Package ListΒΆ

This is a list of things you can install using Spack. It is automatically generated based on the packages in the latest Spack release.

Spack currently has 3908 mainline packages:

abinit oniguruma r-annotationhub
abseil-cpp ont-albacore r-aod
abyss opa-psm2 r-ape
accfft opam r-argparse
ace opari2 r-aroma-light
ack openbabel r-askpass
acpid openblas r-assertthat
activeharmony opencascade r-backports
activemq opencoarrays r-bamsignals
acts-core opencv r-base64
adept-utils openexr r-base64enc
adf openfast r-bayesm
adiak openfdtd r-bbmisc
adios openfoam r-beachmat
adios2 openfoam-org r-beanplot
adlbx openfst r-beeswarm
adol-c opengl r-bfast
advancecomp openglu r-bfastspatial
aegean openimageio r-bglr
aida openjdk r-bh
akantu openjpeg r-biasedurn
alan openkim-models r-bibtex
albany openldap r-bindr
albert openmc r-bindrcpp
alglib openmolcas r-bio3d
allpaths-lg openmpi r-biobase
alluxio openmx r-biocfilecache
alquimia opennurbs r-biocgenerics
alsa-lib openpa r-biocinstaller
aluminum openpmd-api r-biocmanager
amber openresty r-biocneighbors
amdblis openscenegraph r-biocparallel
amg openslide r-biocsingular
amg2013 openspeedshop r-biocstyle
aml openspeedshop-utils r-biom-utils
amp openssh r-biomart
ampliconnoise openssl r-biomartr
amrex openstf r-biomformat
amrvis opentsdb r-biostrings
andi opium r-biovizbase
angsd optional-lite r-bit
ant optipng r-bit64
antlr opus r-bitops
ants orca r-blob
aoflagger orfm r-blockmodeling
aom orthofiller r-bmp
apachetop orthofinder r-bookdown
ape orthomcl r-boot
aperture-photometry osmctools r-brew
apex osqp r-broom
apple-libunwind osu-micro-benchmarks r-bsgenome
applewmproto otf r-bsgenome-hsapiens-ucsc-hg19
appres otf2 r-bumphunter
apr p3dfft3 r-c50
apr-util p4est r-cairo
aragorn p7zip r-callr
arborx pacbio-daligner r-car
archer pacbio-damasker r-cardata
argobots pacbio-dazz-db r-caret
argp-standalone pacbio-dextractor r-caroline
argtable packmol r-category
aria2 pacvim r-catools
arm-forge pagit r-cdcfluview
armadillo pagmo r-cellranger
arpack-ng pal r-checkmate
arrow paml r-checkpoint
asagi panda r-chemometrics
ascent pandaseq r-chron
asciidoc pandoc r-circlize
asciidoctor pango r-class
asdf-cxx pangomm r-classint
aspa papi r-cli
aspcud papyrus r-clipr
aspect paradiseo r-clisymbols
aspell parallel r-clue
aspell6-de parallel-netcdf r-cluster
aspell6-en paraver r-clustergeneration
aspell6-es paraview r-clusterprofiler
aspera-cli parmetis r-cner
assimp parmgridgen r-coda
astra parquet-cpp r-codetools
astral parsimonator r-codex
astyle parsplice r-coin
at-spi2-atk partitionfinder r-colorspace
at-spi2-core pasta r-combinat
athena patch r-commonmark
atk patchelf r-complexheatmap
atlas pathfinder r-compositions
atom-dft pax-utils r-condop
atompaw pbbam r-construct
atop pbmpi r-convevol
attr pbsuite r-copula
audit-userspace pcma r-corhmm
augustus pcre r-corpcor
autoconf pcre2 r-corrplot
autodock-vina pdf2svg r-covr
autofact pdftk r-cowplot
autogen pdsh r-crayon
automaded pdt r-crosstalk
automake pegtl r-crul
avizo pennant r-ctc
aws-parallelcluster percept r-cubature
awscli perl r-cubist
axel perl-acme-damn r-curl
axl perl-algorithm-diff r-dada2
bam-readcount perl-alien-build r-data-table
bamdst perl-alien-libxml2 r-dbi
bamtools perl-app-cmd r-dbplyr
bamutil perl-array-utils r-debugme
barrnap perl-b-hooks-endofscope r-delayedarray
bash perl-bioperl r-delayedmatrixstats
bash-completion perl-bit-vector r-deldir
bats perl-cairo r-dendextend
bazel perl-capture-tiny r-deoptim
bbcp perl-carp-clan r-deoptimr
bbmap perl-cgi r-desc
bc perl-class-data-inheritable r-deseq
bcftools perl-class-inspector r-deseq2
bcl2fastq2 perl-class-load r-desolve
bdftopcf perl-class-load-xs r-devtools
bdw-gc perl-clone r-diagrammer
beagle perl-clone-choose r-dicekriging
bear perl-compress-raw-bzip2 r-dichromat
beast-tracer perl-compress-raw-zlib r-diffusionmap
beast1 perl-config-general r-digest
beast2 perl-contextual-return r-diptest
bedops perl-cpan-meta-check r-dirichletmultinomial
bedtools2 perl-data-dumper r-dismo
beforelight perl-data-optlist r-diversitree
benchmark perl-data-stag r-dnacopy
berkeley-db perl-db-file r-do-db
bertini perl-dbd-mysql r-domc
bib2xhtml perl-dbd-pg r-doparallel
bigreqsproto perl-dbd-sqlite r-dorng
bind9 perl-dbi r-dose
binutils perl-devel-cycle r-dosnow
bioawk perl-devel-globaldestruction r-dotcall64
biobloom perl-devel-overloadinfo r-downloader
biopieces perl-devel-stacktrace r-dplyr
bismark perl-devel-symdump r-dqrng
bison perl-digest-md5 r-dt
bitmap perl-dist-checkconflicts r-dtw
blasr perl-encode-locale r-dygraphs
blasr-libcpp perl-error r-dynamictreecut
blast-legacy perl-eval-closure r-e1071
blast-plus perl-exception-class r-earth
blast2go perl-exporter-tiny r-ecp
blat perl-extutils-config r-edger
blaze perl-extutils-depends r-ellipse
blis perl-extutils-helpers r-ellipsis
bliss perl-extutils-installpaths r-emmli
blitz perl-extutils-makemaker r-energy
blktrace perl-extutils-pkgconfig r-enrichplot
bmake perl-ffi-checklib r-ensembldb
bmi perl-file-chdir r-ergm
bml perl-file-copy-recursive r-europepmc
bohrium perl-file-homedir r-evaluate
bolt perl-file-listing r-evd
bookleaf-cpp perl-file-pushd r-exomecopy
boost perl-file-sharedir-install r-exomedepth
boostmplcartesianproduct perl-file-slurp-tiny r-expint
bowtie perl-file-slurper r-expm
bowtie2 perl-file-which r-factoextra
boxlib perl-font-ttf r-factominer
bpp-core perl-forks r-fansi
bpp-phyl perl-gd r-farver
bpp-seq perl-gdgraph r-fastcluster
bpp-suite perl-gdgraph-histogram r-fastmatch
bracken perl-gdtextutil r-fdb-infiniummethylation-hg18
braker perl-graph r-fdb-infiniummethylation-hg19
branson perl-graph-readwrite r-ff
breakdancer perl-hash-merge r-fftwtools
bref3 perl-html-parser r-fgsea
breseq perl-html-tagset r-fields
bridger perl-http-cookies r-filehash
brigand perl-http-daemon r-findpython
brltty perl-http-date r-fit-models
brotli perl-http-message r-fitdistrplus
bsseeker2 perl-http-negotiate r-flashclust
bucky perl-inline r-flexclust
bumpversion perl-inline-c r-flexmix
busco perl-io-all r-fnn
busybox perl-io-compress r-forcats
butter perl-io-html r-foreach
butterflypack perl-io-prompt r-forecast
bwa perl-io-sessiondata r-foreign
bwtool perl-io-socket-ssl r-formatr
byobu perl-io-string r-formula
bzip2 perl-io-stringy r-fpc
c-ares perl-io-tty r-fracdiff
c-blosc perl-ipc-run r-fs
c-blosc2 perl-json r-futile-logger
c-lime perl-libwww-perl r-futile-options
cabana perl-libxml-perl r-future
caffe perl-list-moreutils r-future-apply
cairo perl-list-moreutils-xs r-gamlss
cairomm perl-log-log4perl r-gamlss-data
caliper perl-logger-simple r-gamlss-dist
callpath perl-lwp-mediatypes r-gbm
camellia perl-lwp-protocol-https r-gbrd
camx perl-mailtools r-gcrma
candle-benchmarks perl-math-bezier r-gdalutils
cantera perl-math-cdf r-gdata
canu perl-math-cephes r-gdsfmt
cap3 perl-math-matrixreal r-geiger
capnproto perl-math-round r-genefilter
capstone perl-math-vecstat r-genelendatabase
cardioid perl-module-build r-genemeta
casacore perl-module-build-tiny r-geneplotter
cask perl-module-implementation r-generics
casper perl-module-runtime r-genetics
cassandra perl-module-runtime-conflicts r-genie3
catalyst perl-moose r-genomeinfodb
catch2 perl-mozilla-ca r-genomeinfodbdata
cbench perl-mro-compat r-genomicalignments
cblas perl-namespace-clean r-genomicfeatures
cbtf perl-net-http r-genomicranges
cbtf-argonavis perl-net-scp-expect r-gensa
cbtf-argonavis-gui perl-net-ssleay r-geomorph
cbtf-krell perl-number-format r-geonames
cbtf-lanl perl-object-insideout r-geoquery
ccache perl-package-deprecationmanager r-geor
ccfits perl-package-stash r-geosphere
ccs-qcd perl-package-stash-xs r-getopt
cctools perl-padwalker r-getoptlong
cdbfasta perl-parallel-forkmanager r-ggally
cdd perl-params-util r-ggbeeswarm
cddlib perl-params-validate r-ggbio
cdecimal perl-parse-recdescent r-ggdendro
cdhit perl-path-tiny r-ggforce
cdo perl-pdf-api2 r-ggjoy
ceed perl-pegex r-ggmap
cereal perl-perl-unsafe-signals r-ggplot2
ceres-solver perl-perl-version r-ggplotify
cfitsio perl-perl4-corelibs r-ggpubr
cgal perl-perl6-slurp r-ggraph
cgdb perl-perlio-gzip r-ggrepel
cgm perl-perlio-utf8-strict r-ggridges
cgns perl-readonly r-ggsci
channelflow perl-regexp-common r-ggsignif
chapel perl-scalar-list-utils r-ggvis
charliecloud perl-scalar-util-numeric r-gh
charmpp perl-set-intervaltree r-gistr
chatterbug perl-set-intspan r-git2r
check perl-set-scalar r-glimma
chgcentre perl-soap-lite r-glmnet
chill perl-star-fusion r-globaloptions
chlorop perl-statistics-basic r-globals
chombo perl-statistics-descriptive r-glue
chrpath perl-statistics-pca r-gmodels
cinch perl-sub-exporter r-gmp
circos perl-sub-exporter-progressive r-go-db
cistem perl-sub-identify r-gofuncr
citcoms perl-sub-install r-googlevis
cityhash perl-sub-name r-goplot
clamav perl-sub-uplevel r-gosemsim
clamr perl-svg r-goseq
clapack perl-swissknife r-gostats
clara perl-sys-sigaction r-gower
claw perl-task-weaken r-gplots
cleaveland4 perl-term-readline-gnu r-graph
cleverleaf perl-termreadkey r-graphlayouts
clfft perl-test-cleannamespaces r-grbase
clhep perl-test-deep r-gridbase
clingo perl-test-differences r-gridextra
cln perl-test-exception r-gridgraphics
cloc perl-test-fatal r-gsa
cloog perl-test-memory-cycle r-gsalib
cloverleaf perl-test-most r-gseabase
cloverleaf3d perl-test-needs r-gsl
clp perl-test-requires r-gss
clustal-omega perl-test-requiresinternet r-gstat
clustalw perl-test-warn r-gsubfn
cmake perl-test-warnings r-gtable
cmocka perl-text-csv r-gtools
cmor perl-text-diff r-gtrellis
cnmem perl-text-format r-gviz
cnpy perl-text-simpletable r-gwmodel
cntk perl-text-soundex r-haven
cntk1bitsgd perl-text-unidecode r-hdf5array
cnvnator perl-time-hires r-hdf5r
codar-cheetah perl-time-piece r-hexbin
codes perl-timedate r-highr
coevp perl-try-tiny r-hmisc
cohmm perl-uri r-hms
coinhsl perl-want r-hoardr
colm perl-www-robotrules r-htmltable
colordiff perl-xml-dom r-htmltools
comd perl-xml-dom-xpath r-htmlwidgets
commons-lang perl-xml-filter-buffertext r-httpcode
commons-lang3 perl-xml-libxml r-httpuv
commons-logging perl-xml-libxslt r-httr
compiz perl-xml-namespacesupport r-hwriter
compositeproto perl-xml-parser r-hypergraph
conduit perl-xml-parser-lite r-ica
connect-proxy perl-xml-quote r-igraph
constype perl-xml-regexp r-illuminahumanmethylation450kanno-ilmn12-hg19
converge perl-xml-sax r-illuminaio
coreutils perl-xml-sax-base r-imager
corset perl-xml-sax-writer r-impute
cosbench perl-xml-simple r-influencer
cosmomc perl-xml-twig r-ini
cosp2 perl-xml-writer r-inline
cotter perl-xml-xpathengine r-interactivedisplaybase
cowsay perl-yaml r-intervals
cp2k perl-yaml-libyaml r-inum
cpio petsc r-ipred
cppad pexsi r-iranges
cppcheck pfft r-irdisplay
cppgsl pflotran r-irkernel
cpprestsdk pfunit r-irlba
cppunit pgdspider r-isdparser
cppzmq pgi r-iso
cpu-features pgmath r-iterators
cpuinfo phantompeakqualtools r-janitor
cquery phast r-jaspar2018
cram phasta r-jomo
cray-libsci phist r-jpeg
cromwell phrap-crossmatch-swat r-jsonlite
cromwell-womtool phred r-kegg-db
cryptopp phylip r-kegggraph
cryptsetup phyluce r-keggrest
cscope picard r-kernlab
csdp picsar r-kernsmooth
ctffind picsarlite r-kknn
cub pidx r-knitr
cube pig r-ks
cubelib pigz r-labeling
cubew pilon r-lambda-r
cuda pindel r-laplacesdemon
cuda-memtest pipework r-lars
cudnn piranha r-later
cufflinks pism r-lattice
cups pixman r-latticeextra
curl pixz r-lava
cvs pkg-config r-lazyeval
cxxopts pkgconf r-ldheatmap
czmq pktools r-leaflet
dakota planck-likelihood r-leaps
daligner plasma r-learnbayes
damageproto platypus r-leiden
damaris plink r-lhs
damselfly plplot r-libcoin
darshan-runtime plumed r-limma
darshan-util pmdk r-listenv
dash pmgr-collective r-lme4
datamash pmix r-lmtest
dataspaces pmlib r-locfit
dateutils pnfft r-log4r
davix pngquant r-loo
dbcsr pngwriter r-lpsolve
dbus pnmpi r-lsei
dcmtk poamsa r-lubridate
dd4hep pocl r-lumi
dealii polymake r-magic
dealii-parameter-gui poppler r-magick
decentralized-internet poppler-data r-magrittr
deconseq-standalone popt r-makecdfenv
dejagnu porta r-maldiquant
delly2 portage r-manipulatewidget
denovogear portcullis r-mapplots
dftfe postgresql r-mapproj
dia powerapi r-maps
dialign ppl r-maptools
dialign-tx pplacer r-markdown
diamond prank r-mass
diffsplice precice r-matr
diffutils presentproto r-matrix
dimemas preseq r-matrixmodels
direnv price r-matrixstats
discovar primer3 r-mclust
discovardenovo prinseq-lite r-mcmcglmm
dislin printproto r-mco
diy prng r-mda
dlpack probconsrna r-memoise
dmd procps r-mergemaid
dmlc-core prodigal r-metap
dmtcp proj r-methylumi
dmxproto protobuf r-mgcv
docbook-xml protobuf-c r-mgraster
docbook-xsl proxymngr r-mice
dos2unix prrte r-mime
dotnet-core-sdk pruners-ninja r-minfi
double-conversion ps-lite r-miniui
doxygen psi4 r-minqa
draco pslib r-misc3d
dri2proto psm r-mitml
dri3proto psmc r-mitools
drill pstreams r-mixtools
ds pugixml r-mlbench
dsdp pumi r-mlinterfaces
dsrc pv r-mlr
dtcmp pvm r-mlrmbo
dyninst pxz r-mmwrweek
dysco py-3to2 r-mnormt
ea-utils py-4suite-xml r-modelmetrics
easybuild py-abipy r-modelr
ebms py-absl-py r-modeltools
eccodes py-adios r-mpm
ecflow py-advancedhtmlparser r-msnbase
eclipse-gcj-parser py-aenum r-multcomp
ecos py-affine r-multicool
ecp-io-sdk py-agate r-multitaper
ecp-proxy-apps py-agate-dbf r-multtest
ecp-viz-sdk py-agate-excel r-munsell
ed py-agate-sql r-mvtnorm
editline py-alabaster r-mzid
editres py-alembic r-mzr
eem py-altgraph r-nanotime
eigen py-amqp r-ncbit
elasticsearch py-ansible r-ncdf4
elemental py-antlr4-python3-runtime r-network
elfutils py-apache-libcloud r-networkd3
elk py-apipkg r-nleqslv
elmerfem py-appdirs r-nlme
elpa py-appnope r-nloptr
elsd py-apscheduler r-nmf
elsdc py-argcomplete r-nmof
elsi py-argparse r-nnet
emacs py-arrow r-nnls
ember py-asciitree r-nor1mix
emboss py-asdf r-nortest
enchant py-ase r-np
energyplus py-asn1crypto r-npsurv
entrezdirect py-aspy-yaml r-numderiv
environment-modules py-asserts r-oligoclasses
eospac py-astor r-openssl
eq-r py-astroid r-openxlsx
er py-astropy r-optparse
erfa py-astunparse r-ordinal
erlang py-async-generator r-org-hs-eg-db
ermod py-atomicwrites r-organismdbi
erne py-atropos r-packrat
es-shell py-attrs r-pacman
esmf py-autopep8 r-paleotree
essl py-avro r-pamr
ethminer py-avro-json-serializer r-pan
ethtool py-babel r-parallelmap
etsf-io py-backcall r-paramhelpers
everytrace py-backports-abc r-party
everytrace-example py-backports-functools-lru-cache r-partykit
evieext py-backports-shutil-get-terminal-size r-pathview
exabayes py-backports-ssl-match-hostname r-pbapply
examinimd py-backports-tempfile r-pbdzmq
exampm py-backports-weakref r-pbkrtest
exasp2 py-basemap r-pcamethods
exchanger py-bcbio-gff r-pcapp
exiv2 py-bcrypt r-permute
exmcutils py-beautifulsoup4 r-pfam-db
exodusii py-billiard r-phangorn
exonerate py-binaryornot r-phantompeakqualtools
expat py-bintrees r-philentropy
expect py-binwalk r-phyloseq
express py-biom-format r-phylostratr
extrae py-biomine r-phytools
exuberant-ctags py-biopython r-picante
eztrace py-bitarray r-pillar
f18 py-bitstring r-pkgbuild
f77-zmq py-black r-pkgconfig
f90cache py-bleach r-pkgload
fabtests py-blessed r-pkgmaker
fairlogger py-blessings r-plogr
falcon py-blinker r-plot3d
fann py-bokeh r-plotly
faodel py-boltons r-plotmo
fast-global-file-status py-boto3 r-plotrix
fasta py-botocore r-pls
fastdfs py-bottleneck r-plyr
fastjar py-breakseq2 r-pmcmr
fastmath py-breathe r-png
fastme py-brian r-polyclip
fastp py-brian2 r-polynom
fastphase py-brotlipy r-popgenome
fastq-screen py-bsddb3 r-popvar
fastqc py-bx-python r-powerlaw
fastqvalidator py-bz2file r-prabclus
fasttree py-cached-property r-praise
fastx-toolkit py-cachetools r-preprocesscore
feh py-cairocffi r-prettyunits
fenics py-cartopy r-processx
fermi py-cclib r-prodlim
fermikit py-cdat-lite r-progress
fermisciencetools py-cdo r-proj
ferret py-cdsapi r-proj4
ffmpeg py-celery r-promises
fftw py-certifi r-protgenerics
fgsl py-certipy r-proto
figtree py-cf-units r-proxy
file py-cffi r-pryr
filebench py-cfgv r-ps
fimpute py-cftime r-pscbs
find-circ py-chai r-pspline
findutils py-chardet r-psych
fio py-checkm-genome r-ptw
fish py-cheetah r-purrr
fixesproto py-cheroot r-qtl
fl py-cherrypy r-quadprog
flac py-cinema-lib r-quantmod
flang py-click r-quantreg
flann py-click-plugins r-quantro
flash py-cligj r-qvalue
flatbuffers py-clipboard r-r-cache
flatcc py-cloudpickle r-r-methodss3
flecsale py-clustershell r-r-oo
flecsi py-codecov r-r-utils
flecsph py-cogent r-r6
flex py-colorama r-randomfields
flibcpp py-coloredlogs r-randomfieldsutils
flink py-colorlog r-randomforest
flint py-colormath r-randomglm
flit py-colorpy r-ranger
fltk py-configobj r-rann
flume py-configparser r-rappdirs
flux-core py-contextlib2 r-raster
flux-sched py-convertdate r-rbgl
fluxbox py-cookiecutter r-rbokeh
fmt py-counter r-rcmdcheck
foam-extend py-cov-core r-rcolorbrewer
folly py-coverage r-rcpp
font-util py-crispresso r-rcppannoy
fontcacheproto py-crossmap r-rcpparmadillo
fontconfig py-cryptography r-rcppblaze
fontsproto py-cssselect r-rcppcctz
fonttosfnt py-csvkit r-rcppcnpy
fp16 py-current r-rcppeigen
fpc py-cutadapt r-rcpphnsw
fpocket py-cvxopt r-rcppparallel
fqtrim py-cvxpy r-rcppprogress
fr-hit py-cycler r-rcurl
freebayes py-cython r-rda
freeglut py-dask r-rdpack
freeimage py-dataclasses r-readbitmap
freetype py-dateparser r-readr
freexl py-dbf r-readxl
fribidi py-dbfread r-recipes
fseq py-decorator r-registry
fsl py-deeptools r-rematch
fslsfonts py-deeptoolsintervals r-remotes
fstobdf py-defusedxml r-reordercluster
fstrack py-dendropy r-reportingtools
ftgl py-deprecation r-repr
fujitsu-mpi py-descartes r-reprex
funhpc py-dill r-reshape
fyba py-discover r-reshape2
fzf py-distributed r-reticulate
g4abla py-dlcpar r-rex
g4emlow py-dnaio r-rgdal
g4ensdfstate py-docopt r-rgenoud
g4ndl py-docutils r-rgeos
g4neutronxs py-docutils-stubs r-rgexf
g4photonevaporation py-doxypy r-rgl
g4pii py-doxypypy r-rgooglemaps
g4radioactivedecay py-dryscrape r-rgraphviz
g4realsurface py-dxchange r-rhdf5
g4saiddata py-dxfile r-rhdf5lib
g4tendl py-earthengine-api r-rhmmer
gams py-easybuild-easyblocks r-rhtslib
gapbs py-easybuild-easyconfigs r-rinside
gapcloser py-easybuild-framework r-rio
gapfiller py-ecdsa r-rjags
gasnet py-ecos r-rjava
gatk py-edffile r-rjson
gaudi py-editdistance r-rjsonio
gaussian py-elasticsearch r-rlang
gawk py-elephant r-rmariadb
gblocks py-emcee r-rmarkdown
gcc py-empy r-rminer
gccmakedep py-entrypoints r-rmpfr
gccxml py-enum34 r-rmpi
gconf py-epydoc r-rmutil
gcta py-espresso r-rmysql
gdal py-espressopp r-rnaseqmap
gdb py-et-xmlfile r-rngtools
gdbm py-eventlet r-rnoaa
gdk-pixbuf py-execnet r-robust
gdl py-exodus-bundler r-robustbase
geant4 py-extras r-roc
geant4-data py-fallocate r-rocr
gearshifft py-fastaindex r-rodbc
gemmlowp py-fastcache r-rook
genemark-et py-fasteners r-rots
genomefinisher py-faststructure r-roxygen2
genometools py-filelock r-rpart
genrich py-filemagic r-rpart-plot
geode py-fiona r-rpostgresql
geopm py-fiscalyear r-rprojroot
geos py-fixtures r-rrblup
gettext py-flake8 r-rrcov
gflags py-flake8-import-order r-rrpp
ghost py-flake8-polyfill r-rsamtools
ghostscript py-flask r-rsnns
ghostscript-fonts py-flask-compress r-rsolnp
giflib py-flask-socketio r-rspectra
ginkgo py-flexx r-rsqlite
git py-flye r-rstan
git-fat-git py-fn-py r-rstantools
git-imerge py-fortranformat r-rstudioapi
git-lfs py-fparser r-rsvd
gl2ps py-freezegun r-rtracklayer
glew py-fsspec r-rtsne
glfmultiples py-funcsigs r-runit
glib py-functools32 r-rvcheck
glibmm py-fusepy r-rvest
glimmer py-future r-rzmq
glm py-futures r-s4vectors
global py-fypp r-samr
globalarrays py-gast r-sandwich
glog py-gdbgui r-scales
gloo py-gdc-client r-scater
glpk py-gee-asset-manager r-scatterplot3d
glproto py-geeadd r-scrime
glvis py-geeup r-sctransform
gmake py-genders r-sdmtools
gmap-gsnap py-genshi r-segmented
gmime py-gensim r-selectr
gmodel py-geoalchemy2 r-seqinr
gmp py-geopandas r-seqlogo
gmsh py-gevent r-sessioninfo
gmt py-gf256 r-seurat
gmtsar py-git-review r-sf
gnat py-gnuplot r-sfsmisc
gnome-common py-goatools r-shape
gnupg py-google-api-core r-shiny
gnuplot py-google-api-python-client r-shinydashboard
gnutls py-google-auth r-shinyfiles
go py-google-auth-httplib2 r-shortread
go-bootstrap py-google-cloud-core r-siggenes
go-md2man py-google-cloud-storage r-simpleaffy
gobject-introspection py-google-pasta r-singlecellexperiment
googletest py-google-resumable-media r-sitmo
gotcha py-googleapis-common-protos r-sm
gource py-gpaw r-smoof
gpdb py-graphviz r-sn
gperf py-greenlet r-snakecase
gperftools py-grequests r-snow
gpgme py-griddataformats r-snowfall
gplates py-grpcio r-snprelate
gprolog py-guidata r-snpstats
gpu-burn py-guiqwt r-som
grackle py-h5glance r-somaticsignatures
gradle py-h5py r-sourcetools
grandr py-h5sh r-sp
graph500 py-hacking r-spacetime
graphicsmagick py-hdfs r-spam
graphite2 py-heapdict r-sparsem
graphlib py-hepdata-validator r-spatial
graphmap py-hpcbench r-spatialreg
graphviz py-hpccm r-spdata
grass py-html2text r-spdep
grep py-html5lib r-speedglm
grib-api py-htmlgen r-spem
grnboost py-htseq r-splancs
groff py-httpbin r-splitstackshape
gromacs py-httplib2 r-sqldf
grpc py-humanfriendly r-squarem
gsl py-humanize r-squash
gslib py-hvac r-sseq
gtkmm py-hypothesis r-stabledist
gtkorvo-atl py-ics r-stanheaders
gtkorvo-cercs-env py-identify r-stargazer
gtkorvo-dill py-idna r-statmod
gtkorvo-enet py-illumina-utils r-statnet-common
gtkplus py-imageio r-stringi
gtksourceview py-imagesize r-stringr
gts py-iminuit r-strucchange
guidance py-importlib r-subplex
guile py-importlib-metadata r-summarizedexperiment
gurobi py-importlib-resources r-suppdists
gzip py-iniparse r-survey
h5cpp py-intervaltree r-survival
h5hut py-invoke r-sva
h5part py-ipaddress r-sys
h5utils py-ipdb r-tarifx
h5z-zfp py-ipykernel r-taxizedb
hacckernels py-ipython r-tclust
hadoop py-ipython-genutils r-teachingdemos
halc py-ipywidgets r-tensora
half py-irpf90 r-testit
hama py-isodate r-testthat
hapcut2 py-isort r-tfbstools
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harfbuzz py-jdcal r-tibble
harminv py-jedi r-tidycensus
hbase py-jellyfish r-tidygraph
hc py-jinja2 r-tidyr
hdf py-jinja2-time r-tidyselect
hdf5 py-jmespath r-tidyverse
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heaptrack py-jplephem r-tigris
heffte py-jprops r-timedate
help2man py-jpype1 r-tinytex
henson py-jsonpatch r-tmixclust
hepmc py-jsonpointer r-topgo
heppdt py-jsonschema r-triebeard
hic-pro py-junit-xml r-trimcluster
highfive py-jupyter r-truncdist
highwayhash py-jupyter-client r-truncnorm
hiop py-jupyter-console r-trust
hipsycl py-jupyter-core r-tseries
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hisea py-keras r-ttr
hive py-keras-applications r-tweenr
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homer py-kitchen r-txdb-hsapiens-ucsc-hg19-knowngene
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hotspot py-kmodes r-ucminf
hpccg py-kombu r-udunits2
hpctoolkit py-lark-parser r-units
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hpgmg py-lazy r-urca
hpl py-lazy-object-proxy r-urltools
hpx py-lazy-property r-usethis
hpx5 py-lazyarray r-utf8
hsakmt py-leather r-uuid
hstr py-libconf r-uwot
htop py-libensemble r-variantannotation
htslib py-ligo-segments r-varselrf
httperf py-line-profiler r-vcd
httpie py-linecache2 r-vctrs
hub py-lit r-vegan
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hunspell py-lmfit r-vgam
hwloc py-localcider r-vioplot
hybpiper py-locket r-vipor
hydra py-lockfile r-viridis
hydrogen py-logilab-common r-viridislite
hyphy py-lru-dict r-visnetwork
hypre py-lscsoft-glue r-vsn
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ibmisc py-lzstring r-wgcna
iceauth py-m2r r-whisker
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icet py-machotools r-xde
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id3lib py-magic r-xlconnect
idba py-mako r-xlconnectjars
iegenlib py-markdown r-xlsx
ignite py-markupsafe r-xlsxjars
igraph py-matplotlib r-xmapbridge
igv py-mccabe r-xml
igvtools py-mdanalysis r-xml2
ilmbase py-mechanize r-xnomial
imagemagick py-memory-profiler r-xopen
imake py-merlin r-xtable
imlib2 py-merlinwf r-xts
imp py-metasv r-xvector
impute2 py-methylcode r-yaml
infernal py-mg-rast-tools r-yapsa
inputproto py-misopy r-yaqcaffy
intel py-mistune r-yarn
intel-daal py-mlxtend r-zeallot
intel-gpu-tools py-mo-pack r-zip
intel-ipp py-mock r-zlibbioc
intel-llvm py-modred r-zoo
intel-mkl py-moltemplate r3d
intel-mkl-dnn py-monotonic rabbitmq
intel-mpi py-monty racon
intel-parallel-studio py-more-itertools raft
intel-pin py-mpi4py ragel
intel-tbb py-mpld3 raja
intel-xed py-mpmath randfold
interproscan py-msgpack random123
intltool py-multi-key-dict randrproto
ioapi py-multiprocess range-v3
ior py-multiqc rankstr
iozone py-munch rapidjson
iperf2 py-mx ravel
iperf3 py-myhdl raxml
ipopt py-mypy ray
isaac py-mypy-extensions rclone
isaac-server py-mysql-connector-python rdma-core
isl py-mysqlclient rdp-classifier
iso-codes py-mysqldb1 rdptools
itstool py-natsort re2c
itsx py-nbconvert readfq
jackcess py-nbformat readline
jafka py-nc-time-axis recon
jags py-neo recordproto
jali py-nestle redis
jansson py-netcdf4 redset
jasper py-netifaces redundans
jbigkit py-networkx reframe
jchronoss py-nodeenv regcm
jdk py-nose relax
jellyfish py-nose-cov relion
jemalloc py-nose2 rempi
jmol py-nosexcover rename
jq py-notebook rendercheck
json-c py-numba renderproto
json-cwx py-numcodecs repeatmasker
json-fortran py-numexpr repeatmodeler
json-glib py-numexpr3 repeatscout
jsoncpp py-numpy resourceproto
jstorm py-numpydoc revbayes
jube py-oauth2client rgb
judy py-oauthlib rhash
julia py-olefile rlwrap
k8 py-onnx rmats
kafka py-ont-fast5-api rmlab
kahip py-openpmd-validator rna-seqc
kaiju py-openpyxl rnaz
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kaldi py-opentuner rocketmq
kallisto py-opppy rocksdb
karma py-opt-einsum rockstar
kbproto py-ordereddict rodinia
kcov py-oset root
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kealib py-overpy ross
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kim-api py-pamela rsbench
kitty py-pandas rsem
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ladot py-pathlib2 ruby-rubyinline
laghos py-pathos ruby-svn2git
lame py-pathspec ruby-terminal-table
lammps py-patsy rust
last py-pauvre rust-bindgen
lastz py-pbr sabre
laszip py-pep8 saga-gis
latte py-pep8-naming sailfish
launchmon py-performance salmon
lazyten py-periodictable sambamba
lbann py-petsc4py samblaster
lbxproxy py-pexpect samrai
lbzip2 py-phonopy samtools
lcals py-pickleshare sandbox
lcms py-picrust sas
lcov py-pil satsuma2
ldc py-pillow savanna
ldc-bootstrap py-pint saws
legion py-pip sbt
lemon py-pipits scala
leveldb py-pispino scalasca
lftp py-pkgconfig scallop
libaec py-pkginfo scalpel
libaio py-planar scan-for-matches
libapplewm py-plotly scons
libarchive py-pluggy scorec-core
libassuan py-ply scorep
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libbeagle py-portend scr
libbeato py-poster screen
libbsd py-pox scripts
libbson py-poyo scrnsaverproto
libcanberra py-ppft scs
libcap py-pre-commit sctk
libceed py-prettytable sdl2
libcerf py-progress sdl2-image
libcint py-progressbar2 sdsl-lite
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libconfig py-prometheus-client sed
libcroco py-prompt-toolkit sensei
libctl py-protobuf sentieon-genomics
libdap4 py-psutil seqan
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libdrm py-ptyprocess seqtk
libdwarf py-pudb serf
libeatmydata py-py sessreg
libedit py-py-cpuinfo setxkbmap
libelf py-py2bit sfcgal
libemos py-py2cairo sga
libepoxy py-py2neo shadow
libev py-py4j shapeit
libevent py-pyani shared-mime-info
libevpath py-pyarrow shiny-server
libexif py-pyasn1 shocklibs
libfabric py-pyasn1-modules shoremap
libfastcommon py-pybedtools shortbred
libffi py-pybigwig shortstack
libffs py-pybind11 showfont
libfive py-pybtex shtools
libflame py-pybtex-docutils shuffile
libfontenc py-pycairo sickle
libfs py-pycares siesta
libgcrypt py-pycbc signalp
libgd py-pychecker signify
libgeotiff py-pycmd silo
libgit2 py-pycodestyle simgrid
libglvnd py-pycparser simmetrix-simmodsuite
libgpg-error py-pycrypto simplemoc
libgpuarray py-pycuda simul
libgridxc py-pycurl simulationio
libgtextutils py-pydatalog singularity
libharu py-pydispatcher singularity-legacy
libhio py-pydot sirius
libiberty py-pydot2 skilion-onedrive
libibumad py-pydotplus skopeo
libice py-pydv sl
libiconv py-pyelftools slate
libid3tag py-pyepsg sleef
libidn2 py-pyfaidx slepc
libint py-pyfasta slurm
libjpeg py-pyfftw smalt
libjpeg-turbo py-pyflakes smof
libkml py-pygdal smproxy
libksba py-pygdbmi snakemake
liblas py-pygit2 snap
liblbxutil py-pyglet snap-berkeley
liblockfile py-pygments snap-korf
libmad py-pygobject snappy
libmatheval py-pygpu snbone
libmaxminddb py-pygresql sniffles
libmesh py-pygtk snpeff
libmmtf-cpp py-pyinstrument snphylo
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libmonitor py-pyke soapdenovo2
libnbc py-pykml sofa-c
libnl py-pykwalify sollve
libnova py-pyliblzma somatic-sniper
libnrm py-pylint sortmerna
libnsl py-pymatgen sosflow
libogg py-pymeeus sowing
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libpaper py-pymol spades
libpcap py-pymongo span-lite
libpciaccess py-pymorph spark
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libplist py-pynn spectrum-mpi
libpmemobj-cpp py-pyodbc speex
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libsecret py-pyproj sqlitebrowser
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libszip py-pysmartdl star-ccm-plus
libtasn1 py-pysocks startup-notification
libtermkey py-pyspark stat
libtiff py-pysqlite stata
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libtomlc99 py-pytest steps
libtool py-pytest-cache storm
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libxaw py-python-gitlab superlu
libxaw3d py-python-igraph superlu-dist
libxc py-python-jenkins superlu-mt
libxcb py-python-ldap supernova
libxcomposite py-python-levenshtein sw4lite
libxcursor py-python-logstash swap-assembler
libxdamage py-python-magic swarm
libxdmcp py-python-mapnik swfft
libxevie py-python-meep swftools
libxext py-python-memcached swiftsim
libxfixes py-python-oauth2 swig
libxfont py-python-rapidjson swipl
libxfont2 py-python-slugify symengine
libxfontcache py-python-socketio sympol
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libxi py-python-utils sz
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libxkbfile py-pytools talass
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libxv py-readme-renderer tecplot
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libxxf86misc py-reportlab tensorflow-serving-client
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libyaml py-requests tethex
libyogrt py-requests-futures texinfo
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liggghts py-requests-toolbelt textparser
lighttpd py-restview tfel
likwid py-retrying the-platinum-searcher
linkphase3 py-rnacocktail the-silver-searcher
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llvm-flang py-rtree time
llvm-openmp py-ruamel-yaml timemory
llvm-openmp-ompt py-s3cmd tinker
lm-sensors py-s3transfer tinyxml
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lndir py-scientificpython tippecanoe
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loki py-scikit-optimize tmalign
lordec py-scipy tmhmm
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lrzip py-scp tmuxinator
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lua-bitlib py-setuptools transposome
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lua-luafilesystem py-setuptools-scm trapproto
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lua-mpack py-sgp4 trf
lucene py-sh triangle
luit py-shapely trilinos
lulesh py-shiboken trilinos-catalyst-ioss-adapter
lumpy-sv py-simplegeneric trimal
lvm2 py-simplejson trimgalore
lwgrp py-simplekml trimmomatic
lwm2 py-singledispatch trinity
lz4 py-sip trinotate
lzma py-six trnascan-se
lzo py-slepc4py turbine
m4 py-slurm-pipeline turbomole
macsio py-smart-open tut
mad-numdiff py-sncosmo twm
mafft py-snowballstemmer tycho2
magics py-snuggs typhon
magma py-sortedcontainers typhonio
makedepend py-soupsieve ucx
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mallocmc py-spdlog ufo-core
man-db py-spectra ufo-filters
manta py-spefile umap
mapnik py-spglib umoci
mapserver py-sphinx umpire
maq py-sphinx-bootstrap-theme unblur
margo py-sphinx-rtd-theme uncrustify
mariadb py-sphinxautomodapi unibilium
mariadb-c-client py-sphinxcontrib-applehelp unifdef
masa py-sphinxcontrib-bibtex unifyfs
masurca py-sphinxcontrib-devhelp unison
mathematica py-sphinxcontrib-htmlhelp units
matio py-sphinxcontrib-issuetracker unittest-cpp
matlab py-sphinxcontrib-jsmath unixodbc
maven py-sphinxcontrib-programoutput unrar
maverick py-sphinxcontrib-qthelp unuran
mawk py-sphinxcontrib-serializinghtml unzip
mbdyn py-sphinxcontrib-websupport upcxx
mbedtls py-spyder uriparser
mc py-spykeutils usearch
mcl py-sqlalchemy utf8proc
mdtest py-statsmodels util-linux
med py-stestr util-macros
meep py-stevedore uuid
mefit py-storm uvw
megadock py-stratify valgrind
megahit py-subprocess32 vampirtrace
memaxes py-subrosa vardictjava
memcached py-svgpathtools variorum
meme py-svgwrite varscan
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meraculous py-sympy vcsh
mercurial py-syned vdt
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mesa py-tables veclibfort
mesa-glu py-tabulate vegas2
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metabat py-tempora verrou
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metaphysicl py-tensorflow-estimator videoproto
metis py-termcolor viennarna
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mii py-testscenarios vizglow
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mindthegap py-tetoolkit voropp
miniaero py-text-unidecode votca-csg
miniamr py-texttable votca-csg-tutorials
miniasm py-theano votca-csgapps
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minife py-toml votca-xtp
minighost py-tomopy vpfft
minigmg py-toolz vpic
minimap2 py-torch vsearch
minimd py-torchvision vt
miniqmc py-tornado vtk
minisign py-tox vtk-h
minismac2d py-tqdm vtk-m
minitri py-traceback2 wannier90
minivite py-traitlets warpx
minixyce py-treehash watch
minizip py-tuiview wcslib
minuit py-twine wget
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miranda py-typed-ast which
mirdeep2 py-typesentry windowswmproto
mitofates py-typing wireshark
mitos py-typing-extensions wordnet
mixcr py-tzlocal workrave
mkfontdir py-ujson wt
mkfontscale py-umalqurra wtdbg2
mlhka py-umi-tools wxpropgrid
mmg py-unicycler wxwidgets
moab py-unittest2 x11perf
modern-wheel py-unittest2py3k xapian-core
mofem-cephas py-uritemplate xauth
mofem-fracture-module py-urllib3 xbacklight
mofem-minimal-surface-equation py-urwid xbiff
mofem-users-modules py-us xbitmaps
molcas py-usgs xbraid
mongo-c-driver py-uwsgi xcalc
mongo-cxx-driver py-vcversioner xcb-demo
mono py-vermin xcb-proto
montage py-vine xcb-util
moosefs py-virtualenv xcb-util-cursor
moreutils py-virtualenv-clone xcb-util-errors
mosh py-virtualenvwrapper xcb-util-image
mothur py-voluptuous xcb-util-keysyms
motif py-vsc-base xcb-util-renderutil
motioncor2 py-vsc-install xcb-util-wm
mount-point-attributes py-wand xcb-util-xrm
mozjs py-warlock xclip
mpark-variant py-wcsaxes xclipboard
mpc py-wcwidth xclock
mpdecimal py-weave xcmiscproto
mpe2 py-webencodings xcmsdb
mpest py-webkit-server xcompmgr
mpfr py-weblogo xconsole
mpi-bash py-werkzeug xcursor-themes
mpich py-whatshap xcursorgen
mpifileutils py-wheel xdbedizzy
mpilander py-whichcraft xditview
mpileaks py-widgetsnbextension xdm
mpip py-wradlib xdmf3
mpir py-wrapt xdpyinfo
mpix-launch-swift py-wub xdriinfo
mpt py-wxmplot xedit
mrbayes py-wxpython xerces-c
mrnet py-xarray xeus
mrtrix3 py-xattr xev
mscgen py-xdot xextproto
msgpack-c py-xenv xeyes
mshadow py-xlrd xf86bigfontproto
msmc py-xlsxwriter xf86dga
mstk py-xlwt xf86dgaproto
multitail py-xmlrunner xf86driproto
multitime py-xmltodict xf86miscproto
multiverso py-xopen xf86rushproto
mummer py-xpyb xf86vidmodeproto
mumps py-xvfbwrapper xfd
munge py-yajl xfindproxy
muparser py-yamlreader xfontsel
muscle py-yapf xfs
muse py-yt xfsinfo
musl py-ytopt xfwp
muster py-zarr xgamma
mutationpp py-zc-buildout xgboost
mvapich2 py-zc-lockfile xgc
mxml py-zict xhmm
mxnet py-zipp xhost
mysql py-zope-event xineramaproto
nag py-zope-interface xinit
nalu py-zxcvbn xinput
nalu-wind pythia6 xios
namd pythia8 xkbcomp
nano python xkbdata
nanoflann qbank xkbevd
nanopb qbox xkbprint
nasm qca xkbutils
nauty qemu xkeyboard-config
ncbi-magicblast qhull xkill
ncbi-rmblastn qjson xload
ncbi-toolkit qmcpack xlogo
nccl qmd-progress xlsatoms
nccmp qnnpack xlsclients
ncdu qorts xlsfonts
ncftp qperf xmag
ncl qrupdate xman
nco qscintilla xmessage
ncurses qt xmh
ncview qt-creator xmlf90
ndiff qtgraph xmlto
nek5000 qthreads xmodmap
nekbone qtkeychain xmore
nekcem quantum-espresso xorg-cf-files
nektar quinoa xorg-docs
nektools qwt xorg-gtest
neovim qwtpolar xorg-server
nest r xorg-sgml-doctools
netcdf-c r-a4 xphelloworld
netcdf-cxx r-a4base xplor-nih
netcdf-cxx4 r-a4classif xplsprinters
netcdf-fortran r-a4core xpr
netgauge r-a4preproc xprehashprinterlist
netgen r-a4reporting xprop
netlib-lapack r-abadata xproto
netlib-scalapack r-abaenrichment xproxymanagementprotocol
netlib-xblas r-abind xqilla
netperf r-absseq xrandr
nettle r-acde xrdb
neuron r-acepack xrefresh
nextflow r-acgh xrootd
nfft r-acme xrx
nghttp2 r-ada xsbench
nginx r-adabag xscope
ngmlr r-ade4 xsd
nicstat r-adegenet xsdk
nim r-adgoftest xsdktrilinos
ninja r-adsplit xset
ninja-fortran r-aer xsetmode
nix r-affxparser xsetpointer
nlohmann-json r-affy xsetroot
nlopt r-affycomp xsimd
nmap r-affycompatible xsm
nnvm r-affycontam xssp
node-js r-affycoretools xstdcmap
notmuch r-affydata xtensor
npb r-affyexpress xtensor-python
npm r-affyilm xterm
npth r-affyio xtl
nrm r-affypdnn xtrans
nseg r-affyplm xtrap
nsimd r-affyqcreport xts
nspr r-affyrnadegradation xvidtune
ntpoly r-agdex xvinfo
numactl r-agilp xwd
numdiff r-agimicrorna xwininfo
nut r-aims xwud
nvptx-tools r-aldex2 xxhash
nwchem r-allelicimbalance xz
nyancat r-alpine yajl
ocaml r-als yambo
occa r-alsace yaml-cpp
oce r-altcdfenvs yara
oclint r-amap yasm
oclock r-ampliqueso yorick
octave r-analysispageserver z3
octave-optim r-anaquin zfp
octave-splines r-aneufinder zip
octave-struct r-aneufinderdata zlib
octopus r-animation zoltan
of-catalyst r-annaffy zookeeper
of-precice r-annotate zsh
omega-h r-annotationdbi zstd
ompss r-annotationfilter zziplib
ompt-openmp r-annotationforge None

abinit

Homepage:
Spack package:
Versions:
8.10.3, 8.8.2, 8.6.3, 8.2.2, 8.0.8b
Build Dependencies:
blas, lapack, mpi, scalapack, fftw, netcdf-fortran, hdf5, libxc
Link Dependencies:
blas, lapack, mpi, scalapack, fftw, netcdf-fortran, hdf5, libxc
Description:
ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave or wavelet basis. ABINIT also includes options to optimize the geometry according to the DFT forces and stresses, or to perform molecular dynamics simulations using these forces, or to generate dynamical matrices, Born effective charges, and dielectric tensors, based on Density-Functional Perturbation Theory, and many more properties. Excited states can be computed within the Many-Body Perturbation Theory (the GW approximation and the Bethe-Salpeter equation), and Time- Dependent Density Functional Theory (for molecules). In addition to the main ABINIT code, different utility programs are provided.

abseil-cpp

Homepage:
Spack package:
Versions:
20190808, 20181200, 20180600
Build Dependencies:
cmake
Description:
Abseil Common Libraries (C++)

abyss

Homepage:
Spack package:
Versions:
2.1.4, 2.0.2, 1.5.2
Build Dependencies:
autoconf, automake, mpi, boost, sparsehash, sqlite, libtool
Link Dependencies:
mpi, boost, sparsehash, sqlite, libtool
Run Dependencies:
bwa
Description:
ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads. The single-processor version is useful for assembling genomes up to 100 Mbases in size.

accfft

Homepage:
Spack package:
Versions:
develop
Build Dependencies:
cuda, cmake, fftw, parallel-netcdf
Link Dependencies:
cuda, fftw, parallel-netcdf
Description:
AccFFT extends existing FFT libraries for CUDA-enabled Graphics Processing Units (GPUs) to distributed memory clusters

ace

Homepage:
Spack package:
Versions:
6.5.6, 6.5.1, 6.5.0
Description:
ACE is an open-source framework that provides many components and patterns for developing high-performance, distributed real-time and embedded systems. ACE provides powerful, yet efficient abstractions for sockets, demultiplexing loops, threads, synchronization primitives.

ack

Homepage:
Spack package:
Versions:
2.22, 2.18, 2.16, 2.14
Build Dependencies:
perl
Link Dependencies:
perl
Description:
ack 2.14 is a tool like grep, optimized for programmers. Designed for programmers with large heterogeneous trees of source code, ack is written purely in portable Perl 5 and takes advantage of the power of Perl's regular expressions.

acpid

Homepage:
Spack package:
Versions:
2.0.28, 2.0.27, 2.0.26, 2.0.25, 2.0.24
Build Dependencies:
autoconf, automake, libtool, m4
Description:
ACPID used to try to handle events internally. Rather than try to climb an ever-growing mountain, ACPID now lets YOU define what events to handle. Any event that publishes itself to /proc/acpi/event can be handled. ACPID reads a set of configuration files which define event->action pairs. This is how you make it do stuff. See the man page for details.

activeharmony

Homepage:
Spack package:
Versions:
4.5
Description:
Active Harmony: a framework for auto-tuning (the automated search for values to improve the performance of a target application).

activemq

Homepage:
Spack package:
Versions:
5.14.0
Description:
Apache ActiveMQ is a high performance Apache 2.0 licensed Message Broker and JMS 1.1 implementation.

acts-core

Homepage:
Spack package:
Versions:
develop, 0.16.0, 0.15.0, 0.14.0, 0.13.0, 0.12.1, 0.12.0, 0.11.1, 0.11.0, 0.10.5, 0.10.4, 0.10.3, 0.10.2, 0.10.1, 0.10.0, 0.09.5, 0.09.4, 0.09.3, 0.09.2, 0.09.1, 0.09.0, 0.08.2, 0.08.1, 0.08.0
Build Dependencies:
cmake, boost, eigen, nlohmann-json, root, dd4hep
Link Dependencies:
boost, nlohmann-json, root, dd4hep
Description:
A Common Tracking Software (ACTS) This project contains an experiment- independent set of track reconstruction tools. The main philosophy is to provide high-level track reconstruction modules that can be used for any tracking detector. The description of the tracking detector's geometry is optimized for efficient navigation and quick extrapolation of tracks. Converters for several common geometry description languages exist. Having a highly performant, yet largely customizable implementation of track reconstruction algorithms was a primary objective for the design of this toolset. Additionally, the applicability to real-life HEP experiments plays major role in the development process. Apart from algorithmic code, this project also provides an event data model for the description of track parameters and measurements. Key features of this project include: tracking geometry description which can be constructed from TGeo, DD4Hep, or GDML input, simple and efficient event data model, performant and highly flexible algorithms for track propagation and fitting, basic seed finding algorithms.

adept-utils

Homepage:
Spack package:
Versions:
1.0.1, 1.0
Build Dependencies:
cmake, boost, mpi
Link Dependencies:
boost, mpi
Description:
Utility libraries for LLNL performance tools.

adf

Homepage:
Spack package:
Versions:
2017.113
Description:
Amsterdam Density Functional (ADF) is a program for first-principles electronic structure calculations that makes use of density functional theory.

adiak

Homepage:
Spack package:
Versions:
0.1.1
Build Dependencies:
cmake, mpi
Link Dependencies:
mpi
Description:
Adiak collects metadata about HPC application runs and provides it to tools.

adios

Homepage:
Spack package:
Versions:
develop, 1.13.1, 1.13.0, 1.12.0, 1.11.1, 1.11.0, 1.10.0, 1.9.0
Build Dependencies:
autoconf, automake, m4, libtool, python, mpi, zlib, bzip2, szip, sz, zfp, lz4, c-blosc, hdf5, netcdf-c, libevpath, dataspaces
Link Dependencies:
mpi, zlib, bzip2, szip, sz, zfp, lz4, c-blosc, hdf5, netcdf-c, libevpath, dataspaces
Description:
The Adaptable IO System (ADIOS) provides a simple, flexible way for scientists to describe the data in their code that may need to be written, read, or processed outside of the running simulation.

adios2

Homepage:
Spack package:
Versions:
develop, 2.5.0, 2.4.0, 2.3.1
Build Dependencies:
cmake, pkgconfig, libffi, libfabric, mpi, libzmq, dataspaces, hdf5, c-blosc, bzip2, libpng, zfp, sz, python, py-numpy, py-mpi4py
Link Dependencies:
libffi, libfabric, mpi, libzmq, dataspaces, hdf5, c-blosc, bzip2, libpng, zfp, sz, python
Run Dependencies:
python, py-numpy, py-mpi4py
Description:
The Adaptable Input Output System version 2, developed in the Exascale Computing Program

adlbx

Homepage:
Spack package:
Versions:
master, 0.9.2, 0.9.1
Build Dependencies:
exmcutils, autoconf, automake, libtool, m4, mpi
Link Dependencies:
exmcutils, mpi
Description:
ADLB/X: Master-worker library + work stealing and data dependencies

adol-c

Homepage:
Spack package:
Versions:
develop, 2.6.3, 2.6.2, 2.6.1, 2.5.2
Build Dependencies:
automake, autoconf, libtool, m4, boost
Link Dependencies:
boost
Description:
A package for the automatic differentiation of first and higher derivatives of vector functions in C and C++ programs by operator overloading.

advancecomp

Homepage:
Spack package:
Versions:
2.1, 2.0, 1.23, 1.22
Build Dependencies:
autoconf, automake, libtool, m4
Description:
AdvanceCOMP contains recompression utilities for your .zip archives, .png images, .mng video clips and .gz files.

aegean

Homepage:
Spack package:
Versions:
0.15.2
Build Dependencies:
genometools
Link Dependencies:
genometools
Description:
The AEGeAn Toolkit is designed for the Analysis and Evaluation of Genome Annotations. The toolkit includes a variety of analysis programs as well as a C library whose API provides access to AEGeAn's core functions and data structures.

aida

Homepage:
Spack package:
Versions:
3.2.1
Description:
Abstract Interfaces for Data Analysis

akantu

Homepage:
Spack package:
Versions:
master, 3.0.0
Build Dependencies:
cmake, boost, lapack, python, py-numpy, py-scipy, py-pybind11, mumps, netlib-scalapack, petsc, mpi, scotch
Link Dependencies:
boost, lapack, python, mumps, netlib-scalapack, petsc, mpi, scotch
Run Dependencies:
python, py-numpy, py-scipy, py-pybind11
Description:
Akantu means a little element in Kinyarwanda, a Bantu language. From now on it is also an opensource object-oriented Finite Element library which has the ambition to be generic and efficient.

alan

Homepage:
Spack package:
Versions:
2.1.1
Description:
Alignment viewer for linux terminal

albany

Homepage:
Spack package:
Versions:
develop
Build Dependencies:
cmake, mpi, trilinos
Link Dependencies:
mpi, trilinos
Description:
Albany is an implicit, unstructured grid, finite element code for the solution and analysis of multiphysics problems. The Albany repository on the GitHub site contains hundreds of regression tests and examples that demonstrate the code's capabilities on a wide variety of problems including fluid mechanics, solid mechanics (elasticity and plasticity), ice-sheet flow, quantum device modeling, and many other applications.

albert

Homepage:
Spack package:
Versions:
4.0a_opt4
Build Dependencies:
readline
Link Dependencies:
readline
Description:
Albert is an interactive program to assist the specialist in the study of nonassociative algebra.

alglib

Homepage:
Spack package:
Versions:
3.11.0
Description:
ALGLIB is a cross-platform numerical analysis and data processing library.

allpaths-lg

Homepage:
Spack package:
Versions:
52488
Description:
ALLPATHS-LG is our original short read assembler and it works on both small and large (mammalian size) genomes.

alluxio

Homepage:
Spack package:
Versions:
2.1.0
Description:
Alluxio (formerly known as Tachyon) is a virtual distributed storage system. It bridges the gap between computation frameworks and storage systems, enabling computation applications to connect to numerous storage systems through a common interface.

alquimia

Homepage:
Spack package:
Versions:
develop, xsdk-0.5.0, xsdk-0.4.0, xsdk-0.3.0, xsdk-0.2.0
Build Dependencies:
cmake, mpi, hdf5, pflotran, petsc
Link Dependencies:
mpi, hdf5, pflotran, petsc
Description:
Alquimia is an interface that exposes the capabilities of mature geochemistry codes such as CrunchFlow and PFLOTRAN

alsa-lib

Homepage:
Spack package:
Versions:
1.1.4.1
Description:
The Advanced Linux Sound Architecture (ALSA) provides audio and MIDI functionality to the Linux operating system. alsa-lib contains the user space library that developers compile ALSA applications against.

aluminum

Homepage:
Spack package:
Versions:
master, 0.3.3, 0.3.2, 0.2.1-1, 0.2.1, 0.2, 0.1
Build Dependencies:
cmake, cuda, mpi, nccl, hwloc, ninja
Link Dependencies:
cuda, mpi, nccl, hwloc
Description:
Aluminum provides a generic interface to high-performance communication libraries, with a focus on allreduce algorithms. Blocking and non- blocking algorithms and GPU-aware algorithms are supported. Aluminum also contains custom implementations of select algorithms to optimize for certain situations.

amber

Homepage:
Spack package:
Versions:
18, 16
Build Dependencies:
cuda, zlib, flex, bison, netcdf-fortran, mpi
Link Dependencies:
cuda, zlib, netcdf-fortran, mpi
Description:
Amber is a suite of biomolecular simulation programs. Note: A manual download is required for Amber. Spack will search your current directory for the download file. Alternatively, add this file to a mirror so that Spack can find it. For instructions on how to set up a mirror, see http://spack.readthedocs.io/en/latest/mirrors.html

blis

Homepage:
Spack package:
Versions:
2.1
Build Dependencies:
python
Run Dependencies:
python
Description:
AMD Optimized BLIS. BLIS is a portable software framework for instantiating high-performance BLAS-like dense linear algebra libraries. The framework was designed to isolate essential kernels of computation that, when optimized, immediately enable optimized implementations of most of its commonly used and computationally intensive operations.

amg

Homepage:
Spack package:
Versions:
develop, 1.2, 1.1, 1.0
Build Dependencies:
mpi
Link Dependencies:
mpi
Description:
AMG is a parallel algebraic multigrid solver for linear systems arising from problems on unstructured grids. The driver provided with AMG builds linear systems for various 3-dimensional problems.

amg2013

Homepage:
Spack package:
Versions:
master
Build Dependencies:
mpi
Link Dependencies:
mpi
Description:
AMG2013 is a parallel algebraic multigrid solver for linear systems arising from problems on unstructured grids. It has been derived directly from the BoomerAMG solver in the hypre library, a large linear solver library that is being developed in the Center for Applied Scientific Computing (CASC) at LLNL.

aml

Homepage:
Spack package:
Versions:
develop, master, 0.1.0
Build Dependencies:
numactl, m4, autoconf, automake, libtool
Link Dependencies:
numactl
Description:
AML: Building Blocks for Memory Management.

amp

Homepage:
Spack package:
Versions:
develop
Build Dependencies:
cmake, blas, lapack, boost, petsc, trilinos, hdf5, silo, zlib, mpi
Link Dependencies:
blas, lapack, boost, petsc, trilinos, hdf5, silo, zlib, mpi
Description:
The Advanced Multi-Physics (AMP) package is an open source parallel object-oriented computational framework that is designed with single and multi-domain multi-physics applications in mind. AMP can be used to build powerful and flexible multi-physics simulation algorithms from lightweight operator, solver, linear algebra, material database, discretization, and meshing components. The AMP design is meant to enable existing investments in application codes to be leveraged without having to adopt dramatically different data structures while developing new computational science applications. Application components are represented as discrete mathematical operators that only require a minimal interface and through operator composition the incremental development of complex parallel applications is enabled. AMP is meant to allow application domain scientists, computer scientists and mathematicians to simulate, collaborate, and conduct research on various aspects of massively parallel simulation algorithms.

ampliconnoise

Homepage:
Spack package:
Versions:
1.29
Build Dependencies:
mpi, gsl
Link Dependencies:
mpi, gsl
Description:
AmpliconNoise is a collection of programs for the removal of noise from 454 sequenced PCR amplicons.

amrex

Homepage:
Spack package:
Versions:
develop, 20.02, 20.01, 19.10, 19.08, 18.10.1, 18.10, 18.09.1
Build Dependencies:
cmake, mpi, sundials, python
Link Dependencies:
mpi, sundials
Description:
AMReX is a publicly available software framework designed for building massively parallel block- structured adaptive mesh refinement (AMR) applications.

amrvis

Homepage:
Spack package:
Versions:
master
Build Dependencies:
gmake, mpi, libsm, libice, libxpm, libx11, libxt, libxext, motif, flex, bison
Link Dependencies:
mpi, libsm, libice, libxpm, libx11, libxt, libxext, motif, flex, bison
Description:
Amrvis is a visualization package specifically designed to read and display output and profiling data from codes built on the AMReX framework.

andi

Homepage:
Spack package:
Versions:
0.10
Build Dependencies:
m4, autoconf, automake, libtool, gsl, libdivsufsort
Link Dependencies:
gsl, libdivsufsort
Description:
andi is used for for estimating the evolutionary distance between closely related genomes.

angsd

Homepage:
Spack package:
Versions:
0.921, 0.919
Build Dependencies:
htslib
Link Dependencies:
htslib
Description:
Angsd is a program for analysing NGS data. The software can handle a number of different input types from mapped reads to imputed genotype probabilities. Most methods take genotype uncertainty into account instead of basing the analysis on called genotypes. This is especially useful for low and medium depth data.

ant

Homepage:
Spack package:
Versions:
1.10.7, 1.10.6, 1.10.5, 1.10.4, 1.10.3, 1.10.2, 1.10.1, 1.10.0, 1.9.9, 1.9.8, 1.9.7, 1.9.6
Build Dependencies:
java
Link Dependencies:
java
Description:
Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files as targets and extension points dependent upon each other

antlr

Homepage:
Spack package:
Versions:
2.7.7
Build Dependencies:
python, java
Link Dependencies:
python
Run Dependencies:
java
Description:
ANTLR (ANother Tool for Language Recognition) is a powerful parser generator for reading, processing, executing, or translating structured text or binary files. It's widely used to build languages, tools, and frameworks. From a grammar, ANTLR generates a parser that can build and walk parse trees.

ants

Homepage:
Spack package:
Versions:
2.2.0
Build Dependencies:
cmake
Link Dependencies:
zlib
Description:
ANTs extracts information from complex datasets that include imaging. Paired with ANTsR (answer), ANTs is useful for managing, interpreting and visualizing multidimensional data. ANTs is popularly considered a state-of-the-art medical image registration and segmentation toolkit. ANTs depends on the Insight ToolKit (ITK), a widely used medical image processing library to which ANTs developers contribute.

aoflagger

Homepage:
Spack package:
Versions:
2.10.0
Build Dependencies:
cmake, casacore, fftw, boost, libxml2, lapack, cfitsio
Link Dependencies:
casacore, fftw, boost, libxml2, lapack, cfitsio
Description:
RFI detector and quality analysis for astronomical radio observations.

aom

Homepage:
Spack package:
Versions:
v1.0.0-errata1
Build Dependencies:
cmake, yasm
Link Dependencies:
yasm
Description:
Alliance for Open Media AOM AV1 Codec Library

apachetop

Homepage:
Spack package:
Versions:
0.19.7, 0.18.4, 0.17.4, 0.15.6
Build Dependencies:
autoconf, automake, libtool, m4, readline
Link Dependencies:
readline
Description:
ApacheTop watches a logfile generated by Apache (in standard common or combined logformat, and generates human-parsable output in realtime.) See the INSTALL file for ./configure options (there's a few newly added since v0.11)

ape

Homepage:
Spack package:
Versions:
2.2.1
Build Dependencies:
gsl, libxc
Link Dependencies:
gsl, libxc
Description:
A tool for generating atomic pseudopotentials within a Density- Functional Theory framework

aperture-photometry

Homepage:
Spack package:
Versions:
2.7.2
Build Dependencies:
java
Link Dependencies:
java
Description:
Aperture Photometry Tool APT is software for astronomical research

apex

Homepage:
Spack package:
Versions:
0.1
Build Dependencies:
cmake, binutils, boost, activeharmony, ompt-openmp
Link Dependencies:
binutils, boost, activeharmony, ompt-openmp
Description:
Autonomic Performance Environment for eXascale (APEX).

apple-libunwind

Homepage:
Spack package:
Description:
Placeholder package for Apple's analogue to non-GNU libunwind

applewmproto

Homepage:
Spack package:
Versions:
1.4.2
Build Dependencies:
pkgconfig, util-macros
Description:
Apple Rootless Window Management Extension. This extension defines a protcol that allows X window managers to better interact with the Mac OS X Aqua user interface when running X11 in a rootless mode.

appres

Homepage:
Spack package:
Versions:
1.0.4
Build Dependencies:
libx11, libxt, xproto, pkgconfig, util-macros
Link Dependencies:
libx11, libxt
Description:
The appres program prints the resources seen by an application (or subhierarchy of an application) with the specified class and instance names. It can be used to determine which resources a particular program will load.

apr

Homepage:
Spack package:
Versions:
1.7.0, 1.6.2, 1.5.2
Description:
Apache portable runtime.

apr-util

Homepage:
Spack package:
Versions:
1.6.1, 1.6.0, 1.5.4
Build Dependencies:
apr, expat, libiconv, openssl, gdbm, postgresql, sqlite, unixodbc
Link Dependencies:
apr, expat, libiconv, openssl, gdbm, postgresql, sqlite, unixodbc
Description:
Apache Portable Runtime Utility

aragorn

Homepage:
Spack package:
Versions:
1.2.38, 1.2.36
Description:
ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences.

arborx

Homepage:
Spack package:
Versions:
master, 0.8-beta2
Build Dependencies:
cmake, cuda, mpi, kokkos
Link Dependencies:
cuda, mpi, kokkos
Description:
ArborX is a performance-portable library for geometric search

archer

Homepage:
Spack package:
Versions:
2.0.0, 1.0.0
Build Dependencies:
cmake, llvm, ninja, llvm-openmp-ompt
Link Dependencies:
llvm, llvm-openmp-ompt
Description:
ARCHER, a data race detection tool for large OpenMP applications.

argobots

Homepage:
Spack package:
Versions:
master, 1.0rc2, 1.0rc1, 1.0b1, 1.0a1
Build Dependencies:
m4, autoconf, automake, libtool, valgrind
Link Dependencies:
valgrind
Description:
Argobots, which was developed as a part of the Argo project, is a lightweight runtime system that supports integrated computation and data movement with massive concurrency. It will directly leverage the lowest- level constructs in the hardware and OS: lightweight notification mechanisms, data movement engines, memory mapping, and data placement strategies. It consists of an execution model and a memory model.

argp-standalone

Homepage:
Spack package:
Versions:
1.3
Description:
Standalone version of the argp interface from glibc for parsing unix- style arguments.

argtable

Homepage:
Spack package:
Versions:
2-13
Description:
Argtable is an ANSI C library for parsing GNU style command line options with a minimum of fuss.

aria2

Homepage:
Spack package:
Versions:
1.34.0
Build Dependencies:
libxml2, libssh2, libgcrypt, zlib, c-ares, sqlite
Link Dependencies:
libxml2, libssh2, libgcrypt, zlib, c-ares, sqlite
Description:
An ultra fast download utility

arm-forge

Homepage:
Spack package:
Versions:
19.0.4-19.0.4-Ubuntu-16.04-x86_64, 19.0.4-Ubuntu-16.04-aarch64, 19.0.4-Ubuntu-14.04-x86_64, 19.0.4-Suse-15-x86_64, 19.0.4-Suse-12-x86_64, 19.0.4-Suse-12-aarch64, 19.0.4-Suse-11-x86_64, 19.0.4-Redhat-7.4-aarch64, 19.0.4-Redhat-7.2-ppc64le, 19.0.4-Redhat-7.0-x86_64, 19.0.4-Redhat-6.0-x86_64, 19.0.3-Ubuntu-16.04-x86_64, 19.0.3-Ubuntu-16.04-aarch64, 19.0.3-Ubuntu-14.04-x86_64, 19.0.3-Suse-12-x86_64, 19.0.3-Suse-12-aarch64, 19.0.3-Suse-11-x86_64, 19.0.3-Redhat-7.4-aarch64, 19.0.3-Redhat-7.2-ppc64le, 19.0.3-Redhat-7.0-x86_64, 19.0.3-Redhat-6.0-x86_64
Description:
Arm Forge is the complete toolsuite for software development - with everything needed to debug, profile, optimize, edit and build C, C++ and Fortran applications on Linux for high performance - from single threads through to complex parallel HPC codes with MPI, OpenMP, threads or CUDA.

armadillo

Homepage:
Spack package:
Versions:
9.800.3, 8.100.1, 7.950.1
Build Dependencies:
cmake, arpack-ng, blas, lapack, superlu, hdf5
Link Dependencies:
arpack-ng, blas, lapack, superlu, hdf5
Description:
Armadillo is a high quality linear algebra library (matrix maths) for the C++ language, aiming towards a good balance between speed and ease of use.

arpack-ng

Homepage:
Spack package:
Versions:
develop, 3.7.0, 3.6.3, 3.6.2, 3.6.0, 3.5.0, 3.4.0, 3.3.0
Build Dependencies:
blas, lapack, automake, autoconf, libtool, cmake, mpi
Link Dependencies:
blas, lapack, mpi
Description:
ARPACK-NG is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems. Important Features: * Reverse Communication Interface. * Single and Double Precision Real Arithmetic Versions for Symmetric, Non-symmetric, Standard or Generalized Problems. * Single and Double Precision Complex Arithmetic Versions for Standard or Generalized Problems. * Routines for Banded Matrices - Standard or Generalized Problems. * Routines for The Singular Value Decomposition. * Example driver routines that may be used as templates to implement numerous Shift-Invert strategies for all problem types, data types and precision. This project is a joint project between Debian, Octave and Scilab in order to provide a common and maintained version of arpack. Indeed, no single release has been published by Rice university for the last few years and since many software (Octave, Scilab, R, Matlab...) forked it and implemented their own modifications, arpack-ng aims to tackle this by providing a common repository and maintained versions. arpack-ng is replacing arpack almost everywhere.

arrow

Homepage:
Spack package:
Versions:
0.15.1, 0.15.0, 0.14.1, 0.12.1, 0.11.0, 0.9.0, 0.8.0
Build Dependencies:
cmake, boost, flatbuffers, python, py-numpy, rapidjson, snappy, zlib, zstd
Link Dependencies:
boost, flatbuffers, python, py-numpy, rapidjson, snappy, zlib, zstd
Description:
A cross-language development platform for in-memory data. This package contains the C++ bindings.

asagi

Homepage:
Spack package:
Versions:
1.0.1, 1.0
Build Dependencies:
cmake, mpi, netcdf-c, numactl
Link Dependencies:
mpi, netcdf-c, numactl
Description:
a pArallel Server for Adaptive GeoInformation.

ascent

Homepage:
Spack package:
Versions:
develop, 0.5.0
Build Dependencies:
cuda, cmake, conduit, python, py-numpy, py-pip, mpi, py-mpi4py, vtk-h, mfem, adios, py-sphinx, py-sphinx-rtd-theme
Link Dependencies:
cuda, conduit, python, mpi, py-mpi4py, vtk-h, mfem, adios
Run Dependencies:
py-numpy, py-pip
Description:
Ascent is an open source many-core capable lightweight in situ visualization and analysis infrastructure for multi-physics HPC simulations.

asciidoc

Homepage:
Spack package:
Versions:
8.6.9
Build Dependencies:
libxml2, libxslt, docbook-xml, docbook-xsl
Link Dependencies:
libxml2, libxslt, docbook-xml, docbook-xsl
Description:
A presentable text document format for writing articles, UNIX man pages and other small to medium sized documents.

asciidoctor

Homepage:
Spack package:
Versions:
1.5.8
Build Dependencies:
ruby
Link Dependencies:
ruby
Description:
Modern asciidoc tool based on ruby

asdf-cxx

Homepage:
Spack package:
Versions:
7.2.1, 7.2.0, 7.1.0, 7.0.0, 6.3.0, 6.0.0, 5.0.0, 4.0.1, 3.1.0, 3.0.0, 2.6.1, 2.5.1, 2.5.0, 2.4.1, 2.4.0, 2.3.1, 2.2.1, 2.1.1, 2.1.0, 1.1.0, 1.0.0
Build Dependencies:
cmake, bzip2, openssl, py-numpy, python, swig, yaml-cpp, zlib
Link Dependencies:
bzip2, openssl, yaml-cpp, zlib
Run Dependencies:
py-numpy, python
Description:
ASDF - Advanced Scientific Data Format, a C++ implementation

aspa

Homepage:
Spack package:
Versions:
master
Build Dependencies:
lapack, blas, mpi, hdf5
Link Dependencies:
lapack, blas, mpi, hdf5
Description:
A fundamental premise in ExMatEx is that scale-bridging performed in heterogeneous MPMD materials science simulations will place important demands upon the exascale ecosystem that need to be identified and quantified.

aspcud

Homepage:
Spack package:
Versions:
1.9.4
Build Dependencies:
cmake, boost, re2c, clingo
Link Dependencies:
clingo
Description:
Aspcud: Package dependency solver Aspcud is a solver for package dependencies. A package universe and a request to install, remove, or upgrade packages have to be encoded in the CUDF format. Such a CUDF document can then be passed to aspcud along with an optimization criteria to obtain a solution to the given package problem.

aspect

Homepage:
Spack package:
Versions:
develop, 2.1.0, 2.0.1, 2.0.0
Build Dependencies:
cmake, dealii, dealii-parameter-gui
Link Dependencies:
dealii, dealii-parameter-gui
Description:
Parallel, extendible finite element code to simulate convection in the Earth's mantle and elsewhere.

aspell

Homepage:
Spack package:
Versions:
0.60.6.1
Description:
GNU Aspell is a Free and Open Source spell checker designed to eventually replace Ispell.

aspell6-de

Homepage:
Spack package:
Versions:
6-de-20030222-1
Build Dependencies:
aspell
Link Dependencies:
aspell
Description:
German (de) dictionary for aspell.

aspell6-en

Homepage:
Spack package:
Versions:
2017.01.22-0
Build Dependencies:
aspell
Link Dependencies:
aspell
Description:
English (en) dictionary for aspell.

aspell6-es

Homepage:
Spack package:
Versions:
1.11-2
Build Dependencies:
aspell
Link Dependencies:
aspell
Description:
Spanish (es) dictionary for aspell.

aspera-cli

Homepage:
Spack package:
Versions:
3.7.7
Description:
The Aspera CLI client for the Fast and Secure Protocol (FASP).

assimp

Homepage:
Spack package:
Versions:
4.0.1
Build Dependencies:
cmake, boost
Link Dependencies:
boost
Description:
Open Asset Import Library (Assimp) is a portable Open Source library to import various well-known 3D model formats in a uniform manner.

astra

Homepage:
Spack package:
Versions:
2016-11-30
Description:
A Space Charge Tracking Algorithm.

astral

Homepage:
Spack package:
Versions:
5.6.1, 4.10.7
Build Dependencies:
java, zip
Run Dependencies:
java
Description:
ASTRAL is a tool for estimating an unrooted species tree given a set of unrooted gene trees.

astyle

Homepage:
Spack package:
Versions:
3.1, 3.0.1, 2.06, 2.05.1, 2.04
Description:
A Free, Fast, and Small Automatic Formatter for C, C++, C++/CLI, Objective-C, C#, and Java Source Code.

at-spi2-atk

Homepage:
Spack package:
Versions:
2.26.2, 2.26.1
Build Dependencies:
meson, ninja, pkgconfig, at-spi2-core, atk
Link Dependencies:
at-spi2-core, atk
Description:
The At-Spi2 Atk package contains a library that bridges ATK to At-Spi2 D-Bus service.

at-spi2-core

Homepage:
Spack package:
Versions:
2.28.0
Build Dependencies:
meson, ninja, glib, dbus, gettext, libx11, libxi, libxtst, recordproto, inputproto, fixesproto, pkgconfig, python
Link Dependencies:
glib, dbus, gettext, libx11, libxi
Description:
The At-Spi2 Core package provides a Service Provider Interface for the Assistive Technologies available on the GNOME platform and a library against which applications can be linked.

athena

Homepage:
Spack package:
Versions:
master, 4.2
Build Dependencies:
autoconf, automake, libtool, m4, mpi, fftw
Link Dependencies:
mpi, fftw
Description:
Athena is a grid-based code for astrophysical magnetohydrodynamics (MHD). It was developed primarily for studies of the interstellar medium, star formation, and accretion flows.

atk

Homepage:
Spack package:
Versions:
2.30.0, 2.28.1, 2.20.0, 2.14.0
Build Dependencies:
meson, glib, gettext, pkgconfig, gobject-introspection, libffi
Link Dependencies:
glib, gettext, gobject-introspection, libffi
Description:
ATK provides the set of accessibility interfaces that are implemented by other toolkits and applications. Using the ATK interfaces, accessibility tools have full access to view and control running applications.

atlas

Homepage:
Spack package:
Versions:
3.11.41, 3.11.39, 3.11.34, 3.10.3, 3.10.2
Description:
Automatically Tuned Linear Algebra Software, generic shared ATLAS is an approach for the automatic generation and optimization of numerical software. Currently ATLAS supplies optimized versions for the complete set of linear algebra kernels known as the Basic Linear Algebra Subroutines (BLAS), and a subset of the linear algebra routines in the LAPACK library.

atom-dft

Homepage:
Spack package:
Versions:
4.2.6
Build Dependencies:
libgridxc, xmlf90
Link Dependencies:
libgridxc, xmlf90
Description:
ATOM is a program for DFT calculations in atoms and pseudopotential generation.

atompaw

Homepage:
Spack package:
Versions:
4.0.0.13, 3.1.0.3
Build Dependencies:
lapack, blas, libxc
Link Dependencies:
lapack, blas, libxc
Description:
A Projector Augmented Wave (PAW) code for generating atom-centered functions. Official website: http://pwpaw.wfu.edu User's guide: ~/doc/atompaw-usersguide.pdf

atop

Homepage:
Spack package:
Versions:
2.5.0, 2.4.0, 2.3.0, 2.2.6, 2.2-3
Build Dependencies:
zlib, ncurses
Link Dependencies:
zlib, ncurses
Description:
Atop is an ASCII full-screen performance monitor for Linux

attr

Homepage:
Spack package:
Versions:
2.4.47, 2.4.46
Description:
Commands for Manipulating Filesystem Extended Attributes

audit-userspace

Homepage:
Spack package:
Versions:
2.8.5, 2.8.4, 2.8.3, 2.8.2
Build Dependencies:
autoconf, automake, libtool, m4, openldap, swig
Link Dependencies:
openldap, swig
Description:
Linux audit userspace

augustus

Homepage:
Spack package:
Versions:
3.3.2, 3.3.1-tag1, 3.3, 3.2.3
Build Dependencies:
perl, bamtools, gsl, boost, zlib, htslib, bcftools, samtools, curl
Link Dependencies:
bamtools, gsl, boost, zlib, htslib, bcftools, samtools, curl
Run Dependencies:
perl
Description:
AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences

autoconf

Homepage:
Spack package:
Versions:
2.69, 2.62, 2.59, 2.13
Build Dependencies:
m4, perl
Run Dependencies:
m4, perl
Description:
Autoconf -- system configuration part of autotools

autodock-vina

Homepage:
Spack package:
Versions:
1_1_2
Build Dependencies:
boost
Link Dependencies:
boost
Description:
AutoDock Vina is an open-source program for doing molecular docking

autofact

Homepage:
Spack package:
Versions:
3_4
Run Dependencies:
perl, perl-bioperl, perl-io-string, perl-libwww-perl, blast-legacy
Description:
An Automatic Functional Annotation and Classification Tool

autogen

Homepage:
Spack package:
Versions:
5.18.12
Build Dependencies:
pkgconfig, guile, libxml2
Link Dependencies:
guile, libxml2
Description:
AutoGen is a tool designed to simplify the creation and maintenance of programs that contain large amounts of repetitious text. It is especially valuable in programs that have several blocks of text that must be kept synchronized.

automaded

Homepage:
Spack package:
Versions:
1.0
Build Dependencies:
cmake, mpi, boost, callpath
Link Dependencies:
mpi, boost, callpath
Description:
AutomaDeD (Automata-based Debugging for Dissimilar parallel tasks) is a tool for automatic diagnosis of performance and correctness problems in MPI applications. It creates control-flow models of each MPI process and, when a failure occurs, these models are leveraged to find the origin of problems automatically. MPI calls are intercepted (using wrappers) to create the models. When an MPI application hangs, AutomaDeD creates a progress-dependence graph that helps finding the process (or group of processes) that caused the hang.

automake

Homepage:
Spack package:
Versions:
1.16.1, 1.15.1, 1.15, 1.14.1, 1.13.4, 1.11.6
Build Dependencies:
autoconf, perl
Run Dependencies:
perl
Description:
Automake -- make file builder part of autotools

avizo

Homepage:
Spack package:
Versions:
9.7.0
Description:
Avizo is a 3D analysis software for scientific and industrial data. Wherever three-dimensional imaging data sets need to be processed, in materials science, geosciences or engineering applications, Avizo offers abundant state-of-the-art image data processing, exploration and analysis features within an intuitive workflow and easy-to-use graphical user interface.

aws-parallelcluster

Homepage:
Spack package:
Versions:
2.5.1, 2.5.0
Build Dependencies:
python, py-setuptools, py-boto3, py-future, py-tabulate, py-ipaddress, py-enum34, py-pyyaml, py-configparser
Link Dependencies:
python
Run Dependencies:
python, py-setuptools, py-boto3, py-future, py-tabulate, py-ipaddress, py-enum34, py-pyyaml, py-configparser
Description:
AWS ParallelCluster is an AWS supported Open Source cluster management tool to deploy and manage HPC clusters in the AWS cloud.

awscli

Homepage:
Spack package:
Versions:
1.16.308, 1.16.179
Build Dependencies:
python, py-setuptools, py-botocore, py-docutils, py-rsa, py-s3transfer, py-argparse, py-pyyaml, py-colorama
Link Dependencies:
python
Run Dependencies:
python, py-botocore, py-docutils, py-rsa, py-s3transfer, py-argparse, py-pyyaml, py-colorama
Test Dependencies:
py-nose, py-mock
Description:
This package provides a unified command line interface to Amazon Web Services

axel

Homepage:
Spack package:
Versions:
2.16.1
Build Dependencies:
m4, autoconf, automake, libtool, pkgconfig, gettext, openssl
Link Dependencies:
gettext, openssl
Description:
Axel is a light command line download accelerator for Linux and Unix

axl

Homepage:
Spack package:
Versions:
master, 0.1.1
Build Dependencies:
cmake, kvtree
Link Dependencies:
kvtree
Description:
Asynchronous transfer library

bam-readcount

Homepage:
Spack package:
Versions:
0.8.0
Build Dependencies:
cmake
Description:
Bam-readcount generates metrics at single nucleotide positions.

bamdst

Homepage:
Spack package:
Versions:
master
Build Dependencies:
zlib
Link Dependencies:
zlib
Description:
Bamdst is a a lightweight bam file depth statistical tool.

bamtools

Homepage:
Spack package:
Versions:
2.5.1, 2.5.0, 2.4.1, 2.4.0, 2.3.0, 2.2.3
Build Dependencies:
cmake
Link Dependencies:
zlib
Description:
C++ API & command-line toolkit for working with BAM data.

bamutil

Homepage:
Spack package:
Versions:
1.0.13
Build Dependencies:
zlib
Link Dependencies:
zlib
Description:
bamUtil is a repository that contains several programs that perform operations on SAM/BAM files. All of these programs are built into a single executable, bam.

barrnap

Homepage:
Spack package:
Versions:
0.8, 0.7, 0.6
Run Dependencies:
hmmer
Description:
Barrnap predicts the location of ribosomal RNA genes in genomes.

bash

Homepage:
Spack package:
Versions:
5.0, 4.4.12, 4.4, 4.3
Build Dependencies:
ncurses, readline, libiconv
Link Dependencies:
ncurses, readline, libiconv
Description:
The GNU Project's Bourne Again SHell.

bash-completion

Homepage:
Spack package:
Versions:
develop, 2.7, 2.3
Build Dependencies:
automake, autoconf, libtool
Run Dependencies:
bash
Description:
Programmable completion functions for bash.

bats

Homepage:
Spack package:
Versions:
0.4.0
Description:
Bats is a TAP-compliant testing framework for Bash.

bazel

Homepage:
Spack package:
Versions:
1.2.1, 1.2.0, 1.1.0, 1.0.1, 1.0.0, 0.29.1, 0.29.0, 0.28.1, 0.28.0, 0.27.2, 0.27.1, 0.27.0, 0.26.1, 0.26.0, 0.25.3, 0.25.2, 0.25.1, 0.25.0, 0.24.1, 0.24.0, 0.23.2, 0.23.1, 0.23.0, 0.22.0, 0.21.0, 0.20.0, 0.19.2, 0.19.1, 0.19.0, 0.18.1, 0.18.0, 0.17.2, 0.17.1, 0.16.1, 0.16.0, 0.15.2, 0.15.1, 0.15.0, 0.14.1, 0.14.0, 0.13.1, 0.13.0, 0.12.0, 0.11.1, 0.11.0, 0.10.1, 0.10.0, 0.9.0, 0.8.1, 0.8.0, 0.7.0, 0.6.1, 0.6.0, 0.5.4, 0.5.3, 0.5.2, 0.5.1, 0.5.0, 0.4.5, 0.4.4, 0.4.3, 0.4.2, 0.4.1, 0.4.0, 0.3.2, 0.3.1, 0.3.0
Build Dependencies:
jdk, python
Run Dependencies:
jdk, python
Description:
Bazel is an open-source build and test tool similar to Make, Maven, and Gradle. It uses a human-readable, high-level build language. Bazel supports projects in multiple languages and builds outputs for multiple platforms. Bazel supports large codebases across multiple repositories, and large numbers of users.

bbcp

Homepage:
Spack package:
Versions:
git
Build Dependencies:
zlib, openssl
Link Dependencies:
zlib, openssl
Description:
Securely and quickly copy data from source to target

bbmap

Homepage:
Spack package:
Versions:
38.63, 37.36
Build Dependencies:
java
Link Dependencies:
java
Description:
Short read aligner for DNA and RNA-seq data.

bc

Homepage:
Spack package:
Versions:
1.07
Build Dependencies:
ed, texinfo
Description:
bc is an arbitrary precision numeric processing language. Syntax is similar to C, but differs in many substantial areas. It supports interactive execution of statements.

bcftools

Homepage:
Spack package:
Versions:
1.10.2, 1.9, 1.8, 1.7, 1.6, 1.4, 1.3.1, 1.2
Build Dependencies:
gsl, perl, htslib
Link Dependencies:
gsl, htslib
Run Dependencies:
py-matplotlib, perl
Description:
BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF- compressed.

bcl2fastq2

Homepage:
Spack package:
Versions:
2.20.0.422, 2.19.1.403
Build Dependencies:
boost, cmake, libxml2, libxslt, libgcrypt, zlib
Link Dependencies:
boost, cmake, libxml2, libxslt, libgcrypt, zlib
Description:
The bcl2fastq2 Conversion Software converts base call (BCL) files from a sequencing run into FASTQ files.

bdftopcf

Homepage:
Spack package:
Versions:
1.0.5
Build Dependencies:
libxfont, pkgconfig, xproto, fontsproto, util-macros
Link Dependencies:
libxfont
Description:
bdftopcf is a font compiler for the X server and font server. Fonts in Portable Compiled Format can be read by any architecture, although the file is structured to allow one particular architecture to read them directly without reformatting. This allows fast reading on the appropriate machine, but the files are still portable (but read more slowly) on other machines.

bdw-gc

Homepage:
Spack package:
Versions:
8.0.0, 7.6.0, 7.4.4
Build Dependencies:
libatomic-ops
Link Dependencies:
libatomic-ops
Description:
The Boehm-Demers-Weiser conservative garbage collector is a garbage collecting replacement for C malloc or C++ new.

beagle

Homepage:
Spack package:
Versions:
5.1, 5.0, 4.1
Run Dependencies:
java
Description:
Beagle is a software package for phasing genotypes and for imputing ungenotyped markers.

bear

Homepage:
Spack package:
Versions:
2.2.0, 2.0.4
Build Dependencies:
cmake, python
Link Dependencies:
python
Description:
Bear is a tool that generates a compilation database for clang tooling from non-cmake build systems.

beast-tracer

Homepage:
Spack package:
Versions:
1.7.1
Build Dependencies:
ant, java
Run Dependencies:
java
Description:
Tracer is a graphical tool for visualization and diagnostics of MCMC output.

beast1

Homepage:
Spack package:
Versions:
1.10.4, 1.8.4
Build Dependencies:
libbeagle
Link Dependencies:
libbeagle
Run Dependencies:
java, libbeagle
Description:
BEAST is a cross-platform program for Bayesian analysis of molecular sequences using MCMC.

beast2

Homepage:
Spack package:
Versions:
2.5.2, 2.4.6
Build Dependencies:
java
Link Dependencies:
java
Description:
BEAST is a cross-platform program for Bayesian inference using MCMC of molecular sequences. It is entirely orientated towards rooted, time- measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology.

bedops

Homepage:
Spack package:
Versions:
2.4.35, 2.4.34, 2.4.30
Description:
BEDOPS is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale.

bedtools2

Homepage:
Spack package:
Versions:
2.27.1, 2.27.0, 2.26.0, 2.25.0, 2.23.0
Build Dependencies:
zlib
Link Dependencies:
zlib
Description:
Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome.

beforelight

Homepage:
Spack package:
Versions:
1.0.5
Build Dependencies:
libx11, libxscrnsaver, libxt, pkgconfig, util-macros
Link Dependencies:
libx11, libxscrnsaver, libxt
Description:
The beforelight program is a sample implementation of a screen saver for X servers supporting the MIT-SCREEN-SAVER extension. It is only recommended for use as a code sample, as it does not include features such as screen locking or configurability.

benchmark

Homepage:
Spack package:
Versions:
develop, 1.5.0, 1.4.1, 1.4.0, 1.3.0, 1.2.0, 1.1.0, 1.0.0
Build Dependencies:
cmake
Description:
A microbenchmark support library

berkeley-db

Homepage:
Spack package:
Versions:
6.2.32, 6.1.29, 6.0.35, 5.3.28
Description:
Oracle Berkeley DB

bertini

Homepage:
Spack package:
Versions:
1.5
Build Dependencies:
flex, bison, gmp, mpfr, mpi
Link Dependencies:
gmp, mpfr, mpi
Description:
Bertini is a general-purpose solver, written in C, that was created for research about polynomial continuation. It solves for the numerical solution of systems of polynomial equations using homotopy continuation.

bib2xhtml

Homepage:
Spack package:
Versions:
3.0-79-ge935
Description:
bib2xhtml is a program that converts BibTeX files into HTML.

bigreqsproto

Homepage:
Spack package:
Versions:
1.1.2
Build Dependencies:
pkgconfig, util-macros
Description:
Big Requests Extension. This extension defines a protocol to enable the use of requests that exceed 262140 bytes in length.

bind9

Homepage:
Spack package:
Versions:
9_14_6
Description:
BIND 9 has evolved to be a very flexible, full-featured DNS system.

binutils

Homepage:
Spack package:
Versions:
2.33.1, 2.32, 2.31.1, 2.29.1, 2.28, 2.27, 2.26, 2.25.1, 2.25, 2.24, 2.23.2, 2.20.1
Build Dependencies:
zlib, gettext, m4, bison
Link Dependencies:
zlib, gettext
Description:
GNU binutils, which contain the linker, assembler, objdump and others

bioawk

Homepage:
Spack package:
Versions:
1.0
Build Dependencies:
zlib, bison
Link Dependencies:
zlib
Description:
Bioawk is an extension to Brian Kernighan's awk, adding the support of several common biological data formats, including optionally gzip'ed BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names.

biobloom

Homepage:
Spack package:
Versions:
2.2.0
Build Dependencies:
boost, sdsl-lite, sparsehash, zlib
Link Dependencies:
boost, sdsl-lite, sparsehash, zlib
Description:
BioBloom Tools (BBT) provides the means to create filters for a given reference and then to categorize sequences.

bismark

Homepage:
Spack package:
Versions:
0.19.0, 0.18.2
Run Dependencies:
bowtie2, perl, samtools
Description:
A tool to map bisulfite converted sequence reads and determine cytosine methylation states

bison

Homepage:
Spack package:
Versions:
3.4.2, 3.4.1, 3.0.5, 3.0.4, 2.7
Build Dependencies:
diffutils, m4, perl, help2man
Run Dependencies:
m4
Description:
Bison is a general-purpose parser generator that converts an annotated context-free grammar into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.

bitmap

Homepage:
Spack package:
Versions:
1.0.8
Build Dependencies:
libx11, libxmu, libxaw, libxt, xbitmaps, xproto, pkgconfig, util-macros
Link Dependencies:
libx11, libxmu, libxaw, libxt
Description:
bitmap, bmtoa, atobm - X bitmap (XBM) editor and converter utilities.

blasr

Homepage:
Spack package:
Versions:
5.3.1
Build Dependencies:
ncurses, hdf5, htslib, zlib, boost, pbbam, blasr-libcpp, python
Link Dependencies:
ncurses, hdf5, htslib, zlib, boost, pbbam, blasr-libcpp
Description:
The PacBio long read aligner.

blasr-libcpp

Homepage:
Spack package:
Versions:
5.3.1
Build Dependencies:
pbbam, hdf5, python
Link Dependencies:
pbbam, hdf5
Description:
Blasr_libcpp is a library used by blasr and other executables such as samtoh5, loadPulses for analyzing PacBio sequences.

blast-legacy

Homepage:
Spack package:
Versions:
2.2.26
Build Dependencies:
tcsh
Description:
Legacy NCBI BLAST distribution -- no longer supported. Contains older programs including `blastall'

blast-plus

Homepage:
Spack package:
Versions:
2.9.0, 2.8.1, 2.7.1, 2.6.0, 2.2.30
Build Dependencies:
jpeg, libpng, freetype, gnutls, openssl, zlib, bzip2, lzo, pcre, python, perl, lmdb
Link Dependencies:
jpeg, libpng, freetype, gnutls, openssl, zlib, bzip2, lzo, pcre, python, perl, lmdb
Description:
Basic Local Alignment Search Tool.

blast2go

Homepage:
Spack package:
Versions:
5.2.5
Build Dependencies:
bash, java
Run Dependencies:
blast-plus
Description:
Blast2GO is a bioinformatics platform for high-quality functional annotation and analysis of genomic datasets.

blat

Homepage:
Spack package:
Versions:
35
Build Dependencies:
libpng
Link Dependencies:
libpng
Description:
BLAT (BLAST-like alignment tool) is a pairwise sequence alignment algorithm.

blaze

Homepage:
Spack package:
Versions:
master, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.6, 2.5, 2.4, 2.3, 2.2, 2.1, 2.0, 1.5, 1.4, 1.3, 1.2, 1.1, 1.0
Build Dependencies:
cmake
Description:
Blaze is an open-source, high-performance C++ math library for dense and sparse arithmetic. With its state-of-the-art Smart Expression Template implementation Blaze combines the elegance and ease of use of a domain- specific language with HPC-grade performance, making it one of the most intuitive and fastest C++ math libraries available.

blis

Homepage:
Spack package:
Versions:
master, 0.6.1, 0.6.0, 0.5.0, 0.4.0, 0.3.2, 0.3.1, 0.3.0, 0.2.2
Build Dependencies:
python
Run Dependencies:
python
Description:
BLIS is a portable software framework for instantiating high-performance BLAS-like dense linear algebra libraries. The framework was designed to isolate essential kernels of computation that, when optimized, immediately enable optimized implementations of most of its commonly used and computationally intensive operations. BLIS is written in ISO C99 and available under a new/modified/3-clause BSD license. While BLIS exports a new BLAS-like API, it also includes a BLAS compatibility layer which gives application developers access to BLIS implementations via traditional BLAS routine calls. An object-based API unique to BLIS is also available.

bliss

Homepage:
Spack package:
Versions:
0.73
Build Dependencies:
gmp, libtool
Link Dependencies:
gmp
Description:
bliss: A Tool for Computing Automorphism Groups and Canonical Labelings of Graphs

blitz

Homepage:
Spack package:
Versions:
1.0.1, 1.0.0
Description:
N-dimensional arrays for C++

blktrace

Homepage:
Spack package:
Versions:
1.2.0, 1.1.0, 1.0.5, 1.0.4, 1.0.3, 1.0.2
Build Dependencies:
libaio
Link Dependencies:
libaio
Description:
blktrace is a block layer IO tracing mechanism which provides detailed information about request queue operations up to user space. There are three major components: a kernel component, a utility to record the i/o trace information for the kernel to user space, and utilities to analyse and view the trace information.

bmake

Homepage:
Spack package:
Versions:
20180512, 20171207
Description:
Portable version of NetBSD make(1).

bmi

Homepage:
Spack package:
Versions:
develop
Build Dependencies:
autoconf, automake
Description:
a communications framework and network abstraction layer

bml

Homepage:
Spack package:
Versions:
develop, 1.3.1, 1.3.0, 1.2.3, 1.2.2, 1.1.0
Build Dependencies:
cmake, blas, lapack, mpi
Link Dependencies:
blas, lapack, mpi
Description:
The basic matrix library (bml) is a collection of various matrix data formats (in dense and sparse) and their associated algorithms for basic matrix operations.

bohrium

Homepage:
Spack package:
Versions:
develop, 0.9.1, 0.9.0
Build Dependencies:
cuda, cmake, python, boost, opencl, netlib-lapack, blas, opencv, py-numpy, swig, py-cython, zlib
Link Dependencies:
cuda, python, boost, opencl, netlib-lapack, blas, opencv, zlib
Run Dependencies:
py-numpy
Test Dependencies:
python, py-numpy
Description:
Library for automatic acceleration of array operations

bolt

Homepage:
Spack package:
Versions:
master, 1.0rc3, 1.0rc2, 1.0rc1, 1.0b1
Build Dependencies:
cmake, argobots, autoconf, automake, libtool
Link Dependencies:
argobots
Description:
BOLT targets a high-performing OpenMP implementation, especially specialized for fine-grain parallelism. Unlike other OpenMP implementations, BOLT utilizes a lightweight threading model for its underlying threading mechanism. It currently adopts Argobots, a new holistic, low-level threading and tasking runtime, in order to overcome shortcomings of conventional OS-level threads. The current BOLT implementation is based on the OpenMP runtime in LLVM, and thus it can be used with LLVM/Clang, Intel OpenMP compiler, and GCC.

bookleaf-cpp

Homepage:
Spack package:
Versions:
develop, 2.0.2, 2.0.1, 2.0
Build Dependencies:
cmake, caliper, parmetis, silo, typhon, mpi, yaml-cpp
Link Dependencies:
caliper, parmetis, silo, typhon, mpi, yaml-cpp
Description:
BookLeaf is a 2D unstructured hydrodynamics mini-app.

boost

Homepage:
Spack package:
Versions:
develop, 1.72.0, 1.71.0, 1.70.0, 1.69.0, 1.68.0, 1.67.0, 1.66.0, 1.65.1, 1.65.0, 1.64.0, 1.63.0, 1.62.0, 1.61.0, 1.60.0, 1.59.0, 1.58.0, 1.57.0, 1.56.0, 1.55.0, 1.54.0, 1.53.0, 1.52.0, 1.51.0, 1.50.0, 1.49.0, 1.48.0, 1.47.0, 1.46.1, 1.46.0, 1.45.0, 1.44.0, 1.43.0, 1.42.0, 1.41.0, 1.40.0, 1.39.0, 1.38.0, 1.37.0, 1.36.0, 1.35.0, 1.34.1, 1.34.0
Build Dependencies:
icu4c, python, mpi, bzip2, zlib, py-numpy
Link Dependencies:
icu4c, python, mpi, bzip2, zlib
Run Dependencies:
py-numpy
Description:
Boost provides free peer-reviewed portable C++ source libraries, emphasizing libraries that work well with the C++ Standard Library. Boost libraries are intended to be widely useful, and usable across a broad spectrum of applications. The Boost license encourages both commercial and non-commercial use.

boostmplcartesianproduct

Homepage:
Spack package:
Versions:
20161205
Description:
Cartesian_product is an extension to the Boost.MPL library and as such requires a version of the Boost libraries on your system.

bowtie

Homepage:
Spack package:
Versions:
1.2.3, 1.2.2_p1, 1.2.2, 1.2.1.1, 1.2.1, 1.2.0, 1.2
Build Dependencies:
tbb, zlib
Link Dependencies:
tbb, zlib
Description:
Bowtie is an ultrafast, memory-efficient short read aligner for short DNA sequences (reads) from next-gen sequencers.

bowtie2

Homepage:
Spack package:
Versions:
2.3.5.1, 2.3.5, 2.3.4.1, 2.3.1, 2.3.0, 2.2.5
Build Dependencies:
tbb, readline, zlib
Link Dependencies:
tbb, readline, zlib
Run Dependencies:
perl, python
Description:
Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences

boxlib

Homepage:
Spack package:
Versions:
16.12.2
Build Dependencies:
cmake, mpi
Link Dependencies:
mpi
Description:
BoxLib, a software framework for massively parallel block-structured adaptive mesh refinement (AMR) codes.

bpp-core

Homepage:
Spack package:
Versions:
2.2.0
Build Dependencies:
cmake
Description:
Bio++ core library.

bpp-phyl

Homepage:
Spack package:
Versions:
2.2.0
Build Dependencies:
cmake, bpp-core, bpp-seq
Link Dependencies:
bpp-core, bpp-seq
Description:
Bio++ phylogeny library.

bpp-seq

Homepage:
Spack package:
Versions:
2.2.0
Build Dependencies:
cmake, bpp-core
Link Dependencies:
bpp-core
Description:
Bio++ seq library.

bpp-suite

Homepage:
Spack package:
Versions:
2.2.0
Build Dependencies:
cmake, texinfo, bpp-core, bpp-seq, bpp-phyl
Link Dependencies:
bpp-core, bpp-seq, bpp-phyl
Description:
BppSuite is a suite of ready-to-use programs for phylogenetic and sequence analysis.

bracken

Homepage:
Spack package:
Versions:
1.0.0
Build Dependencies:
perl, python, perl-exporter-tiny, perl-list-moreutils, perl-parallel-forkmanager
Link Dependencies:
perl, python, perl-exporter-tiny, perl-list-moreutils, perl-parallel-forkmanager
Run Dependencies:
perl, python
Description:
Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.

braker

Homepage:
Spack package:
Versions:
2.1.4, 1.11
Build Dependencies:
perl, perl-scalar-util-numeric, perl-parallel-forkmanager, perl-file-which, perl-yaml, perl-hash-merge, perl-logger-simple, perl-file-homedir, augustus, genemark-et, bamtools, samtools, diamond
Link Dependencies:
augustus, genemark-et, bamtools, samtools, diamond
Run Dependencies:
perl, perl-scalar-util-numeric, perl-parallel-forkmanager, perl-file-which, perl-yaml, perl-hash-merge, perl-logger-simple, perl-file-homedir
Description:
BRAKER is a pipeline for unsupervised RNA-Seq-based genome annotation that combines the advantages of GeneMark-ET and AUGUSTUS

branson

Homepage:
Spack package:
Versions:
develop, 0.82, 0.81, 0.8
Build Dependencies:
cmake, mpi, boost, metis, parmetis
Link Dependencies:
mpi, boost, metis, parmetis
Description:
Branson's purpose is to study different algorithms for parallel Monte Carlo transport. Currently it contains particle passing and mesh passing methods for domain decomposition.

breakdancer

Homepage:
Spack package:
Versions:
master, 1.4.5
Build Dependencies:
cmake, zlib
Link Dependencies:
zlib, ncurses
Run Dependencies:
perl-statistics-descriptive, perl-math-cdf, perl-gdgraph, perl-gdgraph-histogram, perl-list-moreutils, perl-exporter-tiny
Description:
BreakDancer-1.3.6, released under GPLv3, is a perl/Cpp package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads. It includes two complementary programs. BreakDancerMax predicts five types of structural variants: insertions, deletions, inversions, inter- and intra-chromosomal translocations from next-generation short paired-end sequencing reads using read pairs that are mapped with unexpected separation distances or orientation. BreakDancerMini focuses on detecting small indels (usually between 10bp and 100bp) using normally mapped read pairs..

bref3

Homepage:
Spack package:
Versions:
2019-11-25, 2019-07-12, 2018-01-27
Run Dependencies:
java
Description:
Bref3: Converts from VCF format to bref3 format.

breseq

Homepage:
Spack package:
Versions:
0.33.2, 0.33.1, 0.31.1
Build Dependencies:
autoconf, automake, libtool, m4
Link Dependencies:
zlib
Run Dependencies:
bedtools2, r
Description:
breseq is a computational pipeline for finding mutations relative to a reference sequence in short-read DNA re-sequencing data for haploid microbial-sized genomes.

bridger

Homepage:
Spack package:
Versions:
2014-12-01
Build Dependencies:
boost
Link Dependencies:
boost
Run Dependencies:
perl
Description:
Bridger : An Efficient De novo Transcriptome Assembler For RNA-Seq Data

brigand

Homepage:
Spack package:
Versions:
master, 1.3.0, 1.2.0, 1.1.0, 1.0.0
Description:
Brigand Meta-programming library

brltty

Homepage:
Spack package:
Versions:
6.0, 5.6, 5.5, 5.4
Build Dependencies:
autoconf, automake, libtool, m4, expat
Link Dependencies:
expat
Description:
BRLTTY is a background process (daemon) providing access to the Linux/Unix console (when in text mode) for a blind person using a refreshable braille display.

brotli

Homepage:
Spack package:
Versions:
1.0.7
Build Dependencies:
cmake
Description:
Brotli is a generic-purpose lossless compression algorithm

bsseeker2

Homepage:
Spack package:
Versions:
2.1.8, 2.1.7, 2.1.2
Build Dependencies:
python, py-pysam
Run Dependencies:
python, py-pysam
Description:
A versatile aligning pipeline for bisulfite sequencing data.

bucky

Homepage:
Spack package:
Versions:
1.4.4
Description:
BUCKy is a free program to combine molecular data from multiple loci. BUCKy estimates the dominant history of sampled individuals, and how much of the genome supports each relationship, using Bayesian concordance analysis.

bumpversion

Homepage:
Spack package:
Versions:
0.5.3, 0.5.0
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Version-bump your software with a single command.

busco

Homepage:
Spack package:
Versions:
3.0.1, 2.0.1
Build Dependencies:
python, blast-plus, hmmer, augustus
Link Dependencies:
python, blast-plus, hmmer, augustus
Run Dependencies:
python
Description:
Assesses genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs

busybox

Homepage:
Spack package:
Versions:
1.31.1, 1.31.0, 1.30.1, 1.30.0
Description:
BusyBox combines tiny versions of many common UNIX utilities into a single small executable. It provides replacements for most of the utilities you usually find in GNU fileutils, shellutils, etc

butter

Homepage:
Spack package:
Versions:
0.3.3
Build Dependencies:
perl, samtools, bowtie
Link Dependencies:
samtools, bowtie
Run Dependencies:
perl
Description:
butter: Bowtie UTilizing iTerative placEment of Repetitive small rnas. A wrapper for bowtie to produce small RNA-seq alignments where multimapped small RNAs tend to be placed near regions of confidently high density.

butterflypack

Homepage:
Spack package:
Versions:
master, 1.1.0, 1.0.3, 1.0.1, 1.0.0
Build Dependencies:
cmake, mpi, blas, lapack, scalapack, arpack-ng
Link Dependencies:
mpi, blas, lapack, scalapack, arpack-ng
Description:
ButterflyPACK is a mathematical software for rapidly solving large-scale dense linear systems that exhibit off-diagonal rank-deficiency. These systems arise frequently from boundary element methods, or factorization phases in finite-difference/finite-element methods. ButterflyPACK relies on low-rank or butterfly formats under Hierarchical matrix, HODLR or other hierarchically nested frameworks to compress, factor and solve the linear system in quasi-linear time. The computationally most intensive phase, factorization, is accelerated via randomized linear algebras. The butterfly format, originally inspired by the butterfly data flow in fast Fourier Transform, is a linear algebra tool well-suited for compressing matrices arising from high-frequency wave equations or highly oscillatory integral operators.

bwa

Homepage:
Spack package:
Versions:
0.7.17, 0.7.15, 0.7.13, 0.7.12
Build Dependencies:
zlib
Link Dependencies:
zlib
Description:
Burrow-Wheeler Aligner for pairwise alignment between DNA sequences.

bwtool

Homepage:
Spack package:
Versions:
1.0
Build Dependencies:
libbeato
Link Dependencies:
libbeato
Description:
bwtool is a command-line utility for bigWig files.

byobu

Homepage:
Spack package:
Versions:
5.131, 5.127, 5.125, 5.123
Build Dependencies:
tmux
Run Dependencies:
tmux
Description:
Byobu: Text-based window manager and terminal multiplexer.

bzip2

Homepage:
Spack package:
Versions:
1.0.8, 1.0.7, 1.0.6
Build Dependencies:
diffutils
Description:
bzip2 is a freely available, patent free high-quality data compressor. It typically compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical compressors), whilst being around twice as fast at compression and six times faster at decompression.

c-ares

Homepage:
Spack package:
Versions:
master, 1.15.0, 1.13.0
Build Dependencies:
cmake
Description:
c-ares: A C library for asynchronous DNS requests

c-blosc

Homepage:
Spack package:
Versions:
1.17.0, 1.16.3, 1.15.0, 1.12.1, 1.11.1, 1.9.2, 1.9.1, 1.9.0, 1.8.1, 1.8.0
Build Dependencies:
cmake, snappy, zlib, zstd, lz4
Link Dependencies:
snappy, zlib, zstd, lz4
Description:
Blosc, an extremely fast, multi-threaded, meta-compressor library

c-blosc2

Homepage:
Spack package:
Versions:
develop
Build Dependencies:
cmake, lizard, lz4, snappy, zlib, zstd
Link Dependencies:
lizard, lz4, snappy, zlib, zstd
Description:
Next generation c-blosc with a new API, a new container and other bells and whistles

c-lime

Homepage:
Spack package:
Versions:
2-3-9
Description:
LIME (which can stand for Lattice QCD Interchange Message Encapsulation or more generally, Large Internet Message Encapsulation) is a simple packaging scheme for combining records containing ASCII and/or binary data.

cabana

Homepage:
Spack package:
Versions:
develop, 0.1.0-rc0, 0.1.0
Build Dependencies:
cmake, kokkos
Link Dependencies:
kokkos
Description:
The Exascale Co-Design Center for Particle Applications Toolkit

caffe

Homepage:
Spack package:
Versions:
1.0, rc5, rc4, rc3, rc2
Build Dependencies:
cmake, boost, cuda, blas, protobuf, glog, gflags, hdf5, opencv, leveldb, lmdb, python, py-numpy, matlab
Link Dependencies:
boost, cuda, blas, protobuf, glog, gflags, hdf5, opencv, leveldb, lmdb, python, matlab
Run Dependencies:
py-numpy
Description:
Caffe is a deep learning framework made with expression, speed, and modularity in mind. It is developed by the Berkeley Vision and Learning Center (BVLC) and by community contributors.

cairo

Homepage:
Spack package:
Versions:
1.17.2, 1.16.0, 1.14.12, 1.14.8, 1.14.0
Build Dependencies:
libx11, libxext, libxrender, libxcb, python, libpng, librsvg, glib, pixman, automake, autoconf, libtool, m4, freetype, pkgconfig, fontconfig
Link Dependencies:
libx11, libxext, libxrender, libxcb, libpng, librsvg, glib, pixman, freetype, fontconfig
Description:
Cairo is a 2D graphics library with support for multiple output devices.

cairomm

Homepage:
Spack package:
Versions:
1.6.4, 1.6.2
Build Dependencies:
cairo, libsigcpp
Link Dependencies:
cairo, libsigcpp
Description:
Cairomm is a C++ wrapper for the cairo graphics library.

caliper

Homepage:
Spack package:
Versions:
master, 2.2.0, 2.1.1, 2.0.1, 1.9.1, 1.9.0, 1.8.0, 1.7.0
Build Dependencies:
cmake, adiak, gotcha, dyninst, papi, libpfm4, mpi, unwind, sosflow, python
Link Dependencies:
adiak, gotcha, dyninst, papi, libpfm4, mpi, unwind, sosflow
Description:
Caliper is a program instrumentation and performance measurement framework. It is designed as a performance analysis toolbox in a library, allowing one to bake performance analysis capabilities directly into applications and activate them at runtime.

callpath

Homepage:
Spack package:
Versions:
1.0.4, 1.0.2, 1.0.1
Build Dependencies:
cmake, libdwarf, dyninst, adept-utils, mpi
Link Dependencies:
elf, libdwarf, dyninst, adept-utils, mpi
Description:
Library for representing callpaths consistently in distributed-memory performance tools.

camellia

Homepage:
Spack package:
Versions:
master
Build Dependencies:
cmake, trilinos, moab, hdf5, mpi
Link Dependencies:
trilinos, moab, hdf5, mpi
Description:
Camellia: user-friendly MPI-parallel adaptive finite element package, with support for DPG and other hybrid methods, built atop Trilinos.

camx

Homepage:
Spack package:
Versions:
6.50
Build Dependencies:
mpi
Link Dependencies:
mpi
Description:
Comprehensive Air Quality Model with Extensions.

candle-benchmarks

Homepage:
Spack package:
Versions:
0.1
Build Dependencies:
python, py-theano, py-keras, py-matplotlib, py-tqdm, py-scikit-learn, opencv, py-mdanalysis, py-mpi4py, py-h5py, py-requests
Link Dependencies:
python, opencv
Run Dependencies:
py-theano, py-keras, py-matplotlib, py-tqdm, py-scikit-learn, py-mdanalysis, py-mpi4py, py-h5py, py-requests
Description:
ECP-CANDLE Benchmarks

cantera

Homepage:
Spack package:
Versions:
2.4.0, 2.3.0, 2.2.1
Build Dependencies:
scons, fmt, googletest, eigen, boost, sundials, blas, lapack, python, py-cython, py-numpy, py-scipy, py-3to2, py-unittest2, py-unittest2py3k, matlab
Link Dependencies:
fmt, googletest, eigen, boost, sundials, blas, lapack, python, matlab
Run Dependencies:
py-numpy, py-scipy, py-3to2, py-unittest2, py-unittest2py3k
Description:
Cantera is a suite of object-oriented software tools for problems involving chemical kinetics, thermodynamics, and/or transport processes.

canu

Homepage:
Spack package:
Versions:
1.8, 1.7.1, 1.7, 1.5
Run Dependencies:
gnuplot, jdk, perl
Description:
A single molecule sequence assembler for genomes large and small.

cap3

Homepage:
Spack package:
Versions:
2015-02-11
Description:
CAP3 is DNA Sequence Assembly Program

capnproto

Homepage:
Spack package:
Versions:
0.7.0
Description:
Cap'n Proto is an insanely fast data interchange format and capability- based RPC system.

capstone

Homepage:
Spack package:
Versions:
4.0.1
Build Dependencies:
cmake
Description:
Capstone is a lightweight multi-platform, multi-architecture disassembly framework.

cardioid

Homepage:
Spack package:
Versions:
develop, elecfem
Build Dependencies:
cmake, blas, lapack, mpi, cuda, mfem, perl
Link Dependencies:
blas, lapack, mpi, cuda, mfem
Description:
Cardiac simulation suite.

casacore

Homepage:
Spack package:
Versions:
3.2.0, 3.1.2, 3.1.1, 3.1.0, 3.0.0, 2.4.1
Build Dependencies:
cmake, flex, bison, blas, lapack, cfitsio, wcslib, fftw, hdf5, readline, python, boost, py-numpy
Link Dependencies:
blas, lapack, cfitsio, wcslib, fftw, hdf5, readline, python, boost, py-numpy
Description:
A suite of c++ libraries for radio astronomy data processing.

cask

Homepage:
Spack package:
Versions:
0.8.1, 0.7.4
Build Dependencies:
emacs
Run Dependencies:
emacs
Description:
Cask is a project management tool for Emacs Lisp to automate the package development cycle; development, dependencies, testing, building, packaging and more.

casper

Homepage:
Spack package:
Versions:
0.8.2
Build Dependencies:
jellyfish, boost
Link Dependencies:
jellyfish, boost
Description:
CASPER (Context-Aware Scheme for Paired-End Read) is state-of-the art merging tool in terms of accuracy and robustness. Using this sophisticated merging method, we could get elongated reads from the forward and reverse reads.

cassandra

Homepage:
Spack package:
Versions:
4.0-alpha2, 4.0-alpha1, 3.11.5
Description:
Apache Cassandra is a highly-scalable partitioned row store. Rows are organized into tables with a required primary key.

catalyst

Homepage:
Spack package:
Versions:
5.6.0, 5.5.2, 5.5.1, 5.5.0, 5.4.1, 5.4.0, 5.3.0, 5.2.0, 5.1.2, 5.0.1, 4.4.0
Build Dependencies:
cmake, python, git, mpi, py-numpy, py-mpi4py, gl, mesa, glx
Link Dependencies:
python, mpi, gl, mesa, glx
Run Dependencies:
python, py-numpy, py-mpi4py
Description:
Catalyst is an in situ use case library, with an adaptable application programming interface (API), that orchestrates the alliance between simulation and analysis and/or visualization tasks.

catch2

Homepage:
Spack package:
Versions:
2.9.1, 2.9.0, 2.8.0, 2.7.2, 2.7.1, 2.7.0, 2.6.1, 2.6.0, 2.5.0, 2.4.2, 2.4.1, 2.4.0, 2.3.0, 2.2.3, 2.2.2, 2.2.1, 2.1.0, 2.0.1, 1.12.1, 1.12.0, 1.11.0, 1.10.0, 1.9.7, 1.9.6, 1.9.5, 1.9.4, 1.9.3, 1.9.2, 1.9.1, 1.9.0, 1.8.2, 1.8.1, 1.8.0, 1.7.2, 1.7.1, 1.7.0, 1.6.1, 1.6.0, 1.5.9, 1.5.0, 1.4.0, 1.3.5, 1.3.0
Build Dependencies:
cmake
Description:
Catch2 is a multi-paradigm test framework for C++, which also supports Objective-C (and maybe C).

cbench

Homepage:
Spack package:
Versions:
1.3.0
Build Dependencies:
mpi, blas, lapack, fftw
Link Dependencies:
mpi, blas, lapack, fftw
Description:
Cbench is intended as a relatively straightforward toolbox of tests, benchmarks, applications, utilities, and framework to hold them together with the goal to facilitate scalable testing, benchmarking, and analysis of a Linux parallel compute cluster.

cblas

Homepage:
Spack package:
Versions:
2015-06-06
Build Dependencies:
blas
Link Dependencies:
blas
Description:
The BLAS (Basic Linear Algebra Subprograms) are routines that provide standard building blocks for performing basic vector and matrix operations.

cbtf

Homepage:
Spack package:
Versions:
develop, 1.9.3, 1.9.2, 1.9.1.2, 1.9.1.1, 1.9.1.0
Build Dependencies:
cmake, rpcsvc-proto, boost, mrnet, xerces-c, libxml2
Link Dependencies:
libtirpc, boost, mrnet, xerces-c, libxml2
Description:
CBTF project contains the base code for CBTF that supports creating components, component networks and the support to connect these components and component networks into sequential and distributed network tools.

cbtf-argonavis

Homepage:
Spack package:
Versions:
develop, 1.9.3, 1.9.2, 1.9.1.2, 1.9.1.1, 1.9.1.0
Build Dependencies:
cmake, boost, mrnet, cbtf, libmonitor, papi, cbtf-krell, cuda
Link Dependencies:
elf, boost, mrnet, cbtf, libmonitor, papi, cbtf-krell, cuda
Run Dependencies:
mrnet, cbtf, libmonitor, papi, cbtf-krell
Description:
CBTF Argo Navis project contains the CUDA collector and supporting libraries that was done as a result of a DOE SBIR grant.

cbtf-argonavis-gui

Homepage:
Spack package:
Versions:
develop, 1.3.0.0
Build Dependencies:
qt, cmake, boost, mrnet, cbtf, cbtf-krell, cbtf-argonavis, cuda, openspeedshop-utils, xerces-c, graphviz, qtgraph
Link Dependencies:
qt, boost, mrnet, cbtf, cbtf-krell, cbtf-argonavis, cuda, openspeedshop-utils, xerces-c, graphviz, qtgraph
Description:
CBTF Argo Navis GUI project contains the GUI that views OpenSpeedShop performance information by loading in the Sqlite database files.

cbtf-krell

Homepage:
Spack package:
Versions:
develop, 1.9.3, 1.9.2, 1.9.1.2, 1.9.1.1, 1.9.1.0
Build Dependencies:
cmake, rpcsvc-proto, binutils, boost, dyninst, mrnet, xerces-c, cbtf, libmonitor, libunwind, papi, llvm-openmp-ompt, openmpi, mpich, mvapich2, mpt, python, gotcha
Link Dependencies:
libtirpc, binutils, boost, dyninst, mrnet, xerces-c, cbtf, libmonitor, libunwind, papi, llvm-openmp-ompt, openmpi, mpich, mvapich2, mpt, gotcha
Run Dependencies:
mrnet, cbtf, libmonitor, papi, python
Description:
CBTF Krell project contains the Krell Institute contributions to the CBTF project. These contributions include many performance data collectors and support libraries as well as some example tools that drive the data collection at HPC levels of scale.

cbtf-lanl

Homepage:
Spack package:
Versions:
develop, 1.9.3, 1.9.2, 1.9.1.2, 1.9.1.1, 1.9.1.0
Build Dependencies:
cmake, mrnet, xerces-c, cbtf, cbtf-krell
Link Dependencies:
mrnet, xerces-c, cbtf, cbtf-krell
Description:
CBTF LANL project contains a memory tool and data center type system command monitoring tool.

ccache

Homepage:
Spack package:
Versions:
3.7.1, 3.3.4, 3.3.3, 3.3.2, 3.3.1, 3.3, 3.2.9
Build Dependencies:
gperf, libxslt, zlib
Link Dependencies:
gperf, libxslt, zlib
Description:
ccache is a compiler cache. It speeds up recompilation by caching previous compilations and detecting when the same compilation is being done again.

ccfits

Homepage:
Spack package:
Versions:
2.5, 2.4
Build Dependencies:
cfitsio
Link Dependencies:
cfitsio
Description:
CCfits is an object oriented interface to the cfitsio library. It is designed to make the capabilities of cfitsio available to programmers working in C++. It is written in ANSI C++ and implemented using the C++ Standard Library with namespaces, exception handling, and member template functions.

ccs-qcd

Homepage:
Spack package:
Versions:
master, 1.2.1
Build Dependencies:
mpi
Link Dependencies:
mpi
Description:
This program benchmarks the performance of a linear equation solver with a large sparse coefficient matrix appering in a lattice QCD probrem. Lattice QCD describes the property of protons, neutrons and neucleons in terms of more fundamental interacting elementary particles gluon and quarks.

cctools

Homepage:
Spack package:
Versions:
7.0.18, 6.1.1
Build Dependencies:
openssl, perl, python, readline, swig, zlib
Link Dependencies:
openssl, readline, swig, zlib
Run Dependencies:
perl, python
Description:
The Cooperative Computing Tools (cctools) enable large scale distributed computations to harness hundreds to thousands of machines from clusters, clouds, and grids.

cdbfasta

Homepage:
Spack package:
Versions:
2017-03-16
Build Dependencies:
zlib
Link Dependencies:
zlib
Description:
Fast indexing and retrieval of fasta records from flat file databases

cdd

Homepage:
Spack package:
Versions:
0.61a
Build Dependencies:
libtool
Description:
The program cdd+ (cdd, respectively) is a C++ (ANSI C) implementation of the Double Description Method [MRTT53] for generating all vertices (i.e. extreme points) and extreme rays of a general convex polyhedron given by a system of linear inequalities

cddlib

Homepage:
Spack package:
Versions:
0.94h
Build Dependencies:
gmp, libtool
Link Dependencies:
gmp
Description:
The C-library cddlib is a C implementation of the Double Description Method of Motzkin et al. for generating all vertices (i.e. extreme points) and extreme rays of a general convex polyhedron in R^d given by a system of linear inequalities

cdecimal

Homepage:
Spack package:
Versions:
2.3
Description:
cdecimal is a fast drop-in replacement for the decimal module in Python's standard library.

cdhit

Homepage:
Spack package:
Versions:
4.8.1, 4.6.8
Build Dependencies:
perl
Link Dependencies:
zlib
Run Dependencies:
perl
Description:
CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences.

cdo

Homepage:
Spack package:
Versions:
1.9.8, 1.9.7.1, 1.9.6, 1.9.5, 1.9.4, 1.9.3, 1.9.2, 1.9.1, 1.9.0, 1.8.2, 1.7.2
Build Dependencies:
pkgconfig, netcdf-c, hdf5, grib-api, eccodes, szip, udunits, libxml2, proj, curl, fftw, magics, libuuid
Link Dependencies:
netcdf-c, hdf5, grib-api, eccodes, szip, udunits, libxml2, proj, curl, fftw, magics, libuuid
Description:
CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.

ceed

Homepage:
Spack package:
Versions:
2.0
Build Dependencies:
libceed, occa, nek5000, nektools, gslib, nekbone, nekcem, petsc, hpgmg, magma, pumi, mfem, laghos, hypre, suite-sparse
Link Dependencies:
libceed, occa, nek5000, nektools, gslib, nekbone, nekcem, petsc, hpgmg, magma, pumi, mfem, laghos, hypre, suite-sparse
Description:
Ceed is a collection of benchmarks, miniapps, software libraries and APIs for efficient high-order finite element and spectral element discretizations for exascale applications developed in the Department of Energy (DOE) and partially supported by the Exascale Computing Project (ECP). This is a Spack bundle package that installs the CEED software components.

cereal

Homepage:
Spack package:
Versions:
1.2.2, 1.2.1, 1.2.0, 1.1.2, 1.1.1, 1.1.0, 1.0.0, 0.9.1
Build Dependencies:
cmake
Description:
cereal is a header-only C++11 serialization library. cereal takes arbitrary data types and reversibly turns them into different representations, such as compact binary encodings, XML, or JSON. cereal was designed to be fast, light-weight, and easy to extend - it has no external dependencies and can be easily bundled with other code or used standalone.

ceres-solver

Homepage:
Spack package:
Versions:
1.12.0
Build Dependencies:
cmake, eigen, lapack, glog
Link Dependencies:
eigen, lapack, glog
Description:
Ceres Solver is an open source C++ library for modeling and solving large, complicated optimization problems. It can be used to solve Non- linear Least Squares problems with bounds constraints and general unconstrained optimization problems. It is a mature, feature rich, and performant library that has been used in production at Google since 2010.

cfitsio

Homepage:
Spack package:
Versions:
3.450, 3.420, 3.410, 3.370
Build Dependencies:
curl, bzip2
Link Dependencies:
curl, bzip2
Description:
CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format.

cgal

Homepage:
Spack package:
Versions:
4.13, 4.12, 4.11, 4.9.1, 4.9, 4.7, 4.6.3
Build Dependencies:
cmake, boost, gmp, mpfr, zlib, qt
Link Dependencies:
boost, gmp, mpfr, zlib, qt
Description:
The Computational Geometry Algorithms Library (CGAL) is a C++ library that aims to provide easy access to efficient and reliable algorithms in computational geometry. CGAL is used in various areas needing geometric computation, such as geographic information systems, computer aided design, molecular biology, medical imaging, computer graphics, and robotics.

cgdb

Homepage:
Spack package:
Versions:
0.7.0
Build Dependencies:
ncurses, readline
Link Dependencies:
ncurses, readline
Description:
A curses front-end to GDB

cgm

Homepage:
Spack package:
Versions:
16.0, 13.1.1, 13.1.0, 13.1
Build Dependencies:
mpi, oce
Link Dependencies:
mpi, oce
Description:
The Common Geometry Module, Argonne (CGMA) is a code library which provides geometry functionality used for mesh generation and other applications.

cgns

Homepage:
Spack package:
Versions:
develop, master, 3.4.0, 3.3.1, 3.3.0
Build Dependencies:
cmake, hdf5, mpi
Link Dependencies:
hdf5, mpi
Description:
The CFD General Notation System (CGNS) provides a general, portable, and extensible standard for the storage and retrieval of computational fluid dynamics (CFD) analysis data.

channelflow

Homepage:
Spack package:
Versions:
master
Build Dependencies:
cmake, eigen, fftw, mpi, hdf5, netcdf-c, boost
Link Dependencies:
eigen, fftw, mpi, hdf5, netcdf-c, boost
Description:
Channelflow is a software system for numerical analysis of the incompressible fluid flow in channel geometries, written in C++.

chapel

Homepage:
Spack package:
Versions:
1.20.0, 1.19.0, 1.18.0
Description:
Chapel is a modern programming language that is parallel, productive, portable, scalable and open-source.

charliecloud

Homepage:
Spack package:
Versions:
master, 0.13
Build Dependencies:
python, rsync, py-sphinx, py-sphinx-rtd-theme
Run Dependencies:
python, py-lark-parser, skopeo, umoci
Test Dependencies:
bats
Description:
Lightweight user-defined software stacks for HPC.

charmpp

Homepage:
Spack package:
Versions:
develop, 6.10.0, 6.9.0, 6.8.2, 6.8.1, 6.8.0, 6.7.1, 6.7.0, 6.6.1, 6.6.0, 6.5.1
Build Dependencies:
mpi, papi, cuda, automake, autoconf
Link Dependencies:
mpi, papi, cuda, automake, autoconf
Description:
Charm++ is a parallel programming framework in C++ supported by an adaptive runtime system, which enhances user productivity and allows programs to run portably from small multicore computers (your laptop) to the largest supercomputers.

chatterbug

Homepage:
Spack package:
Versions:
develop, 1.0
Build Dependencies:
mpi, scorep
Link Dependencies:
mpi, scorep
Description:
A suite of communication-intensive proxy applications that mimic commonly found communication patterns in HPC codes. These codes can be used as synthetic codes for benchmarking, or for trace generation using Score-P / OTF2.

check

Homepage:
Spack package:
Versions:
0.12.0, 0.11.0, 0.10.0
Description:
Check is a unit testing framework for C. It features a simple interface for defining unit tests, putting little in the way of the developer. Tests are run in a separate address space, so both assertion failures and code errors that cause segmentation faults or other signals can be caught. Test results are reportable in the following: Subunit, TAP, XML, and a generic logging format.

chgcentre

Homepage:
Spack package:
Versions:
1.6
Build Dependencies:
cmake, casacore, gsl
Link Dependencies:
casacore, gsl
Description:
The chgcentre tool can be used to change the phase centre of a measurement set.

chill

Homepage:
Spack package:
Versions:
master, 0.3
Build Dependencies:
boost, rose, autoconf, automake, libtool, m4, iegenlib, bison, flex, python
Link Dependencies:
python
Description:
A polyheadral compiler for autotuning

chlorop

Homepage:
Spack package:
Versions:
1.1
Run Dependencies:
awk
Description:
Chlorop predicts the presence of chloroplast transit peptides in protein sequences and the location of potential cTP cleavage sites. You will need to obtain the tarball by visiting the URL and completing the form. You can then either run spack install with the tarball in the directory, or add it to a mirror. You will need to set the CHLOROTMP environment variable to the full path of the directory you want chlorop to use as a temporary directory.

chombo

Homepage:
Spack package:
Versions:
develop, 3.2
Build Dependencies:
blas, lapack, gmake, mpi, hdf5
Link Dependencies:
blas, lapack, mpi, hdf5
Description:
The Chombo package provides a set of tools for implementing finite difference and finite-volume methods for the solution of partial differential equations on block-structured adaptively refined logically rectangular (i.e. Cartesian) grids.

chrpath

Homepage:
Spack package:
Versions:
0.16
Description:
chrpath: Modifies the dynamic library load path (rpath and runpath) of compiled programs and libraries.

cinch

Homepage:
Spack package:
Versions:
develop, 1.0
Description:
Cinch is a set of utilities and configuration options designed to make cmake builds easy to use and manage.

cistem

Homepage:
Spack package:
Versions:
1.0.0-beta
Build Dependencies:
wxwidgets, fftw
Link Dependencies:
wxwidgets, fftw
Description:
cisTEM is user-friendly software to process cryo-EM images of macromolecular complexes and obtain high-resolution 3D reconstructions from them.

citcoms

Homepage:
Spack package:
Versions:
3.3.1, 3.2.0
Build Dependencies:
mpi, zlib, exchanger, py-pythia, hc, cuda, hdf5
Link Dependencies:
mpi, zlib, exchanger, hc, cuda, hdf5
Run Dependencies:
py-pythia
Description:
CitcomS is a finite element code designed to solve compressible thermochemical convection problems relevant to Earth's mantle.

cityhash

Homepage:
Spack package:
Versions:
master, 2013-07-31
Description:
CityHash, a family of hash functions for strings.

clamav

Homepage:
Spack package:
Versions:
0.101.2
Build Dependencies:
pkgconfig, json-c, openssl, pcre, yara, zlib, bzip2
Link Dependencies:
json-c, openssl, pcre, yara, zlib, bzip2
Description:
Open source antivirus engine for detecting trojans, viruses, malware & other malicious threats.

clamr

Homepage:
Spack package:
Versions:
master
Build Dependencies:
cmake, mpi, mpe
Link Dependencies:
cmake, mpi, mpe
Description:
The CLAMR code is a cell-based adaptive mesh refinement (AMR) mini-app developed as a testbed for hybrid algorithm development using MPI and OpenCL GPU code.

clapack

Homepage:
Spack package:
Versions:
3.2.1
Build Dependencies:
atlas
Link Dependencies:
atlas
Description:
CLAPACK is a f2c'ed version of LAPACK. The CLAPACK library was built using a Fortran to C conversion utility called f2c. The entire Fortran 77 LAPACK library is run through f2c to obtain C code, and then modified to improve readability. CLAPACK's goal is to provide LAPACK for someone who does not have access to a Fortran compiler.

clara

Homepage:
Spack package:
Versions:
1.1.5, 1.1.4, 1.1.3, 1.1.2, 1.1.1, 1.1.0
Build Dependencies:
cmake
Description:
A simple to use, composable, command line parser for C++ 11 and beyond.

claw

Homepage:
Spack package:
Versions:
2.0.1, 2.0, 1.2.3, 1.2.2, 1.2.1, 1.2.0, 1.1.0
Build Dependencies:
cmake, java, ant, libxml2, bison
Link Dependencies:
java, ant, libxml2, bison
Description:
CLAW Compiler targets performance portability problem in climate and weather application written in Fortran. From a single source code, it generates architecture specific code decorated with OpenMP or OpenACC

cleaveland4

Homepage:
Spack package:
Versions:
4.4
Build Dependencies:
perl, perl-math-cdf, bowtie, viennarna, r, samtools
Link Dependencies:
bowtie, viennarna, samtools
Run Dependencies:
perl, perl-math-cdf, r
Description:
CleaveLand4: Analysis of degradome data to find sliced miRNA and siRNA targets

cleverleaf

Homepage:
Spack package:
Versions:
develop
Build Dependencies:
cmake, samrai, hdf5, boost
Link Dependencies:
samrai, hdf5, boost
Description:
CleverLeaf is a hydrodynamics mini-app that extends CloverLeaf with Adaptive Mesh Refinement using the SAMRAI toolkit from Lawrence Livermore National Laboratory. The primary goal of CleverLeaf is to evaluate the application of AMR to the Lagrangian-Eulerian hydrodynamics scheme used by CloverLeaf.

clfft

Homepage:
Spack package:
Versions:
2.12.2
Build Dependencies:
cmake, opencl, boost
Link Dependencies:
opencl, boost
Description:
a software library containing FFT functions written in OpenCL

clhep

Homepage:
Spack package:
Versions:
2.4.1.3, 2.4.1.2, 2.4.1.0, 2.4.0.4, 2.4.0.2, 2.4.0.1, 2.4.0.0, 2.3.4.6, 2.3.4.5, 2.3.4.4, 2.3.4.3, 2.3.4.2, 2.3.3.2, 2.3.3.1, 2.3.3.0, 2.3.2.2, 2.3.1.1, 2.3.1.0, 2.3.0.0, 2.2.0.8, 2.2.0.5, 2.2.0.4
Build Dependencies:
cmake
Description:
CLHEP is a C++ Class Library for High Energy Physics.

clingo

Homepage:
Spack package:
Versions:
5.4.0, 5.3.0, 5.2.2
Build Dependencies:
cmake, doxygen, python
Link Dependencies:
python
Description:
Clingo: A grounder and solver for logic programs Clingo is part of the Potassco project for Answer Set Programming (ASP). ASP offers a simple and powerful modeling language to describe combinatorial problems as logic programs. The clingo system then takes such a logic program and computes answer sets representing solutions to the given problem.

cln

Homepage:
Spack package:
Versions:
1.3.6, 1.3.5, 1.3.4, 1.3.3, 1.3.2, 1.3.1, 1.3.0, 1.2.2, 1.2.1, 1.2.0
Build Dependencies:
autoconf, automake, libtool, m4
Description:
CLN is a library for efficient computations with all kinds of numbers in arbitrary precision. It features number classes for unlimited length integers, rationals, arbitrary precision floating point numbers and much more.

cloc

Homepage:
Spack package:
Versions:
1.84, 1.80, 1.74
Build Dependencies:
perl
Link Dependencies:
perl
Description:
Count, or compute differences of, physical lines of source code in the given files (may be archives such as compressed tarballs or zip files) and/or recursively below the given directories.

cloog

Homepage:
Spack package:
Versions:
0.18.1, 0.18.0, 0.17.0
Build Dependencies:
gmp, isl
Link Dependencies:
gmp, isl
Description:
CLooG is a free software and library to generate code for scanning Z-polyhedra. That is, it finds a code (e.g. in C, FORTRAN...) that reaches each integral point of one or more parameterized polyhedra.

cloverleaf

Homepage:
Spack package:
Versions:
1.1
Build Dependencies:
mpi, cuda
Link Dependencies:
mpi, cuda
Description:
Proxy Application. CloverLeaf is a miniapp that solves the compressible Euler equations on a Cartesian grid, using an explicit, second-order accurate method.

cloverleaf3d

Homepage:
Spack package:
Versions:
1.0
Build Dependencies:
mpi
Link Dependencies:
mpi
Description:
Proxy Application. CloverLeaf3D is 3D version of the CloverLeaf mini- app. CloverLeaf is a mini-app that solves the compressible Euler equations on a Cartesian grid, using an explicit, second-order accurate method.

clp

Homepage:
Spack package:
Versions:
1.16.11
Description:
Clp (Coin-or linear programming) is an open-source linear programming solver written in C++.

clustal-omega

Homepage:
Spack package:
Versions:
1.2.4
Build Dependencies:
argtable
Link Dependencies:
argtable
Description:
Clustal Omega: the last alignment program you'll ever need.

clustalw

Homepage:
Spack package:
Versions:
2.1
Description:
Multiple alignment of nucleic acid and protein sequences.

cmake

Homepage:
Spack package:
Versions:
3.16.2, 3.16.1, 3.16.0, 3.15.5, 3.15.4, 3.15.3, 3.15.2, 3.15.1, 3.15.0, 3.14.5, 3.14.4, 3.14.3, 3.14.2, 3.14.1, 3.14.0, 3.13.4, 3.13.3, 3.13.2, 3.13.1, 3.13.0, 3.12.4, 3.12.3, 3.12.2, 3.12.1, 3.12.0, 3.11.4, 3.11.3, 3.11.2, 3.11.1, 3.11.0, 3.10.3, 3.10.2, 3.10.1, 3.10.0, 3.9.6, 3.9.4, 3.9.0, 3.8.2, 3.8.1, 3.8.0, 3.7.2, 3.7.1, 3.6.1, 3.6.0, 3.5.2, 3.5.1, 3.5.0, 3.4.3, 3.4.0, 3.3.1, 3.1.0, 3.0.2, 2.8.10.2
Build Dependencies:
curl, expat, zlib, bzip2, xz, libarchive, libuv, rhash, qt, python, py-sphinx, openssl, ncurses
Link Dependencies:
curl, expat, zlib, bzip2, xz, libarchive, libuv, rhash, qt, openssl, ncurses
Description:
A cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.

cmocka

Homepage:
Spack package:
Versions:
1.1.1, 1.1.0
Build Dependencies:
cmake
Description:
Unit-testing framework in pure C

cmor

Homepage:
Spack package:
Versions:
3.4.0, 3.3.0, 3.2.0, 3.1.2
Build Dependencies:
uuid, netcdf-c, udunits, hdf5, python, py-numpy
Link Dependencies:
uuid, netcdf-c, udunits, hdf5, python
Run Dependencies:
py-numpy
Description:
Climate Model Output Rewriter is used to produce CF-compliant netCDF files. The structure of the files created by the library and the metadata they contain fulfill the requirements of many of the climate community's standard model experiments.

cnmem

Homepage:
Spack package:
Versions:
git
Build Dependencies:
cmake
Description:
CNMem mempool for CUDA devices

cnpy

Homepage:
Spack package:
Versions:
master
Build Dependencies:
cmake
Link Dependencies:
zlib
Description:
cnpy: library to read/write .npy and .npz files in C/C++.

cntk

Homepage:
Spack package:
Versions:
master, 2.0
Build Dependencies:
libzip, openblas, mpi, boost, protobuf, kaldi, opencv, cuda, cub, cudnn, nccl, cntk1bitsgd, multiverso
Link Dependencies:
libzip, openblas, mpi, boost, protobuf, kaldi, opencv, cuda, cub, cudnn, nccl, cntk1bitsgd, multiverso
Description:
The Microsoft Cognitive Toolkit is a unified deep-learning toolkit that describes neural networks as a series of computational steps via a directed graph.

cntk1bitsgd

Homepage:
Spack package:
Versions:
master, c8b77d
Description:
CNTK1bitSGD is the header-only 1-bit stochastic gradient descent (1bit- SGD) library for the Computational Network Toolkit (CNTK).

cnvnator

Homepage:
Spack package:
Versions:
0.3.3
Build Dependencies:
samtools, htslib, root, bzip2, curl, lzma, zlib
Link Dependencies:
samtools, htslib, root, bzip2, curl, lzma, zlib
Description:
A tool for CNV discovery and genotyping from depth-of-coverage by mapped reads.

codar-cheetah

Homepage:
Spack package:
Versions:
develop, 0.5
Build Dependencies:
python
Link Dependencies:
python
Run Dependencies:
python
Description:
CODAR Cheetah: The CODAR Experiment Harness for Exascale science applications.

codes

Homepage:
Spack package:
Versions:
develop, 1.1.0, 1.0.0
Build Dependencies:
autoconf, automake, libtool, m4, pkgconfig, bison, flex, mpi, ross, sst-dumpi
Link Dependencies:
mpi, ross, sst-dumpi
Description:
CO-Design of multi-layer Exascale Storage (CODES) simulation framework

coevp

Homepage:
Spack package:
Versions:
develop
Build Dependencies:
mpi, silo, flann, lapack
Link Dependencies:
mpi, silo, flann, lapack
Description:
CoEVP is a scale-bridging proxy application for embedded viscoplasticity applications. It is created and maintained by The Exascale Co-Design Center for Materials in Extreme Environments (ExMatEx). The code is intended to serve as a vehicle for co-design by allowing others to extend and/or reimplement it as needed to test performance of new architectures, programming models, etc. Due to the size and complexity of the studied models, as well as restrictions on distribution, the currently available LULESH proxy application provides the coarse-scale model implementation and the ASPA proxy application provides the adaptive sampling support.

cohmm

Homepage:
Spack package:
Versions:
develop
Build Dependencies:
gnuplot
Link Dependencies:
gnuplot
Description:
An anticipated important use-case for next-generation supercomputing is multiscale modeling, in which continuum equations for large-scale material deformation are augmented with high-fidelity, fine-scale simulations that provide constitutive data on demand.

coinhsl

Homepage:
Spack package:
Versions:
2015.06.23, 2014.01.17, 2014.01.10
Build Dependencies:
blas
Link Dependencies:
blas
Description:
CoinHSL is a collection of linear algebra libraries (KB22, MA27, MA28, MA54, MA57, MA64, MA77, MA86, MA97, MC19, MC34, MC64, MC68, MC69, MC78, MC80, OF01, ZB01, ZB11) bundled for use with IPOPT and other applications that use these HSL routines. Note: CoinHSL is licensed software. You will need to request a license from Research Councils UK and download a .tar.gz archive of CoinHSL yourself. Spack will search your current directory for the download file. Alternatively, add this file to a mirror so that Spack can find it. For instructions on how to set up a mirror, see http://spack.readthedocs.io/en/latest/mirrors.html

colm

Homepage:
Spack package:
Versions:
0.12.0
Description:
Colm Programming Language Colm is a programming language designed for the analysis and transformation of computer languages. Colm is influenced primarily by TXL. It is in the family of program transformation languages.

colordiff

Homepage:
Spack package:
Versions:
1.0.18
Build Dependencies:
perl
Link Dependencies:
perl
Description:
Colorful diff utility.

comd

Homepage:
Spack package:
Versions:
develop, 1.1
Build Dependencies:
mpi, graphviz
Link Dependencies:
mpi, graphviz
Description:
CoMD is a reference implementation of classical molecular dynamics algorithms and workloads as used in materials science. It is created and maintained by The Exascale Co-Design Center for Materials in Extreme Environments (ExMatEx). The code is intended to serve as a vehicle for co-design by allowing others to extend and/or reimplement it as needed to test performance of new architectures, programming models, etc. New versions of CoMD will be released to incorporate the lessons learned from the co-design process.

commons-lang

Homepage:
Spack package:
Versions:
2.6, 2.4
Build Dependencies:
jdk
Link Dependencies:
jdk
Run Dependencies:
java
Description:
The standard Java libraries fail to provide enough methods for manipulation of its core classes. Apache Commons Lang provides these extra methods. Lang provides a host of helper utilities for the java.lang API, notably String manipulation methods, basic numerical methods, object reflection, concurrency, creation and serialization and System properties. Additionally it contains basic enhancements to java.util.Date and a series of utilities dedicated to help with building methods, such as hashCode, toString and equals.

commons-lang3

Homepage:
Spack package:
Versions:
3.7
Build Dependencies:
jdk
Link Dependencies:
jdk
Run Dependencies:
java
Description:
The standard Java libraries fail to provide enough methods for manipulation of its core classes. Apache Commons Lang provides these extra methods. Lang provides a host of helper utilities for the java.lang API, notably String manipulation methods, basic numerical methods, object reflection, concurrency, creation and serialization and System properties. Additionally it contains basic enhancements to java.util.Date and a series of utilities dedicated to help with building methods, such as hashCode, toString and equals.

commons-logging

Homepage:
Spack package:
Versions:
1.2, 1.1.3, 1.1.1
Build Dependencies:
jdk
Link Dependencies:
jdk
Run Dependencies:
java
Description:
When writing a library it is very useful to log information. However there are many logging implementations out there, and a library cannot impose the use of a particular one on the overall application that the library is a part of. The Logging package is an ultra-thin bridge between different logging implementations. A library that uses the commons-logging API can be used with any logging implementation at runtime. Commons-logging comes with support for a number of popular logging implementations, and writing adapters for others is a reasonably simple task.

compiz

Homepage:
Spack package:
Versions:
0.7.8
Build Dependencies:
libxcb, libxcomposite, libxfixes, libxdamage, libxrandr, libxinerama, libice, libsm, libxml2, libxslt, libxrender, libpng, glib, gconf
Link Dependencies:
libxcb, libxcomposite, libxfixes, libxdamage, libxrandr, libxinerama, libice, libsm, libxml2, libxslt, libxrender, libpng, glib, gconf
Description:
compiz - OpenGL window and compositing manager. Compiz is an OpenGL compositing manager that use GLX_EXT_texture_from_pixmap for binding redirected top-level windows to texture objects. It has a flexible plug- in system and it is designed to run well on most graphics hardware.

compositeproto

Homepage:
Spack package:
Versions:
0.4.2
Build Dependencies:
pkgconfig, util-macros
Description:
Composite Extension. This package contains header files and documentation for the composite extension. Library and server implementations are separate.

conduit

Homepage:
Spack package:
Versions:
master, 0.5.1, 0.5.0, 0.4.0, 0.3.1, 0.3.0, 0.2.1, 0.2.0
Build Dependencies:
cmake, python, py-numpy, hdf5, silo, adios, zfp, mpi, py-sphinx, py-sphinx-rtd-theme, doxygen
Link Dependencies:
python, hdf5, silo, adios, zfp, mpi, doxygen
Run Dependencies:
py-numpy
Description:
Conduit is an open source project from Lawrence Livermore National Laboratory that provides an intuitive model for describing hierarchical scientific data in C++, C, Fortran, and Python. It is used for data coupling between packages in-core, serialization, and I/O tasks.

connect-proxy

Homepage:
Spack package:
Versions:
1.105
Description:
`connect.c` is a simple relaying command to make network connection via SOCKS and https proxy

constype

Homepage:
Spack package:
Versions:
1.0.4
Build Dependencies:
pkgconfig, util-macros
Description:
constype prints on the standard output the Sun code for the type of display that the specified device is. It was originally written for SunOS, but has been ported to other SPARC OS'es and to Solaris on both SPARC & x86.

converge

Homepage:
Spack package:
Versions:
2.4.10, 2.3.23, 2.2.0, 2.1.0, 2.0.0
Build Dependencies:
mpi, openmpi
Link Dependencies:
mpi, openmpi
Description:
CONVERGE is a revolutionary computational fluid dynamics (CFD) program that eliminates the grid generation bottleneck from the simulation process. CONVERGE was developed by engine simulation experts and is straightforward to use for both engine and non-engine simulations. Unlike many CFD programs, CONVERGE automatically generates a perfectly orthogonal, structured grid at runtime based on simple, user-defined grid control parameters. This grid generation method completely eliminates the need to manually generate a grid. In addition, CONVERGE offers many other features to expedite the setup process and to ensure that your simulations are as computationally efficient as possible.

coreutils

Homepage:
Spack package:
Versions:
8.31, 8.30, 8.29, 8.26, 8.23
Description:
The GNU Core Utilities are the basic file, shell and text manipulation utilities of the GNU operating system. These are the core utilities which are expected to exist on every operating system.

corset

Homepage:
Spack package:
Versions:
1.06
Description:
Corset is a command-line software program to go from a de novo transcriptome assembly to gene-level counts.

cosbench

Homepage:
Spack package:
Versions:
0.4.2, 0.4.1.0, 0.4.0.1
Run Dependencies:
java, curl
Description:
COSBench is a benchmarking tool to measure the performance of Cloud Object Storage services. Object storage is an emerging technology that is different from traditional file systems (e.g., NFS) or block device systems (e.g., iSCSI). Amazon S3 and Openstack* swift are well-known object storage solutions

cosmomc

Homepage:
Spack package:
Versions:
2016.11, 2016.06
Build Dependencies:
python, mpi, planck-likelihood, py-matplotlib, py-numpy, py-pandas, py-scipy, py-six
Link Dependencies:
python, mpi, planck-likelihood
Run Dependencies:
python, py-matplotlib, py-numpy, py-pandas, py-scipy, py-six
Description:
CosmoMC is a Fortran 2008 Markov-Chain Monte-Carlo (MCMC) engine for exploring cosmological parameter space, together with Fortran and python code for analysing Monte-Carlo samples and importance sampling (plus a suite of scripts for building grids of runs, plotting and presenting results).

cosp2

Homepage:
Spack package:
Versions:
master
Build Dependencies:
mpi
Link Dependencies:
mpi
Description:
Proxy Application. CoSP2 represents a sparse linear algebra parallel algorithm for calculating the density matrix in electronic tructure theory. The algorithm is based on a recursive second-order Fermi- Operator expansion method (SP2) and is tailored for density functional based tight-binding calculations of non-metallic systems.

cotter

Homepage:
Spack package:
Versions:
master, 20190205
Build Dependencies:
cmake, erfa, pal, aoflagger
Link Dependencies:
erfa, pal, aoflagger
Description:
Andre Offringa's cotter pre-processing pipeline.

cowsay

Homepage:
Spack package:
Versions:
3.04
Run Dependencies:
perl
Description:
A program that generates ASCII pictures of a cow with a message.

cp2k

Homepage:
Spack package:
Versions:
develop, 6.1, 5.1, 4.1, 3.0
Build Dependencies:
cuda, python, fftw, openblas, lapack, intel-mkl, libxsmm, pkgconfig, libint, libxc, mpi, scalapack, elpa, plumed, pexsi, sirius, py-numpy, wannier90
Link Dependencies:
cuda, fftw, openblas, lapack, intel-mkl, libxsmm, libint, libxc, mpi, scalapack, elpa, plumed, pexsi, sirius
Description:
CP2K is a quantum chemistry and solid state physics software package that can perform atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems

cpio

Homepage:
Spack package:
Versions:
2.13
Description:
GNU cpio copies files into or out of a cpio or tar archive. The archive can be another file on the disk, a magnetic tape, or a pipe.

cppad

Homepage:
Spack package:
Versions:
develop, 20170114
Build Dependencies:
cmake
Description:
A Package for Differentiation of C++ Algorithms.

cppcheck

Homepage:
Spack package:
Versions:
1.87, 1.81, 1.78, 1.72, 1.68
Run Dependencies:
py-pygments
Description:
A tool for static C/C++ code analysis.

cppgsl

Homepage:
Spack package:
Versions:
develop, 2.0.0, 1.0.0
Build Dependencies:
cmake
Description:
C++ Guideline Support Library

cpprestsdk

Homepage:
Spack package:
Versions:
2.9.1
Build Dependencies:
cmake, boost
Link Dependencies:
boost
Description:
The C++ REST SDK is a Microsoft project for cloud-based client-server communication in native code using a modern asynchronous C++ API design. This project aims to help C++ developers connect to and interact with services.

cppunit

Homepage:
Spack package:
Versions:
1.14.0, 1.13.2
Description:
Obsolete Unit testing framework for C++

cppzmq

Homepage:
Spack package:
Versions:
develop, 4.3.0, 4.2.2
Build Dependencies:
cmake, libzmq
Link Dependencies:
libzmq
Description:
C++ binding for 0MQ

cpu-features

Homepage:
Spack package:
Versions:
develop
Build Dependencies:
cmake
Description:
A cross platform C99 library to get cpu features at runtime.

cpuinfo

Homepage:
Spack package:
Versions:
master
Build Dependencies:
cmake
Description:
cpuinfo is a library to detect essential for performance optimization information about host CPU.

cquery

Homepage:
Spack package:
Versions:
2018-08-23
Build Dependencies:
cmake, llvm
Link Dependencies:
llvm
Description:
a C++ header-only library for Nearest Neighbor (NN) search wih KD-trees.

cram

Homepage:
Spack package:
Versions:
1.0.1
Build Dependencies:
cmake, python, mpi
Link Dependencies:
python, mpi
Description:
Cram runs many small MPI jobs inside one large MPI job.

cray-libsci

Homepage:
Spack package:
Versions:
18.11.1.2, 16.11.1, 16.09.1, 16.07.1, 16.06.1, 16.03.1
Description:
The Cray Scientific Libraries package, LibSci, is a collection of numerical routines optimized for best performance on Cray systems.

cromwell

Homepage:
Spack package:
Versions:
44
Run Dependencies:
java
Description:
Cromwell is a Workflow Management System geared towards scientific workflows.

cromwell-womtool

Homepage:
Spack package:
Versions:
44
Run Dependencies:
java
Description:
Command line utilities for interacting with the Workflow Object Model (WOM).

cryptopp

Homepage:
Spack package:
Versions:
7.0.0, 6.1.0, 6.0.0, 5.6.5, 5.6.4, 5.6.3, 5.6.2, 5.6.1
Build Dependencies:
gmake
Description:
Crypto++ is an open-source C++ library of cryptographic schemes. The library supports a number of different cryptography algorithms, including authenticated encryption schemes (GCM, CCM), hash functions (SHA-1, SHA2), public-key encryption (RSA, DSA), and a few obsolete/historical encryption algorithms (MD5, Panama).

cryptsetup

Homepage:
Spack package:
Versions:
2.2.1
Build Dependencies:
libuuid, lvm2, popt, json-c, util-linux, gettext, autoconf, automake, libtool, m4
Link Dependencies:
libuuid, lvm2, popt, json-c, util-linux, gettext
Description:
Cryptsetup and LUKS - open-source disk encryption.

cscope

Homepage:
Spack package:
Versions:
15.8b
Build Dependencies:
ncurses, flex, bison, pkgconfig
Link Dependencies:
ncurses
Description:
Cscope is a developer's tool for browsing source code.

csdp

Homepage:
Spack package:
Versions:
6.1.1
Build Dependencies:
atlas
Link Dependencies:
atlas
Description:
CSDP is a library of routines that implements a predictor corrector variant of the semidefinite programming algorithm of Helmberg, Rendl, Vanderbei, and Wolkowicz

ctffind

Homepage:
Spack package:
Versions:
4.1.8
Build Dependencies:
wxwidgets, fftw
Link Dependencies:
wxwidgets, fftw
Description:
Fast and accurate defocus estimation from electron micrographs.

cub

Homepage:
Spack package:
Versions:
1.8.0, 1.7.5, 1.7.4, 1.7.3, 1.7.2, 1.7.1
Description:
CUB is a C++ header library of cooperative threadblock primitives and other utilities for CUDA kernel programming.

cube

Homepage:
Spack package:
Versions:
4.4.4, 4.4.3, 4.4.2, 4.4, 4.3.5, 4.3.4, 4.3.3, 4.2.3
Build Dependencies:
cubelib, pkgconfig, dbus, zlib, qt
Link Dependencies:
cubelib, dbus, zlib, qt
Description:
Cube the profile viewer for Score-P and Scalasca profiles. It displays a multi-dimensional performance space consisting of the dimensions: - performance metric - call path - system resource

cubelib

Homepage:
Spack package:
Versions:
4.4.4, 4.4.3, 4.4.2, 4.4
Build Dependencies:
pkgconfig, zlib
Link Dependencies:
zlib
Description:
Component of CubeBundle: General purpose C++ library and tools

cubew

Homepage:
Spack package:
Versions:
4.4.3, 4.4.2, 4.4.1, 4.4
Build Dependencies:
pkgconfig, zlib
Link Dependencies:
zlib
Description:
Component of CubeBundle: High performance C Writer library

cuda

Homepage:
Spack package:
Versions:
10.2.89, 10.1.243, 10.0.130, 9.2.88, 9.1.85, 9.0.176, 8.0.61, 8.0.44, 7.5.18, 6.5.14
Build Dependencies:
libxml2
Link Dependencies:
libxml2
Description:
CUDA is a parallel computing platform and programming model invented by NVIDIA. It enables dramatic increases in computing performance by harnessing the power of the graphics processing unit (GPU). Note: This package does not currently install the drivers necessary to run CUDA. These will need to be installed manually. See: https://docs.nvidia.com/cuda/ for details.

cuda-memtest

Homepage:
Spack package:
Versions:
master
Build Dependencies:
cmake, cuda
Link Dependencies:
cuda
Description:
Maintained and updated fork of cuda_memtest. original homepage: http://sourceforge.net/projects/cudagpumemtest . This software tests GPU memory for hardware errors and soft errors using CUDA or OpenCL.

cudnn

Homepage:
Spack package:
Versions:
7.6.5.32-10.2-linux-x64, 7.6.5.32-10.1-osx-x64, 7.6.5.32-10.1-linux-x64, 7.6.5.32-10.1-linux-ppc64le, 7.6.5.32-10.0-osx-x64, 7.6.5.32-10.0-linux-x64, 7.6.5.32-10.0-linux-ppc64le, 7.6.5.32-9.2-linux-x64, 7.6.5.32-9.2-linux-ppc64le, 7.6.5.32-9.0-linux-x64, 7.6.4.38-10.1-osx-x64, 7.6.4.38-10.1-linux-x64, 7.6.4.38-10.1-linux-ppc64le, 7.6.4.38-10.0-osx-x64, 7.6.4.38-10.0-linux-x64, 7.6.4.38-10.0-linux-ppc64le, 7.6.4.38-9.2-linux-x64, 7.6.4.38-9.2-linux-ppc64le, 7.6.4.38-9.0-linux-x64, 7.6.3.30-10.1-linux-x64, 7.6.3.30-10.1-linux-ppc64le, 7.5.1.10-10.1-linux-x64, 7.5.1.10-10.1-linux-ppc64le, 7.5.1.10-10.0-linux-x64, 7.5.1.10-10.0-linux-ppc64le, 7.5.0.56-10.1-linux-x64, 7.5.0.56-10.1-linux-ppc64le, 7.5.0.56-10.0-linux-x64, 7.5.0.56-10.0-linux-ppc64le, 7.3.0.29-9.0-linux-x64, 7.2.1.38-9.0-linux-x64, 7.1.3-9.1-linux-x64, 7.1.3-9.1-linux-ppc64le, 6.0-8.0-linux-x64, 5.1-8.0-linux-x64
Build Dependencies:
cuda
Link Dependencies:
cuda
Description:
NVIDIA cuDNN is a GPU-accelerated library of primitives for deep neural networks

cups

Homepage:
Spack package:
Versions:
2.2.3
Build Dependencies:
gnutls
Link Dependencies:
gnutls
Description:
CUPS is the standards-based, open source printing system developed by Apple Inc. for macOS and other UNIX-like operating systems. CUPS uses the Internet Printing Protocol (IPP) to support printing to local and network printers. This provides the core CUPS libraries, not a complete CUPS install.

curl

Homepage:
Spack package:
Versions:
7.68.0, 7.63.0, 7.60.0, 7.59.0, 7.56.0, 7.54.0, 7.53.1, 7.52.1, 7.50.3, 7.50.2, 7.50.1, 7.49.1, 7.47.1, 7.46.0, 7.45.0, 7.44.0, 7.43.0, 7.42.1
Build Dependencies:
openssl, zlib, nghttp2, libssh2, libssh, krb5
Link Dependencies:
openssl, zlib, nghttp2, libssh2, libssh, krb5
Description:
cURL is an open source command line tool and library for transferring data with URL syntax

cvs

Homepage:
Spack package:
Versions:
1.12.13
Description:
CVS a very traditional source control system

cxxopts

Homepage:
Spack package:
Versions:
2.2.0, 2.1.2, 2.1.1, 2.1.0, 2.0.0, 1.4.4, 1.4.3, 1.4.2, 1.4.1, 1.4.0
Build Dependencies:
cmake, icu4c
Link Dependencies:
icu4c
Description:
Lightweight C++ command line option parser

czmq

Homepage:
Spack package:
Versions:
4.1.1, 4.0.2, 3.0.2
Build Dependencies:
libtool, automake, autoconf, pkgconfig, libuuid, libzmq
Link Dependencies:
libuuid, libzmq
Description:
A C interface to the ZMQ library

dakota

Homepage:
Spack package:
Versions:
6.9, 6.3
Build Dependencies:
cmake, netlib-lapack, blas, mpi, python, boost
Link Dependencies:
netlib-lapack, blas, mpi, python, boost
Description:
The Dakota toolkit provides a flexible, extensible interface between analysis codes and iterative systems analysis methods. Dakota contains algorithms for: - optimization with gradient and non gradient-based methods; - uncertainty quantification with sampling, reliability, stochastic - expansion, and epistemic methods; - parameter estimation with nonlinear least squares methods; - sensitivity/variance analysis with design of experiments and - parameter study methods. These capabilities may be used on their own or as components within advanced strategies such as hybrid optimization, surrogate-based optimization, mixed integer nonlinear programming, or optimization under uncertainty.

daligner

Homepage:
Spack package:
Versions:
1.0
Description:
Daligner: The Dazzler "Overlap" Module.

damageproto

Homepage:
Spack package:
Versions:
1.2.1
Build Dependencies:
pkgconfig, util-macros
Description:
X Damage Extension. This package contains header files and documentation for the X Damage extension. Library and server implementations are separate.

damaris

Homepage:
Spack package:
Versions:
master, 1.3.1
Build Dependencies:
cmake, mpi, boost, xsd, xerces-c, hdf5, catalyst, visit
Link Dependencies:
mpi, boost, xsd, xerces-c, hdf5, catalyst, visit
Description:
Damaris is a middleware for I/O and in situ analytics targeting large- scale, MPI-based HPC simulations.

damselfly

Homepage:
Spack package:
Versions:
1.0
Build Dependencies:
cmake, mpi
Link Dependencies:
mpi
Description:
Damselfly is a model-based parallel network simulator.

darshan-runtime

Homepage:
Spack package:
Versions:
develop, 3.1.7, 3.1.6, 3.1.0, 3.0.0
Build Dependencies:
mpi, zlib
Link Dependencies:
mpi, zlib
Description:
Darshan (runtime) is a scalable HPC I/O characterization tool designed to capture an accurate picture of application I/O behavior, including properties such as patterns of access within files, with minimum overhead. DarshanRuntime package should be installed on systems where you intend to instrument MPI applications.

darshan-util

Homepage:
Spack package:
Versions:
develop, 3.1.7, 3.1.6, 3.1.0, 3.0.0
Build Dependencies:
zlib, bzip2
Link Dependencies:
zlib, bzip2
Run Dependencies:
bzip2
Description:
Darshan (util) is collection of tools for parsing and summarizing log files produced by Darshan (runtime) instrumentation. This package is typically installed on systems (front-end) where you intend to analyze log files produced by Darshan (runtime).

dash

Homepage:
Spack package:
Versions:
0.5.9.1
Build Dependencies:
autoconf, automake, libtool, m4
Link Dependencies:
libedit
Description:
The Debian Almquist Shell.

datamash

Homepage:
Spack package:
Versions:
1.3, 1.1.0, 1.0.7, 1.0.6, 1.0.5
Description:
GNU datamash is a command-line program which performs basic numeric, textual and statistical operations on input textual data files.

dataspaces

Homepage:
Spack package:
Versions:
1.8.0, 1.6.2
Build Dependencies:
m4, automake, autoconf, libtool, mpi
Link Dependencies:
mpi
Description:
an extreme scale data management framework.

dateutils

Homepage:
Spack package:
Versions:
0.4.6, 0.4.5
Description:
Dateutils are a bunch of tools that revolve around fiddling with dates and times in the command line with a strong focus on use cases that arise when dealing with large amounts of financial data.

davix

Homepage:
Spack package:
Versions:
0.7.5, 0.7.3, 0.6.9, 0.6.8
Build Dependencies:
cmake, pkgconfig, libxml2, libuuid, openssl
Link Dependencies:
libxml2, libuuid, openssl
Description:
High-performance file management over WebDAV/HTTP.

dbcsr

Homepage:
Spack package:
Versions:
develop
Build Dependencies:
cmake, blas, lapack, mpi, py-fypp
Link Dependencies:
blas, lapack, mpi, py-fypp
Description:
Distributed Block Compressed Sparse Row matrix library.

dbus

Homepage:
Spack package:
Versions:
1.12.8, 1.11.2, 1.9.0, 1.8.8, 1.8.6, 1.8.4, 1.8.2
Build Dependencies:
pkgconfig, expat, glib
Link Dependencies:
expat, glib
Description:
D-Bus is a message bus system, a simple way for applications to talk to one another. D-Bus supplies both a system daemon (for events such new hardware device printer queue ) and a per-user-login-session daemon (for general IPC needs among user applications). Also, the message bus is built on top of a general one-to-one message passing framework, which can be used by any two applications to communicate directly (without going through the message bus daemon).

dcmtk

Homepage:
Spack package:
Versions:
3.6.3, 3.6.2
Build Dependencies:
cmake, openssl, zlib, libtiff, libpng, libxml2, libiconv
Link Dependencies:
openssl, zlib, libtiff, libpng, libxml2, libiconv
Description:
DCMTK is a collection of libraries and applications implementing large parts of the DICOM standard.

dd4hep

Homepage:
Spack package:
Versions:
master, 1.11.0, 1.10.0
Build Dependencies:
cmake, boost, root, python, xerces-c, geant4
Link Dependencies:
boost, root, python, xerces-c, geant4
Description:
DD4hep is a software framework for providing a complete solution for full detector description (geometry, materials, visualization, readout, alignment, calibration, etc.) for the full experiment life cycle (detector concept development, detector optimization, construction, operation). It offers a consistent description through a single source of detector information for simulation, reconstruction, analysis, etc. It distributed under the LGPLv3 License.

dealii

Homepage:
Spack package:
Versions:
develop, 9.1.1, 9.1.0, 9.0.1, 9.0.0, 8.5.1, 8.5.0, 8.4.2, 8.4.1, 8.4.0, 8.3.0, 8.2.1, 8.1.0
Build Dependencies:
cuda, cmake, blas, boost, bzip2, lapack, suite-sparse, zlib, mpi, adol-c, arpack-ng, assimp, doxygen, graphviz, ginkgo, gmsh, gsl, hdf5, metis, muparser, nanoflann, netcdf-c, netcdf-cxx, oce, p4est, petsc, python, scalapack, slepc, sundials, symengine, tbb, trilinos
Link Dependencies:
cuda, blas, boost, bzip2, lapack, suite-sparse, zlib, mpi, adol-c, arpack-ng, assimp, doxygen, graphviz, ginkgo, gsl, hdf5, metis, muparser, nanoflann, netcdf-c, netcdf-cxx, oce, p4est, petsc, python, scalapack, slepc, sundials, symengine, tbb, trilinos
Run Dependencies:
gmsh
Description:
C++ software library providing well-documented tools to build finite element codes for a broad variety of PDEs.

dealii-parameter-gui

Homepage:
Spack package:
Versions:
develop
Build Dependencies:
cmake, qt
Link Dependencies:
qt
Description:
A qt based graphical user interface for editing deal.II .prm parameter files.

decentralized-internet

Homepage:
Spack package:
Versions:
4.2.3
Description:
A library for building decentralized and grid computing projects

deconseq-standalone

Homepage:
Spack package:
Versions:
0.4.3
Build Dependencies:
perl
Link Dependencies:
perl
Description:
The DeconSeq tool can be used to automatically detect and efficiently remove sequence contaminations from genomic and metagenomic datasets.

dejagnu

Homepage:
Spack package:
Versions:
1.6, 1.4.4
Build Dependencies:
expect, tcl
Link Dependencies:
expect, tcl
Description:
DejaGnu is a framework for testing other programs. Its purpose is to provide a single front end for all tests.

delly2

Homepage:
Spack package:
Versions:
2017-08-03
Build Dependencies:
htslib, boost, bcftools
Link Dependencies:
htslib, boost, bcftools
Description:
Delly2 is an integrated structural variant prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short- read massively parallel sequencing data..

denovogear

Homepage:
Spack package:
Versions:
1.1.1, 1.1.0
Build Dependencies:
cmake, boost, htslib, eigen
Link Dependencies:
zlib
Description:
DeNovoGear is a software package to detect de novo mutations using next- generation sequencing data. It supports the analysis of many differential experimental designs and uses advanced statistical models to reduce the false positve rate.

dftfe

Homepage:
Spack package:
Versions:
0.6.0, 0.5.2, 0.5.1, 0.5.0
Build Dependencies:
cmake, mpi, dealii, scalapack, alglib, libxc, spglib, libxml2
Link Dependencies:
mpi, dealii, scalapack, alglib, libxc, spglib, libxml2
Description:
Real-space DFT calculations using Finite Elements

dia

Homepage:
Spack package:
Versions:
0.97.3
Build Dependencies:
intltool, gettext, pkgconfig, gtkplus, libxslt, python, swig, libsm, libuuid, libxinerama, libxrender, libxml2, freetype
Link Dependencies:
gtkplus, libxslt, python, swig, libsm, libuuid, libxinerama, libxrender, libxml2, freetype
Description:
Dia is a program for drawing structured diagrams.

dialign

Homepage:
Spack package:
Versions:
2.2.1
Description:
DIALIGN is a software program for multiple sequence alignment developed by Burkhard Morgenstern et al..

dialign-tx

Homepage:
Spack package:
Versions:
1.0.2
Description:
DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignment

diamond

Homepage:
Spack package:
Versions:
0.9.25, 0.9.23, 0.9.22, 0.9.21, 0.9.20, 0.9.19, 0.9.14, 0.8.38, 0.8.26
Build Dependencies:
cmake, zlib
Link Dependencies:
zlib
Description:
DIAMOND is a sequence aligner for protein and translated DNA searches, designed for high performance analysis of big sequence data.

diffsplice

Homepage:
Spack package:
Versions:
0.1.2beta, 0.1.1
Description:
A novel tool for discovering and quantitating alternative splicing variants present in an RNA-seq dataset, without relying on annotated transcriptome or pre-determined splice pattern.

diffutils

Homepage:
Spack package:
Versions:
3.7, 3.6
Build Dependencies:
libiconv
Link Dependencies:
libiconv
Description:
GNU Diffutils is a package of several programs related to finding differences between files.

dimemas

Homepage:
Spack package:
Versions:
5.4.1
Build Dependencies:
autoconf, automake, libtool, m4, bison, flex, boost
Link Dependencies:
bison, flex, boost
Run Dependencies:
bison, flex
Description:
High-abstracted network simulator for message-passing programs.

direnv

Homepage:
Spack package:
Versions:
2.20.0, 2.11.3
Build Dependencies:
go
Description:
direnv is an environment switcher for the shell.

discovar

Homepage:
Spack package:
Versions:
52488
Description:
DISCOVAR is a variant caller and small genome assembler.

discovardenovo

Homepage:
Spack package:
Versions:
52488
Build Dependencies:
samtools, jemalloc
Link Dependencies:
samtools, jemalloc
Description:
DISCOVAR de novo is a large (and small) de novo genome assembler. It quickly generates highly accurate and complete assemblies using the same single library data as used by DISCOVAR. It currently doesn't support variant calling, for that, please use DISCOVAR instead.

dislin

Homepage:
Spack package:
Versions:
11.0
Build Dependencies:
motif, gl, glx
Link Dependencies:
motif, gl, glx
Description:
DISLIN is a high level and easy to use graphics library for displaying data as curves, bar graphs, pie charts, 3D-colour plots, surfaces, contours and maps.

diy

Homepage:
Spack package:
Versions:
master, 3.5.0
Build Dependencies:
cmake, mpi
Link Dependencies:
mpi
Description:
Data-parallel out-of-core library

dlpack

Homepage:
Spack package:
Versions:
master
Description:
DLPack is an RFC for common tensor and operator guidelines in deep learning systems.

dmd

Homepage:
Spack package:
Versions:
2.081.1
Build Dependencies:
openssl, curl
Link Dependencies:
openssl, curl
Description:
DMD is the reference compiler for the D programming language.

dmlc-core

Homepage:
Spack package:
Versions:
master, 20170508
Build Dependencies:
cmake
Description:
DMLC-Core is the backbone library to support all DMLC projects, offers the bricks to build efficient and scalable distributed machine learning libraries.

dmtcp

Homepage:
Spack package:
Versions:
2.6.0, 2.5.2
Description:
DMTCP (Distributed MultiThreaded Checkpointing) transparently checkpoints a single-host or distributed computation in user-space -- with no modifications to user code or to the O/S.

dmxproto

Homepage:
Spack package:
Versions:
2.3.1
Build Dependencies:
pkgconfig, util-macros
Description:
Distributed Multihead X (DMX) Extension. This extension defines a protocol for clients to access a front-end proxy X server that controls multiple back-end X servers making up a large display.

docbook-xml

Homepage:
Spack package:
Versions:
4.5
Description:
Docbook DTD XML files.

docbook-xsl

Homepage:
Spack package:
Versions:
1.79.2
Build Dependencies:
docbook-xml
Link Dependencies:
docbook-xml
Description:
DocBook XSLT 1.0 Stylesheets.

dos2unix

Homepage:
Spack package:
Versions:
7.3.4
Description:
DOS/Mac to Unix and vice versa text file format converter.

dotnet-core-sdk

Homepage:
Spack package:
Versions:
2.1.300
Description:
The .NET Core SDK is a powerful development environment to write applications for all types of infrastructure.

double-conversion

Homepage:
Spack package:
Versions:
2.0.1, 2.0.0, 1.1.5, 1.1.4, 1.1.3
Build Dependencies:
cmake
Description:
This project (double-conversion) provides binary-decimal and decimal- binary routines for IEEE doubles. The library consists of efficient conversion routines that have been extracted from the V8 JavaScript engine. The code has been refactored and improved so that it can be used more easily in other projects. There is extensive documentation in src/double-conversion.h. Other examples can be found in test/cctest/test-conversions.cc.

doxygen

Homepage:
Spack package:
Versions:
1.8.15, 1.8.14, 1.8.12, 1.8.11, 1.8.10
Build Dependencies:
cmake, python, libiconv, flex, bison
Link Dependencies:
libiconv
Run Dependencies:
graphviz
Description:
Doxygen is the de facto standard tool for generating documentation from annotated C++ sources, but it also supports other popular programming languages such as C, Objective-C, C#, PHP, Java, Python, IDL (Corba, Microsoft, and UNO/OpenOffice flavors), Fortran, VHDL, Tcl, and to some extent D..

draco

Homepage:
Spack package:
Versions:
develop, 7.4.0, 7.3.0, 7.2.0, 7.1.0, 6.25.0, 6.23.0, 6.22.0, 6.21.0, 6.20.1, 6.20.0
Build Dependencies:
cmake, gsl, mpi, numdiff, python, random123, eospac, lapack, libquo, metis, parmetis, qt, superlu-dist
Link Dependencies:
gsl, mpi, eospac, lapack, libquo, metis, parmetis, qt, superlu-dist
Run Dependencies:
mpi, python, qt
Description:
Draco is an object-oriented component library geared towards numerically intensive, radiation (particle) transport applications built for parallel computing hardware. It consists of semi-independent packages and a robust build system.

dri2proto

Homepage:
Spack package:
Versions:
2.8
Build Dependencies:
pkgconfig, util-macros
Description:
Direct Rendering Infrastructure 2 Extension. This extension defines a protocol to securely allow user applications to access the video hardware without requiring data to be passed through the X server.

dri3proto

Homepage:
Spack package:
Versions:
1.0
Build Dependencies:
pkgconfig, util-macros
Description:
Direct Rendering Infrastructure 3 Extension. This extension defines a protocol to securely allow user applications to access the video hardware without requiring data to be passed through the X server.

drill

Homepage:
Spack package:
Versions:
1.17.0, 1.16.0, 1.15.0, 1.14.0, 1.13.0
Run Dependencies:
java
Description:
Apache Drill is a distributed MPP query layer that supports SQL and alternative query languages against NoSQL and Hadoop data storage systems.

ds

Homepage:
Spack package:
Versions:
9.8.0
Build Dependencies:
autoconf, automake, m4, libtool, libx11, libxml2, libxslt, openssl, tcl, tcl-tclxml, tk
Link Dependencies:
libx11, libxml2, libxslt, openssl, tcl, tcl-tclxml, tk
Description:
SAOImage DS9 is an astronomical imaging and data visualization application.

dsdp

Homepage:
Spack package:
Versions:
5.8
Build Dependencies:
blas, lapack
Link Dependencies:
blas, lapack
Description:
The DSDP software is a free open source implementation of an interior- point method for semidefinite programming. It provides primal and dual solutions, exploits low-rank structure and sparsity in the data, and has relatively low memory requirements for an interior-point method. It allows feasible and infeasible starting points and provides approximate certificates of infeasibility when no feasible solution exists.

dsrc

Homepage:
Spack package:
Versions:
2.0.2
Description:
DNA Sequence Reads Compression is an application designed for compression of data files containing reads from DNA sequencing in FASTQ format.

dtcmp

Homepage:
Spack package:
Versions:
1.1.0, 1.0.3
Build Dependencies:
mpi, lwgrp
Link Dependencies:
mpi, lwgrp
Description:
The Datatype Comparison Library provides comparison operations and parallel sort algorithms for MPI applications.

dyninst

Homepage:
Spack package:
Versions:
develop, 10.1.0, 10.0.0, 9.3.2, 9.3.0, 9.2.0, 9.1.0, 8.2.1
Build Dependencies:
cmake, boost, libiberty, libdwarf, tbb
Link Dependencies:
boost, libiberty, elf, libdwarf, tbb
Description:
API for dynamic binary instrumentation. Modify programs while they are executing without recompiling, re-linking, or re-executing.

dysco

Homepage:
Spack package:
Versions:
1.2
Build Dependencies:
cmake, casacore, gsl, boost
Link Dependencies:
casacore, gsl, boost
Description:
Dysco is a compressing storage manager for Casacore mearement sets.

ea-utils

Homepage:
Spack package:
Versions:
1.04.807
Build Dependencies:
subversion, zlib, gsl, bamtools, perl
Link Dependencies:
subversion, zlib, gsl, bamtools
Description:
Command-line tools for processing biological sequencing data. Barcode demultiplexing, adapter trimming, etc. Primarily written to support an Illumina based pipeline - but should work with any FASTQs.

easybuild

Homepage:
Spack package:
Versions:
4.0.0, 3.1.2
Build Dependencies:
python
Link Dependencies:
python
Run Dependencies:
python, py-easybuild-framework, py-easybuild-easyblocks, py-easybuild-easyconfigs
Description:
EasyBuild is a software build and installation framework for (scientific) software on HPC systems.

ebms

Homepage:
Spack package:
Versions:
develop
Build Dependencies:
mpi
Link Dependencies:
mpi
Description:
This is a miniapp for the Energy Banding Monte Carlo (EBMC) neutron transportation simulation code. It is adapted from a similar miniapp provided by Andrew Siegel, whose algorithm is described in [1], where only one process in a compute node is used, and the compute nodes are divided into memory nodes and tracking nodes. Memory nodes do not participate in particle tracking. Obviously, there is a lot of resource waste in this design.

eccodes

Homepage:
Spack package:
Versions:
2.13.0, 2.5.0, 2.2.0
Build Dependencies:
cmake, netcdf-c, openjpeg, jasper, libpng, libaec, python, py-numpy
Link Dependencies:
netcdf-c, openjpeg, jasper, libpng, libaec, python
Run Dependencies:
python, py-numpy
Description:
ecCodes is a package developed by ECMWF for processing meteorological data in GRIB (1/2), BUFR (3/4) and GTS header formats.

ecflow

Homepage:
Spack package:
Versions:
4.11.1
Build Dependencies:
cmake, boost, qt
Link Dependencies:
boost, qt
Description:
ecFlow is a work flow package that enables users to run a large number of programs (with dependencies on each other and on time) in a controlled environment. It provides tolerance for hardware and software failures, combined with good restart capabilities.

eclipse-gcj-parser

Homepage:
Spack package:
Versions:
4.8
Description:
GCJ requires the Eclipse Java parser, but does not ship with it. This builds that parser into an executable binary, thereby making GCJ work.

ecos

Homepage:
Spack package:
Versions:
2.0.7
Description:
A lightweight conic solver for second-order cone programming.

ecp-io-sdk

Homepage:
Spack package:
Versions:
1.0
Build Dependencies:
cmake, adios2, darshan-runtime, darshan-util, faodel, hdf5, mercury, parallel-netcdf, unifyfs, veloc
Link Dependencies:
adios2, darshan-runtime, darshan-util, faodel, hdf5, mercury, parallel-netcdf, unifyfs, veloc
Description:
ECP I/O Services SDK

ecp-proxy-apps

Homepage:
Spack package:
Versions:
2.1, 2.0, 1.1, 1.0
Build Dependencies:
amg, miniamr, ember, miniqmc, minivite, picsarlite, thornado-mini, candle-benchmarks, laghos, macsio, sw4lite, xsbench, examinimd, nekbone, swfft, minife, minitri, comd
Link Dependencies:
amg, miniamr, ember, miniqmc, minivite, picsarlite, thornado-mini, candle-benchmarks, laghos, macsio, sw4lite, xsbench, examinimd, nekbone, swfft, minife, minitri, comd
Description:
This is a collection of packages that represents the official suite of DOE/ECP proxy applications. This is a Spack bundle package that installs the ECP proxy application suite.

ecp-viz-sdk

Homepage:
Spack package:
Versions:
1.0
Build Dependencies:
cmake, ascent, catalyst, paraview, sz, visit, vtk-m, zfp
Link Dependencies:
ascent, catalyst, paraview, sz, visit, vtk-m, zfp
Description:
ECP Viz & Analysis SDK

ed

Homepage:
Spack package:
Versions:
1.4
Description:
GNU ed is a line-oriented text editor. It is used to create, display, modify and otherwise manipulate text files, both interactively and via shell scripts.

editline

Homepage:
Spack package:
Versions:
1.16.0
Build Dependencies:
autoconf, automake, libtool, m4, ncurses
Link Dependencies:
ncurses
Description:
A readline() replacement for UNIX without termcap (ncurses)

editres

Homepage:
Spack package:
Versions:
1.0.6
Build Dependencies:
libxaw, libx11, libxt, libxmu, pkgconfig, util-macros
Link Dependencies:
libxaw, libx11, libxt, libxmu
Description:
Dynamic resource editor for X Toolkit applications.

eem

Homepage:
Spack package:
Versions:
1.0.1
Build Dependencies:
mpi
Link Dependencies:
mpi
Description:
EEM is a program to extract the gene group and expression modules that are co-expressed in the mRNA expression data.

eigen

Homepage:
Spack package:
Versions:
3.3.7, 3.3.5, 3.3.4, 3.3.3, 3.3.1, 3.2.10, 3.2.9, 3.2.8, 3.2.7
Build Dependencies:
cmake, metis, scotch, fftw, suite-sparse, mpfr, gmp
Link Dependencies:
metis, scotch, fftw, suite-sparse, mpfr, gmp
Description:
Eigen is a C++ template library for linear algebra matrices, vectors, numerical solvers, and related algorithms.

elasticsearch

Homepage:
Spack package:
Versions:
6.4.0, 6.3.0, 6.2.4
Run Dependencies:
jdk
Description:
Elasticsearch is a search engine based on Lucene. It provides a distributed, multitenant-capable full-text search engine with an HTTP web interface and schema-free JSON documents.

elemental

Homepage:
Spack package:
Versions:
develop, 0.87.7, 0.87.6
Build Dependencies:
cmake, blas, openblas, intel-mkl, veclibfort, essl, lapack, netlib-lapack, metis, mpi, scalapack, python, gmp, mpc, mpfr
Link Dependencies:
blas, openblas, intel-mkl, veclibfort, essl, lapack, netlib-lapack, metis, mpi, scalapack, python, gmp, mpc, mpfr
Description:
Elemental: Distributed-memory dense and sparse-direct linear algebra and optimization library.

elfutils

Homepage:
Spack package:
Versions:
0.178, 0.177, 0.176, 0.175, 0.174, 0.173, 0.170, 0.168, 0.163
Build Dependencies:
gettext, m4
Link Dependencies:
bzip2, xz, zlib, gettext
Description:
elfutils is a collection of various binary tools such as eu-objdump, eu- readelf, and other utilities that allow you to inspect and manipulate ELF files. Refer to Table 5.Tools Included in elfutils for Red Hat Developer for a complete list of binary tools that are distributed with the Red Hat Developer Toolset version of elfutils.

elk

Homepage:
Spack package:
Versions:
3.3.17
Build Dependencies:
blas, lapack, fftw, mpi, libxc
Link Dependencies:
blas, lapack, fftw, mpi, libxc
Description:
An all-electron full-potential linearised augmented-plane wave (FP-LAPW) code with many advanced features.

elmerfem

Homepage:
Spack package:
Versions:
8.4, devel
Build Dependencies:
cmake, mpi, netcdf-fortran, blas, lapack, mumps, hypre, trilinos, zoltan, lua
Link Dependencies:
mpi, netcdf-fortran, blas, lapack, mumps, hypre, trilinos, zoltan, lua
Description:
Elmer is an open source multiphysical simulation software. It includes physical models of fluid dynamics, structural mechanics, electromagnetics, heat transfer and acoustics.

elpa

Homepage:
Spack package:
Versions:
2019.05.002, 2018.11.001, 2018.05.001.rc1, 2017.11.001, 2017.05.003, 2017.05.002, 2016.11.001.pre, 2016.05.004, 2016.05.003, 2015.11.001
Build Dependencies:
mpi, blas, lapack, scalapack
Link Dependencies:
mpi, blas, lapack, scalapack
Description:
Eigenvalue solvers for Petaflop-Applications (ELPA)

elsd

Homepage:
Spack package:
Versions:
master
Build Dependencies:
blas, lapack
Link Dependencies:
blas, lapack
Description:
ELSD: Ellipse and Line Segment Detector

elsdc

Homepage:
Spack package:
Versions:
master
Build Dependencies:
blas, lapack
Link Dependencies:
blas, lapack
Description:
ELSDc: Ellipse and Line Segment Detector, with Continuous validation.

elsi

Homepage:
Spack package:
Versions:
2.2.1
Build Dependencies:
cmake, mpi, elpa, ntpoly, slepc, petsc, superlu-dist
Link Dependencies:
blas, lapack, mpi, scalapack, elpa, ntpoly, slepc, petsc, superlu-dist
Description:
ELSI provides a unified interface for electronic structure codes to a variety of eigenvalue solvers.

emacs

Homepage:
Spack package:
Versions:
26.3, 26.2, 26.1, 25.3, 25.2, 25.1, 24.5
Build Dependencies:
pkgconfig, ncurses, pcre, zlib, libtiff, libpng, libxpm, giflib, libx11, libxaw, gtkplus, gnutls, jpeg
Link Dependencies:
ncurses, pcre, zlib, libtiff, libpng, libxpm, giflib, libx11, libxaw, gtkplus, gnutls, jpeg
Description:
The Emacs programmable text editor.

ember

Homepage:
Spack package:
Versions:
1.0.0
Build Dependencies:
mpi
Link Dependencies:
mpi
Description:
Ember Communication Pattern Library The Ember suite provides communication patterns in a simplified setting (simplified by the removal of application calculations, control flow, etc.).

emboss

Homepage:
Spack package:
Versions:
6.6.0
Build Dependencies:
libxpm, libgd, postgresql
Link Dependencies:
libxpm, libgd, postgresql
Description:
EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community

enchant

Homepage:
Spack package:
Versions:
2.2.7, 2.2.6, 2.2.5, 2.2.4, 2.2.3, 2.2.2, 2.2.1, 2.2.0, 2.1.3, 2.1.2, 2.1.1, 2.1.0
Build Dependencies:
glib, aspell, hunspell
Link Dependencies:
glib, aspell, hunspell
Description:
Enchant is a library (and command-line program) that wraps a number of different spelling libraries and programs with a consistent interface.

energyplus

Homepage:
Spack package:
Versions:
8.9.0
Description:
EnergyPlus is a whole building energy simulation program that engineers, architects, and researchers use to model both energy consumption for heating, cooling, ventilation, lighting and plug and process loads and water use in buildings

entrezdirect

Homepage:
Spack package:
Versions:
10.7.20190114
Run Dependencies:
perl, perl-html-parser, perl-libwww-perl, perl-lwp-protocol-https, perl-http-message, perl-xml-simple
Description:
Entrez Direct (EDirect) provides access to the NCBI's suite of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window.

environment-modules

Homepage:
Spack package:
Versions:
4.4.1, 4.4.0, 4.3.1, 4.3.0, 4.2.5, 4.2.4, 4.2.3, 4.2.2, 4.2.1, 4.2.0, 4.1.4, 4.1.3, 4.1.2, 4.1.1, 4.1.0, 4.0.0, 3.2.10
Build Dependencies:
tcl
Link Dependencies:
tcl
Run Dependencies:
tcl
Description:
The Environment Modules package provides for the dynamic modification of a user's environment via module files.

eospac

Homepage:
Spack package:
Versions:
6.4.0beta.4, 6.4.0beta.3, 6.4.0beta.2, 6.4.0beta.1, 6.4.0, 6.3.1
Description:
A collection of C routines that can be used to access the Sesame data library.

eq-r

Homepage:
Spack package:
Versions:
master, 1.0
Build Dependencies:
autoconf, automake, libtool, m4, mpi, r-rinside, r-rcpp, r, tcl, swig
Link Dependencies:
mpi, r-rinside, r-rcpp, r, tcl, swig
Description:
EMEWS Queues for R (EQ/R) Installs EQ/R.

er

Homepage:
Spack package:
Versions:
master, 0.0.3
Build Dependencies:
cmake, mpi, kvtree, redset, shuffile
Link Dependencies:
mpi, kvtree, redset, shuffile
Description:
Encoding and redundancy on a file set

erfa

Homepage:
Spack package:
Versions:
1.4.0
Build Dependencies:
m4, autoconf, automake, libtool
Description:
ERFA(Essential Routines for Fundamental Astronomy) is a C library containing key algorithms for astronomy.

erlang

Homepage:
Spack package:
Versions:
22.2, 22.1, 22.0, 21.3, 21.2
Build Dependencies:
autoconf, automake, m4, libtool
Description:
Erlang is a programming language and runtime system for building massively scalable soft real-time systems with requirements on high availability.

ermod

Homepage:
Spack package:
Versions:
0.3.6, 0.3.5
Build Dependencies:
fftw, blas
Link Dependencies:
fftw, blas
Description:
ERmod (Energy Representation Module) is a program to calculate the solvation free energy based on the energy representation method. The program allows users to calculate the solvation free energy to arbitrary solvents, including inhomogeneous systems, and can run in cooperation with state-of-art molecular simulation softwares, such as NAMD, GROMACS and/or AMBER.

erne

Homepage:
Spack package:
Versions:
2.1.1
Build Dependencies:
boost, openmpi
Link Dependencies:
boost
Run Dependencies:
boost, openmpi
Description:
The Extended Randomized Numerical alignEr using BWT

es-shell

Homepage:
Spack package:
Versions:
0.9.1
Build Dependencies:
readline
Link Dependencies:
readline
Description:
Es is an extensible shell. The language was derived from the Plan 9 shell, rc, and was influenced by functional programming languages, such as Scheme, and the Tcl embeddable programming language. This implementation is derived from Byron Rakitzis's public domain implementation of rc.

esmf

Homepage:
Spack package:
Versions:
7.1.0r
Build Dependencies:
zlib, libxml2, mpi, lapack, netcdf-c, netcdf-fortran, parallel-netcdf, xerces-c
Link Dependencies:
zlib, libxml2, mpi, lapack, netcdf-c, netcdf-fortran, parallel-netcdf, xerces-c
Test Dependencies:
perl
Description:
The Earth System Modeling Framework (ESMF) is high-performance, flexible software infrastructure for building and coupling weather, climate, and related Earth science applications. The ESMF defines an architecture for composing complex, coupled modeling systems and includes data structures and utilities for developing individual models.

essl

Homepage:
Spack package:
Description:
IBM's Engineering and Scientific Subroutine Library (ESSL).

ethminer

Homepage:
Spack package:
Versions:
0.12.0
Build Dependencies:
cmake, python, boost, json-c, curl, zlib, cuda, mesa
Link Dependencies:
python, boost, json-c, curl, zlib, cuda, mesa
Description:
The ethminer is an Ethereum GPU mining worker.

ethtool

Homepage:
Spack package:
Versions:
4.8
Build Dependencies:
autoconf, automake, libtool, m4
Description:
Ethtool is a small utility for examining and tuning your ethernet-based network interface.

etsf-io

Homepage:
Spack package:
Versions:
1.0.4
Build Dependencies:
netcdf-fortran, hdf5
Link Dependencies:
netcdf-fortran, hdf5
Description:
ETSF_IO is a library implementing the Nanoquanta/ETSF file format specifications. ETSF_IO enables an architecture-independent exchange of crystallographic data, electronic wavefunctions, densities and potentials, as well as spectroscopic data. It is meant to be used by quantum-physical and quantum-chemical applications relying upon Density Functional Theory (DFT).

everytrace

Homepage:
Spack package:
Versions:
develop, 0.2.2
Build Dependencies:
cmake, mpi
Link Dependencies:
mpi
Description:
Get stack trace EVERY time a program exits.

everytrace-example

Homepage:
Spack package:
Versions:
develop
Build Dependencies:
cmake, everytrace, openmpi
Link Dependencies:
everytrace, openmpi
Description:
Get stack trace EVERY time a program exits.

evieext

Homepage:
Spack package:
Versions:
1.1.1
Build Dependencies:
pkgconfig, util-macros
Description:
Extended Visual Information Extension (XEVIE). This extension defines a protocol for a client to determine information about core X visuals beyond what the core protocol provides.

exabayes

Homepage:
Spack package:
Versions:
1.5
Build Dependencies:
mpi
Link Dependencies:
mpi
Description:
ExaBayes is a software package for Bayesian tree inference. It is particularly suitable for large-scale analyses on computer clusters.

examinimd

Homepage:
Spack package:
Versions:
develop, 1.0
Build Dependencies:
kokkos, mpi
Link Dependencies:
kokkos, mpi
Description:
ExaMiniMD is a proxy application and research vehicle for particle codes, in particular Molecular Dynamics (MD). Compared to previous MD proxy apps (MiniMD, COMD), its design is significantly more modular in order to allow independent investigation of different aspects. To achieve that the main components such as force calculation, communication, neighbor list construction and binning are derived classes whose main functionality is accessed via virtual functions. This allows a developer to write a new derived class and drop it into the code without touching much of the rest of the application.

exampm

Homepage:
Spack package:
Versions:
develop
Build Dependencies:
cmake
Description:
Exascale Material Point Method (MPM) Mini-App

exasp2

Homepage:
Spack package:
Versions:
develop, 1.0
Build Dependencies:
bml, blas, lapack, mpi
Link Dependencies:
bml, blas, lapack, mpi
Description:
ExaSP2 is a reference implementation of typical linear algebra algorithms and workloads for a quantum molecular dynamics (QMD) electronic structure code. The algorithm is based on a recursive second- order Fermi-Operator expansion method (SP2) and is tailored for density functional based tight-binding calculations of material systems. The SP2 algorithm variants are part of the Los Alamos Transferable Tight-binding for Energetics (LATTE) code, based on a matrix expansion of the Fermi operator in a recursive series of generalized matrix-matrix multiplications. It is created and maintained by Co-Design Center for Particle Applications (CoPA). The code is intended to serve as a vehicle for co-design by allowing others to extend and/or reimplement as needed to test performance of new architectures, programming models, etc.

exchanger

Homepage:
Spack package:
Versions:
1.0.1
Build Dependencies:
python, py-merlin, py-pythia
Run Dependencies:
python, py-pythia
Description:
Exchanger is a package containing several C++ base classes. These classes, when customized for a solver, can provide communication channels between solvers. This packaged is used by CitcomS for solver coupling.

exiv2

Homepage:
Spack package:
Versions:
0.27.2
Build Dependencies:
cmake
Description:
Exiv2 is a Cross-platform C++ library and a command line utility to manage image metadata

exmcutils

Homepage:
Spack package:
Versions:
master, 0.5.7, 0.5.6
Build Dependencies:
m4, autoconf, automake, libtool
Link Dependencies:
m4, autoconf, automake, libtool
Description:
ExM C-Utils: Generic C utility library for ADLB/X and Swift/T

exodusii

Homepage:
Spack package:
Versions:
master, 2016-08-09
Build Dependencies:
cmake, mpi, netcdf-c
Link Dependencies:
mpi, netcdf-c
Description:
Exodus II is a C++/Fortran library developed to store and retrieve data for finite element analyses. It's used for preprocessing (problem definition), postprocessing (results visualization), and data transfer between codes. An Exodus II data file is a random access, machine independent, binary file that is written and read via C, C++, or Fortran API routines.

exonerate

Homepage:
Spack package:
Versions:
2.4.0
Build Dependencies:
pkgconfig, glib
Link Dependencies:
glib
Description:
Pairwise sequence alignment of DNA and proteins

expat

Homepage:
Spack package:
Versions:
2.2.9, 2.2.6, 2.2.5, 2.2.2, 2.2.0
Build Dependencies:
libbsd
Link Dependencies:
libbsd
Description:
Expat is an XML parser library written in C.

expect

Homepage:
Spack package:
Versions:
5.45
Build Dependencies:
tcl, automake, autoconf, libtool, m4
Link Dependencies:
tcl
Description:
Expect is a tool for automating interactive applications such as telnet, ftp, passwd, fsck, rlogin, tip, etc.

express

Homepage:
Spack package:
Versions:
1.5.2, 1.5.1
Build Dependencies:
cmake, boost, bamtools, zlib
Link Dependencies:
boost, bamtools, zlib
Description:
eXpress is a streaming tool for quantifying the abundances of a set of target sequences from sampled subsequences.

extrae

Homepage:
Spack package:
Versions:
3.7.1, 3.4.1
Build Dependencies:
autoconf, automake, libtool, m4, mpi, libunwind, boost, libdwarf, papi, libxml2, numactl, binutils, gettext, dyninst
Link Dependencies:
mpi, libunwind, boost, libdwarf, papi, elf, libxml2, numactl, binutils, gettext, dyninst
Description:
Extrae is the package devoted to generate tracefiles which can be analyzed later by Paraver. Extrae is a tool that uses different interposition mechanisms to inject probes into the target application so as to gather information regarding the application performance. The Extrae instrumentation package can instrument the MPI programin model, and the following parallel programming models either alone or in conjunction with MPI : OpenMP, CUDA, OpenCL, pthread, OmpSs

exuberant-ctags

Homepage:
Spack package:
Versions:
5.8
Description:
The canonical ctags generator

eztrace

Homepage:
Spack package:
Versions:
1.1-8
Build Dependencies:
mpi
Link Dependencies:
mpi
Description:
EZTrace is a tool to automatically generate execution traces of HPC applications.

f18

Homepage:
Spack package:
Versions:
master
Build Dependencies:
cmake, llvm
Link Dependencies:
llvm
Description:
F18 is a front-end for Fortran intended to replace the existing front- end in the Flang compiler

f77-zmq

Homepage:
Spack package:
Versions:
4.3.1
Build Dependencies:
libzmq, python
Link Dependencies:
libzmq
Description:
Fortran binding for the ZeroMQ communication library

f90cache

Homepage:
Spack package:
Versions:
0.99c, 0.99
Description:
f90cache is a compiler cache. It acts as a caching pre-processor to Fortran compilers, using the -E compiler switch and a hash to detect when a compilation can be satisfied from cache. This often results in a great speedup in common compilations.

fabtests

Homepage:
Spack package:
Versions:
1.6.0, 1.5.3
Build Dependencies:
libfabric
Link Dependencies:
libfabric
Description:
Fabtests provides a set of examples that uses libfabric. DEPRECATED. Fabtests has merged with the libfabric git repo.

fairlogger

Homepage:
Spack package:
Versions:
develop, 1.6.1, 1.6.0, 1.5.0, 1.4.0, 1.3.0, 1.2.0, 1.1.0, 1.0.6
Build Dependencies:
cmake, git, boost, fmt
Link Dependencies:
boost, fmt
Description:
Lightweight and fast C++ Logging Library

falcon

Homepage:
Spack package:
Versions:
2017-05-30
Build Dependencies:
python, py-networkx
Link Dependencies:
python
Run Dependencies:
python, py-setuptools, py-pypeflow, py-networkx, pacbio-dazz-db, pacbio-daligner, pacbio-dextractor, pacbio-damasker
Description:
Falcon: a set of tools for fast aligning long reads for consensus and assembly. The Falcon tool kit is a set of simple code collection which I use for studying efficient assembly algorithm for haploid and diploid genomes. It has some back-end code implemented in C for speed and some simple front-end written in Python for convenience.

fann

Homepage:
Spack package:
Versions:
2.2.0
Build Dependencies:
cmake
Description:
Fast Artificial Neural Network Library is a free open source neural network library, which implements multilayer artificial neural networks in C with support for both fully connected and sparsely connected networks. Cross-platform execution in both fixed and floating point are supported. It includes a framework for easy handling of training data sets. It is easy to use, versatile, well documented, and fast. Bindings to more than 20 programming languages are available. An easy to read introduction article and a reference manual accompanies the library with examples and recommendations on how to use the library. Several graphical user interfaces are also available for the library.

faodel

Homepage:
Spack package:
Versions:
1.1906.1, 1.1811.2, 1.1811.1, 1.1803.1
Build Dependencies:
cmake, mpi, boost, hdf5, libfabric, googletest
Link Dependencies:
mpi, boost, hdf5, libfabric
Description:
Flexible, Asynchronous, Object Data-Exchange Libraries

fast-global-file-status

Homepage:
Spack package:
Versions:
1.1
Build Dependencies:
mrnet, mount-point-attributes, mpi
Link Dependencies:
mrnet, mount-point-attributes, mpi
Description:
provides a scalable mechanism to retrieve such information of a file, including its degree of distribution or replication and consistency.

fasta

Homepage:
Spack package:
Versions:
36.3.8g
Build Dependencies:
zlib
Link Dependencies:
zlib
Description:
The FASTA programs find regions of local or global similarity between Protein or DNA sequences, either by searching Protein or DNA databases, or by identifying local duplications within a sequence. Other programs provide information on the statistical significance of an alignment. Like BLAST, FASTA can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.

fastdfs

Homepage:
Spack package:
Versions:
6.05, 6.04, 6.03, 6.02, 6.01
Build Dependencies:
perl, libfastcommon
Description:
FastDFS is an open source high performance distributed file system. It's major functions include: file storing, file syncing and file accessing (file uploading and file downloading), and it can resolve the high capacity and load balancing problem. FastDFS should meet the requirement of the website whose service based on files such as photo sharing site and video sharing site.

fastjar

Homepage:
Spack package:
Versions:
0.98
Build Dependencies:
zlib
Link Dependencies:
zlib
Description:
Fastjar is a version of Sun's 'jar' utility, written entirely in C.

fastmath

Homepage:
Spack package:
Versions:
latest
Build Dependencies:
amrex, chombo, hypre, mpi, arpack-ng, petsc, phasta, pumi, sundials, superlu-dist, trilinos, zoltan
Link Dependencies:
amrex, chombo, hypre, mpi, arpack-ng, petsc, phasta, pumi, sundials, superlu-dist, trilinos, zoltan
Description:
FASTMath is a suite of ~15 numerical libraries frequently used together in various SciDAC and CSE applications. The suite includes discretization libraries for structured, AMR and unstructured grids as well as solver libraries for ODE's, Time Integrators, Iterative, Non- Linear, and Direct Solvers.

fastme

Homepage:
Spack package:
Versions:
2.1.5.1
Build Dependencies:
autoconf, automake, libtool, m4
Description:
FastME is a distance based phylogeny reconstruction program that works on distance matrices and, as of v2.0, sequence data.

fastp

Homepage:
Spack package:
Versions:
0.20.0
Description:
A tool designed to provide fast all-in-one preprocessing for FastQ files.

fastphase

Homepage:
Spack package:
Versions:
2016-03-30
Description:
Software for haplotype reconstruction, and estimating missing genotypes from population data.

fastq-screen

Homepage:
Spack package:
Versions:
0.11.2
Build Dependencies:
bowtie, bowtie2, bwa, samtools
Link Dependencies:
bowtie, bowtie2, bwa, samtools
Run Dependencies:
perl, perl-gdgraph
Description:
FastQ Screen allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect.

fastqc

Homepage:
Spack package:
Versions:
0.11.7, 0.11.5, 0.11.4
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
java
Description:
A quality control tool for high throughput sequence data.

fastqvalidator

Homepage:
Spack package:
Versions:
2017-01-10
Link Dependencies:
zlib
Description:
The fastQValidator validates the format of fastq files.

fasttree

Homepage:
Spack package:
Versions:
2.1.10
Description:
FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of time and memory.

fastx-toolkit

Homepage:
Spack package:
Versions:
0.0.14
Build Dependencies:
libgtextutils
Link Dependencies:
libgtextutils
Description:
The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.

feh

Homepage:
Spack package:
Versions:
3.3, 3.1.1
Build Dependencies:
imlib2, curl, libxinerama, libexif, libxt
Link Dependencies:
imlib2, curl, libxinerama, libexif, libxt
Description:
feh is an X11 image viewer aimed mostly at console users. Unlike most other viewers, it does not have a fancy GUI, but simply displays images. It is controlled via commandline arguments and configurable key/mouse actions.

fenics

Homepage:
Spack package:
Versions:
2016.1.0, 1.6.0
Build Dependencies:
cmake, python, eigen, boost, mpi, hdf5, parmetis, scotch, petsc, slepc, trilinos, vtk, suite-sparse, qt, py-ply, py-six, py-numpy, py-sympy, swig, py-setuptools, py-sphinx
Link Dependencies:
python, eigen, boost, mpi, hdf5, parmetis, scotch, petsc, slepc, trilinos, vtk, suite-sparse, qt
Run Dependencies:
py-ply, py-six, py-numpy, py-sympy, swig
Description:
FEniCS is organized as a collection of interoperable components that together form the FEniCS Project. These components include the problem- solving environment DOLFIN, the form compiler FFC, the finite element tabulator FIAT, the just-in-time compiler Instant, the code generation interface UFC, the form language UFL and a range of additional components.

fermi

Homepage:
Spack package:
Versions:
1.1
Build Dependencies:
zlib
Link Dependencies:
zlib
Run Dependencies:
perl
Description:
A WGS de novo assembler based on the FMD-index for large genomes.

fermikit

Homepage:
Spack package:
Versions:
2017-11-7
Build Dependencies:
zlib
Link Dependencies:
zlib
Description:
De novo assembly based variant calling pipeline for Illumina short reads

fermisciencetools

Homepage:
Spack package:
Versions:
11r5p3
Description:
The Fermi Science Tools consists of the basic tools necessary to analyze Fermi data. This is the binary version for Linux x86_64 with libc-2.17.

ferret

Homepage:
Spack package:
Versions:
7.2, 6.96
Build Dependencies:
hdf5, netcdf-c, netcdf-fortran, readline, zlib, libx11
Link Dependencies:
hdf5, netcdf-c, netcdf-fortran, readline, zlib, libx11
Description:
Ferret is an interactive computer visualization and analysis environment designed to meet the needs of oceanographers and meteorologists analyzing large and complex gridded data sets.

ffmpeg

Homepage:
Spack package:
Versions:
4.1.1, 4.1, 3.2.4
Build Dependencies:
yasm, aom
Link Dependencies:
yasm, aom
Description:
FFmpeg is a complete, cross-platform solution to record, convert and stream audio and video.

fftw

Homepage:
Spack package:
Versions:
3.3.8, 3.3.7, 3.3.6-pl2, 3.3.5, 3.3.4, 2.1.5
Build Dependencies:
mpi, automake, autoconf, libtool
Link Dependencies:
mpi
Description:
FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data (as well as of even/odd data, i.e. the discrete cosine/sine transforms or DCT/DST). We believe that FFTW, which is free software, should become the FFT library of choice for most applications.

fgsl

Homepage:
Spack package:
Versions:
1.3.0, 1.2.0, 1.1.0
Build Dependencies:
autoconf, automake, libtool, m4, gsl
Link Dependencies:
gsl
Description:
Fortran interface to the GNU Scientific Library

figtree

Homepage:
Spack package:
Versions:
1.4.3
Run Dependencies:
java
Description:
FigTree is designed as a graphical viewer of phylogenetic trees and as a program for producing publication-ready figures. As with most of my programs, it was written for my own needs so may not be as polished and feature-complete as a commercial program. In particular it is designed to display summarized and annotated trees produced by BEAST.

file

Homepage:
Spack package:
Versions:
5.37
Description:
The file command is "a file type guesser", that is, a command-line tool that tells you in words what kind of data a file contains

filebench

Homepage:
Spack package:
Versions:
1.4.9.1, 1.4.9
Build Dependencies:
autoconf, automake, libtool, m4, flex, bison
Description:
Filebench is a file system and storage benchmark that can generate a large variety of workloads. Unlike typical benchmarks it is extremely flexible and allows to specify application's I/O behavior using its extensive Workload Model Language (WML). Users can either describe desired workloads from scratch or use(with or without modifications) workload personalities shipped with Filebench(e.g., mail-, web-, file-, and database-server workloads). Filebench is equally good for micro and macro-benchmarking, quick to setup, and relatively easy to use.

fimpute

Homepage:
Spack package:
Versions:
2014-01
Description:
FImpute uses an overlapping sliding window approach to efficiently exploit relationships or haplotype similarities between target and reference individuals.

find-circ

Homepage:
Spack package:
Versions:
1.2
Build Dependencies:
python, py-pysam, py-numpy
Run Dependencies:
python, py-pysam, py-numpy
Description:
Find-circ is a collection of python scripts detecting head-to-tail spliced (back-spliced) sequencing reads, indicative of circular RNA (circRNA) in RNA-seq data.

findutils

Homepage:
Spack package:
Versions:
4.6.0, 4.4.2, 4.4.1, 4.4.0, 4.2.33, 4.2.32, 4.2.31, 4.2.30, 4.2.29, 4.2.28, 4.2.27, 4.2.26, 4.2.25, 4.2.23, 4.2.20, 4.2.18, 4.2.15, 4.1.20, 4.1
Build Dependencies:
autoconf, automake, libtool, m4, texinfo
Description:
The GNU Find Utilities are the basic directory searching utilities of the GNU operating system.

fio

Homepage:
Spack package:
Versions:
3.16, 2.19
Build Dependencies:
gtkplus, cairo, libaio, py-sphinx
Link Dependencies:
gtkplus, cairo, libaio
Description:
Flexible I/O Tester. Fio spawns a number of threads or processes doing a particular type of I/O action as specified by the user. fio takes a number of global parameters, each inherited by the thread unless otherwise parameters given to them overriding that setting is given.

fish

Homepage:
Spack package:
Versions:
3.0.0, 2.7.1, 2.7.0, 2.2.0
Build Dependencies:
ncurses
Link Dependencies:
ncurses
Description:
fish is a smart and user-friendly command line shell for OS X, Linux, and the rest of the family.

fixesproto

Homepage:
Spack package:
Versions:
5.0
Build Dependencies:
pkgconfig, util-macros
Description:
X Fixes Extension. The extension makes changes to many areas of the protocol to resolve issues raised by application interaction with core protocol mechanisms that cannot be adequately worked around on the client side of the wire.

fl

Homepage:
Spack package:
Versions:
0.79.47
Description:
Fawlty Language is an IDL8 (Interactive Data Language) compatible compiler.

flac

Homepage:
Spack package:
Versions:
1.3.2, 1.3.1, 1.3.0
Build Dependencies:
libvorbis, id3lib
Link Dependencies:
libvorbis, id3lib
Description:
Encoder/decoder for the Free Lossless Audio Codec

flang

Homepage:
Spack package:
Versions:
master, 20190329, 20181226, 20180921, 20180612
Build Dependencies:
cuda, cmake, python, llvm-flang, pgmath
Link Dependencies:
cuda, llvm-flang, pgmath
Description:
Flang is a Fortran compiler targeting LLVM.

flann

Homepage:
Spack package:
Versions:
1.9.1, 1.8.5, 1.8.4, 1.8.1, 1.8.0
Build Dependencies:
cmake, python, py-numpy, matlab, cuda, mpi, hdf5, boost, texlive
Link Dependencies:
python, cuda, mpi, hdf5, boost, texlive
Run Dependencies:
py-numpy, matlab
Test Dependencies:
hdf5, googletest
Description:
FLANN is a library for performing fast approximate nearest neighbor searches in high dimensional spaces. It contains a collection of algorithms we found to work best for nearest neighbor search and a system for automatically choosing the best algorithm and optimum parameters depending on the dataset. FLANN is written in C++ and contains bindings for the following languages: C, MATLAB and Python.

flash

Homepage:
Spack package:
Versions:
1.2.11
Build Dependencies:
zlib
Link Dependencies:
zlib
Description:
FLASH (Fast Length Adjustment of SHort reads) is a very fast and accurate software tool to merge paired-end reads from next-generation sequencing experiments.

flatbuffers

Homepage:
Spack package:
Versions:
1.11.0, 1.10.0, 1.9.0, 1.8.0
Build Dependencies:
cmake
Description:
Memory Efficient Serialization Library

flatcc

Homepage:
Spack package:
Versions:
master, 0.5.3, 0.5.2, 0.5.1, 0.5.0, 0.4.3, 0.4.2, 0.4.1
Build Dependencies:
cmake
Description:
FlatBuffers C Compiler (flatcc), a memory-efficient serialization library, is implemented as a standalone tool instead of extending Googles flatc compiler in order to have a pure portable C library implementation of the schema compiler that is designed to fail graciously on abusive input in long running processes. It is also believed a C version may help provide schema parsing to other language interfaces that find interfacing with C easier than C++.

flecsale

Homepage:
Spack package:
Versions:
develop
Build Dependencies:
cmake, pkgconfig, flecsi, python, openssl, boost, exodusii
Link Dependencies:
flecsi, python, openssl, boost, exodusii
Description:
Flecsale is an ALE code based on FleCSI

flecsi

Homepage:
Spack package:
Versions:
master
Build Dependencies:
cmake, cinch, mpi, legion, hpx, boost, metis, parmetis, hdf5, caliper, graphviz, python, llvm
Link Dependencies:
mpi, legion, hpx, boost, metis, parmetis, hdf5, caliper, graphviz, python, llvm
Description:
FleCSI is a compile-time configurable framework designed to support multi-physics application development. As such, FleCSI attempts to provide a very general set of infrastructure design patterns that can be specialized and extended to suit the needs of a broad variety of solver and data requirements. Current support includes multi-dimensional mesh topology, mesh geometry, and mesh adjacency information, n-dimensional hashed-tree data structures, graph partitioning interfaces,and dependency closures.

flecsph

Homepage:
Spack package:
Versions:
develop
Build Dependencies:
cmake, boost, mpi, hdf5, flecsi, gsl
Link Dependencies:
boost, mpi, hdf5, flecsi, gsl
Description:
FleCSPH is a multi-physics compact application that exercises FleCSI parallel data structures for tree-based particle methods. In particular, FleCSPH implements a smoothed-particle hydrodynamics (SPH) solver for the solution of Lagrangian problems in astrophysics and cosmology. FleCSPH includes support for gravitational forces using the fast multipole method (FMM).

flex

Homepage:
Spack package:
Versions:
2.6.4, 2.6.3, 2.6.1, 2.6.0, 2.5.39
Build Dependencies:
bison, gettext, help2man, findutils, diffutils, m4, autoconf, automake, libtool
Description:
Flex is a tool for generating scanners.

flibcpp

Homepage:
Spack package:
Versions:
master, 0.3.1
Build Dependencies:
cmake, swig, py-sphinx
Description:
Fortran bindings to the C++ Standard Library.

flint

Homepage:
Spack package:
Versions:
develop, 2.5.2, 2.4.5
Build Dependencies:
autoconf, gmp, mpfr
Link Dependencies:
gmp, mpfr
Description:
FLINT (Fast Library for Number Theory).

flit

Homepage:
Spack package:
Versions:
2.0-alpha.1
Run Dependencies:
python, py-numpy, py-matplotlib, py-toml
Description:
Floating-point Litmus Tests (FLiT) is a C++ test infrastructure for detecting variability in floating-point code caused by variations in compiler code generation, hardware and execution environments.

fltk

Homepage:
Spack package:
Versions:
1.3.3
Build Dependencies:
libx11
Link Dependencies:
libx11
Description:
FLTK (pronounced "fulltick") is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL and its built-in GLUT emulation. FLTK is designed to be small and modular enough to be statically linked, but works fine as a shared library. FLTK also includes an excellent UI builder called FLUID that can be used to create applications in minutes.

flume

Homepage:
Spack package:
Versions:
1.9.0, 1.8.0, 1.7.0, 1.6.0, 1.5.2
Run Dependencies:
java
Description:
Apache Flume is a distributed, reliable, and available service for efficiently collecting, aggregating, and moving large amounts of log data. It has a simple and flexible architecture based on streaming data flows. It is robust and fault tolerant with tunable reliability mechanisms and many failover and recovery mechanisms. The system is centrally managed and allows for intelligent dynamic management. It uses a simple extensible data model that allows for online analytic application.

flux-core

Homepage:
Spack package:
Versions:
master, 0.11.3, 0.11.2, 0.11.1, 0.11.0, 0.10.0, 0.9.0, 0.8.0
Build Dependencies:
libzmq, czmq, hwloc, lua, lua-luaposix, munge, python, py-cffi, py-six, py-pyyaml, py-jsonschema, jansson, pkgconfig, yaml-cpp, lz4, py-pylint, asciidoc, autoconf, automake, libtool
Link Dependencies:
libzmq, czmq, hwloc, lua, lua-luaposix, munge, python, jansson, pkgconfig, yaml-cpp, lz4
Run Dependencies:
lua, python, py-cffi, py-six, py-pyyaml, py-jsonschema
Test Dependencies:
mpich, valgrind, jq
Description:
A next-generation resource manager (pre-alpha)

flux-sched

Homepage:
Spack package:
Versions:
master, 0.7.1, 0.7.0, 0.6.0, 0.5.0, 0.4.0
Build Dependencies:
boost, py-pyyaml, libxml2, yaml-cpp, libuuid, pkgconfig, flux-core, autoconf, automake, libtool
Link Dependencies:
boost, py-pyyaml, libxml2, yaml-cpp, libuuid, pkgconfig, flux-core
Run Dependencies:
flux-core
Description:
A scheduler for flux-core (pre-alpha)

fluxbox

Homepage:
Spack package:
Versions:
1.3.7
Build Dependencies:
pkgconfig, freetype, libxrender, libxext, expat, libx11
Link Dependencies:
freetype, libxrender, libxext, expat, libx11
Description:
Fluxbox is a windowmanager for X that was based on the Blackbox 0.61.1 code. It is very light on resources and easy to handle but yet full of features to make an easy, and extremely fast, desktop experience.

fmt

Homepage:
Spack package:
Versions:
5.3.0, 5.2.1, 5.2.0, 5.1.0, 5.0.0, 4.1.0, 4.0.0, 3.0.2, 3.0.1, 3.0.0
Build Dependencies:
cmake
Description:
fmt (formerly cppformat) is an open-source formatting library. It can be used as a safe alternative to printf or as a fast alternative to C++ IOStreams.

foam-extend

Homepage:
Spack package:
Versions:
4.0, 3.2, 3.1, 3.0
Build Dependencies:
mpi, python, zlib, flex, cmake, scotch, metis, parmetis, parmgridgen, paraview
Link Dependencies:
mpi, python, zlib, scotch, metis, parmetis, paraview
Description:
The Extend Project is a fork of the OpenFOAM opensource library for Computational Fluid Dynamics (CFD). This offering is not approved or endorsed by OpenCFD Ltd, producer and distributor of the OpenFOAM software via www.openfoam.com, and owner of the OPENFOAM trademark.

folly

Homepage:
Spack package:
Versions:
2017.06.05.00, 2016.11.14.00, 2016.11.07.00, 2016.10.31.00, 2016.10.24.00, 2016.10.17.00
Build Dependencies:
m4, autoconf, automake, libtool, pkgconfig, boost, gflags, glog, double-conversion, libevent
Link Dependencies:
boost, gflags, glog, double-conversion, libevent
Description:
Folly (acronymed loosely after Facebook Open Source Library) is a library of C++11 components designed with practicality and efficiency in mind. Folly contains a variety of core library components used extensively at Facebook. In particular, it's often a dependency of Facebook's other open source C++ efforts and place where those projects can share code.

font-util

Homepage:
Spack package:
Versions:
1.3.2, 1.3.1
Build Dependencies:
autoconf, automake, pkgconfig, util-macros, bdftopcf, mkfontscale, mkfontdir
Description:
X.Org font package creation/installation utilities and fonts.

fontcacheproto

Homepage:
Spack package:
Versions:
0.1.3
Description:
X.org FontcacheProto protocol headers.

fontconfig

Homepage:
Spack package:
Versions:
2.13.1, 2.12.3, 2.12.1, 2.11.1
Build Dependencies:
freetype, gperf, libxml2, pkgconfig, font-util, libuuid
Link Dependencies:
freetype, libxml2, font-util, libuuid
Description:
Fontconfig is a library for configuring/customizing font access

fontsproto

Homepage:
Spack package:
Versions:
2.1.3
Build Dependencies:
pkgconfig, util-macros
Description:
X Fonts Extension.

fonttosfnt

Homepage:
Spack package:
Versions:
1.0.4
Build Dependencies:
freetype, libfontenc, xproto, pkgconfig, util-macros
Link Dependencies:
freetype, libfontenc
Description:
Wrap a bitmap font in a sfnt (TrueType) wrapper.

fp16

Homepage:
Spack package:
Versions:
master
Description:
FP16 is a header-only library for conversion to/from half-precision floating point formats

fpc

Homepage:
Spack package:
Versions:
3.0.2
Description:
Free Pascal is a 32, 64 and 16 bit professional Pascal compiler.

fpocket

Homepage:
Spack package:
Versions:
master
Build Dependencies:
netcdf-c
Link Dependencies:
netcdf-c
Description:
fpocket is a very fast open source protein pocket detection algorithm based on Voronoi tessellation.

fqtrim

Homepage:
Spack package:
Versions:
0.9.7
Description:
fqtrim is a versatile stand-alone utility that can be used to trim adapters, poly-A tails, terminal unknown bases (Ns) and low quality 3' regions in reads from high-throughput next-generation sequencing machines.

fr-hit

Homepage:
Spack package:
Versions:
0.7.1-2013-02-20
Build Dependencies:
perl, python
Link Dependencies:
perl, python
Description:
An efficient algorithm for fragment recruitment for next generation sequences against microbial reference genomes.

freebayes

Homepage:
Spack package:
Versions:
1.1.0
Build Dependencies:
cmake, zlib
Link Dependencies:
zlib
Description:
Bayesian haplotype-based genetic polymorphism discovery and genotyping.

freeglut

Homepage:
Spack package:
Versions:
3.0.0
Build Dependencies:
cmake, gl, glu, libx11, libxrandr, libxi, xrandr, inputproto
Link Dependencies:
gl, glu, libx11, libxrandr, libxi, xrandr, inputproto
Description:
FreeGLUT is a free-software/open-source alternative to the OpenGL Utility Toolkit (GLUT) library

freeimage

Homepage:
Spack package:
Versions:
3.18.0
Description:
FreeImage is an Open Source library project for developers who would like to support popular graphics image formats like PNG, BMP, JPEG, TIFF and others as needed by today's multimedia applications

freetype

Homepage:
Spack package:
Versions:
2.10.1, 2.10.0, 2.9.1, 2.7.1, 2.7, 2.5.3
Build Dependencies:
libpng, bzip2, pkgconfig
Link Dependencies:
libpng, bzip2
Description:
FreeType is a freely available software library to render fonts. It is written in C, designed to be small, efficient, highly customizable, and portable while capable of producing high-quality output (glyph images) of most vector and bitmap font formats.

freexl

Homepage:
Spack package:
Versions:
1.0.5
Description:
FreeXL is an open source library to extract valid data from within an Excel (.xls) spreadsheet.

fribidi

Homepage:
Spack package:
Versions:
1.0.5
Build Dependencies:
m4, autoconf, automake, libtool
Description:
GNU FriBidi: The Free Implementation of the Unicode Bidirectional Algorithm.

fseq

Homepage:
Spack package:
Versions:
1.84
Build Dependencies:
java
Run Dependencies:
java
Description:
F-Seq: A Feature Density Estimator for High-Throughput Sequence Tags

fsl

Homepage:
Spack package:
Versions:
5.0.10
Build Dependencies:
python, expat, libx11, glu, zlib, libpng, boost, sqlite
Link Dependencies:
expat, libx11, glu, zlib, libpng, boost, sqlite
Run Dependencies:
python
Description:
FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data. Note: A manual download is required for FSL. Spack will search your current directory for the download file. Alternatively, add this file to a mirror so that Spack can find it. For instructions on how to set up a mirror, see http://spack.readthedocs.io/en/latest/mirrors.html

fslsfonts

Homepage:
Spack package:
Versions:
1.0.5
Build Dependencies:
libfs, xproto, pkgconfig, util-macros
Link Dependencies:
libfs
Description:
fslsfonts produces a list of fonts served by an X font server.

fstobdf

Homepage:
Spack package:
Versions:
1.0.6
Build Dependencies:
libx11, libfs, xproto, pkgconfig, util-macros
Link Dependencies:
libx11, libfs
Description:
The fstobdf program reads a font from a font server and prints a BDF file on the standard output that may be used to recreate the font. This is useful in testing servers, debugging font metrics, and reproducing lost BDF files.

fstrack

Homepage:
Spack package:
Versions:
0.5.3.092918
Build Dependencies:
gmt, netcdf-c
Link Dependencies:
gmt, netcdf-c
Description:
Package with tools to analyze symmetry components of elastic tensors, predict synthetic waveforms and compute automated shear wave splitting along ray paths, and to track finite strain and predict LPO from mantle flow given on GMT/netcdf grds.

ftgl

Homepage:
Spack package:
Versions:
master, 2.4.0, 2.3.1
Build Dependencies:
cmake, pkgconfig, gl, glu, freetype
Link Dependencies:
gl, glu, freetype
Description:
Library to use arbitrary fonts in OpenGL applications.

fujitsu-mpi

Homepage:
Spack package:
Description:
Fujitsu MPI implementation only for Fujitsu compiler.

funhpc

Homepage:
Spack package:
Versions:
develop, 1.3.0
Build Dependencies:
cmake, cereal, googletest, hwloc, jemalloc, mpi, qthreads
Link Dependencies:
cereal, googletest, hwloc, jemalloc, mpi, qthreads
Description:
FunHPC: Functional HPC Programming

fyba

Homepage:
Spack package:
Versions:
4.1.1
Build Dependencies:
autoconf, automake, libtool, m4
Description:
OpenFYBA is the source code release of the FYBA library, distributed by the National Mapping Authority of Norway (Statens kartverk) to read and write files in the National geodata standard format SOSI.

fzf

Homepage:
Spack package:
Versions:
0.17.5, 0.17.4, 0.17.3, 0.17.1, 0.17.0-2, 0.17.0, 0.16.11, 0.16.10, 0.16.9, 0.16.8
Build Dependencies:
go
Link Dependencies:
go
Description:
fzf is a general-purpose command-line fuzzy finder.

g4abla

Homepage:
Spack package:
Versions:
3.1, 3.0
Description:
Geant4 data for nuclear shell effects in INCL/ABLA hadronic mode

g4emlow

Homepage:
Spack package:
Versions:
7.3, 6.50
Description:
Geant4 data files for low energy electromagnetic processes.

g4ensdfstate

Homepage:
Spack package:
Versions:
2.2, 2.1
Description:
Geant4 data for nuclides properties

g4ndl

Homepage:
Spack package:
Versions:
4.5
Description:
Geant4 Neutron data files with thermal cross sections

g4neutronxs

Homepage:
Spack package:
Versions:
1.4
Description:
Geant4 data for evaluated neutron cross-sections on natural composition of elements

g4photonevaporation

Homepage:
Spack package:
Versions:
5.2, 4.3.2
Description:
Geant4 data for photon evaporation

g4pii

Homepage:
Spack package:
Versions:
1.3
Description:
Geant4 data for shell ionisation cross-sections

g4radioactivedecay

Homepage:
Spack package:
Versions:
5.2, 5.1.1
Description:
Geant4 data files for radio-active decay hadronic processes

g4realsurface

Homepage:
Spack package:
Versions:
2.1.1, 2.1, 1.0
Description:
Geant4 data for measured optical surface reflectance

g4saiddata

Homepage:
Spack package:
Versions:
1.1
Description:
Geant4 data from evaluated cross-sections in SAID data-base

g4tendl

Homepage:
Spack package:
Versions:
1.3.2, 1.3
Description:
Geant4 data for incident particles [optional]

gams

Homepage:
Spack package:
Versions:
27.2
Description:
The General Algebraic Modeling System is a high-level modeling system for mathematical optimization. GAMS is designed for modeling and solving linear, nonlinear, and mixed-integer optimization problems.

gapbs

Homepage:
Spack package:
Versions:
1.0
Description:
The GAP Benchmark Suite is intended to help graph processing research by standardizing evaluations. Fewer differences between graph processing evaluations will make it easier to compare different research efforts and quantify improvements. The benchmark not only specifies graph kernels, input graphs, and evaluation methodologies, but it also provides an optimized baseline implementation (this repo). These baseline implementations are representative of state-of-the-art performance, and thus new contributions should outperform them to demonstrate an improvement.

gapcloser

Homepage:
Spack package:
Versions:
1.12-r6
Description:
The GapCloser is designed to close the gaps emerging during the scaffolding process

gapfiller

Homepage:
Spack package:
Versions:
1.10
Build Dependencies:
perl
Run Dependencies:
perl
Description:
GapFiller is a stand-alone program for closing gaps within pre-assembled scaffolds. Note: A manual download is required for GapFiller. Spack will search your current directory for the download file. Alternatively, add this file to a mirror so that Spack can find it. For instructions on how to set up a mirror, see http://spack.readthedocs.io/en/latest/mirrors.html

gasnet

Homepage:
Spack package:
Versions:
2019.3.0, 1.32.0, 1.30.0, 1.28.2, 1.28.0, 1.24.0
Build Dependencies:
mpi
Link Dependencies:
mpi
Description:
GASNet is a language-independent, low-level networking layer that provides network-independent, high-performance communication primitives tailored for implementing parallel global address space SPMD languages and libraries such as UPC, Co-Array Fortran, SHMEM, Cray Chapel, and Titanium.

gatk

Homepage:
Spack package:
Versions:
4.1.0.0, 4.0.12.0, 4.0.11.0, 4.0.8.1, 4.0.4.0, 3.8-1, 3.8-0
Run Dependencies:
java, python, r
Description:
Genome Analysis Toolkit Variant Discovery in High-Throughput Sequencing Data

gaussian

Homepage:
Spack package:
Versions:
09
Description:
Gaussian is a computer program for computational chemistry

gawk

Homepage:
Spack package:
Versions:
5.0.1, 4.1.4
Build Dependencies:
gettext, libsigsegv, readline, mpfr, gmp
Link Dependencies:
gettext, libsigsegv, readline, mpfr, gmp
Description:
If you are like many computer users, you would frequently like to make changes in various text files wherever certain patterns appear, or extract data from parts of certain lines while discarding the rest. To write a program to do this in a language such as C or Pascal is a time- consuming inconvenience that may take many lines of code. The job is easy with awk, especially the GNU implementation: gawk. The awk utility interprets a special-purpose programming language that makes it possible to handle simple data-reformatting jobs with just a few lines of code.

gblocks

Homepage:
Spack package:
Versions:
0.91b
Description:
Gblocks is a computer program written in ANSI C language that eliminates poorly aligned positions and divergent regions of an alignment of DNA or protein sequences

gcc

Homepage:
Spack package:
Versions:
develop, 9.2.0, 9.1.0, 8.3.0, 8.2.0, 8.1.0, 7.4.0, 7.3.0, 7.2.0, 7.1.0, 6.5.0, 6.4.0, 6.3.0, 6.2.0, 6.1.0, 5.5.0, 5.4.0, 5.3.0, 5.2.0, 5.1.0, 4.9.4, 4.9.3, 4.9.2, 4.9.1, 4.8.5, 4.8.4, 4.7.4, 4.6.4, 4.5.4
Build Dependencies:
gmp, mpfr, mpc, isl, zlib, libiconv, gnat, binutils, zip, cuda
Link Dependencies:
gmp, mpfr, mpc, isl, zlib, libiconv, gnat, binutils, cuda
Test Dependencies:
dejagnu, expect, tcl, autogen, guile
Description:
The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Ada, and Go, as well as libraries for these languages.

gccmakedep

Homepage:
Spack package:
Versions:
1.0.3
Build Dependencies:
pkgconfig
Description:
X.org gccmakedep utilities.

gccxml

Homepage:
Spack package:
Versions:
develop, latest
Build Dependencies:
cmake
Description:
gccxml dumps an XML description of C++ source code using an extension of the GCC C++ compiler.

gconf

Homepage:
Spack package:
Versions:
3.2.6
Build Dependencies:
glib, libxml2
Link Dependencies:
glib, libxml2
Description:
GConf is a system for storing application preferences.

gcta

Homepage:
Spack package:
Versions:
1.91.2beta_mac, 1.91.2beta
Description:
GCTA (Genome-wide Complex Trait Analysis) was originally designed to estimate the proportion of phenotypic variance explained by all genome- wide SNPs for complex traits (the GREML method), and has subsequently extended for many other analyses to better understand the genetic architecture of complex traits. GCTA currently supports the following analyses.

gdal

Homepage:
Spack package:
Versions:
3.0.4, 3.0.3, 3.0.2, 3.0.1, 3.0.0, 2.4.4, 2.4.3, 2.4.2, 2.4.1, 2.4.0, 2.3.3, 2.3.2, 2.3.1, 2.3.0, 2.1.2, 2.0.2, 1.11.5
Build Dependencies:
python, gmake, pkgconfig, libtiff, libgeotiff, json-c, libtool, zlib, libiconv, xz, zstd, postgresql, cfitsio, libpng, jpeg, giflib, fyba, hdf, hdf5, kealib, netcdf-c, jasper, openjpeg, xerces-c, expat, libkml, unixodbc, curl, libxml2, sqlite, pcre, geos, qhull, opencl, poppler, proj, perl, py-setuptools, py-numpy, java, armadillo, cryptopp, openssl
Link Dependencies:
python, libtiff, libgeotiff, json-c, zlib, libiconv, xz, zstd, postgresql, cfitsio, libpng, jpeg, giflib, fyba, hdf, hdf5, kealib, netcdf-c, jasper, openjpeg, xerces-c, expat, libkml, unixodbc, curl, libxml2, sqlite, pcre, geos, qhull, opencl, poppler, proj, java, armadillo, cryptopp, openssl
Run Dependencies:
python, perl, py-numpy, java, jackcess
Description:
GDAL (Geospatial Data Abstraction Library) is a translator library for raster and vector geospatial data formats that is released under an X/MIT style Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single raster abstract data model and vector abstract data model to the calling application for all supported formats. It also comes with a variety of useful command line utilities for data translation and processing.

gdb

Homepage:
Spack package:
Versions:
9.1, 8.3.1, 8.3, 8.2.1, 8.2, 8.1, 8.0.1, 8.0, 7.12.1, 7.11, 7.10.1, 7.10, 7.9.1, 7.9, 7.8.2
Build Dependencies:
texinfo, python, xz
Link Dependencies:
python, xz
Description:
GDB, the GNU Project debugger, allows you to see what is going on 'inside' another program while it executes -- or what another program was doing at the moment it crashed.

gdbm

Homepage:
Spack package:
Versions:
1.18.1, 1.14.1, 1.13, 1.12, 1.11, 1.10, 1.9.1, 1.9
Build Dependencies:
readline
Link Dependencies:
readline
Description:
GNU dbm (or GDBM, for short) is a library of database functions that use extensible hashing and work similar to the standard UNIX dbm. These routines are provided to a programmer needing to create and manipulate a hashed database.

gdk-pixbuf

Homepage:
Spack package:
Versions:
2.38.0, 2.31.2
Build Dependencies:
meson, ninja, shared-mime-info, pkgconfig, libxslt, docbook-xsl, gettext, glib, jpeg, libpng, zlib, libtiff, gobject-introspection
Link Dependencies:
gettext, glib, jpeg, libpng, zlib, libtiff, gobject-introspection
Description:
The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it was distributed as part of GTK+ 2 but it was split off into a separate package in preparation for the change to GTK+ 3.

gdl

Homepage:
Spack package:
Versions:
0.9.9, 0.9.8
Build Dependencies:
cmake, python, graphicsmagick, hdf, hdf5, libx11, plplot, proj, py-numpy, wxwidgets, eigen, fftw, gsl, jpeg, libice, libsm, libxinerama, libxxf86vm, netcdf-c, pslib, readline
Link Dependencies:
python, graphicsmagick, hdf, hdf5, libx11, plplot, proj, wxwidgets, eigen, fftw, gsl, jpeg, libice, libsm, libxinerama, libxxf86vm, netcdf-c, pslib, readline
Run Dependencies:
python, py-numpy
Description:
A free and open-source IDL/PV-WAVE compiler. GNU Data Language (GDL) is a free/libre/open source incremental compiler compatible with IDL and to some extent with PV-WAVE.

geant4

Homepage:
Spack package:
Versions:
10.05.p01, 10.04, 10.03.p03
Build Dependencies:
cmake, xerces-c, clhep, vecgeom, expat, zlib, gl, glx, libx11, libxmu, motif, qt, geant4-data
Link Dependencies:
xerces-c, clhep, vecgeom, expat, zlib, gl, glx, libx11, libxmu, motif, qt, geant4-data
Description:
Geant4 is a toolkit for the simulation of the passage of particles through matter. Its areas of application include high energy, nuclear and accelerator physics, as well as studies in medical and space science.

geant4-data

Homepage:
Spack package:
Versions:
10.04, 10.03.p03
Build Dependencies:
g4abla, g4emlow, g4ndl, g4neutronxs, g4saiddata, g4ensdfstate, g4photonevaporation, g4pii, g4radioactivedecay, g4realsurface, g4tendl
Link Dependencies:
g4abla, g4emlow, g4ndl, g4neutronxs, g4saiddata, g4ensdfstate, g4photonevaporation, g4pii, g4radioactivedecay, g4realsurface, g4tendl
Description:
An umbrella package to hold Geant4 data packages

gearshifft

Homepage:
Spack package:
Versions:
0.2.1-lw
Build Dependencies:
cmake, boost, cuda, opencl, clfft, fftw
Link Dependencies:
boost, cuda, opencl, clfft, fftw
Description:
Benchmark Suite for Heterogenuous FFT Implementations

gemmlowp

Homepage:
Spack package:
Versions:
a6f29d9ac
Description:
Google low-precision matrix multiplication library

genemark-et

Homepage:
Spack package:
Versions:
4.46, 4.38
Build Dependencies:
perl, perl-yaml, perl-hash-merge, perl-logger-simple, perl-parallel-forkmanager
Run Dependencies:
perl, perl-yaml, perl-hash-merge, perl-logger-simple, perl-parallel-forkmanager
Description:
Gene Prediction in Bacteria, archaea, Metagenomes and Metatranscriptomes. When downloaded this file is named the same for all versions. Spack will search your current directory for the download file. Alternatively, add this file to a mirror so that Spack can find it. For instructions on how to set up a mirror, see http://spack.readthedocs.io/en/latest/mirrors.html

genomefinisher

Homepage:
Spack package:
Versions:
1.4
Run Dependencies:
java
Description:
GFinisher is an application tools for refinement and finalization of prokaryotic genomes assemblies using the bias of GC Skew to identify assembly errors and organizes the contigs/scaffolds with genomes references.

genometools

Homepage:
Spack package:
Versions:
1.5.9
Build Dependencies:
perl, cairo, pango
Link Dependencies:
cairo, pango
Run Dependencies:
perl
Description:
genometools is a free collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary named gt.

genrich

Homepage:
Spack package:
Versions:
0.6
Description:
Genrich is a peak-caller for genomic enrichment assays.

geode

Homepage:
Spack package:
Versions:
1.9.2, 1.9.0, 1.8.0, 1.7.0, 1.6.0
Run Dependencies:
java
Description:
Apache Geode is a data management platform that provides real-time, consistent access to data-intensive applications throughout widely distributed cloud architectures.

geopm

Homepage:
Spack package:
Versions:
develop, master, 1.1.0, 1.0.0, 0.6.1, 0.6.0, 0.5.1, 0.5.0, 0.4.0, 0.3.0
Build Dependencies:
ruby-ronn, doxygen, mpi, m4, autoconf, automake, libtool, numactl, hwloc, json-c, py-cycler, py-pandas, py-tables, py-cffi, py-pyyaml, py-mock, py-future, py-numpy, py-setuptools, py-natsort, py-psutil, py-pylint, py-matplotlib
Link Dependencies:
mpi, numactl, hwloc, json-c
Run Dependencies:
py-cycler, py-pandas, py-tables, py-cffi, py-pyyaml, py-mock, py-future, py-numpy, py-natsort, py-psutil, py-pylint, py-matplotlib
Description:
GEOPM is an extensible power management framework targeting HPC. The GEOPM package provides libgeopm, libgeopmpolicy and applications geopmctl and geopmpolicy, as well as tools for postprocessing. GEOPM is designed to be extended for new control algorithms and new hardware power management features via its plugin infrastructure. Note: GEOPM interfaces with hardware using Model Specific Registers (MSRs). For propper usage make sure MSRs are made available directly or via the msr- safe kernel module by your administrator.

geos

Homepage:
Spack package:
Versions:
3.7.2, 3.6.2, 3.6.1, 3.6.0, 3.5.1, 3.5.0, 3.4.3, 3.4.2, 3.4.1, 3.4.0, 3.3.9, 3.3.8, 3.3.7, 3.3.6, 3.3.5, 3.3.4, 3.3.3
Build Dependencies:
ruby, python, swig
Link Dependencies:
ruby, python
Description:
GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS). As such, it aims to contain the complete functionality of JTS in C++. This includes all the OpenGIS Simple Features for SQL spatial predicate functions and spatial operators, as well as specific JTS enhanced topology functions.

gettext

Homepage:
Spack package:
Versions:
0.20.1, 0.19.8.1, 0.19.7
Build Dependencies:
ncurses, libxml2, tar, bzip2, xz, libunistring
Link Dependencies:
ncurses, libxml2, tar, bzip2, xz, libunistring
Run Dependencies:
xz
Description:
GNU internationalization (i18n) and localization (l10n) library.

gflags

Homepage:
Spack package:
Versions:
2.1.2
Build Dependencies:
cmake
Description:
The gflags package contains a C++ library that implements commandline flags processing. It includes built-in support for standard types such as string and the ability to define flags in the source file in which they are used. Online documentation available at: https://gflags.github.io/gflags/

ghost

Homepage:
Spack package:
Versions:
develop
Build Dependencies:
cuda, cmake, hwloc, blas, mpi, scotch, zoltan
Link Dependencies:
cuda, cmake, hwloc, blas, mpi, scotch, zoltan
Description:
GHOST: a General, Hybrid and Optimized Sparse Toolkit. This library provides highly optimized building blocks for implementing sparse iterative eigenvalue and linear solvers multi- and manycore clusters and on heterogenous CPU/GPU machines. For an iterative solver library using these kernels, see the phist package.

ghostscript

Homepage:
Spack package:
Versions:
9.50, 9.27, 9.26, 9.21, 9.18
Build Dependencies:
pkgconfig, freetype, jpeg, lcms, libpng, libtiff, zlib, libxext, gtkplus
Link Dependencies:
freetype, jpeg, lcms, libpng, libtiff, zlib, libxext, gtkplus
Description:
An interpreter for the PostScript language and for PDF.

ghostscript-fonts

Homepage:
Spack package:
Versions:
8.11
Description:
Ghostscript Fonts

giflib

Homepage:
Spack package:
Versions:
5.1.4
Description:
The GIFLIB project maintains the giflib service library, which has been pulling images out of GIFs since 1989.

ginkgo

Homepage:
Spack package:
Versions:
develop, master, 1.1.0, 1.0.0
Build Dependencies:
cuda, cmake
Link Dependencies:
cuda
Description:
High-performance linear algebra library for manycore systems, with a focus on sparse solution of linear systems.

git

Homepage:
Spack package:
Versions:
2.25.0, 2.21.0, 2.20.1, 2.19.2, 2.19.1, 2.18.0, 2.17.1, 2.17.0, 2.15.1, 2.14.1, 2.13.0, 2.12.2, 2.12.1, 2.12.0, 2.11.1, 2.11.0, 2.9.3, 2.9.2, 2.9.1, 2.9.0, 2.8.4, 2.8.3, 2.8.2, 2.8.1, 2.8.0, 2.7.3, 2.7.1
Build Dependencies:
curl, expat, gettext, libiconv, libidn2, openssl, pcre, pcre2, perl, zlib, autoconf, automake, libtool, m4, tk
Link Dependencies:
curl, expat, gettext, libiconv, libidn2, openssl, pcre, pcre2, perl, zlib, tk
Description:
Git is a free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency.

git-fat-git

Homepage:
Spack package:
Versions:
2018-08-21
Run Dependencies:
python, git, rsync
Description:
Simple way to handle fat files without committing them to git, supports synchronization using rsync

git-imerge

Homepage:
Spack package:
Versions:
1.1.0, 1.0.0
Build Dependencies:
python, py-argparse, git
Link Dependencies:
python, py-argparse, git
Description:
git-imerge: Incremental merge & rebase for git Perform a merge between two branches incrementally. If conflicts are encountered, figure out exactly which pairs of commits conflict, and present the user with one pairwise conflict at a time for resolution. git-imerge has two primary design goals: * Reduce the pain of resolving merge conflicts to its unavoidable minimum, by finding and presenting the smallest possible conflicts: those between the changes introduced by one commit from each branch. * Allow a merge to be saved, tested, interrupted, published, and collaborated on while it is in progress.

git-lfs

Homepage:
Spack package:
Versions:
2.9.0, 2.8.0, 2.7.2, 2.7.1, 2.7.0, 2.6.1
Build Dependencies:
go
Run Dependencies:
git
Description:
Git LFS is a system for managing and versioning large files in association with a Git repository. Instead of storing the large files within the Git repository as blobs, Git LFS stores special "pointer files" in the repository, while storing the actual file contents on a Git LFS server.

gl2ps

Homepage:
Spack package:
Versions:
1.4.0, 1.3.9
Build Dependencies:
cmake, freeglut, gl, libice, libsm, libxau, libxdamage, libxdmcp, libxext, libxfixes, libxi, libxmu, libxt, libxxf86vm, libxcb, libdrm, expat, libpng, zlib, texlive
Link Dependencies:
freeglut, gl, libice, libsm, libxau, libxdamage, libxdmcp, libxext, libxfixes, libxi, libxmu, libxt, libxxf86vm, libxcb, libdrm, expat, libpng, zlib
Description:
GL2PS is a C library providing high quality vector output for any OpenGL application.

glew

Homepage:
Spack package:
Versions:
2.0.0
Build Dependencies:
cmake, gl
Link Dependencies:
gl
Description:
The OpenGL Extension Wrangler Library.

glfmultiples

Homepage:
Spack package:
Versions:
2010-06-16
Build Dependencies:
zlib
Link Dependencies:
zlib
Description:
glfMultiples is a GLF-based variant caller for next-generation sequencing data. It takes a set of GLF format genotype likelihood files as input and generates a VCF-format set of variant calls as output.

glib

Homepage:
Spack package:
Versions:
2.56.3, 2.56.2, 2.56.1, 2.56.0, 2.55.1, 2.53.1, 2.49.7, 2.49.4, 2.48.1, 2.42.1
Build Dependencies:
pkgconfig, libffi, zlib, gettext, perl, python, pcre, util-linux, libiconv
Link Dependencies:
libffi, zlib, gettext, pcre, util-linux, libiconv
Run Dependencies:
perl, python
Description:
GLib provides the core application building blocks for libraries and applications written in C. The GLib package contains a low-level libraries useful for providing data structure handling for C, portability wrappers and interfaces for such runtime functionality as an event loop, threads, dynamic loading and an object system.

glibmm

Homepage:
Spack package:
Versions:
2.19.3, 2.16.0, 2.4.8
Build Dependencies:
libsigcpp, glib
Link Dependencies:
libsigcpp, glib
Description:
Glibmm is a C++ wrapper for the glib library.

glimmer

Homepage:
Spack package:
Versions:
3.02b
Description:
Glimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses.

glm

Homepage:
Spack package:
Versions:
0.9.7.1
Build Dependencies:
cmake
Description:
OpenGL Mathematics (GLM) is a header only C++ mathematics library for graphics software based on the OpenGL Shading Language (GLSL) specification

global

Homepage:
Spack package:
Versions:
6.5
Build Dependencies:
exuberant-ctags, ncurses
Link Dependencies:
ncurses
Run Dependencies:
exuberant-ctags
Description:
The Gnu Global tagging system

globalarrays

Homepage:
Spack package:
Versions:
5.7, 5.6.5, 5.6.4, 5.6.3, 5.6.2, 5.6.1, 5.6
Build Dependencies:
mpi, blas, lapack, scalapack
Link Dependencies:
mpi, blas, lapack, scalapack
Description:
Global Arrays (GA) is a Partitioned Global Address Space (PGAS) programming model. It provides primitives for one-sided communication (Get, Put, Accumulate) and Atomic Operations (read increment). It supports blocking and non-blocking primtives, and supports location consistency.

glog

Homepage:
Spack package:
Versions:
0.3.5, 0.3.4, 0.3.3
Build Dependencies:
gflags, cmake
Link Dependencies:
gflags, cmake
Description:
C++ implementation of the Google logging module.

gloo

Homepage:
Spack package:
Versions:
master
Build Dependencies:
cmake
Description:
Gloo is a collective communications library.

glpk

Homepage:
Spack package:
Versions:
4.65, 4.61, 4.57
Build Dependencies:
gmp
Link Dependencies:
gmp
Description:
The GLPK (GNU Linear Programming Kit) package is intended for solving large-scale linear programming (LP), mixed integer programming (MIP), and other related problems. It is a set of routines written in ANSI C and organized in the form of a callable library.

glproto

Homepage:
Spack package:
Versions:
1.4.17
Build Dependencies:
pkgconfig, util-macros
Description:
OpenGL Extension to the X Window System. This extension defines a protocol for the client to send 3D rendering commands to the X server.

glvis

Homepage:
Spack package:
Versions:
develop, 3.4, 3.3, 3.2, 3.1
Build Dependencies:
mfem, gl, glu, libx11, libpng, libtiff, freetype, fontconfig
Link Dependencies:
mfem, gl, glu, libx11, libpng, libtiff, freetype, fontconfig
Description:
GLVis: an OpenGL tool for visualization of FEM meshes and functions

gmake

Homepage:
Spack package:
Versions:
4.2.1, 4.0
Build Dependencies:
gettext, guile, texinfo
Link Dependencies:
gettext, guile
Description:
GNU Make is a tool which controls the generation of executables and other non-source files of a program from the program's source files.

gmap-gsnap

Homepage:
Spack package:
Versions:
2019-05-12, 2019-02-15, 2018-07-04, 2018-03-25, 2018-02-12, 2017-06-16, 2014-12-28
Build Dependencies:
zlib, bzip2
Link Dependencies:
zlib, bzip2
Description:
GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences, and GSNAP: Genomic Short-read Nucleotide Alignment Program

gmime

Homepage:
Spack package:
Versions:
2.6.23
Build Dependencies:
glib, libgpg-error
Link Dependencies:
glib, libgpg-error
Description:
GMime is a C/C++ library which may be used for the creation and parsing of messages using the Multipurpose Internet Mail Extension (MIME).

gmodel

Homepage:
Spack package:
Versions:
2.1.0
Build Dependencies:
cmake
Description:
Gmsh model generation library Gmodel is a C++11 library that implements a minimal CAD kernel based on the .geo format used by the Gmsh mesh generation code, and is designed to make it easier for users to quickly construct CAD models for Gmsh.

gmp

Homepage:
Spack package:
Versions:
6.1.2, 6.1.1, 6.1.0, 6.0.0a, 5.1.3, 4.3.2
Build Dependencies:
autoconf, automake, libtool, m4
Description:
GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating-point numbers.

gmsh

Homepage:
Spack package:
Versions:
develop, 4.4.1, 4.2.2, 4.0.0, 3.0.6, 3.0.1, 2.16.0, 2.15.0, 2.12.0
Build Dependencies:
cmake, blas, lapack, gmp, mpi, fltk, hdf5, netgen, oce, petsc, slepc, tetgen, zlib, metis
Link Dependencies:
blas, lapack, gmp, mpi, fltk, hdf5, netgen, oce, petsc, slepc, tetgen, zlib, metis
Description:
Gmsh is a free 3D finite element grid generator with a built-in CAD engine and post-processor. Its design goal is to provide a fast, light and user-friendly meshing tool with parametric input and advanced visualization capabilities. Gmsh is built around four modules: geometry, mesh, solver and post-processing. The specification of any input to these modules is done either interactively using the graphical user interface or in ASCII text files using Gmsh's own scripting language.

gmt

Homepage:
Spack package:
Versions:
5.4.4, 4.5.9
Build Dependencies:
ghostscript, subversion, cmake, netcdf-c, curl, pcre, gdal, fftw, lapack, blas
Link Dependencies:
ghostscript, subversion, netcdf-c, curl, pcre, gdal, fftw, lapack, blas
Test Dependencies:
graphicsmagick
Description:
GMT (Generic Mapping Tools) is an open source collection of about 80 command-line tools for manipulating geographic and Cartesian data sets (including filtering, trend fitting, gridding, projecting, etc.) and producing PostScript illustrations ranging from simple x-y plots via contour maps to artificially illuminated surfaces and 3D perspective views.

gmtsar

Homepage:
Spack package:
Versions:
5.6
Build Dependencies:
cmake, gmt
Link Dependencies:
gmt
Description:
GMTSAR is an open source (GNU General Public License) InSAR processing system designed for users familiar with Generic Mapping Tools (GMT).

gnat

Homepage:
Spack package:
Versions:
2016
Description:
The GNAT Ada compiler. Ada is a modern programming language designed for large, long-lived applications - and embedded systems in particular - where reliability and efficiency are essential.

gnome-common

Homepage:
Spack package:
Versions:
3.18.0, 3.14.0, 3.12.0, 3.10.0, 3.7.4, 3.6.0, 3.5.91, 3.5.5, 3.4.0.1
Build Dependencies:
m4, autoconf, automake, libtool
Description:
Module containing various files needed to bootstrap GNOME modules built from git.

gnupg

Homepage:
Spack package:
Versions:
2.2.17, 2.2.15, 2.2.3, 2.1.21
Build Dependencies:
libgcrypt, libassuan, libksba, libgpg-error, npth, zlib, libiconv
Link Dependencies:
libgcrypt, libassuan, libksba, libgpg-error, npth, zlib, libiconv
Description:
GnuPG is a complete and free implementation of the OpenPGP standard as defined by RFC4880

gnuplot

Homepage:
Spack package:
Versions:
5.2.8, 5.2.7, 5.2.5, 5.2.2, 5.2.0, 5.0.7, 5.0.6, 5.0.5, 5.0.1
Build Dependencies:
readline, pkgconfig, libxpm, libiconv, libcerf, libgd, cairo, wxwidgets, pango, libx11, qt
Link Dependencies:
readline, libxpm, libiconv, libcerf, libgd, cairo, wxwidgets, pango, libx11, qt
Description:
Gnuplot is a portable command-line driven graphing utility for Linux, OS/2, MS Windows, OSX, VMS, and many other platforms. The source code is copyrighted but freely distributed (i.e., you don't have to pay for it). It was originally created to allow scientists and students to visualize mathematical functions and data interactively, but has grown to support many non-interactive uses such as web scripting. It is also used as a plotting engine by third-party applications like Octave. Gnuplot has been supported and under active development since 1986

gnutls

Homepage:
Spack package:
Versions:
3.6.8, 3.6.7.1, 3.5.19, 3.5.13, 3.5.10, 3.5.9, 3.3.9
Build Dependencies:
nettle, guile, libidn2, zlib, gettext, pkgconfig
Link Dependencies:
nettle, guile, libidn2, zlib, gettext
Description:
GnuTLS is a secure communications library implementing the SSL, TLS and DTLS protocols and technologies around them. It provides a simple C language application programming interface (API) to access the secure communications protocols as well as APIs to parse and write X.509, PKCS #12, OpenPGP and other required structures. It is aimed to be portable and efficient with focus on security and interoperability.

go

Homepage:
Spack package:
Versions:
1.13.8, 1.13.7, 1.13.6, 1.13.5, 1.13.4, 1.13.3, 1.13.2, 1.13.1, 1.13, 1.12.17, 1.12.15, 1.12.14, 1.12.13, 1.12.12, 1.12.11, 1.12.10, 1.12.9, 1.12.8, 1.12.6, 1.12.5, 1.11.13, 1.11.11, 1.11.10, 1.11.5, 1.11.4, 1.11.2, 1.11.1, 1.11, 1.10.3, 1.10.2, 1.10.1, 1.9.5, 1.9.2, 1.9.1, 1.9, 1.8.3, 1.8.1, 1.8, 1.7.5, 1.7.4, 1.6.4
Build Dependencies:
git, go-bootstrap
Link Dependencies:
git
Run Dependencies:
git
Description:
The golang compiler and build environment

go-bootstrap

Homepage:
Spack package:
Versions:
1.4-bootstrap-20171003, 1.4-bootstrap-20170531, 1.4-bootstrap-20161024
Build Dependencies:
git
Link Dependencies:
git
Run Dependencies:
git
Description:
Old C-bootstrapped go to bootstrap real go

go-md2man

Homepage:
Spack package:
Versions:
1.0.10
Build Dependencies:
go
Link Dependencies:
go
Description:
go-md2man converts markdown into roff (man pages)

gobject-introspection

Homepage:
Spack package:
Versions:
1.56.1, 1.49.2, 1.48.0
Build Dependencies:
glib, python, cairo, bison, flex, pkgconfig, sed
Link Dependencies:
glib, python, cairo
Description:
The GObject Introspection is used to describe the program APIs and collect them in a uniform, machine readable format.Cairo is a 2D graphics library with support for multiple output

googletest

Homepage:
Spack package:
Versions:
1.10.0, 1.8.1, 1.8.0, 1.7.0, 1.6.0
Build Dependencies:
cmake
Description:
Google test framework for C++. Also called gtest.

gotcha

Homepage:
Spack package:
Versions:
develop, master, 1.0.2, 0.0.2
Build Dependencies:
cmake
Description:
C software library for shared library function wrapping, enables tools to intercept calls into shared libraries

gource

Homepage:
Spack package:
Versions:
0.44
Build Dependencies:
automake, autoconf, libtool, glm, pkgconfig, freetype, pcre, boost, glew, jpeg, libpng, sdl2, sdl2-image
Link Dependencies:
freetype, pcre, boost, glew, jpeg, libpng, sdl2, sdl2-image
Description:
Software version control visualization.

gpdb

Homepage:
Spack package:
Versions:
6.2.1, 6.1.0, 6.0.1, 6.0.0, 5.24.0, 5.23.0
Build Dependencies:
zstd, apr, libevent, curl, xerces-c, bison, libxml2, flex, readline
Link Dependencies:
zstd, apr, libevent, curl, xerces-c, libxml2, flex, readline
Description:
Greenplum Database (GPDB) is an advanced, fully featured, open source data warehouse, based on PostgreSQL. It provides powerful and rapid analytics on petabyte scale data volumes. Uniquely geared toward big data analytics, Greenplum Database is powered by the world's most advanced cost-based query optimizer delivering high analytical query performance on large data volumes.

gperf

Homepage:
Spack package:
Versions:
3.1, 3.0.4
Description:
GNU gperf is a perfect hash function generator. For a given list of strings, it produces a hash function and hash table, in form of C or C++ code, for looking up a value depending on the input string. The hash function is perfect, which means that the hash table has no collisions, and the hash table lookup needs a single string comparison only.

gperftools

Homepage:
Spack package:
Versions:
2.7, 2.4, 2.3
Build Dependencies:
unwind
Link Dependencies:
unwind
Description:
Google's fast malloc/free implementation, especially for multi-threaded applications. Contains tcmalloc, heap-checker, heap-profiler, and cpu- profiler.

gpgme

Homepage:
Spack package:
Versions:
1.12.0
Build Dependencies:
gnupg, libgpg-error, libassuan
Description:
GPGME is the standard library to access GnuPG functions from programming languages.

gplates

Homepage:
Spack package:
Versions:
2.1.0, 2.0.0
Build Dependencies:
cmake, ninja, qt, qwt, glu, glew, gdal, cgal, proj, boost, python
Link Dependencies:
qt, qwt, glu, glew, gdal, cgal, proj, boost, python
Description:
GPlates is desktop software for the interactive visualisation of plate- tectonics. GPlates offers a novel combination of interactive plate- tectonic reconstructions, geographic information system (GIS) functionality and raster data visualisation. GPlates enables both the visualisation and the manipulation of plate-tectonic reconstructions and associated data through geological time.

gprolog

Homepage:
Spack package:
Versions:
1.4.5
Description:
A free Prolog compiler with constraint solving over finite domains.

gpu-burn

Homepage:
Spack package:
Versions:
1.0
Build Dependencies:
cuda
Link Dependencies:
cuda
Description:
Multi-GPU CUDA stress test. Note that the file pointed to by COMPARE_PTX needs to be copied or linked to the current working directory before running gpu_burn.

grackle

Homepage:
Spack package:
Versions:
3.1, 3.0, 2.2, 2.0.1
Build Dependencies:
libtool, mpi, hdf5
Link Dependencies:
libtool, mpi, hdf5
Description:
Grackle is a chemistry and radiative cooling library for astrophysical simulations with interfaces for C, C++, and Fortran codes. It is a generalized and trimmed down version of the chemistry network of the Enzo simulation code

gradle

Homepage:
Spack package:
Versions:
4.8.1, 3.4, 3.3, 3.2.1, 3.2, 3.1, 3.0, 2.14.1, 2.14, 2.13, 2.12, 2.11, 2.10, 2.9, 2.8, 2.7, 2.6, 2.5, 2.4, 2.3, 2.2.1, 2.2, 2.1, 2.0, 1.12, 1.11, 1.10, 1.9, 1.8, 1.5, 1.4, 1.3, 1.2, 1.1, 1.0, 0.9.2, 0.9.1, 0.9, 0.8, 0.7
Build Dependencies:
java
Link Dependencies:
java
Description:
Gradle is an open source build automation system that builds upon the concepts of Apache Ant and Apache Maven and introduces a Groovy-based domain-specific language (DSL) instead of the XML form used by Apache Maven for declaring the project configuration. Gradle uses a directed acyclic graph ("DAG") to determine the order in which tasks can be run.

grandr

Homepage:
Spack package:
Versions:
0.1
Build Dependencies:
gtkplus, gconf, xrandr
Link Dependencies:
gtkplus, gconf, xrandr
Description:
RandR user interface using GTK+ libraries.

graph500

Homepage:
Spack package:
Versions:
3.0.0
Build Dependencies:
mpi
Link Dependencies:
mpi
Description:
Graph500 reference implementations.

graphicsmagick

Homepage:
Spack package:
Versions:
1.3.34, 1.3.33, 1.3.32, 1.3.31, 1.3.30, 1.3.29
Build Dependencies:
bzip2, ghostscript, ghostscript-fonts, graphviz, jasper, jpeg, lcms, libice, libpng, libsm, libtiff, libtool, libxml2, xz, zlib
Link Dependencies:
bzip2, ghostscript, ghostscript-fonts, graphviz, jasper, jpeg, lcms, libice, libpng, libsm, libtiff, libtool, libxml2, xz, zlib
Description:
GraphicsMagick is the swiss army knife of image processing. Provides a robust and efficient collection of tools and libraries which support reading, writing, and manipulating an image in over 88 major formats including important formats like DPX, GIF, JPEG, JPEG-2000, PNG, PDF, PNM, and TIFF.

graphite2

Homepage:
Spack package:
Versions:
1.3.13
Build Dependencies:
cmake
Description:
Graphite is a system that can be used to create "smart fonts" capable of displaying writing systems with various complex behaviors. A smart font contains not only letter shapes but also additional instructions indicating how to combine and position the letters in complex ways.

graphlib

Homepage:
Spack package:
Versions:
3.0.0, 2.0.0
Build Dependencies:
cmake
Description:
Library to create, manipulate, and export graphs Graphlib.

graphmap

Homepage:
Spack package:
Versions:
0.3.0
Link Dependencies:
zlib
Description:
A highly sensitive and accurate mapper for long, error-prone reads

graphviz

Homepage:
Spack package:
Versions:
2.42.2, 2.40.1
Build Dependencies:
java, swig, expat, libgd, fontconfig, freetype, ghostscript, gtkplus, gts, cairo, glib, libpng, pango, zlib, qt, libx11, pkgconfig, automake, autoconf, bison, flex, libtool
Link Dependencies:
java, swig, expat, libgd, fontconfig, freetype, ghostscript, gtkplus, gts, cairo, glib, libpng, pango, zlib, qt, libx11
Description:
Graph Visualization Software

grass

Homepage:
Spack package:
Versions:
7.8.2, 7.8.1, 7.8.0, 7.6.1, 7.4.4, 7.4.3, 7.4.2, 7.4.1, 7.4.0
Build Dependencies:
gmake, libiconv, zlib, flex, bison, proj, python, py-six, libtiff, libpng, postgresql, mariadb, sqlite, gl, unixodbc, fftw, blas, lapack, cairo, freetype, readline, opencl, bzip2, zstd, gdal, liblas, wxwidgets, py-wxpython, netcdf-c, geos, libx11
Link Dependencies:
libiconv, zlib, proj, libtiff, libpng, postgresql, mariadb, sqlite, gl, unixodbc, fftw, blas, lapack, cairo, freetype, readline, opencl, bzip2, zstd, gdal, liblas, wxwidgets, netcdf-c, geos, libx11
Run Dependencies:
python, py-six, py-wxpython
Description:
GRASS GIS (Geographic Resources Analysis Support System), is a free and open source Geographic Information System (GIS) software suite used for geospatial data management and analysis, image processing, graphics and maps production, spatial modeling, and visualization.

grep

Homepage:
Spack package:
Versions:
3.3
Description:
Grep searches one or more input files for lines containing a match to a specified pattern

grib-api

Homepage:
Spack package:
Versions:
1.24.0, 1.21.0, 1.17.0, 1.16.0
Build Dependencies:
cmake, netcdf-c, openjpeg, jasper, libpng, libaec, python, py-numpy
Link Dependencies:
netcdf-c, openjpeg, jasper, libpng, libaec, python
Run Dependencies:
python, py-numpy
Description:
The ECMWF GRIB API is an application program interface accessible from C, FORTRAN and Python programs developed for encoding and decoding WMO FM-92 GRIB edition 1 and edition 2 messages.

grnboost

Homepage:
Spack package:
Versions:
2017-10-9
Build Dependencies:
sbt, java
Run Dependencies:
java, xgboost, spark
Description:
GRNBoost is a library built on top of Apache Spark that implements a scalable strategy for gene regulatory network (GRN) inference. See https://github.com/aertslab/GRNBoost/blob/master/docs/user_guide.md for the user guide. The location of xgboost4j-<version>.jar and GRNBoost.jar are set to $XGBOOST_JAR and $GRNBOOST_JAR. Path to xgboost4j-<version>.jar is also added to CLASSPATH.

groff

Homepage:
Spack package:
Versions:
1.22.3
Build Dependencies:
gawk, gmake, sed, ghostscript
Link Dependencies:
ghostscript
Description:
Groff (GNU troff) is a typesetting system that reads plain text mixed with formatting commands and produces formatted output. Output may be PostScript or PDF, html, or ASCII/UTF8 for display at the terminal.

gromacs

Homepage:
Spack package:
Versions:
develop, 2020, 2019.5, 2019.4, 2019.3, 2019.2, 2019.1, 2019, 2018.8, 2018.5, 2018.4, 2018.3, 2018.2, 2018.1, 2018, 2016.6, 2016.5, 2016.4, 2016.3, 5.1.5, 5.1.4, 5.1.2, 4.5.5
Build Dependencies:
cmake, mpi, plumed, fftw, cuda, hwloc
Link Dependencies:
mpi, plumed, fftw, cuda, hwloc
Description:
GROMACS (GROningen MAchine for Chemical Simulations) is a molecular dynamics package primarily designed for simulations of proteins, lipids and nucleic acids. It was originally developed in the Biophysical Chemistry department of University of Groningen, and is now maintained by contributors in universities and research centers across the world. GROMACS is one of the fastest and most popular software packages available and can run on CPUs as well as GPUs. It is free, open source released under the GNU General Public License. Starting from version 4.6, GROMACS is released under the GNU Lesser General Public License.

grpc

Homepage:
Spack package:
Versions:
1.27.0, 1.26.0, 1.25.0, 1.24.3, 1.23.1
Build Dependencies:
cmake, protobuf, openssl, zlib, c-ares
Link Dependencies:
protobuf, openssl, zlib, c-ares
Description:
A high performance, open-source universal RPC framework.

gsl

Homepage:
Spack package:
Versions:
2.5, 2.4, 2.3, 2.2.1, 2.1, 2.0, 1.16
Description:
The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. It is free software under the GNU General Public License. The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting. There are over 1000 functions in total with an extensive test suite.

gslib

Homepage:
Spack package:
Versions:
1.0.3, 1.0.2, 1.0.1, 1.0.0
Build Dependencies:
mpi, blas
Link Dependencies:
mpi, blas
Description:
Highly scalable Gather-scatter code with AMG and XXT solvers

gtkmm

Homepage:
Spack package:
Versions:
2.19.7, 2.19.6, 2.19.4, 2.19.2, 2.17.11, 2.17.1, 2.16.0, 2.4.11
Build Dependencies:
glibmm, atk, gtkplus, pangomm, cairomm
Link Dependencies:
glibmm, atk, gtkplus, pangomm, cairomm
Description:
Gtkmm is the official C++ interface for the popular GUI library GTK+.

gtkorvo-atl

Homepage:
Spack package:
Versions:
develop, 2.2, 2.1
Build Dependencies:
cmake, gtkorvo-cercs-env
Link Dependencies:
gtkorvo-cercs-env
Description:
Libatl provides a library for the creation and manipulation of lists of name/value pairs using an efficient binary representation.

gtkorvo-cercs-env

Homepage:
Spack package:
Versions:
develop, 1.0
Build Dependencies:
cmake
Description:
A utility library used by some GTkorvo packages.

gtkorvo-dill

Homepage:
Spack package:
Versions:
develop, 2.4, 2.1
Build Dependencies:
cmake
Description:
DILL provides instruction-level code generation, register allocation and simple optimizations for generating executable code directly into memory regions for immediate use.

gtkorvo-enet

Homepage:
Spack package:
Versions:
1.3.14, 1.3.13
Description:
ENet reliable UDP networking library. This is a downstream branch of lsalzman's ENet. This version has expanded the client ID to handle more clients. The original is at http://github.com/lsalzman/enet.

gtkplus

Homepage:
Spack package:
Versions:
3.20.10, 2.24.32, 2.24.31, 2.24.25
Build Dependencies:
pkgconfig, atk, gdk-pixbuf, glib, shared-mime-info, pango, cairo, gobject-introspection, libepoxy, libxi, inputproto, fixesproto, at-spi2-atk, gettext, cups
Link Dependencies:
atk, gdk-pixbuf, glib, shared-mime-info, pango, cairo, gobject-introspection, libepoxy, libxi, inputproto, fixesproto, at-spi2-atk, gettext, cups
Description:
The GTK+ 2 package contains libraries used for creating graphical user interfaces for applications.

gtksourceview

Homepage:
Spack package:
Versions:
4.2.0, 3.24.11
Build Dependencies:
m4, autoconf, automake, libtool, gobject-introspection, intltool, pkgconfig, gettext, glib, gtkplus, libxml2, pango, gdk-pixbuf, atk, libiconv
Link Dependencies:
gettext, glib, gtkplus, libxml2, pango, gdk-pixbuf, atk, libiconv
Description:
GtkSourceView is a GNOME library that extends GtkTextView, the standard GTK+ widget for multiline text editing. GtkSourceView adds support for syntax highlighting, undo/redo, file loading and saving, search and replace, a completion system, printing, displaying line numbers, and other features typical of a source code editor.

gts

Homepage:
Spack package:
Versions:
121130
Build Dependencies:
glib
Link Dependencies:
glib
Description:
GTS stands for the GNU Triangulated Surface Library. It is an Open Source Free Software Library intended to provide a set of useful functions to deal with 3D surfaces meshed with interconnected triangles. The source code is available free of charge under the Free Software LGPL license. The code is written entirely in C with an object-oriented approach based mostly on the design of GTK+. Careful attention is paid to performance related issues as the initial goal of GTS is to provide a simple and efficient library to scientists dealing with 3D computational surface meshes.

guidance

Homepage:
Spack package:
Versions:
2.02
Build Dependencies:
perl, perl-bioperl, ruby, prank, clustalw, mafft, muscle
Link Dependencies:
ruby, prank, clustalw, mafft, muscle
Run Dependencies:
perl, perl-bioperl
Description:
Guidance: Accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters.

guile

Homepage:
Spack package:
Versions:
2.2.6, 2.2.5, 2.2.4, 2.2.3, 2.2.2, 2.2.1, 2.2.0, 2.0.14, 2.0.11
Build Dependencies:
bdw-gc, gmp, gettext, libtool, libunistring, libffi, readline, pkgconfig
Link Dependencies:
bdw-gc, gmp, gettext, libtool, libunistring, libffi, readline
Description:
Guile is the GNU Ubiquitous Intelligent Language for Extensions, the official extension language for the GNU operating system.

gurobi

Homepage:
Spack package:
Versions:
7.5.2
Description:
The Gurobi Optimizer was designed from the ground up to be the fastest, most powerful solver available for your LP, QP, QCP, and MIP (MILP, MIQP, and MIQCP) problems. Note: Gurobi is licensed software. You will need to create an account on the Gurobi homepage and download Gurobi Optimizer yourself. Spack will search your current directory for the download file. Alternatively, add this file to a mirror so that Spack can find it. For instructions on how to set up a mirror, see http://spack.readthedocs.io/en/latest/mirrors.html Please set the path to licence file with the following command (for bash) export GRB_LICENSE_FILE=/path/to/gurobi/license/. See section 4 in $GUROBI_HOME/docs/quickstart_linux.pdf for more details.

gzip

Homepage:
Spack package:
Versions:
1.10
Build Dependencies:
gmake
Description:
GNU Gzip is a popular data compression program originally written by Jean-loup Gailly for the GNU project.

h5cpp

Homepage:
Spack package:
Versions:
master, 1.10.4-5
Build Dependencies:
cmake, hdf5, mpi
Link Dependencies:
hdf5, mpi
Description:
Easy to use HDF5 C++ templates for Serial and Parallel HDF5

h5hut

Homepage:
Spack package:
Versions:
2.0.0rc3
Build Dependencies:
mpi, hdf5
Link Dependencies:
mpi, hdf5
Description:
H5hut (HDF5 Utility Toolkit). High-Performance I/O Library for Particle- based Simulations.

h5part

Homepage:
Spack package:
Versions:
1.6.6
Build Dependencies:
mpi, hdf5
Link Dependencies:
mpi, hdf5
Description:
Portable High Performance Parallel Data Interface to HDF5

h5utils

Homepage:
Spack package:
Versions:
1.12.1
Build Dependencies:
hdf5, libpng, octave, hdf, libmatheval
Link Dependencies:
hdf5, libpng, octave, hdf, libmatheval
Description:
h5utils is a set of utilities for visualization and conversion of scientific data in the free, portable HDF5 format.

h5z-zfp

Homepage:
Spack package:
Versions:
develop, 0.8.0, 0.7.0
Build Dependencies:
hdf5, zfp
Link Dependencies:
hdf5, zfp
Description:
A highly flexible floating point and integer compression plugin for the HDF5 library using ZFP compression.

hacckernels

Homepage:
Spack package:
Versions:
develop
Build Dependencies:
cmake
Description:
HACCKernels: A Benchmark for HACC's Particle Force Kernels. The Hardware/Hybrid Accelerated Cosmology Code (HACC), a cosmology N-body- code framework, is designed to run efficiently on diverse computing architectures and to scale to millions of cores and beyond.

hadoop

Homepage:
Spack package:
Versions:
3.2.1, 3.1.3, 2.10.0, 2.9.2, 2.8.5, 2.7.7
Run Dependencies:
java
Description:
The Apache Hadoop software library is a framework that allows for the distributed processing of large data sets across clusters of computers using simple programming models.

halc

Homepage:
Spack package:
Versions:
1.1
Build Dependencies:
dos2unix
Run Dependencies:
blasr, lordec, python
Description:
HALC is software that makes error correction for long reads with high throughput.

half

Homepage:
Spack package:
Versions:
2.1.0
Description:
This is a C++ header-only library to provide an IEEE-754 conformant half-precision floating point type along with corresponding arithmetic operators, type conversions and common mathematical functions. It aims for both efficiency and ease of use, trying to accurately mimic the behaviour of the builtin floating point types at the best performance possible. It automatically uses and provides C++11 features when possible, but stays completely C++98-compatible when neccessary.

hama

Homepage:
Spack package:
Versions:
0.7.1
Description:
Apache Hama is a framework for Big Data analytics which uses the Bulk Synchronous Parallel (BSP) computing model, which was established in 2012 as a Top-Level Project of The Apache Software Foundation.

hapcut2

Homepage:
Spack package:
Versions:
2017-07-10
Link Dependencies:
zlib
Description:
HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to 'just work' with excellent speed and accuracy.

hapdip

Homepage:
Spack package:
Versions:
2018.02.20
Run Dependencies:
k8
Description:
The CHM1-NA12878 benchmark for single-sample SNP/INDEL calling from WGS Illumina data.

haploview

Homepage:
Spack package:
Versions:
4.1
Build Dependencies:
java
Run Dependencies:
java
Description:
Haploview is designed to simplify and expedite the process of haplotype analysis.

haproxy

Homepage:
Spack package:
Versions:
2.1.1, 2.1.0
Description:
HAProxy is a single-threaded, event-driven, non-blocking engine combining a very fast I/O layer with a priority-based scheduler.

harfbuzz

Homepage:
Spack package:
Versions:
2.3.1, 2.1.3, 1.9.0, 1.4.6, 0.9.37
Build Dependencies:
pkgconfig, glib, icu4c, freetype, cairo, zlib, graphite2
Link Dependencies:
glib, icu4c, freetype, cairo, zlib, graphite2
Description:
The Harfbuzz package contains an OpenType text shaping engine.

harminv

Homepage:
Spack package:
Versions:
1.4
Build Dependencies:
blas, lapack
Link Dependencies:
blas, lapack
Description:
Harminv is a free program (and accompanying library) to solve the problem of harmonic inversion - given a discrete-time, finite-length signal that consists of a sum of finitely-many sinusoids (possibly exponentially decaying) in a given bandwidth, it determines the frequencies, decay constants, amplitudes, and phases of those sinusoids.

hbase

Homepage:
Spack package:
Versions:
2.2.2, 2.1.8
Run Dependencies:
java
Description:
Apache HBase is an open-source, distributed, versioned, column-oriented store modeled after Google' Bigtable: A Distributed Storage System for Structured Data by Chang et al. Just as Bigtable leverages the distributed data storage provided by the Google File System, HBase provides Bigtable-like capabilities on top of Apache Hadoop.

hc

Homepage:
Spack package:
Versions:
1.0.7
Build Dependencies:
gmt, netcdf-c
Link Dependencies:
gmt, netcdf-c
Description:
HC is a global mantle circulation solver following Hager & O'Connell (1981) which can compute velocities, tractions, and geoid for simple density distributions and plate velocities.

hdf

Homepage:
Spack package:
Versions:
4.2.14, 4.2.13, 4.2.12, 4.2.11
Build Dependencies:
jpeg, szip, zlib, bison, flex
Link Dependencies:
jpeg, szip, zlib
Description:
HDF4 (also known as HDF) is a library and multi-object file format for storing and managing data between machines.

hdf5

Homepage:
Spack package:
Versions:
develop, 1.10.6, 1.10.5, 1.10.4, 1.10.3, 1.10.2, 1.10.1, 1.10.0-patch1, 1.10.0, 1.8.21, 1.8.19, 1.8.18, 1.8.17, 1.8.16, 1.8.15, 1.8.14, 1.8.13, 1.8.12, 1.8.10
Build Dependencies:
autoconf, automake, libtool, m4, mpi, numactl, szip, zlib
Link Dependencies:
mpi, numactl, szip, zlib
Description:
HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data.

hdf5-blosc

Homepage:
Spack package:
Versions:
master
Build Dependencies:
c-blosc, hdf5, libtool
Link Dependencies:
c-blosc, hdf5
Description:
Blosc filter for HDF5

heaptrack

Homepage:
Spack package:
Versions:
1.1.0
Build Dependencies:
cmake, boost, elfutils, libunwind, zlib, zstd
Link Dependencies:
cmake, boost, elfutils, libunwind, zlib, zstd
Description:
Heaptrack is a heap memory profiler that traces all memory allocations and annotates these events with stack traces.

heffte

Homepage:
Spack package:
Versions:
master, 0.2, 0.1
Build Dependencies:
cmake, fftw, mpi, cuda
Link Dependencies:
fftw, mpi, cuda
Description:
Highly Efficient FFT for Exascale

help2man

Homepage:
Spack package:
Versions:
1.47.11, 1.47.8, 1.47.4
Build Dependencies:
gettext, perl
Run Dependencies:
perl
Description:
help2man produces simple manual pages from the '--help' and '--version' output of other commands.

henson

Homepage:
Spack package:
Versions:
master
Build Dependencies:
cmake, mpi, python
Link Dependencies:
mpi, python
Description:
Cooperative multitasking for in situ processing.

hepmc

Homepage:
Spack package:
Versions:
3.2.0, 3.1.2, 3.1.1, 3.1.0, 3.0.0, 2.06.10, 2.06.09, 2.06.08, 2.06.07, 2.06.06, 2.06.05
Build Dependencies:
cmake, python, root
Link Dependencies:
python, root
Description:
The HepMC package is an object oriented, C++ event record for High Energy Physics Monte Carlo generators and simulation.

heppdt

Homepage:
Spack package:
Versions:
3.04.01, 3.04.00, 3.03.02, 3.03.01, 3.03.00, 2.06.01
Description:
The HepPID library contains translation methods for particle ID's to and from various Monte Carlo generators and the PDG standard numbering scheme. We realize that the generators adhere closely to the standard, but there are occasional differences.

hic-pro

Homepage:
Spack package:
Versions:
2.10.0
Build Dependencies:
bowtie2, samtools, python, r, py-numpy, py-scipy, py-pysam, py-bx-python, r-rcolorbrewer, r-ggplot2
Link Dependencies:
bowtie2, samtools, python, r
Run Dependencies:
py-numpy, py-scipy, py-pysam, py-bx-python, r-rcolorbrewer, r-ggplot2
Description:
HiC-Pro is a package designed to process Hi-C data, from raw fastq files (paired-end Illumina data) to the normalized contact maps

highfive

Homepage:
Spack package:
Versions:
2.0, 1.5, 1.2, 1.1, 1.0
Build Dependencies:
cmake, boost, hdf5
Link Dependencies:
boost, hdf5
Description:
HighFive - Header only C++ HDF5 interface

highwayhash

Homepage:
Spack package:
Versions:
dfcb97
Description:
Strong (well-distributed and unpredictable) hashes: - Portable implementation of SipHash - HighwayHash, a 5x faster SIMD hash with security claims

hiop

Homepage:
Spack package:
Versions:
0.1
Build Dependencies:
cmake, mpi, lapack, blas
Link Dependencies:
mpi, lapack, blas
Description:
HiOp is an optimization solver for solving certain mathematical optimization problems expressed as nonlinear programming problems. HiOp is a lightweight HPC solver that leverages application's existing data parallelism to parallelize the optimization iterations by using specialized linear algebra kernels.

hipsycl

Homepage:
Spack package:
Versions:
master, 0.8.0
Build Dependencies:
cmake, boost, python, llvm, cuda
Link Dependencies:
boost, python, llvm, cuda
Description:
hipSYCL is an implementation of the SYCL standard programming model over NVIDIA CUDA/AMD HIP

hisat2

Homepage:
Spack package:
Versions:
2.1.0
Description:
HISAT2 is a fast and sensitive alignment program for mapping next- generation sequencing reads (whole-genome, transcriptome, and exome sequencing data) against the general human population (as well as against a single reference genome).

hisea

Homepage:
Spack package:
Versions:
2017.12.26
Build Dependencies:
boost
Link Dependencies:
boost
Description:
HISEA is an efficient all-vs-all long read aligner for SMRT sequencing data. Its algorithm is designed to produce highest alignment sensitivity among others.

hive

Homepage:
Spack package:
Versions:
3.1.2, 2.3.6, 1.2.2
Run Dependencies:
hadoop
Description:
The Apache Hive data warehouse software facilitates reading, writing, and managing large datasets residing in distributed storage using SQL. Structure can be projected onto data already in storage. A command line tool and JDBC driver are provided to connect users to Hive.

hmmer

Homepage:
Spack package:
Versions:
3.3, 3.2.1, 3.1b2, 3.0, 2.4i, 2.3.2, 2.3.1
Build Dependencies:
mpi, gsl
Link Dependencies:
mpi, gsl
Description:
HMMER is used for searching sequence databases for sequence homologs, and for making sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs).

homer

Homepage:
Spack package:
Versions:
4.9.1
Build Dependencies:
perl
Run Dependencies:
perl, r-biocgenerics, r-biocparallel, r-edger, r-deseq2
Description:
Software for motif discovery and next generation sequencing analysis

hoomd-blue

Homepage:
Spack package:
Versions:
develop, 2.2.2, 2.1.6
Build Dependencies:
cmake, python, py-numpy, pkgconfig, mpi, cuda, doxygen
Link Dependencies:
python, mpi, cuda
Run Dependencies:
py-numpy
Description:
HOOMD-blue is a general-purpose particle simulation toolkit. It scales from a single CPU core to thousands of GPUs. You define particle initial conditions and interactions in a high-level python script. Then tell HOOMD-blue how you want to execute the job and it takes care of the rest. Python job scripts give you unlimited flexibility to create custom initialization routines, control simulation parameters, and perform in situ analysis.

hotspot

Homepage:
Spack package:
Versions:
6.0
Description:
HotSpot is an accurate and fast thermal model suitable for use ini architectural studies.

hpccg

Homepage:
Spack package:
Versions:
1.0
Build Dependencies:
mpi
Link Dependencies:
mpi
Description:
Proxy Application. Intended to be the 'best approximation to an unstructured implicit finite element or finite volume application in 800 lines or fewer.'

hpctoolkit

Homepage:
Spack package:
Versions:
master, 2019.12.28, 2019.08.14, 2018.12.28, 2018.11.05
Build Dependencies:
boost, dyninst, intel-tbb, libdwarf, libmonitor, libunwind, mbedtls, xerces-c, zlib, cuda, intel-xed, papi, libpfm4, mpi
Link Dependencies:
binutils, boost, bzip2, dyninst, elfutils, intel-tbb, libdwarf, libmonitor, libunwind, mbedtls, xerces-c, xz, zlib, cuda, intel-xed, papi, libpfm4, mpi
Description:
HPCToolkit is an integrated suite of tools for measurement and analysis of program performance on computers ranging from multicore desktop systems to the nation's largest supercomputers. By using statistical sampling of timers and hardware performance counters, HPCToolkit collects accurate measurements of a program's work, resource consumption, and inefficiency and attributes them to the full calling context in which they occur.

hpcviewer

Homepage:
Spack package:
Versions:
2020.01, 2019.12, 2019.09, 2019.08, 2019.07, 2019.04, 2019.02
Build Dependencies:
java
Run Dependencies:
java
Description:
Binary distribution of hpcviewer and hpctraceviewer for the Rice HPCToolkit (Linux x86_64, ppc64 and ppc64le). Note: hpctoolkit databases are platform independent, so you don't need to install hpctoolkit to run the viewers and it's common to run hpcrun and hpcviewer on different machines.

hpgmg

Homepage:
Spack package:
Versions:
develop, 0.4, 0.3, a0a5510df23b
Build Dependencies:
petsc, mpi, cuda, python
Link Dependencies:
petsc, mpi, cuda
Description:
HPGMG implements full multigrid (FMG) algorithms using finite-volume and finite-element methods. Different algorithmic variants adjust the arithmetic intensity and architectural properties that are tested. These FMG methods converge up to discretization error in one F-cycle, thus may be considered direct solvers. An F-cycle visits the finest level a total of two times, the first coarsening (8x smaller) 4 times, the second coarsening 6 times, etc.

hpl

Homepage:
Spack package:
Versions:
2.3, 2.2
Build Dependencies:
mpi, blas
Link Dependencies:
mpi, blas
Description:
HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the High Performance Computing Linpack Benchmark.

hpx

Homepage:
Spack package:
Versions:
master, 1.4.0, 1.3.0, 1.2.1, 1.2.0, 1.1.0
Build Dependencies:
cuda, cmake, hwloc, python, pkgconfig, git, boost, gperftools, jemalloc, tbb, mpi, otf2, papi, valgrind
Link Dependencies:
cuda, hwloc, boost, gperftools, jemalloc, tbb, mpi, otf2, papi, valgrind
Run Dependencies:
python
Test Dependencies:
python
Description:
C++ runtime system for parallel and distributed applications.

hpx5

Homepage:
Spack package:
Versions:
4.1.0, 4.0.0, 3.1.0, 3.0.0, 2.2.0, 2.1.0, 2.0.0
Build Dependencies:
autoconf, automake, hwloc, jemalloc, libtool, m4, metis, mpi, opencl, pkgconfig
Link Dependencies:
hwloc, jemalloc, metis, mpi, opencl
Description:
The HPX-5 Runtime System. HPX-5 (High Performance ParalleX) is an open source, portable, performance-oriented runtime developed at CREST (Indiana University). HPX-5 provides a distributed programming model allowing programs to run unmodified on systems from a single SMP to large clusters and supercomputers with thousands of nodes. HPX-5 supports a wide variety of Intel and ARM platforms. It is being used by a broad range of scientific applications enabling scientists to write code that performs and scales better than contemporary runtimes.

hsakmt

Homepage:
Spack package:
Versions:
1.0.0
Description:
hsakmt is a thunk library that provides a userspace interface to amdkfd (AMD's HSA Linux kernel driver). It is the HSA equivalent of libdrm.

hstr

Homepage:
Spack package:
Versions:
1.22
Build Dependencies:
autoconf, automake, libtool, m4, ncurses, readline
Link Dependencies:
ncurses, readline
Description:
hstr(hh) is a shell history suggest box for Bash and Zsh, which enables easy viewing, searching and using your command history.

htop

Homepage:
Spack package:
Versions:
2.2.0, 2.0.2
Build Dependencies:
ncurses
Link Dependencies:
ncurses
Description:
htop is an interactive text-mode process viewer for Unix systems.

htslib

Homepage:
Spack package:
Versions:
1.10.2, 1.9, 1.8, 1.7, 1.6, 1.5, 1.4, 1.3.1, 1.2
Build Dependencies:
zlib, bzip2, xz, curl, m4, autoconf, automake, libtool
Link Dependencies:
zlib, bzip2, xz, curl, m4, autoconf, automake, libtool
Description:
C library for high-throughput sequencing data formats.

httperf

Homepage:
Spack package:
Versions:
master
Build Dependencies:
autoconf, automake, libtool, m4
Description:
Httperf is a tool for measuring web server performance. It provides a flexible facility for generating various HTTP workloads and for measuring server performance.

httpie

Homepage:
Spack package:
Versions:
0.9.9, 0.9.8
Build Dependencies:
python, py-setuptools, py-pygments, py-requests, py-pysocks, py-argparse
Link Dependencies:
python
Run Dependencies:
python, py-setuptools, py-pygments, py-requests, py-pysocks, py-argparse
Description:
Modern command line HTTP client.

hub

Homepage:
Spack package:
Versions:
master, 2.2.2, 2.2.1, 2.2.0, 1.12.4
Build Dependencies:
go
Link Dependencies:
go
Description:
The github git wrapper

hugo

Homepage:
Spack package:
Versions:
0.53
Build Dependencies:
go
Description:
The world's fastest framework for building websites.

hunspell

Homepage:
Spack package:
Versions:
1.7.0, 1.6.0
Build Dependencies:
autoconf, automake, libtool, m4, gettext
Link Dependencies:
gettext
Description:
The most popular spellchecking library (sez the author...).

hwloc

Homepage:
Spack package:
Versions:
master, 2.1.0, 2.0.2, 2.0.1, 2.0.0, 1.11.11, 1.11.10, 1.11.9, 1.11.8, 1.11.7, 1.11.6, 1.11.5, 1.11.4, 1.11.3, 1.11.2, 1.11.1, 1.9
Build Dependencies:
pkgconfig, m4, autoconf, automake, libtool, cuda, gl, libpciaccess, libxml2, cairo, numactl
Link Dependencies:
cuda, gl, libpciaccess, libxml2, cairo, numactl
Description:
The Hardware Locality (hwloc) software project. The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various system attributes such as cache and memory information as well as the locality of I/O devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering information about modern computing hardware so as to exploit it accordingly and efficiently.

hybpiper

Homepage:
Spack package:
Versions:
1.3.1, 1.2.0
Build Dependencies:
python, py-biopython, exonerate, blast-plus, spades, parallel, bwa, samtools
Link Dependencies:
exonerate, blast-plus, spades, parallel, bwa, samtools
Run Dependencies:
python, py-biopython
Description:
HybPiper was designed for targeted sequence capture, in which DNA sequencing libraries are enriched for gene regions of interest, especially for phylogenetics. HybPiper is a suite of Python scripts that wrap and connect bioinformatics tools in order to extract target sequences from high-throughput DNA sequencing reads

hydra

Homepage:
Spack package:
Versions:
3.2
Description:
Hydra is a process management system for starting parallel jobs. Hydra is designed to natively work with existing launcher daemons (such as ssh, rsh, fork), as well as natively integrate with resource management systems (such as slurm, pbs, sge).

hydrogen

Homepage:
Spack package:
Versions:
develop, 1.3.3, 1.3.2, 1.3.1, 1.3.0, 1.2.0, 1.1.0-1, 1.1.0, 1.0.1, 1.0
Build Dependencies:
cmake, openblas, intel-mkl, veclibfort, essl, netlib-lapack, aluminum, lapack, mpi, scalapack, gmp, mpc, mpfr, cuda, cub, half, ninja
Link Dependencies:
openblas, intel-mkl, veclibfort, essl, netlib-lapack, aluminum, lapack, mpi, scalapack, gmp, mpc, mpfr, cuda, cub, half
Description:
Hydrogen: Distributed-memory dense and sparse-direct linear algebra and optimization library. Based on the Elemental library.

hyphy

Homepage:
Spack package:
Versions:
2.3.14
Build Dependencies:
cmake, curl
Link Dependencies:
cmake, curl
Description:
HyPhy: Hypothesis testing using Phylogenies

hypre

Homepage:
Spack package:
Versions:
develop, 2.18.2, 2.18.1, 2.18.0, 2.17.0, 2.16.0, 2.15.1, 2.15.0, 2.14.0, 2.13.0, 2.12.1, 2.11.2, 2.11.1, 2.10.1, 2.10.0b, xsdk-0.2.0
Build Dependencies:
mpi, blas, lapack, superlu-dist
Link Dependencies:
mpi, blas, lapack, superlu-dist
Description:
Hypre is a library of high performance preconditioners that features parallel multigrid methods for both structured and unstructured grid problems.

i3

Homepage:
Spack package:
Versions:
4.14.1
Build Dependencies:
autoconf, automake, libtool, m4, pkgconfig, libev, startup-notification, xcb-util-cursor, xcb-util-keysyms, xcb-util-wm, xcb-util-xrm, libxkbcommon, yajl, cairo, pango
Link Dependencies:
libev, startup-notification, xcb-util-cursor, xcb-util-keysyms, xcb-util-wm, xcb-util-xrm, libxkbcommon, yajl, cairo, pango
Description:
i3, improved tiling wm. i3 is a tiling window manager, completely written from scratch. The target platforms are GNU/Linux and BSD operating systems, our code is Free and Open Source Software (FOSS) under the BSD license. i3 is primarily targeted at advanced users and developers.

ibm-java

Homepage:
Spack package:
Description:
Binary distribution of the IBM Java Software Development Kit for big and little-endian powerpc (power7, 8 and 9).

ibmisc

Homepage:
Spack package:
Versions:
0.1.0
Build Dependencies:
cmake, python, eigen, everytrace, proj, blitz, netcdf-cxx4, udunits, googletest, py-cython, py-numpy, boost, doxygen
Link Dependencies:
python, eigen, everytrace, proj, blitz, netcdf-cxx4, udunits, boost
Run Dependencies:
py-cython, py-numpy
Description:
Misc. reusable utilities used by IceBin.

iceauth

Homepage:
Spack package:
Versions:
1.0.7
Build Dependencies:
libice, xproto, pkgconfig, util-macros
Link Dependencies:
libice
Description:
The iceauth program is used to edit and display the authorization information used in connecting with ICE. It operates very much like the xauth program for X11 connection authentication records.

icedtea

Homepage:
Spack package:
Versions:
3.9.0, 3.8.0, 3.7.0, 3.6.0, 3.5.1, 3.5.0, 3.4.0
Build Dependencies:
pkgconfig, gmake, cups, jdk, libx11, xproto, libxext, libxtst, libxi, libxt, libxinerama, libxrender, libxcomposite, libxau, libxdmcp, gtkplus, freetype, wget, giflib, libpng, jpeg, lcms, zlib, alsa-lib
Link Dependencies:
cups, libx11, xproto, libxext, libxtst, libxi, libxt, libxinerama, libxrender, libxcomposite, libxau, libxdmcp, gtkplus, freetype, giflib, libpng, jpeg, lcms, zlib, alsa-lib
Description:
The IcedTea project provides a harness to build the source code from http://openjdk.java.net using Free Software build tools and adds a number of key features to the upstream OpenJDK codebase. IcedTea requires an existing IcedTea or OpenJDK install to build.

icet

Homepage:
Spack package:
Versions:
develop, 2.1.1
Build Dependencies:
cmake, mpi
Link Dependencies:
mpi
Description:
The Image Composition Engine for Tiles (IceT) is a high-performance sort-last parallel rendering library.

ico

Homepage:
Spack package:
Versions:
1.0.4
Build Dependencies:
libx11, xproto, pkgconfig, util-macros
Link Dependencies:
libx11
Description:
ico is a simple animation program that may be used for testing various X11 operations and extensions. It displays a wire-frame rotating polyhedron, with hidden lines removed, or a solid-fill polyhedron with hidden faces removed.

icu4c

Homepage:
Spack package:
Versions:
65.1, 64.1, 60.1, 58.2, 57.1
Build Dependencies:
python
Description:
ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization support for software applications. ICU4C is the C/C++ interface.

id3lib

Homepage:
Spack package:
Versions:
3.8.3
Build Dependencies:
zlib
Link Dependencies:
zlib
Description:
Library for manipulating ID3v1 and ID3v2 tags

idba

Homepage:
Spack package:
Versions:
1.1.3
Build Dependencies:
m4, autoconf, automake, libtool
Description:
IDBA is a practical iterative De Bruijn Graph De Novo Assembler for sequence assembly in bioinfomatics.

iegenlib

Homepage:
Spack package:
Versions:
master, 2018-07-03
Build Dependencies:
cmake, autoconf, texinfo, isl
Link Dependencies:
isl
Description:
Inspector/Executor Generation Library for manipulating sets and relations with uninterpreted function symbols.

ignite

Homepage:
Spack package:
Versions:
2.6.0, 2.5.0, 2.4.0, 2.3.0, 2.2.0
Run Dependencies:
java
Description:
Apache Ignite is a memory-centric distributed database, caching, and processing platform for transactional, analytical, and streaming workloads delivering in-memory speeds at petabyte scale.

igraph

Homepage:
Spack package:
Versions:
0.7.1
Build Dependencies:
libxml2
Link Dependencies:
libxml2
Description:
igraph is a library for creating and manipulating graphs.

igv

Homepage:
Spack package:
Versions:
2.8.0
Run Dependencies:
java
Description:
The Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations.

igvtools

Homepage:
Spack package:
Versions:
2.3.98
Build Dependencies:
java
Link Dependencies:
java
Description:
IGVTools suite of command-line utilities for preprocessing data files

ilmbase

Homepage:
Spack package:
Versions:
2.3.0, 2.2.0, 2.0.1, 1.0.2, 0.9.0
Description:
OpenEXR ILM Base libraries (high dynamic-range image file format)

imagemagick

Homepage:
Spack package:
Versions:
7.0.8-7, 7.0.5-9, 7.0.2-7, 7.0.2-6
Build Dependencies:
jpeg, pango, libtool, libpng, freetype, fontconfig, libtiff, ghostscript, ghostscript-fonts
Link Dependencies:
jpeg, pango, libpng, freetype, fontconfig, libtiff, ghostscript, ghostscript-fonts
Description:
ImageMagick is a software suite to create, edit, compose, or convert bitmap images.

imake

Homepage:
Spack package:
Versions:
1.0.7
Build Dependencies:
xproto, pkgconfig
Description:
The imake build system.

imlib2

Homepage:
Spack package:
Versions:
1.6.1, 1.6.0, 1.5.1
Build Dependencies:
libtiff, giflib, bzip2, freetype, libxext, libpng, libid3tag, libjpeg-turbo
Link Dependencies:
libtiff, giflib, bzip2, freetype, libxext, libpng, libid3tag, libjpeg-turbo
Description:
Library that does image file loading and saving as well as rendering, manipulation, arbitrary polygon support

imp

Homepage:
Spack package:
Versions:
2.8.0
Build Dependencies:
cmake, python, swig, boost, hdf5, eigen
Link Dependencies:
python, swig, boost, hdf5, eigen
Description:
IMP, the Integrative Modeling Platform.

impute2

Homepage:
Spack package:
Versions:
2.3.2
Description:
IMPUTE2 is a genotype imputation and haplotype phasing program based on ideas from Howie et al. 2009.

infernal

Homepage:
Spack package:
Versions:
1.1.2
Build Dependencies:
mpi
Link Dependencies:
mpi
Description:
Infernal (INFERence of RNA ALignment) is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs).

inputproto

Homepage:
Spack package:
Versions:
2.3.2
Build Dependencies:
pkgconfig, util-macros
Description:
X Input Extension. This extension defines a protocol to provide additional input devices management such as graphic tablets.

intel

Homepage:
Spack package:
Versions:
19.1.0, 19.0.5, 19.0.4, 19.0.3, 19.0.1, 19.0.0, 18.0.4, 18.0.3, 18.0.2, 18.0.1, 18.0.0, 17.0.7, 17.0.6, 17.0.5, 17.0.4, 17.0.3, 17.0.2, 17.0.1, 17.0.0, 16.0.4, 16.0.3, 16.0.2, 15.0.6, 15.0.1
Description:
Intel Compilers.

intel-daal

Homepage:
Spack package:
Versions:
2020.0.166, 2019.5.281, 2019.4.243, 2019.3.199, 2019.2.187, 2019.1.144, 2019.0.117, 2018.3.222, 2018.2.199, 2018.1.163, 2018.0.128, 2017.4.239, 2017.3.196, 2017.2.174, 2017.1.132, 2017.0.098, 2016.3.210, 2016.2.181
Description:
Intel Data Analytics Acceleration Library.

intel-gpu-tools

Homepage:
Spack package:
Versions:
1.16
Build Dependencies:
libdrm, libpciaccess, cairo, glib, flex, bison, python, pkgconfig, util-macros
Link Dependencies:
libdrm, libpciaccess, cairo, glib
Description:
Intel GPU Tools is a collection of tools for development and testing of the Intel DRM driver. There are many macro-level test suites that get used against the driver, including xtest, rendercheck, piglit, and oglconform, but failures from those can be difficult to track down to kernel changes, and many require complicated build procedures or specific testing environments to get useful results. Therefore, Intel GPU Tools includes low-level tools and tests specifically for development and testing of the Intel DRM Driver.

intel-ipp

Homepage:
Spack package:
Versions:
2020.0.166, 2019.5.281, 2019.4.243, 2019.3.199, 2019.2.187, 2019.1.144, 2019.0.117, 2018.4.274, 2018.3.222, 2018.2.199, 2018.0.128, 2017.3.196, 2017.2.174, 2017.1.132, 2017.0.098, 9.0.3.210
Description:
Intel Integrated Performance Primitives.

intel-llvm

Homepage:
Spack package:
Versions:
sycl
Build Dependencies:
cmake
Description:
Intel's version of the LLVM compiler.

intel-mkl

Homepage:
Spack package:
Versions:
2020.0.166, 2019.5.281, 2019.4.243, 2019.3.199, 2019.2.187, 2019.1.144, 2019.0.117, 2018.4.274, 2018.3.222, 2018.2.199, 2018.1.163, 2018.0.128, 2017.4.239, 2017.3.196, 2017.2.174, 2017.1.132, 2017.0.098, 11.3.3.210, 11.3.2.181
Build Dependencies:
cpio
Description:
Intel Math Kernel Library.

intel-mkl-dnn

Homepage:
Spack package:
Versions:
1.2, 1.1.3, 1.1.2, 1.1.1, 1.1, 1.0.4, 1.0.3, 1.0.2, 1.0.1, 1.0, 0.21.3, 0.21.2, 0.21.1, 0.21, 0.20.6, 0.20.5, 0.20.4, 0.20.3, 0.20.2, 0.20.1, 0.20, 0.19, 0.18.1, 0.11, 0.10, 0.9
Build Dependencies:
cmake, intel-mkl, llvm-openmp
Link Dependencies:
intel-mkl, llvm-openmp
Description:
Intel(R) Math Kernel Library for Deep Neural Networks (Intel(R) MKL- DNN).

intel-mpi

Homepage:
Spack package:
Versions:
2019.6.166, 2019.5.281, 2019.4.243, 2019.3.199, 2019.2.187, 2019.1.144, 2019.0.117, 2018.4.274, 2018.3.222, 2018.2.199, 2018.1.163, 2018.0.128, 2017.4.239, 2017.3.196, 2017.2.174, 2017.1.132, 5.1.3.223
Description:
Intel MPI

intel-parallel-studio

Homepage:
Spack package:
Versions:
professional.2020.0, professional.2019.5, professional.2019.4, professional.2019.3, professional.2019.2, professional.2019.1, professional.2019.0, professional.2018.4, professional.2018.3, professional.2018.2, professional.2018.1, professional.2018.0, professional.2017.7, professional.2017.6, professional.2017.5, professional.2017.4, professional.2017.3, professional.2017.2, professional.2017.1, professional.2017.0, professional.2016.4, professional.2016.3, professional.2016.2, professional.2016.1, professional.2016.0, professional.2015.6, professional.2015.1, composer.2020.0, composer.2019.5, composer.2019.4, composer.2019.3, composer.2019.2, composer.2019.1, composer.2019.0, composer.2018.4, composer.2018.3, composer.2018.2, composer.2018.1, composer.2018.0, composer.2017.7, composer.2017.6, composer.2017.5, composer.2017.4, composer.2017.3, composer.2017.2, composer.2017.1, composer.2017.0, composer.2016.4, composer.2016.3, composer.2016.2, composer.2015.6, composer.2015.1, cluster.2020.0, cluster.2019.5, cluster.2019.4, cluster.2019.3, cluster.2019.2, cluster.2019.1, cluster.2019.0, cluster.2018.4, cluster.2018.3, cluster.2018.2, cluster.2018.1, cluster.2018.0, cluster.2017.7, cluster.2017.6, cluster.2017.5, cluster.2017.4, cluster.2017.3, cluster.2017.2, cluster.2017.1, cluster.2017.0, cluster.2016.4, cluster.2016.3, cluster.2016.2, cluster.2016.1, cluster.2016.0, cluster.2015.6, cluster.2015.1
Description:
Intel Parallel Studio.

intel-pin

Homepage:
Spack package:
Versions:
3.11, 3.10, 3.7
Description:
Intel Pin is a dynamic binary instrumentation framework for the IA-32, x86-64 and MIC instruction-set architectures that enables the creation of dynamic program analysis tools.

intel-tbb

Homepage:
Spack package:
Versions:
2020.1, 2020.0, 2019.9, 2019.8, 2019.7, 2019.6, 2019.5, 2019.4, 2019.3, 2019.2, 2019.1, 2019, 2018.6, 2018.5, 2018.4, 2018.3, 2018.2, 2018.1, 2018, 2017.8, 2017.7, 2017.6, 2017.5, 2017.4, 2017.3, 2017.2, 2017.1, 2017, 4.4.6, 4.4.5, 4.4.4, 4.4.3, 4.4.2, 4.4.1, 4.4
Build Dependencies:
cmake
Description:
Widely used C++ template library for task parallelism. Intel Threading Building Blocks (Intel TBB) lets you easily write parallel C++ programs that take full advantage of multicore performance, that are portable and composable, and that have future-proof scalability.

intel-xed

Homepage:
Spack package:
Versions:
develop, 2019.03.01, 2018.02.14
Build Dependencies:
python
Description:
The Intel X86 Encoder Decoder library for encoding and decoding x86 machine instructions (64- and 32-bit). Also includes libxed-ild, a lightweight library for decoding the length of an instruction.

interproscan

Homepage:
Spack package:
Versions:
5.38-76.0, 5.36-75.0, 4.8
Build Dependencies:
java, maven, perl, python, perl-cgi, perl-mailtools, perl-xml-quote, perl-xml-parser, perl-io-string, perl-io-stringy
Run Dependencies:
java, perl, python, perl-cgi, perl-mailtools, perl-xml-quote, perl-xml-parser, perl-io-string, perl-io-stringy
Description:
InterProScan is the software package that allows sequences (protein and nucleic) to be scanned against InterPro's signatures. Signatures are predictive models, provided by several different databases, that make up the InterPro consortium.

intltool

Homepage:
Spack package:
Versions:
0.51.0
Build Dependencies:
perl-xml-parser, perl
Run Dependencies:
perl-xml-parser, perl
Description:
intltool is a set of tools to centralize translation of many different file formats using GNU gettext-compatible PO files.

ioapi

Homepage:
Spack package:
Versions:
3.2
Build Dependencies:
netcdf-c, netcdf-fortran, sed
Link Dependencies:
netcdf-c, netcdf-fortran
Description:
Models-3/EDSS Input/Output Applications Programming Interface.

ior

Homepage:
Spack package:
Versions:
3.2.1, 3.2.0, 3.0.1
Build Dependencies:
autoconf, automake, libtool, m4, mpi, hdf5, parallel-netcdf
Link Dependencies:
mpi, hdf5, parallel-netcdf
Description:
The IOR software is used for benchmarking parallel file systems using POSIX, MPI-IO, or HDF5 interfaces.

iozone

Homepage:
Spack package:
Versions:
3_465
Description:
IOzone is a filesystem benchmark tool. The benchmark generates and measures a variety of file operations. Iozone has been ported to many machines and runs under many operating systems.

iperf2

Homepage:
Spack package:
Versions:
2.0.12
Description:
This code is a continuation based from the no longer maintained iperf 2.0.5 code base. Iperf 2.0.5 is still widely deployed and used by many for testing networks and for qualifying networking products.

iperf3

Homepage:
Spack package:
Versions:
3.6
Description:
The iperf series of tools perform active measurements to determine the maximum achievable bandwidth on IP networks. iperf2 is a separately maintained project.

ipopt

Homepage:
Spack package:
Versions:
3.12.10, 3.12.9, 3.12.8, 3.12.7, 3.12.6, 3.12.5, 3.12.4, 3.12.3, 3.12.2, 3.12.1, 3.12.0
Build Dependencies:
blas, lapack, pkgconfig, mumps, coinhsl, metis
Link Dependencies:
blas, lapack, mumps, coinhsl, metis
Description:
Ipopt (Interior Point OPTimizer, pronounced eye-pea-Opt) is a software package for large-scale nonlinear optimization.

isaac

Homepage:
Spack package:
Versions:
develop, master, 1.4.0, 1.3.3, 1.3.2, 1.3.1, 1.3.0
Build Dependencies:
cmake
Link Dependencies:
jpeg, jansson, boost, cuda, icet, mpi
Description:
In Situ Animation of Accelerated Computations: Header-Only Library

isaac-server

Homepage:
Spack package:
Versions:
develop, master, 1.4.0, 1.3.3, 1.3.2, 1.3.1, 1.3.0
Build Dependencies:
cmake
Link Dependencies:
jpeg, jansson, boost, libwebsockets
Description:
In Situ Animation of Accelerated Computations: Server

isl

Homepage:
Spack package:
Versions:
0.21, 0.20, 0.19, 0.18, 0.15, 0.14
Build Dependencies:
gmp
Link Dependencies:
gmp
Description:
isl (Integer Set Library) is a thread-safe C library for manipulating sets and relations of integer points bounded by affine constraints.

iso-codes

Homepage:
Spack package:
Versions:
4.3
Build Dependencies:
m4, autoconf, automake, libtool, gettext, python
Description:
ISO-codes provides lists of various ISO standards

itstool

Homepage:
Spack package:
Versions:
2.0.2, 2.0.1, 2.0.0, 1.2.0
Description:
ITS Tool allows you to translate your XML documents with PO files, using rules from the W3C Internationalization Tag Set (ITS) to determine what to translate and how to separate it into PO file messages.

itsx

Homepage:
Spack package:
Versions:
1.0.11
Build Dependencies:
perl, hmmer
Link Dependencies:
hmmer
Run Dependencies:
perl
Description:
Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for use in environmental sequencing

jackcess

Homepage:
Spack package:
Versions:
2.1.12, 1.2.14.3
Build Dependencies:
jdk
Link Dependencies:
jdk
Run Dependencies:
java, commons-lang, commons-logging
Description:
Jackcess is a pure Java library for reading from and writing to MS Access databases (currently supporting versions 2000-2016).

jafka

Homepage:
Spack package:
Versions:
3.0.6, 3.0.5, 3.0.4, 3.0.3, 3.0.2, 3.0.1, 3.0.0, 1.6.2
Run Dependencies:
java
Description:
Jafka is a distributed publish-subscribe messaging system.

jags

Homepage:
Spack package:
Versions:
4.3.0, 4.2.0
Build Dependencies:
blas, lapack
Link Dependencies:
blas, lapack
Description:
JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation not wholly unlike BUGS

jali

Homepage:
Spack package:
Versions:
master, 1.1.1, 1.1.0, 1.0.5
Build Dependencies:
cmake, mpi, boost, mstk, zoltan, metis, exodusii
Link Dependencies:
mpi, boost, mstk, zoltan, metis, exodusii
Test Dependencies:
unittest-cpp
Description:
Jali is a parallel, unstructured mesh infrastructure library designed for use by multi-physics simulations.

jansson

Homepage:
Spack package:
Versions:
2.9
Build Dependencies:
cmake
Description:
Jansson is a C library for encoding, decoding and manipulating JSON data.

jasper

Homepage:
Spack package:
Versions:
2.0.14, 1.900.1
Build Dependencies:
cmake, jpeg, gl
Link Dependencies:
jpeg, gl
Description:
Library for manipulating JPEG-2000 images

jbigkit

Homepage:
Spack package:
Versions:
2.1, 1.6
Description:
JBIG-Kit is a software implementation of the JBIG1 data compression standard.

jchronoss

Homepage:
Spack package:
Versions:
1.2, 1.1.1, 1.1, 1.0
Build Dependencies:
cmake, libxml2, libwebsockets, libev, ncurses
Link Dependencies:
libxml2, libwebsockets, libev, ncurses
Description:
JCHRONOSS aims to help HPC application testing process to scale as much as the application does.

jdk

Homepage:
Spack package:
Versions:
12.0.2_10, 12.0.1_12, 11.0.2_9, 11.0.1_13, 10.0.2_13, 10.0.1_10, 1.8.0_241-b07, 1.8.0_231-b11, 1.8.0_212-b10, 1.8.0_202-b08, 1.8.0_141-b15, 1.8.0_131-b11
Description:
The Java Development Kit (JDK) released by Oracle Corporation in the form of a binary product aimed at Java developers. Includes a complete JRE plus tools for developing, debugging, and monitoring Java applications.

jellyfish

Homepage:
Spack package:
Versions:
2.2.7, 1.1.11
Build Dependencies:
perl, python
Run Dependencies:
perl, python
Description:
JELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA.

jemalloc

Homepage:
Spack package:
Versions:
5.2.1, 5.2.0, 4.5.0, 4.4.0, 4.3.1, 4.2.1, 4.2.0, 4.1.0, 4.0.4
Description:
jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and scalable concurrency support.

jmol

Homepage:
Spack package:
Versions:
14.8.0
Run Dependencies:
java
Description:
Jmol: an open-source Java viewer for chemical structures in 3D with features for chemicals, crystals, materials and biomolecules.

jq

Homepage:
Spack package:
Versions:
1.6, 1.5
Build Dependencies:
oniguruma, bison
Link Dependencies:
oniguruma
Description:
jq is a lightweight and flexible command-line JSON processor.

json-c

Homepage:
Spack package:
Versions:
0.13.1, 0.12.1, 0.12, 0.11
Build Dependencies:
autoconf
Description:
A JSON implementation in C.

json-cwx

Homepage:
Spack package:
Versions:
0.12
Build Dependencies:
autoconf, automake, libtool, m4
Description:
JSON-C with Extensions

json-fortran

Homepage:
Spack package:
Versions:
7.1.0, 7.0.0
Build Dependencies:
cmake
Description:
A Fortran 2008 JSON API

json-glib

Homepage:
Spack package:
Versions:
1.2.8
Build Dependencies:
glib
Link Dependencies:
glib
Description:
JSON-GLib is a library for reading and parsing JSON using GLib and GObject data types and API.

jsoncpp

Homepage:
Spack package:
Versions:
1.9.1, 1.9.0, 1.8.4, 1.8.3, 1.8.2, 1.8.1, 1.8.0, 1.7.7, 1.7.6, 1.7.5, 1.7.4, 1.7.3
Build Dependencies:
cmake
Test Dependencies:
python
Description:
JsonCpp is a C++ library that allows manipulating JSON values, including serialization and deserialization to and from strings. It can also preserve existing comment in unserialization/serialization steps, making it a convenient format to store user input files.

jstorm

Homepage:
Spack package:
Versions:
2.4.0
Description:
JStorm is an enterprise fast and stable streaming process engine.

jube

Homepage:
Spack package:
Versions:
2.2.2, 2.2.1, 2.2.0, 2.1.4, 2.1.3, 2.1.2, 2.1.1, 2.1.0, 2.0.1, 2.0.0
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
The Juelich benchmarking environment (JUBE) provides a script based framework to easily create benchmark sets, run those sets on different computer systems and evaluate the results.

judy

Homepage:
Spack package:
Versions:
1.0.5
Description:
Judy: General-purpose dynamic array, associative array and hash-trie.

julia

Homepage:
Spack package:
Versions:
master, 1.3.1, 1.2.0, 1.1.1, 1.0.0, 0.6.2, 0.5.2, 0.5.1, 0.5.0, 0.4.7, 0.4.6, 0.4.5, 0.4.3
Build Dependencies:
m4, python, cmake, git, curl, openssl, mkl
Link Dependencies:
curl, openssl, mkl
Run Dependencies:
cmake, git
Description:
The Julia Language: A fresh approach to technical computing

k8

Homepage:
Spack package:
Versions:
0.2.4
Run Dependencies:
zlib
Description:
K8 is a Javascript shell based on Google's V8 Javascript engine.

kafka

Homepage:
Spack package:
Versions:
2.13-2.4.0, 2.12-2.4.0, 2.12-2.3.1, 2.12-2.3.0, 2.12-2.2.2
Run Dependencies:
java
Description:
Kafka is used for building real-time data pipelines and streaming apps. It is horizontally scalable, fault-tolerant, wicked fast, and runs in production in thousands of companies.

kahip

Homepage:
Spack package:
Versions:
develop, 2.00
Build Dependencies:
scons, argtable, mpi
Link Dependencies:
argtable, mpi
Description:
KaHIP - Karlsruhe High Quality Partitioning - is a family of graph partitioning programs. It includes KaFFPa (Karlsruhe Fast Flow Partitioner), which is a multilevel graph partitioning algorithm, in its variants Strong, Eco and Fast, KaFFPaE (KaFFPaEvolutionary) which is a parallel evolutionary algorithm that uses KaFFPa to provide combine and mutation operations, as well as KaBaPE which extends the evolutionary algorithm. Moreover, specialized techniques are included to partition road networks (Buffoon), to output a vertex separator from a given partition or techniques geared towards efficient partitioning of social networks.

kaiju

Homepage:
Spack package:
Versions:
1.6.2
Run Dependencies:
perl-io-compress, py-htseq
Description:
Kaiju is a program for the taxonomic classification of high-throughput sequencing reads.

kaks-calculator

Homepage:
Spack package:
Versions:
2.0
Description:
KaKs_Calculator adopts model selection and model averaging to calculate nonsynonymous (Ka) and synonymous (Ks) substitution rates, attempting to include as many features as needed for accurately capturing evolutionary information in protein-coding sequences.

kaldi

Homepage:
Spack package:
Versions:
master, 2019-09-29, 2019-07-29, 2018-07-11, 2015-10-07
Build Dependencies:
blas, cuda, openfst, cub
Link Dependencies:
blas, cuda, openfst, cub
Run Dependencies:
sph2pipe, sctk, speex
Description:
Kaldi is a toolkit for speech recognition written in C++ and licensed under the Apache License v2.0. Kaldi is intended for use by speech recognition researchers.

kallisto

Homepage:
Spack package:
Versions:
0.43.1
Build Dependencies:
cmake, zlib, hdf5, mpich
Link Dependencies:
zlib, hdf5, mpich
Description:
kallisto is a program for quantifying abundances of transcripts from RNA-Seq data.

karma

Homepage:
Spack package:
Versions:
1.7.25-common
Build Dependencies:
libx11, libxaw
Run Dependencies:
libx11, libxaw
Description:
Karma is a toolkit for interprocess communications, authentication, encryption, graphics display, user interface and manipulating the Karma network data structure. It contains KarmaLib (the structured libraries and API) and a large number of modules (applications) to perform many standard tasks.

kbproto

Homepage:
Spack package:
Versions:
1.0.7
Build Dependencies:
pkgconfig, util-macros
Description:
X Keyboard Extension. This extension defines a protcol to provide a number of new capabilities and controls for text keyboards.

kcov

Homepage:
Spack package:
Versions:
38
Build Dependencies:
cmake, zlib, curl
Link Dependencies:
zlib, curl
Description:
Code coverage tool for compiled programs, Python and Bash which uses debugging information to collect and report data without special compilation options

kdiff3

Homepage:
Spack package:
Versions:
0.9.98
Build Dependencies:
qt
Link Dependencies:
qt
Description:
Compare and merge 2 or 3 files or directories.

kealib

Homepage:
Spack package:
Versions:
develop, 1.4.11, 1.4.10, 1.4.9, 1.4.8, 1.4.7
Build Dependencies:
cmake, hdf5
Link Dependencies:
hdf5
Description:
An HDF5 Based Raster File Format. KEALib provides an implementation of the GDAL data model. The format supports raster attribute tables, image pyramids, meta-data and in-built statistics while also handling very large files and compression throughout. Based on the HDF5 standard, it also provides a base from which other formats can be derived and is a good choice for long term data archiving. An independent software library (libkea) provides complete access to the KEA image format and a GDAL driver allowing KEA images to be used from any GDAL supported software. Development work on this project has been funded by Landcare Research.

keepalived

Homepage:
Spack package:
Versions:
2.0.19, 2.0.18, 2.0.17, 2.0.16, 2.0.15, 2.0.14, 2.0.13, 2.0.12, 2.0.11
Build Dependencies:
openssl
Description:
Keepalived implements a set of checkers to dynamically and adaptively maintain and manage loadbalanced server pool according their health

kentutils

Homepage:
Spack package:
Versions:
302.1
Build Dependencies:
libpng, openssl, mariadb
Link Dependencies:
libpng, openssl, mariadb
Description:
Jim Kent command line bioinformatic utilities

kibana

Homepage:
Spack package:
Versions:
6.4.0
Run Dependencies:
jdk
Description:
Kibana lets you visualize your Elasticsearch data and navigate the Elastic Stack

kim-api

Homepage:
Spack package:
Versions:
develop, 2.1.3, 2.1.2, 2.1.1, 2.1.0, 2.0.2
Build Dependencies:
cmake
Description:
OpenKIM is an online framework for making molecular simulations reliable, reproducible, and portable. Computer implementations of inter- atomic models are archived in OpenKIM, verified for coding integrity, and tested by computing their predictions for a variety of material properties. Models conforming to the KIM application programming interface (API) work seamlessly with major simulation codes that have adopted the KIM API standard. This package provides the kim-api library and supporting utilities. It also provides a small set of example models. To obtain all models archived at https://openkim.org that are compatible with the kim-api package, install and activate the openkim- models package too.

kitty

Homepage:
Spack package:
Versions:
0.12.3, 0.12.2, 0.12.1, 0.12.0, 0.11.3, 0.11.2, 0.11.1, 0.11.0, 0.10.1, 0.10.0
Build Dependencies:
python, harfbuzz, libxkbcommon, zlib, libpng, gl, pkgconfig, py-setuptools, py-sphinx, freetype, fontconfig, xrandr, libxinerama, xineramaproto, libxi, libxcursor, fixesproto, dbus, xkeyboard-config
Link Dependencies:
python, harfbuzz, libxkbcommon, zlib, libpng, gl, freetype, fontconfig, xrandr, libxinerama, xineramaproto, libxi, libxcursor, fixesproto, dbus, xkeyboard-config
Run Dependencies:
python, gl
Description:
fast, featureful, cross-platform, GPU-based terminal emulator

kmergenie

Homepage:
Spack package:
Versions:
1.7044
Build Dependencies:
python, py-setuptools, r, zlib
Link Dependencies:
zlib
Run Dependencies:
python, py-setuptools, r
Description:
KmerGenie estimates the best k-mer length for genome de novo assembly.

kokkos

Homepage:
Spack package:
Versions:
develop, 2.9.00, 2.8.00, 2.7.24, 2.7.00, 2.5.00, 2.04.11, 2.04.04, 2.04.00, 2.03.13, 2.03.05, 2.03.00, 2.02.15, 2.02.07
Build Dependencies:
hwloc, qthreads, cuda
Link Dependencies:
hwloc, qthreads, cuda
Description:
Kokkos implements a programming model in C++ for writing performance portable applications targeting all major HPC platforms.

kokkos-kernels

Homepage:
Spack package:
Versions:
develop, 2.7.00, 2.6.00, 2.5.00
Build Dependencies:
kokkos
Link Dependencies:
kokkos
Description:
Kokkos C++ Performance Portability Programming EcoSystem: Math Kernels - Provides BLAS, Sparse BLAS and Graph Kernels.

kraken

Homepage:
Spack package:
Versions:
1.0
Build Dependencies:
perl, jellyfish
Link Dependencies:
jellyfish
Run Dependencies:
perl
Description:
Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies.

krb5

Homepage:
Spack package:
Versions:
1.16.1
Build Dependencies:
bison, openssl
Link Dependencies:
openssl
Description:
Network authentication protocol

krims

Homepage:
Spack package:
Versions:
develop, 0.2.1
Build Dependencies:
cmake
Description:
The bucket of Krimskrams every C or C++ project needs

kripke

Homepage:
Spack package:
Versions:
1.1
Build Dependencies:
cmake, mpi
Link Dependencies:
mpi
Description:
Kripke is a simple, scalable, 3D Sn deterministic particle transport proxy/mini app.

kvasir-mpl

Homepage:
Spack package:
Versions:
develop
Description:
Kvasir metaprogramming library

kvtree

Homepage:
Spack package:
Versions:
master, 1.0.2
Build Dependencies:
cmake, mpi
Link Dependencies:
mpi
Description:
KVTree provides a fully extensible C datastructure modeled after perl hashes.

ladot

Homepage:
Spack package:
Versions:
1.2
Run Dependencies:
perl, graphviz
Test Dependencies:
perl, graphviz, texlive
Description:
Ladot is a script that makes using LaTeX in graphs generated by dot (graphviz) relatively easy.

laghos

Homepage:
Spack package:
Versions:
develop, 2.0, 1.1, 1.0
Build Dependencies:
mfem
Link Dependencies:
mfem
Description:
Laghos (LAGrangian High-Order Solver) is a CEED miniapp that solves the time-dependent Euler equations of compressible gas dynamics in a moving Lagrangian frame using unstructured high-order finite element spatial discretization and explicit high-order time-stepping.

lame

Homepage:
Spack package:
Versions:
3.100
Build Dependencies:
nasm
Description:
LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL.

lammps

Homepage:
Spack package:
Versions:
develop, 20190807, 20190605, 20181212, 20181207, 20181127, 20181115, 20181109, 20181024, 20181010, 20180918, 20180905, 20180831, 20180822, 20180629, 20180316, 20180222, 20170922, 20170901
Build Dependencies:
cuda, cmake, mpi, fftw, voropp, netcdf-c, blas, lapack, latte, opencl, python, hdf5, jpeg, libpng, ffmpeg, kokkos
Link Dependencies:
cuda, mpi, fftw, voropp, netcdf-c, blas, lapack, latte, opencl, python, hdf5, jpeg, libpng, ffmpeg, kokkos
Description:
LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel Simulator. This package uses patch releases, not stable release. See https://github.com/spack/spack/pull/5342 for a detailed discussion.

last

Homepage:
Spack package:
Versions:
869
Description:
LAST finds similar regions between sequences, and aligns them. It is designed for comparing large datasets to each other (e.g. vertebrate genomes and/or large numbers of DNA reads).

lastz

Homepage:
Spack package:
Versions:
1.04.00
Description:
LASTZ is a program for aligning DNA sequences, a pairwise aligner.

laszip

Homepage:
Spack package:
Versions:
3.4.1
Build Dependencies:
cmake
Description:
Free and lossless LiDAR compression

latte

Homepage:
Spack package:
Versions:
develop, 1.2.1
Build Dependencies:
cmake, blas, lapack, mpi, qmd-progress
Link Dependencies:
blas, lapack, mpi, qmd-progress
Description:
Open source density functional tight binding molecular dynamics.

launchmon

Homepage:
Spack package:
Versions:
master, 1.0.2
Build Dependencies:
autoconf, automake, libtool, pkgconfig, libgcrypt, libgpg-error, boost, spectrum-mpi
Link Dependencies:
libgcrypt, libgpg-error, elf, boost, spectrum-mpi
Description:
Software infrastructure that enables HPC run-time tools to co-locate tool daemons with a parallel job.

lazyten

Homepage:
Spack package:
Versions:
develop, 0.4.1
Build Dependencies:
cmake, krims, blas, lapack, armadillo, arpack-ng
Link Dependencies:
krims, blas, lapack, armadillo, arpack-ng
Description:
Lightweight linear algebra library based on lazy matrices

lbann

Homepage:
Spack package:
Versions:
develop, 0.99, 0.98.1, 0.98, 0.97.1, 0.97, 0.96, 0.95, 0.94, 0.93, 0.92, 0.91
Build Dependencies:
cmake, hydrogen, elemental, aluminum, cuda, cudnn, cub, mpi, hwloc, opencv, cnpy, nccl, conduit, python, py-setuptools, py-numpy, py-protobuf, py-breathe, py-m2r, cereal, clara, ninja
Link Dependencies:
hydrogen, elemental, aluminum, cuda, cudnn, cub, mpi, hwloc, opencv, cnpy, nccl, conduit, python, cereal, clara
Run Dependencies:
python, py-argparse, py-configparser, py-graphviz, py-matplotlib, py-numpy, py-onnx, py-pandas, py-texttable, py-protobuf
Test Dependencies:
py-pytest, catch2
Description:
LBANN: Livermore Big Artificial Neural Network Toolkit. A distributed memory, HPC-optimized, model and data parallel training toolkit for deep neural networks.

lbxproxy

Homepage:
Spack package:
Versions:
1.0.3
Build Dependencies:
libxext, liblbxutil, libx11, libice, xtrans, xproxymanagementprotocol, bigreqsproto, pkgconfig, util-macros
Link Dependencies:
libxext, liblbxutil, libx11, libice
Description:
lbxproxy accepts client connections, multiplexes them over a single connection to the X server, and performs various optimizations on the X protocol to make it faster over low bandwidth and/or high latency connections. Note that the X server source from X.Org no longer supports the LBX extension, so this program is only useful in connecting to older X servers.

lbzip2

Homepage:
Spack package:
Versions:
2.5
Description:
Multi-threaded compression utility with support for bzip2 compressed file format

lcals

Homepage:
Spack package:
Versions:
1.0.2
Description:
LCALS ("Livermore Compiler Analysis Loop Suite") is a collection of loop kernels based, in part, on historical "Livermore Loops" benchmarks (See the 1986 technical report: "The Livermore Fortran Kernels: A Computer Test of the Numerical Performance Range", by Frank H. McMahon, UCRL-53745.). The suite contains facilities to generate timing statistics and reports.

lcms

Homepage:
Spack package:
Versions:
2.9, 2.8, 2.6
Build Dependencies:
jpeg, libtiff, zlib
Link Dependencies:
jpeg, libtiff, zlib
Description:
Little cms is a color management library. Implements fast transforms between ICC profiles. It is focused on speed, and is portable across several platforms (MIT license).

lcov

Homepage:
Spack package:
Versions:
1.14
Description:
LCOV is a graphical front-end for GCC's coverage testing tool gcov. It collects gcov data for multiple source files and creates HTML pages containing the source code annotated with coverage information. It also adds overview pages for easy navigation within the file structure. LCOV supports statement, function and branch coverage measurement.

ldc

Homepage:
Spack package:
Versions:
1.3.0
Build Dependencies:
cmake, llvm, zlib, libconfig, curl, libedit, binutils, ldc-bootstrap
Link Dependencies:
llvm, zlib, libconfig, curl, libedit, binutils, ldc-bootstrap
Run Dependencies:
binutils
Description:
The LDC project aims to provide a portable D programming language compiler with modern optimization and code generation capabilities. LDC is fully Open Source; the parts of the code not taken/adapted from other projects are BSD-licensed (see the LICENSE file for details). Consult the D wiki for further information: http://wiki.dlang.org/LDC

ldc-bootstrap

Homepage:
Spack package:
Versions:
0.17.4
Build Dependencies:
cmake, llvm, zlib, libconfig, curl, libedit, binutils
Link Dependencies:
llvm, zlib, libconfig, curl, libedit, binutils
Description:
The LDC project aims to provide a portable D programming language compiler with modern optimization and code generation capabilities. LDC is fully Open Source; the parts of the code not taken/adapted from other projects are BSD-licensed (see the LICENSE file for details). Consult the D wiki for further information: http://wiki.dlang.org/LDC This old version of the compiler is needed to bootstrap newer ones.

legion

Homepage:
Spack package:
Versions:
master, 19.06.0, 19.04.0, 18.12.0, 18.09.0, 18.05.0, 18.02.0, 17.10.0, 17.08.0, 17.02.0, ctrl-rep-2, ctrl-rep-1, ctrl-rep-0, ctrl-rep
Build Dependencies:
cmake, gasnet, hdf5
Link Dependencies:
gasnet, hdf5
Description:
Legion is a data-centric parallel programming system for writing portable high performance programs targeted at distributed heterogeneous architectures. Legion presents abstractions which allow programmers to describe properties of program data (e.g. independence, locality). By making the Legion programming system aware of the structure of program data, it can automate many of the tedious tasks programmers currently face, including correctly extracting task- and data-level parallelism and moving data around complex memory hierarchies. A novel mapping interface provides explicit programmer controlled placement of data in the memory hierarchy and assignment of tasks to processors in a way that is orthogonal to correctness, thereby enabling easy porting and tuning of Legion applications to new architectures.

lemon

Homepage:
Spack package:
Versions:
1.3.1
Build Dependencies:
cmake
Description:
LEMON stands for Library for Efficient Modeling and Optimization in Networks. It is a C++ template library providing efficient implementations of common data structures and algorithms with focus on combinatorial optimization tasks connected mainly with graphs and networks.

leveldb

Homepage:
Spack package:
Versions:
master, 1.22, 1.20, 1.18
Build Dependencies:
cmake, snappy
Link Dependencies:
snappy
Description:
LevelDB is a fast key-value storage library written at Google that provides an ordered mapping from string keys to string values.

lftp

Homepage:
Spack package:
Versions:
4.8.1, 4.7.7, 4.6.4
Build Dependencies:
expat, libiconv, ncurses, openssl, readline, zlib
Link Dependencies:
expat, libiconv, ncurses, openssl, readline, zlib
Description:
LFTP is a sophisticated file transfer program supporting a number of network protocols (ftp, http, sftp, fish, torrent).

libaec

Homepage:
Spack package:
Versions:
1.0.2, 1.0.1, 1.0.0
Build Dependencies:
cmake
Description:
Libaec provides fast lossless compression of 1 up to 32 bit wide signed or unsigned integers (samples). It implements Golomb-Rice compression method under the BSD license and includes a free drop-in replacement for the SZIP library.

libaio

Homepage:
Spack package:
Versions:
0.3.110
Description:
Linux native Asynchronous I/O interface library. AIO enables even a single application thread to overlap I/O operations with other processing, by providing an interface for submitting one or more I/O requests in one system call (io_submit()) without waiting for completion, and a separate interface (io_getevents()) to reap completed I/O operations associated with a given completion group.

libapplewm

Homepage:
Spack package:
Versions:
1.4.1
Build Dependencies:
libx11, libxext, xextproto, applewmproto, pkgconfig, util-macros
Link Dependencies:
libx11, libxext
Description:
AppleWM is a simple library designed to interface with the Apple-WM extension. This extension allows X window managers to better interact with the Mac OS X Aqua user interface when running X11 in a rootless mode.

libarchive

Homepage:
Spack package:
Versions:
3.4.1, 3.3.2, 3.2.1, 3.1.2, 3.1.1, 3.1.0
Build Dependencies:
zlib, bzip2, lz4, xz, lzo, nettle, openssl, libxml2, expat
Link Dependencies:
zlib, bzip2, lz4, xz, lzo, nettle, openssl, libxml2, expat
Description:
libarchive: C library and command-line tools for reading and writing tar, cpio, zip, ISO, and other archive formats.

libassuan

Homepage:
Spack package:
Versions:
2.5.3, 2.4.5, 2.4.3
Build Dependencies:
libgpg-error
Link Dependencies:
libgpg-error
Description:
Libassuan is a small library implementing the so-called Assuan protocol.

libatomic-ops

Homepage:
Spack package:
Versions:
7.6.6, 7.4.4
Description:
This package provides semi-portable access to hardware-provided atomic memory update operations on a number architectures.

libbeagle

Homepage:
Spack package:
Versions:
3.1.2, 2.1.2
Build Dependencies:
cuda, autoconf, automake, libtool, m4, subversion, pkgconfig, java
Link Dependencies:
cuda
Description:
Beagle performs genotype calling, genotype phasing, imputation of ungenotyped markers, and identity-by-descent segment detection.

libbeato

Homepage:
Spack package:
Versions:
master
Description:
libbeato is a C library containing routines for various uses in Genomics, and includes a copy of the freeware portion of the C library from UCSC's Genome Browser Group.

libbsd

Homepage:
Spack package:
Versions:
0.10.0, 0.9.1, 0.9.0, 0.8.7, 0.8.6
Description:
This library provides useful functions commonly found on BSD systems, and lacking on others like GNU systems, thus making it easier to port projects with strong BSD origins, without needing to embed the same code over and over again on each project.

libbson

Homepage:
Spack package:
Versions:
1.9.1, 1.8.1, 1.8.0, 1.7.0, 1.6.3, 1.6.2, 1.6.1
Build Dependencies:
autoconf, automake, libtool, m4
Description:
libbson is a library providing useful routines related to building, parsing, and iterating BSON documents.

libcanberra

Homepage:
Spack package:
Versions:
0.30
Build Dependencies:
libxrender, libxext, libx11, libxinerama, libxrandr, libxcursor, libxcomposite, libxdamage, libxfixes, libxcb, libxau, gtkplus, libvorbis, pkgconfig
Link Dependencies:
libxrender, libxext, libx11, libxinerama, libxrandr, libxcursor, libxcomposite, libxdamage, libxfixes, libxcb, libxau, gtkplus, libvorbis
Description:
libcanberra is an implementation of the XDG Sound Theme and Name Specifications, for generating event sounds on free desktops, such as GNOME.

libcap

Homepage:
Spack package:
Versions:
2.25
Description:
Libcap implements the user-space interfaces to the POSIX 1003.1e capabilities available in Linux kernels. These capabilities are a partitioning of the all powerful root privilege into a set of distinct privileges.

libceed

Homepage:
Spack package:
Versions:
develop, 0.5, 0.4, 0.2, 0.1
Build Dependencies:
cuda, occa, libxsmm
Link Dependencies:
cuda, occa, libxsmm
Description:
The CEED API Library: Code for Efficient Extensible Discretizations.

libcerf

Homepage:
Spack package:
Versions:
1.3
Description:
A self-contained C library providing complex error functions, based on Faddeeva's plasma dispersion function w(z). Also provides Dawson's integral and Voigt's convolution of a Gaussian and a Lorentzian

libcint

Homepage:
Spack package:
Versions:
3.0.13, 3.0.12, 3.0.11, 3.0.10, 3.0.8, 3.0.7, 3.0.6, 3.0.5, 3.0.4
Build Dependencies:
cmake, blas, python, py-numpy
Link Dependencies:
blas
Test Dependencies:
python, py-numpy
Description:
Library for analytical Gaussian integrals for quantum chemistry.

libcircle

Homepage:
Spack package:
Versions:
master, 0.3.0, 0.2.1-rc.1
Build Dependencies:
mpi, pkgconfig
Link Dependencies:
mpi
Description:
libcircle provides an efficient distributed queue on a cluster, using self-stabilizing work stealing.

libconfig

Homepage:
Spack package:
Versions:
1.7.2, 1.7.1, 1.5
Build Dependencies:
m4, autoconf, automake, libtool
Description:
C/C++ Configuration File Library

libcroco

Homepage:
Spack package:
Versions:
0.6.12
Build Dependencies:
glib, libxml2
Link Dependencies:
glib, libxml2
Description:
Libcroco is a standalone css2 parsing and manipulation library.

libctl

Homepage:
Spack package:
Versions:
3.2.2
Build Dependencies:
guile
Link Dependencies:
guile
Description:
libctl is a free Guile-based library implementing flexible control files for scientific simulations.

libdap4

Homepage:
Spack package:
Versions:
3.20.4
Build Dependencies:
autoconf, automake, libtool, m4, bison, flex, curl, libxml2, libuuid
Link Dependencies:
flex, curl, libxml2, libuuid
Description:
libdap4 is is a c++ library to serve as a client for the OPeNDAP framework that simplifies all aspects of scientific data networking and provides software which makes local data accessible to remote locations regardless of local storage format.

libdivsufsort

Homepage:
Spack package:
Versions:
2.0.1
Build Dependencies:
cmake
Description:
libdivsufsort is a software library that implements a lightweight suffix array construction algorithm.

libdmx

Homepage:
Spack package:
Versions:
1.1.3
Build Dependencies:
libx11, libxext, xextproto, dmxproto, pkgconfig, util-macros
Link Dependencies:
libx11, libxext
Description:
libdmx - X Window System DMX (Distributed Multihead X) extension library.

libdrm

Homepage:
Spack package:
Versions:
2.4.100, 2.4.81, 2.4.75, 2.4.70, 2.4.59, 2.4.33
Build Dependencies:
pkgconfig, libpciaccess, libpthread-stubs
Link Dependencies:
libpciaccess, libpthread-stubs
Description:
A userspace library for accessing the DRM, direct rendering manager, on Linux, BSD and other systems supporting the ioctl interface.

libdwarf

Homepage:
Spack package:
Versions:
20180129, 20160507, 20130729, 20130207, 20130126
Link Dependencies:
elfutils, elf, zlib
Description:
The DWARF Debugging Information Format is of interest to programmers working on compilers and debuggers (and any one interested in reading or writing DWARF information). It was developed by a committee (known as the PLSIG at the time) starting around 1991. Starting around 1991 SGI developed the libdwarf and dwarfdump tools for internal use and as part of SGI IRIX developer tools. Since that time dwarfdump and libdwarf have been shipped (as an executable and archive respectively, not source) with every release of the SGI MIPS/IRIX C compiler.

libeatmydata

Homepage:
Spack package:
Versions:
105
Test Dependencies:
strace
Description:
libeatmydata is a small LD_PRELOAD library designed to (transparently) disable fsync (and friends, like open(O_SYNC)). This has two side- effects: making software that writes data safely to disk a lot quicker and making this software no longer crash safe.

libedit

Homepage:
Spack package:
Versions:
3.1-20191231, 3.1-20170329, 3.1-20160903, 3.1-20150325
Build Dependencies:
ncurses
Link Dependencies:
ncurses
Description:
An autotools compatible port of the NetBSD editline library

libelf

Homepage:
Spack package:
Versions:
0.8.13
Description:
libelf lets you read, modify or create ELF object files in an architecture-independent way. The library takes care of size and endian issues, e.g. you can process a file for SPARC processors on an Intel- based system. Note: libelf is no longer maintained and packages that depend on libelf should migrate to elfutils.

libemos

Homepage:
Spack package:
Versions:
4.5.1, 4.5.0, 4.4.9, 4.4.7, 4.4.2
Build Dependencies:
cmake, eccodes, grib-api, fftw, pkgconfig
Link Dependencies:
eccodes, grib-api, fftw
Description:
The Interpolation library (EMOSLIB) includes Interpolation software and BUFR & CREX encoding/decoding routines.

libepoxy

Homepage:
Spack package:
Versions:
1.4.3
Build Dependencies:
pkgconfig, meson, gl, libx11
Link Dependencies:
meson, gl, libx11
Description:
Epoxy is a library for handling OpenGL function pointer management for you.

libev

Homepage:
Spack package:
Versions:
develop, 4.24
Build Dependencies:
autoconf, automake, libtool, m4
Description:
A full-featured and high-performance event loop that is loosely modelled after libevent, but without its limitations and bugs.

libevent

Homepage:
Spack package:
Versions:
2.1.8, 2.0.22, 2.0.21, 2.0.20, 2.0.19, 2.0.18, 2.0.17, 2.0.16, 2.0.15, 2.0.14, 2.0.13, 2.0.12
Build Dependencies:
openssl
Link Dependencies:
openssl
Description:
The libevent API provides a mechanism to execute a callback function when a specific event occurs on a file descriptor or after a timeout has been reached. Furthermore, libevent also support callbacks due to signals or regular timeouts.

libevpath

Homepage:
Spack package:
Versions:
develop, 4.4.0, 4.2.4, 4.2.1, 4.1.2, 4.1.1
Build Dependencies:
cmake, gtkorvo-enet, libffs
Link Dependencies:
gtkorvo-enet, libffs
Description:
EVpath is an event transport middleware layer designed to allow for the easy implementation of overlay networks, with active data processing, routing and management at all points in the overlay. EVPath is designed for high performance systems.

libexif

Homepage:
Spack package:
Versions:
0.6.21
Build Dependencies:
glib
Link Dependencies:
glib
Description:
A library to parse an EXIF file and read the data from those tags

libfabric

Homepage:
Spack package:
Versions:
develop, 1.9.0, 1.8.1, 1.8.0, 1.7.1, 1.7.0, 1.6.2, 1.6.1, 1.6.0, 1.5.3, 1.5.0, 1.4.2
Build Dependencies:
rdma-core, opa-psm2, psm, ucx, m4, autoconf, automake, libtool
Link Dependencies:
rdma-core, opa-psm2, psm, ucx
Description:
The Open Fabrics Interfaces (OFI) is a framework focused on exporting fabric communication services to applications.

libfastcommon

Homepage:
Spack package:
Versions:
1.0.43, 1.0.42, 1.0.41, 1.0.40, 1.0.39
Description:
Libfastcommon is a c common functions library extracted from my open source project FastDFS. this library is very simple and stable. functions including: string, logger, chain, hash, socket, ini file reader, base64 encode / decode, url encode / decode, fast timer, skiplist, object pool etc. detail info please see the c header files.

libffi

Homepage:
Spack package:
Versions:
3.2.1
Description:
The libffi library provides a portable, high level programming interface to various calling conventions. This allows a programmer to call any function specified by a call interface description at run time.

libffs

Homepage:
Spack package:
Versions:
develop, 1.5, 1.1.1, 1.1
Build Dependencies:
cmake, flex, bison, gtkorvo-cercs-env, gtkorvo-atl, gtkorvo-dill
Link Dependencies:
gtkorvo-atl, gtkorvo-dill
Description:
FFS is a middleware library for data communication, including representation, processing and marshaling that preserves the performance of traditional approaches while relaxing the requirement of a priori knowledge and providing complex run-time flexibility.

libfive

Homepage:
Spack package:
Versions:
master
Build Dependencies:
cmake, pkgconfig, boost, eigen, libpng, qt, guile
Link Dependencies:
boost, eigen, libpng, qt, guile
Description:
libfive is a software library and set of tools for solid modeling.

libflame

Homepage:
Spack package:
Versions:
master, 5.2.0, 5.1.0
Build Dependencies:
blas
Link Dependencies:
blas
Description:
libflame is a portable library for dense matrix computations, providing much of the functionality present in LAPACK, developed by current and former members of the Science of High-Performance Computing (SHPC) group in the Institute for Computational Engineering and Sciences at The University of Texas at Austin. libflame includes a compatibility layer, lapack2flame, which includes a complete LAPACK implementation.

libfontenc

Homepage:
Spack package:
Versions:
1.1.3
Build Dependencies:
zlib, xproto, pkgconfig, util-macros
Link Dependencies:
zlib
Description:
libfontenc - font encoding library.

libfs

Homepage:
Spack package:
Versions:
1.0.7
Build Dependencies:
xproto, fontsproto, xtrans, pkgconfig, util-macros
Description:
libFS - X Font Service client library. This library is used by clients of X Font Servers (xfs), such as xfsinfo, fslsfonts, and the X servers themselves.

libgcrypt

Homepage:
Spack package:
Versions:
1.8.5, 1.8.4, 1.8.1, 1.7.6, 1.6.2
Build Dependencies:
libgpg-error
Link Dependencies:
libgpg-error
Description:
Libgcrypt is a general purpose cryptographic library based on the code from GnuPG. It provides functions for all cryptographic building blocks: symmetric ciphers, hash algorithms, MACs, public key algorithms, large integer functions, random numbers and a lot of supporting functions.

libgd

Homepage:
Spack package:
Versions:
2.2.4
Build Dependencies:
autoconf, automake, libtool, m4, gettext, pkgconfig, libiconv, libpng, jpeg, libtiff, fontconfig
Link Dependencies:
libiconv, libpng, jpeg, libtiff, fontconfig
Description:
GD is an open source code library for the dynamic creation of images by programmers. GD is written in C, and "wrappers" are available for Perl, PHP and other languages. GD creates PNG, JPEG, GIF, WebP, XPM, BMP images, among other formats. GD is commonly used to generate charts, graphics, thumbnails, and most anything else, on the fly. While not restricted to use on the web, the most common applications of GD involve website development.

libgeotiff

Homepage:
Spack package:
Versions:
1.5.1, 1.5.0, 1.4.3, 1.4.2
Build Dependencies:
zlib, jpeg, libtiff, proj
Link Dependencies:
zlib, jpeg, libtiff, proj
Description:
GeoTIFF represents an effort by over 160 different remote sensing, GIS, cartographic, and surveying related companies and organizations to establish a TIFF based interchange format for georeferenced raster imagery.

libgit2

Homepage:
Spack package:
Versions:
0.28.2, 0.26.0
Build Dependencies:
cmake, libssh2
Link Dependencies:
libssh2
Description:
libgit2 is a portable, pure C implementation of the Git core methods provided as a re-entrant linkable library with a solid API, allowing you to write native speed custom Git applications in any language which supports C bindings.

libglvnd

Homepage:
Spack package:
Versions:
master, 1.1.1
Build Dependencies:
libxext, libx11, glproto
Link Dependencies:
libxext, libx11, glproto
Description:
The GL Vendor-Neutral Dispatch library libglvnd is a vendor-neutral dispatch layer for arbitrating OpenGL API calls between multiple vendors. It allows multiple drivers from different vendors to coexist on the same filesystem, and determines which vendor to dispatch each API call to at runtime. Both GLX and EGL are supported, in any combination with OpenGL and OpenGL ES.

libgpg-error

Homepage:
Spack package:
Versions:
1.36, 1.27, 1.21, 1.18
Build Dependencies:
awk
Description:
Libgpg-error is a small library that defines common error values for all GnuPG components. Among these are GPG, GPGSM, GPGME, GPG-Agent, libgcrypt, Libksba, DirMngr, Pinentry, SmartCard Daemon and possibly more in the future.

libgpuarray

Homepage:
Spack package:
Versions:
0.7.5, 0.7.2, 0.7.1, 0.7.0, 0.6.9, 0.6.2, 0.6.1, 0.6.0
Build Dependencies:
cmake, cuda, check
Link Dependencies:
cuda, check
Description:
Make a common GPU ndarray(n dimensions array) that can be reused by all projects that is as future proof as possible, while keeping it easy to use for simple need/quick test.

libgridxc

Homepage:
Spack package:
Versions:
0.7.6
Description:
A library to compute the exchange and correlation energy and potential in spherical (i.e. an atom) or periodic systems.

libgtextutils

Homepage:
Spack package:
Versions:
0.7
Description:
Gordon's Text utils Library.

libharu

Homepage:
Spack package:
Versions:
master, 2.3.0, 2.2.0
Build Dependencies:
libtool, autoconf, automake, libpng, zlib
Link Dependencies:
libpng, zlib
Description:
libharu - free PDF library. Haru is a free, cross platform, open-sourced software library for generating PDF.

libhio

Homepage:
Spack package:
Versions:
1.4.1.3, 1.4.1.2, 1.4.1.1, 1.4.1.0
Build Dependencies:
json-c, bzip2, pkgconfig, mpi, hdf5
Link Dependencies:
json-c, bzip2, mpi, hdf5
Description:
libHIO is a flexible, high-performance parallel IO package developed at LANL. libHIO supports IO to either a conventional PFS or to Cray DataWarp with management of Cray DataWarp space and stage-in and stage- out from and to the PFS.

libiberty

Homepage:
Spack package:
Versions:
2.33.1, 2.32, 2.31.1, 2.30, 2.29.1, 2.28.1
Description:
The libiberty.a library from GNU binutils. Libiberty provides demangling and support functions for the GNU toolchain.

libibumad

Homepage:
Spack package:
Versions:
25.0
Build Dependencies:
cmake, libnl
Link Dependencies:
libnl
Description:
This package installs the user-space libraries and headers for libibumad. This is a subset of the linux-rdma distribution.

libice

Homepage:
Spack package:
Versions:
1.0.9
Build Dependencies:
xproto, xtrans, pkgconfig, util-macros
Description:
libICE - Inter-Client Exchange Library.

libiconv

Homepage:
Spack package:
Versions:
1.16, 1.15, 1.14
Description:
GNU libiconv provides an implementation of the iconv() function and the iconv program for character set conversion.

libid3tag

Homepage:
Spack package:
Versions:
0.15.1b
Build Dependencies:
zlib, gperf
Link Dependencies:
zlib, gperf
Description:
library for id3 tagging

libidn2

Homepage:
Spack package:
Versions:
2.1.1a, 2.1.1, 2.1.0, 2.0.5
Build Dependencies:
libunistring
Link Dependencies:
libunistring
Description:
Libidn2 is a free software implementation of IDNA2008, Punycode and TR46. Its purpose is to encode and decode internationalized domain names.

libint

Homepage:
Spack package:
Versions:
2.6.0, 2.4.2, 2.4.1, 2.4.0, 2.2.0, 2.1.0, 1.1.6, 1.1.5
Build Dependencies:
autoconf, automake, libtool, boost, gmp
Link Dependencies:
boost, gmp
Description:
Libint is a high-performance library for computing Gaussian integrals in quantum mechanics.

libjpeg

Homepage:
Spack package:
Versions:
9c, 9b, 9a
Description:
libjpeg is a widely used free library with functions for handling the JPEG image data format. It implements a JPEG codec (encoding and decoding) alongside various utilities for handling JPEG data.

libjpeg-turbo

Homepage:
Spack package:
Versions:
2.0.3, 2.0.2, 1.5.90, 1.5.3, 1.5.0, 1.3.1
Build Dependencies:
nasm, autoconf, automake, libtool, cmake
Description:
libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelerate baseline JPEG compression and decompression. libjpeg is a library that implements JPEG image encoding, decoding and transcoding.

libkml

Homepage:
Spack package:
Versions:
1.3.0
Build Dependencies:
cmake, jdk, python, boost, expat, minizip, uriparser, zlib, swig
Link Dependencies:
jdk, python, boost, expat, minizip, uriparser, zlib, googletest
Description:
Reference implementation of OGC KML 2.2.

libksba

Homepage:
Spack package:
Versions:
1.3.5
Build Dependencies:
libgpg-error
Link Dependencies:
libgpg-error
Description:
Libksba is a library to make the tasks of working with X.509 certificates, CMS data and related objects more easy.

liblas

Homepage:
Spack package:
Versions:
1.8.1
Build Dependencies:
cmake, libgeotiff, boost, laszip, gdal
Link Dependencies:
libgeotiff, boost, laszip, gdal
Description:
libLAS is a C/C++ library for reading and writing the very common LAS LiDAR format.

liblbxutil

Homepage:
Spack package:
Versions:
1.1.0
Build Dependencies:
xextproto, xproto, pkgconfig, util-macros
Link Dependencies:
zlib
Description:
liblbxutil - Low Bandwith X extension (LBX) utility routines.

liblockfile

Homepage:
Spack package:
Versions:
1.14
Description:
NFS-safe locking library

libmad

Homepage:
Spack package:
Versions:
0.15.1b
Build Dependencies:
autoconf, automake, libtool, m4
Description:
MAD is a high-quality MPEG audio decoder.

libmatheval

Homepage:
Spack package:
Versions:
1.1.11
Build Dependencies:
guile, flex
Link Dependencies:
flex
Description:
GNU libmatheval is a library (callable from C and Fortran) to parse and evaluate symbolic expressions input as text. It supports expressions in any number of variables of arbitrary names, decimal and symbolic constants, basic unary and binary operators, and elementary mathematical functions. In addition to parsing and evaluation, libmatheval can also compute symbolic derivatives and output expressions to strings.

libmaxminddb

Homepage:
Spack package:
Versions:
1.3.2
Description:
C library for the MaxMind DB file format

libmesh

Homepage:
Spack package:
Versions:
master, 1.4.1, 1.4.0, 1.3.1, 1.3.0, 1.2.1, 1.0.0
Build Dependencies:
boost, eigen, hdf5, mpi, perl, petsc, slepc, tbb, vtk
Link Dependencies:
boost, eigen, hdf5, mpi, perl, petsc, slepc, tbb, vtk
Description:
The libMesh library provides a framework for the numerical simulation of partial differential equations using arbitrary unstructured discretizations on serial and parallel platforms.

libmmtf-cpp

Homepage:
Spack package:
Versions:
1.0.0
Build Dependencies:
cmake, msgpack-c
Link Dependencies:
msgpack-c
Description:
The macromolecular transmission format (MMTF) is a binary encoding of biological structures. This repository holds the C++-03 compatible API, encoding and decoding libraries.

libmng

Homepage:
Spack package:
Versions:
2.0.3, 2.0.2
Build Dependencies:
cmake, jpeg, zlib, lcms
Link Dependencies:
jpeg, zlib, lcms
Description:
THE reference library for reading, displaying, writing and examining Multiple-Image Network Graphics. MNG is the animation extension to the popular PNG image format.

libmo-unpack

Homepage:
Spack package:
Versions:
3.1.2
Build Dependencies:
cmake, check
Link Dependencies:
check
Description:
A library for handling the WGDOS and RLE compression schemes used in UM files.

libmonitor

Homepage:
Spack package:
Versions:
master, 2018.07.18, 2013.02.18
Description:
Libmonitor is a library providing callback functions for the begin and end of processes and threads. It provides a layer on which to build process monitoring tools and profilers.

libnbc

Homepage:
Spack package:
Versions:
1.1.1
Build Dependencies:
mpi
Link Dependencies:
mpi
Description:
LibNBC is a prototypic implementation of a nonblocking interface for MPI collective operations. Based on ANSI C and MPI-1, it supports all MPI-1 collective operations in a nonblocking manner. LibNBC is distributed under the BSD license.

libnl

Homepage:
Spack package:
Versions:
3.3.0
Build Dependencies:
bison, flex, m4
Description:
libnl - Netlink Protocol Library Suite

libnova

Homepage:
Spack package:
Versions:
0.15.0
Build Dependencies:
m4, autoconf, automake, libtool
Link Dependencies:
m4, autoconf, automake, libtool
Description:
"libnova is a general purpose, double precision, Celestial Mechanics, Astrometry and Astrodynamics library.

libnrm

Homepage:
Spack package:
Versions:
0.1.0
Build Dependencies:
m4, autoconf, automake, libtool, pkgconfig, libzmq, mpich
Link Dependencies:
libzmq, mpich
Description:
Libnrm, the application instrumentation library for the Node Resource Manager(NRM).

libnsl

Homepage:
Spack package:
Versions:
1.2.0
Build Dependencies:
autoconf, automake, libtool, m4, pkgconfig, gettext, rpcsvc-proto, libtirpc
Link Dependencies:
gettext, rpcsvc-proto, libtirpc
Description:
This library contains the public client interface for NIS(YP) and NIS+ in a IPv6 ready version.

libogg

Homepage:
Spack package:
Versions:
1.3.2
Description:
Ogg is a multimedia container format, and the native file and stream format for the Xiph.org multimedia codecs.

liboldx

Homepage:
Spack package:
Versions:
1.0.1
Build Dependencies:
libx11, pkgconfig, util-macros
Link Dependencies:
libx11
Description:
X version 10 backwards compatibility.

libpaper

Homepage:
Spack package:
Versions:
1.1.28
Build Dependencies:
autoconf, automake, libtool, m4
Description:
The paper library and accompanying files are intended to provide a simple way for applications to take actions based on a system- or user- specified paper size.

libpcap

Homepage:
Spack package:
Versions:
1.8.1
Build Dependencies:
flex, bison
Description:
libpcap is a portable library in C/C++ for packet capture.

libpciaccess

Homepage:
Spack package:
Versions:
0.13.5, 0.13.4
Build Dependencies:
libtool, pkgconfig, util-macros
Description:
Generic PCI access library.

libpeas

Homepage:
Spack package:
Versions:
1.22.0
Build Dependencies:
m4, autoconf, automake, libtool, gettext, pkgconfig, atk, intltool, xmlto, perl, perl-xml-parser, glib, gobject-introspection, libffi, gtkplus, gdk-pixbuf, pango, gnome-common, py-pygobject, python
Link Dependencies:
atk, intltool, glib, gobject-introspection, libffi, gtkplus, gdk-pixbuf, pango, gnome-common
Description:
libpeas is a gobject-based plugins engine, and is targeted at giving every application the chance to assume its own extensibility.

libpfm4

Homepage:
Spack package:
Versions:
4.10.1, 4.9.0, 4.8.0
Description:
libpfm4 is a userspace library to help setup performance events for use with the perf_events Linux kernel interface.

libpipeline

Homepage:
Spack package:
Versions:
1.4.2
Build Dependencies:
pkgconfig
Test Dependencies:
check
Description:
libpipeline is a C library for manipulating pipelines of subprocesses in a flexible and convenient way.

libplist

Homepage:
Spack package:
Versions:
master, 2.0.0, 1.10, 1.9, 1.8, 1.7, 1.6, 1.5, 1.4, 1.3
Build Dependencies:
autoconf, automake, libtool, pkgconfig
Description:
Library for Apple Binary- and XML-Property Lists.

libpmemobj-cpp

Homepage:
Spack package:
Versions:
develop, 1.6, 1.5.1, 1.5
Build Dependencies:
cmake, pmdk
Link Dependencies:
pmdk
Description:
C++ bindings for libpmemobj (https://github.com/pmem/pmdk)

libpng

Homepage:
Spack package:
Versions:
1.6.37, 1.2.57
Build Dependencies:
zlib
Link Dependencies:
zlib
Description:
libpng is the official PNG reference library.

libpsl

Homepage:
Spack package:
Versions:
0.17.0
Build Dependencies:
icu4c, gettext, pkgconfig, python
Link Dependencies:
icu4c
Test Dependencies:
valgrind
Description:
libpsl - C library to handle the Public Suffix List.

libpthread-stubs

Homepage:
Spack package:
Versions:
0.4, 0.3
Description:
The libpthread-stubs package provides weak aliases for pthread functions not provided in libc or otherwise available by default.

libquo

Homepage:
Spack package:
Versions:
develop, 1.3.1, 1.3, 1.2.9
Build Dependencies:
mpi, m4, autoconf, automake, libtool
Link Dependencies:
mpi
Description:
QUO (as in "status quo") is a runtime library that aids in accommodating thread-level heterogeneity in dynamic, phased MPI+X applications comprising single- and multi-threaded libraries.

librom

Homepage:
Spack package:
Versions:
develop
Build Dependencies:
lapack, mpi, zlib, libszip, hdf5, perl, graphviz, doxygen, boost
Link Dependencies:
lapack, mpi, zlib, libszip, hdf5, perl, graphviz, doxygen, boost
Description:
libROM: library for computing large-scale reduced order models

librsb

Homepage:
Spack package:
Versions:
1.2.0.8
Build Dependencies:
zlib
Link Dependencies:
zlib
Description:
librsb : A shared memory parallel sparse matrix computations library for the Recursive Sparse Blocks format

librsvg

Homepage:
Spack package:
Versions:
2.44.14
Build Dependencies:
gobject-introspection, pkgconfig, rust, cairo, gdk-pixbuf, glib, libcroco, pango, libffi, libxml2
Link Dependencies:
cairo, gdk-pixbuf, glib, libcroco, pango, libffi, libxml2
Description:
Library to render SVG files using Cairo

libseccomp

Homepage:
Spack package:
Versions:
2.3.3
Build Dependencies:
autoconf, automake, libtool, m4, py-cython
Description:
The main libseccomp repository

libsecret

Homepage:
Spack package:
Versions:
0.18.8
Build Dependencies:
glib, libgcrypt, gobject-introspection
Link Dependencies:
glib, libgcrypt, gobject-introspection
Description:
libsecret is a library for storing and retrieving passwords and other secrets. It communicates with the "Secret Service" using D-Bus. gnome- keyring and ksecretservice are both implementations of a Secret Service. libsecret replaces libgnome-keyring

libsharp

Homepage:
Spack package:
Versions:
2018-01-17, 1.0.0
Build Dependencies:
autoconf, mpi
Link Dependencies:
mpi
Description:
Libsharp is a code library for spherical harmonic transforms (SHTs) and spin-weighted spherical harmonic transforms, which evolved from the libpsht library.

libshm

Homepage:
Spack package:
Versions:
master
Description:
Libshm is a header library making an easy C++11 access to a shared memory.

libsigcpp

Homepage:
Spack package:
Versions:
2.99.12, 2.9.3, 2.1.1, 2.0.3
Description:
Libsigc++ is a C++ library for typesafe callbacks

libsigsegv

Homepage:
Spack package:
Versions:
2.12, 2.11, 2.10
Description:
GNU libsigsegv is a library for handling page faults in user mode.

libsm

Homepage:
Spack package:
Versions:
1.2.2
Build Dependencies:
libice, xproto, xtrans, pkgconfig, util-macros
Link Dependencies:
libice
Description:
libSM - X Session Management Library.

libsodium

Homepage:
Spack package:
Versions:
1.0.18, 1.0.17, 1.0.16, 1.0.15, 1.0.13, 1.0.3, 1.0.2, 1.0.1, 1.0.0, 0.7.1
Description:
Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, password hashing and more.

libspatialindex

Homepage:
Spack package:
Versions:
1.8.5
Build Dependencies:
cmake
Description:
C++ implementation of R*-tree, an MVR-tree and a TPR-tree with C API.

libspatialite

Homepage:
Spack package:
Versions:
4.3.0a, 3.0.1
Build Dependencies:
pkgconfig, sqlite, proj, geos, freexl, libiconv, libxml2
Link Dependencies:
sqlite, proj, geos, freexl, libiconv, libxml2
Description:
SpatiaLite is an open source library intended to extend the SQLite core to support fully fledged Spatial SQL capabilities.

libsplash

Homepage:
Spack package:
Versions:
develop, master, 1.7.0, 1.6.0, 1.5.0, 1.4.0, 1.3.1, 1.2.4
Build Dependencies:
cmake, hdf5, mpi
Link Dependencies:
hdf5, mpi
Description:
libSplash aims at developing a HDF5-based I/O library for HPC simulations. It is created as an easy-to-use frontend for the standard HDF5 library with support for MPI processes in a cluster environment. While the standard HDF5 library provides detailed low-level control, libSplash simplifies tasks commonly found in large-scale HPC simulations, such as iterative computations and MPI distributed processes.

libssh

Homepage:
Spack package:
Versions:
0.8.5, 0.7.5
Build Dependencies:
cmake, openssl, zlib
Link Dependencies:
openssl, zlib
Description:
libssh: the SSH library

libssh2

Homepage:
Spack package:
Versions:
1.8.0, 1.7.0, 1.4.3
Build Dependencies:
cmake, openssl, zlib, xz
Link Dependencies:
openssl, zlib, xz
Description:
libssh2 is a client-side C library implementing the SSH2 protocol

libsvm

Homepage:
Spack package:
Versions:
323, 322
Description:
Libsvm is a simple, easy-to-use, and efficient software for SVM classification and regression.

libszip

Homepage:
Spack package:
Versions:
2.1.1, 2.1
Description:
Szip is an implementation of the extended-Rice lossless compression algorithm. It provides lossless compression of scientific data, and is provided with HDF software products.

libtasn1

Homepage:
Spack package:
Versions:
4.13, 4.12, 4.10, 4.9, 4.8, 4.7, 4.6, 4.5, 4.4, 4.3, 4.2, 4.1, 4.0
Description:
ASN.1 structure parser library.

libtermkey

Homepage:
Spack package:
Versions:
0.18, 0.17, 0.16, 0.15b, 0.14
Build Dependencies:
libtool, ncurses
Link Dependencies:
ncurses
Description:
Easy keyboard entry processing for terminal programs

libtiff

Homepage:
Spack package:
Versions:
4.0.10, 4.0.9, 4.0.8, 4.0.7, 4.0.6, 3.9.7
Build Dependencies:
jpeg, zlib, xz
Link Dependencies:
jpeg, zlib, xz
Description:
LibTIFF - Tag Image File Format (TIFF) Library and Utilities.

libtirpc

Homepage:
Spack package:
Versions:
1.1.4
Description:
Libtirpc is a port of Suns Transport-Independent RPC library to Linux.

libtomlc99

Homepage:
Spack package:
Versions:
0.2019.06.24, 0.2019.05.02, 0.2019.03.06
Description:
TOML in c99; v0.4.0 compliant.

libtool

Homepage:
Spack package:
Versions:
develop, 2.4.6, 2.4.2
Build Dependencies:
m4, autoconf, automake, help2man, xz, texinfo
Description:
libtool -- library building part of autotools.

libunistring

Homepage:
Spack package:
Versions:
0.9.10, 0.9.9, 0.9.8, 0.9.7, 0.9.6
Build Dependencies:
libiconv
Link Dependencies:
libiconv
Description:
This library provides functions for manipulating Unicode strings and for manipulating C strings according to the Unicode standard.

libunwind

Homepage:
Spack package:
Versions:
develop, 2018.10.12, 1.4-rc1, 1.3.1, 1.2.1, 1.1
Build Dependencies:
autoconf, automake, libtool, m4
Link Dependencies:
xz
Description:
A portable and efficient C programming interface (API) to determine the call-chain of a program.

libusb

Homepage:
Spack package:
Versions:
master, 1.0.22, 1.0.21, 1.0.20
Build Dependencies:
autoconf, automake, libtool
Description:
Library for USB device access.

libusbmuxd

Homepage:
Spack package:
Versions:
master, 1.0.10, 1.0.9
Build Dependencies:
autoconf, automake, libtool, pkgconfig, libplist
Link Dependencies:
libplist
Description:
A client library to multiplex connections from and to iOS devices.

libuuid

Homepage:
Spack package:
Versions:
1.0.3
Description:
Portable uuid C library

libuv

Homepage:
Spack package:
Versions:
1.25.0, 1.10.0, 1.9.0
Build Dependencies:
automake, autoconf, libtool
Description:
Multi-platform library with a focus on asynchronous IO

libvdwxc

Homepage:
Spack package:
Versions:
0.4.0
Build Dependencies:
fftw, mpi, pfft
Link Dependencies:
fftw, mpi, pfft
Description:
Portable C library of density functionals with van der Waals interactions for density functional theory

libvips

Homepage:
Spack package:
Versions:
8.9.1, 8.9.0
Build Dependencies:
glib, expat, fftw, libjpeg, libtiff, libpng, poppler
Link Dependencies:
glib, expat, fftw, libjpeg, libtiff, libpng, poppler
Description:
libvips is a demand-driven, horizontally threaded image processing library. Compared to similar libraries, libvips runs quickly and uses little memory.

libvorbis

Homepage:
Spack package:
Versions:
1.3.5
Build Dependencies:
libogg, pkgconfig
Link Dependencies:
libogg
Description:
Ogg Vorbis is a fully open, non-proprietary, patent-and-royalty-free, general-purpose compressed audio format for mid to high quality (8kHz- 48.0kHz, 16+ bit, polyphonic) audio and music at fixed and variable bitrates from 16 to 128 kbps/channel.

libvterm

Homepage:
Spack package:
Versions:
681
Build Dependencies:
libtool
Description:
An abstract library implementation of a terminal emulator

libwebp

Homepage:
Spack package:
Versions:
1.0.3
Build Dependencies:
automake, autoconf, libtool, m4
Description:
WebP is a modern image format that provides superior lossless and lossy compression for images on the web. Using WebP, webmasters and web developers can create smaller, richer images that make the web faster.

libwebsockets

Homepage:
Spack package:
Versions:
2.2.1, 2.1.1, 2.1.0, 2.0.3, 1.7.9
Build Dependencies:
cmake, zlib, openssl
Link Dependencies:
zlib, openssl
Description:
C library for lightweight websocket clients and servers.

libwindowswm

Homepage:
Spack package:
Versions:
1.0.1
Build Dependencies:
libx11, libxext, xextproto, windowswmproto, pkgconfig, util-macros
Link Dependencies:
libx11, libxext
Description:
WindowsWM - Cygwin/X rootless window management extension. WindowsWM is a simple library designed to interface with the Windows-WM extension. This extension allows X window managers to better interact with the Cygwin XWin server when running X11 in a rootless mode.

libx11

Homepage:
Spack package:
Versions:
1.6.7, 1.6.5, 1.6.3
Build Dependencies:
libxcb, xproto, xextproto, xtrans, kbproto, inputproto, pkgconfig, util-macros, perl
Link Dependencies:
libxcb, xextproto, kbproto
Description:
libX11 - Core X11 protocol client library.

libxau

Homepage:
Spack package:
Versions:
1.0.8
Build Dependencies:
xproto, pkgconfig, util-macros
Link Dependencies:
xproto
Description:
The libXau package contains a library implementing the X11 Authorization Protocol. This is useful for restricting client access to the display.

libxaw

Homepage:
Spack package:
Versions:
1.0.13, 1.0.12
Build Dependencies:
libx11, libxext, libxt, libxmu, libxpm, xproto, xextproto, pkgconfig, util-macros
Link Dependencies:
libx11, libxext, libxt, libxmu, libxpm
Description:
Xaw is the X Athena Widget Set. Xaw is a widget set based on the X Toolkit Intrinsics (Xt) Library.

libxaw3d

Homepage:
Spack package:
Versions:
1.6.2
Build Dependencies:
libx11, libxt, libxmu, libxext, libxpm, pkgconfig, util-macros
Link Dependencies:
libx11, libxt, libxmu, libxext, libxpm
Description:
Xaw3d is the X 3D Athena Widget Set. Xaw3d is a widget set based on the X Toolkit Intrinsics (Xt) Library.

libxc

Homepage:
Spack package:
Versions:
4.3.2, 4.2.3, 3.0.0, 2.2.2, 2.2.1
Description:
Libxc is a library of exchange-correlation functionals for density- functional theory.

libxcb

Homepage:
Spack package:
Versions:
1.13, 1.12, 1.11.1, 1.11
Build Dependencies:
libpthread-stubs, libxau, libxdmcp, xcb-proto, pkgconfig, util-macros
Link Dependencies:
libpthread-stubs, libxau, libxdmcp
Description:
The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility.

libxcomposite

Homepage:
Spack package:
Versions:
0.4.4
Build Dependencies:
libx11, libxfixes, fixesproto, compositeproto, pkgconfig, util-macros
Link Dependencies:
libx11, libxfixes
Description:
libXcomposite - client library for the Composite extension to the X11 protocol.

libxcursor

Homepage:
Spack package:
Versions:
1.1.14
Build Dependencies:
libxrender, libxfixes, libx11, fixesproto, pkgconfig, util-macros
Link Dependencies:
libxrender, libxfixes, libx11
Description:
libXcursor - X Window System Cursor management library.

libxdamage

Homepage:
Spack package:
Versions:
1.1.4
Build Dependencies:
libxfixes, libx11, damageproto, fixesproto, xextproto, pkgconfig, util-macros
Link Dependencies:
libxfixes, libx11
Description:
This package contains the library for the X Damage extension.

libxdmcp

Homepage:
Spack package:
Versions:
1.1.2
Build Dependencies:
xproto, pkgconfig, util-macros, libbsd
Link Dependencies:
libbsd
Description:
libXdmcp - X Display Manager Control Protocol library.

libxevie

Homepage:
Spack package:
Versions:
1.0.3
Build Dependencies:
libx11, libxext, xproto, xextproto, evieext, pkgconfig, util-macros
Link Dependencies:
libx11, libxext
Description:
Xevie - X Event Interception Extension (XEvIE).

libxext

Homepage:
Spack package:
Versions:
1.3.3
Build Dependencies:
libx11, xproto, xextproto, pkgconfig, util-macros
Link Dependencies:
libx11
Description:
libXext - library for common extensions to the X11 protocol.

libxfixes

Homepage:
Spack package:
Versions:
5.0.2
Build Dependencies:
libx11, xproto, fixesproto, xextproto, pkgconfig, util-macros
Link Dependencies:
libx11
Description:
This package contains header files and documentation for the XFIXES extension. Library and server implementations are separate.

libxfont

Homepage:
Spack package:
Versions:
1.5.2
Build Dependencies:
libfontenc, freetype, xtrans, xproto, fontsproto, pkgconfig, util-macros
Link Dependencies:
libfontenc, freetype
Description:
libXfont provides the core of the legacy X11 font system, handling the index files (fonts.dir, fonts.alias, fonts.scale), the various font file formats, and rasterizing them. It is used by the X servers, the X Font Server (xfs), and some font utilities (bdftopcf for instance), but should not be used by normal X11 clients. X11 clients access fonts via either the new API's in libXft, or the legacy API's in libX11.

libxfont2

Homepage:
Spack package:
Versions:
2.0.1
Build Dependencies:
libfontenc, freetype, xtrans, xproto, fontsproto, pkgconfig, util-macros
Link Dependencies:
libfontenc, freetype
Description:
libXfont provides the core of the legacy X11 font system, handling the index files (fonts.dir, fonts.alias, fonts.scale), the various font file formats, and rasterizing them. It is used by the X servers, the X Font Server (xfs), and some font utilities (bdftopcf for instance), but should not be used by normal X11 clients. X11 clients access fonts via either the new API's in libXft, or the legacy API's in libX11.

libxfontcache

Homepage:
Spack package:
Versions:
1.0.5
Build Dependencies:
libx11, libxext, xextproto, fontcacheproto, pkgconfig, util-macros
Link Dependencies:
libx11, libxext
Description:
Xfontcache - X-TrueType font cache extension client library.

libxft

Homepage:
Spack package:
Versions:
2.3.2
Build Dependencies:
freetype, fontconfig, libx11, libxrender, pkgconfig, util-macros
Link Dependencies:
freetype, fontconfig, libx11, libxrender
Description:
X FreeType library. Xft version 2.1 was the first stand alone release of Xft, a library that connects X applications with the FreeType font rasterization library. Xft uses fontconfig to locate fonts so it has no configuration files.

libxi

Homepage:
Spack package:
Versions:
1.7.6
Build Dependencies:
pkgconfig, libx11, libxext, libxfixes, fixesproto, xproto, xextproto, inputproto
Link Dependencies:
libx11, libxext, libxfixes
Description:
libXi - library for the X Input Extension.

libxinerama

Homepage:
Spack package:
Versions:
1.1.3
Build Dependencies:
libx11, libxext, xextproto, xineramaproto, pkgconfig, util-macros
Link Dependencies:
libx11, libxext
Description:
libXinerama - API for Xinerama extension to X11 Protocol.

libxkbcommon

Homepage:
Spack package:
Versions:
0.8.2, 0.8.0, 0.7.1
Build Dependencies:
pkgconfig, bison, util-macros, xkbdata, libxcb
Link Dependencies:
util-macros, xkbdata, libxcb
Description:
xkbcommon is a library to handle keyboard descriptions, including loading them from disk, parsing them and handling their state. It's mainly meant for client toolkits, window systems, and other system applications.

libxkbfile

Homepage:
Spack package:
Versions:
1.0.9
Build Dependencies:
libx11, kbproto, pkgconfig, util-macros
Link Dependencies:
libx11
Description:
XKB file handling routines.

libxkbui

Homepage:
Spack package:
Versions:
1.0.2
Build Dependencies:
libx11, libxt, libxkbfile, pkgconfig, util-macros
Link Dependencies:
libx11, libxt, libxkbfile
Description:
X.org libxkbui library.

libxml2

Homepage:
Spack package:
Versions:
2.9.9, 2.9.8, 2.9.4, 2.9.2, 2.7.8
Build Dependencies:
pkgconfig, libiconv, zlib, xz, python
Link Dependencies:
libiconv, zlib, xz, python
Description:
Libxml2 is the XML C parser and toolkit developed for the Gnome project (but usable outside of the Gnome platform), it is free software available under the MIT License.

libxmu

Homepage:
Spack package:
Versions:
1.1.2
Build Dependencies:
libxt, libxext, libx11, xextproto, pkgconfig, util-macros
Link Dependencies:
libxt, libxext, libx11
Description:
This library contains miscellaneous utilities and is not part of the Xlib standard. It contains routines which only use public interfaces so that it may be layered on top of any proprietary implementation of Xlib or Xt.

libxp

Homepage:
Spack package:
Versions:
1.0.3
Build Dependencies:
libx11, libxext, libxau, xextproto, printproto, pkgconfig, util-macros
Link Dependencies:
libx11, libxext, libxau
Description:
libXp - X Print Client Library.

libxpm

Homepage:
Spack package:
Versions:
3.5.12, 3.5.11, 3.5.10, 3.5.9, 3.5.8, 3.5.7
Build Dependencies:
gettext, libx11, xproto, pkgconfig, util-macros
Link Dependencies:
gettext, libx11
Description:
libXpm - X Pixmap (XPM) image file format library.

libxpresent

Homepage:
Spack package:
Versions:
1.0.0
Build Dependencies:
libx11, xproto, presentproto, xextproto, pkgconfig, util-macros
Link Dependencies:
libx11
Description:
This package contains header files and documentation for the Present extension. Library and server implementations are separate.

libxprintapputil

Homepage:
Spack package:
Versions:
1.0.1
Build Dependencies:
libx11, libxp, libxprintutil, libxau, printproto, pkgconfig, util-macros
Link Dependencies:
libx11, libxp, libxprintutil, libxau
Description:
Xprint application utility routines.

libxprintutil

Homepage:
Spack package:
Versions:
1.0.1
Build Dependencies:
libx11, libxp, libxt, libxau, printproto, pkgconfig, util-macros
Link Dependencies:
libx11, libxp, libxt, libxau
Description:
Xprint application utility routines.

libxrandr

Homepage:
Spack package:
Versions:
1.5.0
Build Dependencies:
libx11, libxext, libxrender, randrproto, xextproto, renderproto, pkgconfig, util-macros
Link Dependencies:
libx11, libxext, libxrender
Description:
libXrandr - X Resize, Rotate and Reflection extension library.

libxrender

Homepage:
Spack package:
Versions:
0.9.10, 0.9.9
Build Dependencies:
libx11, renderproto, pkgconfig, util-macros
Link Dependencies:
libx11, renderproto
Description:
libXrender - library for the Render Extension to the X11 protocol.

libxres

Homepage:
Spack package:
Versions:
1.0.7
Build Dependencies:
libx11, libxext, xextproto, resourceproto, pkgconfig, util-macros
Link Dependencies:
libx11, libxext
Description:
libXRes - X-Resource extension client library.

libxscrnsaver

Homepage:
Spack package:
Versions:
1.2.2
Build Dependencies:
libx11, libxext, xextproto, scrnsaverproto, pkgconfig, util-macros
Link Dependencies:
libx11, libxext
Description:
XScreenSaver - X11 Screen Saver extension client library

libxshmfence

Homepage:
Spack package:
Versions:
1.3, 1.2
Build Dependencies:
xproto, pkgconfig, util-macros
Description:
libxshmfence - Shared memory 'SyncFence' synchronization primitive. This library offers a CPU-based synchronization primitive compatible with the X SyncFence objects that can be shared between processes using file descriptor passing.

libxslt

Homepage:
Spack package:
Versions:
1.1.33, 1.1.32, 1.1.29, 1.1.28, 1.1.26
Build Dependencies:
pkgconfig, libiconv, libxml2, xz, zlib, libgcrypt, python
Link Dependencies:
libiconv, libxml2, xz, zlib, libgcrypt, python
Description:
Libxslt is the XSLT C library developed for the GNOME project. XSLT itself is a an XML language to define transformation for XML. Libxslt is based on libxml2 the XML C library developed for the GNOME project. It also implements most of the EXSLT set of processor-portable extensions functions and some of Saxon's evaluate and expressions extensions.

libxsmm

Homepage:
Spack package:
Versions:
develop, 1.14, 1.13, 1.12.1, 1.12, 1.11, 1.10, 1.9, 1.8.3, 1.8.2, 1.8.1, 1.8, 1.7.1, 1.7, 1.6.6, 1.6.5, 1.6.4, 1.6.3, 1.6.2, 1.6.1, 1.6, 1.5.2, 1.5.1, 1.5, 1.4.4, 1.4.3, 1.4.2, 1.4.1, 1.4
Description:
Library targeting Intel Architecture for specialized dense and sparse matrix operations, and deep learning primitives.

libxstream

Homepage:
Spack package:
Versions:
0.9.0
Description:
LIBXSTREAM is a library to work with streams, events, and code regions that are able to run asynchronous while preserving the usual stream conditions.

libxt

Homepage:
Spack package:
Versions:
1.1.5
Build Dependencies:
libsm, libice, libx11, xproto, kbproto, pkgconfig, util-macros
Link Dependencies:
libsm, libice, libx11
Description:
libXt - X Toolkit Intrinsics library.

libxtrap

Homepage:
Spack package:
Versions:
1.0.1
Build Dependencies:
libx11, libxt, libxext, trapproto, xextproto, pkgconfig, util-macros
Link Dependencies:
libx11, libxt, libxext
Description:
libXTrap is the Xlib-based client API for the DEC-XTRAP extension. XTrap was a proposed standard extension for X11R5 which facilitated the capturing of server protocol and synthesizing core input events. Digital participated in the X Consortium's xtest working group which chose to evolve XTrap functionality into the XTEST & RECORD extensions for X11R6. As X11R6 was released in 1994, XTrap has now been deprecated for over 15 years, and uses of it should be quite rare.

libxtst

Homepage:
Spack package:
Versions:
1.2.2
Build Dependencies:
libx11, libxext, libxi, recordproto, xextproto, inputproto, fixesproto, pkgconfig, util-macros
Link Dependencies:
libx11, libxext, libxi
Description:
libXtst provides the Xlib-based client API for the XTEST & RECORD extensions. The XTEST extension is a minimal set of client and server extensions required to completely test the X11 server with no user intervention. This extension is not intended to support general journaling and playback of user actions. The RECORD extension supports the recording and reporting of all core X protocol and arbitrary X extension protocol.

libxv

Homepage:
Spack package:
Versions:
1.0.10
Build Dependencies:
libx11, libxext, xextproto, videoproto, pkgconfig, util-macros
Link Dependencies:
libx11, libxext
Description:
libXv - library for the X Video (Xv) extension to the X Window System.

libxvmc

Homepage:
Spack package:
Versions:
1.0.9
Build Dependencies:
libx11, libxext, libxv, xextproto, videoproto, pkgconfig, util-macros
Link Dependencies:
libx11, libxext, libxv
Description:
X.org libXvMC library.

libxxf86dga

Homepage:
Spack package:
Versions:
1.1.4
Build Dependencies:
libx11, libxext, xproto, xextproto, xf86dgaproto, pkgconfig, util-macros
Link Dependencies:
libx11, libxext
Description:
libXxf86dga - Client library for the XFree86-DGA extension.

libxxf86misc

Homepage:
Spack package:
Versions:
1.0.3
Build Dependencies:
libx11, libxext, xproto, xextproto, xf86miscproto, pkgconfig, util-macros
Link Dependencies:
libx11, libxext
Description:
libXxf86misc - Extension library for the XFree86-Misc X extension.

libxxf86vm

Homepage:
Spack package:
Versions:
1.1.4
Build Dependencies:
libx11, libxext, xproto, xextproto, xf86vidmodeproto, pkgconfig, util-macros
Link Dependencies:
libx11, libxext
Description:
libXxf86vm - Extension library for the XFree86-VidMode X extension.

libyaml

Homepage:
Spack package:
Versions:
master, 0.2.2, 0.2.1, 0.1.7, 0.1.6, 0.1.5, 0.1.4, 0.1.3, 0.1.2, 0.1.1
Build Dependencies:
automake, autoconf, libtool, m4
Link Dependencies:
automake, autoconf, libtool, m4
Description:
A C library for parsing and emitting YAML.

libyogrt

Homepage:
Spack package:
Versions:
1.24, 1.23, 1.22, 1.21, 1.20-7, 1.20-6, 1.20-5, 1.20-4, 1.20-3, 1.20-2
Build Dependencies:
slurm
Link Dependencies:
slurm
Description:
Your One Get Remaining Time Library.

libzip

Homepage:
Spack package:
Versions:
1.2.0
Build Dependencies:
zlib
Link Dependencies:
zlib
Description:
libzip is a C library for reading, creating, and modifying zip archives.

libzmq

Homepage:
Spack package:
Versions:
develop, 4.3.2, 4.3.1, 4.3.0, 4.2.5, 4.2.2, 4.1.4, 4.1.2, 4.1.1, 4.0.7, 4.0.6, 4.0.5
Build Dependencies:
libsodium, autoconf, automake, libtool, pkgconfig
Link Dependencies:
libsodium
Description:
The ZMQ networking/concurrency library and core API

liggghts

Homepage:
Spack package:
Versions:
3.8.0
Build Dependencies:
vtk, mpi, jpeg, zlib
Link Dependencies:
vtk, mpi, jpeg, zlib
Description:
Discrete element method particle simulation.

lighttpd

Homepage:
Spack package:
Versions:
1.4.55, 1.4.54, 1.4.53, 1.4.52, 1.4.51, 1.4.50, 1.4.49
Build Dependencies:
cmake, pcre
Link Dependencies:
pcre
Description:
a secure, fast, compliant and very flexible web-server

likwid

Homepage:
Spack package:
Versions:
5.0.0, 4.3.4, 4.3.3, 4.3.2, 4.3.1, 4.3.0
Build Dependencies:
lua, perl
Link Dependencies:
lua
Run Dependencies:
perl
Description:
Likwid is a simple to install and use toolsuite of command line applications for performance oriented programmers. It works for Intel and AMD processors on the Linux operating system. This version uses the perf_event backend which reduces the feature set but allows user installs. See https://github.com/RRZE- HPC/likwid/wiki/TutorialLikwidPerf#feature-limitations for information.

linkphase3

Homepage:
Spack package:
Versions:
2017-06-14
Description:
Haplotype reconstruction in pedigreed populations.

linux-headers

Homepage:
Spack package:
Versions:
4.9.10
Description:
The Linux kernel headers.

listres

Homepage:
Spack package:
Versions:
1.0.3
Build Dependencies:
libxaw, libxt, libxmu, xproto, pkgconfig, util-macros
Link Dependencies:
libxaw, libxt, libxmu
Description:
The listres program generates a list of X resources for a widget in an X client written using a toolkit based on libXt.

lizard

Homepage:
Spack package:
Versions:
develop, 1.0
Description:
Lizard (formerly LZ5) is an efficient compressor with very fast decompression. It achieves compression ratio that is comparable to zip/zlib and zstd/brotli (at low and medium compression levels) at decompression speed of 1000 MB/s and faster.

llvm

Homepage:
Spack package:
Versions:
master, 9.0.1, 9.0.0, 8.0.0, 7.1.0, 7.0.1, 6.0.1, 6.0.0, 5.0.2, 5.0.1, 5.0.0, 4.0.1, 4.0.0, 3.9.1, 3.9.0, 3.8.1, 3.8.0, 3.7.1, 3.7.0, 3.6.2, 3.5.1
Build Dependencies:
cmake, python, perl-data-dumper, ncurses, swig, libedit, py-six, binutils, gmp, isl
Link Dependencies:
python, ncurses, swig, libedit, py-six, binutils, gmp, isl
Description:
The LLVM Project is a collection of modular and reusable compiler and toolchain technologies. Despite its name, LLVM has little to do with traditional virtual machines, though it does provide helpful libraries that can be used to build them. The name "LLVM" itself is not an acronym; it is the full name of the project.

llvm-flang

Homepage:
Spack package:
Versions:
master, 20190329, 20181226_70, 20181226_60, 20180921, 20180328, 20180319, release_70, release_60
Build Dependencies:
cuda, cmake, python, perl-data-dumper, hwloc, libelf, libffi
Link Dependencies:
cuda, hwloc, libelf, libffi
Description:
LLVM-Flang is the Flang fork of LLVM needed by the Flang package.

llvm-openmp

Homepage:
Spack package:
Versions:
9.0.0, 8.0.0
Build Dependencies:
cmake
Description:
The OpenMP subproject of LLVM contains the components required to build an executable OpenMP program that are outside the compiler itself.

llvm-openmp-ompt

Homepage:
Spack package:
Versions:
3.9.2b2, 3.9.2b, tr6_forwards
Build Dependencies:
cmake, llvm, ninja
Link Dependencies:
llvm
Description:
The OpenMP subproject provides an OpenMP runtime for use with the OpenMP implementation in Clang. This branch includes experimental changes for OMPT, the OpenMP Tools interface

lm-sensors

Homepage:
Spack package:
Versions:
3-6-0, 3-5-0, 3-4-0, 3-3-5, 3-3-4, 3-3-3, 3-3-2, 3-3-1, 3-3-0, 3-2-0, 3-1-2, 3-1-1
Build Dependencies:
bison, flex
Run Dependencies:
perl
Description:
The lm-sensors package provides user-space support for the hardware monitoring drivers in Linux.

lmdb

Homepage:
Spack package:
Versions:
0.9.24, 0.9.22, 0.9.21, 0.9.16
Description:
Symas LMDB is an extraordinarily fast, memory-efficient database we developed for the Symas OpenLDAP Project. With memory-mapped files, it has the read performance of a pure in-memory database while retaining the persistence of standard disk-based databases.

lmod

Homepage:
Spack package:
Versions:
8.3, 8.2.10, 8.1.5, 8.0.9, 7.8.15, 7.8, 7.7.29, 7.7.13, 7.7, 7.6.14, 7.4.11, 7.4.10, 7.4.9, 7.4.8, 7.4.5, 7.4.1, 7.3, 6.4.5, 6.4.1, 6.3.7
Build Dependencies:
lua, lua-luaposix, lua-luafilesystem, tcl
Link Dependencies:
lua, tcl
Run Dependencies:
lua-luaposix, lua-luafilesystem, tcl
Description:
Lmod is a Lua based module system that easily handles the MODULEPATH Hierarchical problem. Environment Modules provide a convenient way to dynamically change the users' environment through modulefiles. This includes easily adding or removing directories to the PATH environment variable. Modulefiles for Library packages provide environment variables that specify where the library and header files can be found.

lndir

Homepage:
Spack package:
Versions:
1.0.3
Build Dependencies:
xproto, pkgconfig
Description:
lndir - create a shadow directory of symbolic links to another directory tree.

log4cplus

Homepage:
Spack package:
Versions:
2.0.1, 1.2.1
Build Dependencies:
cmake
Description:
log4cplus is a simple to use C++ logging API providing thread-safe, flexible, and arbitrarily granular control over log management and configuration.

log4cxx

Homepage:
Spack package:
Versions:
0.10.0
Build Dependencies:
apr-util, apr, zip
Link Dependencies:
apr-util, apr, zip
Description:
A C++ port of Log4j

logstash

Homepage:
Spack package:
Versions:
6.6.0
Description:
Logstash is part of the Elastic Stack along with Beats, Elasticsearch and Kibana. Logstash is a server-side data processing pipeline that ingests data from a multitude of sources simultaneously, transforms it, and then sends it to your favorite "stash.

loki

Homepage:
Spack package:
Versions:
0.1.7
Description:
Loki is a C++ library of designs, containing flexible implementations of common design patterns and idioms.

lordec

Homepage:
Spack package:
Versions:
0.8
Build Dependencies:
boost, cmake
Link Dependencies:
boost
Description:
LoRDEC is a program to correct sequencing errors in long reads from 3rd generation sequencing with high error rate, and is especially intended for PacBio reads.

lrslib

Homepage:
Spack package:
Versions:
6.2, 6.1, 6.0, 5.1, 4.3
Build Dependencies:
gmp, libtool
Link Dependencies:
gmp
Description:
lrslib Ver 6.2 is a self-contained ANSI C implementation of the reverse search algorithm for vertex enumeration/convex hull problems and comes with a choice of three arithmetic packages

lrzip

Homepage:
Spack package:
Versions:
master, 0.630, 0.621, 0.616, 0.615
Build Dependencies:
lzo, zlib, bzip2
Link Dependencies:
lzo, zlib, bzip2
Description:
A compression utility that excels at compressing large files (usually > 10-50 MB). Larger files and/or more free RAM means that the utility will be able to more effectively compress your files (ie: faster / smaller size), especially if the filesize(s) exceed 100 MB. You can either choose to optimise for speed (fast compression / decompression) or size, but not both.

lsf

Homepage:
Spack package:
Description:
IBM Platform LSF is a batch scheduler for HPC environments

lshw

Homepage:
Spack package:
Versions:
02.18, 02.17, 02.16, 02.15
Description:
lshw is a small tool to provide detailed information on the hardware configuration of the machine. It can report exact memory configuration, firmware version, mainboard configuration, CPU version and speed, cache configuration, bus speed, etc. on DMI-capable x86 or EFI (IA-64) systems and on some ARM and PowerPC machines.

lsof

Homepage:
Spack package:
Versions:
4.91, 4.90, 4.89
Description:
Lsof displays information about files open to Unix processes.

ltp

Homepage:
Spack package:
Versions:
20190930, 20190517
Build Dependencies:
autoconf, automake, libtool, m4
Description:
Ltp is a joint project started by SGI, developed and maintained by IBM, Cisco, Fujitsu, SUSE, Red Hat and others, that has a goal to deliver test suites to the open source community that validate the reliability, robustness,and stability of Linux. The LTP testsuite contains a collection of tools for testing the Linux kernel and related features.

ltrace

Homepage:
Spack package:
Versions:
0.7.3
Description:
Ltrace intercepts and records dynamic library calls which are called by an executed process and the signals received by that process. It can also intercept and print the system calls executed by the program.

lua

Homepage:
Spack package:
Versions:
5.3.5, 5.3.4, 5.3.2, 5.3.1, 5.3.0, 5.2.4, 5.2.3, 5.2.2, 5.2.1, 5.2.0, 5.1.5, 5.1.4, 5.1.3
Build Dependencies:
ncurses, readline
Link Dependencies:
ncurses, readline
Run Dependencies:
unzip
Description:
The Lua programming language interpreter and library.

lua-bitlib

Homepage:
Spack package:
Versions:
23-2
Build Dependencies:
lua
Link Dependencies:
lua
Description:
Lua-jit-like bitwise operations for lua

lua-lpeg

Homepage:
Spack package:
Versions:
0.12-1
Build Dependencies:
lua
Link Dependencies:
lua
Description:
pattern-matching for lua

lua-luafilesystem

Homepage:
Spack package:
Versions:
1_7_0_2, 1_6_3
Build Dependencies:
git, lua
Link Dependencies:
lua
Description:
LuaFileSystem is a Lua library developed to complement the set of functions related to file systems offered by the standard Lua distribution. LuaFileSystem offers a portable way to access the underlying directory structure and file attributes. LuaFileSystem is free software and uses the same license as Lua 5.1

lua-luajit

Homepage:
Spack package:
Versions:
2.0.4
Description:
Flast flexible JITed lua

lua-luaposix

Homepage:
Spack package:
Versions:
33.4.0
Build Dependencies:
lua
Link Dependencies:
lua
Description:
Lua posix bindings, including ncurses

lua-mpack

Homepage:
Spack package:
Versions:
1.0.6-0
Build Dependencies:
msgpack-c, lua
Link Dependencies:
msgpack-c, lua
Description:
lua bindings to libmpack

lucene

Homepage:
Spack package:
Versions:
8.3.1, 8.3.0, 8.2.0, 8.1.1
Run Dependencies:
java
Description:
Apache Lucene is a high-performance, full featured text search engine library written in Java.

luit

Homepage:
Spack package:
Versions:
1.1.1
Build Dependencies:
libfontenc, libx11, pkgconfig, util-macros
Link Dependencies:
libfontenc, libx11
Description:
Luit is a filter that can be run between an arbitrary application and a UTF-8 terminal emulator such as xterm. It will convert application output from the locale's encoding into UTF-8, and convert terminal input from UTF-8 into the locale's encoding.

lulesh

Homepage:
Spack package:
Versions:
2.0.3
Build Dependencies:
mpi, silo, hdf5
Link Dependencies:
mpi, silo, hdf5
Description:
LULESH is a highly simplified application, hard-coded to only style typical in scientific C or C++ based applications. Hard code to only solve a Sedov blast problem with analytic answer

lumpy-sv

Homepage:
Spack package:
Versions:
0.2.13
Build Dependencies:
htslib
Link Dependencies:
htslib
Description:
A probabilistic framework for structural variant discovery.

lvm2

Homepage:
Spack package:
Versions:
2.03.05, 2.03.04, 2.03.03, 2.03.02, 2.03.01, 2.03.00
Build Dependencies:
libaio, pkgconfig
Link Dependencies:
libaio
Description:
LVM2 is the userspace toolset that provides logical volume management facilities on linux. To use it you need 3 things: device-mapper in your kernel, the userspace device-mapper support library (libdevmapper) and the userspace LVM2 tools (dmsetup). These userspace components, and associated header files, are provided by this package. See http://sources.redhat.com/dm/ for additional information about the device-mapper kernel and userspace components.

lwgrp

Homepage:
Spack package:
Versions:
1.0.2
Build Dependencies:
mpi
Link Dependencies:
mpi
Description:
Thie light-weight group library provides process group representations using O(log N) space and time.

lwm2

Homepage:
Spack package:
Versions:
torus
Build Dependencies:
papi, mpi
Link Dependencies:
papi, mpi
Description:
LWM2: Light Weight Measurement Module. This is a PMPI module that can collect a number of time-sliced MPI and POSIX I/O measurements from a program.

lz4

Homepage:
Spack package:
Versions:
1.9.2, 1.9.0, 1.8.3, 1.8.1.2, 1.7.5, 1.3.1
Test Dependencies:
valgrind
Description:
LZ4 is lossless compression algorithm, providing compression speed at 400 MB/s per core, scalable with multi-cores CPU. It also features an extremely fast decoder, with speed in multiple GB/s per core, typically reaching RAM speed limits on multi-core systems.

lzma

Homepage:
Spack package:
Versions:
4.32.7
Description:
LZMA Utils are legacy data compression software with high compression ratio. LZMA Utils are no longer developed, although critical bugs may be fixed as long as fixing them doesn't require huge changes to the code. Users of LZMA Utils should move to XZ Utils. XZ Utils support the legacy .lzma format used by LZMA Utils, and can also emulate the command line tools of LZMA Utils. This should make transition from LZMA Utils to XZ Utils relatively easy.

lzo

Homepage:
Spack package:
Versions:
2.10, 2.09, 2.08, 2.07, 2.06, 2.05
Description:
Real-time data compression library

m4

Homepage:
Spack package:
Versions:
1.4.18, 1.4.17
Build Dependencies:
libsigsegv
Link Dependencies:
libsigsegv
Description:
GNU M4 is an implementation of the traditional Unix macro processor.

macsio

Homepage:
Spack package:
Versions:
develop, 1.1
Build Dependencies:
cmake, json-cwx, mpi, silo, hdf5, exodusii, typhonio, scr
Link Dependencies:
json-cwx, mpi, silo, hdf5, exodusii, typhonio, scr
Description:
A Multi-purpose, Application-Centric, Scalable I/O Proxy Application.

mad-numdiff

Homepage:
Spack package:
Versions:
develop, 20150724
Build Dependencies:
cmake
Description:
compare unformatted text files with numerical content

mafft

Homepage:
Spack package:
Versions:
7.453, 7.407, 7.221
Description:
MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <~200 sequences), FFT-NS-2 (fast; for alignment of <~30,000 sequences), etc.

magics

Homepage:
Spack package:
Versions:
4.1.0, 2.34.3, 2.34.1, 2.33.0, 2.32.0, 2.31.0, 2.29.6, 2.29.4, 2.29.0
Build Dependencies:
cmake, pkgconfig, python, perl, perl-xml-parser, proj, boost, expat, zlib, libpng, eccodes, grib-api, netcdf-cxx, pango, libemos, qt, py-numpy, swig
Link Dependencies:
python, proj, boost, expat, zlib, libpng, eccodes, grib-api, netcdf-cxx, pango, libemos, qt
Run Dependencies:
python, py-numpy
Description:
Magics is the latest generation of the ECMWF's Meteorological plotting software MAGICS. Although completely redesigned in C++, it is intended to be as backwards-compatible as possible with the Fortran interface.

magma

Homepage:
Spack package:
Versions:
2.5.2, 2.5.1, 2.5.0, 2.4.0, 2.3.0, 2.2.0
Build Dependencies:
cmake, blas, lapack, cuda
Link Dependencies:
blas, lapack, cuda
Description:
The MAGMA project aims to develop a dense linear algebra library similar to LAPACK but for heterogeneous/hybrid architectures, starting with current "Multicore+GPU" systems.

makedepend

Homepage:
Spack package:
Versions:
1.0.5
Build Dependencies:
xproto, pkgconfig
Description:
makedepend - create dependencies in makefiles.

maker

Homepage:
Spack package:
Versions:
2.31.10
Build Dependencies:
perl, perl-module-build, perl-dbi, perl-dbd-pg, perl-dbd-sqlite, perl-forks, perl-file-which, perl-perl-unsafe-signals, perl-bit-vector, perl-inline-c, perl-io-all, perl-io-prompt, perl-bioperl, blast-plus, snap-korf, repeatmasker, exonerate, augustus, interproscan, mpi
Link Dependencies:
blast-plus, snap-korf, repeatmasker, exonerate, augustus, interproscan, mpi
Run Dependencies:
perl, perl-dbi, perl-dbd-pg, perl-dbd-sqlite, perl-forks, perl-file-which, perl-perl-unsafe-signals, perl-bit-vector, perl-inline-c, perl-io-all, perl-io-prompt, perl-bioperl
Description:
MAKER is a portable and easily configurable genome annotation pipeline. It's purpose is to allow smaller eukaryotic and prokaryotic genomeprojects to independently annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values. MAKER is also easily trainable: outputs of preliminary runs can be used to automatically retrain its gene prediction algorithm, producing higher quality gene-models on subsequent runs. MAKER's inputs are minimal and its ouputs can be directly loaded into a GMOD database. They can also be viewed in the Apollo genome browser; this feature of MAKER provides an easy means to annotate, view and edit individual contigs and BACs without the overhead of a database. MAKER should prove especially useful for emerging model organism projects with minimal bioinformatics expertise and computer resources. Note: MAKER requires registration. Fill out the form at http://yandell.topaz.genetics.utah.edu/cgi-bin/maker_license.cgi to get a download link. Spack will search your current directory for the download file. Alternatively, add this file to a mirror so that Spack can find it. For instructions on how to set up a mirror, see http://spack.readthedocs.io/en/latest/mirrors.html

mallocmc

Homepage:
Spack package:
Versions:
develop, master, 2.2.0crp, 2.1.0crp, 2.0.1crp, 2.0.0crp, 1.0.2crp
Build Dependencies:
cmake
Link Dependencies:
boost, cuda
Description:
mallocMC: Memory Allocator for Many Core Architectures. This project provides a framework for fast memory managers on many core accelerators. Currently, it supports NVIDIA GPUs of compute capability sm_20 or higher through the ScatterAlloc algorithm. mallocMC is header-only, but requires a few other C++ libraries to be available.

man-db

Homepage:
Spack package:
Versions:
2.7.6.1
Build Dependencies:
autoconf, automake, gettext, libpipeline, flex, gdbm, groff, bzip2, xz
Link Dependencies:
autoconf, automake, gettext, libpipeline, flex, gdbm, groff, bzip2, xz
Run Dependencies:
groff, bzip2, xz
Description:
man-db is an implementation of the standard Unix documentation system accessed using the man command. It uses a Berkeley DB database in place of the traditional flat-text whatis databases.

manta

Homepage:
Spack package:
Versions:
1.6.0, 1.5.0, 1.4.0, 1.3.2, 1.3.1, 1.3.0
Build Dependencies:
cmake, boost, python, zlib
Link Dependencies:
zlib
Run Dependencies:
python
Description:
Structural variant and indel caller for mapped sequencing data

mapnik

Homepage:
Spack package:
Versions:
3.0.22
Build Dependencies:
python, boost, icu4c, zlib, freetype, libxml2, harfbuzz, libpng, libjpeg, libtiff, proj, cairo, postgresql, gdal, sqlite, libwebp
Link Dependencies:
boost, icu4c, zlib, freetype, libxml2, harfbuzz, libpng, libjpeg, libtiff, proj, cairo, postgresql, gdal, sqlite, libwebp
Run Dependencies:
python, postgresql, gdal, sqlite
Description:
mapnik combines pixel-perfect image output with lightning-fast cartographic algorithms, and exposes interfaces in C++, Python, and Node

mapserver

Homepage:
Spack package:
Versions:
7.2.1
Build Dependencies:
cmake, libpng, freetype, jpeg, zlib, proj, curl, geos, libxml2, gdal, swig, python, ruby, java, perl
Link Dependencies:
libpng, freetype, jpeg, zlib, proj, curl, geos, libxml2, gdal, python, ruby, java, perl
Description:
MapServer is an Open Source geographic data rendering engine written in C. Beyond browsing GIS data, MapServer allows you create "geographic image maps", that is, maps that can direct users to content

maq

Homepage:
Spack package:
Versions:
0.7.1, 0.5.0
Description:
Maq is a software that builds mapping assemblies from short reads generated by the next-generation sequencing machines.

margo

Homepage:
Spack package:
Versions:
develop, 0.4.3
Build Dependencies:
autoconf, automake, libtool, m4, pkgconfig, mercury, argobots
Link Dependencies:
mercury, argobots
Description:
Argobots bindings to the Mercury RPC API

mariadb

Homepage:
Spack package:
Versions:
10.4.8, 10.4.7, 10.2.8, 10.1.23, 10.1.14, 5.5.56, 5.5.49
Build Dependencies:
cmake, boost, pkgconfig, bison, jemalloc, libaio, libedit, libevent, ncurses, zlib, curl, libxml2, lz4, libzmq, msgpack-c, openssl
Link Dependencies:
boost, jemalloc, libaio, libedit, libevent, ncurses, zlib, curl, libxml2, lz4, libzmq, msgpack-c, openssl
Description:
MariaDB Server is one of the most popular database servers in the world. MariaDB turns data into structured information in a wide array of applications, ranging from banking to websites. It is an enhanced, drop- in replacement for MySQL. MariaDB is used because it is fast, scalable and robust, with a rich ecosystem of storage engines, plugins and many other tools make it very versatile for a wide variety of use cases.

mariadb-c-client

Homepage:
Spack package:
Versions:
3.1.6, 3.1.5, 3.1.4, 3.0.9, 3.0.8, 3.0.7, 3.0.6, 3.0.5, 3.0.4, 3.0.3, 3.0.2, 2.3.7, 2.3.6, 2.3.5, 2.3.4, 2.3.3, 2.3.2, 2.3.1, 2.3.0, 2.2.3, 2.2.2, 2.2.1, 2.2.0, 2.1.0
Build Dependencies:
cmake, curl, pcre, openssl, zlib
Link Dependencies:
curl, pcre, openssl, zlib
Description:
MariaDB turns data into structured information in a wide array of applications, ranging from banking to websites. It is an enhanced, drop- in replacement for MySQL. MariaDB is used because it is fast, scalable and robust, with a rich ecosystem of storage engines, plugins and many other tools make it very versatile for a wide variety of use cases. This package comprises only the standalone 'C Connector', which enables connections to MariaDB and MySQL servers.

masa

Homepage:
Spack package:
Versions:
master
Build Dependencies:
autoconf, automake, libtool, swig, python, metaphysicl
Link Dependencies:
python, metaphysicl
Description:
MASA (Manufactured Analytical Solution Abstraction) is a library written in C++ (with C, python and Fortran90 interfaces) which provides a suite of manufactured solutions for the software verification of partial differential equation solvers in multiple dimensions.

masurca

Homepage:
Spack package:
Versions:
3.3.1, 3.2.9
Build Dependencies:
perl, boost, zlib
Link Dependencies:
boost, zlib
Run Dependencies:
perl
Description:
MaSuRCA is whole genome assembly software. It combines the efficiency of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches.

mathematica

Homepage:
Spack package:
Versions:
12.0.0
Description:
Mathematica: high-powered computation with thousands of Wolfram Language functions, natural language input, real-world data, mobile support. Note: A manual download is required for Mathematica. Spack will search your current directory for the download file. Alternatively, add this file to a mirror so that Spack can find it. For instructions on how to set up a mirror, see http://spack.readthedocs.io/en/latest/mirrors.html

matio

Homepage:
Spack package:
Versions:
1.5.13, 1.5.12, 1.5.11, 1.5.10, 1.5.9, 1.5.8, 1.5.7, 1.5.6, 1.5.5, 1.5.4, 1.5.3, 1.5.2
Build Dependencies:
zlib, hdf5
Link Dependencies:
zlib, hdf5
Description:
matio is an C library for reading and writing Matlab MAT files

matlab

Homepage:
Spack package:
Versions:
R2018b, R2016b
Description:
MATLAB (MATrix LABoratory) is a multi-paradigm numerical computing environment and fourth-generation programming language. A proprietary programming language developed by MathWorks, MATLAB allows matrix manipulations, plotting of functions and data, implementation of algorithms, creation of user interfaces, and interfacing with programs written in other languages, including C, C++, C#, Java, Fortran and Python. Note: MATLAB is licensed software. You will need to create an account on the MathWorks homepage and download MATLAB yourself. Spack will search your current directory for the download file. Alternatively, add this file to a mirror so that Spack can find it. For instructions on how to set up a mirror, see http://spack.readthedocs.io/en/latest/mirrors.html

maven

Homepage:
Spack package:
Versions:
3.6.3, 3.6.2, 3.6.1, 3.6.0, 3.5.0, 3.3.9
Build Dependencies:
java
Link Dependencies:
java
Description:
Apache Maven is a software project management and comprehension tool.

maverick

Homepage:
Spack package:
Versions:
1.0.4
Description:
MavericK is a program for inferring population structure on the basis of genetic information.

mawk

Homepage:
Spack package:
Versions:
1.3.4-20171017, 1.3.4
Description:
mawk is an interpreter for the AWK Programming Language.

mbdyn

Homepage:
Spack package:
Versions:
1.7.3
Description:
MBDyn is the first and possibly the only free general purpose multibody dynamics analysis software.

mbedtls

Homepage:
Spack package:
Versions:
2.16.1, 2.7.10, 2.3.0, 2.2.1, 2.2.0, 2.1.4, 2.1.3, 1.3.16
Build Dependencies:
cmake, perl
Description:
mbed TLS (formerly known as PolarSSL) makes it trivially easy for developers to include cryptographic and SSL/TLS capabilities in their (embedded) products, facilitating this functionality with a minimal coding footprint.

mc

Homepage:
Spack package:
Versions:
4.8.23, 4.8.21, 4.8.20
Build Dependencies:
ncurses, pkgconfig, glib, libssh2
Link Dependencies:
ncurses, glib, libssh2
Description:
The GNU Midnight Commander is a visual file manager.

mcl

Homepage:
Spack package:
Versions:
14-137
Description:
The MCL algorithm is short for the Markov Cluster Algorithm, a fast and scalable unsupervised cluster algorithm for graphs (also known as networks) based on simulation of (stochastic) flow in graphs.

mdtest

Homepage:
Spack package:
Versions:
1.9.3
Build Dependencies:
mpi
Link Dependencies:
mpi
Description:
mdtest is an MPI-coordinated metadata benchmark test that performs open/stat/close operations on files and directories and then reports the performance.

med

Homepage:
Spack package:
Versions:
3.2.0
Build Dependencies:
cmake, mpi, hdf5
Link Dependencies:
mpi, hdf5
Description:
The MED file format is a specialization of the HDF5 standard.

meep

Homepage:
Spack package:
Versions:
1.3, 1.2.1, 1.1.1
Build Dependencies:
blas, lapack, harminv, guile, libctl, mpi, hdf5, gsl
Link Dependencies:
blas, lapack, harminv, guile, libctl, mpi, hdf5, gsl
Description:
Meep (or MEEP) is a free finite-difference time-domain (FDTD) simulation software package developed at MIT to model electromagnetic systems.

mefit

Homepage:
Spack package:
Versions:
1.0
Build Dependencies:
py-numpy, py-htseq, jellyfish, casper
Link Dependencies:
py-numpy, py-htseq, jellyfish, casper
Description:
This pipeline will merge overlapping paired-end reads, calculate merge statistics, and filter reads for quality.

megadock

Homepage:
Spack package:
Versions:
4.0.3
Build Dependencies:
cuda, fftw, mpi
Link Dependencies:
cuda, fftw, mpi
Description:
an ultra-high-performance protein-protein docking for heterogeneous supercomputers

megahit

Homepage:
Spack package:
Versions:
1.1.4, 1.1.3
Build Dependencies:
zlib
Link Dependencies:
zlib
Description:
MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

memaxes

Homepage:
Spack package:
Versions:
0.5
Build Dependencies:
cmake, qt
Link Dependencies:
qt
Description:
MemAxes is a visualizer for sampled memory trace data.

memcached

Homepage:
Spack package:
Versions:
1.5.20, 1.5.19, 1.5.18, 1.5.17, 1.5.16, 1.5.15, 1.5.14, 1.5.13
Build Dependencies:
autoconf, automake, libtool, m4, libevent
Description:
Memcached is a high performance multithreaded event-based key/value cache store intended to be used in a distributed system.

meme

Homepage:
Spack package:
Versions:
4.12.0, 4.11.4
Build Dependencies:
perl, python, mpi, imagemagick, perl-xml-parser
Link Dependencies:
zlib, libgcrypt, mpi
Run Dependencies:
perl, python, imagemagick, perl-xml-parser
Description:
The MEME Suite allows the biologist to discover novel motifs in collections of unaligned nucleotide or protein sequences, and to perform a wide variety of other motif-based analyses.

memkind

Homepage:
Spack package:
Versions:
1.7.0
Build Dependencies:
autoconf, automake, libtool, m4, numactl
Link Dependencies:
numactl
Description:
The memkind library is a user extensible heap manager built on top of jemalloc which enables control of memory characteristics and a partitioning of the heap between kinds of memory. The kinds of memory are defined by operating system memory policies that have been applied to virtual address ranges. Memory characteristics supported by memkind without user extension include control of NUMA and page size features. The jemalloc non-standard interface has been extended to enable specialized arenas to make requests for virtual memory from the operating system through the memkind partition interface. Through the other memkind interfaces the user can control and extend memory partition features and allocate memory while selecting enabled features.

memsurfer

Homepage:
Spack package:
Versions:
master, 1.0
Build Dependencies:
python, cmake, swig, py-cython, py-numpy, py-pip, eigen, cgal, vtk, hdf5
Link Dependencies:
python, cmake, swig, py-cython, py-numpy, py-pip, eigen, cgal, vtk, hdf5
Run Dependencies:
python
Description:
MemSurfer is a tool to compute and analyze membrane surfaces found in a wide variety of large-scale molecular simulations.

meraculous

Homepage:
Spack package:
Versions:
2.2.5.1, 2.2.4
Build Dependencies:
cmake, perl, boost, gnuplot, perl-log-log4perl
Link Dependencies:
boost, gnuplot
Run Dependencies:
perl, perl-log-log4perl
Description:
Meraculous is a while genome assembler for Next Generation Sequencing data geared for large genomes.

mercurial

Homepage:
Spack package:
Versions:
5.3, 5.1.2, 5.1.1, 4.9.1, 4.4.1, 4.1.2, 3.9.1, 3.9, 3.8.4, 3.8.3, 3.8.2, 3.8.1
Build Dependencies:
python, py-setuptools, py-docutils, py-pygments, py-certifi
Link Dependencies:
python
Run Dependencies:
python, py-pygments, py-certifi
Description:
Mercurial is a free, distributed source control management tool.

mercury

Homepage:
Spack package:
Versions:
master, 1.0.1, 1.0.0, 0.9.0
Build Dependencies:
cmake, bmi, mpi, libfabric, openpa, boost
Link Dependencies:
bmi, mpi, libfabric, openpa, boost
Description:
Mercury is a C library for implementing RPC, optimized for HPC

mesa

Homepage:
Spack package:
Versions:
18.3.6
Build Dependencies:
autoconf, automake, libtool, m4, pkgconfig, binutils, bison, flex, gettext, python, py-mako, libxml2, zlib, expat, llvm, libx11, libxcb, libxext, glproto
Link Dependencies:
libxml2, zlib, expat, llvm, libx11, libxcb, libxext
Description:
Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics.

mesa-glu

Homepage:
Spack package:
Versions:
9.0.0
Build Dependencies:
gl
Link Dependencies:
gl
Description:
This package provides the Mesa OpenGL Utility library.

meshkit

Homepage:
Spack package:
Versions:
1.5.0
Build Dependencies:
mpi, netgen, cgm, moab
Link Dependencies:
mpi, netgen, cgm, moab
Description:
MeshKit is an open-source library of mesh generation functionality. Its design philosophy is two-fold: it provides a collection of meshing algorithms for use in real meshing problems, along with other tools commonly needed to support mesh generation

meson

Homepage:
Spack package:
Versions:
0.49.1, 0.49.0, 0.42.0, 0.41.2, 0.41.1
Build Dependencies:
python, py-setuptools, ninja
Link Dependencies:
python
Run Dependencies:
python, ninja
Description:
Meson is a portable open source build system meant to be both extremely fast, and as user friendly as possible.

mesquite

Homepage:
Spack package:
Versions:
2.99, 2.3.0, 2.2.0
Build Dependencies:
mpi
Link Dependencies:
mpi
Description:
Mesquite (Mesh Quality Improvement Toolkit) is designed to provide a stand-alone, portable, comprehensive suite of mesh quality improvement algorithms and components that can be used to construct custom quality improvement algorithms. Mesquite provides a robust and effective mesh improvement toolkit that allows both meshing researchers application scientists to benefit from the latest developments in mesh quality control and improvement.

metabat

Homepage:
Spack package:
Versions:
2.14, 2.13, 2.12.1, 2.11.2
Build Dependencies:
scons, boost
Link Dependencies:
zlib, ncurses
Run Dependencies:
boost, perl
Description:
MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities.

metall

Homepage:
Spack package:
Versions:
develop
Build Dependencies:
cmake, boost
Link Dependencies:
boost
Description:
An allocator for persistent memory

metaphysicl

Homepage:
Spack package:
Versions:
0.5.0, 0.3.3, 0.2.0
Build Dependencies:
autoconf, automake, libtool
Description:
Metaprogramming and operator-overloaded classes for numerical simulations.

metis

Homepage:
Spack package:
Versions:
5.1.0
Build Dependencies:
cmake
Description:
METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes.

mfem

Homepage:
Spack package:
Versions:
develop, 4.0.1-xsdk, 4.0.0, 3.4.1-laghos-v2.0, 3.4.0, 3.3.2, 3.3.1-laghos-v1.0, 3.3, 3.2, 3.1
Build Dependencies:
mpi, hypre, metis, blas, lapack, sundials, pumi, suite-sparse, superlu-dist, petsc, mpfr, netcdf-c, unwind, zlib, gnutls, conduit, occa, raja
Link Dependencies:
mpi, hypre, metis, blas, lapack, sundials, pumi, suite-sparse, superlu-dist, petsc, mpfr, netcdf-c, unwind, zlib, gnutls, conduit, occa, raja
Description:
Free, lightweight, scalable C++ library for finite element methods.

mg

Homepage:
Spack package:
Versions:
6.6
Build Dependencies:
ncurses
Link Dependencies:
ncurses
Description:
Mg is intended to be a small, fast, and portable editor for people who can't (or don't want to) run emacs for one reason or another, or are not familiar with the vi editor. It is compatible with emacs because there shouldn't be any reason to learn more editor types than emacs or vi.

mgis

Homepage:
Spack package:
Versions:
master, 1.1, 1.0.1, 1.0, rliv-1.1, rliv-1.0
Build Dependencies:
cmake, tfel, boost, python
Link Dependencies:
tfel, boost, python
Description:
The MFrontGenericInterfaceSupport project (MGIS) provides helper functions for various solvers to interact with behaviour written using MFront generic interface. MGIS is written in C++. Bindings are provided for C and fortran (2003). A FEniCS binding is also available.

microbiomeutil

Homepage:
Spack package:
Versions:
20110519
Build Dependencies:
perl, blast-plus, cdbfasta
Link Dependencies:
blast-plus, cdbfasta
Run Dependencies:
perl
Description:
Microbiome analysis utilities

migrate

Homepage:
Spack package:
Versions:
3.6.11
Build Dependencies:
autoconf, automake, libtool, m4, openmpi
Link Dependencies:
zlib, openmpi
Run Dependencies:
openmpi
Description:
Migrate estimates effective population sizes and past migration rates between n population assuming a migration matrix model with asymmetric migration rates and different subpopulation sizes

mii

Homepage:
Spack package:
Versions:
1.0.3, 1.0.2
Description:
Mii is an inverted indexing system for environment modules. After installation you will no longer need to load modules to run applications. NOTE: Additional steps are required after installing the Spack package to enable Mii in your shell. Please see the README on the homepage for more information.

minced

Homepage:
Spack package:
Versions:
0.3.2, 0.2.0, 0.1.6
Build Dependencies:
java
Run Dependencies:
java
Description:
MinCED is a program to find Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) in full genomes or environmental datasets such as metagenomes, in which sequence size can be anywhere from 100 to 800 bp.

mindthegap

Homepage:
Spack package:
Versions:
2.0.2
Build Dependencies:
cmake, zlib
Link Dependencies:
zlib
Description:
MindTheGap is a software that performs integrated detection and assembly of genomic insertion variants in NGS read datasets with respect to a reference genome.

miniaero

Homepage:
Spack package:
Versions:
2016-11-11
Build Dependencies:
kokkos
Link Dependencies:
kokkos
Description:
Proxy Application. MiniAero is a mini-application for the evaulation of programming models and hardware for next generation platforms.

miniamr

Homepage:
Spack package:
Versions:
develop, 1.4.4, 1.4.3, 1.4.2, 1.4.1, 1.4.0
Build Dependencies:
mpi
Link Dependencies:
mpi
Description:
Proxy Application. 3D stencil calculation with Adaptive Mesh Refinement (AMR)

miniasm

Homepage:
Spack package:
Versions:
2018-3-30
Build Dependencies:
zlib
Link Dependencies:
zlib
Description:
Miniasm is a very fast OLC-based de novo assembler for noisy long reads.

miniconda2

Homepage:
Spack package:
Versions:
4.7.12.1, 4.6.14, 4.5.11, 4.5.4, 4.3.30, 4.3.14, 4.3.11
Description:
The minimalist bootstrap toolset for conda and Python2.

miniconda3

Homepage:
Spack package:
Versions:
4.7.12.1, 4.6.14, 4.5.11, 4.5.4, 4.3.30, 4.3.14, 4.3.11
Description:
The minimalist bootstrap toolset for conda and Python3.

minife

Homepage:
Spack package:
Versions:
2.1.0
Build Dependencies:
mpi, qthreads
Link Dependencies:
mpi, qthreads
Description:
Proxy Application. MiniFE is an proxy application for unstructured implicit finite element codes.

minighost

Homepage:
Spack package:
Versions:
1.0.1
Build Dependencies:
mpi
Link Dependencies:
mpi
Description:
Proxy Application. A Finite Difference proxy application which implements a difference stencil across a homogenous three dimensional domain.

minigmg

Homepage:
Spack package:
Versions:
master
Build Dependencies:
mpi
Link Dependencies:
mpi
Description:
miniGMG is a compact benchmark for understanding the performance challenges associated with geometric multigrid solvers found in applications built from AMR MG frameworks like CHOMBO or BoxLib when running on modern multi- and manycore-based supercomputers. It includes both productive reference examples as well as highly-optimized implementations for CPUs and GPUs. It is sufficiently general that it has been used to evaluate a broad range of research topics including PGAS programming models and algorithmic tradeoffs inherit in multigrid. miniGMG was developed under the CACHE Joint Math-CS Institute. Note, miniGMG code has been supersceded by HPGMG.

minimap2

Homepage:
Spack package:
Versions:
2.14, 2.10, 2.2
Build Dependencies:
python, py-cython
Link Dependencies:
python, zlib
Run Dependencies:
python
Description:
Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database. Mappy provides a convenient interface to minimap2.

minimd

Homepage:
Spack package:
Versions:
1.2
Build Dependencies:
mpi
Link Dependencies:
mpi
Description:
Proxy Application. A simple proxy for the force computations in a typical molecular dynamics applications.

miniqmc

Homepage:
Spack package:
Versions:
0.4.0, 0.3.0, 0.2.0
Build Dependencies:
cmake, mpi, lapack
Link Dependencies:
mpi, lapack
Description:
A simplified real space QMC code for algorithm development, performance portability testing, and computer science experiments

minisign

Homepage:
Spack package:
Versions:
0.7
Build Dependencies:
cmake, libsodium
Link Dependencies:
libsodium
Description:
Minisign is a dead simple tool to sign files and verify signatures.

minismac2d

Homepage:
Spack package:
Versions:
2.0
Build Dependencies:
mpi
Link Dependencies:
mpi
Description:
Proxy Application. Solves the finite-differenced 2D incompressible Navier-Stokes equations with Spalart-Allmaras one-equation turbulence model on a structured body conforming grid.

minitri

Homepage:
Spack package:
Versions:
1.0
Build Dependencies:
mpi
Link Dependencies:
mpi
Description:
A simple, triangle-based data analytics proxy application.

minivite

Homepage:
Spack package:
Versions:
develop, 1.1, 1.0
Build Dependencies:
mpi
Link Dependencies:
mpi
Description:
miniVite is a proxy application that implements a single phase of Louvain method in distributed memory for graph community detection.

minixyce

Homepage:
Spack package:
Versions:
1.0
Build Dependencies:
mpi
Link Dependencies:
mpi
Description:
Proxy Application. A portable proxy of some of the key capabilities in the electrical modeling Xyce.

minizip

Homepage:
Spack package:
Versions:
1.2.11
Build Dependencies:
automake, autoconf, libtool, m4, zlib
Link Dependencies:
zlib
Description:
C library for zip/unzip via zLib.

minuit

Homepage:
Spack package:
Versions:
5.34.14, 5.28.00, 5.27.02, 5.24.00, 5.22.00, 5.21.06, 5.20.00, 5.18.00, 5.16.00, 5.14.00, 5.12.00, 5.10.00, 5.08.00, 1.7.9, 1.7.6, 1.7.1, 1.6.3, 1.6.0, 1.5.2, 1.5.0
Description:
MINUIT is a physics analysis tool for function minimization.

mira

Homepage:
Spack package:
Versions:
4.0.2
Build Dependencies:
boost, expat, gperftools
Link Dependencies:
boost, expat, gperftools
Description:
MIRA is a multi-pass DNA sequence data assembler/mapper for whole genome and EST/RNASeq projects.

miranda

Homepage:
Spack package:
Versions:
3.3a
Description:
miRanda is an algorithm for finding genomic targets for microRNAs.

mirdeep2

Homepage:
Spack package:
Versions:
0.0.8
Build Dependencies:
perl, perl-pdf-api2, bowtie, viennarna, squid, randfold
Link Dependencies:
bowtie, viennarna, squid, randfold
Run Dependencies:
perl, perl-pdf-api2
Description:
miRDeep2 is a completely overhauled tool which discovers microRNA genes by analyzing sequenced RNAs.

mitofates

Homepage:
Spack package:
Versions:
1.2
Build Dependencies:
libsvm
Link Dependencies:
libsvm
Run Dependencies:
perl, perl-inline-c, perl-perl6-slurp, perl-math-cephes
Description:
MitoFates predicts mitochondrial presequence, a cleavable localization signal located in N-terminal, and its cleaved position.

mitos

Homepage:
Spack package:
Versions:
0.9.2, 0.9.1
Build Dependencies:
cmake, dyninst, hwloc, mpi
Link Dependencies:
dyninst, hwloc, mpi
Description:
Mitos is a library and a tool for collecting sampled memory performance data to view with MemAxes

mixcr

Homepage:
Spack package:
Versions:
3.0.2
Build Dependencies:
java
Link Dependencies:
java
Description:
MiXCR is a universal framework that processes big immunome data from raw sequences to quantitated clonotypes. MiXCR efficiently handles paired- and single-end reads, considers sequence quality, corrects PCR errors and identifies germline hypermutations. The software supports both partial- and full-length profiling and employs all available RNA or DNA information, including sequences upstream of V and downstream of J gene segments.

mkfontdir

Homepage:
Spack package:
Versions:
1.0.7
Build Dependencies:
pkgconfig, util-macros
Run Dependencies:
mkfontscale
Description:
mkfontdir creates the fonts.dir files needed by the legacy X server core font system. The current implementation is a simple wrapper script around the mkfontscale program, which must be built and installed first.

mkfontscale

Homepage:
Spack package:
Versions:
1.1.2
Build Dependencies:
libfontenc, freetype, xproto, pkgconfig, util-macros
Link Dependencies:
libfontenc, freetype
Description:
mkfontscale creates the fonts.scale and fonts.dir index files used by the legacy X11 font system.

mlhka

Homepage:
Spack package:
Versions:
2.1
Description:
A maximum likelihood ratio test of natural selection, using polymorphism and divergence data.

mmg

Homepage:
Spack package:
Versions:
5.4.0, 5.3.13
Build Dependencies:
cmake, scotch, doxygen
Link Dependencies:
scotch, doxygen
Description:
Mmg is an open source software for simplicial remeshing. It provides 3 applications and 4 libraries: - the mmg2d application and the libmmg2d library: adaptation and optimization of a two-dimensional triangulation and generation of a triangulation from a set of points or from given boundary edges - the mmgs application and the libmmgs library: adaptation and optimization of a surface triangulation and isovalue discretization - the mmg3d application and the libmmg3d library: adaptation and optimization of a tetrahedral mesh and implicit domain meshing - the libmmg library gathering the libmmg2d, libmmgs and libmmg3d libraries.

moab

Homepage:
Spack package:
Versions:
develop, master, 5.0.2, 5.0.1, 5.0.0, 4.9.2, 4.9.1, 4.9.0, 4.8.2
Build Dependencies:
autoconf, automake, libtool, m4, blas, lapack, mpi, hdf5, netcdf-c, parallel-netcdf, cgm, metis, parmetis, zoltan
Link Dependencies:
blas, lapack, mpi, hdf5, netcdf-c, parallel-netcdf, cgm, metis, parmetis, zoltan
Description:
MOAB is a component for representing and evaluating mesh data. MOAB can store structured and unstructured mesh, consisting of elements in the finite element 'zoo.' The functional interface to MOAB is simple yet powerful, allowing the representation of many types of metadata commonly found on the mesh. MOAB is optimized for efficiency in space and time, based on access to mesh in chunks rather than through individual entities, while also versatile enough to support individual entity access.

modern-wheel

Homepage:
Spack package:
Versions:
1.2, 1.1, 1.0
Build Dependencies:
cmake, boost
Link Dependencies:
boost
Description:
C++ utility collection. Provides various facilities of common use in modern codebases like dynamic linking helpers, loadable plugins facilities and misc patterns.

mofem-cephas

Homepage:
Spack package:
Versions:
develop, 0.8.17, 0.8.16, 0.8.15, 0.8.14, 0.8.13, 0.8.12, 0.8.11, 0.8.10, 0.8.9, 0.8.8, 0.8.7
Build Dependencies:
cmake, mpi, boost, parmetis, hdf5, petsc, slepc, moab, adol-c, tetgen, med
Link Dependencies:
mpi, boost, parmetis, hdf5, petsc, slepc, moab, adol-c, tetgen, med
Description:
MoFEM is finite element core library

mofem-fracture-module

Homepage:
Spack package:
Versions:
develop, 0.9.50, 0.9.49, 0.9.48, 0.9.47, 0.9.46, 0.9.45, 0.9.44, 0.9.42
Build Dependencies:
cmake, mofem-cephas, mofem-users-modules
Link Dependencies:
mofem-cephas, mofem-users-modules
Run Dependencies:
mofem-users-modules
Description:
mofem fracture module

mofem-minimal-surface-equation

Homepage:
Spack package:
Versions:
develop, 0.3.10, 0.3.9
Build Dependencies:
cmake, mofem-cephas, mofem-users-modules
Link Dependencies:
mofem-cephas, mofem-users-modules
Run Dependencies:
mofem-users-modules
Description:
mofem minimal surface equation

mofem-users-modules

Homepage:
Spack package:
Versions:
develop, 0.8.17, 0.8.16, 0.8.15, 0.8.14, 0.8.12, 0.8.11, 0.8.10, 0.8.8, 0.8.7
Build Dependencies:
cmake, mofem-cephas
Link Dependencies:
mofem-cephas
Description:
MofemUsersModules creates installation environment for user-provided modules and extends of mofem-cephas package. For more information how to work with Spack and MoFEM see http://mofem.eng.gla.ac.uk/mofem/html/install_spack.html

molcas

Homepage:
Spack package:
Versions:
8.2
Build Dependencies:
cmake, openmpi, openblas, hdf5
Link Dependencies:
openmpi, openblas, hdf5
Description:
Molcas is an ab initio quantum chemistry software package developed by scientists to be used by scientists. Please set the path to licence file with the following command export MOLCAS_LICENSE=/path/to/molcas/license/

mongo-c-driver

Homepage:
Spack package:
Versions:
1.9.5, 1.9.4, 1.9.3, 1.9.1, 1.8.1, 1.8.0, 1.7.0, 1.6.3, 1.6.2, 1.6.1
Build Dependencies:
autoconf, automake, libtool, m4, pkgconfig, libbson, openssl, snappy, zlib
Link Dependencies:
libbson, openssl, snappy, zlib
Description:
libmongoc is a client library written in C for MongoDB.

mongo-cxx-driver

Homepage:
Spack package:
Versions:
3.2.0
Build Dependencies:
cmake, mongo-c-driver
Link Dependencies:
mongo-c-driver
Description:
C++ Driver for MongoDB

mono

Homepage:
Spack package:
Versions:
6.8.0.105, 5.18.0.240, 5.16.0.220, 5.14.0.177, 5.12.0.309, 5.10.1.57, 5.4.1.7, 5.4.0.167, 5.0.1.1, 4.8.0.524
Build Dependencies:
cmake, libiconv, perl
Link Dependencies:
libiconv
Description:
Mono is a software platform designed to allow developers to easily create cross platform applications. It is an open source implementation of Microsoft's .NET Framework based on the ECMA standards for C# and the Common Language Runtime.

montage

Homepage:
Spack package:
Versions:
6.0
Build Dependencies:
freetype, bzip2, libpng
Link Dependencies:
freetype, bzip2, libpng
Description:
Montage is a toolkit for assembling Flexible Image Transport System (FITS) images into custom mosaics.

moosefs

Homepage:
Spack package:
Versions:
3.0.109, 3.0.108, 3.0.107, 3.0.105, 3.0.104, 3.0.103
Description:
MooseFS is a Petabyte Open Source Network Distributed File System. It is easy to deploy and maintain, fault tolerant, highly performing, easily scalable, POSIX compliant.

moreutils

Homepage:
Spack package:
Versions:
0.63
Build Dependencies:
perl, docbook-xsl, libxml2
Description:
Additional Unix utilities. This is a growing collection of the Unix tools that nobody thought to write long ago, when Unix was young.

mosh

Homepage:
Spack package:
Versions:
1.3.2, 1.3.0, 1.2.6
Build Dependencies:
protobuf, ncurses, zlib, openssl, pkgconfig
Link Dependencies:
protobuf, ncurses, zlib, openssl
Run Dependencies:
perl
Description:
Remote terminal application that allows roaming, supports intermittent connectivity, and provides intelligent local echo and line editing of user keystrokes. Mosh is a replacement for SSH. It's more robust and responsive, especially over Wi-Fi, cellular, and long-distance links.

mothur

Homepage:
Spack package:
Versions:
1.43.0, 1.42.1, 1.40.5, 1.39.5
Build Dependencies:
boost, readline
Link Dependencies:
boost, readline
Run Dependencies:
vsearch
Description:
This project seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community.

motif

Homepage:
Spack package:
Versions:
2.3.8
Build Dependencies:
flex, libx11, libxt, libxext, libxft, libxcomposite, libxfixes, xbitmaps, jpeg, automake, autoconf, m4, libtool
Link Dependencies:
flex, libx11, libxt, libxext, libxft, libxcomposite, libxfixes, xbitmaps, jpeg
Description:
" Motif - Graphical user interface (GUI) specification and the widget toolkit

motioncor2

Homepage:
Spack package:
Versions:
1.1.0, 1.0.5, 1.0.4
Run Dependencies:
cuda, libtiff
Description:
MotionCor2 is a multi-GPU program that corrects beam-induced sample motion recorded on dose fractionated movie stacks. It implements a robust iterative alignment algorithm that delivers precise measurement and correction of both global and non-uniform local motions at single pixel level, suitable for both single-particle and tomographic images. MotionCor2 is sufficiently fast to keep up with automated data collection.

mount-point-attributes

Homepage:
Spack package:
Versions:
1.1
Build Dependencies:
autoconf, automake, libtool
Description:
Library to turn expensive, non-scalable file system calls into simple string comparison operations.

mozjs

Homepage:
Spack package:
Versions:
24.2.0, 17.0.0, 1.8.5
Build Dependencies:
perl, pkgconfig, python, nspr, libffi, readline, zlib
Link Dependencies:
nspr, libffi, readline, zlib
Description:
SpiderMonkey is Mozilla's JavaScript engine written in C/C++. It is used in various Mozilla products, including Firefox, and is available under the MPL2.

mpark-variant

Homepage:
Spack package:
Versions:
1.4.0, 1.3.0
Build Dependencies:
cmake
Description:
C++17 `std::variant` for C++11/14/17

mpc

Homepage:
Spack package:
Versions:
1.1.0, 1.0.3, 1.0.2
Build Dependencies:
gmp, mpfr
Link Dependencies:
gmp, mpfr
Description:
Gnu Mpc is a C library for the arithmetic of complex numbers with arbitrarily high precision and correct rounding of the result.

mpdecimal

Homepage:
Spack package:
Versions:
2.4.2
Build Dependencies:
gmake
Description:
mpdecimal is a package for correctly-rounded arbitrary precision decimal floating point arithmetic.

mpe2

Homepage:
Spack package:
Versions:
1.3.0
Build Dependencies:
mpi, libx11
Link Dependencies:
mpi, libx11
Description:
Message Passing Extensions (MPE): Parallel, shared X window graphics

mpest

Homepage:
Spack package:
Versions:
1.5
Description:
MP-EST estimates species trees from a set of gene trees by maximizing a pseudo-likelihood function.

mpfr

Homepage:
Spack package:
Versions:
4.0.2, 4.0.1, 4.0.0, 3.1.6, 3.1.5, 3.1.4, 3.1.3, 3.1.2
Build Dependencies:
gmp
Link Dependencies:
gmp
Description:
The MPFR library is a C library for multiple-precision floating-point computations with correct rounding.

mpi-bash

Homepage:
Spack package:
Versions:
1.2
Build Dependencies:
bash, mpi, libcircle
Link Dependencies:
bash, mpi, libcircle
Description:
Parallel scripting right from the Bourne-Again Shell (Bash)

mpich

Homepage:
Spack package:
Versions:
develop, 3.3.2, 3.3.1, 3.3, 3.2.1, 3.2, 3.1.4, 3.1.3, 3.1.2, 3.1.1, 3.1, 3.0.4
Build Dependencies:
findutils, pkgconfig, libfabric, ucx, libpciaccess, libxml2, slurm, pmix, automake, libtool, m4, autoconf
Link Dependencies:
libfabric, ucx, libpciaccess, libxml2, slurm, pmix
Description:
MPICH is a high performance and widely portable implementation of the Message Passing Interface (MPI) standard.

mpifileutils

Homepage:
Spack package:
Versions:
develop, 0.10, 0.9.1, 0.9
Build Dependencies:
mpi, libcircle, dtcmp, libarchive, cmake
Link Dependencies:
mpi, libcircle, dtcmp, libarchive
Description:
mpiFileUtils is a suite of MPI-based tools to manage large datasets, which may vary from large directory trees to large files. High- performance computing users often generate large datasets with parallel applications that run with many processes (millions in some cases). However those users are then stuck with single-process tools like cp and rm to manage their datasets. This suite provides MPI-based tools to handle typical jobs like copy, remove, and compare for such datasets, providing speedups of up to 20-30x.

mpilander

Homepage:
Spack package:
Versions:
develop
Build Dependencies:
cmake
Description:
There can only be one (MPI process)!

mpileaks

Homepage:
Spack package:
Versions:
1.0
Build Dependencies:
mpi, adept-utils, callpath
Link Dependencies:
mpi, adept-utils, callpath
Description:
Tool to detect and report MPI objects like MPI_Requests and MPI_Datatypes.

mpip

Homepage:
Spack package:
Versions:
master, 3.4.1
Build Dependencies:
elf, libdwarf, libunwind, mpi
Link Dependencies:
elf, libdwarf, libunwind, mpi
Description:
mpiP: Lightweight, Scalable MPI Profiling

mpir

Homepage:
Spack package:
Versions:
develop, 2.7.0, 2.6.0
Build Dependencies:
autoconf, yasm
Link Dependencies:
yasm
Description:
Multiple Precision Integers and Rationals.

mpix-launch-swift

Homepage:
Spack package:
Versions:
develop
Build Dependencies:
stc, tcl, mpi, swig
Link Dependencies:
stc, tcl, mpi
Description:
Library that allows a child MPI application to be launched inside a subset of processes in a parent MPI application.

mpt

Homepage:
Spack package:
Description:
HPE MPI is HPE's implementation of the Message Passing Interface (MPI) standard. Note: HPE MPI is proprietry software. Spack will search your current directory for the download file. Alternatively, add this file to a mirror so that Spack can find it. For instructions on how to set up a mirror, see http://spack.readthedocs.io/en/latest/mirrors.html

mrbayes

Homepage:
Spack package:
Versions:
3.2.7a, 3.2.7
Build Dependencies:
libbeagle, mpi, readline
Link Dependencies:
libbeagle, mpi, readline
Description:
MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. MrBayes uses Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution of model parameters.

mrnet

Homepage:
Spack package:
Versions:
5.0.1-3, 5.0.1-2, 5.0.1, 4.1.0, 4.0.0
Build Dependencies:
boost
Link Dependencies:
boost
Description:
The MRNet Multi-Cast Reduction Network.

mrtrix3

Homepage:
Spack package:
Versions:
2017-09-25
Build Dependencies:
python, py-numpy, glu, qt, eigen, zlib, libtiff, fftw
Link Dependencies:
glu, qt, eigen, zlib, libtiff, fftw
Run Dependencies:
python, py-numpy
Description:
MRtrix provides a set of tools to perform various advanced diffusion MRI analyses, including constrained spherical deconvolution (CSD), probabilistic tractography, track-density imaging, and apparent fibre density.

mscgen

Homepage:
Spack package:
Versions:
0.20
Build Dependencies:
flex, bison, pkgconfig, libgd
Link Dependencies:
flex, bison, pkgconfig, libgd
Description:
Mscgen is a small program that parses Message Sequence Chart descriptions and produces PNG, SVG, EPS or server side image maps (ismaps) as the output.

msgpack-c

Homepage:
Spack package:
Versions:
3.0.1, 1.4.1
Build Dependencies:
cmake
Test Dependencies:
googletest
Description:
A small, fast binary interchange format convertible to/from JSON

mshadow

Homepage:
Spack package:
Versions:
master, 20170721
Description:
MShadow is a lightweight CPU/GPU Matrix/Tensor C++ Template Library. in C++/CUDA.

msmc

Homepage:
Spack package:
Versions:
1.1.0
Build Dependencies:
gsl, dmd
Run Dependencies:
gsl
Description:
This software implements MSMC, a method to infer population size and gene flow from multiple genome sequences

mstk

Homepage:
Spack package:
Versions:
master, 3.3.2, 3.3.1, 3.3.0, 3.2.1, 3.2.0, 3.1.3, 3.1.2, 3.1.1, 3.1.0, 3.0.4, 3.0.3, 3.0.2, 3.0.1, 3.0.0
Build Dependencies:
cmake, mpi, zoltan, metis, exodusii
Link Dependencies:
mpi, zoltan, metis, exodusii
Test Dependencies:
unittest-cpp
Description:
MSTK is a mesh framework that allows users to represent, manipulate and query unstructured 3D arbitrary topology meshes in a general manner without the need to code their own data structures. MSTK is a flexible framework in that it allows a variety of underlying representations for the mesh while maintaining a common interface. It allows users to choose from different mesh representations either at initialization (implemented) or during the program execution (not yet implemented) so that the optimal data structures are used for the particular algorithm. The interaction of users and applications with MSTK is through a functional interface that acts as though the mesh always contains vertices, edges, faces and regions and maintains connectivity between all these entities.

multitail

Homepage:
Spack package:
Versions:
6.4.2
Build Dependencies:
ncurses
Link Dependencies:
ncurses
Description:
MultiTail allows you to monitor logfiles and command output in multiple windows in a terminal, colorize, filter and merge.

multitime

Homepage:
Spack package:
Versions:
1.4
Description:
multitime is, in essence, a simple extension to time which runs a command multiple times and prints the timing means, standard deviations, mins, medians, and maxes having done so. This can give a much better understanding of the command's performance.

multiverso

Homepage:
Spack package:
Versions:
master, 143187, 0.2
Build Dependencies:
cmake, mpi, boost
Link Dependencies:
mpi, boost
Description:
Multiverso is a parameter server based framework for training machine learning models on big data with numbers of machines.

mummer

Homepage:
Spack package:
Versions:
3.23
Build Dependencies:
gnuplot, perl
Link Dependencies:
gnuplot
Run Dependencies:
perl
Description:
MUMmer is a system for rapidly aligning entire genomes.

mumps

Homepage:
Spack package:
Versions:
5.2.0, 5.1.2, 5.1.1, 5.0.2, 5.0.1
Build Dependencies:
scotch, metis, parmetis, blas, lapack, scalapack, mpi
Link Dependencies:
scotch, metis, parmetis, blas, lapack, scalapack, mpi
Description:
MUMPS: a MUltifrontal Massively Parallel sparse direct Solver

munge

Homepage:
Spack package:
Versions:
0.5.13, 0.5.12, 0.5.11
Build Dependencies:
openssl, libgcrypt
Link Dependencies:
openssl, libgcrypt
Description:
MUNGE Uid 'N' Gid Emporium

muparser

Homepage:
Spack package:
Versions:
2.2.6.1, 2.2.5
Build Dependencies:
cmake
Description:
C++ math expression parser library.

muscle

Homepage:
Spack package:
Versions:
3.8.1551
Description:
MUSCLE is one of the best-performing multiple alignment programs according to published benchmark tests, with accuracy and speed that are consistently better than CLUSTALW.

muse

Homepage:
Spack package:
Versions:
1.0-rc
Link Dependencies:
zlib
Description:
Somatic point mutation caller.

musl

Homepage:
Spack package:
Versions:
1.1.23, 1.1.22, 1.1.21, 1.1.20
Description:
Musl is a libc, an implementation of the standard library functionality described in the ISO C and POSIX standards, plus common extensions, intended for use on Linux-based systems. Whereas the kernel (Linux) governs access to hardware, memory, filesystems, and the privileges for accessing these resources, the C library is responsible for providing the actual C function interfaces userspace applications see, and for constructing higher-level buffered stdio, memory allocation management, thread creation and synchronization operations, and so on using the lower-level interfaces the kernel provides, as well as for implementing pure library routines of the C language like strstr, snprintf, strtol, exp, sqrt, etc. Musl is a new general-purpose implementation of the C library. It is lightweight, fast, simple, free, and aims to be correct in the sense of standards-conformance and safety.

muster

Homepage:
Spack package:
Versions:
1.0.1, 1.0
Build Dependencies:
cmake, boost, mpi
Link Dependencies:
boost, mpi
Description:
The Muster library provides implementations of sequential and parallel K-Medoids clustering algorithms. It is intended as a general framework for parallel cluster analysis, particularly for performance data analysis on systems with very large numbers of processes.

mutationpp

Homepage:
Spack package:
Versions:
1.0.0, 0.3.1
Build Dependencies:
cmake
Description:
Mutation++ is an open-source library originally developed at the von Karman Institute for Fluid Dynamics, designed to couple with conventional computational fluid dynamics codes to provide thermodynamic, transport, chemistry, and energy transfer properties associated with subsonic to hypersonic flows.

mvapich2

Homepage:
Spack package:
Versions:
2.3.2, 2.3.1, 2.3rc2, 2.3rc1, 2.3a, 2.3, 2.2, 2.1
Build Dependencies:
findutils, bison, pkgconfig, zlib, libpciaccess, libxml2, cuda, psm, opa-psm2, rdma-core, libfabric, slurm
Link Dependencies:
zlib, libpciaccess, libxml2, cuda, psm, opa-psm2, rdma-core, libfabric, slurm
Description:
MVAPICH2 is an MPI implementation for Infiniband networks.

mxml

Homepage:
Spack package:
Versions:
2.10, 2.9, 2.8
Description:
Mini-XML is a small XML library that you can use to read and write XML and XML-like data files in your application without requiring large non- standard libraries.

mxnet

Homepage:
Spack package:
Versions:
1.3.0
Build Dependencies:
dmlc-core, mshadow, ps-lite, nnvm, blas, cudnn, cub, opencv, python, py-setuptools
Link Dependencies:
dmlc-core, mshadow, ps-lite, nnvm, blas, cudnn, cub, opencv, python
Run Dependencies:
python
Description:
MXNet is a deep learning framework designed for both efficiency and flexibility.

mysql

Homepage:
Spack package:
Versions:
8.0.19, 8.0.18, 8.0.17, 8.0.16, 8.0.15, 8.0.14, 8.0.13, 8.0.12, 8.0.11, 5.7.26, 5.7.25, 5.7.24, 5.7.23, 5.7.22, 5.7.21, 5.7.20, 5.7.19, 5.7.18, 5.7.17, 5.7.16, 5.7.15, 5.7.14, 5.7.13, 5.7.12, 5.7.11, 5.7.10, 5.7.9, 5.6.44, 5.6.43, 5.5.62
Build Dependencies:
cmake, gmake, pkgconfig, doxygen, boost, ncurses, openssl, libtirpc, perl, bison, m4
Link Dependencies:
boost, ncurses, openssl, libtirpc
Test Dependencies:
perl
Description:
MySQL is an open source relational database management system.

nag

Homepage:
Spack package:
Versions:
7.0, 6.2, 6.1
Description:
The NAG Fortran Compiler.

nalu

Homepage:
Spack package:
Versions:
master
Build Dependencies:
cmake, mpi, yaml-cpp, trilinos, tioga
Link Dependencies:
mpi, yaml-cpp, trilinos, tioga
Description:
Nalu: a generalized unstructured massively parallel low Mach flow code designed to support a variety of energy applications of interest built on the Sierra Toolkit and Trilinos solver Tpetra/Epetra stack

nalu-wind

Homepage:
Spack package:
Versions:
master
Build Dependencies:
cmake, mpi, yaml-cpp, trilinos, openfast, tioga, hypre, trilinos-catalyst-ioss-adapter, fftw
Link Dependencies:
mpi, yaml-cpp, trilinos, openfast, tioga, hypre, trilinos-catalyst-ioss-adapter, fftw
Description:
Nalu-Wind: Wind energy focused variant of Nalu.

namd

Homepage:
Spack package:
Versions:
2.13, 2.12
Build Dependencies:
charmpp, fftw, intel-mkl, tcl, python
Link Dependencies:
charmpp, fftw, intel-mkl, tcl, python
Description:
NAMDis a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.

nano

Homepage:
Spack package:
Versions:
4.4, 4.3, 4.2, 4.1, 4.0, 3.2, 3.1, 3.0, 2.9.8, 2.9.7, 2.9.6, 2.9.5, 2.9.4, 2.9.3, 2.9.2, 2.9.1, 2.9.0, 2.8.7, 2.8.6, 2.8.5, 2.8.4, 2.8.3, 2.8.2, 2.8.1, 2.8.0, 2.7.5, 2.7.4, 2.7.3, 2.7.2, 2.7.1, 2.7.0, 2.6.3, 2.6.2, 2.6.1
Build Dependencies:
ncurses
Link Dependencies:
ncurses
Description:
Tiny little text editor

nanoflann

Homepage:
Spack package:
Versions:
1.2.3
Build Dependencies:
cmake
Description:
a C++ header-only library for Nearest Neighbor (NN) search wih KD-trees.

nanopb

Homepage:
Spack package:
Versions:
0.3.9.1
Build Dependencies:
cmake, protobuf, py-protobuf
Description:
Nanopb is a small code-size Protocol Buffers implementation in ansi C.

nasm

Homepage:
Spack package:
Versions:
2.14.02, 2.13.03, 2.11.06
Description:
NASM (Netwide Assembler) is an 80x86 assembler designed for portability and modularity. It includes a disassembler as well.

nauty

Homepage:
Spack package:
Versions:
2.6r7
Build Dependencies:
m4, autoconf, automake, libtool, pkgconfig, help2man, zlib, gmp
Link Dependencies:
zlib, gmp
Description:
nauty and Traces are programs for computing automorphism groups of graphsq and digraphs

ncbi-magicblast

Homepage:
Spack package:
Versions:
1.3.0
Build Dependencies:
lmdb
Link Dependencies:
lmdb
Description:
Magic-BLAST is a tool for mapping large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome.

ncbi-rmblastn

Homepage:
Spack package:
Versions:
2.9.0
Description:
RMBlast search engine for NCBI

ncbi-toolkit

Homepage:
Spack package:
Versions:
22_0_0, 21_0_0
Build Dependencies:
boost, bzip2, jpeg, libpng, libtiff, libxml2, libxslt, lzo, pcre, giflib, sqlite, zlib, samtools, bamtools
Link Dependencies:
boost, bzip2, jpeg, libpng, libtiff, libxml2, libxslt, lzo, pcre, giflib, sqlite, zlib, samtools, bamtools
Description:
NCBI C++ Toolkit

nccl

Homepage:
Spack package:
Versions:
2.5.7-1, 2.5.6-2, 2.5.6-1, 2.4.8-1, 2.4.6-1, 2.4.2-1, 2.3.7-1, 2.3.5-5, 1.3.4-1, 1.3.0-1
Build Dependencies:
cuda
Link Dependencies:
cuda
Description:
Optimized primitives for collective multi-GPU communication.

nccmp

Homepage:
Spack package:
Versions:
1.8.2.0
Build Dependencies:
netcdf-c
Link Dependencies:
netcdf-c
Description:
Compare NetCDF Files

ncdu

Homepage:
Spack package:
Versions:
1.13, 1.12, 1.11, 1.10, 1.9, 1.8, 1.7
Build Dependencies:
ncurses
Link Dependencies:
ncurses
Description:
Ncdu is a disk usage analyzer with an ncurses interface. It is designed to find space hogs on a remote server where you don't have an entire gaphical setup available, but it is a useful tool even on regular desktop systems. Ncdu aims to be fast, simple and easy to use, and should be able to run in any minimal POSIX-like environment with ncurses installed.

ncftp

Homepage:
Spack package:
Versions:
3.2.6
Build Dependencies:
ncurses
Link Dependencies:
ncurses
Description:
NcFTP Client is a set of application programs implementing the File Transfer Protocol.

ncl

Homepage:
Spack package:
Versions:
6.6.2, 6.5.0, 6.4.0
Build Dependencies:
jpeg, netcdf-c, cairo, bison, flex, libiconv, tcsh, curl, libx11, libxaw, libxmu, pixman, bzip2, freetype, fontconfig, hdf5, szip, hdf, gdal, udunits
Link Dependencies:
jpeg, netcdf-c, cairo, flex, libiconv, tcsh, curl, libx11, libxaw, libxmu, pixman, bzip2, freetype, fontconfig, hdf5, szip, hdf, gdal, udunits
Run Dependencies:
esmf
Description:
NCL is an interpreted language designed specifically for scientific data analysis and visualization. Supports NetCDF 3/4, GRIB 1/2, HDF 4/5, HDF- EOD 2/5, shapefile, ASCII, binary. Numerous analysis functions are built-in.

nco

Homepage:
Spack package:
Versions:
4.7.9, 4.6.7, 4.6.6, 4.6.5, 4.6.4, 4.6.3, 4.6.2, 4.6.1, 4.5.5
Build Dependencies:
netcdf-c, antlr, gsl, udunits, flex, bison, texinfo
Link Dependencies:
netcdf-c, antlr, gsl, udunits
Description:
The NCO toolkit manipulates and analyzes data stored in netCDF- accessible formats

ncurses

Homepage:
Spack package:
Versions:
6.1, 6.0, 5.9
Build Dependencies:
pkgconfig
Description:
The ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, and more. It uses terminfo format, supports pads and color and multiple highlights and forms characters and function-key mapping, and has all the other SYSV-curses enhancements over BSD curses.

ncview

Homepage:
Spack package:
Versions:
2.1.7
Build Dependencies:
netcdf-c, udunits, libpng, libxaw
Link Dependencies:
netcdf-c, udunits, libpng, libxaw
Description:
Simple viewer for NetCDF files.

ndiff

Homepage:
Spack package:
Versions:
2.00, 1.00
Description:
The ndiff tool is a binary utility that compares putatively similar files while ignoring small numeric differernces. This utility is most often used to compare files containing a lot of floating-point numeric data that may be slightly different due to numeric error.

nek5000

Homepage:
Spack package:
Versions:
develop, 17.0
Build Dependencies:
mpi
Link Dependencies:
mpi
Description:
A fast and scalable high-order solver for computational fluid dynamics

nekbone

Homepage:
Spack package:
Versions:
develop, 17.0
Build Dependencies:
mpi
Link Dependencies:
mpi
Description:
NEK5000 emulation software called NEKbone. Nekbone captures the basic structure and user interface of the extensive Nek5000 software. Nek5000 is a high order, incompressible Navier-Stokes solver based on the spectral element method.

nekcem

Homepage:
Spack package:
Versions:
develop, 7332619, 0b8bedd
Build Dependencies:
mpi, blas, lapack, python
Link Dependencies:
mpi, blas, lapack
Description:
Spectral-element solver for Maxwell's equations, drift-diffusion equations, and more.

nektar

Homepage:
Spack package:
Versions:
5.0.0, 4.4.1
Build Dependencies:
cmake, blas, lapack, boost, tinyxml, mpi, fftw, arpack-ng, hdf5, scotch
Link Dependencies:
blas, lapack, boost, tinyxml, mpi, fftw, arpack-ng, hdf5, scotch
Description:
Nektar++: Spectral/hp Element Framework

nektools

Homepage:
Spack package:
Versions:
develop, 17.0
Build Dependencies:
libx11, libxt, xproto, visit
Link Dependencies:
libx11, libxt, xproto, visit
Description:
Tools reuqired by Nek5000

neovim

Homepage:
Spack package:
Versions:
0.3.4, 0.3.1, 0.3.0, 0.2.2, 0.2.1, 0.2.0
Build Dependencies:
cmake, lua, lua-lpeg, lua-mpack, lua-bitlib, libuv, jemalloc, libtermkey, libvterm, unibilium, msgpack-c, gperf
Link Dependencies:
lua, lua-lpeg, lua-mpack, lua-bitlib, libuv, jemalloc, libtermkey, libvterm, unibilium, msgpack-c, gperf
Description:
NeoVim: the future of vim

nest

Homepage:
Spack package:
Versions:
2.14.0, 2.12.0, 2.10.0, 2.8.0, 2.6.0, 2.4.2
Build Dependencies:
cmake, python, py-numpy, py-cython, py-setuptools, mpi, doxygen, gsl, readline, libtool, pkgconfig
Link Dependencies:
python, mpi, gsl, readline, libtool
Run Dependencies:
python, py-numpy
Test Dependencies:
py-nose
Description:
NEST is a simulator for spiking neural network models It focuses on the dynamics, size and structure of neural systems rather than on the exact morphology of individual neurons.

netcdf-c

Homepage:
Spack package:
Versions:
master, 4.7.3, 4.7.2, 4.7.1, 4.7.0, 4.6.3, 4.6.2, 4.6.1, 4.6.0, 4.5.0, 4.4.1.1, 4.4.1, 4.4.0, 4.3.3.1, 4.3.3
Build Dependencies:
autoconf, automake, libtool, m4, hdf, curl, parallel-netcdf, mpi, zlib, hdf5
Link Dependencies:
hdf, curl, parallel-netcdf, mpi, zlib, hdf5
Description:
NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. This is the C distribution.

netcdf-cxx

Homepage:
Spack package:
Versions:
4.2
Build Dependencies:
netcdf-c
Link Dependencies:
netcdf-c
Description:
Deprecated C++ compatibility bindings for NetCDF. These do NOT read or write NetCDF-4 files, and are no longer maintained by Unidata. Developers should migrate to current NetCDF C++ bindings, in Spack package netcdf-cxx4.

netcdf-cxx4

Homepage:
Spack package:
Versions:
4.3.1, 4.3.0
Build Dependencies:
netcdf-c, automake, autoconf, libtool, m4
Link Dependencies:
netcdf-c
Description:
NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. This is the C++ distribution.

netcdf-fortran

Homepage:
Spack package:
Versions:
4.5.2, 4.4.5, 4.4.4, 4.4.3
Build Dependencies:
mpi, netcdf-c
Link Dependencies:
mpi, netcdf-c
Description:
NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. This is the Fortran distribution.

netgauge

Homepage:
Spack package:
Versions:
2.4.6
Build Dependencies:
mpi
Link Dependencies:
mpi
Description:
Netgauge is a high-precision network parameter measurement tool. It supports benchmarking of many different network protocols and communication patterns. The main focus lies on accuracy, statistical analysis and easy extensibility.

netgen

Homepage:
Spack package:
Versions:
5.3.1
Build Dependencies:
zlib, mpi, oce, metis
Link Dependencies:
zlib, mpi, oce, metis
Description:
NETGEN is an automatic 3d tetrahedral mesh generator. It accepts input from constructive solid geometry (CSG) or boundary representation (BRep) from STL file format. The connection to a geometry kernel allows the handling of IGES and STEP files. NETGEN contains modules for mesh optimization and hierarchical mesh refinement.

netlib-lapack

Homepage:
Spack package:
Versions:
3.8.0, 3.7.1, 3.7.0, 3.6.1, 3.6.0, 3.5.0, 3.4.2, 3.4.1, 3.4.0, 3.3.1
Build Dependencies:
cmake, blas, netlib-xblas
Link Dependencies:
blas, netlib-xblas
Test Dependencies:
python
Description:
LAPACK version 3.X is a comprehensive FORTRAN library that does linear algebra operations including matrix inversions, least squared solutions to linear sets of equations, eigenvector analysis, singular value decomposition, etc. It is a very comprehensive and reputable package that has found extensive use in the scientific community.

netlib-scalapack

Homepage:
Spack package:
Versions:
2.1.0, 2.0.2, 2.0.1, 2.0.0
Build Dependencies:
cmake, mpi, lapack, blas
Link Dependencies:
mpi, lapack, blas
Description:
ScaLAPACK is a library of high-performance linear algebra routines for parallel distributed memory machines

netlib-xblas

Homepage:
Spack package:
Versions:
1.0.248
Description:
XBLAS is a reference implementation for extra precision BLAS. XBLAS is a reference implementation for the dense and banded BLAS routines, along with extended and mixed precision version. Extended precision is only used internally; input and output arguments remain the same as in the existing BLAS. Extra precisions is implemented as double-double (i.e., 128-bit total, 106-bit significand). Mixed precision permits some input/output arguments of different types (mixing real and complex) or precisions (mixing single and double). This implementation is proof of concept, and no attempt was made to optimize performance; performance should be as good as straightforward but careful code written by hand.

netperf

Homepage:
Spack package:
Versions:
2.7.0, 2.6.0, 2.5.0
Description:
Netperf is a benchmark that can be used to measure the performance of many different types of networking. It provides tests for both unidirectional throughput, and end-to-end latency.

nettle

Homepage:
Spack package:
Versions:
3.4.1, 3.4, 3.3, 3.2, 2.7.1, 2.7
Build Dependencies:
gmp, m4
Link Dependencies:
gmp
Description:
The Nettle package contains the low-level cryptographic library that is designed to fit easily in many contexts.

neuron

Homepage:
Spack package:
Versions:
develop, 7.5, 7.4, 7.3, 7.2
Build Dependencies:
flex, bison, automake, autoconf, libtool, pkgconfig, mpi, python, ncurses
Link Dependencies:
mpi, python, ncurses
Description:
NEURON is a simulation environment for single and networks of neurons. NEURON is a simulation environment for modeling individual and networks of neurons. NEURON models individual neurons via the use of sections that are automatically subdivided into individual compartments, instead of requiring the user to manually create compartments. The primary scripting language is hoc but a Python interface is also available.

nextflow

Homepage:
Spack package:
Versions:
0.25.6, 0.24.1, 0.23.3, 0.21.0, 0.20.1, 0.17.3
Build Dependencies:
java
Link Dependencies:
java
Description:
Data-driven computational pipelines

nfft

Homepage:
Spack package:
Versions:
3.4.1, 3.3.2
Build Dependencies:
fftw
Link Dependencies:
fftw
Description:
NFFT is a C subroutine library for computing the nonequispaced discrete Fourier transform (NDFT) in one or more dimensions, of arbitrary input size, and of complex data.

nghttp2

Homepage:
Spack package:
Versions:
1.26.0
Build Dependencies:
python, py-cython, py-setuptools
Run Dependencies:
python, py-cython
Description:
nghttp2 is an implementation of HTTP/2 and its header compression algorithm HPACK in C.

nginx

Homepage:
Spack package:
Versions:
1.15.6, 1.13.8, 1.12.0
Build Dependencies:
openssl, pcre, zlib
Link Dependencies:
openssl, pcre, zlib
Description:
nginx [engine x] is an HTTP and reverse proxy server, a mail proxy server, and a generic TCP/UDP proxy server, originally written by Igor Sysoev.

ngmlr

Homepage:
Spack package:
Versions:
0.2.5
Build Dependencies:
cmake
Link Dependencies:
zlib
Description:
Ngmlr is a long-read mapper designed to align PacBilo or Oxford Nanopore to a reference genome with a focus on reads that span structural variations.

nicstat

Homepage:
Spack package:
Versions:
1.95
Description:
Nicstat is a Solaris and Linux command-line that prints out network statistics for all network interface cards (NICs), including packets, kilobytes per second, average packet sizes and more.

nim

Homepage:
Spack package:
Versions:
0.20.0, 0.19.9, 0.19.6
Build Dependencies:
pcre, openssl
Description:
Nim is a statically typed compiled systems programming language. It combines successful concepts from mature languages like Python, Ada and Modula.

ninja

Homepage:
Spack package:
Versions:
1.10.0, 1.9.0, 1.8.2, 1.7.2, 1.6.0, kitware
Build Dependencies:
python
Description:
Ninja is a small build system with a focus on speed. It differs from other build systems in two major respects: it is designed to have its input files generated by a higher-level build system, and it is designed to run builds as fast as possible.

ninja-fortran

Homepage:
Spack package:
Versions:
1.9.0.2.g99df1, 1.9.0.1.g5b44b, 1.9.0.0.gad558, 1.8.2.2.g81279, 1.8.2.1.g3bbbe, 1.8.2.0.g972a7, 1.7.2.1.gaad58, 1.7.2.0.gcc0ea, 1.7.1.0.g7ca7f
Build Dependencies:
python
Description:
A Fortran capable fork of ninja.

nix

Homepage:
Spack package:
Versions:
2.2.1, 2.1.3, 2.0.4
Build Dependencies:
autoconf, automake, bison, flex, libtool, libxslt, boost, brotli, editline, m4, bzip2, curl, libseccomp, openssl, sqlite, xz
Link Dependencies:
boost, brotli, editline, bzip2, curl, libseccomp, openssl, sqlite, xz
Description:
Nix, the purely functional package manager

nlohmann-json

Homepage:
Spack package:
Versions:
3.7.2, 3.7.0, 3.6.1, 3.5.0, 3.4.0, 3.3.0, 3.2.0, 3.1.2, 3.1.1
Build Dependencies:
cmake
Description:
JSON for Modern C++

nlopt

Homepage:
Spack package:
Versions:
master, 2.5.0
Build Dependencies:
cmake, python, py-numpy, swig, guile, octave, matlab
Link Dependencies:
python, swig, guile, octave, matlab
Run Dependencies:
python, py-numpy
Description:
NLopt is a free/open-source library for nonlinear optimization, providing a common interface for a number of different free optimization routines available online as well as original implementations of various other algorithms.

nmap

Homepage:
Spack package:
Versions:
7.70, 7.31, 7.30
Description:
Nmap ("Network Mapper") is a free and open source (license) utility for network discovery and security auditing. It also provides ncat an updated nc

nnvm

Homepage:
Spack package:
Versions:
master, 20170418
Build Dependencies:
cmake, dmlc-core
Link Dependencies:
dmlc-core
Description:
nnvm is a modular, decentralized and lightweight part to help build deep learning libraries.

node-js

Homepage:
Spack package:
Versions:
13.8.0, 13.5.0, 12.16.0, 12.14.0, 11.1.0, 10.13.0, 8.9.1, 7.1.0, 6.3.0, 6.2.2
Build Dependencies:
gmake, libtool, pkgconfig, python, icu4c, openssl, zlib
Link Dependencies:
icu4c, openssl, zlib
Description:
Node.js is a JavaScript runtime built on Chrome's V8 JavaScript engine.

notmuch

Homepage:
Spack package:
Versions:
0.23.7
Build Dependencies:
zlib, talloc, gmime, xapian-core
Link Dependencies:
zlib, talloc, gmime, xapian-core
Description:
Notmuch is a mail indexer. Essentially, is a very thin front end on top of xapian.

npb

Homepage:
Spack package:
Versions:
3.3.1
Build Dependencies:
mpi
Link Dependencies:
mpi
Description:
The NAS Parallel Benchmarks (NPB) are a small set of programs designed to help evaluate the performance of parallel supercomputers. The benchmarks are derived from computational fluid dynamics (CFD) applications and consist of five kernels and three pseudo-applications in the original "pencil-and-paper" specification (NPB 1). The benchmark suite has been extended to include new benchmarks for unstructured adaptive mesh, parallel I/O, multi-zone applications, and computational grids. Problem sizes in NPB are predefined and indicated as different classes. Reference implementations of NPB are available in commonly-used programming models like MPI and OpenMP (NPB 2 and NPB 3).

npm

Homepage:
Spack package:
Versions:
6.13.7, 6.13.4, 3.10.9, 3.10.5
Build Dependencies:
node-js
Run Dependencies:
node-js
Description:
npm: A package manager for javascript.

npth

Homepage:
Spack package:
Versions:
1.6, 1.5, 1.4
Description:
nPth is a library to provide the GNU Pth API and thus a non-preemptive threads implementation.

nrm

Homepage:
Spack package:
Versions:
0.1.0
Build Dependencies:
python, py-setuptools, py-six, py-pyzmq, py-pyyaml, py-tornado, py-numpy, py-argparse, py-jsonschema, py-warlock, py-scipy
Link Dependencies:
python
Run Dependencies:
python, py-six, py-pyzmq, py-pyyaml, py-tornado, py-numpy, py-argparse, py-jsonschema, py-warlock, py-scipy
Description:
Node Resource Manager

nseg

Homepage:
Spack package:
Versions:
1.0
Description:
NSEG - Low complexity sequence identification

nsimd

Homepage:
Spack package:
Versions:
1.0
Build Dependencies:
cmake, python
Description:
NSIMD is a vectorization library that abstracts SIMD programming. It was designed to exploit the maximum power of processors at a low development cost.

nspr

Homepage:
Spack package:
Versions:
4.13.1
Build Dependencies:
perl
Description:
Netscape Portable Runtime (NSPR) provides a platform-neutral API for system level and libc-like functions.

ntpoly

Homepage:
Spack package:
Versions:
2.3.1
Build Dependencies:
cmake, mpi
Link Dependencies:
blas, mpi
Description:
NTPoly - parallel library for computing matrix functions. NTPoly is a library for computing the functions of sparse, hermitian matrices based on polynomial expansions. For sufficiently sparse matrices, most of the matrix functions in NTPoly can be computed in linear time.

numactl

Homepage:
Spack package:
Versions:
2.0.12, 2.0.11
Build Dependencies:
autoconf, automake, libtool, m4
Description:
NUMA support for Linux

numdiff

Homepage:
Spack package:
Versions:
5.9.0, 5.8.1
Build Dependencies:
gettext, gmp
Link Dependencies:
gettext, gmp
Description:
Numdiff is a little program that can be used to compare putatively similar files line by line and field by field, ignoring small numeric differences or/and different numeric formats.

nut

Homepage:
Spack package:
Versions:
master, 0.1.1
Build Dependencies:
cmake, random123
Link Dependencies:
cmake, random123
Description:
NuT is Monte Carlo code for neutrino transport and is a C++ analog to the Haskell McPhD code. NuT is principally aimed at exploring on-node parallelism and performance issues.

nvptx-tools

Homepage:
Spack package:
Versions:
2018-03-01
Build Dependencies:
binutils, cuda
Link Dependencies:
binutils, cuda
Description:
nvptx-tools: A collection of tools for use with nvptx-none GCC toolchains. These tools are necessary when building a version of GCC that enables offloading of OpenMP/OpenACC code to NVIDIA GPUs.

nwchem

Homepage:
Spack package:
Versions:
6.8.1, 6.8
Build Dependencies:
blas, lapack, mpi, scalapack, python
Link Dependencies:
blas, lapack, mpi, scalapack, python
Run Dependencies:
python
Description:
High-performance computational chemistry software

nyancat

Homepage:
Spack package:
Versions:
1.5.2, 1.5.1, 1.5.0, 1.4.5
Description:
Nyancat in your terminal, rendered through ANSI escape sequences.

ocaml

Homepage:
Spack package:
Versions:
4.06.0, 4.03.0
Build Dependencies:
ncurses
Link Dependencies:
ncurses
Description:
OCaml is an industrial strength programming language supporting functional, imperative and object-oriented styles

occa

Homepage:
Spack package:
Versions:
develop, 1.0.8, 1.0.0-alpha.5, 0.2.0, 0.1.0
Build Dependencies:
cuda
Link Dependencies:
cuda
Description:
OCCA is an open-source (MIT license) library used to program current multi-core/many-core architectures. Devices (such as CPUs, GPUs, Intel's Xeon Phi, FPGAs, etc) are abstracted using an offload-model for application development and programming for the devices is done through a C-based (OKL) or Fortran-based kernel language (OFL). OCCA gives developers the ability to target devices at run-time by using run-time compilation for device kernels.

oce

Homepage:
Spack package:
Versions:
0.18.3, 0.18.2, 0.18.1, 0.18, 0.17.2, 0.17.1, 0.17, 0.16.1, 0.16
Build Dependencies:
cmake, tbb
Link Dependencies:
tbb
Description:
Open CASCADE Community Edition: patches/improvements/experiments contributed by users over the official Open CASCADE library.

oclint

Homepage:
Spack package:
Versions:
0.13
Build Dependencies:
python, py-argparse, git, subversion, cmake, ninja, llvm
Link Dependencies:
llvm
Description:
OClint: a static analysis tool for C, C++, and Objective-C code OCLint is a static code analysis tool for improving quality and reducing defects by inspecting C, C++ and Objective-C code and looking for potential problems

oclock

Homepage:
Spack package:
Versions:
1.0.3
Build Dependencies:
libx11, libxmu, libxext, libxt, libxkbfile, pkgconfig, util-macros
Link Dependencies:
libx11, libxmu, libxext, libxt, libxkbfile
Description:
oclock is a simple analog clock using the SHAPE extension to make a round (possibly transparent) window.

octave

Homepage:
Spack package:
Versions:
5.2.0, 5.1.0, 4.4.1, 4.4.0, 4.2.2, 4.2.1, 4.2.0, 4.0.2, 4.0.0
Build Dependencies:
blas, lapack, pcre, pkgconfig, readline, arpack-ng, curl, fftw, fltk, fontconfig, freetype, glpk, gl2ps, gnuplot, imagemagick, hdf5, java, llvm, qhull, qrupdate, qt, suite-sparse, zlib
Link Dependencies:
blas, lapack, pcre, readline, arpack-ng, curl, fftw, fltk, fontconfig, freetype, glpk, gl2ps, gnuplot, imagemagick, hdf5, java, llvm, qhull, qrupdate, qt, suite-sparse, zlib
Description:
GNU Octave is a high-level language, primarily intended for numerical computations. It provides a convenient command line interface for solving linear and nonlinear problems numerically, and for performing other numerical experiments using a language that is mostly compatible with Matlab. It may also be used as a batch-oriented language.

octave-optim

Homepage:
Spack package:
Versions:
1.5.2
Build Dependencies:
octave, octave-struct
Link Dependencies:
octave, octave-struct
Run Dependencies:
octave
Description:
Non-linear optimization toolkit for Octave.

octave-splines

Homepage:
Spack package:
Versions:
1.3.1
Build Dependencies:
octave
Link Dependencies:
octave
Run Dependencies:
octave
Description:
Additional spline functions.

octave-struct

Homepage:
Spack package:
Versions:
1.0.14
Build Dependencies:
octave
Link Dependencies:
octave
Run Dependencies:
octave
Description:
Additional structure manipulation functions for Octave.

octopus

Homepage:
Spack package:
Versions:
7.3, 6.0, 5.0.1
Build Dependencies:
blas, gsl, lapack, libxc, mpi, fftw, metis, parmetis, scalapack, netcdf-fortran, arpack-ng
Link Dependencies:
blas, gsl, lapack, libxc, mpi, fftw, metis, parmetis, scalapack, netcdf-fortran, arpack-ng
Description:
A real-space finite-difference (time-dependent) density-functional theory code.

of-catalyst

Homepage:
Spack package:
Versions:
develop, 1806
Build Dependencies:
cmake, openfoam, catalyst, paraview
Link Dependencies:
openfoam, catalyst, paraview
Run Dependencies:
openfoam
Description:
Of-catalyst is a library for OpenFOAM that provides a runtime-selectable function object for embedding ParaView Catalyst in-situ visualization into arbitrary OpenFOAM simulations. Supports in-situ conversion of the following types: 1) finite volume meshes and fields, single or multi- region; 2) finite area meshes and fields, single region; 3) lagrangian (clouds), single or multiple clouds. This offering is part of the community repository supported by OpenCFD Ltd, producer and distributor of the OpenFOAM software via www.openfoam.com, and owner of the OPENFOAM trademark. OpenCFD Ltd has been developing and releasing OpenFOAM since its debut in 2004.

of-precice

Homepage:
Spack package:
Versions:
develop
Build Dependencies:
openfoam, precice, yaml-cpp
Link Dependencies:
openfoam, precice, yaml-cpp
Description:
preCICE adapter for OpenFOAM

omega-h

Homepage:
Spack package:
Versions:
develop, 9.29.0, 9.27.0, 9.22.2, 9.19.1, 9.19.0, 9.15.0, 9.14.0, 9.13.14, 9.13.13
Build Dependencies:
cmake, gmsh, mpi, trilinos, zlib
Link Dependencies:
mpi, trilinos, zlib
Description:
Omega_h is a C++11 library providing data structures and algorithms for adaptive discretizations. Its specialty is anisotropic triangle and tetrahedral mesh adaptation. It runs efficiently on most modern HPC hardware including GPUs.

ompss

Homepage:
Spack package:
Versions:
14.10
Build Dependencies:
mpi, hwloc, extrae
Link Dependencies:
mpi, hwloc, extrae
Description:
OmpSs is an effort to integrate features from the StarSs programming model developed by BSC into a single programming model. In particular, our objective is to extend OpenMP with new directives to support asynchronous parallelism and heterogeneity (devices like GPUs). However, it can also be understood as new directives extending other accelerator based APIs like CUDA or OpenCL. Our OmpSs environment is built on top of our Mercurium compiler and Nanos++ runtime system.

ompt-openmp

Homepage:
Spack package:
Versions:
0.1
Build Dependencies:
cmake
Description:
LLVM/Clang OpenMP runtime with OMPT support. This is a fork of the OpenMPToolsInterface/LLVM-openmp fork of the official LLVM OpenMP mirror. This library provides a drop-in replacement of the OpenMP runtimes for GCC, Intel and LLVM/Clang.

oniguruma

Homepage:
Spack package:
Versions:
6.9.4, 6.1.3
Description:
Regular expression library.

ont-albacore

Homepage:
Spack package:
Versions:
2.3.1
Build Dependencies:
python, py-setuptools, py-numpy, py-python-dateutil, py-h5py, py-ont-fast5-api, py-pip
Link Dependencies:
python
Run Dependencies:
python, py-setuptools, py-numpy, py-python-dateutil, py-h5py, py-ont-fast5-api
Description:
Albacore is a software project that provides an entry point to the Oxford Nanopore basecalling algorithms. It can be run from the command line on Windows and multiple Linux platforms. A selection of configuration files allow basecalling DNA libraries made with our current range of sequencing kits and Flow Cells.

opa-psm2

Homepage:
Spack package:
Versions:
11.2.77, 11.2.68, 10.3-37, 10.3-17, 10.3-10, 10.3-8, 10.2-260, 10.2-235, 10.2-175
Build Dependencies:
numactl
Link Dependencies:
numactl
Description:
Intel Omni-Path Performance Scaled Messaging 2 (PSM2) library

opam

Homepage:
Spack package:
Versions:
1.2.2, 1.2.1
Build Dependencies:
ocaml
Link Dependencies:
ocaml
Description:
OPAM: OCaml Package Manager OPAM is a source-based package manager for OCaml. It supports multiple simultaneous compiler installations, flexible package constraints, and a Git-friendly development workflow.

opari2

Homepage:
Spack package:
Versions:
2.0.5, 2.0.4, 2.0.3, 2.0.1, 2.0, 1.1.4, 1.1.2
Description:
OPARI2 is a source-to-source instrumentation tool for OpenMP and hybrid codes. It surrounds OpenMP directives and runtime library calls with calls to the POMP2 measurement interface. OPARI2 will provide you with a new initialization method that allows for multi-directory and parallel builds as well as the usage of pre-instrumented libraries. Furthermore, an efficient way of tracking parent-child relationships was added. Additionally, we extended OPARI2 to support instrumentation of OpenMP 3.0 tied tasks.

openbabel

Homepage:
Spack package:
Versions:
master, 3.0.0, 2.4.1, 2.4.0
Build Dependencies:
cmake, python, pkgconfig, swig, boost, cairo, eigen, libxml2, zlib
Link Dependencies:
python, boost, cairo, eigen, libxml2, zlib
Run Dependencies:
python
Description:
Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas.

openblas

Homepage:
Spack package:
Versions:
develop, 0.3.8, 0.3.7, 0.3.6, 0.3.5, 0.3.4, 0.3.3, 0.3.2, 0.3.1, 0.3.0, 0.2.20, 0.2.19, 0.2.18, 0.2.17, 0.2.16, 0.2.15
Description:
OpenBLAS: An optimized BLAS library

opencascade

Homepage:
Spack package:
Versions:
7.4.0
Build Dependencies:
cmake, intel-tbb, vtk, freeimage, rapidjson
Link Dependencies:
intel-tbb, vtk, freeimage, rapidjson
Description:
Open CASCADE Technology is a software development kit (SDK) intended for development of applications dealing with 3D CAD data, freely available in open source. It includes a set of C++ class libraries providing services for 3D surface and solid modeling, visualization, data exchange and rapid application development.

opencoarrays

Homepage:
Spack package:
Versions:
2.7.1, 2.2.0, 1.8.10, 1.8.4, 1.8.0, 1.7.4, 1.6.2
Build Dependencies:
cmake, mpi
Link Dependencies:
mpi
Description:
OpenCoarrays is an open-source software project that produces an application binary interface (ABI) supporting coarray Fortran (CAF) compilers, an application programming interface (API) that supports users of non-CAF compilers, and an associated compiler wrapper and program launcher.

opencv

Homepage:
Spack package:
Versions:
master, 4.2.0, 4.1.2, 4.1.1, 4.1.0-openvino, 4.1.0, 4.0.1-openvino, 4.0.1, 4.0.0-openvino, 4.0.0, 3.4.6, 3.4.5, 3.4.4, 3.4.3, 3.4.1, 3.4.0, 3.3.1, 3.3.0, 3.2.0, 3.1.0, 2.4.13.2, 2.4.13.1, 2.4.13, 2.4.12.3, 2.4.12.2, 2.4.12.1
Build Dependencies:
cuda, cmake, eigen, zlib, libpng, jpeg, libtiff, jasper, gtkplus, vtk, qt, java, py-numpy, protobuf, ffmpeg, mpi, python
Link Dependencies:
cuda, zlib, libpng, jpeg, libtiff, jasper, gtkplus, vtk, qt, java, protobuf, ffmpeg, mpi, python
Run Dependencies:
py-numpy
Description:
OpenCV is released under a BSD license and hence it's free for both academic and commercial use. It has C++, C, Python and Java interfaces and supports Windows, Linux, Mac OS, iOS and Android. OpenCV was designed for computational efficiency and with a strong focus on real- time applications. Written in optimized C/C++, the library can take advantage of multi-core processing. Enabled with OpenCL, it can take advantage of the hardware acceleration of the underlying heterogeneous compute platform. Adopted all around the world, OpenCV has more than 47 thousand people of user community and estimated number of downloads exceeding 9 million. Usage ranges from interactive art, to mines inspection, stitching maps on the web or through advanced robotics.

openexr

Homepage:
Spack package:
Versions:
2.3.0, 2.2.0, 2.1.0, 2.0.1, 1.7.0, 1.6.1, 1.5.0, 1.4.0a, 1.3.2
Build Dependencies:
pkgconfig, ilmbase, zlib
Link Dependencies:
ilmbase, zlib
Description:
OpenEXR Graphics Tools (high dynamic-range image file format)

openfast

Homepage:
Spack package:
Versions:
develop, master
Build Dependencies:
cmake, blas, lapack, mpi, yaml-cpp, hdf5, zlib, libxml2
Link Dependencies:
blas, lapack, mpi, yaml-cpp, hdf5, zlib, libxml2
Description:
Wind turbine simulation package from NREL

openfdtd

Homepage:
Spack package:
Versions:
2.3.0
Build Dependencies:
mpi
Link Dependencies:
mpi
Description:
OpenFDTD is general purpose FDTD simulator applicable to a wide range of applications. The FDTD method (Finite Difference Time Domain method) is a method for numerically calculating the Maxwell equation, which is the basic equation of the electromagnetic field, by the difference method.

openfoam

Homepage:
Spack package:
Versions:
develop, master, 1912, 1906_191103, 1906, 1812_191001, 1812_190531, 1812, 1806, 1712, 1706, 1612
Build Dependencies:
mpi, zlib, fftw, boost, cgal, flex, cmake, scotch, kahip, metis, parmgridgen, zoltan, vtk, adios2, paraview
Link Dependencies:
mpi, zlib, fftw, boost, cgal, flex, scotch, kahip, metis, zoltan, vtk, adios2, paraview
Description:
OpenFOAM is a GPL-opensource C++ CFD-toolbox. This offering is supported by OpenCFD Ltd, producer and distributor of the OpenFOAM software via www.openfoam.com, and owner of the OPENFOAM trademark. OpenCFD Ltd has been developing and releasing OpenFOAM since its debut in 2004.

openfoam-org

Homepage:
Spack package:
Versions:
develop, 7, 6, 5.0, 4.1, 2.4.0
Build Dependencies:
mpi, zlib, flex, cmake, scotch, metis
Link Dependencies:
mpi, zlib, scotch, metis
Description:
OpenFOAM is a GPL-opensource C++ CFD-toolbox. The openfoam.org release is managed by the OpenFOAM Foundation Ltd as a licensee of the OPENFOAM trademark. This offering is not approved or endorsed by OpenCFD Ltd, producer and distributor of the OpenFOAM software via www.openfoam.com, and owner of the OPENFOAM trademark.

openfst

Homepage:
Spack package:
Versions:
1.6.7, 1.6.1, 1.6.0, 1.5.4, 1.5.3, 1.5.2, 1.5.1, 1.5.0, 1.4.1-patch, 1.4.1, 1.4.0
Description:
OpenFst is a library for constructing, combining, optimizing, and searching weighted finite-state transducers (FSTs). Weighted finite- state transducers are automata where each transition has an input label, an output label, and a weight.

opengl

Homepage:
Spack package:
Description:
Placeholder for external OpenGL libraries from hardware vendors

openglu

Homepage:
Spack package:
Description:
Placeholder for external OpenGL utility library (GLU) from hardware vendors

openimageio

Homepage:
Spack package:
Versions:
1.8.15
Build Dependencies:
cmake, boost, libtiff, openexr, libpng, ffmpeg, openjpeg, python, py-numpy, py-pybind11, qt
Link Dependencies:
boost, libtiff, openexr, libpng, ffmpeg, openjpeg, python, qt
Run Dependencies:
py-numpy, py-pybind11
Description:
OpenImageIO is a library for reading and writing images, and a bunch of related classes, utilities, and applications.

openjdk

Homepage:
Spack package:
Versions:
11.0.2, 11.0.1, 1.8.0_202-b08, 1.8.0_40-b25
Description:
The free and opensource java implementation

openjpeg

Homepage:
Spack package:
Versions:
2.3.1, 2.3.0, 2.2.0, 2.1.2, 2.1.1, 2.1.0, 2.0.1, 2.0.0, 1.5.2, 1.5.1
Build Dependencies:
cmake, zlib
Link Dependencies:
zlib
Description:
OpenJPEG is an open-source JPEG 2000 codec written in C language. It has been developed in order to promote the use of JPEG 2000, a still-image compression standard from the Joint Photographic Experts Group (JPEG). Since April 2015, it is officially recognized by ISO/IEC and ITU-T as a JPEG 2000 Reference Software.

openkim-models

Homepage:
Spack package:
Versions:
2019-07-25, 2019-03-29
Build Dependencies:
cmake, kim-api
Link Dependencies:
kim-api
Description:
OpenKIM is an online framework for making molecular simulations reliable, reproducible, and portable. Computer implementations of inter- atomic models are archived in OpenKIM, verified for coding integrity, and tested by computing their predictions for a variety of material properties. Models conforming to the KIM application programming interface (API) work seamlessly with major simulation codes that have adopted the KIM API standard. This package provides all models archived at openkim.org that are compatible with the kim-api package.

openldap

Homepage:
Spack package:
Versions:
2.4.49, 2.4.48
Build Dependencies:
icu4c, gnutls, openssl, unixodbc, postgresql, berkeley-db, perl
Link Dependencies:
icu4c, gnutls, openssl, unixodbc, postgresql, berkeley-db, perl
Description:
OpenLDAP Software is an open source implementation of the Lightweight Directory Access Protocol. The suite includes: slapd - stand-alone LDAP daemon (server) libraries implementing the LDAP protocol, and utilities, tools, and sample clients.

openmc

Homepage:
Spack package:
Versions:
develop, 0.10.0
Build Dependencies:
cmake, hdf5
Link Dependencies:
hdf5
Description:
The OpenMC project aims to provide a fully-featured Monte Carlo particle transport code based on modern methods. It is a constructive solid geometry, continuous-energy transport code that uses ACE format cross sections. The project started under the Computational Reactor Physics Group at MIT.

openmolcas

Homepage:
Spack package:
Versions:
19.11
Build Dependencies:
cmake, hdf5, lapack, openblas, python, py-pyparsing, py-six
Link Dependencies:
hdf5, lapack, openblas
Run Dependencies:
python, py-pyparsing, py-six
Description:
OpenMolcas is a quantum chemistry software package. The key feature of OpenMolcas is the multiconfigurational approach to the electronic structure.

openmpi

Homepage:
Spack package:
Versions:
develop, 4.0.2, 4.0.1, 4.0.0, 3.1.5, 3.1.4, 3.1.3, 3.1.2, 3.1.1, 3.1.0, 3.0.5, 3.0.4, 3.0.3, 3.0.2, 3.0.1, 3.0.0, 2.1.6, 2.1.5, 2.1.4, 2.1.3, 2.1.2, 2.1.1, 2.1.0, 2.0.4, 2.0.3, 2.0.2, 2.0.1, 2.0.0, 1.10.7, 1.10.6, 1.10.5, 1.10.4, 1.10.3, 1.10.2, 1.10.1, 1.10.0, 1.8.8, 1.8.7, 1.8.6, 1.8.5, 1.8.4, 1.8.3, 1.8.2, 1.8.1, 1.8, 1.7.5, 1.7.4, 1.7.3, 1.7.2, 1.7.1, 1.7, 1.6.5, 1.6.4, 1.6.3, 1.6.2, 1.6.1, 1.6, 1.5.5, 1.5.4, 1.5.3, 1.5.2, 1.5.1, 1.5, 1.4.5, 1.4.4, 1.4.3, 1.4.2, 1.4.1, 1.4, 1.3.4, 1.3.3, 1.3.2, 1.3.1, 1.3, 1.2.9, 1.2.8, 1.2.7, 1.2.6, 1.2.5, 1.2.4, 1.2.3, 1.2.2, 1.2.1, 1.2, 1.1.5, 1.1.4, 1.1.3, 1.1.2, 1.1.1, 1.1, 1.0.2, 1.0.1, 1.0
Build Dependencies:
numactl, autoconf, automake, libtool, m4, perl, hwloc, java, sqlite, zlib, valgrind, ucx, libfabric, slurm, lsf, binutils
Link Dependencies:
numactl, hwloc, java, sqlite, zlib, valgrind, ucx, libfabric, slurm, lsf, binutils
Description:
An open source Message Passing Interface implementation. The Open MPI Project is an open source Message Passing Interface implementation that is developed and maintained by a consortium of academic, research, and industry partners. Open MPI is therefore able to combine the expertise, technologies, and resources from all across the High Performance Computing community in order to build the best MPI library available. Open MPI offers advantages for system and software vendors, application developers and computer science researchers.

openmx

Homepage:
Spack package:
Versions:
3.8
Build Dependencies:
mpi, fftw, blas, lapack
Link Dependencies:
mpi, fftw, blas, lapack
Description:
OpenMX (Open source package for Material eXplorer) is a software package for nano-scale material simulations based on density functional theories (DFT), norm-conserving pseudopotentials, and pseudo-atomic localized basis functions.

opennurbs

Homepage:
Spack package:
Versions:
develop, percept
Description:
OpenNURBS is an open-source NURBS-based geometric modeling library and toolset, with meshing and display / output functions.

openpa

Homepage:
Spack package:
Versions:
1.0.4, 1.0.3, 1.0.2, 1.0.1, 1.0.0
Description:
An open source, highly-portable library that provides atomic primitives (and related constructs) for high performance, concurrent software

openpmd-api

Homepage:
Spack package:
Versions:
0.10.3, 0.10.2, 0.10.1, 0.10.0, dev
Build Dependencies:
cmake, mpark-variant, mpi, hdf5, adios, adios2, nlohmann-json, python
Link Dependencies:
mpark-variant, mpi, hdf5, adios, adios2, nlohmann-json, py-pybind11, python
Run Dependencies:
py-numpy, py-mpi4py, python
Test Dependencies:
catch2, py-numpy, py-mpi4py, python
Description:
API for easy reading and writing of openPMD files

openresty

Homepage:
Spack package:
Versions:
1.15.8.2, 1.15.8.1, 1.13.6.2
Build Dependencies:
pcre
Description:
OpenResty is a full-fledged web application server by bundling the standard nginx core, lots of 3rd-party nginx modules, as well as most of their external dependencies.

openscenegraph

Homepage:
Spack package:
Versions:
3.6.4, 3.2.3, 3.1.5
Build Dependencies:
cmake, qt, zlib
Link Dependencies:
qt, zlib
Description:
OpenSceneGraph is an open source, high performance 3D graphics toolkit that's used in a variety of visual simulation applications.

openslide

Homepage:
Spack package:
Versions:
3.4.1
Build Dependencies:
openjpeg, jpeg, libtiff, libxml2, sqlite
Link Dependencies:
openjpeg, jpeg, libtiff, libxml2, sqlite
Description:
OpenSlide reads whole slide image files.

openspeedshop

Homepage:
Spack package:
Versions:
develop, 2.4.1, 2.4.0, 2.3.1.5, 2.3.1.4, 2.3.1.3
Build Dependencies:
cmake, libtool, bison, flex, binutils, libdwarf, sqlite, boost, dyninst, python, libxml2, qt, cbtf, cbtf-krell, cbtf-argonavis, mrnet
Link Dependencies:
binutils, elf, libdwarf, sqlite, boost, dyninst, libxml2, qt, cbtf, cbtf-krell, cbtf-argonavis, mrnet
Run Dependencies:
python, cbtf, cbtf-krell, cbtf-argonavis, mrnet
Description:
OpenSpeedShop is a community effort by The Krell Institute with current direct funding from DOEs NNSA. It builds on top of a broad list of community infrastructures, most notably Dyninst and MRNet from UW, libmonitor from Rice, and PAPI from UTK. OpenSpeedShop is an open source multi platform Linux performance tool which is targeted to support performance analysis of applications running on both single node and large scale IA64, IA32, EM64T, AMD64, PPC, ARM, Power8, Intel Phi, Blue Gene and Cray platforms. OpenSpeedShop development is hosted by the Krell Institute. The infrastructure and base components of OpenSpeedShop are released as open source code primarily under LGPL.

openspeedshop-utils

Homepage:
Spack package:
Versions:
develop, 2.4.1, 2.4.0, 2.3.1.5, 2.3.1.4, 2.3.1.3
Build Dependencies:
cmake, libtool, bison, flex, binutils, libdwarf, sqlite, boost, dyninst, python, libxml2, cbtf, cbtf-krell, cbtf-argonavis, mrnet
Link Dependencies:
elf, libdwarf, sqlite, boost, dyninst, libxml2, cbtf, cbtf-krell, cbtf-argonavis, mrnet
Run Dependencies:
python, cbtf, cbtf-krell, cbtf-argonavis, mrnet
Description:
OpenSpeedShop is a community effort by The Krell Institute with current direct funding from DOEs NNSA. It builds on top of a broad list of community infrastructures, most notably Dyninst and MRNet from UW, libmonitor from Rice, and PAPI from UTK. OpenSpeedShop is an open source multi platform Linux performance tool which is targeted to support performance analysis of applications running on both single node and large scale IA64, IA32, EM64T, AMD64, PPC, ARM, Power8, Intel Phi, Blue Gene and Cray platforms. OpenSpeedShop development is hosted by the Krell Institute. The infrastructure and base components of OpenSpeedShop are released as open source code primarily under LGPL. openspeedshop- utils is a package that does not have the qt3 gui. It was created to avoid a conflict between openspeedshop and cbtf-argonavis-gui based on the fact that spack will not allow a qt3 and qt4/qt5 dependency in a packages dependency tree.

openssh

Homepage:
Spack package:
Versions:
7.9p1, 7.6p1, 7.5p1, 7.4p1, 7.3p1, 7.2p2, 7.1p2, 7.0p1, 6.9p1, 6.8p1, 6.7p1, 6.6p1
Build Dependencies:
openssl, libedit, ncurses, zlib
Link Dependencies:
openssl, libedit, ncurses, zlib
Description:
OpenSSH is the premier connectivity tool for remote login with the SSH protocol. It encrypts all traffic to eliminate eavesdropping, connection hijacking, and other attacks. In addition, OpenSSH provides a large suite of secure tunneling capabilities, several authentication methods, and sophisticated configuration options.

openssl

Homepage:
Spack package:
Versions:
1.1.1d, 1.1.1c, 1.1.1b, 1.1.1a, 1.1.1, 1.1.0l, 1.1.0k, 1.1.0j, 1.1.0i, 1.1.0g, 1.1.0e, 1.1.0d, 1.1.0c, 1.0.2t, 1.0.2s, 1.0.2r, 1.0.2p, 1.0.2o, 1.0.2n, 1.0.2m, 1.0.2k, 1.0.2j, 1.0.2i, 1.0.2h, 1.0.2g, 1.0.2f, 1.0.2e, 1.0.2d, 1.0.1u, 1.0.1t, 1.0.1r, 1.0.1h, 1.0.1e
Build Dependencies:
zlib, perl
Link Dependencies:
zlib
Test Dependencies:
perl
Description:
OpenSSL is an open source project that provides a robust, commercial- grade, and full-featured toolkit for the Transport Layer Security (TLS) and Secure Sockets Layer (SSL) protocols. It is also a general-purpose cryptography library.

openstf

Homepage:
Spack package:
Versions:
1.3.1
Build Dependencies:
mpi
Link Dependencies:
mpi
Description:
OpenSTF is an electrostatic field simulator which can calculate the voltage distribution and the electric field distribution of a system consisting of electrodes and dielectrics.

opentsdb

Homepage:
Spack package:
Versions:
2.4.0, 2.3.2, 2.3.1, 2.3.0, 2.2.2, 2.2.1, 2.2.0
Build Dependencies:
autoconf, automake, libtool, m4
Run Dependencies:
java
Description:
OpenTSDB is a distributed, scalable Time Series Database (TSDB) written on top of HBase. OpenTSDB was written to address a common need: store, index and serve metrics collected from computer systems (network gear, operating systems, applications) at a large scale, and make this data easily accessible and graphable.

opium

Homepage:
Spack package:
Versions:
3.8
Build Dependencies:
blas, lapack
Link Dependencies:
blas, lapack
Description:
DFT pseudopotential generation project

optional-lite

Homepage:
Spack package:
Versions:
3.2.0, 3.1.1, 3.1.0, 3.0.0, 2.3.0, 2.2.0, 2.0.0, 1.0.3
Build Dependencies:
cmake
Description:
A single-file header-only version of a C++17-like optional, a nullable object for C++98, C++11 and later.

optipng

Homepage:
Spack package:
Versions:
0.7.7
Description:
OptiPNG is a PNG optimizer that recompresses image files to a smaller size, without losing any information. This program also converts external formats (BMP, GIF, PNM and TIFF) to optimized PNG, and performs PNG integrity checks and corrections.

opus

Homepage:
Spack package:
Versions:
1.1.4, 1.1.3, 1.1.2, 1.1.1, 1.1, 1.0.3, 1.0.2, 1.0.1, 1.0.0, 0.9.14, 0.9.10, 0.9.9, 0.9.8, 0.9.7, 0.9.6, 0.9.5, 0.9.3, 0.9.2, 0.9.1, 0.9.0
Build Dependencies:
libvorbis
Link Dependencies:
libvorbis
Description:
Opus is a totally open, royalty-free, highly versatile audio codec.

orca

Homepage:
Spack package:
Versions:
4.0.1.2
Build Dependencies:
zstd
Run Dependencies:
openmpi
Description:
An ab initio, DFT and semiempirical SCF-MO package Note: Orca is licensed software. You will need to create an account on the Orca homepage and download Orca yourself. Spack will search your current directory for the download file. Alternatively, add this file to a mirror so that Spack can find it. For instructions on how to set up a mirror, see http://spack.readthedocs.io/en/latest/mirrors.html

orfm

Homepage:
Spack package:
Versions:
0.7.1
Link Dependencies:
zlib
Description:
A simple and not slow open reading frame (ORF) caller. No bells or whistles like frameshift detection, just a straightforward goal of returning a FASTA file of open reading frames over a certain length from a FASTA/Q file of nucleotide sequences.

orthofiller

Homepage:
Spack package:
Versions:
1.1.4
Run Dependencies:
augustus, bedtools2, hmmer, orthofinder, python, py-biopython, py-scipy, r, r-gamlss, mafft
Description:
OrthoFiller: Identifying missing annotations for evolutionarily conserved genes.

orthofinder

Homepage:
Spack package:
Versions:
2.2.0
Run Dependencies:
blast-plus, mcl, fastme, py-dlcpar
Description:
OrthoFinder is a fast, accurate and comprehensive analysis tool for comparative genomics. It finds orthologues and orthogroups infers rooted gene trees for all orthogroups and infers a rooted species tree for the species being analysed. OrthoFinder also provides comprehensive statistics for comparative genomic analyses. OrthoFinder is simple to use and all you need to run it is a set of protein sequence files (one per species) in FASTA format.

orthomcl

Homepage:
Spack package:
Versions:
2.0.9
Build Dependencies:
perl, blast-plus, mcl, mariadb
Link Dependencies:
blast-plus, mcl, mariadb
Run Dependencies:
perl
Description:
OrthoMCL is a genome-scale algorithm for grouping orthologous protein sequences.

osmctools

Homepage:
Spack package:
Versions:
0.9, 0.8
Build Dependencies:
zlib, autoconf, automake, libtool, m4
Link Dependencies:
zlib
Description:
A few really fast tools to convert, filter and update OpenStreetMap data files

osqp

Homepage:
Spack package:
Versions:
master, 0.6.0, 0.5.0
Build Dependencies:
cmake
Description:
The OSQP (Operator Splitting Quadratic Program) solver is a numerical optimization package for solving problems in the form: minimize 0.5 x' P x + q' x, subject to l <= A x <= u, where "x in R^n" is the optimization variable.

osu-micro-benchmarks

Homepage:
Spack package:
Versions:
5.6.2, 5.6.1, 5.5, 5.4, 5.3
Build Dependencies:
mpi, cuda
Link Dependencies:
mpi, cuda
Description:
The Ohio MicroBenchmark suite is a collection of independent MPI message passing performance microbenchmarks developed and written at The Ohio State University. It includes traditional benchmarks and performance measures such as latency, bandwidth and host overhead and can be used for both traditional and GPU-enhanced nodes.

otf

Homepage:
Spack package:
Versions:
1.12.5salmon
Build Dependencies:
zlib
Link Dependencies:
zlib
Description:
To improve scalability for very large and massively parallel traces the Open Trace Format (OTF) is developed at ZIH as a successor format to the Vampir Trace Format (VTF3).

otf2

Homepage:
Spack package:
Versions:
2.2, 2.1.1, 2.1, 2.0, 1.5.1, 1.4, 1.3.1, 1.2.1
Description:
The Open Trace Format 2 is a highly scalable, memory efficient event trace data format plus support library.

p3dfft3

Homepage:
Spack package:
Versions:
develop, 3.0.0
Build Dependencies:
mpi, fftw, essl
Link Dependencies:
mpi, fftw, essl
Description:
P3DFFT++ (a.k.a. P3DFFT v. 3) is a new generation of P3DFFT library that aims to provide a comprehensive framework for simulating multiscale phenomena. It takes the essence of P3DFFT further by creating an extensible, modular structure uniquely adaptable to a greater range of use cases.

p4est

Homepage:
Spack package:
Versions:
2.2, 2.0, 1.1
Build Dependencies:
automake, autoconf, libtool, mpi, zlib
Link Dependencies:
mpi, zlib
Description:
Dynamic management of a collection (a forest) of adaptive octrees in parallel

p7zip

Homepage:
Spack package:
Versions:
16.02
Description:
A Unix port of the 7z file archiver

pacbio-daligner

Homepage:
Spack package:
Versions:
2017-08-05
Build Dependencies:
gmake, pacbio-dazz-db
Link Dependencies:
pacbio-dazz-db
Description:
Daligner: The Dazzler "Overlap" Module. This is a special fork required for some pacbio utilities.

pacbio-damasker

Homepage:
Spack package:
Versions:
2017-02-11
Build Dependencies:
gmake
Description:
Damasker: The Dazzler Repeat Masking Suite. This is a special fork required for some pacbio utilities.

pacbio-dazz-db

Homepage:
Spack package:
Versions:
2017-04-10
Build Dependencies:
gmake
Description:
The Dazzler Database Library. This version is a special fork required for some pacbio utilities.

pacbio-dextractor

Homepage:
Spack package:
Versions:
2016-08-09
Build Dependencies:
hdf5, gmake
Link Dependencies:
hdf5
Description:
The Dextractor and Compression Command Library. This is a special fork required by some pacbio utilities.

packmol

Homepage:
Spack package:
Versions:
18.169
Build Dependencies:
cmake
Description:
Packmol creates an initial point for molecular dynamics simulations by packing molecules in defined regions of space.

pacvim

Homepage:
Spack package:
Versions:
1.1.1
Build Dependencies:
ncurses
Link Dependencies:
ncurses
Description:
Pacvim is a command-line-based game based off of Pacman. The main purpose of this software is to familiarize individuals with Vim.

pagit

Homepage:
Spack package:
Versions:
1.01
Build Dependencies:
java, perl
Run Dependencies:
java, perl
Description:
PAGIT addresses the need for software to generate high quality draft genomes.

pagmo

Homepage:
Spack package:
Versions:
1.1.7
Build Dependencies:
cmake, python, boost, gsl, ipopt, mpi, blas, py-scipy, py-networkx
Link Dependencies:
python, boost, gsl, ipopt, mpi, blas
Run Dependencies:
py-scipy, py-networkx
Description:
Parallel Global Multiobjective Optimizer (and its Python alter ego PyGMO) is a C++ / Python platform to perform parallel computations of optimisation tasks (global and local) via the asynchronous generalized island model.

pal

Homepage:
Spack package:
Versions:
0.9.8
Build Dependencies:
sofa-c, erfa
Link Dependencies:
sofa-c, erfa
Description:
The PAL library is a partial re-implementation of Pat Wallace's popular SLALIB library written in C using a Gnu GPL license and layered on top of the IAU's SOFA library (or the BSD-licensed ERFA) where appropriate.

paml

Homepage:
Spack package:
Versions:
4.9h
Description:
PAML is a package of programs for phylogenetic analyses of DNA or protein sewuences using maximum likelihood.

panda

Homepage:
Spack package:
Versions:
2016-03-07
Build Dependencies:
cmake, mpi
Link Dependencies:
mpi
Description:
PANDA: Parallel AdjaceNcy Decomposition Algorithm

pandaseq

Homepage:
Spack package:
Versions:
2.11, 2.10
Build Dependencies:
autoconf, automake, libtool, m4, zlib, pkgconfig
Link Dependencies:
libtool, bzip2
Description:
PANDASEQ is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence.

pandoc

Homepage:
Spack package:
Versions:
2.7.3
Build Dependencies:
texlive
Link Dependencies:
texlive
Description:
If you need to convert files from one markup format into another, pandoc is your swiss-army knife.

pango

Homepage:
Spack package:
Versions:
1.41.0, 1.40.3, 1.40.1, 1.36.8
Build Dependencies:
pkgconfig, harfbuzz, cairo, libxft, glib, gobject-introspection
Link Dependencies:
harfbuzz, cairo, libxft, glib, gobject-introspection
Description:
Pango is a library for laying out and rendering of text, with an emphasis on internationalization. It can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the context of the GTK+ widget toolkit.

pangomm

Homepage:
Spack package:
Versions:
2.43.1, 2.42.0, 2.41.5, 2.40.2, 2.39.1, 2.38.1, 2.37.2, 2.36.0, 2.35.1, 2.34.0, 2.28.4, 2.27.1, 2.26.3, 2.25.1, 2.24.0, 2.14.1, 2.14.0
Build Dependencies:
pango, glibmm, cairomm
Link Dependencies:
pango, glibmm, cairomm
Description:
Pangomm is a C++ interface to Pango.

papi

Homepage:
Spack package:
Versions:
5.7.0, 5.6.0, 5.5.1, 5.5.0, 5.4.3, 5.4.1, 5.3.0
Build Dependencies:
lm-sensors
Link Dependencies:
lm-sensors
Description:
PAPI provides the tool designer and application engineer with a consistent interface and methodology for use of the performance counter hardware found in most major microprocessors. PAPI enables software engineers to see, in near real time, the relation between software performance and processor events. In addition Component PAPI provides access to a collection of components that expose performance measurement opportunities across the hardware and software stack.

papyrus

Homepage:
Spack package:
Versions:
develop, 1.0.0
Build Dependencies:
cmake, mpi
Link Dependencies:
mpi
Description:
Parallel Aggregate Persistent Storage

paradiseo

Homepage:
Spack package:
Versions:
head, dev-safe
Build Dependencies:
cmake, mpi, doxygen, gnuplot, eigen, boost
Link Dependencies:
mpi, gnuplot, boost
Description:
A C++ white-box object-oriented framework dedicated to the reusable design of metaheuristics.

parallel

Homepage:
Spack package:
Versions:
20190222, 20170322, 20170122, 20160422, 20160322
Build Dependencies:
perl
Run Dependencies:
perl
Description:
GNU parallel is a shell tool for executing jobs in parallel using one or more computers. A job can be a single command or a small script that has to be run for each of the lines in the input.

parallel-netcdf

Homepage:
Spack package:
Versions:
develop, master, 1.12.1, 1.11.2, 1.11.1, 1.11.0, 1.10.0, 1.9.0, 1.8.1, 1.8.0, 1.7.0, 1.6.1
Build Dependencies:
mpi, m4
Link Dependencies:
mpi
Description:
PnetCDF (Parallel netCDF) is a high-performance parallel I/O library for accessing files in format compatibility with Unidata's NetCDF, specifically the formats of CDF-1, 2, and 5.

paraver

Homepage:
Spack package:
Versions:
4.6.3, 4.6.2
Build Dependencies:
boost, wxwidgets, wxpropgrid
Link Dependencies:
boost, wxwidgets, wxpropgrid
Description:
"A very powerful performance visualization and analysis tool based on traces that can be used to analyse any information that is expressed on its input trace format. Traces for parallel MPI, OpenMP and other programs can be genereated with Extrae.

paraview

Homepage:
Spack package:
Versions:
develop, 5.7.0, 5.6.2, 5.6.0, 5.5.2, 5.5.1, 5.5.0, 5.4.1, 5.4.0, 5.3.0, 5.2.0, 5.1.2, 5.0.1, 4.4.0
Build Dependencies:
cuda, cmake, python, py-numpy, py-mpi4py, mpi, qt, mesa, gl, libxt, bzip2, freetype, hdf5, jpeg, libpng, libtiff, libxml2, netcdf-c, expat, zlib
Link Dependencies:
cuda, python, mpi, qt, mesa, gl, libxt, bzip2, freetype, hdf5, jpeg, libpng, libtiff, libxml2, netcdf-c, expat, zlib
Run Dependencies:
python, py-numpy, py-mpi4py, py-matplotlib
Description:
ParaView is an open-source, multi-platform data analysis and visualization application.

parmetis

Homepage:
Spack package:
Versions:
4.0.3, 4.0.2
Build Dependencies:
cmake, mpi, metis
Link Dependencies:
mpi, metis
Description:
ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices.

parmgridgen

Homepage:
Spack package:
Versions:
1.0
Build Dependencies:
mpi
Link Dependencies:
mpi
Description:
MGRIDGEN is a serial library written entirely in ANSI C that implements (serial) algorithms for obtaining a sequence of successive coarse grids that are well-suited for geometric multigrid methods. ParMGridGen is the parallel version of MGridGen.

parquet-cpp

Homepage:
Spack package:
Versions:
1.4.0
Build Dependencies:
cmake, arrow, boost, pkgconfig, thrift
Link Dependencies:
arrow, boost, thrift
Description:
C++ bindings for the Apache Parquet columnar data format.

parsimonator

Homepage:
Spack package:
Versions:
1.0.2
Description:
Parsimonator is a no-frills light-weight implementation for building starting trees under parsimony for RAxML.

parsplice

Homepage:
Spack package:
Versions:
develop, 1.1, multisplice
Build Dependencies:
cmake, berkeley-db, nauty, boost, mpi, eigen, lammps
Link Dependencies:
berkeley-db, nauty, boost, mpi, eigen, lammps
Description:
ParSplice code implements the Parallel Trajectory Splicing algorithm

partitionfinder

Homepage:
Spack package:
Versions:
2.1.1
Build Dependencies:
python, py-numpy, py-pandas, py-tables, py-pyparsing, py-scipy, py-scikit-learn
Run Dependencies:
python, py-numpy, py-pandas, py-tables, py-pyparsing, py-scipy, py-scikit-learn
Description:
PartitionFinder is free open source software to select best-fit partitioning schemes and models of molecular evolution for phylogenetic analyses.

pasta

Homepage:
Spack package:
Versions:
1.8.3
Build Dependencies:
python, py-dendropy, java
Link Dependencies:
python, py-dendropy, java
Description:
PASTA (Practical Alignment using SATe and Transitivity)

patch

Homepage:
Spack package:
Versions:
2.7.6, 2.7.5
Description:
Patch takes a patch file containing a difference listing produced by the diff program and applies those differences to one or more original files, producing patched versions.

patchelf

Homepage:
Spack package:
Versions:
0.10, 0.9, 0.8
Description:
PatchELF is a small utility to modify the dynamic linker and RPATH of ELF executables.

pathfinder

Homepage:
Spack package:
Versions:
1.0.0
Description:
Proxy Application. Signature search.

pax-utils

Homepage:
Spack package:
Versions:
1.2.2
Description:
ELF utils that can check files for security relevant properties

pbbam

Homepage:
Spack package:
Versions:
0.18.0
Build Dependencies:
cmake, zlib, boost, htslib, doxygen
Link Dependencies:
zlib, boost, htslib, doxygen
Description:
The pbbam software package provides components to create, query, & edit PacBio BAM files and associated indices. These components include a core C++ library, bindings for additional languages, and command-line utilities.

pbmpi

Homepage:
Spack package:
Versions:
partition
Build Dependencies:
mpi, libfabric
Link Dependencies:
mpi, libfabric
Description:
A Bayesian software for phylogenetic reconstruction using mixture models

pbsuite

Homepage:
Spack package:
Versions:
15.8.24
Run Dependencies:
blasr, python, py-networkx
Description:
PBJelly is a highly automated pipeline that aligns long sequencing reads (such as PacBio RS reads or long 454 reads in fasta format) to high- confidence draft assembles.

pcma

Homepage:
Spack package:
Versions:
2.0
Description:
PCMA is a progressive multiple sequence alignment program that combines two different alignment strategies.

pcre

Homepage:
Spack package:
Versions:
8.43, 8.42, 8.41, 8.40, 8.39, 8.38
Description:
The PCRE package contains Perl Compatible Regular Expression libraries. These are useful for implementing regular expression pattern matching using the same syntax and semantics as Perl 5.

pcre2

Homepage:
Spack package:
Versions:
10.31, 10.20
Description:
The PCRE2 package contains Perl Compatible Regular Expression libraries. These are useful for implementing regular expression pattern matching using the same syntax and semantics as Perl 5.

pdf2svg

Homepage:
Spack package:
Versions:
0.2.3, 0.2.2
Build Dependencies:
pkgconfig, cairo, poppler
Link Dependencies:
cairo, poppler
Description:
A simple PDF to SVG converter using the Poppler and Cairo libraries.

pdftk

Homepage:
Spack package:
Versions:
2.02
Build Dependencies:
eclipse-gcj-parser
Description:
PDFtk Server is a command-line tool for working with PDFs. It is commonly used for client-side scripting or server-side processing of PDFs.

pdsh

Homepage:
Spack package:
Versions:
2.31
Description:
PDSH: a high performance, parallel remote shell utility

pdt

Homepage:
Spack package:
Versions:
3.25.1, 3.25, 3.24, 3.23, 3.22.1, 3.22, 3.21, 3.20, 3.19, 3.18.1
Description:
Program Database Toolkit (PDT) is a framework for analyzing source code written in several programming languages and for making rich program knowledge accessible to developers of static and dynamic analysis tools. PDT implements a standard program representation, the program database (PDB), that can be accessed in a uniform way through a class library supporting common PDB operations.

pegtl

Homepage:
Spack package:
Versions:
master, 2.1.4, 2.0.0
Build Dependencies:
cmake
Description:
The Parsing Expression Grammar Template Library (PEGTL) is a zero- dependency C++11 header-only library for creating parsers according to a Parsing Expression Grammar (PEG).

pennant

Homepage:
Spack package:
Versions:
0.9, 0.8, 0.7, 0.6, 0.5, 0.4
Build Dependencies:
mpi
Link Dependencies:
mpi
Description:
PENNANT is an unstructured mesh physics mini-app designed for advanced architecture research. It contains mesh data structures and a few physics algorithms adapted from the LANL rad-hydro code FLAG, and gives a sample of the typical memory access patterns of FLAG.

percept

Homepage:
Spack package:
Versions:
master
Build Dependencies:
cmake, googletest, opennurbs, boost, yaml-cpp, trilinos
Link Dependencies:
googletest, opennurbs, boost, yaml-cpp, trilinos
Description:
Parallel mesh refinement and adaptivity tools for the finite element method.

perl

Homepage:
Spack package:
Versions:
5.31.7, 5.31.4, 5.30.1, 5.30.0, 5.28.0, 5.26.2, 5.24.1, 5.22.4, 5.22.3, 5.22.2, 5.22.1, 5.22.0, 5.20.3, 5.18.4, 5.16.3
Build Dependencies:
gdbm
Link Dependencies:
gdbm
Description:
Perl 5 is a highly capable, feature-rich programming language with over 27 years of development.

perl-acme-damn

Homepage:
Spack package:
Versions:
0.08
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Acme::Damn provides a single routine, damn(), which takes a blessed reference (a Perl object), and unblesses it, to return the original reference.

perl-algorithm-diff

Homepage:
Spack package:
Versions:
1.1903
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Compute 'intelligent' differences between two files / lists

perl-alien-build

Homepage:
Spack package:
Versions:
1.86
Build Dependencies:
perl, perl-capture-tiny, perl-ffi-checklib, perl-file-which, perl-file-chdir, perl-path-tiny
Link Dependencies:
perl
Run Dependencies:
perl, perl-capture-tiny, perl-ffi-checklib, perl-file-which, perl-file-chdir, perl-path-tiny
Description:
This module provides tools for building external (non-CPAN) dependencies for CPAN. It is mainly designed to be used at install time of a CPAN client, and work closely with Alien::Base which is used at runtime.

perl-alien-libxml2

Homepage:
Spack package:
Versions:
0.10_01
Build Dependencies:
perl, libxml2, perl-alien-build
Link Dependencies:
perl, libxml2
Run Dependencies:
perl, perl-alien-build
Description:
This module provides libxml2 for other modules to use.

perl-app-cmd

Homepage:
Spack package:
Versions:
0.331
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Write command line apps with less suffering

perl-array-utils

Homepage:
Spack package:
Versions:
0.5
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Small utils for array manipulation

perl-b-hooks-endofscope

Homepage:
Spack package:
Versions:
0.21
Build Dependencies:
perl, perl-sub-exporter-progressive
Link Dependencies:
perl
Run Dependencies:
perl, perl-sub-exporter-progressive
Description:
Execute code after a scope finished compilation.

perl-bioperl

Homepage:
Spack package:
Versions:
1.007002, 1.7.6
Build Dependencies:
perl, perl-module-build, perl-uri, perl-io-string, perl-data-stag, perl-test-most, perl-error, perl-graph, perl-http-message, perl-io-stringy, perl-ipc-run, perl-list-moreutils, perl-set-scalar, perl-test-requiresinternet, perl-xml-dom, perl-xml-dom-xpath, perl-xml-libxml, perl-xml-sax, perl-xml-sax-base, perl-xml-sax-writer, perl-xml-twig, perl-xml-writer, perl-yaml, perl-libwww-perl, perl-libxml-perl
Link Dependencies:
perl
Run Dependencies:
perl, perl-module-build, perl-uri, perl-io-string, perl-data-stag, perl-test-most, perl-error, perl-graph, perl-http-message, perl-io-stringy, perl-ipc-run, perl-list-moreutils, perl-set-scalar, perl-test-requiresinternet, perl-xml-dom, perl-xml-dom-xpath, perl-xml-libxml, perl-xml-sax, perl-xml-sax-base, perl-xml-sax-writer, perl-xml-twig, perl-xml-writer, perl-yaml, perl-libwww-perl, perl-libxml-perl
Description:
BioPerl is the product of a community effort to produce Perl code which is useful in biology. Examples include Sequence objects, Alignment objects and database searching objects. These objects not only do what they are advertised to do in the documentation, but they also interact - Alignment objects are made from the Sequence objects, Sequence objects have access to Annotation and SeqFeature objects and databases, Blast objects can be converted to Alignment objects, and so on. This means that the objects provide a coordinated and extensible framework to do computational biology. BioPerl development focuses on Perl classes, or code that is used to create objects representing biological entities. There are scripts provided in the scripts/ and examples/ directories but scripts are not the main focus of the BioPerl developers. Of course, as the objects do most of the hard work for you, all you have to do is combine a number of objects together sensibly to make useful scripts. The intent of the BioPerl development effort is to make reusable tools that aid people in creating their own sites or job-specific applications. The BioPerl website at http://bioperl.org also attempts to maintain links and archives of standalone bio-related Perl tools that are not affiliated or related to the core BioPerl effort. Check the site for useful code ideas and contribute your own if possible.

perl-bit-vector

Homepage:
Spack package:
Versions:
7.4
Build Dependencies:
perl, perl-carp-clan
Link Dependencies:
perl
Run Dependencies:
perl, perl-carp-clan
Description:
Efficient bit vector, set of integers and "big int" math library

perl-cairo

Homepage:
Spack package:
Versions:
1.106
Build Dependencies:
perl, cairo, perl-extutils-depends, perl-extutils-pkgconfig
Link Dependencies:
perl, cairo, perl-extutils-depends, perl-extutils-pkgconfig
Run Dependencies:
perl
Description:
Perl interface to the cairo 2d vector graphics library

perl-capture-tiny

Homepage:
Spack package:
Versions:
0.46
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Capture STDOUT and STDERR from Perl, XS or external programs

perl-carp-clan

Homepage:
Spack package:
Versions:
6.06
Build Dependencies:
perl, perl-test-exception, perl-sub-uplevel
Link Dependencies:
perl
Run Dependencies:
perl, perl-test-exception, perl-sub-uplevel
Description:
Report errors from perspective of caller of a "clan" of modules

perl-cgi

Homepage:
Spack package:
Versions:
4.40, 4.39, 4.38, 4.37
Build Dependencies:
perl, perl-html-parser
Link Dependencies:
perl
Run Dependencies:
perl, perl-html-parser
Description:
CGI - Handle Common Gateway Interface requests and responses CGI was included in the Perl distribution from 5.4 to 5.20 but has since been removed.

perl-class-data-inheritable

Homepage:
Spack package:
Versions:
0.08
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
For creating accessor/mutators to class data.

perl-class-inspector

Homepage:
Spack package:
Versions:
1.32
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Get information about a class and its structure

perl-class-load

Homepage:
Spack package:
Versions:
0.24
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
A working (require "Class::Name") and more

perl-class-load-xs

Homepage:
Spack package:
Versions:
0.10
Build Dependencies:
perl, perl-class-load
Link Dependencies:
perl
Run Dependencies:
perl, perl-class-load
Description:
This module provides an XS implementation for portions of Class::Load.

perl-clone

Homepage:
Spack package:
Versions:
0.41
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Clone - recursively copy Perl datatypes

perl-clone-choose

Homepage:
Spack package:
Versions:
0.010
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Checks several different modules which provides a clone() function and selects an appropriate one.

perl-compress-raw-bzip2

Homepage:
Spack package:
Versions:
2.081
Build Dependencies:
perl, bzip2, perl-extutils-makemaker
Link Dependencies:
perl, bzip2
Run Dependencies:
perl
Description:
A low-Level Interface to bzip2 compression library.

perl-compress-raw-zlib

Homepage:
Spack package:
Versions:
2.081
Build Dependencies:
perl, zlib, perl-extutils-makemaker
Link Dependencies:
perl, zlib
Run Dependencies:
perl
Description:
A low-Level Interface to zlib compression library.

perl-config-general

Homepage:
Spack package:
Versions:
2.63
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Config::General - Generic Config Module

perl-contextual-return

Homepage:
Spack package:
Versions:
0.004014
Build Dependencies:
perl, perl-want
Link Dependencies:
perl, perl-want
Run Dependencies:
perl
Description:
Create context-sensitive return values

perl-cpan-meta-check

Homepage:
Spack package:
Versions:
0.014
Build Dependencies:
perl, perl-test-deep
Link Dependencies:
perl
Run Dependencies:
perl, perl-test-deep
Description:
This module verifies if requirements described in a CPAN::Meta object are present..

perl-data-dumper

Homepage:
Spack package:
Versions:
2.173
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Stringified perl data structures, suitable for both printing and eval

perl-data-optlist

Homepage:
Spack package:
Versions:
0.110
Build Dependencies:
perl, perl-sub-install
Link Dependencies:
perl
Run Dependencies:
perl, perl-sub-install
Description:
Parse and validate simple name/value option pairs

perl-data-stag

Homepage:
Spack package:
Versions:
0.14
Build Dependencies:
perl, perl-io-string
Link Dependencies:
perl
Run Dependencies:
perl, perl-io-string
Description:
Structured Tags datastructures

perl-db-file

Homepage:
Spack package:
Versions:
1.840
Build Dependencies:
perl, perl-extutils-makemaker, berkeley-db
Link Dependencies:
perl
Run Dependencies:
perl
Description:
DB_File is a module which allows Perl programs to make use of the facilities provided by Berkeley DB version 1.x (if you have a newer version of DB, see "Using DB_File with Berkeley DB version 2 or greater"). It is assumed that you have a copy of the Berkeley DB manual pages at hand when reading this documentation. The interface defined here mirrors the Berkeley DB interface closely.

perl-dbd-mysql

Homepage:
Spack package:
Versions:
4.043
Build Dependencies:
perl, perl-test-deep, perl-dbi, mariadb
Link Dependencies:
perl, mariadb
Run Dependencies:
perl, perl-test-deep, perl-dbi
Description:
MySQL driver for the Perl5 Database Interface (DBI)

perl-dbd-pg

Homepage:
Spack package:
Versions:
3.10.0
Build Dependencies:
perl, postgresql, perl-dbi
Link Dependencies:
perl, postgresql
Run Dependencies:
perl, perl-dbi
Description:
DBD::Pg is a Perl module that works with the DBI module to provide access to PostgreSQL databases.

perl-dbd-sqlite

Homepage:
Spack package:
Versions:
1.59_01, 1.58, 1.57_01, 1.56
Build Dependencies:
perl, perl-dbi
Link Dependencies:
perl
Run Dependencies:
perl, perl-dbi
Description:
DBD::SQLite - Self-contained RDBMS in a DBI Driver

perl-dbi

Homepage:
Spack package:
Versions:
1.636
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
The DBI is the standard database interface module for Perl. It defines a set of methods, variables and conventions that provide a consistent database interface independent of the actual database being used.

perl-devel-cycle

Homepage:
Spack package:
Versions:
1.12
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Find memory cycles in objects

perl-devel-globaldestruction

Homepage:
Spack package:
Versions:
0.14
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Makes Perl's global destruction less tricky to deal with

perl-devel-overloadinfo

Homepage:
Spack package:
Versions:
0.005, 0.004
Build Dependencies:
perl, perl-mro-compat
Link Dependencies:
perl
Run Dependencies:
perl, perl-mro-compat
Description:
Returns information about overloaded operators for a given class

perl-devel-stacktrace

Homepage:
Spack package:
Versions:
2.02
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
An object representing a stack trace.

perl-devel-symdump

Homepage:
Spack package:
Versions:
2.0604
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Devel::Symdump - dump symbol names or the symbol table

perl-digest-md5

Homepage:
Spack package:
Versions:
2.55
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Perl interface to the MD5 Algorithm

perl-dist-checkconflicts

Homepage:
Spack package:
Versions:
0.11
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Declare version conflicts for your dist

perl-encode-locale

Homepage:
Spack package:
Versions:
1.05
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Determine the locale encoding

perl-error

Homepage:
Spack package:
Versions:
0.17028
Build Dependencies:
perl, perl-module-build
Link Dependencies:
perl
Run Dependencies:
perl
Description:
The Error package provides two interfaces. Firstly Error provides a procedural interface to exception handling. Secondly Error is a base class for errors/exceptions that can either be thrown, for subsequent catch, or can simply be recorded.

perl-eval-closure

Homepage:
Spack package:
Versions:
0.14
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Safely and cleanly create closures via string eval

perl-exception-class

Homepage:
Spack package:
Versions:
1.43
Build Dependencies:
perl, perl-devel-stacktrace, perl-class-data-inheritable
Link Dependencies:
perl
Run Dependencies:
perl, perl-devel-stacktrace, perl-class-data-inheritable
Description:
A module that allows you to declare real exception classes in Perl

perl-exporter-tiny

Homepage:
Spack package:
Versions:
1.000000
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
An exporter with the features of Sub::Exporter but only core dependencies

perl-extutils-config

Homepage:
Spack package:
Versions:
0.008
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
ExtUtils::Config - A wrapper for perl's configuration

perl-extutils-depends

Homepage:
Spack package:
Versions:
0.405
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Easily build XS extensions that depend on XS extensions

perl-extutils-helpers

Homepage:
Spack package:
Versions:
0.026
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
ExtUtils::Helpers - Various portability utilities for module builders

perl-extutils-installpaths

Homepage:
Spack package:
Versions:
0.012
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
ExtUtils::InstallPaths - Build.PL install path logic made easy

perl-extutils-makemaker

Homepage:
Spack package:
Versions:
7.24
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
ExtUtils::MakeMaker - Create a module Makefile. This utility is designed to write a Makefile for an extension module from a Makefile.PL. It is based on the Makefile.SH model provided by Andy Dougherty and the perl5-porters.

perl-extutils-pkgconfig

Homepage:
Spack package:
Versions:
1.16
Build Dependencies:
perl, pkgconfig
Link Dependencies:
perl
Run Dependencies:
perl, pkgconfig
Description:
simplistic interface to pkg-config

perl-ffi-checklib

Homepage:
Spack package:
Versions:
0.25
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
This module checks whether a particular dynamic library is available for FFI to use. It is modeled heavily on Devel::CheckLib, but will find dynamic libraries even when development packages are not installed. It also provides a find_lib function that will return the full path to the found dynamic library, which can be feed directly into FFI::Platypus or another FFI system.

perl-file-chdir

Homepage:
Spack package:
Versions:
0.1011
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Perl's chdir() has the unfortunate problem of being very, very, very global. If any part of your program calls chdir() or if any library you use calls chdir(), it changes the current working directory for the *whole* program. This sucks. File::chdir gives you an alternative, $CWD and @CWD. These two variables combine all the power of chdir(), File::Spec and Cwd.

perl-file-copy-recursive

Homepage:
Spack package:
Versions:
0.40, 0.38
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Perl extension for recursively copying files and directories

perl-file-homedir

Homepage:
Spack package:
Versions:
1.004
Build Dependencies:
perl, perl-file-which
Link Dependencies:
perl
Run Dependencies:
perl, perl-file-which
Description:
Find your home and other directories on any platform

perl-file-listing

Homepage:
Spack package:
Versions:
6.04
Build Dependencies:
perl, perl-http-date
Link Dependencies:
perl
Run Dependencies:
perl, perl-http-date
Description:
Parse directory listing

perl-file-pushd

Homepage:
Spack package:
Versions:
1.014
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Change directory temporarily for a limited scope

perl-file-sharedir-install

Homepage:
Spack package:
Versions:
0.11
Build Dependencies:
perl, perl-module-build
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Install shared files

perl-file-slurp-tiny

Homepage:
Spack package:
Versions:
0.004
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
A simple, sane and efficient file slurper

perl-file-slurper

Homepage:
Spack package:
Versions:
0.011
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
A simple, sane and efficient module to slurp a file

perl-file-which

Homepage:
Spack package:
Versions:
1.22
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Perl implementation of the which utility as an API

perl-font-ttf

Homepage:
Spack package:
Versions:
1.06
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Perl module for TrueType Font hacking

perl-forks

Homepage:
Spack package:
Versions:
0.36
Build Dependencies:
perl, perl-acme-damn, perl-devel-symdump, perl-list-moreutils, perl-sys-sigaction
Link Dependencies:
perl
Run Dependencies:
perl, perl-acme-damn, perl-devel-symdump, perl-list-moreutils, perl-sys-sigaction
Description:
The "forks" pragma allows a developer to use threads without having to have a threaded perl, or to even run 5.8.0 or higher.

perl-gd

Homepage:
Spack package:
Versions:
2.53
Build Dependencies:
perl, perl-module-build, perl-extutils-makemaker, perl-extutils-pkgconfig, libgd
Link Dependencies:
perl, libgd
Run Dependencies:
perl, perl-extutils-makemaker, perl-extutils-pkgconfig
Description:
Interface to Gd Graphics Library

perl-gdgraph

Homepage:
Spack package:
Versions:
1.4308
Build Dependencies:
perl, perl-capture-tiny, perl-test-exception, perl-gdtextutil, perl-gd
Link Dependencies:
perl
Run Dependencies:
perl, perl-capture-tiny, perl-test-exception, perl-gdtextutil, perl-gd
Description:
Graph Plotting Module for Perl 5

perl-gdgraph-histogram

Homepage:
Spack package:
Versions:
1.1
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
GD::Graph::histogram extends the GD::Graph module to create histograms. The module allow creation of count or percentage histograms.

perl-gdtextutil

Homepage:
Spack package:
Versions:
0.86
Build Dependencies:
perl, perl-gd
Link Dependencies:
perl
Run Dependencies:
perl, perl-gd
Description:
Text utilities for use with GD

perl-graph

Homepage:
Spack package:
Versions:
0.9704
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Graph data structures and algorithms

perl-graph-readwrite

Homepage:
Spack package:
Versions:
2.09
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Write out directed graph in Dot format

perl-hash-merge

Homepage:
Spack package:
Versions:
0.300
Build Dependencies:
perl, perl-scalar-list-utils, perl-clone-choose
Link Dependencies:
perl
Run Dependencies:
perl, perl-scalar-list-utils, perl-clone-choose
Description:
Hash::Merge merges two arbitrarily deep hashes into a single hash.

perl-html-parser

Homepage:
Spack package:
Versions:
3.72
Build Dependencies:
perl, perl-html-tagset
Link Dependencies:
perl
Run Dependencies:
perl, perl-html-tagset
Description:
HTML parser class

perl-html-tagset

Homepage:
Spack package:
Versions:
3.20
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Data tables useful in parsing HTML

perl-http-cookies

Homepage:
Spack package:
Versions:
6.04
Build Dependencies:
perl, perl-uri, perl-http-message
Link Dependencies:
perl
Run Dependencies:
perl, perl-uri, perl-http-message
Description:
HTTP cookie jars

perl-http-daemon

Homepage:
Spack package:
Versions:
6.01
Build Dependencies:
perl, perl-lwp-mediatypes, perl-http-message, perl-http-date, perl-module-build-tiny
Link Dependencies:
perl
Run Dependencies:
perl, perl-lwp-mediatypes, perl-http-message, perl-http-date
Description:
A simple http server class

perl-http-date

Homepage:
Spack package:
Versions:
6.02
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Date conversion routines

perl-http-message

Homepage:
Spack package:
Versions:
6.13
Build Dependencies:
perl, perl-lwp-mediatypes, perl-encode-locale, perl-io-html, perl-try-tiny, perl-uri, perl-http-date
Link Dependencies:
perl
Run Dependencies:
perl, perl-lwp-mediatypes, perl-encode-locale, perl-io-html, perl-try-tiny, perl-uri, perl-http-date
Description:
HTTP style message (base class)

perl-http-negotiate

Homepage:
Spack package:
Versions:
6.01
Build Dependencies:
perl, perl-http-message
Link Dependencies:
perl
Run Dependencies:
perl, perl-http-message
Description:
Choose a variant to serve

perl-inline

Homepage:
Spack package:
Versions:
0.80
Build Dependencies:
perl, perl-test-warn
Link Dependencies:
perl
Run Dependencies:
perl, perl-test-warn
Description:
Write Perl Subroutines in Other Programming Languages

perl-inline-c

Homepage:
Spack package:
Versions:
0.78
Build Dependencies:
perl, perl-yaml-libyaml, perl-parse-recdescent, perl-inline, perl-pegex, perl-file-copy-recursive
Link Dependencies:
perl
Run Dependencies:
perl, perl-yaml-libyaml, perl-parse-recdescent, perl-inline, perl-pegex, perl-file-copy-recursive
Description:
C Language Support for Inline

perl-io-all

Homepage:
Spack package:
Versions:
0.87
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
IO::All combines all of the best Perl IO modules into a single nifty object oriented interface to greatly simplify your everyday Perl IO idioms. It exports a single function called io, which returns a new IO::All object. And that object can do it all! The IO::All object is a proxy for IO::File, IO::Dir, IO::Socket, Tie::File, File::Spec, File::Path, File::MimeInfo and File::ReadBackwards; as well as all the DBM and MLDBM modules. You can use most of the methods found in these classes and in IO::Handle (which they inherit from). IO::All adds dozens of other helpful idiomatic methods including file stat and manipulation functions. IO::All is pluggable, and modules like IO::All::LWP and IO::All::Mailto add even more functionality. Optionally, every IO::All object can be tied to itself. This means that you can use most perl IO builtins on it: readline, <>, getc, print, printf, syswrite, sysread, close.

perl-io-compress

Homepage:
Spack package:
Versions:
2.081
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl, perl-compress-raw-zlib, perl-compress-raw-bzip2
Description:
A perl library for uncompressing gzip, zip, bzip2 or lzop file/buffer.

perl-io-html

Homepage:
Spack package:
Versions:
1.001
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Open an HTML file with automatic charset detection.

perl-io-prompt

Homepage:
Spack package:
Versions:
0.997004
Build Dependencies:
perl, perl-module-build, perl-termreadkey, perl-want
Link Dependencies:
perl
Run Dependencies:
perl, perl-termreadkey, perl-want
Description:
By default, this module exports a single function prompt. It prompts the user to enter some input, and returns an object that represents the user input. You may specify various flags to the function to affect its behaviour; most notably, it defaults to automatically chomp the input, unless the -line flag is specified. Two other functions are exported at request: hand_print, which simulates hand-typing to the console; and get_input, which is the lower-level function that actually prompts the user for a suitable input. Note that this is an interim re-release. A full release with better documentation will follow in the near future. Meanwhile, please consult the examples directory from this module's CPAN distribution to better understand how to make use of this module.

perl-io-sessiondata

Homepage:
Spack package:
Versions:
1.03
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
A wrapper around a single IO::Socket object

perl-io-socket-ssl

Homepage:
Spack package:
Versions:
2.052
Build Dependencies:
perl, perl-net-ssleay
Link Dependencies:
perl
Run Dependencies:
perl, perl-net-ssleay
Description:
SSL sockets with IO::Socket interface

perl-io-string

Homepage:
Spack package:
Versions:
1.08
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Emulate file interface for in-core strings

perl-io-stringy

Homepage:
Spack package:
Versions:
2.111
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
This toolkit primarily provides modules for performing both traditional and object-oriented i/o) on things other than normal filehandles; in particular, IO::Scalar, IO::ScalarArray, and IO::Lines. In the more- traditional IO::Handle front, we have IO::AtomicFile which may be used to painlessly create files which are updated atomically. And in the "this-may-prove-useful" corner, we have IO::Wrap, whose exported wraphandle() function will clothe anything that's not a blessed object in an IO::Handle-like wrapper... so you can just use OO syntax and stop worrying about whether your function's caller handed you a string, a globref, or a FileHandle.

perl-io-tty

Homepage:
Spack package:
Versions:
1.13_01
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
IO::Tty is used internally by IO::Pty to create a pseudo-tty. You wouldn't want to use it directly except to import constants, use IO::Pty. For a list of importable constants, see IO::Tty::Constant.

perl-ipc-run

Homepage:
Spack package:
Versions:
20180523.0
Build Dependencies:
perl, perl-io-tty, perl-readonly
Link Dependencies:
perl
Run Dependencies:
perl, perl-io-tty
Description:
IPC::Run allows you to run and interact with child processes using files, pipes, and pseudo-ttys. Both system()-style and scripted usages are supported and may be mixed. Likewise, functional and OO API styles are both supported and may be mixed.

perl-json

Homepage:
Spack package:
Versions:
2.97001
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
JSON (JavaScript Object Notation) encoder/decoder

perl-libwww-perl

Homepage:
Spack package:
Versions:
6.33, 6.29
Build Dependencies:
perl, perl-encode-locale, perl-file-listing, perl-html-parser, perl-http-cookies, perl-http-daemon, perl-http-date, perl-http-message, perl-http-negotiate, perl-lwp-mediatypes, perl-net-http, perl-try-tiny, perl-uri, perl-www-robotrules
Link Dependencies:
perl
Run Dependencies:
perl, perl-encode-locale, perl-file-listing, perl-html-parser, perl-http-cookies, perl-http-daemon, perl-http-date, perl-http-message, perl-http-negotiate, perl-lwp-mediatypes, perl-net-http, perl-try-tiny, perl-uri, perl-www-robotrules
Description:
The libwww-perl collection is a set of Perl modules which provides a simple and consistent application programming interface to the World- Wide Web. The main focus of the library is to provide classes and functions that allow you to write WWW clients.

perl-libxml-perl

Homepage:
Spack package:
Versions:
0.08
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
libxml-perl is a collection of smaller Perl modules, scripts, and documents for working with XML in Perl. libxml-perl software works in combination with XML::Parser, PerlSAX, XML::DOM, XML::Grove and others.

perl-list-moreutils

Homepage:
Spack package:
Versions:
0.428
Build Dependencies:
perl, perl-exporter-tiny, perl-list-moreutils-xs
Link Dependencies:
perl
Run Dependencies:
perl, perl-exporter-tiny, perl-list-moreutils-xs
Description:
Provide the stuff missing in List::Util

perl-list-moreutils-xs

Homepage:
Spack package:
Versions:
0.428
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
List::MoreUtils::XS is a backend for List::MoreUtils. Even if it's possible (because of user wishes) to have it practically independent from List::MoreUtils, it technically depend on List::MoreUtils. Since it's only a backend, the API is not public and can change without any warning.

perl-log-log4perl

Homepage:
Spack package:
Versions:
1.46
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Log4j implementation for Perl

perl-logger-simple

Homepage:
Spack package:
Versions:
2.0
Build Dependencies:
perl, perl-object-insideout
Link Dependencies:
perl
Run Dependencies:
perl, perl-object-insideout
Description:
Implementation of the Simran-Log-Log and Simran-Error-Error modules

perl-lwp-mediatypes

Homepage:
Spack package:
Versions:
6.02
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Guess media type for a file or a URL

perl-mailtools

Homepage:
Spack package:
Versions:
2.21
Build Dependencies:
perl, perl-timedate
Link Dependencies:
perl
Run Dependencies:
perl, perl-timedate
Description:
Perl module for handling mail

perl-math-bezier

Homepage:
Spack package:
Versions:
0.01
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Math::Bezier - solution of Bezier Curves

perl-math-cdf

Homepage:
Spack package:
Versions:
0.1
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Generate probabilities and quantiles from several statistical probability functions

perl-math-cephes

Homepage:
Spack package:
Versions:
0.5305
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
This module provides an interface to over 150 functions of the cephes math library of Stephen Moshier.

perl-math-matrixreal

Homepage:
Spack package:
Versions:
2.13
Build Dependencies:
perl, perl-module-build
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Implements the data type "matrix of real numbers" (and consequently also "vector of real numbers").

perl-math-round

Homepage:
Spack package:
Versions:
0.07
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Math::Round - Perl extension for rounding numbers

perl-math-vecstat

Homepage:
Spack package:
Versions:
0.08
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Math::VecStat - Some basic numeric stats on vectors

perl-module-build

Homepage:
Spack package:
Versions:
0.4224, 0.4220
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Module::Build is a system for building, testing, and installing Perl modules. It is meant to be an alternative to ExtUtils::MakeMaker. Developers may alter the behavior of the module through subclassing in a much more straightforward way than with MakeMaker. It also does not require a make on your system - most of the Module::Build code is pure- perl and written in a very cross-platform way.

perl-module-build-tiny

Homepage:
Spack package:
Versions:
0.039
Build Dependencies:
perl, perl-module-build, perl-extutils-config, perl-extutils-helpers, perl-extutils-installpaths
Link Dependencies:
perl
Run Dependencies:
perl, perl-extutils-config, perl-extutils-helpers, perl-extutils-installpaths
Description:
Module::Build::Tiny - A tiny replacement for Module::Build

perl-module-implementation

Homepage:
Spack package:
Versions:
0.09
Build Dependencies:
perl, perl-module-runtime, perl-test-fatal, perl-test-requires, perl-try-tiny
Link Dependencies:
perl
Run Dependencies:
perl, perl-module-runtime, perl-test-fatal, perl-test-requires, perl-try-tiny
Description:
Loads one of several alternate underlying implementations for a module

perl-module-runtime

Homepage:
Spack package:
Versions:
0.016
Build Dependencies:
perl, perl-module-build
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Runtime module handling

perl-module-runtime-conflicts

Homepage:
Spack package:
Versions:
0.003
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Provide information on conflicts for Module::Runtime

perl-mozilla-ca

Homepage:
Spack package:
Versions:
20160104
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Mozilla's CA cert bundle in PEM format

perl-mro-compat

Homepage:
Spack package:
Versions:
0.13
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Provides several utilities for dealing with method resolution order.

perl-namespace-clean

Homepage:
Spack package:
Versions:
0.27
Build Dependencies:
perl, perl-b-hooks-endofscope
Link Dependencies:
perl
Run Dependencies:
perl, perl-b-hooks-endofscope
Description:
Keep imports and functions out of your namespace.

perl-net-http

Homepage:
Spack package:
Versions:
6.17
Build Dependencies:
perl, perl-uri
Link Dependencies:
perl
Run Dependencies:
perl, perl-uri
Description:
Low-level HTTP connection (client)

perl-net-scp-expect

Homepage:
Spack package:
Versions:
0.16
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Wrapper for scp that allows passwords via Expect.

perl-net-ssleay

Homepage:
Spack package:
Versions:
1.85, 1.82
Build Dependencies:
perl, openssl
Link Dependencies:
perl, openssl
Run Dependencies:
perl
Description:
Perl extension for using OpenSSL

perl-number-format

Homepage:
Spack package:
Versions:
1.75
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Number::Format - Perl extension for formatting numbers

perl-object-insideout

Homepage:
Spack package:
Versions:
4.05
Build Dependencies:
perl, perl-module-build, perl-exception-class
Link Dependencies:
perl
Run Dependencies:
perl, perl-exception-class
Description:
Implements inside-out objects as anonymous scalar references that are blessed into a class with the scalar containing the ID for the object (usually a sequence number).

perl-package-deprecationmanager

Homepage:
Spack package:
Versions:
0.17
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Manage deprecation warnings for your distribution

perl-package-stash

Homepage:
Spack package:
Versions:
0.37
Build Dependencies:
perl, perl-test-requires, perl-test-fatal, perl-module-implementation, perl-dist-checkconflicts
Link Dependencies:
perl
Run Dependencies:
perl, perl-test-requires, perl-test-fatal, perl-module-implementation, perl-dist-checkconflicts
Description:
Routines for manipulating stashes

perl-package-stash-xs

Homepage:
Spack package:
Versions:
0.28
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Faster and more correct implementation of the Package::Stash API

perl-padwalker

Homepage:
Spack package:
Versions:
2.2
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
play with other peoples' lexical variables

perl-parallel-forkmanager

Homepage:
Spack package:
Versions:
1.19
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
A simple parallel processing fork manager

perl-params-util

Homepage:
Spack package:
Versions:
1.07
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Simple, compact and correct param-checking functions

perl-params-validate

Homepage:
Spack package:
Versions:
1.29
Build Dependencies:
perl, perl-module-build, perl-module-implementation
Link Dependencies:
perl
Run Dependencies:
perl, perl-module-implementation
Description:
Params::Validate - Validate method/function parameters

perl-parse-recdescent

Homepage:
Spack package:
Versions:
1.967015
Build Dependencies:
perl, perl-module-build
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Generate Recursive-Descent Parsers

perl-path-tiny

Homepage:
Spack package:
Versions:
0.108
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
This module provides a small, fast utility for working with file paths. It is friendlier to use than File::Spec and provides easy access to functions from several other core file handling modules. It aims to be smaller and faster than many alternatives on CPAN, while helping people do many common things in consistent and less error-prone ways.

perl-pdf-api2

Homepage:
Spack package:
Versions:
2.033
Build Dependencies:
perl, perl-test-exception, perl-test-memory-cycle, perl-font-ttf
Link Dependencies:
perl
Run Dependencies:
perl, perl-test-exception, perl-test-memory-cycle, perl-font-ttf
Description:
Facilitates the creation and modification of PDF files

perl-pegex

Homepage:
Spack package:
Versions:
0.64
Build Dependencies:
perl, perl-file-sharedir-install, perl-yaml-libyaml
Link Dependencies:
perl
Run Dependencies:
perl, perl-file-sharedir-install, perl-yaml-libyaml
Description:
Acmeist PEG Parser Framework

perl-perl-unsafe-signals

Homepage:
Spack package:
Versions:
0.03
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Quoting perl581delta: In Perl 5.8.0 the so-called "safe signals" were introduced. This means that Perl no longer handles signals immediately but instead "between opcodes", when it is safe to do so. The earlier immediate handling easily could corrupt the internal state of Perl, resulting in mysterious crashes. It's possible since perl 5.8.1 to globally disable this feature by using the PERL_SIGNALS environment variables (as specified in "PERL_SIGNALS" in perlrun); but there's no way to disable it locally, for a short period of time. That's however something you might want to do, if, for example, your Perl program calls a C routine that will potentially run for a long time and for which you want to set a timeout. This module therefore allows you to define UNSAFE_SIGNALS blocks in which signals will be handled "unsafely". Note that, no matter how short you make the unsafe block, it will still be unsafe. Use with caution.

perl-perl-version

Homepage:
Spack package:
Versions:
1.013_03
Build Dependencies:
perl, perl-file-slurp-tiny
Link Dependencies:
perl
Run Dependencies:
perl, perl-file-slurp-tiny
Description:
Parse and manipulate Perl version strings

perl-perl4-corelibs

Homepage:
Spack package:
Versions:
0.004, 0.003, 0.002, 0.001, 0.000
Build Dependencies:
perl, perl-module-build
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Perl4::CoreLibs - libraries historically supplied with Perl 4

perl-perl6-slurp

Homepage:
Spack package:
Versions:
0.051005
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Perl6::Slurp - Implements the Perl 6 'slurp' built-in

perl-perlio-gzip

Homepage:
Spack package:
Versions:
0.20, 0.19
Build Dependencies:
perl
Link Dependencies:
perl, zlib
Run Dependencies:
perl
Description:
Perl extension to provide a PerlIO layer to gzip/gunzip

perl-perlio-utf8-strict

Homepage:
Spack package:
Versions:
0.002
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
This module provides a fast and correct UTF-8 PerlIO layer.

perl-readonly

Homepage:
Spack package:
Versions:
2.05
Build Dependencies:
perl, perl-module-build-tiny
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Readonly - Facility for creating read-only scalars, arrays, hashes

perl-regexp-common

Homepage:
Spack package:
Versions:
2017060201
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Regexp::Common - Provide commonly requested regular expressions

perl-scalar-list-utils

Homepage:
Spack package:
Versions:
1.50
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Scalar::Util - A selection of general-utility scalar subroutines

perl-scalar-util-numeric

Homepage:
Spack package:
Versions:
0.40
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
This module exports a number of wrappers around perl's builtin grok_number function, which returns the numeric type of its argument, or 0 if it isn't numeric.

perl-set-intervaltree

Homepage:
Spack package:
Versions:
0.10
Build Dependencies:
perl, perl-extutils-makemaker
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Set::IntervalTree uses Interval Trees to store and efficiently look up ranges using a range-based lookup.

perl-set-intspan

Homepage:
Spack package:
Versions:
1.19
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Set::IntSpan - Manages sets of integers

perl-set-scalar

Homepage:
Spack package:
Versions:
1.29
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Set::Scalar - basic set operations

perl-star-fusion

Homepage:
Spack package:
Versions:
master
Build Dependencies:
perl, star, perl-set-intervaltree, perl-dbi, perl-db-file, perl-uri
Link Dependencies:
perl
Run Dependencies:
perl, star, perl-set-intervaltree, perl-dbi, perl-db-file, perl-uri
Description:
STAR-Fusion is a component of the Trinity Cancer Transcriptome Analysis Toolkit (CTAT). STAR-Fusion uses the STAR aligner to identify candidate fusion transcripts supported by Illumina reads. STAR-Fusion further processes the output generated by the STAR aligner to map junction reads and spanning reads to a reference annotation set.

perl-statistics-basic

Homepage:
Spack package:
Versions:
1.6611
Build Dependencies:
perl, perl-number-format, perl-scalar-list-utils
Link Dependencies:
perl
Run Dependencies:
perl, perl-number-format, perl-scalar-list-utils
Description:
Statistics::Basic - A collection of very basic statistics modules

perl-statistics-descriptive

Homepage:
Spack package:
Versions:
3.0612
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Module of basic descriptive statistical functions.

perl-statistics-pca

Homepage:
Spack package:
Versions:
0.0.1
Build Dependencies:
perl, perl-module-build, perl-contextual-return, perl-text-simpletable, perl-math-matrixreal
Link Dependencies:
perl
Run Dependencies:
perl, perl-contextual-return, perl-text-simpletable, perl-math-matrixreal
Description:
A simple Perl implementation of Principal Component Analysis.

perl-sub-exporter

Homepage:
Spack package:
Versions:
0.987
Build Dependencies:
perl, perl-params-util, perl-data-optlist
Link Dependencies:
perl
Run Dependencies:
perl, perl-params-util, perl-data-optlist
Description:
A sophisticated exporter for custom-built routines

perl-sub-exporter-progressive

Homepage:
Spack package:
Versions:
0.001013
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Progressive Sub::Exporter

perl-sub-identify

Homepage:
Spack package:
Versions:
0.14
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Retrieve names of code references

perl-sub-install

Homepage:
Spack package:
Versions:
0.928
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Install subroutines into packages easily

perl-sub-name

Homepage:
Spack package:
Versions:
0.21
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Name or rename a sub

perl-sub-uplevel

Homepage:
Spack package:
Versions:
0.2800
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
apparently run a function in a higher stack frame

perl-svg

Homepage:
Spack package:
Versions:
2.78
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Perl extension for generating Scalable Vector Graphics (SVG) documents.

perl-swissknife

Homepage:
Spack package:
Versions:
1.75
Build Dependencies:
perl, perl-module-build
Link Dependencies:
perl
Run Dependencies:
perl
Description:
An object-oriented Perl library to handle Swiss-Prot entries

perl-sys-sigaction

Homepage:
Spack package:
Versions:
0.23
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Prior to version 5.8.0 perl implemented 'unsafe' signal handling. The reason it is consider unsafe, is that there is a risk that a signal will arrive, and be handled while perl is changing internal data structures. This can result in all kinds of subtle and not so subtle problems. For this reason it has always been recommended that one do as little as possible in a signal handler, and only variables that already exist be manipulated. Perl 5.8.0 and later versions implements 'safe' signal handling on platforms which support the POSIX sigaction() function. This is accomplished by having perl note that a signal has arrived, but deferring the execution of the signal handler until such time as it is safe to do so. Unfortunately these changes can break some existing scripts, if they depended on a system routine being interrupted by the signal's arrival. The perl 5.8.0 implementation was modified further in version 5.8.2

perl-task-weaken

Homepage:
Spack package:
Versions:
1.04
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Ensure that a platform has weaken support

perl-term-readline-gnu

Homepage:
Spack package:
Versions:
1.36
Build Dependencies:
perl, readline
Link Dependencies:
perl, readline
Run Dependencies:
perl
Description:
Perl extension for the GNU Readline/History Library.

perl-termreadkey

Homepage:
Spack package:
Versions:
2.38, 2.37
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Term::ReadKey is a compiled perl module dedicated to providing simple control over terminal driver modes (cbreak, raw, cooked, etc.,) support for non-blocking reads, if the architecture allows, and some generalized handy functions for working with terminals. One of the main goals is to have the functions as portable as possible, so you can just plug in "use Term::ReadKey" on any architecture and have a good likelihood of it working.

perl-test-deep

Homepage:
Spack package:
Versions:
1.127
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Extremely flexible deep comparison

perl-test-differences

Homepage:
Spack package:
Versions:
0.64
Build Dependencies:
perl, perl-module-build, perl-capture-tiny, perl-text-diff
Link Dependencies:
perl
Run Dependencies:
perl, perl-capture-tiny, perl-text-diff
Description:
Test strings and data structures and show differences if not ok

perl-test-exception

Homepage:
Spack package:
Versions:
0.43
Build Dependencies:
perl, perl-sub-uplevel
Link Dependencies:
perl
Run Dependencies:
perl, perl-sub-uplevel
Description:
Test exception-based code

perl-test-fatal

Homepage:
Spack package:
Versions:
0.014
Build Dependencies:
perl, perl-try-tiny
Link Dependencies:
perl
Run Dependencies:
perl, perl-try-tiny
Description:
Incredibly simple helpers for testing code with exceptions

perl-test-memory-cycle

Homepage:
Spack package:
Versions:
1.06
Build Dependencies:
perl, perl-padwalker, perl-devel-cycle
Link Dependencies:
perl
Run Dependencies:
perl, perl-padwalker, perl-devel-cycle
Description:
Check for memory leaks and circular memory references

perl-test-most

Homepage:
Spack package:
Versions:
0.35
Build Dependencies:
perl, perl-exception-class, perl-test-differences, perl-test-exception, perl-test-warn, perl-test-deep
Link Dependencies:
perl
Run Dependencies:
perl, perl-exception-class, perl-test-differences, perl-test-exception, perl-test-warn, perl-test-deep
Description:
Most commonly needed test functions and features.

perl-test-needs

Homepage:
Spack package:
Versions:
0.002005
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Skip tests when modules not available.

perl-test-requires

Homepage:
Spack package:
Versions:
0.10
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Checks to see if the module can be loaded.

perl-test-requiresinternet

Homepage:
Spack package:
Versions:
0.05
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Easily test network connectivity

perl-test-warn

Homepage:
Spack package:
Versions:
0.30
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Perl extension to test methods for warnings

perl-test-warnings

Homepage:
Spack package:
Versions:
0.026
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Test for warnings and the lack of them

perl-text-csv

Homepage:
Spack package:
Versions:
1.95
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Comma-separated values manipulator (using XS or PurePerl)

perl-text-diff

Homepage:
Spack package:
Versions:
1.45
Build Dependencies:
perl, perl-algorithm-diff
Link Dependencies:
perl
Run Dependencies:
perl, perl-algorithm-diff
Description:
Provides a basic set of services akin to the GNU diff utility.

perl-text-format

Homepage:
Spack package:
Versions:
0.61
Build Dependencies:
perl, perl-module-build
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Text::Format - Various subroutines to format text

perl-text-simpletable

Homepage:
Spack package:
Versions:
2.04
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Simple Eyecandy ASCII Tables

perl-text-soundex

Homepage:
Spack package:
Versions:
3.05
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Soundex is a phonetic algorithm for indexing names by sound, as pronounced in English. The goal is for names with the same pronunciation to be encoded to the same representation so that they can be matched despite minor differences in spelling

perl-text-unidecode

Homepage:
Spack package:
Versions:
1.30
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
plain ASCII transliterations of Unicode text

perl-time-hires

Homepage:
Spack package:
Versions:
1.9746
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
High resolution alarm, sleep, gettimeofday, interval timers

perl-time-piece

Homepage:
Spack package:
Versions:
1.3203
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Object Oriented time objects

perl-timedate

Homepage:
Spack package:
Versions:
2.30
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
The parser contained here will only parse absolute dates, if you want a date parser that can parse relative dates then take a look at the Time modules by David Muir on CPAN.

perl-try-tiny

Homepage:
Spack package:
Versions:
0.28
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Minimal try/catch with proper preservation of $@

perl-uri

Homepage:
Spack package:
Versions:
1.72, 1.71
Build Dependencies:
perl, perl-test-needs
Link Dependencies:
perl
Run Dependencies:
perl
Test Dependencies:
perl-test-needs
Description:
Uniform Resource Identifiers (absolute and relative)

perl-want

Homepage:
Spack package:
Versions:
0.29
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
A generalisation of wantarray.

perl-www-robotrules

Homepage:
Spack package:
Versions:
6.02
Build Dependencies:
perl, perl-uri
Link Dependencies:
perl
Run Dependencies:
perl, perl-uri
Description:
Database of robots.txt-derived permissions

perl-xml-dom

Homepage:
Spack package:
Versions:
1.46
Build Dependencies:
perl, perl-xml-parser, perl-xml-regexp, perl-libwww-perl, perl-libxml-perl
Link Dependencies:
perl
Run Dependencies:
perl, perl-xml-parser, perl-xml-regexp, perl-libwww-perl, perl-libxml-perl
Description:
This module extends the XML::Parser module by Clark Cooper. The XML::Parser module is built on top of XML::Parser::Expat, which is a lower level interface to James Clark's expat library.

perl-xml-dom-xpath

Homepage:
Spack package:
Versions:
0.14
Build Dependencies:
perl, perl-xml-dom, perl-xml-xpathengine
Link Dependencies:
perl
Run Dependencies:
perl, perl-xml-dom, perl-xml-xpathengine
Description:
XML::DOM::XPath allows you to use XML::XPath methods to query a DOM. This is often much easier than relying only on getElementsByTagName.

perl-xml-filter-buffertext

Homepage:
Spack package:
Versions:
1.01
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
This is a very simple filter. One common cause of grief (and programmer error) is that XML parsers aren't required to provide character events in one chunk. They can, but are not forced to, and most don't. This filter does the trivial but oft-repeated task of putting all characters into a single event.

perl-xml-libxml

Homepage:
Spack package:
Versions:
2.0201
Build Dependencies:
perl, libxml2, perl-xml-namespacesupport, perl-xml-sax, perl-xml-sax-base, perl-alien-libxml2
Link Dependencies:
perl, libxml2
Run Dependencies:
perl, perl-xml-namespacesupport, perl-xml-sax, perl-xml-sax-base
Description:
This module is an interface to libxml2, providing XML and HTML parsers with DOM, SAX and XMLReader interfaces, a large subset of DOM Layer 3 interface and a XML::XPath-like interface to XPath API of libxml2. The module is split into several packages which are not described in this section; unless stated otherwise, you only need to use XML::LibXML; in your programs.

perl-xml-libxslt

Homepage:
Spack package:
Versions:
1.96
Build Dependencies:
perl, libxslt, perl-xml-libxml
Link Dependencies:
perl, libxslt, perl-xml-libxml
Run Dependencies:
perl
Description:
Interface to the GNOME libxslt library.

perl-xml-namespacesupport

Homepage:
Spack package:
Versions:
1.12_9
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
This module offers a simple to process namespaced XML names (unames) from within any application that may need them. It also helps maintain a prefix to namespace URI map, and provides a number of basic checks.

perl-xml-parser

Homepage:
Spack package:
Versions:
2.44
Build Dependencies:
perl, expat, perl-libwww-perl
Link Dependencies:
perl, expat
Run Dependencies:
perl, perl-libwww-perl
Description:
XML::Parser - A perl module for parsing XML documents

perl-xml-parser-lite

Homepage:
Spack package:
Versions:
0.721
Build Dependencies:
perl, perl-test-requires
Link Dependencies:
perl
Run Dependencies:
perl, perl-test-requires
Description:
Lightweight pure-perl XML Parser (based on regexps)

perl-xml-quote

Homepage:
Spack package:
Versions:
1.02
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
This module provides functions to quote/dequote strings in "xml"-way. All functions are written in XS and are very fast; they correctly process utf8, tied, overloaded variables and all the rest of perl "magic".

perl-xml-regexp

Homepage:
Spack package:
Versions:
0.04
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
This package contains regular expressions for the following XML tokens: BaseChar, Ideographic, Letter, Digit, Extender, CombiningChar, NameChar, EntityRef, CharRef, Reference, Name, NmToken, and AttValue.

perl-xml-sax

Homepage:
Spack package:
Versions:
1.02
Build Dependencies:
perl, perl-xml-namespacesupport, perl-xml-sax-base
Link Dependencies:
perl
Run Dependencies:
perl, perl-xml-namespacesupport, perl-xml-sax-base
Description:
XML::SAX is a SAX parser access API for Perl. It includes classes and APIs required for implementing SAX drivers, along with a factory class for returning any SAX parser installed on the user's system.

perl-xml-sax-base

Homepage:
Spack package:
Versions:
1.09
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
This module has a very simple task - to be a base class for PerlSAX drivers and filters. It's default behaviour is to pass the input directly to the output unchanged. It can be useful to use this module as a base class so you don't have to, for example, implement the characters() callback.

perl-xml-sax-writer

Homepage:
Spack package:
Versions:
0.57
Build Dependencies:
perl, perl-xml-filter-buffertext, perl-xml-namespacesupport, perl-xml-sax-base
Link Dependencies:
perl
Run Dependencies:
perl, perl-xml-filter-buffertext, perl-xml-namespacesupport, perl-xml-sax-base
Description:
A new XML Writer was needed to match the SAX2 effort because quite naturally no existing writer understood SAX2. My first intention had been to start patching XML::Handler::YAWriter as it had previously been my favourite writer in the SAX1 world.

perl-xml-simple

Homepage:
Spack package:
Versions:
2.24
Build Dependencies:
perl, perl-xml-parser
Link Dependencies:
perl
Run Dependencies:
perl, perl-xml-parser
Description:
An API for simple XML files

perl-xml-twig

Homepage:
Spack package:
Versions:
3.52
Build Dependencies:
perl, perl-xml-parser
Link Dependencies:
perl
Run Dependencies:
perl, perl-xml-parser
Description:
This module provides a way to process XML documents. It is build on top of XML::Parser. The module offers a tree interface to the document, while allowing you to output the parts of it that have been completely processed. It allows minimal resource (CPU and memory) usage by building the tree only for the parts of the documents that need actual processing, through the use of the twig_roots and twig_print_outside_roots options. The finish and finish_print methods also help to increase performances. XML::Twig tries to make simple things easy so it tries its best to takes care of a lot of the (usually) annoying (but sometimes necessary) features that come with XML and XML::Parser.

perl-xml-writer

Homepage:
Spack package:
Versions:
0.625
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
XML::Writer is a helper module for Perl programs that write an XML document. The module handles all escaping for attribute values and character data and constructs different types of markup, such as tags, comments, and processing instructions. By default, the module performs several well-formedness checks to catch errors during output. This behaviour can be extremely useful during development and debugging, but it can be turned off for production-grade code. The module can operate either in regular mode in or Namespace processing mode. In Namespace mode, the module will generate Namespace Declarations itself, and will perform additional checks on the output.

perl-xml-xpathengine

Homepage:
Spack package:
Versions:
0.14
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
This module provides an XPath engine, that can be re-used by other module/classes that implement trees.

perl-yaml

Homepage:
Spack package:
Versions:
1.27
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
This module has been released to CPAN as YAML::Old, and soon YAML.pm will be changed to just be a frontend interface module for all the various Perl YAML implementation modules, including YAML::Old

perl-yaml-libyaml

Homepage:
Spack package:
Versions:
0.67
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
perl
Description:
Perl YAML Serialization using XS and libyaml

petsc

Homepage:
Spack package:
Versions:
develop, 3.12.3, 3.12.2, 3.12.1, 3.12.0, 3.11.4, 3.11.3, 3.11.2, 3.11.1, 3.11.0, 3.10.5, 3.10.4, 3.10.3, 3.10.2, 3.10.1, 3.10.0, 3.9.4, 3.9.3, 3.9.2, 3.9.1, 3.9.0, 3.8.4, 3.8.3, 3.8.2, 3.8.1, 3.8.0, 3.7.7, 3.7.6, 3.7.5, 3.7.4, 3.7.2, 3.6.4, 3.6.3, 3.5.3, 3.5.2, 3.5.1, 3.4.4, xsdk-0.2.0
Build Dependencies:
sowing, blas, lapack, mpi, python, metis, hdf5, zlib, parmetis, hypre, superlu-dist, mumps, scalapack, trilinos, fftw, suite-sparse, libx11
Link Dependencies:
sowing, blas, lapack, mpi, metis, hdf5, zlib, parmetis, hypre, superlu-dist, mumps, scalapack, trilinos, fftw, suite-sparse, libx11
Description:
PETSc is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations.

pexsi

Homepage:
Spack package:
Versions:
0.10.2, 0.9.2, 0.9.0
Build Dependencies:
parmetis, superlu-dist
Link Dependencies:
parmetis, superlu-dist
Description:
The PEXSI library is written in C++, and uses message passing interface (MPI) to parallelize the computation on distributed memory computing systems and achieve scalability on more than 10,000 processors. The Pole EXpansion and Selected Inversion (PEXSI) method is a fast method for electronic structure calculation based on Kohn-Sham density functional theory. It efficiently evaluates certain selected elements of matrix functions, e.g., the Fermi-Dirac function of the KS Hamiltonian, which yields a density matrix. It can be used as an alternative to diagonalization methods for obtaining the density, energy and forces in electronic structure calculations.

pfft

Homepage:
Spack package:
Versions:
1.0.8-alpha
Build Dependencies:
fftw, mpi
Link Dependencies:
fftw, mpi
Description:
PFFT is a software library for computing massively parallel, fast Fourier transformations on distributed memory architectures. PFFT can be understood as a generalization of FFTW-MPI to multidimensional data decomposition.

pflotran

Homepage:
Spack package:
Versions:
develop, xsdk-0.5.0, xsdk-0.4.0, xsdk-0.3.0, xsdk-0.2.0
Build Dependencies:
mpi, hdf5, petsc
Link Dependencies:
mpi, hdf5, petsc
Description:
PFLOTRAN is an open source, state-of-the-art massively parallel subsurface flow and reactive transport code.

pfunit

Homepage:
Spack package:
Versions:
3.3.3, 3.3.2, 3.3.1, 3.3.0, 3.2.10, 3.2.9
Build Dependencies:
cmake, python, mpi
Link Dependencies:
mpi
Run Dependencies:
python
Description:
pFUnit is a unit testing framework enabling JUnit-like testing of serial and MPI-parallel software written in Fortran.

pgdspider

Homepage:
Spack package:
Versions:
2.1.1.2
Build Dependencies:
java, bcftools, bwa, samtools
Link Dependencies:
bcftools, bwa, samtools
Run Dependencies:
java
Description:
"PGDSpider is a powerful automated data conversion tool for population genetic and genomics programs

pgi

Homepage:
Spack package:
Versions:
19.4, 19.1, 18.10, 18.4, 17.10, 17.4
Description:
PGI optimizing multi-core x64 compilers for Linux, MacOS & Windows with support for debugging and profiling of local MPI processes. Note: The PGI compilers are licensed software. You will need to create an account on the PGI homepage and download PGI yourself. Spack will search your current directory for the download tarball. Alternatively, add this file to a mirror so that Spack can find it. For instructions on how to set up a mirror, see http://spack.readthedocs.io/en/latest/mirrors.html

pgmath

Homepage:
Spack package:
Versions:
master, 20190329, 20181226, 20180921, 20180612
Build Dependencies:
cmake, awk
Description:
Flang's math library

phantompeakqualtools

Homepage:
Spack package:
Versions:
1.2
Build Dependencies:
r, awk, samtools, r-phantompeakqualtools
Link Dependencies:
r, awk, samtools
Run Dependencies:
r, r-phantompeakqualtools
Description:
This package computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data.

phast

Homepage:
Spack package:
Versions:
1.4
Build Dependencies:
clapack
Link Dependencies:
clapack
Description:
PHAST is a freely available software package for comparative and evolutionary genomics.

phasta

Homepage:
Spack package:
Versions:
develop, 0.0.1
Build Dependencies:
cmake, mpi
Link Dependencies:
mpi
Description:
SCOREC RPI's Parallel Hierarchic Adaptive Stabilized Transient Analysis (PHASTA) of compressible and incompressible Navier Stokes equations.

phist

Homepage:
Spack package:
Versions:
develop, master, 1.8.0, 1.7.5, 1.7.4, 1.7.3, 1.7.2, 1.6.1, 1.6.0, 1.4.3
Build Dependencies:
cmake, blas, lapack, python, mpi, trilinos, petsc, eigen, ghost, parmetis
Link Dependencies:
blas, lapack, mpi, trilinos, petsc, eigen, ghost, parmetis
Description:
The Pipelined, Hybrid-parallel Iterative Solver Toolkit provides implementations of and interfaces to block iterative solvers for sparse linear and eigenvalue problems. In contrast to other libraries we support multiple backends (e.g. Trilinos, PETSc and our own optimized kernels), and interfaces in multiple languages such as C, C++, Fortran 2003 and Python. PHIST has a clear focus on portability and hardware performance: in particular support row-major storage of block vectors and using GPUs (via the ghost library or Trilinos/Tpetra).

phrap-crossmatch-swat

Homepage:
Spack package:
Versions:
1.090518
Description:
phrap is a program for assembling shotgun DNA sequence data. cross_match is a general purpose utility for comparing any two DNA sequence sets using a 'banded' version of swat. swat is a program for searching one or more DNA or protein query sequences, or a query profile, against a sequence database

phred

Homepage:
Spack package:
Versions:
071220
Description:
The phred software reads DNA sequencing trace files, calls bases, and assigns a quality value to each called base.

phylip

Homepage:
Spack package:
Versions:
3.697
Description:
PHYLIP (the PHYLogeny Inference Package) is a package of programs for inferring phylogenies (evolutionary trees).

phyluce

Homepage:
Spack package:
Versions:
1.6.7
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python, py-setuptools, py-biopython, abyss, bcftools, bwa, gatk, gblocks, lastz, mafft, muscle, picard, raxml, samtools, seqtk, spades, trimal, trinity, velvet
Description:
phyluce (phy-loo-chee) is a software package that was initially developed for analyzing data collected from ultraconserved elements in organismal genomes

picard

Homepage:
Spack package:
Versions:
2.20.8, 2.19.0, 2.18.3, 2.18.0, 2.17.0, 2.16.0, 2.15.0, 2.13.2, 2.10.0, 2.9.4, 2.9.3, 2.9.2, 2.9.0, 2.8.3, 2.6.0, 1.140
Run Dependencies:
java
Description:
Picard is a set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

picsar

Homepage:
Spack package:
Versions:
develop
Build Dependencies:
mpi, fftw
Link Dependencies:
mpi, fftw
Description:
PICSAR is a high performance library of optimized versions of the key functionalities of the PIC loop.

picsarlite

Homepage:
Spack package:
Versions:
develop, 0.1
Build Dependencies:
mpi, fftw
Link Dependencies:
mpi, fftw
Description:
PICSARlite is a self-contained proxy that adequately portrays the computational loads and dataflow of more complex PIC codes.

pidx

Homepage:
Spack package:
Versions:
1.0
Build Dependencies:
cmake, mpi
Link Dependencies:
mpi
Description:
PIDX Parallel I/O Library. PIDX is an efficient parallel I/O library that reads and writes multiresolution IDX data files.

pig

Homepage:
Spack package:
Versions:
0.7.0
Description:
Pig is a dataflow programming environment for processing very large files. Pig's language is called Pig Latin. A Pig Latin program consists of a directed acyclic graph where each node represents an operation that transforms data.

pigz

Homepage:
Spack package:
Versions:
2.4, 2.3.4
Build Dependencies:
zlib
Link Dependencies:
zlib
Description:
A parallel implementation of gzip for modern multi-processor, multi-core machines.

pilon

Homepage:
Spack package:
Versions:
1.22, 1.13
Run Dependencies:
java
Description:
Pilon is an automated genome assembly improvement and variant detection tool.

pindel

Homepage:
Spack package:
Versions:
0.2.5b8, 0.2.5b6, 0.2.5b5, 0.2.5b4, 0.2.5b1, 0.2.5a7, 0.2.5
Build Dependencies:
htslib
Link Dependencies:
htslib
Description:
Pindel can detect breakpoints from next-gen sequence data.

pipework

Homepage:
Spack package:
Versions:
master
Description:
Pipework lets you connect together containers in arbitrarily complex scenarios.

piranha

Homepage:
Spack package:
Versions:
develop, 0.5
Build Dependencies:
cmake, python, boost, bzip2, gmp, mpfr
Link Dependencies:
python, boost, bzip2, gmp, mpfr
Description:
Piranha is a computer-algebra library for the symbolic manipulation of sparse multivariate polynomials and other closely-related symbolic objects (such as Poisson series).

pism

Homepage:
Spack package:
Versions:
develop, 1.1.4, 0.7.x, icebin
Build Dependencies:
cmake, fftw, gsl, mpi, netcdf-c, petsc, udunits, proj, everytrace, python, py-matplotlib, py-numpy
Link Dependencies:
fftw, gsl, mpi, netcdf-c, petsc, udunits, proj, everytrace, python, py-matplotlib, py-numpy
Description:
Parallel Ice Sheet Model

pixman

Homepage:
Spack package:
Versions:
0.38.4, 0.38.0, 0.34.0, 0.32.6
Build Dependencies:
pkgconfig, libpng
Link Dependencies:
libpng
Description:
The Pixman package contains a library that provides low-level pixel manipulation features such as image compositing and trapezoid rasterization.

pixz

Homepage:
Spack package:
Versions:
1.0.6
Build Dependencies:
xz, libarchive
Link Dependencies:
xz, libarchive
Description:
Pixz (pronounced pixie) is a parallel, indexing version of xz.

pkg-config

Homepage:
Spack package:
Versions:
0.29.2, 0.29.1, 0.28
Description:
pkg-config is a helper tool used when compiling applications and libraries

pkgconf

Homepage:
Spack package:
Versions:
1.6.3, 1.6.1, 1.6.0, 1.5.4, 1.4.2, 1.4.0, 1.3.10, 1.3.8
Description:
pkgconf is a program which helps to configure compiler and linker flags for development frameworks. It is similar to pkg-config from freedesktop.org, providing additional functionality while also maintaining compatibility.

pktools

Homepage:
Spack package:
Versions:
2.6.7.1, 2.6.7
Build Dependencies:
cmake, gdal, gsl, armadillo, nlopt, boost, fann, liblas
Link Dependencies:
gdal, gsl, armadillo, nlopt, boost, fann, liblas
Description:
Processing Kernel for geospatial data

planck-likelihood

Homepage:
Spack package:
Versions:
2.00
Build Dependencies:
blas, cfitsio, lapack
Link Dependencies:
blas, cfitsio, lapack
Description:
2015 Cosmic Microwave Background (CMB) spectra and likelihood code

plasma

Homepage:
Spack package:
Versions:
develop, 19.8.1, 19.8.0, 18.11.1, 18.11.0, 18.10.0, 18.9.0, 17.1
Build Dependencies:
cmake, lua, blas, lapack
Link Dependencies:
lua, blas, lapack
Description:
Parallel Linear Algebra Software for Multicore Architectures, PLASMA is a software package for solving problems in dense linear algebra using multicore processors and Xeon Phi coprocessors. PLASMA provides implementations of state-of-the-art algorithms using cutting-edge task scheduling techniques. PLASMA currently offers a collection of routines for solving linear systems of equations, least squares problems, eigenvalue problems, and singular value problems.

platypus

Homepage:
Spack package:
Versions:
0.8.1
Build Dependencies:
python, py-cython, htslib
Link Dependencies:
htslib
Run Dependencies:
python
Description:
A Haplotype-Based Variant Caller For Next Generation Sequence Data

plplot

Homepage:
Spack package:
Versions:
5.15.0, 5.14.0, 5.13.0, 5.12.0, 5.11.0
Build Dependencies:
cmake, java, lua, pango, py-numpy, python, qt, tcl, wxwidgets, freetype, gtkplus, libx11, qhull, swig
Link Dependencies:
java, lua, pango, qt, tcl, wxwidgets, freetype, gtkplus, libx11, qhull, swig
Run Dependencies:
py-numpy, python
Description:
PLplot is a cross-platform package for creating scientific plots.

plumed

Homepage:
Spack package:
Versions:
master, 2.6b, 2.5.3, 2.5.2, 2.5.1, 2.5.0, 2.4.6, 2.4.4, 2.4.2, 2.4.1, 2.3.5, 2.3.3, 2.3.0, 2.2.4, 2.2.3
Build Dependencies:
zlib, blas, lapack, libmatheval, mpi, gsl, autoconf, automake, libtool
Link Dependencies:
zlib, blas, lapack, libmatheval, mpi, gsl
Description:
PLUMED is an open source library for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines. Free energy calculations can be performed as a function of many order parameters with a particular focus on biological problems, using state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The software, written in C++, can be easily interfaced with both fortran and C/C++ codes.

pmdk

Homepage:
Spack package:
Versions:
develop, 1.8, 1.7, 1.6, 1.5
Build Dependencies:
ncurses
Link Dependencies:
ncurses
Description:
The Persistent Memory Development Kit (PMDK), formerly known as NVML, is a library for using memory-mapped persistence, optimized specifically for persistent memory

pmgr-collective

Homepage:
Spack package:
Versions:
1.0
Description:
PMGR_COLLECTIVE provides a scalable network for bootstrapping MPI jobs.

pmix

Homepage:
Spack package:
Versions:
3.1.3, 3.1.2, 3.0.2, 3.0.1, 3.0.0, 2.2.2, 2.1.4, 2.1.3, 2.1.2, 2.0.1, 1.2.5
Build Dependencies:
libevent, hwloc
Link Dependencies:
libevent, hwloc
Description:
The Process Management Interface (PMI) has been used for quite some time as a means of exchanging wireup information needed for interprocess communication. However, meeting the significant orchestration challenges presented by exascale systems requires that the process-to-system interface evolve to permit a tighter integration between the different components of the parallel application and existing and future SMS solutions. PMI Exascale (PMIx) addresses these needs by providing an extended version of the PMI definitions specifically designed to support exascale and beyond environments by: (a) adding flexibility to the functionality expressed in the existing APIs, (b) augmenting the interfaces with new APIs that provide extended capabilities, (c) forging a collaboration between subsystem providers including resource manager, fabric, file system, and programming library developers, (d) establishing a standards-like body for maintaining the definitions, and (e) providing a reference implementation of the PMIx standard that demonstrates the desired level of scalability while maintaining strict separation between it and the standard itself.

pmlib

Homepage:
Spack package:
Versions:
master, 6.4.1
Build Dependencies:
cmake, mpi
Link Dependencies:
mpi
Description:
This library records the statistics information of run-time performance and the trace information of a user code and reports its summary. The PMlib is able to use for both serial and parallel environments including hybrid(OpenMP & MPI) code. In addition, PAPI interface allows us to access the information of build-in hardware counter.

pnfft

Homepage:
Spack package:
Versions:
1.0.7-alpha
Build Dependencies:
pfft, gsl
Link Dependencies:
pfft, gsl
Description:
PNFFT is a parallel software library for the calculation of three- dimensional nonequispaced FFTs.

pngquant

Homepage:
Spack package:
Versions:
2.12.5
Build Dependencies:
libpng
Link Dependencies:
libpng
Description:
pngquant is a command-line utility and a library for lossy compression of PNG images.

pngwriter

Homepage:
Spack package:
Versions:
develop, master, 0.7.0, 0.6.0, 0.5.6
Build Dependencies:
cmake, libpng, zlib, freetype
Link Dependencies:
libpng, zlib, freetype
Description:
PNGwriter is a very easy to use open source graphics library that uses PNG as its output format. The interface has been designed to be as simple and intuitive as possible. It supports plotting and reading pixels in the RGB (red, green, blue), HSV (hue, saturation, value/brightness) and CMYK (cyan, magenta, yellow, black) colour spaces, basic shapes, scaling, bilinear interpolation, full TrueType antialiased and rotated text support, bezier curves, opening existing PNG images and more.

pnmpi

Homepage:
Spack package:
Versions:
1.7
Build Dependencies:
cmake, argp-standalone, binutils, help2man, doxygen, mpi
Link Dependencies:
argp-standalone, binutils, help2man, doxygen, mpi
Description:
PnMPI is a dynamic MPI tool infrastructure that builds on top of the standardized PMPI interface.

poamsa

Homepage:
Spack package:
Versions:
2.0
Description:
POA is Partial Order Alignment, a fast program for multiple sequence alignment in bioinformatics. Its advantages are speed, scalability, sensitivity, and the superior ability to handle branching / indels in the alignment.

pocl

Homepage:
Spack package:
Versions:
master, 1.1, 1.0, 0.14, 0.13, 0.12, 0.11, 0.10
Build Dependencies:
cmake, hwloc, libtool, pkgconfig, llvm
Link Dependencies:
hwloc, libtool, llvm
Run Dependencies:
libtool
Description:
Portable Computing Language (pocl) is an open source implementation of the OpenCL standard which can be easily adapted for new targets and devices, both for homogeneous CPU and heterogeneous GPUs/accelerators.

polymake

Homepage:
Spack package:
Versions:
3.5, 3.0r2, 3.0r1
Build Dependencies:
bliss, boost, cddlib, gmp, lrslib, mpfr, ninja, perl, perl-json, perl-termreadkey, perl-term-readline-gnu, perl-xml-libxml, perl-xml-libxslt, perl-xml-writer, ppl, readline
Link Dependencies:
bliss, boost, cddlib, gmp, lrslib, mpfr, perl, perl-json, perl-termreadkey, perl-term-readline-gnu, perl-xml-libxml, perl-xml-libxslt, perl-xml-writer, ppl, readline
Description:
polymake is open source software for research in polyhedral geometry

poppler

Homepage:
Spack package:
Versions:
master, 0.79.0, 0.77.0, 0.72.0, 0.65.0, 0.64.0, 0.61.1
Build Dependencies:
cmake, pkgconfig, poppler-data, fontconfig, freetype, lcms, glib, gobject-introspection, curl, openjpeg, qt, zlib, cairo, libiconv, jpeg, libpng, libtiff
Link Dependencies:
fontconfig, freetype, lcms, glib, gobject-introspection, curl, openjpeg, qt, zlib, cairo, libiconv, jpeg, libpng, libtiff
Run Dependencies:
poppler-data
Description:
Poppler is a PDF rendering library based on the xpdf-3.0 code base.

poppler-data

Homepage:
Spack package:
Versions:
0.4.9
Build Dependencies:
cmake
Description:
This package consists of encoding files for use with poppler. The encoding files are optional and poppler will automatically read them if they are present. When installed, the encoding files enables poppler to correctly render CJK and Cyrrilic properly. While poppler is licensed under the GPL, these encoding files have different license, and thus distributed separately.

popt

Homepage:
Spack package:
Versions:
1.16
Description:
The popt library parses command line options.

porta

Homepage:
Spack package:
Versions:
1.4.1
Build Dependencies:
libtool
Description:
PORTA is a collection of routines for analyzing polytopes and polyhedra

portage

Homepage:
Spack package:
Versions:
develop, 1.2.2, 1.1.1, 1.1.0
Build Dependencies:
cmake, mpi, lapack, boost
Link Dependencies:
mpi, lapack, boost
Description:
Portage is a framework that computational physics applications can use to build a highly customized, hybrid parallel (MPI+X) conservative remapping library for transfer of field data between meshes.

portcullis

Homepage:
Spack package:
Versions:
1.1.2
Build Dependencies:
autoconf, automake, libtool, m4, zlib, samtools, python, py-setuptools, py-pandas, py-sphinx
Link Dependencies:
py-sphinx
Run Dependencies:
python, py-setuptools, py-pandas
Description:
PORTable CULLing of Invalid Splice junctions

postgresql

Homepage:
Spack package:
Versions:
11.2, 11.1, 11.0, 10.7, 10.6, 10.5, 10.4, 10.3, 10.2, 10.1, 10.0, 9.6.12, 9.6.11, 9.5.3, 9.3.4
Build Dependencies:
readline, libedit, openssl, tcl, perl, python
Link Dependencies:
readline, libedit, openssl, tcl, perl, python
Description:
PostgreSQL is a powerful, open source object-relational database system. It has more than 15 years of active development and a proven architecture that has earned it a strong reputation for reliability, data integrity, and correctness.

powerapi

Homepage:
Spack package:
Versions:
2020-01-30, 1.1.1
Build Dependencies:
autoconf, automake, libtool, m4, hwloc, mpi
Link Dependencies:
autoconf, automake, libtool, m4, hwloc, mpi
Description:
This software is a reference implementation of the PowerAPI

ppl

Homepage:
Spack package:
Versions:
1.2, 1.1
Build Dependencies:
gmp
Link Dependencies:
gmp
Description:
The Parma Polyhedra Library (PPL) provides numerical abstractions especially targeted at applications in the field of analysis and verification of complex systems. These abstractions include convex polyhedra, some special classes of polyhedra shapes that offer interesting complexity/precision tradeoffs, and grids which represent regularly spaced points that satisfy a set of linear congruence relations. The library also supports finite powersets and products of polyhedra and grids, a mixed integer linear programming problem solver using an exact-arithmetic version of the simplex algorithm, a parametric integer programming solver, and primitives for termination analysis via the automatic synthesis of linear ranking functions.

pplacer

Homepage:
Spack package:
Versions:
1.1.alpha19
Description:
Pplacer places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference alignment. Pplacer is designed to be fast, to give useful information about uncertainty, and to offer advanced visualization and downstream analysis.

prank

Homepage:
Spack package:
Versions:
170427
Build Dependencies:
mafft, exonerate, bpp-suite
Link Dependencies:
mafft, exonerate, bpp-suite
Description:
A powerful multiple sequence alignment browser.

precice

Homepage:
Spack package:
Versions:
develop, 2.0.0, 1.6.1, 1.6.0, 1.5.2, 1.5.1, 1.5.0, 1.4.1, 1.4.0, 1.3.0, 1.2.0
Build Dependencies:
cmake, boost, eigen, libxml2, mpi, petsc, python, py-numpy
Link Dependencies:
boost, eigen, libxml2, mpi, petsc
Run Dependencies:
python, py-numpy
Description:
preCICE (Precise Code Interaction Coupling Environment) is a coupling library for partitioned multi-physics simulations. Partitioned means that preCICE couples existing programs (solvers) capable of simulating a subpart of the complete physics involved in a simulation.

presentproto

Homepage:
Spack package:
Versions:
1.0
Build Dependencies:
pkgconfig, util-macros
Description:
Present protocol specification and Xlib/Xserver headers.

preseq

Homepage:
Spack package:
Versions:
2.0.2
Build Dependencies:
samtools, gsl
Link Dependencies:
samtools, gsl
Description:
The preseq package is aimed at predicting and estimating the complexity of a genomic sequencing library, equivalent to predicting and estimating the number of redundant reads from a given sequencing depth and how many will be expected from additional sequencing using an initial sequencing experiment.

price

Homepage:
Spack package:
Versions:
140408
Description:
PRICE (Paired-Read Iterative Contig Extension): a de novo genome assembler implemented in C++.

primer3

Homepage:
Spack package:
Versions:
2.3.7
Description:
Primer3 is a widely used program for designing PCR primers (PCR = "Polymerase Chain Reaction"). PCR is an essential and ubiquitous tool in genetics and molecular biology. Primer3 can also design hybridization probes and sequencing primers.

prinseq-lite

Homepage:
Spack package:
Versions:
0.20.4
Run Dependencies:
perl, perl-cairo, perl-digest-md5, perl-json
Description:
PRINSEQ will help you to preprocess your genomic or metagenomic sequence data in FASTA or FASTQ format.

printproto

Homepage:
Spack package:
Versions:
1.0.5
Build Dependencies:
pkgconfig, util-macros
Description:
Xprint extension to the X11 protocol - a portable, network-transparent printing system.

prng

Homepage:
Spack package:
Versions:
3.0.2
Build Dependencies:
automake, autoconf, libtool, m4
Description:
Pseudo-Random Number Generator library.

probconsrna

Homepage:
Spack package:
Versions:
2005-6-7
Description:
Experimental version of PROBCONS with parameters estimated via unsupervised training on BRAliBASE

procps

Homepage:
Spack package:
Versions:
master, 3.3.15
Build Dependencies:
autoconf, automake, libtool, m4, pkgconfig, libiconv, gettext, ncurses
Link Dependencies:
libiconv, gettext, ncurses
Test Dependencies:
dejagnu
Description:
Command line and full screen utilities for browsing procfs, a "pseudo" file system dynamically generated by the kernel to provide information about the status of entries in its process table.

prodigal

Homepage:
Spack package:
Versions:
2.6.3
Description:
Fast, reliable protein-coding gene prediction for prokaryotic genomes.

proj

Homepage:
Spack package:
Versions:
6.2.0, 6.1.0, 6.0.0, 5.2.0, 5.1.0, 5.0.1, 4.9.2, 4.9.1, 4.8.0, 4.7.0, 4.6.1
Build Dependencies:
pkgconfig, sqlite
Link Dependencies:
sqlite
Description:
PROJ is a generic coordinate transformation software, that transforms geospatial coordinates from one coordinate reference system (CRS) to another. This includes cartographic projections as well as geodetic transformations.

protobuf

Homepage:
Spack package:
Versions:
3.11.2, 3.11.1, 3.11.0, 3.10.1, 3.10.0, 3.9.2, 3.9.1, 3.7.1, 3.7.0, 3.6.1, 3.5.2, 3.5.1.1, 3.5.1, 3.5.0.1, 3.5.0, 3.4.1, 3.4.0, 3.3.0, 3.2.0, 3.1.0, 3.0.2
Build Dependencies:
cmake, zlib
Link Dependencies:
zlib
Description:
Google's data interchange format.

protobuf-c

Homepage:
Spack package:
Versions:
1.3.2
Build Dependencies:
protobuf, pkgconfig
Link Dependencies:
protobuf
Description:
Protocol Buffers implementation in C

proxymngr

Homepage:
Spack package:
Versions:
1.0.4
Build Dependencies:
libice, libxt, lbxproxy, xproto, xproxymanagementprotocol, pkgconfig, util-macros
Link Dependencies:
libice, libxt, lbxproxy
Description:
The proxy manager (proxymngr) is responsible for resolving requests from xfindproxy (and other similar clients), starting new proxies when appropriate, and keeping track of all of the available proxy services. The proxy manager strives to reuse existing proxies whenever possible.

prrte

Homepage:
Spack package:
Versions:
develop, 1.0.0
Build Dependencies:
pmix, libevent, hwloc, perl, m4, autoconf, automake, libtool, flex
Link Dependencies:
pmix, libevent, hwloc
Description:
PRRTE is the Reference RunTime Environment implementation for PMIx. It is capable of operating within a host SMS. The reference RTE therefore provides an easy way of exploring PMIx capabilities and testing PMIx- based applications outside of a PMIx-enabled environment.

pruners-ninja

Homepage:
Spack package:
Versions:
1.0.1, 1.0.0
Build Dependencies:
mpi, autoconf, automake, libtool
Link Dependencies:
mpi
Description:
NINJA: Noise Inject agent tool to expose subtle and unintended message races.

ps-lite

Homepage:
Spack package:
Versions:
master, 20170328
Build Dependencies:
cmake, protobuf, libzmq
Link Dependencies:
protobuf, libzmq
Description:
ps-lite is A light and efficient implementation of the parameter server framework.

psi4

Homepage:
Spack package:
Versions:
1.3.2
Build Dependencies:
cmake, blas, lapack, boost, python, py-numpy
Link Dependencies:
blas, lapack, boost, python
Run Dependencies:
py-numpy
Description:
Psi4 is an open-source suite of ab initio quantum chemistry programs designed for efficient, high-accuracy simulations of a variety of molecular properties.

pslib

Homepage:
Spack package:
Versions:
0.4.5
Build Dependencies:
jpeg, libpng
Link Dependencies:
jpeg, libpng
Description:
C-library to create PostScript files on the fly.

psm

Homepage:
Spack package:
Versions:
2017-04-28, 3.3
Build Dependencies:
libuuid
Link Dependencies:
libuuid
Description:
Intel Performance scaled messaging library

psmc

Homepage:
Spack package:
Versions:
2016-1-21
Link Dependencies:
zlib
Description:
mplementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model

pstreams

Homepage:
Spack package:
Versions:
1.0.1
Description:
C++ wrapper for the POSIX.2 functions popen(3) and pclose(3)

pugixml

Homepage:
Spack package:
Versions:
1.8.1
Build Dependencies:
cmake
Description:
Light-weight, simple, and fast XML parser for C++ with XPath support

pumi

Homepage:
Spack package:
Versions:
master, 2.2.2, 2.2.1, 2.2.0, 2.1.0
Build Dependencies:
cmake, mpi, zoltan, simmetrix-simmodsuite
Link Dependencies:
mpi, zoltan, simmetrix-simmodsuite
Description:
SCOREC RPI's Parallel Unstructured Mesh Infrastructure (PUMI). An efficient distributed mesh data structure and methods to support parallel adaptive analysis including general mesh-based operations, such as mesh entity creation/deletion, adjacency and geometric classification, iterators, arbitrary (field) data attachable to mesh entities, efficient communication involving entities duplicated across multiple tasks, migration of mesh entities between tasks, and dynamic load balancing.

pv

Homepage:
Spack package:
Versions:
1.6.6
Description:
Pipe Viewer - is a terminal-based tool for monitoring the progress of data through a pipeline

pvm

Homepage:
Spack package:
Versions:
3.4.6
Description:
PVM (Parallel Virtual Machine) is a software package that permits a heterogeneous collection of Unix and/or Windows computers hooked together by a network to be used as a single large parallel computer.

pxz

Homepage:
Spack package:
Versions:
develop, 4.999.9beta.20091201git
Build Dependencies:
xz
Link Dependencies:
xz
Description:
Pxz is a parallel LZMA compressor using liblzma.

py-3to2

Homepage:
Spack package:
Versions:
1.1.1
Build Dependencies:
python
Link Dependencies:
python
Run Dependencies:
python
Description:
lib3to2 is a set of fixers that are intended to backport code written for Python version 3.x into Python version 2.x.

py-4suite-xml

Homepage:
Spack package:
Versions:
1.0.2
Build Dependencies:
python
Link Dependencies:
python
Run Dependencies:
python
Description:
XML tools and libraries for Python: Domlette, XPath, XSLT, XPointer, XLink, XUpdate

py-absl-py

Homepage:
Spack package:
Versions:
0.7.1, 0.7.0, 0.1.6
Build Dependencies:
python, py-setuptools, py-six, py-enum34
Link Dependencies:
python
Run Dependencies:
python, py-six, py-enum34
Description:
This repository is a collection of Python library code for building Python applications. The code is collected from Google's own Python code base, and has been extensively tested and used in production.

py-adios

Homepage:
Spack package:
Versions:
develop, 1.13.0, 1.12.0, 1.11.1, 1.11.0, 1.10.0, 1.9.0
Build Dependencies:
python, adios, py-numpy, mpi, py-cython
Link Dependencies:
python, adios, mpi
Run Dependencies:
python, adios, py-numpy, py-mpi4py
Description:
NumPy bindings of ADIOS1

py-advancedhtmlparser

Homepage:
Spack package:
Versions:
8.1.4
Build Dependencies:
python, py-setuptools, py-queryablelist
Link Dependencies:
python
Run Dependencies:
python, py-queryablelist
Description:
Fast Indexed python HTML parser which builds a DOM node tree, providing common getElementsBy* functions for scraping, testing, modification, and formatting

py-aenum

Homepage:
Spack package:
Versions:
2.1.2
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Advanced Enumerations (compatible with Python's stdlib Enum), NamedTuples, and NamedConstants.

py-affine

Homepage:
Spack package:
Versions:
2.1.0
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Matrices describing affine transformation of the plane.

py-agate

Homepage:
Spack package:
Versions:
1.6.1
Build Dependencies:
python, py-setuptools, py-six, py-pytimeparse, py-parsedatetime, py-babel, py-isodate, py-python-slugify, py-leather
Link Dependencies:
python
Run Dependencies:
python, py-six, py-pytimeparse, py-parsedatetime, py-babel, py-isodate, py-python-slugify, py-leather
Description:
agate is a Python data analysis library that is optimized for humans instead of machines. It is an alternative to numpy and pandas that solves real-world problems with readable code.

py-agate-dbf

Homepage:
Spack package:
Versions:
0.2.1
Build Dependencies:
python, py-setuptools, py-agate, py-dbfread
Link Dependencies:
python
Run Dependencies:
python, py-agate, py-dbfread
Description:
agate-dbf adds read support for dbf files to agate.

py-agate-excel

Homepage:
Spack package:
Versions:
0.2.3
Build Dependencies:
python, py-setuptools, py-agate, py-xlrd, py-openpyxl
Link Dependencies:
python
Run Dependencies:
python, py-agate, py-xlrd, py-openpyxl
Description:
agate-excel adds read support for Excel files (xls and xlsx) to agate.

py-agate-sql

Homepage:
Spack package:
Versions:
0.5.4
Build Dependencies:
python, py-setuptools, py-agate, py-sqlalchemy
Link Dependencies:
python
Run Dependencies:
python, py-agate, py-sqlalchemy
Description:
agate-sql adds SQL read/write support to agate.

py-alabaster

Homepage:
Spack package:
Versions:
0.7.12, 0.7.10, 0.7.9
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Test Dependencies:
py-pygments
Description:
Alabaster is a visually (c)lean, responsive, configurable theme for the Sphinx documentation system.

py-alembic

Homepage:
Spack package:
Versions:
1.0.7
Build Dependencies:
python, py-setuptools, py-sqlalchemy, py-mako, py-python-dateutil, py-python-editor
Link Dependencies:
python
Run Dependencies:
python, py-sqlalchemy, py-mako, py-python-dateutil, py-python-editor
Description:
Alembic is a database migrations tool.

py-altgraph

Homepage:
Spack package:
Versions:
0.16.1
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
altgraph is a fork of graphlib: a graph (network) package for constructing graphs, BFS and DFS traversals, topological sort, shortest paths, etc. with graphviz output.

py-amqp

Homepage:
Spack package:
Versions:
2.5.2, 2.4.2, 2.4.1
Build Dependencies:
python, py-setuptools, py-vine
Link Dependencies:
python
Run Dependencies:
python, py-vine
Description:
Low-level AMQP client for Python (fork of amqplib).

py-ansible

Homepage:
Spack package:
Versions:
2.9.2, 2.9.1, 2.9.0, 2.8.7, 2.8.6, 2.7.15, 2.7.14, 2.6.20
Build Dependencies:
python, py-setuptools, py-jinja2, py-pyyaml, py-cryptography
Link Dependencies:
python
Run Dependencies:
python, py-jinja2, py-pyyaml, py-cryptography
Description:
Ansible is a radically simple IT automation platform that makes your applications and systems easier to deploy.

py-antlr4-python3-runtime

Homepage:
Spack package:
Versions:
4.7.2
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
This package provides runtime libraries required to use parsers generated for the Python3 language by version 4 of ANTLR (ANother Tool for Language Recognition).

py-apache-libcloud

Homepage:
Spack package:
Versions:
1.2.1
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Python library for multiple cloud provider APIs

py-apipkg

Homepage:
Spack package:
Versions:
1.5, 1.4
Build Dependencies:
python, py-setuptools, py-setuptools-scm
Link Dependencies:
python
Run Dependencies:
python
Test Dependencies:
py-py, py-pytest
Description:
apipkg: namespace control and lazy-import mechanism

py-appdirs

Homepage:
Spack package:
Versions:
1.4.3, 1.4.0
Build Dependencies:
python
Link Dependencies:
python
Run Dependencies:
python
Description:
A small Python module for determining appropriate platform-specific dirs, e.g. a "user data dir".

py-appnope

Homepage:
Spack package:
Versions:
0.1.0
Build Dependencies:
python
Link Dependencies:
python
Run Dependencies:
python
Description:
Disable App Nap on OS X 10.9

py-apscheduler

Homepage:
Spack package:
Versions:
3.3.1, 2.1.0
Build Dependencies:
python, py-setuptools, py-six, py-pytz, py-tzlocal
Link Dependencies:
python
Run Dependencies:
python, py-six, py-pytz, py-tzlocal
Description:
In-process task scheduler with Cron-like capabilities.

py-argcomplete

Homepage:
Spack package:
Versions:
1.1.1
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Bash tab completion for argparse.

py-argparse

Homepage:
Spack package:
Versions:
1.4.0
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Python command-line parsing library.

py-arrow

Homepage:
Spack package:
Versions:
0.14.7, 0.14.1
Build Dependencies:
python, py-setuptools, py-backports-functools-lru-cache, py-python-dateutil
Link Dependencies:
python
Run Dependencies:
python, py-backports-functools-lru-cache, py-python-dateutil
Test Dependencies:
py-chai, py-mock, py-pytz
Description:
Arrow is a Python library that offers a sensible and human-friendly approach to creating, manipulating, formatting and converting dates, times and timestamps. It implements and updates the datetime type, plugging gaps in functionality and providing an intelligent module API that supports many common creation scenarios. Simply put, it helps you work with dates and times with fewer imports and a lot less code.

py-asciitree

Homepage:
Spack package:
Versions:
0.3.3
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Draws ASCII trees.

py-asdf

Homepage:
Spack package:
Versions:
2.4.2
Build Dependencies:
python, py-setuptools, py-setuptools-scm, py-semantic-version, py-pyyaml, py-jsonschema, py-six, py-numpy
Link Dependencies:
python
Run Dependencies:
python, py-semantic-version, py-pyyaml, py-jsonschema, py-six, py-numpy
Description:
The Advanced Scientific Data Format (ASDF) is a next-generation interchange format for scientific data. This package contains the Python implementation of the ASDF Standard.

py-ase

Homepage:
Spack package:
Versions:
3.18.0, 3.15.0, 3.13.0
Build Dependencies:
python, py-numpy, py-matplotlib, py-scipy, py-flask
Link Dependencies:
python
Run Dependencies:
python, py-numpy, py-matplotlib, py-scipy, py-flask
Description:
The Atomic Simulation Environment (ASE) is a set of tools and Python modules for setting up, manipulating, running, visualizing and analyzing atomistic simulations.

py-asn1crypto

Homepage:
Spack package:
Versions:
0.24.0, 0.22.0
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Python ASN.1 library with a focus on performance and a pythonic API

py-aspy-yaml

Homepage:
Spack package:
Versions:
1.3.0
Build Dependencies:
python, py-setuptools, py-pyyaml
Link Dependencies:
python
Run Dependencies:
python, py-pyyaml
Description:
Some extensions to pyyaml.

py-asserts

Homepage:
Spack package:
Versions:
0.10.0, 0.9.1, 0.9.0, 0.8.6
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Stand-alone Assertions.

py-astor

Homepage:
Spack package:
Versions:
0.8.0, 0.6
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Test Dependencies:
py-nose, py-astunparse
Description:
astor is designed to allow easy manipulation of Python source via the AST.

py-astroid

Homepage:
Spack package:
Versions:
2.2.0, 1.6.6, 1.4.5, 1.4.4, 1.4.3, 1.4.2, 1.4.1
Build Dependencies:
python, py-lazy-object-proxy, py-six, py-wrapt, py-enum34, py-singledispatch, py-backports-functools-lru-cache, py-setuptools
Link Dependencies:
python, py-lazy-object-proxy, py-six, py-wrapt, py-enum34, py-singledispatch, py-backports-functools-lru-cache, py-setuptools
Run Dependencies:
python
Description:
A common base representation of python source code for pylint and other projects.

py-astropy

Homepage:
Spack package:
Versions:
3.2.1, 2.0.14, 1.1.2, 1.1.post1
Build Dependencies:
python, py-setuptools, py-numpy, py-scipy, py-h5py, py-beautifulsoup4, py-html5lib, py-bleach, py-pyyaml, py-pandas, py-bintrees, py-sortedcontainers, py-pytz, py-jplephem, py-matplotlib, py-scikit-image, py-mpmath, py-asdf, py-bottleneck, py-pytest, erfa, wcslib, cfitsio, expat
Link Dependencies:
python, erfa, wcslib, cfitsio, expat
Run Dependencies:
python, py-numpy, py-scipy, py-h5py, py-beautifulsoup4, py-html5lib, py-bleach, py-pyyaml, py-pandas, py-bintrees, py-sortedcontainers, py-pytz, py-jplephem, py-matplotlib, py-scikit-image, py-mpmath, py-asdf, py-bottleneck, py-pytest
Description:
The Astropy Project is a community effort to develop a single core package for Astronomy in Python and foster interoperability between Python astronomy packages.

py-astunparse

Homepage:
Spack package:
Versions:
1.6.2
Build Dependencies:
python, py-setuptools, py-wheel, py-six
Link Dependencies:
python
Run Dependencies:
python, py-wheel, py-six
Description:
An AST unparser for Python. This is a factored out version of unparse found in the Python source distribution; under Demo/parser in Python 2 and under Tools/parser in Python 3.

py-async-generator

Homepage:
Spack package:
Versions:
1.10
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Provides async generator functionality to python 3.5.

py-atomicwrites

Homepage:
Spack package:
Versions:
1.3.0, 1.1.5
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Atomic file writes.

py-atropos

Homepage:
Spack package:
Versions:
1.1.22
Build Dependencies:
python, py-setuptools, py-cython, py-tqdm, py-pysam
Link Dependencies:
python
Run Dependencies:
python, py-setuptools, py-tqdm, py-pysam
Description:
Atropos is tool for specific, sensitive, and speedy trimming of NGS reads. It is a fork of the venerable Cutadapt read trimmer.

py-attrs

Homepage:
Spack package:
Versions:
19.2.0, 19.1.0, 18.1.0, 16.3.0
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Test Dependencies:
py-coverage, py-hypothesis, py-pympler, py-pytest, py-six, py-zope-interface
Description:
Classes Without Boilerplate

py-autopep8

Homepage:
Spack package:
Versions:
1.4.4, 1.3.3, 1.2.4, 1.2.2
Build Dependencies:
python, py-pycodestyle, py-setuptools
Link Dependencies:
python
Run Dependencies:
python, py-pycodestyle
Description:
autopep8 automatically formats Python code to conform to the PEP 8 style guide.

py-avro

Homepage:
Spack package:
Versions:
1.8.2
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Avro is a serialization and RPC framework.

py-avro-json-serializer

Homepage:
Spack package:
Versions:
0.4
Build Dependencies:
python, py-setuptools, py-simplejson, py-avro
Link Dependencies:
python
Run Dependencies:
python, py-simplejson, py-avro
Description:
Serializes data into a JSON format using AVRO schema.

py-babel

Homepage:
Spack package:
Versions:
2.7.0, 2.6.0, 2.4.0, 2.3.4
Build Dependencies:
python, py-setuptools, py-pytz
Link Dependencies:
python
Run Dependencies:
python, py-pytz
Test Dependencies:
py-pytest, py-freezegun
Description:
Babel is an integrated collection of utilities that assist in internationalizing and localizing Python applications, with an emphasis on web-based applications.

py-backcall

Homepage:
Spack package:
Versions:
0.1.0
Build Dependencies:
python
Link Dependencies:
python
Run Dependencies:
python
Description:
Specifications for callback functions passed in to an API

py-backports-abc

Homepage:
Spack package:
Versions:
0.5, 0.4
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Backports_ABC: A backport of recent additions to the 'collections.abc' module.

py-backports-functools-lru-cache

Homepage:
Spack package:
Versions:
1.5, 1.4, 1.0.1
Build Dependencies:
python, py-setuptools, py-setuptools-scm
Link Dependencies:
python
Run Dependencies:
python
Description:
Backport of functools.lru_cache from Python 3.3

py-backports-shutil-get-terminal-size

Homepage:
Spack package:
Versions:
1.0.0
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
A backport of the get_terminal_size function from Python 3.3's shutil.

py-backports-ssl-match-hostname

Homepage:
Spack package:
Versions:
3.5.0.1
Build Dependencies:
python
Link Dependencies:
python
Run Dependencies:
python
Description:
The ssl.match_hostname() function from Python 3.5

py-backports-tempfile

Homepage:
Spack package:
Versions:
1.0
Build Dependencies:
python, py-setuptools, py-backports-weakref
Link Dependencies:
python
Run Dependencies:
python, py-backports-weakref
Description:
This package provides backports of new features in Python's tempfile module under the backports namespace

py-backports-weakref

Homepage:
Spack package:
Versions:
1.0rc1, 1.0.post1
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Backports of new features in Python's weakref module

py-basemap

Homepage:
Spack package:
Versions:
1.2.0, 1.0.7
Build Dependencies:
python, py-setuptools, py-numpy, py-matplotlib, py-pyproj, py-pyshp, pil, geos
Link Dependencies:
python, geos
Run Dependencies:
python, py-setuptools, py-numpy, py-matplotlib, py-pyproj, py-pyshp, pil
Description:
The matplotlib basemap toolkit is a library for plotting 2D data on maps in Python.

py-bcbio-gff

Homepage:
Spack package:
Versions:
0.6.2
Build Dependencies:
python, py-setuptools, py-six, py-biopython
Link Dependencies:
python
Run Dependencies:
python, py-six, py-biopython
Description:
Read and write Generic Feature Format (GFF) with Biopython integration.

py-bcrypt

Homepage:
Spack package:
Versions:
3.1.4
Build Dependencies:
python, py-setuptools, py-cffi, py-six
Link Dependencies:
python
Run Dependencies:
python, py-cffi, py-six
Description:
Modern password hashing for your software and your servers

py-beautifulsoup4

Homepage:
Spack package:
Versions:
4.8.0, 4.5.3, 4.5.1, 4.4.1
Build Dependencies:
python, py-setuptools, py-soupsieve
Link Dependencies:
python
Run Dependencies:
python, py-soupsieve
Description:
Beautiful Soup is a Python library for pulling data out of HTML and XML files. It works with your favorite parser to provide idiomatic ways of navigating, searching, and modifying the parse tree.

py-billiard

Homepage:
Spack package:
Versions:
3.6.1.0, 3.6.0.0, 3.5.0.5
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Python multiprocessing fork with improvements and bugfixes

py-binaryornot

Homepage:
Spack package:
Versions:
0.4.4
Build Dependencies:
python, py-setuptools, py-chardet
Link Dependencies:
python, py-chardet
Run Dependencies:
python
Description:
Ultra-lightweight pure Python package to check if a file is binary or text.

py-bintrees

Homepage:
Spack package:
Versions:
2.0.7
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Package provides Binary-, RedBlack- and AVL-Trees in Python and Cython.

py-binwalk

Homepage:
Spack package:
Versions:
2.1.0
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Binwalk is a fast, easy to use tool for analyzing, reverse engineering, and extracting firmware images.

py-biom-format

Homepage:
Spack package:
Versions:
2.1.6
Build Dependencies:
python, py-setuptools, py-cython, py-h5py, py-click, py-numpy, py-future, py-scipy, py-pandas, py-six, py-pyqi
Link Dependencies:
python
Run Dependencies:
python, py-setuptools, py-h5py, py-click, py-numpy, py-future, py-scipy, py-pandas, py-six, py-pyqi
Description:
The BIOM file format (canonically pronounced biome) is designed to be a general-use format for representing biological sample by observation contingency tables.

py-biomine

Homepage:
Spack package:
Versions:
0.9.5
Build Dependencies:
python, py-advancedhtmlparser, py-pysam, py-pyvcf, py-requests
Link Dependencies:
python
Run Dependencies:
python, py-advancedhtmlparser, py-pysam, py-pyvcf, py-requests
Description:
Bioinformatics data-mining.

py-biopython

Homepage:
Spack package:
Versions:
1.73, 1.70, 1.65
Build Dependencies:
python, py-numpy, py-setuptools
Link Dependencies:
python
Run Dependencies:
python, py-numpy
Description:
A distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics.

py-bitarray

Homepage:
Spack package:
Versions:
0.8.1
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Efficient array of booleans - C extension

py-bitstring

Homepage:
Spack package:
Versions:
3.1.5
Build Dependencies:
python
Link Dependencies:
python
Run Dependencies:
python
Description:
Simple construction, analysis and modification of binary data.

py-black

Homepage:
Spack package:
Versions:
19.3b0, 18.9b0
Build Dependencies:
python, py-setuptools, py-attrs, py-click, py-appdirs, py-toml
Link Dependencies:
python
Run Dependencies:
python, py-setuptools, py-attrs, py-click, py-appdirs, py-toml
Description:
Black is the uncompromising Python code formatter. By using it, you agree to cede control over minutiae of hand-formatting. In return, Black gives you speed, determinism, and freedom from pycodestyle nagging about formatting.

py-bleach

Homepage:
Spack package:
Versions:
3.1.0, 1.5.0
Build Dependencies:
python, py-setuptools, py-six, py-webencodings
Link Dependencies:
python
Run Dependencies:
python, py-six, py-webencodings
Description:
An easy whitelist-based HTML-sanitizing tool.

py-blessed

Homepage:
Spack package:
Versions:
1.15.0
Build Dependencies:
python, py-setuptools, py-wcwidth, py-six
Link Dependencies:
python
Run Dependencies:
python, py-wcwidth, py-six
Description:
Blessed is a thin, practical wrapper around terminal capabilities in Python.

py-blessings

Homepage:
Spack package:
Versions:
1.6
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
A nicer, kinder way to write to the terminal

py-blinker

Homepage:
Spack package:
Versions:
1.4
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Fast, simple object-to-object and broadcast signaling

py-bokeh

Homepage:
Spack package:
Versions:
1.3.4, 0.12.2
Build Dependencies:
python, py-requests, py-pillow, py-packaging, py-six, py-pyyaml, py-python-dateutil, py-jinja2, py-numpy, py-tornado, py-futures
Link Dependencies:
python
Run Dependencies:
python, py-requests, py-pillow, py-packaging, py-six, py-pyyaml, py-python-dateutil, py-jinja2, py-numpy, py-tornado, py-futures
Description:
Statistical and novel interactive HTML plots for Python

py-boltons

Homepage:
Spack package:
Versions:
16.5.1
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
When they're not builtins, they're boltons. Functionality that should be in the standard library. Like builtins, but Boltons. Otherwise known as, "everyone's util.py," but cleaned up and tested.

py-boto3

Homepage:
Spack package:
Versions:
1.10.44, 1.10.38, 1.9.169
Build Dependencies:
python, py-setuptools, py-botocore, py-jmespath, py-s3transfer
Link Dependencies:
python
Run Dependencies:
python, py-botocore, py-jmespath, py-s3transfer
Description:
The AWS SDK for Python.

py-botocore

Homepage:
Spack package:
Versions:
1.13.44, 1.13.38, 1.12.169
Build Dependencies:
python, py-setuptools, py-jmespath, py-docutils, py-ordereddict, py-simplejson, py-python-dateutil, py-urllib3
Link Dependencies:
python
Run Dependencies:
python, py-jmespath, py-docutils, py-ordereddict, py-simplejson, py-python-dateutil, py-urllib3
Test Dependencies:
py-mock, py-nose
Description:
Low-level, data-driven core of boto 3.

py-bottleneck

Homepage:
Spack package:
Versions:
1.2.1, 1.0.0
Build Dependencies:
python, py-setuptools, py-numpy
Link Dependencies:
python
Run Dependencies:
python, py-numpy
Test Dependencies:
py-nose
Description:
A collection of fast NumPy array functions written in Cython.

py-breakseq2

Homepage:
Spack package:
Versions:
2.2
Build Dependencies:
python, py-setuptools, py-biopython, py-cython, py-pysam
Link Dependencies:
python
Run Dependencies:
python, py-biopython, py-pysam, bwa, samtools
Description:
nucleotide-resolution analysis of structural variants

py-breathe

Homepage:
Spack package:
Versions:
4.11.1, 4.11.0, 4.10.0, 4.9.1, 4.9.0, 4.8.0, 4.7.3, 4.7.2, 4.7.1, 4.7.0
Build Dependencies:
python, py-setuptools, py-sphinx, py-docutils, py-six, doxygen
Link Dependencies:
python, doxygen
Run Dependencies:
python, py-sphinx, py-docutils, py-six
Description:
This is an extension to reStructuredText and Sphinx to be able to read and render the Doxygen xml output.

py-brian

Homepage:
Spack package:
Versions:
1.4.3
Build Dependencies:
python, py-matplotlib, py-numpy, py-scipy
Link Dependencies:
python
Run Dependencies:
python, py-matplotlib, py-numpy, py-scipy
Description:
A clock-driven simulator for spiking neural networks

py-brian2

Homepage:
Spack package:
Versions:
2.2.2.1, 2.0.1, 2.0rc3
Build Dependencies:
python, py-numpy, py-cython, py-sympy, py-pyparsing, py-jinja2, py-setuptools, py-sphinx
Link Dependencies:
python
Run Dependencies:
python, py-numpy, py-cython, py-sympy, py-pyparsing, py-jinja2, py-setuptools, py-sphinx
Test Dependencies:
py-nose
Description:
A clock-driven simulator for spiking neural networks

py-brotlipy

Homepage:
Spack package:
Versions:
0.7.0
Build Dependencies:
python, py-setuptools, py-cffi, py-enum34
Link Dependencies:
python
Run Dependencies:
python, py-cffi, py-enum34
Description:
Python binding to the Brotli library.

py-bsddb3

Homepage:
Spack package:
Versions:
6.2.5
Build Dependencies:
python, py-setuptools, berkeley-db
Link Dependencies:
python, berkeley-db
Run Dependencies:
python
Description:
This module provides a nearly complete wrapping of the Oracle/Sleepycat C API for the Database Environment, Database, Cursor, Log Cursor, Sequence and Transaction objects, and each of these is exposed as a Python type in the bsddb3.db module.

py-bx-python

Homepage:
Spack package:
Versions:
0.7.4
Build Dependencies:
python, py-setuptools, py-numpy, py-six
Link Dependencies:
python
Run Dependencies:
python, py-numpy, py-six
Description:
The bx-python project is a python library and associated set of scripts to allow for rapid implementation of genome scale analyses.

py-bz2file

Homepage:
Spack package:
Versions:
0.98
Build Dependencies:
python
Link Dependencies:
python
Run Dependencies:
python
Description:
Python library for reading and writing bzip2-compressed files.

py-cached-property

Homepage:
Spack package:
Versions:
1.5.1
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
A decorator for caching properties in classes.

py-cachetools

Homepage:
Spack package:
Versions:
3.1.1
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
This module provides various memoizing collections and decorators, including variants of the Python 3 Standard Library @lru_cache function decorator.

py-cairocffi

Homepage:
Spack package:
Versions:
1.0.2
Build Dependencies:
python, py-setuptools, py-cffi
Link Dependencies:
python
Run Dependencies:
python, py-cffi
Test Dependencies:
py-pytest-runner, py-pytest-cov, py-pytest-flake8, py-pytest-isort
Description:
cairocffi is a CFFI-based drop-in replacement for Pycairo, a set of Python bindings and object-oriented API for cairo. Cairo is a 2D vector graphics library with support for multiple backends including image buffers, PNG, PostScript, PDF, and SVG file output.

py-cartopy

Homepage:
Spack package:
Versions:
0.17.0, 0.16.0
Build Dependencies:
python, py-setuptools, py-cython, py-numpy, py-shapely, py-pyshp, py-six, geos, proj, py-matplotlib, gdal, py-pillow, py-pyepsg, py-scipy, py-owslib
Link Dependencies:
python, geos, proj
Run Dependencies:
python, py-numpy, py-shapely, py-pyshp, py-six, py-matplotlib, gdal, py-pillow, py-pyepsg, py-scipy, py-owslib
Test Dependencies:
py-filelock, py-mock, py-pytest
Description:
Cartopy - a cartographic python library with matplotlib support.

py-cclib

Homepage:
Spack package:
Versions:
1.5.post1
Build Dependencies:
python, py-numpy
Link Dependencies:
python
Run Dependencies:
python, py-numpy
Description:
Open source library for parsing and interpreting the results of computational chemistry packages

py-cdat-lite

Homepage:
Spack package:
Versions:
6.0.1
Build Dependencies:
python, netcdf-c, py-numpy, py-setuptools
Link Dependencies:
python, netcdf-c
Run Dependencies:
python, py-numpy
Description:
Cdat-lite is a Python package for managing and analysing climate science data. It is a subset of the Climate Data Analysis Tools (CDAT) developed by PCMDI at Lawrence Livermore National Laboratory.

py-cdo

Homepage:
Spack package:
Versions:
1.3.2
Build Dependencies:
python, cdo, py-setuptools, py-scipy, py-netcdf4
Link Dependencies:
python, cdo
Run Dependencies:
python, py-scipy, py-netcdf4
Description:
The cdo package provides an interface to the Climate Data Operators from Python.

py-cdsapi

Homepage:
Spack package:
Versions:
0.2.3
Build Dependencies:
python, py-setuptools, py-requests, py-tqdm
Link Dependencies:
python
Run Dependencies:
python, py-requests, py-tqdm
Description:
The Climate Data Store Application Program Interface is a service providing programmatic access to CDS data. Get your UID and API key from the CDS portal at the address https://cds.climate.copernicus.eu/user and write it into the configuration file. Look at https://pypi.org/project/cdsapi/ for an example

py-celery

Homepage:
Spack package:
Versions:
4.3.0
Build Dependencies:
python, py-setuptools, py-redis, py-pytz, py-billiard, py-kombu, py-vine
Link Dependencies:
python
Run Dependencies:
python, py-setuptools, py-redis, py-pytz, py-billiard, py-kombu, py-vine
Description:
Celery - Distributed Task Queue.

py-certifi

Homepage:
Spack package:
Versions:
2019.9.11, 2019.6.16, 2019.3.9, 2017.4.17, 2017.1.23
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Certifi: A carefully curated collection of Root Certificates for validating the trustworthiness of SSL certificates while verifying the identity of TLS hosts.

py-certipy

Homepage:
Spack package:
Versions:
0.1.3
Build Dependencies:
python, py-setuptools, py-pyopenssl
Link Dependencies:
python
Run Dependencies:
python, py-pyopenssl
Description:
A simple python tool for creating certificate authorities and certificates on the fly.

py-cf-units

Homepage:
Spack package:
Versions:
master, 2.1.1
Build Dependencies:
python, py-setuptools, py-six, py-cftime, py-cython, py-numpy, py-antlr4-python3-runtime, py-pytest-runner, udunits
Link Dependencies:
python, udunits
Run Dependencies:
python, py-six, py-cftime, py-cython, py-numpy, py-antlr4-python3-runtime
Description:
Units of measure as required by the Climate and Forecast (CF) metadata conventions.

py-cffi

Homepage:
Spack package:
Versions:
1.13.0, 1.12.2, 1.11.5, 1.10.0, 1.1.2
Build Dependencies:
python, pkgconfig, py-setuptools, py-pycparser, libffi
Link Dependencies:
python, libffi
Run Dependencies:
python, py-pycparser
Test Dependencies:
py-py, py-pytest
Description:
Foreign Function Interface for Python calling C code

py-cfgv

Homepage:
Spack package:
Versions:
2.0.1
Build Dependencies:
python, py-setuptools, py-six
Link Dependencies:
python
Run Dependencies:
python, py-six
Description:
Validate configuration and produce human readable error messages.

py-cftime

Homepage:
Spack package:
Versions:
1.0.3.4
Build Dependencies:
python, py-setuptools, py-cython, py-numpy
Link Dependencies:
python
Run Dependencies:
python, py-numpy
Description:
Python library for decoding time units and variable values in a netCDF file conforming to the Climate and Forecasting (CF) netCDF conventions

py-chai

Homepage:
Spack package:
Versions:
1.1.2
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Chai - Python Mocking Made Easy

py-chardet

Homepage:
Spack package:
Versions:
3.0.4, 3.0.2, 2.3.0
Build Dependencies:
python, py-setuptools, py-pytest-runner
Link Dependencies:
python
Run Dependencies:
python
Test Dependencies:
py-pytest, py-hypothesis
Description:
Universal encoding detector for Python 2 and 3

py-checkm-genome

Homepage:
Spack package:
Versions:
1.0.13, 1.0.11
Build Dependencies:
python, hmmer, pplacer, prodigal, py-backports-functools-lru-cache, py-numpy, py-scipy, py-matplotlib, py-pysam, py-dendropy
Link Dependencies:
python
Run Dependencies:
python, hmmer, pplacer, prodigal, py-backports-functools-lru-cache, py-numpy, py-scipy, py-matplotlib, py-pysam, py-dendropy
Description:
Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes

py-cheetah

Homepage:
Spack package:
Versions:
2.3.0
Build Dependencies:
python
Link Dependencies:
python
Run Dependencies:
python
Description:
Cheetah is a template engine and code generation tool.

py-cheroot

Homepage:
Spack package:
Versions:
6.5.5
Build Dependencies:
python, py-setuptools, py-setuptools-scm, py-setuptools-scm-git-archive, py-more-itertools, py-six, py-backports-functools-lru-cache
Link Dependencies:
python
Run Dependencies:
python, py-more-itertools, py-six, py-backports-functools-lru-cache
Description:
Highly-optimized, pure-python HTTP server

py-cherrypy

Homepage:
Spack package:
Versions:
18.1.1
Build Dependencies:
python, py-setuptools, py-setuptools-scm, py-more-itertools, py-zc-lockfile, py-cheroot, py-portend
Link Dependencies:
python
Run Dependencies:
python, py-more-itertools, py-zc-lockfile, py-cheroot, py-portend
Description:
CherryPy is a pythonic, object-oriented HTTP framework.

py-cinema-lib

Homepage:
Spack package:
Versions:
master, 1.2.1, 1.2.0, 1.1.1, 1.1.0, 1.0.2, 1.0.1, 1.0.0, ECPMilestone201806
Build Dependencies:
python, py-numpy, py-scikit-image, opencv, py-setuptools
Link Dependencies:
python
Run Dependencies:
python, py-numpy, py-scikit-image, opencv, py-setuptools
Description:
cinema_lib is a set of tools and library for interacting with a Cinema database (currently Spec A and Spec D) through Python and the command line tool, cinema.

py-click

Homepage:
Spack package:
Versions:
7.0, 6.6
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
A simple wrapper around optparse for powerful command line utilities.

py-click-plugins

Homepage:
Spack package:
Versions:
1.0.4
Build Dependencies:
python, py-setuptools, py-click
Link Dependencies:
python
Run Dependencies:
python, py-click
Description:
An extension module for py-click to register external CLI commands via setuptools entry-points.

py-cligj

Homepage:
Spack package:
Versions:
0.5.0, 0.4.0
Build Dependencies:
python, py-setuptools, py-click
Link Dependencies:
python
Run Dependencies:
python, py-click
Description:
Click-based argument and option decorators for Python GIS command line programs

py-clipboard

Homepage:
Spack package:
Versions:
0.0.4
Build Dependencies:
python, py-setuptools, py-pyperclip
Link Dependencies:
python
Run Dependencies:
python, py-pyperclip
Description:
A cross platform clipboard operation library of Python.

py-cloudpickle

Homepage:
Spack package:
Versions:
1.2.1, 0.5.2
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Extended pickling support for Python objects.

py-clustershell

Homepage:
Spack package:
Versions:
1.8
Build Dependencies:
python, py-setuptools, py-pyyaml
Link Dependencies:
python, py-pyyaml
Run Dependencies:
python
Description:
Scalable cluster administration Python framework - Manage node sets node groups and execute commands on cluster nodes in parallel.

py-codecov

Homepage:
Spack package:
Versions:
2.0.15
Build Dependencies:
python, py-setuptools, py-requests, py-coverage, py-argparse
Link Dependencies:
python
Run Dependencies:
python, py-requests, py-coverage, py-argparse
Test Dependencies:
py-unittest2, py-linecache2
Description:
Hosted coverage reports for Github, Bitbucket and Gitlab.

py-cogent

Homepage:
Spack package:
Versions:
1.9, 1.5.3
Build Dependencies:
python, py-setuptools, py-numpy, zlib, py-matplotlib, py-mpi4py, py-sqlalchemy, py-pymysql, py-cython
Link Dependencies:
python, zlib
Run Dependencies:
python, py-numpy, py-matplotlib, py-mpi4py, py-sqlalchemy, py-pymysql
Description:
A toolkit for statistical analysis of biological sequences.

py-colorama

Homepage:
Spack package:
Versions:
0.4.1, 0.3.7
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Cross-platform colored terminal text.

py-coloredlogs

Homepage:
Spack package:
Versions:
10.0
Build Dependencies:
python, py-setuptools, py-humanfriendly
Link Dependencies:
python
Run Dependencies:
python, py-humanfriendly
Description:
Colored terminal output for Python's logging module

py-colorlog

Homepage:
Spack package:
Versions:
4.0.2, 3.1.4
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
A colored formatter for the python logging module

py-colormath

Homepage:
Spack package:
Versions:
3.0.0, 2.1.1
Build Dependencies:
python, py-setuptools, py-numpy, py-networkx
Link Dependencies:
python
Run Dependencies:
python, py-numpy, py-networkx
Description:
Color math and conversion library.

py-colorpy

Homepage:
Spack package:
Versions:
0.1.1
Build Dependencies:
python
Link Dependencies:
python
Run Dependencies:
python, py-numpy, py-matplotlib
Description:
ColorPy is a Python package to convert physical descriptions of light - spectra of light intensity vs. wavelength - into RGB colors that can be drawn on a computer screen. It provides a nice set of attractive plots that you can make of such spectra, and some other color related functions as well.

py-configobj

Homepage:
Spack package:
Versions:
5.0.6, 4.7.2
Build Dependencies:
python, py-six
Link Dependencies:
python
Run Dependencies:
python, py-six
Description:
Config file reading, writing and validation.

py-configparser

Homepage:
Spack package:
Versions:
3.5.1, 3.5.0
Build Dependencies:
python, py-setuptools, py-ordereddict
Link Dependencies:
python
Run Dependencies:
python, py-ordereddict
Description:
This library brings the updated configparser from Python 3.5 to Python 2.6-3.5.

py-contextlib2

Homepage:
Spack package:
Versions:
0.6.0
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
contextlib2 is a backport of the standard library's contextlib module to earlier Python versions.

py-convertdate

Homepage:
Spack package:
Versions:
2.2.0
Build Dependencies:
python, py-setuptools, py-pytz, py-pymeeus
Link Dependencies:
python
Run Dependencies:
python, py-pytz, py-pymeeus
Description:
Converts between Gregorian dates and other calendar systems.Calendars included: Baha'i, French Republican, Hebrew, Indian Civil, Islamic, ISO, Julian, Mayan and Persian.

py-cookiecutter

Homepage:
Spack package:
Versions:
1.6.0
Build Dependencies:
python, py-setuptools, py-future, py-binaryornot, py-jinja2, py-click, py-whichcraft, py-poyo, py-jinja2-time, py-requests
Link Dependencies:
python
Run Dependencies:
python, py-future, py-binaryornot, py-jinja2, py-click, py-whichcraft, py-poyo, py-jinja2-time, py-requests
Description:
A command-line utility that creates projects from cookiecutters (project templates). E.g. Python package projects, jQuery plugin projects.

py-counter

Homepage:
Spack package:
Versions:
1.0.0
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Counter package defines the "counter.Counter" class similar to bags or multisets in other languages.

py-cov-core

Homepage:
Spack package:
Versions:
1.15.0
Build Dependencies:
python, py-setuptools, py-coverage
Link Dependencies:
python
Run Dependencies:
python, py-coverage
Description:
plugin core for use by pytest-cov, nose-cov and nose2-cov

py-coverage

Homepage:
Spack package:
Versions:
4.5.4, 4.5.3, 4.3.4, 4.0a6
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Testing coverage checker for python

py-crispresso

Homepage:
Spack package:
Versions:
1.0.8
Build Dependencies:
python, py-setuptools, py-biopython, py-matplotlib, py-numpy, py-pandas, py-seaborn, emboss, flash, java
Link Dependencies:
python
Run Dependencies:
python, py-biopython, py-matplotlib, py-numpy, py-pandas, py-seaborn, emboss, flash, java
Description:
Software pipeline for the analysis of CRISPR-Cas9 genome editing outcomes from deep sequencing data.

py-crossmap

Homepage:
Spack package:
Versions:
0.3.3, 0.2.9
Build Dependencies:
python, py-setuptools, py-numpy, py-cython, py-pysam, py-bx-python, py-pybigwig
Link Dependencies:
python
Run Dependencies:
python, py-numpy, py-cython, py-pysam, py-bx-python, py-pybigwig
Description:
CrossMap is a program for convenient conversion of genome coordinates (or annotation files) between different assemblies

py-cryptography

Homepage:
Spack package:
Versions:
2.7, 2.3.1, 1.8.1
Build Dependencies:
python, py-setuptools, py-cffi, py-asn1crypto, py-six, py-idna, py-enum34, py-ipaddress, openssl
Link Dependencies:
python, openssl
Run Dependencies:
python, py-cffi, py-asn1crypto, py-six, py-idna, py-enum34, py-ipaddress
Description:
cryptography is a package which provides cryptographic recipes and primitives to Python developers

py-cssselect

Homepage:
Spack package:
Versions:
1.1.0, 1.0.3, 1.0.2, 1.0.1, 1.0.0
Build Dependencies:
python
Link Dependencies:
python
Run Dependencies:
python
Description:
Python-cssselect parses CSS3 Selectors and translate them to XPath 1.0 expressions. Such expressions can be used in lxml or another XPath engine to find the matching elements in an XML or HTML document.

py-csvkit

Homepage:
Spack package:
Versions:
1.0.4, 0.9.1
Build Dependencies:
python, py-setuptools, py-six, py-argparse, py-ordereddict, py-simplejson, py-python-dateutil, py-dbf, py-xlrd, py-sqlalchemy, py-openpyxl, py-agate, py-agate-excel, py-agate-dbf, py-agate-sql
Link Dependencies:
python
Run Dependencies:
python, py-setuptools, py-six, py-argparse, py-ordereddict, py-simplejson, py-python-dateutil, py-dbf, py-xlrd, py-sqlalchemy, py-openpyxl, py-agate, py-agate-excel, py-agate-dbf, py-agate-sql
Description:
A library of utilities for working with CSV, the king of tabular file formats

py-current

Homepage:
Spack package:
Versions:
0.3.1
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Current module relative paths and imports

py-cutadapt

Homepage:
Spack package:
Versions:
2.5, 1.13
Build Dependencies:
python, py-setuptools, py-xopen, py-dnaio
Link Dependencies:
python
Run Dependencies:
python, py-setuptools, py-xopen, py-dnaio
Description:
Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.

py-cvxopt

Homepage:
Spack package:
Versions:
1.1.9
Build Dependencies:
python, py-setuptools, blas, lapack, suite-sparse, gsl, fftw, glpk, dsdp
Link Dependencies:
python, blas, lapack, suite-sparse, gsl, fftw, glpk, dsdp
Run Dependencies:
python
Description:
CVXOPT is a free software package for convex optimization based on the Python programming language.

py-cvxpy

Homepage:
Spack package:
Versions:
1.0.25
Build Dependencies:
python, py-setuptools, py-numpy, py-scipy, py-ecos, py-scs, py-osqp, py-multiprocess, py-six
Link Dependencies:
python
Run Dependencies:
python, py-numpy, py-scipy, py-ecos, py-scs, py-osqp, py-multiprocess, py-six
Test Dependencies:
py-nose
Description:
Convex optimization, for everyone.

py-cycler

Homepage:
Spack package:
Versions:
0.10.0
Build Dependencies:
python, py-setuptools, py-six
Link Dependencies:
python
Run Dependencies:
python, py-six
Description:
Composable style cycles.

py-cython

Homepage:
Spack package:
Versions:
0.29.14, 0.29.13, 0.29.10, 0.29.7, 0.29.5, 0.29, 0.28.6, 0.28.3, 0.28.1, 0.25.2, 0.23.5, 0.23.4, 0.21.2
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Test Dependencies:
gdb
Description:
The Cython compiler for writing C extensions for the Python language.

py-dask

Homepage:
Spack package:
Versions:
1.2.2, 1.1.2, 1.1.0, 0.17.4, 0.8.1
Build Dependencies:
python, py-setuptools, py-numpy, py-toolz, py-cloudpickle, py-partd, py-pandas, py-distributed
Link Dependencies:
python
Run Dependencies:
python, py-numpy, py-toolz, py-cloudpickle, py-partd, py-pandas, py-distributed
Test Dependencies:
py-pytest, py-requests, py-pytest-runner
Description:
Dask is a flexible parallel computing library for analytics.

py-dataclasses

Homepage:
Spack package:
Versions:
0.7
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
A backport of the dataclasses module for Python 3.6

py-dateparser

Homepage:
Spack package:
Versions:
0.7.2
Build Dependencies:
python, py-setuptools, py-python-dateutil, py-pytz, py-regex, py-tzlocal, py-umalqurra, py-ruamel-yaml, py-convertdate, py-jdatetime
Link Dependencies:
python
Run Dependencies:
python, py-python-dateutil, py-pytz, py-regex, py-tzlocal, py-umalqurra, py-ruamel-yaml, py-convertdate, py-jdatetime
Test Dependencies:
py-mock, py-nose, py-parameterized, py-six, py-coverage
Description:
dateparser -- python parser for human readable dates

py-dbf

Homepage:
Spack package:
Versions:
0.96.005, 0.94.003
Build Dependencies:
python
Link Dependencies:
python
Run Dependencies:
python
Description:
Pure python package for reading/writing dBase, FoxPro, and Visual FoxPro .dbf files (including memos)

py-dbfread

Homepage:
Spack package:
Versions:
2.0.7
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
DBF is a file format used by databases such dBase, Visual FoxPro, and FoxBase+. This library reads DBF files and returns the data as native Python data types for further processing. It is primarily intended for batch jobs and one-off scripts.

py-decorator

Homepage:
Spack package:
Versions:
4.4.0, 4.3.2, 4.3.0, 4.0.9
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
The aim of the decorator module it to simplify the usage of decorators for the average programmer, and to popularize decorators by showing various non-trivial examples.

py-deeptools

Homepage:
Spack package:
Versions:
3.3.0, 3.2.1, 2.5.2
Build Dependencies:
python, py-setuptools, py-numpy, py-scipy, py-py2bit, py-pybigwig, py-pysam, py-matplotlib, py-numpydoc, py-plotly, py-deeptoolsintervals
Link Dependencies:
python
Run Dependencies:
python, py-numpy, py-scipy, py-py2bit, py-pybigwig, py-pysam, py-matplotlib, py-numpydoc, py-plotly, py-deeptoolsintervals
Test Dependencies:
py-nose
Description:
deepTools addresses the challenge of handling the large amounts of data that are now routinely generated from DNA sequencing centers.

py-deeptoolsintervals

Homepage:
Spack package:
Versions:
0.1.9
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
A python module creating/accessing GTF-based interval trees with associated meta-data.

py-defusedxml

Homepage:
Spack package:
Versions:
0.6.0, 0.5.0
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
defusing XML bombs and other exploits

py-dendropy

Homepage:
Spack package:
Versions:
4.3.0, 3.12.0
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
DendroPy is a Python library for phylogenetic computing. It provides classes and functions for the simulation, processing, and manipulation of phylogenetic trees and character matrices, and supports the reading and writing of phylogenetic data in a range of formats, such as NEXUS, NEWICK, NeXML, Phylip, FASTA, etc.

py-deprecation

Homepage:
Spack package:
Versions:
2.0.7
Build Dependencies:
python, py-setuptools, py-packaging
Link Dependencies:
python
Run Dependencies:
python
Description:
The deprecation library provides a deprecated decorator and a fail_if_not_removed decorator for your tests.

py-descartes

Homepage:
Spack package:
Versions:
1.1.0
Build Dependencies:
python, py-setuptools, py-matplotlib
Link Dependencies:
python
Run Dependencies:
python, py-matplotlib
Description:
Use Shapely or GeoJSON-like geometric objects as matplotlib paths and patches

py-dill

Homepage:
Spack package:
Versions:
0.2.9, 0.2.7, 0.2.6, 0.2.5, 0.2.4, 0.2.3, 0.2.2, 0.2.1, 0.2
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Serialize all of python

py-discover

Homepage:
Spack package:
Versions:
0.4.0
Build Dependencies:
python
Link Dependencies:
python
Run Dependencies:
python
Description:
Test discovery for unittest.

py-dlcpar

Homepage:
Spack package:
Versions:
1.0
Build Dependencies:
python, py-numpy
Link Dependencies:
python
Run Dependencies:
python, py-numpy
Description:
DLCpar is a reconciliation method for inferring gene duplications, losses, and coalescence (accounting for incomplete lineage sorting).

py-dnaio

Homepage:
Spack package:
Versions:
0.3
Build Dependencies:
python, py-setuptools, py-xopen
Link Dependencies:
python
Run Dependencies:
python, py-setuptools, py-xopen
Description:
Read and write FASTQ and FASTA

py-docopt

Homepage:
Spack package:
Versions:
0.6.2
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Command-line interface description language.

py-docutils

Homepage:
Spack package:
Versions:
0.15.2, 0.14, 0.13.1, 0.12
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Docutils is an open-source text processing system for processing plaintext documentation into useful formats, such as HTML, LaTeX, man- pages, open-document or XML. It includes reStructuredText, the easy to read, easy to use, what-you-see-is-what-you-get plaintext markup language.

py-docutils-stubs

Homepage:
Spack package:
Versions:
0.0.21
Build Dependencies:
python, py-setuptools, py-docutils
Link Dependencies:
python
Run Dependencies:
python, py-docutils
Description:
PEP 561 based Type information for docutils.

py-doxypy

Homepage:
Spack package:
Versions:
0.3
Build Dependencies:
python
Link Dependencies:
python
Run Dependencies:
python
Description:
doxypy is an input filter for Doxygen.

py-doxypypy

Homepage:
Spack package:
Versions:
0.8.8.6
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
A Doxygen filter for Python. A more Pythonic version of doxypy, a Doxygen filter for Python.

py-dryscrape

Homepage:
Spack package:
Versions:
develop, 1.0
Build Dependencies:
python, py-lxml, py-webkit-server, py-xvfbwrapper
Link Dependencies:
python
Run Dependencies:
python, py-lxml, py-webkit-server, py-xvfbwrapper
Description:
a lightweight Javascript-aware, headless web scraping library for Python

py-dxchange

Homepage:
Spack package:
Versions:
0.1.2
Build Dependencies:
python, py-setuptools, py-numpy, py-scipy, py-h5py, py-six, py-netcdf4, py-spefile, py-edffile, py-tifffile, py-dxfile, py-olefile, py-astropy
Link Dependencies:
python
Run Dependencies:
python, py-numpy, py-scipy, py-h5py, py-six, py-netcdf4, py-spefile, py-edffile, py-tifffile, py-dxfile, py-olefile, py-astropy
Description:
DXchange provides an interface with tomoPy and raw tomographic data collected at different synchrotron facilities.

py-dxfile

Homepage:
Spack package:
Versions:
0.4
Build Dependencies:
python, py-setuptools, py-h5py
Link Dependencies:
python
Run Dependencies:
python, py-h5py
Description:
Scientific Data Exchange [A1] is a set of guidelines for storing scientific data and metadata in a Hierarchical Data Format 5 [B6] file.

py-earthengine-api

Homepage:
Spack package:
Versions:
0.1.186
Build Dependencies:
python, py-setuptools, py-google-api-python-client, py-google-auth, py-google-auth-httplib2, py-httplib2, py-six
Link Dependencies:
python
Run Dependencies:
python, py-google-api-python-client, py-google-auth, py-google-auth-httplib2, py-httplib2, py-six
Description:
This package allows developers to interact with Google Earth Engine using the Python programming language.

py-easybuild-easyblocks

Homepage:
Spack package:
Versions:
4.0.0, 3.1.2
Build Dependencies:
python
Link Dependencies:
python
Run Dependencies:
python, py-easybuild-framework
Description:
Collection of easyblocks for EasyBuild, a software build and installation framework for (scientific) software on HPC systems.

py-easybuild-easyconfigs

Homepage:
Spack package:
Versions:
4.0.0, 3.1.2
Build Dependencies:
python
Link Dependencies:
python
Run Dependencies:
python, py-easybuild-framework, py-easybuild-easyblocks
Description:
Collection of easyconfig files for EasyBuild, a software build and installation framework for (scientific) software on HPC systems.

py-easybuild-framework

Homepage:
Spack package:
Versions:
4.0.0, 3.1.2
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python, py-setuptools, py-vsc-base
Test Dependencies:
py-vsc-install
Description:
The core of EasyBuild, a software build and installation framework for (scientific) software on HPC systems.

py-ecdsa

Homepage:
Spack package:
Versions:
0.13.2
Build Dependencies:
python, py-setuptools, py-six
Link Dependencies:
python
Run Dependencies:
python, py-six
Test Dependencies:
openssl
Description:
ECDSA cryptographic signature library (pure python)

py-ecos

Homepage:
Spack package:
Versions:
2.0.7.post1
Build Dependencies:
python, py-setuptools, py-numpy, py-scipy
Link Dependencies:
python
Run Dependencies:
python, py-numpy, py-scipy
Test Dependencies:
py-nose
Description:
This is the Python package for ECOS: Embedded Cone Solver.

py-edffile

Homepage:
Spack package:
Versions:
5.0.0
Build Dependencies:
python, py-setuptools, py-numpy
Link Dependencies:
python
Run Dependencies:
python, py-numpy
Description:
Generic class for Edf files manipulation.

py-editdistance

Homepage:
Spack package:
Versions:
0.4
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Fast implementation of the edit distance (Levenshtein distance).

py-elasticsearch

Homepage:
Spack package:
Versions:
7.5.1, 6.4.0, 5.2.0, 2.3.0
Build Dependencies:
python, py-setuptools, py-urllib3
Link Dependencies:
python
Run Dependencies:
python, py-urllib3
Description:
Python client for Elasticsearch

py-elephant

Homepage:
Spack package:
Versions:
0.4.1, 0.3.0
Build Dependencies:
python, py-setuptools, py-neo, py-numpy, py-quantities, py-scipy, py-pandas, py-numpydoc, py-sphinx
Link Dependencies:
python
Run Dependencies:
python, py-neo, py-numpy, py-quantities, py-scipy, py-pandas, py-numpydoc, py-sphinx
Test Dependencies:
py-nose
Description:
Elephant is a package for analysis of electrophysiology data in Python

py-emcee

Homepage:
Spack package:
Versions:
2.2.1, 2.1.0
Build Dependencies:
python, py-setuptools, py-numpy
Link Dependencies:
python
Run Dependencies:
python, py-numpy
Description:
emcee is an MIT licensed pure-Python implementation of Goodman & Weare's Affine Invariant Markov chain Monte Carlo (MCMC) Ensemble sampler.

py-empy

Homepage:
Spack package:
Versions:
3.3.4
Build Dependencies:
python
Link Dependencies:
python
Run Dependencies:
python
Description:
A powerful and robust templating system for Python

py-entrypoints

Homepage:
Spack package:
Versions:
0.3, 0.2.3
Build Dependencies:
python, py-configparser
Link Dependencies:
python
Run Dependencies:
python, py-configparser
Description:
Discover and load entry points from installed packages.

py-enum34

Homepage:
Spack package:
Versions:
1.1.6
Build Dependencies:
python, py-ordereddict, py-setuptools
Link Dependencies:
python
Run Dependencies:
python, py-ordereddict
Description:
Python 3.4 Enum backported to 3.3, 3.2, 3.1, 2.7, 2.6, 2.5, and 2.4.

py-epydoc

Homepage:
Spack package:
Versions:
3.0.1
Build Dependencies:
python
Link Dependencies:
python
Run Dependencies:
python
Description:
Epydoc is a tool for generating API documentation documentation for Python modules, based on their docstrings.

py-espresso

Homepage:
Spack package:
Versions:
develop, 4.0.2, 4.0.1, 4.0.0
Build Dependencies:
cmake, mpi, boost, python, py-cython, py-numpy, fftw, hdf5
Link Dependencies:
mpi, boost, python, fftw, hdf5
Run Dependencies:
py-numpy
Description:
ESPResSo is a highly versatile software package for performing and analyzing scientific Molecular Dynamics many-particle simulations of coarse-grained atomistic or bead-spring models as they are used in soft matter research in physics, chemistry and molecular biology. It can be used to simulate systems such as polymers, liquid crystals, colloids, polyelectrolytes, ferrofluids and biological systems, for example DNA and lipid membranes. It also has a DPD and lattice Boltzmann solver for hydrodynamic interactions, and allows several particle couplings to the LB fluid.

py-espressopp

Homepage:
Spack package:
Versions:
develop, 2.0.2, 1.9.5
Build Dependencies:
cmake, mpi, boost, python, py-mpi4py, fftw, py-sphinx, py-numpy, py-matplotlib, texlive, doxygen
Link Dependencies:
mpi, boost, python, fftw
Run Dependencies:
py-mpi4py, py-numpy
Description:
ESPResSo++ is an extensible, flexible, fast and parallel simulation software for soft matter research. It is a highly versatile software package for the scientific simulation and analysis of coarse-grained atomistic or bead-spring models as they are used in soft matter research

py-et-xmlfile

Homepage:
Spack package:
Versions:
1.0.1
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
An implementation of lxml.xmlfile for the standard library.

py-eventlet

Homepage:
Spack package:
Versions:
0.22.0
Build Dependencies:
python, py-setuptools, py-greenlet, py-enum34
Link Dependencies:
python, py-greenlet
Run Dependencies:
python, py-enum34
Description:
Concurrent networking library for Python

py-execnet

Homepage:
Spack package:
Versions:
1.7.1, 1.4.1
Build Dependencies:
python, py-setuptools, py-setuptools-scm, py-apipkg
Link Dependencies:
python
Run Dependencies:
python, py-apipkg
Description:
execnet provides a share-nothing model with channel-send/receive communication for distributing execution across many Python interpreters across version, platform and network barriers.

py-exodus-bundler

Homepage:
Spack package:
Versions:
2.0.2
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python, musl, py-setuptools
Description:
Exodus is a tool that makes it easy to successfully relocate Linux ELF binaries from one system to another.

py-extras

Homepage:
Spack package:
Versions:
1.0.0
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Useful extra bits for Python - things that shold be in the standard library.

py-fallocate

Homepage:
Spack package:
Versions:
1.6.4
Build Dependencies:
python
Link Dependencies:
python
Run Dependencies:
python
Description:
Module to expose posix_fallocate(3), posix_fadvise(3) and fallocate(2)

py-fastaindex

Homepage:
Spack package:
Versions:
0.11rc7
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
FastA index (.fai) handler compatible with samtools faidx is extended with 4 columns storing counts for A, C, G & T for each sequence..

py-fastcache

Homepage:
Spack package:
Versions:
1.1.0
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
C implementation of Python 3 functools.lru_cache

py-fasteners

Homepage:
Spack package:
Versions:
0.14.1
Build Dependencies:
python, py-setuptools, py-monotonic, py-six
Link Dependencies:
python
Run Dependencies:
python, py-monotonic, py-six
Description:
A python package that provides useful locks.

py-faststructure

Homepage:
Spack package:
Versions:
1.0
Build Dependencies:
python, py-cython, py-numpy, gsl
Link Dependencies:
python, gsl
Run Dependencies:
python, py-numpy
Description:
FastStructure is a fast algorithm for inferring population structure from large SNP genotype data.

py-filelock

Homepage:
Spack package:
Versions:
3.0.4, 3.0.3, 3.0.0, 2.0.13, 2.0.12, 2.0.11, 2.0.10, 2.0.9, 2.0.8
Build Dependencies:
python
Link Dependencies:
python
Run Dependencies:
python
Description:
This package contains a single module, which implements a platform independent file lock in Python, which provides a simple way of inter- process communication

py-filemagic

Homepage:
Spack package:
Versions:
1.6
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Test Dependencies:
py-mock, py-unittest2
Description:
A Python API for libmagic, the library behind the Unix file command

py-fiona

Homepage:
Spack package:
Versions:
1.8.6, 1.7.12
Build Dependencies:
python, gdal, py-setuptools, py-cython, py-attrs, py-click, py-cligj, py-click-plugins, py-six, py-munch, py-argparse, py-ordereddict, py-enum34
Link Dependencies:
python
Run Dependencies:
python, gdal, py-attrs, py-click, py-cligj, py-click-plugins, py-six, py-munch, py-argparse, py-ordereddict, py-enum34
Description:
Alternative Python binding for OGR

py-fiscalyear

Homepage:
Spack package:
Versions:
master, 0.2.0, 0.1.0
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Test Dependencies:
py-pytest, py-pytest-runner, py-pytest-mock
Description:
fiscalyear is a small, lightweight Python module providing helpful utilities for managing the fiscal calendar. It is designed as an extension of the built-in datetime and calendar modules, adding the ability to query the fiscal year and fiscal quarter of a date or datetime object.

py-fixtures

Homepage:
Spack package:
Versions:
3.0.0
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Fixtures, reusable state for writing clean tests and more.

py-flake8

Homepage:
Spack package:
Versions:
3.7.8, 3.7.7, 3.5.0, 3.0.4, 2.5.4
Build Dependencies:
python, py-setuptools, py-entrypoints, py-pyflakes, py-pycodestyle, py-mccabe, py-enum34, py-typing, py-configparser, py-functools32
Link Dependencies:
python
Run Dependencies:
python, py-setuptools, py-entrypoints, py-pyflakes, py-pycodestyle, py-mccabe, py-enum34, py-typing, py-configparser, py-functools32
Description:
Flake8 is a wrapper around PyFlakes, pep8 and Ned Batchelder's McCabe script.

py-flake8-import-order

Homepage:
Spack package:
Versions:
0.18.1
Build Dependencies:
python, py-enum34, py-pycodestyle, py-setuptools
Link Dependencies:
python
Run Dependencies:
python, py-enum34, py-pycodestyle, py-setuptools
Description:
Flake8 and pylama plugin that checks the ordering of import statements.

py-flake8-polyfill

Homepage:
Spack package:
Versions:
1.0.2
Build Dependencies:
python
Link Dependencies:
python
Run Dependencies:
python, py-flake8
Description:
flake8-polyfill is a package that provides some compatibility helpers for Flake8 plugins that intend to support Flake8 2.x and 3.x simultaneously.

py-flask

Homepage:
Spack package:
Versions:
1.1.1, 0.12.2, 0.12.1, 0.11.1
Build Dependencies:
python, py-setuptools, py-werkzeug, py-jinja2, py-itsdangerous, py-click
Link Dependencies:
python
Run Dependencies:
python, py-werkzeug, py-jinja2, py-itsdangerous, py-click
Description:
A simple framework for building complex web applications.

py-flask-compress

Homepage:
Spack package:
Versions:
1.4.0
Build Dependencies:
python, py-setuptools, py-flask
Link Dependencies:
python
Run Dependencies:
python, py-flask
Description:
Flask-Compress allows you to easily compress your Flask application's responses with gzip.

py-flask-socketio

Homepage:
Spack package:
Versions:
2.9.6
Build Dependencies:
python, py-setuptools, py-flask, py-python-socketio, py-werkzeug
Link Dependencies:
python
Run Dependencies:
python, py-flask, py-python-socketio, py-werkzeug
Description:
Flask-SocketIO gives Flask applications access to low latency bi- directional communications between the clients and the server. The client-side application can use any of the SocketIO official clients libraries in Javascript, C++, Java and Swift, or any compatible client to establish a permanent connection to the server.

py-flexx

Homepage:
Spack package:
Versions:
0.4.1
Build Dependencies:
python, py-setuptools, py-tornado
Link Dependencies:
python
Run Dependencies:
python, py-tornado
Description:
Write desktop and web apps in pure Python.

py-flye

Homepage:
Spack package:
Versions:
2.6, 2.4.2
Build Dependencies:
python, py-setuptools, gmake, zlib
Link Dependencies:
python, zlib
Run Dependencies:
python
Description:
Fast and accurate de novo assembler for single molecule sequencing reads

py-fn-py

Homepage:
Spack package:
Versions:
0.5.2
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Functional programming in Python: implementation of missing features to enjoy FP.

py-fortranformat

Homepage:
Spack package:
Versions:
0.2.5
Build Dependencies:
python
Link Dependencies:
python
Run Dependencies:
python
Description:
Mimics Fortran textual IO in Python

py-fparser

Homepage:
Spack package:
Versions:
develop, 0.0.6, 0.0.5
Build Dependencies:
python, py-setuptools, py-numpy, py-nose, py-six
Link Dependencies:
python
Run Dependencies:
python, py-numpy
Test Dependencies:
py-pytest
Description:
Parser for Fortran 77..2003 code.

py-freezegun

Homepage:
Spack package:
Versions:
0.3.12
Build Dependencies:
python, py-setuptools, py-six, py-python-dateutil
Link Dependencies:
python
Run Dependencies:
python, py-six, py-python-dateutil
Test Dependencies:
py-mock, py-nose
Description:
FreezeGun is a library that allows your Python tests to travel through time by mocking the datetime module.

py-fsspec

Homepage:
Spack package:
Versions:
0.4.4
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
A specification for pythonic filesystems.

py-funcsigs

Homepage:
Spack package:
Versions:
1.0.2, 0.4
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Test Dependencies:
py-unittest2
Description:
Python function signatures from PEP362 for Python 2.6, 2.7 and 3.2.

py-functools32

Homepage:
Spack package:
Versions:
3.2.3-2
Build Dependencies:
python
Link Dependencies:
python
Run Dependencies:
python
Description:
Backport of the functools module from Python 3.2.3 for use on 2.7 and PyPy.

py-fusepy

Homepage:
Spack package:
Versions:
2.0.4
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Fusepy is a Python module that provides a simple interface to FUSE and MacFUSE. It's just one file and is implemented using ctypes.

py-future

Homepage:
Spack package:
Versions:
0.17.1, 0.17.0, 0.16.0, 0.15.2
Build Dependencies:
python, py-setuptools, py-importlib, py-argparse
Link Dependencies:
python
Run Dependencies:
python, py-importlib, py-argparse
Description:
Clean single-source support for Python 3 and 2

py-futures

Homepage:
Spack package:
Versions:
3.2.0, 3.0.5
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python, py-setuptools
Description:
Backport of the concurrent.futures package from Python 3.2

py-fypp

Homepage:
Spack package:
Versions:
2.1.1
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Python powered Fortran preprocessor.

py-gast

Homepage:
Spack package:
Versions:
0.3.2, 0.2.2, 0.2.0
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Python AST that abstracts the underlying Python version

py-gdbgui

Homepage:
Spack package:
Versions:
0.11.2.1
Build Dependencies:
python, py-setuptools, py-flask, py-flask-compress, py-flask-socketio, py-gevent, py-pygdbmi, py-pygments
Link Dependencies:
python
Run Dependencies:
python, py-setuptools, py-flask, py-flask-compress, py-flask-socketio, py-gevent, py-pygdbmi, py-pygments, gdb
Description:
gdbgui is a modern, free, browser-based frontend to gdb

py-gdc-client

Homepage:
Spack package:
Versions:
1.4.0
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
The gdc-client provides several convenience functions over the GDC API which provides general download/upload via HTTPS.

py-gee-asset-manager

Homepage:
Spack package:
Versions:
master, 0.1
Build Dependencies:
python, py-setuptools, py-earthengine-api, py-requests, py-retrying, py-beautifulsoup4, py-requests-toolbelt, py-pytest, py-future, py-google-cloud-storage
Link Dependencies:
python
Run Dependencies:
python, py-earthengine-api, py-requests, py-retrying, py-beautifulsoup4, py-requests-toolbelt, py-future, py-google-cloud-storage
Test Dependencies:
py-pytest
Description:
Google Earth Engine Batch Asset Manager.

py-genders

Homepage:
Spack package:
Versions:
1.22
Build Dependencies:
python
Link Dependencies:
python
Description:
Genders is a static cluster configuration database used for cluster configuration management. It is used by a variety of tools and scripts for management of large clusters.

py-genshi

Homepage:
Spack package:
Versions:
0.7, 0.6.1, 0.6
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Python toolkit for generation of output for the web

py-gensim

Homepage:
Spack package:
Versions:
3.8.1, 3.8.0
Build Dependencies:
python, py-setuptools, py-numpy, py-scipy, py-smart-open, py-six
Link Dependencies:
python
Run Dependencies:
python, py-numpy, py-scipy, py-smart-open, py-six
Description:
Gensim is a Python library for topic modelling, document indexing and similarity retrieval with large corpora. Target audience is the natural language processing (NLP) and information retrieval (IR) community.

py-geoalchemy2

Homepage:
Spack package:
Versions:
0.6.3, 0.4.2
Build Dependencies:
python, py-setuptools, py-sqlalchemy, py-shapely
Link Dependencies:
python
Run Dependencies:
python, py-sqlalchemy, py-shapely
Test Dependencies:
py-pycodestyle, py-flake8, py-pytest, py-pytest-cov
Description:
Using SQLAlchemy with Spatial Databases

py-geopandas

Homepage:
Spack package:
Versions:
0.5.0, 0.4.0, 0.3.0
Build Dependencies:
python, py-setuptools, py-pandas, py-shapely, py-fiona, py-pyproj, py-descartes, py-matplotlib
Link Dependencies:
python
Run Dependencies:
python, py-pandas, py-shapely, py-fiona, py-pyproj, py-descartes, py-matplotlib
Description:
GeoPandas is an open source project to make working with geospatial data in python easier. GeoPandas extends the datatypes used by pandas to allow spatial operations on geometric types. Geometric operations are performed by shapely. Geopandas further depends on fiona for file access and descartes and matplotlib for plotting.

py-gevent

Homepage:
Spack package:
Versions:
1.3a2
Build Dependencies:
python, py-setuptools, py-cython, py-cffi, py-greenlet
Link Dependencies:
python
Run Dependencies:
python, py-cffi, py-greenlet
Description:
gevent is a coroutine-based Python networking library.

py-gf256

Homepage:
Spack package:
Versions:
0.2.0
Build Dependencies:
python, py-setuptools, py-cffi
Link Dependencies:
python
Run Dependencies:
python, py-cffi
Description:
GF256 is an implementation of GF(2**8). This Galois Field allows you to perform finite field arithmetic on byte sized integers.

py-git-review

Homepage:
Spack package:
Versions:
1.26.0, 1.25.0
Build Dependencies:
python, py-setuptools, py-pbr, py-requests
Link Dependencies:
python
Run Dependencies:
python, py-pbr, py-requests, git, tk
Description:
git-review is a tool that helps submitting git branches to gerrit

py-gnuplot

Homepage:
Spack package:
Versions:
1.8
Build Dependencies:
python, py-numpy
Link Dependencies:
python
Run Dependencies:
python, py-numpy
Description:
Gnuplot.py is a Python package that allows you to create graphs from within Python using the gnuplot plotting program.

py-goatools

Homepage:
Spack package:
Versions:
0.7.11
Build Dependencies:
python, py-nose, py-numpy, py-pandas, py-pydot, py-pyparsing, py-pytest, py-scipy, py-statsmodels, py-xlrd, py-xlsxwriter
Link Dependencies:
python
Run Dependencies:
python, py-nose, py-numpy, py-pandas, py-pydot, py-pyparsing, py-pytest, py-scipy, py-statsmodels, py-xlrd, py-xlsxwriter
Description:
Python scripts to find enrichment of GO terms

py-google-api-python-client

Homepage:
Spack package:
Versions:
1.7.10
Build Dependencies:
python, py-setuptools, py-httplib2, py-google-auth, py-google-auth-httplib2, py-six, py-uritemplate
Link Dependencies:
python
Run Dependencies:
python, py-httplib2, py-google-auth, py-google-auth-httplib2, py-six, py-uritemplate
Description:
The Google API Client for Python is a client library for accessing the Plus, Moderator, and many other Google APIs.

py-google-auth

Homepage:
Spack package:
Versions:
1.6.3
Build Dependencies:
python, py-setuptools, py-pyasn1-modules, py-rsa, py-six, py-cachetools
Link Dependencies:
python
Run Dependencies:
python, py-pyasn1-modules, py-rsa, py-six, py-cachetools
Description:
This library simplifies using Google's various server-to-server authentication mechanisms to access Google APIs.

py-google-auth-httplib2

Homepage:
Spack package:
Versions:
0.0.3
Build Dependencies:
python, py-setuptools, py-google-auth, py-httplib2
Link Dependencies:
python
Run Dependencies:
python, py-google-auth, py-httplib2
Description:
Google Authentication Library: httplib2 transport.

py-google-cloud-core

Homepage:
Spack package:
Versions:
1.0.3
Build Dependencies:
python, py-setuptools, py-google-api-core
Link Dependencies:
python
Run Dependencies:
python, py-google-api-core
Description:
Google Cloud API client core library.

py-google-cloud-storage

Homepage:
Spack package:
Versions:
1.18.0
Build Dependencies:
python, py-setuptools, py-google-auth, py-google-cloud-core, py-google-resumable-media
Link Dependencies:
python
Run Dependencies:
python, py-google-auth, py-google-cloud-core, py-google-resumable-media
Description:
Google Cloud Storage API client library.

py-google-pasta

Homepage:
Spack package:
Versions:
0.1.8
Build Dependencies:
python, py-setuptools, py-six
Link Dependencies:
python
Run Dependencies:
python, py-six
Description:
pasta is an AST-based Python refactoring library.

py-google-resumable-media

Homepage:
Spack package:
Versions:
0.3.2
Build Dependencies:
python, py-setuptools, py-six
Link Dependencies:
python
Run Dependencies:
python, py-six
Description:
Utilities for Google Media Downloads and Resumable Uploads.

py-googleapis-common-protos

Homepage:
Spack package:
Versions:
1.6.0
Build Dependencies:
python, py-setuptools, py-protobuf
Link Dependencies:
python
Run Dependencies:
python, py-protobuf
Description:
Common protobufs used in Google APIs.

py-gpaw

Homepage:
Spack package:
Versions:
19.8.1, 1.3.0
Build Dependencies:
python, mpi, py-ase, py-numpy, py-scipy, libxc, blas, lapack, fftw, scalapack
Link Dependencies:
python, mpi, libxc, blas, lapack, fftw, scalapack
Run Dependencies:
python, mpi, py-ase, py-numpy, py-scipy
Description:
GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) method and the atomic simulation environment (ASE).

py-graphviz

Homepage:
Spack package:
Versions:
0.11.1, 0.10.1
Build Dependencies:
python, py-setuptools, py-tox, py-flake8, py-pep8-naming, py-wheel, py-twine, py-sphinx, py-sphinx-rtd-theme
Link Dependencies:
python
Run Dependencies:
python, py-tox, py-flake8, py-pep8-naming, py-wheel, py-twine, py-sphinx, py-sphinx-rtd-theme
Test Dependencies:
py-mock, py-pytest, py-pytest-mock, py-pytest-cov
Description:
Simple Python interface for Graphviz

py-greenlet

Homepage:
Spack package:
Versions:
0.4.13
Build Dependencies:
python
Link Dependencies:
python
Run Dependencies:
python
Description:
Lightweight in-process concurrent programming

py-grequests

Homepage:
Spack package:
Versions:
0.4.0, 0.3.0
Build Dependencies:
python, py-setuptools, py-gevent, py-requests
Link Dependencies:
python
Run Dependencies:
python, py-gevent, py-requests
Test Dependencies:
py-nose
Description:
GRequests allows you to use Requests with Gevent to make asynchronous HTTP Requests easily. Note: You should probably use requests-threads or requests-futures instead.

py-griddataformats

Homepage:
Spack package:
Versions:
0.5.0, 0.4.1, 0.3.3
Build Dependencies:
python, py-setuptools, py-numpy, py-six
Link Dependencies:
python
Run Dependencies:
python, py-numpy, py-six
Description:
The gridDataFormats package provides classes to unify reading and writing n-dimensional datasets. One can read grid data from files, make them available as a Grid object, and write out the data again.

py-grpcio

Homepage:
Spack package:
Versions:
1.25.0
Build Dependencies:
python, py-setuptools, py-six, py-futures, py-enum34, py-cython, openssl, zlib, c-ares
Link Dependencies:
python, openssl, zlib, c-ares
Run Dependencies:
python, py-six, py-futures, py-enum34
Description:
HTTP/2-based RPC framework.

py-guidata

Homepage:
Spack package:
Versions:
1.7.5
Build Dependencies:
python, py-setuptools, py-pyqt4, py-spyder, py-h5py
Link Dependencies:
python
Run Dependencies:
python, py-pyqt4, py-spyder, py-h5py
Description:
Automatic graphical user interfaces generation for easy dataset editing and display

py-guiqwt

Homepage:
Spack package:
Versions:
3.0.2
Build Dependencies:
python, py-setuptools, py-numpy, py-scipy, py-guidata, py-pythonqwt, py-pillow
Link Dependencies:
python
Run Dependencies:
python, py-numpy, py-scipy, py-guidata, py-pythonqwt, py-pillow
Description:
guiqwt is a set of tools for curve and image plotting (extension to PythonQwt)

py-h5glance

Homepage:
Spack package:
Versions:
0.4
Build Dependencies:
python, py-h5py, py-htmlgen
Link Dependencies:
python
Run Dependencies:
python, py-h5py, py-htmlgen
Description:
H5Glance lets you explore HDF5 files in the terminal or an HTML interface.

py-h5py

Homepage:
Spack package:
Versions:
2.9.0, 2.8.0, 2.7.1, 2.7.0, 2.6.0, 2.5.0, 2.4.0
Build Dependencies:
python, py-cython, py-pkgconfig, py-setuptools, py-numpy, py-six, hdf5, mpi, py-mpi4py
Link Dependencies:
python, hdf5, mpi
Run Dependencies:
python, py-numpy, py-six, py-mpi4py
Description:
The h5py package provides both a high- and low-level interface to the HDF5 library from Python.

py-h5sh

Homepage:
Spack package:
Versions:
0.1.1
Build Dependencies:
python, py-setuptools, py-h5py, py-numpy, py-prompt-toolkit, py-pygments, py-six
Link Dependencies:
python
Run Dependencies:
python, py-setuptools, py-h5py, py-numpy, py-prompt-toolkit, py-pygments, py-six
Test Dependencies:
py-pytest
Description:
Shell-like environment for HDF5.

py-hacking

Homepage:
Spack package:
Versions:
1.1.0
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
OpenStack Hacking Guideline Enforcement.

py-hdfs

Homepage:
Spack package:
Versions:
2.1.0
Build Dependencies:
python, py-setuptools, py-docopt, py-requests, py-six
Link Dependencies:
python
Run Dependencies:
python, py-docopt, py-requests, py-six
Description:
API and command line interface for HDFS

py-heapdict

Homepage:
Spack package:
Versions:
1.0.1
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
A heap with decrease-key and increase-key operations

py-hepdata-validator

Homepage:
Spack package:
Versions:
0.1.16, 0.1.15, 0.1.14, 0.1.8
Build Dependencies:
python, py-setuptools, py-jsonschema, py-pyyaml
Link Dependencies:
python
Run Dependencies:
python, py-jsonschema, py-pyyaml
Description:
Validation schema and code for HEPdata submissions.

py-hpccm

Homepage:
Spack package:
Versions:
19.2.0
Build Dependencies:
python, py-setuptools, py-enum34, py-six
Link Dependencies:
python
Run Dependencies:
python, py-setuptools, py-enum34, py-six
Description:
HPC Container Maker (HPCCM - pronounced H-P-see-M) is an open source tool to make it easier to generate container specification files.

py-html2text

Homepage:
Spack package:
Versions:
2016.9.19
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Turn HTML into equivalent Markdown-structured text.

py-html5lib

Homepage:
Spack package:
Versions:
1.0.1, 0.9999999
Build Dependencies:
python, py-six, py-setuptools, py-webencodings
Link Dependencies:
python
Run Dependencies:
python, py-six, py-webencodings
Description:
HTML parser based on the WHATWG HTML specification.

py-htmlgen

Homepage:
Spack package:
Versions:
1.2.2
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Test Dependencies:
py-asserts, py-typing
Description:
Library to generate HTML from classes.

py-htseq

Homepage:
Spack package:
Versions:
0.11.2, 0.9.1
Build Dependencies:
python, py-setuptools, py-numpy, py-pysam, py-matplotlib, py-cython, swig
Link Dependencies:
python
Run Dependencies:
python, py-numpy, py-pysam, py-matplotlib, py-cython, swig
Description:
HTSeq is a Python package that provides infrastructure to process data from high-throughput sequencing assays.

py-httpbin

Homepage:
Spack package:
Versions:
0.7.0, 0.5.0
Build Dependencies:
python, py-setuptools, py-flask, py-markupsafe, py-decorator, py-itsdangerous, py-six, py-brotlipy, py-raven, py-werkzeug
Link Dependencies:
python
Run Dependencies:
python, py-flask, py-markupsafe, py-decorator, py-itsdangerous, py-six, py-brotlipy, py-raven, py-werkzeug
Description:
HTTP Request and Response Service

py-httplib2

Homepage:
Spack package:
Versions:
0.13.1
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
A comprehensive HTTP client library.

py-humanfriendly

Homepage:
Spack package:
Versions:
4.18
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Human friendly output for text interfaces using Python

py-humanize

Homepage:
Spack package:
Versions:
0.5.1
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Test Dependencies:
py-mock
Description:
This modest package contains various common humanization utilities, like turning a number into a fuzzy human readable duration ('3 minutes ago') or into a human readable size or throughput. It works with python 2.7 and 3.3 and is localized to Russian, French, Korean and Slovak.

py-hvac

Homepage:
Spack package:
Versions:
0.9.6, 0.9.5, 0.9.4, 0.9.3, 0.2.17
Build Dependencies:
python, py-setuptools, py-requests, py-six
Link Dependencies:
python
Run Dependencies:
python, py-requests, py-six
Description:
HashiCorp Vault API client

py-hypothesis

Homepage:
Spack package:
Versions:
4.41.2, 4.24.3, 4.7.2, 3.7.0
Build Dependencies:
python, py-setuptools, py-attrs, py-enum34
Link Dependencies:
python
Run Dependencies:
python, py-attrs, py-enum34
Description:
A library for property based testing.

py-ics

Homepage:
Spack package:
Versions:
0.6
Build Dependencies:
python, py-setuptools, py-python-dateutil, py-arrow, py-six, py-tatsu
Link Dependencies:
python
Run Dependencies:
python, py-python-dateutil, py-arrow, py-six, py-tatsu
Description:
Ics.py : iCalendar for Humans Ics.py is a pythonic and easy iCalendar library. Its goals are to read and write ics data in a developer friendly way. iCalendar is a widely-used and useful format but not user friendly. Ics.py is there to give you the ability of creating and reading this format without any knowledge of it. It should be able to parse every calendar that respects the rfc5545 and maybe some more. It also outputs rfc compliant calendars. iCalendar (file extension .ics) is used by Google Calendar, Apple Calendar, Android and many more. Ics.py is available for Python>=3.6 and is Apache2 Licensed.

py-identify

Homepage:
Spack package:
Versions:
1.4.7
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
File identification library for Python. Given a file (or some information about a file), return a set of standardized tags identifying what the file is.

py-idna

Homepage:
Spack package:
Versions:
2.8, 2.5
Build Dependencies:
python, py-setuptools
Link Dependencies:
python, py-setuptools
Run Dependencies:
python
Description:
Internationalized Domain Names for Python (IDNA 2008 and UTS #46)

py-illumina-utils

Homepage:
Spack package:
Versions:
2.3, 2.2
Build Dependencies:
python, py-pip, py-setuptools, py-matplotlib, py-numpy, py-python-levenshtein
Link Dependencies:
python
Run Dependencies:
python, py-matplotlib, py-numpy, py-python-levenshtein
Description:
A library and collection of scripts to work with Illumina paired-end data (for CASAVA 1.8+).

py-imageio

Homepage:
Spack package:
Versions:
2.5.0, 2.4.1, 2.3.0
Build Dependencies:
python, py-numpy, py-pillow, py-setuptools
Link Dependencies:
python
Run Dependencies:
python, py-numpy, py-pillow, ffmpeg
Description:
Imageio is a Python library that provides an easy interface to read and write a wide range of image data, including animated images, video, volumetric data, and scientific formats. It is cross-platform, runs on Python 2.7 and 3.4+, and is easy to install.

py-imagesize

Homepage:
Spack package:
Versions:
1.1.0, 0.7.1
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Parses image file headers and returns image size. Supports PNG, JPEG, JPEG2000, and GIF image file formats.

py-iminuit

Homepage:
Spack package:
Versions:
1.3.6, 1.2
Build Dependencies:
python, py-setuptools, py-numpy
Link Dependencies:
python
Run Dependencies:
python, py-numpy
Test Dependencies:
py-matplotlib, py-cython, py-pytest, py-scipy
Description:
Interactive IPython-Friendly Minimizer based on SEAL Minuit2.

py-importlib

Homepage:
Spack package:
Versions:
1.0.4
Build Dependencies:
python
Link Dependencies:
python
Run Dependencies:
python
Description:
Packaging for importlib from Python 2.7

py-importlib-metadata

Homepage:
Spack package:
Versions:
1.2.0, 0.23, 0.19, 0.18
Build Dependencies:
python, py-setuptools, py-setuptools-scm, py-zipp, py-pathlib2, py-contextlib2, py-configparser
Link Dependencies:
python
Run Dependencies:
python, py-zipp, py-pathlib2, py-contextlib2, py-configparser
Test Dependencies:
py-importlib-resources, py-packaging
Description:
Read metadata from Python packages.

py-importlib-resources

Homepage:
Spack package:
Versions:
1.0.2
Build Dependencies:
python, py-setuptools, py-wheel, py-pathlib2, py-typing
Link Dependencies:
python
Run Dependencies:
python, py-pathlib2, py-typing
Description:
Read resources from Python packages

py-iniparse

Homepage:
Spack package:
Versions:
master, 0.4
Build Dependencies:
python
Link Dependencies:
python
Run Dependencies:
python
Description:
Accessing and Modifying INI files

py-intervaltree

Homepage:
Spack package:
Versions:
3.0.2
Build Dependencies:
python, py-sortedcontainers, py-setuptools
Link Dependencies:
python
Run Dependencies:
python, py-sortedcontainers
Test Dependencies:
py-pytest
Description:
Editable interval tree data structure for Python 2 and 3.

py-invoke

Homepage:
Spack package:
Versions:
1.2.0
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Pythonic task execution

py-ipaddress

Homepage:
Spack package:
Versions:
1.0.23, 1.0.22, 1.0.18
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Python 3.3's ipaddress for older Python versions

py-ipdb

Homepage:
Spack package:
Versions:
0.10.1
Build Dependencies:
python, py-setuptools, py-ipython, py-traitlets, py-six, py-pexpect, py-prompt-toolkit
Link Dependencies:
python, py-ipython, py-traitlets, py-six, py-pexpect, py-prompt-toolkit
Run Dependencies:
python
Description:
ipdb is the iPython debugger and has many additional features, including a better interactive debugging experience via colorized output.

py-ipykernel

Homepage:
Spack package:
Versions:
5.1.0, 4.10.0, 4.5.0, 4.4.1, 4.4.0, 4.3.1, 4.3.0, 4.2.2, 4.2.1, 4.2.0, 4.1.1, 4.1.0
Build Dependencies:
python, py-setuptools, py-traitlets, py-tornado, py-ipython, py-jupyter-client, py-pexpect
Link Dependencies:
python
Run Dependencies:
python, py-traitlets, py-tornado, py-ipython, py-jupyter-client, py-pexpect
Description:
IPython Kernel for Jupyter

py-ipython

Homepage:
Spack package:
Versions:
7.3.0, 5.8.0, 5.1.0, 3.1.0, 2.3.1
Build Dependencies:
python, py-backports-shutil-get-terminal-size, py-pathlib2, py-pygments, py-pickleshare, py-simplegeneric, py-prompt-toolkit, py-traitlets, py-decorator, py-pexpect, py-backcall, py-appnope
Link Dependencies:
python
Run Dependencies:
python, py-backports-shutil-get-terminal-size, py-pathlib2, py-pygments, py-pickleshare, py-simplegeneric, py-prompt-toolkit, py-traitlets, py-decorator, py-pexpect, py-backcall, py-appnope
Description:
IPython provides a rich toolkit to help you make the most out of using Python interactively.

py-ipython-genutils

Homepage:
Spack package:
Versions:
0.2.0, 0.1.0
Build Dependencies:
python
Link Dependencies:
python
Run Dependencies:
python
Description:
Vestigial utilities from IPython

py-ipywidgets

Homepage:
Spack package:
Versions:
7.4.2, 5.2.2
Build Dependencies:
python, py-ipython, py-ipykernel, py-traitlets, py-nbformat, py-widgetsnbextension
Link Dependencies:
python
Run Dependencies:
python, py-ipython, py-ipykernel, py-traitlets, py-nbformat, py-widgetsnbextension
Test Dependencies:
py-mock, py-nose
Description:
IPython widgets for the Jupyter Notebook

py-irpf90

Homepage:
Spack package:
Versions:
1.7.7
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
IRPF90 is a Fortran90 preprocessor written in Python for programming using the Implicit Reference to Parameters (IRP) method. It simplifies the development of large fortran codes in the field of scientific high performance computing.

py-isodate

Homepage:
Spack package:
Versions:
0.6.0
Build Dependencies:
python, py-setuptools, py-six
Link Dependencies:
python
Run Dependencies:
python, py-six
Description:
This module implements ISO 8601 date, time and duration parsing. The implementation follows ISO8601:2004 standard, and implements only date/time representations mentioned in the standard. If something is not mentioned there, then it is treated as non existent, and not as an allowed option.

py-isort

Homepage:
Spack package:
Versions:
4.3.20, 4.2.15
Build Dependencies:
python, py-setuptools, py-futures, py-backports-functools-lru-cache
Link Dependencies:
python
Run Dependencies:
python, py-setuptools, py-futures, py-backports-functools-lru-cache
Test Dependencies:
py-pytest, py-mock
Description:
A Python utility / library to sort Python imports.

py-itsdangerous

Homepage:
Spack package:
Versions:
1.1.0, 0.24
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Various helpers to pass trusted data to untrusted environments.

py-jaraco-functools

Homepage:
Spack package:
Versions:
2.0
Build Dependencies:
python, py-setuptools, py-setuptools-scm, py-backports-functools-lru-cache, py-more-itertools
Link Dependencies:
python
Run Dependencies:
python, py-backports-functools-lru-cache, py-more-itertools
Description:
Functools like those found in stdlib

py-jdatetime

Homepage:
Spack package:
Versions:
3.6.2
Build Dependencies:
python
Link Dependencies:
python
Run Dependencies:
python
Description:
jdatetime is Jalali implementation of Python's datetime module

py-jdcal

Homepage:
Spack package:
Versions:
1.3, 1.2
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Julian dates from proleptic Gregorian and Julian calendars

py-jedi

Homepage:
Spack package:
Versions:
0.13.3, 0.10.0, 0.9.0
Build Dependencies:
python, py-setuptools, py-parso
Link Dependencies:
python
Run Dependencies:
python, py-setuptools, py-parso
Description:
An autocompletion tool for Python that can be used for text editors.

py-jellyfish

Homepage:
Spack package:
Versions:
0.6.1, 0.5.6
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
a library for doing approximate and phonetic matching of strings.

py-jinja2

Homepage:
Spack package:
Versions:
2.10.3, 2.10.1, 2.10, 2.9.6, 2.8, 2.7.3, 2.7.2, 2.7.1, 2.7
Build Dependencies:
python, py-setuptools, py-markupsafe, py-babel
Link Dependencies:
python
Run Dependencies:
python, py-markupsafe, py-babel
Description:
Jinja2 is a template engine written in pure Python. It provides a Django inspired non-XML syntax but supports inline expressions and an optional sandboxed environment.

py-jinja2-time

Homepage:
Spack package:
Versions:
0.2.0
Build Dependencies:
python, py-setuptools, py-arrow, py-jinja2
Link Dependencies:
python, py-arrow, py-jinja2
Run Dependencies:
python
Description:
Jinja2 Extension for Dates and Times

py-jmespath

Homepage:
Spack package:
Versions:
0.9.4
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Test Dependencies:
py-nose
Description:
JSON Matching Expressions.

py-joblib

Homepage:
Spack package:
Versions:
0.14.0, 0.13.2, 0.11, 0.10.3, 0.10.2, 0.10.0
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Python function as pipeline jobs

py-jplephem

Homepage:
Spack package:
Versions:
2.9
Build Dependencies:
python, py-numpy
Link Dependencies:
python
Run Dependencies:
python, py-numpy
Description:
This package can load and use a Jet Propulsion Laboratory (JPL) ephemeris for predicting the position and velocity of a planet or other Solar System body.

py-jprops

Homepage:
Spack package:
Versions:
2.0.2
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Java properties file parser for Python

py-jpype1

Homepage:
Spack package:
Versions:
0.6.3, 0.6.2, 0.6.1, 0.6.0
Build Dependencies:
python, py-setuptools, java, py-numpy
Link Dependencies:
python
Run Dependencies:
python, java, py-numpy
Description:
JPype is an effort to allow python programs full access to java class libraries.

py-jsonpatch

Homepage:
Spack package:
Versions:
1.23
Build Dependencies:
python, py-setuptools, py-jsonpointer
Link Dependencies:
python
Run Dependencies:
python, py-jsonpointer
Description:
Library to apply JSON Patches according to RFC 6902

py-jsonpointer

Homepage:
Spack package:
Versions:
2.0
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Library to resolve JSON Pointers according to RFC 6901

py-jsonschema

Homepage:
Spack package:
Versions:
3.0.1, 2.6.0, 2.5.1
Build Dependencies:
python, py-setuptools, py-vcversioner, py-setuptools-scm, py-functools32, py-attrs, py-pyrsistent, py-six
Link Dependencies:
python
Run Dependencies:
python, py-setuptools, py-functools32, py-attrs, py-pyrsistent, py-six
Description:
Jsonschema: An(other) implementation of JSON Schema for Python.

py-junit-xml

Homepage:
Spack package:
Versions:
1.7
Build Dependencies:
python, py-setuptools, py-six
Link Dependencies:
python
Run Dependencies:
python, py-six
Description:
Creates JUnit XML test result documents that can be read by tools such as Jenkins

py-jupyter

Homepage:
Spack package:
Versions:
1.0.0
Build Dependencies:
python, py-notebook, py-qtconsole, py-jupyter-console, py-nbconvert, py-ipykernel, py-ipywidgets
Link Dependencies:
python
Run Dependencies:
python, py-notebook, py-qtconsole, py-jupyter-console, py-nbconvert, py-ipykernel, py-ipywidgets
Description:
Jupyter metapackage. Install all the Jupyter components in one go.

py-jupyter-client

Homepage:
Spack package:
Versions:
5.3.4, 5.2.4, 4.4.0, 4.3.0, 4.2.2, 4.2.1, 4.2.0, 4.1.1, 4.1.0, 4.0.0
Build Dependencies:
python, py-traitlets, py-jupyter-core, py-pyzmq, py-python-dateutil, py-tornado, py-setuptools
Link Dependencies:
python
Run Dependencies:
python, py-traitlets, py-jupyter-core, py-pyzmq, py-python-dateutil, py-tornado
Description:
Jupyter protocol client APIs

py-jupyter-console

Homepage:
Spack package:
Versions:
5.2.0, 5.0.0, 4.1.1, 4.1.0, 4.0.3, 4.0.2
Build Dependencies:
python, py-jupyter-client, py-ipython, py-ipykernel, py-pygments
Link Dependencies:
python
Run Dependencies:
python, py-jupyter-client, py-ipython, py-ipykernel, py-pygments
Description:
Jupyter Terminal Console

py-jupyter-core

Homepage:
Spack package:
Versions:
4.6.0, 4.4.0, 4.2.0, 4.1.1, 4.1.0, 4.0.6, 4.0.5, 4.0.4, 4.0.3, 4.0.2, 4.0.1, 4.0.0
Build Dependencies:
python, py-setuptools, py-traitlets
Link Dependencies:
python
Run Dependencies:
python, py-traitlets
Description:
Core Jupyter functionality

py-keras

Homepage:
Spack package:
Versions:
2.2.4, 2.2.3, 2.2.2, 2.2.1, 2.2.0, 2.1.6, 2.1.5, 2.1.4, 2.1.3, 2.1.2, 2.1.1, 2.1.0, 2.0.9, 2.0.8, 2.0.7, 2.0.6, 2.0.5, 2.0.4, 2.0.3, 1.2.2, 1.2.1, 1.2.0, 1.1.2, 1.1.1, 1.1.0
Build Dependencies:
python, py-setuptools, py-theano, py-pyyaml, py-six
Link Dependencies:
python
Run Dependencies:
python, py-keras-applications, py-keras-preprocessing, py-theano, py-pyyaml, py-six
Description:
Deep Learning library for Python. Convnets, recurrent neural networks, and more. Runs on Theano or TensorFlow.

py-keras-applications

Homepage:
Spack package:
Versions:
1.0.8, 1.0.7, 1.0.6, 1.0.4, 1.0.3, 1.0.2, 1.0.1
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Sample Deep Learning application in Keras. Keras depends on this package to run properly.

py-keras-preprocessing

Homepage:
Spack package:
Versions:
1.1.0, 1.0.9, 1.0.5, 1.0.4, 1.0.3, 1.0.2, 1.0.1
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Utilities for working with image data, text data, and sequence data.

py-kitchen

Homepage:
Spack package:
Versions:
1.2.6, 1.1.1
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Kitchen contains a cornucopia of useful code

py-kiwisolver

Homepage:
Spack package:
Versions:
1.1.0, 1.0.1
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
A fast implementation of the Cassowary constraint solver

py-kmodes

Homepage:
Spack package:
Versions:
0.10.1
Build Dependencies:
python, py-setuptools, py-numpy, py-scikit-learn, py-scipy, py-joblib
Link Dependencies:
python
Run Dependencies:
python, py-numpy, py-scikit-learn, py-scipy, py-joblib
Description:
Python implementations of the k-modes and k-prototypes clustering algorithms for clustering categorical data.

py-kombu

Homepage:
Spack package:
Versions:
4.6.6, 4.5.0, 4.3.0
Build Dependencies:
python, py-setuptools, py-amqp, py-importlib-metadata
Link Dependencies:
python
Run Dependencies:
python, py-amqp, py-importlib-metadata
Description:
Messaging library for Python.

py-lark-parser

Homepage:
Spack package:
Versions:
0.7.1, 0.6.2
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Lark is a modern general-purpose parsing library for Python.

py-latexcodec

Homepage:
Spack package:
Versions:
1.0.4
Build Dependencies:
python, py-setuptools, py-six
Link Dependencies:
python
Run Dependencies:
python, py-six
Description:
A lexer and codec to work with LaTeX code in Python.

py-lazy

Homepage:
Spack package:
Versions:
1.2
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Lazy attributes for Python objects

py-lazy-object-proxy

Homepage:
Spack package:
Versions:
1.3.1
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
A fast and thorough lazy object proxy.

py-lazy-property

Homepage:
Spack package:
Versions:
0.0.1, 0.0.0
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
A package for making properties lazy

py-lazyarray

Homepage:
Spack package:
Versions:
0.2.10, 0.2.8
Build Dependencies:
python, py-numpy
Link Dependencies:
python
Run Dependencies:
python, py-numpy
Description:
a Python package that provides a lazily-evaluated numerical array class, larray, based on and compatible with NumPy arrays.

py-leather

Homepage:
Spack package:
Versions:
0.3.3
Build Dependencies:
python, py-setuptools, py-six
Link Dependencies:
python
Run Dependencies:
python, py-six
Description:
Leather is the Python charting library for those who need charts now and don't care if they're perfect.

py-libconf

Homepage:
Spack package:
Versions:
1.0.1
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
A pure-Python libconfig reader/writer with permissive license

py-libensemble

Homepage:
Spack package:
Versions:
develop, 0.6.0, 0.5.2, 0.5.1, 0.5.0, 0.4.1, 0.4.0, 0.3.0, 0.2.0, 0.1.0
Build Dependencies:
python, py-setuptools, py-numpy, mpi, py-mpi4py, py-scipy, py-petsc4py, nlopt
Link Dependencies:
python, mpi
Run Dependencies:
python, py-numpy, py-mpi4py, py-scipy, py-petsc4py, nlopt
Description:
Library for managing ensemble-like collections of computations.

py-ligo-segments

Homepage:
Spack package:
Versions:
1.2.0
Build Dependencies:
python, py-setuptools, py-six
Link Dependencies:
python
Run Dependencies:
python, py-six
Description:
Representations of semi-open intervals.

py-line-profiler

Homepage:
Spack package:
Versions:
2.1.2, 2.0
Build Dependencies:
python, py-setuptools, py-cython, py-ipython
Link Dependencies:
python
Run Dependencies:
python, py-ipython
Description:
Line-by-line profiler.

py-linecache2

Homepage:
Spack package:
Versions:
1.0.0
Build Dependencies:
python, py-setuptools, py-pbr
Link Dependencies:
python
Run Dependencies:
python
Test Dependencies:
py-fixtures, py-unittest2
Description:
Backports of the linecache module

py-lit

Homepage:
Spack package:
Versions:
0.7.1, 0.5.0
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
lit is a portable tool for executing LLVM and Clang style test suites, summarizing their results, and providing indication of failures. lit is designed to be a lightweight testing tool with as simple a user interface as possible.

py-llvmlite

Homepage:
Spack package:
Versions:
0.29.0, 0.27.1, 0.26.0, 0.25.0, 0.23.0, 0.20.0
Build Dependencies:
python, py-setuptools, py-enum34, llvm, binutils
Link Dependencies:
python, llvm
Run Dependencies:
python, py-enum34
Description:
A lightweight LLVM python binding for writing JIT compilers

py-lmfit

Homepage:
Spack package:
Versions:
0.9.5
Build Dependencies:
python, py-numpy, py-scipy, py-setuptools
Link Dependencies:
python
Run Dependencies:
python, py-numpy, py-scipy
Description:
Least-Squares Minimization with Bounds and Constraints

py-localcider

Homepage:
Spack package:
Versions:
0.1.14
Build Dependencies:
python, py-setuptools, py-numpy, py-matplotlib, py-scipy
Link Dependencies:
python
Run Dependencies:
python, py-numpy, py-matplotlib, py-scipy
Description:
Tools for calculating sequence properties of disordered proteins

py-locket

Homepage:
Spack package:
Versions:
0.2.0
Build Dependencies:
python
Link Dependencies:
python
Run Dependencies:
python
Description:
File-based locks for Python for Linux and Windows.

py-lockfile

Homepage:
Spack package:
Versions:
0.10.2
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
The lockfile package exports a LockFile class which provides a simple API for locking files. Unlike the Windows msvcrt.locking function, the fcntl.lockf and flock functions, and the deprecated posixfile module, the API is identical across both Unix (including Linux and Mac) and Windows platforms. The lock mechanism relies on the atomic nature of the link (on Unix) and mkdir (on Windows) system calls. An implementation based on SQLite is also provided, more as a demonstration of the possibilities it provides than as production-quality code.

py-logilab-common

Homepage:
Spack package:
Versions:
1.4.2, 1.2.0
Build Dependencies:
python, py-setuptools, py-six, py-unittest2
Link Dependencies:
python
Run Dependencies:
python, py-setuptools, py-six, py-unittest2
Test Dependencies:
py-pytz
Description:
Common modules used by Logilab projects

py-lru-dict

Homepage:
Spack package:
Versions:
1.1.6
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
A fast LRU cache

py-lscsoft-glue

Homepage:
Spack package:
Versions:
2.0.0
Build Dependencies:
python, py-setuptools, py-six, py-pyopenssl, py-numpy, py-ligo-segments
Link Dependencies:
python
Run Dependencies:
python, py-six, py-pyopenssl, py-numpy, py-ligo-segments
Description:
Glue (Grid LSC User Environment) is a suite of python modules and programs to allow users to run LSC codes on the grid. It also provides certain metadata services, such as the LSC segment database.

py-luigi

Homepage:
Spack package:
Versions:
2.8.3
Build Dependencies:
python, py-setuptools, py-tornado, py-python-daemon, py-python-dateutil
Link Dependencies:
python
Run Dependencies:
python, py-tornado, py-python-daemon, py-python-dateutil
Test Dependencies:
py-pytest
Description:
Workflow mgmgt + task scheduling + dependency resolution

py-lxml

Homepage:
Spack package:
Versions:
4.4.1, 4.3.3, 4.2.5, 3.7.3, 2.3
Build Dependencies:
python, py-setuptools, libxml2, libxslt, py-html5lib, py-beautifulsoup4, py-cssselect
Link Dependencies:
python
Run Dependencies:
python, libxml2, libxslt, py-html5lib, py-beautifulsoup4, py-cssselect
Description:
lxml is the most feature-rich and easy-to-use library for processing XML and HTML in the Python language.

py-lzstring

Homepage:
Spack package:
Versions:
1.0.3
Build Dependencies:
python, py-setuptools, py-future
Link Dependencies:
python
Run Dependencies:
python, py-future
Description:
lz-string for python.

py-m2r

Homepage:
Spack package:
Versions:
0.2.1, 0.2.0, 0.1.15, 0.1.14, 0.1.13, 0.1.12, 0.1.11, 0.1.10, 0.1.9, 0.1.8
Build Dependencies:
python, py-setuptools, py-mistune, py-docutils
Link Dependencies:
python
Run Dependencies:
python, py-mistune, py-docutils
Description:
M2R converts a markdown file including reStructuredText (rst) markups to a valid rst format.

py-macholib

Homepage:
Spack package:
Versions:
1.11
Build Dependencies:
python, py-setuptools, py-altgraph
Link Dependencies:
python
Run Dependencies:
python, py-setuptools, py-altgraph
Description:
Python package for Mach-O header analysis and editing

py-machotools

Homepage:
Spack package:
Versions:
0.2.0
Build Dependencies:
python, py-setuptools, py-macholib
Link Dependencies:
python
Run Dependencies:
python, py-macholib
Description:
Python package for editing Mach-O headers using macholib

py-macs2

Homepage:
Spack package:
Versions:
2.2.4, 2.1.4, 2.1.1.20160309
Build Dependencies:
python, py-setuptools, py-numpy
Link Dependencies:
python
Run Dependencies:
python, py-setuptools, py-numpy
Description:
MACS2 Model-based Analysis of ChIP-Seq

py-maestrowf

Homepage:
Spack package:
Versions:
develop, master, 1.1.6, 1.1.5dev, 1.1.4dev1.1, 1.1.4dev1.0, 1.1.4, 1.1.2, 1.1.1, 1.1.0, 1.0.1
Build Dependencies:
python, py-setuptools, py-pyyaml, py-six, py-enum34, py-tabulate, py-filelock
Link Dependencies:
python
Run Dependencies:
python, py-pyyaml, py-six, py-enum34, py-tabulate, py-filelock
Description:
A general purpose workflow conductor for running multi-step simulation studies.

py-magic

Homepage:
Spack package:
Versions:
0.4.15
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python, file
Description:
A python wrapper for libmagic.

py-mako

Homepage:
Spack package:
Versions:
1.0.4, 1.0.1
Build Dependencies:
python, py-setuptools, py-markupsafe
Link Dependencies:
python
Run Dependencies:
python, py-markupsafe
Test Dependencies:
py-mock, py-pytest
Description:
A super-fast templating language that borrows the best ideas from the existing templating languages.

py-markdown

Homepage:
Spack package:
Versions:
3.1.1, 2.6.11, 2.6.7, 2.6.6, 2.6.5, 2.6.4, 2.6.3, 2.6.2, 2.6.1, 2.6, 2.5.2, 2.5.1, 2.5
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
This is a Python implementation of John Gruber's Markdown. It is almost completely compliant with the reference implementation, though there are a few very minor differences. See John's Syntax Documentation for the syntax rules.

py-markupsafe

Homepage:
Spack package:
Versions:
1.1.1, 1.0, 0.23, 0.22, 0.21, 0.20, 0.19
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
MarkupSafe is a library for Python that implements a unicode string that is aware of HTML escaping rules and can be used to implement automatic string escaping. It is used by Jinja 2, the Mako templating engine, the Pylons web framework and many more.

py-matplotlib

Homepage:
Spack package:
Versions:
3.1.3, 3.1.2, 3.1.1, 3.0.2, 3.0.0, 2.2.5, 2.2.4, 2.2.3, 2.2.2, 2.0.2, 2.0.0, 1.5.3, 1.5.1, 1.4.3, 1.4.2
Build Dependencies:
python, freetype, libpng, py-numpy, py-setuptools, py-cycler, py-python-dateutil, py-kiwisolver, py-pyparsing, py-pytz, py-subprocess32, py-functools32, py-backports-functools-lru-cache, py-six, ffmpeg, imagemagick, py-pillow, pkgconfig
Link Dependencies:
python, freetype, libpng, ffmpeg, imagemagick
Run Dependencies:
python, py-numpy, py-setuptools, py-cycler, py-python-dateutil, py-kiwisolver, py-pyparsing, py-pytz, py-subprocess32, py-functools32, py-backports-functools-lru-cache, py-six, tk, py-pyqt4, py-pyqt5, py-pygobject, py-wxpython, py-cairocffi, py-tornado, py-pillow, texlive, ghostscript
Test Dependencies:
py-pytest
Description:
matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms.

py-mccabe

Homepage:
Spack package:
Versions:
0.6.1, 0.6.0, 0.5.3, 0.5.2, 0.5.1, 0.5.0, 0.4.0, 0.3.1, 0.3, 0.2.1, 0.2, 0.1
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Test Dependencies:
py-pytest
Description:
Ned's script to check McCabe complexity.

py-mdanalysis

Homepage:
Spack package:
Versions:
0.19.2, 0.19.1, 0.19.0, 0.18.0, 0.17.0, 0.16.2, 0.16.1, 0.16.0, 0.15.0
Build Dependencies:
python, py-setuptools, py-cython, py-numpy, py-six, py-biopython, py-networkx, py-griddataformats, py-matplotlib, py-scipy, py-seaborn, py-netcdf4
Link Dependencies:
python
Run Dependencies:
python, py-numpy, py-six, py-biopython, py-networkx, py-griddataformats, py-matplotlib, py-scipy, py-seaborn, py-netcdf4, hdf5
Description:
MDAnalysis is a Python toolkit to analyze molecular dynamics trajectories generated by a wide range of popular simulation packages including DL_Poly, CHARMM, Amber, NAMD, LAMMPS, and Gromacs. (See the lists of supported trajectory formats and topology formats.)

py-mechanize

Homepage:
Spack package:
Versions:
0.4.3, 0.2.5
Build Dependencies:
python, py-setuptools, py-html5lib
Link Dependencies:
python
Run Dependencies:
python, py-html5lib
Description:
Stateful programmatic web browsing.

py-memory-profiler

Homepage:
Spack package:
Versions:
0.47
Build Dependencies:
python, py-setuptools, py-psutil
Link Dependencies:
python
Run Dependencies:
python, py-psutil
Description:
A module for monitoring memory usage of a python program

py-merlin

Homepage:
Spack package:
Versions:
1.8
Build Dependencies:
python
Link Dependencies:
python
Run Dependencies:
python
Description:
A custom version of Phillip J. Eby's setuptools.

py-merlinwf

Homepage:
Spack package:
Versions:
develop, master, 1.2.3, 1.1.1, 1.0.5
Build Dependencies:
python, py-setuptools, py-cached-property, py-celery, py-coloredlogs, py-cryptography, py-importlib-resources, py-maestrowf, py-numpy, py-parse, py-psutil, py-pyyaml, py-tabulate
Link Dependencies:
python
Run Dependencies:
python, py-setuptools, py-cached-property, py-celery, py-coloredlogs, py-cryptography, py-importlib-resources, py-maestrowf, py-numpy, py-parse, py-psutil, py-pyyaml, py-tabulate
Test Dependencies:
py-pytest
Description:
Merlin Workflow for HPC.

py-metasv

Homepage:
Spack package:
Versions:
0.5.4
Build Dependencies:
python, py-pybedtools, py-pysam, py-pyvcf, py-setuptools
Link Dependencies:
python
Run Dependencies:
python, py-pybedtools, py-pysam, py-pyvcf
Description:
An accurate and integrative structural-variant caller for next generation sequencing

py-methylcode

Homepage:
Spack package:
Versions:
master
Build Dependencies:
python, py-setuptools, py-numpy, py-pyfasta, py-bsddb3, bowtie
Link Dependencies:
python, py-numpy, py-pyfasta, py-bsddb3, bowtie
Run Dependencies:
python
Description:
MethylCoder is a single program that takes of bisulfite-treated reads and outputs per-base methylation data.

py-misopy

Homepage:
Spack package:
Versions:
0.5.4
Build Dependencies:
python, py-setuptools, py-numpy, py-scipy, py-pysam, py-matplotlib, samtools, bedtools2
Link Dependencies:
python, samtools, bedtools2
Run Dependencies:
python, py-numpy, py-scipy, py-pysam, py-matplotlib
Description:
MISO (Mixture of Isoforms) is a probabilistic framework that quantitates the expression level of alternatively spliced genes from RNA-Seq data, and identifies differentially regulated isoforms or exons across samples.

py-mistune

Homepage:
Spack package:
Versions:
0.8.4, 0.8.3, 0.8.2, 0.8.1, 0.8, 0.7.4, 0.7.3, 0.7.2, 0.7.1, 0.7, 0.6, 0.5.1, 0.5
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Python markdown parser

py-mlxtend

Homepage:
Spack package:
Versions:
0.16.0
Build Dependencies:
python, py-setuptools, py-numpy, py-scipy, py-pandas, py-scikit-learn, py-matplotlib
Link Dependencies:
python
Run Dependencies:
python, py-numpy, py-scipy, py-pandas, py-scikit-learn, py-matplotlib
Description:
Mlxtend (machine learning extensions) is a Python library of useful tools for the day-to-day data science tasks.

py-mo-pack

Homepage:
Spack package:
Versions:
0.2.0
Build Dependencies:
python, libmo-unpack, py-numpy, py-cython
Link Dependencies:
python, libmo-unpack
Run Dependencies:
python, py-numpy, py-cython
Description:
Packing methods used to encode and decode the data payloads of Met Office Unified Model 'fields'

py-mock

Homepage:
Spack package:
Versions:
3.0.5, 2.0.0, 1.3.0
Build Dependencies:
python, py-setuptools, py-six, py-funcsigs
Link Dependencies:
python
Run Dependencies:
python, py-six, py-funcsigs
Test Dependencies:
py-pytest, py-pytest-cov
Description:
mock is a library for testing in Python. It allows you to replace parts of your system under test with mock objects and make assertions about how they have been used.

py-modred

Homepage:
Spack package:
Versions:
2.0.4, 2.0.3, 2.0.2, 2.0.1, 2.0.0
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python, py-numpy
Description:
Modred is a parallelized library for finding modal decompositions and reduced-order models.

py-moltemplate

Homepage:
Spack package:
Versions:
2.5.8
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python, py-setuptools
Description:
Moltemplate is a general cross-platform text-based molecule builder for LAMMPS.

py-monotonic

Homepage:
Spack package:
Versions:
1.2
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
An implementation of time.monotonic() for Python 2 & < 3.3

py-monty

Homepage:
Spack package:
Versions:
0.9.6
Build Dependencies:
python, py-setuptools, py-six
Link Dependencies:
python
Run Dependencies:
python, py-six
Description:
Monty is the missing complement to Python.

py-more-itertools

Homepage:
Spack package:
Versions:
7.2.0, 5.0.0, 4.3.0, 4.1.0, 2.2
Build Dependencies:
python, py-setuptools, py-six
Link Dependencies:
python
Run Dependencies:
python, py-six
Description:
Additions to the standard Python itertools package.

py-mpi4py

Homepage:
Spack package:
Versions:
develop, 3.0.3, 3.0.1, 3.0.0, 2.0.0, 1.3.1
Build Dependencies:
python, py-setuptools, mpi, py-cython
Link Dependencies:
python, mpi
Run Dependencies:
python
Description:
This package provides Python bindings for the Message Passing Interface (MPI) standard. It is implemented on top of the MPI-1/MPI-2 specification and exposes an API which grounds on the standard MPI-2 C++ bindings.

py-mpld3

Homepage:
Spack package:
Versions:
0.3
Build Dependencies:
python, py-setuptools, py-matplotlib, py-jinja2
Link Dependencies:
python
Run Dependencies:
python, py-matplotlib, py-jinja2
Description:
An interactive D3js-based viewer which brings matplotlib graphics to the browser.

py-mpmath

Homepage:
Spack package:
Versions:
1.1.0, 1.0.0, 0.19
Build Dependencies:
python
Link Dependencies:
python
Run Dependencies:
python
Description:
A Python library for arbitrary-precision floating-point arithmetic.

py-msgpack

Homepage:
Spack package:
Versions:
0.6.2
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
MessagePack (de)serializer.

py-multi-key-dict

Homepage:
Spack package:
Versions:
2.0.3
Build Dependencies:
python
Link Dependencies:
python
Run Dependencies:
python
Description:
Multi key dictionary implementation

py-multiprocess

Homepage:
Spack package:
Versions:
0.70.7, 0.70.5, 0.70.4
Build Dependencies:
python, py-setuptools, py-dill
Link Dependencies:
python
Run Dependencies:
python, py-dill
Description:
Better multiprocessing and multithreading in Python

py-multiqc

Homepage:
Spack package:
Versions:
1.7, 1.5, 1.3, 1.0
Build Dependencies:
python, py-setuptools, py-click, py-jinja2, py-lzstring, py-future, py-spectra, py-matplotlib, py-numpy, py-pyyaml, py-simplejson, py-requests, py-enum34, py-markdown
Link Dependencies:
python
Run Dependencies:
python, py-click, py-jinja2, py-lzstring, py-future, py-spectra, py-matplotlib, py-numpy, py-pyyaml, py-simplejson, py-requests, py-enum34, py-markdown
Description:
MultiQC is a tool to aggregate bioinformatics results across many samples into a single report. It is written in Python and contains modules for a large number of common bioinformatics tools.

py-munch

Homepage:
Spack package:
Versions:
2.2.0
Build Dependencies:
python, py-setuptools, py-six
Link Dependencies:
python
Run Dependencies:
python, py-six
Description:
A Munch is a Python dictionary that provides attribute-style access (a la JavaScript objects).

py-mx

Homepage:
Spack package:
Versions:
3.2.8
Build Dependencies:
python
Link Dependencies:
python
Run Dependencies:
python
Description:
The eGenix.com mx Base Distribution for Python is a collection of professional quality software tools which enhance Python's usability in many important areas such as fast text searching, date/time processing and high speed data types.

py-myhdl

Homepage:
Spack package:
Versions:
0.9.0
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Python as a Hardware Description Language

py-mypy

Homepage:
Spack package:
Versions:
0.740
Build Dependencies:
python, py-setuptools, py-typed-ast, py-typing-extensions, py-mypy-extensions
Link Dependencies:
python
Run Dependencies:
python, py-typed-ast, py-typing-extensions, py-mypy-extensions
Test Dependencies:
py-pytest, py-virtualenv, py-pip, py-lxml, googletest
Description:
Optional static typing for Python.

py-mypy-extensions

Homepage:
Spack package:
Versions:
0.4.3
Build Dependencies:
python, py-setuptools, py-typing
Link Dependencies:
python
Run Dependencies:
python, py-typing
Description:
Experimental type system extensions for programs checked with the mypy typechecker.

py-mysql-connector-python

Homepage:
Spack package:
Versions:
8.0.13
Build Dependencies:
python, py-setuptools, py-protobuf
Link Dependencies:
python
Run Dependencies:
python, py-setuptools, py-protobuf
Description:
MySQL Connector/Python is implementing the MySQL Client/Server protocol completely in Python. No MySQL libraries are needed, and no compilation is necessary to run this Python DB API v2.0 compliant driver.

py-mysqlclient

Homepage:
Spack package:
Versions:
1.4.4, 1.3.13
Build Dependencies:
python, py-setuptools, mysql
Link Dependencies:
python, mysql
Run Dependencies:
python
Description:
Python interface to MySQL

py-mysqldb1

Homepage:
Spack package:
Versions:
1.2.5
Build Dependencies:
python, mysql, py-setuptools
Link Dependencies:
python, mysql
Run Dependencies:
python
Description:
Legacy mysql bindings for python

py-natsort

Homepage:
Spack package:
Versions:
5.2.0, 5.1.1, 5.1.0, 5.0.3, 5.0.2, 5.0.1, 5.0.0, 4.0.4, 4.0.3, 4.0.1
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Simple yet flexible natural sorting in Python.

py-nbformat

Homepage:
Spack package:
Versions:
4.4.0, 4.1.0, 4.0.1, 4.0.0
Build Dependencies:
python, py-ipython-genutils, py-traitlets, py-jsonschema, py-jupyter-core
Link Dependencies:
python
Run Dependencies:
python, py-ipython-genutils, py-traitlets, py-jsonschema, py-jupyter-core
Description:
The Jupyter Notebook format

py-nc-time-axis

Homepage:
Spack package:
Versions:
1.1.0
Build Dependencies:
python, py-cftime, py-matplotlib, py-numpy, py-six
Link Dependencies:
python
Run Dependencies:
python, py-cftime, py-matplotlib, py-numpy, py-six
Description:
cftime support for matplotlib axis.

py-neo

Homepage:
Spack package:
Versions:
0.5.2, 0.4.1
Build Dependencies:
python, py-setuptools, py-numpy, py-quantities
Link Dependencies:
python
Run Dependencies:
python, py-numpy, py-quantities
Description:
Neo is a package for representing electrophysiology data in Python, together with support for reading a wide range of neurophysiology file formats

py-nestle

Homepage:
Spack package:
Versions:
0.1.1
Build Dependencies:
python, py-numpy, py-scipy
Link Dependencies:
python
Run Dependencies:
python, py-numpy, py-scipy
Description:
Nested sampling algorithms for evaluating Bayesian evidence.

py-netcdf4

Homepage:
Spack package:
Versions:
1.4.2, 1.2.7, 1.2.3.1
Build Dependencies:
python, py-setuptools, py-cython, py-numpy, py-cftime, netcdf-c, hdf5
Link Dependencies:
python, netcdf-c, hdf5
Run Dependencies:
python, py-numpy, py-cftime
Description:
Python interface to the netCDF Library.

py-netifaces

Homepage:
Spack package:
Versions:
0.10.5
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Portable network interface information

py-networkx

Homepage:
Spack package:
Versions:
2.2, 2.1, 1.11, 1.10
Build Dependencies:
python, py-decorator, py-setuptools
Link Dependencies:
python
Run Dependencies:
python, py-decorator
Description:
NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks.

py-nodeenv

Homepage:
Spack package:
Versions:
1.3.3
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Node.js virtual environment

py-nose

Homepage:
Spack package:
Versions:
1.3.7, 1.3.6, 1.3.4
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
nose extends the test loading and running features of unittest, making it easier to write, find and run tests.

py-nose-cov

Homepage:
Spack package:
Versions:
1.6
Build Dependencies:
python, py-setuptools, py-nose, py-cov-core
Link Dependencies:
python
Run Dependencies:
python, py-nose, py-cov-core
Description:
This plugin produces coverage reports.

py-nose2

Homepage:
Spack package:
Versions:
0.9.1, 0.6.0
Build Dependencies:
python, py-setuptools, py-six, py-cov-core, py-coverage, py-mock
Link Dependencies:
python
Run Dependencies:
python, py-six, py-cov-core, py-coverage, py-mock
Description:
unittest2 with plugins, the succesor to nose

py-nosexcover

Homepage:
Spack package:
Versions:
1.0.11
Build Dependencies:
python, py-setuptools, py-nose, py-coverage
Link Dependencies:
python
Run Dependencies:
python, py-nose, py-coverage
Description:
A companion to the built-in nose.plugins.cover, this plugin will write out an XML coverage report to a file named coverage.xml.

py-numba

Homepage:
Spack package:
Versions:
0.40.1, 0.35.0
Build Dependencies:
python, py-numpy, py-setuptools, py-llvmlite, py-argparse, py-funcsigs, py-singledispatch
Link Dependencies:
python
Run Dependencies:
python, py-numpy, py-llvmlite, py-argparse, py-funcsigs, py-singledispatch
Description:
NumPy aware dynamic Python compiler using LLVM

py-numcodecs

Homepage:
Spack package:
Versions:
0.6.4
Build Dependencies:
python, py-setuptools, py-setuptools-scm, py-numpy, py-msgpack
Link Dependencies:
python
Run Dependencies:
python, py-setuptools-scm, py-numpy, py-msgpack
Description:
Numcodecs is a Python package providing buffer compression and transformation codecs for use in data storage and communication applications.

py-numexpr

Homepage:
Spack package:
Versions:
2.7.0, 2.6.9, 2.6.5, 2.6.1, 2.5, 2.4.6
Build Dependencies:
python, py-numpy, py-setuptools
Link Dependencies:
python
Run Dependencies:
python, py-numpy
Description:
Fast numerical expression evaluator for NumPy

py-numexpr3

Homepage:
Spack package:
Versions:
3.0.1a1
Build Dependencies:
python, py-numpy, py-setuptools
Link Dependencies:
python
Run Dependencies:
python, py-numpy
Description:
Numexpr3 is a fast numerical expression evaluator for NumPy. With it, expressions that operate on arrays (like "3*a+4*b") are accelerated and use less memory than doing the same calculation in Python. In addition, its multi-threaded capabilities can make use of all your cores, which may accelerate computations, most specially if they are not memory- bounded (e.g. those using transcendental functions). Compared to NumExpr 2.6, functions have been re-written in a fashion such that gcc can auto- vectorize them with SIMD instruction sets such as SSE2 or AVX2, if your processor supports them. Use of a newer version of gcc such as 5.4 is strongly recommended.

py-numpy

Homepage:
Spack package:
Versions:
master, 1.18.1, 1.18.0, 1.17.5, 1.17.4, 1.17.3, 1.17.2, 1.17.1, 1.17.0, 1.16.6, 1.16.5, 1.16.4, 1.16.3, 1.16.2, 1.16.1, 1.16.0, 1.15.4, 1.15.3, 1.15.2, 1.15.1, 1.15.0, 1.14.6, 1.14.5, 1.14.4, 1.14.3, 1.14.2, 1.14.1, 1.14.0, 1.13.3, 1.13.1, 1.13.0, 1.12.1, 1.12.0, 1.11.3, 1.11.2, 1.11.1, 1.11.0, 1.10.4, 1.9.3, 1.9.2, 1.9.1
Build Dependencies:
python, py-setuptools, py-cython, blas, lapack
Link Dependencies:
python, blas, lapack
Run Dependencies:
python
Test Dependencies:
py-nose, py-pytest
Description:
NumPy is the fundamental package for scientific computing with Python. It contains among other things: a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran code, and useful linear algebra, Fourier transform, and random number capabilities

py-numpydoc

Homepage:
Spack package:
Versions:
0.6.0
Build Dependencies:
python, py-setuptools, py-sphinx
Link Dependencies:
python
Run Dependencies:
python
Description:
numpydoc - Numpy's Sphinx extensions

py-oauth2client

Homepage:
Spack package:
Versions:
4.1.3
Build Dependencies:
python, py-setuptools, py-httplib2, py-pyasn1, py-pyasn1-modules, py-rsa, py-six
Link Dependencies:
python
Run Dependencies:
python, py-httplib2, py-pyasn1, py-pyasn1-modules, py-rsa, py-six
Description:
OAuth 2.0 client library. Note: oauth2client is now deprecated. No more features will be added to the libraries and the core team is turning down support. We recommend you use google-auth and oauthlib.

py-oauthlib

Homepage:
Spack package:
Versions:
3.1.0, 3.0.1, 2.0.2
Build Dependencies:
python, py-setuptools, py-pyjwt, py-blinker, py-cryptography
Link Dependencies:
python
Run Dependencies:
python, py-pyjwt, py-blinker, py-cryptography
Test Dependencies:
py-mock, py-pytest, py-pytest-cov, py-nose, py-unittest2
Description:
A generic, spec-compliant, thorough implementation of the OAuth request-signing logic

py-olefile

Homepage:
Spack package:
Versions:
0.44
Build Dependencies:
python
Link Dependencies:
python
Run Dependencies:
python
Description:
Python package to parse, read and write Microsoft OLE2 files

py-onnx

Homepage:
Spack package:
Versions:
1.5.0
Build Dependencies:
python, py-setuptools, protobuf, py-protobuf, py-numpy, py-six, py-typing, py-typing-extensions
Link Dependencies:
python, protobuf
Run Dependencies:
python, py-protobuf, py-numpy, py-six, py-typing, py-typing-extensions
Description:
Open Neural Network Exchange (ONNX) is an open ecosystem that empowers AI developers to choose the right tools as their project evolves. ONNX provides an open source format for AI models, both deep learning and traditional ML. It defines an extensible computation graph model, as well as definitions of built-in operators and standard data types. Currently we focus on the capabilities needed for inferencing (scoring).

py-ont-fast5-api

Homepage:
Spack package:
Versions:
0.3.2
Build Dependencies:
python, py-setuptools, py-h5py, py-numpy
Link Dependencies:
python
Run Dependencies:
python, py-h5py, py-numpy
Description:
This project provides classes and utility functions for working with read fast5 files. It provides an abstraction layer between the underlying h5py library and the various concepts central to read fast5 files, such as "reads", "analyses", "analysis summaries", and "analysis datasets". Ideally all interaction with a read fast5 file should be possible via this API, without having to directly invoke the h5py library.

py-openpmd-validator

Homepage:
Spack package:
Versions:
1.0.0.2
Build Dependencies:
python, py-setuptools, py-numpy, py-python-dateutil, py-h5py
Link Dependencies:
python
Run Dependencies:
python, py-numpy, py-python-dateutil, py-h5py
Description:
Validator and Example Scripts for the openPMD markup. openPMD is an open standard for particle-mesh data files.

py-openpyxl

Homepage:
Spack package:
Versions:
2.4.5
Build Dependencies:
python, py-setuptools, py-jdcal, py-et-xmlfile
Link Dependencies:
python
Run Dependencies:
python, py-jdcal, py-et-xmlfile
Description:
A Python library to read/write Excel 2010 xlsx/xlsm files

py-openslide-python

Homepage:
Spack package:
Versions:
1.1.1
Build Dependencies:
python, openslide, py-setuptools, py-pillow
Link Dependencies:
python, openslide
Run Dependencies:
python, py-pillow
Description:
OpenSlide Python is a Python interface to the OpenSlide library.

py-opentuner

Homepage:
Spack package:
Versions:
0.8.0
Build Dependencies:
python, py-argparse, py-fn-py, py-numpy, py-pysqlite, py-setuptools, py-sqlalchemy
Link Dependencies:
python
Run Dependencies:
python, py-argparse, py-fn-py, py-numpy, py-pysqlite, py-sqlalchemy
Description:
An extensible framework for program autotuning.

py-opppy

Homepage:
Spack package:
Versions:
master, 0_1_2, 0_1_1
Build Dependencies:
python, py-setuptools, py-numpy, py-argparse, py-scipy, py-matplotlib, py-sphinx
Link Dependencies:
python
Run Dependencies:
python, py-setuptools, py-numpy, py-argparse, py-scipy, py-matplotlib, py-sphinx
Description:
The Output Parse-Plot Python (OPPPY) library is a python based data analysis library designed to extract, store, and plot information from output and dump files generated by scientific software packages.

py-opt-einsum

Homepage:
Spack package:
Versions:
3.1.0
Build Dependencies:
python, py-setuptools, py-numpy
Link Dependencies:
python
Run Dependencies:
python, py-numpy
Test Dependencies:
py-pytest, py-pytest-cov, py-pytest-pep8
Description:
Optimized Einsum: A tensor contraction order optimizer.

py-ordereddict

Homepage:
Spack package:
Versions:
1.1
Build Dependencies:
python
Link Dependencies:
python
Run Dependencies:
python
Description:
A drop-in substitute for Py2.7's new collections. OrderedDict that works in Python 2.4-2.6.

py-oset

Homepage:
Spack package:
Versions:
0.1.3
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Set that remembers original insertion order.

py-osqp

Homepage:
Spack package:
Versions:
0.6.1
Build Dependencies:
python, cmake, py-setuptools, py-numpy, py-scipy, py-future
Link Dependencies:
python
Run Dependencies:
python, py-numpy, py-scipy, py-future
Description:
OSQP: The Operator Splitting QP Solver

py-overpy

Homepage:
Spack package:
Versions:
0.4, 0.3.1
Build Dependencies:
python, py-setuptools, py-pytest-runner
Link Dependencies:
python
Run Dependencies:
python
Test Dependencies:
py-pytest
Description:
A Python Wrapper to access the Overpass API.

py-owslib

Homepage:
Spack package:
Versions:
0.17.1, 0.16.0
Build Dependencies:
python, py-setuptools, py-python-dateutil, py-pytz, py-requests, py-pyproj
Link Dependencies:
python
Run Dependencies:
python, py-python-dateutil, py-pytz, py-requests, py-pyproj
Description:
OWSLib is a Python package for client programming with Open Geospatial Consortium (OGC) web service (hence OWS) interface standards, and their related content models.

py-packaging

Homepage:
Spack package:
Versions:
19.2, 19.1, 19.0, 17.1, 16.8
Build Dependencies:
python, py-attrs, py-pyparsing, py-six
Link Dependencies:
python
Run Dependencies:
python, py-attrs, py-pyparsing, py-six
Description:
Core utilities for Python packages.

py-palettable

Homepage:
Spack package:
Versions:
3.0.0
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Color palettes for Python.

py-pamela

Homepage:
Spack package:
Versions:
1.0.0
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Python wrapper for PAM

py-pandas

Homepage:
Spack package:
Versions:
0.25.1, 0.25.0, 0.24.2, 0.24.1, 0.23.4, 0.21.1, 0.20.0, 0.19.2, 0.19.0, 0.18.0, 0.16.1, 0.16.0
Build Dependencies:
python, py-setuptools, py-numpy, py-python-dateutil, py-pytz, py-numexpr, py-bottleneck
Link Dependencies:
python
Run Dependencies:
python, py-numpy, py-python-dateutil, py-pytz, py-numexpr, py-bottleneck
Test Dependencies:
py-pytest, py-hypothesis, py-pyarrow
Description:
pandas is a Python package providing fast, flexible, and expressive data structures designed to make working with relational or labeled data both easy and intuitive. It aims to be the fundamental high-level building block for doing practical, real world data analysis in Python. Additionally, it has the broader goal of becoming the most powerful and flexible open source data analysis / manipulation tool available in any language.

py-pandocfilters

Homepage:
Spack package:
Versions:
1.4.2
Build Dependencies:
python
Link Dependencies:
python
Run Dependencies:
python
Description:
A python module for writing pandoc filters

py-parameterized

Homepage:
Spack package:
Versions:
0.7.1
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Parameterized testing with any Python test framework.

py-paramiko

Homepage:
Spack package:
Versions:
2.1.2
Build Dependencies:
python, py-setuptools, py-pyasn1, py-cryptography
Link Dependencies:
python
Run Dependencies:
python, py-pyasn1, py-cryptography
Description:
SSH2 protocol library

py-parse

Homepage:
Spack package:
Versions:
1.12.1, 1.11.1
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
parse() is the opposite of format()

py-parsedatetime

Homepage:
Spack package:
Versions:
2.5
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Parse human-readable date/time strings.

py-parso

Homepage:
Spack package:
Versions:
0.6.1
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Test Dependencies:
py-pytest, py-docopt
Description:
Parso is a Python parser that supports error recovery and round-trip parsing for different Python versions (in multiple Python versions). Parso is also able to list multiple syntax errors in your python file.

py-partd

Homepage:
Spack package:
Versions:
0.3.8
Build Dependencies:
python, py-setuptools, py-locket, py-toolz
Link Dependencies:
python
Run Dependencies:
python, py-locket, py-toolz
Description:
Key-value byte store with appendable values.

py-path-py

Homepage:
Spack package:
Versions:
12.0.1, 5.2
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
A module wrapper for os.path

py-pathlib

Homepage:
Spack package:
Versions:
1.0.1
Build Dependencies:
python
Link Dependencies:
python
Run Dependencies:
python
Description:
Object-oriented filesystem paths. Attention: this backport module isn't maintained anymore. If you want to report issues or contribute patches, please consider the pathlib2 project instead.

py-pathlib2

Homepage:
Spack package:
Versions:
2.3.3, 2.3.2, 2.1.0
Build Dependencies:
python, py-setuptools, py-six, py-scandir
Link Dependencies:
python
Run Dependencies:
python, py-six, py-scandir
Description:
Backport of pathlib from python 3.4

py-pathos

Homepage:
Spack package:
Versions:
0.2.3, 0.2.0
Build Dependencies:
python, py-setuptools, py-multiprocess, py-pox, py-ppft, py-dill
Link Dependencies:
python
Run Dependencies:
python, py-multiprocess, py-pox, py-ppft, py-dill
Description:
Parallel graph management and execution in heterogeneous computing

py-pathspec

Homepage:
Spack package:
Versions:
0.3.4
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
pathspec extends the test loading and running features of unittest, making it easier to write, find and run tests.

py-patsy

Homepage:
Spack package:
Versions:
0.5.1, 0.4.1
Build Dependencies:
python, py-setuptools, py-numpy, py-scipy, py-six
Link Dependencies:
python
Run Dependencies:
python, py-numpy, py-scipy, py-six
Test Dependencies:
py-nose
Description:
A Python package for describing statistical models and for building design matrices.

py-pauvre

Homepage:
Spack package:
Versions:
0.1.86
Build Dependencies:
python, py-matplotlib, py-biopython, py-pandas, py-pillow
Link Dependencies:
python
Run Dependencies:
python, py-matplotlib, py-biopython, py-pandas, py-pillow
Description:
pauvre: plotting package designed for nanopore and PacBio long reads

py-pbr

Homepage:
Spack package:
Versions:
5.4.3, 5.2.1, 3.1.1, 2.0.0, 1.10.0, 1.8.1
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Test Dependencies:
py-wheel, py-fixtures, py-hacking, py-mock, py-six, py-stestr, py-testresources, py-testscenarios, py-testtools, py-virtualenv, py-coverage, py-sphinx, py-testrepository
Description:
PBR is a library that injects some useful and sensible default behaviors into your setuptools run.

py-pep8

Homepage:
Spack package:
Versions:
1.7.1
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python, py-setuptools
Description:
Python style guide checker (deprecated, use py-pycodestyle instead).

py-pep8-naming

Homepage:
Spack package:
Versions:
0.7.0
Build Dependencies:
python
Link Dependencies:
python
Run Dependencies:
python, py-flake8-polyfill
Description:
Check PEP-8 naming conventions, plugin for flake8.

py-performance

Homepage:
Spack package:
Versions:
0.6.1, 0.6.0
Build Dependencies:
python, py-setuptools, py-six, py-pyperf
Link Dependencies:
python
Run Dependencies:
python, py-setuptools, py-six, py-pyperf
Description:
The performance project is intended to be an authoritative source of benchmarks for all Python implementations. The focus is on real-world benchmarks, rather than synthetic benchmarks, using whole applications when possible.

py-periodictable

Homepage:
Spack package:
Versions:
1.5.0, 1.4.1
Build Dependencies:
python, py-setuptools, py-numpy, py-pyparsing
Link Dependencies:
python
Run Dependencies:
python, py-numpy, py-pyparsing
Description:
nose extends the test loading and running features of unittest, making it easier to write, find and run tests.

py-petsc4py

Homepage:
Spack package:
Versions:
develop, 3.12.0, 3.11.0, 3.10.1, 3.10.0, 3.9.1, 3.9.0, 3.8.1, 3.8.0, 3.7.0
Build Dependencies:
python, py-cython, py-setuptools, py-numpy, py-mpi4py, petsc
Link Dependencies:
python, petsc
Run Dependencies:
python, py-numpy, py-mpi4py
Description:
This package provides Python bindings for the PETSc package.

py-pexpect

Homepage:
Spack package:
Versions:
4.7.0, 4.6.0, 4.2.1, 3.3
Build Dependencies:
python, py-ptyprocess
Link Dependencies:
python
Run Dependencies:
python, py-ptyprocess
Description:
Pexpect allows easy control of interactive console applications.

py-phonopy

Homepage:
Spack package:
Versions:
1.10.0
Build Dependencies:
python, py-numpy, py-scipy, py-matplotlib, py-pyyaml
Link Dependencies:
python
Run Dependencies:
python, py-numpy, py-scipy, py-matplotlib, py-pyyaml
Description:
Phonopy is an open source package for phonon calculations at harmonic and quasi-harmonic levels.

py-pickleshare

Homepage:
Spack package:
Versions:
0.7.5, 0.7.4
Build Dependencies:
python, py-setuptools, py-pathlib2
Link Dependencies:
python
Run Dependencies:
python, py-pathlib2
Description:
Tiny 'shelve'-like database with concurrency support

py-picrust

Homepage:
Spack package:
Versions:
1.1.3
Build Dependencies:
python, py-cogent, py-biom-format, py-setuptools, py-future, py-numpy
Link Dependencies:
python
Run Dependencies:
python, py-cogent, py-biom-format, py-future, py-numpy
Description:
bioinformatics software package designed to predict metagenome functional content from marker gene surveys and full genomes.

py-pil

Homepage:
Spack package:
Versions:
1.1.7
Build Dependencies:
python
Link Dependencies:
python
Run Dependencies:
python
Description:
The Python Imaging Library (PIL) adds image processing capabilities to your Python interpreter. This library supports many file formats, and provides powerful image processing and graphics capabilities.

py-pillow

Homepage:
Spack package:
Versions:
7.0.0, 6.2.2, 6.2.1, 6.2.0, 6.0.0, 5.4.1, 5.1.0, 3.2.0, 3.0.0
Build Dependencies:
python, py-setuptools, zlib, jpeg, libtiff, freetype, lcms, libwebp, openjpeg
Link Dependencies:
python, zlib, jpeg, libtiff, freetype, lcms, libwebp, openjpeg
Run Dependencies:
python
Test Dependencies:
py-pytest, py-pytest-runner, imagemagick
Description:
Pillow is a fork of the Python Imaging Library (PIL). It adds image processing capabilities to your Python interpreter. This library supports many file formats, and provides powerful image processing and graphics capabilities.

py-pint

Homepage:
Spack package:
Versions:
0.8.1
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Pint is a Python package to define, operate and manipulate physical quantities: the product of a numerical value and a unit of measurement. It allows arithmetic operations between them and conversions from and to different units.

py-pip

Homepage:
Spack package:
Versions:
19.3, 19.1.1, 19.0.3, 18.1, 10.0.1, 9.0.1
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python, py-setuptools
Description:
The PyPA recommended tool for installing Python packages.

py-pipits

Homepage:
Spack package:
Versions:
2.4, 1.5.0
Build Dependencies:
python, py-setuptools, py-pispino, py-biom-format, py-numpy, py-pandas, py-progressbar2, py-requests, java
Link Dependencies:
python
Run Dependencies:
python, py-pispino, vsearch, fastx-toolkit, hmmer, itsx, py-biom-format, rdptools, py-numpy, py-pandas, py-progressbar2, py-requests, seqkit, java, rdp-classifier
Description:
Automated pipeline for analyses of fungal ITS from the Illumina

py-pispino

Homepage:
Spack package:
Versions:
1.1
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python, vsearch, fastx-toolkit
Description:
PISPINO (PIpits SPIN-Off tools).

py-pkgconfig

Homepage:
Spack package:
Versions:
1.5.1, 1.4.0, 1.2.2
Build Dependencies:
python, py-setuptools, pkgconfig, py-nose
Link Dependencies:
python
Run Dependencies:
python, py-setuptools, pkgconfig
Test Dependencies:
py-nose
Description:
Interface Python with pkg-config.

py-pkginfo

Homepage:
Spack package:
Versions:
1.5.0.1
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Test Dependencies:
py-nose, py-coverage
Description:
Query metadatdata from sdists / bdists / installed packages.

py-planar

Homepage:
Spack package:
Versions:
0.4
Build Dependencies:
python
Link Dependencies:
python
Run Dependencies:
python
Description:
2D planar geometry library for Python.

py-plotly

Homepage:
Spack package:
Versions:
2.2.0
Build Dependencies:
python, py-setuptools, py-requests, py-six, py-pytz
Link Dependencies:
python
Run Dependencies:
python, py-requests, py-six, py-pytz
Description:
An interactive, browser-based graphing library for Python

py-pluggy

Homepage:
Spack package:
Versions:
0.13.0, 0.12.0, 0.7.1, 0.6.0
Build Dependencies:
python, py-setuptools, py-setuptools-scm, py-importlib-metadata
Link Dependencies:
python
Run Dependencies:
python, py-importlib-metadata
Description:
Plugin and hook calling mechanisms for python.

py-ply

Homepage:
Spack package:
Versions:
3.11, 3.8
Build Dependencies:
python
Link Dependencies:
python
Run Dependencies:
python
Description:
PLY is nothing more than a straightforward lex/yacc implementation.

py-pmw

Homepage:
Spack package:
Versions:
2.0.1, 2.0.0
Build Dependencies:
python
Link Dependencies:
python
Run Dependencies:
python
Description:
Pmw is a toolkit for building high-level compound widgets, or megawidgets, constructed using other widgets as component parts.

py-portend

Homepage:
Spack package:
Versions:
2.5
Build Dependencies:
python, py-setuptools, py-setuptools-scm, py-tempora
Link Dependencies:
python
Run Dependencies:
python, py-tempora
Description:
TCP port monitoring and discovery

py-poster

Homepage:
Spack package:
Versions:
0.8.1
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Streaming HTTP uploads and multipart/form-data encoding.

py-pox

Homepage:
Spack package:
Versions:
0.2.5, 0.2.3, 0.2.2, 0.2.1
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Utilities for filesystem exploration and automated builds.

py-poyo

Homepage:
Spack package:
Versions:
0.4.1
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
A lightweight YAML Parser for Python

py-ppft

Homepage:
Spack package:
Versions:
1.6.4.9, 1.6.4.7.1, 1.6.4.6, 1.6.4.5
Build Dependencies:
python, py-setuptools, py-six, py-dill
Link Dependencies:
python
Run Dependencies:
python, py-six, py-dill
Description:
Distributed and parallel python

py-pre-commit

Homepage:
Spack package:
Versions:
1.20.0
Build Dependencies:
python, py-setuptools, py-aspy-yaml, py-cfgv, py-identify, py-nodeenv, py-pyyaml, py-six, py-toml, py-virtualenv, py-futures, py-importlib-metadata, py-importlib-resources
Link Dependencies:
python
Run Dependencies:
python, py-aspy-yaml, py-cfgv, py-identify, py-nodeenv, py-pyyaml, py-six, py-toml, py-virtualenv, py-futures, py-importlib-metadata, py-importlib-resources
Description:
A framework for managing and maintaining multi-language pre-commit hooks.

py-prettytable

Homepage:
Spack package:
Versions:
0.7.2
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
PrettyTable is a simple Python library designed to make it quick and easy to represent tabular data in visually appealing ASCII tables.

py-progress

Homepage:
Spack package:
Versions:
1.4
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Easy progress reporting for Python

py-progressbar2

Homepage:
Spack package:
Versions:
3.39.3
Build Dependencies:
python, py-setuptools, py-six, py-python-utils
Link Dependencies:
python
Run Dependencies:
python, py-six, py-python-utils
Description:
A progress bar for Python 2 and Python 3

py-projectq

Homepage:
Spack package:
Versions:
develop, 0.3.6
Build Dependencies:
python, py-setuptools, py-numpy, py-scipy, py-future, py-requests, py-pybind11
Link Dependencies:
python
Run Dependencies:
python, py-numpy, py-scipy, py-future, py-requests, py-pybind11
Test Dependencies:
py-pytest
Description:
ProjectQ is an open-source software framework for quantum computing started at ETH Zurich. It allows users to implement their quantum programs in Python using a powerful and intuitive syntax. ProjectQ can then translate these programs to any type of back-end, be it a simulator run on a classical computer of an actual quantum chip.

py-prometheus-client

Homepage:
Spack package:
Versions:
0.7.1, 0.7.0, 0.5.0
Build Dependencies:
python, py-setuptools, py-twisted
Link Dependencies:
python
Run Dependencies:
python, py-twisted
Description:
Prometheus instrumentation library for Python applications.

py-prompt-toolkit

Homepage:
Spack package:
Versions:
2.0.9, 1.0.16, 1.0.9
Build Dependencies:
python, py-setuptools, py-six, py-wcwidth
Link Dependencies:
python
Run Dependencies:
python, py-six, py-wcwidth
Description:
Library for building powerful interactive command lines in Python

py-protobuf

Homepage:
Spack package:
Versions:
3.11.2, 3.11.1, 3.11.0, 3.10.0, 3.9.2, 3.9.1, 3.7.1, 3.6.1, 3.6.0, 3.5.2, 3.5.1, 3.4.0, 3.3.0, 3.1.0, 3.0.0b2, 3.0.0a3, 3.0.0, 2.6.1, 2.5.0, 2.4.1, 2.3.0
Build Dependencies:
python, py-setuptools, py-six, py-ordereddict, py-unittest2, protobuf
Link Dependencies:
python, protobuf
Run Dependencies:
python, py-setuptools, py-six, py-ordereddict, py-unittest2
Description:
Protocol buffers are Google's language-neutral, platform-neutral, extensible mechanism for serializing structured data - think XML, but smaller, faster, and simpler. You define how you want your data to be structured once, then you can use special generated source code to easily write and read your structured data to and from a variety of data streams and using a variety of languages.

py-psutil

Homepage:
Spack package:
Versions:
5.6.3, 5.6.2, 5.5.1, 5.4.5, 5.0.1
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Test Dependencies:
py-unittest2, py-mock, py-ipaddress
Description:
psutil is a cross-platform library for retrieving information on running processes and system utilization (CPU, memory, disks, network) in Python.

py-psyclone

Homepage:
Spack package:
Versions:
develop, 1.5.1
Build Dependencies:
python, py-setuptools, py-pyparsing, py-fparser
Link Dependencies:
python
Run Dependencies:
python, py-pyparsing, py-fparser
Test Dependencies:
py-numpy, py-nose, py-pytest
Description:
Code generation for the PSyKAl framework from the GungHo project, as used by the LFRic model at the UK Met Office.

py-psycopg2

Homepage:
Spack package:
Versions:
2.7.5
Build Dependencies:
python, py-setuptools, postgresql
Link Dependencies:
python
Run Dependencies:
python, postgresql
Description:
Python interface to PostgreSQL databases

py-ptyprocess

Homepage:
Spack package:
Versions:
0.6.0, 0.5.1
Build Dependencies:
python
Link Dependencies:
python
Run Dependencies:
python
Description:
Run a subprocess in a pseudo terminal

py-pudb

Homepage:
Spack package:
Versions:
2017.1.1, 2016.2
Build Dependencies:
python, py-setuptools, py-urwid, py-pygments
Link Dependencies:
python
Run Dependencies:
python, py-setuptools, py-urwid, py-pygments
Description:
Full-screen console debugger for Python

py-py

Homepage:
Spack package:
Versions:
1.8.0, 1.5.4, 1.5.3, 1.4.33, 1.4.31
Build Dependencies:
python, py-setuptools, py-setuptools-scm
Link Dependencies:
python
Run Dependencies:
python
Description:
Library with cross-python path, ini-parsing, io, code, log facilities

py-py-cpuinfo

Homepage:
Spack package:
Versions:
0.2.3
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Get CPU info with pure Python 2 & 3

py-py2bit

Homepage:
Spack package:
Versions:
0.2.1
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
A package for accessing 2bit files using lib2bit.

py-py2cairo

Homepage:
Spack package:
Versions:
1.10.0
Build Dependencies:
python, cairo, pixman, pkgconfig
Link Dependencies:
python, cairo, pixman
Run Dependencies:
python
Test Dependencies:
py-pytest
Description:
Pycairo is a set of Python bindings for the cairo graphics library.

py-py2neo

Homepage:
Spack package:
Versions:
2.0.8, 2.0.7, 2.0.6, 2.0.5, 2.0.4
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Py2neo is a client library and toolkit for working with Neo4j from within Python applications and from the command line.

py-py4j

Homepage:
Spack package:
Versions:
0.10.7, 0.10.6, 0.10.4, 0.10.3
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Test Dependencies:
py-nose
Description:
Enables Python programs to dynamically access arbitrary Java objects.

py-pyani

Homepage:
Spack package:
Versions:
0.2.7, 0.2.6
Build Dependencies:
python, py-setuptools, py-matplotlib, py-seaborn, py-biopython, py-pandas, py-scipy
Link Dependencies:
python
Run Dependencies:
python, py-matplotlib, py-seaborn, py-biopython, py-pandas, py-scipy, blast-plus, mummer
Description:
pyani is a Python3 module that provides support for calculating average nucleotide identity (ANI) and related measures for whole genome comparisons, and rendering relevant graphical summary output. Where available, it takes advantage of multicore systems, and can integrate with SGE/OGE-type job schedulers for the sequence comparisons.

py-pyarrow

Homepage:
Spack package:
Versions:
0.15.1, 0.12.1, 0.11.0, 0.9.0
Build Dependencies:
python, cmake, pkgconfig, py-setuptools, py-setuptools-scm, py-cython, py-numpy, py-six, py-futures, py-enum34, arrow
Link Dependencies:
python, arrow
Run Dependencies:
python, py-numpy, py-six, py-futures, py-enum34
Test Dependencies:
py-pytest, py-pandas, py-hypothesis, py-pathlib2
Description:
A cross-language development platform for in-memory data. This package contains the Python bindings.

py-pyasn1

Homepage:
Spack package:
Versions:
0.4.6, 0.4.5, 0.2.3
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Pure-Python implementation of ASN.1 types and DER/BER/CER codecs (X.208).

py-pyasn1-modules

Homepage:
Spack package:
Versions:
0.2.6, 0.2.5
Build Dependencies:
python, py-setuptools, py-pyasn1
Link Dependencies:
python
Run Dependencies:
python, py-pyasn1
Description:
A collection of ASN.1 modules expressed in form of pyasn1 classes. Includes protocols PDUs definition (SNMP, LDAP etc.) and various data structures (X.509, PKCS etc.).

py-pybedtools

Homepage:
Spack package:
Versions:
0.6.9
Build Dependencies:
python, py-cython, py-pysam, py-pandas, py-six, py-numpy, py-setuptools
Link Dependencies:
python
Run Dependencies:
python, bedtools2, py-cython, py-pysam, py-pandas, py-six, py-numpy
Description:
Python wrapper -- and more -- for Aaron Quinlan's BEDTools

py-pybigwig

Homepage:
Spack package:
Versions:
0.3.12, 0.3.4
Build Dependencies:
python, curl, py-setuptools, py-numpy
Link Dependencies:
python, curl
Run Dependencies:
python, curl, py-numpy
Description:
A package for accessing bigWig files using libBigWig.

py-pybind11

Homepage:
Spack package:
Versions:
master, 2.4.3, 2.3.0, 2.2.4, 2.2.3, 2.2.2, 2.2.1, 2.2.0, 2.1.1, 2.1.0
Build Dependencies:
cmake, py-setuptools, python
Link Dependencies:
python
Test Dependencies:
py-pytest
Description:
pybind11 -- Seamless operability between C++11 and Python. pybind11 is a lightweight header-only library that exposes C++ types in Python and vice versa, mainly to create Python bindings of existing C++ code. Its goals and syntax are similar to the excellent Boost.Python library by David Abrahams: to minimize boilerplate code in traditional extension modules by inferring type information using compile-time introspection.

py-pybtex

Homepage:
Spack package:
Versions:
0.21
Build Dependencies:
python, py-setuptools, py-latexcodec, py-pyyaml, py-counter
Link Dependencies:
python
Run Dependencies:
python, py-latexcodec, py-pyyaml, py-counter
Description:
Pybtex is a BibTeX-compatible bibliography processor written in Python.

py-pybtex-docutils

Homepage:
Spack package:
Versions:
0.2.1
Build Dependencies:
python, py-setuptools, py-docutils, py-pybtex, py-six
Link Dependencies:
python
Run Dependencies:
python, py-docutils, py-pybtex, py-six
Description:
A docutils backend for pybtex.

py-pycairo

Homepage:
Spack package:
Versions:
1.17.1
Build Dependencies:
python, cairo, pkgconfig, py-setuptools
Link Dependencies:
python, cairo
Run Dependencies:
python
Description:
Pycairo is a set of Python bindings for the cairo graphics library.

py-pycares

Homepage:
Spack package:
Versions:
3.0.0
Build Dependencies:
python, py-cffi
Link Dependencies:
python, py-cffi
Run Dependencies:
python
Description:
pycares is a Python module which provides an interface to c-ares. c-ares is a C library that performs DNS requests and name resolutions asynchronously.

py-pycbc

Homepage:
Spack package:
Versions:
1.14.1
Build Dependencies:
python, py-setuptools, py-numpy, py-mako, py-cython, py-decorator, py-scipy, py-matplotlib, py-pillow, py-h5py, py-jinja2, py-astropy, py-mpld3, py-lscsoft-glue, py-emcee, py-requests, py-beautifulsoup4, py-six, py-ligo-segments, py-weave
Link Dependencies:
python
Run Dependencies:
python, py-numpy, py-mako, py-decorator, py-scipy, py-matplotlib, py-pillow, py-h5py, py-jinja2, py-astropy, py-mpld3, py-lscsoft-glue, py-emcee, py-requests, py-beautifulsoup4, py-six, py-ligo-segments, py-weave
Description:
PyCBC is a software package used to explore astrophysical sources of gravitational waves. It contains algorithms to analyze gravitational- wave data from the LIGO and Virgo detectors, detect coalescing compact binaries, and measure the astrophysical parameters of detected sources. PyCBC was used in the first direct detection of gravitational waves and is used in the flagship analysis of LIGO and Virgo data.

py-pychecker

Homepage:
Spack package:
Versions:
0.8.19
Build Dependencies:
python
Link Dependencies:
python
Run Dependencies:
python
Description:
Python source code checking tool.

py-pycmd

Homepage:
Spack package:
Versions:
1.2
Build Dependencies:
python, py-py, py-setuptools
Link Dependencies:
python
Run Dependencies:
python, py-py
Description:
pycmd is a collection of command line tools for helping with Python development.

py-pycodestyle

Homepage:
Spack package:
Versions:
2.5.0, 2.3.1, 2.3.0, 2.2.0, 2.1.0, 2.0.0, 1.7.0, 1.6.2, 1.6.1, 1.6, 1.5.7, 1.5.6, 1.5.5, 1.5.4
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python, py-setuptools
Description:
pycodestyle is a tool to check your Python code against some of the style conventions in PEP 8. Note: formerly called pep8.

py-pycparser

Homepage:
Spack package:
Versions:
2.19, 2.18, 2.17, 2.13
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
A complete parser of the C language, written in pure python.

py-pycrypto

Homepage:
Spack package:
Versions:
2.6.1
Build Dependencies:
python, gmp
Link Dependencies:
python, gmp
Run Dependencies:
python
Description:
The Python Cryptography Toolkit

py-pycuda

Homepage:
Spack package:
Versions:
2019.1.2, 2016.1.2
Build Dependencies:
python, py-setuptools, cuda, boost, py-numpy
Link Dependencies:
python, cuda, boost
Run Dependencies:
python, py-numpy, py-six, py-decorator, py-appdirs, py-mako
Test Dependencies:
py-pytest
Description:
PyCUDA gives you easy, Pythonic access to Nvidia's CUDA parallel computation API

py-pycurl

Homepage:
Spack package:
Versions:
7.43.0
Build Dependencies:
python, curl
Link Dependencies:
python, curl
Run Dependencies:
python
Description:
PycURL is a Python interface to libcurl. PycURL can be used to fetch objects identified by a URL from a Python program.

py-pydatalog

Homepage:
Spack package:
Versions:
0.17.1
Build Dependencies:
python
Link Dependencies:
python
Run Dependencies:
python
Description:
pyDatalog adds logic programming to Python.

py-pydispatcher

Homepage:
Spack package:
Versions:
2.0.5
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Multi-producer-multi-consumer signal dispatching mechanism.

py-pydot

Homepage:
Spack package:
Versions:
1.4.1, 1.2.3, 1.2.2
Build Dependencies:
python, py-setuptools, py-pyparsing, graphviz
Link Dependencies:
python
Run Dependencies:
python, py-pyparsing, graphviz
Description:
Python interface to Graphviz's Dot language

py-pydot2

Homepage:
Spack package:
Versions:
1.0.33
Build Dependencies:
python, py-setuptools, py-pyparsing
Link Dependencies:
python
Run Dependencies:
python, py-pyparsing
Description:
Python interface to Graphviz's Dot

py-pydotplus

Homepage:
Spack package:
Versions:
2.0.2
Build Dependencies:
python, py-setuptools, py-pyparsing, py-sphinx, py-sphinx-rtd-theme
Link Dependencies:
python
Run Dependencies:
python, py-pyparsing
Test Dependencies:
py-pytest
Description:
Python interface to Graphviz's Dot language

py-pydv

Homepage:
Spack package:
Versions:
2.4.2
Build Dependencies:
python, py-backports-functools-lru-cache, py-cycler, py-python-dateutil, py-matplotlib, py-pyside, py-scipy
Link Dependencies:
python
Run Dependencies:
python, py-backports-functools-lru-cache, py-cycler, py-python-dateutil, py-matplotlib, py-pyside, py-scipy
Description:
PDV is a 1D graphics and data analysis tool, heavily based on the ULTRA plotting tool

py-pyelftools

Homepage:
Spack package:
Versions:
0.23
Build Dependencies:
python
Link Dependencies:
python
Run Dependencies:
python
Description:
A pure-Python library for parsing and analyzing ELF files and DWARF debugging information

py-pyepsg

Homepage:
Spack package:
Versions:
0.3.2
Build Dependencies:
python, py-setuptools, py-requests
Link Dependencies:
python
Run Dependencies:
python, py-requests
Description:
Provides simple access to http://epsg.io/.

py-pyfaidx

Homepage:
Spack package:
Versions:
0.5.5.2
Build Dependencies:
python, py-setuptools, py-six, py-ordereddict, py-argparse
Link Dependencies:
python
Run Dependencies:
python, py-setuptools, py-six, py-ordereddict, py-argparse
Description:
pyfaidx: efficient pythonic random access to fasta subsequences

py-pyfasta

Homepage:
Spack package:
Versions:
0.5.2
Build Dependencies:
python, py-setuptools, py-numpy
Link Dependencies:
python, py-setuptools, py-numpy
Run Dependencies:
python
Description:
Pyfasta: fast, memory-efficient, pythonic (and command-line) access to fasta sequence files

py-pyfftw

Homepage:
Spack package:
Versions:
0.11.1, 0.10.4
Build Dependencies:
python, fftw, py-setuptools, py-cython, py-numpy, py-scipy
Link Dependencies:
python, fftw
Run Dependencies:
python, py-numpy, py-scipy
Description:
A pythonic wrapper around FFTW, the FFT library, presenting a unified interface for all the supported transforms.

py-pyflakes

Homepage:
Spack package:
Versions:
2.1.1, 2.1.0, 1.6.0, 1.5.0, 1.4.0, 1.3.0, 1.2.3, 1.2.2, 1.2.1, 1.2.0, 1.1.0, 1.0.0, 0.9.2, 0.9.1, 0.9.0
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python, py-setuptools
Description:
A simple program which checks Python source files for errors.

py-pygdal

Homepage:
Spack package:
Versions:
3.0.1.5, 2.4.2.5, 2.4.1.6, 2.4.0.6, 1.11.5.3, 1.11.4.3
Build Dependencies:
python, py-setuptools, py-numpy, gdal
Link Dependencies:
python, gdal
Run Dependencies:
python, py-numpy, gdal
Description:
Virtualenv and setuptools friendly version of standard GDAL python bindings. This package is for you if you had problems installing GDAL in your virtualenv. You can install GDAL into your virtualenv using this package but you still need to install GDAL library and its header files on your system.

py-pygdbmi

Homepage:
Spack package:
Versions:
0.8.2.0
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Parse gdb machine interface output with Python

py-pygit2

Homepage:
Spack package:
Versions:
0.24.1
Build Dependencies:
python, py-setuptools, libgit2, py-six, py-cffi
Link Dependencies:
python, libgit2
Run Dependencies:
python, py-six, py-cffi
Description:
Pygit2 is a set of Python bindings to the libgit2 shared library, libgit2 implements the core of Git.

py-pyglet

Homepage:
Spack package:
Versions:
1.4.2, 1.2.1
Build Dependencies:
python, py-setuptools, py-future
Link Dependencies:
python
Run Dependencies:
python, py-future
Description:
pyglet is a cross-platform windowing and multimedia library for Python for developing games and other visually rich applications.

py-pygments

Homepage:
Spack package:
Versions:
2.4.2, 2.3.1, 2.2.0, 2.1.3, 2.0.2, 2.0.1
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Pygments is a syntax highlighting package written in Python.

py-pygobject

Homepage:
Spack package:
Versions:
3.28.3, 2.28.6, 2.28.3
Build Dependencies:
python, py-setuptools, pkgconfig, libffi, glib, py-pycairo, py-py2cairo, gobject-introspection, gtkplus
Link Dependencies:
python, libffi, glib, gobject-introspection, gtkplus
Run Dependencies:
python, py-pycairo, py-py2cairo
Description:
bindings for the GLib, and GObject, to be used in Python.

py-pygpu

Homepage:
Spack package:
Versions:
0.7.5, 0.7.2, 0.7.1, 0.7.0, 0.6.9, 0.6.2, 0.6.1, 0.6.0
Build Dependencies:
python, libgpuarray, py-setuptools, py-cython, py-nose, py-numpy, py-mako, check
Link Dependencies:
python, libgpuarray, check
Run Dependencies:
python, py-setuptools, py-cython, py-nose, py-numpy, py-mako
Description:
Python packge for the libgpuarray C library.

py-pygresql

Homepage:
Spack package:
Versions:
5.0.5
Build Dependencies:
python, py-setuptools, postgresql
Link Dependencies:
python
Run Dependencies:
python, postgresql
Description:
PyGreSQL is an open-source Python module that interfaces to a PostgreSQL database

py-pygtk

Homepage:
Spack package:
Versions:
2.24.0
Build Dependencies:
python, pkgconfig, libffi, atk, cairo, glib, gtkplus, py-pygobject, py-py2cairo
Link Dependencies:
python, libffi, atk, cairo, glib, gtkplus
Run Dependencies:
python, py-pygobject, py-py2cairo
Description:
bindings for the Gtk2 in Python. use pygobject for Gtk3.

py-pyinstrument

Homepage:
Spack package:
Versions:
3.1.0
Build Dependencies:
python, py-setuptools, py-pytest-runner, npm, py-pyinstrument-cext
Link Dependencies:
python
Run Dependencies:
python, py-pyinstrument-cext
Test Dependencies:
py-pytest
Description:
Call stack profiler for Python. Shows you why your code is slow!

py-pyinstrument-cext

Homepage:
Spack package:
Versions:
0.2.2
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Test Dependencies:
py-nose
Description:
A CPython extension supporting pyinstrument.

py-pyjwt

Homepage:
Spack package:
Versions:
1.7.1
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Test Dependencies:
py-pytest, py-pytest-cov, py-pytest-runner
Description:
JSON Web Token implementation in Python

py-pyke

Homepage:
Spack package:
Versions:
1.1.1
Build Dependencies:
python
Link Dependencies:
python
Run Dependencies:
python
Description:
Pyke introduces a form of Logic Programming (inspired by Prolog) to the Python community by providing a knowledge-based inference engine (expert system) written in 100% Python.

py-pykml

Homepage:
Spack package:
Versions:
0.1.3
Build Dependencies:
python, py-setuptools, py-lxml
Link Dependencies:
python
Run Dependencies:
python, py-lxml
Test Dependencies:
py-nose
Description:
pyKML is a Python package for parsing and authoring KML documents. It is based on the lxml.objectify API which provides Pythonic access to XML documents.

py-pykwalify

Homepage:
Spack package:
Versions:
1.7.0, 1.6.1
Build Dependencies:
python, py-setuptools, py-docopt, py-ruamel-yaml, py-python-dateutil, py-pyyaml
Link Dependencies:
python
Run Dependencies:
python, py-docopt, py-ruamel-yaml, py-python-dateutil, py-pyyaml
Description:
Python lib/cli for JSON/YAML schema validation

py-pyliblzma

Homepage:
Spack package:
Versions:
0.5.3
Build Dependencies:
python, py-setuptools, lzma
Link Dependencies:
python, lzma
Run Dependencies:
python
Description:
Python bindings for liblzma

py-pylint

Homepage:
Spack package:
Versions:
2.3.0, 1.9.4, 1.6.5, 1.4.3, 1.4.1
Build Dependencies:
python, py-astroid, py-six, py-isort, py-mccabe, py-editdistance, py-setuptools, py-configparser, py-backports-functools-lru-cache, py-singledispatch
Link Dependencies:
python
Run Dependencies:
python, py-astroid, py-six, py-isort, py-mccabe, py-editdistance, py-configparser, py-backports-functools-lru-cache, py-singledispatch
Description:
array processing for numbers, strings, records, and objects.

py-pymatgen

Homepage:
Spack package:
Versions:
4.7.2, 4.6.2
Build Dependencies:
python, py-setuptools, py-numpy, py-six, py-requests, py-pyyaml, py-monty, py-scipy, py-pydispatcher, py-tabulate, py-spglib, py-matplotlib, py-palettable
Link Dependencies:
python
Run Dependencies:
python, py-numpy, py-six, py-requests, py-pyyaml, py-monty, py-scipy, py-pydispatcher, py-tabulate, py-spglib, py-matplotlib, py-palettable
Description:
Python Materials Genomics is a robust materials analysis code that defines core object representations for structures and molecules with support for many electronic structure codes. It is currently the core analysis code powering the Materials Project.

py-pymeeus

Homepage:
Spack package:
Versions:
0.3.6
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Library of astronomical algorithms in Python.

py-pyminifier

Homepage:
Spack package:
Versions:
2.1
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Pyminifier is a Python code minifier, obfuscator, and compressor.

py-pymol

Homepage:
Spack package:
Versions:
2.3.0
Build Dependencies:
python, freetype, glew, glm, freeglut, py-numpy, tcsh, py-pyqt5, py-pmw, libmmtf-cpp, msgpack-c
Link Dependencies:
python, glew, glm
Run Dependencies:
python, freetype, freeglut, py-numpy, tcsh, py-pyqt5, py-pmw
Description:
PyMOL is a Python-enhanced molecular graphics tool. It excels at 3D visualization of proteins, small molecules, density, surfaces, and trajectories. It also includes molecular editing, ray tracing, and movies. Open Source PyMOL is free to everyone!

py-pymongo

Homepage:
Spack package:
Versions:
3.9.0, 3.6.0, 3.3.0
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
The PyMongo distribution contains tools for interacting with MongoDB database from Python. The bson package is an implementation of the BSON format for Python. The pymongo package is a native Python driver for MongoDB. The gridfs package is a gridfs implementation on top of pymongo. PyMongo supports MongoDB 2.6, 3.0, 3.2, 3.4, 3.6, 4.0 and 4.2.

py-pymorph

Homepage:
Spack package:
Versions:
0.96
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Pymorph is a collection of pure python implementations of many image morphology functions.

py-pympler

Homepage:
Spack package:
Versions:
0.4.3, 0.4.2, 0.4.1, 0.4, 0.3.1
Build Dependencies:
python
Link Dependencies:
python
Run Dependencies:
python
Description:
Development tool to measure, monitor and analyze the memory behavior of Python objects in a running Python application.

py-pymysql

Homepage:
Spack package:
Versions:
0.9.2
Build Dependencies:
python, py-setuptools, py-cryptography
Link Dependencies:
python
Run Dependencies:
python, py-cryptography
Description:
Pure-Python MySQL client library

py-pynio

Homepage:
Spack package:
Versions:
1.5.4
Build Dependencies:
python, libpng, jpeg, zlib, netcdf-c, hdf5, gdal, py-numpy
Link Dependencies:
python, libpng, jpeg, zlib, netcdf-c, hdf5, gdal
Run Dependencies:
python, py-numpy
Description:
PyNIO ("pie-nee-oh") is a Python module that allows read and/or write access to a variety of scientific data formats popular in climate and weather

py-pynn

Homepage:
Spack package:
Versions:
0.9.1, 0.8.3, 0.8.1, 0.8beta, 0.7.5
Build Dependencies:
python, py-jinja2, py-docutils, py-numpy, py-quantities, py-lazyarray, py-neo
Link Dependencies:
python
Run Dependencies:
python, py-jinja2, py-docutils, py-numpy, py-quantities, py-lazyarray, py-neo
Test Dependencies:
py-mock
Description:
A Python package for simulator-independent specification of neuronal network models

py-pyodbc

Homepage:
Spack package:
Versions:
4.0.26
Build Dependencies:
python, py-setuptools, unixodbc
Link Dependencies:
python
Run Dependencies:
python, unixodbc
Description:
A Python DB API 2 module for ODBC. This project provides an up-to-date, convenient interface to ODBC using native data types like datetime and decimal.

py-pyomo

Homepage:
Spack package:
Versions:
5.6.6
Build Dependencies:
python, py-setuptools, py-cython, py-appdirs, py-pyutilib, py-ply, py-six
Link Dependencies:
python
Run Dependencies:
python, py-appdirs, py-pyutilib, py-ply, py-six
Description:
Pyomo is a Python-based open-source software package that supports a diverse set of optimization capabilities for formulating and analyzing optimization models.

py-pyopenssl

Homepage:
Spack package:
Versions:
19.0.0
Build Dependencies:
python, py-setuptools, py-cryptography, py-six
Link Dependencies:
python
Run Dependencies:
python, py-cryptography, py-six
Description:
High-level wrapper around a subset of the OpenSSL library. Note: The Python Cryptographic Authority strongly suggests the use of pyca/cryptography where possible. If you are using pyOpenSSL for anything other than making a TLS connection you should move to cryptography and drop your pyOpenSSL dependency.

py-pypar

Homepage:
Spack package:
Versions:
2.1.5_108
Build Dependencies:
python, mpi, py-numpy
Link Dependencies:
python, mpi
Run Dependencies:
python, py-numpy
Description:
Pypar is an efficient but easy-to-use module that allows programs written in Python to run in parallel on multiple processors and communicate using MPI.

py-pyparsing

Homepage:
Spack package:
Versions:
2.4.2, 2.4.0, 2.3.1, 2.2.0, 2.1.10, 2.0.3
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
A Python Parsing Module.

py-pypeflow

Homepage:
Spack package:
Versions:
2017-05-04
Build Dependencies:
python, py-setuptools, py-networkx
Link Dependencies:
python
Run Dependencies:
python, py-networkx
Description:
pypeFLOW is light weight and reusable make / flow data process library written in Python.

py-pyperclip

Homepage:
Spack package:
Versions:
1.7.0
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
A cross-platform clipboard module for Python.

py-pyperf

Homepage:
Spack package:
Versions:
1.6.1, 1.6.0, 1.5.1
Build Dependencies:
python, py-setuptools, py-six
Link Dependencies:
python
Run Dependencies:
python, py-six
Description:
The Python perf module is a toolkit to write, run and analyze benchmarks.

py-pyprof2html

Homepage:
Spack package:
Versions:
0.3.1
Build Dependencies:
python, py-setuptools, py-jinja2
Link Dependencies:
python
Run Dependencies:
python, py-jinja2
Description:
Python cProfile and hotshot profile's data to HTML Converter

py-pyproj

Homepage:
Spack package:
Versions:
2.2.0, 2.1.3, 1.9.6, 1.9.5.1
Build Dependencies:
python, py-setuptools, py-cython, py-aenum, proj
Link Dependencies:
python, proj
Run Dependencies:
python, py-aenum
Description:
Python interface to the PROJ.4 Library.

py-pyqi

Homepage:
Spack package:
Versions:
0.3.2
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
pyqi (canonically pronounced pie chee) is a Python framework designed to support wrapping general commands in multiple types of interfaces, including at the command line, HTML, and API levels.

py-pyqt4

Homepage:
Spack package:
Versions:
4.12.3, 4.11.3
Build Dependencies:
python, qt, qscintilla
Link Dependencies:
python, qt, qscintilla
Description:
PyQt is a set of Python v2 and v3 bindings for The Qt Company's Qt application framework and runs on all platforms supported by Qt including Windows, OS X, Linux, iOS and Android. PyQt4 supports Qt v4 and will build against Qt v5.

py-pyqt5

Homepage:
Spack package:
Versions:
5.13.0, 5.12.3
Build Dependencies:
python, qt, py-enum34, qscintilla
Link Dependencies:
python, qt, qscintilla
Run Dependencies:
python, py-enum34
Description:
PyQt is a set of Python v2 and v3 bindings for The Qt Company's Qt application framework and runs on all platforms supported by Qt including Windows, OS X, Linux, iOS and Android. PyQt5 supports Qt v5.

py-pyrad

Homepage:
Spack package:
Versions:
3.0.66
Build Dependencies:
python, py-setuptools, py-numpy, py-scipy, vsearch, muscle
Link Dependencies:
python, vsearch, muscle
Run Dependencies:
python, py-numpy, py-scipy
Description:
RADseq for phylogenetics & introgression analyses

py-pyrosar

Homepage:
Spack package:
Versions:
0.8
Build Dependencies:
python, py-setuptools, py-progressbar2, py-pathos, py-numpy, py-scoop, py-spatialist, py-pyyaml, gdal
Link Dependencies:
python, gdal
Run Dependencies:
python, py-progressbar2, py-pathos, py-numpy, py-scoop, py-spatialist, py-pyyaml, gdal
Description:
A framework for large-scale SAR satellite data processing

py-pyrsistent

Homepage:
Spack package:
Versions:
0.15.7
Build Dependencies:
python, py-setuptools, py-six
Link Dependencies:
python
Run Dependencies:
python, py-six
Description:
Pyrsistent is a number of persistent collections (by some referred to as functional data structures). Persistent in the sense that they are immutable.

py-pysam

Homepage:
Spack package:
Versions:
0.15.2, 0.15.1, 0.14.1
Build Dependencies:
python, py-setuptools, py-cython, curl, bcftools, htslib, samtools
Link Dependencies:
python, curl, bcftools, htslib, samtools
Run Dependencies:
python
Description:
A python module for reading, manipulating and writing genomic data sets.

py-pyscaf

Homepage:
Spack package:
Versions:
0.12a4
Build Dependencies:
python, py-setuptools, py-fastaindex
Link Dependencies:
python
Run Dependencies:
python, py-fastaindex
Description:
pyScaf orders contigs from genome assemblies utilising several types of information

py-pyserial

Homepage:
Spack package:
Versions:
3.1.1
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Python Serial Port Extension

py-pyshp

Homepage:
Spack package:
Versions:
2.1.0, 1.2.12
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
The Python Shapefile Library (pyshp) reads and writes ESRI Shapefiles in pure Python.

py-pyside

Homepage:
Spack package:
Versions:
1.2.4, 1.2.2
Build Dependencies:
python, cmake, py-setuptools, py-sphinx, qt, libxml2, libxslt
Link Dependencies:
python, qt, libxml2, libxslt
Run Dependencies:
python, py-sphinx
Description:
Python bindings for Qt.

py-pyside2

Homepage:
Spack package:
Versions:
develop, 5.13.2, 5.13.1, 5.13.0, 5.12.5
Build Dependencies:
python, cmake, llvm, py-setuptools, py-wheel, qt, graphviz, libxml2, libxslt, py-sphinx
Link Dependencies:
python
Run Dependencies:
python, qt
Description:
Python bindings for Qt.

py-pysmartdl

Homepage:
Spack package:
Versions:
1.3.2, 1.2.5
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
A Smart Download Manager for Python.

py-pysocks

Homepage:
Spack package:
Versions:
1.7.1, 1.6.6, 1.5.7
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Test Dependencies:
py-psutil, py-pytest
Description:
A Python SOCKS client module.

py-pyspark

Homepage:
Spack package:
Versions:
2.3.0
Build Dependencies:
python, py-setuptools, py-py4j
Link Dependencies:
python
Run Dependencies:
python, py-py4j
Description:
Python bindings for Apache Spark

py-pysqlite

Homepage:
Spack package:
Versions:
2.8.3
Build Dependencies:
python, sqlite
Link Dependencies:
python
Run Dependencies:
python, sqlite
Description:
Python DB-API module for SQLite 3.

py-pytailf

Homepage:
Spack package:
Versions:
1.1
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Simple python tail -f wrapper

py-pytest

Homepage:
Spack package:
Versions:
5.2.1, 5.1.1, 4.6.5, 4.6.2, 4.3.0, 3.7.2, 3.7.1, 3.5.1, 3.0.7, 3.0.2
Build Dependencies:
python, py-setuptools, py-setuptools-scm, py-py, py-six, py-packaging, py-attrs, py-more-itertools, py-atomicwrites, py-pluggy, py-funcsigs, py-pathlib2, py-importlib-metadata, py-wcwidth
Link Dependencies:
python
Run Dependencies:
python, py-setuptools, py-py, py-six, py-packaging, py-attrs, py-more-itertools, py-atomicwrites, py-pluggy, py-funcsigs, py-pathlib2, py-importlib-metadata, py-wcwidth
Description:
pytest: simple powerful testing with Python.

py-pytest-cache

Homepage:
Spack package:
Versions:
1.0
Build Dependencies:
python, py-setuptools, py-pytest, py-execnet
Link Dependencies:
python
Run Dependencies:
python, py-pytest, py-execnet
Description:
pytest plugin to provide cross-test run caching functionality to plugins and test runs.

py-pytest-cov

Homepage:
Spack package:
Versions:
2.8.1, 2.3.1
Build Dependencies:
python, py-setuptools, py-pytest, py-coverage
Link Dependencies:
python
Run Dependencies:
python, py-pytest, py-coverage
Description:
Pytest plugin for measuring coverage.

py-pytest-flake8

Homepage:
Spack package:
Versions:
0.8.1
Build Dependencies:
python, py-setuptools, py-flake8, py-pytest
Link Dependencies:
python
Run Dependencies:
python, py-flake8, py-pytest
Description:
pytest plugin to check FLAKE8 requirements.

py-pytest-forked

Homepage:
Spack package:
Versions:
1.1.1
Build Dependencies:
python, py-setuptools, py-setuptools-scm, py-pytest
Link Dependencies:
python
Run Dependencies:
python, py-pytest
Description:
Run tests in isolated forked subprocesses.

py-pytest-httpbin

Homepage:
Spack package:
Versions:
1.0.0, 0.2.3, 0.0.7
Build Dependencies:
python, py-setuptools, py-flask, py-decorator, py-httpbin, py-six
Link Dependencies:
python
Run Dependencies:
python, py-flask, py-decorator, py-httpbin, py-six
Test Dependencies:
py-pytest
Description:
Easily test your HTTP library against a local copy of httpbin

py-pytest-isort

Homepage:
Spack package:
Versions:
0.3.1
Build Dependencies:
python, py-pytest, py-isort
Link Dependencies:
python
Run Dependencies:
python, py-pytest, py-isort
Description:
py.test plugin to check import ordering using isort

py-pytest-mock

Homepage:
Spack package:
Versions:
1.11.1, 1.2
Build Dependencies:
python, py-setuptools, py-setuptools-scm, py-pytest
Link Dependencies:
python
Run Dependencies:
python, py-pytest
Description:
Thin-wrapper around the mock package for easier use with py.test

py-pytest-mypy

Homepage:
Spack package:
Versions:
0.4.2
Build Dependencies:
python, py-setuptools, py-pytest, py-mypy
Link Dependencies:
python
Run Dependencies:
python, py-pytest, py-mypy
Description:
Mypy static type checker plugin for Pytest.

py-pytest-pep8

Homepage:
Spack package:
Versions:
1.0.6
Build Dependencies:
python, py-setuptools, py-pytest-cache, py-pytest, py-pep8
Link Dependencies:
python
Run Dependencies:
python, py-pytest-cache, py-pytest, py-pep8
Description:
pytest plugin for efficiently checking PEP8 compliance

py-pytest-runner

Homepage:
Spack package:
Versions:
5.1, 2.11.1
Build Dependencies:
python, py-setuptools, py-setuptools-scm
Link Dependencies:
python
Run Dependencies:
python
Description:
Invoke py.test as distutils command with dependency resolution.

py-pytest-xdist

Homepage:
Spack package:
Versions:
1.30.0, 1.29.0, 1.27.0, 1.24.0, 1.17.0, 1.16.0
Build Dependencies:
python, py-setuptools, py-execnet, py-pytest, py-pytest-forked, py-six
Link Dependencies:
python
Run Dependencies:
python, py-execnet, py-pytest, py-pytest-forked, py-six
Description:
py.test xdist plugin for distributed testing and loop-on-failing mode

py-pythia

Homepage:
Spack package:
Versions:
0.8.1.18
Build Dependencies:
python, py-merlin
Link Dependencies:
python
Run Dependencies:
python
Description:
Pythia refers to the Pyre framework and a collection of packages that interact with it, such as an interface to the ACIS solid modelling package.

py-python-daemon

Homepage:
Spack package:
Versions:
2.0.5
Build Dependencies:
python, py-setuptools, py-lockfile
Link Dependencies:
python
Run Dependencies:
python, py-lockfile
Description:
Library to implement a well-behaved Unix daemon process. This library implements the well-behaved daemon specification of PEP Standard daemon process. A well-behaved Unix daemon process is tricky to get right, but the required steps are much the same for every daemon program. A DaemonContext instance holds the behaviour and configured process environment for the program; use the instance as a context manager to enter a daemon state.

py-python-dateutil

Homepage:
Spack package:
Versions:
2.8.0, 2.7.5, 2.5.2, 2.4.2, 2.4.0, 2.2
Build Dependencies:
python, py-setuptools, py-setuptools-scm, py-six
Link Dependencies:
python
Run Dependencies:
python, py-six
Description:
Extensions to the standard Python datetime module.

py-python-editor

Homepage:
Spack package:
Versions:
1.0.4
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
python-editor is a library that provides the editor module for programmatically interfacing with your system's EDITOR variable.

py-python-engineio

Homepage:
Spack package:
Versions:
2.0.2
Build Dependencies:
python, py-setuptools, py-six
Link Dependencies:
python
Run Dependencies:
python, py-six
Description:
Engine.IO is the implementation of transport-based cross-browser/cross- device bi-directional communication layer for Socket.IO.

py-python-gitlab

Homepage:
Spack package:
Versions:
1.8.0, 0.19, 0.18, 0.17, 0.16
Build Dependencies:
python, py-setuptools, py-six, py-requests
Link Dependencies:
python
Run Dependencies:
python, py-six, py-requests
Description:
Python wrapper for the GitLab API

py-python-igraph

Homepage:
Spack package:
Versions:
0.7.0
Build Dependencies:
python, py-setuptools, igraph
Link Dependencies:
python, igraph
Run Dependencies:
python
Description:
igraph is a collection of network analysis tools with the emphasis on efficiency, portability and ease of use.

py-python-jenkins

Homepage:
Spack package:
Versions:
1.5.0, 1.0.2
Build Dependencies:
python, py-setuptools, py-pbr
Link Dependencies:
python
Run Dependencies:
python, py-pbr, py-six, py-multi-key-dict, py-requests
Description:
Python bindings for the remote Jenkins API

py-python-ldap

Homepage:
Spack package:
Versions:
3.2.0, 3.0.0
Build Dependencies:
python, openldap, py-setuptools, py-pyasn1, py-pyasn1-modules
Link Dependencies:
python, openldap
Run Dependencies:
python, openldap, py-pyasn1, py-pyasn1-modules
Description:
python-ldap provides an object-oriented API to access LDAP directory servers from Python programs.

py-python-levenshtein

Homepage:
Spack package:
Versions:
0.12.0
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Python extension for computing string edit distances and similarities.

py-python-logstash

Homepage:
Spack package:
Versions:
0.4.6
Build Dependencies:
python
Link Dependencies:
python
Run Dependencies:
python
Description:
Python logging handler for Logstash.

py-python-magic

Homepage:
Spack package:
Versions:
0.4.15
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
A python wrapper for libmagic

py-python-mapnik

Homepage:
Spack package:
Versions:
3.0.16, 3.0.13
Build Dependencies:
python, py-setuptools, mapnik, boost, py-pycairo
Link Dependencies:
python, mapnik, boost
Run Dependencies:
python, mapnik, py-pycairo
Description:
Python bindings for mapnik

py-python-meep

Homepage:
Spack package:
Versions:
1.4.2
Build Dependencies:
python, py-numpy, py-scipy, py-matplotlib, mpi, meep, swig
Link Dependencies:
python, mpi, meep, swig
Run Dependencies:
python, py-numpy, py-scipy, py-matplotlib
Description:
Python-meep is a wrapper around libmeep. It allows the scripting of Meep-simulations with Python

py-python-memcached

Homepage:
Spack package:
Versions:
1.59
Build Dependencies:
python, py-setuptools, py-six
Link Dependencies:
python
Run Dependencies:
python, py-six
Description:
This software is a 100% Python interface to the memcached memory cache daemon. It is the client side software which allows storing values in one or more, possibly remote, memcached servers. Search google for memcached for more information.

py-python-oauth2

Homepage:
Spack package:
Versions:
1.1.1
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
python-oauth2 is a framework that aims at making it easy to provide authentication via OAuth 2.0 within an application stack.

py-python-rapidjson

Homepage:
Spack package:
Versions:
0.9.1
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Python wrapper around rapidjson.

py-python-slugify

Homepage:
Spack package:
Versions:
4.0.0
Build Dependencies:
python, py-setuptools, py-text-unidecode
Link Dependencies:
python
Run Dependencies:
python, py-text-unidecode
Description:
A Python Slugify application that handles Unicode

py-python-socketio

Homepage:
Spack package:
Versions:
1.8.4
Build Dependencies:
python, py-setuptools, py-six, py-python-engineio, py-eventlet
Link Dependencies:
python
Run Dependencies:
python, py-six, py-python-engineio, py-eventlet
Description:
Python implementation of the Socket.IO realtime server.

py-python-subunit

Homepage:
Spack package:
Versions:
1.3.0
Build Dependencies:
python, py-setuptools, py-extras, py-testtools
Link Dependencies:
python
Run Dependencies:
python, py-extras, py-testtools
Description:
Python implementation of subunit test streaming protocol.

py-python-utils

Homepage:
Spack package:
Versions:
2.3.0
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Python Utils is a collection of small Python functions and classes which make common patterns shorter and easier.

py-pythonqwt

Homepage:
Spack package:
Versions:
0.5.5
Build Dependencies:
python, py-setuptools, py-numpy, py-sip, py-pyqt4, py-sphinx
Link Dependencies:
python
Run Dependencies:
python, py-numpy, py-sip, py-pyqt4, py-sphinx
Description:
Qt plotting widgets for Python

py-pytimeparse

Homepage:
Spack package:
Versions:
1.1.8
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
A small Python library to parse various kinds of time expressions.

py-pytools

Homepage:
Spack package:
Versions:
2019.1.1, 2016.2.6
Build Dependencies:
python, py-setuptools, py-decorator, py-appdirs, py-six, py-numpy
Link Dependencies:
python
Run Dependencies:
python, py-decorator, py-appdirs, py-six, py-numpy
Description:
A collection of tools for Python

py-pytz

Homepage:
Spack package:
Versions:
2019.3, 2019.1, 2018.4, 2016.10, 2016.6.1, 2016.3, 2015.4, 2014.10, 2014.9
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
World timezone definitions, modern and historical.

py-pyudev

Homepage:
Spack package:
Versions:
0.21.0, 0.15, 0.9
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Pure Python libudev binding

py-pyugrid

Homepage:
Spack package:
Versions:
0.3.1
Build Dependencies:
python, py-setuptools, py-numpy, py-scipy, py-netcdf4, py-matplotlib
Link Dependencies:
python
Run Dependencies:
python, py-numpy, py-scipy, py-netcdf4, py-matplotlib
Description:
Work with triangular unstructured grids and the data on them.

py-pyutilib

Homepage:
Spack package:
Versions:
5.6.2, 5.6.1, 5.6, 5.5.1, 5.5, 5.4.1, 5.4, 5.3.5, 5.3.4, 5.3.3
Build Dependencies:
python, py-nose, py-six
Link Dependencies:
python
Run Dependencies:
python, py-nose, py-six
Description:
The PyUtilib project supports a collection of Python utilities, including a well-developed component architecture and extensions to the PyUnit testing framework. PyUtilib has been developed to support several Python-centric projects, especially Pyomo. PyUtilib is available under the BSD License.

py-pyvcf

Homepage:
Spack package:
Versions:
0.6.0
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
A Variant Call Format reader for Python

py-pywavelets

Homepage:
Spack package:
Versions:
0.5.2
Build Dependencies:
python, py-setuptools, py-cython, py-numpy
Link Dependencies:
python
Run Dependencies:
python, py-numpy
Description:
PyWavelets is a free Open Source library for wavelet transforms in Python

py-pyyaml

Homepage:
Spack package:
Versions:
5.1.2, 5.1, 3.13, 3.12, 3.11
Build Dependencies:
python, libyaml
Link Dependencies:
python, libyaml
Run Dependencies:
python
Description:
PyYAML is a YAML parser and emitter for Python.

py-pyzmq

Homepage:
Spack package:
Versions:
18.1.0, 18.0.1, 17.1.2, 16.0.2, 14.7.0
Build Dependencies:
python, py-cython, py-py, py-cffi, libzmq
Link Dependencies:
python, libzmq
Run Dependencies:
python, py-cython, py-py, py-cffi
Description:
PyZMQ: Python bindings for zeromq.

py-qtawesome

Homepage:
Spack package:
Versions:
0.4.1, 0.3.3
Build Dependencies:
python, py-setuptools, py-qtpy, py-six
Link Dependencies:
python
Run Dependencies:
python, py-qtpy, py-six
Description:
FontAwesome icons in PyQt and PySide applications

py-qtconsole

Homepage:
Spack package:
Versions:
4.5.1, 4.2.1
Build Dependencies:
python, py-ipykernel, py-jupyter-client, py-jupyter-core, py-pygments, py-traitlets, py-ipython-genutils, py-sphinx
Link Dependencies:
python
Run Dependencies:
python, py-ipykernel, py-jupyter-client, py-jupyter-core, py-pygments, py-traitlets, py-ipython-genutils, py-sphinx
Test Dependencies:
py-mock
Description:
Jupyter Qt console

py-qtpy

Homepage:
Spack package:
Versions:
1.7.1, 1.2.1
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python, py-pyqt5, py-pyqt4, py-pyside2, py-pyside
Description:
QtPy: Abtraction layer for PyQt5/PyQt4/PySide/PySide2

py-quantities

Homepage:
Spack package:
Versions:
0.12.1, 0.11.1
Build Dependencies:
python, py-numpy
Link Dependencies:
python
Run Dependencies:
python, py-numpy
Description:
Support for physical quantities with units, based on numpy

py-quast

Homepage:
Spack package:
Versions:
4.6.3, 4.6.1, 4.6.0
Build Dependencies:
python, boost, perl, py-setuptools, py-matplotlib, java, perl-time-hires, gnuplot, mummer, bedtools2, bwa, glimmer
Link Dependencies:
python, boost, perl
Run Dependencies:
python, py-matplotlib, java, perl-time-hires, gnuplot, mummer, bedtools2, bwa, glimmer
Description:
Quality Assessment Tool for Genome Assemblies

py-queryablelist

Homepage:
Spack package:
Versions:
3.1.0
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Python module to add support for ORM-style filtering to any list of items

py-radical-utils

Homepage:
Spack package:
Versions:
0.45, 0.41.1
Build Dependencies:
python, py-setuptools, py-colorama, py-netifaces
Link Dependencies:
python
Run Dependencies:
python, py-colorama, py-netifaces
Description:
Shared code and tools for various RADICAL Projects

py-ranger-fm

Homepage:
Spack package:
Versions:
1.9.2
Build Dependencies:
python
Link Dependencies:
python
Run Dependencies:
python
Description:
A VIM-inspired filemanager for the console

py-rasterio

Homepage:
Spack package:
Versions:
1.0.24, 1.0a12
Build Dependencies:
python, py-setuptools, py-cython, py-affine, py-attrs, py-click, py-cligj, py-numpy, py-snuggs, py-click-plugins, gdal, jpeg
Link Dependencies:
python, gdal, jpeg
Run Dependencies:
python, py-affine, py-attrs, py-click, py-cligj, py-numpy, py-snuggs, py-click-plugins, py-enum34
Test Dependencies:
py-pytest, py-boto3, py-packaging, py-hypothesis, py-futures, py-mock
Description:
Rasterio reads and writes geospatial raster data. Geographic information systems use GeoTIFF and other formats to organize and store gridded, or raster, datasets. Rasterio reads and writes these formats and provides a Python API based on N-D arrays.

py-ratelim

Homepage:
Spack package:
Versions:
0.1.6
Build Dependencies:
python, py-setuptools, py-decorator
Link Dependencies:
python
Run Dependencies:
python, py-decorator
Description:
Makes it easy to respect rate limits.

py-raven

Homepage:
Spack package:
Versions:
6.10.0
Build Dependencies:
python, py-setuptools, py-flask, py-blinker
Link Dependencies:
python
Run Dependencies:
python, py-flask, py-blinker
Description:
Raven is a client for Sentry.

py-readme-renderer

Homepage:
Spack package:
Versions:
24.0, 16.0
Build Dependencies:
python, py-setuptools, py-bleach, py-docutils, py-pygments, py-six
Link Dependencies:
python
Run Dependencies:
python, py-bleach, py-docutils, py-pygments, py-six
Test Dependencies:
py-pytest, py-mock
Description:
readme_renderer is a library for rendering "readme" descriptions for Warehouse.

py-redis

Homepage:
Spack package:
Versions:
3.3.8
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
The Python interface to the Redis key-value store.

py-regex

Homepage:
Spack package:
Versions:
2019.11.1, 2017.07.11
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Alternative regular expression module, to replace re.

py-reportlab

Homepage:
Spack package:
Versions:
3.4.0
Build Dependencies:
python
Link Dependencies:
python
Run Dependencies:
python
Description:
The ReportLab Toolkit. An Open Source Python library for generating PDFs and graphics.

py-repoze-lru

Homepage:
Spack package:
Versions:
0.7
Build Dependencies:
python, py-setuptools, py-sphinx
Link Dependencies:
python
Run Dependencies:
python
Description:
A tiny LRU cache implementation and decorator

py-requests

Homepage:
Spack package:
Versions:
2.22.0, 2.21.0, 2.14.2, 2.13.0, 2.11.1, 2.3.0
Build Dependencies:
python, py-setuptools, py-chardet, py-idna, py-urllib3, py-certifi
Link Dependencies:
python
Run Dependencies:
python, py-chardet, py-idna, py-urllib3, py-certifi
Test Dependencies:
py-pytest-httpbin, py-pytest-cov, py-pytest-mock, py-pytest-xdist, py-pysocks, py-pytest
Description:
Python HTTP for Humans.

py-requests-futures

Homepage:
Spack package:
Versions:
1.0.0
Build Dependencies:
python, py-setuptools, py-futures, py-requests
Link Dependencies:
python
Run Dependencies:
python, py-futures, py-requests
Description:
Asynchronous Python HTTP Requests for Humans using Futures

py-requests-mock

Homepage:
Spack package:
Versions:
1.7.0
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Mock out responses from the requests package.

py-requests-oauthlib

Homepage:
Spack package:
Versions:
1.2.0, 0.3.3
Build Dependencies:
python, py-setuptools, py-oauthlib, py-requests
Link Dependencies:
python
Run Dependencies:
python, py-oauthlib, py-requests
Test Dependencies:
py-mock, py-requests-mock
Description:
This project provides first-class OAuth library support for Requests.

py-requests-toolbelt

Homepage:
Spack package:
Versions:
0.9.1, 0.8.0
Build Dependencies:
python, py-setuptools, py-requests
Link Dependencies:
python
Run Dependencies:
python, py-requests
Description:
A toolbelt of useful classes and functions to be used with python- requests

py-restview

Homepage:
Spack package:
Versions:
2.6.1
Build Dependencies:
python, py-setuptools, py-docutils, py-readme-renderer, py-pygments
Link Dependencies:
python
Run Dependencies:
python, py-docutils, py-readme-renderer, py-pygments
Description:
A viewer for ReStructuredText documents that renders them on the fly.

py-retrying

Homepage:
Spack package:
Versions:
1.3.3
Build Dependencies:
python, py-setuptools, py-six
Link Dependencies:
python
Run Dependencies:
python, py-six
Description:
Retrying is an Apache 2.0 licensed general-purpose retrying library, written in Python, to simplify the task of adding retry behavior to just about anything.

py-rnacocktail

Homepage:
Spack package:
Versions:
0.2.2
Build Dependencies:
python, py-setuptools, py-pybedtools, py-pysam, py-pandas, py-numpy
Link Dependencies:
python
Run Dependencies:
python, py-pybedtools, py-pysam, py-pandas, py-numpy
Description:
RNACocktail: A comprehensive framework for accurate and efficient RNA- Seq analysis.

py-rope

Homepage:
Spack package:
Versions:
0.11.0, 0.10.7, 0.10.6, 0.10.5
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
a python refactoring library.

py-rpy2

Homepage:
Spack package:
Versions:
3.0.0, 2.9.4, 2.8.6, 2.5.6, 2.5.4
Build Dependencies:
python, py-setuptools, r, py-jinja2, py-six, py-singledispatch
Link Dependencies:
python
Run Dependencies:
python, r, py-jinja2, py-six, py-singledispatch
Description:
rpy2 is a redesign and rewrite of rpy. It is providing a low-level interface to R from Python, a proposed high-level interface, including wrappers to graphical libraries, as well as R-like structures and functions.

py-rsa

Homepage:
Spack package:
Versions:
4.0, 3.4.2
Build Dependencies:
python, py-setuptools, py-pyasn1
Link Dependencies:
python
Run Dependencies:
python, py-setuptools, py-pyasn1
Description:
Pure-Python RSA implementation

py-rseqc

Homepage:
Spack package:
Versions:
2.6.4
Build Dependencies:
python, py-setuptools, py-bx-python, py-numpy, py-pysam, r
Link Dependencies:
python
Run Dependencies:
python, py-bx-python, py-numpy, py-pysam, r
Description:
RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA- seq data.

py-rtree

Homepage:
Spack package:
Versions:
0.8.3
Build Dependencies:
python, py-setuptools, libspatialindex
Link Dependencies:
python, libspatialindex
Run Dependencies:
python
Description:
Python interface to the RTREE.4 Library.

py-ruamel-yaml

Homepage:
Spack package:
Versions:
0.16.5, 0.11.7
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
a YAML parser/emitter that supports roundtrip preservation of comments, seq/map flow style, and map key order

py-s3cmd

Homepage:
Spack package:
Versions:
2.0.2, 2.0.1, 2.0.0, 1.6.1, 1.6.0, 1.5.2
Build Dependencies:
python, py-setuptools, py-python-dateutil, py-python-magic
Link Dependencies:
python
Run Dependencies:
python, py-python-dateutil, py-python-magic
Description:
S3cmd (s3cmd) is a free command line tool and client for uploading, retrieving and managing data in Amazon S3 and other cloud storage service providers that use the S3 protocol, such as Google Cloud Storage or DreamHost DreamObjects. It is best suited for power users who are familiar with command line programs.

py-s3transfer

Homepage:
Spack package:
Versions:
0.2.1
Build Dependencies:
python, py-setuptools, py-botocore, py-futures
Link Dependencies:
python
Run Dependencies:
python, py-botocore, py-futures
Test Dependencies:
py-mock
Description:
S3transfer is a Python library for managing Amazon S3 transfers.

py-saga-python

Homepage:
Spack package:
Versions:
0.41.3
Build Dependencies:
python, py-setuptools, py-apache-libcloud, py-radical-utils
Link Dependencies:
python
Run Dependencies:
python, py-apache-libcloud, py-radical-utils
Description:
A light-weight access layer for distributed computing infrastructure

py-scandir

Homepage:
Spack package:
Versions:
1.10.0, 1.9.0, 1.6
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
scandir, a better directory iterator and faster os.walk().

py-scientificpython

Homepage:
Spack package:
Versions:
2.8.1
Build Dependencies:
python, py-numpy
Link Dependencies:
python
Run Dependencies:
python, py-numpy
Description:
ScientificPython is a collection of Python modules for scientific computing. It contains support for geometry, mathematical functions, statistics, physical units, IO, visualization, and parallelization.

py-scikit-build

Homepage:
Spack package:
Versions:
0.10.0
Build Dependencies:
python, py-setuptools, py-packaging, py-wheel
Link Dependencies:
python
Run Dependencies:
python, py-setuptools, py-packaging, py-wheel
Description:
scikit-build is an improved build system generator for CPython C/C++/Fortran/Cython extensions. It provides better support for additional compilers, build systems, cross compilation, and locating dependencies and their associated build requirements. The scikit-build package is fundamentally just glue between the setuptools Python module and CMake.

py-scikit-image

Homepage:
Spack package:
Versions:
0.14.2, 0.12.3
Build Dependencies:
python, py-dask, py-pillow, py-networkx, py-six, py-numpy, py-scipy, py-matplotlib, py-pywavelets, py-cloudpickle, py-setuptools, py-cython
Link Dependencies:
python
Run Dependencies:
python, py-dask, py-pillow, py-networkx, py-six, py-numpy, py-scipy, py-matplotlib, py-pywavelets, py-cloudpickle
Description:
Image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.

py-scikit-learn

Homepage:
Spack package:
Versions:
master, 0.22.1, 0.22, 0.21.3, 0.21.2, 0.21.1, 0.20.3, 0.20.2, 0.20.0, 0.19.1, 0.18.1, 0.17.1, 0.16.1, 0.15.2, 0.13.1
Build Dependencies:
python, py-numpy, py-scipy, py-joblib, py-cython, py-setuptools, llvm-openmp
Link Dependencies:
python, llvm-openmp
Run Dependencies:
python, py-numpy, py-scipy, py-joblib
Test Dependencies:
py-pytest, py-pandas
Description:
A set of python modules for machine learning and data mining.

py-scikit-optimize

Homepage:
Spack package:
Versions:
0.5.2
Build Dependencies:
python, py-setuptools, py-numpy, py-scipy, py-scikit-learn, py-matplotlib
Link Dependencies:
python, py-matplotlib
Run Dependencies:
python, py-numpy, py-scipy, py-scikit-learn
Test Dependencies:
py-pytest
Description:
Scikit-Optimize, or skopt, is a simple and efficient library to minimize (very) expensive and noisy black-box functions. It implements several methods for sequential model-based optimization. skopt aims to be accessible and easy to use in many contexts. The library is built on top of NumPy, SciPy and Scikit-Learn.

py-scipy

Homepage:
Spack package:
Versions:
1.4.1, 1.4.0, 1.3.3, 1.3.2, 1.3.1, 1.3.0, 1.2.3, 1.2.2, 1.2.1, 1.1.0, 1.0.0, 0.19.1, 0.18.1, 0.17.0, 0.15.1, 0.15.0
Build Dependencies:
python, py-setuptools, py-pybind11, py-numpy, blas, lapack
Link Dependencies:
python, blas, lapack
Run Dependencies:
python, py-numpy
Test Dependencies:
py-pytest
Description:
SciPy (pronounced "Sigh Pie") is a Scientific Library for Python. It provides many user-friendly and efficient numerical routines such as routines for numerical integration and optimization.

py-scoop

Homepage:
Spack package:
Versions:
0.7.1.1
Build Dependencies:
python, py-setuptools, py-greenlet, py-pyzmq
Link Dependencies:
python
Run Dependencies:
python, py-greenlet, py-pyzmq
Description:
SCOOP (Scalable COncurrent Operations in Python) is a distributed task module allowing concurrent parallel programming on various environments, from heterogeneous grids to supercomputers.

py-scp

Homepage:
Spack package:
Versions:
0.13.2
Build Dependencies:
python, py-setuptools, py-paramiko
Link Dependencies:
python
Run Dependencies:
python, py-paramiko
Description:
scp module for paramiko

py-scs

Homepage:
Spack package:
Versions:
2.1.1-2
Build Dependencies:
python, py-setuptools, py-numpy, py-scipy
Link Dependencies:
python
Run Dependencies:
python, py-numpy, py-scipy
Description:
SCS: splitting conic solver

py-seaborn

Homepage:
Spack package:
Versions:
0.9.0, 0.7.1
Build Dependencies:
python, py-setuptools, py-numpy, py-scipy, py-matplotlib, py-pandas
Link Dependencies:
python
Run Dependencies:
python, py-numpy, py-scipy, py-matplotlib, py-pandas
Description:
Seaborn: statistical data visualization. Seaborn is a library for making attractive and informative statistical graphics in Python. It is built on top of matplotlib and tightly integrated with the PyData stack, including support for numpy and pandas data structures and statistical routines from scipy and statsmodels.

py-selenium

Homepage:
Spack package:
Versions:
3.141.0
Build Dependencies:
python, py-setuptools, py-urllib3
Link Dependencies:
python
Run Dependencies:
python, py-urllib3
Description:
Python language bindings for Selenium WebDriver. The selenium package is used to automate web browser interaction from Python.

py-semantic-version

Homepage:
Spack package:
Versions:
2.8.2, 2.6.0
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
This small python library provides a few tools to handle SemVer in Python. It follows strictly the 2.0.0 version of the SemVer scheme.

py-semver

Homepage:
Spack package:
Versions:
2.8.1
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
A Python module for semantic versioning. Simplifies comparing versions.

py-send2trash

Homepage:
Spack package:
Versions:
1.5.0
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Python library to send files to Trash/Recycle on all platforms.

py-setuptools

Homepage:
Spack package:
Versions:
41.4.0, 41.0.1, 41.0.0, 40.8.0, 40.4.3, 40.2.0, 39.2.0, 39.0.1, 35.0.2, 34.4.1, 34.2.0, 25.2.0, 20.7.0, 20.6.7, 19.2, 18.1, 16.0, 11.3.1
Build Dependencies:
python, py-packaging, py-six, py-appdirs
Link Dependencies:
python
Run Dependencies:
python, py-packaging, py-six, py-appdirs
Description:
A Python utility that aids in the process of downloading, building, upgrading, installing, and uninstalling Python packages.

py-setuptools-git

Homepage:
Spack package:
Versions:
1.2
Build Dependencies:
python, py-setuptools, git
Link Dependencies:
python, git
Run Dependencies:
python
Description:
Setuptools revision control system plugin for Git

py-setuptools-scm

Homepage:
Spack package:
Versions:
3.3.3, 3.1.0, 1.15.6
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
The blessed package to manage your versions by scm tags.

py-setuptools-scm-git-archive

Homepage:
Spack package:
Versions:
1.1, 1.0
Build Dependencies:
python, py-setuptools, py-setuptools-scm
Link Dependencies:
python
Run Dependencies:
python
Description:
This is a setuptools_scm plugin that adds support for git archives (for example the ones GitHub automatically generates).

py-sfepy

Homepage:
Spack package:
Versions:
2017.3
Build Dependencies:
python, py-numpy, py-setuptools
Link Dependencies:
python
Run Dependencies:
python, py-numpy, py-six, py-scipy, py-matplotlib, py-sympy, hdf5, py-tables, py-petsc4py
Description:
SfePy (http://sfepy.org) is a software for solving systems of coupled partial differential equations (PDEs) by the finite element method in 1D, 2D and 3D. It can be viewed both as black-box PDE solver, and as a Python package which can be used for building custom applications.

py-sgp4

Homepage:
Spack package:
Versions:
1.4
Build Dependencies:
python
Link Dependencies:
python
Run Dependencies:
python
Description:
Track earth satellite TLE orbits using up-to-date 2010 version of SGP4

py-sh

Homepage:
Spack package:
Versions:
1.12.9, 1.11
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Python subprocess interface

py-shapely

Homepage:
Spack package:
Versions:
1.6.4.post2, 1.6.4
Build Dependencies:
python, py-setuptools, py-cython, py-numpy, geos
Link Dependencies:
python, geos
Run Dependencies:
python, py-numpy
Test Dependencies:
py-pytest
Description:
Manipulation and analysis of geometric objects in the Cartesian plane.

py-shiboken

Homepage:
Spack package:
Versions:
1.2.2
Build Dependencies:
python, cmake, py-setuptools, py-sphinx, libxml2, qt
Link Dependencies:
python, libxml2, qt
Run Dependencies:
python, py-sphinx
Description:
Shiboken generates bindings for C++ libraries using CPython.

py-simplegeneric

Homepage:
Spack package:
Versions:
0.8.1, 0.8
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Simple generic functions (similar to Python's own len(), pickle.dump(), etc.)

py-simplejson

Homepage:
Spack package:
Versions:
3.10.0, 3.9.0, 3.8.2, 3.8.1, 3.8.0
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Simplejson is a simple, fast, extensible JSON encoder/decoder for Python

py-simplekml

Homepage:
Spack package:
Versions:
1.3.1
Build Dependencies:
python
Link Dependencies:
python
Run Dependencies:
python
Description:
simplekml is a python package which enables you to generate KML with as little effort as possible.

py-singledispatch

Homepage:
Spack package:
Versions:
3.4.0.3
Build Dependencies:
python, py-setuptools, py-six, py-ordereddict
Link Dependencies:
python
Run Dependencies:
python, py-six, py-ordereddict
Description:
This library brings functools.singledispatch to Python 2.6-3.3.

py-sip

Homepage:
Spack package:
Versions:
develop, 4.19.18, 4.19.15, 4.19.13
Build Dependencies:
python, flex, bison
Link Dependencies:
python
Description:
SIP is a tool that makes it very easy to create Python bindings for C and C++ libraries.

py-six

Homepage:
Spack package:
Versions:
1.12.0, 1.11.0, 1.10.0, 1.9.0, 1.8.0
Build Dependencies:
python
Link Dependencies:
python
Run Dependencies:
python
Description:
Python 2 and 3 compatibility utilities.

py-slepc4py

Homepage:
Spack package:
Versions:
3.12.0, 3.11.0, 3.10.0, 3.9.0, 3.8.0, 3.7.0
Build Dependencies:
python, py-setuptools, py-petsc4py, slepc
Link Dependencies:
python, slepc
Run Dependencies:
python, py-petsc4py
Description:
This package provides Python bindings for the SLEPc package.

py-slurm-pipeline

Homepage:
Spack package:
Versions:
2.0.9, 1.1.13
Build Dependencies:
python, py-setuptools, py-six
Link Dependencies:
python
Run Dependencies:
python, py-six
Description:
A Python class for scheduling SLURM jobs

py-smart-open

Homepage:
Spack package:
Versions:
1.8.4
Build Dependencies:
python, py-setuptools, py-boto3
Link Dependencies:
python
Run Dependencies:
python, py-boto3
Description:
smart_open is a Python 2 & Python 3 library for efficient streaming of very large files from/to S3, HDFS, WebHDFS, HTTP, or local storage. It supports transparent, on-the-fly (de-)compression for a variety of different formats.

py-sncosmo

Homepage:
Spack package:
Versions:
1.2.0
Build Dependencies:
python, py-setuptools, py-numpy, py-scipy, py-astropy, py-matplotlib, py-iminuit, py-emcee, py-nestle
Link Dependencies:
python
Run Dependencies:
python, py-numpy, py-scipy, py-astropy, py-matplotlib, py-iminuit, py-emcee, py-nestle
Description:
SNCosmo is a Python library for high-level supernova cosmology analysis.

py-snowballstemmer

Homepage:
Spack package:
Versions:
2.0.0, 1.2.1
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
This package provides 16 stemmer algorithms (15 + Poerter English stemmer) generated from Snowball algorithms.

py-snuggs

Homepage:
Spack package:
Versions:
1.4.1
Build Dependencies:
python, py-numpy, py-click, py-pyparsing
Link Dependencies:
python
Run Dependencies:
python, py-numpy, py-click, py-pyparsing
Description:
Snuggs are s-expressions for Numpy

py-sortedcontainers

Homepage:
Spack package:
Versions:
2.1.0
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Sorted Containers is an Apache2 licensed sorted collections library, written in pure-Python, and fast as C-extensions.

py-soupsieve

Homepage:
Spack package:
Versions:
1.9.3
Build Dependencies:
python, py-setuptools, py-backports-functools-lru-cache
Link Dependencies:
python
Run Dependencies:
python, py-backports-functools-lru-cache
Description:
A modern CSS selector implementation for Beautiful Soup.

py-spatialist

Homepage:
Spack package:
Versions:
0.2.8
Build Dependencies:
python, py-setuptools, py-progressbar2, py-pathos, py-numpy, py-matplotlib, py-jupyter-core, py-ipython, py-ipywidgets, py-tblib
Link Dependencies:
python
Run Dependencies:
python, py-progressbar2, py-pathos, py-numpy, py-matplotlib, py-jupyter-core, py-ipython, py-ipywidgets, py-tblib
Description:
This package offers functionalities for user-friendly geo data processing using GDAL and OGR.

py-spdlog

Homepage:
Spack package:
Versions:
master, 2.0.0
Build Dependencies:
python, py-pybind11, py-setuptools, py-pytest-runner
Link Dependencies:
python
Run Dependencies:
python, py-pybind11
Test Dependencies:
py-pytest
Description:
The py-spdlog package provides a Python wrapper to the C++ spdlog library.

py-spectra

Homepage:
Spack package:
Versions:
0.0.11, 0.0.8
Build Dependencies:
python, py-setuptools, py-colormath
Link Dependencies:
python
Run Dependencies:
python, py-colormath
Description:
Color scales and color conversion made easy for Python.

py-spefile

Homepage:
Spack package:
Versions:
1.6
Build Dependencies:
python, py-setuptools, py-numpy
Link Dependencies:
python
Run Dependencies:
python, py-numpy
Description:
Reader for SPE files part of pyspec a set of python routines for data analysis of x-ray scattering experiments

py-spglib

Homepage:
Spack package:
Versions:
1.9.9.18
Build Dependencies:
python, py-setuptools, py-numpy
Link Dependencies:
python
Run Dependencies:
python, py-setuptools, py-numpy
Description:
Python bindings for C library for finding and handling crystal symmetries.

py-sphinx-bootstrap-theme

Homepage:
Spack package:
Versions:
0.4.13
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Sphinx Bootstrap Theme.

py-sphinx-rtd-theme

Homepage:
Spack package:
Versions:
0.4.3, 0.2.5b1, 0.1.10a0
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
ReadTheDocs.org theme for Sphinx.

py-sphinxautomodapi

Homepage:
Spack package:
Versions:
0.9
Build Dependencies:
python, py-setuptools, py-sphinx
Link Dependencies:
python
Run Dependencies:
python, py-sphinx
Description:
Provides Sphinx directives to autogenerate API documentation pages

py-sphinxcontrib-applehelp

Homepage:
Spack package:
Versions:
1.0.1
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
sphinxcontrib-applehelp is a sphinx extension which outputs Apple help books.

py-sphinxcontrib-bibtex

Homepage:
Spack package:
Versions:
0.3.5
Build Dependencies:
python, py-setuptools, py-latexcodec, py-pybtex, py-pybtex-docutils, py-six, py-sphinx, py-oset, py-ordereddict
Link Dependencies:
python
Run Dependencies:
python, py-latexcodec, py-pybtex, py-pybtex-docutils, py-six, py-sphinx, py-oset, py-ordereddict
Description:
A Sphinx extension for BibTeX style citations.

py-sphinxcontrib-devhelp

Homepage:
Spack package:
Versions:
1.0.1
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp document.

py-sphinxcontrib-htmlhelp

Homepage:
Spack package:
Versions:
1.0.2
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
sphinxcontrib-htmlhelp is a sphinx extension which outputs htmlhelp document.

py-sphinxcontrib-issuetracker

Homepage:
Spack package:
Versions:
0.11
Build Dependencies:
python, py-setuptools, py-sphinx, py-requests
Link Dependencies:
python
Run Dependencies:
python, py-sphinx, py-requests
Description:
Sphinx integration with different issuetrackers.

py-sphinxcontrib-jsmath

Homepage:
Spack package:
Versions:
1.0.1
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
A sphinx extension which renders display math in HTML via JavaScript.

py-sphinxcontrib-programoutput

Homepage:
Spack package:
Versions:
0.15, 0.10
Build Dependencies:
python, py-setuptools, py-sphinx
Link Dependencies:
python
Run Dependencies:
python, py-sphinx
Description:
A Sphinx extension to literally insert the output of arbitrary commands into documents, helping you to keep your command examples up to date.

py-sphinxcontrib-qthelp

Homepage:
Spack package:
Versions:
1.0.2
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp document.

py-sphinxcontrib-serializinghtml

Homepage:
Spack package:
Versions:
1.1.3
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
sphinxcontrib-serializinghtml is a sphinx extension which outputs "serialized" HTML files (json and pickle).

py-sphinxcontrib-websupport

Homepage:
Spack package:
Versions:
1.1.2, 1.1.0, 1.0.1
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
sphinxcontrib-webuspport provides a Python API to easily integrate Sphinx documentation into your Web application.

py-spykeutils

Homepage:
Spack package:
Versions:
0.4.3
Build Dependencies:
python, py-setuptools, py-scipy, py-quantities, py-neo
Link Dependencies:
python
Run Dependencies:
python, py-scipy, py-quantities, py-neo
Description:
Utilities for analyzing electrophysiological data

py-sqlalchemy

Homepage:
Spack package:
Versions:
1.3.9, 1.2.19, 1.2.10, 1.1.18, 1.0.12
Build Dependencies:
python, py-setuptools, py-mysqlclient, py-pymysql, py-psycopg2
Link Dependencies:
python
Run Dependencies:
python, py-mysqlclient, py-pymysql, py-psycopg2
Test Dependencies:
py-pytest, py-mock, py-pytest-xdist
Description:
The Python SQL Toolkit and Object Relational Mapper

py-statsmodels

Homepage:
Spack package:
Versions:
0.10.1, 0.8.0
Build Dependencies:
python, py-setuptools, py-numpy, py-pandas, py-patsy, py-scipy, py-matplotlib
Link Dependencies:
python
Run Dependencies:
python, py-numpy, py-pandas, py-patsy, py-scipy, py-matplotlib
Test Dependencies:
py-pytest
Description:
Statistical computations and models for use with SciPy

py-stestr

Homepage:
Spack package:
Versions:
2.5.1
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
A parallel Python test runner built around subunit.

py-stevedore

Homepage:
Spack package:
Versions:
1.28.0
Build Dependencies:
python, py-six, py-pbr
Link Dependencies:
python
Run Dependencies:
python, py-six, py-pbr
Description:
Manage Dynamic Plugins for Python Applications.

py-storm

Homepage:
Spack package:
Versions:
0.20
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Storm is an object-relational mapper (ORM) for Python

py-stratify

Homepage:
Spack package:
Versions:
0.1
Build Dependencies:
python, py-setuptools, py-numpy, py-cython
Link Dependencies:
python
Run Dependencies:
python, py-numpy, py-cython
Description:
Vectorized interpolators that are especially useful for Nd vertical interpolation/stratification of atmospheric and oceanographic datasets.

py-subprocess32

Homepage:
Spack package:
Versions:
3.5.4, 3.2.7
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
A backport of the subprocess module from Python 3.2/3.3 for 2.x.

py-subrosa

Homepage:
Spack package:
Versions:
0.1.0
Build Dependencies:
python, py-setuptools, py-gf256
Link Dependencies:
python
Run Dependencies:
python, py-gf256
Description:
Subrosa is a Python implementation of Shamir's Secret Sharing. An algorithm for sharing a secret with a group of people without letting any individual of the group know the secret.

py-svgpathtools

Homepage:
Spack package:
Versions:
1.3.3
Build Dependencies:
python, py-setuptools, py-numpy, py-svgwrite
Link Dependencies:
python
Run Dependencies:
python, py-numpy, py-svgwrite
Description:
A collection of tools for manipulating and analyzing SVG Path objects and Bezier curves.

py-svgwrite

Homepage:
Spack package:
Versions:
1.1.12
Build Dependencies:
python, py-setuptools, py-pyparsing
Link Dependencies:
python
Run Dependencies:
python, py-pyparsing
Description:
A Python library to create SVG drawings.

py-symengine

Homepage:
Spack package:
Versions:
develop, 0.2.0
Build Dependencies:
python, py-setuptools, py-cython, cmake, symengine
Link Dependencies:
python, symengine
Run Dependencies:
python
Description:
Python wrappers for SymEngine, a symbolic manipulation library.

py-symfit

Homepage:
Spack package:
Versions:
0.3.5
Build Dependencies:
python, py-setuptools, py-pbr
Link Dependencies:
python
Run Dependencies:
python, py-numpy, py-scipy, py-sympy, py-funcsigs
Description:
Symbolic Fitting; fitting as it should be.

py-sympy

Homepage:
Spack package:
Versions:
1.4, 1.3, 1.1.1, 1.0, 0.7.6
Build Dependencies:
python, py-mpmath
Link Dependencies:
python
Run Dependencies:
python, py-mpmath
Description:
SymPy is a Python library for symbolic mathematics.

py-syned

Homepage:
Spack package:
Versions:
develop
Build Dependencies:
python, py-numpy, py-scipy, py-setuptools
Link Dependencies:
python, py-numpy, py-scipy, py-setuptools
Run Dependencies:
python
Description:
A python library to define the components of a synchrotron beamline and their positions. They can be read/write to json files. It is used by OASYS as a common tool to define sources and optical systems that are then exported to the different add-ons.

py-systemd-python

Homepage:
Spack package:
Versions:
234
Build Dependencies:
python
Link Dependencies:
python
Run Dependencies:
python
Description:
Python interface for libsystemd

py-tables

Homepage:
Spack package:
Versions:
3.6.1, 3.6.0, 3.5.2, 3.4.4, 3.3.0, 3.2.2
Build Dependencies:
python, py-setuptools, py-cython, py-numpy, py-numexpr, py-six, hdf5, c-blosc, zlib, bzip2, lzo
Link Dependencies:
python, hdf5, c-blosc, zlib, bzip2, lzo
Run Dependencies:
python, py-numpy, py-numexpr, py-six
Test Dependencies:
py-mock
Description:
PyTables is a package for managing hierarchical datasets and designed to efficiently and easily cope with extremely large amounts of data.

py-tabulate

Homepage:
Spack package:
Versions:
0.8.6, 0.8.3, 0.7.7
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Pretty-print tabular data

py-tap-py

Homepage:
Spack package:
Versions:
1.6
Build Dependencies:
python, py-nose, py-pygments, py-setuptools
Link Dependencies:
python
Run Dependencies:
python, py-nose, py-pygments
Description:
Python TAP interface module for unit tests

py-tatsu

Homepage:
Spack package:
Versions:
4.4.0
Build Dependencies:
python, py-setuptools, py-dataclasses, py-regex
Link Dependencies:
python
Run Dependencies:
python, py-dataclasses, py-regex
Test Dependencies:
py-pytest-mypy
Description:
TatSu (the successor to Grako) is a tool that takes grammars in a variation of EBNF as input, and outputs memoizing (Packrat) PEG parsers in Python.

py-tblib

Homepage:
Spack package:
Versions:
1.4.0
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Traceback fiddling library. Allows you to pickle tracebacks.

py-tempora

Homepage:
Spack package:
Versions:
1.14.1
Build Dependencies:
python, py-setuptools, py-setuptools-scm, py-six, py-pytz, py-jaraco-functools
Link Dependencies:
python
Run Dependencies:
python, py-six, py-pytz, py-jaraco-functools
Description:
Objects and routines pertaining to date and time (tempora)

py-tensorflow

Homepage:
Spack package:
Versions:
2.1.0, 2.0.1, 2.0.0, 1.15.2, 1.15.1, 1.15.0, 1.14.0, 1.13.2, 1.13.1, 1.12.3, 1.12.2, 1.12.1, 1.12.0, 1.11.0, 1.10.1, 1.10.0, 1.9.0, 1.8.0, 1.7.1, 1.7.0, 1.6.0, 1.5.1, 1.5.0, 1.4.1, 1.4.0, 1.3.1, 1.3.0, 1.2.1, 1.2.0, 1.1.0, 1.0.1, 1.0.0, 0.12.0, 0.11.0, 0.10.0, 0.9.0, 0.8.0, 0.7.1, 0.7.0, 0.6.0
Build Dependencies:
cuda, python, bazel, swig, py-setuptools, py-future, py-absl-py, py-astor, py-backports-weakref, py-enum34, py-gast, py-google-pasta, py-keras-applications, py-keras-preprocessing, py-numpy, py-opt-einsum, py-protobuf, py-termcolor, py-wrapt, py-wheel, py-mock, py-functools32, py-six, py-scipy, py-grpcio, mkl, curl, cudnn, nccl, mpi
Link Dependencies:
cuda, python, mkl, curl, cudnn, nccl, mpi
Run Dependencies:
py-absl-py, py-astor, py-backports-weakref, py-enum34, py-gast, py-google-pasta, py-keras-applications, py-keras-preprocessing, py-numpy, py-opt-einsum, py-protobuf, py-termcolor, py-wrapt, py-wheel, py-mock, py-functools32, py-six, py-scipy, py-grpcio
Test Dependencies:
py-scipy
Description:
TensorFlow is an Open Source Software Library for Machine Intelligence

py-tensorflow-estimator

Homepage:
Spack package:
Versions:
2.0.0, 1.13.0
Build Dependencies:
python, py-tensorflow, bazel, py-pip, py-funcsigs
Link Dependencies:
python, py-tensorflow
Run Dependencies:
py-funcsigs
Description:
TensorFlow Estimator is a high-level TensorFlow API that greatly simplifies machine learning programming.

py-termcolor

Homepage:
Spack package:
Versions:
1.1.0
Build Dependencies:
python
Link Dependencies:
python
Run Dependencies:
python
Description:
ANSII Color formatting for output in terminal.

py-terminado

Homepage:
Spack package:
Versions:
0.8.2, 0.8.1, 0.6
Build Dependencies:
python, py-tornado, py-ptyprocess
Link Dependencies:
python
Run Dependencies:
python, py-tornado, py-ptyprocess
Description:
Terminals served to term.js using Tornado websockets

py-testinfra

Homepage:
Spack package:
Versions:
1.18.0, 1.13.0, 1.12.0, 1.11.1
Build Dependencies:
python, py-setuptools, py-importlib, py-pytest, py-six, py-paramiko, py-pytest-xdist
Link Dependencies:
python
Run Dependencies:
python, py-importlib, py-pytest, py-six, py-paramiko, py-pytest-xdist
Description:
With Testinfra you can write unit tests in Python to test actual state of your servers configured by management tools like Salt, Ansible, Puppet, Chef and so on.

py-testpath

Homepage:
Spack package:
Versions:
0.4.2
Build Dependencies:
python
Link Dependencies:
python
Run Dependencies:
python
Description:
Testpath is a collection of utilities for Python code working with files and commands.

py-testrepository

Homepage:
Spack package:
Versions:
0.0.20
Build Dependencies:
python, py-setuptools, py-fixtures, py-python-subunit, py-testtools
Link Dependencies:
python
Run Dependencies:
python, py-fixtures, py-python-subunit, py-testtools
Description:
A repository of test results.

py-testresources

Homepage:
Spack package:
Versions:
2.0.1
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Testresources, a pyunit extension for managing expensive test resources.

py-testscenarios

Homepage:
Spack package:
Versions:
0.5.0
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Testscenarios, a pyunit extension for dependency injection

py-testtools

Homepage:
Spack package:
Versions:
2.3.0
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Extensions to the Python standard library unit testing framework.

py-tetoolkit

Homepage:
Spack package:
Versions:
2.0.3, 1.5.1
Build Dependencies:
python, py-setuptools, py-pysam, r-deseq, r-deseq2
Link Dependencies:
python, py-setuptools
Run Dependencies:
python, py-pysam, r-deseq, r-deseq2
Description:
TEToolkit is a software package that utilizes both unambiguously (uniquely) and ambiguously (multi-) mapped reads to perform differential enrichment analyses from high throughput sequencing experiments.

py-text-unidecode

Homepage:
Spack package:
Versions:
1.3
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
text-unidecode is the most basic port of the Text::Unidecode Perl library.

py-texttable

Homepage:
Spack package:
Versions:
1.6.1
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Python module for creating simple ASCII tables.

py-theano

Homepage:
Spack package:
Versions:
master, 1.0.4, 1.0.2, 1.0.1, 0.8.2
Build Dependencies:
cuda, python, py-setuptools, py-numpy, py-scipy, py-six, blas, cudnn, py-pygpu, libgpuarray
Link Dependencies:
cuda, python, blas, cudnn, libgpuarray
Run Dependencies:
python, py-setuptools, py-numpy, py-scipy, py-six, py-pygpu
Test Dependencies:
py-nose, py-parameterized, py-flake8
Description:
Optimizing compiler for evaluating mathematical expressions on CPUs and GPUs.

py-thirdorder

Homepage:
Spack package:
Versions:
1.1.1-8526f47
Build Dependencies:
python, py-numpy, py-scipy, spglib
Link Dependencies:
python
Run Dependencies:
python, py-numpy, py-scipy, spglib
Description:
It helps ShengBTE users create FORCE_CONSTANTS_3RD files efficiently

py-tifffile

Homepage:
Spack package:
Versions:
0.12.1
Build Dependencies:
python, py-setuptools, py-numpy
Link Dependencies:
python
Run Dependencies:
python, py-numpy
Description:
Read and write image data from and to TIFF files.

py-toml

Homepage:
Spack package:
Versions:
0.10.0, 0.9.3
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
A Python library for parsing and creating TOML configuration files. For more information on the TOML standard, see https://github.com/toml- lang/toml.git

py-tomopy

Homepage:
Spack package:
Versions:
1.0.0
Build Dependencies:
python, py-setuptools, py-numpy, py-h5py, py-scipy, py-six, py-scikit-image, py-pywavelets, py-pyfftw, py-dxchange
Link Dependencies:
python
Run Dependencies:
python, py-numpy, py-h5py, py-scipy, py-six, py-scikit-image, py-pywavelets, py-pyfftw, py-dxchange
Description:
TomoPy is an open-source Python package for tomographic data processing and image reconstruction.

py-toolz

Homepage:
Spack package:
Versions:
0.9.0
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
A set of utility functions for iterators, functions, and dictionaries

py-torch

Homepage:
Spack package:
Versions:
master, 1.4.0, 1.3.1, 1.3.0, 1.2.0, 1.1.0, 1.0.1, 1.0.0, 0.4.1, 0.4.0, 0.3.1
Build Dependencies:
cuda, python, cmake, ninja, py-setuptools, py-numpy, py-future, py-pyyaml, py-typing, py-pybind11, blas, lapack, protobuf, eigen, cudnn, magma, intel-mkl-dnn, qnnpack, mpi, nccl, gloo, opencv, llvm-openmp, ffmpeg, leveldb, lmdb, redis, zstd, tbb
Link Dependencies:
cuda, python, blas, lapack, protobuf, eigen, cudnn, magma, intel-mkl-dnn, qnnpack, mpi, nccl, gloo, opencv, llvm-openmp, ffmpeg, leveldb, lmdb, redis, zstd, tbb
Run Dependencies:
cuda, python, py-numpy, py-pyyaml, py-typing, py-pybind11
Test Dependencies:
py-hypothesis, py-six, py-psutil
Description:
Tensors and Dynamic neural networks in Python with strong GPU acceleration.

py-torchvision

Homepage:
Spack package:
Versions:
0.5.0, 0.4.2, 0.4.1, 0.4.0, 0.3.0
Build Dependencies:
python, py-setuptools, py-numpy, py-six, py-torch, py-pillow
Link Dependencies:
python
Run Dependencies:
python, py-numpy, py-six, py-torch, py-pillow
Test Dependencies:
py-scipy
Description:
The torchvision package consists of popular datasets, model architectures, and common image transformations for computer vision.

py-tornado

Homepage:
Spack package:
Versions:
6.0.3, 5.1.1, 4.4.0
Build Dependencies:
python, py-setuptools, py-backports-ssl-match-hostname, py-singledispatch, py-certifi, py-backports-abc, py-futures
Link Dependencies:
python
Run Dependencies:
python, py-backports-ssl-match-hostname, py-singledispatch, py-certifi, py-backports-abc, py-futures
Description:
Tornado is a Python web framework and asynchronous networking library.

py-tox

Homepage:
Spack package:
Versions:
3.14.2
Build Dependencies:
python, py-setuptools, py-importlib-metadata, py-packaging, py-pluggy, py-py, py-six, py-virtualenv, py-toml, py-filelock
Link Dependencies:
python
Run Dependencies:
python, py-importlib-metadata, py-packaging, py-pluggy, py-py, py-six, py-virtualenv, py-toml, py-filelock
Description:
tox is a generic virtualenv management and test command line tool.

py-tqdm

Homepage:
Spack package:
Versions:
4.36.1, 4.8.4
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Test Dependencies:
py-nose, py-flake8, py-coverage
Description:
A Fast, Extensible Progress Meter

py-traceback2

Homepage:
Spack package:
Versions:
1.4.0
Build Dependencies:
python, py-setuptools, py-pbr
Link Dependencies:
python
Run Dependencies:
python
Test Dependencies:
py-contextlib2, py-fixtures, py-testtools, py-unittest2
Description:
Backports of the traceback module

py-traitlets

Homepage:
Spack package:
Versions:
4.3.3, 4.3.2, 4.3.1, 4.3.0, 4.2.2, 4.2.1, 4.2.0, 4.1.0, 4.0.0
Build Dependencies:
python, py-six, py-decorator, py-ipython-genutils, py-enum34
Link Dependencies:
python
Run Dependencies:
python, py-six, py-decorator, py-ipython-genutils, py-enum34
Description:
Traitlets Python config system

py-treehash

Homepage:
Spack package:
Versions:
1.0.2
Build Dependencies:
python
Link Dependencies:
python
Run Dependencies:
python
Description:
Calculates a SHA256 (or, potentially, any other hashlib supported function) "tree" hash, as used by e.g. Amazon Glacier.

py-tuiview

Homepage:
Spack package:
Versions:
1.1.7
Build Dependencies:
python, py-pyqt4, py-numpy, gdal
Link Dependencies:
python, gdal
Run Dependencies:
python, py-pyqt4, py-numpy
Description:
TuiView is a lightweight raster GIS with powerful raster attribute table manipulation abilities.

py-twine

Homepage:
Spack package:
Versions:
2.0.0
Build Dependencies:
python, py-pkginfo, py-readme-renderer, py-requests-toolbelt, py-setuptools, py-tqdm
Link Dependencies:
python
Run Dependencies:
python, py-pkginfo, py-readme-renderer, py-requests-toolbelt, py-setuptools, py-tqdm
Description:
Twine is a utility for publishing Python packages on PyPI.

py-twisted

Homepage:
Spack package:
Versions:
15.4.0, 15.3.0
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
An asynchronous networking framework written in Python

py-typed-ast

Homepage:
Spack package:
Versions:
1.4.0
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
A fork of Python 2 and 3 ast modules with type comment support.

py-typesentry

Homepage:
Spack package:
Versions:
0.2.7
Build Dependencies:
python, py-colorama
Link Dependencies:
python
Run Dependencies:
python, py-colorama
Description:
Python library for run-time type checking for type-annotated functions.

py-typing

Homepage:
Spack package:
Versions:
3.7.4.1, 3.6.6, 3.6.4, 3.6.1
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
This is a backport of the standard library typing module to Python versions older than 3.6.

py-typing-extensions

Homepage:
Spack package:
Versions:
3.7.4, 3.7.2
Build Dependencies:
python, py-setuptools, py-typing
Link Dependencies:
python
Run Dependencies:
python, py-typing
Description:
The typing_extensions module contains both backports of these changes as well as experimental types that will eventually be added to the typing module, such as Protocol (see PEP 544 for details about protocols and static duck typing).

py-tzlocal

Homepage:
Spack package:
Versions:
2.0.0, 1.3
Build Dependencies:
python, py-setuptools, py-pytz
Link Dependencies:
python
Run Dependencies:
python, py-pytz
Description:
tzinfo object for the local timezone.

py-ujson

Homepage:
Spack package:
Versions:
1.35
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Ultra fast JSON decoder and encoder written in C with Python bindings.

py-umalqurra

Homepage:
Spack package:
Versions:
0.2
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Date Api that support Hijri Umalqurra calendar.

py-umi-tools

Homepage:
Spack package:
Versions:
1.0.0, 0.5.5, 0.5.4, 0.5.3
Build Dependencies:
python, py-setuptools, py-numpy, py-pandas, py-pysam, py-future, py-six, py-regex, py-scipy, py-matplotlib
Link Dependencies:
python
Run Dependencies:
python, py-numpy, py-pandas, py-pysam, py-future, py-six, py-regex, py-scipy, py-matplotlib
Description:
Tools for handling Unique Molecular Identifiers in NGS data sets

py-unicycler

Homepage:
Spack package:
Versions:
0.4.7, 0.4.6, 0.4.5
Build Dependencies:
python, py-setuptools, jdk, samtools, racon
Link Dependencies:
python, samtools, racon
Run Dependencies:
python, py-setuptools, spades, pilon, jdk, bowtie2, samtools, racon, blast-plus
Description:
Unicycler is an assembly pipeline for bacterial genomes. It can assemble Illumina-only read sets where it functions as a SPAdes-optimiser. It can also assembly long-read-only sets (PacBio or Nanopore) where it runs a miniasm+Racon pipeline. For the best possible assemblies, give it both Illumina reads and long reads, and it will conduct a hybrid assembly.

py-unittest2

Homepage:
Spack package:
Versions:
1.1.0
Build Dependencies:
python, py-setuptools, py-traceback2, py-six, py-argparse
Link Dependencies:
python
Run Dependencies:
python, py-traceback2, py-six, py-argparse
Description:
unittest2 is a backport of the new features added to the unittest testing framework in Python 2.7 and onwards.

py-unittest2py3k

Homepage:
Spack package:
Versions:
0.5.1
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
unittest2 is a backport of the new features added to the unittest testing framework in Python 2.7 and 3.2. This is a Python 3 compatible version of unittest2.

py-uritemplate

Homepage:
Spack package:
Versions:
3.0.0
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Simple python library to deal with URI Templates.

py-urllib3

Homepage:
Spack package:
Versions:
1.25.6, 1.25.3, 1.21.1, 1.20, 1.14
Build Dependencies:
python, py-setuptools, py-pyopenssl, py-cryptography, py-idna, py-certifi, py-ipaddress, py-pysocks
Link Dependencies:
python, py-pyopenssl, py-cryptography, py-idna, py-certifi, py-ipaddress, py-pysocks
Run Dependencies:
python
Test Dependencies:
py-pytest, py-mock, py-tornado
Description:
HTTP library with thread-safe connection pooling, file post, and more.

py-urwid

Homepage:
Spack package:
Versions:
1.3.0
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
A full-featured console UI library

py-us

Homepage:
Spack package:
Versions:
1.0.0
Build Dependencies:
python, py-setuptools, py-jellyfish
Link Dependencies:
python
Run Dependencies:
python, py-jellyfish
Description:
US state meta information and other fun stuff.

py-usgs

Homepage:
Spack package:
Versions:
0.2.7
Build Dependencies:
python, py-setuptools, py-click, py-requests, py-requests-futures
Link Dependencies:
python
Run Dependencies:
python, py-click, py-requests, py-requests-futures
Test Dependencies:
py-mock, py-pytest
Description:
Client library for interfacing with USGS datasets

py-uwsgi

Homepage:
Spack package:
Versions:
2.0.18
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Web Application framework for low overhead web services

py-vcversioner

Homepage:
Spack package:
Versions:
2.16.0.0
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Vcversioner: Take version numbers from version control.

py-vermin

Homepage:
Spack package:
Versions:
0.10.0
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python, py-setuptools
Description:
Concurrently detect the minimum Python versions needed to run code.

py-vine

Homepage:
Spack package:
Versions:
1.3.0, 1.2.0
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Promises, promises, promises.

py-virtualenv

Homepage:
Spack package:
Versions:
16.7.6, 16.4.1, 16.0.0, 15.1.0, 15.0.1, 13.0.1, 1.11.6
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python, py-setuptools
Description:
virtualenv is a tool to create isolated Python environments.

py-virtualenv-clone

Homepage:
Spack package:
Versions:
0.2.6
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python, py-setuptools
Description:
A script for cloning a non-relocatable virtualenv.

py-virtualenvwrapper

Homepage:
Spack package:
Versions:
4.8.2
Build Dependencies:
python, py-virtualenv, py-virtualenv-clone, py-stevedore, py-setuptools
Link Dependencies:
python
Run Dependencies:
python, py-virtualenv, py-virtualenv-clone, py-stevedore, py-setuptools
Description:
virtualenvwrapper is a set of extensions to Ian Bicking's virtualenv tool. The extensions include wrappers for creating and deleting virtual environments and otherwise managing your development workflow, making it easier to work on more than one project at a time without introducing conflicts in their dependencies.

py-voluptuous

Homepage:
Spack package:
Versions:
0.11.7, 0.11.6, 0.11.5
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Voluptous, despite the name, is a Python data validation library.

py-vsc-base

Homepage:
Spack package:
Versions:
2.5.8
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python, py-setuptools
Description:
Common Python libraries tools created by HPC-UGent

py-vsc-install

Homepage:
Spack package:
Versions:
0.10.25
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python, py-setuptools
Description:
Shared setuptools functions and classes for Python libraries developed by HPC-UGent.

py-wand

Homepage:
Spack package:
Versions:
0.5.6, 0.4.2
Build Dependencies:
python, py-setuptools, imagemagick, py-sphinx
Link Dependencies:
python, imagemagick
Run Dependencies:
python
Test Dependencies:
py-pytest, py-pytest-xdist, py-psutil
Description:
Wand is a ctypes-based simple ImageMagick binding for Python.

py-warlock

Homepage:
Spack package:
Versions:
1.3.3
Build Dependencies:
python, py-setuptools, py-jsonschema, py-jsonpatch, py-six
Link Dependencies:
python
Run Dependencies:
python, py-jsonschema, py-jsonpatch, py-six
Description:
Self-validating Python objects using JSON schema

py-wcsaxes

Homepage:
Spack package:
Versions:
0.8
Build Dependencies:
python, py-setuptools, py-numpy, py-matplotlib, py-astropy
Link Dependencies:
python
Run Dependencies:
python, py-numpy, py-matplotlib, py-astropy
Description:
WCSAxes is a framework for making plots of Astronomical data in Matplotlib.

py-wcwidth

Homepage:
Spack package:
Versions:
0.1.7
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Measures number of Terminal column cells of wide-character codes

py-weave

Homepage:
Spack package:
Versions:
0.17.0
Build Dependencies:
python, py-setuptools, py-numpy
Link Dependencies:
python
Run Dependencies:
python, py-numpy
Description:
Weave provides tools for including C/C++ code within Python code. Weave is the stand-alone version of the now-removed SciPy submodule ``scipy.weave``. It is Python 2.x only, and is provided for users that need new versions of SciPy but have existing code that still depends on ``scipy.weave``. For new code, users are recommended to use Cython.

py-webencodings

Homepage:
Spack package:
Versions:
0.5.1
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
This is a Python implementation of the WHATWG Encoding standard.

py-webkit-server

Homepage:
Spack package:
Versions:
develop, 1.0
Build Dependencies:
python
Link Dependencies:
python
Run Dependencies:
python
Description:
a Webkit-based, headless web client

py-werkzeug

Homepage:
Spack package:
Versions:
0.16.0, 0.15.4, 0.11.15, 0.11.11
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Test Dependencies:
py-pytest, py-hypothesis, py-requests
Description:
The Swiss Army knife of Python web development

py-whatshap

Homepage:
Spack package:
Versions:
0.17
Build Dependencies:
python, py-setuptools, py-cython
Link Dependencies:
python
Run Dependencies:
python, py-cython, py-pysam, py-xopen, py-pyvcf, py-pyfaidx, py-networkx
Description:
WhatsHap is a software for phasing genomic variants using DNA sequencing reads, also called read-based phasing or haplotype assembly.

py-wheel

Homepage:
Spack package:
Versions:
0.33.4, 0.33.1, 0.29.0, 0.26.0
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python, py-setuptools
Test Dependencies:
py-pytest, py-pytest-cov
Description:
A built-package format for Python.

py-whichcraft

Homepage:
Spack package:
Versions:
0.4.1
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Cross-platform cross-python shutil.which functionality.

py-widgetsnbextension

Homepage:
Spack package:
Versions:
3.5.1, 3.4.2, 3.3.0, 1.2.6
Build Dependencies:
python, py-setuptools, py-notebook
Link Dependencies:
python
Run Dependencies:
python, py-notebook
Description:
IPython HTML widgets for Jupyter

py-wradlib

Homepage:
Spack package:
Versions:
1.5.0
Build Dependencies:
python, py-setuptools, py-numpy, py-matplotlib, py-scipy, py-h5py, py-netcdf4, py-xarray, py-xmltodict, py-semver, py-deprecation, py-requests, gdal
Link Dependencies:
python
Run Dependencies:
python, py-numpy, py-matplotlib, py-scipy, py-h5py, py-netcdf4, py-xarray, py-xmltodict, py-semver, py-deprecation, py-requests, gdal
Description:
wradlib is designed to assist you in the most important steps of processing weather radar data. These may include: reading common data formats, georeferencing, converting reflectivity to rainfall intensity, identifying and correcting typical error sources (such as clutter or attenuation) and visualising the data.

py-wrapt

Homepage:
Spack package:
Versions:
1.11.2, 1.11.1, 1.10.10
Build Dependencies:
python
Link Dependencies:
python
Run Dependencies:
python
Description:
Module for decorators, wrappers and monkey patching.

py-wub

Homepage:
Spack package:
Versions:
0.4.0
Build Dependencies:
python, py-six, py-pytest, py-pycmd, py-biopython, py-numpy, py-matplotlib, py-seaborn, py-editdistance, py-pandas, py-pysam, py-tqdm, py-statsmodels, py-setuptools
Link Dependencies:
python
Run Dependencies:
python, py-six, py-pytest, py-pycmd, py-biopython, py-numpy, py-matplotlib, py-seaborn, py-editdistance, py-pandas, py-pysam, py-tqdm, py-statsmodels
Test Dependencies:
py-pytest, py-pycmd, py-numpy, py-editdistance
Description:
Bioinformatics tools and a software library developed by the Oxford Nanopore Technologies Applications group.

py-wxmplot

Homepage:
Spack package:
Versions:
0.9.38
Build Dependencies:
python, py-setuptools, py-numpy, py-six, py-matplotlib, py-wxpython
Link Dependencies:
python
Run Dependencies:
python, py-numpy, py-six, py-matplotlib, py-wxpython
Test Dependencies:
py-pytest
Description:
wxPython plotting widgets using matplotlib.

py-wxpython

Homepage:
Spack package:
Versions:
4.0.6
Build Dependencies:
python, wxwidgets, py-setuptools, py-pathlib2
Link Dependencies:
python, wxwidgets
Run Dependencies:
python, py-numpy, py-pillow, py-six
Description:
Cross platform GUI toolkit for Python.

py-xarray

Homepage:
Spack package:
Versions:
0.14.0, 0.13.0, 0.12.0, 0.11.0, 0.9.1
Build Dependencies:
python, py-setuptools, py-pandas, py-numpy
Link Dependencies:
python
Run Dependencies:
python, py-pandas, py-numpy
Description:
N-D labeled arrays and datasets in Python

py-xattr

Homepage:
Spack package:
Versions:
master, 0.9.6
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
A python interface to access extended file attributes, sans libattr dependency.

py-xdot

Homepage:
Spack package:
Versions:
master, 1.0, 0.9
Build Dependencies:
python, py-setuptools, py-pygobject, py-pycairo, pango, atk, gdk-pixbuf, gtkplus
Link Dependencies:
python
Run Dependencies:
python, py-setuptools, py-pygobject, py-pycairo, pango, atk, gdk-pixbuf, gtkplus
Description:
xdot.py is an interactive viewer for graphs written in Graphviz's dot language.

py-xenv

Homepage:
Spack package:
Versions:
develop_2018-12-20, develop
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Helpers to work with the environment in a platform independent way.

py-xlrd

Homepage:
Spack package:
Versions:
0.9.4
Build Dependencies:
python
Link Dependencies:
python
Run Dependencies:
python
Description:
Library for developers to extract data from Microsoft Excel (tm) spreadsheet files

py-xlsxwriter

Homepage:
Spack package:
Versions:
1.0.2
Build Dependencies:
python
Link Dependencies:
python
Run Dependencies:
python
Description:
XlsxWriter is a Python module for writing files in the Excel 2007+ XLSX file format.

py-xlwt

Homepage:
Spack package:
Versions:
1.3.0
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Library to create spreadsheet files compatible with MS Excel 97/2000/XP/2003 XLS files, on any platform, with Python 2.6, 2.7, 3.3+.

py-xmlrunner

Homepage:
Spack package:
Versions:
1.7.7
Build Dependencies:
python, py-setuptools, py-unittest2
Link Dependencies:
python
Run Dependencies:
python, py-unittest2
Description:
PyUnit-based test runner with JUnit like XML reporting.

py-xmltodict

Homepage:
Spack package:
Versions:
0.12.0
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
xmltodict is a Python module that makes working with XML feel like you are working with JSON.

py-xopen

Homepage:
Spack package:
Versions:
0.8.2, 0.5.0, 0.1.1
Build Dependencies:
python, py-setuptools, py-bz2file
Link Dependencies:
python
Run Dependencies:
python, py-bz2file
Description:
This small Python module provides a xopen function that works like the built-in open function, but can also deal with compressed files. Supported compression formats are gzip, bzip2 and xz. They are automatically recognized by their file extensions .gz, .bz2 or .xz.

py-xpyb

Homepage:
Spack package:
Versions:
1.3.1
Build Dependencies:
python, libxcb, xcb-proto
Link Dependencies:
python, libxcb
Description:
xpyb provides a Python binding to the X Window System protocol via libxcb.

py-xvfbwrapper

Homepage:
Spack package:
Versions:
0.2.9
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
run headless display inside X virtual framebuffer (Xvfb)

py-yajl

Homepage:
Spack package:
Versions:
0.3.5
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Python bindings for the Yajl JSON encoder/decoder library.

py-yamlreader

Homepage:
Spack package:
Versions:
3.0.4
Build Dependencies:
python, py-setuptools, py-pyyaml, py-six
Link Dependencies:
python
Run Dependencies:
python, py-setuptools, py-pyyaml, py-six
Description:
Yamlreader merges YAML data from a directory, a list of files or a file glob.

py-yapf

Homepage:
Spack package:
Versions:
0.2.1
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Yet Another Python Formatter

py-yt

Homepage:
Spack package:
Versions:
develop-4.0, develop, 3.5.1, 3.5.0, 3.4.1, 3.4.0, 3.3.5, 3.3.4, 3.3.3, 3.3.2, 3.3.1, 3.3.0, 3.2.3, 3.2.2
Build Dependencies:
python, py-astropy, py-cython, py-h5py, py-ipython, py-matplotlib, py-numpy, py-scipy, py-setuptools, py-sympy, rockstar
Link Dependencies:
python
Run Dependencies:
python, py-astropy, py-cython, py-h5py, py-ipython, py-matplotlib, py-numpy, py-scipy, py-setuptools, py-sympy, rockstar
Description:
Volumetric Data Analysis yt is a python package for analyzing and visualizing volumetric, multi-resolution data from astrophysical simulations, radio telescopes, and a burgeoning interdisciplinary community.

py-ytopt

Homepage:
Spack package:
Versions:
0.1.0
Build Dependencies:
python, py-scikit-learn, py-scikit-optimize
Link Dependencies:
python
Run Dependencies:
python, py-scikit-learn, py-scikit-optimize
Description:
Ytopt package implements search using Random Forest (SuRF), an autotuning search method developed within Y-Tune ECP project.

py-zarr

Homepage:
Spack package:
Versions:
2.3.2
Build Dependencies:
python, py-asciitree, py-fasteners, py-msgpack, py-setuptools, py-setuptools-scm, py-numcodecs, py-numpy, py-scandir
Link Dependencies:
python
Run Dependencies:
python, py-asciitree, py-fasteners, py-msgpack, py-numcodecs, py-numpy, py-scandir
Description:
Zarr is a Python package providing an implementation of chunked, compressed, N-dimensional arrays.

py-zc-buildout

Homepage:
Spack package:
Versions:
2.13.1
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python, py-setuptools
Description:
System for managing development buildouts

py-zc-lockfile

Homepage:
Spack package:
Versions:
1.4
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python, py-setuptools
Description:
Basic inter-process locks

py-zict

Homepage:
Spack package:
Versions:
1.0.0
Build Dependencies:
python, py-setuptools, py-heapdict
Link Dependencies:
python
Run Dependencies:
python, py-heapdict
Description:
Mutable mapping tools

py-zipp

Homepage:
Spack package:
Versions:
0.6.0, 0.5.1
Build Dependencies:
python, py-setuptools, py-setuptools-scm, py-more-itertools
Link Dependencies:
python
Run Dependencies:
python, py-more-itertools
Description:
Backport of pathlib-compatible object wrapper for zip files.

py-zope-event

Homepage:
Spack package:
Versions:
4.3.0
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Very basic event publishing system.

py-zope-interface

Homepage:
Spack package:
Versions:
4.5.0
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Test Dependencies:
py-zope-event, py-nose, py-coverage
Description:
This package provides an implementation of "object interfaces" for Python. Interfaces are a mechanism for labeling objects as conforming to a given API or contract. So, this package can be considered as implementation of the Design By Contract methodology support in Python.

py-zxcvbn

Homepage:
Spack package:
Versions:
4.4.28, 4.4.27, 4.4.26, 4.4.25
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
A realistic password strength estimator. This is a Python implementation of the library created by the team at Dropbox.

pythia6

Homepage:
Spack package:
Versions:
6.4.28
Build Dependencies:
cmake
Description:
PYTHIA is a program for the generation of high-energy physics events, i.e. for the description of collisions at high energies between elementary particles such as e+, e-, p and pbar in various combinations. PYTHIA6 is a Fortran package which is no longer maintained: new prospective users should use Pythia8 instead. This recipe includes patches required to interoperate with Root.

pythia8

Homepage:
Spack package:
Versions:
8301, 8244, 8240, 8235, 8230, 8212
Build Dependencies:
rsync
Description:
The Pythia program is a standard tool for the generation of events in high-energy collisions, comprising a coherent set of physics models for the evolution from a few-body hard process to a complex multiparticle final state.

python

Homepage:
Spack package:
Versions:
3.8.1, 3.8.0, 3.7.6, 3.7.5, 3.7.4, 3.7.3, 3.7.2, 3.7.1, 3.7.0, 3.6.8, 3.6.7, 3.6.6, 3.6.5, 3.6.4, 3.6.3, 3.6.2, 3.6.1, 3.6.0, 3.5.7, 3.5.2, 3.5.1, 3.5.0, 3.4.10, 3.4.3, 3.3.6, 3.2.6, 3.1.5, 2.7.16, 2.7.15, 2.7.14, 2.7.13, 2.7.12, 2.7.11, 2.7.10, 2.7.9, 2.7.8
Build Dependencies:
pkgconfig, gettext, readline, ncurses, openssl, sqlite, gdbm, libnsl, zlib, bzip2, xz, expat, libffi, tk, tcl, tix, libuuid
Link Dependencies:
gettext, readline, ncurses, openssl, sqlite, gdbm, libnsl, zlib, bzip2, xz, expat, libffi, tk, tcl, tix, libuuid
Description:
The Python programming language.

qbank

Homepage:
Spack package:
Versions:
2.10.4
Build Dependencies:
openssl, perl, perl-dbi
Link Dependencies:
openssl
Run Dependencies:
perl, perl-dbi
Description:
QBank is a unique dynamic reservation-based allocation management system that manages the utilization of computational resources in a multi- project environment. It is used in conjunction with a resource management system allowing an organization to guarantee greater fairness and enforce mission priorities by associating a charge with the use of computational resources and allocating resource credits which limit how much of the resources may be used at what time and by whom. It tracks resource utilization and allows for insightful planning.

qbox

Homepage:
Spack package:
Versions:
1.63.7, 1.63.5, 1.63.4, 1.63.2, 1.63.0, 1.62.3, 1.60.9, 1.60.4, 1.60.0, 1.58.0, 1.56.2, 1.54.4, 1.54.2, 1.52.3, 1.52.2, 1.50.4, 1.50.2, 1.50.1, 1.47.0, 1.45.3, 1.45.1, 1.45.0, 1.44.0
Build Dependencies:
mpi, blas, scalapack, fftw, xerces-c
Link Dependencies:
mpi, blas, scalapack, fftw, xerces-c
Description:
Qbox is a C++/MPI scalable parallel implementation of first-principles molecular dynamics (FPMD) based on the plane-wave, pseudopotential formalism. Qbox is designed for operation on large parallel computers.

qca

Homepage:
Spack package:
Versions:
2.2.1, 2.1.3
Build Dependencies:
cmake, qt
Link Dependencies:
qt
Description:
Taking a hint from the similarly-named Java Cryptography Architecture, QCA aims to provide a straightforward and cross-platform crypto API, using Qt datatypes and conventions. QCA separates the API from the implementation, using plugins known as Providers. The advantage of this model is to allow applications to avoid linking to or explicitly depending on any particular cryptographic library. This allows one to easily change or upgrade crypto implementations without even needing to recompile the application! QCA should work everywhere Qt does, including Windows/Unix/MacOSX.

qemu

Homepage:
Spack package:
Versions:
4.1.1, 4.1.0, 4.0.1, 4.0.0, 3.1.1.1, 3.1.1, 3.1.0, 3.0.1, 3.0.0, 2.12.1, 2.12.0, 2.11.2, 2.11.1, 2.11.0, 2.10.2, 2.10.1, 2.10.0, 2.9.1, 2.9.0, 2.8.1.1, 2.8.1, 2.8.0, 2.7.1, 2.7.0, 2.6.2, 2.6.1, 2.6.0, 2.5.1.1, 2.5.1, 2.5.0, 2.4.1, 2.4.0.1, 2.4.0, 2.3.1, 2.3.0, 2.2.1, 2.2.0, 2.1.3, 2.1.2, 2.1.1, 2.1.0, 2.0.2, 2.0.0, 1.7.2, 1.7.0, 1.6.2, 1.6.1, 1.6.0, 1.5.3, 1.5.2, 1.5.1, 1.5.0, 1.4.2, 1.4.1, 1.4.0, 1.3.1, 1.3.0, 1.2.2, 1.2.1, 1.2.0, 1.1.2, 1.1.1, 1.1.0-1, 1.1.0, 1.0.1, 1.0, 0.15.1, 0.15.0, 0.14.1, 0.14.0, 0.13.0, 0.12.4, 0.12.3, 0.12.2, 0.12.1, 0.12.0, 0.11.0, 0.10.6, 0.10.5, 0.10.4, 0.10.3, 0.10.2, 0.10.1, 0.10.0, 0.9.1
Build Dependencies:
glib, pixman
Link Dependencies:
glib, pixman
Description:
QEMU is a generic and open source machine emulator and virtualizer.

qhull

Homepage:
Spack package:
Versions:
2015.2, 2012.1
Build Dependencies:
cmake
Description:
Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, furt hest-site Delaunay triangulation, and furthest-site Voronoi diagram. The source code runs in 2-d, 3-d, 4-d, and higher dimensions. Qhull implements the Quickhull algorithm for computing the convex hull. It handles roundoff errors from floating point arithmetic. It computes volumes, surface areas, and approximations to the convex hull.

qjson

Homepage:
Spack package:
Versions:
0.9.0
Build Dependencies:
cmake, qt
Link Dependencies:
qt
Description:
QJson is a Qt-based library that maps JSON data to QVariant objects and vice versa.

qmcpack

Homepage:
Spack package:
Versions:
develop, 3.9.1, 3.9.0, 3.8.0, 3.7.0, 3.6.0, 3.5.0, 3.4.0, 3.3.0, 3.2.0, 3.1.1, 3.1.0
Build Dependencies:
cuda, cmake, boost, libxml2, mpi, python, hdf5, blas, lapack, fftw-api
Link Dependencies:
cuda, boost, libxml2, mpi, python, hdf5, blas, lapack, fftw-api
Run Dependencies:
py-numpy, py-matplotlib, quantum-espresso
Description:
QMCPACK, is a modern high-performance open-source Quantum Monte Carlo (QMC) simulation code.

qmd-progress

Homepage:
Spack package:
Versions:
develop, 1.1.0, 1.0.0
Build Dependencies:
cmake, bml, mpi, metis
Link Dependencies:
bml, mpi, metis
Description:
PROGRESS: Parallel, Rapid O(N) and Graph-based Recursive Electronic Structure Solver. This library is focused on the development of general solvers that are commonly used in quantum chemistry packages.

qnnpack

Homepage:
Spack package:
Versions:
master
Build Dependencies:
cmake
Description:
QNNPACK (Quantized Neural Networks PACKage) is a mobile-optimized library for low-precision high-performance neural network inference. QNNPACK provides implementation of common neural network operators on quantized 8-bit tensors.

qorts

Homepage:
Spack package:
Versions:
1.2.42
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r, java
Description:
The QoRTs software package is a fast, efficient, and portable multifunction toolkit designed to assist in the analysis, quality control, and data management of RNA-Seq and DNA-Seq datasets. Its primary function is to aid in the detection and identification of errors, biases, and artifacts produced by high-throughput sequencing technology.

qperf

Homepage:
Spack package:
Versions:
0.4.11, 0.4.10
Build Dependencies:
autoconf, automake, libtool, m4
Description:
The qperf measures bandwidth and latency between two nodes. It can work over TCP/IP as well as the RDMA transports.

qrupdate

Homepage:
Spack package:
Versions:
1.1.2
Build Dependencies:
blas, lapack
Link Dependencies:
blas, lapack
Description:
qrupdate is a Fortran library for fast updates of QR and Cholesky decompositions.

qscintilla

Homepage:
Spack package:
Versions:
2.11.2, 2.10.2
Build Dependencies:
qt
Link Dependencies:
qt
Description:
QScintilla is a port to Qt of Neil Hodgson's Scintilla C++ editor control.

qt

Homepage:
Spack package:
Versions:
5.14.1, 5.14.0, 5.13.1, 5.12.5, 5.12.2, 5.11.3, 5.11.2, 5.10.0, 5.9.1, 5.9.0, 5.8.0, 5.7.1, 5.7.0, 5.5.1, 5.4.2, 5.4.0, 5.3.2, 5.2.1, 4.8.7, 4.8.6, 4.8.5, 3.3.8b
Build Dependencies:
pkgconfig, flex, bison, python, icu4c, jpeg, libmng, libtiff, libxml2, zlib, freetype, gperf, gtkplus, openssl, sqlite, libpng, pcre, inputproto, glib, dbus, gl, harfbuzz, double-conversion, pcre2, fontconfig, libx11, libxcb, libxkbcommon, xcb-util-image, xcb-util-keysyms, xcb-util-renderutil, xcb-util-wm, libxext, libxrender
Link Dependencies:
icu4c, jpeg, libmng, libtiff, libxml2, zlib, freetype, gperf, gtkplus, openssl, libpng, pcre, inputproto, glib, dbus, gl, harfbuzz, double-conversion, pcre2, fontconfig, libx11, libxcb, libxkbcommon, xcb-util-image, xcb-util-keysyms, xcb-util-renderutil, xcb-util-wm, libxext, libxrender
Run Dependencies:
sqlite
Description:
Qt is a comprehensive cross-platform C++ application framework.

qt-creator

Homepage:
Spack package:
Versions:
4.8.0
Build Dependencies:
qt, sqlite
Link Dependencies:
qt, sqlite
Description:
The Qt Creator IDE.

qtgraph

Homepage:
Spack package:
Versions:
develop, 1.0.0.0
Build Dependencies:
qt, graphviz
Link Dependencies:
qt, graphviz
Description:
The baseline library used in the CUDA-centric Open|SpeedShop Graphical User Interface (GUI) which allows Graphviz DOT formatted data to be imported into a Qt application by wrapping the Graphviz libcgraph and libgvc within the Qt Graphics View Framework.

qthreads

Homepage:
Spack package:
Versions:
1.14, 1.12, 1.11, 1.10
Build Dependencies:
hwloc
Link Dependencies:
hwloc
Description:
The qthreads API is designed to make using large numbers of threads convenient and easy, and to allow portable access to threading constructs used in massively parallel shared memory environments. The API maps well to both MTA-style threading and PIM-style threading, and we provide an implementation of this interface in both a standard SMP context as well as the SST context. The qthreads API provides access to full/empty-bit (FEB) semantics, where every word of memory can be marked either full or empty, and a thread can wait for any word to attain either state.

qtkeychain

Homepage:
Spack package:
Versions:
0.9.1
Build Dependencies:
cmake, qt, libsecret
Link Dependencies:
qt, libsecret
Description:
Platform-independent Qt API for storing passwords securely.

quantum-espresso

Homepage:
Spack package:
Versions:
develop, 6.5, 6.4.1, 6.4, 6.3, 6.2.1, 6.2.0, 6.1.0, 6.0.0, 5.4, 5.3
Build Dependencies:
blas, lapack, fftw-api, mpi, scalapack, elpa, hdf5
Link Dependencies:
blas, lapack, fftw-api, mpi, scalapack, elpa, hdf5
Description:
Quantum-ESPRESSO is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.

quinoa

Homepage:
Spack package:
Versions:
develop
Build Dependencies:
cmake, hdf5, charmpp, trilinos, boost, hypre, random123, netlib-lapack, mad-numdiff, h5part, boostmplcartesianproduct, tut, pugixml, pstreams, pegtl
Link Dependencies:
hdf5, charmpp, trilinos, boost, hypre, random123, netlib-lapack, mad-numdiff, h5part, boostmplcartesianproduct, tut, pugixml, pstreams, pegtl
Description:
Quinoa is a set of computational tools that enables research and numerical analysis in fluid dynamics. At this time it is a test-bed to experiment with various algorithms using fully asynchronous runtime systems.

qwt

Homepage:
Spack package:
Versions:
6.1.4, 6.1.3, 5.2.2
Build Dependencies:
qt
Link Dependencies:
qt
Description:
The Qwt library contains GUI Components and utility classes which are primarily useful for programs with a technical background. Beside a framework for 2D plots it provides scales, sliders, dials, compasses, thermometers, wheels and knobs to control or display values, arrays, or ranges of type double.

qwtpolar

Homepage:
Spack package:
Versions:
1.1.1
Build Dependencies:
qt, qwt
Link Dependencies:
qt, qwt
Description:
The QwtPolar library contains classes for displaying values on a polar coordinate system.

r

Homepage:
Spack package:
Versions:
3.6.2, 3.6.1, 3.6.0, 3.5.3, 3.5.2, 3.5.1, 3.5.0, 3.4.4, 3.4.3, 3.4.2, 3.4.1, 3.4.0, 3.3.3, 3.3.2, 3.3.1, 3.3.0, 3.2.5, 3.2.3, 3.2.2, 3.2.1, 3.2.0, 3.1.3, 3.1.2
Build Dependencies:
blas, lapack, readline, ncurses, icu4c, glib, zlib, bzip2, libtiff, jpeg, cairo, pango, freetype, tcl, tk, libx11, libxt, libxmu, curl, pcre, java
Link Dependencies:
blas, lapack, readline, ncurses, icu4c, glib, zlib, bzip2, libtiff, jpeg, cairo, pango, freetype, tcl, tk, libx11, libxt, libxmu, curl, pcre, java
Description:
R is 'GNU S', a freely available language and environment for statistical computing and graphics which provides a wide variety of statistical and graphical techniques: linear and nonlinear modelling, statistical tests, time series analysis, classification, clustering, etc. Please consult the R project homepage for further information.

r-a4

Homepage:
Spack package:
Versions:
1.32.0, 1.30.0, 1.28.0, 1.26.0, 1.24.0
Build Dependencies:
r, r-a4base, r-a4preproc, r-a4classif, r-a4core, r-a4reporting
Link Dependencies:
r
Run Dependencies:
r, r-a4base, r-a4preproc, r-a4classif, r-a4core, r-a4reporting
Description:
Automated Affymetrix Array Analysis Umbrella Package.

r-a4base

Homepage:
Spack package:
Versions:
1.32.0, 1.30.0, 1.28.0, 1.26.0, 1.24.0
Build Dependencies:
r, r-biobase, r-annotationdbi, r-annaffy, r-mpm, r-genefilter, r-limma, r-multtest, r-glmnet, r-a4preproc, r-a4core, r-gplots
Link Dependencies:
r
Run Dependencies:
r, r-biobase, r-annotationdbi, r-annaffy, r-mpm, r-genefilter, r-limma, r-multtest, r-glmnet, r-a4preproc, r-a4core, r-gplots
Description:
Automated Affymetrix Array Analysis Base Package.

r-a4classif

Homepage:
Spack package:
Versions:
1.32.0, 1.30.0, 1.28.0, 1.26.0, 1.24.0
Build Dependencies:
r, r-a4core, r-a4preproc, r-mlinterfaces, r-rocr, r-pamr, r-glmnet, r-varselrf
Link Dependencies:
r
Run Dependencies:
r, r-a4core, r-a4preproc, r-mlinterfaces, r-rocr, r-pamr, r-glmnet, r-varselrf
Description:
Automated Affymetrix Array Analysis Classification Package.

r-a4core

Homepage:
Spack package:
Versions:
1.32.0, 1.30.0, 1.28.0, 1.26.0, 1.24.0
Build Dependencies:
r, r-biobase, r-glmnet
Link Dependencies:
r
Run Dependencies:
r, r-biobase, r-glmnet
Description:
Automated Affymetrix Array Analysis Core Package.

r-a4preproc

Homepage:
Spack package:
Versions:
1.32.0, 1.30.0, 1.28.0, 1.26.0, 1.24.0
Build Dependencies:
r, r-annotationdbi
Link Dependencies:
r
Run Dependencies:
r, r-annotationdbi
Description:
Automated Affymetrix Array Analysis Preprocessing Package.

r-a4reporting

Homepage:
Spack package:
Versions:
1.32.0, 1.30.0, 1.28.0, 1.26.0, 1.24.0
Build Dependencies:
r, r-annaffy, r-xtable
Link Dependencies:
r
Run Dependencies:
r, r-annaffy, r-xtable
Description:
Automated Affymetrix Array Analysis Reporting Package.

r-abadata

Homepage:
Spack package:
Versions:
1.14.0, 1.12.0, 1.10.0, 1.8.0, 1.6.0
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Averaged gene expression in human brain regions from Allen Brain Atlas. Provides the data for the gene expression enrichment analysis conducted in the package 'ABAEnrichment'. The package includes three datasets which are derived from the Allen Brain Atlas: (1) Gene expression data from Human Brain (adults) averaged across donors, (2) Gene expression data from the Developing Human Brain pooled into five age categories and averaged across donors and (3) a developmental effect score based on the Developing Human Brain expression data. All datasets are restricted to protein coding genes.

r-abaenrichment

Homepage:
Spack package:
Versions:
1.14.1, 1.12.0, 1.10.0, 1.8.0, 1.6.0
Build Dependencies:
r, r-rcpp, r-gplots, r-gtools, r-abadata, r-data-table, r-gofuncr
Link Dependencies:
r
Run Dependencies:
r, r-rcpp, r-gplots, r-gtools, r-abadata, r-data-table, r-gofuncr
Description:
Gene expression enrichment in human brain regions. The package ABAEnrichment is designed to test for enrichment of user defined candidate genes in the set of expressed genes in different human brain regions. The core function 'aba_enrich' integrates the expression of the candidate gene set (averaged across donors) and the structural information of the brain using an ontology, both provided by the Allen Brain Atlas project. 'aba_enrich' interfaces the ontology enrichment software FUNC to perform the statistical analyses. Additional functions provided in this package like 'get_expression' and 'plot_expression' facilitate exploring the expression data, and besides the standard candidate vs. background gene set enrichment, also three additional tests are implemented, e.g. for cases when genes are ranked instead of divided into candidate and background.

r-abind

Homepage:
Spack package:
Versions:
1.4-5, 1.4-3
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Combine multidimensional arrays into a single array. This is a generalization of 'cbind' and 'rbind'. Works with vectors, matrices, and higher-dimensional arrays. Also provides functions 'adrop', 'asub', and 'afill' for manipulating, extracting and replacing data in arrays.

r-absseq

Homepage:
Spack package:
Versions:
1.38.0, 1.36.0, 1.34.1, 1.32.3, 1.22.8
Build Dependencies:
r, r-locfit, r-limma
Link Dependencies:
r
Run Dependencies:
r, r-locfit, r-limma
Description:
ABSSeq: a new RNA-Seq analysis method based on modelling absolute expression differences. Inferring differential expression genes by absolute counts difference between two groups, utilizing Negative binomial distribution and moderating fold-change according to heterogeneity of dispersion across expression level.

r-acde

Homepage:
Spack package:
Versions:
1.14.0, 1.12.0, 1.10.0, 1.8.0, 1.6.0
Build Dependencies:
r, r-boot
Link Dependencies:
r
Run Dependencies:
r, r-boot
Description:
Artificial Components Detection of Differentially Expressed Genes. This package provides a multivariate inferential analysis method for detecting differentially expressed genes in gene expression data. It uses artificial components, close to the data's principal components but with an exact interpretation in terms of differential genetic expression, to identify differentially expressed genes while controlling the false discovery rate (FDR). The methods on this package are described in the vignette or in the article 'Multivariate Method for Inferential Identification of Differentially Expressed Genes in Gene Expression Experiments' by J. P. Acosta, L. Lopez-Kleine and S. Restrepo (2015, pending publication).

r-acepack

Homepage:
Spack package:
Versions:
1.4.1
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
ACE and AVAS for Selecting Multiple Regression Transformations.

r-acgh

Homepage:
Spack package:
Versions:
1.62.0, 1.60.0, 1.58.0, 1.56.0, 1.54.0
Build Dependencies:
r, r-cluster, r-survival, r-multtest, r-biobase
Link Dependencies:
r
Run Dependencies:
r, r-cluster, r-survival, r-multtest, r-biobase
Description:
Classes and functions for Array Comparative Genomic Hybridization data.. Functions for reading aCGH data from image analysis output files and clone information files, creation of aCGH S3 objects for storing these data. Basic methods for accessing/replacing, subsetting, printing and plotting aCGH objects.

r-acme

Homepage:
Spack package:
Versions:
2.40.0, 2.38.0, 2.36.0, 2.34.0, 2.32.0
Build Dependencies:
r, r-biobase, r-biocgenerics
Link Dependencies:
r
Run Dependencies:
r, r-biobase, r-biocgenerics
Description:
Algorithms for Calculating Microarray Enrichment (ACME). ACME (Algorithms for Calculating Microarray Enrichment) is a set of tools for analysing tiling array ChIP/chip, DNAse hypersensitivity, or other experiments that result in regions of the genome showing "enrichment". It does not rely on a specific array technology (although the array should be a "tiling" array), is very general (can be applied in experiments resulting in regions of enrichment), and is very insensitive to array noise or normalization methods. It is also very fast and can be applied on whole-genome tiling array experiments quite easily with enough memory.

r-ada

Homepage:
Spack package:
Versions:
2.0-5
Build Dependencies:
r, r-rpart
Link Dependencies:
r
Run Dependencies:
r, r-rpart
Description:
Performs discrete, real, and gentle boost under both exponential and logistic loss on a given data set.

r-adabag

Homepage:
Spack package:
Versions:
4.2, 4.1
Build Dependencies:
r, r-rpart, r-mlbench, r-caret, r-foreach, r-doparallel
Link Dependencies:
r
Run Dependencies:
r, r-rpart, r-mlbench, r-caret, r-foreach, r-doparallel
Description:
Applies Multiclass AdaBoost.M1, SAMME and Bagging.

r-ade4

Homepage:
Spack package:
Versions:
1.7-13, 1.7-11, 1.7-6
Build Dependencies:
r, r-mass
Link Dependencies:
r
Run Dependencies:
r, r-mass
Description:
Analysis of Ecological Data : Exploratory and Euclidean Methods in Environmental Sciences

r-adegenet

Homepage:
Spack package:
Versions:
2.1.1, 2.1.0, 2.0.1
Build Dependencies:
r, r-ade4, r-mass, r-igraph, r-ape, r-shiny, r-ggplot2, r-seqinr, r-spdep, r-reshape2, r-dplyr, r-vegan, r-boot
Link Dependencies:
r
Run Dependencies:
r, r-ade4, r-mass, r-igraph, r-ape, r-shiny, r-ggplot2, r-seqinr, r-spdep, r-reshape2, r-dplyr, r-vegan, r-boot
Description:
Toolset for the exploration of genetic and genomic data. Adegenet provides formal (S4) classes for storing and handling various genetic data, including genetic markers with varying ploidy and hierarchical population structure ('genind' class), alleles counts by populations ('genpop'), and genome-wide SNP data ('genlight'). It also implements original multivariate methods (DAPC, sPCA), graphics, statistical tests, simulation tools, distance and similarity measures, and several spatial methods. A range of both empirical and simulated datasets is also provided to illustrate various methods.

r-adgoftest

Homepage:
Spack package:
Versions:
0.3
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Anderson-Darling GoF test with p-value calculation based on Marsaglia's 2004 paper 'Evaluating the Anderson-Darling Distribution'

r-adsplit

Homepage:
Spack package:
Versions:
1.54.0, 1.52.0, 1.50.0, 1.48.0, 1.46.0
Build Dependencies:
r, r-annotationdbi, r-biobase, r-cluster, r-go-db, r-kegg-db, r-multtest
Link Dependencies:
r
Run Dependencies:
r, r-annotationdbi, r-biobase, r-cluster, r-go-db, r-kegg-db, r-multtest
Description:
Annotation-Driven Clustering. This package implements clustering of microarray gene expression profiles according to functional annotations. For each term genes are annotated to, splits into two subclasses are computed and a significance of the supporting gene set is determined.

r-aer

Homepage:
Spack package:
Versions:
1.2-7, 1.2-6, 1.2-5
Build Dependencies:
r, r-car, r-lmtest, r-sandwich, r-survival, r-zoo, r-formula
Link Dependencies:
r
Run Dependencies:
r, r-car, r-lmtest, r-sandwich, r-survival, r-zoo, r-formula
Description:
Functions, data sets, examples, demos, and vignettes for the book Christian Kleiber and Achim Zeileis (2008), Applied Econometrics with R, Springer-Verlag, New York. ISBN 978-0-387-77316-2.

r-affxparser

Homepage:
Spack package:
Versions:
1.56.0, 1.54.0, 1.52.0, 1.50.0, 1.48.0
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Affymetrix File Parsing SDK. Package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP, BAR). It provides methods for fast and memory efficient parsing of Affymetrix files using the Affymetrix' Fusion SDK. Both ASCII- and binary-based files are supported. Currently, there are methods for reading chip definition file (CDF) and a cell intensity file (CEL). These files can be read either in full or in part. For example, probe signals from a few probesets can be extracted very quickly from a set of CEL files into a convenient list structure.

r-affy

Homepage:
Spack package:
Versions:
1.62.0, 1.60.0, 1.58.0, 1.56.0, 1.54.0
Build Dependencies:
r, r-biocgenerics, r-biobase, r-affyio, r-biocinstaller, r-preprocesscore, r-zlibbioc, r-biocmanager
Link Dependencies:
r
Run Dependencies:
r, r-biocgenerics, r-biobase, r-affyio, r-biocinstaller, r-preprocesscore, r-zlibbioc, r-biocmanager
Description:
Methods for Affymetrix Oligonucleotide Arrays. The package contains functions for exploratory oligonucleotide array analysis. The dependence on tkWidgets only concerns few convenience functions. 'affy' is fully functional without it.

r-affycomp

Homepage:
Spack package:
Versions:
1.60.0, 1.58.0, 1.56.0, 1.54.0, 1.52.0
Build Dependencies:
r, r-biobase
Link Dependencies:
r
Run Dependencies:
r, r-biobase
Description:
Graphics Toolbox for Assessment of Affymetrix Expression Measures. The package contains functions that can be used to compare expression measures for Affymetrix Oligonucleotide Arrays.

r-affycompatible

Homepage:
Spack package:
Versions:
1.44.0, 1.42.0, 1.40.0, 1.38.0, 1.36.0
Build Dependencies:
r, r-xml, r-rcurl, r-biostrings
Link Dependencies:
r
Run Dependencies:
r, r-xml, r-rcurl, r-biostrings
Description:
Affymetrix GeneChip software compatibility. This package provides an interface to Affymetrix chip annotation and sample attribute files. The package allows an easy way for users to download and manage local data bases of Affynmetrix NetAffx annotation files. The package also provides access to GeneChip Operating System (GCOS) and GeneChip Command Console (AGCC)-compatible sample annotation files.

r-affycontam

Homepage:
Spack package:
Versions:
1.42.0, 1.40.0, 1.38.0, 1.36.0, 1.34.0
Build Dependencies:
r, r-biobase, r-affy, r-affydata
Link Dependencies:
r
Run Dependencies:
r, r-biobase, r-affy, r-affydata
Description:
structured corruption of affymetrix cel file data. structured corruption of cel file data to demonstrate QA effectiveness

r-affycoretools

Homepage:
Spack package:
Versions:
1.56.0, 1.54.0, 1.52.2, 1.50.6, 1.48.0
Build Dependencies:
r, r-biobase, r-affy, r-limma, r-gostats, r-gcrma, r-xtable, r-annotationdbi, r-ggplot2, r-gplots, r-oligoclasses, r-reportingtools, r-hwriter, r-lattice, r-s4vectors, r-edger, r-rsqlite, r-biocgenerics, r-dbi
Link Dependencies:
r
Run Dependencies:
r, r-biobase, r-affy, r-limma, r-gostats, r-gcrma, r-xtable, r-annotationdbi, r-ggplot2, r-gplots, r-oligoclasses, r-reportingtools, r-hwriter, r-lattice, r-s4vectors, r-edger, r-rsqlite, r-biocgenerics, r-dbi
Description:
Functions useful for those doing repetitive analyses with Affymetrix GeneChips. Various wrapper functions that have been written to streamline the more common analyses that a core Biostatistician might see.

r-affydata

Homepage:
Spack package:
Versions:
1.32.0, 1.30.0, 1.28.0, 1.26.0, 1.24.0
Build Dependencies:
r, r-affy
Link Dependencies:
r
Run Dependencies:
r, r-affy
Description:
Affymetrix Data for Demonstration Purpose. Example datasets of a slightly large size. They represent 'real world examples', unlike the artificial examples included in the package affy.

r-affyexpress

Homepage:
Spack package:
Versions:
1.50.0, 1.48.0, 1.46.0, 1.44.0, 1.42.0
Build Dependencies:
r, r-affy, r-limma
Link Dependencies:
r
Run Dependencies:
r, r-affy, r-limma
Description:
Affymetrix Quality Assessment and Analysis Tool. The purpose of this package is to provide a comprehensive and easy-to- use tool for quality assessment and to identify differentially expressed genes in the Affymetrix gene expression data.

r-affyilm

Homepage:
Spack package:
Versions:
1.36.0, 1.34.0, 1.32.0, 1.30.0, 1.28.0
Build Dependencies:
r, r-gcrma, r-affxparser, r-affy, r-biobase
Link Dependencies:
r
Run Dependencies:
r, r-gcrma, r-affxparser, r-affy, r-biobase
Description:
Linear Model of background subtraction and the Langmuir isotherm. affyILM is a preprocessing tool which estimates gene expression levels for Affymetrix Gene Chips. Input from physical chemistry is employed to first background subtract intensities before calculating concentrations on behalf of the Langmuir model.

r-affyio

Homepage:
Spack package:
Versions:
1.54.0, 1.52.0, 1.50.0, 1.48.0, 1.46.0
Build Dependencies:
r, r-zlibbioc
Link Dependencies:
r
Run Dependencies:
r, r-zlibbioc
Description:
Tools for parsing Affymetrix data files. Routines for parsing Affymetrix data files based upon file format information. Primary focus is on accessing the CEL and CDF file formats.

r-affypdnn

Homepage:
Spack package:
Versions:
1.58.0, 1.56.0, 1.54.0, 1.52.0, 1.50.0
Build Dependencies:
r, r-affy
Link Dependencies:
r
Run Dependencies:
r, r-affy
Description:
Probe Dependent Nearest Neighbours (PDNN) for the affy package. The package contains functions to perform the PDNN method described by Li Zhang et al.

r-affyplm

Homepage:
Spack package:
Versions:
1.60.0, 1.58.0, 1.56.0, 1.54.0, 1.52.1
Build Dependencies:
r, r-biocgenerics, r-affy, r-biobase, r-gcrma, r-preprocesscore, r-zlibbioc
Link Dependencies:
r
Run Dependencies:
r, r-biocgenerics, r-affy, r-biobase, r-gcrma, r-preprocesscore, r-zlibbioc
Description:
Methods for fitting probe-level models. A package that extends and improves the functionality of the base affy package. Routines that make heavy use of compiled code for speed. Central focus is on implementation of methods for fitting probe-level models and tools using these models. PLM based quality assessment tools.

r-affyqcreport

Homepage:
Spack package:
Versions:
1.62.0, 1.60.0, 1.58.0, 1.56.0, 1.54.0
Build Dependencies:
r, r-biobase, r-affy, r-lattice, r-affyplm, r-genefilter, r-rcolorbrewer, r-simpleaffy, r-xtable
Link Dependencies:
r
Run Dependencies:
r, r-biobase, r-affy, r-lattice, r-affyplm, r-genefilter, r-rcolorbrewer, r-simpleaffy, r-xtable
Description:
QC Report Generation for affyBatch objects. This package creates a QC report for an AffyBatch object. The report is intended to allow the user to quickly assess the quality of a set of arrays in an AffyBatch object.

r-affyrnadegradation

Homepage:
Spack package:
Versions:
1.30.0, 1.28.0, 1.26.0, 1.24.0, 1.22.0
Build Dependencies:
r, r-affy
Link Dependencies:
r
Run Dependencies:
r, r-affy
Description:
Analyze and correct probe positional bias in microarray data due to RNA degradation. The package helps with the assessment and correction of RNA degradation effects in Affymetrix 3' expression arrays. The parameter d gives a robust and accurate measure of RNA integrity. The correction removes the probe positional bias, and thus improves comparability of samples that are affected by RNA degradation.

r-agdex

Homepage:
Spack package:
Versions:
1.32.0, 1.30.0, 1.28.0, 1.26.0, 1.24.0
Build Dependencies:
r, r-biobase, r-gseabase
Link Dependencies:
r
Run Dependencies:
r, r-biobase, r-gseabase
Description:
Agreement of Differential Expression Analysis. A tool to evaluate agreement of differential expression for cross- species genomics

r-agilp

Homepage:
Spack package:
Versions:
3.16.0, 3.14.0, 3.12.0, 3.10.0, 3.8.0
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Agilent expression array processing package. More about what it does (maybe more than one line)

r-agimicrorna

Homepage:
Spack package:
Versions:
2.34.0, 2.32.0, 2.30.0, 2.28.0, 2.26.0
Build Dependencies:
r, r-biobase, r-limma, r-affy, r-preprocesscore, r-affycoretools
Link Dependencies:
r
Run Dependencies:
r, r-biobase, r-limma, r-affy, r-preprocesscore, r-affycoretools
Description:
Processing and Differential Expression Analysis of Agilent microRNA chips.

r-aims

Homepage:
Spack package:
Versions:
1.16.0, 1.14.1, 1.12.0, 1.10.0, 1.8.0
Build Dependencies:
r, r-e1071, r-biobase
Link Dependencies:
r
Run Dependencies:
r, r-e1071, r-biobase
Description:
AIMS : Absolute Assignment of Breast Cancer Intrinsic Molecular Subtype. This package contains the AIMS implementation. It contains necessary functions to assign the five intrinsic molecular subtypes (Luminal A, Luminal B, Her2-enriched, Basal-like, Normal-like). Assignments could be done on individual samples as well as on dataset of gene expression data.

r-aldex2

Homepage:
Spack package:
Versions:
1.16.0, 1.14.1, 1.12.0, 1.10.0, 1.8.0
Build Dependencies:
r, r-s4vectors, r-iranges, r-genomicranges, r-summarizedexperiment, r-biocparallel, r-multtest
Link Dependencies:
r
Run Dependencies:
r, r-s4vectors, r-iranges, r-genomicranges, r-summarizedexperiment, r-biocparallel, r-multtest
Description:
Analysis Of Differential Abundance Taking Sample Variation Into Account. A differential abundance analysis for the comparison of two or more conditions. Useful for analyzing data from standard RNA-seq or meta-RNA- seq assays as well as selected and unselected values from in-vitro sequence selections. Uses a Dirichlet-multinomial model to infer abundance from counts, optimized for three or more experimental replicates. The method infers biological and sampling variation to calculate the expected false discovery rate, given the variation, based on a Wilcoxon Rank Sum test and Welch's t-test (via aldex.ttest), a Kruskal-Wallis test (via aldex.kw), a generalized linear model (via aldex.glm), or a correlation test (via aldex.corr). All tests report p-values and Benjamini-Hochberg corrected p-values.

r-alpine

Homepage:
Spack package:
Versions:
1.10.0, 1.8.0, 1.6.0, 1.4.0, 1.2.0
Build Dependencies:
r, r-biostrings, r-iranges, r-genomicranges, r-genomicalignments, r-rsamtools, r-summarizedexperiment, r-genomicfeatures, r-speedglm, r-graph, r-rbgl, r-stringr, r-genomeinfodb, r-s4vectors
Link Dependencies:
r
Run Dependencies:
r, r-biostrings, r-iranges, r-genomicranges, r-genomicalignments, r-rsamtools, r-summarizedexperiment, r-genomicfeatures, r-speedglm, r-graph, r-rbgl, r-stringr, r-genomeinfodb, r-s4vectors
Description:
alpine. Fragment sequence bias modeling and correction for RNA-seq transcript abundance estimation.

r-als

Homepage:
Spack package:
Versions:
0.0.6
Build Dependencies:
r, r-iso, r-nnls
Link Dependencies:
r
Run Dependencies:
r, r-iso, r-nnls
Description:
Alternating least squares is often used to resolve components contributing to data with a bilinear structure; the basic technique may be extended to alternating constrained least squares. Commonly applied constraints include unimodality, non-negativity, and normalization of components. Several data matrices may be decomposed simultaneously by assuming that one of the two matrices in the bilinear decomposition is shared between datasets.

r-alsace

Homepage:
Spack package:
Versions:
1.20.0, 1.18.0, 1.16.0, 1.14.0, 1.12.0
Build Dependencies:
r, r-als, r-ptw
Link Dependencies:
r
Run Dependencies:
r, r-als, r-ptw
Description:
ALS for the Automatic Chemical Exploration of mixtures. Alternating Least Squares (or Multivariate Curve Resolution) for analytical chemical data, in particular hyphenated data where the first direction is a retention time axis, and the second a spectral axis. Package builds on the basic als function from the ALS package and adds functionality for high-throughput analysis, including definition of time windows, clustering of profiles, retention time correction, etcetera.

r-altcdfenvs

Homepage:
Spack package:
Versions:
2.46.0, 2.44.0, 2.42.0, 2.40.0, 2.38.0
Build Dependencies:
r, r-biocgenerics, r-s4vectors, r-biobase, r-affy, r-makecdfenv, r-biostrings, r-hypergraph
Link Dependencies:
r
Run Dependencies:
r, r-biocgenerics, r-s4vectors, r-biobase, r-affy, r-makecdfenv, r-biostrings, r-hypergraph
Description:
alternative CDF environments (aka probeset mappings). Convenience data structures and functions to handle cdfenvs

r-amap

Homepage:
Spack package:
Versions:
0.8-17, 0.8-16
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Tools for Clustering and Principal Component Analysis (With robust methods, and parallelized functions).

r-ampliqueso

Homepage:
Spack package:
Versions:
1.21.0, 1.20.0, 1.18.0, 1.16.0, 1.14.0
Build Dependencies:
r, r-rnaseqmap, r-knitr, r-rgl, r-ggplot2, r-gplots, r-doparallel, r-foreach, r-variantannotation, r-genefilter, r-statmod, r-xtable, r-edger, r-deseq, r-samr
Link Dependencies:
r
Run Dependencies:
r, r-rnaseqmap, r-knitr, r-rgl, r-ggplot2, r-gplots, r-doparallel, r-foreach, r-variantannotation, r-genefilter, r-statmod, r-xtable, r-edger, r-deseq, r-samr
Description:
Analysis of amplicon enrichment panels. The package provides tools and reports for the analysis of amplicon sequencing panels, such as AmpliSeq

r-analysispageserver

Homepage:
Spack package:
Versions:
1.18.1, 1.16.0, 1.14.0, 1.12.0, 1.10.0
Build Dependencies:
r, r-log4r, r-rjson, r-biobase, r-graph
Link Dependencies:
r
Run Dependencies:
r, r-log4r, r-rjson, r-biobase, r-graph
Description:
A framework for sharing interactive data and plots from R through the web. AnalysisPageServer is a modular system that enables sharing of customizable R analyses via the web.

r-anaquin

Homepage:
Spack package:
Versions:
2.8.0, 2.6.1, 2.4.0, 2.2.0, 1.2.0
Build Dependencies:
r, r-ggplot2, r-rocr, r-knitr, r-qvalue, r-locfit, r-plyr, r-deseq2
Link Dependencies:
r
Run Dependencies:
r, r-ggplot2, r-rocr, r-knitr, r-qvalue, r-locfit, r-plyr, r-deseq2
Description:
Statistical analysis of sequins. The project is intended to support the use of sequins (synthetic sequencing spike-in controls) owned and made available by the Garvan Institute of Medical Research. The goal is to provide a standard open source library for quantitative analysis, modelling and visualization of spike-in controls.

r-aneufinder

Homepage:
Spack package:
Versions:
1.12.1, 1.10.2, 1.8.0, 1.6.0, 1.4.0
Build Dependencies:
r, r-genomicranges, r-cowplot, r-aneufinderdata, r-foreach, r-doparallel, r-biocgenerics, r-s4vectors, r-genomeinfodb, r-iranges, r-rsamtools, r-bamsignals, r-dnacopy, r-biostrings, r-genomicalignments, r-ggplot2, r-reshape2, r-ggdendro, r-ggrepel, r-reordercluster, r-mclust, r-ecp
Link Dependencies:
r
Run Dependencies:
r, r-genomicranges, r-cowplot, r-aneufinderdata, r-foreach, r-doparallel, r-biocgenerics, r-s4vectors, r-genomeinfodb, r-iranges, r-rsamtools, r-bamsignals, r-dnacopy, r-biostrings, r-genomicalignments, r-ggplot2, r-reshape2, r-ggdendro, r-ggrepel, r-reordercluster, r-mclust, r-ecp
Description:
Analysis of Copy Number Variation in Single-Cell-Sequencing Data. AneuFinder implements functions for copy-number detection, breakpoint detection, and karyotype and heterogeneity analysis in single-cell whole genome sequencing and strand-seq data.

r-aneufinderdata

Homepage:
Spack package:
Versions:
1.12.0, 1.10.0, 1.8.0, 1.6.0, 1.4.0
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
WGSCS Data for Demonstration Purposes. Whole-genome single cell sequencing data for demonstration purposes in the AneuFinder package.

r-animation

Homepage:
Spack package:
Versions:
2.6, 2.5
Build Dependencies:
r, r-magick, imagemagick, ffmpeg, swftools, texlive
Link Dependencies:
r, imagemagick, ffmpeg, swftools, texlive
Run Dependencies:
r, r-magick
Description:
Provides functions for animations in statistics, covering topics in probability theory, mathematical statistics, multivariate statistics, non-parametric statistics, sampling survey, linear models, time series, computational statistics, data mining and machine learning. These functions maybe helpful in teaching statistics and data analysis.

r-annaffy

Homepage:
Spack package:
Versions:
1.56.0, 1.54.0, 1.52.0, 1.50.0, 1.48.0
Build Dependencies:
r, r-biobase, r-go-db, r-kegg-db, r-annotationdbi, r-dbi
Link Dependencies:
r
Run Dependencies:
r, r-biobase, r-go-db, r-kegg-db, r-annotationdbi, r-dbi
Description:
Annotation tools for Affymetrix biological metadata. Functions for handling data from Bioconductor Affymetrix annotation data packages. Produces compact HTML and text reports including experimental data and URL links to many online databases. Allows searching biological metadata using various criteria.

r-annotate

Homepage:
Spack package:
Versions:
1.62.0, 1.60.1, 1.58.0, 1.56.2, 1.54.0
Build Dependencies:
r, r-annotationdbi, r-xml, r-biobase, r-dbi, r-xtable, r-biocgenerics, r-rcurl
Link Dependencies:
r
Run Dependencies:
r, r-annotationdbi, r-xml, r-biobase, r-dbi, r-xtable, r-biocgenerics, r-rcurl
Description:
Annotation for microarrays. Using R enviroments for annotation.

r-annotationdbi

Homepage:
Spack package:
Versions:
1.46.1, 1.44.0, 1.42.1, 1.40.0, 1.38.2
Build Dependencies:
r, r-biocgenerics, r-biobase, r-iranges, r-dbi, r-rsqlite, r-s4vectors
Link Dependencies:
r
Run Dependencies:
r, r-biocgenerics, r-biobase, r-iranges, r-dbi, r-rsqlite, r-s4vectors
Description:
Manipulation of SQLite-based annotations in Bioconductor. Implements a user-friendly interface for querying SQLite-based annotation data packages.

r-annotationfilter

Homepage:
Spack package:
Versions:
1.8.0, 1.6.0, 1.4.0, 1.2.0, 1.0.0
Build Dependencies:
r, r-genomicranges, r-lazyeval
Link Dependencies:
r
Run Dependencies:
r, r-genomicranges, r-lazyeval
Description:
Facilities for Filtering Bioconductor Annotation Resources. This package provides class and other infrastructure to implement filters for manipulating Bioconductor annotation resources. The filters will be used by ensembldb, Organism.dplyr, and other packages.

r-annotationforge

Homepage:
Spack package:
Versions:
1.26.0, 1.24.0, 1.22.2, 1.20.0, 1.18.2
Build Dependencies:
r, r-biocgenerics, r-biobase, r-annotationdbi, r-dbi, r-rsqlite, r-xml, r-s4vectors, r-rcurl
Link Dependencies:
r
Run Dependencies:
r, r-biocgenerics, r-biobase, r-annotationdbi, r-dbi, r-rsqlite, r-xml, r-s4vectors, r-rcurl
Description:
Tools for building SQLite-based annotation data packages. Provides code for generating Annotation packages and their databases. Packages produced are intended to be used with AnnotationDbi.

r-annotationhub

Homepage:
Spack package:
Versions:
2.16.1, 2.14.5, 2.12.1, 2.10.1, 2.8.3
Build Dependencies:
r, r-biocgenerics, r-rsqlite, r-biocinstaller, r-annotationdbi, r-s4vectors, r-interactivedisplaybase, r-httr, r-yaml, r-curl, r-biocmanager, r-biocfilecache, r-rappdirs, r-dplyr
Link Dependencies:
r
Run Dependencies:
r, r-biocgenerics, r-rsqlite, r-biocinstaller, r-annotationdbi, r-s4vectors, r-interactivedisplaybase, r-httr, r-yaml, r-curl, r-biocmanager, r-biocfilecache, r-rappdirs, r-dplyr
Description:
Client to access AnnotationHub resources. This package provides a client for the Bioconductor AnnotationHub web resource. The AnnotationHub web resource provides a central location where genomic files (e.g., VCF, bed, wig) and other resources from standard locations (e.g., UCSC, Ensembl) can be discovered. The resource includes metadata about each resource, e.g., a textual description, tags, and date of modification. The client creates and manages a local cache of files retrieved by the user, helping with quick and reproducible access.

r-aod

Homepage:
Spack package:
Versions:
1.3.1
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Provides a set of functions to analyse overdispersed counts or proportions. Most of the methods are already available elsewhere but are scattered in different packages. The proposed functions should be considered as complements to more sophisticated methods such as generalized estimating equations (GEE) or generalized linear mixed effect models (GLMM).

r-ape

Homepage:
Spack package:
Versions:
5.3, 5.2, 5.1, 5.0, 4.1
Build Dependencies:
r, r-nlme, r-lattice, r-rcpp
Link Dependencies:
r
Run Dependencies:
r, r-nlme, r-lattice, r-rcpp
Description:
Functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from DNA sequences, reading and writing nucleotide sequences as well as importing from BioConductor, and several tools such as Mantel's test, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean path lengths and penalized likelihood, dating trees with non- contemporaneous sequences, translating DNA into AA sequences, and assessing sequence alignments. Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and several methods handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions call external applications (PhyML, Clustal, T-Coffee, Muscle) whose results are returned into R.

r-argparse

Homepage:
Spack package:
Versions:
2.0.1, 1.1.1
Build Dependencies:
r, r-proto, r-getopt, r-r6, r-findpython, r-jsonlite
Link Dependencies:
r
Run Dependencies:
r, r-proto, r-getopt, r-r6, r-findpython, r-jsonlite
Description:
A command line parser to be used with Rscript to write "#!" shebang scripts that gracefully accept positional and optional arguments and automatically generate usage.

r-aroma-light

Homepage:
Spack package:
Versions:
3.16.0
Build Dependencies:
r, r-r-methodss3, r-r-oo, r-r-utils, r-matrixstats
Link Dependencies:
r
Run Dependencies:
r, r-r-methodss3, r-r-oo, r-r-utils, r-matrixstats
Description:
Methods for microarray analysis that take basic data types such as matrices and lists of vectors. These methods can be used standalone, be utilized in other packages, or be wrapped up in higher-level classes.

r-askpass

Homepage:
Spack package:
Versions:
1.1
Build Dependencies:
r, r-sys
Link Dependencies:
r
Run Dependencies:
r, r-sys
Description:
Cross-platform utilities for prompting the user for credentials or a passphrase, for example to authenticate with a server or read a protected key. Includes native programs for MacOS and Windows, hence no 'tcltk' is required. Password entry can be invoked in two different ways: directly from R via the askpass() function, or indirectly as password-entry back-end for 'ssh-agent' or 'git-credential' via the SSH_ASKPASS and GIT_ASKPASS environment variables. Thereby the user can be prompted for credentials or a passphrase if needed when R calls out to git or ssh.

r-assertthat

Homepage:
Spack package:
Versions:
0.2.1, 0.2.0, 0.1
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
assertthat is an extension to stopifnot() that makes it easy to declare the pre and post conditions that you code should satisfy, while also producing friendly error messages so that your users know what they've done wrong.

r-backports

Homepage:
Spack package:
Versions:
1.1.4, 1.1.3, 1.1.1, 1.1.0
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Implementations of functions which have been introduced in R since version 3.0.0. The backports are conditionally exported which results in R resolving the function names to the version shipped with R (if available) and uses the implemented backports as fallback. This way package developers can make use of the new functions without worrying about the minimum required R version.

r-bamsignals

Homepage:
Spack package:
Versions:
1.16.0, 1.14.0, 1.12.1, 1.10.0, 1.8.0
Build Dependencies:
r, r-biocgenerics, r-rcpp, r-iranges, r-genomicranges, r-zlibbioc, r-rhtslib
Link Dependencies:
r
Run Dependencies:
r, r-biocgenerics, r-rcpp, r-iranges, r-genomicranges, r-zlibbioc, r-rhtslib
Description:
Extract read count signals from bam files. This package allows to efficiently obtain count vectors from indexed bam files. It counts the number of reads in given genomic ranges and it computes reads profiles and coverage profiles. It also handles paired- end data.

r-base64

Homepage:
Spack package:
Versions:
2.0
Build Dependencies:
r, r-openssl
Link Dependencies:
r
Run Dependencies:
r, r-openssl
Description:
Compatibility wrapper to replace the orphaned package by Romain Francois. New applications should use the 'openssl' or 'base64enc' package instead.

r-base64enc

Homepage:
Spack package:
Versions:
0.1-3
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
This package provides tools for handling base64 encoding. It is more flexible than the orphaned base64 package.

r-bayesm

Homepage:
Spack package:
Versions:
3.1-3, 3.1-2, 3.1-1, 3.1-0.1
Build Dependencies:
r, r-rcpp, r-rcpparmadillo
Link Dependencies:
r
Run Dependencies:
r, r-rcpp, r-rcpparmadillo
Description:
Bayesian Inference for Marketing/Micro-Econometrics

r-bbmisc

Homepage:
Spack package:
Versions:
1.11
Build Dependencies:
r, r-checkmate
Link Dependencies:
r
Run Dependencies:
r, r-checkmate
Description:
Miscellaneous helper functions for and from B. Bischl and some other guys, mainly for package development.

r-beachmat

Homepage:
Spack package:
Versions:
2.0.0, 1.4.0, 1.2.1, 1.0.2
Build Dependencies:
r, r-rhdf5lib, r-hdf5array, r-delayedarray, r-rcpp, r-rhdf5, r-biocgenerics
Link Dependencies:
r
Run Dependencies:
r, r-rhdf5lib, r-hdf5array, r-delayedarray, r-rcpp, r-rhdf5, r-biocgenerics
Description:
Compiling Bioconductor to Handle Each Matrix Type. Provides a consistent C++ class interface for reading from and writing data to a variety of commonly used matrix types. Ordinary matrices and several sparse/dense Matrix classes are directly supported, third-party S4 classes may be supported by external linkage, while all other matrices are handled by DelayedArray block processing.

r-beanplot

Homepage:
Spack package:
Versions:
1.2
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Plots univariate comparison graphs, an alternative to boxplot/stripchart/violin plot.

r-beeswarm

Homepage:
Spack package:
Versions:
0.2.3
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
beeswarm: The Bee Swarm Plot, an Alternative to Stripchart

r-bfast

Homepage:
Spack package:
Versions:
1.5.7
Build Dependencies:
r, r-strucchange, r-zoo, r-forecast, r-sp, r-raster
Link Dependencies:
r
Run Dependencies:
r, r-strucchange, r-zoo, r-forecast, r-sp, r-raster
Description:
bfast: Breaks For Additive Season and Trend (BFAST)

r-bfastspatial

Homepage:
Spack package:
Versions:
0.6.2
Build Dependencies:
r, r-raster, r-bfast, r-gdalutils, r-stringr, r-rgdal, r-bitops, r-zoo, r-sp
Link Dependencies:
r
Run Dependencies:
r, r-raster, r-bfast, r-gdalutils, r-stringr, r-rgdal, r-bitops, r-zoo, r-sp
Description:
Pre-process gridded time-series data in order for them to be analyzed with change detection algorithms such as bfast. Uses classes from the raster package and includes utilities to run the algorithms and post- process the results.

r-bglr

Homepage:
Spack package:
Versions:
1.0.8
Build Dependencies:
r, r-truncnorm
Link Dependencies:
r
Run Dependencies:
r, r-truncnorm
Description:
BGLR: Bayesian Generalized Linear Regression

r-bh

Homepage:
Spack package:
Versions:
1.69.0-1, 1.65.0-1, 1.60.0-2
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Boost provides free peer-reviewed portable C++ source libraries. A large part of Boost is provided as C++ template code which is resolved entirely at compile-time without linking. This package aims to provide the most useful subset of Boost libraries for template use among CRAN package. By placing these libraries in this package, we offer a more efficient distribution system for CRAN as replication of this code in the sources of other packages is avoided. As of release 1.60.0-2, the following Boost libraries are included: 'algorithm' 'any' 'bimap' 'bind' 'circular_buffer' 'concept' 'config' 'container' 'date'_'time' 'detail' 'dynamic_bitset' 'exception' 'filesystem' 'flyweight' 'foreach' 'functional' 'fusion' 'geometry' 'graph' 'heap' 'icl' 'integer' 'interprocess' 'intrusive' 'io' 'iostreams' 'iterator' 'math' 'move' 'mpl' 'multiprcecision' 'numeric' 'pending' 'phoenix' 'preprocessor' 'random' 'range' 'smart_ptr' 'spirit' 'tuple' 'type_trains' 'typeof' 'unordered' 'utility' 'uuid'.

r-biasedurn

Homepage:
Spack package:
Versions:
1.07
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Statistical models of biased sampling in the form of univariate and multivariate noncentral hypergeometric distributions, including Wallenius' noncentral hypergeometric distribution and Fisher's noncentral hypergeometric distribution (also called extended hypergeometric distribution). See vignette("UrnTheory") for explanation of these distributions.

r-bibtex

Homepage:
Spack package:
Versions:
0.4.2
Build Dependencies:
r, r-stringr
Link Dependencies:
r
Run Dependencies:
r, r-stringr
Description:
bibtex: Bibtex Parser Utility to parse a bibtex file.

r-bindr

Homepage:
Spack package:
Versions:
0.1.1, 0.1
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Provides a simple interface for creating active bindings where the bound function accepts additional arguments.

r-bindrcpp

Homepage:
Spack package:
Versions:
0.2.2, 0.2
Build Dependencies:
r, r-rcpp, r-bindr, r-plogr
Link Dependencies:
r
Run Dependencies:
r, r-rcpp, r-bindr, r-plogr
Description:
Provides an easy way to fill an environment with active bindings that call a C++ function.

r-bio3d

Homepage:
Spack package:
Versions:
2.3-4
Build Dependencies:
r, r-rcpp
Link Dependencies:
r
Run Dependencies:
r, r-rcpp
Description:
bio3d: Biological Structure Analysis

r-biobase

Homepage:
Spack package:
Versions:
2.44.0, 2.42.0, 2.40.0, 2.38.0, 2.36.2
Build Dependencies:
r, r-biocgenerics
Link Dependencies:
r
Run Dependencies:
r, r-biocgenerics
Description:
Biobase: Base functions for Bioconductor. Functions that are needed by many other packages or which replace R functions.

r-biocfilecache

Homepage:
Spack package:
Versions:
1.8.0, 1.6.0, 1.4.0, 1.2.3, 1.0.1
Build Dependencies:
r, r-dbplyr, r-dplyr, r-rsqlite, r-dbi, r-rappdirs, r-httr, r-curl
Link Dependencies:
r
Run Dependencies:
r, r-dbplyr, r-dplyr, r-rsqlite, r-dbi, r-rappdirs, r-httr, r-curl
Description:
Manage Files Across Sessions. This package creates a persistent on-disk cache of files that the user can add, update, and retrieve. It is useful for managing resources (such as custom Txdb objects) that are costly or difficult to create, web resources, and data files used across sessions.

r-biocgenerics

Homepage:
Spack package:
Versions:
0.30.0, 0.28.0, 0.26.0, 0.24.0, 0.22.1
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
S4 generic functions used in Bioconductor. The package defines S4 generic functions used in Bioconductor.

r-biocinstaller

Homepage:
Spack package:
Versions:
1.33.1, 1.32.1, 1.30.0, 1.28.0, 1.26.1
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Install/Update Bioconductor, CRAN, and github Packages. This package is used to install and update Bioconductor, CRAN, and (some) github packages.

r-biocmanager

Homepage:
Spack package:
Versions:
1.30.10
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
BiocManager: Access the Bioconductor Project Package Repository

r-biocneighbors

Homepage:
Spack package:
Versions:
1.2.0, 1.0.0
Build Dependencies:
r, r-biocparallel, r-rcpp, r-s4vectors, r-rcppannoy, r-biocgenerics, r-rcpphnsw
Link Dependencies:
r
Run Dependencies:
r, r-biocparallel, r-rcpp, r-s4vectors, r-rcppannoy, r-biocgenerics, r-rcpphnsw
Description:
Nearest Neighbor Detection for Bioconductor Packages. Implements exact and approximate methods for nearest neighbor detection, in a framework that allows them to be easily switched within Bioconductor packages or workflows. Exact searches can be performed using the k-means for k-nearest neighbors algorithm or with vantage point trees. Approximate searches can be performed using the Annoy or HNSW libraries. Searching on either Euclidean or Manhattan distances is supported. Parallelization is achieved for all methods by using BiocParallel. Functions are also provided to search for all neighbors within a given distance.

r-biocparallel

Homepage:
Spack package:
Versions:
1.18.1, 1.16.6, 1.14.2, 1.12.0, 1.10.1
Build Dependencies:
r, r-futile-logger, r-snow, r-bh
Link Dependencies:
r
Run Dependencies:
r, r-futile-logger, r-snow, r-bh
Description:
Bioconductor facilities for parallel evaluation. This package provides modified versions and novel implementation of functions for parallel evaluation, tailored to use with Bioconductor objects.

r-biocsingular

Homepage:
Spack package:
Versions:
1.0.0
Build Dependencies:
r, r-biocgenerics, r-s4vectors, r-matrix, r-delayedarray, r-biocparallel, r-irlba, r-rsvd, r-rcpp, r-beachmat
Link Dependencies:
r
Run Dependencies:
r, r-biocgenerics, r-s4vectors, r-matrix, r-delayedarray, r-biocparallel, r-irlba, r-rsvd, r-rcpp, r-beachmat
Description:
Singular Value Decomposition for Bioconductor Packages. Implements exact and approximate methods for singular value decomposition and principal components analysis, in a framework that allows them to be easily switched within Bioconductor packages or workflows. Where possible, parallelization is achieved using the BiocParallel framework.

r-biocstyle

Homepage:
Spack package:
Versions:
2.12.0, 2.10.0, 2.8.2, 2.6.1, 2.4.1
Build Dependencies:
r, r-bookdown, r-knitr, r-rmarkdown, r-yaml, r-biocmanager
Link Dependencies:
r
Run Dependencies:
r, r-bookdown, r-knitr, r-rmarkdown, r-yaml, r-biocmanager
Description:
Standard styles for vignettes and other Bioconductor documents. Provides standard formatting styles for Bioconductor PDF and HTML documents. Package vignettes illustrate use and functionality.

r-biom-utils

Homepage:
Spack package:
Versions:
0.9
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Provides utilities to facilitate import, export and computation with the BIOM (Biological Observation Matrix) format (http://biom-format.org).

r-biomart

Homepage:
Spack package:
Versions:
2.40.5, 2.38.0, 2.36.1, 2.34.2, 2.32.1
Build Dependencies:
r, r-xml, r-rcurl, r-annotationdbi, r-progress, r-stringr, r-httr
Link Dependencies:
r
Run Dependencies:
r, r-xml, r-rcurl, r-annotationdbi, r-progress, r-stringr, r-httr
Description:
Interface to BioMart databases (i.e. Ensembl). In recent years a wealth of biological data has become available in public data repositories. Easy access to these valuable data resources and firm integration with data analysis is needed for comprehensive bioinformatics data analysis. biomaRt provides an interface to a growing collection of databases implementing the BioMart software suite (<http://www.biomart.org>). The package enables retrieval of large amounts of data in a uniform way without the need to know the underlying database schemas or write complex SQL queries. The most prominent examples of BioMart databases are maintain by Ensembl, which provides biomaRt users direct access to a diverse set of data and enables a wide range of powerful online queries from gene annotation to database mining.

r-biomartr

Homepage:
Spack package:
Versions:
0.9.2
Build Dependencies:
r, r-biomart, r-biostrings, r-curl, r-tibble, r-jsonlite, r-data-table, r-dplyr, r-readr, r-downloader, r-rcurl, r-xml, r-httr, r-stringr, r-purrr, r-r-utils, r-philentropy, r-fs
Link Dependencies:
r
Run Dependencies:
r, r-biomart, r-biostrings, r-curl, r-tibble, r-jsonlite, r-data-table, r-dplyr, r-readr, r-downloader, r-rcurl, r-xml, r-httr, r-stringr, r-purrr, r-r-utils, r-philentropy, r-fs
Description:
Perform large scale genomic data retrieval and functional annotation retrieval. This package aims to provide users with a standardized way to automate genome, proteome, 'RNA', coding sequence ('CDS'), 'GFF', and metagenome retrieval from 'NCBI RefSeq', 'NCBI Genbank', 'ENSEMBL', 'ENSEMBLGENOMES', and 'UniProt' databases. Furthermore, an interface to the 'BioMart' database (Smedley et al. (2009) <doi:10.1186/1471-2164-10-22>) allows users to retrieve functional annotation for genomic loci. In addition, users can download entire databases such as 'NCBI RefSeq' (Pruitt et al. (2007) <doi:10.1093/nar/gkl842>), 'NCBI nr', 'NCBI nt', 'NCBI Genbank' (Benson et al. (2013) <doi:10.1093/nar/gks1195>), etc. as well as 'ENSEMBL' and 'ENSEMBLGENOMES' with only one command.

r-biomformat

Homepage:
Spack package:
Versions:
1.12.0, 1.10.1, 1.8.0, 1.6.0, 1.4.0
Build Dependencies:
r, r-plyr, r-jsonlite, r-matrix, r-rhdf5
Link Dependencies:
r
Run Dependencies:
r, r-plyr, r-jsonlite, r-matrix, r-rhdf5
Description:
An interface package for the BIOM file format. This is an R package for interfacing with the BIOM format. This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object (which is more complex than a single table), as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format project, but with a decidedly "R flavor" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods.

r-biostrings

Homepage:
Spack package:
Versions:
2.52.0, 2.50.2, 2.48.0, 2.46.0, 2.44.2
Build Dependencies:
r, r-biocgenerics, r-s4vectors, r-iranges, r-xvector
Link Dependencies:
r
Run Dependencies:
r, r-biocgenerics, r-s4vectors, r-iranges, r-xvector
Description:
Efficient manipulation of biological strings. Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences.

r-biovizbase

Homepage:
Spack package:
Versions:
1.32.0, 1.30.1, 1.28.2, 1.26.0, 1.24.0
Build Dependencies:
r, r-scales, r-hmisc, r-rcolorbrewer, r-dichromat, r-biocgenerics, r-s4vectors, r-iranges, r-genomeinfodb, r-genomicranges, r-summarizedexperiment, r-biostrings, r-rsamtools, r-genomicalignments, r-genomicfeatures, r-annotationdbi, r-variantannotation, r-ensembldb, r-annotationfilter, r-rlang
Link Dependencies:
r
Run Dependencies:
r, r-scales, r-hmisc, r-rcolorbrewer, r-dichromat, r-biocgenerics, r-s4vectors, r-iranges, r-genomeinfodb, r-genomicranges, r-summarizedexperiment, r-biostrings, r-rsamtools, r-genomicalignments, r-genomicfeatures, r-annotationdbi, r-variantannotation, r-ensembldb, r-annotationfilter, r-rlang
Description:
Basic graphic utilities for visualization of genomic data.. The biovizBase package is designed to provide a set of utilities, color schemes and conventions for genomic data. It serves as the base for various high-level packages for biological data visualization. This saves development effort and encourages consistency.

r-bit

Homepage:
Spack package:
Versions:
1.1-14, 1.1-12
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
A class for vectors of 1-bit booleans.

r-bit64

Homepage:
Spack package:
Versions:
0.9-7
Build Dependencies:
r, r-bit
Link Dependencies:
r
Run Dependencies:
r, r-bit
Description:
Package 'bit64' provides serializable S3 atomic 64bit (signed) integers. These are useful for handling database keys and exact counting in +-2^63. WARNING: do not use them as replacement for 32bit integers, integer64 are not supported for subscripting by R-core and they have different semantics when combined with double, e.g. integer64 + double => integer64. Class integer64 can be used in vectors, matrices, arrays and data.frames. Methods are available for coercion from and to logicals, integers, doubles, characters and factors as well as many elementwise and summary functions. Many fast algorithmic operations such as 'match' and 'order' support inter- active data exploration and manipulation and optionally leverage caching.

r-bitops

Homepage:
Spack package:
Versions:
1.0-6
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Functions for bitwise operations on integer vectors.

r-blob

Homepage:
Spack package:
Versions:
1.2.0, 1.1.0
Build Dependencies:
r, r-tibble, r-prettyunits, r-rlang, r-vctrs
Link Dependencies:
r
Run Dependencies:
r, r-tibble, r-prettyunits, r-rlang, r-vctrs
Description:
R's raw vector is useful for storing a single binary object. What if you want to put a vector of them in a data frame? The blob package provides the blob object, a list of raw vectors, suitable for use as a column in data frame.

r-blockmodeling

Homepage:
Spack package:
Versions:
0.3.4, 0.3.1
Build Dependencies:
r, r-matrix, r-doparallel, r-dorng, r-foreach
Link Dependencies:
r
Run Dependencies:
r, r-matrix, r-doparallel, r-dorng, r-foreach
Description:
blockmodeling: Generalized and Classical Blockmodeling of Valued Networks

r-bmp

Homepage:
Spack package:
Versions:
0.3
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Reads Windows BMP format images. Currently limited to 8 bit greyscale images and 24,32 bit (A)RGB images. Pure R implementation without external dependencies.

r-bookdown

Homepage:
Spack package:
Versions:
0.12, 0.5
Build Dependencies:
r, r-yaml, r-rmarkdown, r-knitr, r-htmltools, r-xfun, r-tinytex, pandoc
Link Dependencies:
r, pandoc
Run Dependencies:
r, r-yaml, r-rmarkdown, r-knitr, r-htmltools, r-xfun, r-tinytex
Description:
Output formats and utilities for authoring books and technical documents with R Markdown.

r-boot

Homepage:
Spack package:
Versions:
1.3-23, 1.3-22, 1.3-20, 1.3-18
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Functions and datasets for bootstrapping from the book "Bootstrap Methods and Their Application" by A. C. Davison and D. V. Hinkley (1997, CUP), originally written by Angelo Canty for S.

r-brew

Homepage:
Spack package:
Versions:
1.0-6
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
brew implements a templating framework for mixing text and R code for report generation. brew template syntax is similar to PHP, Ruby's erb module, Java Server Pages, and Python's psp module.

r-broom

Homepage:
Spack package:
Versions:
0.5.2, 0.5.1, 0.4.2
Build Dependencies:
r, r-plyr, r-dplyr, r-tidyr, r-psych, r-stringr, r-reshape2, r-nlme, r-backports, r-generics, r-purrr, r-tibble
Link Dependencies:
r
Run Dependencies:
r, r-plyr, r-dplyr, r-tidyr, r-psych, r-stringr, r-reshape2, r-nlme, r-backports, r-generics, r-purrr, r-tibble
Description:
Convert statistical analysis objects from R into tidy data frames, so that they can more easily be combined, reshaped and otherwise processed with tools like 'dplyr', 'tidyr' and 'ggplot2'. The package provides three S3 generics: tidy, which summarizes a model's statistical findings such as coefficients of a regression; augment, which adds columns to the original data such as predictions, residuals and cluster assignments; and glance, which provides a one-row summary of model-level statistics.

r-bsgenome

Homepage:
Spack package:
Versions:
1.52.0, 1.50.0, 1.48.0, 1.46.0, 1.44.2
Build Dependencies:
r, r-biocgenerics, r-s4vectors, r-iranges, r-genomeinfodb, r-genomicranges, r-biostrings, r-rtracklayer, r-xvector, r-rsamtools
Link Dependencies:
r
Run Dependencies:
r, r-biocgenerics, r-s4vectors, r-iranges, r-genomeinfodb, r-genomicranges, r-biostrings, r-rtracklayer, r-xvector, r-rsamtools
Description:
Software infrastructure for efficient representation of full genomes and their SNPs.

r-bsgenome-hsapiens-ucsc-hg19

Homepage:
Spack package:
Versions:
1.4.0
Build Dependencies:
r, r-bsgenome
Link Dependencies:
r
Run Dependencies:
r, r-bsgenome
Description:
Full genome sequences for Homo sapiens (Human) as provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects.

r-bumphunter

Homepage:
Spack package:
Versions:
1.26.0, 1.24.5, 1.22.0, 1.20.0, 1.16.0
Build Dependencies:
r, r-s4vectors, r-iranges, r-genomeinfodb, r-genomicranges, r-foreach, r-iterators, r-locfit, r-matrixstats, r-limma, r-dorng, r-biocgenerics, r-genomicfeatures, r-annotationdbi
Link Dependencies:
r
Run Dependencies:
r, r-s4vectors, r-iranges, r-genomeinfodb, r-genomicranges, r-foreach, r-iterators, r-locfit, r-matrixstats, r-limma, r-dorng, r-biocgenerics, r-genomicfeatures, r-annotationdbi
Description:
Bump Hunter. Tools for finding bumps in genomic data

r-c50

Homepage:
Spack package:
Versions:
0.1.2, 0.1.1, 0.1.0-24
Build Dependencies:
r, r-partykit, r-cubist
Link Dependencies:
r
Run Dependencies:
r, r-partykit, r-cubist
Description:
C5.0 decision trees and rule-based models for pattern recognition.

r-cairo

Homepage:
Spack package:
Versions:
1.5-10, 1.5-9
Build Dependencies:
r, cairo
Link Dependencies:
r, cairo
Run Dependencies:
r
Description:
R graphics device using cairo graphics library for creating high-quality bitmap (PNG, JPEG, TIFF), vector (PDF, SVG, PostScript) and display (X11 and Win32) output

r-callr

Homepage:
Spack package:
Versions:
3.3.1, 3.2.0, 3.0.0, 1.0.0
Build Dependencies:
r, r-processx, r-r6
Link Dependencies:
r
Run Dependencies:
r, r-processx, r-r6
Description:
It is sometimes useful to perform a computation in a separate R process, without affecting the current R process at all. This packages does exactly that.

r-car

Homepage:
Spack package:
Versions:
3.0-3, 3.0-2, 2.1-4, 2.1-2
Build Dependencies:
r, r-cardata, r-abind, r-mass, r-mgcv, r-nnet, r-pbkrtest, r-quantreg, r-maptools, r-rio, r-lme4, r-nlme
Link Dependencies:
r
Run Dependencies:
r, r-cardata, r-abind, r-mass, r-mgcv, r-nnet, r-pbkrtest, r-quantreg, r-maptools, r-rio, r-lme4, r-nlme
Description:
Functions and Datasets to Accompany J. Fox and S. Weisberg, An R Companion to Applied Regression, Second Edition, Sage, 2011.

r-cardata

Homepage:
Spack package:
Versions:
3.0-2
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Datasets to Accompany J. Fox and S. Weisberg, An R Companion to Applied Regression, Third Edition, Sage (forthcoming).

r-caret

Homepage:
Spack package:
Versions:
6.0-84, 6.0-83, 6.0-73, 6.0-70
Build Dependencies:
r, r-lattice, r-ggplot2, r-car, r-foreach, r-plyr, r-modelmetrics, r-nlme, r-reshape2, r-recipes, r-withr
Link Dependencies:
r
Run Dependencies:
r, r-lattice, r-ggplot2, r-car, r-foreach, r-plyr, r-modelmetrics, r-nlme, r-reshape2, r-recipes, r-withr
Description:
Misc functions for training and plotting classification and regression models.

r-caroline

Homepage:
Spack package:
Versions:
0.7.6
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
caroline: A Collection of Database, Data Structure, Visualization, andUtility Functions for R

r-category

Homepage:
Spack package:
Versions:
2.50.0, 2.48.1, 2.46.0, 2.44.0, 2.42.1
Build Dependencies:
r, r-biocgenerics, r-annotationdbi, r-biobase, r-matrix, r-graph, r-rbgl, r-gseabase, r-genefilter, r-annotate, r-dbi
Link Dependencies:
r
Run Dependencies:
r, r-biocgenerics, r-annotationdbi, r-biobase, r-matrix, r-graph, r-rbgl, r-gseabase, r-genefilter, r-annotate, r-dbi
Description:
Category Analysis. A collection of tools for performing category (gene set enrichment) analysis.

r-catools

Homepage:
Spack package:
Versions:
1.17.1.2, 1.17.1.1, 1.17.1
Build Dependencies:
r, r-bitops
Link Dependencies:
r
Run Dependencies:
r, r-bitops
Description:
Contains several basic utility functions including: moving (rolling, running) window statistic functions, read/write for GIF and ENVI binary files, fast calculation of AUC, LogitBoost classifier, base64 encoder/decoder, round-off-error-free sum and cumsum, etc.

r-cdcfluview

Homepage:
Spack package:
Versions:
0.9.0, 0.7.0
Build Dependencies:
r, r-httr, r-dplyr, r-jsonlite, r-sf, r-xml2, r-purrr, r-readr, r-mmwrweek, r-units
Link Dependencies:
r
Run Dependencies:
r, r-httr, r-dplyr, r-jsonlite, r-sf, r-xml2, r-purrr, r-readr, r-mmwrweek, r-units
Description:
The 'U.S.' Centers for Disease Control ('CDC') maintains a portal <http://gis.cdc.gov/grasp/fluview/fluportaldashboard.html> for accessing state, regional and national influenza statistics as well as Mortality Surveillance Data. The web interface makes it difficult and time- consuming to select and retrieve influenza data. Tools are provided to access the data provided by the portal's underlying 'API'.

r-cellranger

Homepage:
Spack package:
Versions:
1.1.0
Build Dependencies:
r, r-rematch, r-tibble
Link Dependencies:
r
Run Dependencies:
r, r-rematch, r-tibble
Description:
Helper functions to work with spreadsheets and the "A1:D10" style of cell range specification.

r-checkmate

Homepage:
Spack package:
Versions:
1.9.4, 1.8.4
Build Dependencies:
r, r-backports
Link Dependencies:
r
Run Dependencies:
r, r-backports
Description:
Tests and assertions to perform frequent argument checks. A substantial part of the package was written in C to minimize any worries about execution time overhead.

r-checkpoint

Homepage:
Spack package:
Versions:
0.4.6, 0.4.3, 0.3.15
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
The goal of checkpoint is to solve the problem of package reproducibility in R. Specifically, checkpoint allows you to install packages as they existed on CRAN on a specific snapshot date as if you had a CRAN time machine.

r-chemometrics

Homepage:
Spack package:
Versions:
1.4.2, 1.4.1, 1.3.9, 1.3.8, 1.3.7
Build Dependencies:
r, r-rpart, r-mclust, r-lars, r-robustbase, r-e1071, r-pls, r-som, r-pcapp, r-class, r-mass, r-nnet
Link Dependencies:
r
Run Dependencies:
r, r-rpart, r-mclust, r-lars, r-robustbase, r-e1071, r-pls, r-som, r-pcapp, r-class, r-mass, r-nnet
Description:
R companion to the book "Introduction to Multivariate Statistical Analysis in Chemometrics" written by K. Varmuza and P. Filzmoser (2009).

r-chron

Homepage:
Spack package:
Versions:
2.3-53, 2.3-52, 2.3-47
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Chronological objects which can handle dates and times.

r-circlize

Homepage:
Spack package:
Versions:
0.4.6, 0.4.1, 0.4.0
Build Dependencies:
r, r-globaloptions, r-shape, r-colorspace
Link Dependencies:
r
Run Dependencies:
r, r-globaloptions, r-shape, r-colorspace
Description:
Circular layout is an efficient way for the visualization of huge amounts of information. Here this package provides an implementation of circular layout generation in R as well as an enhancement of available software. The flexibility of the package is based on the usage of low- level graphics functions such that self-defined high-level graphics can be easily implemented by users for specific purposes. Together with the seamless connection between the powerful computational and visual environment in R, it gives users more convenience and freedom to design figures for better understanding complex patterns behind multiple dimensional data.

r-class

Homepage:
Spack package:
Versions:
7.3-15, 7.3-14
Build Dependencies:
r, r-mass
Link Dependencies:
r
Run Dependencies:
r, r-mass
Description:
Various functions for classification, including k-nearest neighbour, Learning Vector Quantization and Self-Organizing Maps.

r-classint

Homepage:
Spack package:
Versions:
0.4-1, 0.3-3, 0.3-1, 0.1-24
Build Dependencies:
r, r-e1071, r-class, r-kernsmooth
Link Dependencies:
r
Run Dependencies:
r, r-e1071, r-class, r-kernsmooth
Description:
Selected commonly used methods for choosing univariate class intervals for mapping or other graphics purposes.

r-cli

Homepage:
Spack package:
Versions:
1.1.0, 1.0.1, 1.0.0
Build Dependencies:
r, r-assertthat, r-crayon
Link Dependencies:
r
Run Dependencies:
r, r-assertthat, r-crayon
Description:
A suite of tools designed to build attractive command line interfaces ('CLIs'). Includes tools for drawing rules, boxes, trees, and 'Unicode' symbols with 'ASCII' alternatives.

r-clipr

Homepage:
Spack package:
Versions:
0.7.0, 0.5.0, 0.4.0
Build Dependencies:
r, xclip
Link Dependencies:
r, xclip
Run Dependencies:
r
Description:
Simple utility functions to read from and write to the Windows, OS X, and X11 clipboards.

r-clisymbols

Homepage:
Spack package:
Versions:
1.2.0
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
A small subset of Unicode symbols, that are useful when building command line applications. They fall back to alternatives on terminals that do not support Unicode. Many symbols were taken from the 'figures' 'npm' package (see <https://github.com/sindresorhus/figures>).

r-clue

Homepage:
Spack package:
Versions:
0.3-57
Build Dependencies:
r, r-cluster
Link Dependencies:
r
Run Dependencies:
r, r-cluster
Description:
clue: Cluster Ensembles

r-cluster

Homepage:
Spack package:
Versions:
2.1.0, 2.0.7-1, 2.0.5, 2.0.4
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Methods for Cluster analysis. Much extended the original from Peter Rousseeuw, Anja Struyf and Mia Hubert, based on Kaufman and Rousseeuw (1990) "Finding Groups in Data".

r-clustergeneration

Homepage:
Spack package:
Versions:
1.3.4
Build Dependencies:
r, r-mass
Link Dependencies:
r
Run Dependencies:
r, r-mass
Description:
Random Cluster Generation (with Specified Degree of Separation)

r-clusterprofiler

Homepage:
Spack package:
Versions:
3.12.0, 3.10.1, 3.8.1, 3.6.0, 3.4.4
Build Dependencies:
r, r-dose, r-annotationdbi, r-ggplot2, r-go-db, r-gosemsim, r-magrittr, r-plyr, r-qvalue, r-rvcheck, r-tidyr, r-enrichplot
Link Dependencies:
r
Run Dependencies:
r, r-dose, r-annotationdbi, r-ggplot2, r-go-db, r-gosemsim, r-magrittr, r-plyr, r-qvalue, r-rvcheck, r-tidyr, r-enrichplot
Description:
statistical analysis and visualization of functional profiles for genes and gene clusters. This package implements methods to analyze and visualize functional profiles (GO and KEGG) of gene and gene clusters.

r-cner

Homepage:
Spack package:
Versions:
1.20.0, 1.18.1, 1.16.1, 1.14.0, 1.12.1
Build Dependencies:
r, r-biostrings, r-rsqlite, r-genomeinfodb, r-genomicranges, r-rtracklayer, r-xvector, r-genomicalignments, r-dbi, r-s4vectors, r-iranges, r-readr, r-biocgenerics, r-reshape2, r-ggplot2, r-powerlaw, r-annotate, r-go-db, r-r-utils, r-keggrest
Link Dependencies:
r
Run Dependencies:
r, r-biostrings, r-rsqlite, r-genomeinfodb, r-genomicranges, r-rtracklayer, r-xvector, r-genomicalignments, r-dbi, r-s4vectors, r-iranges, r-readr, r-biocgenerics, r-reshape2, r-ggplot2, r-powerlaw, r-annotate, r-go-db, r-r-utils, r-keggrest
Description:
CNE Detection and Visualization. Large-scale identification and advanced visualization of sets of conserved noncoding elements.

r-coda

Homepage:
Spack package:
Versions:
0.19-3, 0.19-2, 0.19-1
Build Dependencies:
r, r-lattice
Link Dependencies:
r
Run Dependencies:
r, r-lattice
Description:
Provides functions for summarizing and plotting the output from Markov Chain Monte Carlo (MCMC) simulations, as well as diagnostic tests of convergence to the equilibrium distribution of the Markov chain.

r-codetools

Homepage:
Spack package:
Versions:
0.2-16, 0.2-15, 0.2-14
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Code analysis tools for R.

r-codex

Homepage:
Spack package:
Versions:
1.18.0
Build Dependencies:
r, r-rsamtools, r-genomeinfodb, r-bsgenome-hsapiens-ucsc-hg19, r-iranges, r-biostrings, r-s4vectors
Link Dependencies:
r
Run Dependencies:
r, r-rsamtools, r-genomeinfodb, r-bsgenome-hsapiens-ucsc-hg19, r-iranges, r-biostrings, r-s4vectors
Description:
A normalization and copy number variation calling procedure for whole exome DNA sequencing data. CODEX relies on the availability of multiple samples processed using the same sequencing pipeline for normalization, and does not require matched controls. The normalization model in CODEX includes terms that specifically remove biases due to GC content, exon length and targeting and amplification efficiency, and latent systemic artifacts. CODEX also includes a Poisson likelihood-based recursive segmentation procedure that explicitly models the count-based exome sequencing data.

r-coin

Homepage:
Spack package:
Versions:
1.3-0, 1.2-2, 1.1-3
Build Dependencies:
r, r-survival, r-modeltools, r-mvtnorm, r-multcomp, r-libcoin, r-matrixstats
Link Dependencies:
r
Run Dependencies:
r, r-survival, r-modeltools, r-mvtnorm, r-multcomp, r-libcoin, r-matrixstats
Description:
Conditional inference procedures for the general independence problem including two-sample, K-sample (non-parametric ANOVA), correlation, censored, ordered and multivariate problems.

r-colorspace

Homepage:
Spack package:
Versions:
1.4-1, 1.4-0, 1.3-2, 1.2-6
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Carries out mapping between assorted color spaces including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar CIELAB. Qualitative, sequential, and diverging color palettes based on HCL colors are provided.

r-combinat

Homepage:
Spack package:
Versions:
0.0-8
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
routines for combinatorics

r-commonmark

Homepage:
Spack package:
Versions:
1.7
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
commonmark: CommonMark and Github Markdown Rendering in R

r-complexheatmap

Homepage:
Spack package:
Versions:
2.0.0, 1.20.0, 1.18.1, 1.17.1, 1.14.0
Build Dependencies:
r, r-circlize, r-getoptlong, r-colorspace, r-rcolorbrewer, r-dendextend, r-globaloptions, r-clue, r-png
Link Dependencies:
r
Run Dependencies:
r, r-circlize, r-getoptlong, r-colorspace, r-rcolorbrewer, r-dendextend, r-globaloptions, r-clue, r-png
Description:
Make Complex Heatmaps. Complex heatmaps are efficient to visualize associations between different sources of data sets and reveal potential patterns. Here the ComplexHeatmap package provides a highly flexible way to arrange multiple heatmaps and supports various annotation graphics.

r-compositions

Homepage:
Spack package:
Versions:
1.40-2
Build Dependencies:
r, r-tensora, r-robustbase, r-energy, r-bayesm
Link Dependencies:
r
Run Dependencies:
r, r-tensora, r-robustbase, r-energy, r-bayesm
Description:
Compositional Data Analysis

r-condop

Homepage:
Spack package:
Versions:
1.0
Build Dependencies:
r, r-mclust, r-earth, r-plyr, r-seqinr, r-randomforest, r-rminer, r-genomicranges, r-genomeinfodb, r-s4vectors, r-iranges
Link Dependencies:
r
Run Dependencies:
r, r-mclust, r-earth, r-plyr, r-seqinr, r-randomforest, r-rminer, r-genomicranges, r-genomeinfodb, r-s4vectors, r-iranges
Description:
CONDOP: Condition-Dependent Operon Predictions. An implementation of the computational strategy for the comprehensive analysis of condition- dependent operon maps in prokaryotes proposed by Fortino et al. (2014) <doi:10.1186/1471-2105-15-145>. It uses RNA-seq transcriptome profiles to improve prokaryotic operon map inference.

r-construct

Homepage:
Spack package:
Versions:
1.0.3
Build Dependencies:
r, r-bh, r-caroline, r-doparallel, r-foreach, r-gtools, r-rcpp, r-rcppeigen, r-rstan, r-rstantools, r-stanheaders, gmake
Link Dependencies:
r
Run Dependencies:
r, r-bh, r-caroline, r-doparallel, r-foreach, r-gtools, r-rcpp, r-rcppeigen, r-rstan, r-rstantools, r-stanheaders
Description:
conStruct: Models Spatially Continuous and Discrete Population GeneticStructure

r-convevol

Homepage:
Spack package:
Versions:
1.3
Build Dependencies:
r, r-ape, r-cluster, r-geiger, r-mass, r-phytools
Link Dependencies:
r
Run Dependencies:
r, r-ape, r-cluster, r-geiger, r-mass, r-phytools
Description:
Quantifies and assesses the significance of convergent evolution

r-copula

Homepage:
Spack package:
Versions:
0.999-20
Build Dependencies:
r, r-matrix, r-lattice, r-colorspace, r-gsl, r-adgoftest, r-stabledist, r-mvtnorm, r-pcapp, r-pspline, r-numderiv
Link Dependencies:
r
Run Dependencies:
r, r-matrix, r-lattice, r-colorspace, r-gsl, r-adgoftest, r-stabledist, r-mvtnorm, r-pcapp, r-pspline, r-numderiv
Description:
Classes (S4) of commonly used elliptical, Archimedean, extreme-value and other copula families, as well as their rotations, mixtures and asymmetrizations. Nested Archimedean copulas, related tools and special functions. Methods for density, distribution, random number generation, bivariate dependence measures, Rosenblatt transform, Kendall distribution function, perspective and contour plots. Fitting of copula models with potentially partly fixed parameters, including standard errors. Serial independence tests, copula specification tests (independence, exchangeability, radial symmetry, extreme-value dependence, goodness-of-fit) and model selection based on cross- validation. Empirical copula, smoothed versions, and non-parametric estimators of the Pickands dependence function.

r-corhmm

Homepage:
Spack package:
Versions:
1.22
Build Dependencies:
r, r-ape, r-nloptr, r-gensa, r-expm, r-numderiv, r-nnet, r-corpcor, r-phangorn, r-rmpfr
Link Dependencies:
r
Run Dependencies:
r, r-ape, r-nloptr, r-gensa, r-expm, r-numderiv, r-nnet, r-corpcor, r-phangorn, r-rmpfr
Description:
corHMM: Analysis of Binary Character Evolution Fits a hidden rates model that allows different transition rate classes on different portions of a phylogeny by treating rate classes as hidden states in a Markov process and various other functions for evaluating models of binary character evolution.

r-corpcor

Homepage:
Spack package:
Versions:
1.6.9
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Efficient Estimation of Covariance and (Partial) Correlation

r-corrplot

Homepage:
Spack package:
Versions:
0.84, 0.77
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
A graphical display of a correlation matrix or general matrix. It also contains some algorithms to do matrix reordering.

r-covr

Homepage:
Spack package:
Versions:
3.3.0, 3.2.1, 3.2.0, 3.0.1
Build Dependencies:
r, r-digest, r-jsonlite, r-rex, r-httr, r-crayon, r-withr, r-yaml
Link Dependencies:
r
Run Dependencies:
r, r-digest, r-jsonlite, r-rex, r-httr, r-crayon, r-withr, r-yaml
Description:
Track and report code coverage for your package and (optionally) upload the results to a coverage service like 'Codecov' <http://codecov.io> or 'Coveralls' <http://coveralls.io>. Code coverage is a measure of the amount of code being exercised by a set of tests. It is an indirect measure of test quality and completeness. This package is compatible with any testing methodology or framework and tracks coverage of both R code and compiled C/C++/FORTRAN code.

r-cowplot

Homepage:
Spack package:
Versions:
1.0.0, 0.9.3, 0.9.2, 0.9.1, 0.9.0, 0.8.0
Build Dependencies:
r, r-ggplot2, r-gtable, r-plyr, r-scales, r-rlang
Link Dependencies:
r
Run Dependencies:
r, r-ggplot2, r-gtable, r-plyr, r-scales, r-rlang
Description:
Some helpful extensions and modifications to the 'ggplot2' package. In particular, this package makes it easy to combine multiple 'ggplot2' plots into one and label them with letters, e.g. A, B, C, etc., as is often required for scientific publications. The package also provides a streamlined and clean theme that is used in the Wilke lab, hence the package name, which stands for Claus O. Wilke's plot package.

r-crayon

Homepage:
Spack package:
Versions:
1.3.4, 1.3.2
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Colored terminal output on terminals that support 'ANSI' color and highlight codes. It also works in 'Emacs' 'ESS'. 'ANSI' color support is automatically detected. Colors and highlighting can be combined and nested. New styles can also be created easily. This package was inspired by the 'chalk' 'JavaScript' project.

r-crosstalk

Homepage:
Spack package:
Versions:
1.0.0
Build Dependencies:
r, r-htmltools, r-jsonlite, r-lazyeval, r-ggplot2, r-shiny, r-r6
Link Dependencies:
r
Run Dependencies:
r, r-htmltools, r-jsonlite, r-lazyeval, r-ggplot2, r-shiny, r-r6
Description:
Provides building blocks for allowing HTML widgets to communicate with each other, with Shiny or without (i.e. static .html files).

r-crul

Homepage:
Spack package:
Versions:
0.8.4, 0.7.4
Build Dependencies:
r, r-curl, r-httpcode, r-mime, r-r6, r-urltools, r-jsonlite
Link Dependencies:
r
Run Dependencies:
r, r-curl, r-httpcode, r-mime, r-r6, r-urltools, r-jsonlite
Description:
crul: HTTP Client

r-ctc

Homepage:
Spack package:
Versions:
1.58.0, 1.56.0, 1.54.0, 1.52.0, 1.50.0
Build Dependencies:
r, r-amap
Link Dependencies:
r
Run Dependencies:
r, r-amap
Description:
Cluster and Tree Conversion.. Tools for export and import classification trees and clusters to other programs

r-cubature

Homepage:
Spack package:
Versions:
2.0.3, 2.0.2, 1.1-2
Build Dependencies:
r, r-rcpp
Link Dependencies:
r
Run Dependencies:
r, r-rcpp
Description:
Adaptive multivariate integration over hypercubes

r-cubist

Homepage:
Spack package:
Versions:
0.2.2, 0.2.1, 0.0.19
Build Dependencies:
r, r-lattice, r-reshape2
Link Dependencies:
r
Run Dependencies:
r, r-lattice, r-reshape2
Description:
Regression modeling using rules with added instance-based corrections

r-curl

Homepage:
Spack package:
Versions:
4.3, 4.0, 3.3, 3.0, 2.3, 1.0, 0.9.7
Build Dependencies:
r, curl
Link Dependencies:
r, curl
Run Dependencies:
r
Description:
The curl() and curl_download() functions provide highly configurable drop-in replacements for base url() and download.file() with better performance, support for encryption (https, ftps), gzip compression, authentication, and other libcurl goodies. The core of the package implements a framework for performing fully customized requests where data can be processed either in memory, on disk, or streaming via the callback or connection interfaces. Some knowledge of libcurl is recommended; for a more-user-friendly web client see the 'httr' package which builds on this package with http specific tools and logic.

r-dada2

Homepage:
Spack package:
Versions:
1.14
Build Dependencies:
r, r-rcpp, r-biostrings, r-ggplot2, r-reshape2, r-shortread, r-rcppparallel, r-iranges, r-xvector, r-biocgenerics, gmake
Link Dependencies:
r
Run Dependencies:
r, r-rcpp, r-biostrings, r-ggplot2, r-reshape2, r-shortread, r-rcppparallel, r-iranges, r-xvector, r-biocgenerics
Description:
Accurate sample inference from amplicon data with single nucleotide resolution

r-data-table

Homepage:
Spack package:
Versions:
1.12.2, 1.12.0, 1.11.8, 1.11.6, 1.11.4, 1.11.2, 1.11.0, 1.10.4-3, 1.10.4-2, 1.10.4-1, 1.10.4, 1.10.2, 1.10.0, 1.9.8, 1.9.6
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, fast add/modify/delete of columns by group using no copies at all, list columns and a fast file reader (fread). Offers a natural and flexible syntax, for faster development.

r-dbi

Homepage:
Spack package:
Versions:
1.1.0, 1.0.0, 0.7, 0.4-1
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
A database interface definition for communication between R and relational database management systems. All classes in this package are virtual and need to be extended by the various R/DBMS implementations.

r-dbplyr

Homepage:
Spack package:
Versions:
1.4.2, 1.4.1, 1.2.2, 1.2.1, 1.2.0, 1.1.0
Build Dependencies:
r, r-assertthat, r-dbi, r-dplyr, r-glue, r-purrr, r-r6, r-rlang, r-tibble, r-tidyselect
Link Dependencies:
r
Run Dependencies:
r, r-assertthat, r-dbi, r-dplyr, r-glue, r-purrr, r-r6, r-rlang, r-tibble, r-tidyselect
Description:
A 'dplyr' back end for databases that allows you to work with remote database tables as if they are in-memory data frames. Basic features works with any database that has a 'DBI' back end; more advanced features require 'SQL' translation to be provided by the package author.

r-debugme

Homepage:
Spack package:
Versions:
1.1.0
Build Dependencies:
r, r-crayon
Link Dependencies:
r
Run Dependencies:
r, r-crayon
Description:
Specify debug messages as special string constants, and control debugging of packages via environment variables.

r-delayedarray

Homepage:
Spack package:
Versions:
0.10.0, 0.8.0, 0.6.6, 0.4.1, 0.2.7
Build Dependencies:
r, r-biocgenerics, r-s4vectors, r-iranges, r-matrixstats, r-biocparallel, r-matrix
Link Dependencies:
r
Run Dependencies:
r, r-biocgenerics, r-s4vectors, r-iranges, r-matrixstats, r-biocparallel, r-matrix
Description:
A unified framework for working transparently with on-disk and in-memory array-like datasets. Wrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically with Rle columns), Matrix objects, and ordinary arrays and data frames.

r-delayedmatrixstats

Homepage:
Spack package:
Versions:
1.6.1, 1.4.0, 1.2.0, 1.0.3
Build Dependencies:
r, r-delayedarray, r-matrixstats, r-matrix, r-s4vectors, r-iranges, r-hdf5array, r-biocparallel
Link Dependencies:
r
Run Dependencies:
r, r-delayedarray, r-matrixstats, r-matrix, r-s4vectors, r-iranges, r-hdf5array, r-biocparallel
Description:
Functions that Apply to Rows and Columns of 'DelayedMatrix' Objects. A port of the 'matrixStats' API for use with DelayedMatrix objects from the 'DelayedArray' package. High-performing functions operating on rows and columns of DelayedMatrix objects, e.g. col / rowMedians(), col / rowRanks(), and col / rowSds(). Functions optimized per data type and for subsetted calculations such that both memory usage and processing time is minimized.

r-deldir

Homepage:
Spack package:
Versions:
0.1-23, 0.1-21, 0.1-14
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Calculates the Delaunay triangulation and the Dirichlet or Voronoi tessellation (with respect to the entire plane) of a planar point set. Plots triangulations and tessellations in various ways. Clips tessellations to sub-windows. Calculates perimeters of tessellations. Summarises information about the tiles of the tessellation.

r-dendextend

Homepage:
Spack package:
Versions:
1.12.0, 1.10.0, 1.5.2
Build Dependencies:
r, r-magrittr, r-ggplot2, r-fpc, r-whisker, r-viridis
Link Dependencies:
r
Run Dependencies:
r, r-magrittr, r-ggplot2, r-fpc, r-whisker, r-viridis
Description:
dendextend: Extending 'Dendrogram' Functionality in R

r-deoptim

Homepage:
Spack package:
Versions:
2.2-4, 2.2-3
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Implements the differential evolution algorithm for global optimization of a real-valued function of a real-valued parameter vector.

r-deoptimr

Homepage:
Spack package:
Versions:
1.0-8
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
An implementation of a bespoke jDE variant of the Differential Evolution stochastic algorithm for global optimization of nonlinear programming problems.

r-desc

Homepage:
Spack package:
Versions:
1.2.0
Build Dependencies:
r, r-assertthat, r-r6, r-crayon, r-rprojroot
Link Dependencies:
r
Run Dependencies:
r, r-assertthat, r-r6, r-crayon, r-rprojroot
Description:
desc: Manipulate DESCRIPTION Files

r-deseq

Homepage:
Spack package:
Versions:
1.36.0, 1.34.1, 1.32.0, 1.30.0, 1.28.0
Build Dependencies:
r, r-biocgenerics, r-biobase, r-locfit, r-lattice, r-genefilter, r-geneplotter, r-mass, r-rcolorbrewer
Link Dependencies:
r
Run Dependencies:
r, r-biocgenerics, r-biobase, r-locfit, r-lattice, r-genefilter, r-geneplotter, r-mass, r-rcolorbrewer
Description:
Differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high- throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution

r-deseq2

Homepage:
Spack package:
Versions:
1.24.0, 1.22.2, 1.20.0, 1.18.1, 1.16.1
Build Dependencies:
r, r-s4vectors, r-iranges, r-genomicranges, r-summarizedexperiment, r-biocgenerics, r-biobase, r-biocparallel, r-genefilter, r-locfit, r-geneplotter, r-ggplot2, r-hmisc, r-rcpp, r-rcpparmadillo
Link Dependencies:
r
Run Dependencies:
r, r-s4vectors, r-iranges, r-genomicranges, r-summarizedexperiment, r-biocgenerics, r-biobase, r-biocparallel, r-genefilter, r-locfit, r-geneplotter, r-ggplot2, r-hmisc, r-rcpp, r-rcpparmadillo
Description:
Differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high- throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.

r-desolve

Homepage:
Spack package:
Versions:
1.24, 1.21, 1.20
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Functions that solve initial value problems of a system of first-order ordinary differential equations ('ODE'), of partial differential equations ('PDE'), of differential algebraic equations ('DAE'), and of delay differential equations.

r-devtools

Homepage:
Spack package:
Versions:
2.1.0, 2.0.2, 1.12.0, 1.11.1
Build Dependencies:
r, r-httr, r-memoise, r-whisker, r-digest, r-rstudioapi, r-jsonlite, r-git2r, r-withr, r-usethis, r-callr, r-cli, r-pkgbuild, r-pkgload, r-rcmdcheck, r-remotes, r-roxygen2, r-sessioninfo, r-testthat
Link Dependencies:
r
Run Dependencies:
r, r-httr, r-memoise, r-whisker, r-digest, r-rstudioapi, r-jsonlite, r-git2r, r-withr, r-usethis, r-callr, r-cli, r-pkgbuild, r-pkgload, r-rcmdcheck, r-remotes, r-roxygen2, r-sessioninfo, r-testthat
Description:
Collection of package development tools.

r-dicekriging

Homepage:
Spack package:
Versions:
1.5.6, 1.5.5
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Estimation, validation and prediction of kriging models. Important functions : km, print.km, plot.km, predict.km.

r-dichromat

Homepage:
Spack package:
Versions:
2.0-0
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Collapse red-green or green-blue distinctions to simulate the effects of different types of color-blindness.

r-diffusionmap

Homepage:
Spack package:
Versions:
1.1-0.1, 1.1-0, 1.0-0, 0.0-2, 0.0-1
Build Dependencies:
r, r-matrix, r-scatterplot3d, r-igraph
Link Dependencies:
r
Run Dependencies:
r, r-matrix, r-scatterplot3d, r-igraph
Description:
Allows to display a progress bar in the R console for long running computations taking place in c++ code, and support for interrupting those computations even in multithreaded code, typically using OpenMP.

r-digest

Homepage:
Spack package:
Versions:
0.6.20, 0.6.19, 0.6.12, 0.6.11, 0.6.9
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Implementation of a function 'digest()' for the creation of hash digests of arbitrary R objects (using the md5, sha-1, sha-256, crc32, xxhash and murmurhash algorithms) permitting easy comparison of R language objects, as well as a function 'hmac()' to create hash-based message authentication code. The md5 algorithm by Ron Rivest is specified in RFC 1321, the sha-1 and sha-256 algorithms are specified in FIPS-180-1 and FIPS-180-2, and the crc32 algorithm is described in ftp://ftp.rocksoft.com/cliens/rocksoft/papers/crc_v3.txt. For md5, sha-1, sha-256 and aes, this package uses small standalone implementations that were provided by Christophe Devine. For crc32, code from the zlib library is used. For sha-512, an implementation by Aaron D. Gifford is used. For xxhash, the implementation by Yann Collet is used. For murmurhash, an implementation by Shane Day is used. Please note that this package is not meant to be deployed for cryptographic purposes for which more comprehensive (and widely tested) libraries such as OpenSSL should be used.

r-diptest

Homepage:
Spack package:
Versions:
0.75-7
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
diptest: Hartigan's Dip Test Statistic for Unimodality - Corrected

r-dirichletmultinomial

Homepage:
Spack package:
Versions:
1.26.0, 1.24.1, 1.22.0, 1.20.0, 1.18.0
Build Dependencies:
r, r-s4vectors, r-iranges, r-biocgenerics, gsl
Link Dependencies:
r, gsl
Run Dependencies:
r, r-s4vectors, r-iranges, r-biocgenerics
Description:
Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome Data. Dirichlet-multinomial mixture models can be used to describe variability in microbial metagenomic data. This package is an interface to code originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): 1-15, as discussed further in the man page for this package, ?DirichletMultinomial.

r-dismo

Homepage:
Spack package:
Versions:
1.1-4
Build Dependencies:
r, r-raster, r-sp
Link Dependencies:
r
Run Dependencies:
r, r-raster, r-sp
Description:
Functions for species distribution modeling, that is, predicting entire geographic distributions form occurrences at a number of sites and the environment at these sites.

r-diversitree

Homepage:
Spack package:
Versions:
0.9-11, 0.9-10
Build Dependencies:
r, r-ape, r-desolve, r-subplex, r-rcpp, fftw, gsl
Link Dependencies:
r, fftw, gsl
Run Dependencies:
r, r-ape, r-desolve, r-subplex, r-rcpp
Description:
Contains a number of comparative 'phylogenetic' methods. Mostly focusing on analysing diversification and character evolution. Contains implementations of 'BiSSE' (Binary State 'Speciation' and Extinction) and its unresolved tree extensions, 'MuSSE' (Multiple State 'Speciation' and Extinction), 'QuaSSE', 'GeoSSE', and 'BiSSE-ness' Other included methods include Markov models of discrete and continuous trait evolution and constant rate 'speciation' and extinction.

r-dnacopy

Homepage:
Spack package:
Versions:
1.58.0, 1.56.0, 1.54.0, 1.52.0, 1.50.1
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
DNA copy number data analysis. Implements the circular binary segmentation (CBS) algorithm to segment DNA copy number data and identify genomic regions with abnormal copy number.

r-do-db

Homepage:
Spack package:
Versions:
2.9
Build Dependencies:
r, r-annotationdbi
Link Dependencies:
r
Run Dependencies:
r, r-annotationdbi
Description:
A set of annotation maps describing the entire Disease Ontology assembled using data from DO.

r-domc

Homepage:
Spack package:
Versions:
1.3.6, 1.3.4
Build Dependencies:
r, r-foreach, r-iterators
Link Dependencies:
r
Run Dependencies:
r, r-foreach, r-iterators
Description:
Provides a parallel backend for the %dopar% function using the multicore functionality of the parallel package.

r-doparallel

Homepage:
Spack package:
Versions:
1.0.15, 1.0.11, 1.0.10
Build Dependencies:
r, r-foreach, r-iterators
Link Dependencies:
r
Run Dependencies:
r, r-foreach, r-iterators
Description:
Provides a parallel backend for the %dopar% function using the parallel package.

r-dorng

Homepage:
Spack package:
Versions:
1.7.1, 1.6.6
Build Dependencies:
r, r-foreach, r-rngtools, r-iterators, r-pkgmaker
Link Dependencies:
r
Run Dependencies:
r, r-foreach, r-rngtools, r-iterators, r-pkgmaker
Description:
Provides functions to perform reproducible parallel foreach loops, using independent random streams as generated by L'Ecuyer's combined multiple- recursive generator [L'Ecuyer (1999), <doi:10.1287/opre.47.1.159>]. It enables to easily convert standard %dopar% loops into fully reproducible loops, independently of the number of workers, the task scheduling strategy, or the chosen parallel environment and associated foreach backend.

r-dose

Homepage:
Spack package:
Versions:
3.10.2, 3.8.2, 3.6.1, 3.4.0, 3.2.0
Build Dependencies:
r, r-annotationdbi, r-biocparallel, r-do-db, r-fgsea, r-ggplot2, r-gosemsim, r-igraph, r-qvalue, r-reshape2, r-s4vectors, r-scales, r-rvcheck
Link Dependencies:
r
Run Dependencies:
r, r-annotationdbi, r-biocparallel, r-do-db, r-fgsea, r-ggplot2, r-gosemsim, r-igraph, r-qvalue, r-reshape2, r-s4vectors, r-scales, r-rvcheck
Description:
Disease Ontology Semantic and Enrichment analysis. This package implements five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively for measuring semantic similarities among DO terms and gene products. Enrichment analyses including hypergeometric model and gene set enrichment analysis are also implemented for discovering disease associations of high-throughput biological data.

r-dosnow

Homepage:
Spack package:
Versions:
1.0.18
Build Dependencies:
r, r-foreach, r-iterators, r-snow
Link Dependencies:
r
Run Dependencies:
r, r-foreach, r-iterators, r-snow
Description:
Provides a parallel backend for the %dopar% function using the snow package of Tierney, Rossini, Li, and Sevcikova.

r-dotcall64

Homepage:
Spack package:
Versions:
1.0-0
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
dotCall64: Enhanced Foreign Function Interface Supporting Long Vectors.

r-downloader

Homepage:
Spack package:
Versions:
0.4
Build Dependencies:
r, r-digest
Link Dependencies:
r
Run Dependencies:
r, r-digest
Description:
Provides a wrapper for the download.file function, making it possible to download files over HTTPS on Windows, Mac OS X, and other Unix-like platforms. The 'RCurl' package provides this functionality (and much more) but can be difficult to install because it must be compiled with external dependencies. This package has no external dependencies, so it is much easier to install.

r-dplyr

Homepage:
Spack package:
Versions:
0.8.3, 0.8.2, 0.7.7, 0.7.6, 0.7.5, 0.7.4, 0.7.3, 0.7.2, 0.7.1, 0.7.0, 0.5.0
Build Dependencies:
r, r-assertthat, r-bindrcpp, r-glue, r-magrittr, r-pkgconfig, r-r6, r-rcpp, r-rlang, r-tibble, r-tidyselect, r-bh, r-plogr
Link Dependencies:
r
Run Dependencies:
r, r-assertthat, r-bindrcpp, r-glue, r-magrittr, r-pkgconfig, r-r6, r-rcpp, r-rlang, r-tibble, r-tidyselect, r-bh, r-plogr
Description:
A fast, consistent tool for working with data frame like objects, both in memory and out of memory.

r-dqrng

Homepage:
Spack package:
Versions:
0.2.1
Build Dependencies:
r, r-rcpp, r-bh, r-sitmo
Link Dependencies:
r
Run Dependencies:
r, r-rcpp, r-bh, r-sitmo
Description:
Several fast random number generators are provided as C++ header only libraries: The PCG family by O'Neill (2014 <https://www.cs.hmc.edu/tr/hmc-cs-2014-0905.pdf>) as well as Xoroshiro128+ and Xoshiro256+ by Blackman and Vigna (2018 <arXiv:1805.01407>). In addition fast functions for generating random numbers according to a uniform, normal and exponential distribution are included. The latter two use the Ziggurat algorithm originally proposed by Marsaglia and Tsang (2000, <doi:10.18637/jss.v005.i08>). These functions are exported to R and as a C++ interface and are enabled for use with the default 64 bit generator from the PCG family, Xoroshiro128+ and Xoshiro256+ as well as the 64 bit version of the 20 rounds Threefry engine (Salmon et al., 2011 <doi:10.1145/2063384.2063405>) as provided by the package 'sitmo'.

r-dt

Homepage:
Spack package:
Versions:
0.8, 0.7, 0.6, 0.4, 0.3, 0.2, 0.1
Build Dependencies:
r, r-htmltools, r-htmlwidgets, r-magrittr, r-crosstalk, r-promises, r-jsonlite
Link Dependencies:
r
Run Dependencies:
r, r-htmltools, r-htmlwidgets, r-magrittr, r-crosstalk, r-promises, r-jsonlite
Description:
Data objects in R can be rendered as HTML tables using the JavaScript library 'DataTables' (typically via R Markdown or Shiny). The 'DataTables' library has been included in this R package. The package name 'DT' is an abbreviation of 'DataTables'.

r-dtw

Homepage:
Spack package:
Versions:
1.20-1, 1.18-1, 1.17-1, 1.16, 1.15, 1.14-3
Build Dependencies:
r, r-proxy
Link Dependencies:
r
Run Dependencies:
r, r-proxy
Description:
A comprehensive implementation of dynamic time warping (DTW) algorithms in R. DTW computes the optimal (least cumulative distance) alignment between points of two time series.

r-dygraphs

Homepage:
Spack package:
Versions:
1.1.1.6, 1.1.1.5, 0.9
Build Dependencies:
r, r-magrittr, r-htmlwidgets, r-zoo, r-xts, r-htmltools
Link Dependencies:
r
Run Dependencies:
r, r-magrittr, r-htmlwidgets, r-zoo, r-xts, r-htmltools
Description:
An R interface to the 'dygraphs' JavaScript charting library (a copy of which is included in the package). Provides rich facilities for charting time-series data in R, including highly configurable series- and axis- display and interactive features like zoom/pan and series/point highlighting.

r-dynamictreecut

Homepage:
Spack package:
Versions:
1.63-1
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
dynamicTreeCut: Methods for Detection of Clusters in Hierarchical Clustering Dendrograms

r-e1071

Homepage:
Spack package:
Versions:
1.7-2, 1.7-1, 1.6-7
Build Dependencies:
r, r-class
Link Dependencies:
r
Run Dependencies:
r, r-class
Description:
Functions for latent class analysis, short time Fourier transform, fuzzy clustering, support vector machines, shortest path computation, bagged clustering, naive Bayes classifier, ...

r-earth

Homepage:
Spack package:
Versions:
5.1.2
Build Dependencies:
r, r-formula, r-plotmo, r-teachingdemos
Link Dependencies:
r
Run Dependencies:
r, r-formula, r-plotmo, r-teachingdemos
Description:
earth: Multivariate Adaptive Regression Splines. Build regression models using the techniques in Friedman's papers "Fast MARS" and "Multivariate Adaptive Regression Splines" <doi:10.1214/aos/1176347963>.

r-ecp

Homepage:
Spack package:
Versions:
3.1.1
Build Dependencies:
r, r-rcpp
Link Dependencies:
r
Run Dependencies:
r, r-rcpp
Description:
ecp: Non-Parametric Multiple Change-Point Analysis of MultivariateData

r-edger

Homepage:
Spack package:
Versions:
3.26.8, 3.24.3, 3.22.5, 3.20.9, 3.18.1
Build Dependencies:
r, r-limma, r-locfit, r-rcpp
Link Dependencies:
r
Run Dependencies:
r, r-limma, r-locfit, r-rcpp
Description:
Empirical Analysis of Digital Gene Expression Data in R. Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, Bisulfite-seq, SAGE and CAGE.

r-ellipse

Homepage:
Spack package:
Versions:
0.4.1, 0.3-8
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
This package contains various routines for drawing ellipses and ellipse- like confidence regions.

r-ellipsis

Homepage:
Spack package:
Versions:
0.2.0.1
Build Dependencies:
r, r-rlang
Link Dependencies:
r
Run Dependencies:
r, r-rlang
Description:
The ellipsis is a powerful tool for extending functions. Unfortunately this power comes at a cost: misspelled arguments will be silently ignored. The ellipsis package provides a collection of functions to catch problems and alert the user.

r-emmli

Homepage:
Spack package:
Versions:
0.0.3
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Fit models of modularity to morphological landmarks. Perform model selection on results. Fit models with a single within-module correlation or with separate within-module correlations fitted to each module.

r-energy

Homepage:
Spack package:
Versions:
1.7-6, 1.7-5
Build Dependencies:
r, r-rcpp, r-boot
Link Dependencies:
r
Run Dependencies:
r, r-rcpp, r-boot
Description:
E-Statistics: Multivariate Inference via the Energy of Data

r-enrichplot

Homepage:
Spack package:
Versions:
1.4.0, 1.2.0, 1.0.2
Build Dependencies:
r, r-annotationdbi, r-cowplot, r-dose, r-ggplot2, r-ggraph, r-ggridges, r-gosemsim, r-igraph, r-reshape2, r-upsetr, r-europepmc, r-ggplotify, r-gridextra, r-purrr, r-rcolorbrewer
Link Dependencies:
r
Run Dependencies:
r, r-annotationdbi, r-cowplot, r-dose, r-ggplot2, r-ggraph, r-ggridges, r-gosemsim, r-igraph, r-reshape2, r-upsetr, r-europepmc, r-ggplotify, r-gridextra, r-purrr, r-rcolorbrewer
Description:
Visualization of Functional Enrichment Result. The 'enrichplot' package implements several visualization methods for interpreting functional enrichment results obtained from ORA or GSEA analysis. All the visualization methods are developed based on 'ggplot2' graphics.

r-ensembldb

Homepage:
Spack package:
Versions:
2.8.1, 2.6.8, 2.4.1, 2.2.2, 2.0.4
Build Dependencies:
r, r-biocgenerics, r-genomicranges, r-genomicfeatures, r-annotationfilter, r-rsqlite, r-dbi, r-biobase, r-genomeinfodb, r-annotationdbi, r-rtracklayer, r-s4vectors, r-annotationhub, r-rsamtools, r-iranges, r-protgenerics, r-biostrings, r-curl
Link Dependencies:
r
Run Dependencies:
r, r-biocgenerics, r-genomicranges, r-genomicfeatures, r-annotationfilter, r-rsqlite, r-dbi, r-biobase, r-genomeinfodb, r-annotationdbi, r-rtracklayer, r-s4vectors, r-annotationhub, r-rsamtools, r-iranges, r-protgenerics, r-biostrings, r-curl
Description:
Utilities to create and use Ensembl-based annotation databases. The package provides functions to create and use transcript centric annotation databases/packages. The annotation for the databases are directly fetched from Ensembl using their Perl API. The functionality and data is similar to that of the TxDb packages from the GenomicFeatures package, but, in addition to retrieve all gene/transcript models and annotations from the database, ensembldb provides a filter framework allowing to retrieve annotations for specific entries like genes encoded on a chromosome region or transcript models of lincRNA genes. EnsDb databases built with ensembldb contain also protein annotations and mappings between proteins and their encoding transcripts. Finally, ensembldb provides functions to map between genomic, transcript and protein coordinates.

r-ergm

Homepage:
Spack package:
Versions:
3.10.4, 3.10.1, 3.7.1
Build Dependencies:
r, r-robustbase, r-coda, r-trust, r-matrix, r-lpsolve, r-mass, r-statnet-common, r-network, r-purrr, r-rlang, r-tibble, r-dplyr
Link Dependencies:
r
Run Dependencies:
r, r-robustbase, r-coda, r-trust, r-matrix, r-lpsolve, r-mass, r-statnet-common, r-network, r-purrr, r-rlang, r-tibble, r-dplyr
Description:
An integrated set of tools to analyze and simulate networks based on exponential-family random graph models (ERGM). "ergm" is a part of the "statnet" suite of packages for network analysis.

r-europepmc

Homepage:
Spack package:
Versions:
0.3
Build Dependencies:
r, r-dplyr, r-httr, r-jsonlite, r-plyr, r-progress, r-purrr, r-urltools, r-xml2
Link Dependencies:
r
Run Dependencies:
r, r-dplyr, r-httr, r-jsonlite, r-plyr, r-progress, r-purrr, r-urltools, r-xml2
Description:
europepmc: R Interface to the Europe PubMed Central RESTful Web Service

r-evaluate

Homepage:
Spack package:
Versions:
0.14, 0.10.1, 0.10, 0.9
Build Dependencies:
r, r-stringr
Link Dependencies:
r
Run Dependencies:
r, r-stringr
Description:
Parsing and evaluation tools that make it easy to recreate the command line behaviour of R.

r-evd

Homepage:
Spack package:
Versions:
2.3-3
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
evd: Functions for Extreme Value Distributions

r-exomecopy

Homepage:
Spack package:
Versions:
1.32.0
Build Dependencies:
r, r-iranges, r-genomicranges, r-rsamtools, r-genomeinfodb
Link Dependencies:
r
Run Dependencies:
r, r-iranges, r-genomicranges, r-rsamtools, r-genomeinfodb
Description:
Detection of copy number variants (CNV) from exome sequencing samples, including unpaired samples. The package implements a hidden Markov model which uses positional covariates, such as background read depth and GC- content, to simultaneously normalize and segment the samples into regions of constant copy count.

r-exomedepth

Homepage:
Spack package:
Versions:
1.1.15
Build Dependencies:
r, r-biostrings, r-iranges, r-rsamtools, r-genomicranges, r-aod, r-vgam, r-genomicalignments, r-dplyr, r-magrittr
Link Dependencies:
r
Run Dependencies:
r, r-biostrings, r-iranges, r-rsamtools, r-genomicranges, r-aod, r-vgam, r-genomicalignments, r-dplyr, r-magrittr
Description:
Calls copy number variants (CNVs) from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders.

r-expint

Homepage:
Spack package:
Versions:
0.1-5
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
expint: Exponential Integral and Incomplete Gamma Function

r-expm

Homepage:
Spack package:
Versions:
0.999-4, 0.999-3, 0.999-2
Build Dependencies:
r, r-matrix
Link Dependencies:
r
Run Dependencies:
r, r-matrix
Description:
Computation of the matrix exponential, logarithm, sqrt, and related quantities.

r-factoextra

Homepage:
Spack package:
Versions:
1.0.5, 1.0.4
Build Dependencies:
r, r-ggplot2, r-abind, r-cluster, r-dendextend, r-factominer, r-ggpubr, r-reshape2, r-ggrepel, r-tidyr
Link Dependencies:
r
Run Dependencies:
r, r-ggplot2, r-abind, r-cluster, r-dendextend, r-factominer, r-ggpubr, r-reshape2, r-ggrepel, r-tidyr
Description:
factoextra: Extract and Visualize the Results of Multivariate Data Analyses

r-factominer

Homepage:
Spack package:
Versions:
1.42, 1.41, 1.40, 1.39, 1.38, 1.36, 1.35
Build Dependencies:
r, r-car, r-cluster, r-ellipse, r-flashclust, r-lattice, r-leaps, r-mass, r-scatterplot3d
Link Dependencies:
r
Run Dependencies:
r, r-car, r-cluster, r-ellipse, r-flashclust, r-lattice, r-leaps, r-mass, r-scatterplot3d
Description:
FactoMineR: Multivariate Exploratory Data Analysis and Data Mining

r-fansi

Homepage:
Spack package:
Versions:
0.4.0, 0.3.0, 0.2.3, 0.2.2, 0.2.1
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Counterparts to R string manipulation functions that account for the effects of ANSI text formatting control sequences.

r-farver

Homepage:
Spack package:
Versions:
2.0.1
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
farver: High Performance Colour Space Manipulation

r-fastcluster

Homepage:
Spack package:
Versions:
1.1.25
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
This is a two-in-one package which provides interfaces to both R and 'Python'. It implements fast hierarchical, agglomerative clustering routines. Part of the functionality is designed as drop-in replacement for existing routines: linkage() in the 'SciPy' package 'scipy.cluster.hierarchy', hclust() in R's 'stats' package, and the 'flashClust' package. It provides the same functionality with the benefit of a much faster implementation. Moreover, there are memory- saving routines for clustering of vector data, which go beyond what the existing packages provide. For information on how to install the 'Python' files, see the file INSTALL in the source distribution.

r-fastmatch

Homepage:
Spack package:
Versions:
1.1-0
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Package providing a fast match() replacement for cases that require repeated look-ups. It is slightly faster that R's built-in match() function on first match against a table, but extremely fast on any subsequent lookup as it keeps the hash table in memory.

r-fdb-infiniummethylation-hg18

Homepage:
Spack package:
Versions:
2.2.0
Build Dependencies:
r, r-genomicfeatures, r-txdb-hsapiens-ucsc-hg18-knowngene, r-org-hs-eg-db, r-annotationdbi, r-biostrings
Link Dependencies:
r
Run Dependencies:
r, r-genomicfeatures, r-txdb-hsapiens-ucsc-hg18-knowngene, r-org-hs-eg-db, r-annotationdbi, r-biostrings
Description:
Compiled HumanMethylation27 and HumanMethylation450 annotations

r-fdb-infiniummethylation-hg19

Homepage:
Spack package:
Versions:
2.2.0
Build Dependencies:
r, r-genomicfeatures, r-txdb-hsapiens-ucsc-hg19-knowngene, r-org-hs-eg-db, r-annotationdbi, r-biostrings
Link Dependencies:
r
Run Dependencies:
r, r-genomicfeatures, r-txdb-hsapiens-ucsc-hg19-knowngene, r-org-hs-eg-db, r-annotationdbi, r-biostrings
Description:
Compiled HumanMethylation27 and HumanMethylation450 annotations.

r-ff

Homepage:
Spack package:
Versions:
2.2-14, 2.2-13
Build Dependencies:
r, r-bit
Link Dependencies:
r
Run Dependencies:
r, r-bit
Description:
memory-efficient storage of large data on disk and fast access functions.

r-fftwtools

Homepage:
Spack package:
Versions:
0.9-8
Build Dependencies:
r, fftw
Link Dependencies:
r, fftw
Run Dependencies:
r
Description:
Provides a wrapper for several 'FFTW' functions. This package provides access to the two-dimensional 'FFT', the multivariate 'FFT', and the one-dimensional real to complex 'FFT' using the 'FFTW3' library. The package includes the functions fftw() and mvfftw() which are designed to mimic the functionality of the R functions fft() and mvfft(). The 'FFT' functions have a parameter that allows them to not return the redundant complex conjugate when the input is real data.

r-fgsea

Homepage:
Spack package:
Versions:
1.10.1, 1.8.0, 1.6.0, 1.4.1, 1.2.1
Build Dependencies:
r, r-rcpp, r-data-table, r-biocparallel, r-ggplot2, r-gridextra, r-fastmatch, r-matrix, r-bh
Link Dependencies:
r
Run Dependencies:
r, r-rcpp, r-data-table, r-biocparallel, r-ggplot2, r-gridextra, r-fastmatch, r-matrix, r-bh
Description:
Fast Gene Set Enrichment Analysis. The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction.

r-fields

Homepage:
Spack package:
Versions:
9.9
Build Dependencies:
r, r-maps, r-spam
Link Dependencies:
r
Run Dependencies:
r, r-maps, r-spam
Description:
fields: Tools for Spatial Data

r-filehash

Homepage:
Spack package:
Versions:
2.4-2, 2.4-1, 2.3
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Implements a simple key-value style database where character string keys are associated with data values that are stored on the disk. A simple interface is provided for inserting, retrieving, and deleting data from the database. Utilities are provided that allow 'filehash' databases to be treated much like environments and lists are already used in R. These utilities are provided to encourage interactive and exploratory analysis on large datasets. Three different file formats for representing the database are currently available and new formats can easily be incorporated by third parties for use in the 'filehash' framework.

r-findpython

Homepage:
Spack package:
Versions:
1.0.5, 1.0.4, 1.0.3
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r, python
Description:
Package designed to find an acceptable python binary.

r-fit-models

Homepage:
Spack package:
Versions:
0.5-14, 0.5-13
Build Dependencies:
r, r-lattice
Link Dependencies:
r
Run Dependencies:
r, r-lattice
Description:
Compare Fitted Models

r-fitdistrplus

Homepage:
Spack package:
Versions:
1.0-14
Build Dependencies:
r, r-mass, r-survival, r-npsurv
Link Dependencies:
r
Run Dependencies:
r, r-mass, r-survival, r-npsurv
Description:
Extends the fitdistr() function (of the MASS package) with several functions to help the fit of a parametric distribution to non-censored or censored data. Censored data may contain left censored, right censored and interval censored values, with several lower and upper bounds. In addition to maximum likelihood estimation (MLE), the package provides moment matching (MME), quantile matching (QME) and maximum goodness-of-fit estimation (MGE) methods (available only for non- censored data). Weighted versions of MLE, MME and QME are available. See e.g. Casella & Berger (2002). Statistical inference. Pacific Grove.

r-flashclust

Homepage:
Spack package:
Versions:
1.01-2
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
flashClust: Implementation of optimal hierarchical clustering

r-flexclust

Homepage:
Spack package:
Versions:
1.4-0, 1.3-5
Build Dependencies:
r, r-lattice, r-modeltools, r-class
Link Dependencies:
r
Run Dependencies:
r, r-lattice, r-modeltools, r-class
Description:
The main function kcca implements a general framework for k-centroids cluster analysis supporting arbitrary distance measures and centroid computation. Further cluster methods include hard competitive learning, neural gas, and QT clustering. There are numerous visualization methods for cluster results (neighborhood graphs, convex cluster hulls, barcharts of centroids, ...), and bootstrap methods for the analysis of cluster stability.

r-flexmix

Homepage:
Spack package:
Versions:
2.3-15, 2.3-14
Build Dependencies:
r, r-lattice, r-modeltools, r-nnet
Link Dependencies:
r
Run Dependencies:
r, r-lattice, r-modeltools, r-nnet
Description:
flexmix: Flexible Mixture Modeling

r-fnn

Homepage:
Spack package:
Versions:
1.1.3, 1.1.2.2, 1.1, 1.0, 0.6-4, 0.6-3, 0.6-2
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Cover-tree and kd-tree fast k-nearest neighbor search algorithms and related applications including KNN classification, regression and information measures are implemented.

r-forcats

Homepage:
Spack package:
Versions:
0.4.0, 0.3.0, 0.2.0
Build Dependencies:
r, r-tibble, r-magrittr, r-ellipsis, r-rlang
Link Dependencies:
r
Run Dependencies:
r, r-tibble, r-magrittr, r-ellipsis, r-rlang
Description:
Helpers for reordering factor levels (including moving specified levels to front, ordering by first appearance, reversing, and randomly shuffling), and tools for modifying factor levels (including collapsing rare levels into other, 'anonymising', and manually 'recoding').

r-foreach

Homepage:
Spack package:
Versions:
1.4.7, 1.4.3
Build Dependencies:
r, r-codetools, r-iterators
Link Dependencies:
r
Run Dependencies:
r, r-codetools, r-iterators
Description:
Support for the foreach looping construct. Foreach is an idiom that allows for iterating over elements in a collection, without the use of an explicit loop counter. This package in particular is intended to be used for its return value, rather than for its side effects. In that sense, it is similar to the standard lapply function, but doesn't require the evaluation of a function. Using foreach without side effects also facilitates executing the loop in parallel.

r-forecast

Homepage:
Spack package:
Versions:
8.8, 8.6, 8.2
Build Dependencies:
r, r-magrittr, r-ggplot2, r-colorspace, r-nnet, r-rcpp, r-fracdiff, r-tseries, r-lmtest, r-zoo, r-timedate, r-rcpparmadillo, r-urca
Link Dependencies:
r
Run Dependencies:
r, r-magrittr, r-ggplot2, r-colorspace, r-nnet, r-rcpp, r-fracdiff, r-tseries, r-lmtest, r-zoo, r-timedate, r-rcpparmadillo, r-urca
Description:
Methods and tools for displaying and analysing univariate time series forecasts including exponential smoothing via state space models and automatic ARIMA modelling.

r-foreign

Homepage:
Spack package:
Versions:
0.8-72, 0.8-70.2, 0.8-66
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Functions for reading and writing data stored by some versions of Epi Info, Minitab, S, SAS, SPSS, Stata, Systat and Weka and for reading and writing some dBase files.

r-formatr

Homepage:
Spack package:
Versions:
1.7, 1.6, 1.5, 1.4
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Provides a function tidy_source() to format R source code. Spaces and indent will be added to the code automatically, and comments will be preserved under certain conditions, so that R code will be more human- readable and tidy. There is also a Shiny app as a user interface in this package.

r-formula

Homepage:
Spack package:
Versions:
1.2-3, 1.2-2, 1.2-1
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Infrastructure for extended formulas with multiple parts on the right- hand side and/or multiple responses on the left-hand side.

r-fpc

Homepage:
Spack package:
Versions:
2.2-3, 2.2-2, 2.1-10
Build Dependencies:
r, r-mass, r-cluster, r-mclust, r-flexmix, r-prabclus, r-class, r-diptest, r-mvtnorm, r-robustbase, r-kernlab, r-trimcluster
Link Dependencies:
r
Run Dependencies:
r, r-mass, r-cluster, r-mclust, r-flexmix, r-prabclus, r-class, r-diptest, r-mvtnorm, r-robustbase, r-kernlab, r-trimcluster
Description:
fpc: Flexible Procedures for Clustering

r-fracdiff

Homepage:
Spack package:
Versions:
1.4-2
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Maximum likelihood estimation of the parameters of a fractionally differenced ARIMA(p,d,q) model (Haslett and Raftery, Appl.Statistics, 1989).

r-fs

Homepage:
Spack package:
Versions:
1.3.1
Build Dependencies:
r, r-rcpp, gmake
Link Dependencies:
r
Run Dependencies:
r, r-rcpp
Description:
A cross-platform interface to file system operations, built on top of the 'libuv' C library.

r-futile-logger

Homepage:
Spack package:
Versions:
1.4.3
Build Dependencies:
r, r-lambda-r, r-futile-options
Link Dependencies:
r
Run Dependencies:
r, r-lambda-r, r-futile-options
Description:
Provides a simple yet powerful logging utility. Based loosely on log4j, futile.logger takes advantage of R idioms to make logging a convenient and easy to use replacement for cat and print statements.

r-futile-options

Homepage:
Spack package:
Versions:
1.0.1, 1.0.0
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
A scoped options management framework

r-future

Homepage:
Spack package:
Versions:
1.14.0
Build Dependencies:
r, r-digest, r-globals, r-listenv
Link Dependencies:
r
Run Dependencies:
r, r-digest, r-globals, r-listenv
Description:
The purpose of this package is to provide a lightweight and unified Future API for sequential and parallel processing of R expression via futures. The simplest way to evaluate an expression in parallel is to use 'x %<-% { expression }' with 'plan(multiprocess)'. This package implements sequential, multicore, multisession, and cluster futures. With these, R expressions can be evaluated on the local machine, in parallel a set of local machines, or distributed on a mix of local and remote machines. Extensions to this package implement additional backends for processing futures via compute cluster schedulers etc. Because of its unified API, there is no need to modify any code in order switch from sequential on the local machine to, say, distributed processing on a remote compute cluster. Another strength of this package is that global variables and functions are automatically identified and exported as needed, making it straightforward to tweak existing code to make use of futures.

r-future-apply

Homepage:
Spack package:
Versions:
1.3.0
Build Dependencies:
r, r-future, r-globals
Link Dependencies:
r
Run Dependencies:
r, r-future, r-globals
Description:
Implementations of apply(), by(), eapply(), lapply(), Map(), mapply(), replicate(), sapply(), tapply(), and vapply() that can be resolved using any future-supported backend, e.g. parallel on the local machine or distributed on a compute cluster. These future_*apply() functions come with the same pros and cons as the corresponding base-R *apply() functions but with the additional feature of being able to be processed via the future framework.

r-gamlss

Homepage:
Spack package:
Versions:
5.1-4, 5.1-3, 5.1-2
Build Dependencies:
r, r-gamlss-data, r-gamlss-dist, r-mass, r-survival, r-nlme
Link Dependencies:
r
Run Dependencies:
r, r-gamlss-data, r-gamlss-dist, r-mass, r-survival, r-nlme
Description:
gamlss: Generalised Additive Models for Location Scale and Shape

r-gamlss-data

Homepage:
Spack package:
Versions:
5.1-4, 5.1-3, 5.1-0
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
gamlss.data: GAMLSS Data

r-gamlss-dist

Homepage:
Spack package:
Versions:
5.1-4, 5.1-3, 5.1-1
Build Dependencies:
r, r-mass
Link Dependencies:
r
Run Dependencies:
r, r-mass
Description:
gamlss.dist: Distributions for Generalized Additive Models for Location Scale and Shape

r-gbm

Homepage:
Spack package:
Versions:
2.1.5, 2.1.3
Build Dependencies:
r, r-gridextra, r-survival, r-lattice
Link Dependencies:
r
Run Dependencies:
r, r-gridextra, r-survival, r-lattice
Description:
Generalized Boosted Regression Models.

r-gbrd

Homepage:
Spack package:
Versions:
0.4-11
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Provides utilities for processing Rd objects and files. Extract argument descriptions and other parts of the help pages of functions.

r-gcrma

Homepage:
Spack package:
Versions:
2.56.0, 2.54.0, 2.52.0, 2.50.0, 2.48.0
Build Dependencies:
r, r-affy, r-biobase, r-affyio, r-xvector, r-biostrings, r-biocinstaller, r-biocmanager
Link Dependencies:
r
Run Dependencies:
r, r-affy, r-biobase, r-affyio, r-xvector, r-biostrings, r-biocinstaller, r-biocmanager
Description:
Background Adjustment Using Sequence Information.

r-gdalutils

Homepage:
Spack package:
Versions:
2.0.1.14
Build Dependencies:
r, r-sp, r-foreach, r-r-utils, r-raster, r-rgdal, gdal
Link Dependencies:
r, gdal
Run Dependencies:
r, r-sp, r-foreach, r-r-utils, r-raster, r-rgdal
Description:
gdalUtils: Wrappers for the Geospatial Data Abstraction Library

r-gdata

Homepage:
Spack package:
Versions:
2.18.0, 2.17.0
Build Dependencies:
r, r-gtools, perl
Link Dependencies:
r, perl
Run Dependencies:
r, r-gtools
Description:
Various R programming tools for data manipulation, including: - medical unit conversions ('ConvertMedUnits', 'MedUnits'), - combining objects ('bindData', 'cbindX', 'combine', 'interleave'), - character vector operations ('centerText', 'startsWith', 'trim'), - factor manipulation ('levels', 'reorder.factor', 'mapLevels'), - obtaining information about R objects ('object.size', 'elem', 'env', 'humanReadable', 'is.what', 'll', 'keep', 'ls.funs', 'Args','nPairs', 'nobs'), - manipulating MS- Excel formatted files ('read.xls', 'installXLSXsupport', 'sheetCount', 'xlsFormats'), - generating fixed-width format files ('write.fwf'), - extricating components of date & time objects ('getYear', 'getMonth', 'getDay', 'getHour', 'getMin', 'getSec'), - operations on columns of data frames ('matchcols', 'rename.vars'), - matrix operations ('unmatrix', 'upperTriangle', 'lowerTriangle'), - operations on vectors ('case', 'unknownToNA', 'duplicated2', 'trimSum'), - operations on data frames ('frameApply', 'wideByFactor'), - value of last evaluated expression ('ans'), and - wrapper for 'sample' that ensures consistent behavior for both scalar and vector arguments ('resample').

r-gdsfmt

Homepage:
Spack package:
Versions:
1.20.0, 1.18.1, 1.16.0, 1.14.1, 1.12.0
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
R Interface to CoreArray Genomic Data Structure (GDS) Files. This package provides a high-level R interface to CoreArray Genomic Data Structure (GDS) data files, which are portable across platforms with hierarchical structure to store multiple scalable array-oriented data sets with metadata information. It is suited for large-scale datasets, especially for data which are much larger than the available random- access memory. The gdsfmt package offers the efficient operations specifically designed for integers of less than 8 bits, since a diploid genotype, like single-nucleotide polymorphism (SNP), usually occupies fewer bits than a byte. Data compression and decompression are available with relatively efficient random access. It is also allowed to read a GDS file in parallel with multiple R processes supported by the package parallel.

r-geiger

Homepage:
Spack package:
Versions:
2.0.6.2, 2.0.6.1, 2.0.6
Build Dependencies:
r, r-ape, r-mvtnorm, r-subplex, r-desolve, r-digest, r-rcpp, r-coda, r-ncbit, r-colorspace, r-mass
Link Dependencies:
r
Run Dependencies:
r, r-ape, r-mvtnorm, r-subplex, r-desolve, r-digest, r-rcpp, r-coda, r-ncbit, r-colorspace, r-mass
Description:
Methods for fitting macroevolutionary models to phylogenetic trees.

r-genefilter

Homepage:
Spack package:
Versions:
1.66.0, 1.64.0, 1.62.0, 1.60.0, 1.58.1
Build Dependencies:
r, r-s4vectors, r-annotationdbi, r-annotate, r-biobase, r-survival
Link Dependencies:
r
Run Dependencies:
r, r-s4vectors, r-annotationdbi, r-annotate, r-biobase, r-survival
Description:
genefilter: methods for filtering genes from high-throughput experiments.

r-genelendatabase

Homepage:
Spack package:
Versions:
1.20.0, 1.18.0, 1.16.0, 1.14.0, 1.12.0
Build Dependencies:
r, r-rtracklayer, r-genomicfeatures
Link Dependencies:
r
Run Dependencies:
r, r-rtracklayer, r-genomicfeatures
Description:
Lengths of mRNA transcripts for a number of genomes. Length of mRNA transcripts for a number of genomes and gene ID formats, largely based on UCSC table browser

r-genemeta

Homepage:
Spack package:
Versions:
1.56.0, 1.54.0, 1.52.0, 1.50.0, 1.48.0
Build Dependencies:
r, r-biobase, r-genefilter
Link Dependencies:
r
Run Dependencies:
r, r-biobase, r-genefilter
Description:
MetaAnalysis for High Throughput Experiments. A collection of meta- analysis tools for analysing high throughput experimental data

r-geneplotter

Homepage:
Spack package:
Versions:
1.62.0, 1.60.0, 1.58.0, 1.56.0, 1.54.0
Build Dependencies:
r, r-biobase, r-biocgenerics, r-lattice, r-annotate, r-annotationdbi, r-rcolorbrewer
Link Dependencies:
r
Run Dependencies:
r, r-biobase, r-biocgenerics, r-lattice, r-annotate, r-annotationdbi, r-rcolorbrewer
Description:
Graphics related functions for Bioconductor.

r-generics

Homepage:
Spack package:
Versions:
0.0.2
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
In order to reduce potential package dependencies and conflicts, generics provides a number of commonly used S3 generics.

r-genetics

Homepage:
Spack package:
Versions:
1.3.8.1.2
Build Dependencies:
r, r-combinat, r-gdata, r-gtools, r-mass, r-mvtnorm
Link Dependencies:
r
Run Dependencies:
r, r-combinat, r-gdata, r-gtools, r-mass, r-mvtnorm
Description:
genetics: Population Genetics

r-genie3

Homepage:
Spack package:
Versions:
1.6.0, 1.4.3, 1.2.1, 1.0.0
Build Dependencies:
r, r-reshape2
Link Dependencies:
r
Run Dependencies:
r, r-reshape2
Description:
GEne Network Inference with Ensemble of trees. This package implements the GENIE3 algorithm for inferring gene regulatory networks from expression data.

r-genomeinfodb

Homepage:
Spack package:
Versions:
1.20.0, 1.18.2, 1.16.0, 1.14.0, 1.12.3
Build Dependencies:
r, r-biocgenerics, r-s4vectors, r-iranges, r-rcurl, r-genomeinfodbdata
Link Dependencies:
r
Run Dependencies:
r, r-biocgenerics, r-s4vectors, r-iranges, r-rcurl, r-genomeinfodbdata
Description:
Utilities for manipulating chromosome names, including modifying them to follow a particular naming style. Contains data and functions that define and allow translation between different chromosome sequence naming conventions (e.g., "chr1" versus "1"), including a function that attempts to place sequence names in their natural, rather than lexicographic, order.

r-genomeinfodbdata

Homepage:
Spack package:
Versions:
1.2.1, 1.1.0, 0.99.0
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
for mapping between NCBI taxonomy ID and species. Used by functions in the GenomeInfoDb package.

r-genomicalignments

Homepage:
Spack package:
Versions:
1.20.1, 1.18.1, 1.16.0, 1.14.2, 1.12.2
Build Dependencies:
r, r-biocgenerics, r-s4vectors, r-iranges, r-genomeinfodb, r-genomicranges, r-summarizedexperiment, r-biostrings, r-rsamtools, r-biocparallel
Link Dependencies:
r
Run Dependencies:
r, r-biocgenerics, r-s4vectors, r-iranges, r-genomeinfodb, r-genomicranges, r-summarizedexperiment, r-biostrings, r-rsamtools, r-biocparallel
Description:
Representation and manipulation of short genomic alignments. Provides efficient containers for storing and manipulating short genomic alignments (typically obtained by aligning short reads to a reference genome). This includes read counting, computing the coverage, junction detection, and working with the nucleotide content of the alignments.

r-genomicfeatures

Homepage:
Spack package:
Versions:
1.36.4, 1.34.8, 1.32.3, 1.30.3, 1.28.5
Build Dependencies:
r, r-biocgenerics, r-s4vectors, r-iranges, r-genomeinfodb, r-genomicranges, r-annotationdbi, r-dbi, r-rsqlite, r-rcurl, r-xvector, r-biostrings, r-rtracklayer, r-biomart, r-biobase, r-rmysql
Link Dependencies:
r
Run Dependencies:
r, r-biocgenerics, r-s4vectors, r-iranges, r-genomeinfodb, r-genomicranges, r-annotationdbi, r-dbi, r-rsqlite, r-rcurl, r-xvector, r-biostrings, r-rtracklayer, r-biomart, r-biobase, r-rmysql
Description:
Conveniently import and query gene models. A set of tools and methods for making and manipulating transcript centric annotations. With these tools the user can easily download the genomic locations of the transcripts, exons and cds of a given organism, from either the UCSC Genome Browser or a BioMart database (more sources will be supported in the future). This information is then stored in a local database that keeps track of the relationship between transcripts, exons, cds and genes. Flexible methods are provided for extracting the desired features in a convenient format.

r-genomicranges

Homepage:
Spack package:
Versions:
1.36.1, 1.34.0, 1.32.7, 1.30.3, 1.28.6
Build Dependencies:
r, r-biocgenerics, r-s4vectors, r-iranges, r-genomeinfodb, r-xvector
Link Dependencies:
r
Run Dependencies:
r, r-biocgenerics, r-s4vectors, r-iranges, r-genomeinfodb, r-xvector
Description:
Representation and manipulation of genomic intervals. The ability to efficiently represent and manipulate genomic annotations and alignments is playing a central role when it comes to analyzing high-throughput sequencing data (a.k.a. NGS data). The GenomicRanges package defines general purpose containers for storing and manipulating genomic intervals and variables defined along a genome. More specialized containers for representing and manipulating short alignments against a reference genome, or a matrix-like summarization of an experiment, are defined in the GenomicAlignments and SummarizedExperiment packages, respectively. Both packages build on top of the GenomicRanges infrastructure.

r-gensa

Homepage:
Spack package:
Versions:
1.1.7
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
GenSA: Generalized Simulated Annealing Performs search for global minimum of a very complex non-linear objective function with a very large number of optima.

r-geomorph

Homepage:
Spack package:
Versions:
3.1.2, 3.1.1, 3.0.7, 3.0.5
Build Dependencies:
r, r-rgl, r-ape, r-jpeg, r-geiger, r-matrix, r-rrpp
Link Dependencies:
r
Run Dependencies:
r, r-rgl, r-ape, r-jpeg, r-geiger, r-matrix, r-rrpp
Description:
Read, manipulate, and digitize landmark data, generate shape variables via Procrustes analysis for points, curves and surfaces, perform shape analyses, and provide graphical depictions of shapes and patterns of shape variation.

r-geonames

Homepage:
Spack package:
Versions:
0.999
Build Dependencies:
r, r-rjson
Link Dependencies:
r
Run Dependencies:
r, r-rjson
Description:
geonames: Interface to the "Geonames" Spatial Query Web Service

r-geoquery

Homepage:
Spack package:
Versions:
2.52.0, 2.50.5, 2.48.0, 2.46.15, 2.42.0
Build Dependencies:
r, r-biobase, r-xml, r-rcurl, r-httr, r-readr, r-xml2, r-dplyr, r-tidyr, r-magrittr, r-limma
Link Dependencies:
r
Run Dependencies:
r, r-biobase, r-xml, r-rcurl, r-httr, r-readr, r-xml2, r-dplyr, r-tidyr, r-magrittr, r-limma
Description:
Get data from NCBI Gene Expression Omnibus (GEO). The NCBI Gene Expression Omnibus (GEO) is a public repository of microarray data. Given the rich and varied nature of this resource, it is only natural to want to apply BioConductor tools to these data. GEOquery is the bridge between GEO and BioConductor.

r-geor

Homepage:
Spack package:
Versions:
1.7-5.2.1
Build Dependencies:
r, r-mass, r-sp, r-splancs, r-randomfields
Link Dependencies:
r
Run Dependencies:
r, r-mass, r-sp, r-splancs, r-randomfields
Description:
Geostatistical analysis including traditional, likelihood-based and Bayesian methods.

r-geosphere

Homepage:
Spack package:
Versions:
1.5-10, 1.5-7, 1.5-5
Build Dependencies:
r, r-sp
Link Dependencies:
r
Run Dependencies:
r, r-sp
Description:
Spherical trigonometry for geographic applications. That is, compute distances and related measures for angular (longitude/latitude) locations.

r-getopt

Homepage:
Spack package:
Versions:
1.20.3, 1.20.2, 1.20.1
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Package designed to be used with Rscript to write "#!" shebang scripts that accept short and long flags/options. Many users will prefer using instead the packages optparse or argparse which add extra features like automatically generated help option and usage, support for default values, positional argument support, etc.

r-getoptlong

Homepage:
Spack package:
Versions:
0.1.7, 0.1.6
Build Dependencies:
r, r-rjson, r-globaloptions, perl
Link Dependencies:
r, perl
Run Dependencies:
r, r-rjson, r-globaloptions
Description:
This is yet another command-line argument parser which wraps the powerful Perl module Getopt::Long and with some adaptation for easier use in R. It also provides a simple way for variable interpolation in R.

r-ggally

Homepage:
Spack package:
Versions:
1.4.0, 1.3.2
Build Dependencies:
r, r-ggplot2, r-gtable, r-plyr, r-progress, r-rcolorbrewer, r-reshape, r-rlang, openssl
Link Dependencies:
r, openssl
Run Dependencies:
r, r-ggplot2, r-gtable, r-plyr, r-progress, r-rcolorbrewer, r-reshape, r-rlang
Description:
The R package 'ggplot2' is a plotting system based on the grammar of graphics. 'GGally' extends 'ggplot2' by adding several functions to reduce the complexity of combining geometric objects with transformed data. Some of these functions include a pairwise plot matrix, a two group pairwise plot matrix, a parallel coordinates plot, a survival plot, and several functions to plot networks.

r-ggbeeswarm

Homepage:
Spack package:
Versions:
0.6.0
Build Dependencies:
r, r-beeswarm, r-ggplot2, r-vipor
Link Dependencies:
r
Run Dependencies:
r, r-beeswarm, r-ggplot2, r-vipor
Description:
ggbeeswarm: Categorical Scatter (Violin Point) Plots

r-ggbio

Homepage:
Spack package:
Versions:
1.32.0, 1.30.0, 1.28.5, 1.26.1, 1.24.1
Build Dependencies:
r, r-biocgenerics, r-ggplot2, r-gridextra, r-scales, r-reshape2, r-gtable, r-hmisc, r-biovizbase, r-biobase, r-s4vectors, r-iranges, r-genomeinfodb, r-genomicranges, r-summarizedexperiment, r-biostrings, r-rsamtools, r-genomicalignments, r-bsgenome, r-variantannotation, r-rtracklayer, r-genomicfeatures, r-organismdbi, r-ggally, r-ensembldb, r-annotationdbi, r-annotationfilter, r-rlang
Link Dependencies:
r
Run Dependencies:
r, r-biocgenerics, r-ggplot2, r-gridextra, r-scales, r-reshape2, r-gtable, r-hmisc, r-biovizbase, r-biobase, r-s4vectors, r-iranges, r-genomeinfodb, r-genomicranges, r-summarizedexperiment, r-biostrings, r-rsamtools, r-genomicalignments, r-bsgenome, r-variantannotation, r-rtracklayer, r-genomicfeatures, r-organismdbi, r-ggally, r-ensembldb, r-annotationdbi, r-annotationfilter, r-rlang
Description:
Visualization tools for genomic data. The ggbio package extends and specializes the grammar of graphics for biological data. The graphics are designed to answer common scientific questions, in particular those often asked of high throughput genomics data. All core Bioconductor data structures are supported, where appropriate. The package supports detailed views of particular genomic regions, as well as genome-wide overviews. Supported overviews include ideograms and grand linear views. High-level plots include sequence fragment length, edge-linked interval to data view, mismatch pileup, and several splicing summaries.

r-ggdendro

Homepage:
Spack package:
Versions:
0.1-20
Build Dependencies:
r, r-ggplot2, r-mass
Link Dependencies:
r
Run Dependencies:
r, r-ggplot2, r-mass
Description:
This is a set of tools for dendrograms and tree plots using 'ggplot2'. The 'ggplot2' philosophy is to clearly separate data from the presentation. Unfortunately the plot method for dendrograms plots directly to a plot device without exposing the data. The 'ggdendro' package resolves this by making available functions that extract the dendrogram plot data. The package provides implementations for tree, rpart, as well as diana and agnes cluster diagrams.

r-ggforce

Homepage:
Spack package:
Versions:
0.3.1
Build Dependencies:
r, r-ggplot2, r-gtable, r-mass, r-polyclip, r-rcpp, r-rcppeigen, r-rlang, r-scales, r-tidyselect, r-tweenr, r-withr
Link Dependencies:
r
Run Dependencies:
r, r-ggplot2, r-gtable, r-mass, r-polyclip, r-rcpp, r-rcppeigen, r-rlang, r-scales, r-tidyselect, r-tweenr, r-withr
Description:
ggforce: Accelerating 'ggplot2'

r-ggjoy

Homepage:
Spack package:
Versions:
0.4.1, 0.4.0, 0.3.0, 0.2.0
Build Dependencies:
r, r-ggplot2, r-ggridges
Link Dependencies:
r
Run Dependencies:
r, r-ggplot2, r-ggridges
Description:
Joyplots provide a convenient way of visualizing changes in distributions over time or space.

r-ggmap

Homepage:
Spack package:
Versions:
3.0.0, 2.6.2, 2.6.1
Build Dependencies:
r, r-ggplot2, r-proto, r-rgooglemaps, r-png, r-plyr, r-reshape2, r-rjson, r-mapproj, r-jpeg, r-geosphere, r-digest, r-scales, r-dplyr, r-bitops, r-glue, r-httr, r-stringr, r-purrr, r-magrittr, r-tibble, r-tidyr
Link Dependencies:
r
Run Dependencies:
r, r-ggplot2, r-proto, r-rgooglemaps, r-png, r-plyr, r-reshape2, r-rjson, r-mapproj, r-jpeg, r-geosphere, r-digest, r-scales, r-dplyr, r-bitops, r-glue, r-httr, r-stringr, r-purrr, r-magrittr, r-tibble, r-tidyr
Description:
A collection of functions to visualize spatial data and models on top of static maps from various online sources (e.g Google Maps and Stamen Maps). It includes tools common to those tasks, including functions for geolocation and routing.

r-ggplot2

Homepage:
Spack package:
Versions:
3.2.0, 3.1.1, 2.2.1, 2.1.0
Build Dependencies:
r, r-digest, r-gtable, r-mass, r-plyr, r-reshape2, r-scales, r-tibble, r-lazyeval, r-mgcv, r-rlang, r-viridislite, r-withr
Link Dependencies:
r
Run Dependencies:
r, r-digest, r-gtable, r-mass, r-plyr, r-reshape2, r-scales, r-tibble, r-lazyeval, r-mgcv, r-rlang, r-viridislite, r-withr
Description:
An implementation of the grammar of graphics in R. It combines the advantages of both base and lattice graphics: conditioning and shared axes are handled automatically, and you can still build up a plot step by step from multiple data sources. It also implements a sophisticated multidimensional conditioning system and a consistent interface to map data to aesthetic attributes. See http://ggplot2.org for more information, documentation and examples.

r-ggplotify

Homepage:
Spack package:
Versions:
0.0.3
Build Dependencies:
r, r-ggplot2, r-gridgraphics, r-rvcheck
Link Dependencies:
r
Run Dependencies:
r, r-ggplot2, r-gridgraphics, r-rvcheck
Description:
ggplotify: Convert Plot to 'grob' or 'ggplot' Object

r-ggpubr

Homepage:
Spack package:
Versions:
0.2.2, 0.2.1, 0.2, 0.1.2
Build Dependencies:
r, r-ggplot2, r-magrittr, r-ggrepel, r-ggsci, r-plyr, r-tidyr, r-purrr, r-dplyr, r-cowplot, r-ggsignif, r-scales, r-gridextra, r-glue, r-polynom, r-rlang
Link Dependencies:
r
Run Dependencies:
r, r-ggplot2, r-magrittr, r-ggrepel, r-ggsci, r-plyr, r-tidyr, r-purrr, r-dplyr, r-cowplot, r-ggsignif, r-scales, r-gridextra, r-glue, r-polynom, r-rlang
Description:
ggpubr: 'ggplot2' Based Publication Ready Plots

r-ggraph

Homepage:
Spack package:
Versions:
2.0.0
Build Dependencies:
r, r-ggplot2, r-rcpp, r-dplyr, r-ggforce, r-igraph, r-scales, r-mass, r-digest, r-gtable, r-ggrepel, r-viridis, r-rlang, r-tidygraph, r-graphlayouts
Link Dependencies:
r
Run Dependencies:
r, r-ggplot2, r-rcpp, r-dplyr, r-ggforce, r-igraph, r-scales, r-mass, r-digest, r-gtable, r-ggrepel, r-viridis, r-rlang, r-tidygraph, r-graphlayouts
Description:
ggraph: An Implementation of Grammar of Graphics for Graphs and Networks

r-ggrepel

Homepage:
Spack package:
Versions:
0.8.1, 0.8.0, 0.6.5
Build Dependencies:
r, r-ggplot2, r-rcpp, r-scales
Link Dependencies:
r
Run Dependencies:
r, r-ggplot2, r-rcpp, r-scales
Description:
ggrepel: Repulsive Text and Label Geoms for 'ggplot2'

r-ggridges

Homepage:
Spack package:
Versions:
0.5.1, 0.5.0, 0.4.1, 0.4.0
Build Dependencies:
r, r-ggplot2, r-plyr, r-scales, r-withr
Link Dependencies:
r
Run Dependencies:
r, r-ggplot2, r-plyr, r-scales, r-withr
Description:
Ridgeline plots provide a convenient way of visualizing changes in distributions over time or space.

r-ggsci

Homepage:
Spack package:
Versions:
2.9, 2.8, 2.4
Build Dependencies:
r, r-scales, r-ggplot2
Link Dependencies:
r
Run Dependencies:
r, r-scales, r-ggplot2
Description:
ggsci: Scientific Journal and Sci-Fi Themed Color Palettes for 'ggplot2'

r-ggsignif

Homepage:
Spack package:
Versions:
0.6.0
Build Dependencies:
r, r-ggplot2
Link Dependencies:
r
Run Dependencies:
r, r-ggplot2
Description:
Enrich your 'ggplots' with group-wise comparisons. This package provides an easy way to indicate if two groups are significantly different. Commonly this is shown by a bracket on top connecting the groups of interest which itself is annotated with the level of significance (NS, *, **, ***). The package provides a single layer (geom_signif()) that takes the groups for comparison and the test (t.test(), wilcox.text() etc.) as arguments and adds the annotation to the plot.

r-ggvis

Homepage:
Spack package:
Versions:
0.4.4, 0.4.3, 0.4.2
Build Dependencies:
r, r-assertthat, r-jsonlite, r-shiny, r-magrittr, r-dplyr, r-lazyeval, r-htmltools
Link Dependencies:
r
Run Dependencies:
r, r-assertthat, r-jsonlite, r-shiny, r-magrittr, r-dplyr, r-lazyeval, r-htmltools
Description:
An implementation of an interactive grammar of graphics, taking the best parts of 'ggplot2', combining them with the reactive framework from 'shiny' and web graphics from 'vega'.

r-gh

Homepage:
Spack package:
Versions:
1.0.1
Build Dependencies:
r, r-ini, r-jsonlite, r-httr
Link Dependencies:
r
Run Dependencies:
r, r-ini, r-jsonlite, r-httr
Description:
Minimal client to access the 'GitHub' 'API'.

r-gistr

Homepage:
Spack package:
Versions:
0.4.2, 0.4.0, 0.3.6
Build Dependencies:
r, r-jsonlite, r-httr, r-magrittr, r-assertthat, r-knitr, r-rmarkdown, r-dplyr
Link Dependencies:
r
Run Dependencies:
r, r-jsonlite, r-httr, r-magrittr, r-assertthat, r-knitr, r-rmarkdown, r-dplyr
Description:
Work with 'GitHub' 'gists' from 'R'. This package allows the user to create new 'gists', update 'gists' with new files, rename files, delete files, get and delete 'gists', star and 'un-star' 'gists', fork 'gists', open a 'gist' in your default browser, get embed code for a 'gist', list 'gist' 'commits', and get rate limit information when 'authenticated'. Some requests require authentication and some do not.

r-git2r

Homepage:
Spack package:
Versions:
0.26.1, 0.26.0, 0.18.0, 0.15.0
Build Dependencies:
r, zlib, openssl, libgit2
Link Dependencies:
r, zlib, openssl, libgit2
Run Dependencies:
r
Description:
Interface to the 'libgit2' library, which is a pure C implementation of the 'Git' core methods. Provides access to 'Git' repositories to extract data and running some basic 'Git' commands.

r-glimma

Homepage:
Spack package:
Versions:
1.12.0, 1.10.1, 1.8.2, 1.6.0, 1.4.0
Build Dependencies:
r, r-biobase, r-edger, r-jsonlite, r-scater, r-s4vectors
Link Dependencies:
r
Run Dependencies:
r, r-biobase, r-edger, r-jsonlite, r-scater, r-s4vectors
Description:
Interactive HTML graphics. This package generates interactive visualisations for analysis of RNA- sequencing data using output from limma, edgeR or DESeq2 packages in an HTML page. The interactions are built on top of the popular static representations of analysis results in order to provide additional information.

r-glmnet

Homepage:
Spack package:
Versions:
2.0-18, 2.0-13, 2.0-5
Build Dependencies:
r, r-matrix, r-foreach
Link Dependencies:
r
Run Dependencies:
r, r-matrix, r-foreach
Description:
Extremely efficient procedures for fitting the entire lasso or elastic- net regularization path for linear regression, logistic and multinomial regression models, Poisson regression and the Cox model. Two recent additions are the multiple-response Gaussian, and the grouped multinomial. The algorithm uses cyclical coordinate descent in a path- wise fashion, as described in the paper linked to via the URL below.

r-globaloptions

Homepage:
Spack package:
Versions:
0.1.0, 0.0.12
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
It provides more controls on the option values such as validation and filtering on the values, making options invisible or private.

r-globals

Homepage:
Spack package:
Versions:
0.12.4
Build Dependencies:
r, r-codetools
Link Dependencies:
r
Run Dependencies:
r, r-codetools
Description:
Identifies global ("unknown" or "free") objects in R expressions by code inspection using various strategies, e.g. conservative or liberal. The objective of this package is to make it as simple as possible to identify global objects for the purpose of exporting them in distributed compute environments.

r-glue

Homepage:
Spack package:
Versions:
1.3.1, 1.3.0, 1.2.0
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
An implementation of interpreted string literals, inspired by Python's Literal String Interpolation <https://www.python.org/dev/peps/pep-0498/> and Docstrings <https://www.python.org/dev/peps/pep-0257/> and Julia's Triple-Quoted String Literals <https://docs.julialang.org/en/stable/ manual/strings/#triple-quoted-string-literals>.

r-gmodels

Homepage:
Spack package:
Versions:
2.18.1, 2.16.2
Build Dependencies:
r, r-gdata, r-mass
Link Dependencies:
r
Run Dependencies:
r, r-gdata, r-mass
Description:
Various R programming tools for model fitting.

r-gmp

Homepage:
Spack package:
Versions:
0.5-13.5, 0.5-13.4, 0.5-13.1
Build Dependencies:
r, gmp
Link Dependencies:
r, gmp
Run Dependencies:
r
Description:
Multiple Precision Arithmetic (big integers and rationals, prime number tests, matrix computation), "arithmetic without limitations" using the C library GMP (GNU Multiple Precision Arithmetic).

r-go-db

Homepage:
Spack package:
Versions:
3.4.1
Build Dependencies:
r, r-annotationdbi
Link Dependencies:
r
Run Dependencies:
r, r-annotationdbi
Description:
A set of annotation maps describing the entire Gene Ontology assembled using data from GO.

r-gofuncr

Homepage:
Spack package:
Versions:
1.4.0, 1.2.0, 1.0.0
Build Dependencies:
r, r-vioplot, r-rcpp, r-mapplots, r-gtools, r-genomicranges, r-annotationdbi, r-iranges
Link Dependencies:
r
Run Dependencies:
r, r-vioplot, r-rcpp, r-mapplots, r-gtools, r-genomicranges, r-annotationdbi, r-iranges
Description:
Gene ontology enrichment using FUNC. GOfuncR performs a gene ontology enrichment analysis based on the ontology enrichment software FUNC. GO- annotations are obtained from OrganismDb or OrgDb packages ('Homo.sapiens' by default); the GO-graph is included in the package and updated regularly (27-Mar-2019). GOfuncR provides the standard candidate vs. background enrichment analysis using the hypergeometric test, as well as three additional tests: (i) the Wilcoxon rank-sum test that is used when genes are ranked, (ii) a binomial test that is used when genes are associated with two counts and (iii) a Chi-square or Fisher's exact test that is used in cases when genes are associated with four counts. To correct for multiple testing and interdependency of the tests, family-wise error rates are computed based on random permutations of the gene-associated variables. GOfuncR also provides tools for exploring the ontology graph and the annotations, and options to take gene-length or spatial clustering of genes into account. It is also possible to provide custom gene coordinates, annotations and ontologies.

r-googlevis

Homepage:
Spack package:
Versions:
0.6.4, 0.6.3, 0.6.0
Build Dependencies:
r, r-jsonlite
Link Dependencies:
r
Run Dependencies:
r, r-jsonlite
Description:
R interface to Google Charts API, allowing users to create interactive charts based on data frames. Charts are displayed locally via the R HTTP help server. A modern browser with an Internet connection is required and for some charts a Flash player. The data remains local and is not uploaded to Google.

r-goplot

Homepage:
Spack package:
Versions:
1.0.2
Build Dependencies:
r, r-ggplot2, r-ggdendro, r-gridextra, r-rcolorbrewer
Link Dependencies:
r
Run Dependencies:
r, r-ggplot2, r-ggdendro, r-gridextra, r-rcolorbrewer
Description:
Implementation of multilayered visualizations for enhanced graphical representation of functional analysis data. It combines and integrates omics data derived from expression and functional annotation enrichment analyses. Its plotting functions have been developed with an hierarchical structure in mind: starting from a general overview to identify the most enriched categories (modified bar plot, bubble plot) to a more detailed one displaying different types of relevant information for the molecules in a given set of categories (circle plot, chord plot, cluster plot, Venn diagram, heatmap).

r-gosemsim

Homepage:
Spack package:
Versions:
2.10.0, 2.8.0, 2.6.2, 2.4.1, 2.2.0
Build Dependencies:
r, r-annotationdbi, r-go-db, r-rcpp
Link Dependencies:
r
Run Dependencies:
r, r-annotationdbi, r-go-db, r-rcpp
Description:
GO-terms Semantic Similarity Measures. The semantic comparisons of Gene Ontology (GO) annotations provide quantitative ways to compute similarities between genes and gene groups, and have became important basis for many bioinformatics analysis approaches. GOSemSim is an R package for semantic similarity computation among GO terms, sets of GO terms, gene products and gene clusters. GOSemSim implemented five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively.

r-goseq

Homepage:
Spack package:
Versions:
1.36.0, 1.34.1, 1.32.0, 1.30.0, 1.28.0
Build Dependencies:
r, r-biasedurn, r-genelendatabase, r-mgcv, r-annotationdbi, r-go-db, r-biocgenerics
Link Dependencies:
r
Run Dependencies:
r, r-biasedurn, r-genelendatabase, r-mgcv, r-annotationdbi, r-go-db, r-biocgenerics
Description:
Gene Ontology analyser for RNA-seq and other length biased data. Detects Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data

r-gostats

Homepage:
Spack package:
Versions:
2.50.0, 2.48.0, 2.46.0, 2.44.0, 2.42.0
Build Dependencies:
r, r-biobase, r-category, r-graph, r-annotationdbi, r-go-db, r-rbgl, r-annotate, r-annotationforge, r-rgraphviz
Link Dependencies:
r
Run Dependencies:
r, r-biobase, r-category, r-graph, r-annotationdbi, r-go-db, r-rbgl, r-annotate, r-annotationforge, r-rgraphviz
Description:
Tools for manipulating GO and microarrays. A set of tools for interacting with GO and microarray data. A variety of basic manipulation tools for graphs, hypothesis testing and other simple calculations.

r-gower

Homepage:
Spack package:
Versions:
0.2.1
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Compute Gower's distance (or similarity) coefficient between records. Compute the top-n matches between records. Core algorithms are executed in parallel on systems supporting OpenMP.

r-gplots

Homepage:
Spack package:
Versions:
3.0.1.1, 3.0.1
Build Dependencies:
r, r-gtools, r-gdata, r-catools, r-kernsmooth
Link Dependencies:
r
Run Dependencies:
r, r-gtools, r-gdata, r-catools, r-kernsmooth
Description:
Various R Programming Tools for Plotting Data.

r-graph

Homepage:
Spack package:
Versions:
1.62.0, 1.60.0, 1.58.2, 1.56.0, 1.54.0
Build Dependencies:
r, r-biocgenerics
Link Dependencies:
r
Run Dependencies:
r, r-biocgenerics
Description:
graph: A package to handle graph data structures. A package that implements some simple graph handling capabilities.

r-graphlayouts

Homepage:
Spack package:
Versions:
0.5.0
Build Dependencies:
r, r-igraph, r-rcpp, r-rcpparmadillo
Link Dependencies:
r
Run Dependencies:
r, r-igraph, r-rcpp, r-rcpparmadillo
Description:
graphlayouts: Additional Layout Algorithms for Network Visualizations. Several new layout algorithms to visualize networks are provided which are not part of 'igraph'. Most are based on the concept of stress majorization by Gansner et al. (2004) <doi:10.1007/978-3-540-31843-9_25>. Some more specific algorithms allow to emphasize hidden group structures in networks or focus on specific nodes.

r-grbase

Homepage:
Spack package:
Versions:
1.8-3.4
Build Dependencies:
r, r-graph, r-igraph, r-magrittr, r-matrix, r-rbgl, r-rcpp, r-rcpparmadillo, r-rcppeigen
Link Dependencies:
r
Run Dependencies:
r, r-graph, r-igraph, r-magrittr, r-matrix, r-rbgl, r-rcpp, r-rcpparmadillo, r-rcppeigen
Description:
gRbase: A Package for Graphical Modelling in R

r-gridbase

Homepage:
Spack package:
Versions:
0.4-7
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Integration of base and grid graphics.

r-gridextra

Homepage:
Spack package:
Versions:
2.3, 2.2.1
Build Dependencies:
r, r-gtable
Link Dependencies:
r
Run Dependencies:
r, r-gtable
Description:
Provides a number of user-level functions to work with "grid" graphics, notably to arrange multiple grid-based plots on a page, and draw tables.

r-gridgraphics

Homepage:
Spack package:
Versions:
0.4-1
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
gridGraphics: Redraw Base Graphics Using 'grid' Graphics

r-gsa

Homepage:
Spack package:
Versions:
1.03.1
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Gene Set Analysis.

r-gsalib

Homepage:
Spack package:
Versions:
2.1
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
This package contains utility functions used by the Genome Analysis Toolkit (GATK) to load tables and plot data. The GATK is a toolkit for variant discovery in high-throughput sequencing data.

r-gseabase

Homepage:
Spack package:
Versions:
1.46.0, 1.44.0, 1.42.0, 1.40.1, 1.38.2
Build Dependencies:
r, r-biocgenerics, r-biobase, r-annotate, r-graph, r-annotationdbi, r-xml
Link Dependencies:
r
Run Dependencies:
r, r-biocgenerics, r-biobase, r-annotate, r-graph, r-annotationdbi, r-xml
Description:
Gene set enrichment data structures and methods. This package provides classes and methods to support Gene Set Enrichment Analysis (GSEA).

r-gsl

Homepage:
Spack package:
Versions:
2.1-6
Build Dependencies:
r, gsl
Link Dependencies:
r, gsl
Run Dependencies:
r
Description:
An R wrapper for some of the functionality of the Gnu Scientific Library.

r-gss

Homepage:
Spack package:
Versions:
2.1-10, 2.1-7
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
A comprehensive package for structural multivariate function estimation using smoothing splines.

r-gstat

Homepage:
Spack package:
Versions:
2.0-3
Build Dependencies:
r, r-fnn, r-lattice, r-sp, r-spacetime, r-zoo
Link Dependencies:
r
Run Dependencies:
r, r-fnn, r-lattice, r-sp, r-spacetime, r-zoo
Description:
gstat: Spatial and Spatio-Temporal Geostatistical Modelling, Predictionand Simulation

r-gsubfn

Homepage:
Spack package:
Versions:
0.7, 0.6-6
Build Dependencies:
r, r-proto
Link Dependencies:
r
Run Dependencies:
r, r-proto
Description:
gsubfn is like gsub but can take a replacement function or certain other objects instead of the replacement string. Matches and back references are input to the replacement function and replaced by the function output. gsubfn can be used to split strings based on content rather than delimiters and for quasi-perl-style string interpolation. The package also has facilities for translating formulas to functions and allowing such formulas in function calls instead of functions. This can be used with R functions such as apply, sapply, lapply, optim, integrate, xyplot, Filter and any other function that expects another function as an input argument or functions like cat or sql calls that may involve strings where substitution is desirable.

r-gtable

Homepage:
Spack package:
Versions:
0.3.0, 0.2.0
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Tools to make it easier to work with "tables" of 'grobs'.

r-gtools

Homepage:
Spack package:
Versions:
3.8.1, 3.5.0
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Functions to assist in R programming. Including: - assist in developing, updating, and maintaining R and R packages ('ask', 'checkRVersion', 'getDependencies', 'keywords', 'scat') - calculate the logit and inverse logit transformations ('logit', 'inv.logit') - test if a value is missing, empty or contains only NA and NULL values ('invalid') - manipulate R's .Last function ('addLast') - define macros ('defmacro') - detect odd and even integers ('odd', 'even') - convert strings containing non-ASCII characters (like single quotes) to plain ASCII ('ASCIIfy') - perform a binary search ('binsearch') - sort strings containing both numeric and character components ('mixedsort') - create a factor variable from the quantiles of a continuous variable ('quantcut') - enumerate permutations and combinations ('combinations', 'permutation') - calculate and convert between fold-change and log-ratio ('foldchange', 'logratio2foldchange', 'foldchange2logratio') - calculate probabilities and generate random numbers from Dirichlet distributions ('rdirichlet', 'ddirichlet') - apply a function over adjacent subsets of a vector ('running') - modify the TCP_NODELAY ('de-Nagle') flag for socket objects - efficient 'rbind' of data frames, even if the column names don't match ('smartbind') - generate significance stars from p-values ('stars.pval') - convert characters to/from ASCII codes.

r-gtrellis

Homepage:
Spack package:
Versions:
1.16.1, 1.14.0, 1.12.1, 1.11.1, 1.8.0
Build Dependencies:
r, r-iranges, r-genomicranges, r-circlize, r-getoptlong
Link Dependencies:
r
Run Dependencies:
r, r-iranges, r-genomicranges, r-circlize, r-getoptlong
Description:
Genome Level Trellis Layout. Genome level Trellis graph visualizes genomic data conditioned by genomic categories (e.g. chromosomes). For each genomic category, multiple dimensional data which are represented as tracks describe different features from different aspects. This package provides high flexibility to arrange genomic categories and to add self-defined graphics in the plot.

r-gviz

Homepage:
Spack package:
Versions:
1.28.3, 1.26.5, 1.24.0, 1.22.3, 1.20.0
Build Dependencies:
r, r-s4vectors, r-iranges, r-genomicranges, r-xvector, r-rtracklayer, r-lattice, r-rcolorbrewer, r-biomart, r-annotationdbi, r-biobase, r-genomicfeatures, r-bsgenome, r-biostrings, r-biovizbase, r-rsamtools, r-latticeextra, r-matrixstats, r-genomicalignments, r-genomeinfodb, r-biocgenerics, r-digest
Link Dependencies:
r
Run Dependencies:
r, r-s4vectors, r-iranges, r-genomicranges, r-xvector, r-rtracklayer, r-lattice, r-rcolorbrewer, r-biomart, r-annotationdbi, r-biobase, r-genomicfeatures, r-bsgenome, r-biostrings, r-biovizbase, r-rsamtools, r-latticeextra, r-matrixstats, r-genomicalignments, r-genomeinfodb, r-biocgenerics, r-digest
Description:
Plotting data and annotation information along genomic coordinates. Genomic data analyses requires integrated visualization of known genomic information and new experimental data. Gviz uses the biomaRt and the rtracklayer packages to perform live annotation queries to Ensembl and UCSC and translates this to e.g. gene/transcript structures in viewports of the grid graphics package. This results in genomic information plotted together with your data.

r-gwmodel

Homepage:
Spack package:
Versions:
2.1-3, 2.1-1, 2.0-9
Build Dependencies:
r, r-maptools, r-rcpp, r-rcpparmadillo, r-robustbase, r-sp, r-spacetime, r-spatialreg, r-spdep, r-fnn
Link Dependencies:
r
Run Dependencies:
r, r-maptools, r-rcpp, r-rcpparmadillo, r-robustbase, r-sp, r-spacetime, r-spatialreg, r-spdep, r-fnn
Description:
GWmodel: Geographically-Weighted Models

r-haven

Homepage:
Spack package:
Versions:
2.1.1, 2.1.0, 1.1.0
Build Dependencies:
r, r-rcpp, r-readr, r-hms, r-tibble, r-forcats, gmake
Link Dependencies:
r
Run Dependencies:
r, r-rcpp, r-readr, r-hms, r-tibble, r-forcats
Description:
Import foreign statistical formats into R via the embedded 'ReadStat' C library, <https://github.com/WizardMac/ReadStat>.

r-hdf5array

Homepage:
Spack package:
Versions:
1.12.3, 1.10.1, 1.8.1, 1.6.0, 1.4.8
Build Dependencies:
r, r-delayedarray, r-rhdf5, r-biocgenerics, r-s4vectors, r-iranges, r-rhdf5lib, gmake
Link Dependencies:
r
Run Dependencies:
r, r-delayedarray, r-rhdf5, r-biocgenerics, r-s4vectors, r-iranges, r-rhdf5lib
Description:
HDF5 backend for DelayedArray objects. Implements the HDF5Array and TENxMatrix classes, 2 convenient and memory-efficient array-like containers for on-disk representation of HDF5 datasets. HDF5Array is for datasets that use the conventional (i.e. dense) HDF5 representation. TENxMatrix is for datasets that use the HDF5-based sparse matrix representation from 10x Genomics (e.g. the 1.3 Million Brain Cell Dataset). Both containers being DelayedArray extensions, they support all operations supported by DelayedArray objects. These operations can be either delayed or block-processed.

r-hdf5r

Homepage:
Spack package:
Versions:
1.2.0
Build Dependencies:
r, r-r6, r-bit64, hdf5
Link Dependencies:
r, hdf5
Run Dependencies:
r, r-r6, r-bit64
Description:
'HDF5' is a data model, library and file format for storing and managing large amounts of data. This package provides a nearly feature complete, object oriented wrapper for the 'HDF5' API <https://support.hdfgroup.org/HDF5/doc/RM/RM_H5Front.html> using R6 classes. Additionally, functionality is added so that 'HDF5' objects behave very similar to their corresponding R counterparts.

r-hexbin

Homepage:
Spack package:
Versions:
1.27.3, 1.27.2, 1.27.1
Build Dependencies:
r, r-lattice
Link Dependencies:
r
Run Dependencies:
r, r-lattice
Description:
Binning and plotting functions for hexagonal bins. Now uses and relies on grid graphics and formal (S4) classes and methods.

r-highr

Homepage:
Spack package:
Versions:
0.8, 0.7, 0.6
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Provides syntax highlighting for R source code. Currently it supports LaTeX and HTML output. Source code of other languages is supported via Andre Simon's highlight package.

r-hmisc

Homepage:
Spack package:
Versions:
4.2-0, 4.1-1
Build Dependencies:
r, r-lattice, r-survival, r-formula, r-ggplot2, r-latticeextra, r-acepack, r-gridextra, r-data-table, r-htmltools, r-base64enc, r-htmltable, r-viridis, r-cluster, r-rpart, r-nnet, r-foreign, r-gtable
Link Dependencies:
r
Run Dependencies:
r, r-lattice, r-survival, r-formula, r-ggplot2, r-latticeextra, r-acepack, r-gridextra, r-data-table, r-htmltools, r-base64enc, r-htmltable, r-viridis, r-cluster, r-rpart, r-nnet, r-foreign, r-gtable
Description:
Contains many functions useful for data analysis, high-level graphics, utility operations, functions for computing sample size and power, importing and annotating datasets, imputing missing values, advanced table making, variable clustering, character string manipulation, conversion of R objects to LaTeX and html code, and recoding variables.

r-hms

Homepage:
Spack package:
Versions:
0.5.0, 0.3
Build Dependencies:
r, r-pkgconfig, r-rlang, r-vctrs
Link Dependencies:
r
Run Dependencies:
r, r-pkgconfig, r-rlang, r-vctrs
Description:
Implements an S3 class for storing and formatting time-of-day values, based on the 'difftime' class.

r-hoardr

Homepage:
Spack package:
Versions:
0.5.2
Build Dependencies:
r, r-r6, r-rappdirs, r-digest
Link Dependencies:
r
Run Dependencies:
r, r-r6, r-rappdirs, r-digest
Description:
hoardr: Manage Cached Files

r-htmltable

Homepage:
Spack package:
Versions:
1.13.1, 1.11.2, 1.9
Build Dependencies:
r, r-stringr, r-knitr, r-magrittr, r-checkmate, r-htmlwidgets, r-htmltools, r-rstudioapi
Link Dependencies:
r
Run Dependencies:
r, r-stringr, r-knitr, r-magrittr, r-checkmate, r-htmlwidgets, r-htmltools, r-rstudioapi
Description:
Tables with state-of-the-art layout elements such as row spanners, column spanners, table spanners, zebra striping, and more. While allowing advanced layout, the underlying css-structure is simple in order to maximize compatibility with word processors such as 'MS Word' or 'LibreOffice'. The package also contains a few text formatting functions that help outputting text compatible with HTML/'LaTeX'.

r-htmltools

Homepage:
Spack package:
Versions:
0.3.6, 0.3.5
Build Dependencies:
r, r-digest, r-rcpp
Link Dependencies:
r
Run Dependencies:
r, r-digest, r-rcpp
Description:
Tools for HTML generation and output.

r-htmlwidgets

Homepage:
Spack package:
Versions:
1.3, 0.9, 0.8, 0.6
Build Dependencies:
r, r-htmltools, r-jsonlite, r-yaml
Link Dependencies:
r
Run Dependencies:
r, r-htmltools, r-jsonlite, r-yaml
Description:
A framework for creating HTML widgets that render in various contexts including the R console, 'R Markdown' documents, and 'Shiny' web applications.

r-httpcode

Homepage:
Spack package:
Versions:
0.2.0
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
httpcode: 'HTTP' Status Code Helper

r-httpuv

Homepage:
Spack package:
Versions:
1.5.1, 1.3.5, 1.3.3
Build Dependencies:
r, r-rcpp, r-r6, r-promises, r-later, gmake
Link Dependencies:
r
Run Dependencies:
r, r-rcpp, r-r6, r-promises, r-later
Description:
Provides low-level socket and protocol support for handling HTTP and WebSocket requests directly from within R. It is primarily intended as a building block for other packages, rather than making it particularly easy to create complete web applications using httpuv alone. httpuv is built on top of the libuv and http-parser C libraries, both of which were developed by Joyent, Inc. (See LICENSE file for libuv and http- parser license information.)

r-httr

Homepage:
Spack package:
Versions:
1.4.1, 1.4.0, 1.3.1, 1.2.1, 1.1.0
Build Dependencies:
r, r-jsonlite, r-mime, r-curl, r-openssl, r-r6
Link Dependencies:
r
Run Dependencies:
r, r-jsonlite, r-mime, r-curl, r-openssl, r-r6
Description:
Useful tools for working with HTTP organised by HTTP verbs (GET(), POST(), etc). Configuration functions make it easy to control additional request components (authenticate(), add_headers() and so on).

r-hwriter

Homepage:
Spack package:
Versions:
1.3.2
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Easy-to-use and versatile functions to output R objects in HTML format.

r-hypergraph

Homepage:
Spack package:
Versions:
1.56.0, 1.54.0, 1.52.0, 1.50.0, 1.48.0
Build Dependencies:
r, r-graph
Link Dependencies:
r
Run Dependencies:
r, r-graph
Description:
A package providing hypergraph data structures. A package that implements some simple capabilities for representing and manipulating hypergraphs.

r-ica

Homepage:
Spack package:
Versions:
1.0-2, 1.0-1, 1.0-0
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Independent Component Analysis (ICA) using various algorithms: FastICA, Information-Maximization (Infomax), and Joint Approximate Diagonalization of Eigenmatrices (JADE).

r-igraph

Homepage:
Spack package:
Versions:
1.2.4.1, 1.2.4, 1.1.2, 1.0.1
Build Dependencies:
r, r-matrix, r-magrittr, r-pkgconfig, r-irlba, gmp, libxml2, glpk
Link Dependencies:
r, gmp, libxml2, glpk
Run Dependencies:
r, r-matrix, r-magrittr, r-pkgconfig, r-irlba
Description:
Routines for simple graphs and network analysis. It can handle large graphs very well and provides functions for generating random and regular graphs, graph visualization, centrality methods and much more.

r-illuminahumanmethylation450kanno-ilmn12-hg19

Homepage:
Spack package:
Versions:
0.6.0
Build Dependencies:
r, r-minfi
Link Dependencies:
r
Run Dependencies:
r, r-minfi
Description:
Manifests and annotation for Illumina's 450k array data.

r-illuminaio

Homepage:
Spack package:
Versions:
0.26.0, 0.24.0, 0.22.0, 0.20.0, 0.18.0
Build Dependencies:
r, r-base64
Link Dependencies:
r
Run Dependencies:
r, r-base64
Description:
Parsing Illumina Microarray Output Files. Tools for parsing Illumina's microarray output files, including IDAT.

r-imager

Homepage:
Spack package:
Versions:
0.41.2
Build Dependencies:
r, r-magrittr, r-rcpp, r-stringr, r-png, r-jpeg, r-readbitmap, r-purrr, r-cairo, r-downloader, r-igraph, r-plyr, fftw, libtiff
Link Dependencies:
r, fftw, libtiff
Run Dependencies:
r, r-magrittr, r-rcpp, r-stringr, r-png, r-jpeg, r-readbitmap, r-purrr, r-cairo, r-downloader, r-igraph, r-plyr
Description:
Fast image processing for images in up to 4 dimensions (two spatial dimensions, one time/depth dimension, one colour dimension). Provides most traditional image processing tools (filtering, morphology, transformations, etc.) as well as various functions for easily analysing image data using R. The package wraps 'CImg', <http://cimg.eu>, a simple, modern C++ library for image processing.

r-impute

Homepage:
Spack package:
Versions:
1.58.0, 1.56.0, 1.54.0, 1.52.0, 1.50.1
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
impute: Imputation for microarray data. Imputation for microarray data (currently KNN only)

r-influencer

Homepage:
Spack package:
Versions:
0.1.0
Build Dependencies:
r, r-igraph, r-matrix
Link Dependencies:
r
Run Dependencies:
r, r-igraph, r-matrix
Description:
Provides functionality to compute various node centrality measures on networks. Included are functions to compute betweenness centrality (by utilizing Madduri and Bader's SNAP library), implementations of Burt's constraint and effective network size (ENS) metrics, Borgatti's algorithm to identify key players, and Valente's bridging metric. On Unix systems, the betweenness, Key Players, and bridging implementations are parallelized with OpenMP, which may run faster on systems which have OpenMP configured.

r-ini

Homepage:
Spack package:
Versions:
0.3.1
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Parse simple '.ini' configuration files to an structured list. Users can manipulate this resulting list with lapply() functions. This same structured list can be used to write back to file after modifications.

r-inline

Homepage:
Spack package:
Versions:
0.3.15, 0.3.14
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Functionality to dynamically define R functions and S4 methods with inlined C, C++ or Fortran code supporting .C and .Call calling conventions.

r-interactivedisplaybase

Homepage:
Spack package:
Versions:
1.22.0, 1.20.0, 1.18.0, 1.16.0, 1.14.0
Build Dependencies:
r, r-biocgenerics, r-shiny
Link Dependencies:
r
Run Dependencies:
r, r-biocgenerics, r-shiny
Description:
Base package for enabling powerful shiny web displays of Bioconductor objects. The interactiveDisplayBase package contains the the basic methods needed to generate interactive Shiny based display methods for Bioconductor objects.

r-intervals

Homepage:
Spack package:
Versions:
0.15.1
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
intervals: Tools for Working with Points and Intervals

r-inum

Homepage:
Spack package:
Versions:
1.0-1
Build Dependencies:
r, r-libcoin
Link Dependencies:
r
Run Dependencies:
r, r-libcoin
Description:
Enum-type representation of vectors and representation of intervals, including a method of coercing variables in data frames.

r-ipred

Homepage:
Spack package:
Versions:
0.9-9, 0.9-8, 0.9-5
Build Dependencies:
r, r-rpart, r-mass, r-survival, r-nnet, r-class, r-prodlim
Link Dependencies:
r
Run Dependencies:
r, r-rpart, r-mass, r-survival, r-nnet, r-class, r-prodlim
Description:
Improved predictive models by indirect classification and bagging for classification, regression and survival problems as well as resampling based estimators of prediction error.

r-iranges

Homepage:
Spack package:
Versions:
2.18.3, 2.16.0, 2.14.12, 2.12.0, 2.10.5
Build Dependencies:
r, r-biocgenerics, r-s4vectors
Link Dependencies:
r
Run Dependencies:
r, r-biocgenerics, r-s4vectors
Description:
Foundation of integer range manipulation in Bioconductor. Provides efficient low-level and highly reusable S4 classes for storing, manipulating and aggregating over annotated ranges of integers. Implements an algebra of range operations, including efficient algorithms for finding overlaps and nearest neighbors. Defines efficient list-like classes for storing, transforming and aggregating large grouped data, i.e., collections of atomic vectors and DataFrames.

r-irdisplay

Homepage:
Spack package:
Versions:
0.7.0, 0.4.4
Build Dependencies:
r, r-repr
Link Dependencies:
r
Run Dependencies:
r, r-repr
Description:
An interface to the rich display capabilities of Jupyter front-ends (e.g. 'Jupyter Notebook') Designed to be used from a running IRkernel session

r-irkernel

Homepage:
Spack package:
Versions:
master
Build Dependencies:
r, r-repr, r-irdisplay, r-evaluate, r-crayon, r-pbdzmq, r-devtools, r-uuid, r-digest
Link Dependencies:
r
Run Dependencies:
r, r-repr, r-irdisplay, r-evaluate, r-crayon, r-pbdzmq, r-devtools, r-uuid, r-digest
Description:
R kernel for Jupyter

r-irlba

Homepage:
Spack package:
Versions:
2.3.3, 2.3.2, 2.1.2, 2.0.0
Build Dependencies:
r, r-matrix
Link Dependencies:
r
Run Dependencies:
r, r-matrix
Description:
Fast and memory efficient methods for truncated singular and eigenvalue decompositions and principal component analysis of large sparse or dense matrices.

r-isdparser

Homepage:
Spack package:
Versions:
0.3.0
Build Dependencies:
r, r-data-table, r-tibble
Link Dependencies:
r
Run Dependencies:
r, r-data-table, r-tibble
Description:
isdparser: Parse 'NOAA' Integrated Surface Data Files

r-iso

Homepage:
Spack package:
Versions:
0.0-18, 0.0-17
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Linear order and unimodal order (univariate) isotonic regression; bivariate isotonic regression with linear order on both variables.

r-iterators

Homepage:
Spack package:
Versions:
1.0.12, 1.0.9, 1.0.8
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Support for iterators, which allow a programmer to traverse through all the elements of a vector, list, or other collection of data.

r-janitor

Homepage:
Spack package:
Versions:
1.2.0, 1.1.1, 0.3.0
Build Dependencies:
r, r-dplyr, r-tidyr, r-magrittr, r-snakecase, r-purrr, r-rlang
Link Dependencies:
r
Run Dependencies:
r, r-dplyr, r-tidyr, r-magrittr, r-snakecase, r-purrr, r-rlang
Description:
The main janitor functions can: perfectly format data.frame column names; provide quick one- and two-variable tabulations (i.e., frequency tables and crosstabs); and isolate duplicate records. Other janitor functions nicely format the tabulation results. These tabulate-and- report functions approximate popular features of SPSS and Microsoft Excel. This package follows the principles of the "tidyverse" and works well with the pipe function %>%. janitor was built with beginning-to- intermediate R users in mind and is optimized for user-friendliness. Advanced R users can already do everything covered here, but with janitor they can do it faster and save their thinking for the fun stuff.

r-jaspar2018

Homepage:
Spack package:
Versions:
1.1.0, 1.0.0
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Data package for JASPAR 2018. Data package for JASPAR 2018. To search this databases, please use the package TFBSTools (>= 1.15.6).

r-jomo

Homepage:
Spack package:
Versions:
2.6-9, 2.6-7, 2.6-2
Build Dependencies:
r, r-lme4, r-survival, r-mass, r-ordinal
Link Dependencies:
r
Run Dependencies:
r, r-lme4, r-survival, r-mass, r-ordinal
Description:
Similarly to Schafer's package 'pan', 'jomo' is a package for multilevel joint modelling multiple imputation (Carpenter and Kenward, 2013) <doi:10.1002/9781119942283>. Novel aspects of 'jomo' are the possibility of handling binary and categorical data through latent normal variables, the option to use cluster-specific covariance matrices and to impute compatibly with the substantive model.

r-jpeg

Homepage:
Spack package:
Versions:
0.1-8
Build Dependencies:
r, jpeg
Link Dependencies:
r, jpeg
Run Dependencies:
r
Description:
This package provides an easy and simple way to read, write and display bitmap images stored in the JPEG format. It can read and write both files and in-memory raw vectors.

r-jsonlite

Homepage:
Spack package:
Versions:
1.6, 1.5, 1.2, 1.0, 0.9.21
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
A fast JSON parser and generator optimized for statistical data and the web. Started out as a fork of 'RJSONIO', but has been completely rewritten in recent versions. The package offers flexible, robust, high performance tools for working with JSON in R and is particularly powerful for building pipelines and interacting with a web API. The implementation is based on the mapping described in the vignette (Ooms, 2014). In addition to converting JSON data from/to R objects, 'jsonlite' contains functions to stream, validate, and prettify JSON data. The unit tests included with the package verify that all edge cases are encoded and decoded consistently for use with dynamic data in systems and applications.

r-kegg-db

Homepage:
Spack package:
Versions:
3.2.3
Build Dependencies:
r, r-annotationdbi
Link Dependencies:
r
Run Dependencies:
r, r-annotationdbi
Description:
A set of annotation maps for KEGG assembled using data from KEGG.

r-kegggraph

Homepage:
Spack package:
Versions:
1.44.0, 1.42.0, 1.40.0, 1.38.1, 1.38.0
Build Dependencies:
r, r-xml, r-graph, r-rcurl
Link Dependencies:
r
Run Dependencies:
r, r-xml, r-graph, r-rcurl
Description:
KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor. KEGGGraph is an interface between KEGG pathway and graph object as well as a collection of tools to analyze, dissect and visualize these graphs. It parses the regularly updated KGML (KEGG XML) files into graph models maintaining all essential pathway attributes. The package offers functionalities including parsing, graph operation, visualization and etc.

r-keggrest

Homepage:
Spack package:
Versions:
1.24.1, 1.22.0, 1.20.2, 1.18.1, 1.16.1
Build Dependencies:
r, r-httr, r-png, r-biostrings
Link Dependencies:
r
Run Dependencies:
r, r-httr, r-png, r-biostrings
Description:
Client-side REST access to KEGG. A package that provides a client interface to the KEGG REST server. Based on KEGGSOAP by J. Zhang, R. Gentleman, and Marc Carlson, and KEGG (python package) by Aurelien Mazurie.

r-kernlab

Homepage:
Spack package:
Versions:
0.9-27, 0.9-26, 0.9-25
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Kernel-based machine learning methods for classification, regression, clustering, novelty detection, quantile regression and dimensionality reduction. Among other methods 'kernlab' includes Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes and a QP solver.

r-kernsmooth

Homepage:
Spack package:
Versions:
2.23-15
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Functions for kernel smoothing (and density estimation).

r-kknn

Homepage:
Spack package:
Versions:
1.3.1
Build Dependencies:
r, r-igraph, r-matrix
Link Dependencies:
r
Run Dependencies:
r, r-igraph, r-matrix
Description:
Weighted k-Nearest Neighbors for Classification, Regression and Clustering.

r-knitr

Homepage:
Spack package:
Versions:
1.24, 1.23, 1.17, 1.14
Build Dependencies:
r, r-evaluate, r-digest, r-formatr, r-highr, r-stringr, r-markdown, r-yaml, r-xfun
Link Dependencies:
r
Run Dependencies:
r, r-evaluate, r-digest, r-formatr, r-highr, r-stringr, r-markdown, r-yaml, r-xfun
Description:
Provides a general-purpose tool for dynamic report generation in R using Literate Programming techniques.

r-ks

Homepage:
Spack package:
Versions:
1.11.5, 1.11.4, 1.11.2
Build Dependencies:
r, r-fnn, r-kernlab, r-mclust, r-multicool, r-mvtnorm, r-kernsmooth, r-matrix, r-mgcv
Link Dependencies:
r
Run Dependencies:
r, r-fnn, r-kernlab, r-mclust, r-multicool, r-mvtnorm, r-kernsmooth, r-matrix, r-mgcv
Description:
Kernel smoothers for univariate and multivariate data.

r-labeling

Homepage:
Spack package:
Versions:
0.3
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Provides a range of axis labeling algorithms.

r-lambda-r

Homepage:
Spack package:
Versions:
1.2.3, 1.2
Build Dependencies:
r, r-formatr
Link Dependencies:
r
Run Dependencies:
r, r-formatr
Description:
A language extension to efficiently write functional programs in R. Syntax extensions include multi-part function definitions, pattern matching, guard statements, built-in (optional) type safety.

r-laplacesdemon

Homepage:
Spack package:
Versions:
16.1.1, 16.1.0, 16.0.1
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Provides a complete environment for Bayesian inference using a variety of different samplers (see ?LaplacesDemon for an overview). The README describes the history of the package development process.

r-lars

Homepage:
Spack package:
Versions:
1.2, 1.1, 0.9-8
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Efficient procedures for fitting an entire lasso sequence with the cost of a single least squares fit.

r-later

Homepage:
Spack package:
Versions:
0.8.0
Build Dependencies:
r, r-rcpp, r-rlang, r-bh
Link Dependencies:
r
Run Dependencies:
r, r-rcpp, r-rlang, r-bh
Description:
Executes arbitrary R or C functions some time after the current time, after the R execution stack has emptied.

r-lattice

Homepage:
Spack package:
Versions:
0.20-38, 0.20-35, 0.20-34
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
A powerful and elegant high-level data visualization system inspired by Trellis graphics, with an emphasis on multivariate data. Lattice is sufficient for typical graphics needs, and is also flexible enough to handle most nonstandard requirements. See ?Lattice for an introduction.

r-latticeextra

Homepage:
Spack package:
Versions:
0.6-28
Build Dependencies:
r, r-lattice, r-rcolorbrewer
Link Dependencies:
r
Run Dependencies:
r, r-lattice, r-rcolorbrewer
Description:
Building on the infrastructure provided by the lattice package, this package provides several new high-level functions and methods, as well as additional utilities such as panel and axis annotation functions.

r-lava

Homepage:
Spack package:
Versions:
1.6.6, 1.6.4, 1.4.7
Build Dependencies:
r, r-numderiv, r-survival, r-squarem
Link Dependencies:
r
Run Dependencies:
r, r-numderiv, r-survival, r-squarem
Description:
Estimation and simulation of latent variable models.

r-lazyeval

Homepage:
Spack package:
Versions:
0.2.2, 0.2.1, 0.2.0
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
An alternative approach to non-standard evaluation using formulas. Provides a full implementation of LISP style 'quasiquotation', making it easier to generate code with other code.

r-ldheatmap

Homepage:
Spack package:
Versions:
0.99-7
Build Dependencies:
r, r-genetics, r-rcpp, r-snpstats
Link Dependencies:
r
Run Dependencies:
r, r-genetics, r-rcpp, r-snpstats
Description:
LDheatmap: Graphical Display of Pairwise Linkage Disequilibria Between SNPs

r-leaflet

Homepage:
Spack package:
Versions:
2.0.2, 2.0.1, 1.0.1
Build Dependencies:
r, r-base64enc, r-crosstalk, r-htmlwidgets, r-htmltools, r-magrittr, r-markdown, r-png, r-rcolorbrewer, r-raster, r-scales, r-sp, r-viridis
Link Dependencies:
r
Run Dependencies:
r, r-base64enc, r-crosstalk, r-htmlwidgets, r-htmltools, r-magrittr, r-markdown, r-png, r-rcolorbrewer, r-raster, r-scales, r-sp, r-viridis
Description:
Create and customize interactive maps using the 'Leaflet' JavaScript library and the 'htmlwidgets' package. These maps can be used directly from the R console, from 'RStudio', in Shiny apps and R Markdown documents.

r-leaps

Homepage:
Spack package:
Versions:
3.0
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
leaps: Regression Subset Selection

r-learnbayes

Homepage:
Spack package:
Versions:
2.15.1, 2.15
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
LearnBayes contains a collection of functions helpful in learning the basic tenets of Bayesian statistical inference. It contains functions for summarizing basic one and two parameter posterior distributions and predictive distributions. It contains MCMC algorithms for summarizing posterior distributions defined by the user. It also contains functions for regression models, hierarchical models, Bayesian tests, and illustrations of Gibbs sampling.

r-leiden

Homepage:
Spack package:
Versions:
0.3.1
Build Dependencies:
r, r-reticulate, r-matrix, r-igraph
Link Dependencies:
r
Run Dependencies:
r, r-reticulate, r-matrix, r-igraph
Description:
Implements the 'Python leidenalg' module to be called in R. Enables clustering using the leiden algorithm for partition a graph into communities. See the 'Python' repository for more details: <https://github.com/vtraag/leidenalg> Traag et al (2018) From Louvain to Leiden: guaranteeing well-connected communities. <arXiv:1810.08473>.

r-lhs

Homepage:
Spack package:
Versions:
1.0.1, 1.0, 0.16
Build Dependencies:
r, r-rcpp
Link Dependencies:
r
Run Dependencies:
r, r-rcpp
Description:
Provides a number of methods for creating and augmenting Latin Hypercube Samples.

r-libcoin

Homepage:
Spack package:
Versions:
1.0-4
Build Dependencies:
r, r-mvtnorm
Link Dependencies:
r
Run Dependencies:
r, r-mvtnorm
Description:
Basic infrastructure for linear test statistics and permutation inference in the framework of Strasser and Weber (1999) <http://epub.wu.ac.at/102/>. This package must not be used by end-users. CRAN package 'coin' implements all user interfaces and is ready to be used by anyone.

r-limma

Homepage:
Spack package:
Versions:
3.40.6, 3.38.3, 3.36.5, 3.34.9, 3.32.10
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Linear Models for Microarray Data. Data analysis, linear models and differential expression for microarray data.

r-listenv

Homepage:
Spack package:
Versions:
0.7.0
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
List environments are environments that have list-like properties. For instance, the elements of a list environment are ordered and can be accessed and iterated over using index subsetting.

r-lme4

Homepage:
Spack package:
Versions:
1.1-21, 1.1-20, 1.1-12
Build Dependencies:
r, r-matrix, r-mass, r-lattice, r-nlme, r-minqa, r-nloptr, r-rcpp, r-rcppeigen, r-boot
Link Dependencies:
r
Run Dependencies:
r, r-matrix, r-mass, r-lattice, r-nlme, r-minqa, r-nloptr, r-rcpp, r-rcppeigen, r-boot
Description:
Fit linear and generalized linear mixed-effects models. The models and their components are represented using S4 classes and methods. The core computational algorithms are implemented using the 'Eigen' C++ library for numerical linear algebra and 'RcppEigen' "glue".

r-lmtest

Homepage:
Spack package:
Versions:
0.9-37, 0.9-36, 0.9-34
Build Dependencies:
r, r-zoo
Link Dependencies:
r
Run Dependencies:
r, r-zoo
Description:
A collection of tests, data sets, and examples for diagnostic checking in linear regression models. Furthermore, some generic tools for inference in parametric models are provided.

r-locfit

Homepage:
Spack package:
Versions:
1.5-9.1
Build Dependencies:
r, r-lattice
Link Dependencies:
r
Run Dependencies:
r, r-lattice
Description:
Local regression, likelihood and density estimation.

r-log4r

Homepage:
Spack package:
Versions:
0.3.0, 0.2
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
logr4 provides an object-oriented logging system that uses an API roughly equivalent to log4j and its related variants.

r-loo

Homepage:
Spack package:
Versions:
2.1.0
Build Dependencies:
r, r-checkmate, r-matrixstats, pandoc
Link Dependencies:
r, pandoc
Run Dependencies:
r, r-checkmate, r-matrixstats
Description:
loo: Efficient Leave-One-Out Cross-Validation and WAIC for BayesianModels

r-lpsolve

Homepage:
Spack package:
Versions:
5.6.13.2, 5.6.13.1, 5.6.13
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Lp_solve is freely available (under LGPL 2) software for solving linear, integer and mixed integer programs. In this implementation we supply a "wrapper" function in C and some R functions that solve general linear/integer problems, assignment problems, and transportation problems. This version calls lp_solve

r-lsei

Homepage:
Spack package:
Versions:
1.2-0
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
It contains functions that solve least squares linear regression problems under linear equality/inequality constraints. Functions for solving quadratic programming problems are also available, which transform such problems into least squares ones first. It is developed based on the 'Fortran' program of Lawson and Hanson (1974, 1995), which is public domain and available at <http://www.netlib.org/lawson-hanson>.

r-lubridate

Homepage:
Spack package:
Versions:
1.7.4, 1.7.3, 1.7.1, 1.5.6
Build Dependencies:
r, r-rcpp, r-stringr
Link Dependencies:
r
Run Dependencies:
r, r-rcpp, r-stringr
Description:
Functions to work with date-times and timespans: fast and user friendly parsing of date-time data, extraction and updating of components of a date-time (years, months, days, hours, minutes, and seconds), algebraic manipulation on date-time and timespan objects. The 'lubridate' package has a consistent and memorable syntax that makes working with dates easy and fun.

r-lumi

Homepage:
Spack package:
Versions:
2.38.0
Build Dependencies:
r, r-biobase, r-affy, r-methylumi, r-genomicfeatures, r-genomicranges, r-annotate, r-lattice, r-mgcv, r-nleqslv, r-kernsmooth, r-preprocesscore, r-rsqlite, r-dbi, r-annotationdbi, r-mass
Link Dependencies:
r
Run Dependencies:
r, r-biobase, r-affy, r-methylumi, r-genomicfeatures, r-genomicranges, r-annotate, r-lattice, r-mgcv, r-nleqslv, r-kernsmooth, r-preprocesscore, r-rsqlite, r-dbi, r-annotationdbi, r-mass
Description:
The lumi package provides an integrated solution for the Illumina microarray data analysis. It includes functions of Illumina BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific variance stabilization, normalization and gene annotation at the probe level. It also includes the functions of processing Illumina methylation microarrays, especially Illumina Infinium methylation microarrays.

r-magic

Homepage:
Spack package:
Versions:
1.5-9, 1.5-8, 1.5-6
Build Dependencies:
r, r-abind
Link Dependencies:
r
Run Dependencies:
r, r-abind
Description:
A collection of efficient, vectorized algorithms for the creation and investigation of magic squares and hypercubes, including a variety of functions for the manipulation and analysis of arbitrarily dimensioned arrays.

r-magick

Homepage:
Spack package:
Versions:
2.1
Build Dependencies:
r, r-rcpp, r-magrittr, r-curl, imagemagick
Link Dependencies:
r, imagemagick
Run Dependencies:
r, r-rcpp, r-magrittr, r-curl
Description:
Bindings to 'ImageMagick': the most comprehensive open-source image processing library available. Supports many common formats (png, jpeg, tiff, pdf, etc) and manipulations (rotate, scale, crop, trim, flip, blur, etc). All operations are vectorized via the Magick++ STL meaning they operate either on a single frame or a series of frames for working with layers, collages, or animation. In RStudio images are automatically previewed when printed to the console, resulting in an interactive editing environment. The latest version of the package includes a native graphics device for creating in-memory graphics or drawing onto images using pixel coordinates.

r-magrittr

Homepage:
Spack package:
Versions:
1.5
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Provides a mechanism for chaining commands with a new forward-pipe operator, %>%. This operator will forward a value, or the result of an expression, into the next function call/expression. There is flexible support for the type of right-hand side expressions. For more information, see package vignette.

r-makecdfenv

Homepage:
Spack package:
Versions:
1.60.0, 1.58.0, 1.56.0, 1.54.0, 1.52.0
Build Dependencies:
r, r-affyio, r-biobase, r-affy, r-zlibbioc
Link Dependencies:
r
Run Dependencies:
r, r-affyio, r-biobase, r-affy, r-zlibbioc
Description:
CDF Environment Maker. This package has two functions. One reads a Affymetrix chip description file (CDF) and creates a hash table environment containing the location/probe set membership mapping. The other creates a package that automatically loads that environment.

r-maldiquant

Homepage:
Spack package:
Versions:
1.19.3, 1.19.2, 1.16.4
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
A complete analysis pipeline for matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) and other two- dimensional mass spectrometry data. In addition to commonly used plotting and processing methods it includes distinctive features, namely baseline subtraction methods such as morphological filters (TopHat) or the statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak alignment using warping functions, handling of replicated measurements as well as allowing spectra with different resolutions.

r-manipulatewidget

Homepage:
Spack package:
Versions:
0.10.0, 0.9.0, 0.8.0, 0.7.0, 0.6.0, 0.5.1, 0.5.0, 0.4.0
Build Dependencies:
r, r-base64enc, r-codetools, r-htmltools, r-htmlwidgets, r-knitr, r-miniui, r-shiny, r-webshot
Link Dependencies:
r
Run Dependencies:
r, r-base64enc, r-codetools, r-htmltools, r-htmlwidgets, r-knitr, r-miniui, r-shiny, r-webshot
Description:
Like package 'manipulate' does for static graphics, this package helps to easily add controls like sliders, pickers, checkboxes, etc. that can be used to modify the input data or the parameters of an interactive chart created with package 'htmlwidgets'.

r-mapplots

Homepage:
Spack package:
Versions:
1.5.1
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
mapplots: Data Visualisation on Maps

r-mapproj

Homepage:
Spack package:
Versions:
1.2.6, 1.2-5, 1.2-4
Build Dependencies:
r, r-maps
Link Dependencies:
r
Run Dependencies:
r, r-maps
Description:
Converts latitude/longitude into projected coordinates.

r-maps

Homepage:
Spack package:
Versions:
3.3.0, 3.2.0, 3.1.1
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Display of maps. Projection code and larger maps are in separate packages ('mapproj' and 'mapdata').

r-maptools

Homepage:
Spack package:
Versions:
0.9-5, 0.9-4, 0.8-39
Build Dependencies:
r, r-sp, r-foreign, r-lattice
Link Dependencies:
r
Run Dependencies:
r, r-sp, r-foreign, r-lattice
Description:
Set of tools for manipulating and reading geographic data, in particular ESRI shapefiles; C code used from shapelib. It includes binary access to GSHHG shoreline files. The package also provides interface wrappers for exchanging spatial objects with packages such as PBSmapping, spatstat, maps, RArcInfo, Stata tmap, WinBUGS, Mondrian, and others.

r-markdown

Homepage:
Spack package:
Versions:
1.1, 1.0, 0.9, 0.8, 0.7.7
Build Dependencies:
r, r-mime, r-xfun
Link Dependencies:
r
Run Dependencies:
r, r-mime, r-xfun
Description:
Provides R bindings to the 'Sundown' 'Markdown' rendering library (https://github.com/vmg/sundown). 'Markdown' is a plain-text formatting syntax that can be converted to 'XHTML' or other formats. See http://en.wikipedia.org/wiki/Markdown for more information about 'Markdown'.

r-mass

Homepage:
Spack package:
Versions:
7.3-51.5, 7.3-51.4, 7.3-51.3, 7.3-47
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Functions and datasets to support Venables and Ripley, "Modern Applied Statistics with S" (4th edition, 2002).

r-matr

Homepage:
Spack package:
Versions:
0.9.1, 0.9
Build Dependencies:
r, r-mgraster, r-biom-utils
Link Dependencies:
r
Run Dependencies:
r, r-mgraster, r-biom-utils
Description:
Package matR (Metagenomics Analysis Tools for R) is an analysis client for the MG-RAST metagenome annotation engine, part of the US Department of Energy (DOE) Systems Biology Knowledge Base (KBase). Customized analysis and visualization tools securely access remote data and metadata within the popular open source R language and environment for statistical computing.

r-matrix

Homepage:
Spack package:
Versions:
1.2-17, 1.2-14, 1.2-11, 1.2-8, 1.2-6
Build Dependencies:
r, r-lattice
Link Dependencies:
r
Run Dependencies:
r, r-lattice
Description:
Classes and methods for dense and sparse matrices and operations on them using 'LAPACK' and 'SuiteSparse'.

r-matrixmodels

Homepage:
Spack package:
Versions:
0.4-1
Build Dependencies:
r, r-matrix
Link Dependencies:
r
Run Dependencies:
r, r-matrix
Description:
Modelling with sparse and dense 'Matrix' matrices, using modular prediction and response module classes.

r-matrixstats

Homepage:
Spack package:
Versions:
0.55.0, 0.54.0, 0.52.2
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
High-performing functions operating on rows and columns of matrices, e.g. col / rowMedians(), col / rowRanks(), and col / rowSds(). Functions optimized per data type and for subsetted calculations such that both memory usage and processing time is minimized. There are also optimized vector-based methods, e.g. binMeans(), madDiff() and weightedMedian().

r-mclust

Homepage:
Spack package:
Versions:
5.4.5, 5.4.4, 5.3
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
mclust: Gaussian Mixture Modelling for Model-Based Clustering, Classification, and Density Estimation

r-mcmcglmm

Homepage:
Spack package:
Versions:
2.29, 2.28, 2.25
Build Dependencies:
r, r-matrix, r-coda, r-ape, r-corpcor, r-tensora, r-cubature
Link Dependencies:
r
Run Dependencies:
r, r-matrix, r-coda, r-ape, r-corpcor, r-tensora, r-cubature
Description:
MCMC Generalised Linear Mixed Models.

r-mco

Homepage:
Spack package:
Versions:
1.0-15.1, 1.0-15
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Functions for multiple criteria optimization using genetic algorithms and related test problems

r-mda

Homepage:
Spack package:
Versions:
0.4-10, 0.4-9
Build Dependencies:
r, r-class
Link Dependencies:
r
Run Dependencies:
r, r-class
Description:
Mixture and flexible discriminant analysis, multivariate adaptive regression splines (MARS), BRUTO.

r-memoise

Homepage:
Spack package:
Versions:
1.1.0, 1.0.0
Build Dependencies:
r, r-digest
Link Dependencies:
r
Run Dependencies:
r, r-digest
Description:
Cache the results of a function so that when you call it again with the same arguments it returns the pre-computed value.

r-mergemaid

Homepage:
Spack package:
Versions:
2.56.0, 2.54.0, 2.52.0, 2.50.0, 2.48.0
Build Dependencies:
r, r-survival, r-biobase, r-mass
Link Dependencies:
r
Run Dependencies:
r, r-survival, r-biobase, r-mass
Description:
Merge Maid. The functions in this R extension are intended for cross- study comparison of gene expression array data. Required from the user is gene expression matrices, their corresponding gene-id vectors and other useful information, and they could be 'list','matrix', or 'ExpressionSet'. The main function is 'mergeExprs' which transforms the input objects into data in the merged format, such that common genes in different datasets can be easily found. And the function 'intcor' calculate the correlation coefficients. Other functions use the output from 'modelOutcome' to graphically display the results and cross- validate associations of gene expression data with survival.

r-metap

Homepage:
Spack package:
Versions:
1.1
Build Dependencies:
r, r-lattice, r-rdpack
Link Dependencies:
r
Run Dependencies:
r, r-lattice, r-rdpack
Description:
The canonical way to perform meta-analysis involves using effect sizes. When they are not available this package provides a number of methods for meta-analysis of significance values including the methods of Edgington, Fisher, Lancaster, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate published results; and a routine for graphical display.

r-methylumi

Homepage:
Spack package:
Versions:
2.32.0
Build Dependencies:
r, r-biobase, r-scales, r-reshape2, r-ggplot2, r-matrixstats, r-fdb-infiniummethylation-hg19, r-minfi, r-biocgenerics, r-iranges, r-genomeinfodb, r-genomicranges, r-summarizedexperiment, r-lattice, r-annotate, r-genefilter, r-annotationdbi, r-illuminaio
Link Dependencies:
r
Run Dependencies:
r, r-biobase, r-scales, r-reshape2, r-ggplot2, r-matrixstats, r-fdb-infiniummethylation-hg19, r-minfi, r-biocgenerics, r-iranges, r-genomeinfodb, r-genomicranges, r-summarizedexperiment, r-lattice, r-annotate, r-genefilter, r-annotationdbi, r-illuminaio
Description:
This package provides classes for holding and manipulating Illumina methylation data. Based on eSet, it can contain MIAME information, sample information, feature information, and multiple matrices of data. An "intelligent" import function, methylumiR can read the Illumina text files and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from HumanMethylation27 and HumanMethylation450 microarrays. Normalization, background correction, and quality control features for GoldenGate, Infinium, and Infinium HD arrays are also included.

r-mgcv

Homepage:
Spack package:
Versions:
1.8-28, 1.8-27, 1.8-22, 1.8-21, 1.8-20, 1.8-19, 1.8-18, 1.8-17, 1.8-16, 1.8-13
Build Dependencies:
r, r-nlme, r-matrix
Link Dependencies:
r
Run Dependencies:
r, r-nlme, r-matrix
Description:
GAMs, GAMMs and other generalized ridge regression with multiple smoothing parameter estimation by GCV, REML or UBRE/AIC. Includes a gam() function, a wide variety of smoothers, JAGS support and distributions beyond the exponential family.

r-mgraster

Homepage:
Spack package:
Versions:
0.9
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Convenience Functions for R Language Access to the v.1 API of the MG- RAST Metagenome Annotation Server, part of the US Department of Energy (DOE) Systems Biology Knowledge Base (KBase).

r-mice

Homepage:
Spack package:
Versions:
3.6.0, 3.5.0, 3.0.0
Build Dependencies:
r, r-broom, r-dplyr, r-mass, r-mitml, r-nnet, r-rcpp, r-rlang, r-rpart, r-survival, r-lattice
Link Dependencies:
r
Run Dependencies:
r, r-broom, r-dplyr, r-mass, r-mitml, r-nnet, r-rcpp, r-rlang, r-rpart, r-survival, r-lattice
Description:
Multiple imputation using Fully Conditional Specification (FCS) implemented by the MICE algorithm as described in Van Buuren and Groothuis-Oudshoorn (2011) <doi:10.18637/jss.v045.i03>. Each variable has its own imputation model. Built-in imputation models are provided for continuous data (predictive mean matching, normal), binary data (logistic regression), unordered categorical data (polytomous logistic regression) and ordered categorical data (proportional odds). MICE can also impute continuous two-level data (normal model, pan, second-level variables). Passive imputation can be used to maintain consistency between variables. Various diagnostic plots are available to inspect the quality of the imputations.

r-mime

Homepage:
Spack package:
Versions:
0.7, 0.6, 0.5, 0.4
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Guesses the MIME type from a filename extension using the data derived from /etc/mime.types in UNIX-type systems.

r-miniui

Homepage:
Spack package:
Versions:
0.1.1.1
Build Dependencies:
r, r-shiny, r-htmltools
Link Dependencies:
r
Run Dependencies:
r, r-shiny, r-htmltools
Description:
Provides UI widget and layout functions for writing Shiny apps that work well on small screens.

r-minqa

Homepage:
Spack package:
Versions:
1.2.4
Build Dependencies:
r, r-rcpp, gmake
Link Dependencies:
r
Run Dependencies:
r, r-rcpp
Description:
Derivative-free optimization by quadratic approximation based on an interface to Fortran implementations by M. J. D. Powell.

r-misc3d

Homepage:
Spack package:
Versions:
0.8-4
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
A collection of miscellaneous 3d plots, including isosurfaces.

r-mitml

Homepage:
Spack package:
Versions:
0.3-7, 0.3-6, 0.3-5
Build Dependencies:
r, r-pan, r-jomo, r-haven
Link Dependencies:
r
Run Dependencies:
r, r-pan, r-jomo, r-haven
Description:
Provides tools for multiple imputation of missing data in multilevel modeling. Includes a user-friendly interface to the packages 'pan' and 'jomo', and several functions for visualization, data management and the analysis of multiply imputed data sets.

r-mitools

Homepage:
Spack package:
Versions:
2.4
Build Dependencies:
r, r-dbi
Link Dependencies:
r
Run Dependencies:
r, r-dbi
Description:
Tools to perform analyses and combine results from multiple-imputation datasets.

r-mixtools

Homepage:
Spack package:
Versions:
1.1.0, 1.0.4
Build Dependencies:
r, r-mass, r-segmented, r-survival
Link Dependencies:
r
Run Dependencies:
r, r-mass, r-segmented, r-survival
Description:
mixtools: Tools for Analyzing Finite Mixture Models Analyzes finite mixture models for various parametric and semiparametric settings.

r-mlbench

Homepage:
Spack package:
Versions:
2.1-1
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
A collection of artificial and real-world machine learning benchmark problems, including, e.g., several data sets from the UCI repository.

r-mlinterfaces

Homepage:
Spack package:
Versions:
1.64.1, 1.62.1, 1.60.1, 1.58.1, 1.56.0
Build Dependencies:
r, r-biocgenerics, r-biobase, r-annotate, r-cluster, r-gdata, r-pls, r-sfsmisc, r-mass, r-rpart, r-rda, r-genefilter, r-fpc, r-ggvis, r-shiny, r-gbm, r-rcolorbrewer, r-hwriter, r-threejs, r-mlbench
Link Dependencies:
r
Run Dependencies:
r, r-biocgenerics, r-biobase, r-annotate, r-cluster, r-gdata, r-pls, r-sfsmisc, r-mass, r-rpart, r-rda, r-genefilter, r-fpc, r-ggvis, r-shiny, r-gbm, r-rcolorbrewer, r-hwriter, r-threejs, r-mlbench
Description:
Uniform interfaces to R machine learning procedures for data in Bioconductor containers. This package provides uniform interfaces to machine learning code for data in R and Bioconductor containers.

r-mlr

Homepage:
Spack package:
Versions:
2.15.0, 2.14.0, 2.13, 2.12.1, 2.12
Build Dependencies:
r, r-paramhelpers, r-bbmisc, r-backports, r-ggplot2, r-stringi, r-checkmate, r-data-table, r-parallelmap, r-survival, r-xml
Link Dependencies:
r
Run Dependencies:
r, r-paramhelpers, r-bbmisc, r-backports, r-ggplot2, r-stringi, r-checkmate, r-data-table, r-parallelmap, r-survival, r-xml
Description:
Interface to a large number of classification and regression techniques, including machine-readable parameter descriptions. There is also an experimental extension for survival analysis, clustering and general, example-specific cost-sensitive learning. Generic resampling, including cross-validation, bootstrapping and subsampling. Hyperparameter tuning with modern optimization techniques, for single- and multi-objective problems. Filter and wrapper methods for feature selection. Extension of basic learners with additional operations common in machine learning, also allowing for easy nested resampling. Most operations can be parallelized.

r-mlrmbo

Homepage:
Spack package:
Versions:
1.1.2, 1.1.1, 1.1.0
Build Dependencies:
r, r-mlr, r-paramhelpers, r-smoof, r-backports, r-bbmisc, r-checkmate, r-data-table, r-lhs, r-parallelmap
Link Dependencies:
r
Run Dependencies:
r, r-mlr, r-paramhelpers, r-smoof, r-backports, r-bbmisc, r-checkmate, r-data-table, r-lhs, r-parallelmap
Description:
Flexible and comprehensive R toolbox for model-based optimization ('MBO'), also known as Bayesian optimization. It is designed for both single- and multi-objective optimization with mixed continuous, categorical and conditional parameters. The machine learning toolbox 'mlr' provide dozens of regression learners to model the performance of the target algorithm with respect to the parameter settings. It provides many different infill criteria to guide the search process. Additional features include multi-point batch proposal, parallel execution as well as visualization and sophisticated logging mechanisms, which is especially useful for teaching and understanding of algorithm behavior. 'mlrMBO' is implemented in a modular fashion, such that single components can be easily replaced or adapted by the user for specific use cases.

r-mmwrweek

Homepage:
Spack package:
Versions:
0.1.1
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
The first day of any MMWR week is Sunday. MMWR week numbering is sequential beginning with 1 and incrementing with each week to a maximum of 52 or 53. MMWR week #1 of an MMWR year is the first week of the year that has at least four days in the calendar year. This package provides functionality to convert Dates to MMWR day, week, and year and the reverse.

r-mnormt

Homepage:
Spack package:
Versions:
1.5-5
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Functions are provided for computing the density and the distribution function of multivariate normal and "t" random variables, and for generating random vectors sampled from these distributions. Probabilities are computed via non-Monte Carlo methods; different routines are used in the case d=1, d=2, d>2, if d denotes the number of dimensions.

r-modelmetrics

Homepage:
Spack package:
Versions:
1.2.2, 1.2.0, 1.1.0
Build Dependencies:
r, r-rcpp, r-data-table
Link Dependencies:
r
Run Dependencies:
r, r-rcpp, r-data-table
Description:
Collection of metrics for evaluating models written in C++ using 'Rcpp'.

r-modelr

Homepage:
Spack package:
Versions:
0.1.5, 0.1.4, 0.1.3, 0.1.1
Build Dependencies:
r, r-magrittr, r-purrr, r-lazyeval, r-tibble, r-broom, r-dplyr, r-tidyr, r-rlang
Link Dependencies:
r
Run Dependencies:
r, r-magrittr, r-purrr, r-lazyeval, r-tibble, r-broom, r-dplyr, r-tidyr, r-rlang
Description:
Functions for modelling that help you seamlessly integrate modelling into a pipeline of data manipulation and visualisation.

r-modeltools

Homepage:
Spack package:
Versions:
0.2-22, 0.2-21
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
A collection of tools to deal with statistical models.

r-mpm

Homepage:
Spack package:
Versions:
1.0-22
Build Dependencies:
r, r-mass, r-kernsmooth
Link Dependencies:
r
Run Dependencies:
r, r-mass, r-kernsmooth
Description:
Exploratory graphical analysis of multivariate data, specifically gene expression data with different projection methods: principal component analysis, correspondence analysis, spectral map analysis.

r-msnbase

Homepage:
Spack package:
Versions:
2.10.1, 2.8.3, 2.6.4, 2.4.2, 2.2.0
Build Dependencies:
r, r-biocgenerics, r-biobase, r-mzr, r-biocparallel, r-protgenerics, r-plyr, r-iranges, r-preprocesscore, r-vsn, r-affy, r-impute, r-pcamethods, r-mzid, r-maldiquant, r-digest, r-lattice, r-ggplot2, r-s4vectors, r-xml, r-rcpp, r-scales, r-mass
Link Dependencies:
r
Run Dependencies:
r, r-biocgenerics, r-biobase, r-mzr, r-biocparallel, r-protgenerics, r-plyr, r-iranges, r-preprocesscore, r-vsn, r-affy, r-impute, r-pcamethods, r-mzid, r-maldiquant, r-digest, r-lattice, r-ggplot2, r-s4vectors, r-xml, r-rcpp, r-scales, r-mass
Description:
Base Functions and Classes for Mass Spectrometry and Proteomics. MSnbase provides infrastructure for manipulation, processing and visualisation of mass spectrometry and proteomics data, ranging from raw to quantitative and annotated data.

r-multcomp

Homepage:
Spack package:
Versions:
1.4-10, 1.4-8, 1.4-6
Build Dependencies:
r, r-mvtnorm, r-survival, r-th-data, r-sandwich, r-codetools
Link Dependencies:
r
Run Dependencies:
r, r-mvtnorm, r-survival, r-th-data, r-sandwich, r-codetools
Description:
Simultaneous tests and confidence intervals for general linear hypotheses in parametric models, including linear, generalized linear, linear mixed effects, and survival models. The package includes demos reproducing analyzes presented in the book "Multiple Comparisons Using R" (Bretz, Hothorn, Westfall, 2010, CRC Press).

r-multicool

Homepage:
Spack package:
Versions:
0.1-9
Build Dependencies:
r, r-rcpp
Link Dependencies:
r
Run Dependencies:
r, r-rcpp
Description:
Permutations of multisets in cool-lex order.

r-multitaper

Homepage:
Spack package:
Versions:
1.0-14
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
multitaper: Spectral Analysis Tools using the Multitaper Method

r-multtest

Homepage:
Spack package:
Versions:
2.40.0, 2.38.0, 2.36.0, 2.34.0, 2.32.0
Build Dependencies:
r, r-biocgenerics, r-biobase, r-survival, r-mass
Link Dependencies:
r
Run Dependencies:
r, r-biocgenerics, r-biobase, r-survival, r-mass
Description:
Resampling-based multiple hypothesis testing. Non-parametric bootstrap and permutation resampling-based multiple testing procedures (including empirical Bayes methods) for controlling the family-wise error rate (FWER), generalized family-wise error rate (gFWER), tail probability of the proportion of false positives (TPPFP), and false discovery rate (FDR). Several choices of bootstrap-based null distribution are implemented (centered, centered and scaled, quantile- transformed). Single-step and step-wise methods are available. Tests based on a variety of t- and F-statistics (including t-statistics based on regression parameters from linear and survival models as well as those based on correlation parameters) are included. When probing hypotheses with t-statistics, users may also select a potentially faster null distribution which is multivariate normal with mean zero and variance covariance matrix derived from the vector influence function. Results are reported in terms of adjusted p-values, confidence regions and test statistic cutoffs. The procedures are directly applicable to identifying differentially expressed genes in DNA microarray experiments.

r-munsell

Homepage:
Spack package:
Versions:
0.5.0, 0.4.3
Build Dependencies:
r, r-colorspace
Link Dependencies:
r
Run Dependencies:
r, r-colorspace
Description:
Provides easy access to, and manipulation of, the Munsell colours. Provides a mapping between Munsell's original notation (e.g. "5R 5/10") and hexadecimal strings suitable for use directly in R graphics. Also provides utilities to explore slices through the Munsell colour tree, to transform Munsell colours and display colour palettes.

r-mvtnorm

Homepage:
Spack package:
Versions:
1.0-11, 1.0-10, 1.0-6, 1.0-5
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Computes multivariate normal and t probabilities, quantiles, random deviates and densities.

r-mzid

Homepage:
Spack package:
Versions:
1.22.0, 1.20.1, 1.18.0, 1.16.0, 1.14.0
Build Dependencies:
r, r-xml, r-plyr, r-doparallel, r-foreach, r-iterators, r-protgenerics
Link Dependencies:
r
Run Dependencies:
r, r-xml, r-plyr, r-doparallel, r-foreach, r-iterators, r-protgenerics
Description:
An mzIdentML parser for R. A parser for mzIdentML files implemented using the XML package. The parser tries to be general and able to handle all types of mzIdentML files with the drawback of having less 'pretty' output than a vendor specific parser. Please contact the maintainer with any problems and supply an mzIdentML file so the problems can be fixed quickly.

r-mzr

Homepage:
Spack package:
Versions:
2.18.1, 2.16.2, 2.14.0, 2.12.0, 2.10.0
Build Dependencies:
r, r-rcpp, r-biobase, r-biocgenerics, r-protgenerics, r-zlibbioc, r-rhdf5lib, r-ncdf4, gmake
Link Dependencies:
r
Run Dependencies:
r, r-rcpp, r-biobase, r-biocgenerics, r-protgenerics, r-zlibbioc, r-rhdf5lib, r-ncdf4
Description:
parser for netCDF, mzXML, mzData and mzML and mzIdentML files (mass spectrometry data). mzR provides a unified API to the common file formats and parsers available for mass spectrometry data. It comes with a wrapper for the ISB random access parser for mass spectrometry mzXML, mzData and mzML files. The package contains the original code written by the ISB, and a subset of the proteowizard library for mzML and mzIdentML. The netCDF reading code has previously been used in XCMS.

r-nanotime

Homepage:
Spack package:
Versions:
0.2.4, 0.2.3, 0.2.0
Build Dependencies:
r, r-bit64, r-rcppcctz, r-zoo
Link Dependencies:
r
Run Dependencies:
r, r-bit64, r-rcppcctz, r-zoo
Description:
Full 64-bit resolution date and time support with resolution up to nanosecond granularity is provided, with easy transition to and from the standard 'POSIXct' type.

r-ncbit

Homepage:
Spack package:
Versions:
2013.03.29
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Making NCBI taxonomic data locally available and searchable as an R object.

r-ncdf4

Homepage:
Spack package:
Versions:
1.16.1, 1.16, 1.15
Build Dependencies:
r, netcdf-c
Link Dependencies:
r, netcdf-c
Run Dependencies:
r
Description:
Provides a high-level R interface to data files written using Unidata's netCDF library (version 4 or earlier), which are binary data files that are portable across platforms and include metadata information in addition to the data sets. Using this package, netCDF files (either version 4 or "classic" version 3) can be opened and data sets read in easily. It is also easy to create new netCDF dimensions, variables, and files, in either version 3 or 4 format, and manipulate existing netCDF files. This package replaces the former ncdf package, which only worked with netcdf version 3 files. For various reasons the names of the functions have had to be changed from the names in the ncdf package. The old ncdf package is still available at the URL given below, if you need to have backward compatibility. It should be possible to have both the ncdf and ncdf4 packages installed simultaneously without a problem. However, the ncdf package does not provide an interface for netcdf version 4 files.

r-network

Homepage:
Spack package:
Versions:
1.15, 1.14-377, 1.13.0
Build Dependencies:
r, r-tibble, r-magrittr
Link Dependencies:
r
Run Dependencies:
r, r-tibble, r-magrittr
Description:
Tools to create and modify network objects. The network class can represent a range of relational data types, and supports arbitrary vertex/edge/graph attributes.

r-networkd3

Homepage:
Spack package:
Versions:
0.4, 0.3, 0.2.12
Build Dependencies:
r, r-htmlwidgets, r-igraph, r-magrittr
Link Dependencies:
r
Run Dependencies:
r, r-htmlwidgets, r-igraph, r-magrittr
Description:
Creates 'D3' 'JavaScript' network, tree, dendrogram, and Sankey graphs from 'R'.

r-nleqslv

Homepage:
Spack package:
Versions:
3.3.2
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
nleqslv: Solve Systems of Nonlinear Equations

r-nlme

Homepage:
Spack package:
Versions:
3.1-141, 3.1-139, 3.1-131, 3.1-130
Build Dependencies:
r, r-lattice
Link Dependencies:
r
Run Dependencies:
r, r-lattice
Description:
Fit and compare Gaussian linear and nonlinear mixed-effects models.

r-nloptr

Homepage:
Spack package:
Versions:
1.2.1, 1.0.4
Build Dependencies:
r, nlopt
Link Dependencies:
r, nlopt
Run Dependencies:
r
Description:
nloptr is an R interface to NLopt. NLopt is a free/open-source library for nonlinear optimization, providing a common interface for a number of different free optimization routines available online as well as original implementations of various other algorithms. See http://ab- initio.mit.edu/wiki/index.php/NLopt _Introduction for more information on the available algorithms. During installation on Unix the NLopt code is downloaded and compiled from the NLopt website.

r-nmf

Homepage:
Spack package:
Versions:
0.21.0
Build Dependencies:
r, r-pkgmaker, r-registry, r-rngtools, r-cluster, r-stringr, r-digest, r-gridbase, r-colorspace, r-rcolorbrewer, r-foreach, r-doparallel, r-ggplot2, r-reshape2
Link Dependencies:
r
Run Dependencies:
r, r-pkgmaker, r-registry, r-rngtools, r-cluster, r-stringr, r-digest, r-gridbase, r-colorspace, r-rcolorbrewer, r-foreach, r-doparallel, r-ggplot2, r-reshape2
Description:
Provides a framework to perform Non-negative Matrix Factorization (NMF). The package implements a set of already published algorithms and seeding methods, and provides a framework to test, develop and plug new/custom algorithms. Most of the built-in algorithms have been optimized in C++, and the main interface function provides an easy way of performing parallel computations on multicore machines..

r-nmof

Homepage:
Spack package:
Versions:
1.6-0
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Functions, examples and data from the book "Numerical Methods and Optimization in Finance" by M. Gilli, D. Maringer and E. Schumann (2011), ISBN 978-0123756626. The package provides implementations of several optimisation heuristics, such as Differential Evolution, Genetic Algorithms and Threshold Accepting. There are also functions for the valuation of financial instruments, such as bonds and options, and functions that help with stochastic simulations.

r-nnet

Homepage:
Spack package:
Versions:
7.3-12
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Software for feed-forward neural networks with a single hidden layer, and for multinomial log-linear models.

r-nnls

Homepage:
Spack package:
Versions:
1.4
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
An R interface to the Lawson-Hanson implementation of an algorithm for non-negative least squares (NNLS). Also allows the combination of non- negative and non-positive constraints.

r-nor1mix

Homepage:
Spack package:
Versions:
1.3-0, 1.2-3
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Onedimensional Normal Mixture Models Classes, for, e.g., density estimation or clustering algorithms research and teaching; providing the widely used Marron-Wand densities. Efficient random number generation and graphics; now fitting to data by ML (Maximum Likelihood) or EM estimation.

r-nortest

Homepage:
Spack package:
Versions:
1.0-4
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
nortest: Tests for Normality Five omnibus tests for testing the composite hypothesis of normality.

r-np

Homepage:
Spack package:
Versions:
0.60-9, 0.60-8, 0.60-2
Build Dependencies:
r, r-boot, r-cubature, r-quadprog, r-quantreg
Link Dependencies:
r
Run Dependencies:
r, r-boot, r-cubature, r-quadprog, r-quantreg
Description:
This package provides a variety of nonparametric (and semiparametric) kernel methods that seamlessly handle a mix of continuous, unordered, and ordered factor data types. We would like to gratefully acknowledge support from the Natural Sciences and Engineering Research Council of Canada (NSERC:www.nserc.ca), the Social Sciences and Humanities Research Council of Canada (SSHRC:www.sshrc.ca), and the Shared Hierarchical Academic Research Computing Network (SHARCNET:www.sharcnet.ca).

r-npsurv

Homepage:
Spack package:
Versions:
0.4-0
Build Dependencies:
r, r-lsei
Link Dependencies:
r
Run Dependencies:
r, r-lsei
Description:
Contains functions for non-parametric survival analysis of exact and interval-censored observations.

r-numderiv

Homepage:
Spack package:
Versions:
2016.8-1.1, 2016.8-1
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Methods for calculating (usually) accurate numerical first and second order derivatives.

r-oligoclasses

Homepage:
Spack package:
Versions:
1.46.0, 1.44.0, 1.42.0, 1.40.0, 1.38.0
Build Dependencies:
r, r-biocgenerics, r-biobase, r-iranges, r-genomicranges, r-summarizedexperiment, r-biostrings, r-affyio, r-ff, r-foreach, r-biocinstaller, r-s4vectors, r-rsqlite, r-dbi, r-biocmanager
Link Dependencies:
r
Run Dependencies:
r, r-biocgenerics, r-biobase, r-iranges, r-genomicranges, r-summarizedexperiment, r-biostrings, r-affyio, r-ff, r-foreach, r-biocinstaller, r-s4vectors, r-rsqlite, r-dbi, r-biocmanager
Description:
Classes for high-throughput arrays supported by oligo and crlmm. This package contains class definitions, validity checks, and initialization methods for classes used by the oligo and crlmm packages.

r-openssl

Homepage:
Spack package:
Versions:
1.4.1, 1.3, 0.9.7, 0.9.6, 0.9.4
Build Dependencies:
r, r-askpass, openssl
Link Dependencies:
r, openssl
Run Dependencies:
r, r-askpass
Description:
Bindings to OpenSSL libssl and libcrypto, plus custom SSH pubkey parsers. Supports RSA, DSA and EC curves P-256, P-384 and P-521. Cryptographic signatures can either be created and verified manually or via x509 certificates. AES can be used in cbc, ctr or gcm mode for symmetric encryption; RSA for asymmetric (public key) encryption or EC for Diffie Hellman. High-level envelope functions combine RSA and AES for encrypting arbitrary sized data. Other utilities include key generators, hash functions (md5, sha1, sha256, etc), base64 encoder, a secure random number generator, and 'bignum' math methods for manually performing crypto calculations on large multibyte integers.

r-openxlsx

Homepage:
Spack package:
Versions:
4.1.0.1
Build Dependencies:
r, r-rcpp, r-zip
Link Dependencies:
r
Run Dependencies:
r, r-rcpp, r-zip
Description:
Simplifies the creation of Excel .xlsx files by providing a high level interface to writing, styling and editing worksheets. Through the use of 'Rcpp', read/write times are comparable to the 'xlsx' and 'XLConnect' packages with the added benefit of removing the dependency on Java.

r-optparse

Homepage:
Spack package:
Versions:
1.6.2, 1.6.1, 1.6.0
Build Dependencies:
r, r-getopt
Link Dependencies:
r
Run Dependencies:
r, r-getopt
Description:
A command line parser inspired by Python's 'optparse' library to be used with Rscript to write "#!" shebang scripts that accept short and long flag/options

r-ordinal

Homepage:
Spack package:
Versions:
2019.4-25
Build Dependencies:
r, r-ucminf, r-mass, r-matrix, r-numderiv
Link Dependencies:
r
Run Dependencies:
r, r-ucminf, r-mass, r-matrix, r-numderiv
Description:
Implementation of cumulative link (mixed) models also known as ordered regression models, proportional odds models, proportional hazards models for grouped survival times and ordered logit/probit/... models. Estimation is via maximum likelihood and mixed models are fitted with the Laplace approximation and adaptive Gauss-Hermite quadrature. Multiple random effect terms are allowed and they may be nested, crossed or partially nested/crossed. Restrictions of symmetry and equidistance can be imposed on the thresholds (cut-points/intercepts). Standard model methods are available (summary, anova, drop-methods, step, confint, predict etc.) in addition to profile methods and slice methods for visualizing the likelihood function and checking convergence.

r-org-hs-eg-db

Homepage:
Spack package:
Versions:
3.8.2, 3.4.1
Build Dependencies:
r, r-annotationdbi
Link Dependencies:
r
Run Dependencies:
r, r-annotationdbi
Description:
Genome wide annotation for Human, primarily based on mapping using Entrez Gene identifiers.

r-organismdbi

Homepage:
Spack package:
Versions:
1.26.0, 1.24.0, 1.22.0, 1.20.0, 1.18.1
Build Dependencies:
r, r-biocgenerics, r-annotationdbi, r-genomicfeatures, r-biobase, r-biocinstaller, r-genomicranges, r-graph, r-iranges, r-rbgl, r-dbi, r-s4vectors, r-biocmanager
Link Dependencies:
r
Run Dependencies:
r, r-biocgenerics, r-annotationdbi, r-genomicfeatures, r-biobase, r-biocinstaller, r-genomicranges, r-graph, r-iranges, r-rbgl, r-dbi, r-s4vectors, r-biocmanager
Description:
Software to enable the smooth interfacing of different database packages. The package enables a simple unified interface to several annotation packages each of which has its own schema by taking advantage of the fact that each of these packages implements a select methods.

r-packrat

Homepage:
Spack package:
Versions:
0.5.0, 0.4.9-3, 0.4.8-1, 0.4.7-1
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Manage the R packages your project depends on in an isolated, portable, and reproducible way.

r-pacman

Homepage:
Spack package:
Versions:
0.5.1, 0.5.0, 0.4.1
Build Dependencies:
r, r-devtools, r-remotes
Link Dependencies:
r
Run Dependencies:
r, r-devtools, r-remotes
Description:
Tools to more conveniently perform tasks associated with add-on packages. pacman conveniently wraps library and package related functions and names them in an intuitive and consistent fashion. It seeks to combine functionality from lower level functions which can speed up workflow.

r-paleotree

Homepage:
Spack package:
Versions:
3.3.0, 3.1.3
Build Dependencies:
r, r-ape, r-phangorn, r-phytools, r-jsonlite, r-png, r-rcurl
Link Dependencies:
r
Run Dependencies:
r, r-ape, r-phangorn, r-phytools, r-jsonlite, r-png, r-rcurl
Description:
Provides tools for transforming, a posteriori time-scaling, and modifying phylogenies containing extinct (i.e. fossil) lineages

r-pamr

Homepage:
Spack package:
Versions:
1.56.1, 1.55
Build Dependencies:
r, r-cluster, r-survival
Link Dependencies:
r
Run Dependencies:
r, r-cluster, r-survival
Description:
Some functions for sample classification in microarrays.

r-pan

Homepage:
Spack package:
Versions:
1.6, 1.4
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Multiple imputation for multivariate panel or clustered data.

r-parallelmap

Homepage:
Spack package:
Versions:
1.4, 1.3
Build Dependencies:
r, r-bbmisc, r-checkmate
Link Dependencies:
r
Run Dependencies:
r, r-bbmisc, r-checkmate
Description:
Unified parallelization framework for multiple back-end, designed for internal package and interactive usage. The main operation is a parallel "map" over lists. Supports local, multicore, mpi and BatchJobs mode. Allows "tagging" of the parallel operation with a level name that can be later selected by the user to switch on parallel execution for exactly this operation.

r-paramhelpers

Homepage:
Spack package:
Versions:
1.12, 1.11, 1.10
Build Dependencies:
r, r-bbmisc, r-checkmate, r-backports, r-fastmatch
Link Dependencies:
r
Run Dependencies:
r, r-bbmisc, r-checkmate, r-backports, r-fastmatch
Description:
Functions for parameter descriptions and operations in black-box optimization, tuning and machine learning. Parameters can be described (type, constraints, defaults, etc.), combined to parameter sets and can in general be programmed on. A useful OptPath object (archive) to log function evaluations is also provided.

r-party

Homepage:
Spack package:
Versions:
1.3-3, 1.3-2, 1.1-2
Build Dependencies:
r, r-mvtnorm, r-modeltools, r-strucchange, r-survival, r-coin, r-zoo, r-sandwich
Link Dependencies:
r
Run Dependencies:
r, r-mvtnorm, r-modeltools, r-strucchange, r-survival, r-coin, r-zoo, r-sandwich
Description:
A computational toolbox for recursive partitioning.

r-partykit

Homepage:
Spack package:
Versions:
1.2-5, 1.2-3, 1.1-1
Build Dependencies:
r, r-survival, r-formula, r-libcoin, r-mvtnorm, r-inum, r-rpart
Link Dependencies:
r
Run Dependencies:
r, r-survival, r-formula, r-libcoin, r-mvtnorm, r-inum, r-rpart
Description:
A toolkit with infrastructure for representing, summarizing, and visualizing tree-structured regression and classification models. This unified infrastructure can be used for reading/coercing tree models from different sources ('rpart', 'RWeka', 'PMML') yielding objects that share functionality for print()/plot()/predict() methods. Furthermore, new and improved reimplementations of conditional inference trees (ctree()) and model-based recursive partitioning (mob()) from the 'party' package are provided based on the new infrastructure.

r-pathview

Homepage:
Spack package:
Versions:
1.24.0, 1.22.3, 1.20.0, 1.18.2, 1.16.7
Build Dependencies:
r, r-org-hs-eg-db, r-kegggraph, r-xml, r-rgraphviz, r-graph, r-png, r-annotationdbi, r-keggrest
Link Dependencies:
r
Run Dependencies:
r, r-org-hs-eg-db, r-kegggraph, r-xml, r-rgraphviz, r-graph, r-png, r-annotationdbi, r-keggrest
Description:
a tool set for pathway based data integration and visualization. Pathview is a tool set for pathway based data integration and visualization. It maps and renders a wide variety of biological data on relevant pathway graphs. All users need is to supply their data and specify the target pathway. Pathview automatically downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, Pathview also seamlessly integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis.

r-pbapply

Homepage:
Spack package:
Versions:
1.4-1, 1.3-4, 1.3-3, 1.3-2, 1.3-1, 1.3-0, 1.2-2
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
A lightweight package that adds progress bar to vectorized R apply functions.

r-pbdzmq

Homepage:
Spack package:
Versions:
0.3-3, 0.3-2, 0.2-4
Build Dependencies:
r, r-r6, libzmq
Link Dependencies:
r, libzmq
Run Dependencies:
r, r-r6
Description:
'ZeroMQ' is a well-known library for high-performance asynchronous messaging in scalable, distributed applications. This package provides high level R wrapper functions to easily utilize 'ZeroMQ'. We mainly focus on interactive client/server programming frameworks. For convenience, a minimal 'ZeroMQ' library (4.1.0 rc1) is shipped with 'pbdZMQ', which can be used if no system installation of 'ZeroMQ' is available. A few wrapper functions compatible with 'rzmq' are also provided.

r-pbkrtest

Homepage:
Spack package:
Versions:
0.4-7, 0.4-6, 0.4-4
Build Dependencies:
r, r-lme4, r-matrix, r-mass
Link Dependencies:
r
Run Dependencies:
r, r-lme4, r-matrix, r-mass
Description:
Test in mixed effects models. Attention is on mixed effects models as implemented in the 'lme4' package. This package implements a parametric bootstrap test and a Kenward Roger modification of F-tests for linear mixed effects models and a parametric bootstrap test for generalized linear mixed models.

r-pcamethods

Homepage:
Spack package:
Versions:
1.76.0, 1.74.0, 1.72.0, 1.70.0, 1.68.0
Build Dependencies:
r, r-biobase, r-biocgenerics, r-rcpp, r-mass
Link Dependencies:
r
Run Dependencies:
r, r-biobase, r-biocgenerics, r-rcpp, r-mass
Description:
A collection of PCA methods. Provides Bayesian PCA, Probabilistic PCA, Nipals PCA, Inverse Non-Linear PCA and the conventional SVD PCA. A cluster based method for missing value estimation is included for comparison. BPCA, PPCA and NipalsPCA may be used to perform PCA on incomplete data as well as for accurate missing value estimation. A set of methods for printing and plotting the results is also provided. All PCA methods make use of the same data structure (pcaRes) to provide a common interface to the PCA results. Initiated at the Max-Planck Institute for Molecular Plant Physiology, Golm, Germany.

r-pcapp

Homepage:
Spack package:
Versions:
1.9-73, 1.9-72.1, 1.9-72, 1.9-70, 1.9-61, 1.9-60, 1.9-50
Build Dependencies:
r, r-mvtnorm
Link Dependencies:
r
Run Dependencies:
r, r-mvtnorm
Description:
Provides functions for robust PCA by projection pursuit.

r-permute

Homepage:
Spack package:
Versions:
0.9-5, 0.9-4
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
A set of restricted permutation designs for freely exchangeable, line transects (time series), and spatial grid designs plus permutation of blocks (groups of samples) is provided. 'permute' also allows split-plot designs, in which the whole-plots or split-plots or both can be freely- exchangeable or one of the restricted designs. The 'permute' package is modelled after the permutation schemes of 'Canoco 3.1' (and later) by Cajo ter Braak.

r-pfam-db

Homepage:
Spack package:
Versions:
3.10.0, 3.4.1
Build Dependencies:
r, r-annotationdbi
Link Dependencies:
r
Run Dependencies:
r, r-annotationdbi
Description:
A set of protein ID mappings for PFAM assembled using data from public repositories.

r-phangorn

Homepage:
Spack package:
Versions:
2.5.5, 2.5.3, 2.3.1
Build Dependencies:
r, r-ape, r-quadprog, r-igraph, r-matrix, r-fastmatch, r-magrittr, r-rcpp
Link Dependencies:
r
Run Dependencies:
r, r-ape, r-quadprog, r-igraph, r-matrix, r-fastmatch, r-magrittr, r-rcpp
Description:
Package contains methods for estimation of phylogenetic trees and networks using Maximum Likelihood, Maximum Parsimony, distance methods and Hadamard conjugation. Allows to compare trees, models selection and offers visualizations for trees and split networks.

r-phantompeakqualtools

Homepage:
Spack package:
Versions:
1.14
Build Dependencies:
r, boost, r-catools, r-snow, r-snowfall, r-bitops, r-rsamtools
Link Dependencies:
r, boost
Run Dependencies:
r, r-catools, r-snow, r-snowfall, r-bitops, r-rsamtools
Description:
Computes informative enrichment and quality measures for ChIP-seq/DNase- seq/FAIRE-seq/MNase-seq data. This is a modified version of r-spp to be used in conjunction with the phantompeakqualtools package.

r-philentropy

Homepage:
Spack package:
Versions:
0.4.0
Build Dependencies:
r, r-rcpp, r-dplyr, r-kernsmooth
Link Dependencies:
r
Run Dependencies:
r, r-rcpp, r-dplyr, r-kernsmooth
Description:
Computes 46 optimized distance and similarity measures for comparing probability functions (Drost (2018) <doi:10.21105/joss.00765>). These comparisons between probability functions have their foundations in a broad range of scientific disciplines from mathematics to ecology. The aim of this package is to provide a core framework for clustering, classification, statistical inference, goodness-of-fit, non-parametric statistics, information theory, and machine learning tasks that are based on comparing univariate or multivariate probability functions.

r-phyloseq

Homepage:
Spack package:
Versions:
1.28.0, 1.26.1, 1.24.2, 1.22.3, 1.20.0
Build Dependencies:
r, r-biocgenerics, r-ade4, r-ape, r-biomformat, r-biostrings, r-cluster, r-data-table, r-foreach, r-ggplot2, r-igraph, r-multtest, r-plyr, r-reshape2, r-scales, r-vegan, r-biobase
Link Dependencies:
r
Run Dependencies:
r, r-biocgenerics, r-ade4, r-ape, r-biomformat, r-biostrings, r-cluster, r-data-table, r-foreach, r-ggplot2, r-igraph, r-multtest, r-plyr, r-reshape2, r-scales, r-vegan, r-biobase
Description:
Handling and analysis of high-throughput microbiome census data. phyloseq provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data.

r-phylostratr

Homepage:
Spack package:
Versions:
20190323
Build Dependencies:
r, r-ape, r-biostrings, r-curl, r-dplyr, r-ggplot2, r-scales, r-glue, r-gridextra, r-magrittr, r-purrr, r-readr, r-reshape2, r-rhmmer, r-rlang, r-tibble, r-taxizedb, r-tidyr
Link Dependencies:
r
Run Dependencies:
r, r-ape, r-biostrings, r-curl, r-dplyr, r-ggplot2, r-scales, r-glue, r-gridextra, r-magrittr, r-purrr, r-readr, r-reshape2, r-rhmmer, r-rlang, r-tibble, r-taxizedb, r-tidyr
Description:
Predict and explore the age of genes using phylostratigraphic methods

r-phytools

Homepage:
Spack package:
Versions:
0.6-99, 0.6-60
Build Dependencies:
r, r-animation, r-ape, r-clustergeneration, r-coda, r-combinat, r-expm, r-mass, r-maps, r-mnormt, r-nlme, r-numderiv, r-phangorn, r-plotrix, r-scatterplot3d, r-gtools
Link Dependencies:
r
Run Dependencies:
r, r-animation, r-ape, r-clustergeneration, r-coda, r-combinat, r-expm, r-mass, r-maps, r-mnormt, r-nlme, r-numderiv, r-phangorn, r-plotrix, r-scatterplot3d, r-gtools
Description:
Phylogenetic Tools for Comparative Biology (and Other Things)

r-picante

Homepage:
Spack package:
Versions:
1.8, 1.7, 1.6-2, 1.6-1
Build Dependencies:
r, r-ape, r-nlme, r-vegan
Link Dependencies:
r
Run Dependencies:
r, r-ape, r-nlme, r-vegan
Description:
R tools for integrating phylogenies and ecology

r-pillar

Homepage:
Spack package:
Versions:
1.4.2, 1.4.1, 1.3.1, 1.3.0, 1.2.3, 1.2.2, 1.2.1, 1.2.0, 1.1.0, 1.0.1, 1.0.0
Build Dependencies:
r, r-cli, r-crayon, r-fansi, r-rlang, r-utf8, r-vctrs
Link Dependencies:
r
Run Dependencies:
r, r-cli, r-crayon, r-fansi, r-rlang, r-utf8, r-vctrs
Description:
Provides a 'pillar' generic designed for formatting columns of data using the full range of colours provided by modern terminals.

r-pkgbuild

Homepage:
Spack package:
Versions:
1.0.4, 1.0.3
Build Dependencies:
r, r-callr, r-cli, r-crayon, r-desc, r-prettyunits, r-r6, r-rprojroot, r-withr
Link Dependencies:
r
Run Dependencies:
r, r-callr, r-cli, r-crayon, r-desc, r-prettyunits, r-r6, r-rprojroot, r-withr
Description:
pkgbuild: Find Tools Needed to Build R Packages

r-pkgconfig

Homepage:
Spack package:
Versions:
2.0.2, 2.0.1
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Set configuration options on a per-package basis. Options set by a given package only apply to that package, other packages are unaffected.

r-pkgload

Homepage:
Spack package:
Versions:
1.0.2
Build Dependencies:
r, r-desc, r-pkgbuild, r-rlang, r-rprojroot, r-rstudioapi, r-withr
Link Dependencies:
r
Run Dependencies:
r, r-desc, r-pkgbuild, r-rlang, r-rprojroot, r-rstudioapi, r-withr
Description:
pkgload: Simulate Package Installation and Attach

r-pkgmaker

Homepage:
Spack package:
Versions:
0.27
Build Dependencies:
r, r-registry, r-codetools, r-digest, r-stringi, r-magrittr, r-stringr, r-xtable, r-withr, r-bibtex
Link Dependencies:
r
Run Dependencies:
r, r-registry, r-codetools, r-digest, r-stringi, r-magrittr, r-stringr, r-xtable, r-withr, r-bibtex
Description:
This package provides some low-level utilities to use for package development. It currently provides managers for multiple package specific options and registries, vignette, unit test and bibtex related utilities. It serves as a base package for packages like NMF, RcppOctave, doRNG, and as an incubator package for other general purposes utilities, that will eventually be packaged separately. It is still under heavy development and changes in the interface(s) are more than likely to happen.

r-plogr

Homepage:
Spack package:
Versions:
0.2.0, 0.1-1
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
A simple header-only logging library for C++. Add 'LinkingTo: plogr' to 'DESCRIPTION', and '#include <plogr.h>' in your C++ modules to use it.

r-plot3d

Homepage:
Spack package:
Versions:
1.1.1
Build Dependencies:
r, r-misc3d
Link Dependencies:
r
Run Dependencies:
r, r-misc3d
Description:
Functions for viewing 2-D and 3-D data, including perspective plots, slice plots, surface plots, scatter plots, etc. Includes data sets from oceanography.

r-plotly

Homepage:
Spack package:
Versions:
4.9.0, 4.8.0, 4.7.1, 4.7.0, 4.6.0, 4.5.6, 4.5.2
Build Dependencies:
r, r-ggplot2, r-httr, r-base64enc, r-htmltools, r-tidyr, r-dplyr, r-htmlwidgets, r-data-table, r-hexbin, r-purrr, r-crosstalk, r-scales, r-jsonlite, r-magrittr, r-digest, r-viridislite, r-tibble, r-lazyeval, r-rcolorbrewer, r-rlang, r-promises
Link Dependencies:
r
Run Dependencies:
r, r-ggplot2, r-httr, r-base64enc, r-htmltools, r-tidyr, r-dplyr, r-htmlwidgets, r-data-table, r-hexbin, r-purrr, r-crosstalk, r-scales, r-jsonlite, r-magrittr, r-digest, r-viridislite, r-tibble, r-lazyeval, r-rcolorbrewer, r-rlang, r-promises
Description:
Easily translate 'ggplot2' graphs to an interactive web-based version and/or create custom web-based visualizations directly from R.

r-plotmo

Homepage:
Spack package:
Versions:
3.5.6
Build Dependencies:
r, r-formula, r-plotrix, r-teachingdemos
Link Dependencies:
r
Run Dependencies:
r, r-formula, r-plotrix, r-teachingdemos
Description:
plotmo: Plot a Model's Residuals, Response, and Partial Dependence Plots. Plot model surfaces for a wide variety of models using partial dependence plots and other techniques. Also plot model residuals and other information on the model.

r-plotrix

Homepage:
Spack package:
Versions:
3.7-6, 3.7-5, 3.6-4, 3.6-3
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Lots of plots, various labeling, axis and color scaling functions.

r-pls

Homepage:
Spack package:
Versions:
2.7-1, 2.7-0, 2.6-0
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Multivariate regression methods Partial Least Squares Regression (PLSR), Principal Component Regression (PCR) and Canonical Powered Partial Least Squares (CPPLS).

r-plyr

Homepage:
Spack package:
Versions:
1.8.4
Build Dependencies:
r, r-rcpp
Link Dependencies:
r
Run Dependencies:
r, r-rcpp
Description:
A set of tools that solves a common set of problems: you need to break a big problem down into manageable pieces, operate on each piece and then put all the pieces back together. For example, you might want to fit a model to each spatial location or time point in your study, summarise data by panels or collapse high-dimensional arrays to simpler summary statistics. The development of 'plyr' has been generously supported by 'Becton Dickinson'.

r-pmcmr

Homepage:
Spack package:
Versions:
4.3, 4.1
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
The Kruskal and Wallis one-way analysis of variance by ranks or van der Waerden's normal score test can be employed, if the data do not meet the assumptions for one-way ANOVA. Provided that significant differences were detected by the omnibus test, one may be interested in applying post-hoc tests for pairwise multiple comparisons (such as Nemenyi's test, Dunn's test, Conover's test, van der Waerden's test). Similarly, one-way ANOVA with repeated measures that is also referred to as ANOVA with unreplicated block design can also be conducted via the Friedman- Test or the Quade-test. The consequent post-hoc pairwise multiple comparison tests according to Nemenyi, Conover and Quade are also provided in this package. Finally Durbin's test for a two-way balanced incomplete block design (BIBD) is also given in this package.

r-png

Homepage:
Spack package:
Versions:
0.1-7
Build Dependencies:
r, libpng
Link Dependencies:
r, libpng
Run Dependencies:
r
Description:
This package provides an easy and simple way to read, write and display bitmap images stored in the PNG format. It can read and write both files and in-memory raw vectors.

r-polyclip

Homepage:
Spack package:
Versions:
1.10-0
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
polyclip: Polygon Clipping

r-polynom

Homepage:
Spack package:
Versions:
1.4-0
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
A collection of functions to implement a class for univariate polynomial manipulations.

r-popgenome

Homepage:
Spack package:
Versions:
2.7.1, 2.6.1
Build Dependencies:
r, r-ff
Link Dependencies:
r
Run Dependencies:
r, r-ff
Description:
PopGenome is an efficient Swiss army knife for population genetics data analysis, able to process individual loci, large sets of loci, or whole genomes.

r-popvar

Homepage:
Spack package:
Versions:
1.2.1
Build Dependencies:
r, r-bglr, r-qtl, r-rrblup
Link Dependencies:
r
Run Dependencies:
r, r-bglr, r-qtl, r-rrblup
Description:
PopVar: Genomic Breeding Tools: Genetic Variance Prediction andCross- Validation

r-powerlaw

Homepage:
Spack package:
Versions:
0.70.2, 0.70.1
Build Dependencies:
r, r-vgam
Link Dependencies:
r
Run Dependencies:
r, r-vgam
Description:
An implementation of maximum likelihood estimators for a variety of heavy tailed distributions, including both the discrete and continuous power law distributions. Additionally, a goodness-of-fit based approach is used to estimate the lower cut-off for the scaling region.

r-prabclus

Homepage:
Spack package:
Versions:
2.3-1, 2.2-7.1, 2.2-6
Build Dependencies:
r, r-mass, r-mclust
Link Dependencies:
r
Run Dependencies:
r, r-mass, r-mclust
Description:
prabclus: Functions for Clustering of Presence-Absence, Abundance and Multilocus Genetic Data

r-praise

Homepage:
Spack package:
Versions:
1.0.0
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Build friendly R packages that praise their users if they have done something good, or they just need it to feel better.

r-preprocesscore

Homepage:
Spack package:
Versions:
1.46.0, 1.44.0, 1.42.0, 1.40.0, 1.38.1
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
A collection of pre-processing functions. A library of core preprocessing routines.

r-prettyunits

Homepage:
Spack package:
Versions:
1.0.2
Build Dependencies:
r, r-magrittr, r-assertthat
Link Dependencies:
r
Run Dependencies:
r, r-magrittr, r-assertthat
Description:
Pretty, human readable formatting of quantities. Time intervals: 1337000 -> 15d 11h 23m 20s. Vague time intervals: 2674000 -> about a month ago. Bytes: 1337 -> 1.34 kB.

r-processx

Homepage:
Spack package:
Versions:
3.4.1, 3.3.1, 3.2.0, 3.1.0, 3.0.3, 2.0.0.1, 2.0.0
Build Dependencies:
r, r-assertthat, r-crayon, r-ps, r-r6, r-debugme
Link Dependencies:
r
Run Dependencies:
r, r-assertthat, r-crayon, r-ps, r-r6, r-debugme
Description:
Tools to run system processes in the background

r-prodlim

Homepage:
Spack package:
Versions:
2018.04.18, 1.6.1, 1.5.9
Build Dependencies:
r, r-rcpp, r-survival, r-kernsmooth, r-lava
Link Dependencies:
r
Run Dependencies:
r, r-rcpp, r-survival, r-kernsmooth, r-lava
Description:
Product-Limit Estimation for Censored Event History Analysis. Fast and user friendly implementation of nonparametric estimators for censored event history (survival) analysis. Kaplan-Meier and Aalen-Johansen method.

r-progress

Homepage:
Spack package:
Versions:
1.2.2, 1.2.1, 1.1.2
Build Dependencies:
r, r-r6, r-prettyunits, r-hms, r-crayon
Link Dependencies:
r
Run Dependencies:
r, r-r6, r-prettyunits, r-hms, r-crayon
Description:
Configurable Progress bars, they may include percentage, elapsed time, and/or the estimated completion time. They work in terminals, in 'Emacs' 'ESS', 'RStudio', 'Windows' 'Rgui' and the 'macOS' 'R.app'. The package also provides a 'C++' 'API', that works with or without 'Rcpp'.

r-proj

Homepage:
Spack package:
Versions:
0.1.0
Build Dependencies:
r, proj
Link Dependencies:
r, proj
Run Dependencies:
r
Description:
A wrapper around the generic coordinate transformation software 'PROJ' that transforms geospatial coordinates from one coordinate reference system ('CRS') to another. This includes cartographic projections as well as geodetic transformations. Version 6.0.0 or higher is required. The intention is for this package to be used by user-packages such as 'reproj', and that the older 'PROJ.4' and version 5 pathways be provided by the legacy package. The 'PROJ' library is available from <https://proj.org/>.

r-proj4

Homepage:
Spack package:
Versions:
1.0-8.1
Build Dependencies:
r, proj
Link Dependencies:
r, proj
Run Dependencies:
r
Description:
A simple interface to lat/long projection and datum transformation of the PROJ.4 cartographic projections library. It allows transformation of geographic coordinates from one projection and/or datum to another.

r-promises

Homepage:
Spack package:
Versions:
1.0.1
Build Dependencies:
r, r-r6, r-rcpp, r-later, r-rlang, r-magrittr
Link Dependencies:
r
Run Dependencies:
r, r-r6, r-rcpp, r-later, r-rlang, r-magrittr
Description:
Provides fundamental abstractions for doing asynchronous programming in R using promises. Asynchronous programming is useful for allowing a single R process to orchestrate multiple tasks in the background while also attending to something else. Semantics are similar to 'JavaScript' promises, but with a syntax that is idiomatic R.

r-protgenerics

Homepage:
Spack package:
Versions:
1.16.0, 1.14.0, 1.12.0, 1.10.0, 1.8.0
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
S4 generic functions for Bioconductor proteomics infrastructure. S4 generic functions needed by Bioconductor proteomics packages.

r-proto

Homepage:
Spack package:
Versions:
1.0.0, 0.3-10
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
An object oriented system using object-based, also called prototype- based, rather than class-based object oriented ideas.

r-proxy

Homepage:
Spack package:
Versions:
0.4-23, 0.4-19
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Provides an extensible framework for the efficient calculation of auto- and cross-proximities, along with implementations of the most popular ones.

r-pryr

Homepage:
Spack package:
Versions:
0.1.4, 0.1.3, 0.1.2
Build Dependencies:
r, r-stringr, r-rcpp, r-codetools
Link Dependencies:
r
Run Dependencies:
r, r-stringr, r-rcpp, r-codetools
Description:
Useful tools to pry back the covers of R and understand the language at a deeper level.

r-ps

Homepage:
Spack package:
Versions:
1.3.0, 1.2.1, 1.1.0, 1.0.0
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Manipulate processes on Windows, Linux and MacOS

r-pscbs

Homepage:
Spack package:
Versions:
0.65.0
Build Dependencies:
r, r-r-methodss3, r-r-oo, r-r-utils, r-r-cache, r-matrixstats, r-aroma-light, r-dnacopy, r-listenv, r-future
Link Dependencies:
r
Run Dependencies:
r, r-r-methodss3, r-r-oo, r-r-utils, r-r-cache, r-matrixstats, r-aroma-light, r-dnacopy, r-listenv, r-future
Description:
Segmentation of allele-specific DNA copy number data and detection of regions with abnormal copy number within each parental chromosome. Both tumor-normal paired and tumor-only analyses are supported.

r-pspline

Homepage:
Spack package:
Versions:
1.0-18
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Smoothing splines with penalties on order m derivatives.

r-psych

Homepage:
Spack package:
Versions:
1.8.12, 1.8.10, 1.7.8
Build Dependencies:
r, r-mnormt, r-foreign, r-lattice, r-nlme
Link Dependencies:
r
Run Dependencies:
r, r-mnormt, r-foreign, r-lattice, r-nlme
Description:
A general purpose toolbox for personality, psychometric theory and experimental psychology. Functions are primarily for multivariate analysis and scale construction using factor analysis, principal component analysis, cluster analysis and reliability analysis, although others provide basic descriptive statistics. Item Response Theory is done using factor analysis of tetrachoric and polychoric correlations. Functions for analyzing data at multiple levels include within and between group statistics, including correlations and factor analysis. Functions for simulating and testing particular item and test structures are included. Several functions serve as a useful front end for structural equation modeling. Graphical displays of path diagrams, factor analysis and structural equation models are created using basic graphics. Some of the functions are written to support a book on psychometric theory as well as publications in personality research. For more information, see the <http://personality-project.org/r> web page.

r-ptw

Homepage:
Spack package:
Versions:
1.9-13, 1.9-12
Build Dependencies:
r, r-nloptr
Link Dependencies:
r
Run Dependencies:
r, r-nloptr
Description:
Parametric Time Warping aligns patterns, i.e. it aims to put corresponding features at the same locations. The algorithm searches for an optimal polynomial describing the warping. It is possible to align one sample to a reference, several samples to the same reference, or several samples to several references. One can choose between calculating individual warpings, or one global warping for a set of samples and one reference. Two optimization criteria are implemented: RMS (Root Mean Square error) and WCC (Weighted Cross Correlation). Both warping of peak profiles and of peak lists are supported.

r-purrr

Homepage:
Spack package:
Versions:
0.3.2, 0.3.1, 0.2.4
Build Dependencies:
r, r-magrittr, r-rlang, r-tibble
Link Dependencies:
r
Run Dependencies:
r, r-magrittr, r-rlang, r-tibble
Description:
A complete and consistent functional programming toolkit for R.

r-qtl

Homepage:
Spack package:
Versions:
1.44-9
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
qtl: Tools for Analyzing QTL Experiments

r-quadprog

Homepage:
Spack package:
Versions:
1.5-7, 1.5-6, 1.5-5
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
This package contains routines and documentation for solving quadratic programming problems.

r-quantmod

Homepage:
Spack package:
Versions:
0.4-15, 0.4-14, 0.4-10, 0.4-5
Build Dependencies:
r, r-xts, r-zoo, r-ttr, r-curl
Link Dependencies:
r
Run Dependencies:
r, r-xts, r-zoo, r-ttr, r-curl
Description:
Specify, build, trade, and analyse quantitative financial trading strategies.

r-quantreg

Homepage:
Spack package:
Versions:
5.51, 5.42.1, 5.40, 5.29, 5.26
Build Dependencies:
r, r-sparsem, r-matrix, r-matrixmodels
Link Dependencies:
r
Run Dependencies:
r, r-sparsem, r-matrix, r-matrixmodels
Description:
Estimation and inference methods for models of conditional quantiles: Linear and nonlinear parametric and non-parametric (total variation penalized) models for conditional quantiles of a univariate response and several methods for handling censored survival data. Portfolio selection methods based on expected shortfall risk are also included.

r-quantro

Homepage:
Spack package:
Versions:
1.18.0, 1.16.0, 1.14.0, 1.12.0, 1.10.0
Build Dependencies:
r, r-biobase, r-minfi, r-doparallel, r-foreach, r-iterators, r-ggplot2, r-rcolorbrewer
Link Dependencies:
r
Run Dependencies:
r, r-biobase, r-minfi, r-doparallel, r-foreach, r-iterators, r-ggplot2, r-rcolorbrewer
Description:
A test for when to use quantile normalization. A data-driven test for the assumptions of quantile normalization using raw data such as objects that inherit eSets (e.g. ExpressionSet, MethylSet). Group level information about each sample (such as Tumor / Normal status) must also be provided because the test assesses if there are global differences in the distributions between the user-defined groups.

r-qvalue

Homepage:
Spack package:
Versions:
2.16.0, 2.14.1, 2.12.0, 2.10.0, 2.8.0
Build Dependencies:
r, r-ggplot2, r-reshape2
Link Dependencies:
r
Run Dependencies:
r, r-ggplot2, r-reshape2
Description:
Q-value estimation for false discovery rate control. This package takes a list of p-values resulting from the simultaneous testing of many hypotheses and estimates their q-values and local FDR values. The q-value of a test measures the proportion of false positives incurred (called the false discovery rate) when that particular test is called significant. The local FDR measures the posterior probability the null hypothesis is true given the test's p-value. Various plots are automatically generated, allowing one to make sensible significance cut- offs. Several mathematical results have recently been shown on the conservative accuracy of the estimated q-values from this software. The software can be applied to problems in genomics, brain imaging, astrophysics, and data mining.

r-r-cache

Homepage:
Spack package:
Versions:
0.14.0
Build Dependencies:
r, r-r-methodss3, r-r-oo, r-r-utils, r-digest
Link Dependencies:
r
Run Dependencies:
r, r-r-methodss3, r-r-oo, r-r-utils, r-digest
Description:
Memoization can be used to speed up repetitive and computational expensive function calls. The first time a function that implements memoization is called the results are stored in a cache memory. The next time the function is called with the same set of parameters, the results are momentarily retrieved from the cache avoiding repeating the calculations. With this package, any R object can be cached in a key- value storage where the key can be an arbitrary set of R objects. The cache memory is persistent (on the file system).

r-r-methodss3

Homepage:
Spack package:
Versions:
1.7.1
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Methods that simplify the setup of S3 generic functions and S3 methods. Major effort has been made in making definition of methods as simple as possible with a minimum of maintenance for package developers. For example, generic functions are created automatically, if missing, and naming conflict are automatically solved, if possible. The method setMethodS3() is a good start for those who in the future may want to migrate to S4. This is a cross-platform package implemented in pure R that generates standard S3 methods.

r-r-oo

Homepage:
Spack package:
Versions:
1.23.0, 1.22.0, 1.21.0
Build Dependencies:
r, r-r-methodss3
Link Dependencies:
r
Run Dependencies:
r, r-r-methodss3
Description:
Methods and classes for object-oriented programming in R with or without references. Large effort has been made on making definition of methods as simple as possible with a minimum of maintenance for package developers. The package has been developed since 2001 and is now considered very stable. This is a cross-platform package implemented in pure R that defines standard S3 classes without any tricks.

r-r-utils

Homepage:
Spack package:
Versions:
2.9.0, 2.5.0
Build Dependencies:
r, r-r-oo, r-r-methodss3
Link Dependencies:
r
Run Dependencies:
r, r-r-oo, r-r-methodss3
Description:
Utility functions useful when programming and developing R packages.

r-r6

Homepage:
Spack package:
Versions:
2.4.0, 2.2.2, 2.2.0, 2.1.2
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
The R6 package allows the creation of classes with reference semantics, similar to R's built-in reference classes. Compared to reference classes, R6 classes are simpler and lighter-weight, and they are not built on S4 classes so they do not require the methods package. These classes allow public and private members, and they support inheritance, even when the classes are defined in different packages.

r-randomfields

Homepage:
Spack package:
Versions:
3.3.6, 3.3.4, 3.1.50
Build Dependencies:
r, r-sp, r-randomfieldsutils
Link Dependencies:
r
Run Dependencies:
r, r-sp, r-randomfieldsutils
Description:
Methods for the inference on and the simulation of Gaussian fields are provided, as well as methods for the simulation of extreme value random fields.

r-randomfieldsutils

Homepage:
Spack package:
Versions:
0.5.3, 0.5.1
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Various utilities are provided that might be used in spatial statistics and elsewhere. It delivers a method for solving linear equations that checks the sparsity of the matrix before any algorithm is used. Furthermore, it includes the Struve functions.

r-randomforest

Homepage:
Spack package:
Versions:
4.6-14, 4.6-12
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Classification and regression based on a forest of trees using random inputs.

r-randomglm

Homepage:
Spack package:
Versions:
1.02-1
Build Dependencies:
r, r-doparallel, r-foreach, r-mass
Link Dependencies:
r
Run Dependencies:
r, r-doparallel, r-foreach, r-mass
Description:
randomGLM: Random General Linear Model Prediction

r-ranger

Homepage:
Spack package:
Versions:
0.11.2, 0.11.1, 0.8.0, 0.7.0, 0.6.0, 0.5.0, 0.4.0
Build Dependencies:
r, r-matrix, r-rcpp, r-rcppeigen
Link Dependencies:
r
Run Dependencies:
r, r-matrix, r-rcpp, r-rcppeigen
Description:
A fast implementation of Random Forests, particularly suited for high dimensional data.

r-rann

Homepage:
Spack package:
Versions:
2.6.1
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Finds the k nearest neighbours for every point in a given dataset in O(N log N) time using Arya and Mount's ANN library (v1.1.3). There is support for approximate as well as exact searches, fixed radius searches and 'bd' as well as 'kd' trees. The distance is computed using the L2 (Euclidean) metric. Please see package 'RANN.L1' for the same functionality using the L1 (Manhattan, taxicab) metric.

r-rappdirs

Homepage:
Spack package:
Versions:
0.3.1
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
An easy way to determine which directories on the users computer you should use to save data, caches and logs. A port of Python's 'Appdirs' to R.

r-raster

Homepage:
Spack package:
Versions:
2.9-23, 2.9-22, 2.5-8
Build Dependencies:
r, r-sp, r-rcpp
Link Dependencies:
r
Run Dependencies:
r, r-sp, r-rcpp
Description:
Reading, writing, manipulating, analyzing and modeling of gridded spatial data. The package implements basic and high-level functions. Processing of very large files is supported.

r-rbgl

Homepage:
Spack package:
Versions:
1.60.0, 1.58.2, 1.56.0, 1.54.0, 1.52.0
Build Dependencies:
r, r-graph, r-bh
Link Dependencies:
r
Run Dependencies:
r, r-graph, r-bh
Description:
An interface to the BOOST graph library. A fairly extensive and comprehensive interface to the graph algorithms contained in the BOOST library.

r-rbokeh

Homepage:
Spack package:
Versions:
0.5.0
Build Dependencies:
r, r-htmlwidgets, r-maps, r-jsonlite, r-digest, r-hexbin, r-lazyeval, r-pryr, r-magrittr, r-ggplot2, r-scales, r-gistr
Link Dependencies:
r
Run Dependencies:
r, r-htmlwidgets, r-maps, r-jsonlite, r-digest, r-hexbin, r-lazyeval, r-pryr, r-magrittr, r-ggplot2, r-scales, r-gistr
Description:
R interface for creating plots in Bokeh. Bokeh by Continuum Analytics.

r-rcmdcheck

Homepage:
Spack package:
Versions:
1.3.3
Build Dependencies:
r, r-callr, r-cli, r-crayon, r-desc, r-digest, r-pkgbuild, r-prettyunits, r-r6, r-rprojroot, r-sessioninfo, r-withr, r-xopen
Link Dependencies:
r
Run Dependencies:
r, r-callr, r-cli, r-crayon, r-desc, r-digest, r-pkgbuild, r-prettyunits, r-r6, r-rprojroot, r-sessioninfo, r-withr, r-xopen
Description:
Run 'R CMD check' from 'R' and capture the results of the individual checks. Supports running checks in the background, timeouts, pretty printing and comparing check results.

r-rcolorbrewer

Homepage:
Spack package:
Versions:
1.1-2
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Provides color schemes for maps (and other graphics) designed by Cynthia Brewer as described at http://colorbrewer2.org

r-rcpp

Homepage:
Spack package:
Versions:
1.0.2, 1.0.0, 0.12.19, 0.12.18, 0.12.17, 0.12.16, 0.12.15, 0.12.14, 0.12.13, 0.12.12, 0.12.11, 0.12.9, 0.12.6, 0.12.5
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
The 'Rcpp' package provides R functions as well as C++ classes which offer a seamless integration of R and C++. Many R data types and objects can be mapped back and forth to C++ equivalents which facilitates both writing of new code as well as easier integration of third-party libraries. Documentation about 'Rcpp' is provided by several vignettes included in this package, via the 'Rcpp Gallery' site at <http://gallery.rcpp.org>, the paper by Eddelbuettel and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see 'citation("Rcpp")' for details on these last two.

r-rcppannoy

Homepage:
Spack package:
Versions:
0.0.12
Build Dependencies:
r, r-rcpp
Link Dependencies:
r
Run Dependencies:
r, r-rcpp
Description:
'Annoy' is a small C++ library for Approximate Nearest Neighbors written for efficient memory usage as well an ability to load from / save to disk. This package provides an R interface by relying on the 'Rcpp' package, exposing the same interface as the original Python wrapper to 'Annoy'. See <https://github.com/spotify/annoy> for more on 'Annoy'. 'Annoy' is released under Version 2.0 of the Apache License. Also included is a small Windows port of 'mmap' which is released under the MIT license.

r-rcpparmadillo

Homepage:
Spack package:
Versions:
0.9.600.4.0, 0.9.400.3.0, 0.8.100.1.0
Build Dependencies:
r, r-rcpp
Link Dependencies:
r
Run Dependencies:
r, r-rcpp
Description:
'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra Library.

r-rcppblaze

Homepage:
Spack package:
Versions:
0.2.2
Build Dependencies:
r, r-rcpp, r-matrix, r-bh
Link Dependencies:
r
Run Dependencies:
r, r-rcpp, r-matrix, r-bh
Description:
'Blaze' is an open-source, high-performance C++ math library for dense and sparse arithmetic. With its state-of-the-art Smart Expression Template implementation 'Blaze' combines the elegance and ease of use of a domain-specific language with 'HPC'-grade performance, making it one of the most intuitive and fastest C++ math libraries available. The 'Blaze' library offers: - high performance through the integration of 'BLAS' libraries and manually tuned 'HPC' math kernels - vectorization by 'SSE', 'SSE2', 'SSE3', 'SSSE3', 'SSE4', 'AVX', 'AVX2', 'AVX-512', 'FMA', and 'SVML' - parallel execution by 'OpenMP', C++11 threads and 'Boost' threads ('Boost' threads are disabled in 'RcppBlaze') - the intuitive and easy to use API of a domain specific language - unified arithmetic with dense and sparse vectors and matrices - thoroughly tested matrix and vector arithmetic - completely portable, high quality C++ source code. The 'RcppBlaze' package includes the header files from the 'Blaze' library with disabling some functionalities related to link to the thread and system libraries which make 'RcppBlaze' be a header- only library. Therefore, users do not need to install 'Blaze' and the dependency 'Boost'. 'Blaze' is licensed under the New (Revised) BSD license, while 'RcppBlaze' (the 'Rcpp' bindings/bridge to 'Blaze') is licensed under the GNU GPL version 2 or later, as is the rest of 'Rcpp'. Note that since 'Blaze' has committed to 'C++14' commit to 'C++14' which does not used by most R users from version 3.0, we will use the version 2.6 of 'Blaze' which is 'C++98' compatible to support the most compilers and system.

r-rcppcctz

Homepage:
Spack package:
Versions:
0.2.6, 0.2.4, 0.2.3
Build Dependencies:
r, r-rcpp
Link Dependencies:
r
Run Dependencies:
r, r-rcpp
Description:
'Rcpp' Access to the 'CCTZ' timezone library is provided. 'CCTZ' is a C++ library for translating between absolute and civil times using the rules of a time zone. The 'CCTZ' source code, released under the Apache 2.0 License, is included in this package. See <https://github.com/google/cctz> for more details.

r-rcppcnpy

Homepage:
Spack package:
Versions:
0.2.10, 0.2.9
Build Dependencies:
r, r-rcpp
Link Dependencies:
r
Run Dependencies:
r, r-rcpp
Description:
Rcpp bindings for NumPy files.

r-rcppeigen

Homepage:
Spack package:
Versions:
0.3.3.5.0, 0.3.3.4.0, 0.3.3.3.1, 0.3.2.9.0, 0.3.2.8.1
Build Dependencies:
r, r-matrix, r-rcpp
Link Dependencies:
r
Run Dependencies:
r, r-matrix, r-rcpp
Description:
R and 'Eigen' integration using 'Rcpp'. 'Eigen' is a C++ template library for linear algebra: matrices, vectors, numerical solvers and related algorithms. It supports dense and sparse matrices on integer, floating point and complex numbers, decompositions of such matrices, and solutions of linear systems. Its performance on many algorithms is comparable with some of the best implementations based on 'Lapack' and level-3 'BLAS'. The 'RcppEigen' package includes the header files from the 'Eigen' C++ template library (currently version 3.2.8). Thus users do not need to install 'Eigen' itself in order to use 'RcppEigen'. Since version 3.1.1, 'Eigen' is licensed under the Mozilla Public License (version 2); earlier version were licensed under the GNU LGPL version 3 or later. 'RcppEigen' (the 'Rcpp' bindings/bridge to 'Eigen') is licensed under the GNU GPL version 2 or later, as is the rest of 'Rcpp'.

r-rcpphnsw

Homepage:
Spack package:
Versions:
0.1.0
Build Dependencies:
r, r-rcpp
Link Dependencies:
r
Run Dependencies:
r, r-rcpp
Description:
RcppHNSW: 'Rcpp' Bindings for 'hnswlib', a Library for Approximate NearestNeighbors

r-rcppparallel

Homepage:
Spack package:
Versions:
4.4.3
Build Dependencies:
r, gmake
Link Dependencies:
r
Run Dependencies:
r
Description:
High level functions for parallel programming with 'Rcpp'. For example, the 'parallelFor()' function can be used to convert the work of a standard serial "for" loop into a parallel one and the 'parallelReduce()' function can be used for accumulating aggregate or other values.

r-rcppprogress

Homepage:
Spack package:
Versions:
0.4.1, 0.4, 0.3, 0.2.1, 0.2, 0.1
Build Dependencies:
r, r-rcpp
Link Dependencies:
r
Run Dependencies:
r, r-rcpp
Description:
Allows to display a progress bar in the R console for long running computations taking place in c++ code, and support for interrupting those computations even in multithreaded code, typically using OpenMP.

r-rcurl

Homepage:
Spack package:
Versions:
1.95-4.12, 1.95-4.8
Build Dependencies:
r, r-bitops, curl, gmake
Link Dependencies:
r, curl
Run Dependencies:
r, r-bitops
Description:
A wrapper for 'libcurl' <http://curl.haxx.se/libcurl/> Provides functions to allow one to compose general HTTP requests and provides convenient functions to fetch URIs, get & post forms, etc. and process the results returned by the Web server. This provides a great deal of control over the HTTP/FTP/... connection and the form of the request while providing a higher-level interface than is available just using R socket connections. Additionally, the underlying implementation is robust and extensive, supporting FTP/FTPS/TFTP (uploads and downloads), SSL/HTTPS, telnet, dict, ldap, and also supports cookies, redirects, authentication, etc.

r-rda

Homepage:
Spack package:
Versions:
1.0.2-2.1, 1.0.2-2, 1.0.2-1
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Shrunken Centroids Regularized Discriminant Analysis for the classification purpose in high dimensional data.

r-rdpack

Homepage:
Spack package:
Versions:
0.11-0
Build Dependencies:
r, r-bibtex, r-gbrd
Link Dependencies:
r
Run Dependencies:
r, r-bibtex, r-gbrd
Description:
Functions for manipulation of R documentation objects, including functions reprompt() and ereprompt() for updating 'Rd' documentation for functions, methods and classes; 'Rd' macros for citations and import of references from 'bibtex' files for use in 'Rd' files and 'roxygen2' comments; 'Rd' macros for evaluating and inserting snippets of 'R' code and the results of its evaluation or creating graphics on the fly; and many functions for manipulation of references and Rd files.

r-readbitmap

Homepage:
Spack package:
Versions:
0.1.5
Build Dependencies:
r, r-bmp, r-jpeg, r-png, r-tiff, jpeg, libpng
Link Dependencies:
r, jpeg, libpng
Run Dependencies:
r, r-bmp, r-jpeg, r-png, r-tiff
Description:
Identifies and reads Windows BMP, JPEG, PNG, and TIFF format bitmap images. Identification defaults to the use of the magic number embedded in the file rather than the file extension. Reading of JPEG and PNG image depends on libjpg and libpng libraries. See file INSTALL for details if necessary.

r-readr

Homepage:
Spack package:
Versions:
1.3.1, 1.1.1
Build Dependencies:
r, r-rcpp, r-tibble, r-hms, r-r6, r-bh, r-clipr, r-crayon, gmake
Link Dependencies:
r
Run Dependencies:
r, r-rcpp, r-tibble, r-hms, r-r6, r-bh, r-clipr, r-crayon
Description:
The goal of 'readr' is to provide a fast and friendly way to read rectangular data (like 'csv', 'tsv', and 'fwf'). It is designed to flexibly parse many types of data found in the wild, while still cleanly failing when data unexpectedly changes.

r-readxl

Homepage:
Spack package:
Versions:
1.3.1, 1.3.0, 1.1.0, 1.0.0
Build Dependencies:
r, r-tibble, r-rcpp, r-cellranger, r-progress
Link Dependencies:
r
Run Dependencies:
r, r-tibble, r-rcpp, r-cellranger, r-progress
Description:
Import excel files into R. Supports '.xls' via the embedded 'libxls' C library <https://sourceforge.net/projects/libxls/> and '.xlsx' via the embedded 'RapidXML' C++ library <https://rapidxml.sourceforge.net>. Works on Windows, Mac and Linux without external dependencies.

r-recipes

Homepage:
Spack package:
Versions:
0.1.6
Build Dependencies:
r, r-dplyr, r-generics, r-glue, r-gower, r-ipred, r-lubridate, r-magrittr, r-matrix, r-purrr, r-rlang, r-tibble, r-tidyr, r-tidyselect, r-timedate, r-withr
Link Dependencies:
r
Run Dependencies:
r, r-dplyr, r-generics, r-glue, r-gower, r-ipred, r-lubridate, r-magrittr, r-matrix, r-purrr, r-rlang, r-tibble, r-tidyr, r-tidyselect, r-timedate, r-withr
Description:
An extensible framework to create and preprocess design matrices. Recipes consist of one or more data manipulation and analysis "steps". Statistical parameters for the steps can be estimated from an initial data set and then applied to other data sets. The resulting design matrices can then be used as inputs into statistical or machine learning models.

r-registry

Homepage:
Spack package:
Versions:
0.5-1, 0.5, 0.3
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Provides a generic infrastructure for creating and using registries.

r-rematch

Homepage:
Spack package:
Versions:
1.0.1
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
A small wrapper on 'regexpr' to extract the matches and captured groups from the match of a regular expression to a character vector.

r-remotes

Homepage:
Spack package:
Versions:
2.1.0
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Download and install R packages stored in 'GitHub', 'BitBucket', or plain 'subversion' or 'git' repositories. This package provides the 'install_*' functions in 'devtools'. Indeed most of the code was copied over from 'devtools'.

r-reordercluster

Homepage:
Spack package:
Versions:
1.0
Build Dependencies:
r, r-gplots, r-rcpp
Link Dependencies:
r
Run Dependencies:
r, r-gplots, r-rcpp
Description:
Tools for performing the leaf reordering for the dendrogram that preserves the hierarchical clustering result and at the same time tries to group instances from the same class together.

r-reportingtools

Homepage:
Spack package:
Versions:
2.24.0, 2.22.1, 2.20.0, 2.17.3, 2.16.0
Build Dependencies:
r, r-knitr, r-biobase, r-hwriter, r-category, r-gostats, r-limma, r-lattice, r-annotationdbi, r-edger, r-annotate, r-pfam-db, r-gseabase, r-biocgenerics, r-xml, r-r-utils, r-deseq2, r-ggplot2, r-ggbio, r-iranges
Link Dependencies:
r
Run Dependencies:
r, r-knitr, r-biobase, r-hwriter, r-category, r-gostats, r-limma, r-lattice, r-annotationdbi, r-edger, r-annotate, r-pfam-db, r-gseabase, r-biocgenerics, r-xml, r-r-utils, r-deseq2, r-ggplot2, r-ggbio, r-iranges
Description:
Tools for making reports in various formats. The ReportingTools software package enables users to easily display reports of analysis results generated from sources such as microarray and sequencing data. The package allows users to create HTML pages that may be viewed on a web browser such as Safari, or in other formats readable by programs such as Excel. Users can generate tables with sortable and filterable columns, make and display plots, and link table entries to other data sources such as NCBI or larger plots within the HTML page. Using the package, users can also produce a table of contents page to link various reports together for a particular project that can be viewed in a web browser. For more examples, please visit our site: http:// research- pub.gene.com/ReportingTools.

r-repr

Homepage:
Spack package:
Versions:
1.0.1, 1.0.0, 0.9
Build Dependencies:
r, r-htmltools, r-base64enc, r-jsonlite, r-pillar
Link Dependencies:
r
Run Dependencies:
r, r-htmltools, r-base64enc, r-jsonlite, r-pillar
Description:
String and binary representations of objects for several formats and mime types.

r-reprex

Homepage:
Spack package:
Versions:
0.3.0, 0.2.1, 0.1.1
Build Dependencies:
r, r-callr, r-clipr, r-knitr, r-rmarkdown, r-whisker, r-rlang, r-withr, r-fs, pandoc
Link Dependencies:
r, pandoc
Run Dependencies:
r, r-callr, r-clipr, r-knitr, r-rmarkdown, r-whisker, r-rlang, r-withr, r-fs
Description:
Convenience wrapper that uses the 'rmarkdown' package to render small snippets of code to target formats that include both code and output. The goal is to encourage the sharing of small, reproducible, and runnable examples on code-oriented websites, such as <http://stackoverflow.com> and <https://github.com>, or in email. 'reprex' also extracts clean, runnable R code from various common formats, such as copy/paste from an R session.

r-reshape

Homepage:
Spack package:
Versions:
0.8.8, 0.8.7
Build Dependencies:
r, r-plyr
Link Dependencies:
r
Run Dependencies:
r, r-plyr
Description:
Flexibly restructure and aggregate data using just two functions: melt and cast.

r-reshape2

Homepage:
Spack package:
Versions:
1.4.3, 1.4.2, 1.4.1
Build Dependencies:
r, r-plyr, r-stringr, r-rcpp
Link Dependencies:
r
Run Dependencies:
r, r-plyr, r-stringr, r-rcpp
Description:
Flexibly restructure and aggregate data using just two functions: melt and dcast (or acast).

r-reticulate

Homepage:
Spack package:
Versions:
1.13
Build Dependencies:
r, r-jsonlite, r-rcpp, r-matrix, python
Link Dependencies:
r, python
Run Dependencies:
r, r-jsonlite, r-rcpp, r-matrix
Description:
Interface to 'Python' modules, classes, and functions. When calling into 'Python', R data types are automatically converted to their equivalent 'Python' types. When values are returned from 'Python' to R they are converted back to R types. Compatible with all versions of 'Python' >= 2.7.

r-rex

Homepage:
Spack package:
Versions:
1.1.2
Build Dependencies:
r, r-lazyeval, r-magrittr
Link Dependencies:
r
Run Dependencies:
r, r-lazyeval, r-magrittr
Description:
A friendly interface for the construction of regular expressions.

r-rgdal

Homepage:
Spack package:
Versions:
1.4-4, 1.3-9, 1.2-16
Build Dependencies:
r, r-sp, gdal, proj
Link Dependencies:
r, gdal, proj
Run Dependencies:
r, r-sp
Description:
Provides bindings to the 'Geospatial' Data Abstraction Library ('GDAL') (>= 1.6.3) and access to projection/transformation operations from the 'PROJ.4' library. The 'GDAL' and 'PROJ.4' libraries are external to the package, and, when installing the package from source, must be correctly installed first. Both 'GDAL' raster and 'OGR' vector map data can be imported into R, and 'GDAL' raster data and 'OGR' vector data exported. Use is made of classes defined in the 'sp' package. Windows and Mac Intel OS X binaries (including 'GDAL', 'PROJ.4' and 'Expat') are provided on 'CRAN'.

r-rgenoud

Homepage:
Spack package:
Versions:
5.8-3.0, 5.8-2.0, 5.8-1.0
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
A genetic algorithm plus derivative optimizer.

r-rgeos

Homepage:
Spack package:
Versions:
0.5-1, 0.3-26
Build Dependencies:
r, r-sp, geos
Link Dependencies:
r, geos
Run Dependencies:
r, r-sp
Description:
Interface to Geometry Engine - Open Source ('GEOS') using the C 'API' for topology operations on geometries. The 'GEOS' library is external to the package, and, when installing the package from source, must be correctly installed first. Windows and Mac Intel OS X binaries are provided on 'CRAN'.

r-rgexf

Homepage:
Spack package:
Versions:
0.15.3
Build Dependencies:
r, r-xml, r-rook, r-igraph
Link Dependencies:
r
Run Dependencies:
r, r-xml, r-rook, r-igraph
Description:
Create, read and write GEXF (Graph Exchange XML Format) graph files (used in Gephi and others). Using the XML package, it allows the user to easily build/read graph files including attributes, GEXF viz attributes (such as color, size, and position), network dynamics (for both edges and nodes) and edge weighting. Users can build/handle graphs element-by- element or massively through data-frames, visualize the graph on a web browser through "sigmajs" (a javascript library) and interact with the igraph package.

r-rgl

Homepage:
Spack package:
Versions:
0.100.26, 0.100.24, 0.100.19, 0.99.16, 0.98.1
Build Dependencies:
r, r-htmlwidgets, r-htmltools, r-knitr, r-jsonlite, r-shiny, r-magrittr, r-crosstalk, r-manipulatewidget, libx11, gl, glu, pandoc
Link Dependencies:
r, zlib, libpng, libx11, freetype, gl, glu
Run Dependencies:
r, r-htmlwidgets, r-htmltools, r-knitr, r-jsonlite, r-shiny, r-magrittr, r-crosstalk, r-manipulatewidget
Description:
Provides medium to high level functions for 3D interactive graphics, including functions modelled on base graphics (plot3d(), etc.) as well as functions for constructing representations of geometric objects (cube3d(), etc.). Output may be on screen using OpenGL, or to various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D image formats, including PNG, Postscript, SVG, PGF.

r-rgooglemaps

Homepage:
Spack package:
Versions:
1.4.3, 1.4.2, 1.2.0.7
Build Dependencies:
r, r-png, r-rjsonio
Link Dependencies:
r
Run Dependencies:
r, r-png, r-rjsonio
Description:
This package serves two purposes: (i) Provide a comfortable R interface to query the Google server for static maps, and (ii) Use the map as a background image to overlay plots within R. This requires proper coordinate scaling.

r-rgraphviz

Homepage:
Spack package:
Versions:
2.28.0, 2.26.0, 2.24.0, 2.22.0, 2.20.0
Build Dependencies:
r, r-graph
Link Dependencies:
r
Run Dependencies:
r, r-graph, graphviz
Description:
Provides plotting capabilities for R graph objects. Interfaces R with the AT and T graphviz library for plotting R graph objects from the graph package.

r-rhdf5

Homepage:
Spack package:
Versions:
2.28.1, 2.26.2, 2.24.0, 2.22.0, 2.20.0
Build Dependencies:
r, r-zlibbioc, r-rhdf5lib, gmake
Link Dependencies:
r
Run Dependencies:
r, r-zlibbioc, r-rhdf5lib
Description:
R Interface to HDF5. This package provides an interface between HDF5 and R. HDF5's main features are the ability to store and access very large and/or complex datasets and a wide variety of metadata on mass storage (disk) through a completely portable file format. The rhdf5 package is thus suited for the exchange of large and/or complex datasets between R and other software package, and for letting R applications work on datasets that are larger than the available RAM.

r-rhdf5lib

Homepage:
Spack package:
Versions:
1.6.3, 1.4.3, 1.2.1, 1.0.0
Build Dependencies:
r, gmake
Link Dependencies:
r
Run Dependencies:
r
Description:
hdf5 library as an R package. Provides C and C++ hdf5 libraries.

r-rhmmer

Homepage:
Spack package:
Versions:
0.1.0
Build Dependencies:
r, r-magrittr, r-readr, r-dplyr, r-tidyr, r-rlang
Link Dependencies:
r
Run Dependencies:
r, r-magrittr, r-readr, r-dplyr, r-tidyr, r-rlang
Description:
rhmmer: Utilities Parsing 'HMMER' Results

r-rhtslib

Homepage:
Spack package:
Versions:
1.18.1, 1.16.3, 1.14.1, 1.12.1, 1.10.0, 1.8.0
Build Dependencies:
r, r-zlibbioc, bzip2, xz, curl, gmake, patchelf
Link Dependencies:
r, bzip2, xz, curl
Run Dependencies:
r, r-zlibbioc, bzip2, xz, curl
Description:
HTSlib high-throughput sequencing library as an R package. This package provides version 1.7 of the 'HTSlib' C library for high- throughput sequence analysis. The package is primarily useful to developers of other R packages who wish to make use of HTSlib. Motivation and instructions for use of this package are in the vignette, vignette(package="Rhtslib", "Rhtslib").

r-rinside

Homepage:
Spack package:
Versions:
0.2.15, 0.2.14, 0.2.13
Build Dependencies:
r, r-rcpp
Link Dependencies:
r
Run Dependencies:
r, r-rcpp
Description:
C++ classes to embed R in C++ applications The 'RInside' packages makes it easier to have "R inside" your C++ application by providing a C++ wrapperclass providing the R interpreter. As R itself is embedded into your application, a shared library build of R is required. This works on Linux, OS X and even on Windows provided you use the same tools used to build R itself. Numerous examples are provided in the eight subdirectories of the examples/ directory of the installed package: standard, mpi (for parallel computing) qt (showing how to embed 'RInside' inside a Qt GUI application), wt (showing how to build a "web- application" using the Wt toolkit), armadillo (for 'RInside' use with 'RcppArmadillo') and eigen (for 'RInside' use with 'RcppEigen'). The example use GNUmakefile(s) with GNU extensions, so a GNU make is required (and will use the GNUmakefile automatically). Doxygen-generated documentation of the C++ classes is available at the 'RInside' website as well.

r-rio

Homepage:
Spack package:
Versions:
0.5.16
Build Dependencies:
r, r-foreign, r-haven, r-curl, r-data-table, r-readxl, r-openxlsx, r-tibble
Link Dependencies:
r
Run Dependencies:
r, r-foreign, r-haven, r-curl, r-data-table, r-readxl, r-openxlsx, r-tibble
Description:
Streamlined data import and export by making assumptions that the user is probably willing to make: 'import()' and 'export()' determine the data structure from the file extension, reasonable defaults are used for data import and export (e.g., 'stringsAsFactors=FALSE'), web-based import is natively supported (including from SSL/HTTPS), compressed files can be read directly without explicit decompression, and fast import packages are used where appropriate. An additional convenience function, 'convert()', provides a simple method for converting between file types.

r-rjags

Homepage:
Spack package:
Versions:
4-8, 4-6
Build Dependencies:
r, r-coda
Link Dependencies:
r, jags
Run Dependencies:
r, r-coda
Description:
Interface to the JAGS MCMC library. Usage: $ spack load r-rjags

r-rjava

Homepage:
Spack package:
Versions:
0.9-11, 0.9-8
Build Dependencies:
r, java, gmake
Link Dependencies:
r, java
Run Dependencies:
r
Description:
Low-level interface to Java VM very much like .C/.Call and friends. Allows creation of objects, calling methods and accessing fields.

r-rjson

Homepage:
Spack package:
Versions:
0.2.20, 0.2.19, 0.2.15
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Converts R object into JSON objects and vice-versa.

r-rjsonio

Homepage:
Spack package:
Versions:
1.3-1.2, 1.3-1.1, 1.3-0
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
This is a package that allows conversion to and from data in Javascript object notation (JSON) format. This allows R objects to be inserted into Javascript/ECMAScript/ActionScript code and allows R programmers to read and convert JSON content to R objects. This is an alternative to rjson package. Originally, that was too slow for converting large R objects to JSON and was not extensible. rjson's performance is now similar to this package, and perhaps slightly faster in some cases. This package uses methods and is readily extensible by defining methods for different classes, vectorized operations, and C code and callbacks to R functions for deserializing JSON objects to R. The two packages intentionally share the same basic interface. This package (RJSONIO) has many additional options to allow customizing the generation and processing of JSON content. This package uses libjson rather than implementing yet another JSON parser. The aim is to support other general projects by building on their work, providing feedback and benefit from their ongoing development.

r-rlang

Homepage:
Spack package:
Versions:
0.4.0, 0.3.4, 0.3.1, 0.3.0.1, 0.3.0, 0.2.2, 0.1.4, 0.1.2, 0.1.1
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
A toolbox for working with base types, core R features like the condition system, and core 'Tidyverse' features like tidy evaluation.

r-rmariadb

Homepage:
Spack package:
Versions:
1.0.8
Build Dependencies:
r, r-bit64, r-dbi, r-hms, r-rcpp, r-bh, r-plogr, mariadb-client
Link Dependencies:
r, mariadb-client
Run Dependencies:
r, r-bit64, r-dbi, r-hms, r-rcpp, r-bh, r-plogr
Description:
Implements a 'DBI'-compliant interface to 'MariaDB' (<https://mariadb.org/>) and 'MySQL' (<https://www.mysql.com/>) databases.

r-rmarkdown

Homepage:
Spack package:
Versions:
1.14, 1.13, 1.7, 1.0
Build Dependencies:
r, r-knitr, r-yaml, r-htmltools, r-evaluate, r-base64enc, r-jsonlite, r-rprojroot, r-mime, r-stringr, r-catools, r-tinytex, r-xfun, pandoc
Link Dependencies:
r, pandoc
Run Dependencies:
r, r-knitr, r-yaml, r-htmltools, r-evaluate, r-base64enc, r-jsonlite, r-rprojroot, r-mime, r-stringr, r-catools, r-tinytex, r-xfun
Description:
Convert R Markdown documents into a variety of formats.

r-rminer

Homepage:
Spack package:
Versions:
1.4.2
Build Dependencies:
r, r-plotrix, r-lattice, r-nnet, r-kknn, r-pls, r-mass, r-mda, r-rpart, r-randomforest, r-adabag, r-party, r-cubist, r-kernlab, r-e1071, r-glmnet, r-xgboost
Link Dependencies:
r
Run Dependencies:
r, r-plotrix, r-lattice, r-nnet, r-kknn, r-pls, r-mass, r-mda, r-rpart, r-randomforest, r-adabag, r-party, r-cubist, r-kernlab, r-e1071, r-glmnet, r-xgboost
Description:
Facilitates the use of data mining algorithms in classification and regression (including time series forecasting) tasks by presenting a short and coherent set of functions.

r-rmpfr

Homepage:
Spack package:
Versions:
0.7-2, 0.7-1, 0.6-1
Build Dependencies:
r, r-gmp, mpfr, gmp
Link Dependencies:
r, mpfr, gmp
Run Dependencies:
r, r-gmp
Description:
Arithmetic (via S4 classes and methods) for arbitrary precision floating point numbers, including transcendental ("special") functions. To this end, Rmpfr interfaces to the LGPL'ed MPFR (Multiple Precision Floating- Point Reliable) Library which itself is based on the GMP (GNU Multiple Precision) Library.

r-rmpi

Homepage:
Spack package:
Versions:
0.6-9, 0.6-8, 0.6-6
Build Dependencies:
r, mpi
Link Dependencies:
r, mpi
Run Dependencies:
r
Description:
An interface (wrapper) to MPI APIs. It also provides interactive R manager and worker environment.

r-rmutil

Homepage:
Spack package:
Versions:
1.1.3
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
rmutil: Utilities for Nonlinear Regression and Repeated MeasurementsModels

r-rmysql

Homepage:
Spack package:
Versions:
0.10.17, 0.10.9
Build Dependencies:
r, r-dbi, mariadb
Link Dependencies:
r, mariadb
Run Dependencies:
r, r-dbi
Description:
Implements 'DBI' Interface to 'MySQL' and 'MariaDB' Databases.

r-rnaseqmap

Homepage:
Spack package:
Versions:
2.42.0, 2.40.1, 2.38.0, 2.36.0, 2.34.0
Build Dependencies:
r, r-biobase, r-rsamtools, r-genomicalignments, r-genomicranges, r-iranges, r-edger, r-deseq, r-dbi
Link Dependencies:
r
Run Dependencies:
r, r-biobase, r-rsamtools, r-genomicalignments, r-genomicranges, r-iranges, r-edger, r-deseq, r-dbi
Description:
rnaSeq secondary analyses. The rnaSeqMap library provides classes and functions to analyze the RNA- sequencing data using the coverage profiles in multiple samples at a time

r-rngtools

Homepage:
Spack package:
Versions:
1.4, 1.3.1.1, 1.3.1
Build Dependencies:
r, r-pkgmaker, r-stringr, r-digest
Link Dependencies:
r
Run Dependencies:
r, r-pkgmaker, r-stringr, r-digest
Description:
This package contains a set of functions for working with Random Number Generators (RNGs). In particular, it defines a generic S4 framework for getting/setting the current RNG, or RNG data that are embedded into objects for reproducibility. Notably, convenient default methods greatly facilitate the way current RNG settings can be changed.

r-rnoaa

Homepage:
Spack package:
Versions:
0.8.4
Build Dependencies:
r, r-crul, r-dplyr, r-geonames, r-ggplot2, r-gridextra, r-hoardr, r-isdparser, r-jsonlite, r-lubridate, r-rappdirs, r-scales, r-tibble, r-tidyr, r-xml, r-xml2
Link Dependencies:
r
Run Dependencies:
r, r-crul, r-dplyr, r-geonames, r-ggplot2, r-gridextra, r-hoardr, r-isdparser, r-jsonlite, r-lubridate, r-rappdirs, r-scales, r-tibble, r-tidyr, r-xml, r-xml2
Description:
rnoaa: 'NOAA' Weather Data from R

r-robust

Homepage:
Spack package:
Versions:
0.4-18.1, 0.4-18
Build Dependencies:
r, r-lattice, r-mass, r-robustbase, r-rrcov, r-fit-models
Link Dependencies:
r
Run Dependencies:
r, r-lattice, r-mass, r-robustbase, r-rrcov, r-fit-models
Description:
robust: Port of the S+ Robust Library

r-robustbase

Homepage:
Spack package:
Versions:
0.93-5, 0.93-4, 0.92-7
Build Dependencies:
r, r-deoptimr
Link Dependencies:
r
Run Dependencies:
r, r-deoptimr
Description:
"Essential" Robust Statistics. Tools allowing to analyze data with robust methods. This includes regression methodology including model selections and multivariate statistics where we strive to cover the book "Robust Statistics, Theory and Methods" by 'Maronna, Martin and Yohai'; Wiley 2006.

r-roc

Homepage:
Spack package:
Versions:
1.62.0
Build Dependencies:
r, r-knitr
Link Dependencies:
r
Run Dependencies:
r, r-knitr
Description:
Provide utilities for ROC, with microarray focus.

r-rocr

Homepage:
Spack package:
Versions:
1.0-7
Build Dependencies:
r, r-gplots
Link Dependencies:
r
Run Dependencies:
r, r-gplots
Description:
ROC graphs, sensitivity/specificity curves, lift charts, and precision/recall plots are popular examples of trade-off visualizations for specific pairs of performance measures. ROCR is a flexible tool for creating cutoff-parameterized 2D performance curves by freely combining two from over 25 performance measures (new performance measures can be added using a standard interface). Curves from different cross- validation or bootstrapping runs can be averaged by different methods, and standard deviations, standard errors or box plots can be used to visualize the variability across the runs. The parameterization can be visualized by printing cutoff values at the corresponding curve positions, or by coloring the curve according to cutoff. All components of a performance plot can be quickly adjusted using a flexible parameter dispatching mechanism. Despite its flexibility, ROCR is easy to use, with only three commands and reasonable default values for all optional parameters.

r-rodbc

Homepage:
Spack package:
Versions:
1.3-15, 1.3-13
Build Dependencies:
r, unixodbc
Link Dependencies:
r, unixodbc
Run Dependencies:
r
Description:
An ODBC database interface.

r-rook

Homepage:
Spack package:
Versions:
1.1-1
Build Dependencies:
r, r-brew
Link Dependencies:
r
Run Dependencies:
r, r-brew
Description:
This package contains the Rook specification and convenience software for building and running Rook applications. To get started, be sure and read the 'Rook' help file first.

r-rots

Homepage:
Spack package:
Versions:
1.12.0, 1.10.1, 1.8.0, 1.6.0, 1.4.0
Build Dependencies:
r, r-rcpp, r-biobase
Link Dependencies:
r
Run Dependencies:
r, r-rcpp, r-biobase
Description:
Reproducibility-Optimized Test Statistic. Calculates the Reproducibility-Optimized Test Statistic (ROTS) for differential testing in omics data.

r-roxygen2

Homepage:
Spack package:
Versions:
6.1.1, 5.0.1
Build Dependencies:
r, r-brew, r-commonmark, r-desc, r-digest, r-pkgload, r-purrr, r-r6, r-rcpp, r-stringi, r-stringr, r-xml2
Link Dependencies:
r
Run Dependencies:
r, r-brew, r-commonmark, r-desc, r-digest, r-pkgload, r-purrr, r-r6, r-rcpp, r-stringi, r-stringr, r-xml2
Description:
A 'Doxygen'-like in-source documentation system for Rd, collation, and 'NAMESPACE' files.

r-rpart

Homepage:
Spack package:
Versions:
4.1-15, 4.1-13, 4.1-11, 4.1-10
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Recursive partitioning for classification, regression and survival trees.

r-rpart-plot

Homepage:
Spack package:
Versions:
3.0.7, 3.0.6, 2.1.0
Build Dependencies:
r, r-rpart
Link Dependencies:
r
Run Dependencies:
r, r-rpart
Description:
Plot 'rpart' models. Extends plot.rpart() and text.rpart() in the 'rpart' package.

r-rpostgresql

Homepage:
Spack package:
Versions:
0.6-2, 0.4-1
Build Dependencies:
r, r-dbi, postgresql
Link Dependencies:
r, postgresql
Run Dependencies:
r, r-dbi
Description:
Database interface and PostgreSQL driver for R This package provides a Database Interface (DBI) compliant driver for R to access PostgreSQL database systems. In order to build and install this package from source, PostgreSQL itself must be present your system to provide PostgreSQL functionality via its libraries and header files. These files are provided as postgresql-devel package under some Linux distributions. On Microsoft Windows system the attached libpq library source will be used. A wiki and issue tracking system for the package are available at Google Code at https://code.google.com/p/rpostgresql/.

r-rprojroot

Homepage:
Spack package:
Versions:
1.3-2, 1.2
Build Dependencies:
r, r-backports
Link Dependencies:
r
Run Dependencies:
r, r-backports
Description:
Robust, reliable and flexible paths to files below a project root. The 'root' of a project is defined as a directory that matches a certain criterion, e.g., it contains a certain regular file.

r-rrblup

Homepage:
Spack package:
Versions:
4.6
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
rrBLUP: Ridge Regression and Other Kernels for Genomic Selection

r-rrcov

Homepage:
Spack package:
Versions:
1.4-7
Build Dependencies:
r, r-robustbase, r-mvtnorm, r-lattice, r-cluster, r-pcapp
Link Dependencies:
r
Run Dependencies:
r, r-robustbase, r-mvtnorm, r-lattice, r-cluster, r-pcapp
Description:
rrcov: Scalable Robust Estimators with High Breakdown Point

r-rrpp

Homepage:
Spack package:
Versions:
0.4.2, 0.4.1, 0.3.0
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Linear model calculations are made for many random versions of data. Using residual randomization in a permutation procedure, sums of squares are calculated over many permutations to generate empirical probability distributions for evaluating model effects. This method is described by Collyer, Sekora, & Adams (2015) <doi:10.1038/hdy.2014.75>. Additionally, coefficients, statistics, fitted values, and residuals generated over many permutations can be used for various procedures including pairwise tests, prediction, classification, and model comparison. This package should provide most tools one could need for the analysis of high- dimensional data, especially in ecology and evolutionary biology, but certainly other fields, as well.

r-rsamtools

Homepage:
Spack package:
Versions:
2.2.1, 2.0.3, 1.34.1, 1.32.3, 1.30.0, 1.28.0
Build Dependencies:
r, r-genomeinfodb, r-genomicranges, r-biostrings, r-biocgenerics, r-s4vectors, r-iranges, r-xvector, r-zlibbioc, r-bitops, r-biocparallel, r-rhtslib, gmake
Link Dependencies:
r
Run Dependencies:
r, r-genomeinfodb, r-genomicranges, r-biostrings, r-biocgenerics, r-s4vectors, r-iranges, r-xvector, r-zlibbioc, r-bitops, r-biocparallel, r-rhtslib
Description:
Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import. This package provides an interface to the 'samtools', 'bcftools', and 'tabix' utilities for manipulating SAM (Sequence Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed tab-delimited (tabix) files.

r-rsnns

Homepage:
Spack package:
Versions:
0.4-11, 0.4-10.1, 0.4-7
Build Dependencies:
r, r-rcpp
Link Dependencies:
r
Run Dependencies:
r, r-rcpp
Description:
The Stuttgart Neural Network Simulator (SNNS) is a library containing many standard implementations of neural networks. This package wraps the SNNS functionality to make it available from within R. Using the RSNNS low-level interface, all of the algorithmic functionality and flexibility of SNNS can be accessed. Furthermore, the package contains a convenient high-level interface, so that the most common neural network topologies and learning algorithms integrate seamlessly into R.

r-rsolnp

Homepage:
Spack package:
Versions:
1.16
Build Dependencies:
r, r-truncnorm
Link Dependencies:
r
Run Dependencies:
r, r-truncnorm
Description:
General Non-linear Optimization Using Augmented Lagrange Multiplier Method.

r-rspectra

Homepage:
Spack package:
Versions:
0.15-0
Build Dependencies:
r, r-matrix, r-rcpp, r-rcppeigen
Link Dependencies:
r
Run Dependencies:
r, r-matrix, r-rcpp, r-rcppeigen
Description:
R interface to the 'Spectra' library <https://spectralib.org/> for large-scale eigenvalue and SVD problems. It is typically used to compute a few eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues, which is usually more efficient than eigen() if k << n. This package provides the 'eigs()' function that does the similar job as in 'Matlab', 'Octave', 'Python SciPy' and 'Julia'. It also provides the 'svds()' function to calculate the largest k singular values and corresponding singular vectors of a real matrix. The matrix to be computed on can be dense, sparse, or in the form of an operator defined by the user.

r-rsqlite

Homepage:
Spack package:
Versions:
2.1.2, 2.1.0, 2.0
Build Dependencies:
r, r-dbi, r-bit64, r-blob, r-memoise, r-pkgconfig, r-rcpp, r-bh, r-plogr
Link Dependencies:
r
Run Dependencies:
r, r-dbi, r-bit64, r-blob, r-memoise, r-pkgconfig, r-rcpp, r-bh, r-plogr
Description:
This package embeds the SQLite database engine in R and provides an interface compliant with the DBI package. The source for the SQLite engine (version 3.8.6) is included.

r-rstan

Homepage:
Spack package:
Versions:
2.19.2, 2.18.2, 2.17.2, 2.10.1
Build Dependencies:
r, r-stanheaders, r-ggplot2, r-inline, r-gridextra, r-rcpp, r-loo, r-pkgbuild, r-rcppeigen, r-bh, gmake, pandoc
Link Dependencies:
r
Run Dependencies:
r, r-stanheaders, r-ggplot2, r-inline, r-gridextra, r-rcpp, r-loo, r-pkgbuild, r-rcppeigen, r-bh
Description:
User-facing R functions are provided to parse, compile, test, estimate, and analyze Stan models by accessing the header-only Stan library provided by the 'StanHeaders' package. The Stan project develops a probabilistic programming language that implements full Bayesian statistical inference via Markov Chain Monte Carlo, rough Bayesian inference via variational approximation, and (optionally penalized) maximum likelihood estimation via optimization. In all three cases, automatic differentiation is used to quickly and accurately evaluate gradients without burdening the user with the need to derive the partial derivatives.

r-rstantools

Homepage:
Spack package:
Versions:
1.5.1
Build Dependencies:
r, pandoc
Link Dependencies:
r
Run Dependencies:
r
Description:
rstantools: Tools for Developing R Packages Interfacing with 'Stan'

r-rstudioapi

Homepage:
Spack package:
Versions:
0.10, 0.9.0, 0.7, 0.6, 0.5
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Access the RStudio API (if available) and provide informative error messages when it's not.

r-rsvd

Homepage:
Spack package:
Versions:
1.0.2
Build Dependencies:
r, r-matrix
Link Dependencies:
r
Run Dependencies:
r, r-matrix
Description:
Low-rank matrix decompositions are fundamental tools and widely used for data analysis, dimension reduction, and data compression. Classically, highly accurate deterministic matrix algorithms are used for this task. However, the emergence of large-scale data has severely challenged our computational ability to analyze big data. The concept of randomness has been demonstrated as an effective strategy to quickly produce approximate answers to familiar problems such as the singular value decomposition (SVD). The rsvd package provides several randomized matrix algorithms such as the randomized singular value decomposition (rsvd), randomized principal component analysis (rpca), randomized robust principal component analysis (rrpca), randomized interpolative decomposition (rid), and the randomized CUR decomposition (rcur). In addition several plot functions are provided. The methods are discussed in detail by Erichson et al. (2016) <arXiv:1608.02148>.

r-rtracklayer

Homepage:
Spack package:
Versions:
1.44.4, 1.42.2, 1.40.6, 1.38.3, 1.36.6
Build Dependencies:
r, r-genomicranges, r-xml, r-biocgenerics, r-s4vectors, r-iranges, r-xvector, r-genomeinfodb, r-biostrings, r-zlibbioc, r-rcurl, r-rsamtools, r-genomicalignments
Link Dependencies:
r
Run Dependencies:
r, r-genomicranges, r-xml, r-biocgenerics, r-s4vectors, r-iranges, r-xvector, r-genomeinfodb, r-biostrings, r-zlibbioc, r-rcurl, r-rsamtools, r-genomicalignments
Description:
R interface to genome annotation files and the UCSC genome browser. Extensible framework for interacting with multiple genome browsers (currently UCSC built-in) and manipulating annotation tracks in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit built-in). The user may export/import tracks to/from the supported browsers, as well as query and modify the browser state, such as the current viewport.

r-rtsne

Homepage:
Spack package:
Versions:
0.15, 0.13, 0.11, 0.10
Build Dependencies:
r, r-rcpp
Link Dependencies:
r
Run Dependencies:
r, r-rcpp
Description:
An R wrapper around the fast T-distributed Stochastic Neighbor Embedding implementation.

r-runit

Homepage:
Spack package:
Versions:
0.4.32
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
RUnit: R Unit Test Framework

r-rvcheck

Homepage:
Spack package:
Versions:
0.1.3, 0.0.9
Build Dependencies:
r, r-rlang
Link Dependencies:
r
Run Dependencies:
r, r-rlang
Description:
Check latest release version of R and R package (both in 'CRAN', 'Bioconductor' or 'Github').

r-rvest

Homepage:
Spack package:
Versions:
0.3.4, 0.3.3, 0.3.2
Build Dependencies:
r, r-xml2, r-httr, r-selectr, r-magrittr
Link Dependencies:
r
Run Dependencies:
r, r-xml2, r-httr, r-selectr, r-magrittr
Description:
Wrappers around the 'xml2' and 'httr' packages to make it easy to download, then manipulate, HTML and XML.

r-rzmq

Homepage:
Spack package:
Versions:
0.9.6, 0.9.4, 0.7.7
Build Dependencies:
r, libzmq
Link Dependencies:
r, libzmq
Run Dependencies:
r
Description:
Interface to the ZeroMQ lightweight messaging kernel.

r-s4vectors

Homepage:
Spack package:
Versions:
0.22.1, 0.20.1, 0.18.3, 0.16.0, 0.14.7
Build Dependencies:
r, r-biocgenerics
Link Dependencies:
r
Run Dependencies:
r, r-biocgenerics
Description:
Foundation of vector-like and list-like containers in Bioconductor. The S4Vectors package defines the Vector and List virtual classes and a set of generic functions that extend the semantic of ordinary vectors and lists in R. Package developers can easily implement vector-like or list- like objects as concrete subclasses of Vector or List. In addition, a few low-level concrete subclasses of general interest (e.g. DataFrame, Rle, and Hits) are implemented in the S4Vectors package itself (many more are implemented in the IRanges package and in other Bioconductor infrastructure packages).

r-samr

Homepage:
Spack package:
Versions:
3.0, 2.0
Build Dependencies:
r, r-impute, r-matrixstats, r-shiny, r-shinyfiles, r-openxlsx, r-gsa
Link Dependencies:
r
Run Dependencies:
r, r-impute, r-matrixstats, r-shiny, r-shinyfiles, r-openxlsx, r-gsa
Description:
Significance Analysis of Microarrays.

r-sandwich

Homepage:
Spack package:
Versions:
2.5-1, 2.5-0, 2.3-4
Build Dependencies:
r, r-zoo
Link Dependencies:
r
Run Dependencies:
r, r-zoo
Description:
Model-robust standard error estimators for cross-sectional, time series, and longitudinal data.

r-scales

Homepage:
Spack package:
Versions:
1.0.0, 0.5.0, 0.4.1, 0.4.0
Build Dependencies:
r, r-rcolorbrewer, r-dichromat, r-plyr, r-munsell, r-labeling, r-rcpp, r-r6, r-viridislite
Link Dependencies:
r
Run Dependencies:
r, r-rcolorbrewer, r-dichromat, r-plyr, r-munsell, r-labeling, r-rcpp, r-r6, r-viridislite
Description:
Graphical scales map data to aesthetics, and provide methods for automatically determining breaks and labels for axes and legends.

r-scatterplot3d

Homepage:
Spack package:
Versions:
0.3-41, 0.3-40
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
scatterplot3d: 3D Scatter Plot

r-scrime

Homepage:
Spack package:
Versions:
1.3.5
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
scrime: Analysis of High-Dimensional Categorical Data Such as SNP Data

r-sctransform

Homepage:
Spack package:
Versions:
0.2.0
Build Dependencies:
r, r-mass, r-matrix, r-future, r-future-apply, r-ggplot2, r-reshape2, r-gridextra, r-rcpp, r-rcppeigen
Link Dependencies:
r
Run Dependencies:
r, r-mass, r-matrix, r-future, r-future-apply, r-ggplot2, r-reshape2, r-gridextra, r-rcpp, r-rcppeigen
Description:
A normalization method for single-cell UMI count data using a variance stabilizing transformation. The transformation is based on a negative binomial regression model with regularized parameters. As part of the same regression framework, this package also provides functions for batch correction, and data correction. See Hafemeister and Satija 2019 <doi:10.1101/576827> for more details.

r-sdmtools

Homepage:
Spack package:
Versions:
1.1-221.1, 1.1-221, 1.1-20, 1.1-13, 1.1-12, 1.1-11
Build Dependencies:
r, r-r-utils
Link Dependencies:
r
Run Dependencies:
r, r-r-utils
Description:
Species Distribution Modelling Tools: Tools for processing data associated with species distribution modelling exercises This packages provides a set of tools for post processing the outcomes of species distribution modeling exercises.

r-segmented

Homepage:
Spack package:
Versions:
1.0-0, 0.5-4.0, 0.5-2.2, 0.5-1.4
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Given a regression model, segmented 'updates' the model by adding one or more segmented (i.e., piecewise-linear) relationships. Several variables with multiple breakpoints are allowed.

r-selectr

Homepage:
Spack package:
Versions:
0.4-1, 0.4-0, 0.3-1
Build Dependencies:
r, r-stringr, r-r6
Link Dependencies:
r
Run Dependencies:
r, r-stringr, r-r6
Description:
Translates a CSS3 selector into an equivalent XPath expression. This allows us to use CSS selectors when working with the XML package as it can only evaluate XPath expressions. Also provided are convenience functions useful for using CSS selectors on XML nodes. This package is a port of the Python package 'cssselect' (<https://pythonhosted.org/cssselect/>).

r-seqinr

Homepage:
Spack package:
Versions:
3.4-5, 3.3-6
Build Dependencies:
r, r-ade4, r-segmented, zlib
Link Dependencies:
r, zlib
Run Dependencies:
r, r-ade4, r-segmented
Description:
Exploratory data analysis and data visualization for biological sequence (DNA and protein) data. Includes also utilities for sequence data management under the ACNUC system.

r-sessioninfo

Homepage:
Spack package:
Versions:
1.1.1
Build Dependencies:
r, r-cli, r-withr
Link Dependencies:
r
Run Dependencies:
r, r-cli, r-withr
Description:
Query and print information about the current R session. It is similar to 'utils::sessionInfo()', but includes more information about packages, and where they were installed from.

r-seurat

Homepage:
Spack package:
Versions:
3.1.0, 3.0.2, 3.0.1, 2.1.0, 2.0.1
Build Dependencies:
r, r-ggplot2, r-gplots, r-reshape2, r-ape, r-tidyr, r-caret, r-gdata, r-gridextra, r-cowplot, r-rocr, r-hmisc, r-nmf, r-irlba, r-igraph, r-fpc, r-rcppprogress, r-lars, r-dtw, r-mixtools, r-ica, r-diffusionmap, r-tsne, r-rtsne, r-ranger, r-pbapply, r-ggjoy, r-plotly, r-sdmtools, r-tclust, r-fnn, r-vgam, r-matrix, r-rcolorbrewer, r-mass, r-rcpp, r-rcppeigen, r-ggridges, r-e1071, r-compositions, r-nmof, r-metap, r-cluster, r-fitdistrplus, r-png, r-lmtest, r-rann, r-reticulate, r-stringr, r-dplyr, r-httr, r-dosnow, r-foreach, r-hdf5r, r-future, r-future-apply, r-ggrepel, r-kernsmooth, r-rlang, r-rsvd, r-scales, r-sctransform, r-leiden, r-rcppannoy, r-uwot, java
Link Dependencies:
r, java
Run Dependencies:
r, r-ggplot2, r-gplots, r-reshape2, r-ape, r-tidyr, r-caret, r-gdata, r-gridextra, r-cowplot, r-rocr, r-hmisc, r-nmf, r-irlba, r-igraph, r-fpc, r-rcppprogress, r-lars, r-dtw, r-mixtools, r-ica, r-diffusionmap, r-tsne, r-rtsne, r-ranger, r-pbapply, r-ggjoy, r-plotly, r-sdmtools, r-tclust, r-fnn, r-vgam, r-matrix, r-rcolorbrewer, r-mass, r-rcpp, r-rcppeigen, r-ggridges, r-e1071, r-compositions, r-nmof, r-metap, r-cluster, r-fitdistrplus, r-png, r-lmtest, r-rann, r-reticulate, r-stringr, r-dplyr, r-httr, r-dosnow, r-foreach, r-hdf5r, r-future, r-future-apply, r-ggrepel, r-kernsmooth, r-rlang, r-rsvd, r-scales, r-sctransform, r-leiden, r-rcppannoy, r-uwot
Description:
Seurat is an R package designed for QC, analysis, and exploration of single cell RNA-seq data.

r-sf

Homepage:
Spack package:
Versions:
0.7-7, 0.7-5, 0.5-5
Build Dependencies:
r, r-rcpp, r-dbi, r-units, r-classint, r-magrittr, gdal, geos, proj
Link Dependencies:
r, gdal, geos, proj
Run Dependencies:
r, r-rcpp, r-dbi, r-units, r-classint, r-magrittr
Description:
Support for simple features, a standardized way to encode spatial vector data. Binds to GDAL for reading and writing data, to GEOS for geometrical operations, and to Proj.4 for projection conversions and datum transformations.

r-sfsmisc

Homepage:
Spack package:
Versions:
1.1-4, 1.1-3, 1.1-0
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Useful utilities ['goodies'] from Seminar fuer Statistik ETH Zurich, quite a few related to graphics; some were ported from S-plus.

r-shape

Homepage:
Spack package:
Versions:
1.4.4, 1.4.3, 1.4.2
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Functions for plotting graphical shapes such as ellipses, circles, cylinders, arrows, ...

r-shiny

Homepage:
Spack package:
Versions:
1.3.2, 1.0.5, 0.13.2
Build Dependencies:
r, r-httpuv, r-mime, r-jsonlite, r-xtable, r-digest, r-htmltools, r-r6, r-sourcetools, r-later, r-promises, r-crayon, r-rlang
Link Dependencies:
r
Run Dependencies:
r, r-httpuv, r-mime, r-jsonlite, r-xtable, r-digest, r-htmltools, r-r6, r-sourcetools, r-later, r-promises, r-crayon, r-rlang
Description:
Makes it incredibly easy to build interactive web applications with R. Automatic "reactive" binding between inputs and outputs and extensive pre-built widgets make it possible to build beautiful, responsive, and powerful applications with minimal effort.

r-shinydashboard

Homepage:
Spack package:
Versions:
0.7.1, 0.7.0, 0.6.1
Build Dependencies:
r, r-htmltools, r-shiny, r-promises
Link Dependencies:
r
Run Dependencies:
r, r-htmltools, r-shiny, r-promises
Description:
Create Dashboards with 'Shiny'

r-shinyfiles

Homepage:
Spack package:
Versions:
0.7.3
Build Dependencies:
r, r-htmltools, r-jsonlite, r-shiny, r-fs, r-tibble
Link Dependencies:
r
Run Dependencies:
r, r-htmltools, r-jsonlite, r-shiny, r-fs, r-tibble
Description:
Provides functionality for client-side navigation of the server side file system in shiny apps. In case the app is running locally this gives the user direct access to the file system without the need to "download" files to a temporary location. Both file and folder selection as well as file saving is available.

r-shortread

Homepage:
Spack package:
Versions:
1.42.0, 1.40.0, 1.38.0, 1.36.1, 1.34.2
Build Dependencies:
r, r-biocgenerics, r-biocparallel, r-biostrings, r-rsamtools, r-genomicalignments, r-biobase, r-s4vectors, r-iranges, r-genomeinfodb, r-genomicranges, r-hwriter, r-zlibbioc, r-lattice, r-latticeextra, r-xvector
Link Dependencies:
r
Run Dependencies:
r, r-biocgenerics, r-biocparallel, r-biostrings, r-rsamtools, r-genomicalignments, r-biobase, r-s4vectors, r-iranges, r-genomeinfodb, r-genomicranges, r-hwriter, r-zlibbioc, r-lattice, r-latticeextra, r-xvector
Description:
FASTQ input and manipulation. This package implements sampling, iteration, and input of FASTQ files. The package includes functions for filtering and trimming reads, and for generating a quality assessment report. Data are represented as DNAStringSet-derived objects, and easily manipulated for a diversity of purposes. The package also contains legacy support for early single-end, ungapped alignment formats.

r-siggenes

Homepage:
Spack package:
Versions:
1.58.0, 1.56.0, 1.54.0, 1.52.0, 1.50.0
Build Dependencies:
r, r-biobase, r-multtest, r-scrime
Link Dependencies:
r
Run Dependencies:
r, r-biobase, r-multtest, r-scrime
Description:
Multiple Testing using SAM and Efron's Empirical Bayes Approaches. Identification of differentially expressed genes and estimation of the False Discovery Rate (FDR) using both the Significance Analysis of Microarrays (SAM) and the Empirical Bayes Analyses of Microarrays (EBAM).

r-simpleaffy

Homepage:
Spack package:
Versions:
2.60.0, 2.58.0, 2.56.0, 2.54.0, 2.52.0
Build Dependencies:
r, r-biocgenerics, r-biobase, r-affy, r-genefilter, r-gcrma
Link Dependencies:
r
Run Dependencies:
r, r-biocgenerics, r-biobase, r-affy, r-genefilter, r-gcrma
Description:
Very simple high level analysis of Affymetrix data. Provides high level functions for reading Affy .CEL files, phenotypic data, and then computing simple things with it, such as t-tests, fold changes and the like. Makes heavy use of the affy library. Also has some basic scatter plot functions and mechanisms for generating high resolution journal figures...

r-singlecellexperiment

Homepage:
Spack package:
Versions:
1.6.0, 1.4.1, 1.2.0, 1.0.0
Build Dependencies:
r, r-summarizedexperiment, r-s4vectors, r-biocgenerics
Link Dependencies:
r
Run Dependencies:
r, r-summarizedexperiment, r-s4vectors, r-biocgenerics
Description:
S4 Classes for Single Cell Data. Defines a S4 class for storing data from single-cell experiments. This includes specialized methods to store and retrieve spike-in information, dimensionality reduction coordinates and size factors for each cell, along with the usual metadata for genes and libraries.

r-sitmo

Homepage:
Spack package:
Versions:
2.0.1
Build Dependencies:
r, r-rcpp
Link Dependencies:
r
Run Dependencies:
r, r-rcpp
Description:
Provided within are two high quality and fast PPRNGs that may be used in an 'OpenMP' parallel environment. In addition, there is a generator for one dimensional low-discrepancy sequence. The objective of this library to consolidate the distribution of the 'sitmo' (C++98 & C++11), 'threefry' and 'vandercorput' (C++11-only) engines on CRAN by enabling others to link to the header files inside of 'sitmo' instead of including a copy of each engine within their individual package. Lastly, the package contains example implementations using the 'sitmo' package and three accompanying vignette that provide additional information.

r-sm

Homepage:
Spack package:
Versions:
2.2-5.6, 2.2-5.5
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
This is software linked to the book 'Applied Smoothing Techniques for Data Analysis - The Kernel Approach with S-Plus Illustrations' Oxford University Press.

r-smoof

Homepage:
Spack package:
Versions:
1.5.1, 1.5
Build Dependencies:
r, r-paramhelpers, r-bbmisc, r-checkmate, r-ggplot2, r-rcolorbrewer, r-plot3d, r-plotly, r-mco, r-rcpp, r-rjsonio, r-rcpparmadillo
Link Dependencies:
r
Run Dependencies:
r, r-paramhelpers, r-bbmisc, r-checkmate, r-ggplot2, r-rcolorbrewer, r-plot3d, r-plotly, r-mco, r-rcpp, r-rjsonio, r-rcpparmadillo
Description:
Provides generators for a high number of both single- and multi- objective test functions which are frequently used for the benchmarking of (numerical) optimization algorithms. Moreover, it offers a set of convenient functions to generate, plot and work with objective functions.

r-sn

Homepage:
Spack package:
Versions:
1.5-4, 1.5-3, 1.5-0, 1.4-0, 1.3-0, 1.2-4, 1.2-3
Build Dependencies:
r, r-mnormt, r-numderiv
Link Dependencies:
r
Run Dependencies:
r, r-mnormt, r-numderiv
Description:
Build and manipulate probability distributions of the skew-normal family and some related ones, notably the skew-t family, and provide related statistical methods for data fitting and diagnostics, in the univariate and the multivariate case.

r-snakecase

Homepage:
Spack package:
Versions:
0.11.0
Build Dependencies:
r, r-stringr, r-stringi
Link Dependencies:
r
Run Dependencies:
r, r-stringr, r-stringi
Description:
A consistent, flexible and easy to use tool to parse and convert strings into cases like snake or camel among others.

r-snow

Homepage:
Spack package:
Versions:
0.4-3, 0.4-2
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Support for simple parallel computing in R.

r-snowfall

Homepage:
Spack package:
Versions:
1.84-6.1
Build Dependencies:
r, r-snow
Link Dependencies:
r
Run Dependencies:
r, r-snow
Description:
Usability wrapper around snow for easier development of parallel R programs. This package offers e.g. extended error checks, and additional functions. All functions work in sequential mode, too, if no cluster is present or wished. Package is also designed as connector to the cluster management tool sfCluster, but can also used without it.

r-snprelate

Homepage:
Spack package:
Versions:
1.18.1, 1.16.0, 1.14.0, 1.12.2, 1.10.2
Build Dependencies:
r, r-gdsfmt
Link Dependencies:
r
Run Dependencies:
r, r-gdsfmt
Description:
Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data. Genome-wide association studies (GWAS) are widely used to investigate the genetic basis of diseases and traits, but they pose many computational challenges. We developed an R package SNPRelate to provide a binary format for single-nucleotide polymorphism (SNP) data in GWAS utilizing CoreArray Genomic Data Structure (GDS) data files. The GDS format offers the efficient operations specifically designed for integers with two bits, since a SNP could occupy only two bits. SNPRelate is also designed to accelerate two key computations on SNP data using parallel computing for multi-core symmetric multiprocessing computer architectures: Principal Component Analysis (PCA) and relatedness analysis using Identity-By-Descent measures. The SNP GDS format is also used by the GWASTools package with the support of S4 classes and generic functions. The extended GDS format is implemented in the SeqArray package to support the storage of single nucleotide variations (SNVs), insertion/deletion polymorphism (indel) and structural variation calls.

r-snpstats

Homepage:
Spack package:
Versions:
1.34.0, 1.32.0, 1.30.0, 1.28.0, 1.26.0
Build Dependencies:
r, r-survival, r-matrix, r-biocgenerics, r-zlibbioc
Link Dependencies:
r
Run Dependencies:
r, r-survival, r-matrix, r-biocgenerics, r-zlibbioc
Description:
SnpMatrix and XSnpMatrix classes and methods. Classes and statistical methods for large SNP association studies. This extends the earlier snpMatrix package, allowing for uncertainty in genotypes.

r-som

Homepage:
Spack package:
Versions:
0.3-5.1, 0.3-5, 0.3-4, 0.3-3, 0.3-2
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Self-Organizing Map (with application in gene clustering).

r-somaticsignatures

Homepage:
Spack package:
Versions:
2.20.0, 2.18.0, 2.16.0, 2.14.0, 2.12.1
Build Dependencies:
r, r-variantannotation, r-genomicranges, r-nmf, r-s4vectors, r-iranges, r-genomeinfodb, r-biostrings, r-ggplot2, r-ggbio, r-reshape2, r-pcamethods, r-biobase, r-proxy
Link Dependencies:
r
Run Dependencies:
r, r-variantannotation, r-genomicranges, r-nmf, r-s4vectors, r-iranges, r-genomeinfodb, r-biostrings, r-ggplot2, r-ggbio, r-reshape2, r-pcamethods, r-biobase, r-proxy
Description:
Somatic Signatures. The SomaticSignatures package identifies mutational signatures of single nucleotide variants (SNVs). It provides a infrastructure related to the methodology described in Nik-Zainal (2012, Cell), with flexibility in the matrix decomposition algorithms.

r-sourcetools

Homepage:
Spack package:
Versions:
0.1.7, 0.1.6, 0.1.5
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Tools for Reading, Tokenizing and Parsing R Code.

r-sp

Homepage:
Spack package:
Versions:
1.3-1, 1.2-7, 1.2-3
Build Dependencies:
r, r-lattice
Link Dependencies:
r
Run Dependencies:
r, r-lattice
Description:
Classes and methods for spatial data; the classes document where the spatial location information resides, for 2D or 3D data. Utility functions are provided, e.g. for plotting data as maps, spatial selection, as well as methods for retrieving coordinates, for subsetting, print, summary, etc.

r-spacetime

Homepage:
Spack package:
Versions:
1.2-2
Build Dependencies:
r, r-intervals, r-lattice, r-sp, r-xts, r-zoo
Link Dependencies:
r
Run Dependencies:
r, r-intervals, r-lattice, r-sp, r-xts, r-zoo
Description:
spacetime: Classes and Methods for Spatio-Temporal Data

r-spam

Homepage:
Spack package:
Versions:
2.3-0.2
Build Dependencies:
r, r-dotcall64
Link Dependencies:
r
Run Dependencies:
r, r-dotcall64
Description:
spam: SPArse Matrix

r-sparsem

Homepage:
Spack package:
Versions:
1.77, 1.76, 1.74, 1.7
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Some basic linear algebra functionality for sparse matrices is provided: including Cholesky decomposition and backsolving as well as standard R subsetting and Kronecker products.

r-spatial

Homepage:
Spack package:
Versions:
7.3-11
Build Dependencies:
r, r-mass
Link Dependencies:
r
Run Dependencies:
r, r-mass
Description:
spatial: Functions for Kriging and Point Pattern Analysis

r-spatialreg

Homepage:
Spack package:
Versions:
1.1-3
Build Dependencies:
r, r-boot, r-coda, r-expm, r-gmodels, r-learnbayes, r-mass, r-matrix, r-nlme, r-spdata, r-spdep
Link Dependencies:
r
Run Dependencies:
r, r-boot, r-coda, r-expm, r-gmodels, r-learnbayes, r-mass, r-matrix, r-nlme, r-spdata, r-spdep
Description:
spatialreg: Spatial Regression Analysis

r-spdata

Homepage:
Spack package:
Versions:
0.3.0
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
spData: Datasets for Spatial Analysis

r-spdep

Homepage:
Spack package:
Versions:
1.1-2, 1.0-2, 0.6-13
Build Dependencies:
r, r-sp, r-learnbayes, r-deldir, r-coda, r-gmodels, r-expm, r-matrix, r-mass, r-boot, r-nlme, r-spdata, r-sf
Link Dependencies:
r
Run Dependencies:
r, r-sp, r-learnbayes, r-deldir, r-coda, r-gmodels, r-expm, r-matrix, r-mass, r-boot, r-nlme, r-spdata, r-sf
Description:
A collection of functions to create spatial weights matrix objects from polygon contiguities, from point patterns by distance and tessellations, for summarizing these objects, and for permitting their use in spatial data analysis, including regional aggregation by minimum spanning tree; a collection of tests for spatial autocorrelation, including global Moran's I, APLE, Geary's C, Hubert/Mantel general cross product statistic, Empirical Bayes estimates and AssunasReis Index, Getis/Ord G and multicoloured join count statistics, local Moran's I and Getis/Ord G, saddlepoint approximations and exact tests for global and local Moran's I; and functions for estimating spatial simultaneous autoregressive (SAR) lag and error models, impact measures for lag models, weighted and unweighted SAR and CAR spatial regression models, semi-parametric and Moran eigenvector spatial filtering, GM SAR error models, and generalized spatial two stage least squares models.

r-speedglm

Homepage:
Spack package:
Versions:
0.3-2
Build Dependencies:
r, r-mass, r-matrix
Link Dependencies:
r
Run Dependencies:
r, r-mass, r-matrix
Description:
Fitting linear models and generalized linear models to large data sets by updating algorithms.

r-spem

Homepage:
Spack package:
Versions:
1.24.0, 1.22.0, 1.20.0, 1.18.0, 1.16.0
Build Dependencies:
r, r-rsolnp, r-biobase
Link Dependencies:
r
Run Dependencies:
r, r-rsolnp, r-biobase
Description:
S-system parameter estimation method. This package can optimize the parameter in S-system models given time series data

r-splancs

Homepage:
Spack package:
Versions:
2.01-40
Build Dependencies:
r, r-sp
Link Dependencies:
r
Run Dependencies:
r, r-sp
Description:
Spatial and Space-Time Point Pattern Analysis

r-splitstackshape

Homepage:
Spack package:
Versions:
1.4.8, 1.4.6, 1.4.4
Build Dependencies:
r, r-data-table
Link Dependencies:
r
Run Dependencies:
r, r-data-table
Description:
Stack and Reshape Datasets After Splitting Concatenated Values. Online data collection tools like Google Forms often export multiple-response questions with data concatenated in cells. The concat.split (cSplit) family of functions splits such data into separate cells. The package also includes functions to stack groups of columns and to reshape wide data, even when the data are "unbalanced" something which reshape (from base R) does not handle, and which melt and dcast from reshape2 do not easily handle.

r-sqldf

Homepage:
Spack package:
Versions:
0.4-11
Build Dependencies:
r, r-gsubfn, r-proto, r-rsqlite, r-dbi, r-chron
Link Dependencies:
r
Run Dependencies:
r, r-gsubfn, r-proto, r-rsqlite, r-dbi, r-chron
Description:
The sqldf() function is typically passed a single argument which is an SQL select statement where the table names are ordinary R data frame names. sqldf() transparently sets up a database, imports the data frames into that database, performs the SQL select or other statement and returns the result using a heuristic to determine which class to assign to each column of the returned data frame. The sqldf() or read.csv.sql() functions can also be used to read filtered files into R even if the original files are larger than R itself can handle. 'RSQLite', 'RH2', 'RMySQL' and 'RPostgreSQL' backends are supported.

r-squarem

Homepage:
Spack package:
Versions:
2017.10-1
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Algorithms for accelerating the convergence of slow, monotone sequences from smooth, contraction mapping such as the EM algorithm. It can be used to accelerate any smooth, linearly convergent acceleration scheme. A tutorial style introduction to this package is available in a vignette on the CRAN download page or, when the package is loaded in an R session, with vignette("SQUAREM").

r-squash

Homepage:
Spack package:
Versions:
1.0.8, 1.0.7
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Color-Based Plots for Multivariate Visualization

r-sseq

Homepage:
Spack package:
Versions:
1.22.0, 1.20.1, 1.18.0, 1.16.0, 1.14.0
Build Dependencies:
r, r-catools, r-rcolorbrewer
Link Dependencies:
r
Run Dependencies:
r, r-catools, r-rcolorbrewer
Description:
Shrinkage estimation of dispersion in Negative Binomial models for RNA- seq experiments with small sample size. The purpose of this package is to discover the genes that are differentially expressed between two conditions in RNA-seq experiments. Gene expression is measured in counts of transcripts and modeled with the Negative Binomial (NB) distribution using a shrinkage approach for dispersion estimation. The method of moment (MM) estimates for dispersion are shrunk towards an estimated target, which minimizes the average squared difference between the shrinkage estimates and the initial estimates. The exact per-gene probability under the NB model is calculated, and used to test the hypothesis that the expected expression of a gene in two conditions identically follow a NB distribution.

r-stabledist

Homepage:
Spack package:
Versions:
0.7-1
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Density, Probability and Quantile functions, and random number generation for (skew) stable distributions, using the parametrizations of Nolan.

r-stanheaders

Homepage:
Spack package:
Versions:
2.18.1-10, 2.18.1, 2.17.1, 2.10.0-2
Build Dependencies:
r, pandoc
Link Dependencies:
r
Run Dependencies:
r
Description:
The C++ header files of the Stan project are provided by this package, but it contains no R code, vignettes, or function documentation. There is a shared object containing part of the CVODES library, but it is not accessible from R. StanHeaders is only useful for developers who want to utilize the LinkingTo directive of their package's DESCRIPTION file to build on the Stan library without incurring unnecessary dependencies. The Stan project develops a probabilistic programming language that implements full or approximate Bayesian statistical inference via Markov Chain Monte Carlo or variational methods and implements (optionally penalized) maximum likelihood estimation via optimization. The Stan library includes an advanced automatic differentiation scheme, templated statistical and linear algebra functions that can handle the automatically differentiable scalar types (and doubles, ints, etc.), and a parser for the Stan language. The 'rstan' package provides user-facing R functions to parse, compile, test, estimate, and analyze Stan models.

r-stargazer

Homepage:
Spack package:
Versions:
5.2.2
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
stargazer: Well-Formatted Regression and Summary Statistics Tables

r-statmod

Homepage:
Spack package:
Versions:
1.4.32, 1.4.30
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
A collection of algorithms and functions to aid statistical modeling. Includes growth curve comparisons, limiting dilution analysis (aka ELDA), mixed linear models, heteroscedastic regression, inverse-Gaussian probability calculations, Gauss quadrature and a secure convergence algorithm for nonlinear models. Includes advanced generalized linear model functions that implement secure convergence, dispersion modeling and Tweedie power-law families.

r-statnet-common

Homepage:
Spack package:
Versions:
4.3.0, 4.2.0, 3.3.0
Build Dependencies:
r, r-coda
Link Dependencies:
r
Run Dependencies:
r, r-coda
Description:
Non-statistical utilities used by the software developed by the Statnet Project. They may also be of use to others.

r-stringi

Homepage:
Spack package:
Versions:
1.4.3, 1.3.1, 1.1.5, 1.1.3, 1.1.2, 1.1.1
Build Dependencies:
r, icu4c
Link Dependencies:
r, icu4c
Run Dependencies:
r
Description:
Allows for fast, correct, consistent, portable, as well as convenient character string/text processing in every locale and any native encoding. Owing to the use of the ICU library, the package provides R users with platform-independent functions known to Java, Perl, Python, PHP, and Ruby programmers. Among available features there are: pattern searching (e.g., with ICU Java-like regular expressions or the Unicode Collation Algorithm), random string generation, case mapping, string transliteration, concatenation, Unicode normalization, date-time formatting and parsing, etc.

r-stringr

Homepage:
Spack package:
Versions:
1.4.0, 1.3.1, 1.2.0, 1.1.0, 1.0.0
Build Dependencies:
r, r-stringi, r-magrittr, r-glue
Link Dependencies:
r
Run Dependencies:
r, r-stringi, r-magrittr, r-glue
Description:
A consistent, simple and easy to use set of wrappers around the fantastic 'stringi' package. All function and argument names (and positions) are consistent, all functions deal with "NA"'s and zero length vectors in the same way, and the output from one function is easy to feed into the input of another.

r-strucchange

Homepage:
Spack package:
Versions:
1.5-1
Build Dependencies:
r, r-zoo, r-sandwich
Link Dependencies:
r
Run Dependencies:
r, r-zoo, r-sandwich
Description:
Testing, monitoring and dating structural changes in (linear) regression models.

r-subplex

Homepage:
Spack package:
Versions:
1.5-4, 1.5-2, 1.4-1
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Unconstrained Optimization using the Subplex Algorithm

r-summarizedexperiment

Homepage:
Spack package:
Versions:
1.14.1, 1.12.0, 1.10.1, 1.8.1, 1.6.5
Build Dependencies:
r, r-genomicranges, r-biobase, r-delayedarray, r-matrix, r-biocgenerics, r-s4vectors, r-iranges, r-genomeinfodb
Link Dependencies:
r
Run Dependencies:
r, r-genomicranges, r-biobase, r-delayedarray, r-matrix, r-biocgenerics, r-s4vectors, r-iranges, r-genomeinfodb
Description:
SummarizedExperiment container. The SummarizedExperiment container contains one or more assays, each represented by a matrix-like object of numeric or other mode. The rows typically represent genomic ranges of interest and the columns represent samples.

r-suppdists

Homepage:
Spack package:
Versions:
1.1-9.5
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Ten distributions supplementing those built into R. Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi squared, Spearman's rho, maximum F ratio, the Pearson product moment correlation coefficient, Johnson distributions, normal scores and generalized hypergeometric distributions.

r-survey

Homepage:
Spack package:
Versions:
3.36, 3.35-1, 3.30-3
Build Dependencies:
r, r-matrix, r-survival, r-lattice, r-minqa, r-numderiv, r-mitools
Link Dependencies:
r
Run Dependencies:
r, r-matrix, r-survival, r-lattice, r-minqa, r-numderiv, r-mitools
Description:
Summary statistics, two-sample tests, rank tests, generalised linear models, cumulative link models, Cox models, loglinear models, and general maximum pseudolikelihood estimation for multistage stratified, cluster-sampled, unequally weighted survey samples. Variances by Taylor series linearisation or replicate weights. Post-stratification, calibration, and raking. Two-phase subsampling designs. Graphics. PPS sampling without replacement. Principal components, factor analysis.

r-survival

Homepage:
Spack package:
Versions:
2.44-1.1, 2.44-1, 2.41-3, 2.40-1, 2.39-5
Build Dependencies:
r, r-matrix
Link Dependencies:
r
Run Dependencies:
r, r-matrix
Description:
Contains the core survival analysis routines, including definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models, and parametric accelerated failure time models.

r-sva

Homepage:
Spack package:
Versions:
3.32.1, 3.30.1, 3.28.0, 3.26.0, 3.24.4
Build Dependencies:
r, r-mgcv, r-genefilter, r-biocparallel, r-matrixstats, r-limma
Link Dependencies:
r
Run Dependencies:
r, r-mgcv, r-genefilter, r-biocparallel, r-matrixstats, r-limma
Description:
Surrogate Variable Analysis. The sva package contains functions for removing batch effects and other unwanted variation in high-throughput experiment. Specifically, the sva package contains functions for the identifying and building surrogate variables for high-dimensional data sets. Surrogate variables are covariates constructed directly from high- dimensional data (like gene expression/RNA sequencing/methylation/brain imaging data) that can be used in subsequent analyses to adjust for unknown, unmodeled, or latent sources of noise. The sva package can be used to remove artifacts in three ways: (1) identifying and estimating surrogate variables for unknown sources of variation in high-throughput experiments (Leek and Storey 2007 PLoS Genetics,2008 PNAS), (2) directly removing known batch effects using ComBat (Johnson et al. 2007 Biostatistics) and (3) removing batch effects with known control probes (Leek 2014 biorXiv). Removing batch effects and using surrogate variables in differential expression analysis have been shown to reduce dependence, stabilize error rate estimates, and improve reproducibility, see (Leek and Storey 2007 PLoS Genetics, 2008 PNAS or Leek et al. 2011 Nat. Reviews Genetics).

r-sys

Homepage:
Spack package:
Versions:
3.2
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Drop-in replacements for the base system2() function with fine control and consistent behavior across platforms. Supports clean interruption, timeout, background tasks, and streaming STDIN / STDOUT / STDERR over binary or text connections. Arguments on Windows automatically get encoded and quoted to work on different locales.

r-tarifx

Homepage:
Spack package:
Versions:
1.0.6.1, 1.0.6
Build Dependencies:
r, r-reshape2, r-plyr
Link Dependencies:
r
Run Dependencies:
r, r-reshape2, r-plyr
Description:
A collection of various utility and convenience functions.

r-taxizedb

Homepage:
Spack package:
Versions:
0.1.4
Build Dependencies:
r, r-curl, r-dbi, r-rpostgresql, r-rmysql, r-rsqlite, r-dplyr, r-dbplyr, r-magrittr, r-hoardr
Link Dependencies:
r
Run Dependencies:
r, r-curl, r-dbi, r-rpostgresql, r-rmysql, r-rsqlite, r-dplyr, r-dbplyr, r-magrittr, r-hoardr
Description:
taxizedb: Tools for Working with 'Taxonomic' Databases

r-tclust

Homepage:
Spack package:
Versions:
1.4-1, 1.3-1, 1.2-7, 1.2-3, 1.1-03, 1.1-02
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Provides functions for robust trimmed clustering.

r-teachingdemos

Homepage:
Spack package:
Versions:
2.10
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
TeachingDemos: Demonstrations for Teaching and Learning. Demonstration functions that can be used in a classroom to demonstrate statistical concepts, or on your own to better understand the concepts or the programming.

r-tensora

Homepage:
Spack package:
Versions:
0.36.1, 0.36
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
The package provides convenience functions for advance linear algebra with tensors and computation with datasets of tensors on a higher level abstraction.

r-testit

Homepage:
Spack package:
Versions:
0.9, 0.8, 0.7, 0.5
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Provides two convenience functions assert() and test_pkg() to facilitate testing R packages.

r-testthat

Homepage:
Spack package:
Versions:
2.2.1, 2.1.0, 1.0.2
Build Dependencies:
r, r-digest, r-crayon, r-praise, r-magrittr, r-r6, r-cli, r-rlang, r-withr, r-evaluate
Link Dependencies:
r
Run Dependencies:
r, r-digest, r-crayon, r-praise, r-magrittr, r-r6, r-cli, r-rlang, r-withr, r-evaluate
Description:
A unit testing system designed to be fun, flexible and easy to set up.

r-tfbstools

Homepage:
Spack package:
Versions:
1.22.0, 1.20.0, 1.18.0, 1.16.0, 1.14.2
Build Dependencies:
r, r-biobase, r-biostrings, r-biocgenerics, r-biocparallel, r-bsgenome, r-catools, r-cner, r-dirichletmultinomial, r-genomeinfodb, r-genomicranges, r-gtools, r-iranges, r-dbi, r-rsqlite, r-rtracklayer, r-seqlogo, r-s4vectors, r-tfmpvalue, r-xml, r-xvector
Link Dependencies:
r
Run Dependencies:
r, r-biobase, r-biostrings, r-biocgenerics, r-biocparallel, r-bsgenome, r-catools, r-cner, r-dirichletmultinomial, r-genomeinfodb, r-genomicranges, r-gtools, r-iranges, r-dbi, r-rsqlite, r-rtracklayer, r-seqlogo, r-s4vectors, r-tfmpvalue, r-xml, r-xvector
Description:
Software Package for Transcription Factor Binding Site (TFBS) Analysis. TFBSTools is a package for the analysis and manipulation of transcription factor binding sites. It includes matrices conversion between Position Frequency Matirx (PFM), Position Weight Matirx (PWM) and Information Content Matrix (ICM). It can also scan putative TFBS from sequence/alignment, query JASPAR database and provides a wrapper of de novo motif discovery software.

r-tfmpvalue

Homepage:
Spack package:
Versions:
0.0.8, 0.0.6
Build Dependencies:
r, r-rcpp
Link Dependencies:
r
Run Dependencies:
r, r-rcpp
Description:
In putative Transcription Factor Binding Sites (TFBSs) identification from sequence/alignments, we are interested in the significance of certain match score. TFMPvalue provides the accurate calculation of P-value with score threshold for Position Weight Matrices, or the score with given P-value. This package is an interface to code originally made available by Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15.

r-th-data

Homepage:
Spack package:
Versions:
1.0-10, 1.0-9, 1.0-8, 1.0-7
Build Dependencies:
r, r-survival, r-mass
Link Dependencies:
r
Run Dependencies:
r, r-survival, r-mass
Description:
Contains data sets used in other packages Torsten Hothorn maintains.

r-threejs

Homepage:
Spack package:
Versions:
0.3.1, 0.2.2
Build Dependencies:
r, r-htmlwidgets, r-base64enc, r-matrix, r-jsonlite, r-igraph, r-crosstalk
Link Dependencies:
r
Run Dependencies:
r, r-htmlwidgets, r-base64enc, r-matrix, r-jsonlite, r-igraph, r-crosstalk
Description:
Create interactive 3D scatter plots, network plots, and globes using the 'three.js' visualization library ("http://threejs.org").

r-tibble

Homepage:
Spack package:
Versions:
2.1.3, 2.0.1, 2.0.0, 1.4.2, 1.4.1, 1.3.4, 1.2, 1.1
Build Dependencies:
r, r-assertthat, r-lazyeval, r-rcpp, r-rlang, r-cli, r-crayon, r-pillar, r-pkgconfig, r-fansi
Link Dependencies:
r
Run Dependencies:
r, r-assertthat, r-lazyeval, r-rcpp, r-rlang, r-cli, r-crayon, r-pillar, r-pkgconfig, r-fansi
Description:
Provides a 'tbl_df' class that offers better checking and printing capabilities than traditional data frames.

r-tidycensus

Homepage:
Spack package:
Versions:
0.9.2, 0.3.1
Build Dependencies:
r, r-httr, r-sf, r-dplyr, r-tigris, r-stringr, r-jsonlite, r-purrr, r-rvest, r-tidyr, r-rappdirs, r-readr, r-xml2, r-units
Link Dependencies:
r
Run Dependencies:
r, r-httr, r-sf, r-dplyr, r-tigris, r-stringr, r-jsonlite, r-purrr, r-rvest, r-tidyr, r-rappdirs, r-readr, r-xml2, r-units
Description:
An integrated R interface to the decennial US Census and American Community Survey APIs and the US Census Bureau's geographic boundary files. Allows R users to return Census and ACS data as tidyverse-ready data frames, and optionally returns a list-column with feature geometry for many geographies.

r-tidygraph

Homepage:
Spack package:
Versions:
1.1.2
Build Dependencies:
r, r-tibble, r-dplyr, r-igraph, r-magrittr, r-rlang, r-r6, r-rcpp, r-tidyr, r-pillar
Link Dependencies:
r
Run Dependencies:
r, r-tibble, r-dplyr, r-igraph, r-magrittr, r-rlang, r-r6, r-rcpp, r-tidyr, r-pillar
Description:
tidygraph: A Tidy API for Graph Manipulation. A graph, while not "tidy" in itself, can be thought of as two tidy data frames describing node and edge data respectively. 'tidygraph' provides an approach to manipulate these two virtual data frames using the API defined in the 'dplyr' package, as well as provides tidy interfaces to a lot of common graph algorithms.

r-tidyr

Homepage:
Spack package:
Versions:
0.8.3, 0.8.2, 0.7.2, 0.5.1
Build Dependencies:
r, r-tibble, r-dplyr, r-stringi, r-magrittr, r-glue, r-rcpp, r-purrr, r-tidyselect, r-rlang
Link Dependencies:
r
Run Dependencies:
r, r-tibble, r-dplyr, r-stringi, r-magrittr, r-glue, r-rcpp, r-purrr, r-tidyselect, r-rlang
Description:
An evolution of 'reshape2'. It's designed specifically for data tidying (not general reshaping or aggregating) and works well with 'dplyr' data pipelines.

r-tidyselect

Homepage:
Spack package:
Versions:
0.2.5, 0.2.4, 0.2.3
Build Dependencies:
r, r-glue, r-purrr, r-rlang, r-rcpp
Link Dependencies:
r
Run Dependencies:
r, r-glue, r-purrr, r-rlang, r-rcpp
Description:
A backend for the selecting functions of the 'tidyverse'. It makes it easy to implement select-like functions in your own packages in a way that is consistent with other 'tidyverse' interfaces for selection.

r-tidyverse

Homepage:
Spack package:
Versions:
1.2.1
Build Dependencies:
r, r-broom, r-cli, r-crayon, r-dplyr, r-dbplyr, r-forcats, r-ggplot2, r-haven, r-hms, r-httr, r-jsonlite, r-lubridate, r-magrittr, r-modelr, r-purrr, r-readr, r-readxl, r-reprex, r-rlang, r-rstudioapi, r-rvest, r-stringr, r-tibble, r-tidyr, r-xml2
Link Dependencies:
r
Run Dependencies:
r, r-broom, r-cli, r-crayon, r-dplyr, r-dbplyr, r-forcats, r-ggplot2, r-haven, r-hms, r-httr, r-jsonlite, r-lubridate, r-magrittr, r-modelr, r-purrr, r-readr, r-readxl, r-reprex, r-rlang, r-rstudioapi, r-rvest, r-stringr, r-tibble, r-tidyr, r-xml2
Description:
The 'tidyverse' is a set of packages that work in harmony because they share common data representations and 'API' design. This package is designed to make it easy to install and load multiple 'tidyverse' packages in a single step.

r-tiff

Homepage:
Spack package:
Versions:
0.1-5
Build Dependencies:
r, jpeg, libtiff
Link Dependencies:
r, jpeg, libtiff
Run Dependencies:
r
Description:
This package provides an easy and simple way to read, write and display bitmap images stored in the TIFF format. It can read and write both files and in-memory raw vectors.

r-tigris

Homepage:
Spack package:
Versions:
0.8.2, 0.5.3
Build Dependencies:
r, r-stringr, r-magrittr, r-rgdal, r-rgeos, r-sp, r-rappdirs, r-maptools, r-httr, r-uuid, r-sf, r-dplyr
Link Dependencies:
r
Run Dependencies:
r, r-stringr, r-magrittr, r-rgdal, r-rgeos, r-sp, r-rappdirs, r-maptools, r-httr, r-uuid, r-sf, r-dplyr
Description:
Download TIGER/Line shapefiles from the United States Census Bureau and load into R as 'SpatialDataFrame' or 'sf' objects.

r-timedate

Homepage:
Spack package:
Versions:
3043.102, 3042.101, 3012.100
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Environment for teaching "Financial Engineering and Computational Finance". Managing chronological and calendar objects.

r-tinytex

Homepage:
Spack package:
Versions:
0.15
Build Dependencies:
r, r-xfun
Link Dependencies:
r
Run Dependencies:
r, r-xfun
Description:
Helper functions to install and maintain the 'LaTeX' distribution named 'TinyTeX' (<https://yihui.name/tinytex/>), a lightweight, cross- platform, portable, and easy-to-maintain version of 'TeX Live'. This package also contains helper functions to compile 'LaTeX' documents, and install missing 'LaTeX' packages automatically.

r-tmixclust

Homepage:
Spack package:
Versions:
1.6.0, 1.4.0, 1.2.0, 1.0.1
Build Dependencies:
r, r-gss, r-mvtnorm, r-zoo, r-cluster, r-biocparallel, r-flexclust, r-biobase, r-spem
Link Dependencies:
r
Run Dependencies:
r, r-gss, r-mvtnorm, r-zoo, r-cluster, r-biocparallel, r-flexclust, r-biobase, r-spem
Description:
Time Series Clustering of Gene Expression with Gaussian Mixed-Effects Models and Smoothing Splines. Implementation of a clustering method for time series gene expression data based on mixed-effects models with Gaussian variables and non- parametric cubic splines estimation. The method can robustly account for the high levels of noise present in typical gene expression time series datasets.

r-topgo

Homepage:
Spack package:
Versions:
2.36.0, 2.34.0, 2.32.0, 2.30.1, 2.28.0
Build Dependencies:
r, r-biocgenerics, r-graph, r-biobase, r-go-db, r-annotationdbi, r-sparsem, r-lattice, r-matrixstats, r-dbi
Link Dependencies:
r
Run Dependencies:
r, r-biocgenerics, r-graph, r-biobase, r-go-db, r-annotationdbi, r-sparsem, r-lattice, r-matrixstats, r-dbi
Description:
Enrichment Analysis for Gene Ontology. topGO package provides tools for testing GO terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be implemented and applied.

r-triebeard

Homepage:
Spack package:
Versions:
0.3.0
Build Dependencies:
r, r-rcpp
Link Dependencies:
r
Run Dependencies:
r, r-rcpp
Description:
triebeard: 'Radix' Trees in 'Rcpp'

r-trimcluster

Homepage:
Spack package:
Versions:
0.1-2.1, 0.1-2
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
trimcluster: Cluster analysis with trimming

r-truncdist

Homepage:
Spack package:
Versions:
1.0-2
Build Dependencies:
r, r-evd
Link Dependencies:
r
Run Dependencies:
r, r-evd
Description:
truncdist: Truncated Random Variables

r-truncnorm

Homepage:
Spack package:
Versions:
1.0-8
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Density, probability, quantile and random number generation functions for the truncated normal distribution.

r-trust

Homepage:
Spack package:
Versions:
0.1-7
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Does local optimization using two derivatives and trust regions. Guaranteed to converge to local minimum of objective function.

r-tseries

Homepage:
Spack package:
Versions:
0.10-47, 0.10-46, 0.10-42
Build Dependencies:
r, r-quadprog, r-zoo, r-quantmod
Link Dependencies:
r
Run Dependencies:
r, r-quadprog, r-zoo, r-quantmod
Description:
Time series analysis and computational finance.

r-tsne

Homepage:
Spack package:
Versions:
0.1-3, 0.1-2, 0.1-1
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
A "pure R" implementation of the t-SNE algorithm.

r-ttr

Homepage:
Spack package:
Versions:
0.23-4, 0.23-3, 0.23-1
Build Dependencies:
r, r-xts, r-zoo, r-curl
Link Dependencies:
r
Run Dependencies:
r, r-xts, r-zoo, r-curl
Description:
Functions and data to construct technical trading rules with R.

r-tweenr

Homepage:
Spack package:
Versions:
1.0.1
Build Dependencies:
r, r-farver, r-magrittr, r-rcpp, r-rlang
Link Dependencies:
r
Run Dependencies:
r, r-farver, r-magrittr, r-rcpp, r-rlang
Description:
tweenr: Interpolate Data for Smooth Animations

r-txdb-hsapiens-ucsc-hg18-knowngene

Homepage:
Spack package:
Versions:
3.2.2
Build Dependencies:
r, r-genomicfeatures, r-annotationdbi
Link Dependencies:
r
Run Dependencies:
r, r-genomicfeatures, r-annotationdbi
Description:
Exposes an annotation databases generated from UCSC by exposing these as TxDb objects

r-txdb-hsapiens-ucsc-hg19-knowngene

Homepage:
Spack package:
Versions:
3.2.2
Build Dependencies:
r, r-genomicfeatures, r-annotationdbi
Link Dependencies:
r
Run Dependencies:
r, r-genomicfeatures, r-annotationdbi
Description:
Exposes an annotation databases generated from UCSC by exposing these as TxDb objects.

r-tximport

Homepage:
Spack package:
Versions:
1.12.3, 1.10.1, 1.8.0, 1.6.0, 1.4.0
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Import and summarize transcript-level estimates for transcript- and gene-level analysis. Imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level analysis packages. Average transcript length, weighted by sample- specific transcript abundance estimates, is provided as a matrix which can be used as an offset for different expression of gene-level counts.

r-ucminf

Homepage:
Spack package:
Versions:
1.1-4
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
An algorithm for general-purpose unconstrained non-linear optimization. The algorithm is of quasi-Newton type with BFGS updating of the inverse Hessian and soft line search with a trust region type monitoring of the input to the line search algorithm. The interface of 'ucminf' is designed for easy interchange with 'optim'.

r-udunits2

Homepage:
Spack package:
Versions:
0.13
Build Dependencies:
r, udunits
Link Dependencies:
r, udunits
Run Dependencies:
r
Description:
Provides simple bindings to Unidata's udunits library.

r-units

Homepage:
Spack package:
Versions:
0.6-3, 0.6-2, 0.4-6
Build Dependencies:
r, r-udunits2, r-rcpp, udunits
Link Dependencies:
r, udunits
Run Dependencies:
r, r-udunits2, r-rcpp
Description:
Support for measurement units in R vectors, matrices and arrays: automatic propagation, conversion, derivation and simplification of units; raising errors in case of unit incompatibility. Compatible with the POSIXct, Date and difftime classes. Uses the UNIDATA udunits library and unit database for unit compatibility checking and conversion.

r-upsetr

Homepage:
Spack package:
Versions:
1.4.0
Build Dependencies:
r, r-ggplot2, r-gridextra, r-plyr, r-scales
Link Dependencies:
r
Run Dependencies:
r, r-ggplot2, r-gridextra, r-plyr, r-scales
Description:
UpSetR: A More Scalable Alternative to Venn and Euler Diagrams forVisualizing Intersecting Sets

r-urca

Homepage:
Spack package:
Versions:
1.3-0
Build Dependencies:
r, r-nlme
Link Dependencies:
r
Run Dependencies:
r, r-nlme
Description:
Unit root and cointegration tests encountered in applied econometric analysis are implemented.

r-urltools

Homepage:
Spack package:
Versions:
1.7.3
Build Dependencies:
r, r-rcpp, r-triebeard
Link Dependencies:
r
Run Dependencies:
r, r-rcpp, r-triebeard
Description:
urltools: Vectorised Tools for URL Handling and Parsing

r-usethis

Homepage:
Spack package:
Versions:
1.5.1
Build Dependencies:
r, r-clipr, r-clisymbols, r-crayon, r-curl, r-desc, r-fs, r-gh, r-git2r, r-glue, r-purrr, r-rlang, r-rprojroot, r-rstudioapi, r-whisker, r-withr, r-yaml
Link Dependencies:
r
Run Dependencies:
r, r-clipr, r-clisymbols, r-crayon, r-curl, r-desc, r-fs, r-gh, r-git2r, r-glue, r-purrr, r-rlang, r-rprojroot, r-rstudioapi, r-whisker, r-withr, r-yaml
Description:
Automate package and project setup tasks that are otherwise performed manually. This includes setting up unit testing, test coverage, continuous integration, Git, 'GitHub', licenses, 'Rcpp', 'RStudio' projects, and more.

r-utf8

Homepage:
Spack package:
Versions:
1.1.4, 1.1.3, 1.1.2, 1.1.1, 1.1.0, 1.0.0
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Process and print 'UTF-8' encoded international text (Unicode). Input, validate, normalize, encode, format, and display.

r-uuid

Homepage:
Spack package:
Versions:
0.1-2
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Tools for generating and handling of UUIDs (Universally Unique Identifiers).

r-uwot

Homepage:
Spack package:
Versions:
0.1.3
Build Dependencies:
r, r-matrix, r-rcpp, r-fnn, r-rspectra, r-rcppannoy, r-rcppparallel, r-irlba, r-rcppprogress, r-dqrng, gmake
Link Dependencies:
r
Run Dependencies:
r, r-matrix, r-rcpp, r-fnn, r-rspectra, r-rcppannoy, r-rcppparallel, r-irlba, r-rcppprogress, r-dqrng
Description:
An implementation of the Uniform Manifold Approximation and Projection dimensionality reduction by McInnes et al. (2018) <arXiv:1802.03426>. It also provides means to transform new data and to carry out supervised dimensionality reduction. An implementation of the related LargeVis method of Tang et al. (2016) <arXiv:1602.00370> is also provided. This is a complete re-implementation in R (and C++, via the 'Rcpp' package): no Python installation is required. See the uwot website (<https://github.com/jlmelville/uwot>) for more documentation and examples.

r-variantannotation

Homepage:
Spack package:
Versions:
1.30.1, 1.28.13, 1.26.1, 1.24.5, 1.22.3
Build Dependencies:
r, r-biocgenerics, r-genomeinfodb, r-genomicranges, r-summarizedexperiment, r-rsamtools, r-dbi, r-zlibbioc, r-biobase, r-s4vectors, r-iranges, r-xvector, r-biostrings, r-annotationdbi, r-bsgenome, r-rtracklayer, r-genomicfeatures, r-rhtslib, gmake
Link Dependencies:
r
Run Dependencies:
r, r-biocgenerics, r-genomeinfodb, r-genomicranges, r-summarizedexperiment, r-rsamtools, r-dbi, r-zlibbioc, r-biobase, r-s4vectors, r-iranges, r-xvector, r-biostrings, r-annotationdbi, r-bsgenome, r-rtracklayer, r-genomicfeatures, r-rhtslib
Description:
Annotation of Genetic Variants. Annotate variants, compute amino acid coding changes, predict coding outcomes.

r-varselrf

Homepage:
Spack package:
Versions:
0.7-8
Build Dependencies:
r, r-randomforest
Link Dependencies:
r
Run Dependencies:
r, r-randomforest
Description:
Variable selection from random forests using both backwards variable elimination (for the selection of small sets of non-redundant variables) and selection based on the importance spectrum (somewhat similar to scree plots; for the selection of large, potentially highly-correlated variables) . Main applications in high-dimensional data (e.g., microarray data, and other genomics and proteomics applications).

r-vcd

Homepage:
Spack package:
Versions:
1.4-4, 1.4-3, 1.4-1
Build Dependencies:
r, r-mass, r-colorspace, r-lmtest
Link Dependencies:
r
Run Dependencies:
r, r-mass, r-colorspace, r-lmtest
Description:
Visualization techniques, data sets, summary and inference procedures aimed particularly at categorical data. Special emphasis is given to highly extensible grid graphics. The package was package was originally inspired by the book "Visualizing Categorical Data" by Michael Friendly and is now the main support package for a new book, "Discrete Data Analysis with R" by Michael Friendly and David Meyer (2015).

r-vctrs

Homepage:
Spack package:
Versions:
0.2.0
Build Dependencies:
r, r-backports, r-ellipsis, r-digest, r-glue, r-rlang, r-zeallot
Link Dependencies:
r
Run Dependencies:
r, r-backports, r-ellipsis, r-digest, r-glue, r-rlang, r-zeallot
Description:
Defines new notions of prototype and size that are used to provide tools for consistent and well-founded type-coercion and size-recycling, and are in turn connected to ideas of type- and size-stability useful for analyzing function interfaces.

r-vegan

Homepage:
Spack package:
Versions:
2.5-5, 2.5-4, 2.4-3
Build Dependencies:
r, r-permute, r-lattice, r-mass, r-cluster, r-mgcv
Link Dependencies:
r
Run Dependencies:
r, r-permute, r-lattice, r-mass, r-cluster, r-mgcv
Description:
Ordination methods, diversity analysis and other functions for community and vegetation ecologists.

r-vfs

Homepage:
Spack package:
Versions:
1.0.2
Build Dependencies:
r, r-e1071, r-nleqslv
Link Dependencies:
r
Run Dependencies:
r, r-e1071, r-nleqslv
Description:
VFS: Vegetated Filter Strip and Erosion Model

r-vgam

Homepage:
Spack package:
Versions:
1.1-1, 1.0-6, 1.0-4, 1.0-3, 1.0-2, 1.0-1, 1.0-0
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
An implementation of about 6 major classes of statistical regression models.

r-vioplot

Homepage:
Spack package:
Versions:
0.3.2
Build Dependencies:
r, r-sm, r-zoo
Link Dependencies:
r
Run Dependencies:
r, r-sm, r-zoo
Description:
vioplot: Violin Plot

r-vipor

Homepage:
Spack package:
Versions:
0.4.5, 0.4.4
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Plot Categorical Data Using Quasirandom Noise and Density Estimates

r-viridis

Homepage:
Spack package:
Versions:
0.5.1, 0.5.0, 0.4.0
Build Dependencies:
r, r-viridislite, r-ggplot2, r-gridextra
Link Dependencies:
r
Run Dependencies:
r, r-viridislite, r-ggplot2, r-gridextra
Description:
viridis: Default Color Maps from 'matplotlib'

r-viridislite

Homepage:
Spack package:
Versions:
0.3.0, 0.2.0
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
viridisLite: Default Color Maps from 'matplotlib' (Lite Version)

r-visnetwork

Homepage:
Spack package:
Versions:
2.0.7, 2.0.6, 1.0.1
Build Dependencies:
r, r-htmlwidgets, r-htmltools, r-jsonlite, r-magrittr
Link Dependencies:
r
Run Dependencies:
r, r-htmlwidgets, r-htmltools, r-jsonlite, r-magrittr
Description:
Provides an R interface to the 'vis.js' JavaScript charting library. It allows an interactive visualization of networks.

r-vsn

Homepage:
Spack package:
Versions:
3.52.0, 3.50.0, 3.48.1, 3.46.0, 3.44.0
Build Dependencies:
r, r-biobase, r-affy, r-limma, r-lattice, r-ggplot2, r-hexbin
Link Dependencies:
r
Run Dependencies:
r, r-biobase, r-affy, r-limma, r-lattice, r-ggplot2, r-hexbin
Description:
Variance stabilization and calibration for microarray data. The package implements a method for normalising microarray intensities, and works for single- and multiple-color arrays. It can also be used for data from other technologies, as long as they have similar format. The method uses a robust variant of the maximum-likelihood estimator for an additive- multiplicative error model and affine calibration. The model incorporates data calibration step (a.k.a. normalization), a model for the dependence of the variance on the mean intensity and a variance stabilizing data transformation. Differences between transformed intensities are analogous to "normalized log-ratios". However, in contrast to the latter, their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription.

r-watermelon

Homepage:
Spack package:
Versions:
1.30.0
Build Dependencies:
r, r-biobase, r-limma, r-matrixstats, r-methylumi, r-lumi, r-roc, r-illuminahumanmethylation450kanno-ilmn12-hg19, r-illuminaio
Link Dependencies:
r
Run Dependencies:
r, r-biobase, r-limma, r-matrixstats, r-methylumi, r-lumi, r-roc, r-illuminahumanmethylation450kanno-ilmn12-hg19, r-illuminaio
Description:
Illumina 450 methylation array normalization and metrics.

r-webshot

Homepage:
Spack package:
Versions:
0.5.1
Build Dependencies:
r, r-magrittr, r-jsonlite, r-callr
Link Dependencies:
r
Run Dependencies:
r, r-magrittr, r-jsonlite, r-callr
Description:
webshot: Take Screenshots of Web Pages

r-wgcna

Homepage:
Spack package:
Versions:
1.68, 1.67, 1.64-1
Build Dependencies:
r, r-dynamictreecut, r-fastcluster, r-matrixstats, r-hmisc, r-impute, r-foreach, r-doparallel, r-preprocesscore, r-survival, r-go-db, r-annotationdbi, r-rcpp, r-robust
Link Dependencies:
r
Run Dependencies:
r, r-dynamictreecut, r-fastcluster, r-matrixstats, r-hmisc, r-impute, r-foreach, r-doparallel, r-preprocesscore, r-survival, r-go-db, r-annotationdbi, r-rcpp, r-robust
Description:
WGCNA: Weighted Correlation Network Analysis

r-whisker

Homepage:
Spack package:
Versions:
0.3-2
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
logicless templating, reuse templates in many programming languages including R

r-withr

Homepage:
Spack package:
Versions:
2.1.2, 1.0.2, 1.0.1
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
A set of functions to run code 'with' safely and temporarily modified global state. Many of these functions were originally a part of the 'devtools' package, this provides a simple package with limited dependencies to provide access to these functions.

r-xde

Homepage:
Spack package:
Versions:
2.30.0, 2.28.0, 2.26.0, 2.24.0, 2.22.0
Build Dependencies:
r, r-biobase, r-biocgenerics, r-genefilter, r-gtools, r-mergemaid, r-mvtnorm, r-rcolorbrewer, r-genemeta, r-siggenes
Link Dependencies:
r
Run Dependencies:
r, r-biobase, r-biocgenerics, r-genefilter, r-gtools, r-mergemaid, r-mvtnorm, r-rcolorbrewer, r-genemeta, r-siggenes
Description:
XDE: a Bayesian hierarchical model for cross-study analysis of differential gene expression.

r-xfun

Homepage:
Spack package:
Versions:
0.8
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Miscellaneous functions commonly used in other packages maintained by 'Yihui Xie'.

r-xgboost

Homepage:
Spack package:
Versions:
0.90.0.2, 0.81.0.1, 0.6-4, 0.4-4
Build Dependencies:
r, r-matrix, r-data-table, r-magrittr, r-stringi, r-stringr
Link Dependencies:
r
Run Dependencies:
r, r-matrix, r-data-table, r-magrittr, r-stringi, r-stringr
Description:
Extreme Gradient Boosting, which is an efficient implementation of gradient boosting framework. This package is its R interface. The package includes efficient linear model solver and tree learning algorithms. The package can automatically do parallel computation on a single machine which could be more than 10 times faster than existing gradient boosting packages. It supports various objective functions, including regression, classification and ranking. The package is made to be extensible, so that users are also allowed to define their own objectives easily.

r-xlconnect

Homepage:
Spack package:
Versions:
0.2-15, 0.2-14, 0.2-12, 0.2-11
Build Dependencies:
r, r-xlconnectjars, r-rjava, java
Link Dependencies:
r, java
Run Dependencies:
r, r-xlconnectjars, r-rjava
Description:
Provides comprehensive functionality to read, write and format Excel data.

r-xlconnectjars

Homepage:
Spack package:
Versions:
0.2-15, 0.2-14, 0.2-12, 0.2-9
Build Dependencies:
r, r-rjava, java
Link Dependencies:
r, java
Run Dependencies:
r, r-rjava
Description:
Provides external JAR dependencies for the XLConnect package.

r-xlsx

Homepage:
Spack package:
Versions:
0.6.1
Build Dependencies:
r, r-rjava, r-xlsxjars, java
Link Dependencies:
r, java
Run Dependencies:
r, r-rjava, r-xlsxjars
Description:
Provide R functions to read/write/format Excel 2007 and Excel 97/2000/XP/2003 file formats.

r-xlsxjars

Homepage:
Spack package:
Versions:
0.6.1
Build Dependencies:
r, r-rjava
Link Dependencies:
r
Run Dependencies:
r, r-rjava
Description:
The xlsxjars package collects all the external jars required for the xlxs package. This release corresponds to POI 3.10.1.

r-xmapbridge

Homepage:
Spack package:
Versions:
1.42.0, 1.40.0, 1.38.0, 1.36.0, 1.34.0
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Export plotting files to the xmapBridge for visualisation in X:Map. xmapBridge can plot graphs in the X:Map genome browser. This package exports plotting files in a suitable format.

r-xml

Homepage:
Spack package:
Versions:
3.98-1.20, 3.98-1.19, 3.98-1.9, 3.98-1.5, 3.98-1.4
Build Dependencies:
r, libxml2
Link Dependencies:
r, libxml2
Run Dependencies:
r
Description:
Many approaches for both reading and creating XML (and HTML) documents (including DTDs), both local and accessible via HTTP or FTP. Also offers access to an 'XPath' "interpreter".

r-xml2

Homepage:
Spack package:
Versions:
1.2.2, 1.2.1, 1.1.1
Build Dependencies:
r, r-rcpp, r-bh, libxml2
Link Dependencies:
r, libxml2
Run Dependencies:
r, r-rcpp, r-bh
Description:
Work with XML files using a simple, consistent interface. Built on top of the 'libxml2' C library.

r-xnomial

Homepage:
Spack package:
Versions:
1.0.4
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
XNomial: Exact Goodness-of-Fit Test for Multinomial Data with Fixed Probabilities

r-xopen

Homepage:
Spack package:
Versions:
1.0.0
Build Dependencies:
r, r-processx
Link Dependencies:
r
Run Dependencies:
r, r-processx
Description:
Cross platform solution to open files, directories or 'URLs' with their associated programs.

r-xtable

Homepage:
Spack package:
Versions:
1.8-4, 1.8-3, 1.8-2
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Coerce data to LaTeX and HTML tables.

r-xts

Homepage:
Spack package:
Versions:
0.11-2, 0.9-7
Build Dependencies:
r, r-zoo
Link Dependencies:
r
Run Dependencies:
r, r-zoo
Description:
Provide for uniform handling of R's different time-based data classes by extending zoo, maximizing native format information preservation and allowing for user level customization and extension, while simplifying cross-class interoperability.

r-xvector

Homepage:
Spack package:
Versions:
0.24.0, 0.22.0, 0.20.0, 0.18.0, 0.16.0
Build Dependencies:
r, r-biocgenerics, r-s4vectors, r-iranges, r-zlibbioc
Link Dependencies:
r
Run Dependencies:
r, r-biocgenerics, r-s4vectors, r-iranges, r-zlibbioc
Description:
Foundation of external vector representation and manipulation in Bioconductor. Provides memory efficient S4 classes for storing sequences "externally" (e.g. behind an R external pointer, or on disk).

r-yaml

Homepage:
Spack package:
Versions:
2.2.0, 2.1.19, 2.1.14, 2.1.13
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
This package implements the libyaml YAML 1.1 parser and emitter (http://pyyaml.org/wiki/LibYAML) for R.

r-yapsa

Homepage:
Spack package:
Versions:
1.10.0, 1.8.0, 1.6.0, 1.4.0, 1.2.0
Build Dependencies:
r, r-genomicranges, r-ggplot2, r-lsei, r-somaticsignatures, r-variantannotation, r-genomeinfodb, r-reshape2, r-gridextra, r-corrplot, r-dendextend, r-getoptlong, r-circlize, r-gtrellis, r-pmcmr, r-complexheatmap, r-keggrest
Link Dependencies:
r
Run Dependencies:
r, r-genomicranges, r-ggplot2, r-lsei, r-somaticsignatures, r-variantannotation, r-genomeinfodb, r-reshape2, r-gridextra, r-corrplot, r-dendextend, r-getoptlong, r-circlize, r-gtrellis, r-pmcmr, r-complexheatmap, r-keggrest
Description:
Yet Another Package for Signature Analysis. This package provides functions and routines useful in the analysis of somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular, functions to perform a signature analysis with known signatures (LCD = linear combination decomposition) and a signature analysis on stratified mutational catalogue (SMC = stratify mutational catalogue) are provided.

r-yaqcaffy

Homepage:
Spack package:
Versions:
1.44.0, 1.42.0, 1.40.0, 1.38.0, 1.36.0
Build Dependencies:
r, r-simpleaffy
Link Dependencies:
r
Run Dependencies:
r, r-simpleaffy
Description:
Affymetrix expression data quality control and reproducibility analysis. Quality control of Affymetrix GeneChip expression data and reproducibility analysis of human whole genome chips with the MAQC reference datasets.

r-yarn

Homepage:
Spack package:
Versions:
1.10.0, 1.8.1, 1.6.0, 1.4.0, 1.2.0
Build Dependencies:
r, r-biobase, r-biomart, r-downloader, r-edger, r-gplots, r-limma, r-matrixstats, r-preprocesscore, r-readr, r-rcolorbrewer, r-quantro
Link Dependencies:
r
Run Dependencies:
r, r-biobase, r-biomart, r-downloader, r-edger, r-gplots, r-limma, r-matrixstats, r-preprocesscore, r-readr, r-rcolorbrewer, r-quantro
Description:
YARN: Robust Multi-Condition RNA-Seq Preprocessing and Normalization. Expedite large RNA-Seq analyses using a combination of previously developed tools. YARN is meant to make it easier for the user in performing basic mis-annotation quality control, filtering, and condition-aware normalization. YARN leverages many Bioconductor tools and statistical techniques to account for the large heterogeneity and sparsity found in very large RNA-seq experiments.

r-zeallot

Homepage:
Spack package:
Versions:
0.1.0
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Provides a %<-% operator to perform multiple, unpacking, and destructuring assignment in R. The operator unpacks the right-hand side of an assignment into multiple values and assigns these values to variables on the left-hand side of the assignment.

r-zip

Homepage:
Spack package:
Versions:
2.0.3
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
Cross-Platform 'zip' Compression Library. A replacement for the 'zip' function, that does not require any additional external tools on any platform.

r-zlibbioc

Homepage:
Spack package:
Versions:
1.30.0, 1.28.0, 1.26.0, 1.24.0, 1.22.0
Build Dependencies:
r
Link Dependencies:
r
Run Dependencies:
r
Description:
An R packaged zlib-1.2.5. This package uses the source code of zlib-1.2.5 to create libraries for systems that do not have these available via other means (most Linux and Mac users should have system- level access to zlib, and no direct need for this package). See the vignette for instructions on use.

r-zoo

Homepage:
Spack package:
Versions:
1.8-6, 1.8-5, 1.7-14, 1.7-13
Build Dependencies:
r, r-lattice
Link Dependencies:
r
Run Dependencies:
r, r-lattice
Description:
An S3 class with methods for totally ordered indexed observations. It is particularly aimed at irregular time series of numeric vectors/matrices and factors. zoo's key design goals are independence of a particular index/date/time class and consistency with ts and base R by providing methods to extend standard generics.

r3d

Homepage:
Spack package:
Versions:
2019-04-24, 2018-12-19, 2018-01-07
Description:
Fast, robust polyhedral intersections, analytic integration, and conservative voxelization.

rabbitmq

Homepage:
Spack package:
Versions:
3.6.15
Description:
RabbitMQ is lightweight and easy to deploy on premises and in the cloud. It supports multiple messaging protocols. RabbitMQ can be deployed in distributed and federated configurations to meet high-scale, high-availability requirements.

racon

Homepage:
Spack package:
Versions:
1.4.3, 1.4.2, 1.4.0, 1.3.3, 1.3.2, 1.3.1, 1.3.0, 1.2.1
Build Dependencies:
cmake, python
Description:
Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads.

raft

Homepage:
Spack package:
Versions:
develop, 1.2.3
Build Dependencies:
cmake, mpi, hdf5, fftw, cuda
Link Dependencies:
mpi, hdf5, fftw, cuda
Description:
RAFT: Reconstruct Algorithms for Tomography. Toolbox under development at Brazilian Synchrotron Light Source.

ragel

Homepage:
Spack package:
Versions:
6.10
Build Dependencies:
colm
Description:
Ragel State Machine Compiler Ragel compiles executable finite state machines from regular languages. Ragel targets C, C++ and ASM. Ragel state machines can not only recognize byte sequences as regular expression machines do, but can also execute code at arbitrary points in the recognition of a regular language. Code embedding is done using inline operators that do not disrupt the regular language syntax.

raja

Homepage:
Spack package:
Versions:
develop, master, 0.11.0, 0.10.0, 0.9.0, 0.8.0, 0.7.0, 0.6.0, 0.5.3, 0.5.2, 0.5.1, 0.5.0, 0.4.1, 0.4.0
Build Dependencies:
cmake, cuda
Link Dependencies:
cuda
Description:
RAJA Parallel Framework.

randfold

Homepage:
Spack package:
Versions:
2.0.1
Build Dependencies:
squid
Link Dependencies:
squid
Description:
Minimum free energy of folding randomization test software

random123

Homepage:
Spack package:
Versions:
1.09
Description:
Random123 is a library of 'counter-based' random number generators (CBRNGs), in which the Nth random number can be obtained by applying a stateless mixing function to N instead of the conventional approach of using N iterations of a stateful transformation.

randrproto

Homepage:
Spack package:
Versions:
1.5.0
Build Dependencies:
pkgconfig, util-macros
Description:
X Resize and Rotate Extension (RandR). This extension defines a protocol for clients to dynamically change X screens, so as to resize, rotate and reflect the root window of a screen.

range-v3

Homepage:
Spack package:
Versions:
develop, 0.5.0, 0.4.0, 0.3.7, 0.3.6, 0.3.5, 0.3.0, 0.2.6, 0.2.5, 0.2.4, 0.2.3, 0.2.2, 0.2.1, 0.2.0
Build Dependencies:
cmake, doxygen, boost
Description:
Range v3 forms the basis of a proposal to add range support to the standard library (N4128: Ranges for the Standard Library). It also will be the reference implementation for an upcoming Technical Specification. These are the first steps toward turning ranges into an international standard.

rankstr

Homepage:
Spack package:
Versions:
master, 0.0.2
Build Dependencies:
cmake, mpi
Link Dependencies:
mpi
Description:
Assign one-to-one mapping of MPI ranks to strings

rapidjson

Homepage:
Spack package:
Versions:
1.1.0, 1.0.2, 1.0.1, 1.0.0
Build Dependencies:
cmake
Description:
A fast JSON parser/generator for C++ with both SAX/DOM style API

ravel

Homepage:
Spack package:
Versions:
1.0.0
Build Dependencies:
cmake, muster, otf, otf2, qt
Link Dependencies:
muster, otf, otf2, qt
Description:
Ravel is a parallel communication trace visualization tool that orders events according to logical time.

raxml

Homepage:
Spack package:
Versions:
8.2.11
Build Dependencies:
mpi
Link Dependencies:
mpi
Description:
RAxML (Randomized Axelerated Maximum Likelihood) is a program for sequential and parallel Maximum Likelihood based inference of large phylogenetic trees.

ray

Homepage:
Spack package:
Versions:
2.3.1
Build Dependencies:
cmake, mpi
Link Dependencies:
mpi
Description:
Parallel genome assemblies for parallel DNA sequencing

rclone

Homepage:
Spack package:
Versions:
1.51.0, 1.50.2, 1.50.1, 1.50.0, 1.49.5, 1.49.4, 1.43
Build Dependencies:
go
Description:
Rclone is a command line program to sync files and directories to and from various cloud storage providers

rdma-core

Homepage:
Spack package:
Versions:
20, 17.1, 13
Build Dependencies:
cmake, pkgconfig, libnl
Link Dependencies:
libnl
Description:
RDMA core userspace libraries and daemons

rdp-classifier

Homepage:
Spack package:
Versions:
2.12
Build Dependencies:
java
Run Dependencies:
java
Description:
The RDP Classifier is a naive Bayesian classifier that can rapidly and accurately provides taxonomic assignments from domain to genus, with confidence estimates for each assignment.

rdptools

Homepage:
Spack package:
Versions:
2.0.2
Build Dependencies:
java, ant, python
Link Dependencies:
java, ant, python
Description:
Collection of commonly used RDP Tools for easy building.

re2c

Homepage:
Spack package:
Versions:
1.2.1
Description:
re2c: a free and open-source lexer generator for C and C++

readfq

Homepage:
Spack package:
Versions:
2013.04.10
Description:
Readfq is a collection of routines for parsing the FASTA/FASTQ format. It seamlessly parses both FASTA and multi-line FASTQ with a simple interface.

readline

Homepage:
Spack package:
Versions:
8.0, 7.0, 6.3
Build Dependencies:
ncurses
Link Dependencies:
ncurses
Description:
The GNU Readline library provides a set of functions for use by applications that allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. The Readline library includes additional functions to maintain a list of previously-entered command lines, to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.

recon

Homepage:
Spack package:
Versions:
1.05
Run Dependencies:
perl
Description:
RECON: a package for automated de novo identification of repeat families from genomic sequences.

recordproto

Homepage:
Spack package:
Versions:
1.14.2
Build Dependencies:
pkgconfig, util-macros
Description:
X Record Extension. This extension defines a protocol for the recording and playback of user actions in the X Window System.

redis

Homepage:
Spack package:
Versions:
5.0.3, 5.0.2, 5.0.1, 5.0.0, 4.0.13, 4.0.12, 4.0.11
Description:
Redis is an open source (BSD licensed), in-memory data structure store, used as a database, cache and message broker. It supports data structures such as strings, hashes, lists, sets, sorted sets with range queries, bitmaps, hyperloglogs, geospatial indexes with radius queries and streams. Redis has built-in replication, Lua scripting, LRU eviction, transactions and different levels of on-disk persistence, and provides high availability via Redis Sentinel and automatic partitioning with Redis Cluster

redset

Homepage:
Spack package:
Versions:
master, 0.0.3
Build Dependencies:
cmake, mpi, rankstr, kvtree
Link Dependencies:
mpi, rankstr, kvtree
Description:
Create MPI communicators for disparate redundancy sets

redundans

Homepage:
Spack package:
Versions:
0.14a, 0.13c
Build Dependencies:
python, py-pyscaf, py-fastaindex, py-numpy, perl, sspace-standard, bwa, last, gapcloser, parallel, snap-berkeley
Link Dependencies:
sspace-standard, bwa, last, gapcloser, parallel
Run Dependencies:
python, py-pyscaf, py-fastaindex, py-numpy, perl, snap-berkeley
Description:
Redundans pipeline assists an assembly of heterozygous genomes.

reframe

Homepage:
Spack package:
Versions:
master, 2.21, 2.20, 2.17.3, 2.17.2, 2.17.1
Run Dependencies:
python
Description:
ReFrame is a framework for writing regression tests for HPC systems. The goal of this framework is to abstract away the complexity of the interactions with the system, separating the logic of a regression test from the low-level details, which pertain to the system configuration and setup. This allows users to write easily portable regression tests, focusing only on the functionality.

regcm

Homepage:
Spack package:
Versions:
4.7.0
Build Dependencies:
netcdf-c, netcdf-fortran, hdf5, mpi
Link Dependencies:
netcdf-c, netcdf-fortran, hdf5, mpi
Description:
RegCM, ICTP Regional Climate Model (https://ictp.it).

relax

Homepage:
Spack package:
Versions:
root6
Build Dependencies:
cmake, clhep, gsl, hepmc, root
Link Dependencies:
clhep, gsl, hepmc, root
Description:
A set of Reflex libraries for the most common used general data types in the LHC Computing Grid

relion

Homepage:
Spack package:
Versions:
master, 3.1_beta, 3.0.8, 3.0.7
Build Dependencies:
cuda, cmake, mpi, fftw, fltk, libtiff
Link Dependencies:
cuda, mpi, fftw, fltk, libtiff
Description:
RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computer program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM).

rempi

Homepage:
Spack package:
Versions:
1.1.0, 1.0.0
Build Dependencies:
mpi, zlib, autoconf, automake, libtool
Link Dependencies:
mpi, zlib
Description:
ReMPI is a record-and-replay tool for MPI applications.

rename

Homepage:
Spack package:
Versions:
1.600
Build Dependencies:
perl
Run Dependencies:
perl
Description:
Perl-powered file rename script with many helpful built-ins.

rendercheck

Homepage:
Spack package:
Versions:
1.5
Build Dependencies:
libxrender, libx11, xproto, pkgconfig, util-macros
Link Dependencies:
libxrender, libx11
Description:
rendercheck is a program to test a Render extension implementation against separate calculations of expected output.

renderproto

Homepage:
Spack package:
Versions:
0.11.1
Build Dependencies:
pkgconfig, util-macros
Description:
X Rendering Extension. This extension defines the protcol for a digital image composition as the foundation of a new rendering model within the X Window System.

repeatmasker

Homepage:
Spack package:
Versions:
4.0.9, 4.0.7
Build Dependencies:
perl, perl-text-soundex, hmmer, ncbi-rmblastn, trf, phrap-crossmatch-swat
Link Dependencies:
hmmer, ncbi-rmblastn, trf
Run Dependencies:
perl, perl-text-soundex, phrap-crossmatch-swat
Description:
RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.

repeatmodeler

Homepage:
Spack package:
Versions:
1.0.11
Build Dependencies:
perl, perl-json, perl-uri, perl-libwww-perl
Run Dependencies:
perl, perl-json, perl-uri, perl-libwww-perl, repeatmasker, recon, repeatscout, trf, nseg, ncbi-rmblastn
Description:
RepeatModeler is a de-novo repeat family identification and modeling package.

repeatscout

Homepage:
Spack package:
Versions:
1.0.5
Run Dependencies:
perl, trf, nseg
Description:
RepeatScout - De Novo Repeat Finder, Price A.L., Jones N.C. and Pevzner P.A.

resourceproto

Homepage:
Spack package:
Versions:
1.2.0
Build Dependencies:
pkgconfig, util-macros
Description:
X Resource Extension. This extension defines a protocol that allows a client to query the X server about its usage of various resources.

revbayes

Homepage:
Spack package:
Versions:
develop, 1.0.13, 1.0.12, 1.0.11, 1.0.10
Build Dependencies:
cmake, boost, mpi
Link Dependencies:
boost, mpi
Description:
Bayesian phylogenetic inference using probabilistic graphical models and an interpreted language.

rgb

Homepage:
Spack package:
Versions:
1.0.6
Build Dependencies:
xorg-server, xproto
Link Dependencies:
xorg-server
Description:
X color name database. This package includes both the list mapping X color names to RGB values (rgb.txt) and, if configured to use a database for color lookup, the rgb program to convert the text file into the binary database format. The "others" subdirectory contains some alternate color databases.

rhash

Homepage:
Spack package:
Versions:
1.3.5
Description:
RHash is a console utility for computing and verifying hash sums of files. It supports CRC32, MD4, MD5, SHA1, SHA256, SHA512, SHA3, Tiger, TTH, Torrent BTIH, AICH, ED2K, GOST R 34.11-94, RIPEMD-160, HAS-160, EDON-R 256/512, WHIRLPOOL and SNEFRU hash sums.

rlwrap

Homepage:
Spack package:
Versions:
0.43
Build Dependencies:
readline
Link Dependencies:
readline
Description:
rlwrap is a 'readline wrapper', a small utility that uses the GNU readline library to allow the editing of keyboard input for any command.

rmats

Homepage:
Spack package:
Versions:
4.0.2
Build Dependencies:
py-numpy, openblas
Link Dependencies:
openblas
Run Dependencies:
python, py-numpy
Description:
MATS is a computational tool to detect differential alternative splicing events from RNA-Seq data.

rmlab

Homepage:
Spack package:
Versions:
develop
Build Dependencies:
cmake, pngwriter
Link Dependencies:
pngwriter
Description:
C++ File API for the reMarkable tablet

rna-seqc

Homepage:
Spack package:
Versions:
1.1.8, 1.1.7, 1.1.6, 1.1.5, 1.1.4
Run Dependencies:
jdk
Description:
RNA-SeQC is a java program which computes a series of quality control metrics for RNA-seq data.

rnaz

Homepage:
Spack package:
Versions:
2.1
Description:
RNAz - predicting structural noncoding RNAs.

rngstreams

Homepage:
Spack package:
Versions:
1.0.1
Description:
Multiple independent streams of pseudo-random numbers.

rocketmq

Homepage:
Spack package:
Versions:
4.6.0, 4.5.2, 4.5.1, 4.5.0, 4.4.0, 4.3.2
Run Dependencies:
java
Description:
Apache RocketMQ is a distributed messaging and streaming platform with low latency, high performance and reliability, trillion-level capacity and flexible scalability.

rocksdb

Homepage:
Spack package:
Versions:
develop, 6.5.3, 5.18.3, 5.17.2, 5.16.6, 5.15.10
Build Dependencies:
bzip2, gflags, lz4, snappy, zlib, zstd, tbb
Link Dependencies:
bzip2, gflags, lz4, snappy, zlib, zstd, tbb
Description:
RocksDB: A Persistent Key-Value Store for Flash and RAM Storage

rockstar

Homepage:
Spack package:
Versions:
develop, yt
Build Dependencies:
hdf5
Link Dependencies:
hdf5
Description:
The Rockstar Halo Finder

rodinia

Homepage:
Spack package:
Versions:
3.1
Build Dependencies:
cuda, freeglut, glew, gl, glu
Link Dependencies:
cuda, freeglut, glew, gl, glu
Description:
Rodinia: Accelerating Compute-Intensive Applications with Accelerators

root

Homepage:
Spack package:
Versions:
master, 6.18.04, 6.18.02, 6.18.00, 6.16.00, 6.14.08, 6.14.06, 6.14.04, 6.14.02, 6.14.00, 6.12.06, 6.10.08, 6.08.06, 6.06.08, 6.06.06, 6.06.04, 6.06.02
Build Dependencies:
cmake, pkgconfig, blas, freetype, jpeg, libice, libpng, lz4, ncurses, pcre, xxhash, xz, zlib, libx11, libxext, libxft, libxpm, libsm, ftgl, glew, gl, glu, gl2ps, qt, py-numpy, davix, cfitsio, fftw, graphviz, gsl, jemalloc, mysql-client, openssl, postgresql, pythia6, pythia8, python, r, r-rcpp, r-rinside, shadow, sqlite, tbb, unuran, vc, vdt, libxml2, xrootd
Link Dependencies:
blas, freetype, jpeg, libice, libpng, lz4, ncurses, pcre, xxhash, xz, zlib, libx11, libxext, libxft, libxpm, libsm, ftgl, glew, gl, glu, gl2ps, qt, py-numpy, davix, cfitsio, fftw, graphviz, gsl, jemalloc, mysql-client, openssl, postgresql, pythia6, pythia8, shadow, sqlite, tbb, unuran, vc, vdt, libxml2, xrootd
Run Dependencies:
python, r, r-rcpp, r-rinside
Description:
ROOT is a data analysis framework.

rose

Homepage:
Spack package:
Versions:
develop, 0.9.13.0
Build Dependencies:
autoconf, automake, libtool, boost, mvapich2, libgcrypt, java, z3, git
Link Dependencies:
boost, mvapich2, java, z3, git
Run Dependencies:
py-binwalk
Description:
A compiler infrastructure to build source-to-source program transformation and analysis tools. (Developed at Lawrence Livermore National Lab)

ross

Homepage:
Spack package:
Versions:
develop, master, 7.2.0, 7.1.1, 7.1.0, 7.0.1, 7.0.0, 6.0.0
Build Dependencies:
cmake, mpi
Link Dependencies:
mpi
Description:
Rensselaer Optimistic Simulation System

routino

Homepage:
Spack package:
Versions:
3.2
Build Dependencies:
zlib, bzip2
Link Dependencies:
zlib, bzip2
Description:
Routino is an application for finding a route between two points using the dataset of topographical information collected by http://www.OpenStreetMap.org.

rpcsvc-proto

Homepage:
Spack package:
Versions:
1.4
Build Dependencies:
gettext
Link Dependencies:
gettext
Description:
rpcsvc protocol definitions from glibc.

rr

Homepage:
Spack package:
Versions:
4.5.0, 4.4.0, 4.3.0
Build Dependencies:
cmake, gdb, git, zlib, pkgconfig
Link Dependencies:
gdb, git, zlib
Test Dependencies:
py-pexpect
Description:
Application execution recorder, player and debugger

rsbench

Homepage:
Spack package:
Versions:
2, 0
Description:
A mini-app to represent the multipole resonance representation lookup cross section algorithm.

rsem

Homepage:
Spack package:
Versions:
1.3.1, 1.3.0
Build Dependencies:
r, perl, python, bowtie, bowtie2, star
Link Dependencies:
bowtie, bowtie2, star
Run Dependencies:
r, perl, python
Description:
RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data.

rstart

Homepage:
Spack package:
Versions:
1.0.5
Build Dependencies:
xproto, pkgconfig, util-macros
Description:
This package includes both the client and server sides implementing the protocol described in the "A Flexible Remote Execution Protocol Based on rsh" paper found in the specs/ subdirectory. This software has been deprecated in favor of the X11 forwarding provided in common ssh implementations.

rsync

Homepage:
Spack package:
Versions:
3.1.3, 3.1.2, 3.1.1
Build Dependencies:
zlib, popt
Link Dependencies:
zlib, popt
Description:
An open source utility that provides fast incremental file transfer.

rt-tests

Homepage:
Spack package:
Versions:
1.2
Description:
Suite of real-time tests - cyclictest, hwlatdetect, pip_stress, pi_stress, pmqtest, ptsematest, rt-migrate-test, sendme, signaltest, sigwaittest, svsematest.

rtags

Homepage:
Spack package:
Versions:
2.17
Build Dependencies:
cmake, llvm, zlib, openssl, lua, bash-completion, pkgconfig
Link Dependencies:
llvm, zlib, openssl, lua, bash-completion
Description:
RTags is a client/server application that indexes C/C++ code

rtax

Homepage:
Spack package:
Versions:
0.984
Build Dependencies:
usearch
Link Dependencies:
usearch
Description:
Rapid and accurate taxonomic classification of short paired-end sequence reads from the 16S ribosomal RNA gene

ruby

Homepage:
Spack package:
Versions:
2.6.2, 2.5.3, 2.2.0
Build Dependencies:
pkgconfig, libffi, zlib, libx11, tcl, tk, openssl, readline
Link Dependencies:
libffi, zlib, libx11, tcl, tk, openssl, readline
Description:
A dynamic, open source programming language with a focus on simplicity and productivity.

ruby-gnuplot

Homepage:
Spack package:
Versions:
2.6.2
Build Dependencies:
gnuplot, ruby
Link Dependencies:
gnuplot, ruby
Description:
Utility library to aid in interacting with gnuplot from ruby

ruby-narray

Homepage:
Spack package:
Versions:
0.9.0.9
Build Dependencies:
ruby
Link Dependencies:
ruby
Description:
Numo::NArray is an Numerical N-dimensional Array class for fast processing and easy manipulation of multi-dimensional numerical data, similar to numpy.ndaray.

ruby-ronn

Homepage:
Spack package:
Versions:
0.7.3, 0.7.0
Build Dependencies:
ruby
Link Dependencies:
ruby
Description:
Ronn builds manuals. It converts simple, human readable textfiles to roff for terminal display, and also to HTML for the web.

ruby-rubyinline

Homepage:
Spack package:
Versions:
3.12.4
Build Dependencies:
ruby
Link Dependencies:
ruby
Description:
Inline allows you to write foreign code within your ruby code.

ruby-svn2git

Homepage:
Spack package:
Versions:
2.4.0
Build Dependencies:
git, subversion, ruby
Link Dependencies:
git, subversion, ruby
Description:
svn2git is a tiny utility for migrating projects from Subversion to Git while keeping the trunk, branches and tags where they should be. It uses git-svn to clone an svn repository and does some clean-up to make sure branches and tags are imported in a meaningful way, and that the code checked into master ends up being what's currently in your svn trunk rather than whichever svn branch your last commit was in.

ruby-terminal-table

Homepage:
Spack package:
Versions:
1.8.0
Build Dependencies:
ruby
Link Dependencies:
ruby
Description:
Simple, feature rich ascii table generation library

rust

Homepage:
Spack package:
Versions:
develop, 1.41.0, 1.34.0, 1.32.0, 1.31.1, 1.31.0, 1.30.1
Build Dependencies:
llvm, curl, git, cmake, binutils, python, openssl
Link Dependencies:
llvm, curl, git, cmake, binutils, python, openssl
Description:
The rust programming language toolchain

rust-bindgen

Homepage:
Spack package:
Versions:
0.20.5
Build Dependencies:
rust, llvm
Link Dependencies:
rust, llvm
Description:
The rust programming language toolchain

sabre

Homepage:
Spack package:
Versions:
2013-09-27
Build Dependencies:
zlib
Link Dependencies:
zlib
Description:
Sabre is a tool that will demultiplex barcoded reads into separate files. It will work on both single-end and paired-end data in fastq format. It simply compares the provided barcodes with each read and separates the read into its appropriate barcode file, after stripping the barcode from the read (and also stripping the quality values of the barcode bases). If a read does not have a recognized barcode, then it is put into the unknown file.

saga-gis

Homepage:
Spack package:
Versions:
develop, 7.4.0, 7.3.0, 7.1.1, 7.1.0, 7.0.0, 6.4.0, 6.3.0, 6.2.0, 6.1.0, 6.0.0, 5.0.1, 5.0.0, 4.1.0, 4.0.0, 3.0.0, 2.3.1, 2.3.0, 2.3-lts
Build Dependencies:
autoconf, automake, libtool, m4, libharu, wxwidgets, postgresql, unixodbc, proj, opencv, libjpeg, hdf5, gdal, libgeotiff, swig, python
Link Dependencies:
libharu, wxwidgets, postgresql, unixodbc, proj, opencv, libjpeg, hdf5, gdal, libgeotiff, python
Description:
SAGA is a GIS for Automated Geoscientific Analyses and has been designed for an easy and effective implementation of spatial algorithms. It offers a comprehensive, growing set of geoscientific methods and provides an easily approachable user interface with many visualisation options

sailfish

Homepage:
Spack package:
Versions:
0.10.1
Build Dependencies:
cmake, boost, tbb
Link Dependencies:
boost, tbb
Description:
Sailfish is a tool for transcript quantification from RNA-seq data.

salmon

Homepage:
Spack package:
Versions:
0.14.1, 0.12.0, 0.9.1, 0.8.2
Build Dependencies:
cmake, tbb, boost, curl
Link Dependencies:
tbb, boost, curl
Description:
Salmon is a tool for quantifying the expression of transcripts using RNA-seq data.

sambamba

Homepage:
Spack package:
Versions:
0.6.6
Build Dependencies:
ldc, python
Link Dependencies:
ldc
Description:
Sambamba: process your BAM data faster (bioinformatics)

samblaster

Homepage:
Spack package:
Versions:
0.1.24, 0.1.23
Description:
A tool to mark duplicates and extract discordant and split reads from sam files.

samrai

Homepage:
Spack package:
Versions:
3.12.0, 3.11.5, 3.11.4, 3.11.2, 3.11.1, 3.10.0, 3.9.1, 3.8.0, 3.7.3, 3.7.2, 3.6.3-beta, 3.5.2-beta, 3.5.0-beta, 3.4.1-beta, 3.3.3-beta, 3.3.2-beta, 2.4.4
Build Dependencies:
mpi, zlib, hdf5, m4, boost, silo
Link Dependencies:
mpi, zlib, hdf5, silo
Description:
SAMRAI (Structured Adaptive Mesh Refinement Application Infrastructure) is an object-oriented C++ software library enables exploration of numerical, algorithmic, parallel computing, and software issues associated with applying structured adaptive mesh refinement (SAMR) technology in large-scale parallel application development.

samtools

Homepage:
Spack package:
Versions:
1.10, 1.9, 1.8, 1.7, 1.6, 1.5, 1.4, 1.3.1, 1.2
Build Dependencies:
zlib, ncurses, htslib
Link Dependencies:
zlib, ncurses, htslib
Run Dependencies:
perl, python
Description:
SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format

sandbox

Homepage:
Spack package:
Versions:
2.12
Description:
sandbox'd LD_PRELOAD hack by Gentoo Linux

sas

Homepage:
Spack package:
Versions:
0.2.0, 0.1.4, 0.1.3
Build Dependencies:
cmake, python, llvm
Link Dependencies:
python, llvm
Description:
SAS (Static Analysis Suite) is a powerful tool for running static analysis on C++ code.

satsuma2

Homepage:
Spack package:
Versions:
2016-11-22
Build Dependencies:
cmake
Description:
Satsuma2 is an optimsed version of Satsuma, a tool to reliably align large and complex DNA sequences providing maximum sensitivity (to find all there is to find), specificity (to only find real homology) and speed (to accomodate the billions of base pairs in vertebrate genomes).

savanna

Homepage:
Spack package:
Versions:
develop, 0.5
Build Dependencies:
mpi, stc, adios, mpix-launch-swift, tau
Link Dependencies:
mpi, stc, adios, mpix-launch-swift, tau
Description:
CODARcode Savanna runtime framework for high performance, workflow management using Swift/T and ADIOS.

saws

Homepage:
Spack package:
Versions:
develop, 0.1.0
Description:
The Scientific Application Web server (SAWs) turns any C or C++ scientific or engineering application code into a webserver, allowing one to examine (and even modify) the state of the simulation with any browser from anywhere.

sbt

Homepage:
Spack package:
Versions:
1.1.6, 1.1.5, 1.1.4, 0.13.17
Build Dependencies:
java
Link Dependencies:
java
Description:
Scala Build Tool

scala

Homepage:
Spack package:
Versions:
2.13.1, 2.12.10, 2.12.5, 2.12.1, 2.11.11, 2.10.6
Build Dependencies:
java
Link Dependencies:
java
Description:
Scala is a general-purpose programming language providing support for functional programming and a strong static type system. Designed to be concise, many of Scala's design decisions were designed to build from criticisms of Java.

scalasca

Homepage:
Spack package:
Versions:
2.5, 2.4, 2.3.1, 2.2.2, 2.1
Build Dependencies:
mpi, cubew, otf2, cube
Link Dependencies:
mpi, cubew, otf2, cube
Description:
Scalasca is a software tool that supports the performance optimization of parallel programs by measuring and analyzing their runtime behavior. The analysis identifies potential performance bottlenecks - in particular those concerning communication and synchronization - and offers guidance in exploring their causes.

scallop

Homepage:
Spack package:
Versions:
0.10.3
Build Dependencies:
clp, boost, htslib
Link Dependencies:
clp, boost, htslib
Description:
Scallop is a reference-based transcriptome assembler for RNA-seq

scalpel

Homepage:
Spack package:
Versions:
0.5.4, 0.5.3
Build Dependencies:
perl
Link Dependencies:
perl
Description:
Scalpel is a software package for detecting INDELs (INsertions and DELetions) mutations in a reference genome which has been sequenced with next-generation sequencing technology.

scan-for-matches

Homepage:
Spack package:
Versions:
2010-7-16
Description:
scan_for_matches is a utility written in C for locating patterns in DNA or protein FASTA files.

scons

Homepage:
Spack package:
Versions:
3.1.2, 3.1.1, 3.1.0, 3.0.5, 3.0.4, 3.0.1, 2.5.1, 2.5.0
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
SCons is a software construction tool

scorec-core

Homepage:
Spack package:
Versions:
develop
Build Dependencies:
cmake, mpi, zoltan
Link Dependencies:
mpi, zoltan
Description:
The SCOREC Core is a set of C/C++ libraries for unstructured mesh simulations on supercomputers.

scorep

Homepage:
Spack package:
Versions:
6.0, 5.0, 4.1, 4.0, 3.1, 3.0, 2.0.2, 1.4.2, 1.3
Build Dependencies:
otf2, opari2, cubew, cubelib, cube, mpi, papi, pdt
Link Dependencies:
otf2, opari2, cubew, cubelib, cube, mpi, papi, pdt
Description:
The Score-P measurement infrastructure is a highly scalable and easy-to- use tool suite for profiling, event tracing, and online analysis of HPC applications.

scotch

Homepage:
Spack package:
Versions:
6.0.8, 6.0.6, 6.0.5a, 6.0.4, 6.0.3, 6.0.0, 5.1.10b
Build Dependencies:
flex, bison, mpi, zlib
Link Dependencies:
mpi, zlib
Description:
Scotch is a software package for graph and mesh/hypergraph partitioning, graph clustering, and sparse matrix ordering.

scr

Homepage:
Spack package:
Versions:
master, 1.2.2, 1.2.1, 1.2.0
Build Dependencies:
cmake, pdsh, zlib, mpi, dtcmp, libyogrt
Link Dependencies:
zlib, mpi, dtcmp, libyogrt
Run Dependencies:
pdsh
Description:
SCR caches checkpoint data in storage on the compute nodes of a Linux cluster to provide a fast, scalable checkpoint/restart capability for MPI codes

screen

Homepage:
Spack package:
Versions:
4.6.2, 4.3.1, 4.3.0, 4.2.1, 4.2.0, 4.0.3, 4.0.2, 3.9.15, 3.9.11, 3.9.10, 3.9.9, 3.9.8, 3.9.4, 3.7.6, 3.7.4, 3.7.2, 3.7.1
Build Dependencies:
ncurses
Link Dependencies:
ncurses
Description:
Screen is a full-screen window manager that multiplexes a physical terminal between several processes, typically interactive shells.

scripts

Homepage:
Spack package:
Versions:
1.0.1
Build Dependencies:
libx11, pkgconfig, util-macros
Link Dependencies:
libx11
Description:
Various X related scripts.

scrnsaverproto

Homepage:
Spack package:
Versions:
1.2.2
Build Dependencies:
pkgconfig, util-macros
Description:
MIT Screen Saver Extension. This extension defines a protocol to control screensaver features and also to query screensaver info on specific windows.

scs

Homepage:
Spack package:
Versions:
2.1.1
Build Dependencies:
blas, lapack, cuda
Link Dependencies:
blas, lapack, cuda
Description:
A C package that solves convex cone problems via operator splitting

sctk

Homepage:
Spack package:
Versions:
2.4.10, 2.4.9, 2.4.8, 2.4.0
Description:
The NIST Scoring Toolkit (SCTK) is a collection of software tools designed to score benchmark test evaluations of Automatic Speech Recognition (ASR) Systems. The toolkit is currently used by NIST, benchmark test participants, and reserchers worldwide to as a common scoring engine.

sdl2

Homepage:
Spack package:
Versions:
2.0.5
Build Dependencies:
cmake
Link Dependencies:
libxext
Description:
Simple DirectMedia Layer is a cross-platform development library designed to provide low level access to audio, keyboard, mouse, joystick, and graphics hardware via OpenGL and Direct3D.

sdl2-image

Homepage:
Spack package:
Versions:
2.0.1
Build Dependencies:
sdl2
Link Dependencies:
sdl2
Description:
SDL is designed to provide the bare bones of creating a graphical program.

sdsl-lite

Homepage:
Spack package:
Versions:
2.1.1
Build Dependencies:
cmake, tar
Description:
SDSL - Succinct Data Structure Library The Succinct Data Structure Library (SDSL) is a powerful and flexible C++11 library implementing succinct data structures.

seacas

Homepage:
Spack package:
Versions:
master, 2019-12-18, 2019-10-14, 2019-08-20, 2019-07-26
Build Dependencies:
cmake, netcdf-c, cgns, adios2, matio, metis, parmetis, mpi
Link Dependencies:
netcdf-c, cgns, adios2, matio, metis, parmetis, mpi
Description:
The SEACAS Project contains the Exodus and IOSS libraries and a collection of applications which create, query, modify, or translate exodus databases. Default is to build the exodus and IOSS libraries and the io_shell, io_info, struc_to_unstruc apps.

sed

Homepage:
Spack package:
Versions:
4.2.2
Description:
GNU implementation of the famous stream editor.

sensei

Homepage:
Spack package:
Versions:
master, 3.1.0, 3.0.0, 2.1.1, 2.1.0, 2.0.0, 1.1.0, 1.0.0
Build Dependencies:
cmake, paraview, visit, vtk, adios, hdf5, python, py-numpy, py-mpi4py, swig
Link Dependencies:
paraview, visit, vtk, adios, hdf5
Run Dependencies:
python, py-numpy, py-mpi4py
Description:
SENSEI is a platform for scalable in-situ analysis and visualization. Its design motto is 'Write once, run everywhere', this means that once the application is instrumented with SENSEI it can use existing and future analysis backends. Existing backends include: Paraview/Catalyst, Visit/Libsim, ADIOS, Python scripts, and so on.

sentieon-genomics

Homepage:
Spack package:
Versions:
201808.07, 201808.01
Description:
Sentieon provides complete solutions for secondary DNA analysis. Our software improves upon BWA, GATK, Mutect, and Mutect2 based pipelines. The Sentieon tools are deployable on any CPU-based computing system. Please set the path to the sentieon license server with: export SENTIEON_LICENSE=[FQDN]:[PORT] Note: A manual download is required. Spack will search your current directory for the download file. Alternatively, add this file to a mirror so that Spack can find it. For instructions on how to set up a mirror, see http://spack.readthedocs.io/en/latest/mirrors.html

seqan

Homepage:
Spack package:
Versions:
2.4.0
Build Dependencies:
cmake, python, py-nose, py-sphinx, boost, zlib, bzip2
Link Dependencies:
boost, zlib, bzip2
Description:
SeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data. Our library applies a unique generic design that guarantees high performance, generality, extensibility, and integration with other libraries. SeqAn is easy to use and simplifies the development of new software tools with a minimal loss of performance

seqkit

Homepage:
Spack package:
Versions:
0.10.1
Description:
A cross-platform and ultrafast toolkit for FASTA/Q file manipulation in Golang.

seqprep

Homepage:
Spack package:
Versions:
1.3.2
Link Dependencies:
zlib
Description:
SeqPrep is a program to merge paired end Illumina reads that are overlapping into a single longer read.

seqtk

Homepage:
Spack package:
Versions:
1.3, 1.2, 1.1
Build Dependencies:
zlib
Link Dependencies:
zlib
Description:
Toolkit for processing sequences in FASTA/Q formats.

serf

Homepage:
Spack package:
Versions:
1.3.9, 1.3.8
Build Dependencies:
scons, apr, apr-util, openssl, zlib
Link Dependencies:
apr, apr-util, openssl, zlib
Description:
Apache Serf - a high performance C-based HTTP client library built upon the Apache Portable Runtime (APR) library

sessreg

Homepage:
Spack package:
Versions:
1.1.0
Build Dependencies:
xproto, pkgconfig, util-macros
Description:
Sessreg is a simple program for managing utmp/wtmp entries for X sessions. It was originally written for use with xdm, but may also be used with other display managers such as gdm or kdm.

setxkbmap

Homepage:
Spack package:
Versions:
1.3.1
Build Dependencies:
libxkbfile, libx11, pkgconfig, util-macros
Link Dependencies:
libxkbfile, libx11
Description:
setxkbmap is an X11 client to change the keymaps in the X server for a specified keyboard to use the layout determined by the options listed on the command line.

sfcgal

Homepage:
Spack package:
Versions:
1.3.7
Build Dependencies:
cmake, cgal, boost, mpfr, gmp
Link Dependencies:
cgal, boost, mpfr, gmp
Description:
SFCGAL is a C++ wrapper library around CGAL with the aim of supporting ISO 19107:2013 and OGC Simple Features Access 1.2 for 3D operations. SFCGAL provides standard compliant geometry types and operations, that can be accessed from its C or C++ APIs.

sga

Homepage:
Spack package:
Versions:
0.10.15, 0.10.14, 0.10.13, 0.10.12, 0.10.11, 0.10.10, 0.10.9, 0.10.8, 0.10.3
Build Dependencies:
zlib, sparsehash, jemalloc, bamtools, autoconf, automake, libtool
Link Dependencies:
zlib, sparsehash, jemalloc, bamtools
Description:
SGA is a de novo genome assembler based on the concept of string graphs. The major goal of SGA is to be very memory efficient, which is achieved by using a compressed representation of DNA sequence reads.

shadow

Homepage:
Spack package:
Versions:
4.7, 4.6
Description:
Tools to help unprivileged users create uid and gid mappings in user namespaces.

shapeit

Homepage:
Spack package:
Versions:
2.837
Description:
SHAPEIT is a fast and accurate method for estimation of haplotypes (aka phasing) from genotype or sequencing data.

shared-mime-info

Homepage:
Spack package:
Versions:
1.9, 1.8
Build Dependencies:
glib, libxml2, intltool, gettext, pkgconfig
Link Dependencies:
glib, libxml2
Description:
Database of common MIME types.

shiny-server

Homepage:
Spack package:
Versions:
1.5.3.838
Build Dependencies:
cmake, python, git, r, openssl
Link Dependencies:
cmake, python, git, r, openssl
Description:
Shiny server lets you put shiny web applications and interactive documents online. Take your shiny apps and share them with your organization or the world.

shocklibs

Homepage:
Spack package:
Versions:
0.9.24
Description:
The lib for shock: An object store for scientific data.

shoremap

Homepage:
Spack package:
Versions:
3.6
Build Dependencies:
dislin
Link Dependencies:
dislin
Description:
SHOREmap is a computational tool implementing a method that enables simple and straightforward mapping-by-sequencing analysis. Whole genome resequencing of pools of recombinant mutant genomes allows directly linking phenotypic traits to causal mutations. Such an analysis, called mapping-by-sequencing, combines classical genetic mapping and next generation sequencing by relying on selection-induced patterns within genome-wide allele frequency in pooled genomes.

shortbred

Homepage:
Spack package:
Versions:
0.9.4
Build Dependencies:
blast-plus, cdhit, muscle, python, py-biopython, usearch
Link Dependencies:
blast-plus, cdhit, muscle, python, py-biopython, usearch
Description:
ShortBRED is a system for profiling protein families of interest at very high specificity in shotgun meta'omic sequencing data.

shortstack

Homepage:
Spack package:
Versions:
3.8.3
Build Dependencies:
perl, samtools, viennarna, bowtie
Link Dependencies:
samtools, viennarna, bowtie
Run Dependencies:
perl
Description:
ShortStack is a tool developed to process and analyze smallRNA-seq data with respect to a reference genome, and output a comprehensive and informative annotation of all discovered small RNA genes.

showfont

Homepage:
Spack package:
Versions:
1.0.5
Build Dependencies:
libfs, pkgconfig, util-macros
Link Dependencies:
libfs
Description:
showfont displays data about a font from an X font server. The information shown includes font information, font properties, character metrics, and character bitmaps.

shtools

Homepage:
Spack package:
Versions:
4.5
Build Dependencies:
blas, fftw, lapack
Link Dependencies:
blas, fftw, lapack
Description:
SHTOOLS - Spherical Harmonic Tools

shuffile

Homepage:
Spack package:
Versions:
master, 0.0.3
Build Dependencies:
cmake, mpi, kvtree
Link Dependencies:
mpi, kvtree
Description:
Shuffle files between MPI ranks

sickle

Homepage:
Spack package:
Versions:
1.33
Build Dependencies:
zlib
Link Dependencies:
zlib
Description:
Sickle is a tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads and also determines when the quality is sufficiently high enough to trim the 5'-end of reads.

siesta

Homepage:
Spack package:
Versions:
4.0.1, 3.2-pl-5
Build Dependencies:
mpi, blas, lapack, scalapack, netcdf-c, netcdf-fortran
Link Dependencies:
mpi, blas, lapack, scalapack, netcdf-c, netcdf-fortran
Description:
SIESTA performs electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids.

signalp

Homepage:
Spack package:
Versions:
4.1f
Build Dependencies:
perl, gnuplot
Link Dependencies:
gnuplot
Run Dependencies:
perl
Description:
SignalP predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms: Gram-positive bacteria, Gram-negative bacteria, and eukaryotes. Note: A manual download is required for SignalP. Spack will search your current directory for the download file. Alternatively, add this file to a mirror so that Spack can find it. For instructions on how to set up a mirror, see http://spack.readthedocs.io/en/latest/mirrors.html

signify

Homepage:
Spack package:
Versions:
23
Build Dependencies:
libbsd
Link Dependencies:
libbsd
Description:
OpenBSD tool to signs and verify signatures on files.

silo

Homepage:
Spack package:
Versions:
4.10.2-bsd, 4.10.2, 4.9, 4.8
Build Dependencies:
hdf5, mpi, qt, zlib
Link Dependencies:
hdf5, mpi, qt, zlib
Description:
Silo is a library for reading and writing a wide variety of scientific data to binary, disk files.

simgrid

Homepage:
Spack package:
Versions:
3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14.159, 3.13, 3.12, 3.11, git
Build Dependencies:
cmake, boost
Link Dependencies:
boost
Description:
To study the behavior of large-scale distributed systems such as Grids, Clouds, HPC or P2P systems.

MeshSimAdvanced

Homepage:
Spack package:
Versions:
14.0-191122, 12.0-191027
Build Dependencies:
mpi
Link Dependencies:
mpi
Description:
Simmetrix' Simulation Modeling Suite is a set of component software toolkits that allow developers to easily implement geometry-based simulation applications. Each component of the Simulation Modeling Suite is designed to address specific capabilities: | MeshSim - automatic mesh generation | FieldSim - simulation data management | GeomSim - direct, untranslated access to geometry from a wide variety of sources

simplemoc

Homepage:
Spack package:
Versions:
4
Build Dependencies:
mpi
Link Dependencies:
mpi
Description:
The purpose of this mini-app is to demonstrate the performance characterterics and viability of the Method of Characteristics (MOC) for 3D neutron transport calculations in the context of full scale light water reactor simulation.

simul

Homepage:
Spack package:
Versions:
1.16, 1.15, 1.14, 1.13
Build Dependencies:
mpi
Link Dependencies:
mpi
Description:
simul is an MPI coordinated test of parallel filesystem system calls and library functions.

simulationio

Homepage:
Spack package:
Versions:
develop, 9.0.1
Build Dependencies:
cmake, hdf5, julia, py-h5py, py-numpy, python, swig
Link Dependencies:
hdf5, python
Run Dependencies:
julia, py-h5py, py-numpy, python
Description:
SimulationIO: Efficient and convenient I/O for large PDE simulations

singularity

Homepage:
Spack package:
Versions:
master, 3.5.2, 3.4.1, 3.4.0, 3.3.0, 3.2.1, 3.1.1
Build Dependencies:
go, libuuid, libgpg-error, git, cryptsetup
Link Dependencies:
go, libuuid, libgpg-error, git
Run Dependencies:
squashfs, shadow, cryptsetup
Description:
Singularity is a container technology focused on building portable encapsulated environments to support "Mobility of Compute" For older versions of Singularity (pre 3.0) you should use singularity-legacy, which has a different install base (Autotools). Needs post-install chmod/chown steps to enable full functionality. See package definition or `spack-build-out.txt` build log for details.

singularity-legacy

Homepage:
Spack package:
Versions:
2.6.1, 2.6.0, 2.6-release, 2.5.2
Build Dependencies:
libarchive, m4, autoconf, automake, libtool
Link Dependencies:
libarchive
Description:
Singularity is a container platform focused on supporting 'Mobility of Compute'. The software changed the installation method from AutoTools to GoLang, so we have two separate package names to support that. The legacy package is pre-version 3.0.0

sirius

Homepage:
Spack package:
Versions:
develop, master, 6.4.3, 6.4.2, 6.4.1, 6.4.0, 6.3.4, 6.3.3, 6.3.2, 6.1.5
Build Dependencies:
cuda, cmake, python, mpi, gsl, lapack, fftw, libxc, spglib, hdf5, pkgconfig, py-numpy, py-scipy, py-h5py, py-mpi4py, py-pyyaml, py-voluptuous, py-pybind11, magma, spfft, elpa, libvdwxc, scalapack
Link Dependencies:
cuda, python, mpi, gsl, lapack, fftw, libxc, spglib, hdf5, magma, spfft, elpa, libvdwxc, scalapack
Run Dependencies:
python, py-numpy, py-scipy, py-h5py, py-mpi4py, py-pyyaml, py-voluptuous, py-pybind11
Description:
Domain specific library for electronic structure calculations

skilion-onedrive

Homepage:
Spack package:
Versions:
1.1.1
Build Dependencies:
dmd, curl, sqlite
Link Dependencies:
dmd, curl, sqlite
Description:
A complete tool to interact with OneDrive on Linux, developed by Skilion, following the UNIX philosophy.

skopeo

Homepage:
Spack package:
Versions:
0.1.40, 0.1.39, 0.1.38, 0.1.37, 0.1.36
Build Dependencies:
go, go-md2man, gpgme, libassuan, libgpg-error, lvm2
Link Dependencies:
go, gpgme, libassuan, libgpg-error, lvm2
Description:
skopeo is a command line utility that performs various operations on container images and image repositories.

sl

Homepage:
Spack package:
Versions:
5.02
Build Dependencies:
ncurses
Link Dependencies:
ncurses
Description:
SL: Cure your bad habit of mistyping

slate

Homepage:
Spack package:
Versions:
develop
Build Dependencies:
cuda, intel-mkl, mercurial, mpi
Link Dependencies:
cuda, intel-mkl, mpi
Description:
The Software for Linear Algebra Targeting Exascale (SLATE) project is to provide fundamental dense linear algebra capabilities to the US Department of Energy and to the high-performance computing (HPC) community at large. To this end, SLATE will provide basic dense matrix operations (e.g., matrix multiplication, rank-k update, triangular solve), linear systems solvers, least square solvers, singular value and eigenvalue solvers.

sleef

Homepage:
Spack package:
Versions:
3.2
Build Dependencies:
cmake
Description:
SIMD Library for Evaluating Elementary Functions, vectorized libm and DFT.

slepc

Homepage:
Spack package:
Versions:
develop, 3.12.0, 3.11.2, 3.11.1, 3.11.0, 3.10.2, 3.10.1, 3.10.0, 3.9.2, 3.9.1, 3.9.0, 3.8.2, 3.8.0, 3.7.4, 3.7.3, 3.7.1, 3.6.3, 3.6.2
Build Dependencies:
python, petsc, arpack-ng
Link Dependencies:
petsc, arpack-ng
Description:
Scalable Library for Eigenvalue Problem Computations.

slurm

Homepage:
Spack package:
Versions:
18-08-0-1, 17-11-9-2, 17-02-6-1
Build Dependencies:
curl, glib, json-c, lz4, munge, openssl, pkgconfig, readline, zlib, gtkplus, hdf5, hwloc, mariadb, pmix
Link Dependencies:
curl, glib, json-c, lz4, munge, openssl, readline, zlib, gtkplus, hdf5, hwloc, mariadb, pmix
Description:
Slurm is an open source, fault-tolerant, and highly scalable cluster management and job scheduling system for large and small Linux clusters. Slurm requires no kernel modifications for its operation and is relatively self-contained. As a cluster workload manager, Slurm has three key functions. First, it allocates exclusive and/or non-exclusive access to resources (compute nodes) to users for some duration of time so they can perform work. Second, it provides a framework for starting, executing, and monitoring work (normally a parallel job) on the set of allocated nodes. Finally, it arbitrates contention for resources by managing a queue of pending work.

smalt

Homepage:
Spack package:
Versions:
0.7.6
Description:
SMALT aligns DNA sequencing reads with a reference genome.

smof

Homepage:
Spack package:
Versions:
2.13.1
Run Dependencies:
python
Description:
Explore and analyze biological sequence data

smproxy

Homepage:
Spack package:
Versions:
1.0.6
Build Dependencies:
libsm, libice, libxt, libxmu, pkgconfig, util-macros
Link Dependencies:
libsm, libice, libxt, libxmu
Description:
smproxy allows X applications that do not support X11R6 session management to participate in an X11R6 session.

snakemake

Homepage:
Spack package:
Versions:
3.11.2
Build Dependencies:
python, py-requests, py-setuptools, py-wrapt
Link Dependencies:
python
Run Dependencies:
python, py-requests, py-setuptools, py-wrapt
Description:
Snakemake is an MIT-licensed workflow management system.

snap

Homepage:
Spack package:
Versions:
master
Build Dependencies:
mpi
Link Dependencies:
mpi
Description:
SNAP serves as a proxy application to model the performance of a modern discrete ordinates neutral particle transport application. SNAP may be considered an update to Sweep3D, intended for hybrid computing architectures. It is modeled off the Los Alamos National Laboratory code PARTISN.

snap-berkeley

Homepage:
Spack package:
Versions:
1.0beta.18, 0.15
Build Dependencies:
zlib
Link Dependencies:
zlib
Description:
SNAP is a fast and accurate aligner for short DNA reads. It is optimized for modern read lengths of 100 bases or higher, and takes advantage of these reads to align data quickly through a hash-based indexing scheme.

snap-korf

Homepage:
Spack package:
Versions:
2013-11-29
Build Dependencies:
perl, boost, sqlite, sparsehash
Link Dependencies:
boost, sqlite, sparsehash
Run Dependencies:
perl
Description:
SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes.

snappy

Homepage:
Spack package:
Versions:
1.1.7
Build Dependencies:
cmake
Test Dependencies:
googletest
Description:
A fast compressor/decompressor: https://code.google.com/p/snappy

snbone

Homepage:
Spack package:
Versions:
develop
Build Dependencies:
metis
Link Dependencies:
metis
Description:
This application targets the primary computational solve burden of a SN, continuous finite element based transport equation solver.

sniffles

Homepage:
Spack package:
Versions:
1.0.7, 1.0.5
Build Dependencies:
cmake
Link Dependencies:
zlib, bamtools
Description:
Structural variation caller using third generation sequencing.

snpeff

Homepage:
Spack package:
Versions:
2017-11-24
Build Dependencies:
jdk
Run Dependencies:
jdk
Description:
SnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of genetic variants (such as amino acid changes).

snphylo

Homepage:
Spack package:
Versions:
2016-02-04
Build Dependencies:
python, r, r-phangorn, r-gdsfmt, r-snprelate, r-getopt, muscle, phylip
Link Dependencies:
muscle, phylip
Run Dependencies:
python, r, r-phangorn, r-gdsfmt, r-snprelate, r-getopt
Description:
A pipeline to generate a phylogenetic tree from huge SNP data

snptest

Homepage:
Spack package:
Versions:
2.5.2
Description:
SNPTEST is a program for the analysis of single SNP association in genome-wide studies.

soapdenovo-trans

Homepage:
Spack package:
Versions:
1.0.4
Description:
SOAPdenovo-Trans is a de novo transcriptome assembler basing on the SOAPdenovo framework, adapt to alternative splicing and different expression level among transcripts.

soapdenovo2

Homepage:
Spack package:
Versions:
240
Description:
SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for the human-sized genomes. The program is specially designed to assemble Illumina GA short reads. It creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost effective way.

sofa-c

Homepage:
Spack package:
Versions:
20180130
Description:
Standards of Fundamental Astronomy (SOFA) library for ANSI C.

sollve

Homepage:
Spack package:
Versions:
develop, 1.0a2
Build Dependencies:
cmake, python, perl-data-dumper, argobots, ncurses, swig, libedit, py-six, binutils
Link Dependencies:
python, argobots, ncurses, swig, libedit, binutils
Run Dependencies:
py-six
Description:
The SOLLVE Project aims at scaling OpenMP by leveraging LLVM for exascale performance and portability of applications. This package provides a collection of Clang/LLVM compilers and an OpenMP runtime library.

somatic-sniper

Homepage:
Spack package:
Versions:
1.0.5.0
Build Dependencies:
cmake, ncurses
Link Dependencies:
ncurses
Description:
A tool to call somatic single nucleotide variants.

sortmerna

Homepage:
Spack package:
Versions:
2017-07-13
Build Dependencies:
cmake, zlib
Link Dependencies:
zlib
Description:
SortMeRNA is a program tool for filtering, mapping and OTU-picking NGS reads in metatranscriptomic and metagenomic data

sosflow

Homepage:
Spack package:
Versions:
spack
Build Dependencies:
cmake, libevpath, sqlite, pkgconfig, mpi
Link Dependencies:
libevpath, sqlite, pkgconfig, mpi
Description:
SOSflow provides a flexible, scalable, and programmable framework for observation, introspection, feedback, and control of HPC applications.

sowing

Homepage:
Spack package:
Versions:
1.1.25-p1, 1.1.23-p1
Description:
Sowing generates Fortran interfaces and documentation for PETSc and MPICH.

sox

Homepage:
Spack package:
Versions:
14.4.2
Build Dependencies:
bzip2, flac, id3lib, libvorbis, opus, lame, libmad
Link Dependencies:
bzip2, flac, id3lib, libvorbis, opus, lame, libmad
Description:
SoX, the Swiss Army knife of sound processing programs.

spades

Homepage:
Spack package:
Versions:
3.13.0, 3.12.0, 3.11.1, 3.10.1
Build Dependencies:
cmake, python, zlib, bzip2
Link Dependencies:
zlib, bzip2
Run Dependencies:
python
Description:
SPAdes - St. Petersburg genome assembler - is intended for both standard isolates and single-cell MDA bacteria assemblies.

span-lite

Homepage:
Spack package:
Versions:
0.5.0, 0.4.0, 0.3.0, 0.2.0, 0.1.0
Build Dependencies:
cmake
Description:
A single-file header-only version of a C++20-like span for C++98, C++11 and later

spark

Homepage:
Spack package:
Versions:
2.3.0, 2.1.0, 2.0.2, 2.0.0, 1.6.2, 1.6.1, 1.6.0
Build Dependencies:
java, hadoop
Run Dependencies:
java, hadoop
Description:
Apache Spark is a fast and general engine for large-scale data processing.

sparsehash

Homepage:
Spack package:
Versions:
2.0.3
Description:
Sparse and dense hash-tables for C++ by Google

sparta

Homepage:
Spack package:
Versions:
1.25
Build Dependencies:
bowtie2, python, py-scipy, py-numpy
Link Dependencies:
bowtie2
Run Dependencies:
python, py-scipy, py-numpy
Description:
small RNA-PARE Target Analyzer (sPARTA) is a tool which utilizes high- throughput sequencing to profile genome-wide cleavage products.

spdlog

Homepage:
Spack package:
Versions:
1.4.1, 1.2.1, 1.2.0, 1.1.0, 1.0.0, 0.17.0, 0.16.3, 0.16.2, 0.16.1, 0.16.0, 0.14.0, 0.13.0, 0.12.0, 0.11.0, 0.10.0, 0.9.0
Build Dependencies:
cmake
Description:
Very fast, header only, C++ logging library

spectrum-mpi

Homepage:
Spack package:
Description:
IBM MPI implementation from Spectrum MPI.

speex

Homepage:
Spack package:
Versions:
1.2.0
Description:
Speex is an Open Source/Free Software patent-free audio compression format designed for speech.

spfft

Homepage:
Spack package:
Versions:
0.9.10, 0.9.9, 0.9.8
Build Dependencies:
cmake, fftw, mpi, cuda
Link Dependencies:
fftw, mpi, cuda
Description:
Sparse 3D FFT library with MPI, OpenMP, CUDA and ROCm support.

spglib

Homepage:
Spack package:
Versions:
1.10.3, 1.10.0
Build Dependencies:
cmake
Description:
C library for finding and handling crystal symmetries.

sph2pipe

Homepage:
Spack package:
Versions:
2.5
Build Dependencies:
cmake
Description:
Sph2pipe is a portable tool for converting SPHERE files to other formats.

spherepack

Homepage:
Spack package:
Versions:
3.2
Description:
SPHEREPACK - A Package for Modeling Geophysical Processes

spindle

Homepage:
Spack package:
Versions:
0.8.1
Build Dependencies:
launchmon
Link Dependencies:
launchmon
Description:
Spindle improves the library-loading performance of dynamically linked HPC applications. Without Spindle large MPI jobs can overload on a shared file system when loading dynamically linked libraries, causing site-wide performance problems.

spm

Homepage:
Spack package:
Versions:
12_r7219
Build Dependencies:
zip
Run Dependencies:
matlab
Description:
Statistical Parametric Mapping refers to the construction and assessment of spatially extended statistical processes used to test hypotheses about functional imaging data. These ideas have been instantiated in software that is called SPM.

spot

Homepage:
Spack package:
Versions:
1.99.3, 1.2.6
Build Dependencies:
python, boost
Link Dependencies:
python, boost
Description:
Spot is a C++11 library for omega-automata manipulation and model checking.

sqlite

Homepage:
Spack package:
Versions:
3.30.1, 3.30.0, 3.29.0, 3.28.0, 3.27.2, 3.27.1, 3.27.0, 3.26.0
Build Dependencies:
readline, zlib
Link Dependencies:
readline, zlib
Description:
SQLite3 is an SQL database engine in a C library. Programs that link the SQLite3 library can have SQL database access without running a separate RDBMS process.

sqlitebrowser

Homepage:
Spack package:
Versions:
3.10.1
Build Dependencies:
cmake, sqlite, qt
Link Dependencies:
sqlite, qt
Description:
DB Browser for SQLite (DB4S) is a high quality, visual, open source tool to create, design, and edit database files compatible with SQLite.

squashfs

Homepage:
Spack package:
Versions:
4.4, 4.3, 4.2, 4.1, 4.0
Build Dependencies:
m4, autoconf, automake, libtool, zlib
Link Dependencies:
zlib
Description:
Squashfs - read only compressed filesystem

squid

Homepage:
Spack package:
Versions:
1.9g
Description:
C function library for sequence analysis.

sratoolkit

Homepage:
Spack package:
Versions:
2.9.6, 2.9.2, 2.8.2-1
Description:
The NCBI SRA Toolkit enables reading ("dumping") of sequencing files from the SRA database and writing ("loading") files into the .sra format.

ssht

Homepage:
Spack package:
Versions:
1.2b1
Build Dependencies:
fftw
Link Dependencies:
fftw
Description:
The SSHT code provides functionality to perform fast and exact spin spherical harmonic transforms.

sspace-longread

Homepage:
Spack package:
Versions:
1.1
Build Dependencies:
perl
Run Dependencies:
perl
Description:
SSPACE-LongRead is a stand-alone program for scaffolding pre-assembled contigs using long reads Note: A manual download is required for SSPACE- LongRead. Spack will search your current directory for the download file. Alternatively, add this file to a mirror so that Spack can find it. For instructions on how to set up a mirror, see http://spack.readthedocs.io/en/latest/mirrors.html

sspace-standard

Homepage:
Spack package:
Versions:
3.0
Build Dependencies:
perl, perl-perl4-corelibs
Run Dependencies:
perl, perl-perl4-corelibs
Description:
SSPACE standard is a stand-alone program for scaffolding pre-assembled contigs using NGS paired-read data Note: A manual download is required for SSPACE-Standard. Spack will search your current directory for the download file. Alternatively, add this file to a mirror so that Spack can find it. For instructions on how to set up a mirror, see http://spack.readthedocs.io/en/latest/mirrors.html

sst-core

Homepage:
Spack package:
Versions:
develop, 8.0.0
Build Dependencies:
autoconf, automake, libtool, m4, python, zlib, mpi, boost
Link Dependencies:
python, mpi
Description:
The Structural Simulation Toolkit (SST) was developed to explore innovations in highly concurrent systems where the ISA, microarchitecture, and memory interact with the programming model and communications system

sst-dumpi

Homepage:
Spack package:
Versions:
master, 6.1.0
Build Dependencies:
autoconf, automake, libtool, m4
Description:
The DUMPI package provides libraries to collect and read traces of MPI applications. Traces are created by linking an application with a library that uses the PMPI interface to intercept MPI calls. DUMPI records signatures of all MPI-1 and MPI-2 subroutine calls, return values, request information, and PAPI counters.

sst-macro

Homepage:
Spack package:
Versions:
develop, 8.0.0, 6.1.0
Build Dependencies:
boost, autoconf, automake, libtool, m4, binutils, zlib, otf2, llvm, mpi, sst-core
Link Dependencies:
boost, zlib, otf2, llvm, mpi, sst-core
Description:
The Structural Simulation Toolkit Macroscale Element Library simulates large-scale parallel computer architectures for the coarse-grained study of distributed-memory applications. The simulator is driven from either a trace file or skeleton application. SST/macro's modular architecture can be extended with additional network models, trace file formats, software services, and processor models.

stacks

Homepage:
Spack package:
Versions:
2.3b, 1.46
Build Dependencies:
perl, sparsehash, zlib
Link Dependencies:
sparsehash, zlib
Run Dependencies:
perl
Description:
Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform.

staden-io-lib

Homepage:
Spack package:
Versions:
1.14.8
Build Dependencies:
zlib
Link Dependencies:
zlib
Description:
Io_lib is a library for reading/writing various bioinformatics file formats.

star

Homepage:
Spack package:
Versions:
2.7.0e, 2.7.0d, 2.6.1b, 2.6.1a, 2.6.0c, 2.6.0b, 2.6.0a, 2.5.4b, 2.5.4a, 2.5.3a, 2.5.2b, 2.5.2a, 2.4.2a
Build Dependencies:
zlib
Link Dependencies:
zlib
Description:
STAR is an ultrafast universal RNA-seq aligner.

star-ccm-plus

Homepage:
Spack package:
Versions:
11.06.010_02
Description:
STAR-CCM+ (Computational Continuum Mechanics) CFD solver.

startup-notification

Homepage:
Spack package:
Versions:
0.12
Build Dependencies:
libx11, libxcb, xcb-util
Link Dependencies:
libx11, libxcb, xcb-util
Description:
startup-notification contains a reference implementation of the freedesktop startup notification protocol.

stat

Homepage:
Spack package:
Versions:
develop, 4.0.1, 4.0.0, 3.0.1, 3.0.0, 2.2.0, 2.1.0, 2.0.0
Build Dependencies:
autoconf, automake, libtool, dyninst, fast-global-file-status, graphlib, graphviz, launchmon, mrnet, python, py-pygtk, py-xdot, swig, mpi, boost
Link Dependencies:
dyninst, fast-global-file-status, graphlib, graphviz, launchmon, mrnet, python, py-xdot, swig, mpi, boost
Run Dependencies:
graphviz, py-pygtk, py-enum34
Description:
Library to create, manipulate, and export graphs Graphlib.

stata

Homepage:
Spack package:
Versions:
15
Build Dependencies:
libpng
Link Dependencies:
libpng
Description:
STATA is a general-purpose statistical software package developed by StataCorp.

stc

Homepage:
Spack package:
Versions:
master, 0.8.3, 0.8.2
Build Dependencies:
java, ant, turbine, zsh, autoconf, automake, libtool
Run Dependencies:
java, turbine, zsh
Description:
STC: The Swift-Turbine Compiler

steps

Homepage:
Spack package:
Versions:
develop, 3.3.0, 3.2.0
Build Dependencies:
cmake, blas, lapack, mpi, petsc, python, py-cython
Link Dependencies:
blas, lapack, mpi, petsc, python, py-cython
Description:
STochastic Engine for Pathway Simulation

storm

Homepage:
Spack package:
Versions:
2.1.0, 2.0.0, 1.2.3
Run Dependencies:
java
Description:
Storm is a distributed realtime computation system. Similar to how Hadoop provides a set of general primitives for doing batch processing, Storm provides a set of general primitives for doing realtime computation.

stow

Homepage:
Spack package:
Versions:
2.2.2, 2.2.0, 2.1.3, 2.1.2, 2.1.1, 2.1.0
Build Dependencies:
perl
Link Dependencies:
perl
Description:
GNU Stow: a symlink farm manager GNU Stow is a symlink farm manager which takes distinct packages of software and/or data located in separate directories on the filesystem, and makes them appear to be installed in the same place.

strace

Homepage:
Spack package:
Versions:
5.2, 5.1, 5.0, 4.21
Description:
Strace is a diagnostic, debugging and instructional userspace utility for Linux. It is used to monitor and tamper with interactions between processes and the Linux kernel, which include system calls, signal deliveries, and changes of process state.

stream

Homepage:
Spack package:
Versions:
5.10
Description:
The STREAM benchmark is a simple synthetic benchmark program that measures sustainable memory bandwidth (in MB/s) and the corresponding computation rate for simple vector kernels.

strelka

Homepage:
Spack package:
Versions:
2.8.2
Build Dependencies:
cmake, python, zlib, bzip2, boost
Link Dependencies:
cmake, python, zlib, bzip2, boost
Description:
Somatic and germline small variant caller for mapped sequencing data.

stress

Homepage:
Spack package:
Versions:
1.0.4
Description:
stress is a deliberately simple workload generator for POSIX systems. It imposes a configurable amount of CPU, memory, I/O, and disk stress on the system. It is written in C, and is free software licensed under the GPLv2.

string-view-lite

Homepage:
Spack package:
Versions:
1.2.0, 1.1.0, 1.0.0, 0.2.0, 0.1.0
Build Dependencies:
cmake
Description:
A single-file header-only version of a C++17-like string_view for C++98, C++11 and later

stringtie

Homepage:
Spack package:
Versions:
1.3.4d, 1.3.4a, 1.3.3b
Build Dependencies:
samtools
Link Dependencies:
samtools
Description:
StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.

structure

Homepage:
Spack package:
Versions:
2.3.4
Build Dependencies:
jdk
Run Dependencies:
jdk
Description:
Structure is a free software package for using multi-locus genotype data to investigate population structure.

strumpack

Homepage:
Spack package:
Versions:
master, 3.3.0, 3.2.0, 3.1.1, 3.1.0, 3.0.3, 3.0.2, 3.0.1, 3.0.0, 2.2.0
Build Dependencies:
cmake, mpi, blas, lapack, scalapack, metis, parmetis, scotch, butterflypack
Link Dependencies:
mpi, blas, lapack, scalapack, metis, parmetis, scotch, butterflypack
Description:
STRUMPACK -- STRUctured Matrix PACKage - provides linear solvers for sparse matrices and for dense rank-structured matrices, i.e., matrices that exhibit some kind of low-rank property. It provides a distributed memory fully algebraic sparse solver and preconditioner. The preconditioner is mostly aimed at large sparse linear systems which result from the discretization of a partial differential equation, but is not limited to any particular type of problem. STRUMPACK also provides preconditioned GMRES and BiCGStab iterative solvers.

sublime-text

Homepage:
Spack package:
Versions:
3.2.2.3211, 3.2.1.3207, 3.1.1.3176, 3.0.3126, 2.0.2
Run Dependencies:
gtkplus, glib, libx11, pcre, libffi, libxcb, libxau
Description:
Sublime Text is a sophisticated text editor for code, markup and prose.

subread

Homepage:
Spack package:
Versions:
2.0.0, 1.6.4, 1.6.2, 1.6.0, 1.5.2
Build Dependencies:
zlib
Link Dependencies:
zlib
Description:
The Subread software package is a tool kit for processing next-gen sequencing data.

subversion

Homepage:
Spack package:
Versions:
1.12.2, 1.9.7, 1.9.6, 1.9.5, 1.9.3, 1.8.17, 1.8.13
Build Dependencies:
apr, apr-util, zlib, sqlite, expat, lz4, utf8proc, serf, perl, swig, perl-termreadkey
Link Dependencies:
apr, apr-util, zlib, sqlite, expat, lz4, utf8proc, serf, perl, swig, perl-termreadkey
Description:
Apache Subversion - an open source version control system.

suite-sparse

Homepage:
Spack package:
Versions:
5.6.0, 5.5.0, 5.4.0, 5.3.0, 5.2.0, 5.1.2, 5.1.0, 5.0.0, 4.5.6, 4.5.5, 4.5.3
Build Dependencies:
blas, lapack, m4, cmake, metis, tbb, cuda
Link Dependencies:
blas, lapack, metis, tbb, cuda
Description:
SuiteSparse is a suite of sparse matrix algorithms

sumaclust

Homepage:
Spack package:
Versions:
1.0.20
Description:
Sumaclust aims to cluster sequences in a way that is fast and exact at the same time.

sundials

Homepage:
Spack package:
Versions:
develop, 5.1.0, 5.0.0, 4.1.0, 4.0.1, 3.2.1, 3.2.0, 3.1.2, 3.1.1, 3.1.0, 3.0.0, 2.7.0, 2.6.2
Build Dependencies:
cmake, mpi, cuda, raja, lapack, suite-sparse, petsc, hypre, superlu-dist, trilinos, superlu-mt
Link Dependencies:
mpi, cuda, raja, lapack, suite-sparse, petsc, hypre, superlu-dist, trilinos, superlu-mt
Description:
SUNDIALS (SUite of Nonlinear and DIfferential/ALgebraic equation Solvers)

superlu

Homepage:
Spack package:
Versions:
5.2.1, 4.3
Build Dependencies:
cmake, blas
Link Dependencies:
blas
Description:
SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines. SuperLU is designed for sequential machines.

superlu-dist

Homepage:
Spack package:
Versions:
develop, 6.1.1, 6.1.0, 6.0.0, 5.4.0, 5.3.0, 5.2.2, 5.2.1, 5.1.3, 5.1.2, 5.1.0, 5.0.0, xsdk-0.2.0
Build Dependencies:
cmake, mpi, blas, lapack, parmetis, metis
Link Dependencies:
mpi, blas, lapack, parmetis, metis
Description:
A general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines.

superlu-mt

Homepage:
Spack package:
Versions:
3.1
Build Dependencies:
blas
Link Dependencies:
blas
Description:
SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines. SuperLU_MT is designed for shared memory parallel machines.

supernova

Homepage:
Spack package:
Versions:
2.1.1, 2.0.1
Build Dependencies:
bcl2fastq2
Link Dependencies:
bcl2fastq2
Description:
Supernova is a software package for de novo assembly from Chromium Linked-Reads that are made from a single whole-genome library from an individual DNA source. A key feature of Supernova is that it creates diploid assemblies, thus separately representing maternal and paternal chromosomes over very long distances. Almost all other methods instead merge homologous chromosomes into single incorrect 'consensus' sequences. Supernova is the only practical method for creating diploid assemblies of large genomes. To install this package, you will need to go to the supernova download page of supernova, register with your email address and download supernova yourself. Spack will search your current directory for the download file. Alternatively, add this file yo a mirror so that Spack can find it. For instructions on how to set up a mirror, see http://spack.readthedocs.io/en/latest/mirrors.html

sw4lite

Homepage:
Spack package:
Versions:
develop, 1.1, 1.0
Build Dependencies:
blas, lapack, mpi
Link Dependencies:
blas, lapack, mpi
Description:
Sw4lite is a bare bone version of SW4 intended for testing performance optimizations in a few important numerical kernels of SW4.

swap-assembler

Homepage:
Spack package:
Versions:
0.4
Build Dependencies:
mpich
Link Dependencies:
mpich
Description:
A scalable and fully parallelized genome assembler.

swarm

Homepage:
Spack package:
Versions:
2.1.13
Description:
A robust and fast clustering method for amplicon-based studies.

swfft

Homepage:
Spack package:
Versions:
develop, 1.0
Build Dependencies:
mpi, fftw
Link Dependencies:
mpi, fftw
Description:
A stand-alone version of HACC's distributed-memory, pencil-decomposed, parallel 3D FFT.

swftools

Homepage:
Spack package:
Versions:
0.9.2
Build Dependencies:
giflib, lame, poppler, freetype, jpeg, fftw
Link Dependencies:
giflib, lame, poppler, freetype, jpeg, fftw
Description:
SWFTools is a collection of utilities for working with Adobe Flash files (SWF files). The tool collection includes programs for reading SWF files, combining them, and creating them from other content (like images, sound files, videos or sourcecode). SWFTools is released under the GPL.

swiftsim

Homepage:
Spack package:
Versions:
0.7.0, 0.3.0
Build Dependencies:
autoconf, automake, libtool, m4, mpi, metis, hdf5
Link Dependencies:
mpi, metis, hdf5
Description:
SPH With Inter-dependent Fine-grained Tasking (SWIFT) provides astrophysicists with a state of the art framework to perform particle based simulations.

swig

Homepage:
Spack package:
Versions:
master, 4.0.0, 3.0.12, 3.0.11, 3.0.10, 3.0.8, 3.0.2, 2.0.12, 2.0.2, 1.3.40, fortran
Build Dependencies:
pcre, autoconf, automake, libtool, pkgconfig
Link Dependencies:
pcre
Description:
SWIG is an interface compiler that connects programs written in C and C++ with scripting languages such as Perl, Python, Ruby, and Tcl. It works by taking the declarations found in C/C++ header files and using them to generate the wrapper code that scripting languages need to access the underlying C/C++ code. In addition, SWIG provides a variety of customization features that let you tailor the wrapping process to suit your application.

swipl

Homepage:
Spack package:
Versions:
8.0.3
Build Dependencies:
cmake, uuid, readline, gmp, unwind, unixodbc, openssl, zlib, libxt, libx11, libjpeg, libxpm, libxft, fontconfig, pkgconfig
Link Dependencies:
uuid, readline, gmp, unwind, unixodbc, openssl, zlib, libxt, libx11, libjpeg, libxpm, libxft, fontconfig
Description:
SWI-Prolog is a versatile implementation of the Prolog language. Although SWI-Prolog gained its popularity primarily in education, its development is mostly driven by the needs for application development. This is facilitated by a rich interface to other IT components by supporting many document types and (network) protocols as well as a comprehensive low-level interface to C that is the basis for high-level interfaces to C++, Java (bundled), C#, Python, etc (externally available). Data type extensions such as dicts and strings as well as full support for Unicode and unbounded integers simplify smooth exchange of data with other components.

symengine

Homepage:
Spack package:
Versions:
develop, 0.5.0, 0.4.0, 0.3.0, 0.2.0, 0.1.0
Build Dependencies:
cmake, boost, gmp, llvm, mpc, mpfr, flint, piranha
Link Dependencies:
boost, gmp, llvm, mpc, mpfr, flint, piranha
Description:
SymEngine is a fast symbolic manipulation library, written in C++.

sympol

Homepage:
Spack package:
Versions:
0.1.8
Build Dependencies:
cmake, bliss, boost, gmp, lrslib
Link Dependencies:
bliss, boost, gmp, lrslib
Description:
SymPol is a C++ tool to work with symmetric polyhedra

sysstat

Homepage:
Spack package:
Versions:
12.2.0, 12.1.7, 12.1.6, 12.1.5
Description:
The sysstat package contains various utilities, common to many commercial Unixes, to monitor system performance and usage activity Sysstat also contains tools you can schedule via cron or systemd to collect and historize performance and activity data.

sz

Homepage:
Spack package:
Versions:
develop, 2.1.8.0, 2.0.2.0, 1.4.13.5, 1.4.13.4, 1.4.13.3, 1.4.13.2, 1.4.13.0, 1.4.12.3, 1.4.12.1, 1.4.11.1, 1.4.11.0, 1.4.10.0, 1.4.9.2
Description:
Error-bounded Lossy Compressor for HPC Data.

tabix

Homepage:
Spack package:
Versions:
2013-12-16
Build Dependencies:
perl, python
Link Dependencies:
zlib
Run Dependencies:
perl, python
Description:
Generic indexer for TAB-delimited genome position files

tajo

Homepage:
Spack package:
Versions:
0.11.3, 0.11.2, 0.11.1, 0.11.0, 0.10.1, 0.10.0
Run Dependencies:
java
Description:
Tajo is a relational and distributed data warehouse system for Hadoop Tajo is designed for low-latency and scalable ad-hoc queries, online aggregation and ETL on large-data sets by leveraging advanced database techniques. It supports SQL standards. It has its own query engine which allows direct control of distributed execution and data flow. As a result, Tajo has a variety of query evaluation strategies and more optimization opportunities. In addition, Tajo will have a native columnar execution and and its optimizer.

talass

Homepage:
Spack package:
Versions:
2018-10-29
Build Dependencies:
cmake
Description:
TALASS: Topological Analysis of Large-Scale Simulations This package compiles the talass tool chain thar implements various topological algorithms to analyze large scale data. The package is organized hierarchical FileFormat < Statistics < StreamingTopology and any of the subsets can be build stand- alone.

talloc

Homepage:
Spack package:
Versions:
2.1.9
Description:
Talloc provides a hierarchical, reference counted memory pool system with destructors. It is the core memory allocator used in Samba.

tantan

Homepage:
Spack package:
Versions:
13
Description:
tantan is a tool to mask simple regions (low complexity and short-period tandem repeats) in DNA, RNA, and protein sequences.

tar

Homepage:
Spack package:
Versions:
1.32, 1.31, 1.30, 1.29, 1.28
Build Dependencies:
libiconv
Link Dependencies:
libiconv
Description:
GNU Tar provides the ability to create tar archives, as well as various other kinds of manipulation.

targetp

Homepage:
Spack package:
Versions:
1.1b
Build Dependencies:
chlorop, signalp
Link Dependencies:
chlorop, signalp
Run Dependencies:
perl, awk
Description:
TargetP predicts the subcellular location of eukaryotic protein sequences. Note: A manual download is required for TargetP. Spack will search your current directory for the download file. Alternatively, add this file to a mirror so that Spack can find it. For instructions on how to set up a mirror, see http://spack.readthedocs.io/en/latest/mirrors.html

task

Homepage:
Spack package:
Versions:
2.5.1, 2.4.4
Build Dependencies:
cmake, gnutls, libuuid
Link Dependencies:
gnutls, libuuid
Description:
Feature-rich console based todo list manager

taskd

Homepage:
Spack package:
Versions:
1.1.0
Build Dependencies:
cmake, libuuid, gnutls
Link Dependencies:
libuuid, gnutls
Description:
TaskWarrior task synchronization daemon

tasmanian

Homepage:
Spack package:
Versions:
develop, 7.0, 6.0, 5.1, 5.0
Build Dependencies:
cmake, python, py-numpy, mpi, blas, cuda, magma
Link Dependencies:
python
Run Dependencies:
python, py-numpy, mpi, blas, cuda, magma
Description:
The Toolkit for Adaptive Stochastic Modeling and Non-Intrusive ApproximatioN is a robust library for high dimensional integration and interpolation as well as parameter calibration.

tassel

Homepage:
Spack package:
Versions:
2017-07-22
Build Dependencies:
java, perl
Run Dependencies:
java, perl
Description:
TASSEL is a software package to evaluate traits associations, evolutionary patterns, and linkage disequilibrium.

tau

Homepage:
Spack package:
Versions:
develop, 2.29, 2.28.2, 2.28.1, 2.28, 2.27.2p1, 2.27.2, 2.27.1, 2.27, 2.26.3, 2.26.2, 2.26.1, 2.26, 2.25, 2.24.1, 2.24, 2.23.1
Build Dependencies:
pdt, scorep, otf2, likwid, papi, libdwarf, libelf, binutils, python, libunwind, mpi, cuda, gasnet
Link Dependencies:
zlib, pdt, scorep, otf2, likwid, papi, libdwarf, libelf, binutils, python, libunwind, mpi, cuda, gasnet
Description:
A portable profiling and tracing toolkit for performance analysis of parallel programs written in Fortran, C, C++, UPC, Java, Python.

tcl

Homepage:
Spack package:
Versions:
8.6.8, 8.6.6, 8.6.5, 8.6.4, 8.6.3, 8.5.19
Build Dependencies:
zlib
Link Dependencies:
zlib
Description:
Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more. Open source and business-friendly, Tcl is a mature yet evolving language that is truly cross platform, easily deployed and highly extensible.

tcl-itcl

Homepage:
Spack package:
Versions:
4.0.4
Build Dependencies:
tcl
Link Dependencies:
tcl
Description:
[incr Tcl] is the most widely used O-O system for Tcl. The name is a play on C++, and [incr Tcl] provides a similar object model, including multiple inheritence and public and private classes and variables.

tcl-tcllib

Homepage:
Spack package:
Versions:
1.19, 1.18, 1.17, 1.16, 1.15, 1.14
Build Dependencies:
tcl
Link Dependencies:
tcl
Description:
Tcllib is a collection of utility modules for Tcl. These modules provide a wide variety of functionality, from implementations of standard data structures to implementations of common networking protocols. The intent is to collect commonly used function into a single library, which users can rely on to be available and stable.

tcl-tclxml

Homepage:
Spack package:
Versions:
3.2, 3.1
Build Dependencies:
tcl, tcl-tcllib, libxml2, libxslt
Link Dependencies:
tcl, tcl-tcllib, libxml2, libxslt
Description:
TclXML is an API for parsing XML documents using the Tcl scripting language. It is also a package including a DOM implementation (TclDOM) and XSL Transformations (TclXSLT). These allow Tcl scripts to read, manipulate and write XML documents.

tclap

Homepage:
Spack package:
Versions:
1.2.2, 1.2.1
Description:
Templatized C++ Command Line Parser

tcoffee

Homepage:
Spack package:
Versions:
2017-08-17
Build Dependencies:
perl, blast-plus, dialign-tx, viennarna, clustalw, tmalign, muscle, mafft, pcma, poamsa, probconsrna
Link Dependencies:
blast-plus, dialign-tx, viennarna, clustalw, tmalign, muscle, mafft, pcma, poamsa, probconsrna
Run Dependencies:
perl
Description:
T-Coffee is a multiple sequence alignment program.

tcptrace

Homepage:
Spack package:
Versions:
6.6.7
Build Dependencies:
bison, flex, libpcap
Link Dependencies:
libpcap
Description:
tcptrace is a tool written by Shawn Ostermann at Ohio University for analysis of TCP dump files. It can take as input the files produced by several popular packet-capture programs, including tcpdump, snoop, etherpeek, HP Net Metrix, and WinDump.

tcsh

Homepage:
Spack package:
Versions:
6.21.00, 6.20.00
Build Dependencies:
ncurses
Link Dependencies:
ncurses
Description:
Tcsh is an enhanced but completely compatible version of csh, the C shell. Tcsh is a command language interpreter which can be used both as an interactive login shell and as a shell script command processor. Tcsh includes a command line editor, programmable word completion, spelling correction, a history mechanism, job control and a C language like syntax.

tealeaf

Homepage:
Spack package:
Versions:
1.0
Build Dependencies:
mpi
Link Dependencies:
mpi
Description:
Proxy Application. TeaLeaf is a mini-app that solves the linear heat conduction equation on a spatially decomposed regularly grid using a 5 point stencil with implicit solvers.

teckit

Homepage:
Spack package:
Versions:
2.5.9
Build Dependencies:
expat, zlib
Link Dependencies:
expat, zlib
Description:
TECkit is a low-level toolkit intended to be used by applications for conversions between text encodings. For example, it can be used when importing legacy text into a Unicode-based application. The primary component of TECkit is a library: the TECkit engine. The engine relies on mapping tables in a specific, documented binary format. The TECkit compiler creates these tables from plain-text, human-readable descriptions.

tecplot

Homepage:
Spack package:
Versions:
2018r2, 2017r1
Description:
Tecplot 360 is a Computational Fluid Dynamics (CFD) and numerical simulation software package used in post-processing simulation results. It is also used in chemistry applications to visualize molecule structure by post-processing charge density data.

templight

Homepage:
Spack package:
Versions:
develop, 2019.01.09, 2018.07.20
Build Dependencies:
cmake, python, py-lit
Link Dependencies:
python
Run Dependencies:
py-lit
Description:
Templight is a Clang-based tool to profile the time and memory consumption of template instantiations and to perform interactive debugging sessions to gain introspection into the template instantiation process.

templight-tools

Homepage:
Spack package:
Versions:
develop
Build Dependencies:
cmake, boost
Link Dependencies:
boost
Description:
Supporting tools for the Templight Profiler

tensorflow-serving-client

Homepage:
Spack package:
Versions:
2.1.0, 2.0.0
Build Dependencies:
cmake, protobuf, grpc
Link Dependencies:
protobuf, grpc
Description:
A prebuilt tensorflow serving client from the tensorflow serving proto files

tetgen

Homepage:
Spack package:
Versions:
1.5.0, 1.4.3
Description:
TetGen is a program and library that can be used to generate tetrahedral meshes for given 3D polyhedral domains. TetGen generates exact constrained Delaunay tetrahedralizations, boundary conforming Delaunay meshes, and Voronoi paritions.

tethex

Homepage:
Spack package:
Versions:
develop, 0.0.7
Build Dependencies:
cmake
Description:
Tethex is designed to convert triangular (in 2D) or tetrahedral (in 3D) Gmsh's mesh to quadrilateral or hexahedral one respectively. These meshes can be used in software packages working with hexahedrals only - for example, deal.II.

texinfo

Homepage:
Spack package:
Versions:
6.5, 6.3, 6.0, 5.2, 5.1, 5.0
Build Dependencies:
perl
Link Dependencies:
perl
Description:
Texinfo is the official documentation format of the GNU project. It was invented by Richard Stallman and Bob Chassell many years ago, loosely based on Brian Reid's Scribe and other formatting languages of the time. It is used by many non-GNU projects as well.

texlive

Homepage:
Spack package:
Versions:
20190410, live
Build Dependencies:
perl, pkgconfig, cairo, freetype, ghostscript, gmp, harfbuzz, icu4c, libgd, libpaper, libpng, libxaw, libxt, mpfr, pixman, poppler, teckit, zlib, zziplib
Link Dependencies:
perl, cairo, freetype, ghostscript, gmp, harfbuzz, icu4c, libgd, libpaper, libpng, libxaw, libxt, mpfr, pixman, poppler, teckit, zlib, zziplib
Description:
TeX Live is an easy (we hope) way to get up and running with the TeX document production system. It provides a comprehensive TeX system with binaries for most flavors of Unix, including GNU/Linux, macOS, and also Windows. It includes all the major TeX-related programs, macro packages, and fonts that are free software, including support for many languages around the world.

texstudio

Homepage:
Spack package:
Versions:
master, 2.12.16, 2.12.14, 2.12.12, 2.12.10
Build Dependencies:
qt, poppler
Link Dependencies:
qt, poppler
Description:
TeXstudio is a fully featured LaTeX editor, whose goal is to make writing LaTeX documents as easy and comfortable as possible.

textparser

Homepage:
Spack package:
Versions:
master, 1.8.8
Build Dependencies:
cmake, mpi
Link Dependencies:
mpi
Description:
Text Parser library allows us to describe and to parse JSON like simple parameter structure.

tfel

Homepage:
Spack package:
Versions:
master, 3.3.0, 3.2.2, 3.2.1, 3.2.0, 3.1.5, 3.1.4, 3.1.3, 3.1.2, 3.1.1, 3.1.0, 3.0.5, 3.0.4, 3.0.3, 3.0.2, 3.0.1, 3.0.0, 2.0.4, rliv-3.3, rliv-3.2, rliv-3.1, rliv-3.0, rliv-2.0, rliv-1.2
Build Dependencies:
cmake, java, python, boost
Link Dependencies:
java, python, boost
Run Dependencies:
python
Description:
The TFEL project is a collaborative development of CEA (French Alternative Energies and Atomic Energy Commission) and EDF (Electricite de France). It mostly contains the MFront code generator which translates a set of closely related domain specific languages into plain C++ on top of the TFEL libraries. MFront handles material properties, mechanical behaviours and simple point-wise models. Interfaces are provided for several finite element solvers, such as: Abaqus/Standard, Abaqus/Explicit, Ansys APDL, Cast3M, Europlexus, Code_Aster, CalculiX and a few others. MFront comes with an handy easy-to-use tool called MTest that can test the local behaviour of a material, by imposing independent constraints on each component of the strain or the stress.

the-platinum-searcher

Homepage:
Spack package:
Versions:
head
Build Dependencies:
go
Link Dependencies:
go
Description:
Fast parallel recursive grep alternative

the-silver-searcher

Homepage:
Spack package:
Versions:
2.1.0, 0.32.0, 0.30.0
Build Dependencies:
pcre, xz, zlib, pkgconfig
Link Dependencies:
pcre, xz, zlib
Description:
Fast recursive grep alternative

thornado-mini

Homepage:
Spack package:
Versions:
1.0
Build Dependencies:
mpi, hdf5, lapack
Link Dependencies:
mpi, hdf5, lapack
Description:
Code to solve the equation of radiative transfer in the multi-group two- moment approximation

thrift

Homepage:
Spack package:
Versions:
0.13.0, 0.12.0, 0.11.0, 0.10.0, 0.9.3
Build Dependencies:
pkgconfig, java, autoconf, automake, libtool, boost, bison, flex, openssl, python, zlib, libevent
Link Dependencies:
java, boost, openssl, python, zlib, libevent
Description:
Software framework for scalable cross-language services development. Thrift combines a software stack with a code generation engine to build services that work efficiently and seamlessly between C++, Java, Python, PHP, Ruby, Erlang, Perl, Haskell, C#, Cocoa, JavaScript, Node.js, Smalltalk, OCaml and Delphi and other languages.

thrust

Homepage:
Spack package:
Versions:
1.9.4, 1.9.3, 1.9.2, 1.9.1, 1.9.0, 1.8.2
Description:
Thrust is a parallel algorithms library which resembles the C++ Standard Template Library (STL).

tig

Homepage:
Spack package:
Versions:
2.2.2
Build Dependencies:
ncurses
Link Dependencies:
ncurses
Description:
Text-mode interface for git

time

Homepage:
Spack package:
Versions:
1.9
Description:
The time command runs another program, then displays information about the resources used by that program.

timemory

Homepage:
Spack package:
Versions:
develop, master, 3.0.1, 3.0.0
Build Dependencies:
cmake, python, mpi, tau, papi, cuda, upcxx, gotcha, likwid, caliper, gperftools
Link Dependencies:
python, mpi, tau, papi, cuda, upcxx, gotcha, likwid, caliper, gperftools
Run Dependencies:
python, py-numpy, py-pillow, py-matplotlib
Description:
Timing + Memory + Hardware Counter Utilities for C/C++/CUDA/Python

tinker

Homepage:
Spack package:
Versions:
8.7.1
Build Dependencies:
cmake, fftw
Link Dependencies:
fftw
Description:
The Tinker molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers.

tinyxml

Homepage:
Spack package:
Versions:
2.6.2
Build Dependencies:
cmake
Description:
Simple, small, efficient, C++ XML parser

tinyxml2

Homepage:
Spack package:
Versions:
4.0.1, 4.0.0, 3.0.0, 2.2.0, 2.1.0, 2.0.2
Build Dependencies:
cmake
Description:
Simple, small, efficient, C++ XML parser

tioga

Homepage:
Spack package:
Versions:
master
Build Dependencies:
cmake, mpi
Link Dependencies:
mpi
Description:
Topology Independent Overset Grid Assembly (TIOGA)

tippecanoe

Homepage:
Spack package:
Versions:
1.34.3
Build Dependencies:
sqlite, zlib
Link Dependencies:
sqlite, zlib
Description:
Build vector tilesets from large collections of GeoJSON features.

tix

Homepage:
Spack package:
Versions:
8.4.3
Build Dependencies:
tcl, tk
Link Dependencies:
tcl, tk
Description:
Tix is a powerful high-level widget set that expands the capabilities of your Tk/Tcl and Python applications.

tk

Homepage:
Spack package:
Versions:
8.6.8, 8.6.6, 8.6.5, 8.6.3, 8.5.19
Build Dependencies:
tcl, libx11, libxft, libxscrnsaver
Link Dependencies:
tcl, libx11, libxft, libxscrnsaver
Description:
Tk is a graphical user interface toolkit that takes developing desktop applications to a higher level than conventional approaches. Tk is the standard GUI not only for Tcl, but for many other dynamic languages, and can produce rich, native applications that run unchanged across Windows, Mac OS X, Linux and more.

tldd

Homepage:
Spack package:
Versions:
master, 2018-10-05
Build Dependencies:
pstreams
Link Dependencies:
pstreams
Description:
A program similar to ldd(1) but showing the output as a tree.

tmalign

Homepage:
Spack package:
Versions:
2016-05-25
Description:
TM-align is an algorithm for sequence-order independent protein structure comparisons.

tmhmm

Homepage:
Spack package:
Versions:
2.0c
Run Dependencies:
perl
Description:
Transmembrane helices in proteins Note: A manual download is required for TMHMM. Spack will search your current directory for the download file. Alternatively, add this file to a mirror so that Spack can find it. For instructions on how to set up a mirror, see http://spack.readthedocs.io/en/latest/mirrors.html

tmux

Homepage:
Spack package:
Versions:
3.0a, 2.9, 2.8, 2.7, 2.6, 2.5, 2.4, 2.3, 2.2, 2.1, 1.9a
Build Dependencies:
libevent, ncurses
Link Dependencies:
libevent, ncurses
Description:
Tmux is a terminal multiplexer. What is a terminal multiplexer? It lets you switch easily between several programs in one terminal, detach them (they keep running in the background) and reattach them to a different terminal. And do a lot more.

tmuxinator

Homepage:
Spack package:
Versions:
0.6.11
Build Dependencies:
ruby
Link Dependencies:
ruby
Description:
A session configuration creator and manager for tmux

tomcat

Homepage:
Spack package:
Versions:
9.0.30, 9.0.29, 9.0.27, 9.0.26, 9.0.24
Description:
The Apache Tomcat software is an open source implementation of the Java Servlet, JavaServer Pages, Java Expression Language and Java WebSocket technologies.

tophat

Homepage:
Spack package:
Versions:
2.1.2, 2.1.1
Build Dependencies:
autoconf, automake, libtool, m4, boost
Link Dependencies:
boost
Run Dependencies:
bowtie2
Description:
Spliced read mapper for RNA-Seq.

tppred

Homepage:
Spack package:
Versions:
2.0
Build Dependencies:
emboss
Link Dependencies:
emboss
Run Dependencies:
python, py-scikit-learn
Description:
TPPRED is a software package for the prediction of mitochondrial targeting peptides from protein primary sequence.

tracer

Homepage:
Spack package:
Versions:
develop, 2.2
Build Dependencies:
mpi, codes, otf2
Link Dependencies:
mpi, codes, otf2
Description:
Trace Replay and Network Simulation Framework

transabyss

Homepage:
Spack package:
Versions:
1.5.5
Build Dependencies:
abyss, python, py-python-igraph, blat
Link Dependencies:
abyss, blat
Run Dependencies:
python, py-python-igraph
Description:
De novo assembly of RNAseq data using ABySS

transdecoder

Homepage:
Spack package:
Versions:
5.5.0, 3.0.1
Build Dependencies:
perl
Run Dependencies:
perl, perl-uri
Description:
TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.

transposome

Homepage:
Spack package:
Versions:
0.11.2
Build Dependencies:
perl, blast-plus
Link Dependencies:
perl, blast-plus
Run Dependencies:
perl
Description:
A toolkit for annotation of transposable element families from unassembled sequence reads.

transset

Homepage:
Spack package:
Versions:
1.0.1
Build Dependencies:
libx11, xproto, pkgconfig, util-macros
Link Dependencies:
libx11
Description:
transset is an utility for setting opacity property.

trapproto

Homepage:
Spack package:
Versions:
3.4.3
Description:
X.org TrapProto protocol headers.

tree

Homepage:
Spack package:
Versions:
1.7.0
Description:
Tree is a recursive directory listing command that produces a depth indented listing of files, which is colorized ala dircolors if the LS_COLORS environment variable is set and output is to tty. Tree has been ported and reported to work under the following operating systems: Linux, FreeBSD, OS X, Solaris, HP/UX, Cygwin, HP Nonstop and OS/2.

treesub

Homepage:
Spack package:
Versions:
0.2, 0.1
Build Dependencies:
ant
Run Dependencies:
jdk, paml, raxml, figtree
Description:
A small program (which glues together other programs) that allows a user to input a codon alignment in FASTA format and produce an annotated phylogenetic tree showing which substitutions occurred on a given branch. Originally written for colleagues at the MRC NIMR.

trf

Homepage:
Spack package:
Versions:
4.09, 4.07b
Description:
Tandem Repeats Finder is a program to locate and display tandem repeats in DNA sequences. Note: A manual download is required for TRF. Spack will search your current directory for the download file. Alternatively, add this file to a mirror so that Spack can find it. For instructions on how to set up a mirror, see http://spack.readthedocs.io/en/latest/mirrors.html

triangle

Homepage:
Spack package:
Versions:
1.6
Description:
Triangle is a two-dimensional mesh generator and Delaunay triangulator. Triangle generates exact Delaunay triangulations, constrained Delaunay triangulations, conforming Delaunay triangulations, Voronoi diagrams, and high-quality triangular meshes.

trilinos

Homepage:
Spack package:
Versions:
develop, master, 12.18.1, 12.14.1, 12.12.1, 12.10.1, 12.8.1, 12.6.4, 12.6.3, 12.6.2, 12.6.1, 12.4.2, 12.2.1, 12.0.1, 11.14.3, 11.14.2, 11.14.1, xsdk-0.2.0
Build Dependencies:
cmake, blas, lapack, boost, matio, glm, metis, suite-sparse, zlib, mpi, netcdf-c, parallel-netcdf, parmetis, cgns, adios2, mumps, scalapack, superlu-dist, superlu, hypre, hdf5, python, py-numpy, swig
Link Dependencies:
blas, lapack, boost, matio, glm, metis, suite-sparse, zlib, mpi, netcdf-c, parallel-netcdf, parmetis, cgns, adios2, mumps, scalapack, superlu-dist, superlu, hypre, hdf5, python, swig
Run Dependencies:
py-numpy
Description:
The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented software framework for the solution of large-scale, complex multi-physics engineering and scientific problems. A unique design feature of Trilinos is its focus on packages.

trilinos-catalyst-ioss-adapter

Homepage:
Spack package:
Versions:
develop, master
Build Dependencies:
cmake, bison, flex, paraview, py-numpy, netcdf-c
Link Dependencies:
paraview, netcdf-c
Run Dependencies:
py-numpy
Description:
Adapter for Trilinos Seacas Ioss and Paraview Catalyst

trimal

Homepage:
Spack package:
Versions:
1.4.1
Description:
A tool for automated alignment trimming in large-scale phylogenetic analyses

trimgalore

Homepage:
Spack package:
Versions:
0.6.4, 0.6.3, 0.6.2, 0.6.1, 0.6.0, 0.4.5, 0.4.4
Build Dependencies:
perl, py-cutadapt, fastqc
Link Dependencies:
fastqc
Run Dependencies:
perl, py-cutadapt
Description:
Trim Galore! is a wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data.

trimmomatic

Homepage:
Spack package:
Versions:
0.38, 0.36, 0.33
Run Dependencies:
java
Description:
A flexible read trimming tool for Illumina NGS data.

trinity

Homepage:
Spack package:
Versions:
2.6.6
Build Dependencies:
java, bowtie2, jellyfish, salmon, perl, autoconf, automake, libtool
Link Dependencies:
bowtie2, jellyfish, salmon
Run Dependencies:
java, perl, blast-plus, bowtie, r, r-tidyverse, r-edger, r-deseq2, r-ape, r-gplots, r-biobase, r-qvalue, rsem, kallisto, fastqc, samtools, py-numpy, express, perl-db-file, perl-uri, r-fastcluster, r-ctc, r-goseq, r-glimma, r-rots, r-goplot, r-argparse, r-sm
Description:
Trinity, developed at the Broad Institute and the Hebrew University of Jerusalem, represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-seq reads. Trinity partitions the sequence data into many individual de Bruijn graphs, each representing the transcriptional complexity at a given gene or locus, and then processes each graph independently to extract full-length splicing isoforms and to tease apart transcripts derived from paralogous genes.

trinotate

Homepage:
Spack package:
Versions:
3.1.1
Run Dependencies:
trinity, transdecoder, sqlite, ncbi-rmblastn, hmmer, perl, lighttpd, perl-dbi, perl-cgi, perl-dbd-sqlite
Description:
Trinotate is a comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms

trnascan-se

Homepage:
Spack package:
Versions:
2.0.0
Run Dependencies:
infernal
Description:
Seaching for tRNA genes in genomic sequence

turbine

Homepage:
Spack package:
Versions:
master, 1.2.3, 1.1.0
Build Dependencies:
adlbx, tcl, zsh, swig, python, r, r-rinside, hdf5, mpi, autoconf, automake, libtool, m4
Link Dependencies:
adlbx, python, r, r-rinside, hdf5, mpi
Run Dependencies:
tcl, zsh, m4
Description:
Turbine: The Swift/T runtime

turbomole

Homepage:
Spack package:
Versions:
7.0.2
Description:
TURBOMOLE: Program Package for ab initio Electronic Structure Calculations. Note: Turbomole requires purchase of a license to download. Go to the Turbomole home page, http://www.turbomole-gmbh.com, for details. Spack will search the current directory for this file. It is probably best to add this file to a Spack mirror so that it can be found from anywhere. For information on setting up a Spack mirror see http://spack.readthedocs.io/en/latest/mirrors.html

tut

Homepage:
Spack package:
Versions:
2016-12-19
Build Dependencies:
python
Description:
TUT is a small and portable unit test framework for C++.

twm

Homepage:
Spack package:
Versions:
1.0.9
Build Dependencies:
libx11, libxext, libxt, libxmu, libice, libsm, xproto, bison, flex, pkgconfig, util-macros
Link Dependencies:
libx11, libxext, libxt, libxmu, libice, libsm
Description:
twm is a window manager for the X Window System. It provides titlebars, shaped windows, several forms of icon management, user-defined macro functions, click-to-type and pointer-driven keyboard focus, and user- specified key and pointer button bindings.

tycho2

Homepage:
Spack package:
Versions:
develop
Build Dependencies:
mpi
Link Dependencies:
mpi
Description:
A neutral particle transport mini-app to study performance of sweeps on unstructured, 3D tetrahedral meshes.

typhon

Homepage:
Spack package:
Versions:
develop, 3.0.2, 3.0.1, 3.0
Build Dependencies:
cmake, mpi
Link Dependencies:
mpi
Description:
Typhon is a distributed communications library for unstructured mesh applications.

typhonio

Homepage:
Spack package:
Versions:
develop, 1.6_CMake
Build Dependencies:
cmake, mpi, hdf5
Link Dependencies:
mpi, hdf5
Description:
TyphonIO is a library of routines that perform input/output (I/O) of scientific data within application codes

ucx

Homepage:
Spack package:
Versions:
1.6.1, 1.6.0, 1.5.2, 1.5.1, 1.5.0, 1.4.0, 1.3.1, 1.3.0, 1.2.2, 1.2.1, 1.2.0
Build Dependencies:
numactl, rdma-core
Link Dependencies:
numactl, rdma-core
Description:
a communication library implementing high-performance messaging for MPI/PGAS frameworks

udunits

Homepage:
Spack package:
Versions:
2.2.24, 2.2.23, 2.2.21
Build Dependencies:
expat
Link Dependencies:
expat
Description:
Automated units conversion

ufo-core

Homepage:
Spack package:
Versions:
0.14.0
Build Dependencies:
cmake, glib, json-glib
Link Dependencies:
glib, json-glib
Description:
The UFO data processing framework is a C library suited to build general purpose streams data processing on heterogeneous architectures such as CPUs, GPUs or clusters. This package contains the run-time system and development files.

ufo-filters

Homepage:
Spack package:
Versions:
0.14.1
Build Dependencies:
cmake, ufo-core
Link Dependencies:
ufo-core
Description:
The UFO data processing framework is a C library suited to build general purpose streams data processing on heterogeneous architectures such as CPUs, GPUs or clusters. This package contains filter plugins.

umap

Homepage:
Spack package:
Versions:
develop, 2.0.0, 1.0.0, 0.0.4, 0.0.3, 0.0.2, 0.0.1
Build Dependencies:
cmake
Description:
Umap is a library that provides an mmap()-like interface to a simple, user-space page fault handler based on the userfaultfd Linux feature (starting with 4.3 linux kernel).

umoci

Homepage:
Spack package:
Versions:
0.4.4, 0.4.3, 0.4.2, 0.4.1, 0.4.0
Build Dependencies:
go, go-md2man
Link Dependencies:
go
Description:
umoci modifies Open Container images, intending to be a complete manipulation tool for OCI images.

umpire

Homepage:
Spack package:
Versions:
develop, master, 0.3.3, 0.3.2, 0.3.1, 0.3.0, 0.2.4, 0.2.3, 0.2.2, 0.2.1, 0.2.0, 0.1.4, 0.1.3
Build Dependencies:
cmake, cuda
Link Dependencies:
cuda
Description:
An application-focused API for memory management on NUMA & GPU architectures

unblur

Homepage:
Spack package:
Versions:
1.0.2
Build Dependencies:
zlib, jpeg, libtiff, gsl, jbigkit, fftw
Link Dependencies:
zlib, jpeg, libtiff, gsl, jbigkit, fftw
Description:
Unblur is used to align the frames of movies recorded on an electron microscope to reduce image blurring due to beam-induced motion.

uncrustify

Homepage:
Spack package:
Versions:
0.67, 0.61
Build Dependencies:
cmake
Description:
Source Code Beautifier for C, C++, C#, ObjectiveC, Java, and others.

unibilium

Homepage:
Spack package:
Versions:
1.2.0
Build Dependencies:
libtool
Description:
A terminfo parsing library

unifdef

Homepage:
Spack package:
Versions:
2.11
Description:
The unifdef utility selectively processes conditional C preprocessor #if and #ifdef directives. It removes from a file both the directives and the additional text that they delimit, while otherwise leaving the file alone.

unifyfs

Homepage:
Spack package:
Versions:
develop, 0.9.0
Build Dependencies:
autoconf, automake, libtool, m4, pkgconfig, flatcc, gotcha, leveldb, margo, mercury, mpi, hdf5
Link Dependencies:
flatcc, gotcha, leveldb, margo, mercury, mpi, hdf5
Description:
User level file system that enables applications to use node-local storage as burst buffers for shared files. Supports scalable and efficient aggregation of I/O bandwidth from burst buffers while having the same life cycle as a batch-submitted job. UnifyFS is designed to support common I/O workloads, including checkpoint/restart. While primarily designed for N-N write/read, UnifyFS compliments its functionality with the support for N-1 write/read.

unison

Homepage:
Spack package:
Versions:
2.48.4
Build Dependencies:
ocaml
Description:
Unison is a file-synchronization tool for OSX, Unix, and Windows. It allows two replicas of a collection of files and directories to be stored on different hosts (or different disks on the same host), modified separately, and then brought up to date by propagating the changes in each replica to the other.

units

Homepage:
Spack package:
Versions:
2.13
Build Dependencies:
python
Run Dependencies:
python
Description:
GNU units converts between different systems of units

unittest-cpp

Homepage:
Spack package:
Versions:
2.0.0, 1.6.0
Build Dependencies:
cmake
Description:
UnitTest++ is a lightweight unit testing framework for C++. It was designed to do test-driven development on a wide variety of platforms. Simplicity, portability, speed, and small footprint are all very important aspects of UnitTest++. UnitTest++ is mostly standard C++ and makes minimal use of advanced library and language features, which means it should be easily portable to just about any platform.

unixodbc

Homepage:
Spack package:
Versions:
2.3.4
Build Dependencies:
libiconv, libtool
Link Dependencies:
libiconv, libtool
Description:
ODBC is an open specification for providing application developers with a predictable API with which to access Data Sources. Data Sources include SQL Servers and any Data Source with an ODBC Driver.

unrar

Homepage:
Spack package:
Versions:
5.8.2, 5.8.1
Description:
RAR archive extraction utility

unuran

Homepage:
Spack package:
Versions:
1.8.1
Build Dependencies:
gsl, rngstreams
Link Dependencies:
gsl, rngstreams
Description:
Universal Non-Uniform Random number generator.

unzip

Homepage:
Spack package:
Versions:
6.0
Description:
Unzip is a compression and file packaging/archive utility.

upcxx

Homepage:
Spack package:
Versions:
2019.9.0, 2019.3.2
Build Dependencies:
cuda, python
Link Dependencies:
cuda
Run Dependencies:
python
Description:
UPC++ is a C++ library that supports Partitioned Global Address Space (PGAS) programming, and is designed to interoperate smoothly and efficiently with MPI, OpenMP, CUDA and AMTs. It leverages GASNet-EX to deliver low-overhead, fine-grained communication, including Remote Memory Access (RMA) and Remote Procedure Call (RPC).

uriparser

Homepage:
Spack package:
Versions:
0.9.3
Build Dependencies:
cmake, doxygen, graphviz
Link Dependencies:
googletest
Description:
uriparser is a strictly RFC 3986 compliant URI parsing and handling library written in C89 ("ANSI C").

usearch

Homepage:
Spack package:
Versions:
10.0.240
Description:
USEARCH is a unique sequence analysis tool with thousands of users world-wide. Note: A manual download is required for USEARCH. Spack will search your current directory for the download file. Alternatively, add this file to a mirror so that Spack can find it. For instructions on how to set up a mirror, see http://spack.readthedocs.io/en/latest/mirrors.html

utf8proc

Homepage:
Spack package:
Versions:
2.4.0
Build Dependencies:
cmake
Description:
A clean C library for processing UTF-8 Unicode data: normalization, case-folding, graphemes, and more

util-linux

Homepage:
Spack package:
Versions:
2.29.2, 2.29.1, 2.25
Build Dependencies:
python, pkgconfig
Link Dependencies:
python, pkgconfig
Description:
Util-linux is a suite of essential utilities for any Linux system.

util-macros

Homepage:
Spack package:
Versions:
1.19.1, 1.19.0
Description:
This is a set of autoconf macros used by the configure.ac scripts in other Xorg modular packages, and is needed to generate new versions of their configure scripts with autoconf.

uuid

Homepage:
Spack package:
Versions:
1.6.2
Description:
OSSP uuid is a ISO-C:1999 application programming interface (API) and corresponding command line interface (CLI) for the generation of DCE 1.1, ISO/IEC 11578:1996 and RFC 4122 compliant Universally Unique Identifier (UUID).

uvw

Homepage:
Spack package:
Versions:
1.14.0, 1.13.0, 1.12.0
Build Dependencies:
cmake, doxygen
Link Dependencies:
libuv
Description:
uvw is a header-only, event based, tiny and easy to use libuv wrapper in modern C++.

valgrind

Homepage:
Spack package:
Versions:
develop, 3.15.0, 3.14.0, 3.13.0, 3.12.0, 3.11.0, 3.10.1, 3.10.0
Build Dependencies:
mpi, boost, autoconf, automake, libtool
Link Dependencies:
mpi, boost
Description:
An instrumentation framework for building dynamic analysis. There are Valgrind tools that can automatically detect many memory management and threading bugs, and profile your programs in detail. You can also use Valgrind to build new tools. Valgrind is Open Source / Free Software, and is freely available under the GNU General Public License, version 2.

vampirtrace

Homepage:
Spack package:
Versions:
5.14.4
Build Dependencies:
mpi, otf, papi, zlib
Link Dependencies:
mpi, otf, papi, zlib
Description:
VampirTrace is an open source library that allows detailed logging of program execution for parallel applications using message passing (MPI) and threads (OpenMP, Pthreads).

vardictjava

Homepage:
Spack package:
Versions:
1.5.1
Run Dependencies:
java
Description:
VarDictJava is a variant discovery program written in Java. It is a partial Java port of VarDict variant caller.

variorum

Homepage:
Spack package:
Versions:
0.1.0
Build Dependencies:
cmake, hwloc, py-sphinx
Link Dependencies:
hwloc
Description:
Variorum is a library providing vendor-neutral interfaces for monitoring and controlling underlying hardware features.

varscan

Homepage:
Spack package:
Versions:
2.4.2
Build Dependencies:
java
Run Dependencies:
java
Description:
Variant calling and somatic mutation/CNV detection for next-generation sequencing data

vc

Homepage:
Spack package:
Versions:
1.4.1, 1.3.0, 1.2.0, 1.1.0
Build Dependencies:
cmake
Description:
SIMD Vector Classes for C++

vcftools

Homepage:
Spack package:
Versions:
0.1.14
Build Dependencies:
perl, zlib
Link Dependencies:
zlib
Run Dependencies:
perl
Description:
VCFtools is a program package designed for working with VCF files, such as those generated by the 1000 Genomes Project. The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files.

vcsh

Homepage:
Spack package:
Versions:
1.20151229-1, 1.20151229, 1.20150502, 1.20141026, 1.20141025
Run Dependencies:
git
Description:
config manager based on git

vdt

Homepage:
Spack package:
Versions:
0.4.3, 0.3.9, 0.3.8, 0.3.7, 0.3.6
Build Dependencies:
cmake
Description:
Vectorised math. A collection of fast and inline implementations of mathematical functions.

vecgeom

Homepage:
Spack package:
Versions:
01.01.03, 01.00.00, 00.05.00, 0.3.rc
Build Dependencies:
cmake
Description:
The vectorized geometry library for particle-detector simulation (toolkits).

veclibfort

Homepage:
Spack package:
Versions:
develop, 0.4.2
Description:
Lightweight but flexible shim designed to rectify the incompatibilities between the Accelerate/vecLib BLAS and LAPACK libraries shipped with macOS and FORTRAN code compiled with modern compilers such as GNU Fortran.

vegas2

Homepage:
Spack package:
Versions:
2
Build Dependencies:
plink
Link Dependencies:
plink
Run Dependencies:
perl, r, r-mvtnorm, r-corpcor
Description:
"VEGAS2 is an extension that uses 1,000 Genomes data to model SNP correlations across the autosomes and chromosome X

veloc

Homepage:
Spack package:
Versions:
master, 1.1, 1.0rc1, 1.0
Build Dependencies:
cmake, boost, libpthread-stubs, mpi, er, axl, pdsh
Link Dependencies:
boost, libpthread-stubs, mpi, er, axl, pdsh
Description:
Very-Low Overhead Checkpointing System. VELOC is a multi-level checkpoint-restart runtime for HPC supercomputing infrastructures

velvet

Homepage:
Spack package:
Versions:
1.2.10
Build Dependencies:
zlib
Link Dependencies:
zlib
Description:
Velvet is a de novo genomic assembler specially designed for short read sequencing technologies.

verilator

Homepage:
Spack package:
Versions:
3.920, 3.904
Build Dependencies:
bison, flex, perl
Link Dependencies:
flex
Run Dependencies:
perl
Description:
Verilator is the fastest free Verilog HDL simulator. It compiles synthesizable Verilog (not test-bench code!), plus some PSL, SystemVerilog and Synthesis assertions into C++ or SystemC code. It is designed for large projects where fast simulation performance is of primary concern, and is especially well suited to generate executable models of CPUs for embedded software design teams. Please do not download this program if you are expecting a full featured replacement for NC-Verilog, VCS or another commercial Verilog simulator or Verilog compiler for a little project! (Try Icarus instead.) However, if you are looking for a path to migrate synthesizable Verilog to C++ or SystemC, and writing just a touch of C code and Makefiles doesn't scare you off, this is the free Verilog compiler for you. Verilator supports the synthesis subset of Verilog, plus initial statements, proper blocking/non-blocking assignments, functions, tasks, multi-dimensional arrays, and signed numbers. It also supports very simple forms of SystemVerilog assertions and coverage analysis. Verilator supports the more important Verilog 2005 constructs, and some SystemVerilog features, with additional constructs being added as users request them. Verilator has been used to simulate many very large multi-million gate designs with thousands of modules.

verrou

Homepage:
Spack package:
Versions:
develop, 2.2.0, 2.1.0, 2.0.0, 1.1.0
Build Dependencies:
autoconf, automake, libtool, m4, python
Link Dependencies:
python
Run Dependencies:
python
Description:
A floating-point error checker. Verrou helps you look for floating-point round-off errors in programs. It implements a stochastic floating-point arithmetic based on random rounding: all floating-point operations are perturbed by randomly switching rounding modes. This can be seen as an asynchronous variant of the CESTAC method, or a subset of Monte Carlo Arithmetic, performing only output randomization through random rounding.

vesta

Homepage:
Spack package:
Versions:
3.4.6
Build Dependencies:
gtkplus, mesa, cairo
Link Dependencies:
gtkplus, mesa, cairo
Description:
VESTA is a 3D visualization program for structural models, volumetric data such as electron/nuclear densities, and crystal morphologies.

videoproto

Homepage:
Spack package:
Versions:
2.3.3
Build Dependencies:
pkgconfig, util-macros
Description:
X Video Extension. This extension provides a protocol for a video output mechanism, mainly to rescale video playback in the video controller hardware.

viennarna

Homepage:
Spack package:
Versions:
2.4.3, 2.3.5
Build Dependencies:
perl, python, libsvm, gsl
Link Dependencies:
libsvm, gsl
Run Dependencies:
perl, python
Description:
The ViennaRNA Package consists of a C code library and several stand- alone programs for the prediction and comparison of RNA secondary structures.

viewres

Homepage:
Spack package:
Versions:
1.0.4
Build Dependencies:
libxaw, libxmu, libxt, pkgconfig, util-macros
Link Dependencies:
libxaw, libxmu, libxt
Description:
viewres displays a tree showing the widget class hierarchy of the Athena Widget Set (libXaw).

vigra

Homepage:
Spack package:
Versions:
1.11.1
Build Dependencies:
cmake, libtiff, libpng, jpeg, hdf5, fftw, openexr, py-numpy, boost, py-sphinx, doxygen, python, py-nose
Link Dependencies:
libtiff, libpng, jpeg, hdf5, fftw, openexr, boost, python
Run Dependencies:
py-numpy
Test Dependencies:
py-nose
Description:
VIGRA stands for "Vision with Generic Algorithms". It's an image processing and analysis library that puts its main emphasis on customizable algorithms and data structures

vim

Homepage:
Spack package:
Versions:
8.1.2141, 8.1.0338, 8.1.0001, 8.0.1376, 8.0.0503, 8.0.0454, 8.0.0134, 7.4.2367
Build Dependencies:
python, ruby, lua, perl, libx11, libsm, libxpm, libxt, libxtst, ncurses, findutils
Link Dependencies:
python, ruby, lua, perl, libx11, libsm, libxpm, libxt, libxtst, ncurses
Run Dependencies:
cscope
Description:
Vim is a highly configurable text editor built to enable efficient text editing. It is an improved version of the vi editor distributed with most UNIX systems. Vim is often called a "programmer's editor," and so useful for programming that many consider it an entire IDE. It's not just for programmers, though. Vim is perfect for all kinds of text editing, from composing email to editing configuration files.

virtualgl

Homepage:
Spack package:
Versions:
2.5.2
Build Dependencies:
cmake, jpeg, glu
Link Dependencies:
jpeg, glu
Description:
VirtualGL redirects 3D commands from a Unix/Linux OpenGL application onto a server-side GPU and converts the rendered 3D images into a video stream with which remote clients can interact to view and control the 3D application in real time.

visit

Homepage:
Spack package:
Versions:
3.0.1, 2.13.3, 2.13.0, 2.12.3, 2.12.2, 2.10.3, 2.10.2, 2.10.1
Build Dependencies:
cmake, vtk, qt, qwt, python, silo, hdf5, mpi, adios2
Link Dependencies:
vtk, qt, qwt, python, silo, hdf5, mpi, adios2
Description:
VisIt is an Open Source, interactive, scalable, visualization, animation and analysis tool.

vizglow

Homepage:
Spack package:
Versions:
2.2alpha20, 2.2alpha17, 2.2alpha15
Build Dependencies:
zlib, freetype, fontconfig, libxrender, xterm, libcanberra
Link Dependencies:
zlib, freetype, fontconfig, libxrender, xterm, libcanberra
Description:
VizGlow software tool is used for high-fidelity multi-dimensional modeling of non-equilibrium plasma discharges. Note: VizGlow is licensed software. You will need to create an account on the EsgeeTech homepage and download VizGlow yourself. Spack will search your current directory for a file of this format. Alternatively, add this file to a mirror so that Spack can find it. For instructions on how to set up a mirror, see http://spack.readthedocs.io/en/latest/mirrors.html

vmatch

Homepage:
Spack package:
Versions:
2.3.0
Description:
Vmatch is a versatile software tool for efficiently solving large scale sequence matching tasks

voropp

Homepage:
Spack package:
Versions:
0.4.6
Description:
Voro++ is a open source software library for the computation of the Voronoi diagram, a widely-used tessellation that has applications in many scientific fields.

votca-csg

Homepage:
Spack package:
Versions:
develop, 1.6_rc1, 1.5.1, 1.5, 1.4.1, 1.4
Build Dependencies:
cmake, votca-tools, boost, gromacs, hdf5
Link Dependencies:
votca-tools, boost, gromacs, hdf5
Description:
Versatile Object-oriented Toolkit for Coarse-graining Applications (VOTCA) is a package intended to reduce the amount of routine work when doing systematic coarse-graining of various systems. The core is written in C++. This package contains the VOTCA coarse-graining engine.

votca-csg-tutorials

Homepage:
Spack package:
Versions:
develop, 1.6_rc1, 1.5.1, 1.5, 1.4.1, 1.4
Build Dependencies:
cmake, votca-csg, boost
Link Dependencies:
votca-csg, boost
Description:
Versatile Object-oriented Toolkit for Coarse-graining Applications (VOTCA) is a package intended to reduce the amount of routine work when doing systematic coarse-graining of various systems. The core is written in C++. This package contains the VOTCA coarse-graining tutorials.

votca-csgapps

Homepage:
Spack package:
Versions:
develop, 1.6_rc1, 1.5.1, 1.5, 1.4.1, 1.4
Build Dependencies:
cmake, votca-csg, boost
Link Dependencies:
votca-csg, boost
Description:
Versatile Object-oriented Toolkit for Coarse-graining Applications (VOTCA) is a package intended to reduce the amount of routine work when doing systematic coarse-graining of various systems. The core is written in C++. This package contains the VOTCA coarse-graining extra apps.

votca-ctp

Homepage:
Spack package:
Versions:
develop, 1.5.1, 1.5
Build Dependencies:
cmake, votca-tools, votca-csg, gsl
Link Dependencies:
votca-tools, votca-csg, gsl
Description:
Versatile Object-oriented Toolkit for Coarse-graining Applications (VOTCA) is a package intended to reduce the amount of routine work when doing systematic coarse-graining of various systems. The core is written in C++. This package contains the VOTCA charge transport engine.

votca-tools

Homepage:
Spack package:
Versions:
develop, 1.6_rc1, 1.5.1, 1.5, 1.4.1, 1.4
Build Dependencies:
cmake, expat, fftw, gsl, eigen, boost, sqlite
Link Dependencies:
expat, fftw, gsl, eigen, boost, sqlite
Description:
Versatile Object-oriented Toolkit for Coarse-graining Applications (VOTCA) is a package intended to reduce the amount of routine work when doing systematic coarse-graining of various systems. The core is written in C++. This package contains the basic tools library of VOTCA.

votca-xtp

Homepage:
Spack package:
Versions:
develop, 1.6_rc1, 1.5.1, 1.5, 1.4.1
Build Dependencies:
cmake, votca-tools, votca-csg, libxc, ceres-solver, hdf5
Link Dependencies:
votca-tools, votca-csg, libxc, ceres-solver, hdf5
Description:
Versatile Object-oriented Toolkit for Coarse-graining Applications (VOTCA) is a package intended to reduce the amount of routine work when doing systematic coarse-graining of various systems. The core is written in C++. This package contains the VOTCA exciton transport engine.

vpfft

Homepage:
Spack package:
Versions:
develop
Build Dependencies:
eigen, fftw, mpi
Link Dependencies:
eigen, fftw, mpi
Description:
Proxy Application. VPFFT is an implementation of a mesoscale micromechanical materials model. By solving the viscoplasticity model, VPFFT simulates the evolution of a material under deformation. The solution time to the viscoplasticity model, described by a set of partial differential equations, is significantly reduced by the application of Fast Fourier Transform in the VPFFT algorithm.

vpic

Homepage:
Spack package:
Versions:
develop
Build Dependencies:
cmake, mpi
Link Dependencies:
mpi
Description:
VPIC is a general purpose particle-in-cell simulation code for modeling kinetic plasmas in one, two, or three spatial dimensions. It employs a second-order, explicit, leapfrog algorithm to update charged particle positions and velocities in order to solve the relativistic kinetic equation for each species in the plasma, along with a full Maxwell description for the electric and magnetic fields evolved via a second- order finite-difference-time-domain (FDTD) solve.

vsearch

Homepage:
Spack package:
Versions:
2.14.1, 2.13.3, 2.4.3
Build Dependencies:
m4, autoconf, automake, libtool
Description:
VSEARCH is a versatile open-source tool for metagenomics.

vt

Homepage:
Spack package:
Versions:
0.5772, 0.577
Build Dependencies:
zlib
Link Dependencies:
zlib
Description:
A tool set for short variant discovery in genetic sequence data.

vtk

Homepage:
Spack package:
Versions:
8.2.0, 8.1.2, 8.1.1, 8.1.0, 8.0.1, 7.1.0, 7.0.0, 6.3.0, 6.1.0
Build Dependencies:
cmake, python, gl, glx, libxt, mesa, qt, boost, ffmpeg, mpi, expat, freetype, glew, hdf5, jpeg, jsoncpp, libxml2, lz4, netcdf-c, netcdf-cxx, libpng, libtiff, zlib, eigen, double-conversion, sqlite
Link Dependencies:
python, gl, glx, libxt, mesa, qt, boost, ffmpeg, mpi, expat, freetype, glew, hdf5, jpeg, jsoncpp, libxml2, lz4, netcdf-c, netcdf-cxx, libpng, libtiff, zlib, eigen, double-conversion, sqlite
Run Dependencies:
python, py-mpi4py
Description:
The Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computer graphics, image processing and visualization.

vtk-h

Homepage:
Spack package:
Versions:
develop, 0.5.0
Build Dependencies:
cuda, cmake, mpi, vtk-m
Link Dependencies:
cuda, mpi, vtk-m
Description:
VTK-h is a toolkit of scientific visualization algorithms for emerging processor architectures. VTK-h brings together several projects like VTK-m and DIY2 to provide a toolkit with hybrid parallel capabilities.

vtk-m

Homepage:
Spack package:
Versions:
master, 1.5.0, 1.4.0, 1.3.0, 1.2.0, 1.1.0
Build Dependencies:
cuda, cmake, tbb, mpi
Link Dependencies:
cuda, cmake, tbb, mpi
Description:
VTK-m is a toolkit of scientific visualization algorithms for emerging processor architectures. VTK-m supports the fine-grained concurrency for data analysis and visualization algorithms required to drive extreme scale computing by providing abstract models for data and execution that can be applied to a variety of algorithms across many different processor architectures.

wannier90

Homepage:
Spack package:
Versions:
2.1.0, 2.0.1
Build Dependencies:
mpi, lapack, blas
Link Dependencies:
mpi, lapack, blas
Description:
Wannier90 calculates maximally-localised Wannier functions (MLWFs). Wannier90 is released under the GNU General Public License.

warpx

Homepage:
Spack package:
Versions:
master
Build Dependencies:
mpi, fftw
Link Dependencies:
mpi, fftw
Description:
WarpX is an advanced electromagnetic Particle-In-Cell code. It supports many features including Perfectly-Matched Layers (PML) and mesh refinement. In addition, WarpX is a highly-parallel and highly-optimized code and features hybrid OpenMP/MPI parallelization, advanced vectorization techniques and load balancing capabilities.

watch

Homepage:
Spack package:
Versions:
master, 3.3.15
Build Dependencies:
autoconf, automake, libtool, m4, pkgconfig, gettext, ncurses
Link Dependencies:
ncurses
Description:
Executes a program periodically, showing output fullscreen.

wcslib

Homepage:
Spack package:
Versions:
6.4
Build Dependencies:
gmake, flex, cfitsio, libx11
Link Dependencies:
cfitsio, libx11
Description:
WCSLIB a C implementation of the coordinate transformations defined in the FITS WCS papers.

wget

Homepage:
Spack package:
Versions:
1.20.3, 1.19.1, 1.17, 1.16
Build Dependencies:
gnutls, openssl, gettext, python, zlib, libpsl, pcre, perl, pkgconfig, libiconv
Link Dependencies:
gnutls, openssl, zlib, libpsl, pcre, libiconv
Test Dependencies:
valgrind
Description:
GNU Wget is a free software package for retrieving files using HTTP, HTTPS and FTP, the most widely-used Internet protocols. It is a non- interactive commandline tool, so it may easily be called from scripts, cron jobs, terminals without X-Windows support, etc.

wgsim

Homepage:
Spack package:
Versions:
2011.10.17
Build Dependencies:
zlib
Link Dependencies:
zlib
Description:
Wgsim is a small tool for simulating sequence reads from a reference genome. It is able to simulate diploid genomes with SNPs and insertion/deletion (INDEL) polymorphisms, and simulate reads with uniform substitution sequencing errors. It does not generate INDEL sequencing errors, but this can be partly compensated by simulating INDEL polymorphisms.

which

Homepage:
Spack package:
Versions:
2.21
Description:
GNU which - is a utility that is used to find which executable (or alias or shell function) is executed when entered on the shell prompt.

windowswmproto

Homepage:
Spack package:
Versions:
1.0.4
Description:
This module provides the definition of the WindowsWM extension to the X11 protocol, used for coordination between an X11 server and the Microsoft Windows native window manager. WindowsWM is only intended to be used on Cygwin when running a rootless XWin server.

wireshark

Homepage:
Spack package:
Versions:
3.2.1, 3.2.0, 3.1.0, 3.0.8, 2.6.0
Build Dependencies:
cmake, bison, c-ares, doxygen, flex, git, glib, gnutls, libgcrypt, libmaxminddb, libtool, libpcap, lua, krb5, pkgconfig, libssh, nghttp2, qt
Link Dependencies:
c-ares, glib, gnutls, libgcrypt, libmaxminddb, libpcap, lua, krb5, libssh, nghttp2, qt
Description:
Graphical network analyzer and capture tool

wordnet

Homepage:
Spack package:
Versions:
3.0
Build Dependencies:
tk, tcl
Link Dependencies:
tk, tcl
Description:
WordNet is a large lexical database of English. Nouns, verbs, adjectives and adverbs are grouped into sets of cognitive synonyms (synsets), each expressing a distinct concept.

workrave

Homepage:
Spack package:
Versions:
1_10_20, 1_10_19, 1_10_18, 1_10_17, 1_10_16, 1_10_15, 1_10_14, 1_10_13, 1_10_12, 1_10_10
Build Dependencies:
autoconf, automake, libtool, m4, libx11, py-cheetah, glib, glibmm, gtkplus, gtkmm, libsigcpp
Link Dependencies:
libx11, py-cheetah, glib, glibmm, gtkplus, gtkmm, libsigcpp
Description:
Workrave is a program that assists in the recovery and prevention of Repetitive Strain Injury (RSI). The program frequently alerts you to take micro-pauses, rest breaks and restricts you to your daily limit. The program runs on GNU/Linux and Microsoft Windows.

wt

Homepage:
Spack package:
Versions:
master, 3.3.7
Build Dependencies:
cmake, pkgconfig, boost, openssl, libharu, sqlite, mariadb, postgresql, pango, zlib
Link Dependencies:
boost, openssl, libharu, sqlite, mariadb, postgresql, pango, zlib
Description:
Wt, C++ Web Toolkit. Wt is a C++ library for developing web applications.

wtdbg2

Homepage:
Spack package:
Versions:
2.3
Build Dependencies:
zlib
Link Dependencies:
zlib
Description:
A fuzzy Bruijn graph approach to long noisy reads assembly

wxpropgrid

Homepage:
Spack package:
Versions:
1.4.15
Build Dependencies:
wxwidgets
Link Dependencies:
wxwidgets
Description:
wxPropertyGrid is a property sheet control for wxWidgets. In other words, it is a specialized two-column grid for editing properties such as strings, numbers, flagsets, string arrays, and colours.

wxwidgets

Homepage:
Spack package:
Versions:
develop, 3.1.0, 3.0.2, 3.0.1
Build Dependencies:
pkgconfig, gtkplus
Link Dependencies:
gtkplus
Description:
wxWidgets is a C++ library that lets developers create applications for Windows, Mac OS X, Linux and other platforms with a single code base. It has popular language bindings for Python, Perl, Ruby and many other languages, and unlike other cross-platform toolkits, wxWidgets gives applications a truly native look and feel because it uses the platform's native API rather than emulating the GUI. It's also extensive, free, open-source and mature.

x11perf

Homepage:
Spack package:
Versions:
1.6.0
Build Dependencies:
libx11, libxmu, libxrender, libxft, xproto, pkgconfig, util-macros
Link Dependencies:
libx11, libxmu, libxrender, libxft
Description:
Simple X server performance benchmarker.

xapian-core

Homepage:
Spack package:
Versions:
1.4.11, 1.4.3
Build Dependencies:
zlib
Link Dependencies:
zlib
Description:
Xapian is a highly adaptable toolkit which allows developers to easily add advanced indexing and search facilities to their own applications. It supports the Probabilistic Information Retrieval model and also supports a rich set of boolean query operators.

xauth

Homepage:
Spack package:
Versions:
1.0.9
Build Dependencies:
libx11, libxau, libxext, libxmu, xproto, pkgconfig, util-macros
Link Dependencies:
libx11, libxau, libxext, libxmu, xproto
Description:
The xauth program is used to edit and display the authorization information used in connecting to the X server.

xbacklight

Homepage:
Spack package:
Versions:
1.2.1
Build Dependencies:
libxcb, xcb-util, pkgconfig, util-macros
Link Dependencies:
libxcb, xcb-util
Description:
Xbacklight is used to adjust the backlight brightness where supported. It uses the RandR extension to find all outputs on the X server supporting backlight brightness control and changes them all in the same way.

xbiff

Homepage:
Spack package:
Versions:
1.0.3
Build Dependencies:
libxaw, libxmu, libxext, libx11, xbitmaps, pkgconfig, util-macros
Link Dependencies:
libxaw, libxmu, libxext, libx11
Description:
xbiff provides graphical notification of new e-mail. It only handles mail stored in a filesystem accessible file, not via IMAP, POP or other remote access protocols.

xbitmaps

Homepage:
Spack package:
Versions:
1.1.1
Build Dependencies:
pkgconfig, util-macros
Description:
The xbitmaps package contains bitmap images used by multiple applications built in Xorg.

xbraid

Homepage:
Spack package:
Versions:
2.2.0
Build Dependencies:
mpi
Link Dependencies:
mpi
Description:
XBraid: Parallel time integration with Multigrid

xcalc

Homepage:
Spack package:
Versions:
1.0.6
Build Dependencies:
libxaw, libxt, libx11, xproto, pkgconfig, util-macros
Link Dependencies:
libxaw, libxt, libx11
Description:
xcalc is a scientific calculator X11 client that can emulate a TI-30 or an HP-10C.

xcb-demo

Homepage:
Spack package:
Versions:
0.1
Build Dependencies:
libxcb, xcb-util, xcb-util-image, xcb-util-wm, pkgconfig
Link Dependencies:
libxcb, xcb-util, xcb-util-image, xcb-util-wm
Description:
xcb-demo: A collection of demo programs that use the XCB library.

xcb-proto

Homepage:
Spack package:
Versions:
1.13, 1.12, 1.11
Description:
xcb-proto provides the XML-XCB protocol descriptions that libxcb uses to generate the majority of its code and API.

xcb-util

Homepage:
Spack package:
Versions:
0.4.0
Build Dependencies:
libxcb, pkgconfig
Link Dependencies:
libxcb
Description:
The XCB util modules provides a number of libraries which sit on top of libxcb, the core X protocol library, and some of the extension libraries. These experimental libraries provide convenience functions and interfaces which make the raw X protocol more usable. Some of the libraries also provide client-side code which is not strictly part of the X protocol but which have traditionally been provided by Xlib.

xcb-util-cursor

Homepage:
Spack package:
Versions:
0.1.3
Build Dependencies:
libxcb, xcb-util-renderutil, xcb-util-image, pkgconfig
Link Dependencies:
libxcb, xcb-util-renderutil, xcb-util-image
Description:
The XCB util modules provides a number of libraries which sit on top of libxcb, the core X protocol library, and some of the extension libraries. These experimental libraries provide convenience functions and interfaces which make the raw X protocol more usable. Some of the libraries also provide client-side code which is not strictly part of the X protocol but which have traditionally been provided by Xlib.

xcb-util-errors

Homepage:
Spack package:
Versions:
1.0
Build Dependencies:
libxcb, xcb-proto, pkgconfig
Link Dependencies:
libxcb
Description:
The XCB util modules provides a number of libraries which sit on top of libxcb, the core X protocol library, and some of the extension libraries. These experimental libraries provide convenience functions and interfaces which make the raw X protocol more usable. Some of the libraries also provide client-side code which is not strictly part of the X protocol but which have traditionally been provided by Xlib.

xcb-util-image

Homepage:
Spack package:
Versions:
0.4.0
Build Dependencies:
libxcb, xcb-util, xproto, pkgconfig
Link Dependencies:
libxcb, xcb-util
Description:
The XCB util modules provides a number of libraries which sit on top of libxcb, the core X protocol library, and some of the extension libraries. These experimental libraries provide convenience functions and interfaces which make the raw X protocol more usable. Some of the libraries also provide client-side code which is not strictly part of the X protocol but which have traditionally been provided by Xlib.

xcb-util-keysyms

Homepage:
Spack package:
Versions:
0.4.0
Build Dependencies:
libxcb, xproto, pkgconfig
Link Dependencies:
libxcb
Description:
The XCB util modules provides a number of libraries which sit on top of libxcb, the core X protocol library, and some of the extension libraries. These experimental libraries provide convenience functions and interfaces which make the raw X protocol more usable. Some of the libraries also provide client-side code which is not strictly part of the X protocol but which have traditionally been provided by Xlib.

xcb-util-renderutil

Homepage:
Spack package:
Versions:
0.3.9
Build Dependencies:
libxcb, pkgconfig
Link Dependencies:
libxcb
Description:
The XCB util modules provides a number of libraries which sit on top of libxcb, the core X protocol library, and some of the extension libraries. These experimental libraries provide convenience functions and interfaces which make the raw X protocol more usable. Some of the libraries also provide client-side code which is not strictly part of the X protocol but which have traditionally been provided by Xlib.

xcb-util-wm

Homepage:
Spack package:
Versions:
0.4.1
Build Dependencies:
m4, libxcb, pkgconfig
Link Dependencies:
libxcb
Description:
The XCB util modules provides a number of libraries which sit on top of libxcb, the core X protocol library, and some of the extension libraries. These experimental libraries provide convenience functions and interfaces which make the raw X protocol more usable. Some of the libraries also provide client-side code which is not strictly part of the X protocol but which have traditionally been provided by Xlib.

xcb-util-xrm

Homepage:
Spack package:
Versions:
1.2
Build Dependencies:
autoconf, automake, libtool, m4, pkgconfig, libxcb
Link Dependencies:
libxcb
Description:
XCB util-xrm module provides the 'xrm' library, i.e. utility functions for the X resource manager.

xclip

Homepage:
Spack package:
Versions:
0.13
Build Dependencies:
libxmu, libx11, autoconf, automake, libtool, m4
Link Dependencies:
libxmu, libx11
Description:
xclip is a command line utility that is designed to run on any system with an X11 implementation. It provides an interface to X selections ("the clipboard") from the command line. It can read data from standard in or a file and place it in an X selection for pasting into other X applications. xclip can also print an X selection to standard out, which can then be redirected to a file or another program.

xclipboard

Homepage:
Spack package:
Versions:
1.1.3
Build Dependencies:
libxaw, libxmu, libxt, libx11, libxkbfile, xproto, pkgconfig, util-macros
Link Dependencies:
libxaw, libxmu, libxt, libx11, libxkbfile
Description:
xclipboard is used to collect and display text selections that are sent to the CLIPBOARD by other clients. It is typically used to save CLIPBOARD selections for later use. It stores each CLIPBOARD selection as a separate string, each of which can be selected.

xclock

Homepage:
Spack package:
Versions:
1.0.7
Build Dependencies:
libxaw, libxmu, libx11, libxrender, libxft, libxkbfile, libxt, xproto, pkgconfig, util-macros
Link Dependencies:
libxaw, libxmu, libx11, libxrender, libxft, libxkbfile, libxt
Description:
xclock is the classic X Window System clock utility. It displays the time in analog or digital form, continuously updated at a frequency which may be specified by the user.

xcmiscproto

Homepage:
Spack package:
Versions:
1.2.2
Build Dependencies:
pkgconfig, util-macros
Description:
XC-MISC Extension. This extension defines a protocol that provides Xlib two ways to query the server for available resource IDs.

xcmsdb

Homepage:
Spack package:
Versions:
1.0.5
Build Dependencies:
libx11, pkgconfig, util-macros
Link Dependencies:
libx11
Description:
xcmsdb is used to load, query, or remove Device Color Characterization data stored in properties on the root window of the screen as specified in section 7, Device Color Characterization, of the X11 Inter-Client Communication Conventions Manual (ICCCM).

xcompmgr

Homepage:
Spack package:
Versions:
1.1.7
Build Dependencies:
libxcomposite, libxfixes, libxdamage, libxrender, libxext, pkgconfig, util-macros
Link Dependencies:
libxcomposite, libxfixes, libxdamage, libxrender, libxext
Description:
xcompmgr is a sample compositing manager for X servers supporting the XFIXES, DAMAGE, RENDER, and COMPOSITE extensions. It enables basic eye- candy effects.

xconsole

Homepage:
Spack package:
Versions:
1.0.6
Build Dependencies:
libxaw, libxmu, libxt, libx11, xproto, pkgconfig, util-macros
Link Dependencies:
libxaw, libxmu, libxt, libx11, xproto
Description:
xconsole displays in a X11 window the messages which are usually sent to /dev/console.

xcursor-themes

Homepage:
Spack package:
Versions:
1.0.4
Build Dependencies:
libxcursor, xcursorgen, pkgconfig, util-macros
Link Dependencies:
libxcursor
Description:
This is a default set of cursor themes for use with libXcursor, originally created for the XFree86 Project, and now shipped as part of the X.Org software distribution.

xcursorgen

Homepage:
Spack package:
Versions:
1.0.6
Build Dependencies:
libx11, libxcursor, libpng, pkgconfig, util-macros
Link Dependencies:
libx11, libxcursor, libpng
Description:
xcursorgen prepares X11 cursor sets for use with libXcursor.

xdbedizzy

Homepage:
Spack package:
Versions:
1.1.0
Build Dependencies:
libx11, libxext, pkgconfig, util-macros
Link Dependencies:
libx11, libxext
Description:
xdbedizzy is a demo of the X11 Double Buffer Extension (DBE) creating a double buffered spinning scene.

xditview

Homepage:
Spack package:
Versions:
1.0.4
Build Dependencies:
libxaw, libxmu, libxt, libx11, pkgconfig, util-macros
Link Dependencies:
libxaw, libxmu, libxt, libx11
Description:
xditview displays ditroff output on an X display.

xdm

Homepage:
Spack package:
Versions:
1.1.11
Build Dependencies:
libxmu, libx11, libxau, libxinerama, libxft, libxpm, libxaw, libxdmcp, libxt, libxext, pkgconfig, util-macros
Link Dependencies:
libxmu, libx11, libxau, libxinerama, libxft, libxpm, libxaw, libxdmcp, libxt, libxext
Description:
X Display Manager / XDMCP server.

xdmf3

Homepage:
Spack package:
Versions:
2019-01-14
Build Dependencies:
cmake, libxml2, boost, mpi, hdf5
Link Dependencies:
libxml2, boost, mpi, hdf5
Description:
XDMF, or eXtensible Data Model and Format (XDMF), is a common data model format to exchange scientific data between High Performance Computing codes and tools.

xdpyinfo

Homepage:
Spack package:
Versions:
1.3.2
Build Dependencies:
libxext, libx11, libxtst, libxcb, xproto, recordproto, inputproto, fixesproto, pkgconfig, util-macros
Link Dependencies:
libxext, libx11, libxtst, libxcb
Description:
xdpyinfo is a utility for displaying information about an X server. It is used to examine the capabilities of a server, the predefined values for various parameters used in communicating between clients and the server, and the different types of screens, visuals, and X11 protocol extensions that are available.

xdriinfo

Homepage:
Spack package:
Versions:
1.0.5
Build Dependencies:
libx11, expat, libxshmfence, libxext, libxdamage, libxfixes, pcre, glproto, pkgconfig, util-macros
Link Dependencies:
libx11, expat, libxshmfence, libxext, libxdamage, libxfixes, pcre
Description:
xdriinfo - query configuration information of X11 DRI drivers.

xedit

Homepage:
Spack package:
Versions:
1.2.2
Build Dependencies:
libxaw, libxmu, libxt, libx11, pkgconfig, util-macros
Link Dependencies:
libxaw, libxmu, libxt, libx11
Description:
Xedit is a simple text editor for X.

xerces-c

Homepage:
Spack package:
Versions:
3.2.2, 3.2.1, 3.1.4, 3.1.3
Link Dependencies:
libiconv, icu4c
Description:
Xerces-C++ is a validating XML parser written in a portable subset of C++. Xerces-C++ makes it easy to give your application the ability to read and write XML data. A shared library is provided for parsing, generating, manipulating, and validating XML documents using the DOM, SAX, and SAX2 APIs.

xeus

Homepage:
Spack package:
Versions:
develop, 0.15.0, 0.14.1
Build Dependencies:
cmake, libzmq, cppzmq, cryptopp, xtl, nlohmann-json, libuuid
Link Dependencies:
libzmq, cppzmq, cryptopp, xtl, nlohmann-json, libuuid
Description:
QuantStack C++ implementation of Jupyter kernel protocol

xev

Homepage:
Spack package:
Versions:
1.2.2
Build Dependencies:
libxrandr, libx11, xproto, pkgconfig, util-macros
Link Dependencies:
libxrandr, libx11
Description:
xev creates a window and then asks the X server to send it X11 events whenever anything happens to the window (such as it being moved, resized, typed in, clicked in, etc.). You can also attach it to an existing window. It is useful for seeing what causes events to occur and to display the information that they contain; it is essentially a debugging and development tool, and should not be needed in normal usage.

xextproto

Homepage:
Spack package:
Versions:
7.3.0
Build Dependencies:
pkgconfig, util-macros
Description:
X Protocol Extensions.

xeyes

Homepage:
Spack package:
Versions:
1.1.1
Build Dependencies:
libx11, libxt, libxext, libxmu, libxrender, pkgconfig, util-macros
Link Dependencies:
libx11, libxt, libxext, libxmu, libxrender
Description:
xeyes - a follow the mouse X demo, using the X SHAPE extension

xf86bigfontproto

Homepage:
Spack package:
Versions:
1.2.0
Description:
X.org XF86BigFontProto protocol headers.

xf86dga

Homepage:
Spack package:
Versions:
1.0.3
Build Dependencies:
libx11, libxxf86dga, pkgconfig, util-macros
Link Dependencies:
libx11, libxxf86dga
Description:
dga is a simple test client for the XFree86-DGA extension.

xf86dgaproto

Homepage:
Spack package:
Versions:
2.1
Description:
X.org XF86DGAProto protocol headers.

xf86driproto

Homepage:
Spack package:
Versions:
2.1.1
Build Dependencies:
pkgconfig, util-macros
Description:
XFree86 Direct Rendering Infrastructure Extension. This extension defines a protocol to allow user applications to access the video hardware without requiring data to be passed through the X server.

xf86miscproto

Homepage:
Spack package:
Versions:
0.9.3
Description:
This package includes the protocol definitions of the "XFree86-Misc" extension to the X11 protocol. The "XFree86-Misc" extension is supported by the XFree86 X server and versions of the Xorg X server prior to Xorg 1.6.

xf86rushproto

Homepage:
Spack package:
Versions:
1.1.2
Description:
X.org XF86RushProto protocol headers.

xf86vidmodeproto

Homepage:
Spack package:
Versions:
2.3.1
Build Dependencies:
pkgconfig, util-macros
Description:
XFree86 Video Mode Extension. This extension defines a protocol for dynamically configuring modelines and gamma.

xfd

Homepage:
Spack package:
Versions:
1.1.3, 1.1.2
Build Dependencies:
fontconfig, gettext, libxaw, libxft, libxrender, libxmu, libxt, xproto, pkgconfig, util-macros
Link Dependencies:
fontconfig, gettext, libxaw, libxft, libxrender, libxmu, libxt
Description:
xfd - display all the characters in a font using either the X11 core protocol or libXft2.

xfindproxy

Homepage:
Spack package:
Versions:
1.0.4
Build Dependencies:
libice, libxt, xproto, xproxymanagementprotocol, pkgconfig, util-macros
Link Dependencies:
libice, libxt
Description:
xfindproxy is used to locate available X11 proxy services. It utilizes the Proxy Management Protocol to communicate with a proxy manager. The proxy manager keeps track of all available proxy services, starts new proxies when necessary, and makes sure that proxies are shared whenever possible.

xfontsel

Homepage:
Spack package:
Versions:
1.0.5
Build Dependencies:
libxaw, libxmu, libxt, libx11, pkgconfig, util-macros
Link Dependencies:
libxaw, libxmu, libxt, libx11
Description:
xfontsel application provides a simple way to display the X11 core protocol fonts known to your X server, examine samples of each, and retrieve the X Logical Font Description ("XLFD") full name for a font.

xfs

Homepage:
Spack package:
Versions:
1.1.4
Build Dependencies:
libxfont, font-util, xproto, fontsproto, xtrans, pkgconfig, util-macros
Link Dependencies:
libxfont, font-util
Description:
X Font Server.

xfsinfo

Homepage:
Spack package:
Versions:
1.0.5
Build Dependencies:
libfs, xproto, pkgconfig, util-macros
Link Dependencies:
libfs
Description:
xfsinfo is a utility for displaying information about an X font server. It is used to examine the capabilities of a server, the predefined values for various parameters used in communicating between clients and the server, and the font catalogues and alternate servers that are available.

xfwp

Homepage:
Spack package:
Versions:
1.0.3
Build Dependencies:
libice, xproto, xproxymanagementprotocol, pkgconfig, util-macros
Link Dependencies:
libice
Description:
xfwp proxies X11 protocol connections, such as through a firewall.

xgamma

Homepage:
Spack package:
Versions:
1.0.6
Build Dependencies:
libx11, libxxf86vm, xproto, pkgconfig, util-macros
Link Dependencies:
libx11, libxxf86vm
Description:
xgamma allows X users to query and alter the gamma correction of a monitor via the X video mode extension (XFree86-VidModeExtension).

xgboost

Homepage:
Spack package:
Versions:
0.81
Build Dependencies:
cuda, cmake
Link Dependencies:
cuda
Description:
Scalable, Portable and Distributed Gradient Boosting (GBDT, GBRT or GBM) Library, for Python, R, Java, Scala, C++ and more. Runs on single machine, Hadoop, Spark, Flink and DataFlow

xgc

Homepage:
Spack package:
Versions:
1.0.5
Build Dependencies:
libxaw, libxt, flex, bison, pkgconfig, util-macros
Link Dependencies:
libxaw, libxt
Description:
xgc is an X11 graphics demo that shows various features of the X11 core protocol graphics primitives.

xhmm

Homepage:
Spack package:
Versions:
20160104
Build Dependencies:
lapack
Link Dependencies:
lapack
Description:
The XHMM C++ software suite was written to call copy number variation (CNV) from next-generation sequencing projects, where exome capture was used (or targeted sequencing, more generally).

xhost

Homepage:
Spack package:
Versions:
1.0.7
Build Dependencies:
libx11, libxmu, libxau, xproto, pkgconfig, util-macros
Link Dependencies:
libx11, libxmu, libxau
Description:
xhost is used to manage the list of host names or user names allowed to make connections to the X server.

xineramaproto

Homepage:
Spack package:
Versions:
1.2.1
Build Dependencies:
pkgconfig, util-macros
Description:
X Xinerama Extension. This is an X extension that allows multiple physical screens controlled by a single X server to appear as a single screen.

xinit

Homepage:
Spack package:
Versions:
1.3.4
Build Dependencies:
libx11, xproto, pkgconfig, util-macros
Link Dependencies:
libx11
Description:
The xinit program is used to start the X Window System server and a first client program on systems that are not using a display manager such as xdm.

xinput

Homepage:
Spack package:
Versions:
1.6.2
Build Dependencies:
libx11, libxext, libxi, libxrandr, libxinerama, inputproto, fixesproto, randrproto, xineramaproto, pkgconfig, util-macros
Link Dependencies:
libx11, libxext, libxi, libxrandr, libxinerama
Description:
xinput is a utility to configure and test XInput devices.

xios

Homepage:
Spack package:
Versions:
develop, 1.0
Build Dependencies:
netcdf-c, netcdf-fortran, hdf5, mpi, boost, blitz, perl, perl-uri, gmake
Link Dependencies:
netcdf-c, netcdf-fortran, hdf5, mpi, boost, blitz
Description:
XML-IO-SERVER library for IO management of climate models.

xkbcomp

Homepage:
Spack package:
Versions:
1.3.1
Build Dependencies:
libx11, libxkbfile, xproto, bison, pkgconfig, util-macros
Link Dependencies:
libx11, libxkbfile
Description:
The X Keyboard (XKB) Extension essentially replaces the core protocol definition of a keyboard. The extension makes it possible to specify clearly and explicitly most aspects of keyboard behaviour on a per-key basis, and to track more closely the logical and physical state of a keyboard. It also includes a number of keyboard controls designed to make keyboards more accessible to people with physical impairments.

xkbdata

Homepage:
Spack package:
Versions:
1.0.1
Build Dependencies:
xkbcomp
Description:
The XKB data files for the various keyboard models, layouts, and locales.

xkbevd

Homepage:
Spack package:
Versions:
1.1.4
Build Dependencies:
libxkbfile, libx11, bison, pkgconfig, util-macros
Link Dependencies:
libxkbfile, libx11
Description:
XKB event daemon demo.

xkbprint

Homepage:
Spack package:
Versions:
1.0.4
Build Dependencies:
libxkbfile, libx11, xproto, pkgconfig, util-macros
Link Dependencies:
libxkbfile, libx11
Description:
xkbprint generates a printable or encapsulated PostScript description of an XKB keyboard description.

xkbutils

Homepage:
Spack package:
Versions:
1.0.4
Build Dependencies:
libxaw, libxt, libx11, xproto, inputproto, pkgconfig, util-macros
Link Dependencies:
libxaw, libxt, libx11
Description:
xkbutils is a collection of small utilities utilizing the XKeyboard (XKB) extension to the X11 protocol.

xkeyboard-config

Homepage:
Spack package:
Versions:
2.18
Build Dependencies:
libx11, libxslt, pkgconfig, intltool, xproto
Link Dependencies:
libx11
Description:
This project provides a consistent, well-structured, frequently released, open source database of keyboard configuration data. The project is targeted to XKB-based systems.

xkill

Homepage:
Spack package:
Versions:
1.0.4
Build Dependencies:
libx11, libxmu, xproto, pkgconfig, util-macros
Link Dependencies:
libx11, libxmu
Description:
xkill is a utility for forcing the X server to close connections to clients. This program is very dangerous, but is useful for aborting programs that have displayed undesired windows on a user's screen.

xload

Homepage:
Spack package:
Versions:
1.1.2
Build Dependencies:
libxaw, libxmu, libxt, libx11, xproto, pkgconfig, util-macros
Link Dependencies:
libxaw, libxmu, libxt, libx11
Description:
xload displays a periodically updating histogram of the system load average.

xlsatoms

Homepage:
Spack package:
Versions:
1.1.2
Build Dependencies:
libxcb, libx11, pkgconfig, util-macros
Link Dependencies:
libxcb, libx11
Description:
xlsatoms lists the interned atoms defined on an X11 server.

xlsclients

Homepage:
Spack package:
Versions:
1.1.3
Build Dependencies:
libxcb, libx11, pkgconfig, util-macros
Link Dependencies:
libxcb, libx11
Description:
xlsclients is a utility for listing information about the client applications running on a X11 server.

xlsfonts

Homepage:
Spack package:
Versions:
1.0.5
Build Dependencies:
libx11, xproto, pkgconfig, util-macros
Link Dependencies:
libx11
Description:
xlsfonts lists fonts available from an X server via the X11 core protocol.

xmag

Homepage:
Spack package:
Versions:
1.0.6
Build Dependencies:
libxaw, libxmu, libxt, libx11, pkgconfig, util-macros
Link Dependencies:
libxaw, libxmu, libxt, libx11
Description:
xmag displays a magnified snapshot of a portion of an X11 screen.

xman

Homepage:
Spack package:
Versions:
1.1.4
Build Dependencies:
libxaw, libxt, xproto, pkgconfig, util-macros
Link Dependencies:
libxaw, libxt
Description:
xman is a graphical manual page browser using the Athena Widgets (Xaw) toolkit.

xmessage

Homepage:
Spack package:
Versions:
1.0.4
Build Dependencies:
libxaw, libxt, pkgconfig, util-macros
Link Dependencies:
libxaw, libxt
Description:
xmessage displays a message or query in a window. The user can click on an "okay" button to dismiss it or can select one of several buttons to answer a question. xmessage can also exit after a specified time.

xmh

Homepage:
Spack package:
Versions:
1.0.3
Build Dependencies:
libxaw, libxmu, libxt, libx11, xbitmaps, pkgconfig, util-macros
Link Dependencies:
libxaw, libxmu, libxt, libx11
Description:
The xmh program provides a graphical user interface to the MH Message Handling System. To actually do things with your mail, it makes calls to the MH package.

xmlf90

Homepage:
Spack package:
Versions:
1.5.2
Build Dependencies:
autoconf, automake, libtool, m4
Description:
xmlf90 is a suite of libraries to handle XML in Fortran.

xmlto

Homepage:
Spack package:
Versions:
0.0.28
Build Dependencies:
libxslt
Link Dependencies:
libxslt
Description:
Utility xmlto is a simple shell script for converting XML files to various formats. It serves as easy to use command line frontend to make fine output without remembering many long options and searching for the syntax of the backends.

xmodmap

Homepage:
Spack package:
Versions:
1.0.9
Build Dependencies:
libx11, xproto, pkgconfig, util-macros
Link Dependencies:
libx11
Description:
The xmodmap program is used to edit and display the keyboard modifier map and keymap table that are used by client applications to convert event keycodes into keysyms. It is usually run from the user's session startup script to configure the keyboard according to personal tastes.

xmore

Homepage:
Spack package:
Versions:
1.0.2
Build Dependencies:
libxaw, libxt, pkgconfig, util-macros
Link Dependencies:
libxaw, libxt
Description:
xmore - plain text display program for the X Window System.

xorg-cf-files

Homepage:
Spack package:
Versions:
1.0.6
Build Dependencies:
pkgconfig
Description:
The xorg-cf-files package contains the data files for the imake utility, defining the known settings for a wide variety of platforms (many of which have not been verified or tested in over a decade), and for many of the libraries formerly delivered in the X.Org monolithic releases.

xorg-docs

Homepage:
Spack package:
Versions:
1.7.1
Build Dependencies:
pkgconfig, util-macros, xorg-sgml-doctools, xmlto
Description:
This package provides miscellaneous documentation for the X Window System that doesn't better fit into other packages. The preferred documentation format for these documents is DocBook XML.

xorg-gtest

Homepage:
Spack package:
Versions:
0.7.1
Build Dependencies:
libx11, libxi, xorg-server, pkgconfig, util-macros
Link Dependencies:
libx11, libxi, xorg-server
Description:
Provides a Google Test environment for starting and stopping a X server for testing purposes.

xorg-sgml-doctools

Homepage:
Spack package:
Versions:
1.11
Build Dependencies:
pkgconfig, util-macros
Description:
This package provides a common set of SGML entities and XML/CSS style sheets used in building/formatting the documentation provided in other X.Org packages.

xphelloworld

Homepage:
Spack package:
Versions:
1.0.1
Build Dependencies:
libx11, libxaw, libxprintapputil, libxprintutil, libxp, libxt, pkgconfig, util-macros
Link Dependencies:
libx11, libxaw, libxprintapputil, libxprintutil, libxp, libxt
Description:
Xprint sample applications.

xplor-nih

Homepage:
Spack package:
Versions:
2.45
Build Dependencies:
python
Run Dependencies:
python
Description:
XPLOR-NIH is a structure determination program. Note: A manual download is required for XPLOR-NIH. Spack will search your current directory for the download file. Alternatively, add this file to a mirror so that Spack can find it. For instructions on how to set up a mirror, see http://spack.readthedocs.io/en/latest/mirrors.html

xplsprinters

Homepage:
Spack package:
Versions:
1.0.1
Build Dependencies:
libxp, libxprintutil, libx11, pkgconfig, util-macros
Link Dependencies:
libxp, libxprintutil, libx11
Description:
List Xprint printers.

xpr

Homepage:
Spack package:
Versions:
1.0.4
Build Dependencies:
libxmu, libx11, xproto, pkgconfig, util-macros
Link Dependencies:
libxmu, libx11
Description:
xpr takes as input a window dump file produced by xwd and formats it for output on various types of printers.

xprehashprinterlist

Homepage:
Spack package:
Versions:
1.0.1
Build Dependencies:
libxp, libx11, pkgconfig, util-macros
Link Dependencies:
libxp, libx11
Description:
Rehash list of Xprint printers.

xprop

Homepage:
Spack package:
Versions:
1.2.2
Build Dependencies:
libx11, xproto, pkgconfig, util-macros
Link Dependencies:
libx11
Description:
xprop is a command line tool to display and/or set window and font properties of an X server.

xproto

Homepage:
Spack package:
Versions:
7.0.31, 7.0.29
Build Dependencies:
pkgconfig, util-macros
Description:
X Window System Core Protocol. This package provides the headers and specification documents defining the X Window System Core Protocol, Version 11. It also includes a number of headers that aren't purely protocol related, but are depended upon by many other X Window System packages to provide common definitions and porting layer.

xproxymanagementprotocol

Homepage:
Spack package:
Versions:
1.0.3
Description:
The Proxy Management Protocol is an ICE based protocol that provides a way for application servers to easily locate proxy services available to them.

xqilla

Homepage:
Spack package:
Versions:
2.3.3
Build Dependencies:
xerces-c
Link Dependencies:
xerces-c
Description:
XQilla is an XQuery and XPath 2 library and command line utility written in C++, implemented on top of the Xerces-C library.

xrandr

Homepage:
Spack package:
Versions:
1.5.0
Build Dependencies:
libxrandr, libxrender, libx11, randrproto, xproto, pkgconfig, util-macros
Link Dependencies:
libxrandr, libxrender, libx11, randrproto
Description:
xrandr - primitive command line interface to X11 Resize, Rotate, and Reflect (RandR) extension.

xrdb

Homepage:
Spack package:
Versions:
1.1.0
Build Dependencies:
libxmu, libx11, xproto, pkgconfig, util-macros
Link Dependencies:
libxmu, libx11
Description:
xrdb - X server resource database utility.

xrefresh

Homepage:
Spack package:
Versions:
1.0.5
Build Dependencies:
libx11, xproto, pkgconfig, util-macros
Link Dependencies:
libx11
Description:
xrefresh - refresh all or part of an X screen.

xrootd

Homepage:
Spack package:
Versions:
4.10.0, 4.8.5, 4.8.4, 4.8.3, 4.8.2, 4.8.1, 4.8.0, 4.7.1, 4.7.0, 4.6.1, 4.6.0, 4.5.0, 4.4.1, 4.4.0, 4.3.0
Build Dependencies:
cmake, bzip2, libxml2, openssl, python, readline, xz, zlib
Link Dependencies:
bzip2, libxml2, openssl, python, readline, xz, zlib
Description:
The XROOTD project aims at giving high performance, scalable fault tolerant access to data repositories of many kinds.

xrx

Homepage:
Spack package:
Versions:
1.0.4
Build Dependencies:
libx11, libxt, libxext, libxau, libice, libxaw, xtrans, xproxymanagementprotocol, pkgconfig, util-macros
Link Dependencies:
libx11, libxt, libxext, libxau, libice, libxaw
Description:
The remote execution (RX) service specifies a MIME format for invoking applications remotely, for example via a World Wide Web browser. This RX format specifies a syntax for listing network services required by the application, for example an X display server. The requesting Web browser must identify specific instances of the services in the request to invoke the application.

xsbench

Homepage:
Spack package:
Versions:
19, 18, 14, 13
Build Dependencies:
mpi
Link Dependencies:
mpi
Description:
XSBench is a mini-app representing a key computational kernel of the Monte Carlo neutronics application OpenMC. A full explanation of the theory and purpose of XSBench is provided in docs/XSBench_Theory.pdf.

xscope

Homepage:
Spack package:
Versions:
1.4.1
Build Dependencies:
xproto, xtrans, pkgconfig, util-macros
Description:
XSCOPE -- a program to monitor X11/Client conversations.

xsd

Homepage:
Spack package:
Versions:
4.0.0
Build Dependencies:
xerces-c, libtool
Link Dependencies:
xerces-c
Description:
CodeSynthesis XSD is an open-source, cross-platform W3C XML Schema to C++ data binding compiler. It support in-memory and event-driven XML processing models and is available for a wide range of C++ compilers and platforms.

xsdk

Homepage:
Spack package:
Versions:
develop, 0.5.0, 0.4.0, 0.3.0, xsdk-0.2.0
Build Dependencies:
hypre, mfem, superlu-dist, trilinos, petsc, dealii, pflotran, alquimia, sundials, plasma, magma, amrex, slepc, omega-h, strumpack, pumi, tasmanian, phist, ginkgo, precice, butterflypack
Link Dependencies:
hypre, mfem, superlu-dist, trilinos, petsc, dealii, pflotran, alquimia, sundials, plasma, magma, amrex, slepc, omega-h, strumpack, pumi, tasmanian, phist, ginkgo, precice, butterflypack
Run Dependencies:
py-libensemble
Description:
Xsdk is a suite of Department of Energy (DOE) packages for numerical simulation. This is a Spack bundle package that installs the xSDK packages

xsdktrilinos

Homepage:
Spack package:
Versions:
develop, 12.8.1, 12.6.4, xsdk-0.2.0
Build Dependencies:
cmake, mpi, hypre, petsc, trilinos
Link Dependencies:
mpi, hypre, petsc, trilinos
Description:
xSDKTrilinos contains the portions of Trilinos that depend on PETSc because they would cause a circular dependency if built as part of Trilinos.

xset

Homepage:
Spack package:
Versions:
1.2.3
Build Dependencies:
libxmu, libx11, xproto, pkgconfig, util-macros
Link Dependencies:
libxmu, libx11
Description:
User preference utility for X.

xsetmode

Homepage:
Spack package:
Versions:
1.0.0
Build Dependencies:
libxi, libx11, pkgconfig, util-macros
Link Dependencies:
libxi, libx11
Description:
Set the mode for an X Input device.

xsetpointer

Homepage:
Spack package:
Versions:
1.0.1
Build Dependencies:
libxi, libx11, inputproto, pkgconfig, util-macros
Link Dependencies:
libxi, libx11
Description:
Set an X Input device as the main pointer.

xsetroot

Homepage:
Spack package:
Versions:
1.1.1
Build Dependencies:
libxmu, libx11, libxcursor, xbitmaps, xproto, pkgconfig, util-macros
Link Dependencies:
libxmu, libx11, libxcursor
Description:
xsetroot - root window parameter setting utility for X.

xsimd

Homepage:
Spack package:
Versions:
develop, 7.2.3, 4.0.0, 3.1.0
Build Dependencies:
cmake
Test Dependencies:
googletest
Description:
C++ wrappers for SIMD intrinsics

xsm

Homepage:
Spack package:
Versions:
1.0.3
Build Dependencies:
libx11, libxt, libice, libsm, libxaw, pkgconfig, util-macros
Link Dependencies:
libx11, libxt, libice, libsm, libxaw
Description:
X Session Manager.

xssp

Homepage:
Spack package:
Versions:
3.0.10, 3.0.9, 3.0.8, 3.0.7, 3.0.6, 3.0.5, 3.0.4, 3.0.3, 3.0.2, 3.0.1
Build Dependencies:
autoconf, automake, libtool, m4, boost
Link Dependencies:
boost
Description:
The source code for building the mkdssp, mkhssp, hsspconv, and hsspsoap programs is bundled in the xssp project

xstdcmap

Homepage:
Spack package:
Versions:
1.0.3
Build Dependencies:
libxmu, libx11, xproto, pkgconfig, util-macros
Link Dependencies:
libxmu, libx11
Description:
The xstdcmap utility can be used to selectively define standard colormap properties. It is intended to be run from a user's X startup script to create standard colormap definitions in order to facilitate sharing of scarce colormap resources among clients using PseudoColor visuals.

xtensor

Homepage:
Spack package:
Versions:
develop, 0.20.7, 0.15.1, 0.13.1
Build Dependencies:
cmake, xtl, xsimd, intel-tbb
Link Dependencies:
xtl, xsimd, intel-tbb
Description:
Multi-dimensional arrays with broadcasting and lazy computing

xtensor-python

Homepage:
Spack package:
Versions:
develop, 0.23.1, 0.17.0
Build Dependencies:
cmake, xtensor, xtl, py-pybind11, py-numpy, python
Link Dependencies:
xtensor, xtl, py-pybind11, py-numpy, python
Run Dependencies:
python
Description:
Python bindings for the xtensor C++ multi-dimensional array library

xterm

Homepage:
Spack package:
Versions:
353, 350, 340, 330, 327
Build Dependencies:
libxft, fontconfig, libxaw, libxmu, libxt, libx11, libxinerama, libxpm, libice, freetype, libxrender, libxext, libsm, libxcb, libxau, bzip2, pkgconfig
Link Dependencies:
libxft, fontconfig, libxaw, libxmu, libxt, libx11, libxinerama, libxpm, libice, freetype, libxrender, libxext, libsm, libxcb, libxau, bzip2
Description:
The xterm program is a terminal emulator for the X Window System. It provides DEC VT102 and Tektronix 4014 compatible terminals for programs that can't use the window system directly.

xtl

Homepage:
Spack package:
Versions:
develop, 0.6.4, 0.4.0, 0.3.4, 0.3.3
Build Dependencies:
cmake
Description:
QuantStack tools library

xtrans

Homepage:
Spack package:
Versions:
1.3.5
Build Dependencies:
pkgconfig, util-macros
Description:
xtrans is a library of code that is shared among various X packages to handle network protocol transport in a modular fashion, allowing a single place to add new transport types. It is used by the X server, libX11, libICE, the X font server, and related components.

xtrap

Homepage:
Spack package:
Versions:
1.0.2
Build Dependencies:
libx11, libxtrap, pkgconfig, util-macros
Link Dependencies:
libx11, libxtrap
Description:
XTrap sample clients.

xts

Homepage:
Spack package:
Versions:
0.99.1
Build Dependencies:
libx11, libxext, libxi, libxtst, libxau, libxt, libxmu, libxaw, xtrans, bdftopcf, mkfontdir, perl, xset, xdpyinfo
Link Dependencies:
libx11, libxext, libxi, libxtst, libxau, libxt, libxmu, libxaw
Description:
This is a revamped version of X Test Suite (XTS) which removes some of the ugliness of building and running the tests.

xvidtune

Homepage:
Spack package:
Versions:
1.0.3
Build Dependencies:
libxxf86vm, libxt, libxaw, libxmu, libx11, pkgconfig, util-macros
Link Dependencies:
libxxf86vm, libxt, libxaw, libxmu, libx11
Description:
xvidtune is a client interface to the X server video mode extension (XFree86-VidModeExtension).

xvinfo

Homepage:
Spack package:
Versions:
1.1.3
Build Dependencies:
libxv, libx11, xproto, pkgconfig, util-macros
Link Dependencies:
libxv, libx11
Description:
xvinfo prints out the capabilities of any video adaptors associated with the display that are accessible through the X-Video extension.

xwd

Homepage:
Spack package:
Versions:
1.0.6
Build Dependencies:
libx11, libxkbfile, xproto, pkgconfig, util-macros
Link Dependencies:
libx11, libxkbfile
Description:
xwd - dump an image of an X window.

xwininfo

Homepage:
Spack package:
Versions:
1.1.3
Build Dependencies:
libxcb, libx11, xproto, pkgconfig, util-macros
Link Dependencies:
libxcb, libx11
Description:
xwininfo prints information about windows on an X server. Various information is displayed depending on which options are selected.

xwud

Homepage:
Spack package:
Versions:
1.0.4
Build Dependencies:
libx11, xproto, pkgconfig, util-macros
Link Dependencies:
libx11
Description:
xwud allows X users to display in a window an image saved in a specially formatted dump file, such as produced by xwd.

xxhash

Homepage:
Spack package:
Versions:
0.6.5, 0.6.4, 0.6.3, 0.6.2, 0.6.1, 0.6.0, 0.5.1, 0.5.0
Description:
xxHash is an Extremely fast Hash algorithm, running at RAM speed limits. It successfully completes the SMHasher test suite which evaluates collision, dispersion and randomness qualities of hash functions. Code is highly portable, and hashes are identical on all platforms (little / big endian).

xz

Homepage:
Spack package:
Versions:
5.2.4, 5.2.3, 5.2.2, 5.2.0
Description:
XZ Utils is free general-purpose data compression software with high compression ratio. XZ Utils were written for POSIX-like systems, but also work on some not-so-POSIX systems. XZ Utils are the successor to LZMA Utils.

yajl

Homepage:
Spack package:
Versions:
develop, 2.1.0
Build Dependencies:
cmake
Description:
Yet Another JSON Library (YAJL)

yambo

Homepage:
Spack package:
Versions:
4.2.2, 4.2.1, 4.2.0
Build Dependencies:
blas, lapack, mpi, netcdf-c, hdf5, fftw, scalapack, netcdf-fortran, libxc
Link Dependencies:
blas, lapack, mpi, netcdf-c, hdf5, fftw, scalapack, netcdf-fortran, libxc
Description:
Yambo is a FORTRAN/C code for Many-Body calculations in solid state and molecular physics. Yambo relies on the Kohn-Sham wavefunctions generated by two DFT public codes: abinit, and PWscf. The code was originally developed in the Condensed Matter Theoretical Group of the Physics Department at the University of Rome "Tor Vergata" by Andrea Marini. Previous to its release under the GPL license, yambo was known as SELF.

yaml-cpp

Homepage:
Spack package:
Versions:
develop, 0.6.3, 0.6.2, 0.5.3
Build Dependencies:
cmake, boost
Link Dependencies:
boost
Description:
A YAML parser and emitter in C++

yara

Homepage:
Spack package:
Versions:
3.9.0
Build Dependencies:
autoconf, automake, libtool, m4
Description:
YARA is a tool aimed at (but not limited to) helping malware researchers to identify and classify malware samples

yasm

Homepage:
Spack package:
Versions:
develop, 1.3.0
Build Dependencies:
autoconf, automake, libtool, m4
Link Dependencies:
autoconf, automake, libtool, m4
Description:
Yasm is a complete rewrite of the NASM-2.11.06 assembler. It supports the x86 and AMD64 instruction sets, accepts NASM and GAS assembler syntaxes and outputs binary, ELF32 and ELF64 object formats.

yorick

Homepage:
Spack package:
Versions:
master, 2.2.04, f90-plugin
Build Dependencies:
libx11
Link Dependencies:
libx11
Description:
Yorick is an interpreted programming language for scientific simulations or calculations, postprocessing or steering large simulation codes, interactive scientific graphics, and reading, writing, or translating files of numbers. Yorick includes an interactive graphics package, and a binary file package capable of translating to and from the raw numeric formats of all modern computers. Yorick is written in ANSI C and runs on most operating systems (*nix systems, MacOS X, Windows).

z3

Homepage:
Spack package:
Versions:
4.5.0, 4.4.1, 4.4.0
Build Dependencies:
python
Link Dependencies:
python
Run Dependencies:
python
Description:
Z3 is a theorem prover from Microsoft Research. It is licensed under the MIT license.

zfp

Homepage:
Spack package:
Versions:
0.5.5, 0.5.4, 0.5.2, 0.5.1
Build Dependencies:
cmake
Description:
zfp is an open source C/C++ library for high-fidelity, high-throughput lossy compression of floating-point and integer multi-dimensional arrays.

zip

Homepage:
Spack package:
Versions:
3.0
Build Dependencies:
bzip2
Link Dependencies:
bzip2
Description:
Zip is a compression and file packaging/archive utility.

zlib

Homepage:
Spack package:
Versions:
1.2.11, 1.2.8, 1.2.3
Description:
A free, general-purpose, legally unencumbered lossless data-compression library.

zoltan

Homepage:
Spack package:
Versions:
3.83, 3.8, 3.6, 3.3
Build Dependencies:
mpi, parmetis, metis, perl, autoconf, automake, m4
Link Dependencies:
mpi, parmetis, metis
Description:
The Zoltan library is a toolkit of parallel combinatorial algorithms for parallel, unstructured, and/or adaptive scientific applications. Zoltan's largest component is a suite of dynamic load-balancing and partitioning algorithms that increase applications' parallel performance by reducing idle time. Zoltan also has graph coloring and graph ordering algorithms, which are useful in task schedulers and parallel preconditioners.

zookeeper

Homepage:
Spack package:
Versions:
3.4.11
Description:
Apache ZooKeeper is an effort to develop and maintain an open-source server which enables highly reliable distributed coordination.

zsh

Homepage:
Spack package:
Versions:
5.4.2, 5.3.1, 5.1.1
Build Dependencies:
pcre, ncurses
Link Dependencies:
pcre, ncurses
Description:
Zsh is a shell designed for interactive use, although it is also a powerful scripting language. Many of the useful features of bash, ksh, and tcsh were incorporated into zsh; many original features were added.

zstd

Homepage:
Spack package:
Versions:
1.4.3, 1.4.2, 1.4.0, 1.3.8, 1.3.0, 1.1.2
Build Dependencies:
zlib
Link Dependencies:
zlib
Description:
Zstandard, or zstd as short version, is a fast lossless compression algorithm, targeting real-time compression scenarios at zlib-level and better compression ratios.

zziplib

Homepage:
Spack package:
Versions:
0.13.69
Build Dependencies:
python, zlib
Link Dependencies:
zlib
Description:
The zziplib provides read access to zipped files in a zip-archive, using compression based solely on free algorithms provided by zlib. It also provides a functionality to overlay the archive filesystem with the filesystem of the operating system environment.