パッケージ一覧<a class="headerlink" href="#package-list" title="このヘッドラインへのパーマリンク">¶

Description:

A package for the automatic differentiation of first and higher derivatives of vector functions in C and C++ programs by operator overloading.

aegean¶

Homepage:

http://brendelgroup.github.io/AEGeAn/

Spack package:

aegean/package.py

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:

http://aida.freehep.org/

Spack package:

aida/package.py

Versions:

3.2.1

Description:

Abstract Interfaces for Data Analysis

albany¶

Homepage:

http://gahansen.github.io/Albany

Spack package:

albany/package.py

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:

https://people.cs.clemson.edu/~dpj/albertstuff/albert.html

Spack package:

albert/package.py

Versions:

4.0a_opt4

Build Dependencies:

Link Dependencies:

Description:

Albert is an interactive program to assist the specialist in the study of nonassociative algebra.

alglib¶

Homepage:

http://www.alglib.net

Spack package:

alglib/package.py

Versions:

3.11.0

Description:

ALGLIB is a cross-platform numerical analysis and data processing library.

allinea-reports¶

Homepage:

http://www.allinea.com/products/allinea-performance-reports

Spack package:

allinea-reports/package.py

Versions:

6.0.4

Description:

Allinea Performance Reports are the most effective way to characterize and understand the performance of HPC application runs. One single-page HTML report elegantly answers a range of vital questions for any HPC site

allpaths-lg¶

Homepage:

http://www.broadinstitute.org/software/allpaths-lg/blog/

Spack package:

allpaths-lg/package.py

Versions:

52488

Description:

ALLPATHS-LG is our original short read assembler and it works on both small and large (mammalian size) genomes.

alquimia¶

Homepage:

https://github.com/LBL-EESA/alquimia-dev

Spack package:

alquimia/package.py

Versions:

develop, 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:

https://www.alsa-project.org

Spack package:

alsa-lib/package.py

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:

https://github.com/LLNL/Aluminum

Spack package:

aluminum/package.py

Versions:

master, 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.

amg¶

Homepage:

https://computation.llnl.gov/projects/co-design/amg2013

Spack package:

amg/package.py

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:

https://computation.llnl.gov/projects/co-design/amg2013

Spack package:

amg2013/package.py

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.

amp¶

Homepage:

https://bitbucket.org/AdvancedMultiPhysics/amp

Spack package:

amp/package.py

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:

https://code.google.com/archive/p/ampliconnoise/

Spack package:

ampliconnoise/package.py

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:

https://amrex-codes.github.io/amrex/

Spack package:

amrex/package.py

Versions:

develop, 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:

https://github.com/AMReX-Codes/Amrvis

Spack package:

amrvis/package.py

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:

https://github.com/EvolBioInf/andi

Spack package:

andi/package.py

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:

https://github.com/ANGSD/angsd

Spack package:

angsd/package.py

Versions:

0.921, 0.919

Build Dependencies:

Link Dependencies:

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:

http://ant.apache.org/

Spack package:

ant/package.py

Versions:

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:

http://www.antlr2.org/

Spack package:

antlr/package.py

Versions:

2.7.7

Build Dependencies:

python, java

Link Dependencies:

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:

http://stnava.github.io/ANTs/

Spack package:

ants/package.py

Versions:

2.2.0

Build Dependencies:

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:

https://sourceforge.net/projects/aoflagger/

Spack package:

aoflagger/package.py

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:

https://aomedia.googlesource.com/aom

Spack package:

aom/package.py

Versions:

v1.0.0-errata1

Build Dependencies:

cmake, yasm

Link Dependencies:

yasm

Description:

Alliance for Open Media AOM AV1 Codec Library

ape¶

Homepage:

http://www.tddft.org/programs/APE/

Spack package:

ape/package.py

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:

http://www.aperturephotometry.org/aptool/

Spack package:

aperture-photometry/package.py

Versions:

2.7.2

Build Dependencies:

java

Link Dependencies:

java

Description:

Aperture Photometry Tool APT is software for astronomical research

apex¶

Homepage:

http://github.com/khuck/xpress-apex

Spack package:

apex/package.py

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:

https://opensource.apple.com/source/libunwind/libunwind-35.3/

Spack package:

apple-libunwind/package.py

Description:

Placeholder package for Apple's analogue to non-GNU libunwind

applewmproto¶

Homepage:

http://cgit.freedesktop.org/xorg/proto/applewmproto

Spack package:

applewmproto/package.py

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:

http://cgit.freedesktop.org/xorg/app/appres

Spack package:

appres/package.py

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:

https://apr.apache.org/

Spack package:

apr/package.py

Versions:

1.6.2, 1.5.2

Description:

Apache portable runtime.

apr-util¶

Homepage:

https://apr.apache.org/

Spack package:

apr-util/package.py

Versions:

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:

http://mbio-serv2.mbioekol.lu.se/ARAGORN

Spack package:

aragorn/package.py

Versions:

1.2.38, 1.2.36

Description:

ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences.

archer¶

Homepage:

https://github.com/PRUNERS/ARCHER

Spack package:

archer/package.py

Versions:

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:

http://www.argobots.org/

Spack package:

argobots/package.py

Versions:

develop, 1.0rc1, 1.0b1, 1.0a1

Build Dependencies:

m4, autoconf, automake, libtool, valgrind

Link Dependencies:

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:

https://www.lysator.liu.se/~nisse/misc

Spack package:

argp-standalone/package.py

Versions:

1.3

Description:

Standalone version of the argp interface from glibc for parsing unix- style arguments.

argtable¶

Homepage:

http://argtable.sourceforge.net/

Spack package:

argtable/package.py

Versions:

2-13

Description:

Argtable is an ANSI C library for parsing GNU style command line options with a minimum of fuss.

arlecore¶

Homepage:

http://cmpg.unibe.ch/software/arlequin35/

Spack package:

arlecore/package.py

Versions:

3.5.2.2

Build Dependencies:

Run Dependencies:

Description:

An Integrated Software for Population Genetics Data Analysis

arm-forge¶

Homepage:

http://www.allinea.com/products/develop-allinea-forge

Spack package:

arm-forge/package.py

Versions:

19.0.4-linux-ubuntu16.04-x86_64, 19.0.4-linux-ubuntu16.04-aarch64, 19.0.4-linux-ubuntu14.04-x86_64, 19.0.4-linux-sles15-x86_64, 19.0.4-linux-sles12-x86_64, 19.0.4-linux-sles12-aarch64, 19.0.4-linux-sles11-x86_64, 19.0.4-linux-rhel7-x86_64, 19.0.4-linux-rhel7-ppc64le, 19.0.4-linux-rhel7-aarch64, 19.0.4-linux-rhel6-x86_64, 19.0.3-linux-ubuntu16.04-x86_64, 19.0.3-linux-ubuntu16.04-aarch64, 19.0.3-linux-ubuntu14.04-x86_64, 19.0.3-linux-sles12-x86_64, 19.0.3-linux-sles12-aarch64, 19.0.3-linux-sles11-x86_64, 19.0.3-linux-rhel7-x86_64, 19.0.3-linux-rhel7-ppc64le, 19.0.3-linux-rhel7-aarch64, 19.0.3-linux-rhel6-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:

http://arma.sourceforge.net/

Spack package:

armadillo/package.py

Versions:

8.100.1, 7.950.1, 7.900.1, 7.500.0, 7.200.2, 7.200.1

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:

https://github.com/opencollab/arpack-ng

Spack package:

arpack-ng/package.py

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:

http://arrow.apache.org

Spack package:

arrow/package.py

Versions:

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.

ascent¶

Homepage:

https://github.com/Alpine-DAV/ascent

Spack package:

ascent/package.py

Versions:

develop

Build Dependencies:

cmake, conduit, python, py-numpy, mpi, py-mpi4py, vtkh, mfem, adios, py-sphinx

Link Dependencies:

conduit, python, mpi, py-mpi4py, vtkh, mfem, adios

Run Dependencies:

Description:

Ascent is an open source many-core capable lightweight in situ visualization and analysis infrastructure for multi-physics HPC simulations.

asciidoc¶

Homepage:

http://asciidoc.org

Spack package:

asciidoc/package.py

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:

https://asciidoctor.org/

Spack package:

asciidoctor/package.py

Versions:

1.5.8

Build Dependencies:

ruby

Link Dependencies:

ruby

Description:

Modern asciidoc tool based on ruby

aspa¶

Homepage:

http://www.exmatex.org/aspa.html

Spack package:

aspa/package.py

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:

https://potassco.org/aspcud

Spack package:

aspcud/package.py

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:

https://aspect.geodynamics.org

Spack package:

aspect/package.py

Versions:

develop, 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:

http://aspell.net/

Spack package:

aspell/package.py

Versions:

0.60.6.1

Description:

GNU Aspell is a Free and Open Source spell checker designed to eventually replace Ispell.

aspell6-de¶

Homepage:

http://aspell.net/

Spack package:

aspell6-de/package.py

Versions:

6-de-20030222-1

Build Dependencies:

Link Dependencies:

Description:

German (de) dictionary for aspell.

aspell6-en¶

Homepage:

http://aspell.net/

Spack package:

aspell6-en/package.py

Versions:

2017.01.22-0

Build Dependencies:

Link Dependencies:

Description:

English (en) dictionary for aspell.

aspell6-es¶

Homepage:

http://aspell.net/

Spack package:

aspell6-es/package.py

Versions:

1.11-2

Build Dependencies:

Link Dependencies:

Description:

Spanish (es) dictionary for aspell.

aspera-cli¶

Homepage:

https://asperasoft.com

Spack package:

aspera-cli/package.py

Versions:

3.7.7

Description:

The Aspera CLI client for the Fast and Secure Protocol (FASP).

assimp¶

Homepage:

https://www.assimp.org

Spack package:

assimp/package.py

Versions:

4.0.1

Build Dependencies:

Link Dependencies:

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:

http://www.desy.de/~mpyflo/

Spack package:

astra/package.py

Versions:

2016-11-30

Description:

A Space Charge Tracking Algorithm.

astral¶

Homepage:

https://github.com/smirarab/ASTRAL

Spack package:

astral/package.py

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:

http://astyle.sourceforge.net/

Spack package:

astyle/package.py

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:

http://www.linuxfromscratch.org/blfs/view/cvs/x/at-spi2-atk.html

Spack package:

at-spi2-atk/package.py

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:

http://www.linuxfromscratch.org/blfs/view/cvs/x/at-spi2-core.html

Spack package:

at-spi2-core/package.py

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.

atk¶

Homepage:

https://developer.gnome.org/atk/

Spack package:

atk/package.py

Versions:

2.30.0, 2.28.1, 2.20.0, 2.14.0

Build Dependencies:

meson, glib, gettext, pkgconfig, gobject-introspection

Link Dependencies:

glib, gettext, gobject-introspection

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:

http://math-atlas.sourceforge.net/

Spack package:

atlas/package.py

Versions:

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:

https://departments.icmab.es/leem/siesta/Pseudopotentials/

Spack package:

atom-dft/package.py

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:

http://users.wfu.edu/natalie/papers/pwpaw/man.html

Spack package:

atompaw/package.py

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:

http://www.atoptool.nl/index.php

Spack package:

atop/package.py

Versions:

2.2-3

Build Dependencies:

zlib, ncurses

Link Dependencies:

zlib, ncurses

Description:

Atop is an ASCII full-screen performance monitor for Linux

augustus¶

Homepage:

http://bioinf.uni-greifswald.de/augustus/

Spack package:

augustus/package.py

Versions:

3.3.2, 3.3.1, 3.3, 3.2.3

Build Dependencies:

bamtools, gsl, boost, zlib, htslib, bcftools, samtools, tabix, curl

Link Dependencies:

bamtools, gsl, boost, zlib, htslib, bcftools, samtools, tabix, curl

Description:

AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences

autoconf¶

Homepage:

https://www.gnu.org/software/autoconf/

Spack package:

autoconf/package.py

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:

http://vina.scripps.edu/

Spack package:

autodock-vina/package.py

Versions:

1_1_2

Build Dependencies:

Link Dependencies:

Description:

AutoDock Vina is an open-source program for doing molecular docking

autofact¶

Homepage:

http://megasun.bch.umontreal.ca/Software/AutoFACT.htm

Spack package:

autofact/package.py

Versions:

3_4

Run Dependencies:

perl, perl-bio-perl, perl-io-string, perl-lwp, blast-legacy

Description:

An Automatic Functional Annotation and Classification Tool

autogen¶

Homepage:

https://www.gnu.org/software/autogen/index.html

Spack package:

autogen/package.py

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:

https://github.com/llnl/AutomaDeD

Spack package:

automaded/package.py

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:

http://www.gnu.org/software/automake/

Spack package:

automake/package.py

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

axel¶

Homepage:

https://github.com/axel-download-accelerator/axel

Spack package:

axel/package.py

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:

https://github.com/ECP-VeloC/AXL

Spack package:

axl/package.py

Versions:

master, 0.1.1

Build Dependencies:

cmake, kvtree

Link Dependencies:

kvtree

Description:

Asynchronous transfer library

bamdst¶

Homepage:

https://github.com/shiquan/bamdst

Spack package:

bamdst/package.py

Versions:

master

Build Dependencies:

zlib

Link Dependencies:

zlib

Description:

Bamdst is a a lightweight bam file depth statistical tool.

bamtools¶

Homepage:

https://github.com/pezmaster31/bamtools

Spack package:

bamtools/package.py

Versions:

2.5.1, 2.5.0, 2.4.1, 2.4.0, 2.3.0, 2.2.3

Build Dependencies:

Link Dependencies:

zlib

Description:

C++ API & command-line toolkit for working with BAM data.

bamutil¶

Homepage:

http://genome.sph.umich.edu/wiki/BamUtil

Spack package:

bamutil/package.py

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:

https://github.com/tseemann/barrnap

Spack package:

barrnap/package.py

Versions:

0.8, 0.7, 0.6

Run Dependencies:

hmmer

Description:

Barrnap predicts the location of ribosomal RNA genes in genomes.

bash¶

Homepage:

https://www.gnu.org/software/bash/

Spack package:

bash/package.py

Versions:

5.0, 4.4.12, 4.4, 4.3

Build Dependencies:

Link Dependencies:

Description:

The GNU Project's Bourne Again SHell.

bash-completion¶

Homepage:

https://github.com/scop/bash-completion

Spack package:

bash-completion/package.py

Versions:

develop, 2.7, 2.3

Build Dependencies:

Run Dependencies:

bash

Description:

Programmable completion functions for bash.

bats¶

Homepage:

https://github.com/sstephenson/bats

Spack package:

bats/package.py

Versions:

0.4.0

Description:

Bats is a TAP-compliant testing framework for Bash.

bazel¶

Homepage:

https://www.bazel.io

Spack package:

bazel/package.py

Versions:

0.17.2, 0.16.1, 0.15.0, 0.14.1, 0.13.0, 0.12.0, 0.11.1, 0.11.0, 0.10.1, 0.10.0, 0.9.0, 0.4.5, 0.4.4, 0.3.1, 0.3.0, 0.2.3, 0.2.2b, 0.2.2

Build Dependencies:

java, zip

Link Dependencies:

java, zip

Run Dependencies:

java

Description:

Bazel is Google's own build tool

bbcp¶

Homepage:

http://www.slac.stanford.edu/~abh/bbcp/

Spack package:

bbcp/package.py

Versions:

git

Build Dependencies:

zlib, openssl

Link Dependencies:

zlib, openssl

Description:

Securely and quickly copy data from source to target

bbmap¶

Homepage:

http://sourceforge.net/projects/bbmap/

Spack package:

bbmap/package.py

Versions:

37.36

Build Dependencies:

java

Link Dependencies:

java

Description:

Short read aligner for DNA and RNA-seq data.

bc¶

Homepage:

https://www.gnu.org/software/bc

Spack package:

bc/package.py

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:

http://samtools.github.io/bcftools/

Spack package:

bcftools/package.py

Versions:

1.9, 1.8, 1.7, 1.6, 1.4, 1.3.1, 1.2

Build Dependencies:

libzip, htslib

Link Dependencies:

libzip, htslib

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:

https://support.illumina.com/downloads/bcl2fastq-conversion-software-v2-20.html

Spack package:

bcl2fastq2/package.py

Versions:

2.20.0.422, 2.19.1.403, 2.18.0.12, 2.17.1.14

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:

http://cgit.freedesktop.org/xorg/app/bdftopcf

Spack package:

bdftopcf/package.py

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:

https://www.hboehm.info/gc/

Spack package:

bdw-gc/package.py

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.

bear¶

Homepage:

https://github.com/rizsotto/Bear

Spack package:

bear/package.py

Versions:

2.2.0, 2.0.4

Build Dependencies:

cmake, python

Link Dependencies:

Description:

Bear is a tool that generates a compilation database for clang tooling from non-cmake build systems.

beast-tracer¶

Homepage:

http://beast.community/tracer

Spack package:

beast-tracer/package.py

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:

http://beast.community/

Spack package:

beast1/package.py

Versions:

1.10.4, 1.10.0, 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:

http://beast2.org/

Spack package:

beast2/package.py

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:

https://bedops.readthedocs.io

Spack package:

bedops/package.py

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:

https://github.com/arq5x/bedtools2

Spack package:

bedtools2/package.py

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:

http://cgit.freedesktop.org/xorg/app/beforelight

Spack package:

beforelight/package.py

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:

https://github.com/google/benchmark

Spack package:

benchmark/package.py

Versions:

develop, 1.4.0, 1.3.0, 1.2.0, 1.1.0, 1.0.0

Build Dependencies:

Description:

A microbenchmark support library

berkeley-db¶

Homepage:

http://www.oracle.com/technetwork/database/database-technologies/berkeleydb/overview/index.html

Spack package:

berkeley-db/package.py

Versions:

6.2.32, 6.1.29, 6.0.35, 5.3.28

Description:

Oracle Berkeley DB

bertini¶

Homepage:

https://bertini.nd.edu/

Spack package:

bertini/package.py

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:

http://www.spinellis.gr/sw/textproc/bib2xhtml/

Spack package:

bib2xhtml/package.py

Versions:

3.0-15-gf506

Description:

bib2xhtml is a program that converts BibTeX files into HTML.

bigreqsproto¶

Homepage:

http://cgit.freedesktop.org/xorg/proto/bigreqsproto

Spack package:

bigreqsproto/package.py

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.

binutils¶

Homepage:

http://www.gnu.org/software/binutils/

Spack package:

binutils/package.py

Versions:

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:

https://github.com/lh3/bioawk

Spack package:

bioawk/package.py

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:

https://github.com/bcgsc/biobloom

Spack package:

biobloom/package.py

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.

biopieces¶

Homepage:

http://maasha.github.io/biopieces/

Spack package:

biopieces/package.py

Versions:

2016-04-12

Build Dependencies:

perl, perl-module-build, perl-bit-vector, perl-svg, perl-term-readkey, perl-time-hires, perl-dbi, perl-xml-parser, perl-carp-clan, perl-class-inspector, perl-html-parser, perl-lwp, perl-soap-lite, perl-uri, perl-inline, perl-inline-c, perl-parse-recdescent, perl-version, perl-dbfile, perl-dbd-mysql, ruby, ruby-gnuplot, ruby-narray, ruby-rubyinline, ruby-terminal-table, python, blast-plus, muscle, mummer, blat, vmatch, bowtie, bwa, usearch, velvet, idba, ray, scan-for-matches

Link Dependencies:

ruby, ruby-gnuplot, ruby-narray, ruby-rubyinline, ruby-terminal-table, blast-plus, muscle, mummer, blat, vmatch, bowtie, bwa, usearch, velvet, idba, ray, scan-for-matches

Run Dependencies:

Description:

The Biopieces are a collection of bioinformatics tools that can be pieced together in a very easy and flexible manner to perform both simple and complex tasks.

bismark¶

Homepage:

https://www.bioinformatics.babraham.ac.uk/projects/bismark

Spack package:

bismark/package.py

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:

http://www.gnu.org/software/bison/

Spack package:

bison/package.py

Versions:

3.0.5, 3.0.4, 2.7

Build Dependencies:

diffutils, m4, perl, help2man

Run Dependencies:

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:

http://cgit.freedesktop.org/xorg/app/bitmap

Spack package:

bitmap/package.py

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:

https://github.com/PacificBiosciences/blasr/wiki

Spack package:

blasr/package.py

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:

https://github.com/PacificBiosciences/blasr_libcpp

Spack package:

blasr-libcpp/package.py

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:

https://www.ncbi.nlm.nih.gov/

Spack package:

blast-legacy/package.py

Versions:

2.2.26

Build Dependencies:

tcsh

Description:

Legacy NCBI BLAST distribution -- no longer supported. Contains older programs including `blastall'

blast-plus¶

Homepage:

http://blast.ncbi.nlm.nih.gov/

Spack package:

blast-plus/package.py

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:

https://www.blast2go.com/

Spack package:

blast2go/package.py

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:

https://genome.ucsc.edu/FAQ/FAQblat.html

Spack package:

blat/package.py

Versions:

Build Dependencies:

Link Dependencies:

Description:

BLAT (BLAST-like alignment tool) is a pairwise sequence alignment algorithm.

blaze¶

Homepage:

https://bitbucket.org/blaze-lib/blaze/overview

Spack package:

blaze/package.py

Versions:

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

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:

https://github.com/flame/blis

Spack package:

blis/package.py

Versions:

develop, 0.4.0, 0.3.2, 0.3.1, 0.3.0, 0.2.2

Build Dependencies:

Run Dependencies:

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:

http://www.tcs.hut.fi/Software/bliss/

Spack package:

bliss/package.py

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:

http://github.com/blitzpp/blitz

Spack package:

blitz/package.py

Versions:

1.0.1, 1.0.0

Description:

N-dimensional arrays for C++

bmake¶

Homepage:

http://www.crufty.net/help/sjg/bmake.htm

Spack package:

bmake/package.py

Versions:

20180512, 20171207

Description:

Portable version of NetBSD make(1).

bmi¶

Homepage:

http://git.mcs.anl.gov/bmi.git/

Spack package:

bmi/package.py

Versions:

develop

Build Dependencies:

autoconf

Description:

a communications framework and network abstraction layer

bml¶

Homepage:

http://lanl.github.io/bml/

Spack package:

bml/package.py

Versions:

develop, 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:

http://bh107.org

Spack package:

bohrium/package.py

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:

Test Dependencies:

Description:

Library for automatic acceleration of array operations

bolt¶

Homepage:

http://www.bolt-omp.org/

Spack package:

bolt/package.py

Versions:

1.0b1

Build Dependencies:

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:

https://github.com/UK-MAC/BookLeaf_Cpp

Spack package:

bookleaf-cpp/package.py

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:

http://www.boost.org

Spack package:

boost/package.py

Versions:

develop, 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:

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:

http://www.organicvectory.com/index.php?option=com_content&view=article&id=75:boostmplcartesianproduct&catid=42:boost&Itemid=78

Spack package:

boostmplcartesianproduct/package.py

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:

https://sourceforge.net/projects/bowtie-bio/

Spack package:

bowtie/package.py

Versions:

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:

bowtie-bio.sourceforge.net/bowtie2/index.shtml

Spack package:

bowtie2/package.py

Versions:

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:

Description:

Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences

boxlib¶

Homepage:

https://ccse.lbl.gov/BoxLib/

Spack package:

boxlib/package.py

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:

http://biopp.univ-montp2.fr/wiki/index.php/Installation

Spack package:

bpp-core/package.py

Versions:

2.2.0

Build Dependencies:

perl-statistics-descriptive, perl-math-cdf, perl-gd-graph, perl-gdgraph-histogram, perl-list-moreutils, perl-exporter-tiny

Description:

Bio++ core library.

bpp-phyl¶

Homepage:

http://biopp.univ-montp2.fr/wiki/index.php/Installation

Spack package:

bpp-phyl/package.py

Versions:

2.2.0

Build Dependencies:

cmake, bpp-core, bpp-seq

Link Dependencies:

bpp-core, bpp-seq

Description:

Bio++ phylogeny library.

bpp-seq¶

Homepage:

http://biopp.univ-montp2.fr/wiki/index.php/Installation

Spack package:

bpp-seq/package.py

Versions:

2.2.0

Build Dependencies:

cmake, bpp-core

Link Dependencies:

bpp-core

Description:

Bio++ seq library.

bpp-suite¶

Homepage:

http://biopp.univ-montp2.fr/wiki/index.php/BppSuite

Spack package:

bpp-suite/package.py

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:

https://ccb.jhu.edu/software/bracken

Spack package:

bracken/package.py

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

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:

http://exon.gatech.edu/braker1.html

Spack package:

braker/package.py

Versions:

2.1.0, 1.11

Build Dependencies:

perl, perl-scalar-util-numeric, perl-parallel-forkmanager, perl-file-which, augustus, genemark-et, bamtools, samtools

Link Dependencies:

augustus, genemark-et, bamtools, samtools

Run Dependencies:

perl, perl-scalar-util-numeric, perl-parallel-forkmanager, perl-file-which

Description:

BRAKER is a pipeline for unsupervised RNA-Seq-based genome annotation that combines the advantages of GeneMark-ET and AUGUSTUS

branson¶

Homepage:

https://github.com/lanl/branson

Spack package:

branson/package.py

Versions:

develop, 1.01, 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:

http://gmt.genome.wustl.edu/packages/breakdancer

Spack package:

breakdancer/package.py

Versions:

master, 1.4.5

Build Dependencies:

cmake, zlib

Link Dependencies:

zlib

Run Dependencies:

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..

breseq¶

Homepage:

http://barricklab.org/breseq

Spack package:

breseq/package.py

Versions:

0.33.2, 0.33.1, 0.31.1

Build Dependencies:

autoconf, automake, libtool, m4, 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:

https://sourceforge.net/projects/rnaseqassembly/

Spack package:

bridger/package.py

Versions:

2014-12-01

Build Dependencies:

Link Dependencies:

Run Dependencies:

perl

Description:

Bridger : An Efficient De novo Transcriptome Assembler For RNA-Seq Data

brigand¶

Homepage:

https://github.com/edouarda/brigand

Spack package:

brigand/package.py

Versions:

master, 1.3.0, 1.2.0, 1.1.0, 1.0.0

Description:

Brigand Meta-programming library

brotli¶

Homepage:

https://github.com/google/brotli

Spack package:

brotli/package.py

Versions:

1.0.7

Build Dependencies:

Description:

Brotli is a generic-purpose lossless compression algorithm

bsseeker2¶

Homepage:

http://pellegrini.mcdb.ucla.edu/BS_Seeker2

Spack package:

bsseeker2/package.py

Versions:

2.1.8, 2.1.5, 2.1.2

Build Dependencies:

python, py-pysam

Run Dependencies:

python, py-pysam

Description:

A versatile aligning pipeline for bisulfite sequencing data.

bucky¶

Homepage:

http://www.stat.wisc.edu/~ane/bucky/index.html

Spack package:

bucky/package.py

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:

https://pypi.python.org/pypi/bumpversion

Spack package:

bumpversion/package.py

Versions:

0.5.3, 0.5.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Version-bump your software with a single command.

busco¶

Homepage:

http://busco.ezlab.org/

Spack package:

busco/package.py

Versions:

3.0.1, 2.0.1

Build Dependencies:

python, blast-plus, hmmer, augustus

Link Dependencies:

python, blast-plus, hmmer, augustus

Run Dependencies:

Description:

Assesses genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs

butter¶

Homepage:

https://github.com/MikeAxtell/butter

Spack package:

butter/package.py

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.

bwa¶

Homepage:

http://github.com/lh3/bwa

Spack package:

bwa/package.py

Versions:

0.7.17, 0.7.16a, 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:

https://github.com/CRG-Barcelona/bwtool

Spack package:

bwtool/package.py

Versions:

1.0

Build Dependencies:

libbeato

Link Dependencies:

libbeato

Description:

bwtool is a command-line utility for bigWig files.

byobu¶

Homepage:

http://www.byobu.co

Spack package:

byobu/package.py

Versions:

5.127, 5.125, 5.123

Build Dependencies:

tmux

Run Dependencies:

tmux

Description:

Byobu: Text-based window manager and terminal multiplexer.

bzip2¶

Homepage:

https://sourceware.org/bzip2/

Spack package:

bzip2/package.py

Versions:

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-blosc¶

Homepage:

http://www.blosc.org

Spack package:

c-blosc/package.py

Versions:

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-lime¶

Homepage:

https://usqcd-software.github.io/c-lime/

Spack package:

c-lime/package.py

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:

https://github.com/ECP-copa/Cabana

Spack package:

cabana/package.py

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:

http://caffe.berkeleyvision.org

Spack package:

caffe/package.py

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:

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:

https://www.cairographics.org/

Spack package:

cairo/package.py

Versions:

1.16.0, 1.14.12, 1.14.8, 1.14.0

Build Dependencies:

libx11, libxext, libxrender, libxcb, python, libpng, glib, pixman, freetype, pkgconfig, fontconfig

Link Dependencies:

libx11, libxext, libxrender, libxcb, libpng, glib, pixman, freetype, fontconfig

Description:

Cairo is a 2D graphics library with support for multiple output devices.

cairomm¶

Homepage:

https://www.cairographics.org/cairomm/

Spack package:

cairomm/package.py

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:

https://github.com/LLNL/Caliper

Spack package:

caliper/package.py

Versions:

master, 2.0.1, 1.9.1, 1.9.0, 1.8.0, 1.7.0

Build Dependencies:

cmake, gotcha, dyninst, papi, libpfm4, mpi, unwind, sosflow, python

Link Dependencies:

gotcha, dyninst, papi, libpfm4, mpi, unwind, sosflow

Description:

Caliper is a program instrumentation and performance measurement framework. It provides data collection mechanisms and a source-code annotation API for a variety of performance engineering use cases, e.g., performance profiling, tracing, monitoring, and auto-tuning.

callpath¶

Homepage:

https://github.com/llnl/callpath

Spack package:

callpath/package.py

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:

https://bitbucket.org/nateroberts/Camellia

Spack package:

camellia/package.py

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.

candle-benchmarks¶

Homepage:

https://github.com/ECP-CANDLE/Benchmarks

Spack package:

candle-benchmarks/package.py

Versions:

0.1, 0.0

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:

http://www.cantera.org/docs/sphinx/html/index.html

Spack package:

cantera/package.py

Versions:

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:

http://canu.readthedocs.io/

Spack package:

canu/package.py

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:

http://seq.cs.iastate.edu/

Spack package:

cap3/package.py

Versions:

2015-02-11

Description:

CAP3 is DNA Sequence Assembly Program

capstone¶

Homepage:

http://www.capstone-engine.org/

Spack package:

capstone/package.py

Versions:

4.0.1

Build Dependencies:

Description:

Capstone is a lightweight multi-platform, multi-architecture disassembly framework.

cardioid¶

Homepage:

https://baasic.llnl.gov/comp-bio/cardioid-code.php

Spack package:

cardioid/package.py

Versions:

develop, elecfem

Build Dependencies:

cmake, blas, lapack, mpi, cuda, mfem, perl

Link Dependencies:

blas, lapack, mpi, cuda, mfem

Description:

Cardiac simulation suite.

cares¶

Homepage:

https://c-ares.haxx.se

Spack package:

cares/package.py

Versions:

develop, 1.13.0

Build Dependencies:

Description:

c-ares: A C library for asynchronous DNS requests

casacore¶

Homepage:

https://github.com/casacore/casacore

Spack package:

casacore/package.py

Versions:

2.4.1

Build Dependencies:

cmake, flex, bison, blas, lapack, cfitsio, wcslib, fftw, sofa-c, hdf5, ncurses, python, boost, py-numpy

Link Dependencies:

blas, lapack, cfitsio, wcslib, fftw, sofa-c, hdf5, ncurses, python, boost, py-numpy

Description:

A suite of c++ libraries for radio astronomy data processing.

cask¶

Homepage:

http://cask.readthedocs.io/en/latest/

Spack package:

cask/package.py

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:

http://best.snu.ac.kr/casper/index.php?name=main

Spack package:

casper/package.py

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.

catalyst¶

Homepage:

http://www.paraview.org

Spack package:

catalyst/package.py

Versions:

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, git, mpi, python, gl, mesa, glx

Link Dependencies:

mpi, python, gl, mesa, glx

Run Dependencies:

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.

catch¶

Homepage:

https://github.com/catchorg/Catch2

Spack package:

catch/package.py

Versions:

2.6.1, 2.6.0, 2.5.0, 2.4.0, 2.3.0, 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:

Description:

Catch tests

cbench¶

Homepage:

https://sourceforge.net/projects/cbench/

Spack package:

cbench/package.py

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:

http://www.netlib.org/blas/_cblas/

Spack package:

cblas/package.py

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:

http://sourceforge.net/p/cbtf/wiki/Home

Spack package:

cbtf/package.py

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, xerces-c, libxml2

Link Dependencies:

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:

http://sourceforge.net/p/cbtf/wiki/Home/

Spack package:

cbtf-argonavis/package.py

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

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:

http://sourceforge.net/p/cbtf/wiki/Home/

Spack package:

cbtf-argonavis-gui/package.py

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:

http://sourceforge.net/p/cbtf/wiki/Home/

Spack package:

cbtf-krell/package.py

Versions:

develop, 1.9.3, 1.9.2, 1.9.1.2, 1.9.1.1, 1.9.1.0

Build Dependencies:

cmake, binutils, boost, dyninst, mrnet, xerces-c, cbtf, libmonitor, libunwind, papi, llvm-openmp-ompt, openmpi, mpich, mpich2, mvapich2, mvapich, mpt, python, gotcha

Link Dependencies:

binutils, boost, dyninst, mrnet, xerces-c, cbtf, libmonitor, libunwind, papi, llvm-openmp-ompt, openmpi, mpich, mpich2, mvapich2, mvapich, mpt, gotcha

Run Dependencies:

mrnet, cbtf, 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:

http://sourceforge.net/p/cbtf/wiki/Home/

Spack package:

cbtf-lanl/package.py

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:

https://ccache.samba.org/

Spack package:

ccache/package.py

Versions:

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:

https://heasarc.gsfc.nasa.gov/fitsio/CCfits/

Spack package:

ccfits/package.py

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.

cctools¶

Homepage:

https://github.com/cooperative-computing-lab/cctools

Spack package:

cctools/package.py

Versions:

6.1.1

Build Dependencies:

openssl, perl, python, readline, swig, zlib

Link Dependencies:

openssl, readline, swig, zlib

Run Dependencies:

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:

https://github.com/gpertea/cdbfasta

Spack package:

cdbfasta/package.py

Versions:

2017-03-16

Build Dependencies:

zlib

Link Dependencies:

zlib

Description:

Fast indexing and retrieval of fasta records from flat file databases

cdd¶

Homepage:

https://www.inf.ethz.ch/personal/fukudak/cdd_home/cdd.html

Spack package:

cdd/package.py

Versions:

0.61a

Build Dependencies:

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:

https://www.inf.ethz.ch/personal/fukudak/cdd_home/

Spack package:

cddlib/package.py

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:

https://www.bytereef.org/mpdecimal/

Spack package:

cdecimal/package.py

Versions:

2.3

Description:

cdecimal is a fast drop-in replacement for the decimal module in Python's standard library.

cdhit¶

Homepage:

http://cd-hit.org/

Spack package:

cdhit/package.py

Versions:

4.8.1, 4.6.8

Build Dependencies:

perl

Run Dependencies:

perl

Description:

CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences.

cdo¶

Homepage:

https://code.mpimet.mpg.de/projects/cdo

Spack package:

cdo/package.py

Versions:

1.9.7rc2, 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, hdf5, grib-api, eccodes, szip, udunits2, libxml2, proj, curl, fftw, magics, libuuid

Link Dependencies:

netcdf, hdf5, grib-api, eccodes, szip, udunits2, 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:

https://ceed.exascaleproject.org

Spack package:

ceed/package.py

Versions:

2.0.0, 1.0.0

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:

http://uscilab.github.io/cereal/

Spack package:

cereal/package.py

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:

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:

http://ceres-solver.org

Spack package:

ceres-solver/package.py

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:

http://heasarc.gsfc.nasa.gov/fitsio/

Spack package:

cfitsio/package.py

Versions:

3.450, 3.420, 3.410, 3.370

Build Dependencies:

Link Dependencies:

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:

http://www.cgal.org/

Spack package:

cgal/package.py

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.

cgm¶

Homepage:

http://sigma.mcs.anl.gov/cgm-library

Spack package:

cgm/package.py

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:

http://cgns.github.io/

Spack package:

cgns/package.py

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:

https://github.com/epfl-ecps/channelflow

Spack package:

channelflow/package.py

Versions:

develop

Build Dependencies:

cmake, eigen, fftw, mpi, hdf5, netcdf, boost

Link Dependencies:

eigen, fftw, mpi, hdf5, netcdf, boost

Description:

Channelflow is a software system for numerical analysis of the incompressible fluid flow in channel geometries, written in C++.

chapel¶

Homepage:

https://chapel-lang.org/

Spack package:

chapel/package.py

Versions:

1.19.0, 1.18.0

Description:

Chapel is a modern programming language that is parallel, productive, portable, scalable and open-source.

charliecloud¶

Homepage:

https://hpc.github.io/charliecloud

Spack package:

charliecloud/package.py

Versions:

0.9.9, 0.9.8, 0.9.7, 0.9.6, 0.9.3, 0.9.2, 0.9.1, 0.9.0, 0.2.4

Description:

Lightweight user-defined software stacks for HPC.

charmpp¶

Homepage:

http://charmplusplus.org

Spack package:

charmpp/package.py

Versions:

develop, 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:

https://chatterbug.readthedocs.io

Spack package:

chatterbug/package.py

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:

https://libcheck.github.io/check/index.html

Spack package:

check/package.py

Versions:

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.

chlorop¶

Homepage:

http://www.cbs.dtu.dk/services/ChloroP/

Spack package:

chlorop/package.py

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:

https://commons.lbl.gov/display/chombo

Spack package:

chombo/package.py

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:

https://directory.fsf.org/wiki/Chrpath

Spack package:

chrpath/package.py

Versions:

0.16

Description:

chrpath: Modifies the dynamic library load path (rpath and runpath) of compiled programs and libraries.

circos¶

Homepage:

http://circos.ca/

Spack package:

circos/package.py

Versions:

0.69-6

Run Dependencies:

perl, perl-clone, perl-config-general, perl-exporter-tiny, perl-font-ttf, perl-gd, perl-io-string, perl-list-moreutils, perl-math-round, perl-math-bezier, perl-math-vecstat, perl-params-validate, perl-readonly, perl-regexp-common, perl-set-intspan, perl-statistics-basic, perl-svg, perl-text-format

Description:

Circos is a software package for visualizing data and information.

cistem¶

Homepage:

https://cistem.org/

Spack package:

cistem/package.py

Versions:

1.0.0-beta

Build Dependencies:

wx, fftw

Link Dependencies:

wx, 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:

https://geodynamics.org/cig/software/citcoms/

Spack package:

citcoms/package.py

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:

https://github.com/google/cityhash

Spack package:

cityhash/package.py

Versions:

master, 2013-07-31

Description:

CityHash, a family of hash functions for strings.

clamr¶

Homepage:

https://github.com/lanl/CLAMR

Spack package:

clamr/package.py

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:

http://www.netlib.org/clapack/

Spack package:

clapack/package.py

Versions:

3.2.1

Build Dependencies:

Link Dependencies:

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.

claw¶

Homepage:

https://claw-project.github.io/

Spack package:

claw/package.py

Versions:

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:

https://github.com/MikeAxtell/CleaveLand4

Spack package:

cleaveland4/package.py

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:

http://uk-mac.github.io/CleverLeaf/

Spack package:

cleverleaf/package.py

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:

https://github.com/clMathLibraries/clFFT

Spack package:

clfft/package.py

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:

http://proj-clhep.web.cern.ch/proj-clhep/

Spack package:

clhep/package.py

Versions:

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:

Description:

CLHEP is a C++ Class Library for High Energy Physics.

clingo¶

Homepage:

https://potassco.org/clingo/

Spack package:

clingo/package.py

Versions:

5.2.2

Build Dependencies:

cmake, doxygen, python

Link Dependencies:

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:

https://www.ginac.de/CLN/

Spack package:

cln/package.py

Versions:

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:

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:

https://github.com/AlDanial/cloc/

Spack package:

cloc/package.py

Versions:

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:

http://www.cloog.org

Spack package:

cloog/package.py

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:

http://uk-mac.github.io/CloverLeaf

Spack package:

cloverleaf/package.py

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:

http://uk-mac.github.io/CloverLeaf3D/

Spack package:

cloverleaf3d/package.py

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:

https://projects.coin-or.org/Clp

Spack package:

clp/package.py

Versions:

1.16.11

Description:

Clp (Coin-or linear programming) is an open-source linear programming solver written in C++.

clustalo¶

Homepage:

http://www.clustal.org/omega/

Spack package:

clustalo/package.py

Versions:

1.2.4

Build Dependencies:

argtable

Link Dependencies:

argtable

Description:

Clustal Omega: the last alignment program you'll ever need.

clustalw¶

Homepage:

http://www.clustal.org/clustal2/

Spack package:

clustalw/package.py

Versions:

2.1

Description:

Multiple alignment of nucleic acid and protein sequences.

cmake¶

Homepage:

https://www.cmake.org

Spack package:

cmake/package.py

Versions:

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, gnutls

Link Dependencies:

curl, expat, zlib, bzip2, xz, libarchive, libuv, rhash, qt, openssl, ncurses, gnutls

Description:

A cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.

cmocka¶

Homepage:

https://cmocka.org/

Spack package:

cmocka/package.py

Versions:

1.1.1, 1.1.0, 1.0.1

Build Dependencies:

Description:

Unit-testing framework in pure C

cmor¶

Homepage:

http://cmor.llnl.gov

Spack package:

cmor/package.py

Versions:

3.3.0, 3.2.0, 3.1.2

Build Dependencies:

uuid, netcdf, udunits2, hdf5, python, py-numpy

Link Dependencies:

uuid, netcdf, udunits2, hdf5, python

Run Dependencies:

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:

https://github.com/NVIDIA/cnmem

Spack package:

cnmem/package.py

Versions:

git

Build Dependencies:

Description:

CNMem mempool for CUDA devices

cnpy¶

Homepage:

https://github.com/rogersce/cnpy

Spack package:

cnpy/package.py

Versions:

master

Build Dependencies:

Description:

cnpy: library to read/write .npy and .npz files in C/C++.

cntk¶

Homepage:

https://www.microsoft.com/en-us/research/product/cognitive-toolkit

Spack package:

cntk/package.py

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:

https://github.com/CNTK-components/CNTK1bitSGD

Spack package:

cntk1bitsgd/package.py

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:

https://github.com/abyzovlab/CNVnator

Spack package:

cnvnator/package.py

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:

https://github.com/CODARcode/cheetah

Spack package:

codar-cheetah/package.py

Versions:

develop, 0.1

Build Dependencies:

python, savanna

Link Dependencies:

savanna

Run Dependencies:

Description:

CODAR Cheetah: The CODAR Experiment Harness for Exascale science applications.

codes¶

Homepage:

http://www.mcs.anl.gov/projects/codes

Spack package:

codes/package.py

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:

https://github.com/exmatex/CoEVP

Spack package:

coevp/package.py

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:

http://www.exmatex.org/cohmm.html

Spack package:

cohmm/package.py

Versions:

develop

Build Dependencies:

Link Dependencies:

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:

http://www.hsl.rl.ac.uk/ipopt/

Spack package:

coinhsl/package.py

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:

http://www.colm.net/open-source/colm

Spack package:

colm/package.py

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:

https://www.colordiff.org

Spack package:

colordiff/package.py

Versions:

1.0.18

Build Dependencies:

perl

Link Dependencies:

perl

Description:

Colorful diff utility.

comd¶

Homepage:

http://www.exmatex.org/comd.html

Spack package:

comd/package.py

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:

http://commons.apache.org/proper/commons-lang/

Spack package:

commons-lang/package.py

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:

http://commons.apache.org/proper/commons-lang/

Spack package:

commons-lang3/package.py

Versions:

3.7

Build Dependencies:

jdk

Link Dependencies:

jdk

Run Dependencies:

java

Description:

commons-logging¶

Homepage:

http://commons.apache.org/proper/commons-logging/

Spack package:

commons-logging/package.py

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:

http://www.compiz.org/

Spack package:

compiz/package.py

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:

http://cgit.freedesktop.org/xorg/proto/compositeproto

Spack package:

compositeproto/package.py

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:

http://software.llnl.gov/conduit

Spack package:

conduit/package.py

Versions:

master, 0.4.0, 0.3.1, 0.3.0, 0.2.1, 0.2.0

Build Dependencies:

cmake, python, py-numpy, hdf5, silo, adios, mpi, py-sphinx, doxygen

Link Dependencies:

python, hdf5, silo, adios, mpi, doxygen

Run Dependencies:

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:

https://bitbucket.org/gotoh/connect

Spack package:

connect-proxy/package.py

Versions:

1.105

Description:

`connect.c` is a simple relaying command to make network connection via SOCKS and https proxy

constype¶

Homepage:

http://cgit.freedesktop.org/xorg/app/constype

Spack package:

constype/package.py

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:

https://www.convergecfd.com/

Spack package:

converge/package.py

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:

http://www.gnu.org/software/coreutils/

Spack package:

coreutils/package.py

Versions:

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:

https://github.com/Oshlack/Corset/wiki

Spack package:

corset/package.py

Versions:

1.06

Description:

Corset is a command-line software program to go from a de novo transcriptome assembly to gene-level counts.

cosmomc¶

Homepage:

http://cosmologist.info/cosmomc/

Spack package:

cosmomc/package.py

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:

http://www.exmatex.org/cosp2.html

Spack package:

cosp2/package.py

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:

https://github.com/MWATelescope/cotter

Spack package:

cotter/package.py

Versions:

master, 20190205

Build Dependencies:

cmake, erfa, pal, aoflagger

Link Dependencies:

erfa, pal, aoflagger

Description:

Andre Offringa's cotter pre-processing pipeline.

cp2k¶

Homepage:

https://www.cp2k.org

Spack package:

cp2k/package.py

Versions:

develop, 6.1, 5.1, 4.1, 3.0

Build Dependencies:

python, fftw, openblas, lapack, intel-mkl, libxsmm, pkgconfig, libint, libxc, mpi, scalapack, elpa, plumed, pexsi, sirius, json-fortran, wannier90

Link Dependencies:

fftw, openblas, lapack, intel-mkl, libxsmm, mpi, scalapack, elpa, plumed, pexsi, sirius, json-fortran

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

cppad¶

Homepage:

https://www.coin-or.org/CppAD/

Spack package:

cppad/package.py

Versions:

develop, 20170114

Build Dependencies:

Description:

A Package for Differentiation of C++ Algorithms.

cppcheck¶

Homepage:

http://cppcheck.sourceforge.net/

Spack package:

cppcheck/package.py

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:

https://github.com/Microsoft/GSL

Spack package:

cppgsl/package.py

Versions:

develop, 2.0.0, 1.0.0

Build Dependencies:

Description:

C++ Guideline Support Library

cpprestsdk¶

Homepage:

https://github.com/Microsoft/cpprestsdk

Spack package:

cpprestsdk/package.py

Versions:

2.9.1

Build Dependencies:

Link Dependencies:

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:

https://wiki.freedesktop.org/www/Software/cppunit/

Spack package:

cppunit/package.py

Versions:

1.14.0, 1.13.2

Description:

Obsolete Unit testing framework for C++

cppzmq¶

Homepage:

http://www.zeromq.org

Spack package:

cppzmq/package.py

Versions:

develop, 4.3.0, 4.2.2

Build Dependencies:

cmake, zeromq

Link Dependencies:

zeromq

Description:

C++ binding for 0MQ

cpu-features¶

Homepage:

https://github.com/google/cpu_features

Spack package:

cpu-features/package.py

Versions:

develop

Build Dependencies:

Description:

A cross platform C99 library to get cpu features at runtime.

cpuinfo¶

Homepage:

https://github.com/Maratyszcza/cpuinfo/

Spack package:

cpuinfo/package.py

Versions:

master

Build Dependencies:

Description:

cpuinfo is a library to detect essential for performance optimization information about host CPU.

cquery¶

Homepage:

https://github.com/cquery-project/cquery

Spack package:

cquery/package.py

Versions:

v20180823

Build Dependencies:

cmake, llvm

Link Dependencies:

llvm

Description:

a C++ header-only library for Nearest Neighbor (NN) search wih KD-trees.

cram¶

Homepage:

https://github.com/llnl/cram

Spack package:

cram/package.py

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.

cryptopp¶

Homepage:

http://www.cryptopp.com

Spack package:

cryptopp/package.py

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:

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).

cscope¶

Homepage:

http://cscope.sourceforge.net/

Spack package:

cscope/package.py

Versions:

15.8b

Build Dependencies:

ncurses, flex, bison, pkgconfig

Link Dependencies:

Description:

Cscope is a developer's tool for browsing source code.

csdp¶

Homepage:

https://projects.coin-or.org/Csdp

Spack package:

csdp/package.py

Versions:

6.1.1

Build Dependencies:

Link Dependencies:

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:

http://grigoriefflab.janelia.org/ctffind4

Spack package:

ctffind/package.py

Versions:

4.1.8

Build Dependencies:

wx, fftw

Link Dependencies:

wx, fftw

Description:

Fast and accurate defocus estimation from electron micrographs.

cub¶

Homepage:

https://nvlabs.github.com/cub

Spack package:

cub/package.py

Versions:

1.7.1, 1.6.4, 1.4.1

Description:

CUB is a C++ header library of cooperative threadblock primitives and other utilities for CUDA kernel programming.

cube¶

Homepage:

http://www.scalasca.org/software/cube-4.x/download.html

Spack package:

cube/package.py

Versions:

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:

http://www.scalasca.org/software/cube-4.x/download.html

Spack package:

cubelib/package.py

Versions:

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:

http://www.scalasca.org/software/cube-4.x/download.html

Spack package:

cubew/package.py

Versions:

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:

https://developer.nvidia.com/cuda-zone

Spack package:

cuda/package.py

Versions:

10.0.130, 9.2.88, 9.1.85, 9.0.176, 8.0.61, 8.0.44, 7.5.18, 6.5.14

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:

https://github.com/ComputationalRadiationPhysics/cuda_memtest

Spack package:

cuda-memtest/package.py

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:

https://developer.nvidia.com/cudnn

Spack package:

cudnn/package.py

Versions:

7.5.1-10.1-x86_64, 7.5.1-10.1-ppc64le, 7.5.1-10.0-x86_64, 7.5.1-10.0-ppc64le, 7.5.0-10.1-x86_64, 7.5.0-10.1-ppc64le, 7.5.0-10.0-x86_64, 7.5.0-10.0-ppc64le, 7.3.0, 7.2.1, 6.0, 5.1

Build Dependencies:

cuda

Link Dependencies:

cuda

Description:

NVIDIA cuDNN is a GPU-accelerated library of primitives for deep neural networks

cufflinks¶

Homepage:

http://cole-trapnell-lab.github.io/cufflinks

Spack package:

cufflinks/package.py

Versions:

2.2.1

Description:

Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples.

cups¶

Homepage:

https://www.cups.org/

Spack package:

cups/package.py

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:

http://curl.haxx.se

Spack package:

curl/package.py

Versions:

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:

http://www.nongnu.org/cvs/

Spack package:

cvs/package.py

Versions:

1.12.13

Description:

CVS a very traditional source control system

czmq¶

Homepage:

http://czmq.zeromq.org

Spack package:

czmq/package.py

Versions:

4.1.1, 4.0.2, 3.0.2

Build Dependencies:

libtool, automake, autoconf, pkgconfig, libuuid, zeromq

Link Dependencies:

libuuid, zeromq

Description:

A C interface to the ZMQ library

dakota¶

Homepage:

https://dakota.sandia.gov/

Spack package:

dakota/package.py

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:

https://github.com/thegenemyers/DALIGNER

Spack package:

daligner/package.py

Versions:

1.0

Description:

Daligner: The Dazzler "Overlap" Module.

damageproto¶

Homepage:

https://cgit.freedesktop.org/xorg/proto/damageproto

Spack package:

damageproto/package.py

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:

https://project.inria.fr/damaris/

Spack package:

damaris/package.py

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:

https://github.com/llnl/damselfly

Spack package:

damselfly/package.py

Versions:

1.0

Build Dependencies:

Description:

Damselfly is a model-based parallel network simulator.

darshan-runtime¶

Homepage:

http://www.mcs.anl.gov/research/projects/darshan/

Spack package:

darshan-runtime/package.py

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:

http://www.mcs.anl.gov/research/projects/darshan/

Spack package:

darshan-util/package.py

Versions:

develop, 3.1.7, 3.1.6, 3.1.0, 3.0.0

Build Dependencies:

zlib, bzip2

Link Dependencies:

zlib, bzip2

Run Dependencies:

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:

https://git.kernel.org/pub/scm/utils/dash/dash.git

Spack package:

dash/package.py

Versions:

0.5.9.1

Build Dependencies:

Link Dependencies:

libedit

Description:

The Debian Almquist Shell.

datamash¶

Homepage:

https://www.gnu.org/software/datamash/

Spack package:

datamash/package.py

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:

http://www.dataspaces.org

Spack package:

dataspaces/package.py

Versions:

develop, 1.6.2

Build Dependencies:

m4, automake, autoconf, libtool, mpi

Link Dependencies:

mpi

Description:

an extreme scale data management framework.

davix¶

Homepage:

https://dmc.web.cern.ch/projects/davix

Spack package:

davix/package.py

Versions:

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:

https://github.com/cp2k/dbcsr

Spack package:

dbcsr/package.py

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:

http://dbus.freedesktop.org/

Spack package:

dbus/package.py

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:

https://dicom.offis.de

Spack package:

dcmtk/package.py

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:

https://dd4hep.web.cern.ch/dd4hep/

Spack package:

dd4hep/package.py

Versions:

develop, 1.10.0

Build Dependencies:

cmake, root, boost, xerces-c, geant4

Link Dependencies:

root, boost, 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:

https://www.dealii.org

Spack package:

dealii/package.py

Versions:

develop, 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, tbb, zlib, mpi, adol-c, arpack-ng, assimp, doxygen, graphviz, ginkgo, gmsh, gsl, hdf5, metis, muparser, nanoflann, netcdf, netcdf-cxx, oce, p4est, petsc, python, scalapack, slepc, sundials, symengine, trilinos

Link Dependencies:

cuda, blas, boost, bzip2, lapack, suite-sparse, tbb, zlib, mpi, adol-c, arpack-ng, assimp, doxygen, graphviz, ginkgo, gsl, hdf5, metis, muparser, nanoflann, netcdf, netcdf-cxx, oce, p4est, petsc, python, scalapack, slepc, sundials, symengine, 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:

https://github.com/dealii/parameter_gui

Spack package:

dealii-parameter-gui/package.py

Versions:

develop

Build Dependencies:

cmake, qt

Link Dependencies:

Description:

A qt based graphical user interface for editing deal.II .prm parameter files.

deconseq-standalone¶

Homepage:

http://deconseq.sourceforge.net

Spack package:

deconseq-standalone/package.py

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:

https://www.gnu.org/software/dejagnu/

Spack package:

dejagnu/package.py

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:

https://github.com/dellytools/delly

Spack package:

delly2/package.py

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:

https://github.com/denovogear/denovogear

Spack package:

denovogear/package.py

Versions:

1.1.1, 1.1.0

Build Dependencies:

cmake, boost, htslib, eigen

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:

https://sites.google.com/umich.edu/dftfe/

Spack package:

dftfe/package.py

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:

https://wiki.gnome.org/Apps/Dia

Spack package:

dia/package.py

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-tx¶

Homepage:

http://dialign-tx.gobics.de/

Spack package:

dialign-tx/package.py

Versions:

1.0.2

Description:

DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignment

diamond¶

Homepage:

https://ab.inf.uni-tuebingen.de/software/diamond

Spack package:

diamond/package.py

Versions:

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:

http://www.netlab.uky.edu/p/bioinfo/DiffSplice

Spack package:

diffsplice/package.py

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:

https://www.gnu.org/software/diffutils/

Spack package:

diffutils/package.py

Versions:

3.7, 3.6

Description:

GNU Diffutils is a package of several programs related to finding differences between files.

direnv¶

Homepage:

https://direnv.net/

Spack package:

direnv/package.py

Versions:

2.11.3

Build Dependencies:

Description:

direnv is an environment switcher for the shell.

discovar¶

Homepage:

https://software.broadinstitute.org/software/discovar/blog/

Spack package:

discovar/package.py

Versions:

52488

Description:

DISCOVAR is a variant caller and small genome assembler.

discovardenovo¶

Homepage:

https://software.broadinstitute.org/software/discovar/blog/

Spack package:

discovardenovo/package.py

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:

http://www.mps.mpg.de/dislin

Spack package:

dislin/package.py

Versions:

11.1.linux.i586_64, 11.0.linux.i586_64

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:

https://github.com/diatomic/diy

Spack package:

diy/package.py

Versions:

master, 3.5.0

Build Dependencies:

Description:

Data-parallel out-of-core library

dlpack¶

Homepage:

https://github.com/sjtuhpcc/dlpack

Spack package:

dlpack/package.py

Versions:

master

Description:

DLPack is an RFC for common tensor and operator guidelines in deep learning systems.

dmd¶

Homepage:

https://github.com/dlang/dmd

Spack package:

dmd/package.py

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:

https://github.com/dmlc/dmlc-core

Spack package:

dmlc-core/package.py

Versions:

master, 20170508

Build Dependencies:

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:

http://dmtcp.sourceforge.net/

Spack package:

dmtcp/package.py

Versions:

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:

http://dmx.sourceforge.net/

Spack package:

dmxproto/package.py

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:

https://www.oasis-open.org/docbook

Spack package:

docbook-xml/package.py

Versions:

4.5

Description:

Docbook DTD XML files.

docbook-xsl¶

Homepage:

https://github.com/docbook/xslt10-stylesheets

Spack package:

docbook-xsl/package.py

Versions:

1.79.2

Build Dependencies:

docbook-xml

Link Dependencies:

docbook-xml

Description:

DocBook XSLT 1.0 Stylesheets.

dos2unix¶

Homepage:

https://waterlan.home.xs4all.nl/dos2unix.html

Spack package:

dos2unix/package.py

Versions:

7.3.4

Description:

DOS/Mac to Unix and vice versa text file format converter.

dotnet-core-sdk¶

Homepage:

https://www.microsoft.com/net/

Spack package:

dotnet-core-sdk/package.py

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:

https://github.com/google/double-conversion

Spack package:

double-conversion/package.py

Versions:

2.0.1, 2.0.0, 1.1.5, 1.1.4, 1.1.3

Build Dependencies:

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:

https://github.com/doxygen/doxygen/

Spack package:

doxygen/package.py

Versions:

1.8.15, 1.8.14, 1.8.12, 1.8.11, 1.8.10

Build Dependencies:

cmake, flex, bison

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:

https://github.com/lanl/draco

Spack package:

draco/package.py

Versions:

develop, 7_1_0, 6_25_0, 6_23_0, 6_22_0, 6_21_0, 6_20_1, 6_20_0

Build Dependencies:

cmake, mpi, random123, gsl, python, lapack, eospac, parmetis, qt, superlu-dist

Run Dependencies:

mpi, python, numdiff, 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:

https://cgit.freedesktop.org/xorg/proto/dri2proto/

Spack package:

dri2proto/package.py

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:

https://cgit.freedesktop.org/xorg/proto/dri3proto/

Spack package:

dri3proto/package.py

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.

ds¶

Homepage:

http://ds9.si.edu/

Spack package:

ds/package.py

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:

http://www.mcs.anl.gov/hs/software/DSDP/

Spack package:

dsdp/package.py

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:

http://sun.aei.polsl.pl/dsrc

Spack package:

dsrc/package.py

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:

https://github.com/hpc/dtcmp

Spack package:

dtcmp/package.py

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:

https://dyninst.org

Spack package:

dyninst/package.py

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:

https://github.com/aroffringa/dysco

Spack package:

dysco/package.py

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:

http://expressionanalysis.github.io/ea-utils/

Spack package:

ea-utils/package.py

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:

http://hpcugent.github.io/easybuild/

Spack package:

easybuild/package.py

Versions:

3.1.2

Build Dependencies:

Link Dependencies:

python, py-easybuild-framework, py-easybuild-easyblocks, py-easybuild-easyconfigs

Run Dependencies:

Description:

EasyBuild is a software build and installation framework for (scientific) software on HPC systems.

ebms¶

Homepage:

https://github.com/ANL-CESAR/EBMS

Spack package:

ebms/package.py

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:

https://software.ecmwf.int/wiki/display/ECC/ecCodes+Home

Spack package:

eccodes/package.py

Versions:

2.5.0, 2.2.0

Build Dependencies:

cmake, netcdf, openjpeg, jasper, libpng, libaec, python, py-numpy

Link Dependencies:

netcdf, openjpeg, jasper, libpng, libaec, python

Run Dependencies:

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:

https://confluence.ecmwf.int/display/ECFLOW/

Spack package:

ecflow/package.py

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:

https://github.com/spack/spack/issues/8165

Spack package:

eclipse-gcj-parser/package.py

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.

ecp-io-sdk¶

Homepage:

https://github.com/chuckatkins/ecp-data-viz-sdk

Spack package:

ecp-io-sdk/package.py

Versions:

1.0

Build Dependencies:

cmake, hdf5, adios2, parallel-netcdf, veloc, unifycr, darshan-runtime, darshan-util, mercury

Link Dependencies:

hdf5, adios2, parallel-netcdf, veloc, unifycr, darshan-runtime, darshan-util, mercury

Description:

ECP I/O Services SDK

ecp-proxy-apps¶

Homepage:

https://proxyapps.exascaleproject.org

Spack package:

ecp-proxy-apps/package.py

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:

https://github.com/chuckatkins/ecp-data-viz-sdk

Spack package:

ecp-viz-sdk/package.py

Versions:

1.0

Build Dependencies:

cmake, paraview, catalyst, vtkm, ascent, visit, zfp, sz

Link Dependencies:

paraview, catalyst, vtkm, ascent, visit, zfp, sz

Description:

ECP Viz & Analysis SDK

ed¶

Homepage:

https://www.gnu.org/software/ed

Spack package:

ed/package.py

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:

http://troglobit.com/editline.html

Spack package:

editline/package.py

Versions:

1.16.0

Build Dependencies:

autoconf, automake, libtool, m4, ncurses

Link Dependencies:

Description:

A readline() replacement for UNIX without termcap (ncurses)

editres¶

Homepage:

http://cgit.freedesktop.org/xorg/app/editres

Spack package:

editres/package.py

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.

eigen¶

Homepage:

http://eigen.tuxfamily.org/

Spack package:

eigen/package.py

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:

https://www.elastic.co/

Spack package:

elasticsearch/package.py

Versions:

6.4.0, 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:

http://libelemental.org

Spack package:

elemental/package.py

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:

https://fedorahosted.org/elfutils/

Spack package:

elfutils/package.py

Versions:

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:

http://elk.sourceforge.net/

Spack package:

elk/package.py

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.

elmer-fem¶

Homepage:

https://www.csc.fi/web/elmer

Spack package:

elmer-fem/package.py

Versions:

8.4

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:

http://elpa.mpcdf.mpg.de/

Spack package:

elpa/package.py

Versions:

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:

http://ubee.enseeiht.fr/vision/ELSD/

Spack package:

elsd/package.py

Versions:

master

Build Dependencies:

blas, lapack

Link Dependencies:

blas, lapack

Description:

ELSD: Ellipse and Line Segment Detector

elsdc¶

Homepage:

http://ubee.enseeiht.fr/vision/ELSD/

Spack package:

elsdc/package.py

Versions:

master

Build Dependencies:

blas, lapack

Link Dependencies:

blas, lapack

Description:

ELSDc: Ellipse and Line Segment Detector, with Continuous validation.

emacs¶

Homepage:

https://www.gnu.org/software/emacs

Spack package:

emacs/package.py

Versions:

26.1, 25.3, 25.2, 25.1, 24.5

Build Dependencies:

pkgconfig, ncurses, pcre, zlib, libtiff, libpng, libxpm, giflib, libx11, libxaw, gtkplus, gnutls

Link Dependencies:

ncurses, pcre, zlib, libtiff, libpng, libxpm, giflib, libx11, libxaw, gtkplus, gnutls

Description:

The Emacs programmable text editor.

ember¶

Homepage:

http://sst-simulator.org/SSTPages/SSTElementEmber/

Spack package:

ember/package.py

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:

http://emboss.sourceforge.net/

Spack package:

emboss/package.py

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

encodings¶

Homepage:

http://cgit.freedesktop.org/xorg/font/encodings

Spack package:

encodings/package.py

Versions:

1.0.4

Build Dependencies:

font-util, mkfontscale, pkgconfig, util-macros

Link Dependencies:

Description:

X.org encodings font.

energyplus¶

Homepage:

https://energyplus.net

Spack package:

energyplus/package.py

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:

https://www.ncbi.nlm.nih.gov/books/NBK179288/

Spack package:

entrezdirect/package.py

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:

https://cea-hpc.github.io/modules/

Spack package:

environment-modules/package.py

Versions:

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:

https://laws.lanl.gov/projects/data/eos.html

Spack package:

eospac/package.py

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.

eqr¶

Homepage:

http://emews.org

Spack package:

eqr/package.py

Versions:

develop, 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:

https://github.com/ECP-VeloC/er

Spack package:

er/package.py

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:

https://github.com/liberfa/erfa

Spack package:

erfa/package.py

Versions:

1.4.0

Build Dependencies:

Description:

ERFA(Essential Routines for Fundamental Astronomy) is a C library containing key algorithms for astronomy.

erne¶

Homepage:

http://erne.sourceforge.net/

Spack package:

erne/package.py

Versions:

2.1.1

Build Dependencies:

boost, openmpi

Link Dependencies:

Run Dependencies:

boost, openmpi

Description:

The Extended Randomized Numerical alignEr using BWT

es¶

Homepage:

http://wryun.github.io/es-shell/

Spack package:

es/package.py

Versions:

0.9.1

Build Dependencies:

Link Dependencies:

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:

https://www.earthsystemcog.org/projects/esmf/

Spack package:

esmf/package.py

Versions:

7.0.1

Build Dependencies:

zlib, libxml2, mpi, lapack, netcdf, netcdf-fortran, parallel-netcdf, xerces-c

Link Dependencies:

zlib, libxml2, mpi, lapack, netcdf, 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:

https://www.ibm.com/systems/power/software/essl/

Spack package:

essl/package.py

Description:

IBM's Engineering and Scientific Subroutine Library (ESSL).

ethminer¶

Homepage:

https://github.com/ethereum-mining/ethminer

Spack package:

ethminer/package.py

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.

etsf-io¶

Homepage:

http://www.etsf.eu/resources/software/libraries_and_tools

Spack package:

etsf-io/package.py

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:

https://github.com/citibeth/everytrace

Spack package:

everytrace/package.py

Versions:

develop, 0.2.2

Build Dependencies:

cmake, mpi

Link Dependencies:

mpi

Description:

Get stack trace EVERY time a program exits.

everytrace-example¶

Homepage:

https://github.com/citibeth/everytrace-example

Spack package:

everytrace-example/package.py

Versions:

develop

Build Dependencies:

cmake, everytrace, openmpi

Link Dependencies:

everytrace, openmpi

Description:

Get stack trace EVERY time a program exits.

evieext¶

Homepage:

http://cgit.freedesktop.org/xorg/proto/evieproto

Spack package:

evieext/package.py

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:

https://sco.h-its.org/exelixis/web/software/exabayes/

Spack package:

exabayes/package.py

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:

https://github.com/ECP-copa/ExaMiniMD

Spack package:

examinimd/package.py

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:

https://github.com/ECP-copa/ExaMPM

Spack package:

exampm/package.py

Versions:

develop

Build Dependencies:

Description:

Exascale Material Point Method (MPM) Mini-App

exasp2¶

Homepage:

https://github.com/ECP-copa/ExaSP2

Spack package:

exasp2/package.py

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:

https://geodynamics.org/cig/software/exchanger/

Spack package:

exchanger/package.py

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.

exmcutils¶

Homepage:

http://swift-lang.org/Swift-T

Spack package:

exmcutils/package.py

Versions:

0.5.6

Description:

ExM C-Utils: Generic C utility library for ADLB/X and Swift/T

exodusii¶

Homepage:

https://github.com/gsjaardema/seacas

Spack package:

exodusii/package.py

Versions:

master, 2016-08-09

Build Dependencies:

cmake, mpi, netcdf

Link Dependencies:

mpi, netcdf

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:

http://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate

Spack package:

exonerate/package.py

Versions:

2.4.0

Build Dependencies:

pkgconfig, glib

Link Dependencies:

glib

Description:

Pairwise sequence alignment of DNA and proteins

expat¶

Homepage:

https://libexpat.github.io/

Spack package:

expat/package.py

Versions:

2.2.5, 2.2.2, 2.2.0

Build Dependencies:

Link Dependencies:

Description:

Expat is an XML parser library written in C.

expect¶

Homepage:

http://expect.sourceforge.net/

Spack package:

expect/package.py

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:

http://bio.math.berkeley.edu/eXpress/

Spack package:

express/package.py

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:

https://tools.bsc.es/extrae

Spack package:

extrae/package.py

Versions:

3.4.1

Build Dependencies:

mpi, dyninst, libunwind, boost, libdwarf, papi, libxml2, gettext, binutils

Link Dependencies:

mpi, dyninst, libunwind, boost, libdwarf, papi, elf, libxml2, gettext, binutils

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:

ctags.sourceforge.net

Spack package:

exuberant-ctags/package.py

Versions:

5.8

Description:

The canonical ctags generator

eztrace¶

Homepage:

http://eztrace.gforge.inria.fr

Spack package:

eztrace/package.py

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:

https://github.com/flang-compiler/f18

Spack package:

f18/package.py

Versions:

develop

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

f90cache¶

Homepage:

https://perso.univ-rennes1.fr/edouard.canot/f90cache/

Spack package:

f90cache/package.py

Versions:

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:

http://libfabric.org

Spack package:

fabtests/package.py

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.

falcon¶

Homepage:

https://github.com/PacificBiosciences/FALCON

Spack package:

falcon/package.py

Versions:

2017-05-30

Build Dependencies:

python, py-networkx

Link Dependencies:

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.

faodel¶

Homepage:

https://github.com/faodel/faodel

Spack package:

faodel/package.py

Versions:

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:

https://github.com/LLNL/FastGlobalFileStatus

Spack package:

fast-global-file-status/package.py

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:

https://fasta.bioch.virginia.edu/fasta_www2/fasta_list2.shtml

Spack package:

fasta/package.py

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.

fastjar¶

Homepage:

http://savannah.nongnu.org/projects/fastjar/

Spack package:

fastjar/package.py

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:

www.fastmath-scidac.org/

Spack package:

fastmath/package.py

Versions:

1.0

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:

http://www.atgc-montpellier.fr/fastme/

Spack package:

fastme/package.py

Versions:

2.1.5.1

Build Dependencies:

Description:

FastME is a distance based phylogeny reconstruction program that works on distance matrices and, as of v2.0, sequence data.

fastphase¶

Homepage:

http://stephenslab.uchicago.edu/software.html

Spack package:

fastphase/package.py

Versions:

2016-03-30

Description:

Software for haplotype reconstruction, and estimating missing genotypes from population data.

fastq-screen¶

Homepage:

https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/

Spack package:

fastq-screen/package.py

Versions:

0.11.2

Build Dependencies:

bowtie, bowtie2, bwa, samtools

Link Dependencies:

bowtie, bowtie2, bwa, samtools

Run Dependencies:

perl, perl-gd-graph

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:

http://www.bioinformatics.babraham.ac.uk/projects/fastqc/

Spack package:

fastqc/package.py

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:

http://genome.sph.umich.edu/wiki/FastQValidator

Spack package:

fastqvalidator/package.py

Versions:

2017-01-10

Description:

The fastQValidator validates the format of fastq files.

fasttree¶

Homepage:

http://www.microbesonline.org/fasttree

Spack package:

fasttree/package.py

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:

http://hannonlab.cshl.edu/fastx_toolkit/

Spack package:

fastx-toolkit/package.py

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.

fenics¶

Homepage:

http://fenicsproject.org/

Spack package:

fenics/package.py

Versions:

2016.1.0, 1.6.0, 1.5.0

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:

https://github.com/lh3/fermi

Spack package:

fermi/package.py

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:

https://github.com/lh3/fermikit

Spack package:

fermikit/package.py

Versions:

2017-11-7

Build Dependencies:

zlib

Link Dependencies:

zlib

Description:

De novo assembly based variant calling pipeline for Illumina short reads

fermisciencetools¶

Homepage:

https://fermi.gsfc.nasa.gov/ssc/data/analysis/software/

Spack package:

fermisciencetools/package.py

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:

http://ferret.pmel.noaa.gov/Ferret/home

Spack package:

ferret/package.py

Versions:

6.96

Build Dependencies:

hdf5, netcdf, netcdf-fortran, readline, zlib

Link Dependencies:

hdf5, netcdf, netcdf-fortran, readline, zlib

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:

https://ffmpeg.org

Spack package:

ffmpeg/package.py

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:

http://www.fftw.org

Spack package:

fftw/package.py

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.

figtree¶

Homepage:

https://github.com/rambaut/figtree

Spack package:

figtree/package.py

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.

fimpute¶

Homepage:

http://www.aps.uoguelph.ca/~msargol/fimpute/

Spack package:

fimpute/package.py

Versions:

2014-01

Description:

FImpute uses an overlapping sliding window approach to efficiently exploit relationships or haplotype similarities between target and reference individuals.

findutils¶

Homepage:

https://www.gnu.org/software/findutils/

Spack package:

findutils/package.py

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:

https://github.com/axboe/fio

Spack package:

fio/package.py

Versions:

2.19

Build Dependencies:

gtkplus, cairo, libaio, py-sphinx

Link Dependencies:

gtkplus, cairo, libaio

Description:

Flexible I/O Tester.

fish¶

Homepage:

https://fishshell.com/

Spack package:

fish/package.py

Versions:

3.0.0, 2.7.1, 2.7.0, 2.2.0

Build Dependencies:

Link Dependencies:

Description:

fish is a smart and user-friendly command line shell for OS X, Linux, and the rest of the family.

fixesproto¶

Homepage:

http://cgit.freedesktop.org/xorg/proto/fixesproto

Spack package:

fixesproto/package.py

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.

flac¶

Homepage:

https://xiph.org/flac/index.html

Spack package:

flac/package.py

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:

https://github.com/flang-compiler/flang

Spack package:

flang/package.py

Versions:

develop, 20180921, 20180612

Build Dependencies:

cmake, llvm, pgmath

Link Dependencies:

llvm, pgmath

Description:

Flang is a Fortran compiler targeting LLVM.

flann¶

Homepage:

http://www.cs.ubc.ca/research/flann/

Spack package:

flann/package.py

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, latex

Link Dependencies:

python, cuda, mpi, hdf5, boost, latex

Run Dependencies:

py-numpy, matlab

Test Dependencies:

hdf5, gtest

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:

https://ccb.jhu.edu/software/FLASH/

Spack package:

flash/package.py

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:

http://google.github.io/flatbuffers/

Spack package:

flatbuffers/package.py

Versions:

1.10.0, 1.9.0, 1.8.0

Build Dependencies:

Description:

Memory Efficient Serialization Library

flatcc¶

Homepage:

https://github.com/dvidelabs/flatcc

Spack package:

flatcc/package.py

Versions:

master, 0.5.2, 0.5.1, 0.5.0, 0.4.3, 0.4.2, 0.4.1

Build Dependencies:

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:

https://github.com/laristra/flecsale

Spack package:

flecsale/package.py

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:

http://flecsi.lanl.gov/

Spack package:

flecsi/package.py

Versions:

develop

Build Dependencies:

cmake, mpi, gasnet, legion, boost, metis, parmetis, caliper, gotcha, graphviz

Link Dependencies:

cmake, mpi, gasnet, legion, boost, metis, parmetis, caliper, gotcha, graphviz

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.

flex¶

Homepage:

https://github.com/westes/flex

Spack package:

flex/package.py

Versions:

2.6.4, 2.6.3, 2.6.1, 2.6.0, 2.5.39

Build Dependencies:

bison, gettext, help2man, m4, autoconf, automake, libtool

Description:

Flex is a tool for generating scanners.

flint¶

Homepage:

http://www.flintlib.org

Spack package:

flint/package.py

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:

https://pruners.github.io/flit

Spack package:

flit/package.py

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:

http://www.fltk.org/

Spack package:

fltk/package.py

Versions:

1.3.3

Build Dependencies:

Link Dependencies:

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.

flux-core¶

Homepage:

https://github.com/flux-framework/flux-core

Spack package:

flux-core/package.py

Versions:

master, 0.11.0, 0.10.0, 0.9.0, 0.8.0

Build Dependencies:

zeromq, 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:

zeromq, czmq, hwloc, lua, lua-luaposix, munge, python, jansson, pkgconfig, yaml-cpp, lz4

Run Dependencies:

lua, python, py-cffi, py-six, py-pyyaml, py-jsonschema

Description:

A next-generation resource manager (pre-alpha)

flux-sched¶

Homepage:

https://github.com/flux-framework/flux-sched

Spack package:

flux-sched/package.py

Versions:

master, 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:

http://fluxbox.org/

Spack package:

fluxbox/package.py

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:

http://fmtlib.net/latest/index.html

Spack package:

fmt/package.py

Versions:

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:

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:

http://www.extend-project.de/

Spack package:

foam-extend/package.py

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:

https://github.com/facebook/folly

Spack package:

folly/package.py

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-adobe-100dpi¶

Homepage:

http://cgit.freedesktop.org/xorg/font/adobe-100dpi

Spack package:

font-adobe-100dpi/package.py

Versions:

1.0.3

Build Dependencies:

font-util, fontconfig, mkfontdir, bdftopcf, pkgconfig, util-macros

Link Dependencies:

Description:

X.org adobe-100dpi font.

font-adobe-75dpi¶

Homepage:

http://cgit.freedesktop.org/xorg/font/adobe-75dpi

Spack package:

font-adobe-75dpi/package.py

Versions:

1.0.3

Build Dependencies:

font-util, fontconfig, mkfontdir, bdftopcf, pkgconfig, util-macros

Link Dependencies:

Description:

X.org adobe-75dpi font.

font-adobe-utopia-100dpi¶

Homepage:

http://cgit.freedesktop.org/xorg/font/adobe-utopia-100dpi

Spack package:

font-adobe-utopia-100dpi/package.py

Versions:

1.0.4

Build Dependencies:

font-util, fontconfig, mkfontdir, bdftopcf, pkgconfig, util-macros

Link Dependencies:

Description:

X.org adobe-utopia-100dpi font.

font-adobe-utopia-75dpi¶

Homepage:

http://cgit.freedesktop.org/xorg/font/adobe-utopia-75dpi

Spack package:

font-adobe-utopia-75dpi/package.py

Versions:

1.0.4

Build Dependencies:

font-util, fontconfig, mkfontdir, bdftopcf, pkgconfig, util-macros

Link Dependencies:

Description:

X.org adobe-utopia-75dpi font.

font-adobe-utopia-type1¶

Homepage:

https://cgit.freedesktop.org/xorg/font/adobe-utopia-type1

Spack package:

font-adobe-utopia-type1/package.py

Versions:

1.0.4

Build Dependencies:

font-util, fontconfig, mkfontdir, mkfontscale, pkgconfig, util-macros

Description:

X.org adobe-utopia-type1 font.

font-alias¶

Homepage:

http://cgit.freedesktop.org/xorg/font/alias

Spack package:

font-alias/package.py

Versions:

1.0.3

Build Dependencies:

font-util, pkgconfig, util-macros

Link Dependencies:

Description:

X.org alias font.

font-arabic-misc¶

Homepage:

http://cgit.freedesktop.org/xorg/font/arabic-misc

Spack package:

font-arabic-misc/package.py

Versions:

1.0.3

Build Dependencies:

font-util, fontconfig, mkfontdir, bdftopcf, pkgconfig, util-macros

Link Dependencies:

Description:

X.org arabic-misc font.

font-bh-100dpi¶

Homepage:

http://cgit.freedesktop.org/xorg/font/bh-100dpi

Spack package:

font-bh-100dpi/package.py

Versions:

1.0.3

Build Dependencies:

font-util, fontconfig, mkfontdir, bdftopcf, pkgconfig, util-macros

Link Dependencies:

Description:

X.org bh-100dpi font.

font-bh-75dpi¶

Homepage:

http://cgit.freedesktop.org/xorg/font/bh-75dpi

Spack package:

font-bh-75dpi/package.py

Versions:

1.0.3

Build Dependencies:

font-util, fontconfig, mkfontdir, bdftopcf, pkgconfig, util-macros

Link Dependencies:

Description:

X.org bh-75dpi font.

font-bh-lucidatypewriter-100dpi¶

Homepage:

http://cgit.freedesktop.org/xorg/font/bh-lucidatypewriter-100dpi

Spack package:

font-bh-lucidatypewriter-100dpi/package.py

Versions:

1.0.3

Build Dependencies:

font-util, fontconfig, mkfontdir, bdftopcf, pkgconfig, util-macros

Link Dependencies:

Description:

X.org bh-lucidatypewriter-100dpi font.

font-bh-lucidatypewriter-75dpi¶

Homepage:

http://cgit.freedesktop.org/xorg/font/bh-lucidatypewriter-75dpi

Spack package:

font-bh-lucidatypewriter-75dpi/package.py

Versions:

1.0.3

Build Dependencies:

font-util, fontconfig, mkfontdir, bdftopcf, pkgconfig, util-macros

Link Dependencies:

Description:

X.org bh-lucidatypewriter-75dpi font.

font-bh-ttf¶

Homepage:

http://cgit.freedesktop.org/xorg/font/bh-ttf

Spack package:

font-bh-ttf/package.py

Versions:

1.0.3

Build Dependencies:

font-util, fontconfig, mkfontdir, bdftopcf, pkgconfig, util-macros

Link Dependencies:

Description:

X.org bh-ttf font.

font-bh-type1¶

Homepage:

http://cgit.freedesktop.org/xorg/font/bh-type1

Spack package:

font-bh-type1/package.py

Versions:

1.0.3

Build Dependencies:

font-util, fontconfig, mkfontdir, mkfontscale, pkgconfig, util-macros

Link Dependencies:

Description:

X.org bh-type1 font.

font-bitstream-100dpi¶

Homepage:

http://cgit.freedesktop.org/xorg/font/bitstream-100dpi

Spack package:

font-bitstream-100dpi/package.py

Versions:

1.0.3

Build Dependencies:

font-util, fontconfig, mkfontdir, bdftopcf, pkgconfig, util-macros

Link Dependencies:

Description:

X.org bitstream-100dpi font.

font-bitstream-75dpi¶

Homepage:

http://cgit.freedesktop.org/xorg/font/bitstream-75dpi

Spack package:

font-bitstream-75dpi/package.py

Versions:

1.0.3

Build Dependencies:

font-util, fontconfig, mkfontdir, bdftopcf, pkgconfig, util-macros

Link Dependencies:

Description:

X.org bitstream-75dpi font.

font-bitstream-speedo¶

Homepage:

http://cgit.freedesktop.org/xorg/font/bitstream-speedo

Spack package:

font-bitstream-speedo/package.py

Versions:

1.0.2

Build Dependencies:

font-util, fontconfig, mkfontdir, mkfontscale, pkgconfig, util-macros

Link Dependencies:

Description:

X.org bitstream-speedo font.

font-bitstream-type1¶

Homepage:

http://cgit.freedesktop.org/xorg/font/bitstream-type1

Spack package:

font-bitstream-type1/package.py

Versions:

1.0.3

Build Dependencies:

font-util, fontconfig, mkfontdir, mkfontscale, pkgconfig, util-macros

Link Dependencies:

Description:

X.org bitstream-type1 font.

font-cronyx-cyrillic¶

Homepage:

http://cgit.freedesktop.org/xorg/font/cronyx-cyrillic

Spack package:

font-cronyx-cyrillic/package.py

Versions:

1.0.3

Build Dependencies:

font-util, fontconfig, mkfontdir, bdftopcf, pkgconfig, util-macros

Link Dependencies:

Description:

X.org cronyx-cyrillic font.

font-cursor-misc¶

Homepage:

http://cgit.freedesktop.org/xorg/font/cursor-misc

Spack package:

font-cursor-misc/package.py

Versions:

1.0.3

Build Dependencies:

font-util, fontconfig, mkfontdir, bdftopcf, pkgconfig, util-macros

Link Dependencies:

Description:

X.org cursor-misc font.

font-daewoo-misc¶

Homepage:

http://cgit.freedesktop.org/xorg/font/daewoo-misc

Spack package:

font-daewoo-misc/package.py

Versions:

1.0.3

Build Dependencies:

font-util, fontconfig, mkfontdir, bdftopcf, pkgconfig, util-macros

Link Dependencies:

Description:

X.org daewoo-misc font.

font-dec-misc¶

Homepage:

http://cgit.freedesktop.org/xorg/font/dec-misc

Spack package:

font-dec-misc/package.py

Versions:

1.0.3

Build Dependencies:

font-util, fontconfig, mkfontdir, bdftopcf, pkgconfig, util-macros

Link Dependencies:

Description:

X.org dec-misc font.

font-ibm-type1¶

Homepage:

http://cgit.freedesktop.org/xorg/font/ibm-type1

Spack package:

font-ibm-type1/package.py

Versions:

1.0.3

Build Dependencies:

font-util, fontconfig, mkfontdir, mkfontscale, pkgconfig, util-macros

Link Dependencies:

Description:

X.org ibm-type1 font.

font-isas-misc¶

Homepage:

http://cgit.freedesktop.org/xorg/font/isas-misc

Spack package:

font-isas-misc/package.py

Versions:

1.0.3

Build Dependencies:

font-util, fontconfig, mkfontdir, bdftopcf, pkgconfig, util-macros

Link Dependencies:

Description:

X.org isas-misc font.

font-jis-misc¶

Homepage:

http://cgit.freedesktop.org/xorg/font/jis-misc

Spack package:

font-jis-misc/package.py

Versions:

1.0.3

Build Dependencies:

font-util, fontconfig, mkfontdir, bdftopcf, pkgconfig, util-macros

Link Dependencies:

Description:

X.org jis-misc font.

font-micro-misc¶

Homepage:

http://cgit.freedesktop.org/xorg/font/micro-misc

Spack package:

font-micro-misc/package.py

Versions:

1.0.3

Build Dependencies:

font-util, fontconfig, mkfontdir, bdftopcf, pkgconfig, util-macros

Link Dependencies:

Description:

X.org micro-misc font.

font-misc-cyrillic¶

Homepage:

http://cgit.freedesktop.org/xorg/font/misc-cyrillic

Spack package:

font-misc-cyrillic/package.py

Versions:

1.0.3

Build Dependencies:

font-util, fontconfig, mkfontdir, bdftopcf, pkgconfig, util-macros

Link Dependencies:

Description:

X.org misc-cyrillic font.

font-misc-ethiopic¶

Homepage:

http://cgit.freedesktop.org/xorg/font/misc-ethiopic

Spack package:

font-misc-ethiopic/package.py

Versions:

1.0.3

Build Dependencies:

font-util, fontconfig, mkfontdir, mkfontscale, pkgconfig, util-macros

Link Dependencies:

Description:

X.org misc-ethiopic font.

font-misc-meltho¶

Homepage:

http://cgit.freedesktop.org/xorg/font/misc-meltho

Spack package:

font-misc-meltho/package.py

Versions:

1.0.3

Build Dependencies:

font-util, fontconfig, mkfontdir, mkfontscale, pkgconfig, util-macros

Link Dependencies:

Description:

X.org misc-meltho font.

font-misc-misc¶

Homepage:

http://cgit.freedesktop.org/xorg/font/misc-misc

Spack package:

font-misc-misc/package.py

Versions:

1.1.2

Build Dependencies:

font-util, fontconfig, mkfontdir, bdftopcf, pkgconfig, util-macros

Link Dependencies:

Description:

X.org misc-misc font.

font-mutt-misc¶

Homepage:

http://cgit.freedesktop.org/xorg/font/mutt-misc

Spack package:

font-mutt-misc/package.py

Versions:

1.0.3

Build Dependencies:

font-util, fontconfig, mkfontdir, bdftopcf, pkgconfig, util-macros

Link Dependencies:

Description:

X.org mutt-misc font.

font-schumacher-misc¶

Homepage:

http://cgit.freedesktop.org/xorg/font/schumacher-misc

Spack package:

font-schumacher-misc/package.py

Versions:

1.1.2

Build Dependencies:

font-util, fontconfig, mkfontdir, bdftopcf, pkgconfig, util-macros

Link Dependencies:

Description:

X.org schumacher-misc font.

font-screen-cyrillic¶

Homepage:

http://cgit.freedesktop.org/xorg/font/screen-cyrillic

Spack package:

font-screen-cyrillic/package.py

Versions:

1.0.4

Build Dependencies:

font-util, fontconfig, mkfontdir, bdftopcf, pkgconfig, util-macros

Link Dependencies:

Description:

X.org screen-cyrillic font.

font-sony-misc¶

Homepage:

http://cgit.freedesktop.org/xorg/font/sony-misc

Spack package:

font-sony-misc/package.py

Versions:

1.0.3

Build Dependencies:

font-util, fontconfig, mkfontdir, bdftopcf, pkgconfig, util-macros

Link Dependencies:

Description:

X.org sony-misc font.

font-sun-misc¶

Homepage:

http://cgit.freedesktop.org/xorg/font/sun-misc

Spack package:

font-sun-misc/package.py

Versions:

1.0.3

Build Dependencies:

font-util, fontconfig, mkfontdir, bdftopcf, pkgconfig, util-macros

Link Dependencies:

Description:

X.org sun-misc font.

font-util¶

Homepage:

http://cgit.freedesktop.org/xorg/font/util

Spack package:

font-util/package.py

Versions:

1.3.1

Build Dependencies:

pkgconfig, util-macros

Description:

X.Org font package creation/installation utilities.

font-winitzki-cyrillic¶

Homepage:

http://cgit.freedesktop.org/xorg/font/winitzki-cyrillic

Spack package:

font-winitzki-cyrillic/package.py

Versions:

1.0.3

Build Dependencies:

font-util, fontconfig, mkfontdir, bdftopcf, pkgconfig, util-macros

Link Dependencies:

Description:

X.org winitzki-cyrillic font.

font-xfree86-type1¶

Homepage:

http://cgit.freedesktop.org/xorg/font/xfree86-type1

Spack package:

font-xfree86-type1/package.py

Versions:

1.0.4

Build Dependencies:

font-util, fontconfig, mkfontdir, mkfontscale, pkgconfig, util-macros

Link Dependencies:

Description:

X.org xfree86-type1 font.

fontcacheproto¶

Homepage:

http://cgit.freedesktop.org/xorg/proto/fontcacheproto

Spack package:

fontcacheproto/package.py

Versions:

0.1.3

Description:

X.org FontcacheProto protocol headers.

fontconfig¶

Homepage:

http://www.freedesktop.org/wiki/Software/fontconfig/

Spack package:

fontconfig/package.py

Versions:

2.12.3, 2.12.1, 2.11.1

Build Dependencies:

freetype, gperf, libxml2, pkgconfig, font-util

Link Dependencies:

freetype, libxml2, font-util

Description:

Fontconfig is a library for configuring/customizing font access

fontsproto¶

Homepage:

http://cgit.freedesktop.org/xorg/proto/fontsproto

Spack package:

fontsproto/package.py

Versions:

2.1.3

Build Dependencies:

pkgconfig, util-macros

Description:

X Fonts Extension.

fonttosfnt¶

Homepage:

http://cgit.freedesktop.org/xorg/app/fonttosfnt

Spack package:

fonttosfnt/package.py

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:

https://github.com/Maratyszcza/FP16/

Spack package:

fp16/package.py

Versions:

master

Description:

FP16 is a header-only library for conversion to/from half-precision floating point formats

fpc¶

Homepage:

https://www.freepascal.org/

Spack package:

fpc/package.py

Versions:

3.0.2

Description:

Free Pascal is a 32, 64 and 16 bit professional Pascal compiler.

fqtrim¶

Homepage:

https://ccb.jhu.edu/software/fqtrim/

Spack package:

fqtrim/package.py

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:

http://weizhong-lab.ucsd.edu/frhit

Spack package:

fr-hit/package.py

Versions:

0.7.1-2013-02-20

Build Dependencies:

Link Dependencies:

Description:

An efficient algorithm for fragment recruitment for next generation sequences against microbial reference genomes.

freebayes¶

Homepage:

https://github.com/ekg/freebayes

Spack package:

freebayes/package.py

Versions:

1.1.0

Build Dependencies:

cmake, zlib

Link Dependencies:

zlib

Description:

Bayesian haplotype-based genetic polymorphism discovery and genotyping.

freeglut¶

Homepage:

http://freeglut.sourceforge.net/

Spack package:

freeglut/package.py

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

freetype¶

Homepage:

https://www.freetype.org/index.html

Spack package:

freetype/package.py

Versions:

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:

http://www.gaia-gis.it

Spack package:

freexl/package.py

Versions:

1.0.5

Description:

FreeXL is an open source library to extract valid data from within an Excel (.xls) spreadsheet.

fseq¶

Homepage:

http://fureylab.web.unc.edu/software/fseq/

Spack package:

fseq/package.py

Versions:

1.84

Build Dependencies:

java

Run Dependencies:

java

Description:

F-Seq: A Feature Density Estimator for High-Throughput Sequence Tags

fsl¶

Homepage:

https://fsl.fmrib.ox.ac.uk

Spack package:

fsl/package.py

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:

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:

http://cgit.freedesktop.org/xorg/app/fslsfonts

Spack package:

fslsfonts/package.py

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:

http://cgit.freedesktop.org/xorg/app/fstobdf

Spack package:

fstobdf/package.py

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:

http://www-udc.ig.utexas.edu/external/becker/data.html#fstrack

Spack package:

fstrack/package.py

Versions:

0.5.3.092918

Build Dependencies:

gmt, netcdf

Link Dependencies:

gmt, netcdf

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:

http://ftgl.sourceforge.net/docs/html/

Spack package:

ftgl/package.py

Versions:

2.1.3-rc5, 2.1.2

Build Dependencies:

autoconf, automake, libtool, m4, pkgconfig, gl, glu, freetype, doxygen

Link Dependencies:

gl, glu, freetype

Description:

Library to use arbitrary fonts in OpenGL applications.

funhpc¶

Homepage:

https://github.com/eschnett/FunHPC.cxx

Spack package:

funhpc/package.py

Versions:

develop, 1.3.0, 1.2.0, 1.1.1, 1.1.0, 1.0.0, 0.1.1, 0.1.0

Build Dependencies:

cmake, cereal, googletest, hwloc, jemalloc, mpi, qthreads

Link Dependencies:

cereal, googletest, hwloc, jemalloc, mpi, qthreads

Description:

FunHPC: Functional HPC Programming

fyba¶

Homepage:

https://github.com/kartverket/fyba

Spack package:

fyba/package.py

Versions:

4.1.1

Build Dependencies:

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:

https://github.com/junegunn/fzf

Spack package:

fzf/package.py

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:

Link Dependencies:

Description:

fzf is a general-purpose command-line fuzzy finder.

g4abla¶

Homepage:

http://geant4.web.cern.ch

Spack package:

g4abla/package.py

Versions:

3.1, 3.0

Description:

Geant4 data for nuclear shell effects in INCL/ABLA hadronic mode

g4emlow¶

Homepage:

http://geant4.web.cern.ch

Spack package:

g4emlow/package.py

Versions:

7.3, 6.50

Description:

Geant4 data files for low energy electromagnetic processes.

g4ensdfstate¶

Homepage:

http://geant4.web.cern.ch

Spack package:

g4ensdfstate/package.py

Versions:

2.2, 2.1

Description:

Geant4 data for nuclides properties

g4ndl¶

Homepage:

http://geant4.web.cern.ch

Spack package:

g4ndl/package.py

Versions:

4.5

Description:

Geant4 Neutron data files with thermal cross sections

g4neutronxs¶

Homepage:

http://geant4.web.cern.ch

Spack package:

g4neutronxs/package.py

Versions:

1.4

Description:

Geant4 data for evaluated neutron cross-sections on natural composition of elements

g4photonevaporation¶

Homepage:

http://geant4.web.cern.ch

Spack package:

g4photonevaporation/package.py

Versions:

5.2, 4.3.2

Description:

Geant4 data for photon evaporation

g4pii¶

Homepage:

http://geant4.web.cern.ch

Spack package:

g4pii/package.py

Versions:

1.3

Description:

Geant4 data for shell ionisation cross-sections

g4radioactivedecay¶

Homepage:

http://geant4.web.cern.ch

Spack package:

g4radioactivedecay/package.py

Versions:

5.2, 5.1.1

Description:

Geant4 data files for radio-active decay hadronic processes

g4realsurface¶

Homepage:

http://geant4.web.cern.ch

Spack package:

g4realsurface/package.py

Versions:

2.1.1, 2.1, 1.0

Description:

Geant4 data for measured optical surface reflectance

g4saiddata¶

Homepage:

http://geant4.web.cern.ch

Spack package:

g4saiddata/package.py

Versions:

1.1

Description:

Geant4 data from evaluated cross-sections in SAID data-base

g4tendl¶

Homepage:

http://geant4.web.cern.ch

Spack package:

g4tendl/package.py

Versions:

1.3.2, 1.3

Description:

Geant4 data for incident particles [optional]

gapbs¶

Homepage:

http://gap.cs.berkeley.edu/benchmark.html

Spack package:

gapbs/package.py

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:

https://sourceforge.net/projects/soapdenovo2/files/GapCloser/

Spack package:

gapcloser/package.py

Versions:

1.12-r6

Description:

The GapCloser is designed to close the gaps emerging during the scaffolding process

gapfiller¶

Homepage:

https://www.baseclear.com/genomics/bioinformatics/basetools/gapfiller

Spack package:

gapfiller/package.py

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:

http://gasnet.lbl.gov

Spack package:

gasnet/package.py

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:

https://software.broadinstitute.org/gatk/

Spack package:

gatk/package.py

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

gaudi¶

Homepage:

http://gaudi.web.cern.ch/gaudi/

Spack package:

gaudi/package.py

Versions:

develop, 31.0, 30.5

Build Dependencies:

cmake, boost, intel-tbb, libuuid, python, py-xenv, range-v3, root, zlib, aida, clhep, cppunit, gdb, gperftools, heppdt, py-networkx, py-nose, py-setuptools, relax, xerces-c, cppgsl, doxygen, gsl, jemalloc, libpng, libunwind, intel-parallel-studio

Link Dependencies:

boost, intel-tbb, libuuid, python, py-xenv, range-v3, root, zlib, aida, clhep, cppunit, gdb, gperftools, heppdt, py-networkx, py-nose, py-setuptools, relax, xerces-c, cppgsl, doxygen, gsl, jemalloc, libpng, libunwind, intel-parallel-studio

Description:

An experiment-independent HEP event data processing framework

gaussian¶

Homepage:

http://www.gaussian.com/

Spack package:

gaussian/package.py

Versions:

Description:

Gaussian is a computer program for computational chemistry

gawk¶

Homepage:

https://www.gnu.org/software/gawk/

Spack package:

gawk/package.py

Versions:

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:

http://molevol.cmima.csic.es/castresana/Gblocks.html

Spack package:

gblocks/package.py

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:

https://gcc.gnu.org

Spack package:

gcc/package.py

Versions:

develop, 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, gnat, binutils, zip, cuda

Link Dependencies:

gmp, mpfr, mpc, isl, zlib, 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:

https://cgit.freedesktop.org/xorg/util/gccmakedep/

Spack package:

gccmakedep/package.py

Versions:

1.0.3

Build Dependencies:

pkgconfig

Description:

X.org gccmakedep utilities.

gccxml¶

Homepage:

http://gccxml.github.io

Spack package:

gccxml/package.py

Versions:

develop, latest

Build Dependencies:

Description:

gccxml dumps an XML description of C++ source code using an extension of the GCC C++ compiler.

gconf¶

Homepage:

https://projects.gnome.org/gconf/

Spack package:

gconf/package.py

Versions:

3.2.6

Build Dependencies:

Link Dependencies:

Description:

GConf is a system for storing application preferences.

gcta¶

Homepage:

http://cnsgenomics.com/software/gcta/#Overview

Spack package:

gcta/package.py

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:

http://www.gdal.org/

Spack package:

gdal/package.py

Versions:

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, jasper, openjpeg, xerces-c, expat, 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, jasper, openjpeg, xerces-c, expat, 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:

https://www.gnu.org/software/gdb

Spack package:

gdb/package.py

Versions:

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:

http://www.gnu.org.ua/software/gdbm/gdbm.html

Spack package:

gdbm/package.py

Versions:

1.18.1, 1.14.1, 1.13, 1.12, 1.11, 1.10, 1.9.1, 1.9

Build Dependencies:

Link Dependencies:

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:

https://developer.gnome.org/gdk-pixbuf/

Spack package:

gdk-pixbuf/package.py

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:

https://github.com/gnudatalanguage/gdl

Spack package:

gdl/package.py

Versions:

0.9.8

Build Dependencies:

cmake, python, graphicsmagick, hdf, hdf5, libx11, plplot, proj, py-numpy, wx, eigen, fftw, gsl, jpeg, libice, libsm, libxinerama, libxxf86vm, netcdf, pslib, readline

Link Dependencies:

python, graphicsmagick, hdf, hdf5, libx11, plplot, proj, wx, eigen, fftw, gsl, jpeg, libice, libsm, libxinerama, libxxf86vm, netcdf, pslib, readline

Run Dependencies:

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:

http://geant4.cern.ch/

Spack package:

geant4/package.py

Versions:

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:

http://geant4.cern.ch

Spack package:

geant4-data/package.py

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:

https://github.com/mpicbg-scicomp/gearshifft

Spack package:

gearshifft/package.py

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:

https://github.com/google/gemmlowp

Spack package:

gemmlowp/package.py

Versions:

a6f29d9ac

Description:

Google low-precision matrix multiplication library

genemark-et¶

Homepage:

http://topaz.gatech.edu/GeneMark

Spack package:

genemark-et/package.py

Versions:

4.38, 4.33

Build Dependencies:

perl

Run Dependencies:

perl

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:

http://gfinisher.sourceforge.net

Spack package:

genomefinisher/package.py

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:

http://genometools.org/

Spack package:

genometools/package.py

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.

geopm¶

Homepage:

https://geopm.github.io

Spack package:

geopm/package.py

Versions:

develop, master, 1.0.0-rc2, 1.0.0-rc1, 0.6.1, 0.6.0, 0.5.1, 0.5.0, 0.4.0, 0.3.0

Build Dependencies:

m4, automake, autoconf, libtool, ruby-ronn, doxygen, numactl, mpi, hwloc, json-c

Link Dependencies:

numactl, mpi, hwloc, json-c

Run Dependencies:

py-pandas, py-numpy, py-natsort, 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:

http://trac.osgeo.org/geos/

Spack package:

geos/package.py

Versions:

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:

https://www.gnu.org/software/gettext/

Spack package:

gettext/package.py

Versions:

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:

Description:

GNU internationalization (i18n) and localization (l10n) library.

gflags¶

Homepage:

https://gflags.github.io/gflags

Spack package:

gflags/package.py

Versions:

2.1.2

Build Dependencies:

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:

https://www.bitbucket.org/essex/ghost/

Spack package:

ghost/package.py

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:

http://ghostscript.com/

Spack package:

ghostscript/package.py

Versions:

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:

http://ghostscript.com/

Spack package:

ghostscript-fonts/package.py

Versions:

8.11

Description:

Ghostscript Fonts

giflib¶

Homepage:

http://giflib.sourceforge.net/

Spack package:

giflib/package.py

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:

https://ginkgo-project.github.io/

Spack package:

ginkgo/package.py

Versions:

develop, master, 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:

http://git-scm.com

Spack package:

git/package.py

Versions:

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, openssl, pcre, perl, zlib, autoconf, automake, libtool, m4, tk

Link Dependencies:

curl, expat, gettext, libiconv, openssl, pcre, 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:

https://github.com/jedbrown/git-fat

Spack package:

git-fat-git/package.py

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:

https://github.com/mhagger/git-imerge

Spack package:

git-imerge/package.py

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:

https://git-lfs.github.com

Spack package:

git-lfs/package.py

Versions:

2.7.2, 2.7.1, 2.7.0, 2.6.1

Build Dependencies:

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:

http://www.geuz.org/gl2ps/

Spack package:

gl2ps/package.py

Versions:

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:

http://glew.sourceforge.net/

Spack package:

glew/package.py

Versions:

2.0.0

Build Dependencies:

cmake, gl

Link Dependencies:

Description:

The OpenGL Extension Wrangler Library.

glfmultiples¶

Homepage:

https://genome.sph.umich.edu/wiki/GlfMultiples

Spack package:

glfmultiples/package.py

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:

https://developer.gnome.org/glib/

Spack package:

glib/package.py

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:

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:

https://developer.gnome.org/glib/

Spack package:

glibmm/package.py

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:

https://ccb.jhu.edu/software/glimmer

Spack package:

glimmer/package.py

Versions:

3.02b

Description:

Glimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses.

glm¶

Homepage:

https://github.com/g-truc/glm

Spack package:

glm/package.py

Versions:

0.9.7.1

Build Dependencies:

Description:

OpenGL Mathematics (GLM) is a header only C++ mathematics library for graphics software based on the OpenGL Shading Language (GLSL) specification

global¶

Homepage:

http://www.gnu.org/software/global

Spack package:

global/package.py

Versions:

6.5

Build Dependencies:

exuberant-ctags, ncurses

Link Dependencies:

Run Dependencies:

exuberant-ctags

Description:

The Gnu Global tagging system

globalarrays¶

Homepage:

http://hpc.pnl.gov/globalarrays/

Spack package:

globalarrays/package.py

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.

globus-toolkit¶

Homepage:

http://toolkit.globus.org

Spack package:

globus-toolkit/package.py

Versions:

6.0.1506371041, 6.0.1493989444

Build Dependencies:

pkgconfig, openssl

Link Dependencies:

Description:

The Globus Toolkit is an open source software toolkit used for building grids

glog¶

Homepage:

https://github.com/google/glog

Spack package:

glog/package.py

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:

https://github.com/facebookincubator/gloo

Spack package:

gloo/package.py

Versions:

master

Build Dependencies:

Description:

Gloo is a collective communications library.

glpk¶

Homepage:

https://www.gnu.org/software/glpk

Spack package:

glpk/package.py

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:

https://www.x.org/wiki/

Spack package:

glproto/package.py

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:

http://glvis.org

Spack package:

glvis/package.py

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:

https://www.gnu.org/software/make/

Spack package:

gmake/package.py

Versions:

4.2.1, 4.0

Build Dependencies:

gettext, guile

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:

http://research-pub.gene.com/gmap/

Spack package:

gmap-gsnap/package.py

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:

http://spruce.sourceforge.net/gmime/

Spack package:

gmime/package.py

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:

https://github.com/ibaned/gmodel

Spack package:

gmodel/package.py

Versions:

2.1.0

Build Dependencies:

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:

https://gmplib.org

Spack package:

gmp/package.py

Versions:

6.1.2, 6.1.1, 6.1.0, 6.0.0a, 6.0.0, 5.1.3, 4.3.2

Build Dependencies:

Description:

GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating-point numbers.

gmsh¶

Homepage:

http://gmsh.info

Spack package:

gmsh/package.py

Versions:

develop, 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:

http://gmt.soest.hawaii.edu/

Spack package:

gmt/package.py

Versions:

5.4.4, 4.5.9

Build Dependencies:

ghostscript, subversion, cmake, netcdf, curl, pcre, gdal, fftw, lapack, blas

Link Dependencies:

ghostscript, subversion, netcdf, 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:

https://topex.ucsd.edu/gmtsar/

Spack package:

gmtsar/package.py

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:

https://libre.adacore.com/tools/gnat-gpl-edition/

Spack package:

gnat/package.py

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.

gnu-prolog¶

Homepage:

http://www.gprolog.org/

Spack package:

gnu-prolog/package.py

Versions:

1.4.4

Description:

A free Prolog compiler with constraint solving over finite domains.

gnupg¶

Homepage:

https://gnupg.org/index.html

Spack package:

gnupg/package.py

Versions:

2.2.15, 2.2.3, 2.1.21

Build Dependencies:

libgcrypt, libassuan, libksba, libgpg-error, npth

Link Dependencies:

libgcrypt, libassuan, libksba, libgpg-error, npth

Description:

GnuPG is a complete and free implementation of the OpenPGP standard as defined by RFC4880

gnuplot¶

Homepage:

http://www.gnuplot.info

Spack package:

gnuplot/package.py

Versions:

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, wx, pango, libx11, qt

Link Dependencies:

readline, libxpm, libiconv, libcerf, libgd, cairo, wx, 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:

http://www.gnutls.org

Spack package:

gnutls/package.py

Versions:

3.6.7.1, 3.5.19, 3.5.13, 3.5.10, 3.5.9, 3.3.9

Build Dependencies:

nettle, libidn2, zlib, gettext, pkgconfig

Link Dependencies:

nettle, 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:

https://golang.org

Spack package:

go/package.py

Versions:

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:

https://golang.org

Spack package:

go-bootstrap/package.py

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

gobject-introspection¶

Homepage:

https://wiki.gnome.org/Projects/GObjectIntrospection

Spack package:

gobject-introspection/package.py

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:

https://github.com/google/googletest

Spack package:

googletest/package.py

Versions:

1.8.1, 1.8.0, 1.7.0, 1.6.0

Build Dependencies:

Description:

Google test framework for C++. Also called gtest.

gotcha¶

Homepage:

http://github.com/LLNL/gotcha

Spack package:

gotcha/package.py

Versions:

develop, master, 1.0.2, 0.0.2

Build Dependencies:

Description:

C software library for shared library function wrapping, enables tools to intercept calls into shared libraries

gource¶

Homepage:

http://gource.io

Spack package:

gource/package.py

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.

gperf¶

Homepage:

https://www.gnu.org/software/gperf/

Spack package:

gperf/package.py

Versions:

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:

https://github.com/gperftools/gperftools

Spack package:

gperftools/package.py

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:

https://www.gnupg.org/software/gpgme/index.html

Spack package:

gpgme/package.py

Versions:

1.12.0

Build Dependencies:

libgpg-error, libassuan

Description:

GPGME is the standard library to access GnuPG functions from programming languages.

gplates¶

Homepage:

https://www.gplates.org

Spack package:

gplates/package.py

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.

grackle¶

Homepage:

http://grackle.readthedocs.io/en/grackle-3.1/

Spack package:

grackle/package.py

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:

https://gradle.org

Spack package:

gradle/package.py

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:

https://cgit.freedesktop.org/xorg/app/grandr

Spack package:

grandr/package.py

Versions:

0.1

Build Dependencies:

gtkplus, gconf, xrandr

Link Dependencies:

gtkplus, gconf, xrandr

Description:

RandR user interface using GTK+ libraries.

graph500¶

Homepage:

https://graph500.org

Spack package:

graph500/package.py

Versions:

3.0.0

Build Dependencies:

mpi

Link Dependencies:

mpi

Description:

Graph500 reference implementations.

graphicsmagick¶

Homepage:

http://www.graphicsmagick.org/

Spack package:

graphicsmagick/package.py

Versions:

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.

graphlib¶

Homepage:

https://github.com/LLNL/graphlib

Spack package:

graphlib/package.py

Versions:

3.0.0, 2.0.0

Build Dependencies:

Description:

Library to create, manipulate, and export graphs Graphlib.

graphmap¶

Homepage:

https://github.com/isovic/graphmap

Spack package:

graphmap/package.py

Versions:

0.3.0

Description:

A highly sensitive and accurate mapper for long, error-prone reads

graphviz¶

Homepage:

http://www.graphviz.org

Spack package:

graphviz/package.py

Versions:

2.40.1

Build Dependencies:

swig, java, python, cairo, pango, freetype, glib, fontconfig, libpng, zlib, libgd, gts, expat, ghostscript, qt, gtkplus, pkgconfig, automake, autoconf, bison, flex, libtool

Link Dependencies:

java, python, cairo, pango, freetype, glib, fontconfig, libpng, zlib, libgd, gts, expat, ghostscript, qt, gtkplus

Description:

Graph Visualization Software

grass¶

Homepage:

http://grass.osgeo.org

Spack package:

grass/package.py

Versions:

7.6.1, 7.4.4, 7.4.3, 7.4.2, 7.4.1, 7.4.0

Build Dependencies:

gmake, zlib, flex, bison, proj, gdal, python, libx11, libtiff, libpng, postgresql, mariadb, sqlite, gl, fftw, blas, lapack, cairo, freetype, readline, opencl, bzip2, netcdf, geos

Link Dependencies:

zlib, proj, gdal, libx11, libtiff, libpng, postgresql, mariadb, sqlite, gl, fftw, blas, lapack, cairo, freetype, readline, opencl, bzip2, netcdf, geos

Run Dependencies:

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.

grib-api¶

Homepage:

https://software.ecmwf.int/wiki/display/GRIB/Home

Spack package:

grib-api/package.py

Versions:

1.24.0, 1.21.0, 1.17.0, 1.16.0

Build Dependencies:

cmake, netcdf, openjpeg, jasper, libpng, libaec, python, py-numpy

Link Dependencies:

netcdf, openjpeg, jasper, libpng, libaec, python

Run Dependencies:

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:

https://github.com/aertslab/GRNBoost

Spack package:

grnboost/package.py

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:

https://www.gnu.org/software/groff/

Spack package:

groff/package.py

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:

http://www.gromacs.org

Spack package:

gromacs/package.py

Versions:

develop, 2019.2, 2019.1, 2019, 2018.4, 2018.3, 2018.2, 2018.1, 2018, 2016.5, 2016.4, 2016.3, 5.1.5, 5.1.4, 5.1.2

Build Dependencies:

cmake, mpi, plumed, fftw, cuda

Link Dependencies:

mpi, plumed, fftw, cuda

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.

gsl¶

Homepage:

http://www.gnu.org/software/gsl

Spack package:

gsl/package.py

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:

https://github.com/gslib/gslib

Spack package:

gslib/package.py

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:

https://www.gtkmm.org/en/

Spack package:

gtkmm/package.py

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:

https://github.com/GTkorvo/atl

Spack package:

gtkorvo-atl/package.py

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:

https://github.com/GTkorvo/cercs_env

Spack package:

gtkorvo-cercs-env/package.py

Versions:

develop, 1.0

Build Dependencies:

Description:

A utility library used by some GTkorvo packages.

gtkorvo-dill¶

Homepage:

https://github.com/GTkorvo/dill

Spack package:

gtkorvo-dill/package.py

Versions:

develop, 2.4, 2.1

Build Dependencies:

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:

http://www.github.com/GTkorvo/enet

Spack package:

gtkorvo-enet/package.py

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:

http://www.gtk.org

Spack package:

gtkplus/package.py

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

Link Dependencies:

atk, gdk-pixbuf, glib, shared-mime-info, pango, cairo, gobject-introspection, libepoxy, libxi, inputproto, fixesproto, at-spi2-atk, gettext

Description:

The GTK+ 2 package contains libraries used for creating graphical user interfaces for applications.

gts¶

Homepage:

http://gts.sourceforge.net/index.html

Spack package:

gts/package.py

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:

http://guidance.tau.ac.il/ver2/

Spack package:

guidance/package.py

Versions:

2.02

Build Dependencies:

perl, perl-bio-perl, ruby, prank, clustalw, mafft, muscle

Link Dependencies:

ruby, prank, clustalw, mafft, muscle

Run Dependencies:

perl, perl-bio-perl

Description:

Guidance: Accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters.

guile¶

Homepage:

https://www.gnu.org/software/guile/

Spack package:

guile/package.py

Versions:

2.2.0, 2.0.14, 2.0.11

Build Dependencies:

gmp, gettext, libtool, libunistring, bdw-gc, libffi, readline, pkgconfig

Link Dependencies:

gmp, gettext, libtool, libunistring, bdw-gc, libffi, readline

Description:

Guile is the GNU Ubiquitous Intelligent Language for Extensions, the official extension language for the GNU operating system.

gurobi¶

Homepage:

http://www.gurobi.com/index

Spack package:

gurobi/package.py

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.

h5hut¶

Homepage:

https://amas.psi.ch/H5hut/

Spack package:

h5hut/package.py

Versions:

1.99.13

Build Dependencies:

mpi, hdf5

Link Dependencies:

mpi, hdf5

Description:

H5hut (HDF5 Utility Toolkit). High-Performance I/O Library for Particle- based Simulations.

h5part¶

Homepage:

http://vis.lbl.gov/Research/H5Part/

Spack package:

h5part/package.py

Versions:

1.6.6

Build Dependencies:

mpi, hdf5

Link Dependencies:

mpi, hdf5

Description:

Portable High Performance Parallel Data Interface to HDF5

h5utils¶

Homepage:

http://ab-initio.mit.edu/wiki/index.php/H5utils

Spack package:

h5utils/package.py

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:

http://h5z-zfp.readthedocs.io/en/latest

Spack package:

h5z-zfp/package.py

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:

https://xgitlab.cels.anl.gov/hacc/HACCKernels

Spack package:

hacckernels/package.py

Versions:

develop

Build Dependencies:

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:

http://hadoop.apache.org/

Spack package:

hadoop/package.py

Versions:

3.1.1, 2.9.0

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:

https://github.com/lanl001/halc

Spack package:

halc/package.py

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.

hapcut2¶

Homepage:

https://github.com/vibansal/HapCUT2

Spack package:

hapcut2/package.py

Versions:

2017-07-10

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:

https://github.com/lh3/hapdip

Spack package:

hapdip/package.py

Versions:

2018.02.20

Run Dependencies:

Description:

The CHM1-NA12878 benchmark for single-sample SNP/INDEL calling from WGS Illumina data.

haploview¶

Homepage:

http://www.broadinstitute.org/haploview/haploview

Spack package:

haploview/package.py

Versions:

4.1

Build Dependencies:

java

Run Dependencies:

java

Description:

Haploview is designed to simplify and expedite the process of haplotype analysis.

harfbuzz¶

Homepage:

http://www.freedesktop.org/wiki/Software/HarfBuzz/

Spack package:

harfbuzz/package.py

Versions:

2.3.1, 2.1.3, 1.9.0, 1.4.6, 0.9.37

Build Dependencies:

pkgconfig, glib, icu4c, freetype, cairo, zlib

Link Dependencies:

glib, icu4c, freetype, cairo, zlib

Description:

The Harfbuzz package contains an OpenType text shaping engine.

harminv¶

Homepage:

http://ab-initio.mit.edu/wiki/index.php/Harminv

Spack package:

harminv/package.py

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.

hc¶

Homepage:

https://geodynamics.org/cig/software/hc/

Spack package:

hc/package.py

Versions:

1.0.7

Build Dependencies:

gmt, netcdf

Link Dependencies:

gmt, netcdf

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:

https://support.hdfgroup.org/products/hdf4/

Spack package:

hdf/package.py

Versions:

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:

https://support.hdfgroup.org/HDF5/

Spack package:

hdf5/package.py

Versions:

develop, 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:

https://github.com/Blosc/hdf5-blosc

Spack package:

hdf5-blosc/package.py

Versions:

master

Build Dependencies:

c-blosc, hdf5, libtool

Link Dependencies:

c-blosc, hdf5

Description:

Blosc filter for HDF5

help2man¶

Homepage:

https://www.gnu.org/software/help2man/

Spack package:

help2man/package.py

Versions:

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:

https://github.com/henson-insitu/henson

Spack package:

henson/package.py

Versions:

develop

Build Dependencies:

cmake, mpi, python

Link Dependencies:

mpi, python

Description:

Cooperative multitasking for in situ processing.

hepmc¶

Homepage:

http://hepmc.web.cern.ch/hepmc/

Spack package:

hepmc/package.py

Versions:

3.0.0, 2.06.09, 2.06.08, 2.06.07, 2.06.06, 2.06.05

Build Dependencies:

Description:

The HepMC package is an object oriented, C++ event record for High Energy Physics Monte Carlo generators and simulation.

heppdt¶

Homepage:

http://lcgapp.cern.ch/project/simu/HepPDT/

Spack package:

heppdt/package.py

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:

https://github.com/nservant/HiC-Pro

Spack package:

hic-pro/package.py

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:

https://github.com/BlueBrain/HighFive

Spack package:

highfive/package.py

Versions:

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:

https://github.com/google/highwayhash

Spack package:

highwayhash/package.py

Versions:

dfcb97

Description:

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

hiop¶

Homepage:

https://github.com/LLNL/hiop

Spack package:

hiop/package.py

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.

hisat2¶

Homepage:

http://ccb.jhu.edu/software/hisat2

Spack package:

hisat2/package.py

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:

https://doi.org/10.1186/s12859-017-1953-9

Spack package:

hisea/package.py

Versions:

2017.12.26

Build Dependencies:

Link Dependencies:

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.

hmmer¶

Homepage:

http://www.hmmer.org

Spack package:

hmmer/package.py

Versions:

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:

http://homer.ucsd.edu/homer

Spack package:

homer/package.py

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:

http://glotzerlab.engin.umich.edu/hoomd-blue/

Spack package:

hoomd-blue/package.py

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:

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.

hpccg¶

Homepage:

https://mantevo.org/about/applications/

Spack package:

hpccg/package.py

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:

http://hpctoolkit.org

Spack package:

hpctoolkit/package.py

Versions:

develop, 2018.12.28, 2018.11.05

Build Dependencies:

binutils, boost, bzip2, dyninst, elfutils, intel-tbb, libdwarf, libmonitor, libunwind, xerces-c, xz, zlib, intel-xed, papi, libpfm4, mpi

Link Dependencies:

binutils, boost, bzip2, dyninst, elfutils, intel-tbb, libdwarf, libmonitor, libunwind, xerces-c, xz, zlib, 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:

http://hpctoolkit.org

Spack package:

hpcviewer/package.py

Versions:

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:

https://bitbucket.org/hpgmg/hpgmg

Spack package:

hpgmg/package.py

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:

http://www.netlib.org/benchmark/hpl/

Spack package:

hpl/package.py

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:

http://stellar.cct.lsu.edu/tag/hpx/

Spack package:

hpx/package.py

Versions:

1.2.1, 1.2.0, 1.1.0, 1.0.0

Build Dependencies:

cuda, cmake, boost, hwloc, python, pkgconfig, git, gperftools, jemalloc, tbb, apex, papi, valgrind

Link Dependencies:

cuda, boost, hwloc, gperftools, jemalloc, tbb, apex, papi, valgrind

Run Dependencies:

Test Dependencies:

Description:

C++ runtime system for parallel and distributed applications.

hpx5¶

Homepage:

http://hpx.crest.iu.edu

Spack package:

hpx5/package.py

Versions:

4.1.0, 4.0.0, 3.1.0, 2.0.0, 1.3.0, 1.2.0, 1.1.0, 1.0.0

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:

https://cgit.freedesktop.org/amd/hsakmt/

Spack package:

hsakmt/package.py

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:

https://github.com/dvorka/hstr

Spack package:

hstr/package.py

Versions:

1.22

Build Dependencies:

autoconf, automake, libtool, m4, ncurses, readline

Link Dependencies:

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:

https://github.com/hishamhm/htop

Spack package:

htop/package.py

Versions:

2.2.0, 2.0.2

Build Dependencies:

Link Dependencies:

Description:

htop is an interactive text-mode process viewer for Unix systems.

htslib¶

Homepage:

https://github.com/samtools/htslib

Spack package:

htslib/package.py

Versions:

1.9, 1.8, 1.7, 1.6, 1.5, 1.4, 1.3.1, 1.2

Build Dependencies:

zlib, bzip2, xz, m4, autoconf, automake, libtool

Link Dependencies:

zlib, bzip2, xz, m4, autoconf, automake, libtool

Description:

C library for high-throughput sequencing data formats.

httpie¶

Homepage:

https://httpie.org/

Spack package:

httpie/package.py

Versions:

0.9.9, 0.9.8

Build Dependencies:

python, py-setuptools, py-pygments, py-requests, py-pysocks, py-argparse

Link Dependencies:

Run Dependencies:

python, py-setuptools, py-pygments, py-requests, py-pysocks, py-argparse

Description:

Modern command line HTTP client.

hub¶

Homepage:

https://github.com/github/hub

Spack package:

hub/package.py

Versions:

head, 2.2.3, 2.2.2, 2.2.1, 2.2.0, 1.12.4

Build Dependencies:

Link Dependencies:

Description:

The github git wrapper

hugo¶

Homepage:

https://gohugo.io

Spack package:

hugo/package.py

Versions:

0.53

Build Dependencies:

Description:

The world's fastest framework for building websites.

hunspell¶

Homepage:

http://hunspell.github.io/

Spack package:

hunspell/package.py

Versions:

1.6.0

Build Dependencies:

Description:

The most popular spellchecking library (sez the author...).

hwloc¶

Homepage:

http://www.open-mpi.org/projects/hwloc/

Spack package:

hwloc/package.py

Versions:

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, 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:

https://github.com/mossmatters/HybPiper

Spack package:

hybpiper/package.py

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:

http://www.mpich.org

Spack package:

hydra/package.py

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:

http://libelemental.org

Spack package:

hydrogen/package.py

Versions:

develop, 1.1.0, 1.0.1, 1.0, 0.99

Build Dependencies:

cmake, openblas, intel-mkl, veclibfort, essl, netlib-lapack, aluminum, lapack, mpi, scalapack, gmp, mpc, mpfr, cuda, cub, ninja

Link Dependencies:

openblas, intel-mkl, veclibfort, essl, netlib-lapack, aluminum, lapack, mpi, scalapack, gmp, mpc, mpfr, cuda, cub

Description:

Hydrogen: Distributed-memory dense and sparse-direct linear algebra and optimization library. Based on the Elemental library.

hyphy¶

Homepage:

http://www.hyphy.org/

Spack package:

hyphy/package.py

Versions:

2.3.14

Build Dependencies:

cmake, curl

Link Dependencies:

cmake, curl

Description:

HyPhy: Hypothesis testing using Phylogenies

hypre¶

Homepage:

http://computation.llnl.gov/project/linear_solvers/software.php

Spack package:

hypre/package.py

Versions:

develop, 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:

https://i3wm.org/

Spack package:

i3/package.py

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:

https://developer.ibm.com/javasdk/

Spack package:

ibm-java/package.py

Versions:

8.0.5.30

Description:

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

ibmisc¶

Homepage:

https://github.com/citibeth/ibmisc

Spack package:

ibmisc/package.py

Versions:

0.1.0

Build Dependencies:

cmake, python, eigen, everytrace, proj, blitz, netcdf-cxx4, udunits2, googletest, py-cython, py-numpy, boost, doxygen

Link Dependencies:

python, eigen, everytrace, proj, blitz, netcdf-cxx4, udunits2, boost

Run Dependencies:

py-cython, py-numpy

Description:

Misc. reusable utilities used by IceBin.

iceauth¶

Homepage:

http://cgit.freedesktop.org/xorg/app/iceauth

Spack package:

iceauth/package.py

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:

http://icedtea.classpath.org/wiki/Main_Page

Spack package:

icedtea/package.py

Versions:

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:

http://icet.sandia.gov

Spack package:

icet/package.py

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:

http://cgit.freedesktop.org/xorg/app/ico

Spack package:

ico/package.py

Versions:

1.0.4

Build Dependencies:

libx11, xproto, pkgconfig, util-macros

Link Dependencies:

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:

http://site.icu-project.org/

Spack package:

icu4c/package.py

Versions:

60.1, 58.2, 57.1

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:

http://id3lib.sourceforge.net/

Spack package:

id3lib/package.py

Versions:

3.8.3

Build Dependencies:

zlib

Link Dependencies:

zlib

Description:

Library for manipulating ID3v1 and ID3v2 tags

idba¶

Homepage:

http://i.cs.hku.hk/~alse/hkubrg/projects/idba/

Spack package:

idba/package.py

Versions:

1.1.3

Build Dependencies:

Description:

IDBA is a practical iterative De Bruijn Graph De Novo Assembler for sequence assembly in bioinfomatics.

igraph¶

Homepage:

http://igraph.org/

Spack package:

igraph/package.py

Versions:

0.7.1

Build Dependencies:

libxml2

Link Dependencies:

libxml2

Description:

igraph is a library for creating and manipulating graphs.

igvtools¶

Homepage:

https://software.broadinstitute.org/software/igv/home

Spack package:

igvtools/package.py

Versions:

2.3.98

Build Dependencies:

java

Link Dependencies:

java

Description:

IGVTools suite of command-line utilities for preprocessing data files

ilmbase¶

Homepage:

http://www.openexr.com/

Spack package:

ilmbase/package.py

Versions:

2.3.0, 2.2.0, 2.1.0, 2.0.1, 1.0.2, 0.9.0

Description:

OpenEXR ILM Base libraries (high dynamic-range image file format)

image-magick¶

Homepage:

http://www.imagemagick.org

Spack package:

image-magick/package.py

Versions:

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:

http://www.snake.net/software/imake-stuff/

Spack package:

imake/package.py

Versions:

1.0.7

Build Dependencies:

xproto, pkgconfig

Description:

The imake build system.

imp¶

Homepage:

https://integrativemodeling.org

Spack package:

imp/package.py

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:

https://mathgen.stats.ox.ac.uk/impute/impute_v2.html#home

Spack package:

impute2/package.py

Versions:

2.3.2

Description:

IMPUTE2 is a genotype imputation and haplotype phasing program based on ideas from Howie et al. 2009.

infernal¶

Homepage:

http://eddylab.org/infernal/

Spack package:

infernal/package.py

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:

http://cgit.freedesktop.org/xorg/proto/inputproto

Spack package:

inputproto/package.py

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:

https://software.intel.com/en-us/intel-parallel-studio-xe

Spack package:

intel/package.py

Versions:

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:

https://software.intel.com/en-us/daal

Spack package:

intel-daal/package.py

Versions:

2019.3.199, 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:

https://cgit.freedesktop.org/xorg/app/intel-gpu-tools/

Spack package:

intel-gpu-tools/package.py

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:

https://software.intel.com/en-us/intel-ipp

Spack package:

intel-ipp/package.py

Versions:

2019.3.199, 2019.1.144, 2019.0.117, 2018.4.274, 2018.3.222, 2018.2.199, 2018.1.163, 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-mkl¶

Homepage:

https://software.intel.com/en-us/intel-mkl

Spack package:

intel-mkl/package.py

Versions:

2019.3.199, 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

Description:

Intel Math Kernel Library.

intel-mkl-dnn¶

Homepage:

https://01.org/mkl-dnn

Spack package:

intel-mkl-dnn/package.py

Versions:

1.0-pc2, 0.19, 0.18.1, 0.11, 0.10, 0.9

Build Dependencies:

cmake, intel-mkl

Link Dependencies:

intel-mkl

Description:

Intel(R) Math Kernel Library for Deep Neural Networks (Intel(R) MKL- DNN).

intel-mpi¶

Homepage:

https://software.intel.com/en-us/intel-mpi-library

Spack package:

intel-mpi/package.py

Versions:

2019.3.199, 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:

https://software.intel.com/en-us/intel-parallel-studio-xe

Spack package:

intel-parallel-studio/package.py

Versions:

professional.2019.3, 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.2019.3, 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.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:

http://www.pintool.org

Spack package:

intel-pin/package.py

Versions:

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:

http://www.threadingbuildingblocks.org/

Spack package:

intel-tbb/package.py

Versions:

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:

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:

https://intelxed.github.io/

Spack package:

intel-xed/package.py

Versions:

develop, 2019.03.01, 2018.02.14

Build Dependencies:

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.

intltool¶

Homepage:

https://freedesktop.org/wiki/Software/intltool/

Spack package:

intltool/package.py

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.

ior¶

Homepage:

https://github.com/hpc/ior

Spack package:

ior/package.py

Versions:

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:

http://www.iozone.org/

Spack package:

iozone/package.py

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:

https://sourceforge.net/projects/iperf2

Spack package:

iperf2/package.py

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:

https://software.es.net/iperf/

Spack package:

iperf3/package.py

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:

https://projects.coin-or.org/Ipopt

Spack package:

ipopt/package.py

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:

http://computationalradiationphysics.github.io/isaac/

Spack package:

isaac/package.py

Versions:

develop, master, 1.4.0, 1.3.3, 1.3.2, 1.3.1, 1.3.0

Build Dependencies:

Link Dependencies:

jpeg, jansson, boost, cuda, icet, mpi

Description:

In Situ Animation of Accelerated Computations: Header-Only Library

isaac-server¶

Homepage:

http://computationalradiationphysics.github.io/isaac/

Spack package:

isaac-server/package.py

Versions:

develop, master, 1.4.0, 1.3.3, 1.3.2, 1.3.1, 1.3.0

Build Dependencies:

Link Dependencies:

jpeg, jansson, boost, libwebsockets

Description:

In Situ Animation of Accelerated Computations: Server

isl¶

Homepage:

http://isl.gforge.inria.fr

Spack package:

isl/package.py

Versions:

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.

itstool¶

Homepage:

http://itstool.org/

Spack package:

itstool/package.py

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:

http://microbiology.se/software/itsx/

Spack package:

itsx/package.py

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:

http://jackcess.sourceforge.net/

Spack package:

jackcess/package.py

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).

jags¶

Homepage:

http://mcmc-jags.sourceforge.net/

Spack package:

jags/package.py

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

jansson¶

Homepage:

http://www.digip.org/jansson/

Spack package:

jansson/package.py

Versions:

2.9

Build Dependencies:

Description:

Jansson is a C library for encoding, decoding and manipulating JSON data.

jasper¶

Homepage:

https://www.ece.uvic.ca/~frodo/jasper/

Spack package:

jasper/package.py

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:

http://www.cl.cam.ac.uk/~mgk25/jbigkit/

Spack package:

jbigkit/package.py

Versions:

2.1, 1.6

Description:

JBIG-Kit is a software implementation of the JBIG1 data compression standard.

jchronoss¶

Homepage:

http://jchronoss.hpcframework.com

Spack package:

jchronoss/package.py

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:

http://www.oracle.com/technetwork/java/javase/downloads/index.html

Spack package:

jdk/package.py

Versions:

11.0.2_9, 11.0.1_13, 10.0.2_13, 10.0.1_10, 1.8.0_202, 1.8.0_181-b13, 1.8.0_172-b11, 1.8.0_141-b15, 1.8.0_131-b11, 1.8.0_92-b14, 1.8.0_73-b02, 1.8.0_66-b17, 1.7.0_80-b0

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:

http://www.cbcb.umd.edu/software/jellyfish/

Spack package:

jellyfish/package.py

Versions:

2.2.7, 1.1.11

Build Dependencies:

Run Dependencies:

Description:

JELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA.

jemalloc¶

Homepage:

http://www.canonware.com/jemalloc/

Spack package:

jemalloc/package.py

Versions:

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:

http://jmol.sourceforge.net/

Spack package:

jmol/package.py

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:

https://stedolan.github.io/jq/

Spack package:

jq/package.py

Versions:

1.5

Build Dependencies:

oniguruma, bison

Link Dependencies:

oniguruma

Description:

jq is a lightweight and flexible command-line JSON processor.

json-c¶

Homepage:

https://github.com/json-c/json-c/wiki

Spack package:

json-c/package.py

Versions:

0.13.1, 0.12.1, 0.11

Build Dependencies:

autoconf

Description:

A JSON implementation in C.

json-cwx¶

Homepage:

https://github.com/LLNL/json-cwx

Spack package:

json-cwx/package.py

Versions:

0.12

Build Dependencies:

Description:

JSON-C with Extensions

json-fortran¶

Homepage:

http://jacobwilliams.github.io/json-fortran/

Spack package:

json-fortran/package.py

Versions:

7.0.0

Build Dependencies:

Description:

A Fortran 2008 JSON API

json-glib¶

Homepage:

https://developer.gnome.org/json-glib

Spack package:

json-glib/package.py

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:

https://github.com/open-source-parsers/jsoncpp

Spack package:

jsoncpp/package.py

Versions:

1.7.3

Build Dependencies:

Test Dependencies:

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.

judy¶

Homepage:

http://judy.sourceforge.net/

Spack package:

judy/package.py

Versions:

1.0.5

Description:

Judy: General-purpose dynamic array, associative array and hash-trie.

julia¶

Homepage:

http://julialang.org

Spack package:

julia/package.py

Versions:

master, 0.6.2, 0.5.2, 0.5.1, 0.5.0, 0.4.7, 0.4.6, 0.4.5, 0.4.3, release-0.5, release-0.4

Build Dependencies:

m4, binutils, cmake, curl, git, openssl, python

Link Dependencies:

binutils, cmake, curl, git, openssl, python

Run Dependencies:

hdf5, mpi, py-matplotlib

Description:

The Julia Language: A fresh approach to technical computing

k8¶

Homepage:

https://github.com/attractivechaos/k8

Spack package:

k8/package.py

Versions:

0.2.4

Run Dependencies:

zlib

Description:

K8 is a Javascript shell based on Google's V8 Javascript engine.

kahip¶

Homepage:

http://algo2.iti.kit.edu/documents/kahip/index.html

Spack package:

kahip/package.py

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:

https://github.com/bioinformatics-centre/kaiju

Spack package:

kaiju/package.py

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:

https://sourceforge.net/projects/kakscalculator2

Spack package:

kaks-calculator/package.py

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:

https://github.com/kaldi-asr/kaldi

Spack package:

kaldi/package.py

Versions:

master, 2018-07-11, 2015-10-07

Build Dependencies:

blas, cuda, openfst

Link Dependencies:

blas, cuda, openfst

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:

http://pachterlab.github.io/kallisto

Spack package:

kallisto/package.py

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:

https://www.atnf.csiro.au/computing/software/karma/

Spack package:

karma/package.py

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:

https://cgit.freedesktop.org/xorg/proto/kbproto

Spack package:

kbproto/package.py

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.

kdiff3¶

Homepage:

http://kdiff3.sourceforge.net/

Spack package:

kdiff3/package.py

Versions:

0.9.98

Build Dependencies:

Link Dependencies:

Description:

Compare and merge 2 or 3 files or directories.

kealib¶

Homepage:

http://www.kealib.org/

Spack package:

kealib/package.py

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.

kentutils¶

Homepage:

https://github.com/ENCODE-DCC/kentUtils

Spack package:

kentutils/package.py

Versions:

302.1

Build Dependencies:

libpng, openssl, mariadb

Link Dependencies:

libpng, openssl, mariadb

Description:

Jim Kent command line bioinformatic utilities

kibana¶

Homepage:

https://www.elastic.co/products/kibana

Spack package:

kibana/package.py

Versions:

6.4.0

Run Dependencies:

jdk

Description:

Kibana lets you visualize your Elasticsearch data and navigate the Elastic Stack

kim-api¶

Homepage:

https://openkim.org/

Spack package:

kim-api/package.py

Versions:

develop, 2.0.2

Build Dependencies:

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 pacakge too.

kitty¶

Homepage:

https://sw.kovidgoyal.net/kitty/index.html

Spack package:

kitty/package.py

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:

http://kmergenie.bx.psu.edu/

Spack package:

kmergenie/package.py

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:

https://github.com/kokkos/kokkos

Spack package:

kokkos/package.py

Versions:

develop, 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.

kraken¶

Homepage:

https://ccb.jhu.edu/software/kraken/

Spack package:

kraken/package.py

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:

https://kerberos.org

Spack package:

krb5/package.py

Versions:

1.16.1

Build Dependencies:

bison, openssl

Link Dependencies:

Description:

Network authentication protocol

krims¶

Homepage:

http://lazyten.org/krims

Spack package:

krims/package.py

Versions:

develop, 0.2.1

Build Dependencies:

Description:

The bucket of Krimskrams every C or C++ project needs

kripke¶

Homepage:

https://computation.llnl.gov/projects/co-design/kripke

Spack package:

kripke/package.py

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:

https://github.com/kvasir-io/mpl

Spack package:

kvasir-mpl/package.py

Versions:

develop

Description:

Kvasir metaprogramming library

kvtree¶

Homepage:

https://github.com/ECP-VeloC/KVTree

Spack package:

kvtree/package.py

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:

https://brighten.bigw.org/projects/ladot/

Spack package:

ladot/package.py

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:

https://computation.llnl.gov/projects/co-design/laghos

Spack package:

laghos/package.py

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.

lammps¶

Homepage:

http://lammps.sandia.gov/

Spack package:

lammps/package.py

Versions:

develop, 20181212, 20181207, 20181127, 20181115, 20181109, 20181024, 20181010, 20180918, 20180905, 20180831, 20180822, 20180629, 20180316, 20180222, 20170922, 20170901

Build Dependencies:

cmake, mpi, fftw, voropp, netcdf, blas, lapack, latte, python, hdf5

Link Dependencies:

mpi, fftw, voropp, netcdf, blas, lapack, latte, python, hdf5

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:

http://last.cbrc.jp/

Spack package:

last/package.py

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:

https://lastz.github.io/lastz

Spack package:

lastz/package.py

Versions:

1.04.00

Description:

LASTZ is a program for aligning DNA sequences, a pairwise aligner.

latte¶

Homepage:

https://github.com/lanl/latte

Spack package:

latte/package.py

Versions:

develop, 1.2.1, 1.2.0, 1.1.1, 1.0.1

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:

https://github.com/LLNL/LaunchMON

Spack package:

launchmon/package.py

Versions:

1.0.2

Build Dependencies:

autoconf, automake, libtool, 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:

http://lazyten.org

Spack package:

lazyten/package.py

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:

http://software.llnl.gov/lbann/

Spack package:

lbann/package.py

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, protobuf, cnpy, nccl, conduit, python, py-setuptools, py-numpy, py-breathe, py-m2r, cereal, ninja

Link Dependencies:

hydrogen, elemental, aluminum, cuda, cudnn, cub, mpi, hwloc, opencv, protobuf, cnpy, nccl, conduit, python, cereal

Run Dependencies:

python, py-argparse, py-configparser, py-graphviz, py-matplotlib, py-numpy, py-onnx, py-pandas, py-texttable

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:

http://cgit.freedesktop.org/xorg/app/lbxproxy

Spack package:

lbxproxy/package.py

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:

http://lbzip2.org/

Spack package:

lbzip2/package.py

Versions:

2.5

Description:

Multi-threaded compression utility with support for bzip2 compressed file format

lcals¶

Homepage:

https://computation.llnl.gov/projects/co-design/lcals

Spack package:

lcals/package.py

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:

http://www.littlecms.com

Spack package:

lcms/package.py

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).

ldc¶

Homepage:

https://dlang.org/

Spack package:

ldc/package.py

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:

https://dlang.org/

Spack package:

ldc-bootstrap/package.py

Versions:

0.17.4

Build Dependencies:

cmake, llvm, zlib, libconfig, curl, libedit, binutils

Link Dependencies:

llvm, zlib, libconfig, curl, libedit, binutils

Description:

legion¶

Homepage:

http://legion.stanford.edu/

Spack package:

legion/package.py

Versions:

develop, 18.05.0, 18.02.0, 17.10.0, 17.08.0, 17.02.0

Build Dependencies:

cmake, gasnet

Link Dependencies:

gasnet

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:

http://lemon.cs.elte.hu/trac/lemon

Spack package:

lemon/package.py

Versions:

1.3.1

Build Dependencies:

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:

https://github.com/google/leveldb

Spack package:

leveldb/package.py

Versions:

master, 1.20, 1.18

Build Dependencies:

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:

http://lftp.yar.ru/

Spack package:

lftp/package.py

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:

https://gitlab.dkrz.de/k202009/libaec

Spack package:

libaec/package.py

Versions:

1.0.2, 1.0.1, 1.0.0

Build Dependencies:

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:

http://lse.sourceforge.net/io/aio.html

Spack package:

libaio/package.py

Versions:

0.3.110

Description:

This is the linux native Asynchronous I/O interface library.

libapplewm¶

Homepage:

http://cgit.freedesktop.org/xorg/lib/libAppleWM

Spack package:

libapplewm/package.py

Versions:

1.4.1

Build Dependencies:

libx11, libxext, xextproto, applewmproto, pkgconfig, util-macros

Link Dependencies:

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:

http://www.libarchive.org

Spack package:

libarchive/package.py

Versions:

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:

https://gnupg.org/software/libassuan/index.html

Spack package:

libassuan/package.py

Versions:

2.5.3, 2.4.5, 2.4.3

Build Dependencies:

Link Dependencies:

Description:

Libassuan is a small library implementing the so-called Assuan protocol.

libatomic-ops¶

Homepage:

https://www.hboehm.info/gc/

Spack package:

libatomic-ops/package.py

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:

https://github.com/beagle-dev/beagle-lib

Spack package:

libbeagle/package.py

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:

https://github.com/CRG-Barcelona/libbeato

Spack package:

libbeato/package.py

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:

https://libbsd.freedesktop.org/wiki/

Spack package:

libbsd/package.py

Versions:

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:

https://github.com/mongodb/libbson

Spack package:

libbson/package.py

Versions:

1.9.1, 1.8.1, 1.8.0, 1.7.0, 1.6.3, 1.6.2, 1.6.1

Build Dependencies:

Description:

libbson is a library providing useful routines related to building, parsing, and iterating BSON documents.

libcanberra¶

Homepage:

http://0pointer.de/lennart/projects/libcanberra/

Spack package:

libcanberra/package.py

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:

https://sites.google.com/site/fullycapable/

Spack package:

libcap/package.py

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:

https://github.com/CEED/libCEED

Spack package:

libceed/package.py

Versions:

develop, 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:

http://sourceforge.net/projects/libcerf

Spack package:

libcerf/package.py

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

libcheck¶

Homepage:

https://libcheck.github.io/check/index.html

Spack package:

libcheck/package.py

Versions:

0.12.0, 0.11.0, 0.10.0

Build Dependencies:

Description:

A unit testing framework for C.

libcint¶

Homepage:

https://github.com/sunqm/libcint

Spack package:

libcint/package.py

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:

Description:

Library for analytical Gaussian integrals for quantum chemistry.

libcircle¶

Homepage:

https://github.com/hpc/libcircle

Spack package:

libcircle/package.py

Versions:

0.2.1-rc.1

Build Dependencies:

mpi

Link Dependencies:

mpi

Description:

libcircle provides an efficient distributed queue on a cluster, using self-stabilizing work stealing.

libconfig¶

Homepage:

http://www.hyperrealm.com/libconfig/

Spack package:

libconfig/package.py

Versions:

1.5

Build Dependencies:

Description:

C/C++ Configuration File Library

libcroco¶

Homepage:

https://developer.gnome.org/libcroco

Spack package:

libcroco/package.py

Versions:

0.6.12

Build Dependencies:

Link Dependencies:

Description:

Libcroco is a standalone css2 parsing and manipulation library.

libctl¶

Homepage:

http://ab-initio.mit.edu/wiki/index.php/Libctl

Spack package:

libctl/package.py

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.

libdivsufsort¶

Homepage:

https://github.com/y-256/libdivsufsort

Spack package:

libdivsufsort/package.py

Versions:

2.0.1

Build Dependencies:

Description:

libdivsufsort is a software library that implements a lightweight suffix array construction algorithm.

libdmx¶

Homepage:

http://cgit.freedesktop.org/xorg/lib/libdmx

Spack package:

libdmx/package.py

Versions:

1.1.3

Build Dependencies:

libx11, libxext, xextproto, dmxproto, pkgconfig, util-macros

Link Dependencies:

Description:

libdmx - X Window System DMX (Distributed Multihead X) extension library.

libdrm¶

Homepage:

http://dri.freedesktop.org/libdrm/

Spack package:

libdrm/package.py

Versions:

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:

http://www.prevanders.net/dwarf.html

Spack package:

libdwarf/package.py

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:

https://www.flamingspork.com/projects/libeatmydata/

Spack package:

libeatmydata/package.py

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:

http://thrysoee.dk/editline/

Spack package:

libedit/package.py

Versions:

3.1-20170329, 3.1-20160903, 3.1-20150325

Build Dependencies:

Link Dependencies:

Description:

An autotools compatible port of the NetBSD editline library

libelf¶

Homepage:

https://directory.fsf.org/wiki/Libelf

Spack package:

libelf/package.py

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:

https://software.ecmwf.int/wiki/display/EMOS/Emoslib

Spack package:

libemos/package.py

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:

https://github.com/anholt/libepoxy

Spack package:

libepoxy/package.py

Versions:

1.4.3, 1.3.1

Build Dependencies:

pkgconfig, meson, gl

Link Dependencies:

meson, gl

Description:

Epoxy is a library for handling OpenGL function pointer management for you.

libev¶

Homepage:

http://software.schmorp.de/pkg/libev.html

Spack package:

libev/package.py

Versions:

develop, 4.24

Build Dependencies:

Description:

A full-featured and high-performance event loop that is loosely modelled after libevent, but without its limitations and bugs.

libevent¶

Homepage:

http://libevent.org

Spack package:

libevent/package.py

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:

Link Dependencies:

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:

https://github.com/GTkorvo/evpath

Spack package:

libevpath/package.py

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.

libfabric¶

Homepage:

https://libfabric.org/

Spack package:

libfabric/package.py

Versions:

develop, 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.

libffi¶

Homepage:

https://sourceware.org/libffi/

Spack package:

libffi/package.py

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:

http://www.cc.gatech.edu/systems/projects/FFS

Spack package:

libffs/package.py

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.

libfontenc¶

Homepage:

http://cgit.freedesktop.org/xorg/lib/libfontenc

Spack package:

libfontenc/package.py

Versions:

1.1.3

Build Dependencies:

zlib, xproto, pkgconfig, util-macros

Link Dependencies:

zlib

Description:

libfontenc - font encoding library.

libfs¶

Homepage:

http://cgit.freedesktop.org/xorg/lib/libFS

Spack package:

libfs/package.py

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:

http://www.gnu.org/software/libgcrypt/

Spack package:

libgcrypt/package.py

Versions:

1.8.4, 1.8.1, 1.7.6, 1.6.2

Build Dependencies:

Link Dependencies:

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:

https://github.com/libgd/libgd

Spack package:

libgd/package.py

Versions:

2.2.4, 2.2.3, 2.1.1

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:

https://trac.osgeo.org/geotiff/

Spack package:

libgeotiff/package.py

Versions:

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:

https://libgit2.github.com/

Spack package:

libgit2/package.py

Versions:

0.26.0, 0.24.2

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.

libgpg-error¶

Homepage:

https://www.gnupg.org/related_software/libgpg-error

Spack package:

libgpg-error/package.py

Versions:

1.36, 1.27, 1.21, 1.18

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:

http://deeplearning.net/software/libgpuarray/

Spack package:

libgpuarray/package.py

Versions:

0.7.5, 0.7.4, 0.7.3, 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, libcheck

Link Dependencies:

cuda, libcheck

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:

https://launchpad.net/libgridxc

Spack package:

libgridxc/package.py

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:

https://github.com/agordon/libgtextutils

Spack package:

libgtextutils/package.py

Versions:

0.7

Description:

Gordon's Text utils Library.

libharu¶

Homepage:

http://libharu.org

Spack package:

libharu/package.py

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:

https://github.com/hpc/libhio

Spack package:

libhio/package.py

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:

https://www.gnu.org/software/binutils/

Spack package:

libiberty/package.py

Versions:

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.

libice¶

Homepage:

http://cgit.freedesktop.org/xorg/lib/libICE

Spack package:

libice/package.py

Versions:

1.0.9

Build Dependencies:

xproto, xtrans, pkgconfig, util-macros

Description:

libICE - Inter-Client Exchange Library.

libiconv¶

Homepage:

https://www.gnu.org/software/libiconv/

Spack package:

libiconv/package.py

Versions:

1.15, 1.14

Description:

GNU libiconv provides an implementation of the iconv() function and the iconv program for character set conversion.

libidn2¶

Homepage:

https://gitlab.com/libidn/libidn2

Spack package:

libidn2/package.py

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:

https://github.com/evaleev/libint

Spack package:

libint/package.py

Versions:

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:

http://www.ijg.org

Spack package:

libjpeg/package.py

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:

https://libjpeg-turbo.org/

Spack package:

libjpeg-turbo/package.py

Versions:

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.

libksba¶

Homepage:

https://gnupg.org/software/libksba/index.html

Spack package:

libksba/package.py

Versions:

1.3.5

Build Dependencies:

Link Dependencies:

Description:

Libksba is a library to make the tasks of working with X.509 certificates, CMS data and related objects more easy.

liblbxutil¶

Homepage:

http://cgit.freedesktop.org/xorg/lib/liblbxutil

Spack package:

liblbxutil/package.py

Versions:

1.1.0

Build Dependencies:

xextproto, xproto, pkgconfig, util-macros

Description:

liblbxutil - Low Bandwith X extension (LBX) utility routines.

liblockfile¶

Homepage:

https://github.com/miquels/liblockfile

Spack package:

liblockfile/package.py

Versions:

1.14

Description:

NFS-safe locking library

libmatheval¶

Homepage:

https://www.gnu.org/software/libmatheval/

Spack package:

libmatheval/package.py

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:

https://github.com/maxmind/libmaxminddb

Spack package:

libmaxminddb/package.py

Versions:

1.3.2

Description:

C library for the MaxMind DB file format

libmesh¶

Homepage:

http://libmesh.github.io/

Spack package:

libmesh/package.py

Versions:

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.

libmng¶

Homepage:

http://sourceforge.net/projects/libmng/

Spack package:

libmng/package.py

Versions:

2.0.3, 2.0.2

Build Dependencies:

jpeg, zlib, lcms

Link Dependencies:

jpeg, zlib, lcms

Description:

libmng -THE reference library for reading, displaying, writing and examining Multiple-Image Network Graphics. MNG is the animation extension to the popular PNG image-format.

libmongoc¶

Homepage:

https://github.com/mongodb/mongo-c-driver

Spack package:

libmongoc/package.py

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.

libmonitor¶

Homepage:

https://github.com/HPCToolkit/libmonitor

Spack package:

libmonitor/package.py

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:

http://unixer.de/research/nbcoll/libnbc/

Spack package:

libnbc/package.py

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:

https://www.infradead.org/~tgr/libnl/

Spack package:

libnl/package.py

Versions:

3.3.0, 3.2.25

Build Dependencies:

bison, flex, m4

Description:

libnl - Netlink Protocol Library Suite

libnova¶

Homepage:

http://libnova.sourceforge.net

Spack package:

libnova/package.py

Versions:

0.15.0

Build Dependencies:

Link Dependencies:

Description:

"libnova is a general purpose, double precision, Celestial Mechanics, Astrometry and Astrodynamics library.

libnsl¶

Homepage:

https://github.com/thkukuk/libnsl

Spack package:

libnsl/package.py

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:

https://www.xiph.org/ogg/

Spack package:

libogg/package.py

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:

https://cgit.freedesktop.org/xorg/lib/liboldX/

Spack package:

liboldx/package.py

Versions:

1.0.1

Build Dependencies:

libx11, pkgconfig, util-macros

Link Dependencies:

Description:

X version 10 backwards compatibility.

libpcap¶

Homepage:

http://www.tcpdump.org/

Spack package:

libpcap/package.py

Versions:

1.8.1

Build Dependencies:

flex, bison

Description:

libpcap is a portable library in C/C++ for packet capture.

libpciaccess¶

Homepage:

http://cgit.freedesktop.org/xorg/lib/libpciaccess/

Spack package:

libpciaccess/package.py

Versions:

0.13.5, 0.13.4

Build Dependencies:

libtool, pkgconfig, util-macros

Description:

Generic PCI access library.

libpfm4¶

Homepage:

http://perfmon2.sourceforge.net

Spack package:

libpfm4/package.py

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:

http://libpipeline.nongnu.org/

Spack package:

libpipeline/package.py

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:

https://www.libimobiledevice.org/

Spack package:

libplist/package.py

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:

https://github.com/pmem/libpmemobj-cpp

Spack package:

libpmemobj-cpp/package.py

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:

http://www.libpng.org/pub/png/libpng.html

Spack package:

libpng/package.py

Versions:

1.6.34, 1.6.29, 1.6.28, 1.6.27, 1.2.57

Build Dependencies:

zlib

Link Dependencies:

zlib

Description:

libpng is the official PNG reference library.

libpsl¶

Homepage:

https://github.com/rockdaboot/libpsl

Spack package:

libpsl/package.py

Versions:

0.17.0

Build Dependencies:

icu4c, gettext, pkgconfig, python

Link Dependencies:

icu4c

Test Dependencies:

Description:

libpsl - C library to handle the Public Suffix List.

libpthread-stubs¶

Homepage:

https://xcb.freedesktop.org/

Spack package:

libpthread-stubs/package.py

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:

https://github.com/lanl/libquo

Spack package:

libquo/package.py

Versions:

develop, 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:

https://github.com/LLNL/libROM

Spack package:

librom/package.py

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

libseccomp¶

Homepage:

https://github.com/seccomp/libseccomp

Spack package:

libseccomp/package.py

Versions:

2.3.3

Build Dependencies:

autoconf, automake, libtool, m4, py-cython

Description:

The main libseccomp repository

libsharp¶

Homepage:

https://github.com/Libsharp/libsharp

Spack package:

libsharp/package.py

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:

https://github.com/afeldman/libshm

Spack package:

libshm/package.py

Versions:

master

Description:

Libshm is a header library making an easy C++11 access to a shared memory.

libsigcpp¶

Homepage:

https://libsigcplusplus.github.io/libsigcplusplus/index.html

Spack package:

libsigcpp/package.py

Versions:

2.99.12, 2.9.3, 2.1.1, 2.0.3

Description:

Libsigc++ is a C++ library for typesafe callbacks

libsigsegv¶

Homepage:

https://www.gnu.org/software/libsigsegv/

Spack package:

libsigsegv/package.py

Versions:

2.11, 2.10

Description:

GNU libsigsegv is a library for handling page faults in user mode.

libsm¶

Homepage:

http://cgit.freedesktop.org/xorg/lib/libSM

Spack package:

libsm/package.py

Versions:

1.2.2

Build Dependencies:

libice, xproto, xtrans, pkgconfig, util-macros

Link Dependencies:

libice

Description:

libSM - X Session Management Library.

libsodium¶

Homepage:

https://download.libsodium.org/doc/

Spack package:

libsodium/package.py

Versions:

1.0.17, 1.0.16, 1.0.15, 1.0.13, 1.0.12, 1.0.11, 1.0.10, 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:

https://libspatialindex.org/

Spack package:

libspatialindex/package.py

Versions:

1.8.5

Build Dependencies:

Description:

C++ implementation of R*-tree, an MVR-tree and a TPR-tree with C API.

libspatialite¶

Homepage:

http://www.gaia-gis.it

Spack package:

libspatialite/package.py

Versions:

4.3.0a

Build Dependencies:

sqlite, proj, geos, freexl

Link Dependencies:

sqlite, proj, geos, freexl

Description:

SpatiaLite is an open source library intended to extend the SQLite core to support fully fledged Spatial SQL capabilities.

libsplash¶

Homepage:

https://github.com/ComputationalRadiationPhysics/libSplash

Spack package:

libsplash/package.py

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:

https://www.libssh.org

Spack package:

libssh/package.py

Versions:

0.8.5, 0.7.5

Build Dependencies:

cmake, openssl, zlib

Link Dependencies:

openssl, zlib

Description:

libssh: the SSH library

libssh2¶

Homepage:

https://www.libssh2.org/

Spack package:

libssh2/package.py

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:

https://www.csie.ntu.edu.tw/~cjlin/libsvm/

Spack package:

libsvm/package.py

Versions:

322

Description:

Libsvm is a simple, easy-to-use, and efficient software for SVM classification and regression.

libszip¶

Homepage:

https://support.hdfgroup.org/doc_resource/SZIP/

Spack package:

libszip/package.py

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:

https://www.gnu.org/software/libtasn1/

Spack package:

libtasn1/package.py

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:

http://www.leonerd.org.uk/code/libtermkey/

Spack package:

libtermkey/package.py

Versions:

0.18, 0.17, 0.16, 0.15b, 0.14

Build Dependencies:

libtool, ncurses

Link Dependencies:

Description:

Easy keyboard entry processing for terminal programs

libtiff¶

Homepage:

http://www.simplesystems.org/libtiff/

Spack package:

libtiff/package.py

Versions:

4.0.9, 4.0.8, 4.0.7, 4.0.6, 4.0.3, 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:

https://sourceforge.net/projects/libtirpc/

Spack package:

libtirpc/package.py

Versions:

1.1.4

Description:

Libtirpc is a port of Suns Transport-Independent RPC library to Linux.

libtool¶

Homepage:

https://www.gnu.org/software/libtool/

Spack package:

libtool/package.py

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:

https://www.gnu.org/software/libunistring/

Spack package:

libunistring/package.py

Versions:

0.9.10, 0.9.9, 0.9.8, 0.9.7, 0.9.6

Description:

This library provides functions for manipulating Unicode strings and for manipulating C strings according to the Unicode standard.

libunwind¶

Homepage:

http://www.nongnu.org/libunwind/

Spack package:

libunwind/package.py

Versions:

develop, 2018.10.12, 1.3-rc1, 1.2.1, 1.1

Build Dependencies:

Link Dependencies:

Description:

A portable and efficient C programming interface (API) to determine the call-chain of a program.

libusb¶

Homepage:

https://libusb.info/

Spack package:

libusb/package.py

Versions:

master, 1.0.22, 1.0.21, 1.0.20

Build Dependencies:

autoconf, automake, libtool

Description:

Library for USB device access.

libusbmuxd¶

Homepage:

https://www.libimobiledevice.org/

Spack package:

libusbmuxd/package.py

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:

http://sourceforge.net/projects/libuuid/

Spack package:

libuuid/package.py

Versions:

1.0.3

Description:

Portable uuid C library

libuv¶

Homepage:

http://libuv.org

Spack package:

libuv/package.py

Versions:

1.25.0, 1.10.0, 1.9.0

Build Dependencies:

Description:

Multi-platform library with a focus on asynchronous IO

libvdwxc¶

Homepage:

https://libvdwxc.gitlab.io/libvdwxc/

Spack package:

libvdwxc/package.py

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

libvorbis¶

Homepage:

https://xiph.org/vorbis/

Spack package:

libvorbis/package.py

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:

http://www.leonerd.org.uk/code/libvterm/

Spack package:

libvterm/package.py

Versions:

681

Build Dependencies:

Description:

An abstract library implementation of a terminal emulator

libwebsockets¶

Homepage:

https://github.com/warmcat/libwebsockets

Spack package:

libwebsockets/package.py

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:

http://cgit.freedesktop.org/xorg/lib/libWindowsWM

Spack package:

libwindowswm/package.py

Versions:

1.0.1

Build Dependencies:

libx11, libxext, xextproto, windowswmproto, pkgconfig, util-macros

Link Dependencies:

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:

https://www.x.org/

Spack package:

libx11/package.py

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:

https://cgit.freedesktop.org/xorg/lib/libXau/

Spack package:

libxau/package.py

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:

http://cgit.freedesktop.org/xorg/lib/libXaw

Spack package:

libxaw/package.py

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:

http://cgit.freedesktop.org/xorg/lib/libXaw3d

Spack package:

libxaw3d/package.py

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:

http://www.tddft.org/programs/octopus/wiki/index.php/Libxc

Spack package:

libxc/package.py

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:

https://xcb.freedesktop.org/

Spack package:

libxcb/package.py

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:

http://cgit.freedesktop.org/xorg/lib/libXcomposite

Spack package:

libxcomposite/package.py

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:

http://cgit.freedesktop.org/xorg/lib/libXcursor

Spack package:

libxcursor/package.py

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:

http://cgit.freedesktop.org/xorg/lib/libXdamage

Spack package:

libxdamage/package.py

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:

http://cgit.freedesktop.org/xorg/lib/libXdmcp

Spack package:

libxdmcp/package.py

Versions:

1.1.2

Build Dependencies:

xproto, pkgconfig, util-macros, libbsd

Link Dependencies:

Description:

libXdmcp - X Display Manager Control Protocol library.

libxevie¶

Homepage:

http://cgit.freedesktop.org/xorg/lib/libXevie

Spack package:

libxevie/package.py

Versions:

1.0.3

Build Dependencies:

libx11, libxext, xproto, xextproto, evieext, pkgconfig, util-macros

Link Dependencies:

Description:

Xevie - X Event Interception Extension (XEvIE).

libxext¶

Homepage:

http://cgit.freedesktop.org/xorg/lib/libXext

Spack package:

libxext/package.py

Versions:

1.3.3

Build Dependencies:

libx11, xproto, xextproto, pkgconfig, util-macros

Link Dependencies:

Description:

libXext - library for common extensions to the X11 protocol.

libxfixes¶

Homepage:

http://cgit.freedesktop.org/xorg/lib/libXfixes

Spack package:

libxfixes/package.py

Versions:

5.0.2

Build Dependencies:

libx11, xproto, fixesproto, xextproto, pkgconfig, util-macros

Link Dependencies:

Description:

This package contains header files and documentation for the XFIXES extension. Library and server implementations are separate.

libxfont¶

Homepage:

http://cgit.freedesktop.org/xorg/lib/libXfont

Spack package:

libxfont/package.py

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:

http://cgit.freedesktop.org/xorg/lib/libXfont

Spack package:

libxfont2/package.py

Versions:

2.0.1

Build Dependencies:

libfontenc, freetype, xtrans, xproto, fontsproto, pkgconfig, util-macros

Link Dependencies:

libfontenc, freetype

Description:

libxfontcache¶

Homepage:

http://cgit.freedesktop.org/xorg/lib/libXfontcache

Spack package:

libxfontcache/package.py

Versions:

1.0.5

Build Dependencies:

libx11, libxext, xextproto, fontcacheproto, pkgconfig, util-macros

Link Dependencies:

Description:

Xfontcache - X-TrueType font cache extension client library.

libxft¶

Homepage:

http://cgit.freedesktop.org/xorg/lib/libXft

Spack package:

libxft/package.py

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:

http://cgit.freedesktop.org/xorg/lib/libXi

Spack package:

libxi/package.py

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:

http://cgit.freedesktop.org/xorg/lib/libXinerama

Spack package:

libxinerama/package.py

Versions:

1.1.3

Build Dependencies:

libx11, libxext, xextproto, xineramaproto, pkgconfig, util-macros

Link Dependencies:

Description:

libXinerama - API for Xinerama extension to X11 Protocol.

libxkbcommon¶

Homepage:

https://xkbcommon.org/

Spack package:

libxkbcommon/package.py

Versions:

0.8.2, 0.8.0

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:

https://cgit.freedesktop.org/xorg/lib/libxkbfile

Spack package:

libxkbfile/package.py

Versions:

1.0.9

Build Dependencies:

libx11, kbproto, pkgconfig, util-macros

Link Dependencies:

Description:

XKB file handling routines.

libxkbui¶

Homepage:

https://cgit.freedesktop.org/xorg/lib/libxkbui/

Spack package:

libxkbui/package.py

Versions:

1.0.2

Build Dependencies:

libx11, libxt, libxkbfile, pkgconfig, util-macros

Link Dependencies:

libx11, libxt, libxkbfile

Description:

X.org libxkbui library.

libxml2¶

Homepage:

http://xmlsoft.org

Spack package:

libxml2/package.py

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:

http://cgit.freedesktop.org/xorg/lib/libXmu

Spack package:

libxmu/package.py

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:

http://cgit.freedesktop.org/xorg/lib/libXp

Spack package:

libxp/package.py

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:

http://cgit.freedesktop.org/xorg/lib/libXpm

Spack package:

libxpm/package.py

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:

https://cgit.freedesktop.org/xorg/lib/libXpresent/

Spack package:

libxpresent/package.py

Versions:

1.0.0

Build Dependencies:

libx11, xproto, presentproto, xextproto, pkgconfig, util-macros

Link Dependencies:

Description:

This package contains header files and documentation for the Present extension. Library and server implementations are separate.

libxprintapputil¶

Homepage:

https://cgit.freedesktop.org/xorg/lib/libXprintAppUtil/

Spack package:

libxprintapputil/package.py

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:

https://cgit.freedesktop.org/xorg/lib/libXprintUtil/

Spack package:

libxprintutil/package.py

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:

http://cgit.freedesktop.org/xorg/lib/libXrandr

Spack package:

libxrandr/package.py

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:

http://cgit.freedesktop.org/xorg/lib/libXrender

Spack package:

libxrender/package.py

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:

http://cgit.freedesktop.org/xorg/lib/libXRes

Spack package:

libxres/package.py

Versions:

1.0.7

Build Dependencies:

libx11, libxext, xextproto, resourceproto, pkgconfig, util-macros

Link Dependencies:

Description:

libXRes - X-Resource extension client library.

libxscrnsaver¶

Homepage:

http://cgit.freedesktop.org/xorg/lib/libXScrnSaver

Spack package:

libxscrnsaver/package.py

Versions:

1.2.2

Build Dependencies:

libx11, libxext, xextproto, scrnsaverproto, pkgconfig, util-macros

Link Dependencies:

Description:

XScreenSaver - X11 Screen Saver extension client library

libxshmfence¶

Homepage:

https://cgit.freedesktop.org/xorg/lib/libxshmfence/

Spack package:

libxshmfence/package.py

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:

http://www.xmlsoft.org/XSLT/index.html

Spack package:

libxslt/package.py

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:

https://github.com/hfp/libxsmm

Spack package:

libxsmm/package.py

Versions:

develop, 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:

https://github.com/hfp/libxstream

Spack package:

libxstream/package.py

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:

http://cgit.freedesktop.org/xorg/lib/libXt

Spack package:

libxt/package.py

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:

http://cgit.freedesktop.org/xorg/lib/libXTrap

Spack package:

libxtrap/package.py

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:

http://cgit.freedesktop.org/xorg/lib/libXtst

Spack package:

libxtst/package.py

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:

http://cgit.freedesktop.org/xorg/lib/libXv

Spack package:

libxv/package.py

Versions:

1.0.10

Build Dependencies:

libx11, libxext, xextproto, videoproto, pkgconfig, util-macros

Link Dependencies:

Description:

libXv - library for the X Video (Xv) extension to the X Window System.

libxvmc¶

Homepage:

https://cgit.freedesktop.org/xorg/lib/libXvMC

Spack package:

libxvmc/package.py

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:

http://cgit.freedesktop.org/xorg/lib/libXxf86dga

Spack package:

libxxf86dga/package.py

Versions:

1.1.4

Build Dependencies:

libx11, libxext, xproto, xextproto, xf86dgaproto, pkgconfig, util-macros

Link Dependencies:

Description:

libXxf86dga - Client library for the XFree86-DGA extension.

libxxf86misc¶

Homepage:

http://cgit.freedesktop.org/xorg/lib/libXxf86misc

Spack package:

libxxf86misc/package.py

Versions:

1.0.3

Build Dependencies:

libx11, libxext, xproto, xextproto, xf86miscproto, pkgconfig, util-macros

Link Dependencies:

Description:

libXxf86misc - Extension library for the XFree86-Misc X extension.

libxxf86vm¶

Homepage:

http://cgit.freedesktop.org/xorg/lib/libXxf86vm

Spack package:

libxxf86vm/package.py

Versions:

1.1.4

Build Dependencies:

libx11, libxext, xproto, xextproto, xf86vidmodeproto, pkgconfig, util-macros

Link Dependencies:

Description:

libXxf86vm - Extension library for the XFree86-VidMode X extension.

libyaml¶

Homepage:

https://github.com/yaml/libyaml

Spack package:

libyaml/package.py

Versions:

master, 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:

Link Dependencies:

Description:

A C library for parsing and emitting YAML.

libyogrt¶

Homepage:

https://github.com/LLNL/libyogrt

Spack package:

libyogrt/package.py

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:

https://nih.at/libzip/index.html

Spack package:

libzip/package.py

Versions:

1.2.0

Build Dependencies:

zlib

Link Dependencies:

zlib

Description:

libzip is a C library for reading, creating, and modifying zip archives.

lighttpd¶

Homepage:

https://www.lighttpd.net

Spack package:

lighttpd/package.py

Versions:

1.4.50, 1.4.49

Build Dependencies:

Description:

a secure, fast, compliant and very flexible web-server

likwid¶

Homepage:

https://github.com/RRZE-HPC/likwid

Spack package:

likwid/package.py

Versions:

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:

https://github.com/tdruet/LINKPHASE3

Spack package:

linkphase3/package.py

Versions:

2017-06-14

Description:

Haplotype reconstruction in pedigreed populations.

linux-headers¶

Homepage:

https://www.kernel.org/

Spack package:

linux-headers/package.py

Versions:

4.9.10

Description:

The Linux kernel headers.

listres¶

Homepage:

http://cgit.freedesktop.org/xorg/app/listres

Spack package:

listres/package.py

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.

llvm¶

Homepage:

http://llvm.org/

Spack package:

llvm/package.py

Versions:

develop, 8.0.0, 7.0.1, 7.0.0, 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, 3.0, flang-develop, flang-20180921, flang-20180612, flang-ppc64le-20180921, flang-ppc64le-20180612

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-openmp-ompt¶

Homepage:

https://github.com/OpenMPToolsInterface/LLVM-openmp

Spack package:

llvm-openmp-ompt/package.py

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:

https://github.com/groeck/lm-sensors/

Spack package:

lm-sensors/package.py

Versions:

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:

https://lmdb.tech/

Spack package:

lmdb/package.py

Versions:

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:

https://www.tacc.utexas.edu/research-development/tacc-projects/lmod

Spack package:

lmod/package.py

Versions:

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, 6.0.1

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:

http://cgit.freedesktop.org/xorg/util/lndir

Spack package:

lndir/package.py

Versions:

1.0.3

Build Dependencies:

xproto, pkgconfig

Description:

lndir - create a shadow directory of symbolic links to another directory tree.

log4cplus¶

Homepage:

https://sourceforge.net/projects/log4cplus/

Spack package:

log4cplus/package.py

Versions:

2.0.1, 1.2.1, 1.2.0

Build Dependencies:

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:

https://logging.apache.org/log4cxx/latest_stable/

Spack package:

log4cxx/package.py

Versions:

0.10.0

Build Dependencies:

apr-util, apr, zip

Link Dependencies:

apr-util, apr, zip

Description:

A C++ port of Log4j

loki¶

Homepage:

http://loki-lib.sourceforge.net

Spack package:

loki/package.py

Versions:

0.1.7

Description:

Loki is a C++ library of designs, containing flexible implementations of common design patterns and idioms.

lordec¶

Homepage:

http://www.atgc-montpellier.fr/lordec/

Spack package:

lordec/package.py

Versions:

0.8

Build Dependencies:

boost, cmake

Link Dependencies:

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:

http://cgm.cs.mcgill.ca/~avis/C/lrs.html

Spack package:

lrslib/package.py

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:

http://lrzip.kolivas.org

Spack package:

lrzip/package.py

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.

lsof¶

Homepage:

https://people.freebsd.org/~abe/

Spack package:

lsof/package.py

Versions:

4.89

Description:

Lsof displays information about files open to Unix processes.

ltrace¶

Homepage:

https://www.ltrace.org

Spack package:

ltrace/package.py

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:

http://www.lua.org

Spack package:

lua/package.py

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:

Link Dependencies:

Run Dependencies:

unzip

Description:

The Lua programming language interpreter and library.

lua-bitlib¶

Homepage:

http://luaforge.net/projects/bitlib

Spack package:

lua-bitlib/package.py

Versions:

Build Dependencies:

lua

Link Dependencies:

lua

Description:

Lua-jit-like bitwise operations for lua

lua-jit¶

Homepage:

http://www.luajit.org

Spack package:

lua-jit/package.py

Versions:

2.0.4

Description:

Flast flexible JITed lua

lua-lpeg¶

Homepage:

http://www.inf.puc-rio.br/~roberto/lpeg/

Spack package:

lua-lpeg/package.py

Versions:

0.12.1

Build Dependencies:

lua

Link Dependencies:

lua

Description:

pattern-matching for lua

lua-luafilesystem¶

Homepage:

http://keplerproject.github.io/luafilesystem

Spack package:

lua-luafilesystem/package.py

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-luaposix¶

Homepage:

https://github.com/luaposix/luaposix/

Spack package:

lua-luaposix/package.py

Versions:

33.4.0

Build Dependencies:

lua

Link Dependencies:

lua

Description:

Lua posix bindings, including ncurses

lua-mpack¶

Homepage:

https://luarocks.org/modules/tarruda/mpack

Spack package:

lua-mpack/package.py

Versions:

1.0.0-0

Build Dependencies:

msgpack-c, lua

Link Dependencies:

msgpack-c, lua

Description:

lua bindings to libmpack

luit¶

Homepage:

http://cgit.freedesktop.org/xorg/app/luit

Spack package:

luit/package.py

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:

https://computation.llnl.gov/projects/co-design/lulesh

Spack package:

lulesh/package.py

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:

https://github.com/arq5x/lumpy-sv

Spack package:

lumpy-sv/package.py

Versions:

0.2.13

Build Dependencies:

Link Dependencies:

Description:

A probabilistic framework for structural variant discovery.

lwgrp¶

Homepage:

https://github.com/hpc/lwgrp

Spack package:

lwgrp/package.py

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:

https://jay.grs.rwth-aachen.de/redmine/projects/lwm2

Spack package:

lwm2/package.py

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:

http://lz4.github.io/lz4/

Spack package:

lz4/package.py

Versions:

1.9.0, 1.8.3, 1.8.1.2, 1.7.5, 1.3.1

Test Dependencies:

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:

http://tukaani.org/lzma/

Spack package:

lzma/package.py

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:

https://www.oberhumer.com/opensource/lzo/

Spack package:

lzo/package.py

Versions:

2.10, 2.09, 2.08, 2.07, 2.06, 2.05

Description:

Real-time data compression library

m4¶

Homepage:

https://www.gnu.org/software/m4/m4.html

Spack package:

m4/package.py

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:

https://computation.llnl.gov/projects/co-design/macsio

Spack package:

macsio/package.py

Versions:

develop, 1.1, 1.0

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:

https://github.com/quinoacomputing/ndiff

Spack package:

mad-numdiff/package.py

Versions:

develop, 20150724

Build Dependencies:

Description:

compare unformatted text files with numerical content

mafft¶

Homepage:

http://mafft.cbrc.jp/alignment/software/index.html

Spack package:

mafft/package.py

Versions:

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:

https://software.ecmwf.int/wiki/display/MAGP/Magics

Spack package:

magics/package.py

Versions:

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:

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:

http://icl.cs.utk.edu/magma/

Spack package:

magma/package.py

Versions:

2.5.1-alpha1, 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:

http://cgit.freedesktop.org/xorg/util/makedepend

Spack package:

makedepend/package.py

Versions:

1.0.5

Build Dependencies:

xproto, pkgconfig

Description:

makedepend - create dependencies in makefiles.

mallocmc¶

Homepage:

https://github.com/ComputationalRadiationPhysics/mallocMC

Spack package:

mallocmc/package.py

Versions:

develop, master, 2.2.0crp, 2.1.0crp, 2.0.1crp, 2.0.0crp, 1.0.2crp

Build Dependencies:

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:

http://www.nongnu.org/man-db/

Spack package:

man-db/package.py

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:

https://github.com/Illumina/manta

Spack package:

manta/package.py

Versions:

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:

Description:

Structural variant and indel caller for mapped sequencing data

mapserver¶

Homepage:

http://www.mapserver.org/

Spack package:

mapserver/package.py

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:

http://maq.sourceforge.net/

Spack package:

maq/package.py

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:

https://xgitlab.cels.anl.gov/sds/margo

Spack package:

margo/package.py

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:

https://mariadb.org/about/

Spack package:

mariadb/package.py

Versions:

10.2.8, 10.1.23, 10.1.14, 5.5.56, 5.5.49

Build Dependencies:

cmake, boost, jemalloc, libaio, libedit, libevent, ncurses, zlib

Link Dependencies:

boost, jemalloc, libaio, libedit, libevent, ncurses, 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.

mariadb-c-client¶

Homepage:

http://mariadb.org/about/

Spack package:

mariadb-c-client/package.py

Versions:

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:

masa¶

Homepage:

https://github.com/manufactured-solutions/MASA

Spack package:

masa/package.py

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:

http://www.genome.umd.edu/masurca.html

Spack package:

masurca/package.py

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.

matio¶

Homepage:

https://sourceforge.net/projects/matio/

Spack package:

matio/package.py

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:

https://www.mathworks.com/products/matlab.html

Spack package:

matlab/package.py

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:

https://maven.apache.org/index.html

Spack package:

maven/package.py

Versions:

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:

https://github.com/bobverity/MavericK

Spack package:

maverick/package.py

Versions:

1.0.4

Description:

MavericK is a program for inferring population structure on the basis of genetic information.

mawk¶

Homepage:

http://invisible-island.net/mawk/mawk.html

Spack package:

mawk/package.py

Versions:

1.3.4-20171017, 1.3.4

Description:

mawk is an interpreter for the AWK Programming Language.

mbedtls¶

Homepage:

https://tls.mbed.org

Spack package:

mbedtls/package.py

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:

https://midnight-commander.org

Spack package:

mc/package.py

Versions:

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:

https://www.micans.org/mcl/index.html

Spack package:

mcl/package.py

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:

https://github.com/LLNL/mdtest

Spack package:

mdtest/package.py

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:

http://docs.salome-platform.org/latest/dev/MEDCoupling/med-file.html

Spack package:

med/package.py

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:

http://ab-initio.mit.edu/wiki/index.php/Meep

Spack package:

meep/package.py

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:

https://github.com/nisheth/MeFiT

Spack package:

mefit/package.py

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:

http://www.bi.cs.titech.ac.jp/megadock/

Spack package:

megadock/package.py

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:

https://github.com/voutcn/megahit

Spack package:

megahit/package.py

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:

https://github.com/llnl/MemAxes

Spack package:

memaxes/package.py

Versions:

0.5

Build Dependencies:

cmake, qt

Link Dependencies:

Description:

MemAxes is a visualizer for sampled memory trace data.

meme¶

Homepage:

http://meme-suite.org

Spack package:

meme/package.py

Versions:

4.12.0, 4.11.4

Build Dependencies:

perl, python, mpi, image-magick, perl-xml-parser

Link Dependencies:

zlib, libgcrypt, mpi

Run Dependencies:

perl, python, image-magick, 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:

https://github.com/memkind/memkind

Spack package:

memkind/package.py

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:

https://github.com/LLNL/MemSurfer

Spack package:

memsurfer/package.py

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:

Description:

MemSurfer is a tool to compute and analyze membrane surfaces found in a wide variety of large-scale molecular simulations.

meraculous¶

Homepage:

http://jgi.doe.gov/data-and-tools/meraculous/

Spack package:

meraculous/package.py

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:

https://www.mercurial-scm.org

Spack package:

mercurial/package.py

Versions:

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-docutils, py-pygments, py-certifi

Link Dependencies:

Run Dependencies:

python, py-pygments, py-certifi

Description:

Mercurial is a free, distributed source control management tool.

mercury¶

Homepage:

https://mercury-hpc.github.io/

Spack package:

mercury/package.py

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:

http://www.mesa3d.org

Spack package:

mesa/package.py

Versions:

develop, 19.1.develop, 19.0.develop, 19.0.4, 19.0.3, 19.0.2, 19.0.1, 19.0.0

Build Dependencies:

meson, ninja, binutils, bison, flex, gettext, pkgconfig, 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:

https://www.mesa3d.org

Spack package:

mesa-glu/package.py

Versions:

9.0.0

Build Dependencies:

Link Dependencies:

Description:

This package provides the Mesa OpenGL Utility library.

meshkit¶

Homepage:

http://sigma.mcs.anl.gov/meshkit-library

Spack package:

meshkit/package.py

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:

http://mesonbuild.com/

Spack package:

meson/package.py

Versions:

0.49.1, 0.49.0, 0.42.0, 0.41.2, 0.41.1

Build Dependencies:

python, py-setuptools, ninja

Link Dependencies:

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:

https://software.sandia.gov/mesquite

Spack package:

mesquite/package.py

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:

https://bitbucket.org/berkeleylab/metabat

Spack package:

metabat/package.py

Versions:

2.12.1, 2.11.2

Build Dependencies:

scons, boost

Run Dependencies:

boost, perl

Description:

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities.

metaphysicl¶

Homepage:

https://github.com/roystgnr/MetaPhysicL

Spack package:

metaphysicl/package.py

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:

http://glaros.dtc.umn.edu/gkhome/metis/metis/overview

Spack package:

metis/package.py

Versions:

5.1.0, 5.0.2, 4.0.3

Build Dependencies:

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:

http://www.mfem.org

Spack package:

mfem/package.py

Versions:

develop, 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, unwind, zlib, gnutls, conduit

Link Dependencies:

mpi, hypre, metis, blas, lapack, sundials, pumi, suite-sparse, superlu-dist, petsc, mpfr, netcdf, unwind, zlib, gnutls, conduit

Description:

Free, lightweight, scalable C++ library for finite element methods.

mgis¶

Homepage:

https://thelfer.github.io/mgis/web/index.html

Spack package:

mgis/package.py

Versions:

master, 1.0.1, 1.0, 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:

http://microbiomeutil.sourceforge.net/

Spack package:

microbiomeutil/package.py

Versions:

20110519

Build Dependencies:

perl, blast-plus, cdbfasta

Link Dependencies:

blast-plus, cdbfasta

Run Dependencies:

perl

Description:

Microbiome analysis utilities

migrate¶

Homepage:

http://popgen.sc.fsu.edu/

Spack package:

migrate/package.py

Versions:

3.6.11

Build Dependencies:

autoconf, automake, libtool, m4, openmpi

Link Dependencies:

autoconf, automake, libtool, m4, 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

minced¶

Homepage:

https://github.com/ctSkennerton/minced

Spack package:

minced/package.py

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:

https://gatb.inria.fr/software/mind-the-gap/

Spack package:

mindthegap/package.py

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:

http://mantevo.org

Spack package:

miniaero/package.py

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:

https://mantevo.org

Spack package:

miniamr/package.py

Versions:

develop, 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:

http://www.example.co://github.com/lh3/miniasm

Spack package:

miniasm/package.py

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:

https://conda.io/miniconda.html

Spack package:

miniconda2/package.py

Versions:

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:

https://conda.io/miniconda.html

Spack package:

miniconda3/package.py

Versions:

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:

https://mantevo.org/

Spack package:

minife/package.py

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:

http://mantevo.org

Spack package:

minighost/package.py

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:

http://crd.lbl.gov/departments/computer-science/PAR/research/previous-projects/miniGMG/

Spack package:

minigmg/package.py

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:

https://github.com/lh3/minimap2

Spack package:

minimap2/package.py

Versions:

2.14, 2.10, 2.2

Build Dependencies:

py-mappy, zlib

Link Dependencies:

zlib

Run Dependencies:

py-mappy

Description:

Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database.

minimd¶

Homepage:

http://mantevo.org

Spack package:

minimd/package.py

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:

https://github.com/QMCPACK/miniqmc

Spack package:

miniqmc/package.py

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:

https://jedisct1.github.io/minisign/

Spack package:

minisign/package.py

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:

http://mantevo.org

Spack package:

minismac2d/package.py

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:

https://github.com/Mantevo/miniTri

Spack package:

minitri/package.py

Versions:

1.0

Build Dependencies:

mpi

Link Dependencies:

mpi

Description:

A simple, triangle-based data analytics proxy application.

minivite¶

Homepage:

http://hpc.pnl.gov/people/hala/grappolo.html

Spack package:

minivite/package.py

Versions:

develop, 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:

https://mantevo.org

Spack package:

minixyce/package.py

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.

minuit¶

Homepage:

https://seal.web.cern.ch/seal/snapshot/work-packages/mathlibs/minuit/home.html

Spack package:

minuit/package.py

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:

http://sourceforge.net/projects/mira-assembler/

Spack package:

mira/package.py

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.

mirdeep2¶

Homepage:

https://www.mdc-berlin.de/8551903/en/

Spack package:

mirdeep2/package.py

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:

http://mitf.cbrc.jp/MitoFates/cgi-bin/top.cgi

Spack package:

mitofates/package.py

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:

https://github.com/llnl/Mitos

Spack package:

mitos/package.py

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:

https://mixcr.readthedocs.io/en/master/index.html

Spack package:

mixcr/package.py

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:

http://cgit.freedesktop.org/xorg/app/mkfontdir

Spack package:

mkfontdir/package.py

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:

http://cgit.freedesktop.org/xorg/app/mkfontscale

Spack package:

mkfontscale/package.py

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:

https://wright.eeb.utoronto.ca

Spack package:

mlhka/package.py

Versions:

2.1

Description:

A maximum likelihood ratio test of natural selection, using polymorphism and divergence data.

mmg¶

Homepage:

http://www.mmgtools.org/

Spack package:

mmg/package.py

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:

https://bitbucket.org/fathomteam/moab

Spack package:

moab/package.py

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, parallel-netcdf, cgm, metis, parmetis, zoltan

Link Dependencies:

blas, lapack, mpi, hdf5, netcdf, 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:

https://github.com/alalazo/modern_wheel

Spack package:

modern-wheel/package.py

Versions:

1.2, 1.1, 1.0

Build Dependencies:

Link Dependencies:

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:

http://mofem.eng.gla.ac.uk

Spack package:

mofem-cephas/package.py

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:

http://mofem.eng.gla.ac.uk

Spack package:

mofem-fracture-module/package.py

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:

http://mofem.eng.gla.ac.uk

Spack package:

mofem-minimal-surface-equation/package.py

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:

http://mofem.eng.gla.ac.uk

Spack package:

mofem-users-modules/package.py

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:

http://www.molcas.org/

Spack package:

molcas/package.py

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-cxx-driver¶

Homepage:

http://www.mongocxx.org

Spack package:

mongo-cxx-driver/package.py

Versions:

3.2.0

Build Dependencies:

cmake, libmongoc

Link Dependencies:

libmongoc

Description:

C++ Driver for MongoDB

mono¶

Homepage:

http://www.mono-project.com/

Spack package:

mono/package.py

Versions:

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.

mosh¶

Homepage:

https://mosh.org/

Spack package:

mosh/package.py

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:

https://github.com/mothur/mothur

Spack package:

mothur/package.py

Versions:

1.40.5, 1.39.5

Build Dependencies:

boost, readline

Link Dependencies:

boost, readline

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:

http://motif.ics.com/

Spack package:

motif/package.py

Versions:

2.3.8

Build Dependencies:

flex, libx11, libxt, libxext, libxft, libxcomposite, libxfixes, xbitmaps

Link Dependencies:

flex, libx11, libxt, libxext, libxft, libxcomposite, libxfixes, xbitmaps

Description:

" Motif - Graphical user interface (GUI) specification and the widget toolkit

motioncor2¶

Homepage:

http://msg.ucsf.edu/em/software

Spack package:

motioncor2/package.py

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:

https://github.com/LLNL/MountPointAttributes

Spack package:

mount-point-attributes/package.py

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:

https://developer.mozilla.org/en-US/docs/Mozilla/Projects/SpiderMonkey

Spack package:

mozjs/package.py

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:

https://mpark.github.io/variant

Spack package:

mpark-variant/package.py

Versions:

1.4.0, 1.3.0

Build Dependencies:

Description:

C++17 `std::variant` for C++11/14/17

mpc¶

Homepage:

http://www.multiprecision.org

Spack package:

mpc/package.py

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:

https://www.bytereef.org/mpdecimal/

Spack package:

mpdecimal/package.py

Versions:

2.4.2

Build Dependencies:

Description:

mpdecimal is a package for correctly-rounded arbitrary precision decimal floating point arithmetic.

mpe2¶

Homepage:

http://www.mcs.anl.gov/research/projects/perfvis/software/MPE/

Spack package:

mpe2/package.py

Versions:

1.3.0

Build Dependencies:

mpi

Link Dependencies:

mpi

Description:

Message Passing Extensions (MPE): Parallel, shared X window graphics

mpest¶

Homepage:

http://faculty.franklin.uga.edu/lliu/content/mp-est

Spack package:

mpest/package.py

Versions:

1.5

Description:

MP-EST estimates species trees from a set of gene trees by maximizing a pseudo-likelihood function.

mpfr¶

Homepage:

http://www.mpfr.org

Spack package:

mpfr/package.py

Versions:

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.

mpibash¶

Homepage:

https://github.com/lanl/MPI-Bash

Spack package:

mpibash/package.py

Versions:

1.2

Build Dependencies:

bash, mpi, libcircle

Link Dependencies:

bash, mpi, libcircle

Description:

Parallel scripting right from the Bourne-Again Shell (Bash)

mpiblast¶

Homepage:

http://www.mpiblast.org/

Spack package:

mpiblast/package.py

Versions:

1.6.0

Build Dependencies:

mpi

Link Dependencies:

mpi

Description:

mpiBLAST is a freely available, open-source, parallel implementation of NCBI BLAST

mpich¶

Homepage:

http://www.mpich.org

Spack package:

mpich/package.py

Versions:

develop, 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, libpciaccess, libxml2, slurm, pmix

Link Dependencies:

libfabric, libpciaccess, libxml2, slurm, pmix

Description:

MPICH is a high performance and widely portable implementation of the Message Passing Interface (MPI) standard.

mpifileutils¶

Homepage:

https://github.com/hpc/mpifileutils

Spack package:

mpifileutils/package.py

Versions:

develop, 0.9.1, 0.9, 0.8.1, 0.8, 0.7, 0.6

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:

https://github.com/MPILander/MPILander

Spack package:

mpilander/package.py

Versions:

develop

Build Dependencies:

Description:

There can only be one (MPI process)!

mpileaks¶

Homepage:

https://github.com/hpc/mpileaks

Spack package:

mpileaks/package.py

Versions:

1.0

Build Dependencies:

mpi, adept-utils, callpath

Link Dependencies:

mpi, adept-utils, callpath

Description:

Tool to detect and report leaked MPI objects like MPI_Requests and MPI_Datatypes.

mpip¶

Homepage:

http://mpip.sourceforge.net/

Spack package:

mpip/package.py

Versions:

3.4.1

Build Dependencies:

elf, libdwarf, libunwind, mpi

Link Dependencies:

elf, libdwarf, libunwind, mpi

Description:

mpiP: Lightweight, Scalable MPI Profiling

mpir¶

Homepage:

https://github.com/wbhart/mpir

Spack package:

mpir/package.py

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:

https://bitbucket.org/kshitijvmehta/mpix_launch_swift

Spack package:

mpix-launch-swift/package.py

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.

mrbayes¶

Homepage:

http://mrbayes.sourceforge.net

Spack package:

mrbayes/package.py

Versions:

2017-11-22

Build Dependencies:

autoconf, automake, libtool, m4, libbeagle, mpi

Link Dependencies:

libbeagle, mpi

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:

http://paradyn.org/mrnet

Spack package:

mrnet/package.py

Versions:

5.0.1-3, 5.0.1-2, 5.0.1, 4.1.0, 4.0.0

Build Dependencies:

boost, cti

Link Dependencies:

boost, cti

Description:

The MRNet Multi-Cast Reduction Network.

mrtrix3¶

Homepage:

http://www.mrtrix.org/

Spack package:

mrtrix3/package.py

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:

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:

http://www.mcternan.me.uk/mscgen/

Spack package:

mscgen/package.py

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:

http://www.msgpack.org

Spack package:

msgpack-c/package.py

Versions:

3.0.1, 1.4.1

Build Dependencies:

Test Dependencies:

googletest

Description:

A small, fast binary interchange format convertible to/from JSON

mshadow¶

Homepage:

https://github.com/dmlc/mshadow

Spack package:

mshadow/package.py

Versions:

master, 20170721

Description:

MShadow is a lightweight CPU/GPU Matrix/Tensor C++ Template Library. in C++/CUDA.

msmc¶

Homepage:

https://github.com/stschiff/msmc

Spack package:

msmc/package.py

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

multitail¶

Homepage:

https://www.vanheusden.com/multitail/index.php

Spack package:

multitail/package.py

Versions:

6.4.2

Build Dependencies:

Link Dependencies:

Description:

MultiTail allows you to monitor logfiles and command output in multiple windows in a terminal, colorize, filter and merge.

multitime¶

Homepage:

https://tratt.net/laurie/src/multitime/

Spack package:

multitime/package.py

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:

https://github.com/Microsoft/Multiverso

Spack package:

multiverso/package.py

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:

http://mummer.sourceforge.net/

Spack package:

mummer/package.py

Versions:

3.23

Build Dependencies:

gnuplot, perl

Link Dependencies:

Run Dependencies:

perl

Description:

MUMmer is a system for rapidly aligning entire genomes.

mumps¶

Homepage:

http://mumps.enseeiht.fr

Spack package:

mumps/package.py

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:

https://code.google.com/p/munge/

Spack package:

munge/package.py

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:

http://muparser.beltoforion.de/

Spack package:

muparser/package.py

Versions:

2.2.6.1, 2.2.5

Build Dependencies:

Description:

C++ math expression parser library.

muscle¶

Homepage:

http://drive5.com/muscle/

Spack package:

muscle/package.py

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:

http://bioinformatics.mdanderson.org/main/MuSE

Spack package:

muse/package.py

Versions:

1.0-rc

Description:

Somatic point mutation caller.

muster¶

Homepage:

https://github.com/llnl/muster

Spack package:

muster/package.py

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.

mvapich2¶

Homepage:

http://mvapich.cse.ohio-state.edu/

Spack package:

mvapich2/package.py

Versions:

2.3.1, 2.3rc2, 2.3rc1, 2.3a, 2.3, 2.2, 2.1, 2.0

Build Dependencies:

findutils, bison, pkgconfig, zlib, libpciaccess, libxml2, cuda, psm, opa-psm2, rdma-core, libfabric

Link Dependencies:

zlib, libpciaccess, libxml2, cuda, psm, opa-psm2, rdma-core, libfabric

Description:

MVAPICH2 is an MPI implementation for Infiniband networks.

mxml¶

Homepage:

http://michaelrsweet.github.io/mxml/

Spack package:

mxml/package.py

Versions:

2.10, 2.9, 2.8, 2.7, 2.6, 2.5

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:

http://mxnet.io

Spack package:

mxnet/package.py

Versions:

1.3.0, 0.10.0.post2, 0.10.0.post1, 0.10.0

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:

Description:

MXNet is a deep learning framework designed for both efficiency and flexibility.

mysql¶

Homepage:

https://www.mysql.com/

Spack package:

mysql/package.py

Versions:

8.0.15, 8.0.14, 8.0.13, 8.0.12, 8.0.11, 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, 5.6.43, 5.5.62

Build Dependencies:

cmake, gmake, boost, ncurses, openssl, bison, m4

Link Dependencies:

boost, ncurses, openssl

Test Dependencies:

perl

Description:

MySQL is an open source relational database management system.

nag¶

Homepage:

http://www.nag.com/nagware/np.asp

Spack package:

nag/package.py

Versions:

6.2, 6.1, 6.0

Description:

The NAG Fortran Compiler.

nalu¶

Homepage:

https://github.com/NaluCFD/Nalu

Spack package:

nalu/package.py

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:

https://github.com/exawind/nalu-wind

Spack package:

nalu-wind/package.py

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:

http://www.ks.uiuc.edu/Research/namd/

Spack package:

namd/package.py

Versions:

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:

http://www.nano-editor.org

Spack package:

nano/package.py

Versions:

2.6.3, 2.6.2

Build Dependencies:

Link Dependencies:

Description:

Tiny little text editor

nanoflann¶

Homepage:

https://github.com/jlblancoc/nanoflann

Spack package:

nanoflann/package.py

Versions:

1.2.3

Build Dependencies:

Description:

a C++ header-only library for Nearest Neighbor (NN) search wih KD-trees.

nanopb¶

Homepage:

https://jpa.kapsi.fi/nanopb/

Spack package:

nanopb/package.py

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:

http://www.nasm.us

Spack package:

nasm/package.py

Versions:

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:

http://pallini.di.uniroma1.it/index.html

Spack package:

nauty/package.py

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:

https://ncbi.github.io/magicblast/

Spack package:

ncbi-magicblast/package.py

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:

https://www.ncbi.nlm.nih.gov/

Spack package:

ncbi-rmblastn/package.py

Versions:

2.2.28

Description:

RMBlast search engine for NCBI

ncbi-toolkit¶

Homepage:

https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/

Spack package:

ncbi-toolkit/package.py

Versions:

21_0_0

Build Dependencies:

boost, bzip2, libjpeg, libpng, libtiff, libxml2, libxslt, lzo, pcre, giflib, sqlite, zlib, samtools, bamtools

Link Dependencies:

boost, bzip2, libjpeg, libpng, libtiff, libxml2, libxslt, lzo, pcre, giflib, sqlite, zlib, samtools, bamtools

Description:

NCBI C++ Toolkit

nccl¶

Homepage:

https://github.com/NVIDIA/nccl

Spack package:

nccl/package.py

Versions:

2.4.6-1, 2.4.2-1, 2.3.7-1, 2.3.5-5, 2.2, 1.3.4-1, 1.3.0-1

Build Dependencies:

cuda

Link Dependencies:

cuda

Description:

Optimized primitives for collective multi-GPU communication.

nccmp¶

Homepage:

http://nccmp.sourceforge.net/

Spack package:

nccmp/package.py

Versions:

1.8.2.0

Build Dependencies:

Link Dependencies:

Description:

Compare NetCDF Files

ncdu¶

Homepage:

http://dev.yorhel.nl/ncdu

Spack package:

ncdu/package.py

Versions:

1.13, 1.12, 1.11, 1.10, 1.9, 1.8, 1.7

Build Dependencies:

Link Dependencies:

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:

http://www.ncftp.com/

Spack package:

ncftp/package.py

Versions:

3.2.6

Build Dependencies:

Link Dependencies:

Description:

NcFTP Client is a set of application programs implementing the File Transfer Protocol.

ncl¶

Homepage:

https://www.ncl.ucar.edu

Spack package:

ncl/package.py

Versions:

6.6.2, 6.5.0, 6.4.0

Build Dependencies:

jpeg, netcdf, cairo, bison, flex, libiconv, tcsh, curl, libx11, libxaw, libxmu, hdf5, szip, hdf, gdal, udunits2

Link Dependencies:

jpeg, netcdf, cairo, flex, libiconv, tcsh, curl, libx11, libxaw, libxmu, hdf5, szip, hdf, gdal, udunits2

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:

http://nco.sourceforge.net/

Spack package:

nco/package.py

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, antlr, gsl, udunits2, flex, bison, texinfo

Link Dependencies:

netcdf, antlr, gsl, udunits2

Description:

The NCO toolkit manipulates and analyzes data stored in netCDF- accessible formats

ncurses¶

Homepage:

http://invisible-island.net/ncurses/ncurses.html

Spack package:

ncurses/package.py

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:

http://meteora.ucsd.edu/~pierce/ncview_home_page.html

Spack package:

ncview/package.py

Versions:

2.1.7

Build Dependencies:

netcdf, udunits2, libpng, libxaw

Link Dependencies:

netcdf, udunits2, libpng, libxaw

Description:

Simple viewer for NetCDF files.

ndiff¶

Homepage:

http://ftp.math.utah.edu/pub/ndiff/

Spack package:

ndiff/package.py

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:

https://nek5000.mcs.anl.gov/

Spack package:

nek5000/package.py

Versions:

develop, 17.0

Build Dependencies:

mpi

Link Dependencies:

mpi

Description:

A fast and scalable high-order solver for computational fluid dynamics

nekbone¶

Homepage:

https://github.com/Nek5000/Nekbone

Spack package:

nekbone/package.py

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:

https://nekcem.mcs.anl.gov

Spack package:

nekcem/package.py

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:

https://www.nektar.info/

Spack package:

nektar/package.py

Versions:

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:

https://nek5000.mcs.anl.gov/

Spack package:

nektools/package.py

Versions:

develop, 17.0

Build Dependencies:

libx11, libxt, xproto, visit

Link Dependencies:

libx11, libxt, xproto, visit

Description:

Tools reuqired by Nek5000

neovim¶

Homepage:

http://neovim.io

Spack package:

neovim/package.py

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:

http://www.nest-simulator.org

Spack package:

nest/package.py

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:

Test Dependencies:

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¶

Homepage:

http://www.unidata.ucar.edu/software/netcdf

Spack package:

netcdf/package.py

Versions:

master, 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 is a set of software libraries and self-describing, machine- independent data formats that support the creation, access, and sharing of array-oriented scientific data.

netcdf-cxx¶

Homepage:

http://www.unidata.ucar.edu/software/netcdf

Spack package:

netcdf-cxx/package.py

Versions:

4.2

Build Dependencies:

Link Dependencies:

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:

http://www.unidata.ucar.edu/software/netcdf

Spack package:

netcdf-cxx4/package.py

Versions:

4.3.0, 4.2.1

Build Dependencies:

netcdf, automake, autoconf, libtool

Link Dependencies:

Description:

C++ interface for NetCDF4

netcdf-fortran¶

Homepage:

http://www.unidata.ucar.edu/software/netcdf

Spack package:

netcdf-fortran/package.py

Versions:

4.4.4, 4.4.3

Build Dependencies:

Link Dependencies:

Description:

Fortran interface for NetCDF4

netgauge¶

Homepage:

http://unixer.de/research/netgauge/

Spack package:

netgauge/package.py

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:

https://ngsolve.org/

Spack package:

netgen/package.py

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:

http://www.netlib.org/lapack/

Spack package:

netlib-lapack/package.py

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:

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:

http://www.netlib.org/scalapack/

Spack package:

netlib-scalapack/package.py

Versions:

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:

http://www.netlib.org/xblas

Spack package:

netlib-xblas/package.py

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.

nettle¶

Homepage:

https://www.lysator.liu.se/~nisse/nettle/

Spack package:

nettle/package.py

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:

https://www.neuron.yale.edu/

Spack package:

neuron/package.py

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:

http://www.nextflow.io

Spack package:

nextflow/package.py

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:

https://www-user.tu-chemnitz.de/~potts/nfft

Spack package:

nfft/package.py

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:

https://nghttp2.org/

Spack package:

nghttp2/package.py

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:

https://nginx.org/en/

Spack package:

nginx/package.py

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:

https://github.com/philres/ngmlr

Spack package:

ngmlr/package.py

Versions:

0.2.5

Build Dependencies:

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.

ninja¶

Homepage:

https://ninja-build.org/

Spack package:

ninja/package.py

Versions:

1.9.0, 1.8.2, 1.7.2, 1.6.0, kitware

Build Dependencies:

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:

https://github.com/Kitware/ninja

Spack package:

ninja-fortran/package.py

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:

Description:

A Fortran capable fork of ninja.

nix¶

Homepage:

http://nixos.org/nix

Spack package:

nix/package.py

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:

https://nlohmann.github.io/json/

Spack package:

nlohmann-json/package.py

Versions:

3.5.0, 3.4.0, 3.3.0, 3.2.0, 3.1.2, 3.1.1

Build Dependencies:

Description:

JSON for Modern C++

nlopt¶

Homepage:

https://nlopt.readthedocs.io

Spack package:

nlopt/package.py

Versions:

develop, 2.5.0

Build Dependencies:

cmake, python, py-numpy, swig, guile, octave, matlab

Link Dependencies:

python, swig, guile, octave, matlab

Run Dependencies:

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:

https://nmap.org

Spack package:

nmap/package.py

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:

https://github.com/dmlc/nnvm

Spack package:

nnvm/package.py

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:

https://nodejs.org/

Spack package:

node-js/package.py

Versions:

11.1.0, 10.13.0, 8.9.1, 7.1.0, 6.3.0, 6.2.2

Build Dependencies:

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:

https://notmuchmail.org/

Spack package:

notmuch/package.py

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:

https://www.nas.nasa.gov/publications/npb.html

Spack package:

npb/package.py

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:

https://github.com/npm/npm

Spack package:

npm/package.py

Versions:

3.10.9, 3.10.5

Build Dependencies:

node-js

Run Dependencies:

node-js

Description:

npm: A package manager for javascript.

npth¶

Homepage:

https://gnupg.org/software/npth/index.html

Spack package:

npth/package.py

Versions:

1.5, 1.4

Description:

nPth is a library to provide the GNU Pth API and thus a non-preemptive threads implementation.

nseg¶

Homepage:

ftp://ftp.ncbi.nih.gov/pub/seg/nseg/

Spack package:

nseg/package.py

Versions:

1.0

Description:

NSEG - Low complexity sequence identification

nspr¶

Homepage:

https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSPR

Spack package:

nspr/package.py

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:

https://william-dawson.github.io/NTPoly/

Spack package:

ntpoly/package.py

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:

http://oss.sgi.com/projects/libnuma/

Spack package:

numactl/package.py

Versions:

2.0.12, 2.0.11

Build Dependencies:

Description:

NUMA support for Linux

numdiff¶

Homepage:

https://www.nongnu.org/numdiff

Spack package:

numdiff/package.py

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:

https://github.com/lanl/NuT

Spack package:

nut/package.py

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:

https://github.com/MentorEmbedded/nvptx-tools

Spack package:

nvptx-tools/package.py

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:

http://www.nwchem-sw.org

Spack package:

nwchem/package.py

Versions:

6.8.1, 6.8, 6.6

Build Dependencies:

blas, lapack, mpi, scalapack, python

Link Dependencies:

blas, lapack, mpi, scalapack, python

Run Dependencies:

Description:

High-performance computational chemistry software

nyancat¶

Homepage:

http://nyancat.dakko.us/

Spack package:

nyancat/package.py

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:

http://ocaml.org/

Spack package:

ocaml/package.py

Versions:

4.06.0, 4.03.0

Build Dependencies:

Link Dependencies:

Description:

OCaml is an industrial strength programming language supporting functional, imperative and object-oriented styles

occa¶

Homepage:

http://libocca.org

Spack package:

occa/package.py

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:

https://github.com/tpaviot/oce

Spack package:

oce/package.py

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:

http://oclint.org/

Spack package:

oclint/package.py

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:

http://cgit.freedesktop.org/xorg/app/oclock

Spack package:

oclock/package.py

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:

https://www.gnu.org/software/octave/

Spack package:

octave/package.py

Versions:

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, image-magick, 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, image-magick, 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:

https://octave.sourceforge.io/optim/

Spack package:

octave-optim/package.py

Versions:

1.5.2

Build Dependencies:

octave, octave-struct

Link Dependencies:

octave, octave-struct

Run Dependencies:

Description:

Non-linear optimization toolkit for Octave.

octave-splines¶

Homepage:

http://octave.sourceforge.net/splines/index.html

Spack package:

octave-splines/package.py

Versions:

1.3.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Additional spline functions.

octave-struct¶

Homepage:

https://octave.sourceforge.io/struct/

Spack package:

octave-struct/package.py

Versions:

1.0.14

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Additional structure manipulation functions for Octave.

octopus¶

Homepage:

http://www.tddft.org/programs/octopus/

Spack package:

octopus/package.py

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-adios-write¶

Homepage:

https://develop.openfoam.com/Community/feature-adiosWrite/

Spack package:

of-adios-write/package.py

Versions:

develop, 1706, 1612

Build Dependencies:

openfoam-com, adios

Link Dependencies:

openfoam-com, adios

Description:

adios-write supplies additional libraries and function objects for reading/writing OpenFOAM data with ADIOS. 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-catalyst¶

Homepage:

https://develop.openfoam.com/Community/catalyst

Spack package:

of-catalyst/package.py

Versions:

develop, 1806

Build Dependencies:

cmake, openfoam-com, catalyst, paraview

Link Dependencies:

openfoam-com, catalyst, paraview

Run Dependencies:

openfoam-com

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:

https://www.precice.org

Spack package:

of-precice/package.py

Versions:

develop

Build Dependencies:

openfoam, precice, yaml-cpp

Link Dependencies:

openfoam, precice, yaml-cpp

Description:

preCICE adapter for OpenFOAM

omega-h¶

Homepage:

https://github.com/SNLComputation/omega_h

Spack package:

omega-h/package.py

Versions:

develop, 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:

http://pm.bsc.es/

Spack package:

ompss/package.py

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:

https://github.com/OpenMPToolsInterface/LLVM-openmp

Spack package:

ompt-openmp/package.py

Versions:

0.1

Build Dependencies:

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:

https://github.com/kkos/oniguruma

Spack package:

oniguruma/package.py

Versions:

6.1.3

Description:

Regular expression library.

ont-albacore¶

Homepage:

https://nanoporetech.com

Spack package:

ont-albacore/package.py

Versions:

2.3.1, 2.1.2, 1.2.4, 1.1.0

Build Dependencies:

python, py-setuptools, py-numpy, py-dateutil, py-h5py, py-ont-fast5-api, py-pip

Link Dependencies:

Run Dependencies:

python, py-setuptools, py-numpy, py-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:

http://github.com/intel/opa-psm2

Spack package:

opa-psm2/package.py

Versions:

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:

https://opam.ocaml.org/

Spack package:

opam/package.py

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:

http://www.vi-hps.org/projects/score-p

Spack package:

opari2/package.py

Versions:

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:

http://openbabel.org/wiki/Main_Page

Spack package:

openbabel/package.py

Versions:

2.4.1

Build Dependencies:

cmake, python, pkgconfig, cairo, eigen, libxml2, zlib

Link Dependencies:

python, cairo, eigen, libxml2, zlib

Run Dependencies:

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:

http://www.openblas.net

Spack package:

openblas/package.py

Versions:

develop, 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

opencoarrays¶

Homepage:

http://www.opencoarrays.org/

Spack package:

opencoarrays/package.py

Versions:

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:

http://opencv.org/

Spack package:

opencv/package.py

Versions:

master, 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:

cmake, eigen, zlib, libpng, jpeg, libtiff, jasper, cuda, gtkplus, vtk, qt, java, py-numpy, protobuf, ffmpeg, mpi, python

Link Dependencies:

zlib, libpng, jpeg, libtiff, jasper, cuda, gtkplus, vtk, qt, java, protobuf, ffmpeg, mpi, python

Run Dependencies:

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:

http://www.openexr.com/

Spack package:

openexr/package.py

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:

http://openfast.readthedocs.io/en/latest/

Spack package:

openfast/package.py

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

openfoam-com¶

Homepage:

http://www.openfoam.com/

Spack package:

openfoam-com/package.py

Versions:

develop, 1812, 1806, 1712, 1706, 1612

Build Dependencies:

mpi, zlib, fftw, boost, cgal, flex, cmake, scotch, kahip, metis, parmgridgen, zoltan, vtk, paraview

Link Dependencies:

mpi, zlib, fftw, boost, cgal, flex, scotch, kahip, metis, zoltan, vtk, 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:

http://www.openfoam.org/

Spack package:

openfoam-org/package.py

Versions:

develop, 5.0, 4.1, 2.4.0

Build Dependencies:

mpi, zlib, flex, cmake, scotch

Link Dependencies:

mpi, zlib, scotch

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:

http://www.openfst.org

Spack package:

openfst/package.py

Versions:

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:

https://www.opengl.org/

Spack package:

opengl/package.py

Description:

Placeholder for external OpenGL libraries from hardware vendors

openglu¶

Homepage:

https://www.opengl.org/resources/libraries

Spack package:

openglu/package.py

Description:

Placeholder for external OpenGL utility library (GLU) from hardware vendors

openimageio¶

Homepage:

http://www.openimageio.org

Spack package:

openimageio/package.py

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:

https://jdk.java.net

Spack package:

openjdk/package.py

Versions:

11.0.1

Description:

The free and opensource java implementation

openjpeg¶

Homepage:

https://github.com/uclouvain/openjpeg

Spack package:

openjpeg/package.py

Versions:

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:

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:

https://openkim.org/

Spack package:

openkim-models/package.py

Versions:

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.

openmc¶

Homepage:

http://openmc.readthedocs.io/

Spack package:

openmc/package.py

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.

openmpi¶

Homepage:

http://www.open-mpi.org

Spack package:

openmpi/package.py

Versions:

develop, 4.0.1, 4.0.0, 3.1.4, 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, 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, binutils

Link Dependencies:

numactl, hwloc, java, sqlite, zlib, valgrind, ucx, libfabric, slurm, 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.

opennurbs¶

Homepage:

https://github.com/OpenNURBS/OpenNURBS

Spack package:

opennurbs/package.py

Versions:

develop, percept

Description:

OpenNURBS is an open-source NURBS-based geometric modeling library and toolset, with meshing and display / output functions.

openpa¶

Homepage:

https://trac.mpich.org/projects/openpa

Spack package:

openpa/package.py

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:

http://www.openPMD.org

Spack package:

openpmd-api/package.py

Versions:

develop

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:

catch, py-numpy, py-mpi4py, python

Description:

API for easy reading and writing of openPMD files

openscenegraph¶

Homepage:

http://www.openscenegraph.org

Spack package:

openscenegraph/package.py

Versions:

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:

http://openslide.org/

Spack package:

openslide/package.py

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:

http://www.openspeedshop.org

Spack package:

openspeedshop/package.py

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:

http://www.openspeedshop.org

Spack package:

openspeedshop-utils/package.py

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:

openssh¶

Homepage:

https://www.openssh.com/

Spack package:

openssh/package.py

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:

http://www.openssl.org

Spack package:

openssl/package.py

Versions:

1.1.1b, 1.1.1a, 1.1.1, 1.1.0j, 1.1.0i, 1.1.0g, 1.1.0e, 1.1.0d, 1.1.0c, 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.

opium¶

Homepage:

https://opium.sourceforge.net/index.html

Spack package:

opium/package.py

Versions:

3.8

Build Dependencies:

blas, lapack

Link Dependencies:

blas, lapack

Description:

DFT pseudopotential generation project

optional-lite¶

Homepage:

https://github.com/martinmoene/optional-lite

Spack package:

optional-lite/package.py

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:

Description:

A single-file header-only version of a C++17-like optional, a nullable object for C++98, C++11 and later.

opus¶

Homepage:

http://opus-codec.org/

Spack package:

opus/package.py

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:

https://cec.mpg.de

Spack package:

orca/package.py

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:

https://github.com/wwood/OrfM

Spack package:

orfm/package.py

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:

https://github.com/mpdunne/orthofiller/

Spack package:

orthofiller/package.py

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:

https://github.com/davidemms/OrthoFinder

Spack package:

orthofinder/package.py

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:

http://orthomcl.org/orthomcl/

Spack package:

orthomcl/package.py

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:

https://gitlab.com/osm-c-tools/osmctools

Spack package:

osmctools/package.py

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

osu-micro-benchmarks¶

Homepage:

http://mvapich.cse.ohio-state.edu/benchmarks/

Spack package:

osu-micro-benchmarks/package.py

Versions:

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:

http://tu-dresden.de/die_tu_dresden/zentrale_einrichtungen/zih/forschung/projekte/otf/index_html/document_view?set_language=en

Spack package:

otf/package.py

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:

http://www.vi-hps.org/projects/score-p

Spack package:

otf2/package.py

Versions:

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.

p4est¶

Homepage:

http://www.p4est.org

Spack package:

p4est/package.py

Versions:

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:

http://p7zip.sourceforge.net

Spack package:

p7zip/package.py

Versions:

16.02

Description:

A Unix port of the 7z file archiver

pacbio-daligner¶

Homepage:

https://github.com/PacificBiosciences/DALIGNER

Spack package:

pacbio-daligner/package.py

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:

https://github.com/PacificBiosciences/DAMASKER

Spack package:

pacbio-damasker/package.py

Versions:

2017-02-11

Build Dependencies:

Description:

Damasker: The Dazzler Repeat Masking Suite. This is a special fork required for some pacbio utilities.

pacbio-dazz-db¶

Homepage:

https://github.com/PacificBiosciences/DAZZ_DB

Spack package:

pacbio-dazz-db/package.py

Versions:

2017-04-10

Build Dependencies:

Description:

The Dazzler Database Library. This version is a special fork required for some pacbio utilities.

pacbio-dextractor¶

Homepage:

https://github.com/PacificBiosciences/DEXTRACTOR

Spack package:

pacbio-dextractor/package.py

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:

http://m3g.iqm.unicamp.br/packmol/home.shtml

Spack package:

packmol/package.py

Versions:

18.169

Build Dependencies:

Description:

Packmol creates an initial point for molecular dynamics simulations by packing molecules in defined regions of space.

pacvim¶

Homepage:

https://github.com/jmoon018/PacVim

Spack package:

pacvim/package.py

Versions:

1.1.1

Build Dependencies:

Link Dependencies:

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:

http://www.sanger.ac.uk/science/tools/pagit

Spack package:

pagit/package.py

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:

https://esa.github.io/pagmo/

Spack package:

pagmo/package.py

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:

https://github.com/Starlink/pal

Spack package:

pal/package.py

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:

http://abacus.gene.ucl.ac.uk/software/paml.html

Spack package:

paml/package.py

Versions:

4.9h

Description:

PAML is a package of programs for phylogenetic analyses of DNA or protein sewuences using maximum likelihood.

panda¶

Homepage:

http://comopt.ifi.uni-heidelberg.de/software/PANDA/index.html

Spack package:

panda/package.py

Versions:

2016-03-07

Build Dependencies:

cmake, mpi

Link Dependencies:

mpi

Description:

PANDA: Parallel AdjaceNcy Decomposition Algorithm

pandaseq¶

Homepage:

https://github.com/neufeld/pandaseq

Spack package:

pandaseq/package.py

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.

pango¶

Homepage:

http://www.pango.org

Spack package:

pango/package.py

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:

http://www.pango.org/

Spack package:

pangomm/package.py

Versions:

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:

http://icl.cs.utk.edu/papi/index.html

Spack package:

papi/package.py

Versions:

5.7.0, 5.6.0, 5.5.1, 5.5.0, 5.4.3, 5.4.1, 5.3.0

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 opportunites across the hardware and software stack.

papyrus¶

Homepage:

https://code.ornl.gov/eck/papyrus

Spack package:

papyrus/package.py

Versions:

develop, 1.0.0

Build Dependencies:

cmake, mpi

Link Dependencies:

mpi

Description:

Parallel Aggregate Persistent Storage

paradiseo¶

Homepage:

http://paradiseo.gforge.inria.fr/

Spack package:

paradiseo/package.py

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:

http://www.gnu.org/software/parallel/

Spack package:

parallel/package.py

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:

https://parallel-netcdf.github.io/

Spack package:

parallel-netcdf/package.py

Versions:

develop, master, 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:

https://tools.bsc.es/paraver

Spack package:

paraver/package.py

Versions:

4.6.3, 4.6.2

Build Dependencies:

boost, wx, wxpropgrid

Link Dependencies:

boost, wx, 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:

http://www.paraview.org

Spack package:

paraview/package.py

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, py-numpy, py-mpi4py, mpi, qt, mesa, gl, libxt, bzip2, freetype, hdf5, jpeg, libpng, libtiff, libxml2, netcdf, expat, zlib

Link Dependencies:

python, mpi, qt, mesa, gl, libxt, bzip2, freetype, hdf5, jpeg, libpng, libtiff, libxml2, netcdf, expat, zlib

Run Dependencies:

py-numpy, py-mpi4py, py-matplotlib

Description:

ParaView is an open-source, multi-platform data analysis and visualization application.

parmetis¶

Homepage:

http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview

Spack package:

parmetis/package.py

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:

http://www-users.cs.umn.edu/~moulitsa/software.html

Spack package:

parmgridgen/package.py

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¶

Homepage:

https://github.com/apache/parquet-cpp

Spack package:

parquet/package.py

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:

http://www.exelixis-lab.org/

Spack package:

parsimonator/package.py

Versions:

1.0.2

Description:

Parsimonator is a no-frills light-weight implementation for building starting trees under parsimony for RAxML

parsplice¶

Homepage:

https://gitlab.com/exaalt/parsplice

Spack package:

parsplice/package.py

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:

https://github.com/brettc/partitionfinder

Spack package:

partitionfinder/package.py

Versions:

2.1.1

Build Dependencies:

python, py-numpy, py-pandas, py-pytables, py-pyparsing, py-scipy, py-scikit-learn

Run Dependencies:

python, py-numpy, py-pandas, py-pytables, 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:

https://github.com/smirarab/pasta

Spack package:

pasta/package.py

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:

http://savannah.gnu.org/projects/patch/

Spack package:

patch/package.py

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:

https://nixos.org/patchelf.html

Spack package:

patchelf/package.py

Versions:

0.9, 0.8

Description:

PatchELF is a small utility to modify the dynamic linker and RPATH of ELF executables.

pathfinder¶

Homepage:

https://mantevo.org/packages/

Spack package:

pathfinder/package.py

Versions:

1.0.0

Description:

Proxy Application. Signature search.

pax-utils¶

Homepage:

https://wiki.gentoo.org/index.php?title=Project:Hardened/PaX_Utilities

Spack package:

pax-utils/package.py

Versions:

1.2.2

Description:

ELF utils that can check files for security relevant properties

pbbam¶

Homepage:

https://github.com/PacificBiosciences/pbbam

Spack package:

pbbam/package.py

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:

http://megasun.bch.umontreal.ca/People/lartillot/www/index.htm

Spack package:

pbmpi/package.py

Versions:

partition

Build Dependencies:

mpi, libfabric

Link Dependencies:

mpi, libfabric

Description:

A Bayesian software for phylogenetic reconstruction using mixture models

pbsuite¶

Homepage:

https://sourceforge.net/p/pb-jelly/wiki/Home/

Spack package:

pbsuite/package.py

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:

http://prodata.swmed.edu/pcma/pcma.php

Spack package:

pcma/package.py

Versions:

2.0

Description:

PCMA is a progressive multiple sequence alignment program that combines two different alignment strategies.

pcre¶

Homepage:

http://www.pcre.org

Spack package:

pcre/package.py

Versions:

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:

http://www.pcre.org

Spack package:

pcre2/package.py

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:

http://www.cityinthesky.co.uk/opensource/pdf2svg

Spack package:

pdf2svg/package.py

Versions:

0.2.3, 0.2.2

Run Dependencies:

cairo, poppler

Description:

A simple PDF to SVG converter using the Poppler and Cairo libraries.

pdftk¶

Homepage:

https://www.pdflabs.com/tools/pdftk-server

Spack package:

pdftk/package.py

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:

https://github.com/grondo/pdsh

Spack package:

pdsh/package.py

Versions:

2.31

Description:

PDSH: a high performance, parallel remote shell utility

pdt¶

Homepage:

https://www.cs.uoregon.edu/research/pdt/home.php

Spack package:

pdt/package.py

Versions:

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:

https://github.com/taocpp/PEGTL

Spack package:

pegtl/package.py

Versions:

develop, 2.1.4, 2.0.0

Build Dependencies:

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:

https://github.com/lanl/PENNANT

Spack package:

pennant/package.py

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:

https://github.com/PerceptTools/percept

Spack package:

percept/package.py

Versions:

develop

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:

http://www.perl.org

Spack package:

perl/package.py

Versions:

5.28.0, 5.26.2, 5.25.11, 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-algorithm-diff¶

Homepage:

http://search.cpan.org/~tyemq/Algorithm-Diff-1.1903/lib/Algorithm/Diff.pm

Spack package:

perl-algorithm-diff/package.py

Versions:

1.1903

Build Dependencies:

perl

Link Dependencies:

perl

Run Dependencies:

perl

Description:

Compute 'intelligent' differences between two files / lists

perl-app-cmd¶

Homepage:

http://search.cpan.org/~rjbs/App-Cmd/lib/App/Cmd.pm

Spack package:

perl-app-cmd/package.py

Versions:

0.331

Build Dependencies:

perl

Link Dependencies:

perl

Run Dependencies:

perl

Description:

Write command line apps with less suffering

perl-array-utils¶

Homepage:

http://search.cpan.org/~zmij/Array-Utils/Utils.pm

Spack package:

perl-array-utils/package.py

Versions:

0.5

Build Dependencies:

perl

Link Dependencies:

perl

Run Dependencies:

perl

Description:

Small utils for array manipulation

perl-b-hooks-endofscope¶

Homepage:

http://search.cpan.org/~ether/B-Hooks-EndOfScope-0.21/lib/B/Hooks/EndOfScope.pm

Spack package:

perl-b-hooks-endofscope/package.py

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-bio-perl¶

Homepage:

http://search.cpan.org/~cjfields/BioPerl-1.007002/Bio/Perl.pm

Spack package:

perl-bio-perl/package.py

Versions:

1.007002

Build Dependencies:

perl, perl-module-build, perl-uri-escape, perl-io-string, perl-data-stag, perl-test-most

Link Dependencies:

perl

Run Dependencies:

perl, perl-uri-escape, perl-io-string, perl-data-stag, perl-test-most

Description:

Functional access to BioPerl for people who don't know objects

perl-bit-vector¶

Homepage:

http://search.cpan.org/~stbey/Bit-Vector-7.4/Vector.pod

Spack package:

perl-bit-vector/package.py

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:

http://search.cpan.org/~xaoc/Cairo/lib/Cairo.pm

Spack package:

perl-cairo/package.py

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:

http://search.cpan.org/~dagolden/Capture-Tiny-0.46/lib/Capture/Tiny.pm

Spack package:

perl-capture-tiny/package.py

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:

http://search.cpan.org/~kentnl/Carp-Clan-6.06/lib/Carp/Clan.pod

Spack package:

perl-carp-clan/package.py

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:

https://metacpan.org/pod/CGI

Spack package:

perl-cgi/package.py

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:

http://search.cpan.org/~tmtm/Class-Data-Inheritable-0.08/lib/Class/Data/Inheritable.pm

Spack package:

perl-class-data-inheritable/package.py

Versions:

0.08

Build Dependencies:

perl

Link Dependencies:

perl

Run Dependencies:

perl

Description:

For creating accessor/mutators to class data.

perl-class-inspector¶

Homepage:

http://search.cpan.org/~plicease/Class-Inspector-1.32/lib/Class/Inspector.pm

Spack package:

perl-class-inspector/package.py

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:

http://search.cpan.org/~ether/Class-Load-0.24/lib/Class/Load.pm

Spack package:

perl-class-load/package.py

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:

http://search.cpan.org/~ether/Class-Load-XS-0.10/lib/Class/Load/XS.pm

Spack package:

perl-class-load-xs/package.py

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:

https://metacpan.org/pod/Clone

Spack package:

perl-clone/package.py

Versions:

0.41

Build Dependencies:

perl

Link Dependencies:

perl

Run Dependencies:

perl

Description:

Clone - recursively copy Perl datatypes

perl-clone-choose¶

Homepage:

https://metacpan.org/pod/Clone::Choose

Spack package:

perl-clone-choose/package.py

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:

http://search.cpan.org/~pmqs/Compress-Raw-Bzip2-2.081/lib/Compress/Raw/Bzip2.pm

Spack package:

perl-compress-raw-bzip2/package.py

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:

http://search.cpan.org/~pmqs/Compress-Raw-Zlib-2.081/lib/Compress/Raw/Zlib.pm

Spack package:

perl-compress-raw-zlib/package.py

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:

https://metacpan.org/pod/Config::General

Spack package:

perl-config-general/package.py

Versions:

2.63

Build Dependencies:

perl

Link Dependencies:

perl

Run Dependencies:

perl

Description:

Config::General - Generic Config Module

perl-contextual-return¶

Homepage:

http://search.cpan.org/~dconway/Contextual-Return/lib/Contextual/Return.pm

Spack package:

perl-contextual-return/package.py

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:

http://search.cpan.org/~leont/CPAN-Meta-Check-0.014/lib/CPAN/Meta/Check.pm

Spack package:

perl-cpan-meta-check/package.py

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:

http://search.cpan.org/dist/Data-Dumper/Dumper.pm

Spack package:

perl-data-dumper/package.py

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:

http://search.cpan.org/~rjbs/Data-OptList-0.110/lib/Data/OptList.pm

Spack package:

perl-data-optlist/package.py

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:

http://search.cpan.org/~cmungall/Data-Stag-0.14/Data/Stag.pm

Spack package:

perl-data-stag/package.py

Versions:

0.14

Build Dependencies:

perl, perl-io-string

Link Dependencies:

perl

Run Dependencies:

perl, perl-io-string

Description:

Structured Tags datastructures

perl-dbd-mysql¶

Homepage:

http://search.cpan.org/~michielb/DBD-mysql-4.043/lib/DBD/mysql.pm

Spack package:

perl-dbd-mysql/package.py

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-sqlite¶

Homepage:

https://metacpan.org/pod/DBD::SQLite

Spack package:

perl-dbd-sqlite/package.py

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-dbfile¶

Homepage:

https://metacpan.org/pod/DB_File

Spack package:

perl-dbfile/package.py

Versions:

1.840

Build Dependencies:

perl, perl-extutils-makemaker

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-dbi¶

Homepage:

https://dbi.perl.org/

Spack package:

perl-dbi/package.py

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:

http://search.cpan.org/~lds/Devel-Cycle-1.12/lib/Devel/Cycle.pm

Spack package:

perl-devel-cycle/package.py

Versions:

1.12

Build Dependencies:

perl

Link Dependencies:

perl

Run Dependencies:

perl

Description:

Find memory cycles in objects

perl-devel-globaldestruction¶

Homepage:

http://search.cpan.org/~haarg/Devel-GlobalDestruction-0.14/lib/Devel/GlobalDestruction.pm

Spack package:

perl-devel-globaldestruction/package.py

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:

http://search.cpan.org/~ilmari/Devel-OverloadInfo-0.004/lib/Devel/OverloadInfo.pm

Spack package:

perl-devel-overloadinfo/package.py

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:

http://search.cpan.org/~drolsky/Devel-StackTrace-2.02/lib/Devel/StackTrace.pm

Spack package:

perl-devel-stacktrace/package.py

Versions:

2.02

Build Dependencies:

perl

Link Dependencies:

perl

Run Dependencies:

perl

Description:

An object representing a stack trace.

perl-digest-md5¶

Homepage:

http://search.cpan.org/dist/Digest-MD5/MD5.pm

Spack package:

perl-digest-md5/package.py

Versions:

2.55

Build Dependencies:

perl

Link Dependencies:

perl

Run Dependencies:

perl

Description:

Perl interface to the MD5 Algorithm

perl-dist-checkconflicts¶

Homepage:

http://search.cpan.org/~doy/Dist-CheckConflicts-0.11/lib/Dist/CheckConflicts.pm

Spack package:

perl-dist-checkconflicts/package.py

Versions:

0.11

Build Dependencies:

perl

Link Dependencies:

perl

Run Dependencies:

perl

Description:

Declare version conflicts for your dist

perl-encode-locale¶

Homepage:

http://search.cpan.org/~gaas/Encode-Locale-1.05/lib/Encode/Locale.pm

Spack package:

perl-encode-locale/package.py

Versions:

1.05

Build Dependencies:

perl

Link Dependencies:

perl

Run Dependencies:

perl

Description:

Determine the locale encoding

perl-eval-closure¶

Homepage:

http://search.cpan.org/~doy/Eval-Closure-0.14/lib/Eval/Closure.pm

Spack package:

perl-eval-closure/package.py

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:

http://search.cpan.org/~drolsky/Exception-Class-1.43/lib/Exception/Class.pm

Spack package:

perl-exception-class/package.py

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:

http://search.cpan.org/~tobyink/Exporter-Tiny/lib/Exporter/Tiny.pm

Spack package:

perl-exporter-tiny/package.py

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:

https://metacpan.org/pod/ExtUtils::Config

Spack package:

perl-extutils-config/package.py

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:

http://search.cpan.org/~xaoc/ExtUtils-Depends/lib/ExtUtils/Depends.pm

Spack package:

perl-extutils-depends/package.py

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:

https://metacpan.org/pod/ExtUtils::Helpers

Spack package:

perl-extutils-helpers/package.py

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:

https://metacpan.org/pod/ExtUtils::InstallPaths

Spack package:

perl-extutils-installpaths/package.py

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:

https://github.com/Perl-Toolchain-Gang/ExtUtils-MakeMaker

Spack package:

perl-extutils-makemaker/package.py

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:

http://search.cpan.org/~xaoc/ExtUtils-PkgConfig-1.16/lib/ExtUtils/PkgConfig.pm

Spack package:

perl-extutils-pkgconfig/package.py

Versions:

1.16

Build Dependencies:

perl, pkgconfig

Link Dependencies:

perl

Run Dependencies:

perl, pkgconfig

Description:

simplistic interface to pkg-config

perl-file-copy-recursive¶

Homepage:

http://search.cpan.org/~dmuey/File-Copy-Recursive-0.38/Recursive.pm

Spack package:

perl-file-copy-recursive/package.py

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:

https://metacpan.org/pod/File::HomeDir

Spack package:

perl-file-homedir/package.py

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:

http://search.cpan.org/~gaas/File-Listing-6.04/lib/File/Listing.pm

Spack package:

perl-file-listing/package.py

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:

http://search.cpan.org/~dagolden/File-pushd-1.014/lib/File/pushd.pm

Spack package:

perl-file-pushd/package.py

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:

http://search.cpan.org/~ether/File-ShareDir-Install-0.11/lib/File/ShareDir/Install.pm

Spack package:

perl-file-sharedir-install/package.py

Versions:

0.11

Build Dependencies:

Link Dependencies:

perl

Run Dependencies:

perl

Description:

Install shared files

perl-file-slurp-tiny¶

Homepage:

http://search.cpan.org/~leont/File-Slurp-Tiny-0.004/lib/File/Slurp/Tiny.pm

Spack package:

perl-file-slurp-tiny/package.py

Versions:

0.004

Build Dependencies:

perl

Link Dependencies:

perl

Run Dependencies:

perl

Description:

A simple, sane and efficient file slurper

perl-file-slurper¶

Homepage:

http://search.cpan.org/~leont/File-Slurper/lib/File/Slurper.pm

Spack package:

perl-file-slurper/package.py

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:

http://cpansearch.perl.org/src/PLICEASE/File-Which-1.22/lib/File/Which.pm

Spack package:

perl-file-which/package.py

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:

http://search.cpan.org/~bhallissy/Font-TTF-1.06/lib/Font/TTF.pm

Spack package:

perl-font-ttf/package.py

Versions:

1.06

Build Dependencies:

perl

Link Dependencies:

perl

Run Dependencies:

perl

Description:

Perl module for TrueType Font hacking

perl-gd¶

Homepage:

http://search.cpan.org/~lds/GD-2.53/GD.pm

Spack package:

perl-gd/package.py

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-gd-graph¶

Homepage:

http://search.cpan.org/~bwarfield/GDGraph/Graph.pm

Spack package:

perl-gd-graph/package.py

Versions:

1.4308

Build Dependencies:

perl, perl-capture-tiny, perl-test-exception, perl-gd-text, perl-gd

Link Dependencies:

perl

Run Dependencies:

perl, perl-capture-tiny, perl-test-exception, perl-gd-text, perl-gd

Description:

Graph Plotting Module for Perl 5

perl-gd-text¶

Homepage:

http://search.cpan.org/~mverb/GDTextUtil-0.86/Text.pm

Spack package:

perl-gd-text/package.py

Versions:

0.86

Build Dependencies:

perl, perl-gd

Link Dependencies:

perl

Run Dependencies:

perl, perl-gd

Description:

Text utilities for use with GD

perl-gdgraph-histogram¶

Homepage:

https://metacpan.org/pod/GD::Graph::histogram

Spack package:

perl-gdgraph-histogram/package.py

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-graph¶

Homepage:

http://search.cpan.org/~jhi/Graph/lib/Graph.pod

Spack package:

perl-graph/package.py

Versions:

0.9704

Build Dependencies:

perl

Link Dependencies:

perl

Run Dependencies:

perl

Description:

Graph data structures and algorithms

perl-graph-readwrite¶

Homepage:

http://search.cpan.org/~neilb/Graph-ReadWrite/lib/Graph/Writer/Dot.pm

Spack package:

perl-graph-readwrite/package.py

Versions:

2.09

Build Dependencies:

perl

Link Dependencies:

perl

Run Dependencies:

perl

Description:

Write out directed graph in Dot format

perl-hash-merge¶

Homepage:

https://metacpan.org/pod/Hash::Merge

Spack package:

perl-hash-merge/package.py

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:

http://search.cpan.org/~gaas/HTML-Parser-3.72/Parser.pm

Spack package:

perl-html-parser/package.py

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:

http://search.cpan.org/~petdance/HTML-Tagset-3.20/Tagset.pm

Spack package:

perl-html-tagset/package.py

Versions:

3.20

Build Dependencies:

perl

Link Dependencies:

perl

Run Dependencies:

perl

Description:

Data tables useful in parsing HTML

perl-http-cookies¶

Homepage:

http://search.cpan.org/~oalders/HTTP-Cookies-6.04/lib/HTTP/Cookies.pm

Spack package:

perl-http-cookies/package.py

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:

http://search.cpan.org/~gaas/HTTP-Daemon-6.01/lib/HTTP/Daemon.pm

Spack package:

perl-http-daemon/package.py

Versions:

6.01

Build Dependencies:

perl, perl-lwp-mediatypes, perl-http-message

Link Dependencies:

perl

Run Dependencies:

perl, perl-lwp-mediatypes, perl-http-message

Description:

A simple http server class

perl-http-date¶

Homepage:

http://search.cpan.org/~gaas/HTTP-Date-6.02/lib/HTTP/Date.pm

Spack package:

perl-http-date/package.py

Versions:

6.02

Build Dependencies:

perl

Link Dependencies:

perl

Run Dependencies:

perl

Description:

Date conversion routines

perl-http-message¶

Homepage:

http://search.cpan.org/~oalders/HTTP-Message-6.13/lib/HTTP/Status.pm

Spack package:

perl-http-message/package.py

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:

http://search.cpan.org/~gaas/HTTP-Negotiate-6.01/lib/HTTP/Negotiate.pm

Spack package:

perl-http-negotiate/package.py

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:

http://search.cpan.org/~ingy/Inline-0.80/lib/Inline.pod

Spack package:

perl-inline/package.py

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:

http://search.cpan.org/~tinita/Inline-C-0.78/lib/Inline/C.pod

Spack package:

perl-inline-c/package.py

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-intervaltree¶

Homepage:

https://metacpan.org/release/Set-IntervalTree

Spack package:

perl-intervaltree/package.py

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-io-compress¶

Homepage:

http://search.cpan.org/~pmqs/IO-Compress-2.070/lib/IO/Uncompress/AnyUncompress.pm

Spack package:

perl-io-compress/package.py

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:

http://search.cpan.org/~cjm/IO-HTML-1.001/lib/IO/HTML.pm

Spack package:

perl-io-html/package.py

Versions:

1.001

Build Dependencies:

perl

Link Dependencies:

perl

Run Dependencies:

perl

Description:

Open an HTML file with automatic charset detection.

perl-io-sessiondata¶

Homepage:

http://search.cpan.org/~phred/IO-SessionData-1.03/

Spack package:

perl-io-sessiondata/package.py

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:

http://search.cpan.org/~sullr/IO-Socket-SSL-2.052/lib/IO/Socket/SSL.pod

Spack package:

perl-io-socket-ssl/package.py

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:

http://search.cpan.org/~gaas/IO-String-1.08/String.pm

Spack package:

perl-io-string/package.py

Versions:

1.08

Build Dependencies:

perl

Link Dependencies:

perl

Run Dependencies:

perl

Description:

Emulate file interface for in-core strings

perl-json¶

Homepage:

http://search.cpan.org/~ishigaki/JSON/lib/JSON.pm

Spack package:

perl-json/package.py

Versions:

2.97001

Build Dependencies:

perl

Link Dependencies:

perl

Run Dependencies:

perl

Description:

JSON (JavaScript Object Notation) encoder/decoder

perl-libwww-perl¶

Homepage:

https://github.com/libwww-perl/libwww-perl

Spack package:

perl-libwww-perl/package.py

Versions:

6.33

Build Dependencies:

perl

Link Dependencies:

perl

Run Dependencies:

perl

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-list-moreutils¶

Homepage:

http://search.cpan.org/~rehsack/List-MoreUtils/lib/List/MoreUtils.pm

Spack package:

perl-list-moreutils/package.py

Versions:

0.428

Build Dependencies:

perl

Link Dependencies:

perl

Run Dependencies:

perl

Description:

Provide the stuff missing in List::Util

perl-log-log4perl¶

Homepage:

http://search.cpan.org/~mschilli/Log-Log4perl-1.44/lib/Log/Log4perl.pm

Spack package:

perl-log-log4perl/package.py

Versions:

146

Build Dependencies:

perl

Link Dependencies:

perl

Run Dependencies:

perl

Description:

Log4j implementation for Perl

perl-logger-simple¶

Homepage:

https://metacpan.org/pod/Logger::Simple

Spack package:

perl-logger-simple/package.py

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¶

Homepage:

http://search.cpan.org/~oalders/libwww-perl-6.29/lib/LWP.pm

Spack package:

perl-lwp/package.py

Versions:

6.29

Build Dependencies:

perl, perl-test-requiresinternet, perl-http-message, perl-file-listing, perl-http-daemon, perl-html-parser, perl-http-cookies, perl-www-robotrules, perl-test-fatal, perl-http-negotiate, perl-net-http

Link Dependencies:

perl

Run Dependencies:

perl, perl-test-requiresinternet, perl-http-message, perl-file-listing, perl-http-daemon, perl-html-parser, perl-http-cookies, perl-www-robotrules, perl-test-fatal, perl-http-negotiate, perl-net-http

Description:

The World-Wide Web library for Perl

perl-lwp-mediatypes¶

Homepage:

http://search.cpan.org/~gaas/LWP-MediaTypes-6.02/lib/LWP/MediaTypes.pm

Spack package:

perl-lwp-mediatypes/package.py

Versions:

6.02

Build Dependencies:

perl

Link Dependencies:

perl

Run Dependencies:

perl

Description:

Guess media type for a file or a URL

perl-lwp-protocol-https¶

Homepage:

http://search.cpan.org/~gaas/LWP-Protocol-https-6.04/lib/LWP/Protocol/https.pm

Spack package:

perl-lwp-protocol-https/package.py

Versions:

6.04

Build Dependencies:

perl, perl-test-requiresinternet, perl-io-socket-ssl, perl-net-http, perl-mozilla-ca, perl-lwp

Link Dependencies:

perl

Run Dependencies:

perl, perl-test-requiresinternet, perl-io-socket-ssl, perl-net-http, perl-mozilla-ca, perl-lwp

Description:

Provide https support for LWP::UserAgent

perl-math-bezier¶

Homepage:

https://metacpan.org/pod/Math::Bezier

Spack package:

perl-math-bezier/package.py

Versions:

0.01

Build Dependencies:

perl

Link Dependencies:

perl

Run Dependencies:

perl

Description:

Math::Bezier - solution of Bezier Curves

perl-math-cdf¶

Homepage:

http://search.cpan.org/~callahan/Math-CDF-0.1/CDF.pm

Spack package:

perl-math-cdf/package.py

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:

http://search.cpan.org/~shlomif/Math-Cephes/lib/Math/Cephes.pod

Spack package:

perl-math-cephes/package.py

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:

http://search.cpan.org/~leto/Math-MatrixReal/lib/Math/MatrixReal.pm

Spack package:

perl-math-matrixreal/package.py

Versions:

2.13

Build Dependencies:

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:

https://metacpan.org/pod/Math::Round

Spack package:

perl-math-round/package.py

Versions:

0.07

Build Dependencies:

perl

Link Dependencies:

perl

Run Dependencies:

perl

Description:

Math::Round - Perl extension for rounding numbers

perl-math-vecstat¶

Homepage:

https://metacpan.org/pod/Math::VecStat

Spack package:

perl-math-vecstat/package.py

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:

http://search.cpan.org/perldoc/Module::Build

Spack package:

perl-module-build/package.py

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:

https://metacpan.org/pod/Module::Build::Tiny

Spack package:

perl-module-build-tiny/package.py

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:

http://search.cpan.org/~drolsky/Module-Implementation/lib/Module/Implementation.pm

Spack package:

perl-module-implementation/package.py

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:

http://search.cpan.org/~zefram/Module-Runtime/lib/Module/Runtime.pm

Spack package:

perl-module-runtime/package.py

Versions:

0.016

Build Dependencies:

perl, perl-cpan-meta-check, perl-test-cleannamespaces, perl-devel-overloadinfo, perl-class-load-xs, perl-devel-stacktrace, perl-eval-closure, perl-sub-name, perl-module-runtime-conflicts, perl-devel-globaldestruction, perl-package-deprecationmanager, perl-package-stash-xs

Link Dependencies:

perl

Run Dependencies:

perl

Description:

Runtime module handling

perl-module-runtime-conflicts¶

Homepage:

http://search.cpan.org/~ether/Module-Runtime-Conflicts-0.003/lib/Module/Runtime/Conflicts.pm

Spack package:

perl-module-runtime-conflicts/package.py

Versions:

0.003

Build Dependencies:

perl

Link Dependencies:

perl

Run Dependencies:

perl

Description:

Provide information on conflicts for Module::Runtime

perl-moose¶

Homepage:

http://search.cpan.org/~ether/Moose-2.2006/lib/Moose.pm

Spack package:

perl-moose/package.py

Versions:

2.2010, 2.2009, 2.2007, 2.2006

Build Dependencies:

Link Dependencies:

perl

Run Dependencies:

Description:

A postmodern object system for Perl 5

perl-mozilla-ca¶

Homepage:

http://search.cpan.org/~abh/Mozilla-CA-20160104/lib/Mozilla/CA.pm

Spack package:

perl-mozilla-ca/package.py

Versions:

20160104

Build Dependencies:

perl

Link Dependencies:

perl

Run Dependencies:

perl

Description:

Mozilla's CA cert bundle in PEM format

perl-mro-compat¶

Homepage:

http://search.cpan.org/~haarg/MRO-Compat-0.13/lib/MRO/Compat.pm

Spack package:

perl-mro-compat/package.py

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:

http://search.cpan.org/~ribasushi/namespace-clean-0.27/lib/namespace/clean.pm

Spack package:

perl-namespace-clean/package.py

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:

http://search.cpan.org/~oalders/Net-HTTP-6.17/lib/Net/HTTP.pm

Spack package:

perl-net-http/package.py

Versions:

6.17

Build Dependencies:

Link Dependencies:

perl

Run Dependencies:

Description:

Low-level HTTP connection (client)

perl-net-scp-expect¶

Homepage:

http://search.cpan.org/~rybskej/Net-SCP-Expect/Expect.pm

Spack package:

perl-net-scp-expect/package.py

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:

http://search.cpan.org/~mikem/Net-SSLeay-1.82/lib/Net/SSLeay.pod

Spack package:

perl-net-ssleay/package.py

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:

https://metacpan.org/pod/Number::Format

Spack package:

perl-number-format/package.py

Versions:

1.75

Build Dependencies:

perl

Link Dependencies:

perl

Run Dependencies:

perl

Description:

Number::Format - Perl extension for formatting numbers

perl-object-insideout¶

Homepage:

https://metacpan.org/pod/Object::InsideOut

Spack package:

perl-object-insideout/package.py

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:

http://search.cpan.org/~drolsky/Package-DeprecationManager-0.17/lib/Package/DeprecationManager.pm

Spack package:

perl-package-deprecationmanager/package.py

Versions:

0.17

Build Dependencies:

perl

Link Dependencies:

perl

Run Dependencies:

perl

Description:

Manage deprecation warnings for your distribution

perl-package-stash¶

Homepage:

http://search.cpan.org/~doy/Package-Stash-0.37/lib/Package/Stash.pm

Spack package:

perl-package-stash/package.py

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:

http://search.cpan.org/~doy/Package-Stash-XS-0.28/lib/Package/Stash/XS.pm

Spack package:

perl-package-stash-xs/package.py

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:

http://search.cpan.org/~robin/PadWalker-2.2/PadWalker.pm

Spack package:

perl-padwalker/package.py

Versions:

2.2

Build Dependencies:

perl

Link Dependencies:

perl

Run Dependencies:

perl

Description:

play with other peoples' lexical variables

perl-parallel-forkmanager¶

Homepage:

http://search.cpan.org/~yanick/Parallel-ForkManager/lib/Parallel/ForkManager.pm

Spack package:

perl-parallel-forkmanager/package.py

Versions:

1.19

Build Dependencies:

perl

Link Dependencies:

perl

Run Dependencies:

perl

Description:

A simple parallel processing fork manager

perl-params-util¶

Homepage:

http://search.cpan.org/~adamk/Params-Util-1.07/lib/Params/Util.pm

Spack package:

perl-params-util/package.py

Versions:

1.07

Build Dependencies:

perl

Link Dependencies:

perl

Run Dependencies:

perl

Description:

Simple, compact and correct param-checking functions

perl-params-validate¶

Homepage:

https://metacpan.org/pod/Params::Validate

Spack package:

perl-params-validate/package.py

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:

http://search.cpan.org/~jtbraun/Parse-RecDescent-1.967015/lib/Parse/RecDescent.pm

Spack package:

perl-parse-recdescent/package.py

Versions:

1.967015

Build Dependencies:

Link Dependencies:

perl

Run Dependencies:

perl

Description:

Generate Recursive-Descent Parsers

perl-pdf-api2¶

Homepage:

http://search.cpan.org/~ssimms/PDF-API2-2.033/lib/PDF/API2.pm

Spack package:

perl-pdf-api2/package.py

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:

http://search.cpan.org/~ingy/Pegex-0.64/lib/Pegex.pod

Spack package:

perl-pegex/package.py

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-perl4-corelibs¶

Homepage:

https://metacpan.org/pod/release/ZEFRAM/Perl4-CoreLibs-0.003/lib/Perl4/CoreLibs.pm

Spack package:

perl-perl4-corelibs/package.py

Versions:

0.004, 0.003, 0.002, 0.001, 0.000

Build Dependencies:

Link Dependencies:

perl

Run Dependencies:

perl

Description:

Perl4::CoreLibs - libraries historically supplied with Perl 4

perl-perl6-slurp¶

Homepage:

http://search.cpan.org/~dconway/Perl6-Slurp-0.051005/lib/Perl6/Slurp.pm

Spack package:

perl-perl6-slurp/package.py

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:

http://search.cpan.org/~nwclark/PerlIO-gzip/gzip.pm

Spack package:

perl-perlio-gzip/package.py

Versions:

0.20, 0.19

Build Dependencies:

perl

Link Dependencies:

perl

Run Dependencies:

perl

Description:

Perl extension to provide a PerlIO layer to gzip/gunzip

perl-perlio-utf8-strict¶

Homepage:

http://search.cpan.org/~leont/PerlIO-utf8_strict/lib/PerlIO/utf8_strict.pm

Spack package:

perl-perlio-utf8-strict/package.py

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:

https://metacpan.org/pod/Readonly

Spack package:

perl-readonly/package.py

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:

https://metacpan.org/pod/Regexp::Common

Spack package:

perl-regexp-common/package.py

Versions:

2017060201

Build Dependencies:

perl

Link Dependencies:

perl

Run Dependencies:

perl

Description:

Regexp::Common - Provide commonly requested regular expressions

perl-scalar-list-utils¶

Homepage:

https://metacpan.org/pod/Scalar::Util

Spack package:

perl-scalar-list-utils/package.py

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:

https://metacpan.org/pod/Scalar::Util::Numeric

Spack package:

perl-scalar-util-numeric/package.py

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-intspan¶

Homepage:

https://metacpan.org/pod/Set::IntSpan

Spack package:

perl-set-intspan/package.py

Versions:

1.19

Build Dependencies:

perl

Link Dependencies:

perl

Run Dependencies:

perl

Description:

Set::IntSpan - Manages sets of integers

perl-soap-lite¶

Homepage:

http://search.cpan.org/~phred/SOAP-Lite-1.20/lib/SOAP/Lite.pm

Spack package:

perl-soap-lite/package.py

Versions:

1.22

Build Dependencies:

perl, perl-io-sessiondata, perl-lwp-protocol-https, perl-task-weaken, perl-xml-parser-lite, perl-xml-parser, perl-test-warn, perl-class-inspector

Link Dependencies:

perl

Run Dependencies:

perl, perl-io-sessiondata, perl-lwp-protocol-https, perl-task-weaken, perl-xml-parser-lite, perl-xml-parser, perl-test-warn, perl-class-inspector

Description:

Perl's Web Services Toolkit

perl-star-fusion¶

Homepage:

https://github.com/STAR-Fusion/STAR-Fusion

Spack package:

perl-star-fusion/package.py

Versions:

master

Build Dependencies:

perl, star, perl-intervaltree, perl-dbi, perl-dbfile, perl-uri-escape

Link Dependencies:

perl

Run Dependencies:

perl, star, perl-intervaltree, perl-dbi, perl-dbfile, perl-uri-escape

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:

https://metacpan.org/pod/distribution/Statistics-Basic/lib/Statistics/Basic.pod

Spack package:

perl-statistics-basic/package.py

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:

http://search.cpan.org/~shlomif/Statistics-Descriptive-3.0612/lib/Statistics/Descriptive.pm

Spack package:

perl-statistics-descriptive/package.py

Versions:

3.0612

Build Dependencies:

perl

Link Dependencies:

perl

Run Dependencies:

perl

Description:

Module of basic descriptive statistical functions.

perl-statistics-pca¶

Homepage:

http://search.cpan.org/~dsth/Statistics-PCA/lib/Statistics/PCA.pm

Spack package:

perl-statistics-pca/package.py

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:

http://search.cpan.org/~rjbs/Sub-Exporter-0.987/lib/Sub/Exporter.pm

Spack package:

perl-sub-exporter/package.py

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:

http://search.cpan.org/~frew/Sub-Exporter-Progressive-0.001013/lib/Sub/Exporter/Progressive.pm

Spack package:

perl-sub-exporter-progressive/package.py

Versions:

0.001013

Build Dependencies:

perl

Link Dependencies:

perl

Run Dependencies:

perl

Description:

Progressive Sub::Exporter

perl-sub-identify¶

Homepage:

http://search.cpan.org/~rgarcia/Sub-Identify-0.14/lib/Sub/Identify.pm

Spack package:

perl-sub-identify/package.py

Versions:

0.14

Build Dependencies:

perl

Link Dependencies:

perl

Run Dependencies:

perl

Description:

Retrieve names of code references

perl-sub-install¶

Homepage:

http://search.cpan.org/~rjbs/Sub-Install-0.928/lib/Sub/Install.pm

Spack package:

perl-sub-install/package.py

Versions:

0.928

Build Dependencies:

perl

Link Dependencies:

perl

Run Dependencies:

perl

Description:

Install subroutines into packages easily

perl-sub-name¶

Homepage:

http://search.cpan.org/~ether/Sub-Name-0.21/lib/Sub/Name.pm

Spack package:

perl-sub-name/package.py

Versions:

0.21

Build Dependencies:

perl

Link Dependencies:

perl

Run Dependencies:

perl

Description:

Name or rename a sub

perl-sub-uplevel¶

Homepage:

http://search.cpan.org/~dagolden/Sub-Uplevel-0.2800/lib/Sub/Uplevel.pm

Spack package:

perl-sub-uplevel/package.py

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:

http://search.cpan.org/~manwar/SVG-2.78/lib/SVG.pm

Spack package:

perl-svg/package.py

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:

http://swissknife.sourceforge.net

Spack package:

perl-swissknife/package.py

Versions:

1.75

Build Dependencies:

Link Dependencies:

perl

Run Dependencies:

perl

Description:

An object-oriented Perl library to handle Swiss-Prot entries

perl-task-weaken¶

Homepage:

http://search.cpan.org/~adamk/Task-Weaken-1.04/lib/Task/Weaken.pm

Spack package:

perl-task-weaken/package.py

Versions:

1.04

Build Dependencies:

perl

Link Dependencies:

perl

Run Dependencies:

perl

Description:

Ensure that a platform has weaken support

perl-term-readkey¶

Homepage:

http://search.cpan.org/perldoc/Term::ReadKey

Spack package:

perl-term-readkey/package.py

Versions:

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-cleannamespaces¶

Homepage:

http://search.cpan.org/~ether/Test-CleanNamespaces-0.22/lib/Test/CleanNamespaces.pm

Spack package:

perl-test-cleannamespaces/package.py

Versions:

0.22

Build Dependencies:

perl, perl-sub-exporter, perl-module-runtime, perl-test-needs, perl-test-deep, perl-test-warnings, perl-file-pushd, perl-package-stash, perl-sub-identify, perl-namespace-clean

Link Dependencies:

perl

Run Dependencies:

perl, perl-sub-exporter, perl-module-runtime, perl-test-needs, perl-test-deep, perl-test-warnings, perl-file-pushd, perl-package-stash, perl-sub-identify, perl-namespace-clean

Description:

This module lets you check your module's namespaces for imported functions you might have forgotten to remove

perl-test-deep¶

Homepage:

http://search.cpan.org/~rjbs/Test-Deep-1.127/lib/Test/Deep.pm

Spack package:

perl-test-deep/package.py

Versions:

1.127

Build Dependencies:

perl

Link Dependencies:

perl

Run Dependencies:

perl

Description:

Extremely flexible deep comparison

perl-test-differences¶

Homepage:

http://search.cpan.org/~dcantrell/Test-Differences-0.64/lib/Test/Differences.pm

Spack package:

perl-test-differences/package.py

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:

http://search.cpan.org/~exodist/Test-Exception-0.43/lib/Test/Exception.pm

Spack package:

perl-test-exception/package.py

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:

http://search.cpan.org/~rjbs/Test-Fatal-0.014/lib/Test/Fatal.pm

Spack package:

perl-test-fatal/package.py

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:

http://search.cpan.org/~petdance/Test-Memory-Cycle-1.06/Cycle.pm

Spack package:

perl-test-memory-cycle/package.py

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:

http://search.cpan.org/~ovid/Test-Most-0.35/lib/Test/Most.pm

Spack package:

perl-test-most/package.py

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:

http://search.cpan.org/~haarg/Test-Needs-0.002005/lib/Test/Needs.pm

Spack package:

perl-test-needs/package.py

Versions:

0.002005

Build Dependencies:

perl

Link Dependencies:

perl

Run Dependencies:

perl

Description:

Skip tests when modules not available.

perl-test-requires¶

Homepage:

http://search.cpan.org/~tokuhirom/Test-Requires-0.10/lib/Test/Requires.pm

Spack package:

perl-test-requires/package.py

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:

http://search.cpan.org/~mallen/Test-RequiresInternet-0.05/lib/Test/RequiresInternet.pm

Spack package:

perl-test-requiresinternet/package.py

Versions:

0.05

Build Dependencies:

perl

Link Dependencies:

perl

Run Dependencies:

perl

Description:

Easily test network connectivity

perl-test-warn¶

Homepage:

http://search.cpan.org/~chorny/Test-Warn-0.30/Warn.pm

Spack package:

perl-test-warn/package.py

Versions:

0.30

Build Dependencies:

perl

Link Dependencies:

perl

Run Dependencies:

perl

Description:

Perl extension to test methods for warnings

perl-test-warnings¶

Homepage:

http://deps.cpantesters.org/?module=Test%3A%3ACleanNamespaces;perl=latest

Spack package:

perl-test-warnings/package.py

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:

http://search.cpan.org/~ishigaki/Text-CSV/lib/Text/CSV.pm

Spack package:

perl-text-csv/package.py

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:

http://search.cpan.org/~neilb/Text-Diff-1.45/lib/Text/Diff.pm

Spack package:

perl-text-diff/package.py

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:

https://metacpan.org/pod/Text::Format

Spack package:

perl-text-format/package.py

Versions:

0.61

Build Dependencies:

Link Dependencies:

perl

Run Dependencies:

perl

Description:

Text::Format - Various subroutines to format text

perl-text-simpletable¶

Homepage:

http://search.cpan.org/~mramberg/Text-SimpleTable/lib/Text/SimpleTable.pm

Spack package:

perl-text-simpletable/package.py

Versions:

2.04

Build Dependencies:

perl

Link Dependencies:

perl

Run Dependencies:

perl

Description:

Simple Eyecandy ASCII Tables

perl-text-soundex¶

Homepage:

http://search.cpan.org/~rjbs/Text-Soundex-3.05/Soundex.pm

Spack package:

perl-text-soundex/package.py

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:

http://search.cpan.org/~sburke/Text-Unidecode/lib/Text/Unidecode.pm

Spack package:

perl-text-unidecode/package.py

Versions:

1.30

Build Dependencies:

perl

Link Dependencies:

perl

Run Dependencies:

perl

Description:

plain ASCII transliterations of Unicode text

perl-time-hires¶

Homepage:

http://search.cpan.org/~jhi/Time-HiRes-1.9746/HiRes.pm

Spack package:

perl-time-hires/package.py

Versions:

1.9746

Build Dependencies:

perl

Link Dependencies:

perl

Run Dependencies:

perl

Description:

High resolution alarm, sleep, gettimeofday, interval timers

perl-time-piece¶

Homepage:

http://search.cpan.org/~esaym/Time-Piece/Piece.pm

Spack package:

perl-time-piece/package.py

Versions:

1.3203

Build Dependencies:

perl

Link Dependencies:

perl

Run Dependencies:

perl

Description:

Object Oriented time objects

perl-try-tiny¶

Homepage:

http://search.cpan.org/~ether/Try-Tiny-0.28/lib/Try/Tiny.pm

Spack package:

perl-try-tiny/package.py

Versions:

0.28

Build Dependencies:

perl

Link Dependencies:

perl

Run Dependencies:

perl

Description:

Minimal try/catch with proper preservation of $@

perl-uri¶

Homepage:

http://search.cpan.org/~ether/URI-1.72/lib/URI.pm

Spack package:

perl-uri/package.py

Versions:

1.72

Build Dependencies:

perl, perl-test-needs

Link Dependencies:

perl

Run Dependencies:

perl, perl-test-needs

Description:

Uniform Resource Identifiers (absolute and relative)

perl-uri-escape¶

Homepage:

https://metacpan.org/pod/URI::Escape

Spack package:

perl-uri-escape/package.py

Versions:

1.71

Build Dependencies:

perl, perl-extutils-makemaker

Link Dependencies:

perl

Run Dependencies:

perl

Description:

This module provides functions to percent-encode and percent-decode URI strings as defined by RFC 3986. Percent-encoding URI's is informally called "URI escaping". This is the terminology used by this module, which predates the formalization of the terms by the RFC by several years.

perl-version¶

Homepage:

http://search.cpan.org/~bdfoy/Perl-Version-1.013/lib/Perl/Version.pm

Spack package:

perl-version/package.py

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-want¶

Homepage:

search.cpan.org/~robin/Want/Want.pm

Spack package:

perl-want/package.py

Versions:

0.29

Build Dependencies:

perl

Link Dependencies:

perl

Run Dependencies:

perl

Description:

A generalisation of wantarray.

perl-www-robotrules¶

Homepage:

http://deps.cpantesters.org/?module=WWW%3A%3ARobotRules;perl=latest

Spack package:

perl-www-robotrules/package.py

Versions:

6.02

Build Dependencies:

Link Dependencies:

perl

Run Dependencies:

Description:

Database of robots.txt-derived permissions

perl-xml-parser¶

Homepage:

http://search.cpan.org/perldoc/XML::Parser

Spack package:

perl-xml-parser/package.py

Versions:

2.44

Build Dependencies:

perl, expat

Link Dependencies:

perl, expat

Run Dependencies:

perl

Description:

XML::Parser - A perl module for parsing XML documents

perl-xml-parser-lite¶

Homepage:

http://search.cpan.org/~phred/XML-Parser-Lite-0.721/lib/XML/Parser/Lite.pm

Spack package:

perl-xml-parser-lite/package.py

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-simple¶

Homepage:

http://search.cpan.org/~grantm/XML-Simple/lib/XML/Simple.pm

Spack package:

perl-xml-simple/package.py

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-yaml¶

Homepage:

https://metacpan.org/pod/YAML

Spack package:

perl-yaml/package.py

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:

http://search.cpan.org/~tinita/YAML-LibYAML/

Spack package:

perl-yaml-libyaml/package.py

Versions:

0.67

Build Dependencies:

perl

Link Dependencies:

perl

Run Dependencies:

perl

Description:

Perl YAML Serialization using XS and libyaml

petsc¶

Homepage:

http://www.mcs.anl.gov/petsc/index.html

Spack package:

petsc/package.py

Versions:

develop, 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:

https://math.berkeley.edu/~linlin/pexsi/index.html

Spack package:

pexsi/package.py

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:

https://www-user.tu-chemnitz.de/~potts/workgroup/pippig/software.php.en

Spack package:

pfft/package.py

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:

http://www.pflotran.org

Spack package:

pflotran/package.py

Versions:

develop, 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:

http://pfunit.sourceforge.net/

Spack package:

pfunit/package.py

Versions:

3.2.9

Build Dependencies:

cmake, python, mpi

Link Dependencies:

mpi

Run Dependencies:

Description:

pFUnit is a unit testing framework enabling JUnit-like testing of serial and MPI-parallel software written in Fortran.

pgdspider¶

Homepage:

http://www.cmpg.unibe.ch/software/PGDSpider

Spack package:

pgdspider/package.py

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:

http://www.pgroup.com/

Spack package:

pgi/package.py

Versions:

19.4, 19.1, 18.10, 18.4, 17.10, 17.4, 17.3, 16.10, 16.5, 16.3, 15.7

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:

https://github.com/flang-compiler/flang

Spack package:

pgmath/package.py

Versions:

develop, 20180921, 20180612

Build Dependencies:

cmake, awk

Description:

Flang's math library

phantompeakqualtools¶

Homepage:

https://github.com/kundajelab/phantompeakqualtools

Spack package:

phantompeakqualtools/package.py

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:

http://compgen.cshl.edu/phast/index.php

Spack package:

phast/package.py

Versions:

1.4

Build Dependencies:

clapack

Link Dependencies:

clapack

Description:

PHAST is a freely available software package for comparative and evolutionary genomics.

phasta¶

Homepage:

https://www.scorec.rpi.edu/software.php

Spack package:

phasta/package.py

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:

https://bitbucket.org/essex/phist/

Spack package:

phist/package.py

Versions:

develop, master, 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:

http://www.phrap.org/phredphrapconsed.html

Spack package:

phrap-crossmatch-swat/package.py

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:

http://www.phrap.org/phredphrapconsed.html

Spack package:

phred/package.py

Versions:

071220

Description:

The phred software reads DNA sequencing trace files, calls bases, and assigns a quality value to each called base.

phylip¶

Homepage:

http://evolution.genetics.washington.edu/phylip/

Spack package:

phylip/package.py

Versions:

3.697, 3.696

Description:

PHYLIP (the PHYLogeny Inference Package) is a package of programs for inferring phylogenies (evolutionary trees).

phyluce¶

Homepage:

https://github.com/faircloth-lab/phyluce

Spack package:

phyluce/package.py

Versions:

1.6.7

Build Dependencies:

Link Dependencies:

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:

http://broadinstitute.github.io/picard/

Spack package:

picard/package.py

Versions:

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:

https://picsar.net

Spack package:

picsar/package.py

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:

https://picsar.net

Spack package:

picsarlite/package.py

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:

http://www.cedmav.com/pidx

Spack package:

pidx/package.py

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.

pigz¶

Homepage:

http://zlib.net/pigz/

Spack package:

pigz/package.py

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:

https://github.com/broadinstitute/pilon

Spack package:

pilon/package.py

Versions:

1.22, 1.13

Run Dependencies:

java

Description:

Pilon is an automated genome assembly improvement and variant detection tool.

pindel¶

Homepage:

http://gmt.genome.wustl.edu/packages/pindel/

Spack package:

pindel/package.py

Versions:

0.2.5b8, 0.2.5b6, 0.2.5b5, 0.2.5b4, 0.2.5b1, 0.2.5a7, 0.2.5

Build Dependencies:

Link Dependencies:

Description:

Pindel can detect breakpoints from next-gen sequence data.

piranha¶

Homepage:

https://bluescarni.github.io/piranha/sphinx/

Spack package:

piranha/package.py

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:

http://pism-docs.org/wiki/doku.php:=

Spack package:

pism/package.py

Versions:

develop, 0.7.3, 0.7.x, icebin

Build Dependencies:

cmake, fftw, gsl, mpi, netcdf, petsc, udunits2, proj, everytrace, python, py-matplotlib, py-numpy

Link Dependencies:

fftw, gsl, mpi, netcdf, petsc, udunits2, proj, everytrace, python, py-matplotlib, py-numpy

Description:

Parallel Ice Sheet Model

pixman¶

Homepage:

http://www.pixman.org

Spack package:

pixman/package.py

Versions:

0.38.0, 0.34.0, 0.32.6

Build Dependencies:

pkgconfig, libpng

Link Dependencies:

Description:

The Pixman package contains a library that provides low-level pixel manipulation features such as image compositing and trapezoid rasterization.

pkg-config¶

Homepage:

http://www.freedesktop.org/wiki/Software/pkg-config/

Spack package:

pkg-config/package.py

Versions:

0.29.2, 0.29.1, 0.28

Description:

pkg-config is a helper tool used when compiling applications and libraries

pkgconf¶

Homepage:

http://pkgconf.org/

Spack package:

pkgconf/package.py

Versions:

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.

planck-likelihood¶

Homepage:

https://wiki.cosmos.esa.int/planckpla2015/index.php/CMB_spectrum_%26_Likelihood_Code

Spack package:

planck-likelihood/package.py

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:

https://bitbucket.org/icl/plasma/

Spack package:

plasma/package.py

Versions:

develop, 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:

http://www.well.ox.ac.uk/platypus

Spack package:

platypus/package.py

Versions:

0.8.1

Build Dependencies:

python, py-cython, htslib

Link Dependencies:

Run Dependencies:

Description:

A Haplotype-Based Variant Caller For Next Generation Sequence Data

plink¶

Homepage:

https://www.cog-genomics.org/plink/1.9/

Spack package:

plink/package.py

Versions:

1.9-beta5, 1.07

Build Dependencies:

atlas, netlib-lapack

Link Dependencies:

atlas, netlib-lapack

Description:

PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.

plplot¶

Homepage:

http://plplot.sourceforge.net/

Spack package:

plplot/package.py

Versions:

5.13.0, 5.12.0, 5.11.0

Build Dependencies:

cmake, java, lua, pango, py-numpy, python, qt, tcl, wx, freetype, gtkplus, libx11, qhull, swig

Link Dependencies:

java, lua, pango, qt, tcl, wx, freetype, gtkplus, libx11, qhull, swig

Run Dependencies:

py-numpy, python

Description:

PLplot is a cross-platform package for creating scientific plots.

plumed¶

Homepage:

http://www.plumed.org/

Spack package:

plumed/package.py

Versions:

2.5.0, 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:

http://pmem.io/pmdk/

Spack package:

pmdk/package.py

Versions:

develop, 1.6, 1.5

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:

http://www.sourceforge.net/projects/pmgrcollective

Spack package:

pmgr-collective/package.py

Versions:

1.0

Description:

PMGR_COLLECTIVE provides a scalable network for bootstrapping MPI jobs.

pmix¶

Homepage:

https://pmix.org

Spack package:

pmix/package.py

Versions:

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.

pnfft¶

Homepage:

https://www-user.tu-chemnitz.de/~potts/workgroup/pippig/software.php.en

Spack package:

pnfft/package.py

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.

pngwriter¶

Homepage:

http://pngwriter.sourceforge.net/

Spack package:

pngwriter/package.py

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:

https://github.com/LLNL/PnMPI

Spack package:

pnmpi/package.py

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:

https://sourceforge.net/projects/poamsa

Spack package:

poamsa/package.py

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:

http://portablecl.org

Spack package:

pocl/package.py

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:

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:

https://polymake.org/doku.php

Spack package:

polymake/package.py

Versions:

3.0r2, 3.0r1

Build Dependencies:

bliss, boost, cddlib, gmp, lrslib, mpfr, ppl

Link Dependencies:

bliss, boost, cddlib, gmp, lrslib, mpfr, ppl

Description:

polymake is open source software for research in polyhedral geometry

poppler¶

Homepage:

https://poppler.freedesktop.org

Spack package:

poppler/package.py

Versions:

0.72.0, 0.65.0, 0.64.0

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:

https://poppler.freedesktop.org/

Spack package:

poppler-data/package.py

Versions:

0.4.9

Build Dependencies:

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.

porta¶

Homepage:

http://porta.zib.de

Spack package:

porta/package.py

Versions:

1.4.1

Build Dependencies:

Description:

PORTA is a collection of routines for analyzing polytopes and polyhedra

portage¶

Homepage:

http://portage.lanl.gov/

Spack package:

portage/package.py

Versions:

develop, 1.1.1, 1.1.0

Build Dependencies:

cmake, mpi, lapack

Link Dependencies:

mpi, lapack

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:

https://github.com/maplesond/portcullis

Spack package:

portcullis/package.py

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:

http://www.postgresql.org/

Spack package:

postgresql/package.py

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.

ppl¶

Homepage:

http://bugseng.com/products/ppl/

Spack package:

ppl/package.py

Versions:

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:

http://matsen.fhcrc.org/pplacer/

Spack package:

pplacer/package.py

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:

http://wasabiapp.org/software/prank/

Spack package:

prank/package.py

Versions:

170427, 150803

Build Dependencies:

mafft, exonerate, bpp-suite

Link Dependencies:

mafft, exonerate, bpp-suite

Description:

A powerful multiple sequence alignment browser.

precice¶

Homepage:

https://www.precice.org

Spack package:

precice/package.py

Versions:

develop, 1.4.1, 1.4.0, 1.3.0, 1.2.0

Build Dependencies:

cmake, boost, eigen, libxml2, mpi, petsc, python

Link Dependencies:

boost, eigen, libxml2, mpi, petsc

Run Dependencies:

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:

https://cgit.freedesktop.org/xorg/proto/presentproto/

Spack package:

presentproto/package.py

Versions:

1.0

Build Dependencies:

pkgconfig, util-macros

Description:

Present protocol specification and Xlib/Xserver headers.

preseq¶

Homepage:

https://github.com/smithlabcode/preseq

Spack package:

preseq/package.py

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:

http://derisilab.ucsf.edu/software/price/

Spack package:

price/package.py

Versions:

140408

Description:

PRICE (Paired-Read Iterative Contig Extension): a de novo genome assembler implemented in C++.

primer3¶

Homepage:

http://primer3.sourceforge.net/

Spack package:

primer3/package.py

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:

http://prinseq.sourceforge.net

Spack package:

prinseq-lite/package.py

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:

http://cgit.freedesktop.org/xorg/proto/printproto

Spack package:

printproto/package.py

Versions:

1.0.5

Build Dependencies:

pkgconfig, util-macros

Description:

Xprint extension to the X11 protocol - a portable, network-transparent printing system.

prng¶

Homepage:

http://statmath.wu.ac.at/prng/

Spack package:

prng/package.py

Versions:

3.0.2

Build Dependencies:

automake, autoconf, libtool, m4

Description:

Pseudo-Random Number Generator library.

probconsrna¶

Homepage:

http://probcons.stanford.edu/

Spack package:

probconsrna/package.py

Versions:

2005-6-7

Description:

Experimental version of PROBCONS with parameters estimated via unsupervised training on BRAliBASE

prodigal¶

Homepage:

https://github.com/hyattpd/Prodigal

Spack package:

prodigal/package.py

Versions:

2.6.3

Description:

Fast, reliable protein-coding gene prediction for prokaryotic genomes.

proj¶

Homepage:

https://proj4.org/

Spack package:

proj/package.py

Versions:

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:

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:

https://developers.google.com/protocol-buffers

Spack package:

protobuf/package.py

Versions:

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.

proxymngr¶

Homepage:

http://cgit.freedesktop.org/xorg/app/proxymngr

Spack package:

proxymngr/package.py

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.

pruners-ninja¶

Homepage:

https://github.com/PRUNERS/NINJA

Spack package:

pruners-ninja/package.py

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:

https://github.com/dmlc/ps-lite

Spack package:

ps-lite/package.py

Versions:

master, 20170328

Build Dependencies:

cmake, protobuf, zeromq

Link Dependencies:

protobuf, zeromq

Description:

ps-lite is A light and efficient implementation of the parameter server framework.

psi4¶

Homepage:

http://www.psicode.org/

Spack package:

psi4/package.py

Versions:

0.5

Build Dependencies:

cmake, blas, lapack, boost, python, py-numpy

Link Dependencies:

blas, lapack, boost, python

Run Dependencies:

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:

http://pslib.sourceforge.net/

Spack package:

pslib/package.py

Versions:

0.4.5

Build Dependencies:

jpeg, libpng

Link Dependencies:

jpeg, libpng

Description:

C-library to create PostScript files on the fly.

psm¶

Homepage:

https://github.com/intel/psm

Spack package:

psm/package.py

Versions:

2017-04-28, 3.3

Build Dependencies:

libuuid

Link Dependencies:

libuuid

Description:

Intel Performance scaled messaging library

psmc¶

Homepage:

https://github.com/lh3/psmc

Spack package:

psmc/package.py

Versions:

2016-1-21

Description:

mplementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model

pstreams¶

Homepage:

http://pstreams.sourceforge.net/

Spack package:

pstreams/package.py

Versions:

1.0.1

Description:

C++ wrapper for the POSIX.2 functions popen(3) and pclose(3)

pugixml¶

Homepage:

http://pugixml.org/

Spack package:

pugixml/package.py

Versions:

1.8.1

Build Dependencies:

Description:

Light-weight, simple, and fast XML parser for C++ with XPath support

pumi¶

Homepage:

https://www.scorec.rpi.edu/pumi

Spack package:

pumi/package.py

Versions:

develop, 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:

http://www.ivarch.com/programs/pv.shtml

Spack package:

pv/package.py

Versions:

1.6.6

Description:

Pipe Viewer - is a terminal-based tool for monitoring the progress of data through a pipeline

pvm¶

Homepage:

http://www.csm.ornl.gov/pvm/pvm_home.html

Spack package:

pvm/package.py

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:

https://jnovy.fedorapeople.org/pxz/pxz.html

Spack package:

pxz/package.py

Versions:

develop, 4.999.9beta.20091201git

Build Dependencies:

Link Dependencies:

Description:

Pxz is a parallel LZMA compressor using liblzma.

py-3to2¶

Homepage:

https://pypi.python.org/pypi/3to2

Spack package:

py-3to2/package.py

Versions:

1.1.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

http://4suite.org/

Spack package:

py-4suite-xml/package.py

Versions:

1.0.2

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

XML tools and libraries for Python: Domlette, XPath, XSLT, XPointer, XLink, XUpdate

py-abipy¶

Homepage:

https://github.com/abinit/abipy

Spack package:

py-abipy/package.py

Versions:

0.2.0

Build Dependencies:

python, py-setuptools, py-cython, py-six, py-prettytable, py-tabulate, py-apscheduler, py-pydispatcher, py-tqdm, py-html2text, py-pyyaml, py-pandas, py-numpy, py-scipy, py-spglib, py-pymatgen, py-netcdf4, py-matplotlib, py-seaborn, py-wxpython, py-wxmplot, py-ipython, py-jupyter, py-nbformat

Link Dependencies:

Run Dependencies:

python, py-six, py-prettytable, py-tabulate, py-apscheduler, py-pydispatcher, py-tqdm, py-html2text, py-pyyaml, py-pandas, py-numpy, py-scipy, py-spglib, py-pymatgen, py-netcdf4, py-matplotlib, py-seaborn, py-wxpython, py-wxmplot, py-ipython, py-jupyter, py-nbformat

Description:

Python package to automate ABINIT calculations and analyze the results.

py-adios¶

Homepage:

https://www.olcf.ornl.gov/center-projects/adios/

Spack package:

py-adios/package.py

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:

https://github.com/kata198/AdvancedHTMLParser

Spack package:

py-advancedhtmlparser/package.py

Versions:

8.1.4

Build Dependencies:

python, py-setuptools, py-queryablelist

Link Dependencies:

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-affine¶

Homepage:

https://github.com/sgillies/affine

Spack package:

py-affine/package.py

Versions:

2.1.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Matrices describing affine transformation of the plane.

py-alabaster¶

Homepage:

https://alabaster.readthedocs.io/

Spack package:

py-alabaster/package.py

Versions:

0.7.12, 0.7.10, 0.7.9

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Alabaster is a visually (c)lean, responsive, configurable theme for the Sphinx documentation system.

py-alembic¶

Homepage:

https://pypi.org/project/alembic/

Spack package:

py-alembic/package.py

Versions:

1.0.7

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Alembic is a database migrations tool.

py-apache-libcloud¶

Homepage:

http://libcloud.apache.org

Spack package:

py-apache-libcloud/package.py

Versions:

1.2.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Python library for multiple cloud provider APIs

py-apipkg¶

Homepage:

https://pypi.python.org/pypi/apipkg

Spack package:

py-apipkg/package.py

Versions:

1.4

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

apipkg: namespace control and lazy-import mechanism

py-appdirs¶

Homepage:

https://github.com/ActiveState/appdirs

Spack package:

py-appdirs/package.py

Versions:

1.4.3, 1.4.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

A small Python module for determining appropriate platform-specific dirs, e.g. a "user data dir".

py-appnope¶

Homepage:

https://github.com/minrk/appnope

Spack package:

py-appnope/package.py

Versions:

0.1.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Disable App Nap on OS X 10.9

py-apscheduler¶

Homepage:

https://github.com/agronholm/apscheduler

Spack package:

py-apscheduler/package.py

Versions:

3.3.1, 2.1.0

Build Dependencies:

python, py-setuptools, py-six, py-pytz, py-tzlocal

Link Dependencies:

Run Dependencies:

python, py-six, py-pytz, py-tzlocal

Description:

In-process task scheduler with Cron-like capabilities.

py-argcomplete¶

Homepage:

https://pypi.python.org/pypi/argcomplete

Spack package:

py-argcomplete/package.py

Versions:

1.1.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Bash tab completion for argparse.

py-argparse¶

Homepage:

https://github.com/ThomasWaldmann/argparse/

Spack package:

py-argparse/package.py

Versions:

1.4.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Python command-line parsing library.

py-ase¶

Homepage:

https://wiki.fysik.dtu.dk/ase/

Spack package:

py-ase/package.py

Versions:

3.15.0, 3.13.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

https://github.com/wbond/asn1crypto

Spack package:

py-asn1crypto/package.py

Versions:

0.22.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Python ASN.1 library with a focus on performance and a pythonic API

py-astroid¶

Homepage:

https://github.com/PyCQA/astroid

Spack package:

py-astroid/package.py

Versions:

2.2.0, 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:

Description:

A common base representation of python source code for pylint and other projects.

py-astropy¶

Homepage:

http://www.astropy.org/

Spack package:

py-astropy/package.py

Versions:

1.1.2, 1.1.post1

Build Dependencies:

python, py-setuptools, py-numpy, py-h5py, py-beautifulsoup4, py-pyyaml, py-scipy, libxml2, py-matplotlib, py-pytz, py-scikit-image, py-pandas, py-markupsafe, cfitsio, expat

Link Dependencies:

python, libxml2, cfitsio, expat

Run Dependencies:

python, py-numpy, py-h5py, py-beautifulsoup4, py-pyyaml, py-scipy, py-matplotlib, py-pytz, py-scikit-image, py-pandas, py-markupsafe

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-async-generator¶

Homepage:

https://pypi.org/project/async_generator/

Spack package:

py-async-generator/package.py

Versions:

1.10

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Provides async generator functionality to python 3.5.

py-atomicwrites¶

Homepage:

https://github.com/untitaker/python-atomicwrites

Spack package:

py-atomicwrites/package.py

Versions:

1.1.5

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Atomic file writes.

py-attrs¶

Homepage:

http://attrs.org/

Spack package:

py-attrs/package.py

Versions:

18.1.0, 16.3.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Test Dependencies:

py-coverage, py-hypothesis, py-pympler, py-pytest, py-six, py-zope-interface

Description:

Classes Without Boilerplate

py-autopep8¶

Homepage:

https://github.com/hhatto/autopep8

Spack package:

py-autopep8/package.py

Versions:

1.3.3, 1.2.4, 1.2.2

Build Dependencies:

python, py-pycodestyle, py-setuptools

Link Dependencies:

Run Dependencies:

python, py-pycodestyle

Description:

autopep8 automatically formats Python code to conform to the PEP 8 style guide.

py-avro¶

Homepage:

http://avro.apache.org/docs/current/

Spack package:

py-avro/package.py

Versions:

1.8.2

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Avro is a serialization and RPC framework.

py-avro-json-serializer¶

Homepage:

https://github.com/linkedin/python-avro-json-serializer

Spack package:

py-avro-json-serializer/package.py

Versions:

0.4

Build Dependencies:

python, py-setuptools, py-simplejson, py-avro

Link Dependencies:

Run Dependencies:

python, py-simplejson, py-avro

Description:

Serializes data into a JSON format using AVRO schema.

py-babel¶

Homepage:

http://babel.pocoo.org/en/latest/

Spack package:

py-babel/package.py

Versions:

2.6.0, 2.4.0, 2.3.4

Build Dependencies:

python, py-setuptools, py-pytz

Link Dependencies:

Run Dependencies:

python, py-pytz

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:

https://github.com/takluyver/backcall

Spack package:

py-backcall/package.py

Versions:

0.1.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Specifications for callback functions passed in to an API

py-backports-abc¶

Homepage:

https://github.com/cython/backports_abc

Spack package:

py-backports-abc/package.py

Versions:

0.4

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Backports_ABC: A backport of recent additions to the 'collections.abc' module.

py-backports-functools-lru-cache¶

Homepage:

https://github.com/jaraco/backports.functools_lru_cache

Spack package:

py-backports-functools-lru-cache/package.py

Versions:

1.5, 1.4, 1.0.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Backport of functools.lru_cache from Python 3.3

py-backports-shutil-get-terminal-size¶

Homepage:

https://pypi.python.org/pypi/backports.shutil_get_terminal_size

Spack package:

py-backports-shutil-get-terminal-size/package.py

Versions:

1.0.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

A backport of the get_terminal_size function from Python 3.3's shutil.

py-backports-ssl-match-hostname¶

Homepage:

https://pypi.python.org/pypi/backports.ssl_match_hostname

Spack package:

py-backports-ssl-match-hostname/package.py

Versions:

3.5.0.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

The ssl.match_hostname() function from Python 3.5

py-basemap¶

Homepage:

http://matplotlib.org/basemap/

Spack package:

py-basemap/package.py

Versions:

1.2.0, 1.0.7

Build Dependencies:

python, 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:

https://pypi.python.org/pypi/bcbio-gff/0.6.2

Spack package:

py-bcbio-gff/package.py

Versions:

0.6.2

Build Dependencies:

python, py-setuptools, py-six, py-biopython

Link Dependencies:

Run Dependencies:

python, py-six, py-biopython

Description:

Read and write Generic Feature Format (GFF) with Biopython integration.

py-beautifulsoup4¶

Homepage:

https://www.crummy.com/software/BeautifulSoup

Spack package:

py-beautifulsoup4/package.py

Versions:

4.5.3, 4.5.1, 4.4.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

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-binwalk¶

Homepage:

https://github.com/devttys0/binwalk

Spack package:

py-binwalk/package.py

Versions:

2.1.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Binwalk is a fast, easy to use tool for analyzing, reverse engineering, and extracting firmware images.

py-biom-format¶

Homepage:

https://pypi.python.org/pypi/biom-format/2.1.6

Spack package:

py-biom-format/package.py

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:

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:

https://github.com/AdamDS/BioMine

Spack package:

py-biomine/package.py

Versions:

0.9.5

Build Dependencies:

python, py-advancedhtmlparser, py-pysam, py-pyvcf, py-requests

Link Dependencies:

Run Dependencies:

python, py-advancedhtmlparser, py-pysam, py-pyvcf, py-requests

Description:

Bioinformatics data-mining.

py-biopython¶

Homepage:

http://biopython.org/wiki/Main_Page

Spack package:

py-biopython/package.py

Versions:

1.73, 1.70, 1.65

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

https://pypi.python.org/pypi/bitarray

Spack package:

py-bitarray/package.py

Versions:

0.8.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Efficient array of booleans - C extension

py-bitstring¶

Homepage:

http://pythonhosted.org/bitstring

Spack package:

py-bitstring/package.py

Versions:

3.1.5

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Simple construction, analysis and modification of binary data.

py-black¶

Homepage:

https://github.com/ambv/black

Spack package:

py-black/package.py

Versions:

18.9b0

Build Dependencies:

python, py-setuptools, py-attrs, py-click, py-appdirs, py-toml

Link Dependencies:

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:

http://github.com/mozilla/bleach

Spack package:

py-bleach/package.py

Versions:

1.5.0

Build Dependencies:

python, py-setuptools, py-six, py-html5lib

Link Dependencies:

Run Dependencies:

python, py-six, py-html5lib

Description:

An easy whitelist-based HTML-sanitizing tool.

py-blessings¶

Homepage:

https://github.com/erikrose/blessings

Spack package:

py-blessings/package.py

Versions:

1.6

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

A nicer, kinder way to write to the terminal

py-bokeh¶

Homepage:

http://github.com/bokeh/bokeh

Spack package:

py-bokeh/package.py

Versions:

0.12.2

Build Dependencies:

python, py-six, py-requests, py-pyyaml, py-dateutil, py-jinja2, py-numpy, py-tornado, py-futures

Link Dependencies:

Run Dependencies:

python, py-six, py-requests, py-pyyaml, py-dateutil, py-jinja2, py-numpy, py-tornado, py-futures

Description:

Statistical and novel interactive HTML plots for Python

py-boltons¶

Homepage:

https://boltons.readthedocs.io/

Spack package:

py-boltons/package.py

Versions:

16.5.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

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-bottleneck¶

Homepage:

https://pypi.python.org/pypi/Bottleneck/1.0.0

Spack package:

py-bottleneck/package.py

Versions:

1.2.1, 1.0.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

A collection of fast NumPy array functions written in Cython.

py-breakseq2¶

Homepage:

http://bioinform.github.io/breakseq2/

Spack package:

py-breakseq2/package.py

Versions:

2.2

Build Dependencies:

python, py-setuptools, py-biopython, py-cython, py-pysam

Link Dependencies:

Run Dependencies:

python, py-biopython, py-pysam, bwa, samtools

Description:

nucleotide-resolution analysis of structural variants

py-breathe¶

Homepage:

https://github.com/michaeljones/breathe

Spack package:

py-breathe/package.py

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:

http://www.briansimulator.org

Spack package:

py-brian/package.py

Versions:

1.4.3

Build Dependencies:

python, py-matplotlib, py-numpy, py-scipy

Link Dependencies:

Run Dependencies:

python, py-matplotlib, py-numpy, py-scipy

Description:

A clock-driven simulator for spiking neural networks

py-brian2¶

Homepage:

http://www.briansimulator.org

Spack package:

py-brian2/package.py

Versions:

2.0.1, 2.0rc3

Build Dependencies:

python, py-setuptools, py-numpy, py-sympy, py-pyparsing, py-jinja2, py-cpuinfo, py-sphinx

Link Dependencies:

Run Dependencies:

python, py-numpy, py-sympy, py-pyparsing, py-jinja2, py-cpuinfo, py-sphinx

Test Dependencies:

py-nosetests

Description:

A clock-driven simulator for spiking neural networks

py-bsddb3¶

Homepage:

https://pypi.python.org/pypi/bsddb3/6.2.5

Spack package:

py-bsddb3/package.py

Versions:

6.2.5

Build Dependencies:

python, py-setuptools, berkeley-db

Link Dependencies:

python, berkeley-db

Run Dependencies:

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:

https://github.com/bxlab/bx-python

Spack package:

py-bx-python/package.py

Versions:

0.7.4

Build Dependencies:

python, py-setuptools, py-numpy, py-six

Link Dependencies:

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-cartopy¶

Homepage:

http://scitools.org.uk/cartopy/

Spack package:

py-cartopy/package.py

Versions:

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-mock, py-pytest

Description:

Cartopy - a cartographic python library with matplotlib support.

py-cclib¶

Homepage:

https://cclib.github.io/

Spack package:

py-cclib/package.py

Versions:

1.5.post1

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Open source library for parsing and interpreting the results of computational chemistry packages

py-cdat-lite¶

Homepage:

http://proj.badc.rl.ac.uk/cedaservices/wiki/CdatLite

Spack package:

py-cdat-lite/package.py

Versions:

6.0.1

Build Dependencies:

python, netcdf, py-numpy, py-setuptools

Link Dependencies:

python, netcdf

Run Dependencies:

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:

https://pypi.python.org/pypi/cdo

Spack package:

py-cdo/package.py

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-certifi¶

Homepage:

http://certifi.io/

Spack package:

py-certifi/package.py

Versions:

2017.4.17, 2017.1.23, 2016.02.28

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Certifi: A carefully curated collection of Root Certificates for validating the trustworthiness of SSL certificates while verifying the identity of TLS hosts.

py-cffi¶

Homepage:

http://cffi.readthedocs.org/en/latest/

Spack package:

py-cffi/package.py

Versions:

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

Description:

Foreign Function Interface for Python calling C code

py-cftime¶

Homepage:

https://unidata.github.io/cftime/

Spack package:

py-cftime/package.py

Versions:

1.0.3.4

Build Dependencies:

python, py-setuptools, py-cython, py-numpy

Link Dependencies:

Run Dependencies:

Description:

Python library for decoding time units and variable values in a netCDF file conforming to the Climate and Forecasting (CF) netCDF conventions

py-chardet¶

Homepage:

https://github.com/chardet/chardet

Spack package:

py-chardet/package.py

Versions:

3.0.2, 2.3.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Universal encoding detector for Python 2 and 3

py-checkm-genome¶

Homepage:

https://ecogenomics.github.io/CheckM

Spack package:

py-checkm-genome/package.py

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:

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:

https://pypi.python.org/pypi/Cheetah/2.4.4

Spack package:

py-cheetah/package.py

Versions:

2.3.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Cheetah is a template engine and code generation tool.

py-click¶

Homepage:

http://github.com/mitsuhiko/click

Spack package:

py-click/package.py

Versions:

6.6

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

A simple wrapper around optparse for powerful command line utilities.

py-click-plugins¶

Homepage:

https://pypi.org/project/click-plugins/

Spack package:

py-click-plugins/package.py

Versions:

1.0.4

Build Dependencies:

python, py-setuptools, py-click

Link Dependencies:

Run Dependencies:

python, py-click

Description:

An extension module for py-click to register external CLI commands via setuptools entry-points.

py-cligj¶

Homepage:

https://github.com/mapbox/cligj

Spack package:

py-cligj/package.py

Versions:

0.4.0

Build Dependencies:

python, py-setuptools, py-click

Link Dependencies:

Run Dependencies:

python, py-click

Description:

Click-based argument and option decorators for Python GIS command line programs

py-cloudpickle¶

Homepage:

https://github.com/cloudpipe/cloudpickle

Spack package:

py-cloudpickle/package.py

Versions:

0.5.2

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Extended pickling support for Python objects.

py-cogent¶

Homepage:

http://pycogent.org

Spack package:

py-cogent/package.py

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:

https://github.com/tartley/colorama

Spack package:

py-colorama/package.py

Versions:

0.3.7

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Cross-platform colored terminal text.

py-colormath¶

Homepage:

https://pypi.python.org/pypi/colormath/2.1.1

Spack package:

py-colormath/package.py

Versions:

3.0.0, 2.1.1

Build Dependencies:

python, py-setuptools, py-numpy, py-networkx

Link Dependencies:

Run Dependencies:

python, py-numpy, py-networkx

Description:

Color math and conversion library.

py-configparser¶

Homepage:

https://docs.python.org/3/library/configparser.html

Spack package:

py-configparser/package.py

Versions:

3.5.1, 3.5.0

Build Dependencies:

python, py-setuptools, py-ordereddict

Link Dependencies:

Run Dependencies:

python, py-ordereddict

Description:

This library brings the updated configparser from Python 3.5 to Python 2.6-3.5.

py-counter¶

Homepage:

https://github.com/KelSolaar/Counter

Spack package:

py-counter/package.py

Versions:

1.0.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Counter package defines the "counter.Counter" class similar to bags or multisets in other languages.

py-coverage¶

Homepage:

http://nedbatchelder.com/code/coverage/

Spack package:

py-coverage/package.py

Versions:

4.3.4, 4.0a6

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Testing coverage checker for python

py-cpuinfo¶

Homepage:

https://github.com/workhorsy/py-cpuinfo

Spack package:

py-cpuinfo/package.py

Versions:

0.2.3

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Get CPU info with pure Python 2 & 3

py-crispresso¶

Homepage:

https://github.com/lucapinello/CRISPResso

Spack package:

py-crispresso/package.py

Versions:

1.0.8

Build Dependencies:

python, py-setuptools, py-biopython, py-matplotlib, py-numpy, py-pandas, py-seaborn, emboss, flash, java

Link Dependencies:

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:

http://crossmap.sourceforge.net/

Spack package:

py-crossmap/package.py

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:

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:

https://pypi.python.org/pypi/cryptography

Spack package:

py-cryptography/package.py

Versions:

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-csvkit¶

Homepage:

http://csvkit.rtfd.org/

Spack package:

py-csvkit/package.py

Versions:

0.9.1

Build Dependencies:

python, py-setuptools, py-dateutil, py-dbf, py-xlrd, py-sqlalchemy, py-six, py-openpyxl

Link Dependencies:

Run Dependencies:

python, py-dateutil, py-dbf, py-xlrd, py-sqlalchemy, py-six, py-openpyxl

Description:

A library of utilities for working with CSV, the king of tabular file formats

py-current¶

Homepage:

http://github.com/xflr6/current

Spack package:

py-current/package.py

Versions:

0.3.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Current module relative paths and imports

py-cutadapt¶

Homepage:

https://cutadapt.readthedocs.io

Spack package:

py-cutadapt/package.py

Versions:

1.13

Build Dependencies:

python, py-setuptools, py-xopen

Link Dependencies:

Run Dependencies:

python, py-setuptools, py-xopen

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:

http://cvxopt.org/

Spack package:

py-cvxopt/package.py

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:

Description:

CVXOPT is a free software package for convex optimization based on the Python programming language.

py-cycler¶

Homepage:

http://matplotlib.org/cycler/

Spack package:

py-cycler/package.py

Versions:

0.10.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Composable style cycles.

py-cython¶

Homepage:

https://pypi.python.org/pypi/cython

Spack package:

py-cython/package.py

Versions:

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, 0.22, 0.21.2

Build Dependencies:

Link Dependencies:

Run Dependencies:

Test Dependencies:

gdb

Description:

The Cython compiler for writing C extensions for the Python language.

py-dask¶

Homepage:

https://github.com/dask/dask/

Spack package:

py-dask/package.py

Versions:

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

Link Dependencies:

Run Dependencies:

python, py-numpy, py-toolz, py-cloudpickle, py-partd, py-pandas

Test Dependencies:

py-pytest, py-requests

Description:

Dask is a flexible parallel computing library for analytics.

py-dateutil¶

Homepage:

https://pypi.python.org/pypi/dateutil

Spack package:

py-dateutil/package.py

Versions:

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:

Run Dependencies:

Description:

Extensions to the standard Python datetime module.

py-dbf¶

Homepage:

https://pypi.python.org/pypi/dbf

Spack package:

py-dbf/package.py

Versions:

0.96.005, 0.94.003

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Pure python package for reading/writing dBase, FoxPro, and Visual FoxPro .dbf files (including memos)

py-decorator¶

Homepage:

https://github.com/micheles/decorator

Spack package:

py-decorator/package.py

Versions:

4.3.0, 4.0.9

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

https://pypi.io/packages/source/d/deepTools

Spack package:

py-deeptools/package.py

Versions:

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

Link Dependencies:

Run Dependencies:

python, py-numpy, py-scipy, py-py2bit, py-pybigwig, py-pysam, py-matplotlib, py-numpydoc

Description:

deepTools addresses the challenge of handling the large amounts of data that are now routinely generated from DNA sequencing centers.

py-dendropy¶

Homepage:

https://www.dendropy.org

Spack package:

py-dendropy/package.py

Versions:

4.3.0, 3.12.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

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-descartes¶

Homepage:

https://pypi.org/project/descartes/

Spack package:

py-descartes/package.py

Versions:

1.1.0

Build Dependencies:

python, py-setuptools, py-matplotlib

Link Dependencies:

Run Dependencies:

python, py-matplotlib

Description:

Use Shapely or GeoJSON-like geometric objects as matplotlib paths and patches

py-dill¶

Homepage:

https://github.com/uqfoundation/dill

Spack package:

py-dill/package.py

Versions:

0.2.6, 0.2.5, 0.2.4, 0.2.3, 0.2.2, 0.2.1, 0.2

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Serialize all of python

py-discover¶

Homepage:

https://pypi.python.org/pypi/discover

Spack package:

py-discover/package.py

Versions:

0.4.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Test discovery for unittest.

py-dlcpar¶

Homepage:

https://www.cs.hmc.edu/~yjw/software/dlcpar/

Spack package:

py-dlcpar/package.py

Versions:

1.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

DLCpar is a reconciliation method for inferring gene duplications, losses, and coalescence (accounting for incomplete lineage sorting).

py-docopt¶

Homepage:

http://docopt.org/

Spack package:

py-docopt/package.py

Versions:

0.6.2

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Command-line interface description language.

py-docutils¶

Homepage:

http://docutils.sourceforge.net/

Spack package:

py-docutils/package.py

Versions:

0.14, 0.13.1, 0.12

Build Dependencies:

Link Dependencies:

Run Dependencies:

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-doxypy¶

Homepage:

https://pypi.python.org/pypi/doxypy

Spack package:

py-doxypy/package.py

Versions:

0.3

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

doxypy is an input filter for Doxygen.

py-doxypypy¶

Homepage:

https://github.com/Feneric/doxypypy

Spack package:

py-doxypypy/package.py

Versions:

0.8.8.6

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

A Doxygen filter for Python. A more Pythonic version of doxypy, a Doxygen filter for Python.

py-dryscrape¶

Homepage:

https://github.com/niklasb/dryscrape

Spack package:

py-dryscrape/package.py

Versions:

develop, 1.0

Build Dependencies:

python, py-lxml, py-webkit-server, py-xvfbwrapper

Link Dependencies:

Run Dependencies:

python, py-lxml, py-webkit-server, py-xvfbwrapper

Description:

a lightweight Javascript-aware, headless web scraping library for Python

py-dxchange¶

Homepage:

https://github.com/data-exchange/dxchange

Spack package:

py-dxchange/package.py

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:

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:

https://github.com/data-exchange/dxfile

Spack package:

py-dxfile/package.py

Versions:

0.4

Build Dependencies:

python, py-setuptools, py-h5py

Link Dependencies:

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-easybuild-easyblocks¶

Homepage:

http://hpcugent.github.io/easybuild/

Spack package:

py-easybuild-easyblocks/package.py

Versions:

3.1.2

Build Dependencies:

Link Dependencies:

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:

http://hpcugent.github.io/easybuild/

Spack package:

py-easybuild-easyconfigs/package.py

Versions:

3.1.2

Build Dependencies:

Link Dependencies:

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:

http://hpcugent.github.io/easybuild/

Spack package:

py-easybuild-framework/package.py

Versions:

3.1.2

Build Dependencies:

Link Dependencies:

Run Dependencies:

python, py-setuptools, py-vsc-base, py-vsc-install

Description:

The core of EasyBuild, a software build and installation framework for (scientific) software on HPC systems.

py-edffile¶

Homepage:

https://github.com/vasole/pymca/blob/master/PyMca5/PyMcaIO/EdfFile.py

Spack package:

py-edffile/package.py

Versions:

5.0.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Generic class for Edf files manipulation.

py-editdistance¶

Homepage:

https://github.com/aflc/editdistance

Spack package:

py-editdistance/package.py

Versions:

0.4

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Fast implementation of the edit distance (Levenshtein distance).

py-elasticsearch¶

Homepage:

https://github.com/elastic/elasticsearch-py

Spack package:

py-elasticsearch/package.py

Versions:

5.2.0, 2.3.0

Build Dependencies:

python, py-setuptools, py-urllib3

Link Dependencies:

Run Dependencies:

python, py-urllib3

Description:

Python client for Elasticsearch

py-elephant¶

Homepage:

http://neuralensemble.org/elephant

Spack package:

py-elephant/package.py

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:

Run Dependencies:

python, py-neo, py-numpy, py-quantities, py-scipy, py-pandas, py-numpydoc, py-sphinx

Test Dependencies:

Description:

Elephant is a package for analysis of electrophysiology data in Python

py-emcee¶

Homepage:

http://dan.iel.fm/emcee/current/

Spack package:

py-emcee/package.py

Versions:

2.1.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

emcee is an MIT licensed pure-Python implementation of Goodman & Weare's Affine Invariant Markov chain Monte Carlo (MCMC) Ensemble sampler.

py-entrypoints¶

Homepage:

https://pypi.python.org/pypi/entrypoints

Spack package:

py-entrypoints/package.py

Versions:

0.3, 0.2.3

Build Dependencies:

python, py-configparser

Link Dependencies:

Run Dependencies:

python, py-configparser

Description:

Discover and load entry points from installed packages.

py-enum34¶

Homepage:

https://pypi.python.org/pypi/enum34

Spack package:

py-enum34/package.py

Versions:

1.1.6

Build Dependencies:

python, py-ordereddict, py-setuptools

Link Dependencies:

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:

https://pypi.python.org/pypi/epydoc

Spack package:

py-epydoc/package.py

Versions:

3.0.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Epydoc is a tool for generating API documentation documentation for Python modules, based on their docstrings.

py-espresso¶

Homepage:

http://espressomd.org/

Spack package:

py-espresso/package.py

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:

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:

https://espressopp.github.io

Spack package:

py-espressopp/package.py

Versions:

develop, 2.0.2, 1.9.5, 1.9.4.1, 1.9.4

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:

https://bitbucket.org/openpyxl/et_xmlfile

Spack package:

py-et-xmlfile/package.py

Versions:

1.0.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

An implementation of lxml.xmlfile for the standard library.

py-eventlet¶

Homepage:

https://github.com/eventlet/eventlet

Spack package:

py-eventlet/package.py

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:

http://codespeak.net/execnet

Spack package:

py-execnet/package.py

Versions:

1.4.1

Build Dependencies:

python, py-setuptools, py-setuptools-scm, py-apipkg

Link Dependencies:

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-fastaindex¶

Homepage:

https://github.com/lpryszcz/FastaIndex

Spack package:

py-fastaindex/package.py

Versions:

0.11rc7

Build Dependencies:

Link Dependencies:

Run Dependencies:

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-fasteners¶

Homepage:

https://github.com/harlowja/fasteners

Spack package:

py-fasteners/package.py

Versions:

0.14.1

Build Dependencies:

python, py-setuptools, py-monotonic, py-six

Link Dependencies:

Run Dependencies:

python, py-monotonic, py-six

Description:

A python package that provides useful locks.

py-faststructure¶

Homepage:

https://github.com/rajanil/fastStructure

Spack package:

py-faststructure/package.py

Versions:

1.0

Build Dependencies:

python, py-cython, py-numpy, gsl

Link Dependencies:

python, gsl

Run Dependencies:

Description:

FastStructure is a fast algorithm for inferring population structure from large SNP genotype data.

py-filelock¶

Homepage:

https://github.com/benediktschmitt/py-filelock

Spack package:

py-filelock/package.py

Versions:

3.0.4, 3.0.3, 3.0.1, 3.0.0, 2.0.13, 2.0.12, 2.0.11, 2.0.10, 2.0.9, 2.0.8

Build Dependencies:

Link Dependencies:

Run Dependencies:

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-fiona¶

Homepage:

http://toblerity.org/fiona/

Spack package:

py-fiona/package.py

Versions:

1.7.12

Build Dependencies:

python, py-cligj, py-six, py-munch, py-argparse, py-ordereddict, gdal, py-click-plugins, py-setuptools, py-cython

Link Dependencies:

Run Dependencies:

python, py-cligj, py-six, py-munch, py-argparse, py-ordereddict, gdal, py-click-plugins

Test Dependencies:

Description:

Alternative Python binding for OGR

py-fiscalyear¶

Homepage:

https://github.com/adamjstewart/fiscalyear

Spack package:

py-fiscalyear/package.py

Versions:

master, 0.1.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Test Dependencies:

py-pytest, py-pytest-runner

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-flake8¶

Homepage:

https://github.com/PyCQA/flake8

Spack package:

py-flake8/package.py

Versions:

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-configparser, py-enum34, py-functools32, py-typing

Link Dependencies:

Run Dependencies:

python, py-setuptools, py-entrypoints, py-pyflakes, py-pycodestyle, py-mccabe, py-configparser, py-enum34, py-functools32, py-typing

Test Dependencies:

Description:

Flake8 is a wrapper around PyFlakes, pep8 and Ned Batchelder's McCabe script.

py-flake8-polyfill¶

Homepage:

https://pypi.org/project/flake8-polyfill/

Spack package:

py-flake8-polyfill/package.py

Versions:

1.0.2

Build Dependencies:

Link Dependencies:

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:

http://github.com/pallets/flask

Spack package:

py-flask/package.py

Versions:

0.12.2, 0.12.1, 0.11.1

Build Dependencies:

python, py-setuptools, py-werkzeug, py-jinja2, py-itsdangerous, py-click

Link Dependencies:

Run Dependencies:

python, py-werkzeug, py-jinja2, py-itsdangerous, py-click

Description:

A microframework based on Werkzeug, Jinja2 and good intentions

py-flask-compress¶

Homepage:

https://github.com/libwilliam/flask-compress

Spack package:

py-flask-compress/package.py

Versions:

1.4.0

Build Dependencies:

python, py-setuptools, py-flask

Link Dependencies:

Run Dependencies:

python, py-flask

Description:

Flask-Compress allows you to easily compress your Flask application's responses with gzip.

py-flask-socketio¶

Homepage:

https://flask-socketio.readthedocs.io

Spack package:

py-flask-socketio/package.py

Versions:

2.9.6

Build Dependencies:

python, py-setuptools, py-flask, py-python-socketio, py-werkzeug

Link Dependencies:

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:

http://flexx.readthedocs.io

Spack package:

py-flexx/package.py

Versions:

0.4.1

Build Dependencies:

python, py-setuptools, py-tornado

Link Dependencies:

Run Dependencies:

python, py-tornado

Description:

Write desktop and web apps in pure Python.

py-fn¶

Homepage:

https://github.com/fnpy/fn.py

Spack package:

py-fn/package.py

Versions:

0.5.2

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Functional programming in Python: implementation of missing features to enjoy FP.

py-fparser¶

Homepage:

https://github.com/stfc/fparser

Spack package:

py-fparser/package.py

Versions:

develop, 0.0.6, 0.0.5

Build Dependencies:

python, py-setuptools, py-numpy, py-nose, py-six

Link Dependencies:

Run Dependencies:

Test Dependencies:

Description:

Parser for Fortran 77..2003 code.

py-funcsigs¶

Homepage:

https://pypi.python.org/pypi/funcsigs

Spack package:

py-funcsigs/package.py

Versions:

1.0.2, 0.4

Build Dependencies:

Link Dependencies:

Run Dependencies:

Test Dependencies:

py-unittest2

Description:

Python function signatures from PEP362 for Python 2.6, 2.7 and 3.2.

py-functools32¶

Homepage:

https://github.com/MiCHiLU/python-functools32

Spack package:

py-functools32/package.py

Versions:

3.2.3-2

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Backport of the functools module from Python 3.2.3 for use on 2.7 and PyPy.

py-future¶

Homepage:

https://python-future.org/

Spack package:

py-future/package.py

Versions:

0.16.0, 0.15.2

Build Dependencies:

python, py-setuptools, py-importlib, py-argparse

Link Dependencies:

Run Dependencies:

python, py-importlib, py-argparse

Description:

Clean single-source support for Python 3 and 2

py-futures¶

Homepage:

https://pypi.python.org/pypi/futures

Spack package:

py-futures/package.py

Versions:

3.0.5

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Backport of the concurrent.futures package from Python 3.2

py-fypp¶

Homepage:

https://github.com/aradi/fypp

Spack package:

py-fypp/package.py

Versions:

2.1.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Python powered Fortran preprocessor.

py-gdbgui¶

Homepage:

https://gdbgui.com

Spack package:

py-gdbgui/package.py

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:

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-genders¶

Homepage:

https://github.com/chaos/genders

Spack package:

py-genders/package.py

Versions:

1.22

Build Dependencies:

Link Dependencies:

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:

https://genshi.edgewall.org/

Spack package:

py-genshi/package.py

Versions:

0.7, 0.6.1, 0.6

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Python toolkit for generation of output for the web

py-geopandas¶

Homepage:

http://geopandas.org/

Spack package:

py-geopandas/package.py

Versions:

0.4.0, 0.3.0

Build Dependencies:

python, py-setuptools, py-descartes, py-matplotlib, py-fiona, py-pyproj, py-shapely, py-pandas

Link Dependencies:

Run Dependencies:

python, py-descartes, py-matplotlib, py-fiona, py-pyproj, py-shapely, py-pandas

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:

http://www.gevent.org

Spack package:

py-gevent/package.py

Versions:

1.3a2

Build Dependencies:

python, py-setuptools, py-cython, py-cffi, py-greenlet

Link Dependencies:

Run Dependencies:

python, py-cffi, py-greenlet

Description:

gevent is a coroutine-based Python networking library.

py-git-review¶

Homepage:

http://docs.openstack.org/infra/git-review

Spack package:

py-git-review/package.py

Versions:

1.26.0, 1.25.0, 1.24, 1.23, 1.22, 1.21

Build Dependencies:

python, py-setuptools, py-pbr, py-requests

Link Dependencies:

Run Dependencies:

python, py-pbr, py-requests, git, tk

Description:

git-review is a tool that helps submitting git branches to gerrit

py-git2¶

Homepage:

http://www.pygit2.org/

Spack package:

py-git2/package.py

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-gnuplot¶

Homepage:

http://gnuplot-py.sourceforge.net/

Spack package:

py-gnuplot/package.py

Versions:

1.8

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Gnuplot.py is a Python package that allows you to create graphs from within Python using the gnuplot plotting program.

py-goatools¶

Homepage:

https://github.com/tanghaibao/goatools

Spack package:

py-goatools/package.py

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:

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-gpaw¶

Homepage:

https://wiki.fysik.dtu.dk/gpaw/index.html

Spack package:

py-gpaw/package.py

Versions:

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:

https://github.com/xflr6/graphviz

Spack package:

py-graphviz/package.py

Versions:

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:

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:

https://github.com/python-greenlet/greenlet

Spack package:

py-greenlet/package.py

Versions:

0.4.13

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Lightweight in-process concurrent programming

py-griddataformats¶

Homepage:

http://www.mdanalysis.org/GridDataFormats

Spack package:

py-griddataformats/package.py

Versions:

0.3.3

Build Dependencies:

python, py-setuptools, py-numpy, py-six

Link Dependencies:

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-guidata¶

Homepage:

https://github.com/PierreRaybaut/guidata

Spack package:

py-guidata/package.py

Versions:

1.7.5

Build Dependencies:

python, py-setuptools, py-pyqt, py-spyder, py-h5py

Link Dependencies:

Run Dependencies:

python, py-pyqt, py-spyder, py-h5py

Description:

Automatic graphical user interfaces generation for easy dataset editing and display

py-guiqwt¶

Homepage:

https://github.com/PierreRaybaut/guiqwt

Spack package:

py-guiqwt/package.py

Versions:

3.0.2

Build Dependencies:

python, py-setuptools, py-numpy, py-scipy, py-guidata, py-pythonqwt, py-pillow

Link Dependencies:

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:

https://github.com/European-XFEL/h5glance

Spack package:

py-h5glance/package.py

Versions:

0.4

Build Dependencies:

python, py-h5py

Link Dependencies:

Run Dependencies:

python, py-h5py, py-python-htmlgen

Description:

H5Glance lets you explore HDF5 files in the terminal or an HTML interface.

py-h5py¶

Homepage:

http://www.h5py.org/

Spack package:

py-h5py/package.py

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-hdfs¶

Homepage:

https://hdfscli.readthedocs.io/en/latest/

Spack package:

py-hdfs/package.py

Versions:

2.1.0

Build Dependencies:

python, py-setuptools, py-docopt, py-requests, py-six

Link Dependencies:

Run Dependencies:

python, py-docopt, py-requests, py-six

Description:

API and command line interface for HDFS

py-hepdata-validator¶

Homepage:

https://github.com/hepdata/hepdata-validator

Spack package:

py-hepdata-validator/package.py

Versions:

0.1.16, 0.1.15, 0.1.14, 0.1.8

Build Dependencies:

python, py-setuptools, py-jsonschema, py-pyyaml

Link Dependencies:

Run Dependencies:

python, py-jsonschema, py-pyyaml

Description:

Validation schema and code for HEPdata submissions.

py-hpccm¶

Homepage:

https://github.com/NVIDIA/hpc-container-maker

Spack package:

py-hpccm/package.py

Versions:

19.2.0

Build Dependencies:

python, py-setuptools, py-enum34, py-six

Link Dependencies:

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:

https://github.com/Alir3z4/html2text/

Spack package:

py-html2text/package.py

Versions:

2016.9.19

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Turn HTML into equivalent Markdown-structured text.

py-html5lib¶

Homepage:

https://github.com/html5lib/html5lib-python

Spack package:

py-html5lib/package.py

Versions:

1.0.1, 0.9999999

Build Dependencies:

python, py-six, py-setuptools, py-webencodings

Link Dependencies:

Run Dependencies:

python, py-six, py-webencodings

Description:

HTML parser based on the WHATWG HTML specification.

py-htseq¶

Homepage:

http://htseq.readthedocs.io/en/release_0.9.1/overview.html

Spack package:

py-htseq/package.py

Versions:

0.11.2, 0.9.1

Build Dependencies:

python, py-setuptools, py-numpy, py-pysam, py-matplotlib, py-cython, swig

Link Dependencies:

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:

https://github.com/Runscope/httpbin

Spack package:

py-httpbin/package.py

Versions:

0.5.0

Build Dependencies:

python, py-setuptools, py-decorator, py-flask, py-itsdangerous, py-markupsafe, py-six

Link Dependencies:

Run Dependencies:

python, py-decorator, py-flask, py-itsdangerous, py-markupsafe, py-six

Description:

HTTP Request and Response Service

py-hypothesis¶

Homepage:

https://github.com/HypothesisWorks/hypothesis-python

Spack package:

py-hypothesis/package.py

Versions:

4.7.2, 3.7.0

Build Dependencies:

python, py-setuptools, py-enum34

Link Dependencies:

Run Dependencies:

python, py-enum34

Description:

A library for property based testing.

py-idna¶

Homepage:

https://github.com/kjd/idna

Spack package:

py-idna/package.py

Versions:

2.5

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Internationalized Domain Names for Python (IDNA 2008 and UTS #46)

py-igraph¶

Homepage:

http://igraph.org/

Spack package:

py-igraph/package.py

Versions:

0.7.0

Build Dependencies:

python, py-setuptools, igraph

Link Dependencies:

python, igraph

Run Dependencies:

Description:

igraph is a collection of network analysis tools with the emphasis on efficiency, portability and ease of use.

py-illumina-utils¶

Homepage:

https://github.com/meren/illumina-utils

Spack package:

py-illumina-utils/package.py

Versions:

2.3, 2.2

Build Dependencies:

python, py-pip, py-setuptools, py-matplotlib, py-numpy, py-python-levenshtein

Link Dependencies:

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:

http://imageio.github.io/

Spack package:

py-imageio/package.py

Versions:

2.3.0

Build Dependencies:

python, py-numpy, py-pillow, py-setuptools

Link Dependencies:

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:

https://github.com/shibukawa/imagesize_py

Spack package:

py-imagesize/package.py

Versions:

1.1.0, 0.7.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Parses image file headers and returns image size. Supports PNG, JPEG, JPEG2000, and GIF image file formats.

py-iminuit¶

Homepage:

https://pypi.python.org/pypi/iminuit

Spack package:

py-iminuit/package.py

Versions:

1.2

Build Dependencies:

python, py-setuptools, py-numpy, py-matplotlib, py-cython

Link Dependencies:

Run Dependencies:

python, py-numpy, py-matplotlib

Description:

Interactive IPython-Friendly Minimizer based on SEAL Minuit2.

py-importlib¶

Homepage:

https://github.com/brettcannon/importlib

Spack package:

py-importlib/package.py

Versions:

1.0.4

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Packaging for importlib from Python 2.7

py-invoke¶

Homepage:

http://www.pyinvoke.org/

Spack package:

py-invoke/package.py

Versions:

1.2.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Pythonic task execution

py-ipaddress¶

Homepage:

https://github.com/phihag/ipaddress

Spack package:

py-ipaddress/package.py

Versions:

1.0.18

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Python 3.3's ipaddress for older Python versions

py-ipdb¶

Homepage:

https://pypi.python.org/pypi/ipdb

Spack package:

py-ipdb/package.py

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:

Description:

ipdb is the iPython debugger and has many additional features, including a better interactive debugging experience via colorized output.

py-ipykernel¶

Homepage:

https://pypi.python.org/pypi/ipykernel

Spack package:

py-ipykernel/package.py

Versions:

5.1.0, 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:

Run Dependencies:

python, py-traitlets, py-tornado, py-ipython, py-jupyter-client, py-pexpect

Description:

IPython Kernel for Jupyter

py-ipython¶

Homepage:

https://pypi.python.org/pypi/ipython

Spack package:

py-ipython/package.py

Versions:

7.3.0, 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

Link Dependencies:

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

Description:

IPython provides a rich toolkit to help you make the most out of using Python interactively.

py-ipython-genutils¶

Homepage:

https://pypi.python.org/pypi/ipython_genutils

Spack package:

py-ipython-genutils/package.py

Versions:

0.2.0, 0.1.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Vestigial utilities from IPython

py-ipywidgets¶

Homepage:

https://github.com/ipython/ipywidgets

Spack package:

py-ipywidgets/package.py

Versions:

5.2.2

Build Dependencies:

python, py-ipython, py-ipykernel, py-traitlets

Link Dependencies:

Run Dependencies:

python, py-ipython, py-ipykernel, py-traitlets

Description:

IPython widgets for the Jupyter Notebook

py-isort¶

Homepage:

https://github.com/timothycrosley/isort

Spack package:

py-isort/package.py

Versions:

4.2.15

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

A Python utility / library to sort Python imports.

py-itsdangerous¶

Homepage:

http://github.com/mitsuhiko/itsdangerous

Spack package:

py-itsdangerous/package.py

Versions:

0.24

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Various helpers to pass trusted data to untrusted environments.

py-jdcal¶

Homepage:

http://github.com/phn/jdcal

Spack package:

py-jdcal/package.py

Versions:

1.3, 1.2

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Julian dates from proleptic Gregorian and Julian calendars

py-jedi¶

Homepage:

https://github.com/davidhalter/jedi

Spack package:

py-jedi/package.py

Versions:

0.10.0, 0.9.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

An autocompletion tool for Python that can be used for text editors.

py-jinja2¶

Homepage:

http://jinja.pocoo.org/

Spack package:

py-jinja2/package.py

Versions:

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:

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-joblib¶

Homepage:

http://packages.python.org/joblib/

Spack package:

py-joblib/package.py

Versions:

0.13.2, 0.10.3, 0.10.2, 0.10.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Python function as pipeline jobs

py-jprops¶

Homepage:

https://github.com/mgood/jprops/

Spack package:

py-jprops/package.py

Versions:

2.0.2

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Java properties file parser for Python

py-jpype¶

Homepage:

https://github.com/originell/jpype

Spack package:

py-jpype/package.py

Versions:

0.6.2, 0.6.1, 0.6.0

Build Dependencies:

python, py-setuptools, java

Link Dependencies:

Run Dependencies:

python, java

Description:

JPype is an effort to allow python programs full access to java class libraries.

py-jsonschema¶

Homepage:

http://github.com/Julian/jsonschema

Spack package:

py-jsonschema/package.py

Versions:

2.5.1

Build Dependencies:

python, py-setuptools, py-vcversioner, py-functools32

Link Dependencies:

Run Dependencies:

python, py-vcversioner, py-functools32

Description:

Jsonschema: An(other) implementation of JSON Schema for Python.

py-junit-xml¶

Homepage:

https://github.com/kyrus/python-junit-xml

Spack package:

py-junit-xml/package.py

Versions:

1.7

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Creates JUnit XML test result documents that can be read by tools such as Jenkins

py-jupyter-client¶

Homepage:

https://github.com/jupyter/jupyter_client

Spack package:

py-jupyter-client/package.py

Versions:

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-zmq

Link Dependencies:

Run Dependencies:

python, py-traitlets, py-jupyter-core, py-zmq

Description:

Jupyter protocol client APIs

py-jupyter-console¶

Homepage:

https://github.com/jupyter/jupyter_console

Spack package:

py-jupyter-console/package.py

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:

Run Dependencies:

python, py-jupyter-client, py-ipython, py-ipykernel, py-pygments

Description:

Jupyter Terminal Console

py-jupyter-core¶

Homepage:

http://jupyter-core.readthedocs.io/

Spack package:

py-jupyter-core/package.py

Versions:

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

Build Dependencies:

python, py-traitlets

Link Dependencies:

Run Dependencies:

python, py-traitlets

Description:

Core Jupyter functionality

py-jupyter-notebook¶

Homepage:

https://github.com/jupyter/notebook

Spack package:

py-jupyter-notebook/package.py

Versions:

4.2.3, 4.2.2, 4.2.1, 4.2.0, 4.1.0, 4.0.6, 4.0.5, 4.0.4, 4.0.3, 4.0.2

Build Dependencies:

python, npm, node-js, py-jinja2, py-tornado, py-ipython-genutils, py-traitlets, py-jupyter-core, py-jupyter-client, py-jupyter-console, py-nbformat, py-nbconvert, py-ipykernel, py-terminado, py-ipywidgets

Link Dependencies:

Run Dependencies:

python, node-js, py-jinja2, py-tornado, py-ipython-genutils, py-traitlets, py-jupyter-core, py-jupyter-client, py-jupyter-console, py-nbformat, py-nbconvert, py-ipykernel, py-terminado, py-ipywidgets

Description:

Jupyter Interactive Notebook

py-jupyterhub¶

Homepage:

https://pypi.org/project/jupyterhub

Spack package:

py-jupyterhub/package.py

Versions:

0.9.4

Build Dependencies:

python, node-js, py-setuptools

Link Dependencies:

Run Dependencies:

python, node-js, py-dateutil, py-jinja2, py-sqlalchemy, py-tornado, py-traitlets, py-alembic, py-mako, py-async-generator, py-jupyter-notebook, py-prometheus-client, py-send2trash, py-requests

Description:

Multi-user server for Jupyter notebooks.

py-keras¶

Homepage:

http://keras.io

Spack package:

py-keras/package.py

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:

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:

http://keras.io

Spack package:

py-keras-applications/package.py

Versions:

1.0.7, 1.0.6, 1.0.4, 1.0.3, 1.0.2, 1.0.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Sample Deep Learning application in Keras. Keras depends on this package to run properly.

py-keras-preprocessing¶

Homepage:

http://keras.io

Spack package:

py-keras-preprocessing/package.py

Versions:

1.0.9, 1.0.5, 1.0.4, 1.0.3, 1.0.2, 1.0.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Utilities for working with image data, text data, and sequence data.

py-kiwisolver¶

Homepage:

https://github.com/nucleic/kiwi

Spack package:

py-kiwisolver/package.py

Versions:

1.0.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

A fast implementation of the Cassowary constraint solver

py-kmodes¶

Homepage:

https://github.com/nicodv/kmodes

Spack package:

py-kmodes/package.py

Versions:

0.10.1

Build Dependencies:

python, py-setuptools, py-numpy, py-scikit-learn, py-scipy, py-joblib

Link Dependencies:

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-lark-parser¶

Homepage:

https://github.com/lark-parser/lark/

Spack package:

py-lark-parser/package.py

Versions:

0.6.2

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Lark is a modern general-purpose parsing library for Python.

py-latexcodec¶

Homepage:

http://latexcodec.readthedocs.io

Spack package:

py-latexcodec/package.py

Versions:

1.0.4

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

A lexer and codec to work with LaTeX code in Python.

py-lazy¶

Homepage:

https://pypi.python.org/pypi/lazy

Spack package:

py-lazy/package.py

Versions:

1.2

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Lazy attributes for Python objects

py-lazy-object-proxy¶

Homepage:

https://github.com/ionelmc/python-lazy-object-proxy

Spack package:

py-lazy-object-proxy/package.py

Versions:

1.3.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

A fast and thorough lazy object proxy.

py-lazy-property¶

Homepage:

https://github.com/jackmaney/lazy-property

Spack package:

py-lazy-property/package.py

Versions:

0.0.1, 0.0.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

A package for making properties lazy

py-lazyarray¶

Homepage:

http://bitbucket.org/apdavison/lazyarray/

Spack package:

py-lazyarray/package.py

Versions:

0.2.10, 0.2.8

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

a Python package that provides a lazily-evaluated numerical array class, larray, based on and compatible with NumPy arrays.

py-libconf¶

Homepage:

https://pypi.python.org/pypi/libconf

Spack package:

py-libconf/package.py

Versions:

1.0.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

A pure-Python libconfig reader/writer with permissive license

py-libensemble¶

Homepage:

https://libensemble.readthedocs.io

Spack package:

py-libensemble/package.py

Versions:

develop, 0.5.0, 0.4.1, 0.4.0, 0.3.0, 0.2.0, 0.1.0

Build Dependencies:

python, py-setuptools, mpi, py-mpi4py, py-numpy, py-scipy, py-petsc4py, nlopt

Link Dependencies:

python, mpi

Run Dependencies:

python, py-mpi4py, py-numpy, py-scipy, py-petsc4py, nlopt

Description:

Library for managing ensemble-like collections of computations.

py-line-profiler¶

Homepage:

https://github.com/rkern/line_profiler

Spack package:

py-line-profiler/package.py

Versions:

2.0

Build Dependencies:

python, py-setuptools, py-cython, py-ipython

Link Dependencies:

Run Dependencies:

python, py-ipython

Description:

Line-by-line profiler.

py-linecache2¶

Homepage:

https://github.com/testing-cabal/linecache2

Spack package:

py-linecache2/package.py

Versions:

1.0.0

Build Dependencies:

python, py-setuptools, py-pbr

Link Dependencies:

Run Dependencies:

python, py-pbr

Description:

Backports of the linecache module

py-lit¶

Homepage:

https://pypi.python.org/pypi/lit

Spack package:

py-lit/package.py

Versions:

0.7.1, 0.5.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

http://llvmlite.readthedocs.io/en/latest/index.html

Spack package:

py-llvmlite/package.py

Versions:

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:

http://lmfit.github.io/lmfit-py/

Spack package:

py-lmfit/package.py

Versions:

0.9.5

Build Dependencies:

python, py-numpy, py-scipy, py-setuptools

Link Dependencies:

Run Dependencies:

Description:

Least-Squares Minimization with Bounds and Constraints

py-localcider¶

Homepage:

http://pappulab.github.io/localCIDER

Spack package:

py-localcider/package.py

Versions:

0.1.14

Build Dependencies:

python, py-setuptools, py-numpy, py-matplotlib, py-scipy

Link Dependencies:

Run Dependencies:

python, py-numpy, py-matplotlib, py-scipy

Description:

Tools for calculating sequence properties of disordered proteins

py-locket¶

Homepage:

http://github.com/mwilliamson/locket.py

Spack package:

py-locket/package.py

Versions:

0.2.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

File-based locks for Python for Linux and Windows.

py-lockfile¶

Homepage:

https://pypi.python.org/pypi/lockfile

Spack package:

py-lockfile/package.py

Versions:

0.10.2

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

https://www.logilab.org/project/logilab-common

Spack package:

py-logilab-common/package.py

Versions:

1.2.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Common modules used by Logilab projects

py-lrudict¶

Homepage:

https://github.com/amitdev/lru-dict

Spack package:

py-lrudict/package.py

Versions:

1.1.6

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

A fast LRU cache

py-luigi¶

Homepage:

https://github.com/spotify/luigi

Spack package:

py-luigi/package.py

Versions:

2.8.3

Build Dependencies:

python, py-setuptools, py-tornado, py-python-daemon, py-dateutil

Link Dependencies:

Run Dependencies:

python, py-tornado, py-python-daemon, py-dateutil

Test Dependencies:

py-test

Description:

Workflow mgmgt + task scheduling + dependency resolution

py-lxml¶

Homepage:

http://lxml.de/

Spack package:

py-lxml/package.py

Versions:

4.2.5, 3.7.3, 2.3

Build Dependencies:

python, py-setuptools, py-cython, libxml2, libxslt

Link Dependencies:

Run Dependencies:

python, libxml2, libxslt

Description:

lxml is the most feature-rich and easy-to-use library for processing XML and HTML in the Python language.

py-lzstring¶

Homepage:

https://github.com/gkovacs/lz-string-python

Spack package:

py-lzstring/package.py

Versions:

1.0.3

Build Dependencies:

python, py-setuptools, py-future

Link Dependencies:

Run Dependencies:

python, py-future

Description:

lz-string for python.

py-m2r¶

Homepage:

https://github.com/miyakogi/m2r

Spack package:

py-m2r/package.py

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:

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:

https://pypi.python.org/pypi/macholib

Spack package:

py-macholib/package.py

Versions:

1.8

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Python package for Mach-O header analysis and editing

py-machotools¶

Homepage:

https://pypi.python.org/pypi/machotools

Spack package:

py-machotools/package.py

Versions:

0.2.0

Build Dependencies:

python, py-setuptools, py-macholib

Link Dependencies:

Run Dependencies:

python, py-macholib

Description:

Python package for editing Mach-O headers using macholib

py-macs2¶

Homepage:

https://github.com/taoliu/MACS

Spack package:

py-macs2/package.py

Versions:

2.1.1.20160309

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

MACS2 Model-based Analysis of ChIP-Seq

py-maestrowf¶

Homepage:

https://github.com/LLNL/maestrowf/

Spack package:

py-maestrowf/package.py

Versions:

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:

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-mako¶

Homepage:

https://pypi.python.org/pypi/mako

Spack package:

py-mako/package.py

Versions:

1.0.4, 1.0.1

Build Dependencies:

python, py-setuptools, py-markupsafe

Link Dependencies:

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-mappy¶

Homepage:

https://pypi.python.org/pypi/mappy

Spack package:

py-mappy/package.py

Versions:

2.2

Build Dependencies:

python, zlib

Link Dependencies:

python, zlib

Run Dependencies:

Description:

Mappy provides a convenient interface to minimap2.

py-markdown¶

Homepage:

https://pythonhosted.org/Markdown/

Spack package:

py-markdown/package.py

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:

Link Dependencies:

Run Dependencies:

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:

http://www.pocoo.org/projects/markupsafe/

Spack package:

py-markupsafe/package.py

Versions:

1.0, 0.23, 0.22, 0.21, 0.20, 0.19

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

https://pypi.python.org/pypi/matplotlib

Spack package:

py-matplotlib/package.py

Versions:

3.0.2, 3.0.0, 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, py-setuptools, libpng, freetype, py-numpy, py-dateutil, py-pyparsing, py-pytz, py-cycler, py-subprocess32, py-functools32, py-kiwisolver, tk, qt, py-pyside, image-magick, pkgconfig, pil, py-ipython, qhull, py-six

Link Dependencies:

python, libpng, freetype, tk, qt, image-magick, qhull

Run Dependencies:

python, py-setuptools, py-numpy, py-dateutil, py-pyparsing, py-pytz, py-cycler, py-subprocess32, py-functools32, py-kiwisolver, py-pyside, pil, py-ipython, ghostscript, texlive, py-six

Test Dependencies:

py-nose, py-mock

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:

https://github.com/PyCQA/mccabe

Spack package:

py-mccabe/package.py

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:

Link Dependencies:

Run Dependencies:

Test Dependencies:

Description:

Ned's script to check McCabe complexity.

py-mdanalysis¶

Homepage:

http://www.mdanalysis.org

Spack package:

py-mdanalysis/package.py

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:

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-meep¶

Homepage:

https://launchpad.net/python-meep

Spack package:

py-meep/package.py

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-memory-profiler¶

Homepage:

https://github.com/fabianp/memory_profiler

Spack package:

py-memory-profiler/package.py

Versions:

0.47

Build Dependencies:

python, py-setuptools, py-psutil

Link Dependencies:

Run Dependencies:

python, py-psutil

Description:

A module for monitoring memory usage of a python program

py-merlin¶

Homepage:

https://pypi.org/project/merlin/

Spack package:

py-merlin/package.py

Versions:

1.8

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

A custom version of Phillip J. Eby's setuptools.

py-metasv¶

Homepage:

http://bioinform.github.io/metasv/

Spack package:

py-metasv/package.py

Versions:

0.5.4

Build Dependencies:

python, py-pybedtools, py-pysam, py-pyvcf, py-setuptools

Link Dependencies:

Run Dependencies:

python, py-pybedtools, py-pysam, py-pyvcf

Description:

An accurate and integrative structural-variant caller for next generation sequencing

py-methylcode¶

Homepage:

https://github.com/brentp/methylcode

Spack package:

py-methylcode/package.py

Versions:

1.0.0

Build Dependencies:

python, py-six, py-setuptools, py-numpy, py-pyparsing, py-pyfasta, py-bsddb3, bowtie

Link Dependencies:

python, py-six, py-setuptools, py-numpy, py-pyparsing, py-pyfasta, py-bsddb3, bowtie

Run Dependencies:

Description:

MethylCoder is a single program that takes of bisulfite-treated reads and outputs per-base methylation data.

py-mg-rast-tools¶

Homepage:

https://github.com/MG-RAST/MG-RAST-Tools

Spack package:

py-mg-rast-tools/package.py

Versions:

2018.04.17

Build Dependencies:

python, perl, py-setuptools, py-prettytable, py-poster, py-requests, py-requests-toolbelt, py-scipy, py-numpy, r-matr, shocklibs, perl-list-moreutils, perl-exporter-tiny, perl-libwww-perl, perl-http-message, perl-json

Link Dependencies:

python, shocklibs

Run Dependencies:

python, perl, py-prettytable, py-poster, py-requests, py-requests-toolbelt, py-scipy, py-numpy, r-matr, perl-list-moreutils, perl-exporter-tiny, perl-libwww-perl, perl-http-message, perl-json

Description:

Repository of scripts and libraries for using the MG-RAST API and MG- RAST data.

py-misopy¶

Homepage:

http://miso.readthedocs.io/en/fastmiso/

Spack package:

py-misopy/package.py

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:

http://mistune.readthedocs.org/en/latest/

Spack package:

py-mistune/package.py

Versions:

0.7.1, 0.7, 0.6, 0.5.1, 0.5

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Python markdown parser

py-mock¶

Homepage:

https://github.com/testing-cabal/mock

Spack package:

py-mock/package.py

Versions:

2.0.0, 1.3.0

Build Dependencies:

python, py-pbr, py-six, py-funcsigs, py-setuptools

Link Dependencies:

Run Dependencies:

python, py-pbr, py-six, py-funcsigs

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:

http://github.com/belson17/modred

Spack package:

py-modred/package.py

Versions:

2.0.4, 2.0.3, 2.0.2, 2.0.1, 2.0.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Modred is a parallelized library for finding modal decompositions and reduced-order models.

py-moltemplate¶

Homepage:

http://moltemplate.org

Spack package:

py-moltemplate/package.py

Versions:

2.5.8

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Moltemplate is a general cross-platform text-based molecule builder for LAMMPS.

py-mongo¶

Homepage:

http://github.com/mongodb/mongo-python-driver

Spack package:

py-mongo/package.py

Versions:

3.6.0, 3.3.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Python driver for MongoDB <http://www.mongodb.org>

py-monotonic¶

Homepage:

https://pypi.python.org/pypi/monotonic

Spack package:

py-monotonic/package.py

Versions:

1.2

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

An implementation of time.monotonic() for Python 2 & < 3.3

py-monty¶

Homepage:

https://github.com/materialsvirtuallab/monty

Spack package:

py-monty/package.py

Versions:

0.9.6

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Monty is the missing complement to Python.

py-more-itertools¶

Homepage:

https://github.com/erikrose/more-itertools

Spack package:

py-more-itertools/package.py

Versions:

4.3.0, 4.1.0, 2.2

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Additions to the standard Python itertools package.

py-mpi4py¶

Homepage:

https://pypi.python.org/pypi/mpi4py

Spack package:

py-mpi4py/package.py

Versions:

develop, 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:

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-mpmath¶

Homepage:

http://mpmath.org

Spack package:

py-mpmath/package.py

Versions:

1.1.0, 1.0.0, 0.19

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

A Python library for arbitrary-precision floating-point arithmetic.

py-multiprocess¶

Homepage:

https://github.com/uqfoundation/multiprocess

Spack package:

py-multiprocess/package.py

Versions:

0.70.5, 0.70.4

Build Dependencies:

python, py-setuptools, py-dill

Link Dependencies:

Run Dependencies:

python, py-dill

Description:

Better multiprocessing and multithreading in Python

py-multiqc¶

Homepage:

https://multiqc.info

Spack package:

py-multiqc/package.py

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:

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:

https://github.com/Infinidat/munch

Spack package:

py-munch/package.py

Versions:

2.2.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

A Munch is a Python dictionary that provides attribute-style access (a la JavaScript objects).

py-mx¶

Homepage:

http://www.egenix.com/products/python/mxBase/

Spack package:

py-mx/package.py

Versions:

3.2.8

Build Dependencies:

Link Dependencies:

Run Dependencies:

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-mxnet¶

Homepage:

http://mxnet.io

Spack package:

py-mxnet/package.py

Versions:

0.10.0.post2

Build Dependencies:

python, py-setuptools, py-numpy, mxnet

Link Dependencies:

Run Dependencies:

python, py-setuptools, py-numpy, mxnet

Description:

Python binding for DMLC/MXNet.

py-myhdl¶

Homepage:

http://www.myhdl.org

Spack package:

py-myhdl/package.py

Versions:

0.9.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Python as a Hardware Description Language

py-mysql-connector¶

Homepage:

https://github.com/mysql/mysql-connector-python

Spack package:

py-mysql-connector/package.py

Versions:

8.0.13

Build Dependencies:

python, py-setuptools, py-protobuf

Link Dependencies:

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-mysqldb1¶

Homepage:

https://github.com/farcepest/MySQLdb1

Spack package:

py-mysqldb1/package.py

Versions:

1.2.5

Build Dependencies:

python, mysql, py-setuptools

Link Dependencies:

python, mysql

Run Dependencies:

Description:

Legacy mysql bindings for python

py-natsort¶

Homepage:

https://pypi.org/project/natsort/

Spack package:

py-natsort/package.py

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:

Link Dependencies:

Run Dependencies:

Description:

Simple yet flexible natural sorting in Python.

py-nbconvert¶

Homepage:

https://github.com/jupyter/nbconvert

Spack package:

py-nbconvert/package.py

Versions:

4.2.0, 4.1.0, 4.0.0

Build Dependencies:

python, py-pycurl, py-mistune, py-jinja2, py-pygments, py-traitlets, py-jupyter-core, py-nbformat, py-entrypoints, py-tornado, py-jupyter-client

Link Dependencies:

Run Dependencies:

python, py-mistune, py-jinja2, py-pygments, py-traitlets, py-jupyter-core, py-nbformat, py-entrypoints, py-tornado, py-jupyter-client

Description:

Jupyter Notebook Conversion

py-nbformat¶

Homepage:

https://github.com/jupyter/nbformat

Spack package:

py-nbformat/package.py

Versions:

4.1.0, 4.0.1, 4.0.0

Build Dependencies:

python, py-ipython-genutils, py-traitlets, py-jsonschema, py-jupyter-core

Link Dependencies:

Run Dependencies:

python, py-ipython-genutils, py-traitlets, py-jsonschema, py-jupyter-core

Description:

The Jupyter Notebook format

py-neo¶

Homepage:

http://neuralensemble.org/neo

Spack package:

py-neo/package.py

Versions:

0.5.2, 0.4.1

Build Dependencies:

python, py-setuptools, py-numpy, py-quantities

Link Dependencies:

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:

http://kbarbary.github.io/nestle/

Spack package:

py-nestle/package.py

Versions:

0.1.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Nested sampling algorithms for evaluating Bayesian evidence.

py-netcdf4¶

Homepage:

https://github.com/Unidata/netcdf4-python

Spack package:

py-netcdf4/package.py

Versions:

1.4.2, 1.2.7, 1.2.3.1

Build Dependencies:

python, py-setuptools, py-cython, py-numpy, py-cftime, netcdf, hdf5

Link Dependencies:

python, netcdf, hdf5

Run Dependencies:

python, py-numpy, py-cftime

Description:

Python interface to the netCDF Library.

py-netifaces¶

Homepage:

https://bitbucket.org/al45tair/netifaces

Spack package:

py-netifaces/package.py

Versions:

0.10.5

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Portable network interface information

py-networkx¶

Homepage:

http://networkx.github.io/

Spack package:

py-networkx/package.py

Versions:

2.2, 2.1, 1.11, 1.10

Build Dependencies:

python, py-decorator, py-setuptools

Link Dependencies:

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-nose¶

Homepage:

https://pypi.python.org/pypi/nose

Spack package:

py-nose/package.py

Versions:

1.3.7, 1.3.6, 1.3.4

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

nose extends the test loading and running features of unittest, making it easier to write, find and run tests.

py-nosexcover¶

Homepage:

https://github.com/cmheisel/nose-xcover

Spack package:

py-nosexcover/package.py

Versions:

1.0.11

Build Dependencies:

python, py-setuptools, py-nose, py-coverage

Link Dependencies:

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:

https://numba.pydata.org/

Spack package:

py-numba/package.py

Versions:

0.40.1, 0.35.0

Build Dependencies:

python, py-numpy, py-setuptools, py-llvmlite, py-argparse, py-funcsigs, py-singledispatch

Link Dependencies:

Run Dependencies:

python, py-numpy, py-llvmlite, py-argparse, py-funcsigs, py-singledispatch

Description:

NumPy aware dynamic Python compiler using LLVM

py-numexpr¶

Homepage:

https://pypi.python.org/pypi/numexpr

Spack package:

py-numexpr/package.py

Versions:

2.6.9, 2.6.5, 2.6.1, 2.5, 2.4.6

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Fast numerical expression evaluator for NumPy

py-numexpr3¶

Homepage:

https://github.com/pydata/numexpr/tree/numexpr-3.0

Spack package:

py-numexpr3/package.py

Versions:

3.0.1.a1

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

http://www.numpy.org/

Spack package:

py-numpy/package.py

Versions:

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, blas, lapack

Link Dependencies:

python, blas, lapack

Run Dependencies:

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:

https://github.com/numpy/numpydoc

Spack package:

py-numpydoc/package.py

Versions:

0.6.0

Build Dependencies:

python, py-setuptools, py-sphinx

Link Dependencies:

Run Dependencies:

Description:

numpydoc - Numpy's Sphinx extensions

py-olefile¶

Homepage:

https://www.decalage.info/python/olefileio

Spack package:

py-olefile/package.py

Versions:

0.44

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Python package to parse, read and write Microsoft OLE2 files

py-onnx¶

Homepage:

https://github.com/onnx/onnx

Spack package:

py-onnx/package.py

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:

https://github.com/nanoporetech/ont_fast5_api

Spack package:

py-ont-fast5-api/package.py

Versions:

0.3.2

Build Dependencies:

python, py-setuptools, py-h5py, py-numpy

Link Dependencies:

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:

http://www.openPMD.org

Spack package:

py-openpmd-validator/package.py

Versions:

1.0.0.2

Build Dependencies:

python, py-setuptools, py-numpy, py-dateutil, py-h5py

Link Dependencies:

Run Dependencies:

python, py-numpy, py-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:

http://openpyxl.readthedocs.org/

Spack package:

py-openpyxl/package.py

Versions:

2.4.5, 2.2.0-b1

Build Dependencies:

python, py-setuptools, py-jdcal, py-et-xmlfile

Link Dependencies:

Run Dependencies:

python, py-jdcal, py-et-xmlfile

Description:

A Python library to read/write Excel 2010 xlsx/xlsm files

py-openslide-python¶

Homepage:

https://github.com/openslide/openslide-python

Spack package:

py-openslide-python/package.py

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:

http://opentuner.org/

Spack package:

py-opentuner/package.py

Versions:

0.8.0

Build Dependencies:

python, py-argparse, py-fn, py-numpy, py-pysqlite, py-setuptools, py-sqlalchemy

Link Dependencies:

Run Dependencies:

python, py-argparse, py-fn, py-numpy, py-pysqlite, py-sqlalchemy

Description:

An extensible framework for program autotuning.

py-ordereddict¶

Homepage:

https://pypi.python.org/pypi/ordereddict

Spack package:

py-ordereddict/package.py

Versions:

1.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

A drop-in substitute for Py2.7's new collections. OrderedDict that works in Python 2.4-2.6.

py-oset¶

Homepage:

https://pypi.python.org/pypi/oset

Spack package:

py-oset/package.py

Versions:

0.1.3

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Set that remembers original insertion order.

py-owslib¶

Homepage:

http://http://geopython.github.io/OWSLib/#installation

Spack package:

py-owslib/package.py

Versions:

0.16.0

Build Dependencies:

python, py-setuptools, py-dateutil, py-pytz, py-requests, py-pyproj

Link Dependencies:

Run Dependencies:

python, py-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:

https://github.com/pypa/packaging

Spack package:

py-packaging/package.py

Versions:

17.1, 16.8

Build Dependencies:

Link Dependencies:

Run Dependencies:

python, py-six, py-pyparsing

Description:

Core utilities for Python packages.

py-palettable¶

Homepage:

https://jiffyclub.github.io/palettable/

Spack package:

py-palettable/package.py

Versions:

3.0.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Color palettes for Python.

py-pandas¶

Homepage:

http://pandas.pydata.org/

Spack package:

py-pandas/package.py

Versions:

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-dateutil, py-numpy, py-setuptools, py-cython, py-pytz, py-numexpr, py-bottleneck

Link Dependencies:

Run Dependencies:

python, py-dateutil, py-numpy, py-pytz, py-numexpr, py-bottleneck

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-paramiko¶

Homepage:

http://www.paramiko.org/

Spack package:

py-paramiko/package.py

Versions:

2.1.2

Build Dependencies:

python, py-setuptools, py-pyasn1, py-cryptography

Link Dependencies:

Run Dependencies:

python, py-pyasn1, py-cryptography

Description:

SSH2 protocol library

py-partd¶

Homepage:

http://github.com/dask/partd/

Spack package:

py-partd/package.py

Versions:

0.3.8

Build Dependencies:

python, py-setuptools, py-locket, py-toolz

Link Dependencies:

Run Dependencies:

python, py-locket, py-toolz

Description:

Key-value byte store with appendable values.

py-pathlib2¶

Homepage:

https://pypi.python.org/pypi/pathlib2

Spack package:

py-pathlib2/package.py

Versions:

2.3.2, 2.1.0

Build Dependencies:

python, py-setuptools, py-six, py-scandir

Link Dependencies:

Run Dependencies:

python, py-six, py-scandir

Description:

Backport of pathlib from python 3.4

py-pathos¶

Homepage:

https://github.com/uqfoundation/pathos

Spack package:

py-pathos/package.py

Versions:

0.2.0

Build Dependencies:

python, py-setuptools, py-multiprocess, py-pox, py-ppft, py-dill

Link Dependencies:

Run Dependencies:

python, py-multiprocess, py-pox, py-ppft, py-dill

Description:

Parallel graph management and execution in heterogeneous computing

py-pathspec¶

Homepage:

https://pypi.python.org/pypi/pathspec

Spack package:

py-pathspec/package.py

Versions:

0.3.4

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

pathspec extends the test loading and running features of unittest, making it easier to write, find and run tests.

py-patsy¶

Homepage:

https://github.com/pydata/patsy

Spack package:

py-patsy/package.py

Versions:

0.4.1

Build Dependencies:

python, py-setuptools, py-numpy, py-scipy, py-six

Link Dependencies:

Run Dependencies:

python, py-numpy, py-scipy, py-six

Test Dependencies:

Description:

A Python package for describing statistical models and for building design matrices.

py-pauvre¶

Homepage:

https://github.com/conchoecia/pauvre

Spack package:

py-pauvre/package.py

Versions:

0.1.86

Build Dependencies:

python, py-matplotlib, py-biopython, py-pandas, py-pillow

Link Dependencies:

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:

https://pypi.python.org/pypi/pbr

Spack package:

py-pbr/package.py

Versions:

3.1.1, 2.0.0, 1.10.0, 1.8.1

Build Dependencies:

python, py-setuptools, py-enum34

Link Dependencies:

Run Dependencies:

Description:

PBR is a library that injects some useful and sensible default behaviors into your setuptools run.

py-pep8-naming¶

Homepage:

https://pypi.org/project/pep8-naming/

Spack package:

py-pep8-naming/package.py

Versions:

0.7.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

python, py-flake8-polyfill

Description:

Check PEP-8 naming conventions, plugin for flake8.

py-perf¶

Homepage:

https://pypi.python.org/pypi/perf

Spack package:

py-perf/package.py

Versions:

1.5.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

The Python perf module is a toolkit to write, run and analyze benchmarks.

py-performance¶

Homepage:

http://pyperformance.readthedocs.io/

Spack package:

py-performance/package.py

Versions:

0.6.1, 0.6.0

Build Dependencies:

python, py-setuptools, py-six, py-perf

Link Dependencies:

Run Dependencies:

python, py-setuptools, py-six, py-perf

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:

https://pypi.python.org/pypi/periodictable

Spack package:

py-periodictable/package.py

Versions:

1.5.0, 1.4.1

Build Dependencies:

python, py-setuptools, py-numpy, py-pyparsing

Link Dependencies:

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:

https://bitbucket.org/petsc/petsc4py

Spack package:

py-petsc4py/package.py

Versions:

develop, 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:

https://pypi.python.org/pypi/pexpect

Spack package:

py-pexpect/package.py

Versions:

4.6.0, 4.2.1, 3.3

Build Dependencies:

python, py-ptyprocess

Link Dependencies:

Run Dependencies:

python, py-ptyprocess

Description:

Pexpect allows easy control of interactive console applications.

py-phonopy¶

Homepage:

http://atztogo.github.io/phonopy/index.html

Spack package:

py-phonopy/package.py

Versions:

1.10.0

Build Dependencies:

python, py-numpy, py-scipy, py-matplotlib, py-pyyaml

Link Dependencies:

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:

https://pypi.python.org/pypi/pickleshare

Spack package:

py-pickleshare/package.py

Versions:

0.7.4

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Tiny 'shelve'-like database with concurrency support

py-picrust¶

Homepage:

http://picrust.github.io/picrust/index.html

Spack package:

py-picrust/package.py

Versions:

1.1.3

Build Dependencies:

python, py-cogent, py-biom-format, py-setuptools, py-future, py-numpy

Link Dependencies:

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:

http://www.pythonware.com/products/pil/

Spack package:

py-pil/package.py

Versions:

1.1.7

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

https://python-pillow.org/

Spack package:

py-pillow/package.py

Versions:

5.4.1, 5.1.0, 3.2.0, 3.0.0

Build Dependencies:

python, binutils, py-setuptools, jpeg, zlib, libtiff, freetype, lcms, openjpeg

Link Dependencies:

python, jpeg, zlib, libtiff, freetype, lcms, openjpeg

Run Dependencies:

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:

https://pypi.python.org/pypi/pint

Spack package:

py-pint/package.py

Versions:

0.8.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

https://pypi.python.org/pypi/pip

Spack package:

py-pip/package.py

Versions:

19.0.3, 18.1, 10.0.1, 9.0.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

The PyPA recommended tool for installing Python packages.

py-pipits¶

Homepage:

https://github.com/hsgweon/pipits

Spack package:

py-pipits/package.py

Versions:

1.5.0

Build Dependencies:

python, py-biom-format, py-numpy, java, hmmer, fastx-toolkit, vsearch, itsx, rdp-classifier

Link Dependencies:

python, hmmer, fastx-toolkit, vsearch, itsx, rdp-classifier

Run Dependencies:

python, py-biom-format, py-numpy, java

Description:

Automated pipeline for analyses of fungal ITS from the Illumina

py-pkgconfig¶

Homepage:

http://github.com/matze/pkgconfig

Spack package:

py-pkgconfig/package.py

Versions:

1.4.0, 1.2.2

Build Dependencies:

python, py-setuptools, pkgconfig, py-nose

Link Dependencies:

Run Dependencies:

python, pkgconfig

Test Dependencies:

Description:

Interface Python with pkg-config.

py-plotly¶

Homepage:

https://plot.ly/python/

Spack package:

py-plotly/package.py

Versions:

2.2.0

Build Dependencies:

python, py-setuptools, py-requests, py-six, py-pytz

Link Dependencies:

Run Dependencies:

python, py-requests, py-six, py-pytz

Description:

An interactive, browser-based graphing library for Python

py-pluggy¶

Homepage:

https://github.com/pytest-dev/pluggy

Spack package:

py-pluggy/package.py

Versions:

0.7.1, 0.6.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Plugin and hook calling mechanisms for python.

py-ply¶

Homepage:

http://www.dabeaz.com/ply

Spack package:

py-ply/package.py

Versions:

3.11, 3.8

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

PLY is nothing more than a straightforward lex/yacc implementation.

py-pmw¶

Homepage:

https://pypi.python.org/pypi/Pmw

Spack package:

py-pmw/package.py

Versions:

2.0.1, 2.0.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Pmw is a toolkit for building high-level compound widgets, or megawidgets, constructed using other widgets as component parts.

py-poster¶

Homepage:

https://pypi.org/project/poster/

Spack package:

py-poster/package.py

Versions:

0.8.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Streaming HTTP uploads and multipart/form-data encoding.

py-pox¶

Homepage:

https://github.com/uqfoundation/pox

Spack package:

py-pox/package.py

Versions:

0.2.3, 0.2.2, 0.2.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Utilities for filesystem exploration and automated builds.

py-ppft¶

Homepage:

https://github.com/uqfoundation/ppft

Spack package:

py-ppft/package.py

Versions:

1.6.4.7.1, 1.6.4.6, 1.6.4.5

Build Dependencies:

python, py-setuptools, py-six, py-dill

Link Dependencies:

Run Dependencies:

python, py-six, py-dill

Description:

Distributed and parallel python

py-prettytable¶

Homepage:

https://code.google.com/archive/p/prettytable/

Spack package:

py-prettytable/package.py

Versions:

0.7.2

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

https://github.com/verigak/progress/

Spack package:

py-progress/package.py

Versions:

1.4

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Easy progress reporting for Python

py-progressbar2¶

Homepage:

https://github.com/WoLpH/python-progressbar

Spack package:

py-progressbar2/package.py

Versions:

3.39.3

Build Dependencies:

python, py-setuptools, py-six, py-python-utils

Link Dependencies:

Run Dependencies:

python, py-six, py-python-utils

Description:

A progress bar for Python 2 and Python 3

py-projectq¶

Homepage:

https://projectq.ch

Spack package:

py-projectq/package.py

Versions:

develop, 0.3.6

Build Dependencies:

python, py-setuptools, py-numpy, py-scipy, py-future, py-requests, py-pybind11

Link Dependencies:

Run Dependencies:

python, py-numpy, py-scipy, py-future, py-requests, py-pybind11

Test Dependencies:

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:

https://pypi.org/project/prometheus_client/

Spack package:

py-prometheus-client/package.py

Versions:

0.5.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Prometheus instrumentation library for Python applications.

py-prompt-toolkit¶

Homepage:

https://pypi.python.org/pypi/prompt_toolkit

Spack package:

py-prompt-toolkit/package.py

Versions:

2.0.9, 1.0.9

Build Dependencies:

python, py-setuptools, py-six, py-wcwidth

Link Dependencies:

Run Dependencies:

python, py-six, py-wcwidth

Description:

Library for building powerful interactive command lines in Python

py-protobuf¶

Homepage:

https://developers.google.com/protocol-buffers/

Spack package:

py-protobuf/package.py

Versions:

3.7.1, 3.6.1, 3.5.2.post1, 3.5.2, 3.5.1, 3.0.0b2, 2.6.1, 2.5.0, 2.4.1, 2.3.0

Build Dependencies:

python, py-setuptools, protobuf

Link Dependencies:

python, protobuf

Run Dependencies:

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:

https://pypi.python.org/pypi/psutil

Spack package:

py-psutil/package.py

Versions:

5.5.1, 5.4.5, 5.0.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

https://github.com/stfc/PSyclone

Spack package:

py-psyclone/package.py

Versions:

develop, 1.5.1

Build Dependencies:

python, py-setuptools, py-pyparsing, py-fparser

Link Dependencies:

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:

http://initd.org/psycopg/

Spack package:

py-psycopg2/package.py

Versions:

2.7.5

Build Dependencies:

python, py-setuptools, postgresql

Link Dependencies:

Run Dependencies:

python, postgresql

Description:

Python interface to PostgreSQL databases

py-ptyprocess¶

Homepage:

https://pypi.python.org/pypi/ptyprocess

Spack package:

py-ptyprocess/package.py

Versions:

0.5.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Run a subprocess in a pseudo terminal

py-pudb¶

Homepage:

http://mathema.tician.de/software/pudb

Spack package:

py-pudb/package.py

Versions:

2017.1.1, 2016.2

Build Dependencies:

python, py-setuptools, py-urwid, py-pygments

Link Dependencies:

Run Dependencies:

python, py-setuptools, py-urwid, py-pygments

Description:

Full-screen console debugger for Python

py-py¶

Homepage:

http://pylib.readthedocs.io/en/latest/

Spack package:

py-py/package.py

Versions:

1.5.4, 1.5.3, 1.4.33, 1.4.31

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Library with cross-python path, ini-parsing, io, code, log facilities

py-py2bit¶

Homepage:

https://pypi.python.org/pypi/py2bit

Spack package:

py-py2bit/package.py

Versions:

0.2.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

A package for accessing 2bit files using lib2bit.

py-py2cairo¶

Homepage:

https://www.cairographics.org/pycairo/

Spack package:

py-py2cairo/package.py

Versions:

1.10.0

Build Dependencies:

python, cairo, pixman, pkgconfig

Link Dependencies:

python, cairo, pixman

Run Dependencies:

Test Dependencies:

Description:

Pycairo is a set of Python bindings for the cairo graphics library.

py-py2neo¶

Homepage:

http://py2neo.org/

Spack package:

py-py2neo/package.py

Versions:

2.0.8, 2.0.7, 2.0.6, 2.0.5, 2.0.4

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Py2neo is a client library and toolkit for working with Neo4j from within Python applications and from the command line.

py-py4j¶

Homepage:

https://www.py4j.org/

Spack package:

py-py4j/package.py

Versions:

0.10.6, 0.10.4, 0.10.3

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Enables Python programs to dynamically access arbitrary Java objects.

py-pyani¶

Homepage:

http://widdowquinn.github.io/pyani

Spack package:

py-pyani/package.py

Versions:

0.2.7, 0.2.6

Build Dependencies:

python, py-setuptools, py-matplotlib, py-seaborn, py-biopython, py-pandas, py-scipy

Link Dependencies:

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:

http://arrow.apache.org

Spack package:

py-pyarrow/package.py

Versions:

0.12.1, 0.11.0, 0.9.0

Build Dependencies:

python, cmake, pkgconfig, py-setuptools, py-cython, arrow

Link Dependencies:

python, arrow

Run Dependencies:

Description:

A cross-language development platform for in-memory data. This package contains the Python bindings.

py-pyasn1¶

Homepage:

https://github.com/etingof/pyasn1

Spack package:

py-pyasn1/package.py

Versions:

0.2.3

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Generic ASN.1 library for Python http://pyasn1.sf.net

py-pybedtools¶

Homepage:

http://daler.github.io/pybedtools

Spack package:

py-pybedtools/package.py

Versions:

0.6.9

Build Dependencies:

python, py-cython, py-pysam, py-pandas, py-six, py-numpy, py-setuptools

Link Dependencies:

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:

https://pypi.python.org/pypi/pyBigWig

Spack package:

py-pybigwig/package.py

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:

https://pybind11.readthedocs.io

Spack package:

py-pybind11/package.py

Versions:

develop, 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:

Test Dependencies:

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:

https://pybtex.org

Spack package:

py-pybtex/package.py

Versions:

0.21

Build Dependencies:

python, py-setuptools, py-latexcodec, py-pyyaml, py-counter

Link Dependencies:

Run Dependencies:

python, py-latexcodec, py-pyyaml, py-counter

Description:

Pybtex is a BibTeX-compatible bibliography processor written in Python.

py-pybtex-docutils¶

Homepage:

https://pypi.python.org/pypi/pybtex-docutils/

Spack package:

py-pybtex-docutils/package.py

Versions:

0.2.1

Build Dependencies:

python, py-setuptools, py-docutils, py-pybtex, py-six

Link Dependencies:

Run Dependencies:

python, py-docutils, py-pybtex, py-six

Description:

A docutils backend for pybtex.

py-pycairo¶

Homepage:

https://www.cairographics.org/pycairo/

Spack package:

py-pycairo/package.py

Versions:

1.17.1

Build Dependencies:

python, cairo, pkgconfig, py-setuptools

Link Dependencies:

python, cairo

Run Dependencies:

Description:

Pycairo is a set of Python bindings for the cairo graphics library.

py-pycares¶

Homepage:

https://github.com/saghul/pycares

Spack package:

py-pycares/package.py

Versions:

3.0.0

Build Dependencies:

python, py-cffi

Link Dependencies:

python, py-cffi

Run Dependencies:

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-pychecker¶

Homepage:

http://pychecker.sourceforge.net/

Spack package:

py-pychecker/package.py

Versions:

0.8.19

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Python source code checking tool.

py-pycodestyle¶

Homepage:

https://github.com/PyCQA/pycodestyle

Spack package:

py-pycodestyle/package.py

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:

Link Dependencies:

Run Dependencies:

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:

https://github.com/eliben/pycparser

Spack package:

py-pycparser/package.py

Versions:

2.18, 2.17, 2.13

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

A complete parser of the C language, written in pure python.

py-pycrypto¶

Homepage:

https://www.dlitz.net/software/pycrypto/

Spack package:

py-pycrypto/package.py

Versions:

2.6.1

Build Dependencies:

python, gmp

Link Dependencies:

python, gmp

Run Dependencies:

Description:

The Python Cryptography Toolkit

py-pycurl¶

Homepage:

http://pycurl.io/

Spack package:

py-pycurl/package.py

Versions:

7.43.0

Build Dependencies:

python, curl

Link Dependencies:

python, curl

Run Dependencies:

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:

https://pypi.python.org/pypi/pyDatalog/

Spack package:

py-pydatalog/package.py

Versions:

0.17.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

pyDatalog adds logic programming to Python.

py-pydispatcher¶

Homepage:

http://pydispatcher.sourceforge.net/

Spack package:

py-pydispatcher/package.py

Versions:

2.0.5

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Multi-producer-multi-consumer signal dispatching mechanism.

py-pydot¶

Homepage:

https://github.com/erocarrera/pydot/

Spack package:

py-pydot/package.py

Versions:

1.4.1, 1.2.3, 1.2.2

Build Dependencies:

python, py-setuptools, py-pyparsing, graphviz

Link Dependencies:

Run Dependencies:

python, py-pyparsing, graphviz

Description:

Python interface to Graphviz's Dot language

py-pydv¶

Homepage:

https://github.com/griffin28/PyDV

Spack package:

py-pydv/package.py

Versions:

2.4.2

Build Dependencies:

python, py-backports-functools-lru-cache, py-cycler, py-dateutil, py-matplotlib, py-pyside, py-scipy

Link Dependencies:

python, py-backports-functools-lru-cache, py-cycler, py-dateutil, py-matplotlib, py-pyside, py-scipy

Run Dependencies:

Description:

PDV is a 1D graphics and data analysis tool, heavily based on the ULTRA plotting tool

py-pyelftools¶

Homepage:

https://pypi.python.org/pypi/pyelftools

Spack package:

py-pyelftools/package.py

Versions:

0.23

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

A pure-Python library for parsing and analyzing ELF files and DWARF debugging information

py-pyepsg¶

Homepage:

https://pyepsg.readthedocs.io/en/latest/

Spack package:

py-pyepsg/package.py

Versions:

0.3.2

Build Dependencies:

python, py-setuptools, py-requests

Link Dependencies:

Run Dependencies:

python, py-requests

Description:

Provides simple access to http://epsg.io/.

py-pyfaidx¶

Homepage:

https://pypi.org/project/pyfaidx/

Spack package:

py-pyfaidx/package.py

Versions:

0.5.5.2

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

pyfaidx: efficient pythonic random access to fasta subsequences

py-pyfasta¶

Homepage:

https://pypi.python.org/pypi/pyfasta/

Spack package:

py-pyfasta/package.py

Versions:

0.5.2

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Pyfasta: fast, memory-efficient, pythonic (and command-line) access to fasta sequence files

py-pyfftw¶

Homepage:

http://hgomersall.github.com/pyFFTW

Spack package:

py-pyfftw/package.py

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:

Description:

A pythonic wrapper around FFTW, the FFT library, presenting a unified interface for all the supported transforms.

py-pyflakes¶

Homepage:

https://github.com/PyCQA/pyflakes

Spack package:

py-pyflakes/package.py

Versions:

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:

Link Dependencies:

Run Dependencies:

Description:

A simple program which checks Python source files for errors.

py-pygdbmi¶

Homepage:

https://github.com/cs01/pygdbmi

Spack package:

py-pygdbmi/package.py

Versions:

0.8.2.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Parse gdb machine interface output with Python

py-pygments¶

Homepage:

http://pygments.org/

Spack package:

py-pygments/package.py

Versions:

2.3.1, 2.2.0, 2.1.3, 2.0.2, 2.0.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Pygments is a syntax highlighting package written in Python.

py-pygobject¶

Homepage:

https://pypi.python.org/pypi/pygobject

Spack package:

py-pygobject/package.py

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:

http://deeplearning.net/software/libgpuarray/

Spack package:

py-pygpu/package.py

Versions:

0.7.5, 0.7.4, 0.7.3, 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, libcheck

Link Dependencies:

python, libgpuarray, libcheck

Run Dependencies:

python, py-setuptools, py-cython, py-nose, py-numpy, py-mako

Description:

Python packge for the libgpuarray C library.

py-pygresql¶

Homepage:

http://www.pygresql.org

Spack package:

py-pygresql/package.py

Versions:

5.0.5

Build Dependencies:

python, py-setuptools, postgresql

Link Dependencies:

Run Dependencies:

python, postgresql

Description:

PyGreSQL is an open-source Python module that interfaces to a PostgreSQL database

py-pygtk¶

Homepage:

http://www.pygtk.org/

Spack package:

py-pygtk/package.py

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-pylint¶

Homepage:

https://pypi.python.org/pypi/pylint

Spack package:

py-pylint/package.py

Versions:

2.3.0, 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, py-isort, py-mccabe, py-editdistance, py-configparser, py-backports-functools-lru-cache, py-singledispatch

Run Dependencies:

python, py-astroid, py-six

Description:

array processing for numbers, strings, records, and objects.

py-pymatgen¶

Homepage:

http://www.pymatgen.org/

Spack package:

py-pymatgen/package.py

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:

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-pyminifier¶

Homepage:

http://liftoff.github.io/pyminifier/

Spack package:

py-pyminifier/package.py

Versions:

2.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Pyminifier is a Python code minifier, obfuscator, and compressor.

py-pymol¶

Homepage:

https://pymol.org

Spack package:

py-pymol/package.py

Versions:

2.1.0

Build Dependencies:

python, tcl, tk, py-pmw, gl, glu, glew, libpng, freetype, libxml2, msgpack-c, py-pyqt, freeglut

Link Dependencies:

python, tcl, tk, py-pmw, gl, glu, glew, libpng, freetype, libxml2, msgpack-c, freeglut

Run Dependencies:

python, py-pyqt

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-pympler¶

Homepage:

https://github.com/pympler/pympler

Spack package:

py-pympler/package.py

Versions:

0.4.3, 0.4.2, 0.4.1, 0.4, 0.3.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Development tool to measure, monitor and analyze the memory behavior of Python objects in a running Python application.

py-pymysql¶

Homepage:

https://github.com/PyMySQL/PyMySQL/

Spack package:

py-pymysql/package.py

Versions:

0.9.2

Build Dependencies:

python, py-setuptools, py-cryptography

Link Dependencies:

Run Dependencies:

python, py-cryptography

Description:

Pure-Python MySQL client library

py-pynio¶

Homepage:

https://www.pyngl.ucar.edu/Nio.shtml

Spack package:

py-pynio/package.py

Versions:

1.5.4

Build Dependencies:

python, libpng, jpeg, zlib, netcdf, hdf5, gdal, py-numpy

Link Dependencies:

python, libpng, jpeg, zlib, netcdf, hdf5, gdal

Run Dependencies:

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:

http://neuralensemble.org/PyNN/

Spack package:

py-pynn/package.py

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:

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:

https://github.com/mkleehammer/pyodbc

Spack package:

py-pyodbc/package.py

Versions:

4.0.26

Build Dependencies:

python, py-setuptools, unixodbc

Link Dependencies:

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-pypar¶

Homepage:

http://code.google.com/p/pypar/

Spack package:

py-pypar/package.py

Versions:

2.1.5_108

Build Dependencies:

python, mpi, py-numpy

Link Dependencies:

python, mpi

Run Dependencies:

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:

http://pyparsing.wikispaces.com/

Spack package:

py-pyparsing/package.py

Versions:

2.3.1, 2.2.0, 2.1.10, 2.0.3

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

A Python Parsing Module.

py-pypeflow¶

Homepage:

https://github.com/PacificBiosciences/pypeFLOW

Spack package:

py-pypeflow/package.py

Versions:

2017-05-04

Build Dependencies:

python, py-setuptools, py-networkx

Link Dependencies:

Run Dependencies:

python, py-networkx

Description:

pypeFLOW is light weight and reusable make / flow data process library written in Python.

py-pyprof2html¶

Homepage:

https://pypi.python.org/pypi/pyprof2html/

Spack package:

py-pyprof2html/package.py

Versions:

0.3.1

Build Dependencies:

python, py-setuptools, py-jinja2

Link Dependencies:

Run Dependencies:

python, py-jinja2

Description:

Python cProfile and hotshot profile's data to HTML Converter

py-pyproj¶

Homepage:

http://jswhit.github.io/pyproj/

Spack package:

py-pyproj/package.py

Versions:

1.9.5.1.1, 1.9.5.1

Build Dependencies:

python, py-cython, py-setuptools

Link Dependencies:

Run Dependencies:

Description:

Python interface to the PROJ.4 Library.

py-pyqi¶

Homepage:

https://pyqi.readthedocs.io

Spack package:

py-pyqi/package.py

Versions:

0.3.2

Build Dependencies:

Link Dependencies:

Run Dependencies:

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-pyqt¶

Homepage:

http://www.riverbankcomputing.com/software/pyqt/intro

Spack package:

py-pyqt/package.py

Versions:

4.11.3

Build Dependencies:

python, py-sip, qt

Link Dependencies:

python, qt

Run Dependencies:

py-sip

Description:

PyQt is a set of Python v2 and v3 bindings for Digia's Qt application framework and runs on all platforms supported by Qt including Windows, MacOS/X and Linux.

py-pyrad¶

Homepage:

http://dereneaton.com/software/pyrad/

Spack package:

py-pyrad/package.py

Versions:

3.0.66

Build Dependencies:

python, py-setuptools, py-numpy, py-scipy, vsearch, muscle

Link Dependencies:

python, vsearch, muscle

Run Dependencies:

Description:

RADseq for phylogenetics & introgression analyses

py-pyrosar¶

Homepage:

https://github.com/johntruckenbrodt/pyroSAR

Spack package:

py-pyrosar/package.py

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-pysam¶

Homepage:

https://pypi.python.org/pypi/pysam

Spack package:

py-pysam/package.py

Versions:

0.15.2, 0.15.1, 0.14.1, 0.13, 0.11.2.2, 0.7.7

Build Dependencies:

python, py-setuptools, py-cython, curl, bcftools, htslib, samtools

Link Dependencies:

python, curl, bcftools, htslib, samtools

Run Dependencies:

Description:

A python module for reading, manipulating and writing genomic data sets.

py-pyscaf¶

Homepage:

https://pypi.python.org/pypi/pyScaf

Spack package:

py-pyscaf/package.py

Versions:

0.12a4

Build Dependencies:

python, py-setuptools, py-fastaindex

Link Dependencies:

Run Dependencies:

python, py-fastaindex

Description:

pyScaf orders contigs from genome assemblies utilising several types of information

py-pyserial¶

Homepage:

https://github.com/pyserial/pyserial

Spack package:

py-pyserial/package.py

Versions:

3.1.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Python Serial Port Extension

py-pyshp¶

Homepage:

https://github.com/GeospatialPython/pyshp

Spack package:

py-pyshp/package.py

Versions:

1.2.12

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

The Python Shapefile Library (pyshp) reads and writes ESRI Shapefiles in pure Python.

py-pyside¶

Homepage:

https://pypi.python.org/pypi/pyside

Spack package:

py-pyside/package.py

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:

Description:

Python bindings for Qt.

py-pysocks¶

Homepage:

https://github.com/Anorov/PySocks

Spack package:

py-pysocks/package.py

Versions:

1.6.6, 1.5.7

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

A Python SOCKS client module.

py-pyspark¶

Homepage:

http://spark.apache.org

Spack package:

py-pyspark/package.py

Versions:

2.3.0

Build Dependencies:

python, py-setuptools, py-py4j

Link Dependencies:

Run Dependencies:

python, py-py4j

Description:

Python bindings for Apache Spark

py-pysqlite¶

Homepage:

https://github.com/ghaering/pysqlite

Spack package:

py-pysqlite/package.py

Versions:

2.8.3

Build Dependencies:

python, sqlite

Link Dependencies:

Run Dependencies:

python, sqlite

Description:

Python DB-API module for SQLite 3.

py-pytables¶

Homepage:

http://www.pytables.org/

Spack package:

py-pytables/package.py

Versions:

3.4.4, 3.3.0, 3.2.2

Build Dependencies:

python, hdf5, py-numpy, py-numexpr, py-cython, py-six, py-setuptools

Link Dependencies:

python, hdf5

Run Dependencies:

python, py-numpy, py-numexpr, py-cython, py-six, py-setuptools

Description:

PyTables is a package for managing hierarchical datasets and designed to efficiently and easily cope with extremely large amounts of data.

py-pytest¶

Homepage:

http://pytest.org/

Spack package:

py-pytest/package.py

Versions:

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-attrs, py-more-itertools, py-atomicwrites, py-pluggy, py-funcsigs, py-pathlib2

Link Dependencies:

Run Dependencies:

python, py-setuptools, py-py, py-six, py-attrs, py-more-itertools, py-atomicwrites, py-pluggy, py-funcsigs, py-pathlib2

Description:

pytest: simple powerful testing with Python.

py-pytest-cov¶

Homepage:

https://github.com/pytest-dev/pytest-cov

Spack package:

py-pytest-cov/package.py

Versions:

2.3.1

Build Dependencies:

python, py-setuptools, py-pytest, py-coverage

Link Dependencies:

Run Dependencies:

python, py-pytest, py-coverage

Description:

Pytest plugin for measuring coverage.

py-pytest-flake8¶

Homepage:

https://github.com/tholo/pytest-flake8

Spack package:

py-pytest-flake8/package.py

Versions:

0.8.1

Build Dependencies:

python, py-setuptools, py-flake8, py-pytest

Link Dependencies:

Run Dependencies:

python, py-flake8, py-pytest

Description:

pytest plugin to check FLAKE8 requirements.

py-pytest-httpbin¶

Homepage:

https://github.com/kevin1024/pytest-httpbin

Spack package:

py-pytest-httpbin/package.py

Versions:

0.2.3

Build Dependencies:

python, py-setuptools, py-flask, py-decorator, py-httpbin, py-six

Link Dependencies:

Run Dependencies:

python, py-flask, py-decorator, py-httpbin, py-six

Description:

Easily test your HTTP library against a local copy of httpbin

py-pytest-mock¶

Homepage:

https://github.com/pytest-dev/pytest-mock

Spack package:

py-pytest-mock/package.py

Versions:

1.2

Build Dependencies:

python, py-setuptools, py-pytest, py-mock

Link Dependencies:

Run Dependencies:

python, py-pytest, py-mock

Description:

Thin-wrapper around the mock package for easier use with py.test

py-pytest-runner¶

Homepage:

https://github.com/pytest-dev/pytest-runner

Spack package:

py-pytest-runner/package.py

Versions:

2.11.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Invoke py.test as distutils command with dependency resolution.

py-pytest-xdist¶

Homepage:

https://github.com/pytest-dev/pytest-xdist

Spack package:

py-pytest-xdist/package.py

Versions:

1.16.0

Build Dependencies:

python, py-setuptools, py-execnet, py-pytest, py-py

Link Dependencies:

Run Dependencies:

python, py-execnet, py-pytest, py-py

Description:

py.test xdist plugin for distributed testing and loop-on-failing mode

py-pythia¶

Homepage:

https://geodynamics.org/cig/software/pythia/

Spack package:

py-pythia/package.py

Versions:

0.8.1.18

Build Dependencies:

python, py-merlin

Link Dependencies:

Run Dependencies:

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:

https://pypi.python.org/pypi/python-daemon/

Spack package:

py-python-daemon/package.py

Versions:

2.0.5

Build Dependencies:

python, py-setuptools, py-lockfile

Link Dependencies:

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-engineio¶

Homepage:

http://python-engineio.readthedocs.io/en/latest/

Spack package:

py-python-engineio/package.py

Versions:

2.0.2

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Engine.IO is the implementation of transport-based cross-browser/cross- device bi-directional communication layer for Socket.IO.

py-python-gitlab¶

Homepage:

https://github.com/gpocentek/python-gitlab

Spack package:

py-python-gitlab/package.py

Versions:

0.19, 0.18, 0.17, 0.16

Build Dependencies:

python, py-setuptools, py-six, py-requests

Link Dependencies:

Run Dependencies:

python, py-six, py-requests

Description:

Python wrapper for the GitLab API

py-python-htmlgen¶

Homepage:

https://github.com/srittau/python-htmlgen

Spack package:

py-python-htmlgen/package.py

Versions:

1.2.2

Build Dependencies:

Link Dependencies:

Run Dependencies:

Test Dependencies:

py-typing, py-python-asserts

Description:

Library to generate HTML from classes.

py-python-levenshtein¶

Homepage:

https://github.com/ztane/python-Levenshtein

Spack package:

py-python-levenshtein/package.py

Versions:

0.12.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Python extension for computing string edit distances and similarities.

py-python-socketio¶

Homepage:

https://github.com/miguelgrinberg/python-socketio

Spack package:

py-python-socketio/package.py

Versions:

1.8.4

Build Dependencies:

python, py-setuptools, py-six, py-python-engineio, py-eventlet

Link Dependencies:

Run Dependencies:

python, py-six, py-python-engineio, py-eventlet

Description:

Python implementation of the Socket.IO realtime server.

py-python-utils¶

Homepage:

https://github.com/WoLpH/python-utils

Spack package:

py-python-utils/package.py

Versions:

2.3.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Python Utils is a collection of small Python functions and classes which make common patterns shorter and easier.

py-pythonqwt¶

Homepage:

https://github.com/PierreRaybaut/PythonQwt

Spack package:

py-pythonqwt/package.py

Versions:

0.5.5

Build Dependencies:

python, py-setuptools, py-numpy, py-sip, py-pyqt, py-sphinx

Link Dependencies:

Run Dependencies:

python, py-numpy, py-sip, py-pyqt, py-sphinx

Description:

Qt plotting widgets for Python

py-pytorch¶

Homepage:

http://pytorch.org/

Spack package:

py-pytorch/package.py

Versions:

1.0.0, 0.4.1, 0.4.0, 0.3.1

Build Dependencies:

python, py-setuptools, py-cffi, py-numpy, blas, lapack, py-pyyaml, py-typing, intel-mkl, cuda, cudnn, nccl, magma

Link Dependencies:

python, blas, lapack, intel-mkl, cuda, cudnn, nccl, magma

Run Dependencies:

python, py-numpy, py-pyyaml, py-typing, cuda

Description:

Tensors and Dynamic neural networks in Python with strong GPU acceleration.

py-pytz¶

Homepage:

http://pythonhosted.org/pytz

Spack package:

py-pytz/package.py

Versions:

2018.4, 2017.2, 2016.10, 2016.6.1, 2016.3, 2015.4, 2014.10, 2014.9

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

World timezone definitions, modern and historical.

py-pyutilib¶

Homepage:

https://github.com/PyUtilib/pyutilib

Spack package:

py-pyutilib/package.py

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:

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:

http://pyvcf.readthedocs.org/en/latest/index.html

Spack package:

py-pyvcf/package.py

Versions:

0.6.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

A Variant Call Format reader for Python

py-pywavelets¶

Homepage:

https://github.com/PyWavelets

Spack package:

py-pywavelets/package.py

Versions:

0.5.2

Build Dependencies:

python, py-setuptools, py-cython, py-numpy

Link Dependencies:

Run Dependencies:

Description:

PyWavelets is a free Open Source library for wavelet transforms in Python

py-pyyaml¶

Homepage:

http://pyyaml.org/wiki/PyYAML

Spack package:

py-pyyaml/package.py

Versions:

3.13, 3.12, 3.11

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

PyYAML is a YAML parser and emitter for Python.

py-qtawesome¶

Homepage:

https://github.com/spyder-ide/qtawesome

Spack package:

py-qtawesome/package.py

Versions:

0.4.1, 0.3.3

Build Dependencies:

python, py-setuptools, py-qtpy, py-six

Link Dependencies:

Run Dependencies:

python, py-qtpy, py-six

Description:

FontAwesome icons in PyQt and PySide applications

py-qtconsole¶

Homepage:

http://ipython.org

Spack package:

py-qtconsole/package.py

Versions:

4.2.1

Build Dependencies:

python, py-ipykernel, py-jupyter-client, py-jupyter-core, py-pygments, py-traitlets, py-sphinx

Link Dependencies:

Run Dependencies:

python, py-ipykernel, py-jupyter-client, py-jupyter-core, py-pygments, py-traitlets, py-sphinx

Test Dependencies:

py-mock

Description:

Jupyter Qt console

py-qtpy¶

Homepage:

https://github.com/spyder-ide/qtpy

Spack package:

py-qtpy/package.py

Versions:

1.2.1

Build Dependencies:

python, py-setuptools, py-pyqt

Link Dependencies:

Run Dependencies:

python, py-pyqt

Description:

QtPy: Abtraction layer for PyQt5/PyQt4/PySide

py-quantities¶

Homepage:

http://python-quantities.readthedocs.org

Spack package:

py-quantities/package.py

Versions:

0.12.1, 0.11.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Support for physical quantities with units, based on numpy

py-quast¶

Homepage:

http://cab.spbu.ru/software/quast

Spack package:

py-quast/package.py

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:

https://github.com/kata198/QueryableList

Spack package:

py-queryablelist/package.py

Versions:

3.1.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Python module to add support for ORM-style filtering to any list of items

py-radical-utils¶

Homepage:

http://radical.rutgers.edu

Spack package:

py-radical-utils/package.py

Versions:

0.45, 0.41.1

Build Dependencies:

python, py-setuptools, py-colorama, py-netifaces

Link Dependencies:

Run Dependencies:

python, py-colorama, py-netifaces

Description:

Shared code and tools for various RADICAL Projects

py-ranger¶

Homepage:

http://ranger.nongnu.org/

Spack package:

py-ranger/package.py

Versions:

1.7.2

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

A VIM-inspired filemanager for the console

py-rasterio¶

Homepage:

https://github.com/mapbox/rasterio

Spack package:

py-rasterio/package.py

Versions:

1.0a12

Build Dependencies:

python, py-setuptools, py-cython, py-attrs, py-numpy, py-cligj, py-click, py-affine, py-snuggs, gdal, jpeg

Link Dependencies:

python, gdal, jpeg

Run Dependencies:

python, py-enum34, py-attrs, py-numpy, py-cligj, py-click, py-affine, py-snuggs

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-readme-renderer¶

Homepage:

https://github.com/pypa/readme_renderer

Spack package:

py-readme-renderer/package.py

Versions:

16.0

Build Dependencies:

python, py-setuptools, py-bleach, py-docutils, py-pygments, py-six

Link Dependencies:

Run Dependencies:

python, py-bleach, py-docutils, py-pygments, py-six

Description:

readme_renderer is a library for rendering "readme" descriptions for Warehouse.

py-regex¶

Homepage:

https://pypi.python.org/pypi/regex/

Spack package:

py-regex/package.py

Versions:

2017.07.11

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Alternative regular expression module, to replace re.

py-reportlab¶

Homepage:

https://pypi.python.org/pypi/reportlab

Spack package:

py-reportlab/package.py

Versions:

3.4.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

The ReportLab Toolkit. An Open Source Python library for generating PDFs and graphics.

py-requests¶

Homepage:

http://python-requests.org

Spack package:

py-requests/package.py

Versions:

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:

Run Dependencies:

python, py-chardet, py-idna, py-urllib3, py-certifi

Test Dependencies:

py-pytest, py-pytest-cov, py-pytest-httpbin, py-pytest-mock

Description:

Python HTTP for Humans.

py-requests-toolbelt¶

Homepage:

https://toolbelt.readthedocs.org/

Spack package:

py-requests-toolbelt/package.py

Versions:

0.8.0

Build Dependencies:

python, py-setuptools, py-requests

Link Dependencies:

Run Dependencies:

python, py-requests

Description:

A toolbelt of useful classes and functions to be used with python- requests

py-restview¶

Homepage:

https://mg.pov.lt/restview/

Spack package:

py-restview/package.py

Versions:

2.6.1

Build Dependencies:

python, py-setuptools, py-docutils, py-readme-renderer, py-pygments

Link Dependencies:

Run Dependencies:

python, py-docutils, py-readme-renderer, py-pygments

Description:

A viewer for ReStructuredText documents that renders them on the fly.

py-rope¶

Homepage:

https://github.com/python-rope/rope

Spack package:

py-rope/package.py

Versions:

0.11.0, 0.10.7, 0.10.6, 0.10.5

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

a python refactoring library.

py-rpy2¶

Homepage:

https://pypi.python.org/pypi/rpy2

Spack package:

py-rpy2/package.py

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:

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:

https://stuvel.eu/rsa

Spack package:

py-rsa/package.py

Versions:

3.4.2

Build Dependencies:

python, py-setuptools, py-pyasn1

Link Dependencies:

Run Dependencies:

python, py-setuptools, py-pyasn1

Description:

Pure-Python RSA implementation

py-rseqc¶

Homepage:

http://rseqc.sourceforge.net

Spack package:

py-rseqc/package.py

Versions:

2.6.4

Build Dependencies:

python, py-setuptools, py-bx-python, py-numpy, py-pysam, r

Link Dependencies:

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:

http://toblerity.org/rtree/

Spack package:

py-rtree/package.py

Versions:

0.8.3

Build Dependencies:

python, py-setuptools, libspatialindex

Link Dependencies:

python, libspatialindex

Run Dependencies:

Description:

Python interface to the RTREE.4 Library.

py-saga-python¶

Homepage:

http://radical.rutgers.edu

Spack package:

py-saga-python/package.py

Versions:

0.41.3

Build Dependencies:

python, py-setuptools, py-apache-libcloud, py-radical-utils

Link Dependencies:

Run Dependencies:

python, py-apache-libcloud, py-radical-utils

Description:

A light-weight access layer for distributed computing infrastructure

py-scandir¶

Homepage:

https://github.com/benhoyt/scandir

Spack package:

py-scandir/package.py

Versions:

1.9.0, 1.6

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

scandir, a better directory iterator and faster os.walk().

py-scientificpython¶

Homepage:

https://sourcesup.renater.fr/projects/scientific-py/

Spack package:

py-scientificpython/package.py

Versions:

2.8.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

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-image¶

Homepage:

http://scikit-image.org/

Spack package:

py-scikit-image/package.py

Versions:

0.14.2, 0.12.3

Build Dependencies:

python, py-dask, pil, py-networkx, py-six, py-scipy, py-matplotlib, py-setuptools, py-cython

Link Dependencies:

Run Dependencies:

python, py-dask, pil, py-networkx, py-six, py-scipy, py-matplotlib

Description:

Image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.

py-scikit-learn¶

Homepage:

https://pypi.python.org/pypi/scikit-learn

Spack package:

py-scikit-learn/package.py

Versions:

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-cython, py-setuptools

Link Dependencies:

Run Dependencies:

Test Dependencies:

py-test

Description:

A set of python modules for machine learning and data mining.

py-scikit-optimize¶

Homepage:

https://scikit-optimize.github.io

Spack package:

py-scikit-optimize/package.py

Versions:

0.5.2

Build Dependencies:

python, py-setuptools, py-numpy, py-scikit-learn, py-scipy, py-matplotlib

Link Dependencies:

python, py-matplotlib

Run Dependencies:

python, py-numpy, py-scikit-learn, py-scipy

Test Dependencies:

py-test

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:

http://www.scipy.org/

Spack package:

py-scipy/package.py

Versions:

1.2.1, 1.1.0, 1.0.0, 0.19.1, 0.19.0, 0.18.1, 0.17.0, 0.15.1, 0.15.0

Build Dependencies:

python, py-setuptools, py-numpy, blas, lapack

Link Dependencies:

python, blas, lapack

Run Dependencies:

Test Dependencies:

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:

https://github.com/soravux/scoop

Spack package:

py-scoop/package.py

Versions:

0.7.1.1

Build Dependencies:

python, py-setuptools, py-greenlet, py-zmq

Link Dependencies:

Run Dependencies:

python, py-greenlet, py-zmq

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-seaborn¶

Homepage:

http://seaborn.pydata.org/

Spack package:

py-seaborn/package.py

Versions:

0.9.0, 0.7.1

Build Dependencies:

python, py-setuptools, py-numpy, py-scipy, py-matplotlib, py-pandas

Link Dependencies:

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-send2trash¶

Homepage:

https://github.com/hsoft/send2trash

Spack package:

py-send2trash/package.py

Versions:

1.5.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Python library to send files to Trash/Recycle on all platforms.

py-setuptools¶

Homepage:

https://github.com/pypa/setuptools

Spack package:

py-setuptools/package.py

Versions:

41.0.1, 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, 20.5, 19.2, 18.1, 16.0, 11.3.1

Build Dependencies:

python, py-packaging, py-six, py-appdirs

Link Dependencies:

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:

https://pypi.python.org/pypi/setuptools-git

Spack package:

py-setuptools-git/package.py

Versions:

1.2

Build Dependencies:

python, py-setuptools, git

Link Dependencies:

python, git

Run Dependencies:

Description:

Setuptools revision control system plugin for Git

py-setuptools-scm¶

Homepage:

https://github.com/pypa/setuptools_scm

Spack package:

py-setuptools-scm/package.py

Versions:

3.1.0, 1.15.6

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

The blessed package to manage your versions by scm tags.

py-sfepy¶

Homepage:

http://sfepy.org

Spack package:

py-sfepy/package.py

Versions:

2017.3

Build Dependencies:

Link Dependencies:

Run Dependencies:

python, py-numpy, py-six, py-scipy, py-matplotlib, py-sympy, hdf5, py-pytables, 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-sh¶

Homepage:

https://github.com/amoffat/sh

Spack package:

py-sh/package.py

Versions:

1.12.9, 1.11

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Python subprocess interface

py-shapely¶

Homepage:

https://github.com/Toblerity/Shapely

Spack package:

py-shapely/package.py

Versions:

1.6.4

Build Dependencies:

python, py-setuptools, py-cython, py-numpy, geos

Link Dependencies:

python, geos

Run Dependencies:

Description:

Manipulation and analysis of geometric objects in the Cartesian plane.

py-shiboken¶

Homepage:

https://shiboken.readthedocs.org/

Spack package:

py-shiboken/package.py

Versions:

1.2.2

Build Dependencies:

python, cmake, py-setuptools, py-sphinx, libxml2, qt

Link Dependencies:

python, libxml2, qt

Run Dependencies:

Description:

Shiboken generates bindings for C++ libraries using CPython.

py-simplegeneric¶

Homepage:

https://pypi.python.org/pypi/simplegeneric

Spack package:

py-simplegeneric/package.py

Versions:

0.8.1, 0.8

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Simple generic functions (similar to Python's own len(), pickle.dump(), etc.)

py-simplejson¶

Homepage:

https://github.com/simplejson/simplejson

Spack package:

py-simplejson/package.py

Versions:

3.10.0, 3.9.0, 3.8.2, 3.8.1, 3.8.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Simplejson is a simple, fast, extensible JSON encoder/decoder for Python

py-singledispatch¶

Homepage:

https://pypi.python.org/pypi/singledispatch

Spack package:

py-singledispatch/package.py

Versions:

3.4.0.3

Build Dependencies:

python, py-setuptools, py-six, py-ordereddict

Link Dependencies:

Run Dependencies:

python, py-six, py-ordereddict

Description:

This library brings functools.singledispatch to Python 2.6-3.3.

py-sip¶

Homepage:

http://www.riverbankcomputing.com/software/sip/intro

Spack package:

py-sip/package.py

Versions:

4.19.13, 4.16.7, 4.16.5

Build Dependencies:

Link Dependencies:

Description:

SIP is a tool that makes it very easy to create Python bindings for C and C++ libraries.

py-six¶

Homepage:

https://pypi.python.org/pypi/six

Spack package:

py-six/package.py

Versions:

1.12.0, 1.11.0, 1.10.0, 1.9.0, 1.8.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Python 2 and 3 compatibility utilities.

py-slepc4py¶

Homepage:

https://bitbucket.org/slepc/slepc4py

Spack package:

py-slepc4py/package.py

Versions:

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:

https://github.com/acorg/slurm-pipeline

Spack package:

py-slurm-pipeline/package.py

Versions:

2.0.9, 1.1.13

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

A Python class for scheduling SLURM jobs

py-sncosmo¶

Homepage:

http://sncosmo.readthedocs.io/

Spack package:

py-sncosmo/package.py

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:

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:

https://github.com/shibukawa/snowball_py

Spack package:

py-snowballstemmer/package.py

Versions:

1.2.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

This package provides 16 stemmer algorithms (15 + Poerter English stemmer) generated from Snowball algorithms.

py-snuggs¶

Homepage:

https://github.com/mapbox/snuggs

Spack package:

py-snuggs/package.py

Versions:

1.4.1

Build Dependencies:

python, py-numpy, py-click, py-pyparsing

Link Dependencies:

Run Dependencies:

python, py-numpy, py-click, py-pyparsing

Description:

Snuggs are s-expressions for Numpy

py-spatialist¶

Homepage:

https://github.com/johntruckenbrodt/spatialist

Spack package:

py-spatialist/package.py

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:

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-spectra¶

Homepage:

https://pypi.python.org/pypi/spectra/0.0.8

Spack package:

py-spectra/package.py

Versions:

0.0.11, 0.0.8

Build Dependencies:

python, py-setuptools, py-colormath

Link Dependencies:

Run Dependencies:

python, py-colormath

Description:

Color scales and color conversion made easy for Python.

py-spefile¶

Homepage:

https://github.com/conda-forge/spefile-feedstock

Spack package:

py-spefile/package.py

Versions:

1.6

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Reader for SPE files part of pyspec a set of python routines for data analysis of x-ray scattering experiments

py-spglib¶

Homepage:

http://atztogo.github.io/spglib/

Spack package:

py-spglib/package.py

Versions:

1.9.9.18

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Python bindings for C library for finding and handling crystal symmetries.

py-sphinx¶

Homepage:

http://sphinx-doc.org

Spack package:

py-sphinx/package.py

Versions:

1.8.4, 1.8.2, 1.7.4, 1.6.3, 1.6.1, 1.5.5, 1.4.5, 1.3.1

Build Dependencies:

python, py-setuptools, py-six, py-jinja2, py-pygments, py-docutils, py-snowballstemmer, py-babel, py-alabaster, py-imagesize, py-requests, py-sphinx-rtd-theme, py-packaging, py-sphinxcontrib-websupport, py-typing

Link Dependencies:

Run Dependencies:

Test Dependencies:

py-pytest, py-mock, py-simplejson, py-html5lib

Description:

Sphinx Documentation Generator.

py-sphinx-bootstrap-theme¶

Homepage:

https://pypi.python.org/pypi/sphinx-bootstrap-theme/

Spack package:

py-sphinx-bootstrap-theme/package.py

Versions:

0.4.13

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Sphinx Bootstrap Theme.

py-sphinx-rtd-theme¶

Homepage:

https://github.com/rtfd/sphinx_rtd_theme/

Spack package:

py-sphinx-rtd-theme/package.py

Versions:

0.4.3, 0.2.5b1, 0.1.10a0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

ReadTheDocs.org theme for Sphinx.

py-sphinxautomodapi¶

Homepage:

https://sphinx-automodapi.readthedocs.io/en/latest/

Spack package:

py-sphinxautomodapi/package.py

Versions:

0.9

Build Dependencies:

python, py-setuptools, py-sphinx

Link Dependencies:

Run Dependencies:

Description:

Provides Sphinx directives to autogenerate API documentation pages

py-sphinxcontrib-bibtex¶

Homepage:

https://pypi.python.org/pypi/sphinxcontrib-bibtex

Spack package:

py-sphinxcontrib-bibtex/package.py

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:

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-programoutput¶

Homepage:

https://sphinxcontrib-programoutput.readthedocs.org/

Spack package:

py-sphinxcontrib-programoutput/package.py

Versions:

0.10

Build Dependencies:

python, py-setuptools, py-sphinx

Link Dependencies:

Run Dependencies:

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-websupport¶

Homepage:

http://sphinx-doc.org/

Spack package:

py-sphinxcontrib-websupport/package.py

Versions:

1.1.0, 1.0.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

Test Dependencies:

py-pytest, py-mock

Description:

sphinxcontrib-webuspport provides a Python API to easily integrate Sphinx documentation into your Web application.

py-spyder¶

Homepage:

https://github.com/spyder-ide/spyder

Spack package:

py-spyder/package.py

Versions:

3.1.3, 2.3.9

Build Dependencies:

python, py-rope, py-jedi, py-pyflakes, py-pygments, py-qtconsole, py-nbconvert, py-sphinx, py-pycodestyle, py-pylint, py-psutil, py-qtawesome, py-qtpy, qt, py-pickleshare, py-zmq, py-chardet, py-numpydoc

Link Dependencies:

Run Dependencies:

Description:

Scientific PYthon Development EnviRonment

py-spykeutils¶

Homepage:

https://github.com/rproepp/spykeutils

Spack package:

py-spykeutils/package.py

Versions:

0.4.3

Build Dependencies:

python, py-setuptools, py-scipy, py-quantities, py-neo

Link Dependencies:

Run Dependencies:

python, py-scipy, py-quantities, py-neo

Description:

Utilities for analyzing electrophysiological data

py-sqlalchemy¶

Homepage:

http://www.sqlalchemy.org/

Spack package:

py-sqlalchemy/package.py

Versions:

1.0.12

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

The Python SQL Toolkit and Object Relational Mapper

py-statsmodels¶

Homepage:

http://www.statsmodels.org

Spack package:

py-statsmodels/package.py

Versions:

0.8.0

Build Dependencies:

python, py-setuptools, py-numpy, py-scipy, py-pandas, py-patsy, py-cython

Link Dependencies:

Run Dependencies:

python, py-numpy, py-scipy, py-pandas, py-patsy, py-cython, py-matplotlib

Description:

Statistical computations and models for use with SciPy

py-stevedore¶

Homepage:

https://docs.openstack.org/stevedore/latest/

Spack package:

py-stevedore/package.py

Versions:

1.28.0

Build Dependencies:

python, py-six, py-pbr

Link Dependencies:

Run Dependencies:

python, py-six, py-pbr

Description:

Manage Dynamic Plugins for Python Applications.

py-storm¶

Homepage:

https://storm.canonical.com/

Spack package:

py-storm/package.py

Versions:

0.20

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Storm is an object-relational mapper (ORM) for Python

py-subprocess32¶

Homepage:

https://pypi.python.org/pypi/subprocess32

Spack package:

py-subprocess32/package.py

Versions:

3.2.7

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

A backport of the subprocess module from Python 3.2/3.3 for 2.x.

py-symengine¶

Homepage:

https://github.com/symengine/symengine.py

Spack package:

py-symengine/package.py

Versions:

develop, 0.2.0

Build Dependencies:

python, py-setuptools, py-cython, cmake, symengine

Link Dependencies:

python, symengine

Run Dependencies:

Description:

Python wrappers for SymEngine, a symbolic manipulation library.

py-symfit¶

Homepage:

http://symfit.readthedocs.org

Spack package:

py-symfit/package.py

Versions:

0.3.5

Build Dependencies:

python, py-setuptools, py-pbr

Link Dependencies:

Run Dependencies:

python, py-numpy, py-scipy, py-sympy, py-funcsigs

Description:

Symbolic Fitting; fitting as it should be.

py-sympy¶

Homepage:

https://pypi.python.org/pypi/sympy

Spack package:

py-sympy/package.py

Versions:

1.3, 1.1.1, 1.0, 0.7.6

Build Dependencies:

python, py-mpmath

Link Dependencies:

Run Dependencies:

python, py-mpmath

Description:

SymPy is a Python library for symbolic mathematics.

py-tabulate¶

Homepage:

https://bitbucket.org/astanin/python-tabulate

Spack package:

py-tabulate/package.py

Versions:

0.7.7

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Pretty-print tabular data

py-tappy¶

Homepage:

https://github.com/mblayman/tappy

Spack package:

py-tappy/package.py

Versions:

1.6

Build Dependencies:

python, py-nose, py-pygments, py-setuptools

Link Dependencies:

Run Dependencies:

python, py-nose, py-pygments

Description:

Python TAP interface module for unit tests

py-tblib¶

Homepage:

https://github.com/ionelmc/python-tblib

Spack package:

py-tblib/package.py

Versions:

1.4.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Traceback fiddling library. Allows you to pickle tracebacks.

py-terminado¶

Homepage:

https://pypi.python.org/pypi/terminado

Spack package:

py-terminado/package.py

Versions:

0.8.1, 0.6

Build Dependencies:

python, py-tornado, py-ptyprocess

Link Dependencies:

Run Dependencies:

python, py-tornado, py-ptyprocess

Description:

Terminals served to term.js using Tornado websockets

py-testinfra¶

Homepage:

https://testinfra.readthedocs.io

Spack package:

py-testinfra/package.py

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:

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-tetoolkit¶

Homepage:

http://hammelllab.labsites.cshl.edu/software

Spack package:

py-tetoolkit/package.py

Versions:

2.0.3, 1.5.1

Build Dependencies:

python, py-setuptools, py-pysam, r-deseq, r-deseq2

Link Dependencies:

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-texttable¶

Homepage:

https://github.com/foutaise/texttable/

Spack package:

py-texttable/package.py

Versions:

1.6.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Python module for creating simple ASCII tables.

py-theano¶

Homepage:

http://deeplearning.net/software/theano/

Spack package:

py-theano/package.py

Versions:

master, 1.0.4, 1.0.2, 1.0.1, 0.8.2

Build Dependencies:

python, py-setuptools, py-scipy, py-numpy, py-six, blas, cuda, cudnn, py-pygpu, libgpuarray

Link Dependencies:

python, blas, cuda, cudnn, libgpuarray

Run Dependencies:

python, py-setuptools, py-scipy, py-numpy, py-six, py-pygpu

Test Dependencies:

py-nose, py-nose-parameterized

Description:

Optimizing compiler for evaluating mathematical expressions on CPUs and GPUs.

py-tifffile¶

Homepage:

https://github.com/blink1073/tifffile

Spack package:

py-tifffile/package.py

Versions:

0.12.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Read and write image data from and to TIFF files.

py-toml¶

Homepage:

https://github.com/uiri/toml.git

Spack package:

py-toml/package.py

Versions:

0.10.0, 0.9.3

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

http://tomopy.readthedocs.io/en/latest/index.html

Spack package:

py-tomopy/package.py

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:

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:

http://github.com/pytoolz/toolz/

Spack package:

py-toolz/package.py

Versions:

0.9.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

A set of utility functions for iterators, functions, and dictionaries

py-tornado¶

Homepage:

https://github.com/tornadoweb/tornado

Spack package:

py-tornado/package.py

Versions:

4.4.0

Build Dependencies:

python, py-setuptools, py-backports-ssl-match-hostname, py-singledispatch, py-certifi, py-backports-abc

Link Dependencies:

Run Dependencies:

python, py-backports-ssl-match-hostname, py-singledispatch, py-certifi, py-backports-abc

Description:

Tornado is a Python web framework and asynchronous networking library.

py-tqdm¶

Homepage:

https://github.com/tqdm/tqdm

Spack package:

py-tqdm/package.py

Versions:

4.8.4

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

A Fast, Extensible Progress Meter

py-traceback2¶

Homepage:

https://github.com/testing-cabal/traceback2

Spack package:

py-traceback2/package.py

Versions:

1.4.0

Build Dependencies:

python, py-setuptools, py-linecache2, py-pbr

Link Dependencies:

Run Dependencies:

python, py-linecache2, py-pbr

Description:

Backports of the traceback module

py-traitlets¶

Homepage:

https://pypi.python.org/pypi/traitlets

Spack package:

py-traitlets/package.py

Versions:

4.3.1, 4.3.0, 4.2.2, 4.2.1, 4.2.0, 4.1.0, 4.0.0, 4.0

Build Dependencies:

python, py-decorator, py-ipython-genutils, py-enum34

Link Dependencies:

Run Dependencies:

python, py-decorator, py-ipython-genutils, py-enum34

Description:

Traitlets Python config system

py-treehash¶

Homepage:

https://github.com/jdswinbank/treehash

Spack package:

py-treehash/package.py

Versions:

1.0.2

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Calculates a SHA256 (or, potentially, any other hashlib supported function) "tree" hash, as used by e.g. Amazon Glacier.

py-tuiview¶

Homepage:

https://bitbucket.org/chchrsc/tuiview

Spack package:

py-tuiview/package.py

Versions:

1.1.7

Build Dependencies:

python, py-pyqt, py-numpy, gdal

Link Dependencies:

python, gdal

Run Dependencies:

python, py-pyqt, py-numpy

Description:

TuiView is a lightweight raster GIS with powerful raster attribute table manipulation abilities.

py-twisted¶

Homepage:

https://twistedmatrix.com/

Spack package:

py-twisted/package.py

Versions:

15.4.0, 15.3.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

An asynchronous networking framework written in Python

py-typing¶

Homepage:

https://docs.python.org/3/library/typing.html

Spack package:

py-typing/package.py

Versions:

3.6.4, 3.6.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

This is a backport of the standard library typing module to Python versions older than 3.6.

py-typing-extensions¶

Homepage:

https://github.com/python/typing/tree/master/typing_extensions

Spack package:

py-typing-extensions/package.py

Versions:

3.7.2

Build Dependencies:

python, py-setuptools, py-typing

Link Dependencies:

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:

https://github.com/regebro/tzlocal

Spack package:

py-tzlocal/package.py

Versions:

1.3

Build Dependencies:

python, py-setuptools, py-pytz

Link Dependencies:

Run Dependencies:

python, py-pytz

Description:

tzinfo object for the local timezone.

py-udunits¶

Homepage:

https://github.com/SciTools/cf_units

Spack package:

py-udunits/package.py

Versions:

1.1.3

Build Dependencies:

python, py-setuptools, py-six, py-netcdf4, udunits2

Link Dependencies:

python, udunits2

Run Dependencies:

python, py-six, py-netcdf4

Description:

The MetOffice cf_units Python interface to the UDUNITS-2 Library.

py-umi-tools¶

Homepage:

https://github.com/CGATOxford/UMI-tools

Spack package:

py-umi-tools/package.py

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:

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:

https://github.com/rrwick/Unicycler

Spack package:

py-unicycler/package.py

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:

https://pypi.python.org/pypi/unittest2

Spack package:

py-unittest2/package.py

Versions:

1.1.0

Build Dependencies:

python, py-setuptools, py-enum34, py-traceback2, py-six, py-argparse

Link Dependencies:

Run Dependencies:

python, py-enum34, 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:

https://pypi.python.org/pypi/unittest2py3k

Spack package:

py-unittest2py3k/package.py

Versions:

0.5.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

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-urllib3¶

Homepage:

https://urllib3.readthedocs.io/

Spack package:

py-urllib3/package.py

Versions:

1.21.1, 1.20, 1.14

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

HTTP library with thread-safe connection pooling, file post, and more.

py-urwid¶

Homepage:

http://urwid.org/

Spack package:

py-urwid/package.py

Versions:

1.3.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

A full-featured console UI library

py-vcversioner¶

Homepage:

https://github.com/habnabit/vcversioner

Spack package:

py-vcversioner/package.py

Versions:

2.16.0.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Vcversioner: Take version numbers from version control.

py-virtualenv¶

Homepage:

https://virtualenv.pypa.io/

Spack package:

py-virtualenv/package.py

Versions:

16.4.1, 16.0.0, 15.1.0, 15.0.1, 13.0.1, 1.11.6

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

virtualenv is a tool to create isolated Python environments.

py-virtualenv-clone¶

Homepage:

https://github.com/edwardgeorge/virtualenv-clone

Spack package:

py-virtualenv-clone/package.py

Versions:

0.2.6

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

A script for cloning a non-relocatable virtualenv.

py-virtualenvwrapper¶

Homepage:

https://bitbucket.org/virtualenvwrapper/virtualenvwrapper.git

Spack package:

py-virtualenvwrapper/package.py

Versions:

4.8.2

Build Dependencies:

python, py-virtualenv, py-virtualenv-clone, py-stevedore, py-setuptools

Link Dependencies:

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-vsc-base¶

Homepage:

https://github.com/hpcugent/vsc-base/

Spack package:

py-vsc-base/package.py

Versions:

2.5.8

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Common Python libraries tools created by HPC-UGent

py-vsc-install¶

Homepage:

https://github.com/hpcugent/vsc-install/

Spack package:

py-vsc-install/package.py

Versions:

0.10.25

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Shared setuptools functions and classes for Python libraries developed by HPC-UGent.

py-wcsaxes¶

Homepage:

http://wcsaxes.readthedocs.io/en/latest/index.html

Spack package:

py-wcsaxes/package.py

Versions:

0.8

Build Dependencies:

python, py-setuptools, py-numpy, py-matplotlib, py-astropy

Link Dependencies:

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:

https://pypi.python.org/pypi/wcwidth

Spack package:

py-wcwidth/package.py

Versions:

0.1.7

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Measures number of Terminal column cells of wide-character codes

py-webencodings¶

Homepage:

https://github.com/gsnedders/python-webencodings

Spack package:

py-webencodings/package.py

Versions:

0.5.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

This is a Python implementation of the WHATWG Encoding standard.

py-webkit-server¶

Homepage:

https://github.com/niklasb/webkit-server

Spack package:

py-webkit-server/package.py

Versions:

develop, 1.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

a Webkit-based, headless web client

py-weblogo¶

Homepage:

http://weblogo.threeplusone.com

Spack package:

py-weblogo/package.py

Versions:

3.6.0

Build Dependencies:

python, py-setuptools, ghostscript, pdf2svg, py-numpy

Link Dependencies:

Run Dependencies:

python, ghostscript, pdf2svg, py-numpy

Description:

WebLogo is a web based application designed to make the generation of sequence logos as easy and painless as possible.

py-werkzeug¶

Homepage:

http://werkzeug.pocoo.org

Spack package:

py-werkzeug/package.py

Versions:

0.11.15, 0.11.11

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

The Swiss Army knife of Python web development

py-whatshap¶

Homepage:

https://whatshap.readthedocs.io/en/latest/

Spack package:

py-whatshap/package.py

Versions:

0.17

Build Dependencies:

python, py-setuptools, py-cython

Link Dependencies:

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:

https://pypi.python.org/pypi/wheel

Spack package:

py-wheel/package.py

Versions:

0.33.1, 0.29.0, 0.26.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

A built-package format for Python.

py-widgetsnbextension¶

Homepage:

https://pypi.python.org/pypi/widgetsnbextension

Spack package:

py-widgetsnbextension/package.py

Versions:

1.2.6

Build Dependencies:

python, py-setuptools, py-jupyter-notebook

Link Dependencies:

Run Dependencies:

python, py-jupyter-notebook

Description:

IPython HTML widgets for Jupyter

py-wrapt¶

Homepage:

https://github.com/GrahamDumpleton/wrapt

Spack package:

py-wrapt/package.py

Versions:

1.10.10

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Module for decorators, wrappers and monkey patching.

py-xarray¶

Homepage:

https://github.com/pydata/xarray

Spack package:

py-xarray/package.py

Versions:

0.9.1

Build Dependencies:

python, py-setuptools, py-pandas, py-numpy

Link Dependencies:

Run Dependencies:

python, py-pandas, py-numpy

Description:

N-D labeled arrays and datasets in Python

py-xattr¶

Homepage:

http://pyxattr.k1024.org/

Spack package:

py-xattr/package.py

Versions:

develop

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

A python interface to access extended file attributes, sans libattr dependency

py-xdot¶

Homepage:

https://github.com/jrfonseca/xdot.py

Spack package:

py-xdot/package.py

Versions:

master, 1.0, 0.9

Build Dependencies:

python, py-setuptools, py-pygobject, py-pycairo, pango, atk, gdk-pixbuf, gtkplus

Link Dependencies:

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:

https://gitlab.cern.ch/gaudi/xenv

Spack package:

py-xenv/package.py

Versions:

develop_2018-12-20, develop

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Helpers to work with the environment in a platform independent way.

py-xlrd¶

Homepage:

http://www.python-excel.org/

Spack package:

py-xlrd/package.py

Versions:

0.9.4

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Library for developers to extract data from Microsoft Excel (tm) spreadsheet files

py-xlsxwriter¶

Homepage:

https://pypi.python.org/pypi/XlsxWriter

Spack package:

py-xlsxwriter/package.py

Versions:

1.0.2

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

XlsxWriter is a Python module for writing files in the Excel 2007+ XLSX file format.

py-xmlrunner¶

Homepage:

https://github.com/pycontribs/xmlrunner

Spack package:

py-xmlrunner/package.py

Versions:

1.7.7

Build Dependencies:

python, py-setuptools, py-unittest2

Link Dependencies:

Run Dependencies:

python, py-unittest2

Description:

PyUnit-based test runner with JUnit like XML reporting.

py-xopen¶

Homepage:

https://github.com/marcelm/xopen

Spack package:

py-xopen/package.py

Versions:

0.5.0, 0.1.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

https://xcb.freedesktop.org/

Spack package:

py-xpyb/package.py

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:

https://pypi.python.org/pypi/xvfbwrapper/0.2.9

Spack package:

py-xvfbwrapper/package.py

Versions:

0.2.9

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

run headless display inside X virtual framebuffer (Xvfb)

py-yamlreader¶

Homepage:

http://pyyaml.org/wiki/PyYAML

Spack package:

py-yamlreader/package.py

Versions:

3.0.4

Build Dependencies:

python, py-setuptools, py-pyyaml, py-six

Link Dependencies:

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:

https://github.com/google/yapf

Spack package:

py-yapf/package.py

Versions:

0.2.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Yet Another Python Formatter

py-yt¶

Homepage:

http://yt-project.org

Spack package:

py-yt/package.py

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:

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:

https://xgitlab.cels.anl.gov/pbalapra/ytopt

Spack package:

py-ytopt/package.py

Versions:

0.1.0

Build Dependencies:

python, py-scikit-learn, py-scikit-optimize

Link Dependencies:

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-zmq¶

Homepage:

https://github.com/zeromq/pyzmq

Spack package:

py-zmq/package.py

Versions:

17.1.2, 16.0.2, 14.7.0

Build Dependencies:

python, py-cython, py-py, py-cffi, zeromq

Link Dependencies:

python, zeromq

Run Dependencies:

python, py-cython, py-py, py-cffi

Description:

PyZMQ: Python bindings for zeromq.

py-zope-event¶

Homepage:

http://github.com/zopefoundation/zope.event

Spack package:

py-zope-event/package.py

Versions:

4.3.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Very basic event publishing system.

py-zope-interface¶

Homepage:

https://github.com/zopefoundation/zope.interface

Spack package:

py-zope-interface/package.py

Versions:

4.5.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

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.

pythia6¶

Homepage:

https://pythiasix.hepforge.org/

Spack package:

pythia6/package.py

Versions:

6.4.28

Build Dependencies:

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.

python¶

Homepage:

https://www.python.org/

Spack package:

python/package.py

Versions:

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, readline, ncurses, openssl, sqlite, gdbm, libnsl, zlib, bzip2, xz, expat, libffi, tk, tcl, libuuid

Link Dependencies:

readline, ncurses, openssl, sqlite, gdbm, libnsl, zlib, bzip2, xz, expat, libffi, tk, tcl, libuuid

Description:

The Python programming language.

qbank¶

Homepage:

http://www.pnnl.gov/

Spack package:

qbank/package.py

Versions:

2.10.4

Build Dependencies:

openssl, perl, perl-dbi

Link Dependencies:

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:

http://qboxcode.org/

Spack package:

qbox/package.py

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:

https://userbase.kde.org/QCA

Spack package:

qca/package.py

Versions:

2.1.3

Build Dependencies:

cmake, qt

Link Dependencies:

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.

qhull¶

Homepage:

http://www.qhull.org

Spack package:

qhull/package.py

Versions:

2015.2, 2012.1

Build Dependencies:

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:

http://qjson.sourceforge.net/

Spack package:

qjson/package.py

Versions:

0.9.0

Build Dependencies:

cmake, qt

Link Dependencies:

Description:

QJson is a Qt-based library that maps JSON data to QVariant objects and vice versa.

qmcpack¶

Homepage:

http://www.qmcpack.org/

Spack package:

qmcpack/package.py

Versions:

develop, 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, hdf5, blas, lapack, fftw-api

Link Dependencies:

cuda, boost, libxml2, mpi, 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:

https://github.com/lanl/qmd-progress

Spack package:

qmd-progress/package.py

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.

qorts¶

Homepage:

https://github.com/hartleys/QoRTs

Spack package:

qorts/package.py

Versions:

1.2.42

Build Dependencies:

Link Dependencies:

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.

qrupdate¶

Homepage:

http://sourceforge.net/projects/qrupdate/

Spack package:

qrupdate/package.py

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.

qt¶

Homepage:

http://qt.io

Spack package:

qt/package.py

Versions:

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, 4.8.6, 4.8.5, 3.3.8b

Build Dependencies:

pkgconfig, openssl, glib, gtkplus, libxml2, zlib, dbus, libtiff, libpng, libmng, jpeg, icu4c, fontconfig, freetype, sqlite, pcre, pcre2, double-conversion, harfbuzz, python, gl, libxcb, xcb-util-image, xcb-util-keysyms, xcb-util-wm, xcb-util-renderutil, libxkbcommon, inputproto, libx11, libxext, flex, bison, gperf

Link Dependencies:

openssl, glib, gtkplus, libxml2, zlib, dbus, libtiff, libpng, libmng, jpeg, icu4c, fontconfig, freetype, pcre, pcre2, double-conversion, harfbuzz, gl, libxcb, xcb-util-image, xcb-util-keysyms, xcb-util-wm, xcb-util-renderutil, libxkbcommon, inputproto, libx11, libxext, gperf

Run Dependencies:

sqlite

Description:

Qt is a comprehensive cross-platform C++ application framework.

qt-creator¶

Homepage:

https://www.qt.io/ide/

Spack package:

qt-creator/package.py

Versions:

4.8.0, 4.4.0, 4.3.1, 4.1.0

Build Dependencies:

qt, sqlite

Link Dependencies:

qt, sqlite

Description:

The Qt Creator IDE.

qtgraph¶

Homepage:

https://github.com/OpenSpeedShop/QtGraph

Spack package:

qtgraph/package.py

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:

http://www.cs.sandia.gov/qthreads/

Spack package:

qthreads/package.py

Versions:

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.

quantum-espresso¶

Homepage:

http://quantum-espresso.org

Spack package:

quantum-espresso/package.py

Versions:

develop, 6.4, 6.3, 6.2.1, 6.2.0, 6.1.0, 6.0.0, 5.4, 5.3, latest-backports

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:

http://quinoacomputing.org

Spack package:

quinoa/package.py

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:

http://qwt.sourceforge.net/

Spack package:

qwt/package.py

Versions:

6.1.3, 5.2.2

Build Dependencies:

Link Dependencies:

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.

r¶

Homepage:

https://www.r-project.org

Spack package:

r/package.py

Versions:

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, curl, pcre, java

Link Dependencies:

blas, lapack, readline, ncurses, icu4c, glib, zlib, bzip2, libtiff, jpeg, cairo, pango, freetype, tcl, tk, libx11, libxt, 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:

https://www.bioconductor.org/packages/a4/

Spack package:

r-a4/package.py

Versions:

1.24.0

Build Dependencies:

r, r-a4base, r-a4preproc, r-a4classif, r-a4core, r-a4reporting

Link Dependencies:

Run Dependencies:

r, r-a4base, r-a4preproc, r-a4classif, r-a4core, r-a4reporting

Description:

Automated Affymetrix Array Analysis Umbrella Package.

r-a4base¶

Homepage:

https://www.bioconductor.org/packages/a4Base/

Spack package:

r-a4base/package.py

Versions:

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:

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.

r-a4classif¶

Homepage:

https://www.bioconductor.org/packages/a4Classif/

Spack package:

r-a4classif/package.py

Versions:

1.24.0

Build Dependencies:

r, r-a4core, r-a4preproc, r-mlinterfaces, r-rocr, r-pamr, r-glmnet, r-varselrf

Link Dependencies:

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:

https://www.bioconductor.org/packages/a4Core/

Spack package:

r-a4core/package.py

Versions:

1.24.0

Build Dependencies:

r, r-biobase, r-glmnet

Link Dependencies:

Run Dependencies:

r, r-biobase, r-glmnet

Description:

Automated Affymetrix Array Analysis Core Package.

r-a4preproc¶

Homepage:

https://www.bioconductor.org/packages/a4Preproc/

Spack package:

r-a4preproc/package.py

Versions:

1.24.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Automated Affymetrix Array Analysis Preprocessing Package.

r-a4reporting¶

Homepage:

https://www.bioconductor.org/packages/a4Reporting

Spack package:

r-a4reporting/package.py

Versions:

1.24.0

Build Dependencies:

r, r-annaffy, r-xtable

Link Dependencies:

Run Dependencies:

r, r-annaffy, r-xtable

Description:

Automated Affymetrix Array Analysis Reporting Package.

r-abadata¶

Homepage:

https://bioconductor.org/packages/ABAData/

Spack package:

r-abadata/package.py

Versions:

1.6.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

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:

https://bioconductor.org/packages/ABAEnrichment/

Spack package:

r-abaenrichment/package.py

Versions:

1.6.0

Build Dependencies:

r, r-rcpp, r-gplots, r-gtools, r-abadata

Link Dependencies:

Run Dependencies:

r, r-rcpp, r-gplots, r-gtools, r-abadata

Description:

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. From version 1.3.5 onwards genomic regions can be provided as input, too; and from version 1.5.9 onwards the function 'get_annotated_genes' offers an easy way to obtain annotations of genes to enriched or user-defined brain regions.

r-abind¶

Homepage:

https://cran.r-project.org/

Spack package:

r-abind/package.py

Versions:

1.4-3

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

https://www.bioconductor.org/packages/ABSSeq/

Spack package:

r-absseq/package.py

Versions:

1.22.8

Build Dependencies:

r, r-locfit, r-limma

Link Dependencies:

Run Dependencies:

r, r-locfit, r-limma

Description:

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:

https://www.bioconductor.org/packages/acde/

Spack package:

r-acde/package.py

Versions:

1.6.0

Build Dependencies:

r, r-boot

Link Dependencies:

Run Dependencies:

r, r-boot

Description:

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:

https://CRAN.R-project.org/package=acepack

Spack package:

r-acepack/package.py

Versions:

1.4.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

ACE and AVAS for Selecting Multiple Regression Transformations.

r-acgh¶

Homepage:

https://www.bioconductor.org/packages/aCGH/

Spack package:

r-acgh/package.py

Versions:

1.54.0

Build Dependencies:

r, r-cluster, r-survival, r-multtest, r-biobase

Link Dependencies:

Run Dependencies:

r, r-cluster, r-survival, r-multtest, r-biobase

Description:

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:

https://www.bioconductor.org/packages/ACME/

Spack package:

r-acme/package.py

Versions:

2.32.0

Build Dependencies:

r, r-biobase, r-biocgenerics

Link Dependencies:

Run Dependencies:

r, r-biobase, r-biocgenerics

Description:

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:

https://cran.r-project.org/web/packages/ada/index.html

Spack package:

r-ada/package.py

Versions:

2.0-5

Build Dependencies:

r, r-rpart

Link Dependencies:

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:

https://cran.r-project.org/package=adabag

Spack package:

r-adabag/package.py

Versions:

4.1

Build Dependencies:

r, r-rpart, r-mlbench, r-caret

Link Dependencies:

Run Dependencies:

r, r-rpart, r-mlbench, r-caret

Description:

Applies Multiclass AdaBoost.M1, SAMME and Bagging.

r-ade4¶

Homepage:

http://pbil.univ-lyon1.fr/ADE-4

Spack package:

r-ade4/package.py

Versions:

1.7-6

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Analysis of Ecological Data : Exploratory and Euclidean Methods in Environmental Sciences

r-adegenet¶

Homepage:

https://github.com/thibautjombart/adegenet/wiki

Spack package:

r-adegenet/package.py

Versions:

2.0.1

Build Dependencies:

r, r-ade4, r-igraph, r-ape, r-shiny, r-ggplot2, r-seqinr, r-spdep, r-reshape2, r-dplyr, r-vegan

Link Dependencies:

Run Dependencies:

r, r-ade4, r-igraph, r-ape, r-shiny, r-ggplot2, r-seqinr, r-spdep, r-reshape2, r-dplyr, r-vegan

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-adsplit¶

Homepage:

https://www.bioconductor.org/packages/adSplit/

Spack package:

r-adsplit/package.py

Versions:

1.46.0

Build Dependencies:

r, r-annotationdbi, r-biobase, r-cluster, r-go-db, r-kegg-db, r-multtest

Link Dependencies:

Run Dependencies:

r, r-annotationdbi, r-biobase, r-cluster, r-go-db, r-kegg-db, r-multtest

Description:

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:

https://cran.r-project.org/web/packages/AER/index.html

Spack package:

r-aer/package.py

Versions:

1.2-5

Build Dependencies:

r, r-car, r-lmtest, r-sandwich, r-survival, r-zoo, r-formula

Link Dependencies:

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:

https://www.bioconductor.org/packages/affxparser/

Spack package:

r-affxparser/package.py

Versions:

1.48.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

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:

https://bioconductor.org/packages/affy/

Spack package:

r-affy/package.py

Versions:

1.54.0

Build Dependencies:

r, r-biocgenerics, r-biobase, r-affyio, r-biocinstaller, r-preprocesscore, r-zlibbioc

Link Dependencies:

Run Dependencies:

r, r-biocgenerics, r-biobase, r-affyio, r-biocinstaller, r-preprocesscore, r-zlibbioc

Description:

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:

https://www.bioconductor.org/packages/affycomp/

Spack package:

r-affycomp/package.py

Versions:

1.52.0

Build Dependencies:

r, r-biobase

Link Dependencies:

Run Dependencies:

r, r-biobase

Description:

The package contains functions that can be used to compare expression measures for Affymetrix Oligonucleotide Arrays.

r-affycompatible¶

Homepage:

https://www.bioconductor.org/packages/AffyCompatible/

Spack package:

r-affycompatible/package.py

Versions:

1.36.0

Build Dependencies:

r, r-xml, r-rcurl, r-biostrings

Link Dependencies:

Run Dependencies:

r, r-xml, r-rcurl, r-biostrings

Description:

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:

https://www.bioconductor.org/packages/affyContam/

Spack package:

r-affycontam/package.py

Versions:

1.34.0

Build Dependencies:

r, r-biobase, r-affy, r-affydata

Link Dependencies:

Run Dependencies:

r, r-biobase, r-affy, r-affydata

Description:

structured corruption of cel file data to demonstrate QA effectiveness.

r-affycoretools¶

Homepage:

https://www.bioconductor.org/packages/affycoretools/

Spack package:

r-affycoretools/package.py

Versions:

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

Link Dependencies:

Run Dependencies:

Description:

Various wrapper functions that have been written to streamline the more common analyses that a core Biostatistician might see.

r-affydata¶

Homepage:

https://www.bioconductor.org/packages/affydata/

Spack package:

r-affydata/package.py

Versions:

1.24.0

Build Dependencies:

r, r-affy

Link Dependencies:

Run Dependencies:

r, r-affy

Description:

Example datasets of a slightly large size. They represent 'real world examples', unlike the artificial examples included in the package affy.

r-affyexpress¶

Homepage:

https://www.bioconductor.org/packages/AffyExpress/

Spack package:

r-affyexpress/package.py

Versions:

1.42.0

Build Dependencies:

r, r-affy, r-limma

Link Dependencies:

Run Dependencies:

r, r-affy, r-limma

Description:

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:

https://www.bioconductor.org/packages/affyILM/

Spack package:

r-affyilm/package.py

Versions:

1.28.0

Build Dependencies:

r, r-gcrma, r-affxparser, r-affy, r-biobase

Link Dependencies:

Run Dependencies:

r, r-gcrma, r-affxparser, r-affy, r-biobase

Description:

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:

https://bioconductor.org/packages/affyio/

Spack package:

r-affyio/package.py

Versions:

1.46.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

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:

https://www.bioconductor.org/packages/affypdnn/

Spack package:

r-affypdnn/package.py

Versions:

1.50.0

Build Dependencies:

r, r-affy

Link Dependencies:

Run Dependencies:

r, r-affy

Description:

The package contains functions to perform the PDNN method described by Li Zhang et al.

r-affyplm¶

Homepage:

https://www.bioconductor.org/packages/affyPLM/

Spack package:

r-affyplm/package.py

Versions:

1.52.1

Build Dependencies:

r, r-biocgenerics, r-affy, r-biobase, r-gcrma, r-preprocesscore, r-zlibbioc

Link Dependencies:

Run Dependencies:

r, r-biocgenerics, r-affy, r-biobase, r-gcrma, r-preprocesscore, r-zlibbioc

Description:

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:

https://www.bioconductor.org/packages/affyQCReport/

Spack package:

r-affyqcreport/package.py

Versions:

1.54.0

Build Dependencies:

r, r-biobase, r-affy, r-lattice, r-affyplm, r-genefilter, r-rcolorbrewer, r-simpleaffy, r-xtable

Link Dependencies:

Run Dependencies:

r, r-biobase, r-affy, r-lattice, r-affyplm, r-genefilter, r-rcolorbrewer, r-simpleaffy, r-xtable

Description:

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:

https://www.bioconductor.org/packages/AffyRNADegradation/

Spack package:

r-affyrnadegradation/package.py

Versions:

1.22.0

Build Dependencies:

r, r-affy

Link Dependencies:

Run Dependencies:

r, r-affy

Description:

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:

http://bioconductor.org/packages/AGDEX/

Spack package:

r-agdex/package.py

Versions:

1.24.0

Build Dependencies:

r, r-biobase, r-gseabase

Link Dependencies:

Run Dependencies:

r, r-biobase, r-gseabase

Description:

A tool to evaluate agreement of differential expression for cross- species genomics.

r-agilp¶

Homepage:

http://bioconductor.org/packages/agilp/

Spack package:

r-agilp/package.py

Versions:

3.8.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Agilent expression array processing package.

r-agimicrorna¶

Homepage:

https://www.bioconductor.org/packages/AgiMicroRna/

Spack package:

r-agimicrorna/package.py

Versions:

2.26.0

Build Dependencies:

r, r-affycoretools, r-preprocesscore, r-affy, r-limma, r-biobase

Link Dependencies:

Run Dependencies:

r, r-affycoretools, r-preprocesscore, r-affy, r-limma, r-biobase

Description:

Processing and Analysis of Agilent microRNA data.

r-aims¶

Homepage:

http://bioconductor.org/packages/AIMS/

Spack package:

r-aims/package.py

Versions:

1.8.0

Build Dependencies:

r, r-e1071, r-biobase

Link Dependencies:

Run Dependencies:

r, r-e1071, r-biobase

Description:

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:

http://bioconductor.org/packages/ALDEx2/

Spack package:

r-aldex2/package.py

Versions:

1.8.0

Build Dependencies:

r, r-s4vectors, r-iranges, r-genomicranges, r-summarizedexperiment, r-biocparallel

Link Dependencies:

Run Dependencies:

r, r-s4vectors, r-iranges, r-genomicranges, r-summarizedexperiment, r-biocparallel

Description:

A differential abundance analysis for the comparison of two or more conditions. For example, single-organism and meta-RNA-seq high- throughput sequencing assays, or of selected and unselected values from in-vitro sequence selections. Uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected false discovery rate given the biological and sampling variation using the Wilcox rank test or Welches t-test (aldex.ttest) or the glm and Kruskal Wallis tests (aldex.glm). Reports both P and fdr values calculated by the Benjamini Hochberg correction.

r-allelicimbalance¶

Homepage:

http://bioconductor.org/packages/AllelicImbalance/

Spack package:

r-allelicimbalance/package.py

Versions:

1.14.0

Build Dependencies:

r, r-genomicranges, r-summarizedexperiment, r-genomicalignments, r-biocgenerics, r-annotationdbi, r-bsgenome, r-variantannotation, r-biostrings, r-s4vectors, r-iranges, r-rsamtools, r-genomicfeatures, r-gviz, r-lattice, r-latticeextra, r-gridextra, r-seqinr, r-genomeinfodb, r-nlme

Link Dependencies:

Run Dependencies:

Description:

Provides a framework for allelic specific expression investigation using RNA-seq data.

r-alpine¶

Homepage:

http://bioconductor.org/packages/alpine/

Spack package:

r-alpine/package.py

Versions:

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:

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:

Fragment sequence bias modeling and correction for RNA-seq transcript abundance estimation.

r-als¶

Homepage:

https://cran.r-project.org/package=ALS

Spack package:

r-als/package.py

Versions:

0.0.6

Build Dependencies:

r, r-iso, r-nnls

Link Dependencies:

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:

https://www.bioconductor.org/packages/alsace/

Spack package:

r-alsace/package.py

Versions:

1.12.0

Build Dependencies:

r, r-als, r-ptw

Link Dependencies:

Run Dependencies:

r, r-als, r-ptw

Description:

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:

https://www.bioconductor.org/packages/altcdfenvs/

Spack package:

r-altcdfenvs/package.py

Versions:

2.38.0

Build Dependencies:

r, r-biocgenerics, r-s4vectors, r-biobase, r-affy, r-makecdfenv, r-biostrings, r-hypergraph

Link Dependencies:

Run Dependencies:

r, r-biocgenerics, r-s4vectors, r-biobase, r-affy, r-makecdfenv, r-biostrings, r-hypergraph

Description:

Convenience data structures and functions to handle cdfenvs.

r-amap¶

Homepage:

http://mulcyber.toulouse.inra.fr/projects/amap/

Spack package:

r-amap/package.py

Versions:

0.8-16

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Tools for Clustering and Principal Component Analysis (With robust methods, and parallelized functions).

r-ampliqueso¶

Homepage:

https://www.bioconductor.org/packages/ampliQueso/

Spack package:

r-ampliqueso/package.py

Versions:

1.14.0

Build Dependencies:

r, r-samr, r-deseq, r-edger, r-xtable, r-statmod, r-genefilter, r-variantannotation, r-foreach, r-doparallel, r-gplots, r-ggplot2, r-rgl, r-knitr, r-rnaseqmap

Link Dependencies:

Run Dependencies:

r, r-samr, r-deseq, r-edger, r-xtable, r-statmod, r-genefilter, r-variantannotation, r-foreach, r-doparallel, r-gplots, r-ggplot2, r-rgl, r-knitr, r-rnaseqmap

Description:

The package provides tools and reports for the analysis of amplicon sequencing panels, such as AmpliSeq.

r-analysispageserver¶

Homepage:

https://www.bioconductor.org/packages/AnalysisPageServer/

Spack package:

r-analysispageserver/package.py

Versions:

1.10.0

Build Dependencies:

r, r-log4r, r-rjson, r-biobase, r-graph

Link Dependencies:

Run Dependencies:

r, r-log4r, r-rjson, r-biobase, r-graph

Description:

AnalysisPageServer is a modular system that enables sharing of customizable R analyses via the web.

r-anaquin¶

Homepage:

https://www.bioconductor.org/packages/Anaquin/

Spack package:

r-anaquin/package.py

Versions:

1.2.0

Build Dependencies:

r, r-deseq2, r-plyr, r-locfit, r-qvalue, r-knitr, r-rocr, r-ggplot2

Link Dependencies:

Run Dependencies:

r, r-deseq2, r-plyr, r-locfit, r-qvalue, r-knitr, r-rocr, r-ggplot2

Description:

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:

https://www.bioconductor.org/packages/AneuFinder/

Spack package:

r-aneufinder/package.py

Versions:

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-reordercluster, r-mclust, r-ggrepel

Link Dependencies:

Run Dependencies:

Description:

This package implements functions for CNV calling, plotting, export and analysis from whole-genome single cell sequencing data.

r-aneufinderdata¶

Homepage:

https://www.bioconductor.org/packages/AneuFinderData/

Spack package:

r-aneufinderdata/package.py

Versions:

1.4.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Whole-genome single cell sequencing data for demonstration purposes in the AneuFinder package.

r-animation¶

Homepage:

https://cran.r-project.org/package=animation

Spack package:

r-animation/package.py

Versions:

2.5

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

https://www.bioconductor.org/packages/annaffy/

Spack package:

r-annaffy/package.py

Versions:

1.48.0

Build Dependencies:

r, r-biobase, r-go-db, r-kegg-db

Link Dependencies:

Run Dependencies:

r, r-biobase, r-go-db, r-kegg-db

Description:

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:

https://www.bioconductor.org/packages/annotate/

Spack package:

r-annotate/package.py

Versions:

1.58.0, 1.54.0

Build Dependencies:

r, r-annotationdbi, r-xml, r-rcurl, r-xtable

Link Dependencies:

Run Dependencies:

r, r-annotationdbi, r-xml, r-rcurl, r-xtable

Description:

Using R enviroments for annotation.

r-annotationdbi¶

Homepage:

https://www.bioconductor.org/packages/AnnotationDbi/

Spack package:

r-annotationdbi/package.py

Versions:

1.42.1, 1.38.2

Build Dependencies:

r, r-biocgenerics, r-biobase, r-iranges, r-dbi, r-rsqlite

Link Dependencies:

Run Dependencies:

r, r-biocgenerics, r-biobase, r-iranges, r-dbi, r-rsqlite

Description:

Provides user interface and database connection code for annotation data packages using SQLite data storage.

r-annotationfilter¶

Homepage:

https://bioconductor.org/packages/AnnotationFilter/

Spack package:

r-annotationfilter/package.py

Versions:

1.0.0

Build Dependencies:

r, r-genomicranges, r-lazyeval

Link Dependencies:

Run Dependencies:

r, r-genomicranges, r-lazyeval

Description:

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:

https://www.bioconductor.org/packages/AnnotationForge/

Spack package:

r-annotationforge/package.py

Versions:

1.18.2

Build Dependencies:

r, r-biocgenerics, r-biobase, r-annotationdbi, r-dbi, r-rsqlite, r-xml, r-s4vectors, r-rcurl

Link Dependencies:

Run Dependencies:

r, r-biocgenerics, r-biobase, r-annotationdbi, r-dbi, r-rsqlite, r-xml, r-s4vectors, r-rcurl

Description:

Provides code for generating Annotation packages and their databases. Packages produced are intended to be used with AnnotationDbi.

r-annotationhub¶

Homepage:

https://bioconductor.org/packages/AnnotationHub/

Spack package:

r-annotationhub/package.py

Versions:

2.8.3

Build Dependencies:

r, r-rsqlite, r-biocinstaller, r-annotationdbi, r-s4vectors, r-interactivedisplaybase, r-httr, r-yaml

Link Dependencies:

Run Dependencies:

r, r-rsqlite, r-biocinstaller, r-annotationdbi, r-s4vectors, r-interactivedisplaybase, r-httr, r-yaml

Description:

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-ape¶

Homepage:

http://ape-package.ird.fr/

Spack package:

r-ape/package.py

Versions:

5.2, 5.1, 5.0, 4.1

Build Dependencies:

r, r-nlme, r-lattice, r-rcpp

Link Dependencies:

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:

https://github.com/trevorld/argparse

Spack package:

r-argparse/package.py

Versions:

1.1.1

Build Dependencies:

r, r-proto, r-findpython, r-getopt, r-jsonlite

Link Dependencies:

Run Dependencies:

r, r-proto, r-findpython, r-getopt, 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-assertthat¶

Homepage:

https://cran.r-project.org/package=assertthat

Spack package:

r-assertthat/package.py

Versions:

0.2.0, 0.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

https://cran.r-project.org/package=backports

Spack package:

r-backports/package.py

Versions:

1.1.1, 1.1.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

https://www.bioconductor.org/packages/bamsignals/

Spack package:

r-bamsignals/package.py

Versions:

1.8.0

Build Dependencies:

r, r-biocgenerics, r-rcpp, r-iranges, r-genomicranges, r-zlibbioc, r-rhtslib

Link Dependencies:

Run Dependencies:

r, r-biocgenerics, r-rcpp, r-iranges, r-genomicranges, r-zlibbioc, r-rhtslib

Description:

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:

https://cran.r-project.org/package=base64

Spack package:

r-base64/package.py

Versions:

2.0

Build Dependencies:

r, r-openssl

Link Dependencies:

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:

http://www.rforge.net/base64enc

Spack package:

r-base64enc/package.py

Versions:

0.1-3

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

This package provides tools for handling base64 encoding. It is more flexible than the orphaned base64 package.

r-bayesm¶

Homepage:

https://cran.r-project.org/web/packages/bayesm/index.html

Spack package:

r-bayesm/package.py

Versions:

3.1-0.1

Build Dependencies:

r, r-rcpp, r-rcpparmadillo

Link Dependencies:

Run Dependencies:

r, r-rcpp, r-rcpparmadillo

Description:

Bayesian Inference for Marketing/Micro-Econometrics

r-bbmisc¶

Homepage:

https://github.com/berndbischl/BBmisc

Spack package:

r-bbmisc/package.py

Versions:

1.11

Build Dependencies:

r, r-checkmate

Link Dependencies:

Run Dependencies:

r, r-checkmate

Description:

Miscellaneous helper functions for and from B. Bischl and some other guys, mainly for package development.

r-beanplot¶

Homepage:

https://cran.r-project.org/web/packages/beanplot/index.html

Spack package:

r-beanplot/package.py

Versions:

1.2

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Plots univariate comparison graphs, an alternative to boxplot/stripchart/violin plot.

r-bfast¶

Homepage:

https://cran.r-project.org/package=bfast

Spack package:

r-bfast/package.py

Versions:

1.5.7

Build Dependencies:

r, r-strucchange, r-zoo, r-forecast, r-sp, r-raster

Link Dependencies:

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:

https://github.com/loicdtx/bfastSpatial

Spack package:

r-bfastspatial/package.py

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:

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:

https://cran.r-project.org/package=BGLR

Spack package:

r-bglr/package.py

Versions:

1.0.8

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

BGLR: Bayesian Generalized Linear Regression

r-bh¶

Homepage:

https://cran.r-project.org/web/packages/BH/index.html

Spack package:

r-bh/package.py

Versions:

1.69.0-1, 1.65.0-1, 1.60.0-2

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

http://www.agner.org/random/

Spack package:

r-biasedurn/package.py

Versions:

1.07

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

https://cran.r-project.org/package=bibtex

Spack package:

r-bibtex/package.py

Versions:

0.4.2

Build Dependencies:

r, r-stringr, r-testthat

Link Dependencies:

Run Dependencies:

r, r-stringr, r-testthat

Description:

bibtex: Bibtex Parser Utility to parse a bibtex file.

r-bindr¶

Homepage:

https://github.com/krlmlr/bindr

Spack package:

r-bindr/package.py

Versions:

0.1.1, 0.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Provides a simple interface for creating active bindings where the bound function accepts additional arguments.

r-bindrcpp¶

Homepage:

https://github.com/krlmlr/bindrcpp

Spack package:

r-bindrcpp/package.py

Versions:

0.2.2, 0.2

Build Dependencies:

r, r-rcpp, r-bindr, r-plogr

Link Dependencies:

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-biobase¶

Homepage:

https://www.bioconductor.org/packages/Biobase/

Spack package:

r-biobase/package.py

Versions:

2.40.0, 2.38.0, 2.36.2

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Functions that are needed by many other packages or which replace R functions.

r-biocgenerics¶

Homepage:

https://www.bioconductor.org/packages/BiocGenerics/

Spack package:

r-biocgenerics/package.py

Versions:

0.26.0, 0.24.0, 0.22.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

S4 generic functions needed by many Bioconductor packages.

r-biocinstaller¶

Homepage:

https://bioconductor.org/packages/BiocInstaller/

Spack package:

r-biocinstaller/package.py

Versions:

1.26.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

This package is used to install and update Bioconductor, CRAN, and (some) github packages.

r-biocparallel¶

Homepage:

https://bioconductor.org/packages/BiocParallel/

Spack package:

r-biocparallel/package.py

Versions:

1.14.2, 1.10.1

Build Dependencies:

r, r-futile-logger, r-snow, r-bh

Link Dependencies:

r, r-bh

Run Dependencies:

r, r-futile-logger, r-snow, r-bh

Description:

This package provides modified versions and novel implementation of functions for parallel evaluation, tailored to use with Bioconductor objects.

r-biocstyle¶

Homepage:

https://www.bioconductor.org/packages/BiocStyle/

Spack package:

r-biocstyle/package.py

Versions:

2.4.1

Build Dependencies:

r, r-bookdown, r-knitr, r-rmarkdown, r-yaml

Link Dependencies:

Run Dependencies:

r, r-bookdown, r-knitr, r-rmarkdown, r-yaml

Description:

Provides standard formatting styles for Bioconductor PDF and HTML documents. Package vignettes illustrate use and functionality.

r-biom-utils¶

Homepage:

https://github.com/braithwaite/BIOM.utils/

Spack package:

r-biom-utils/package.py

Versions:

0.9

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Provides utilities to facilitate import, export and computation with the BIOM (Biological Observation Matrix) format (http://biom-format.org).

r-biomart¶

Homepage:

https://bioconductor.org/packages/biomaRt/

Spack package:

r-biomart/package.py

Versions:

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:

Run Dependencies:

r, r-xml, r-rcurl, r-annotationdbi, r-progress, r-stringr, r-httr

Description:

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. Examples of BioMart databases are Ensembl, COSMIC, Uniprot, HGNC, Gramene, Wormbase and dbSNP mapped to Ensembl. These major databases give biomaRt users direct access to a diverse set of data and enable a wide range of powerful online queries from gene annotation to database mining.

r-biomformat¶

Homepage:

https://www.bioconductor.org/packages/biomformat/

Spack package:

r-biomformat/package.py

Versions:

1.4.0

Build Dependencies:

r, r-plyr, r-jsonlite, r-matrix, r-rhdf5

Link Dependencies:

Run Dependencies:

r, r-plyr, r-jsonlite, r-matrix, r-rhdf5

Description:

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:

https://bioconductor.org/packages/Biostrings/

Spack package:

r-biostrings/package.py

Versions:

2.48.0, 2.44.2

Build Dependencies:

r, r-biocgenerics, r-s4vectors, r-iranges, r-xvector

Link Dependencies:

Run Dependencies:

r, r-biocgenerics, r-s4vectors, r-iranges, r-xvector

Description:

Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences.

r-biovizbase¶

Homepage:

http://bioconductor.org/packages/biovizBase/

Spack package:

r-biovizbase/package.py

Versions:

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

Link Dependencies:

Run Dependencies:

Description:

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:

https://cran.rstudio.com/web/packages/bit/index.html

Spack package:

r-bit/package.py

Versions:

1.1-12

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

A class for vectors of 1-bit booleans.

r-bit64¶

Homepage:

https://cran.rstudio.com/web/packages/bit64/index.html

Spack package:

r-bit64/package.py

Versions:

0.9-7

Build Dependencies:

r, r-bit

Link Dependencies:

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:

https://cran.r-project.org/package=bitops

Spack package:

r-bitops/package.py

Versions:

1.0-6

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Functions for bitwise operations on integer vectors.

r-blob¶

Homepage:

https://cran.rstudio.com/web/packages/blob/index.html

Spack package:

r-blob/package.py

Versions:

1.1.0

Build Dependencies:

r, r-tibble

Link Dependencies:

Run Dependencies:

r, r-tibble

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:

https://cran.r-project.org/package=blockmodeling

Spack package:

r-blockmodeling/package.py

Versions:

0.3.1

Build Dependencies:

r, r-matrix, r-doparallel, r-dorng, r-foreach

Link Dependencies:

Run Dependencies:

r, r-matrix, r-doparallel, r-dorng, r-foreach

Description:

blockmodeling: Generalized and Classical Blockmodeling of Valued Networks

r-bookdown¶

Homepage:

https://cran.r-project.org/package=bookdown

Spack package:

r-bookdown/package.py

Versions:

0.5

Build Dependencies:

r, r-yaml, r-rmarkdown, r-knitr, r-htmltools

Link Dependencies:

Run Dependencies:

r, r-yaml, r-rmarkdown, r-knitr, r-htmltools

Description:

Output formats and utilities for authoring books and technical documents with R Markdown.

r-boot¶

Homepage:

https://cran.r-project.org/package=boot

Spack package:

r-boot/package.py

Versions:

1.3-20, 1.3-18

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

https://cran.r-project.org/package=brew

Spack package:

r-brew/package.py

Versions:

1.0-6

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

http://github.com/tidyverse/broom

Spack package:

r-broom/package.py

Versions:

0.4.2

Build Dependencies:

r, r-plyr, r-dplyr, r-tidyr, r-psych, r-stringr, r-reshape2, r-nlme

Link Dependencies:

Run Dependencies:

r, r-plyr, r-dplyr, r-tidyr, r-psych, r-stringr, r-reshape2, r-nlme

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:

https://www.bioconductor.org/packages/BSgenome/

Spack package:

r-bsgenome/package.py

Versions:

1.46.0, 1.44.2

Build Dependencies:

r, r-biocgenerics, r-s4vectors, r-iranges, r-genomeinfodb, r-genomicranges, r-biostrings, r-rtracklayer, r-rsamtools, r-xvector

Link Dependencies:

Run Dependencies:

r, r-biocgenerics, r-s4vectors, r-iranges, r-genomeinfodb, r-genomicranges, r-biostrings, r-rtracklayer, r-rsamtools, r-xvector

Description:

Infrastructure shared by all the Biostrings-based genome data packages.

r-bumphunter¶

Homepage:

http://bioconductor.org/packages/bumphunter/

Spack package:

r-bumphunter/package.py

Versions:

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:

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:

Tools for finding bumps in genomic data

r-c50¶

Homepage:

https://cran.r-project.org/package=C50

Spack package:

r-c50/package.py

Versions:

0.1.0-24

Build Dependencies:

r, r-partykit

Link Dependencies:

Run Dependencies:

r, r-partykit

Description:

C5.0 decision trees and rule-based models for pattern recognition.

r-cairo¶

Homepage:

https://cran.r-project.org/web/packages/Cairo/index.html

Spack package:

r-cairo/package.py

Versions:

1.5-9

Build Dependencies:

r, cairo

Link Dependencies:

r, cairo

Run Dependencies:

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:

https://github.com/MangoTheCat/callr

Spack package:

r-callr/package.py

Versions:

3.0.0, 1.0.0

Build Dependencies:

r, r-base64enc, r-processx, r-r6, r-utils

Link Dependencies:

Run Dependencies:

r, r-base64enc, r-processx, r-r6, r-utils

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:

https://r-forge.r-project.org/projects/car/

Spack package:

r-car/package.py

Versions:

2.1-4, 2.1-2

Build Dependencies:

r, r-mass, r-mgcv, r-nnet, r-pbkrtest, r-quantreg

Link Dependencies:

Run Dependencies:

r, r-mass, r-mgcv, r-nnet, r-pbkrtest, r-quantreg

Description:

Functions and Datasets to Accompany J. Fox and S. Weisberg, An R Companion to Applied Regression, Second Edition, Sage, 2011.

r-caret¶

Homepage:

https://github.com/topepo/caret/

Spack package:

r-caret/package.py

Versions:

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

Link Dependencies:

Run Dependencies:

r, r-lattice, r-ggplot2, r-car, r-foreach, r-plyr, r-modelmetrics, r-nlme, r-reshape2

Description:

Misc functions for training and plotting classification and regression models.

r-caroline¶

Homepage:

https://cran.r-project.org/package=caroline

Spack package:

r-caroline/package.py

Versions:

0.7.6

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

caroline: A Collection of Database, Data Structure, Visualization, andUtility Functions for R

r-category¶

Homepage:

https://www.bioconductor.org/packages/Category/

Spack package:

r-category/package.py

Versions:

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:

Run Dependencies:

r, r-biocgenerics, r-annotationdbi, r-biobase, r-matrix, r-graph, r-rbgl, r-gseabase, r-genefilter, r-annotate, r-dbi

Description:

A collection of tools for performing category analysis.

r-catools¶

Homepage:

https://cran.r-project.org/package=caTools

Spack package:

r-catools/package.py

Versions:

1.17.1

Build Dependencies:

r, r-bitops

Link Dependencies:

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:

https://cran.r-project.org/package=cdcfluview

Spack package:

r-cdcfluview/package.py

Versions:

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:

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:

https://cran.r-project.org/package=cellranger

Spack package:

r-cellranger/package.py

Versions:

1.1.0

Build Dependencies:

r, r-rematch, r-tibble

Link Dependencies:

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:

https://cran.r-project.org/package=checkmate

Spack package:

r-checkmate/package.py

Versions:

1.8.4

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

https://cran.r-project.org/package=checkpoint

Spack package:

r-checkpoint/package.py

Versions:

0.3.18, 0.3.15

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

https://cran.r-project.org/web/packages/chemometrics/index.html

Spack package:

r-chemometrics/package.py

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

Link Dependencies:

Run Dependencies:

r, r-rpart, r-mclust, r-lars, r-robustbase, r-e1071, r-pls, r-som, r-pcapp

Description:

R companion to the book "Introduction to Multivariate Statistical Analysis in Chemometrics" written by K. Varmuza and P. Filzmoser (2009).

r-chron¶

Homepage:

https://cran.r-project.org/package=chron

Spack package:

r-chron/package.py

Versions:

2.3-47

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Chronological objects which can handle dates and times.

r-circlize¶

Homepage:

https://cran.r-project.org/package=circlize

Spack package:

r-circlize/package.py

Versions:

0.4.1, 0.4.0

Build Dependencies:

r, r-globaloptions, r-shape, r-colorspace

Link Dependencies:

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:

http://www.stats.ox.ac.uk/pub/MASS4/

Spack package:

r-class/package.py

Versions:

7.3-14

Build Dependencies:

r, r-mass

Link Dependencies:

Run Dependencies:

r, r-mass

Description:

Various functions for classification, including k-nearest neighbour, Learning Vector Quantization and Self-Organizing Maps.

r-classint¶

Homepage:

https://cran.r-project.org/package=classInt

Spack package:

r-classint/package.py

Versions:

0.1-24

Build Dependencies:

r, r-e1071, r-class

Link Dependencies:

Run Dependencies:

r, r-e1071, r-class

Description:

Selected commonly used methods for choosing univariate class intervals for mapping or other graphics purposes.

r-cli¶

Homepage:

https://github.com/r-lib/cli#readme

Spack package:

r-cli/package.py

Versions:

1.0.1, 1.0.0

Build Dependencies:

r, r-assertthat, r-crayon

Link Dependencies:

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:

https://github.com/mdlincoln/clipr

Spack package:

r-clipr/package.py

Versions:

0.4.0

Build Dependencies:

r, r-rstudioapi, r-testthat, xclip

Link Dependencies:

r, xclip

Run Dependencies:

r, r-rstudioapi, r-testthat

Description:

Simple utility functions to read from and write to the Windows, OS X, and X11 clipboards.

r-cluster¶

Homepage:

https://cran.r-project.org/web/packages/cluster/index.html

Spack package:

r-cluster/package.py

Versions:

2.0.7-1, 2.0.5, 2.0.4

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

https://cran.r-project.org/package=clusterGeneration

Spack package:

r-clustergeneration/package.py

Versions:

1.3.4

Build Dependencies:

r, r-mass

Link Dependencies:

Run Dependencies:

r, r-mass

Description:

Random Cluster Generation (with Specified Degree of Separation)

r-clusterprofiler¶

Homepage:

https://www.bioconductor.org/packages/clusterProfiler/

Spack package:

r-clusterprofiler/package.py

Versions:

3.4.4

Build Dependencies:

r, r-tidyr, r-rvcheck, r-qvalue, r-plyr, r-magrittr, r-gosemsim, r-go-db, r-ggplot2, r-annotationdbi, r-dose

Link Dependencies:

Run Dependencies:

r, r-tidyr, r-rvcheck, r-qvalue, r-plyr, r-magrittr, r-gosemsim, r-go-db, r-ggplot2, r-annotationdbi, r-dose

Description:

This package implements methods to analyze and visualize functional profiles (GO and KEGG) of gene and gene clusters.

r-cner¶

Homepage:

https://bioconductor.org/packages/CNEr/

Spack package:

r-cner/package.py

Versions:

1.14.0

Build Dependencies:

r, r-biostrings, r-dbi, r-rsqlite, r-genomeinfodb, r-genomicranges, r-rtracklayer, r-xvector, r-genomicalignments, r-s4vectors, r-iranges, r-readr, r-biocgenerics, r-reshape2, r-ggplot2, r-powerlaw, r-annotate, r-go-db, r-keggrest, r-utils

Link Dependencies:

Run Dependencies:

Description:

"Large-scale identification and advanced visualization of sets of conserved noncoding elements.

r-coda¶

Homepage:

https://cran.r-project.org/web/packages/coda/index.html

Spack package:

r-coda/package.py

Versions:

0.19-1

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

https://cran.r-project.org/web/packages/codetools/index.html

Spack package:

r-codetools/package.py

Versions:

0.2-15, 0.2-14

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Code analysis tools for R.

r-coin¶

Homepage:

https://cran.r-project.org/package=coin

Spack package:

r-coin/package.py

Versions:

1.1-3

Build Dependencies:

r, r-survival, r-modeltools, r-mvtnorm, r-multcomp

Link Dependencies:

Run Dependencies:

r, r-survival, r-modeltools, r-mvtnorm, r-multcomp

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:

https://cran.r-project.org/web/packages/colorspace/index.html

Spack package:

r-colorspace/package.py

Versions:

1.3-2, 1.2-6

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

https://cran.r-project.org/package=combinat

Spack package:

r-combinat/package.py

Versions:

0.0-8

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

routines for combinatorics

r-commonmark¶

Homepage:

https://cran.r-project.org/package=commonmark

Spack package:

r-commonmark/package.py

Versions:

1.7

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

commonmark: CommonMark and Github Markdown Rendering in R

r-complexheatmap¶

Homepage:

https://bioconductor.org/packages/ComplexHeatmap/

Spack package:

r-complexheatmap/package.py

Versions:

1.14.0

Build Dependencies:

r, r-circlize, r-getoptlong, r-colorspace, r-rcolorbrewer, r-dendextend, r-globaloptions

Link Dependencies:

Run Dependencies:

r, r-circlize, r-getoptlong, r-colorspace, r-rcolorbrewer, r-dendextend, r-globaloptions

Description:

Complex heatmaps are efficient to visualize associations between different sources of data sets and reveal potential structures. Here the ComplexHeatmap package provides a highly flexible way to arrange multiple heatmaps and supports self-defined annotation graphics.

r-compositions¶

Homepage:

https://cran.r-project.org/web/packages/compositions/index.html

Spack package:

r-compositions/package.py

Versions:

1.40-2

Build Dependencies:

r, r-tensora, r-robustbase, r-energy, r-bayesm

Link Dependencies:

Run Dependencies:

r, r-tensora, r-robustbase, r-energy, r-bayesm

Description:

Compositional Data Analysis

r-construct¶

Homepage:

https://cran.r-project.org/package=conStruct

Spack package:

r-construct/package.py

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

Link Dependencies:

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:

https://cran.r-project.org/package=convevol

Spack package:

r-convevol/package.py

Versions:

1.3

Build Dependencies:

r, r-ape, r-cluster, r-geiger, r-mass, r-phytools

Link Dependencies:

Run Dependencies:

r, r-ape, r-cluster, r-geiger, r-mass, r-phytools

Description:

Quantifies and assesses the significance of convergent evolution

r-corhmm¶

Homepage:

https://cran.r-project.org/package=corHMM

Spack package:

r-corhmm/package.py

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:

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:

https://cran.r-project.org/package=corpcor

Spack package:

r-corpcor/package.py

Versions:

1.6.9

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Efficient Estimation of Covariance and (Partial) Correlation

r-corrplot¶

Homepage:

https://cran.r-project.org/package=corrplot

Spack package:

r-corrplot/package.py

Versions:

0.77

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

A graphical display of a correlation matrix or general matrix. It also contains some algorithms to do matrix reordering.

r-covr¶

Homepage:

https://cran.r-project.org/package=covr

Spack package:

r-covr/package.py

Versions:

3.0.1

Build Dependencies:

r, r-jsonlite, r-rex, r-httr, r-crayon, r-withr

Link Dependencies:

Run Dependencies:

r, r-jsonlite, r-rex, r-httr, r-crayon, r-withr

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:

https://cran.r-project.org/package=cowplot

Spack package:

r-cowplot/package.py

Versions:

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

Link Dependencies:

Run Dependencies:

r, r-ggplot2, r-gtable, r-plyr, r-scales

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:

https://cran.r-project.org/package=sourcetools

Spack package:

r-crayon/package.py

Versions:

1.3.4, 1.3.2

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

https://cran.r-project.org/web/packages/crosstalk/index.html

Spack package:

r-crosstalk/package.py

Versions:

1.0.0

Build Dependencies:

r, r-htmltools, r-jsonlite, r-lazyeval, r-ggplot2, r-shiny

Link Dependencies:

Run Dependencies:

r, r-htmltools, r-jsonlite, r-lazyeval, r-ggplot2, r-shiny

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:

https://cran.r-project.org/package=crul

Spack package:

r-crul/package.py

Versions:

0.7.4

Build Dependencies:

r, r-curl, r-httpcode, r-mime, r-r6, r-urltools

Link Dependencies:

Run Dependencies:

r, r-curl, r-httpcode, r-mime, r-r6, r-urltools

Description:

crul: HTTP Client

r-ctc¶

Homepage:

https://www.bioconductor.org/packages/release/bioc/html/ctc.html

Spack package:

r-ctc/package.py

Versions:

1.54.0

Build Dependencies:

r, r-amap

Link Dependencies:

Run Dependencies:

r, r-amap

Description:

Tools for export and import classification trees and clusters to other programs

r-cubature¶

Homepage:

https://cran.r-project.org/package=cubature

Spack package:

r-cubature/package.py

Versions:

1.1-2

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Adaptive multivariate integration over hypercubes

r-cubist¶

Homepage:

https://cran.r-project.org/package=Cubist

Spack package:

r-cubist/package.py

Versions:

0.0.19

Build Dependencies:

r, r-lattice, r-reshape2

Link Dependencies:

Run Dependencies:

r, r-lattice, r-reshape2

Description:

Regression modeling using rules with added instance-based corrections

r-curl¶

Homepage:

https://github.com/jeroenooms/curl

Spack package:

r-curl/package.py

Versions:

3.3, 3.0, 2.3, 1.0, 0.9.7

Build Dependencies:

r, curl

Link Dependencies:

r, curl

Run Dependencies:

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-data-table¶

Homepage:

https://github.com/Rdatatable/data.table/wiki

Spack package:

r-data-table/package.py

Versions:

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:

Link Dependencies:

Run Dependencies:

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:

http://rstats-db.github.io/DBI

Spack package:

r-dbi/package.py

Versions:

0.7, 0.4-1

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

https://github.com/tidyverse/dbplyr

Spack package:

r-dbplyr/package.py

Versions:

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:

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-delayedarray¶

Homepage:

https://bioconductor.org/packages/DelayedArray/

Spack package:

r-delayedarray/package.py

Versions:

0.6.5, 0.4.1, 0.2.7

Build Dependencies:

r, r-biocparallel, r-biocgenerics, r-s4vectors, r-iranges, r-matrixstats

Link Dependencies:

Run Dependencies:

r, r-biocparallel, r-biocgenerics, r-s4vectors, r-iranges, r-matrixstats

Description:

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. 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-deldir¶

Homepage:

https://CRAN.R-project.org/package=deldir

Spack package:

r-deldir/package.py

Versions:

0.1-14

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

https://CRAN.R-project.org/package=dendextend

Spack package:

r-dendextend/package.py

Versions:

1.5.2

Build Dependencies:

r, r-magrittr, r-ggplot2, r-fpc, r-whisker, r-viridis

Link Dependencies:

Run Dependencies:

r, r-magrittr, r-ggplot2, r-fpc, r-whisker, r-viridis

Description:

dendextend: Extending 'Dendrogram' Functionality in R

r-deoptim¶

Homepage:

https://cran.r-project.org/package=DEoptim

Spack package:

r-deoptim/package.py

Versions:

2.2-3

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Implements the differential evolution algorithm for global optimization of a real-valued function of a real-valued parameter vector.

r-deoptimr¶

Homepage:

https://cran.r-project.org/web/packages/DEoptimR/index.html

Spack package:

r-deoptimr/package.py

Versions:

1.0-8

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

An implementation of a bespoke jDE variant of the Differential Evolution stochastic algorithm for global optimization of nonlinear programming problems.

r-desc¶

Homepage:

https://cran.r-project.org/package=desc

Spack package:

r-desc/package.py

Versions:

1.2.0

Build Dependencies:

r, r-assertthat, r-r6, r-crayon, r-rprojroot

Link Dependencies:

Run Dependencies:

r, r-assertthat, r-r6, r-crayon, r-rprojroot

Description:

desc: Manipulate DESCRIPTION Files

r-deseq¶

Homepage:

https://www.bioconductor.org/packages/DESeq/

Spack package:

r-deseq/package.py

Versions:

1.28.0

Build Dependencies:

r, r-biocgenerics, r-biobase, r-locfit, r-lattice, r-genefilter, r-geneplotter, r-mass, r-rcolorbrewer

Link Dependencies:

Run Dependencies:

r, r-biocgenerics, r-biobase, r-locfit, r-lattice, r-genefilter, r-geneplotter, r-mass, r-rcolorbrewer

Description:

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:

https://www.bioconductor.org/packages/DESeq2/

Spack package:

r-deseq2/package.py

Versions:

1.20.0, 1.18.1, 1.16.1

Build Dependencies:

r, r-rcpparmadillo, 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

Link Dependencies:

Run Dependencies:

r, r-rcpparmadillo, 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

Description:

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:

https://cran.r-project.org/package=deSolve

Spack package:

r-desolve/package.py

Versions:

1.20

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

https://github.com/hadley/devtools

Spack package:

r-devtools/package.py

Versions:

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

Link Dependencies:

Run Dependencies:

r, r-httr, r-memoise, r-whisker, r-digest, r-rstudioapi, r-jsonlite, r-git2r, r-withr

Description:

Collection of package development tools.

r-diagrammer¶

Homepage:

https://github.com/rich-iannone/DiagrammeR

Spack package:

r-diagrammer/package.py

Versions:

0.8.4

Build Dependencies:

r, r-htmlwidgets, r-igraph, r-influencer, r-rstudioapi, r-stringr, r-visnetwork, r-scales

Link Dependencies:

Run Dependencies:

r, r-htmlwidgets, r-igraph, r-influencer, r-rstudioapi, r-stringr, r-visnetwork, r-scales

Description:

Create graph diagrams and flowcharts using R.

r-dicekriging¶

Homepage:

http://dice.emse.fr/

Spack package:

r-dicekriging/package.py

Versions:

1.5.5

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Estimation, validation and prediction of kriging models. Important functions : km, print.km, plot.km, predict.km.

r-dichromat¶

Homepage:

https://cran.r-project.org/web/packages/dichromat/index.html

Spack package:

r-dichromat/package.py

Versions:

2.0-0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Collapse red-green or green-blue distinctions to simulate the effects of different types of color-blindness.

r-diffusionmap¶

Homepage:

https://cran.r-project.org/web/packages/diffusionMap/index.html

Spack package:

r-diffusionmap/package.py

Versions:

1.1-0, 1.0-0, 0.0-2, 0.0-1

Build Dependencies:

r, r-matrix, r-scatterplot3d, r-igraph

Link Dependencies:

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:

http://dirk.eddelbuettel.com/code/digest.html

Spack package:

r-digest/package.py

Versions:

0.6.12, 0.6.11, 0.6.9

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

https://CRAN.R-project.org/package=diptest

Spack package:

r-diptest/package.py

Versions:

0.75-7

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

diptest: Hartigan's Dip Test Statistic for Unimodality - Corrected

r-dirichletmultinomial¶

Homepage:

https://bioconductor.org/packages/DirichletMultinomial/

Spack package:

r-dirichletmultinomial/package.py

Versions:

1.20.0

Build Dependencies:

r, r-s4vectors, r-iranges, gsl

Link Dependencies:

r, gsl

Run Dependencies:

r, r-s4vectors, r-iranges

Description:

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:

https://cran.r-project.org/package=dismo

Spack package:

r-dismo/package.py

Versions:

1.1-4

Build Dependencies:

r, r-raster, r-sp

Link Dependencies:

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:

http://www.zoology.ubc.ca/prog/diversitree

Spack package:

r-diversitree/package.py

Versions:

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:

https://www.bioconductor.org/packages/DNAcopy/

Spack package:

r-dnacopy/package.py

Versions:

1.50.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

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:

https://bioconductor.org/packages/DO.db/

Spack package:

r-do-db/package.py

Versions:

2.9

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

A set of annotation maps describing the entire Disease Ontology assembled using data from DO.

r-domc¶

Homepage:

https://cran.r-project.org/package=doMC

Spack package:

r-domc/package.py

Versions:

1.3.4

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Provides a parallel backend for the %dopar% function using the multicore functionality of the parallel package.

r-doparallel¶

Homepage:

https://cran.r-project.org/web/packages/doParallel/index.html

Spack package:

r-doparallel/package.py

Versions:

1.0.11, 1.0.10

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Provides a parallel backend for the %dopar% function using the parallel package.

r-dorng¶

Homepage:

https://cran.rstudio.com/web/packages/doRNG/index.html

Spack package:

r-dorng/package.py

Versions:

1.6.6

Build Dependencies:

r, r-foreach, r-rngtools, r-iterators, r-pkgmaker

Link Dependencies:

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:

https://www.bioconductor.org/packages/DOSE/

Spack package:

r-dose/package.py

Versions:

3.2.0

Build Dependencies:

r, r-scales, r-s4vectors, r-reshape2, r-qvalue, r-igraph, r-gosemsim, r-ggplot2, r-fgsea, r-do-db, r-biocparallel, r-annotationdbi

Link Dependencies:

Run Dependencies:

r, r-scales, r-s4vectors, r-reshape2, r-qvalue, r-igraph, r-gosemsim, r-ggplot2, r-fgsea, r-do-db, r-biocparallel, r-annotationdbi

Description:

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-downloader¶

Homepage:

https://cran.rstudio.com/web/packages/downloader/index.html

Spack package:

r-downloader/package.py

Versions:

0.4

Build Dependencies:

r, r-digest

Link Dependencies:

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:

https://cran.r-project.org/package=dplyr

Spack package:

r-dplyr/package.py

Versions:

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

Link Dependencies:

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

Description:

A fast, consistent tool for working with data frame like objects, both in memory and out of memory.

r-dt¶

Homepage:

http://rstudio.github.io/DT

Spack package:

r-dt/package.py

Versions:

0.4, 0.3, 0.2, 0.1

Build Dependencies:

r, r-htmltools, r-htmlwidgets, r-magrittr, r-crosstalk

Link Dependencies:

Run Dependencies:

r, r-htmltools, r-htmlwidgets, r-magrittr, r-crosstalk

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:

https://cran.r-project.org/web/packages/dtw/index.html

Spack package:

r-dtw/package.py

Versions:

1.18-1, 1.17-1, 1.16, 1.15, 1.14-3

Build Dependencies:

r, r-proxy

Link Dependencies:

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:

https://cran.r-project.org/web/packages/dygraphs/index.html

Spack package:

r-dygraphs/package.py

Versions:

0.9

Build Dependencies:

r, r-magrittr, r-htmlwidgets, r-zoo, r-xts

Link Dependencies:

Run Dependencies:

r, r-magrittr, r-htmlwidgets, r-zoo, r-xts

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:

https://cran.r-project.org/package=dynamicTreeCut

Spack package:

r-dynamictreecut/package.py

Versions:

1.63-1

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

dynamicTreeCut: Methods for Detection of Clusters in Hierarchical Clustering Dendrograms

r-e1071¶

Homepage:

https://cran.r-project.org/package=e1071

Spack package:

r-e1071/package.py

Versions:

1.6-7

Build Dependencies:

r, r-class

Link Dependencies:

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-edger¶

Homepage:

https://bioconductor.org/packages/edgeR/

Spack package:

r-edger/package.py

Versions:

3.22.3, 3.18.1

Build Dependencies:

r, r-limma, r-locfit, r-rcpp

Link Dependencies:

r, r-rcpp

Run Dependencies:

r, r-limma, r-locfit, r-rcpp

Description:

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, SAGE and CAGE.

r-ellipse¶

Homepage:

https://cran.r-project.org/package=ellipse

Spack package:

r-ellipse/package.py

Versions:

0.3-8

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

This package contains various routines for drawing ellipses and ellipse- like confidence regions.

r-emmli¶

Homepage:

https://cran.r-project.org/package=EMMLi

Spack package:

r-emmli/package.py

Versions:

0.0.3

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

https://cran.r-project.org/web/packages/energy/index.html

Spack package:

r-energy/package.py

Versions:

1.7-5

Build Dependencies:

r, r-rcpp, r-boot

Link Dependencies:

Run Dependencies:

r, r-rcpp, r-boot

Description:

E-Statistics: Multivariate Inference via the Energy of Data

r-ensembldb¶

Homepage:

https://bioconductor.org/packages/ensembldb/

Spack package:

r-ensembldb/package.py

Versions:

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:

Run Dependencies:

Description:

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, the ensembldb package provides also a filter framework allowing to retrieve annotations for specific entries like genes encoded on a chromosome region or transcript models of lincRNA genes.

r-ergm¶

Homepage:

http://statnet.org

Spack package:

r-ergm/package.py

Versions:

3.7.1

Build Dependencies:

r, r-robustbase, r-coda, r-trust, r-matrix, r-lpsolve, r-mass, r-statnet-common, r-network

Link Dependencies:

Run Dependencies:

r, r-robustbase, r-coda, r-trust, r-matrix, r-lpsolve, r-mass, r-statnet-common, r-network

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-evaluate¶

Homepage:

https://cran.r-project.org/package=evaluate

Spack package:

r-evaluate/package.py

Versions:

0.10.1, 0.10, 0.9

Build Dependencies:

r, r-stringr

Link Dependencies:

Run Dependencies:

r, r-stringr

Description:

Parsing and evaluation tools that make it easy to recreate the command line behaviour of R.

r-expint¶

Homepage:

https://cran.r-project.org/package=expint

Spack package:

r-expint/package.py

Versions:

0.1-5

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

expint: Exponential Integral and Incomplete Gamma Function

r-expm¶

Homepage:

http://R-Forge.R-project.org/projects/expm

Spack package:

r-expm/package.py

Versions:

0.999-2

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Computation of the matrix exponential, logarithm, sqrt, and related quantities.

r-factoextra¶

Homepage:

http://www.sthda.com/english/rpkgs/factoextra

Spack package:

r-factoextra/package.py

Versions:

1.0.4

Build Dependencies:

r, r-ggplot2, r-abind, r-dendextend, r-factominer, r-ggpubr, r-reshape2, r-ggrepel, r-tidyr

Link Dependencies:

Run Dependencies:

r, r-ggplot2, r-abind, 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:

http://factominer.free.fr

Spack package:

r-factominer/package.py

Versions:

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:

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:

https://cran.r-project.org/package=fansi

Spack package:

r-fansi/package.py

Versions:

0.4.0, 0.3.0, 0.2.3, 0.2.2, 0.2.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Counterparts to R string manipulation functions that account for the effects of ANSI text formatting control sequences.

r-fastcluster¶

Homepage:

http://danifold.net/fastcluster.html

Spack package:

r-fastcluster/package.py

Versions:

1.1.25

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

http://www.rforge.net/fastmatch

Spack package:

r-fastmatch/package.py

Versions:

1.1-0

Build Dependencies:

Link Dependencies:

Run Dependencies:

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-ff¶

Homepage:

http://ff.r-forge.r-project.org/

Spack package:

r-ff/package.py

Versions:

2.2-13

Build Dependencies:

r, r-bit

Link Dependencies:

Run Dependencies:

r, r-bit

Description:

memory-efficient storage of large data on disk and fast access functions.

r-fftwtools¶

Homepage:

https://github.com/krahim/fftwtools

Spack package:

r-fftwtools/package.py

Versions:

0.9-8

Build Dependencies:

r, fftw

Link Dependencies:

r, fftw

Run Dependencies:

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:

https://www.bioconductor.org/packages/fgsea/

Spack package:

r-fgsea/package.py

Versions:

1.2.1

Build Dependencies:

r, r-fastmatch, r-gridextra, r-ggplot2, r-biocparallel, r-data-table, r-rcpp

Link Dependencies:

Run Dependencies:

r, r-fastmatch, r-gridextra, r-ggplot2, r-biocparallel, r-data-table, r-rcpp

Description:

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-filehash¶

Homepage:

https://cran.r-project.org/

Spack package:

r-filehash/package.py

Versions:

2.3

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

https://github.com/trevorld/findpython

Spack package:

r-findpython/package.py

Versions:

1.0.3

Build Dependencies:

Link Dependencies:

Run Dependencies:

r, python

Description:

Package designed to find an acceptable python binary.

r-fit-models¶

Homepage:

https://cran.r-project.org/package=fit.models

Spack package:

r-fit-models/package.py

Versions:

0.5-14, 0.5-13

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Compare Fitted Models

r-flashclust¶

Homepage:

https://CRAN.R-project.org/package=flashClust

Spack package:

r-flashclust/package.py

Versions:

1.01-2

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

flashClust: Implementation of optimal hierarchical clustering

r-flexclust¶

Homepage:

https://cran.r-project.org/package=flexclust

Spack package:

r-flexclust/package.py

Versions:

1.3-5

Build Dependencies:

r, r-lattice, r-modeltools

Link Dependencies:

Run Dependencies:

r, r-lattice, r-modeltools

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:

https://CRAN.R-project.org/package=flexmix

Spack package:

r-flexmix/package.py

Versions:

2.3-14

Build Dependencies:

r, r-modeltools

Link Dependencies:

Run Dependencies:

r, r-modeltools

Description:

flexmix: Flexible Mixture Modeling

r-fnn¶

Homepage:

https://cran.r-project.org/web/packages/FNN/index.html

Spack package:

r-fnn/package.py

Versions:

1.1, 1.0, 0.6-4, 0.6-3, 0.6-2

Build Dependencies:

r, r-mvtnorm, r-chemometrics

Link Dependencies:

Run Dependencies:

r, r-mvtnorm, r-chemometrics

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:

http://forcats.tidyverse.org/

Spack package:

r-forcats/package.py

Versions:

0.2.0

Build Dependencies:

r, r-tibble, r-magrittr

Link Dependencies:

Run Dependencies:

r, r-tibble, r-magrittr

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:

https://cran.r-project.org/web/packages/foreach/index.html

Spack package:

r-foreach/package.py

Versions:

1.4.3

Build Dependencies:

r, r-codetools, r-iterators

Link Dependencies:

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:

https://cran.r-project.org/package=forecast

Spack package:

r-forecast/package.py

Versions:

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

Link Dependencies:

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

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:

https://cran.r-project.org/web/packages/foreign/index.html

Spack package:

r-foreign/package.py

Versions:

0.8-66

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

https://cran.r-project.org/package=formatR

Spack package:

r-formatr/package.py

Versions:

1.5, 1.4

Build Dependencies:

r, r-codetools, r-shiny, r-testit

Link Dependencies:

Run Dependencies:

r, r-codetools, r-shiny, r-testit

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:

https://cran.r-project.org/package=Formula

Spack package:

r-formula/package.py

Versions:

1.2-2, 1.2-1

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

http://www.homepages.ucl.ac.uk/~ucakche

Spack package:

r-fpc/package.py

Versions:

2.1-10

Build Dependencies:

r, r-mclust, r-flexmix, r-prabclus, r-diptest, r-mvtnorm, r-robustbase, r-kernlab, r-trimcluster

Link Dependencies:

Run Dependencies:

r, r-mclust, r-flexmix, r-prabclus, r-diptest, r-mvtnorm, r-robustbase, r-kernlab, r-trimcluster

Description:

fpc: Flexible Procedures for Clustering

r-fracdiff¶

Homepage:

https://cran.r-project.org/package=fracdiff

Spack package:

r-fracdiff/package.py

Versions:

1.4-2

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Maximum likelihood estimation of the parameters of a fractionally differenced ARIMA(p,d,q) model (Haslett and Raftery, Appl.Statistics, 1989).

r-futile-logger¶

Homepage:

https://cran.rstudio.com/web/packages/futile.logger/index.html

Spack package:

r-futile-logger/package.py

Versions:

1.4.3

Build Dependencies:

r, r-lambda-r, r-futile-options

Link Dependencies:

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:

https://cran.rstudio.com/web/packages/futile.options/index.html

Spack package:

r-futile-options/package.py

Versions:

1.0.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

A scoped options management framework

r-gamlss¶

Homepage:

https://cran.r-project.org/package=gamlss

Spack package:

r-gamlss/package.py

Versions:

5.1-2

Build Dependencies:

r, r-gamlss-data, r-gamlss-dist, r-mass, r-survival, r-nlme

Link Dependencies:

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:

https://cran.r-project.org/package=gamlss.data

Spack package:

r-gamlss-data/package.py

Versions:

5.1-0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

gamlss.data: GAMLSS Data

r-gamlss-dist¶

Homepage:

https://cran.r-project.org/package=gamlss.dist

Spack package:

r-gamlss-dist/package.py

Versions:

5.1-1

Build Dependencies:

r, r-mass

Link Dependencies:

Run Dependencies:

r, r-mass

Description:

gamlss.dist: Distributions for Generalized Additive Models for Location Scale and Shape

r-gbm¶

Homepage:

https://cran.rstudio.com/web/packages/gbm/index.html

Spack package:

r-gbm/package.py

Versions:

2.1.3

Build Dependencies:

r, r-survival, r-lattice

Link Dependencies:

Run Dependencies:

r, r-survival, r-lattice

Description:

Generalized Boosted Regression Models.

r-gcrma¶

Homepage:

https://bioconductor.org/packages/gcrma/

Spack package:

r-gcrma/package.py

Versions:

2.48.0

Build Dependencies:

r, r-affy, r-biobase, r-affyio, r-xvector, r-biostrings, r-biocinstaller

Link Dependencies:

Run Dependencies:

r, r-affy, r-biobase, r-affyio, r-xvector, r-biostrings, r-biocinstaller

Description:

Background adjustment using sequence information

r-gdalutils¶

Homepage:

https://cran.r-project.org/package=gdalUtils

Spack package:

r-gdalutils/package.py

Versions:

2.0.1.14

Build Dependencies:

r, r-sp, r-foreach, r-utils, r-raster, r-rgdal

Link Dependencies:

Run Dependencies:

r, r-sp, r-foreach, r-utils, r-raster, r-rgdal

Description:

gdalUtils: Wrappers for the Geospatial Data Abstraction Library

r-gdata¶

Homepage:

https://cran.r-project.org/package=gdata

Spack package:

r-gdata/package.py

Versions:

2.18.0, 2.17.0

Build Dependencies:

r, r-gtools

Link Dependencies:

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:

http://bioconductor.org/packages/gdsfmt/

Spack package:

r-gdsfmt/package.py

Versions:

1.14.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

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:

https://cran.r-project.org/package=geiger

Spack package:

r-geiger/package.py

Versions:

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:

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:

https://bioconductor.org/packages/genefilter/

Spack package:

r-genefilter/package.py

Versions:

1.62.0, 1.58.1

Build Dependencies:

r, r-s4vectors, r-annotationdbi, r-annotate, r-biobase

Link Dependencies:

Run Dependencies:

r, r-s4vectors, r-annotationdbi, r-annotate, r-biobase

Description:

Some basic functions for filtering genes

r-genelendatabase¶

Homepage:

https://bioconductor.org/packages/release/data/experiment/html/geneLenDataBase.html

Spack package:

r-genelendatabase/package.py

Versions:

1.16.0

Build Dependencies:

r, r-rtracklayer, r-genomicfeatures

Link Dependencies:

Run Dependencies:

r, r-rtracklayer, r-genomicfeatures

Description:

Length of mRNA transcripts for a number of genomes and gene ID formats, largely based on UCSC table browser

r-geneplotter¶

Homepage:

https://www.bioconductor.org/packages/geneplotter/

Spack package:

r-geneplotter/package.py

Versions:

1.58.0, 1.54.0

Build Dependencies:

r, r-biobase, r-biocgenerics, r-lattice, r-annotate, r-annotationdbi, r-rcolorbrewer

Link Dependencies:

Run Dependencies:

r, r-biobase, r-biocgenerics, r-lattice, r-annotate, r-annotationdbi, r-rcolorbrewer

Description:

Functions for plotting genomic data.

r-genie3¶

Homepage:

https://bioconductor.org/packages/GENIE3/

Spack package:

r-genie3/package.py

Versions:

1.2.0

Build Dependencies:

r, r-reshape2

Link Dependencies:

Run Dependencies:

r, r-reshape2

Description:

This package implements the GENIE3 algorithm for inferring gene regulatory networks from expression data.

r-genomeinfodb¶

Homepage:

https://bioconductor.org/packages/GenomeInfoDb/

Spack package:

r-genomeinfodb/package.py

Versions:

1.16.0, 1.14.0, 1.12.3

Build Dependencies:

r, r-biocgenerics, r-s4vectors, r-iranges, r-rcurl, r-genomeinfodbdata

Link Dependencies:

Run Dependencies:

r, r-biocgenerics, r-s4vectors, r-iranges, r-rcurl, r-genomeinfodbdata

Description:

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:

https://bioconductor.org/packages/GenomeInfoDbData/

Spack package:

r-genomeinfodbdata/package.py

Versions:

1.1.0, 0.99.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

for mapping between NCBI taxonomy ID and species. Used by functions in the GenomeInfoDb package.

r-genomicalignments¶

Homepage:

https://bioconductor.org/packages/GenomicAlignments/

Spack package:

r-genomicalignments/package.py

Versions:

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:

Run Dependencies:

r, r-biocgenerics, r-s4vectors, r-iranges, r-genomeinfodb, r-genomicranges, r-summarizedexperiment, r-biostrings, r-rsamtools, r-biocparallel

Description:

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:

http://bioconductor.org/packages/GenomicFeatures/

Spack package:

r-genomicfeatures/package.py

Versions:

1.32.2, 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

Link Dependencies:

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

Description:

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:

https://bioconductor.org/packages/GenomicRanges/

Spack package:

r-genomicranges/package.py

Versions:

1.32.6, 1.30.3, 1.28.6

Build Dependencies:

r, r-biocgenerics, r-s4vectors, r-iranges, r-genomeinfodb, r-xvector

Link Dependencies:

Run Dependencies:

r, r-biocgenerics, r-s4vectors, r-iranges, r-genomeinfodb, r-xvector

Description:

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:

https://cran.r-project.org/package=GenSA

Spack package:

r-gensa/package.py

Versions:

1.1.7

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

https://cran.r-project.org/package=geomorph

Spack package:

r-geomorph/package.py

Versions:

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:

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:

https://cran.r-project.org/package=geonames

Spack package:

r-geonames/package.py

Versions:

0.999

Build Dependencies:

r, r-rjson

Link Dependencies:

Run Dependencies:

r, r-rjson

Description:

geonames: Interface to the "Geonames" Spatial Query Web Service

r-geoquery¶

Homepage:

https://bioconductor.org/packages/GEOquery/

Spack package:

r-geoquery/package.py

Versions:

2.42.0

Build Dependencies:

r, r-biobase, r-xml, r-rcurl, r-httr

Link Dependencies:

Run Dependencies:

r, r-biobase, r-xml, r-rcurl, r-httr

Description:

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:

https://cran.r-project.org/web/packages/geoR/

Spack package:

r-geor/package.py

Versions:

1.7-5.2.1

Build Dependencies:

r, r-mass, r-sp, r-splancs, r-randomfields

Link Dependencies:

Run Dependencies:

r, r-mass, r-sp, r-splancs, r-randomfields

Description:

Geostatistical analysis including traditional, likelihood-based and Bayesian methods.

r-geosphere¶

Homepage:

https://cran.r-project.org/package=geosphere

Spack package:

r-geosphere/package.py

Versions:

1.5-5

Build Dependencies:

r, r-sp

Link Dependencies:

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:

https://github.com/trevorld/getopt

Spack package:

r-getopt/package.py

Versions:

1.20.2, 1.20.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

https://cran.rstudio.com/web/packages/GetoptLong/index.html

Spack package:

r-getoptlong/package.py

Versions:

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:

https://cran.r-project.org/package=GGally

Spack package:

r-ggally/package.py

Versions:

1.3.2

Build Dependencies:

r, r-ggplot2, r-gtable, r-plyr, r-progress, r-rcolorbrewer, r-reshape

Link Dependencies:

Run Dependencies:

r, r-ggplot2, r-gtable, r-plyr, r-progress, r-rcolorbrewer, r-reshape

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-ggbio¶

Homepage:

http://bioconductor.org/packages/ggbio/

Spack package:

r-ggbio/package.py

Versions:

1.24.1

Build Dependencies:

r, 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

Link Dependencies:

Run Dependencies:

Description:

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:

https://cran.r-project.org/package=ggdendro

Spack package:

r-ggdendro/package.py

Versions:

0.1-20

Build Dependencies:

r, r-ggplot2, r-mass

Link Dependencies:

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-ggjoy¶

Homepage:

https://cran.r-project.org/web/packages/ggjoy/index.html

Spack package:

r-ggjoy/package.py

Versions:

0.4.0, 0.3.0, 0.2.0

Build Dependencies:

r, r-ggplot2, r-ggridges

Link Dependencies:

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:

https://github.com/dkahle/ggmap

Spack package:

r-ggmap/package.py

Versions:

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

Link Dependencies:

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

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:

http://ggplot2.org/

Spack package:

r-ggplot2/package.py

Versions:

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

Link Dependencies:

Run Dependencies:

r, r-digest, r-gtable, r-mass, r-plyr, r-reshape2, r-scales, r-tibble, r-lazyeval

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-ggpubr¶

Homepage:

http://www.sthda.com/english/rpkgs/ggpubr

Spack package:

r-ggpubr/package.py

Versions:

0.1.2

Build Dependencies:

r, r-ggplot2, r-ggrepel, r-ggsci, r-plyr

Link Dependencies:

Run Dependencies:

r, r-ggplot2, r-ggrepel, r-ggsci, r-plyr

Description:

ggpubr: 'ggplot2' Based Publication Ready Plots

r-ggrepel¶

Homepage:

http://github.com/slowkow/ggrepel

Spack package:

r-ggrepel/package.py

Versions:

0.6.5

Build Dependencies:

r, r-ggplot2, r-rcpp, r-scales

Link Dependencies:

Run Dependencies:

r, r-ggplot2, r-rcpp, r-scales

Description:

ggrepel: Repulsive Text and Label Geoms for 'ggplot2'

r-ggridges¶

Homepage:

https://cran.r-project.org/web/packages/ggridges/index.html

Spack package:

r-ggridges/package.py

Versions:

0.4.1, 0.4.0

Build Dependencies:

r, r-ggplot2

Link Dependencies:

Run Dependencies:

r, r-ggplot2

Description:

Ridgeline plots provide a convenient way of visualizing changes in distributions over time or space.

r-ggsci¶

Homepage:

https://github.com/road2stat/ggsci

Spack package:

r-ggsci/package.py

Versions:

2.4

Build Dependencies:

r, r-scales, r-ggplot2

Link Dependencies:

Run Dependencies:

r, r-scales, r-ggplot2

Description:

ggsci: Scientific Journal and Sci-Fi Themed Color Palettes for 'ggplot2'

r-ggvis¶

Homepage:

http://ggvis.rstudio.com/

Spack package:

r-ggvis/package.py

Versions:

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:

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-gistr¶

Homepage:

https://github.com/ropensci/gistr

Spack package:

r-gistr/package.py

Versions:

0.3.6

Build Dependencies:

r, r-jsonlite, r-httr, r-magrittr, r-assertthat, r-knitr, r-rmarkdown, r-dplyr

Link Dependencies:

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:

https://github.com/ropensci/git2r

Spack package:

r-git2r/package.py

Versions:

0.18.0, 0.15.0

Build Dependencies:

r, zlib, openssl

Link Dependencies:

r, zlib, openssl

Run Dependencies:

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:

https://bioconductor.org/packages/release/bioc/html/Glimma.html

Spack package:

r-glimma/package.py

Versions:

1.8.2

Build Dependencies:

r, r-edger, r-jsonlite, r-s4vectors

Link Dependencies:

Run Dependencies:

r, r-edger, r-jsonlite, r-s4vectors

Description:

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:

https://cran.rstudio.com/web/packages/glmnet/index.html

Spack package:

r-glmnet/package.py

Versions:

2.0-13, 2.0-5

Build Dependencies:

r, r-matrix, r-foreach

Link Dependencies:

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:

https://cran.r-project.org/package=GlobalOptions

Spack package:

r-globaloptions/package.py

Versions:

0.0.12

Build Dependencies:

r, r-testthat, r-knitr, r-markdown

Link Dependencies:

Run Dependencies:

r, r-testthat, r-knitr, r-markdown

Description:

It provides more controls on the option values such as validation and filtering on the values, making options invisible or private.

r-glue¶

Homepage:

https://github.com/tidyverse/glue

Spack package:

r-glue/package.py

Versions:

1.2.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

http://www.sf.net/projects/r-gregmisc

Spack package:

r-gmodels/package.py

Versions:

2.16.2

Build Dependencies:

r, r-gdata

Link Dependencies:

Run Dependencies:

r, r-gdata

Description:

Various R programming tools for model fitting.

r-gmp¶

Homepage:

http://mulcyber.toulouse.inra.fr/projects/gmp

Spack package:

r-gmp/package.py

Versions:

0.5-13.1

Build Dependencies:

r, gmp

Link Dependencies:

r, gmp

Run Dependencies:

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:

https://www.bioconductor.org/packages/GO.db/

Spack package:

r-go-db/package.py

Versions:

3.4.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

A set of annotation maps describing the entire Gene Ontology assembled using data from GO.

r-googlevis¶

Homepage:

https://github.com/mages/googleVis#googlevis

Spack package:

r-googlevis/package.py

Versions:

0.6.0

Build Dependencies:

r, r-jsonlite

Link Dependencies:

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:

https://github.com/wencke/wencke.github.io/issues

Spack package:

r-goplot/package.py

Versions:

1.0.2

Build Dependencies:

r, r-ggplot2, r-ggdendro, r-gridextra, r-rcolorbrewer

Link Dependencies:

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:

https://www.bioconductor.org/packages/GOSemSim/

Spack package:

r-gosemsim/package.py

Versions:

2.2.0

Build Dependencies:

r, r-annotationdbi, r-go-db, r-rcpp

Link Dependencies:

Run Dependencies:

r, r-annotationdbi, r-go-db, r-rcpp

Description:

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:

https://bioconductor.org/packages/release/bioc/html/goseq.html

Spack package:

r-goseq/package.py

Versions:

1.32.0

Build Dependencies:

r, r-biasedurn, r-genelendatabase, r-mgcv, r-annotationdbi, r-go-db, r-biocgenerics

Link Dependencies:

Run Dependencies:

r, r-biasedurn, r-genelendatabase, r-mgcv, r-annotationdbi, r-go-db, r-biocgenerics

Description:

Detects Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data

r-gostats¶

Homepage:

https://www.bioconductor.org/packages/GOstats/

Spack package:

r-gostats/package.py

Versions:

2.42.0

Build Dependencies:

r, r-biobase, r-category, r-go-db, r-graph, r-annotationdbi, r-rbgl, r-annotate, r-annotationforge

Link Dependencies:

Run Dependencies:

r, r-biobase, r-category, r-go-db, r-graph, r-annotationdbi, r-rbgl, r-annotate, r-annotationforge

Description:

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-gplots¶

Homepage:

https://cran.r-project.org/package=gplots

Spack package:

r-gplots/package.py

Versions:

3.0.1

Build Dependencies:

r, r-gtools, r-gdata, r-catools, r-kernsmooth

Link Dependencies:

Run Dependencies:

r, r-gtools, r-gdata, r-catools, r-kernsmooth

Description:

Various R Programming Tools for Plotting Data.

r-graph¶

Homepage:

https://www.bioconductor.org/packages/graph/

Spack package:

r-graph/package.py

Versions:

1.54.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

A package that implements some simple graph handling capabilities.

r-gridbase¶

Homepage:

https://cran.r-project.org/web/packages/gridBase/index.html

Spack package:

r-gridbase/package.py

Versions:

0.4-7

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Integration of base and grid graphics.

r-gridextra¶

Homepage:

https://cran.r-project.org/package=gridExtra

Spack package:

r-gridextra/package.py

Versions:

2.3, 2.2.1

Build Dependencies:

r, r-gtable

Link Dependencies:

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-gseabase¶

Homepage:

https://www.bioconductor.org/packages/GSEABase/

Spack package:

r-gseabase/package.py

Versions:

1.38.2

Build Dependencies:

r, r-biocgenerics, r-biobase, r-annotate, r-graph, r-annotationdbi, r-xml

Link Dependencies:

Run Dependencies:

r, r-biocgenerics, r-biobase, r-annotate, r-graph, r-annotationdbi, r-xml

Description:

This package provides classes and methods to support Gene Set Enrichment Analysis (GSEA).

r-gss¶

Homepage:

https://cran.r-project.org/package=gss

Spack package:

r-gss/package.py

Versions:

2.1-7

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

A comprehensive package for structural multivariate function estimation using smoothing splines.

r-gsubfn¶

Homepage:

https://cran.r-project.org/package=gsubfn

Spack package:

r-gsubfn/package.py

Versions:

0.6-6

Build Dependencies:

r, r-proto

Link Dependencies:

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:

https://cran.r-project.org/web/packages/gtable/index.html

Spack package:

r-gtable/package.py

Versions:

0.2.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Tools to make it easier to work with "tables" of 'grobs'.

r-gtools¶

Homepage:

https://cran.r-project.org/package=gtools

Spack package:

r-gtools/package.py

Versions:

3.5.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

https://bioconductor.org/packages/gtrellis/

Spack package:

r-gtrellis/package.py

Versions:

1.8.0

Build Dependencies:

r, r-iranges, r-genomicranges, r-circlize, r-getoptlong

Link Dependencies:

Run Dependencies:

r, r-iranges, r-genomicranges, r-circlize, r-getoptlong

Description:

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:

http://bioconductor.org/packages/Gviz/

Spack package:

r-gviz/package.py

Versions:

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:

Run Dependencies:

Description:

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-haven¶

Homepage:

http://haven.tidyverse.org/

Spack package:

r-haven/package.py

Versions:

1.1.0

Build Dependencies:

r, r-rcpp, r-readr, r-hms, r-tibble, r-forcats

Link Dependencies:

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-hexbin¶

Homepage:

http://github.com/edzer/hexbin

Spack package:

r-hexbin/package.py

Versions:

1.27.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Binning and plotting functions for hexagonal bins. Now uses and relies on grid graphics and formal (S4) classes and methods.

r-highr¶

Homepage:

https://github.com/yihui/highr

Spack package:

r-highr/package.py

Versions:

0.6

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

http://biostat.mc.vanderbilt.edu/Hmisc

Spack package:

r-hmisc/package.py

Versions:

4.1-1, 4.0-3

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

Link Dependencies:

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

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:

https://cran.rstudio.com/web/packages/hms/index.html

Spack package:

r-hms/package.py

Versions:

0.3

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Implements an S3 class for storing and formatting time-of-day values, based on the 'difftime' class.

r-hoardr¶

Homepage:

https://cran.r-project.org/package=hoardr

Spack package:

r-hoardr/package.py

Versions:

0.5.2

Build Dependencies:

r, r-r6, r-rappdirs, r-digest, r-roxygen2, r-testthat, r-knitr, r-rmarkdown

Link Dependencies:

Run Dependencies:

r, r-r6, r-rappdirs, r-digest, r-roxygen2, r-testthat, r-knitr, r-rmarkdown

Description:

hoardr: Manage Cached Files

r-htmltable¶

Homepage:

https://CRAN.R-project.org/package=htmlTable

Spack package:

r-htmltable/package.py

Versions:

1.11.2, 1.9

Build Dependencies:

r, r-stringr, r-knitr, r-magrittr, r-checkmate, r-htmlwidgets, r-rstudioapi

Link Dependencies:

Run Dependencies:

r, r-stringr, r-knitr, r-magrittr, r-checkmate, r-htmlwidgets, 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:

https://github.com/rstudio/htmltools

Spack package:

r-htmltools/package.py

Versions:

0.3.6, 0.3.5

Build Dependencies:

r, r-digest, r-rcpp

Link Dependencies:

Run Dependencies:

r, r-digest, r-rcpp

Description:

Tools for HTML generation and output.

r-htmlwidgets¶

Homepage:

https://cran.r-project.org/package=htmlTable

Spack package:

r-htmlwidgets/package.py

Versions:

0.9, 0.8, 0.6

Build Dependencies:

r, r-htmltools, r-jsonlite, r-yaml

Link Dependencies:

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:

https://github.com/sckott/httpcode

Spack package:

r-httpcode/package.py

Versions:

0.2.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

httpcode: 'HTTP' Status Code Helper

r-httpuv¶

Homepage:

https://github.com/rstudio/httpuv

Spack package:

r-httpuv/package.py

Versions:

1.3.5, 1.3.3

Build Dependencies:

r, r-rcpp

Link Dependencies:

Run Dependencies:

r, r-rcpp

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:

https://github.com/hadley/httr

Spack package:

r-httr/package.py

Versions:

1.3.1, 1.2.1, 1.1.0

Build Dependencies:

r, r-jsonlite, r-mime, r-curl, r-openssl, r-r6

Link Dependencies:

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:

https://cran.rstudio.com/web/packages/hwriter/index.html

Spack package:

r-hwriter/package.py

Versions:

1.3.2

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Easy-to-use and versatile functions to output R objects in HTML format.

r-hypergraph¶

Homepage:

https://www.bioconductor.org/packages/hypergraph/

Spack package:

r-hypergraph/package.py

Versions:

1.48.0

Build Dependencies:

r, r-graph

Link Dependencies:

Run Dependencies:

r, r-graph

Description:

A package that implements some simple capabilities for representing and manipulating hypergraphs.

r-ica¶

Homepage:

https://cran.r-project.org/web/packages/ica/index.html

Spack package:

r-ica/package.py

Versions:

1.0-1, 1.0-0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Independent Component Analysis (ICA) using various algorithms: FastICA, Information-Maximization (Infomax), and Joint Approximate Diagonalization of Eigenmatrices (JADE).

r-igraph¶

Homepage:

http://igraph.org/

Spack package:

r-igraph/package.py

Versions:

1.1.2, 1.0.1

Build Dependencies:

r, r-matrix, r-magrittr, r-pkgconfig, r-irlba, gmp, libxml2

Link Dependencies:

r, gmp, libxml2

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-illuminaio¶

Homepage:

http://bioconductor.org/packages/illuminaio/

Spack package:

r-illuminaio/package.py

Versions:

0.18.0

Build Dependencies:

r, r-base64

Link Dependencies:

Run Dependencies:

r, r-base64

Description:

Tools for parsing Illumina's microarray output files, including IDAT.

r-impute¶

Homepage:

https://www.bioconductor.org/packages/impute/

Spack package:

r-impute/package.py

Versions:

1.56.0, 1.50.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Imputation for microarray data (currently KNN only).

r-influencer¶

Homepage:

https://github.com/rcc-uchicago/influenceR

Spack package:

r-influencer/package.py

Versions:

0.1.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

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-inline¶

Homepage:

https://cran.r-project.org/web/packages/inline/index.html

Spack package:

r-inline/package.py

Versions:

0.3.14

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

https://bioconductor.org/packages/interactiveDisplayBase/

Spack package:

r-interactivedisplaybase/package.py

Versions:

1.14.0

Build Dependencies:

r, r-biocgenerics, r-shiny

Link Dependencies:

Run Dependencies:

r, r-biocgenerics, r-shiny

Description:

The interactiveDisplayBase package contains the the basic methods needed to generate interactive Shiny based display methods for Bioconductor objects.

r-ipred¶

Homepage:

https://cran.r-project.org/package=ipred

Spack package:

r-ipred/package.py

Versions:

0.9-5

Build Dependencies:

r, r-rpart, r-mass, r-survival, r-nnet, r-class, r-prodlim

Link Dependencies:

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:

https://www.bioconductor.org/packages/IRanges/

Spack package:

r-iranges/package.py

Versions:

2.14.10, 2.12.0, 2.10.5

Build Dependencies:

r, r-biocgenerics, r-s4vectors

Link Dependencies:

Run Dependencies:

r, r-biocgenerics, r-s4vectors

Description:

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:

https://irkernel.github.io

Spack package:

r-irdisplay/package.py

Versions:

0.4.4

Build Dependencies:

r, r-repr

Link Dependencies:

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:

https://irkernel.github.io/

Spack package:

r-irkernel/package.py

Versions:

master

Build Dependencies:

r, r-repr, r-irdisplay, r-evaluate, r-crayon, r-pbdzmq, r-devtools, r-uuid, r-digest

Link Dependencies:

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:

https://cran.r-project.org/web/packages/irlba/index.html

Spack package:

r-irlba/package.py

Versions:

2.1.2, 2.0.0

Build Dependencies:

r, r-matrix

Link Dependencies:

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:

https://github.com/ropensci/isdparser

Spack package:

r-isdparser/package.py

Versions:

0.3.0

Build Dependencies:

r, r-data-table, r-tibble

Link Dependencies:

Run Dependencies:

r, r-data-table, r-tibble

Description:

isdparser: Parse 'NOAA' Integrated Surface Data Files

r-iso¶

Homepage:

https://cran.r-project.org/package=Iso

Spack package:

r-iso/package.py

Versions:

0.0-17

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Linear order and unimodal order (univariate) isotonic regression; bivariate isotonic regression with linear order on both variables.

r-iterators¶

Homepage:

https://cran.r-project.org/web/packages/iterators/index.html

Spack package:

r-iterators/package.py

Versions:

1.0.8

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

https://github.com/sfirke/janitor

Spack package:

r-janitor/package.py

Versions:

0.3.0

Build Dependencies:

r, r-dplyr, r-tidyr, r-magrittr

Link Dependencies:

Run Dependencies:

r, r-dplyr, r-tidyr, r-magrittr

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:

http://jaspar.genereg.net/

Spack package:

r-jaspar2018/package.py

Versions:

1.0.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Data package for JASPAR 2018. To search this databases, please use the package TFBSTools (>= 1.15.6).

r-jomo¶

Homepage:

https://cran.r-project.org/package=jomo

Spack package:

r-jomo/package.py

Versions:

2.6-2

Build Dependencies:

r, r-lme4, r-survival

Link Dependencies:

Run Dependencies:

r, r-lme4, r-survival

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:

http://www.rforge.net/jpeg/

Spack package:

r-jpeg/package.py

Versions:

0.1-8

Build Dependencies:

r, jpeg

Link Dependencies:

r, jpeg

Run Dependencies:

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:

https://github.com/jeroenooms/jsonlite

Spack package:

r-jsonlite/package.py

Versions:

1.5, 1.2, 1.0, 0.9.21

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

https://www.bioconductor.org/packages/KEGG.db/

Spack package:

r-kegg-db/package.py

Versions:

3.2.3

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

A set of annotation maps for KEGG assembled using data from KEGG.

r-kegggraph¶

Homepage:

https://www.bioconductor.org/packages/KEGGgraph/

Spack package:

r-kegggraph/package.py

Versions:

1.38.1

Build Dependencies:

r, r-graph, r-xml

Link Dependencies:

Run Dependencies:

r, r-graph, r-xml

Description:

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:

http://bioconductor.org/packages/KEGGREST

Spack package:

r-keggrest/package.py

Versions:

1.18.1, 1.2.0

Build Dependencies:

r, r-httr, r-png, r-biostrings

Link Dependencies:

Run Dependencies:

r, r-httr, r-png, r-biostrings

Description:

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-kernlab¶

Homepage:

https://cran.r-project.org/package=kernlab

Spack package:

r-kernlab/package.py

Versions:

0.9-25

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

https://cran.r-project.org/package=KernSmooth

Spack package:

r-kernsmooth/package.py

Versions:

2.23-15

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Functions for kernel smoothing (and density estimation).

r-kknn¶

Homepage:

https://cran.r-project.org/package=kknn

Spack package:

r-kknn/package.py

Versions:

1.3.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Weighted k-Nearest Neighbors for Classification, Regression and Clustering.

r-knitr¶

Homepage:

https://cran.r-project.org/package=knitr

Spack package:

r-knitr/package.py

Versions:

1.17, 1.14, 0.6

Build Dependencies:

r, r-evaluate, r-digest, r-formatr, r-highr, r-stringr, r-markdown, r-yaml

Link Dependencies:

Run Dependencies:

r, r-evaluate, r-digest, r-formatr, r-highr, r-stringr, r-markdown, r-yaml

Description:

Provides a general-purpose tool for dynamic report generation in R using Literate Programming techniques.

r-ks¶

Homepage:

https://cran.r-project.org/package=ks

Spack package:

r-ks/package.py

Versions:

1.11.2

Build Dependencies:

r, r-fnn, r-kernlab, r-mclust, r-multicool, r-mvtnorm, r-kernsmooth, r-matrix, r-mgcv

Link Dependencies:

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:

https://cran.r-project.org/web/packages/labeling/index.html

Spack package:

r-labeling/package.py

Versions:

0.3

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Provides a range of axis labeling algorithms.

r-lambda-r¶

Homepage:

https://cran.rstudio.com/web/packages/lambda.r/index.html

Spack package:

r-lambda-r/package.py

Versions:

1.2

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

https://github.com/LaplacesDemonR/LaplacesDemon

Spack package:

r-laplacesdemon/package.py

Versions:

16.0.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

https://cran.r-project.org/web/packages/lars/index.html

Spack package:

r-lars/package.py

Versions:

1.2, 1.1, 0.9-8

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Efficient procedures for fitting an entire lasso sequence with the cost of a single least squares fit.

r-lattice¶

Homepage:

http://lattice.r-forge.r-project.org/

Spack package:

r-lattice/package.py

Versions:

0.20-35, 0.20-34

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

http://latticeextra.r-forge.r-project.org/

Spack package:

r-latticeextra/package.py

Versions:

0.6-28

Build Dependencies:

r, r-lattice, r-rcolorbrewer

Link Dependencies:

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:

https://cran.r-project.org/package=lava

Spack package:

r-lava/package.py

Versions:

1.4.7

Build Dependencies:

r, r-numderiv, r-survival

Link Dependencies:

Run Dependencies:

r, r-numderiv, r-survival

Description:

Estimation and simulation of latent variable models.

r-lazyeval¶

Homepage:

https://cran.r-project.org/web/packages/lazyeval/index.html

Spack package:

r-lazyeval/package.py

Versions:

0.2.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

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-leaflet¶

Homepage:

http://rstudio.github.io/leaflet/

Spack package:

r-leaflet/package.py

Versions:

1.0.1

Build Dependencies:

r, r-base64enc, r-htmlwidgets, r-htmltools, r-magrittr, r-markdown, r-png, r-rcolorbrewer, r-raster, r-scales, r-sp

Link Dependencies:

Run Dependencies:

r, r-base64enc, r-htmlwidgets, r-htmltools, r-magrittr, r-markdown, r-png, r-rcolorbrewer, r-raster, r-scales, r-sp

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:

https://CRAN.R-project.org/package=leaps

Spack package:

r-leaps/package.py

Versions:

3.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

leaps: Regression Subset Selection

r-learnbayes¶

Homepage:

https://CRAN.R-project.org/package=LearnBayes

Spack package:

r-learnbayes/package.py

Versions:

2.15

Build Dependencies:

Link Dependencies:

Run Dependencies:

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-lhs¶

Homepage:

http://lhs.r-forge.r-project.org/

Spack package:

r-lhs/package.py

Versions:

0.16

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Provides a number of methods for creating and augmenting Latin Hypercube Samples.

r-limma¶

Homepage:

https://www.bioconductor.org/packages/limma/

Spack package:

r-limma/package.py

Versions:

3.36.2, 3.34.9, 3.32.10

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Data analysis, linear models and differential expression for microarray data.

r-lme4¶

Homepage:

https://github.com/lme4/lme4/

Spack package:

r-lme4/package.py

Versions:

1.1-12

Build Dependencies:

r, r-matrix, r-mass, r-lattice, r-nlme, r-minqa, r-nloptr, r-rcpp, r-rcppeigen

Link Dependencies:

Run Dependencies:

r, r-matrix, r-mass, r-lattice, r-nlme, r-minqa, r-nloptr, r-rcpp, r-rcppeigen

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:

https://cran.r-project.org/package=lmtest

Spack package:

r-lmtest/package.py

Versions:

0.9-34

Build Dependencies:

r, r-zoo

Link Dependencies:

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:

https://cran.rstudio.com/web/packages/locfit/index.html

Spack package:

r-locfit/package.py

Versions:

1.5-9.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Local regression, likelihood and density estimation.

r-log4r¶

Homepage:

https://cran.r-project.org/package=log4r

Spack package:

r-log4r/package.py

Versions:

0.2

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

logr4 provides an object-oriented logging system that uses an API roughly equivalent to log4j and its related variants.

r-loo¶

Homepage:

https://mc-stan.org/loo

Spack package:

r-loo/package.py

Versions:

2.1.0

Build Dependencies:

r, r-checkmate, r-matrixstats

Link Dependencies:

Run Dependencies:

r, r-checkmate, r-matrixstats

Description:

loo: Efficient Leave-One-Out Cross-Validation and WAIC for BayesianModels

r-lpsolve¶

Homepage:

https://cran.r-project.org/web/packages/lpSolve/index.html

Spack package:

r-lpsolve/package.py

Versions:

5.6.13

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

https://cran.r-project.org/package=lsei

Spack package:

r-lsei/package.py

Versions:

1.2-0

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

https://cran.r-project.org/web/packages/lubridate/index.html

Spack package:

r-lubridate/package.py

Versions:

1.7.1, 1.5.6

Build Dependencies:

r, r-rcpp, r-stringr

Link Dependencies:

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-magic¶

Homepage:

https://cran.r-project.org/

Spack package:

r-magic/package.py

Versions:

1.5-6

Build Dependencies:

r, r-abind

Link Dependencies:

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-magrittr¶

Homepage:

https://cran.r-project.org/web/packages/magrittr/index.html

Spack package:

r-magrittr/package.py

Versions:

1.5

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

https://www.bioconductor.org/packages/makecdfenv/

Spack package:

r-makecdfenv/package.py

Versions:

1.52.0

Build Dependencies:

r, r-affyio, r-biobase, r-affy, r-zlibbioc

Link Dependencies:

Run Dependencies:

r, r-affyio, r-biobase, r-affy, r-zlibbioc

Description:

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:

https://cran.r-project.org/package=MALDIquant

Spack package:

r-maldiquant/package.py

Versions:

1.16.4

Build Dependencies:

r, r-knitr, r-testthat

Link Dependencies:

Run Dependencies:

r, r-knitr, r-testthat

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:

https://github.com/rte-antares-rpackage/manipulateWidget

Spack package:

r-manipulatewidget/package.py

Versions:

0.10.0

Build Dependencies:

r, r-base64enc, r-codetools, r-htmltools, r-htmlwidgets, r-knitr, r-miniui, r-shiny, r-webshot

Link Dependencies:

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-mapproj¶

Homepage:

https://cran.r-project.org/package=mapproj

Spack package:

r-mapproj/package.py

Versions:

1.2-4

Build Dependencies:

r, r-maps

Link Dependencies:

Run Dependencies:

r, r-maps

Description:

Converts latitude/longitude into projected coordinates.

r-maps¶

Homepage:

https://cran.r-project.org/

Spack package:

r-maps/package.py

Versions:

3.1.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Display of maps. Projection code and larger maps are in separate packages ('mapproj' and 'mapdata').

r-maptools¶

Homepage:

http://r-forge.r-project.org/projects/maptools/

Spack package:

r-maptools/package.py

Versions:

0.8-39

Build Dependencies:

r, r-sp, r-foreign, r-lattice

Link Dependencies:

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:

https://cran.r-project.org/package=markdown

Spack package:

r-markdown/package.py

Versions:

0.8, 0.7.7

Build Dependencies:

r, r-mime

Link Dependencies:

Run Dependencies:

r, r-mime

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:

https://cran.r-project.org/web/packages/MASS/index.html

Spack package:

r-mass/package.py

Versions:

7.3-47, 7.3-45

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Functions and datasets to support Venables and Ripley, "Modern Applied Statistics with S" (4th edition, 2002).

r-matr¶

Homepage:

https://github.com/MG-RAST/matR

Spack package:

r-matr/package.py

Versions:

0.9.1, 0.9

Build Dependencies:

r, r-mgraster, r-biom-utils

Link Dependencies:

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:

http://matrix.r-forge.r-project.org/

Spack package:

r-matrix/package.py

Versions:

1.2-14, 1.2-12, 1.2-11, 1.2-8, 1.2-6

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Classes and methods for dense and sparse matrices and operations on them using 'LAPACK' and 'SuiteSparse'.

r-matrixmodels¶

Homepage:

http://matrix.r-forge.r-project.org/

Spack package:

r-matrixmodels/package.py

Versions:

0.4-1

Build Dependencies:

r, r-matrix

Link Dependencies:

Run Dependencies:

r, r-matrix

Description:

Modelling with sparse and dense 'Matrix' matrices, using modular prediction and response module classes.

r-matrixstats¶

Homepage:

https://cran.rstudio.com/web/packages/matrixStats/index.html

Spack package:

r-matrixstats/package.py

Versions:

0.52.2

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

http://www.stat.washington.edu/mclust

Spack package:

r-mclust/package.py

Versions:

5.3

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

mclust: Gaussian Mixture Modelling for Model-Based Clustering, Classification, and Density Estimation

r-mcmcglmm¶

Homepage:

https://cran.r-project.org/web/packages/MCMCglmm/index.html

Spack package:

r-mcmcglmm/package.py

Versions:

2.25

Build Dependencies:

r, r-matrix, r-coda, r-ape, r-corpcor, r-tensora, r-cubature

Link Dependencies:

Run Dependencies:

r, r-matrix, r-coda, r-ape, r-corpcor, r-tensora, r-cubature

Description:

MCMC Generalised Linear Mixed Models.

r-mco¶

Homepage:

https://github.com/cran/mco

Spack package:

r-mco/package.py

Versions:

1.0-15.1, 1.0-15

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Functions for multiple criteria optimization using genetic algorithms and related test problems

r-mda¶

Homepage:

https://cran.r-project.org/package=mda

Spack package:

r-mda/package.py

Versions:

0.4-9

Build Dependencies:

r, r-class

Link Dependencies:

Run Dependencies:

r, r-class

Description:

Mixture and flexible discriminant analysis, multivariate adaptive regression splines (MARS), BRUTO.

r-memoise¶

Homepage:

https://github.com/hadley/memoise

Spack package:

r-memoise/package.py

Versions:

1.1.0, 1.0.0

Build Dependencies:

r, r-digest

Link Dependencies:

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:

https://www.bioconductor.org/packages/MergeMaid/

Spack package:

r-mergemaid/package.py

Versions:

2.48.0

Build Dependencies:

r, r-survival, r-biobase, r-mass

Link Dependencies:

Run Dependencies:

r, r-survival, r-biobase, r-mass

Description:

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-methodss3¶

Homepage:

https://cran.r-project.org/package=R.methodsS3

Spack package:

r-methodss3/package.py

Versions:

1.7.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

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-mgcv¶

Homepage:

https://cran.r-project.org/package=mgcv

Spack package:

r-mgcv/package.py

Versions:

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:

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:

https://github.com/braithwaite/MGRASTer/

Spack package:

r-mgraster/package.py

Versions:

0.9

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

https://cran.r-project.org/package=mice

Spack package:

r-mice/package.py

Versions:

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:

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:

https://github.com/yihui/mime

Spack package:

r-mime/package.py

Versions:

0.5, 0.4

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Guesses the MIME type from a filename extension using the data derived from /etc/mime.types in UNIX-type systems.

r-minfi¶

Homepage:

https://bioconductor.org/packages/minfi/

Spack package:

r-minfi/package.py

Versions:

1.22.1

Build Dependencies:

r, r-biocgenerics, r-genomicranges, r-summarizedexperiment, r-biostrings, r-bumphunter, r-s4vectors, r-genomeinfodb, r-biobase, r-iranges, r-beanplot, r-rcolorbrewer, r-lattice, r-nor1mix, r-siggenes, r-limma, r-preprocesscore, r-illuminaio, r-matrixstats, r-mclust, r-genefilter, r-nlme, r-reshape, r-mass, r-quadprog, r-data-table, r-geoquery

Link Dependencies:

Run Dependencies:

Description:

Tools to analyze & visualize Illumina Infinium methylation arrays.

r-miniui¶

Homepage:

https://cran.r-project.org/package=miniUI

Spack package:

r-miniui/package.py

Versions:

0.1.1.1

Build Dependencies:

r, r-shiny, r-htmltools

Link Dependencies:

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:

http://optimizer.r-forge.r-project.org/

Spack package:

r-minqa/package.py

Versions:

1.2.4

Build Dependencies:

r, r-rcpp

Link Dependencies:

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:

https://cran.r-project.org/web/packages/misc3d/index.html

Spack package:

r-misc3d/package.py

Versions:

0.8-4

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

A collection of miscellaneous 3d plots, including isosurfaces.

r-mitml¶

Homepage:

https://cran.r-project.org/package=mitml

Spack package:

r-mitml/package.py

Versions:

0.3-5

Build Dependencies:

r, r-pan, r-jomo, r-haven

Link Dependencies:

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-mixtools¶

Homepage:

https://cran.r-project.org/web/packages/mixtools/index.html

Spack package:

r-mixtools/package.py

Versions:

1.1.0, 1.0.4

Build Dependencies:

r, r-mass, r-segmented, r-survival

Link Dependencies:

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:

https://cran.r-project.org/web/packages/mlbench/index.html

Spack package:

r-mlbench/package.py

Versions:

2.1-1

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

https://www.bioconductor.org/packages/MLInterfaces/

Spack package:

r-mlinterfaces/package.py

Versions:

1.56.0

Build Dependencies:

r, r-biocgenerics, r-biobase, r-gdata, r-pls, r-sfsmisc, r-rda, r-genefilter, r-fpc, r-ggvis, r-shiny, r-gbm, r-rcolorbrewer, r-hwriter, r-threejs, r-mlbench

Link Dependencies:

Run Dependencies:

r, r-biocgenerics, r-biobase, r-gdata, r-pls, r-sfsmisc, r-rda, r-genefilter, r-fpc, r-ggvis, r-shiny, r-gbm, r-rcolorbrewer, r-hwriter, r-threejs, r-mlbench

Description:

This package provides uniform interfaces to machine learning code for data in R and Bioconductor containers.

r-mlr¶

Homepage:

https://github.com/mlr-org/mlr/

Spack package:

r-mlr/package.py

Versions:

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-xml

Link Dependencies:

Run Dependencies:

r, r-paramhelpers, r-bbmisc, r-backports, r-ggplot2, r-stringi, r-checkmate, r-data-table, r-parallelmap, 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:

https://github.com/mlr-org/mlrMBO/

Spack package:

r-mlrmbo/package.py

Versions:

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:

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:

https://cran.r-project.org/package=MMWRweek

Spack package:

r-mmwrweek/package.py

Versions:

0.1.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

http://azzalini.stat.unipd.it/SW/Pkg-mnormt

Spack package:

r-mnormt/package.py

Versions:

1.5-5

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

https://cran.r-project.org/package=ModelMetrics

Spack package:

r-modelmetrics/package.py

Versions:

1.1.0

Build Dependencies:

r, r-rcpp

Link Dependencies:

Run Dependencies:

r, r-rcpp

Description:

Collection of metrics for evaluating models written in C++ using 'Rcpp'.

r-modelr¶

Homepage:

https://github.com/hadley/modelr

Spack package:

r-modelr/package.py

Versions:

0.1.1

Build Dependencies:

r, r-magrittr, r-purrr, r-lazyeval, r-tibble, r-broom, r-dplyr, r-tidyr

Link Dependencies:

Run Dependencies:

r, r-magrittr, r-purrr, r-lazyeval, r-tibble, r-broom, r-dplyr, r-tidyr

Description:

Functions for modelling that help you seamlessly integrate modelling into a pipeline of data manipulation and visualisation.

r-modeltools¶

Homepage:

https://cran.r-project.org/package=modeltools

Spack package:

r-modeltools/package.py

Versions:

0.2-21

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

A collection of tools to deal with statistical models.

r-mpm¶

Homepage:

https://cran.rstudio.com/web/packages/mpm/index.html

Spack package:

r-mpm/package.py

Versions:

1.0-22

Build Dependencies:

r, r-kernsmooth

Link Dependencies:

Run Dependencies:

r, 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:

https://www.bioconductor.org/packages/MSnbase/

Spack package:

r-msnbase/package.py

Versions:

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

Link Dependencies:

Run Dependencies:

Description:

Manipulation, processing and visualisation of mass spectrometry and proteomics data.

r-multcomp¶

Homepage:

http://multcomp.r-forge.r-project.org/

Spack package:

r-multcomp/package.py

Versions:

1.4-6

Build Dependencies:

r, r-mvtnorm, r-survival, r-th-data, r-sandwich, r-codetools

Link Dependencies:

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:

https://cran.r-project.org/package=multicool

Spack package:

r-multicool/package.py

Versions:

0.1-9

Build Dependencies:

r, r-rcpp

Link Dependencies:

Run Dependencies:

r, r-rcpp

Description:

Permutations of multisets in cool-lex order.

r-multitaper¶

Homepage:

https://github.com/krahim/multitaper/

Spack package:

r-multitaper/package.py

Versions:

1.0-14

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

multitaper: Spectral Analysis Tools using the Multitaper Method

r-multtest¶

Homepage:

https://www.bioconductor.org/packages/multtest/

Spack package:

r-multtest/package.py

Versions:

2.32.0

Build Dependencies:

r, r-biocgenerics, r-biobase

Link Dependencies:

Run Dependencies:

r, r-biocgenerics, r-biobase

Description:

Resampling-based multiple hypothesis testing

r-munsell¶

Homepage:

https://cran.r-project.org/web/packages/munsell/index.html

Spack package:

r-munsell/package.py

Versions:

0.4.3

Build Dependencies:

r, r-colorspace

Link Dependencies:

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:

http://mvtnorm.r-forge.r-project.org/

Spack package:

r-mvtnorm/package.py

Versions:

1.0-6, 1.0-5

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Computes multivariate normal and t probabilities, quantiles, random deviates and densities.

r-mzid¶

Homepage:

https://www.bioconductor.org/packages/mzID/

Spack package:

r-mzid/package.py

Versions:

1.14.0

Build Dependencies:

r, r-xml, r-plyr, r-doparallel, r-foreach, r-iterators, r-protgenerics

Link Dependencies:

Run Dependencies:

r, r-xml, r-plyr, r-doparallel, r-foreach, r-iterators, r-protgenerics

Description:

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:

https://www.bioconductor.org/packages/mzR/

Spack package:

r-mzr/package.py

Versions:

2.10.0

Build Dependencies:

r, r-biobase, r-biocgenerics, r-protgenerics, r-rcpp, r-zlibbioc, netcdf

Link Dependencies:

r, netcdf

Run Dependencies:

r, r-biobase, r-biocgenerics, r-protgenerics, r-rcpp, r-zlibbioc

Description:

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:

https://cran.r-project.org/package=nanotime

Spack package:

r-nanotime/package.py

Versions:

0.2.0

Build Dependencies:

r, r-bit64, r-rcppcctz, r-zoo

Link Dependencies:

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:

https://cran.r-project.org/package=ncbit

Spack package:

r-ncbit/package.py

Versions:

2013.03.29

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Making NCBI taxonomic data locally available and searchable as an R object.

r-ncdf4¶

Homepage:

http://cirrus.ucsd.edu/~pierce/ncdf

Spack package:

r-ncdf4/package.py

Versions:

1.15

Build Dependencies:

r, netcdf

Link Dependencies:

r, netcdf

Run Dependencies:

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:

https://statnet.org

Spack package:

r-network/package.py

Versions:

1.13.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

http://cran.r-project.org/package=networkD3

Spack package:

r-networkd3/package.py

Versions:

0.2.12

Build Dependencies:

r, r-htmlwidgets, r-igraph, r-magrittr

Link Dependencies:

Run Dependencies:

r, r-htmlwidgets, r-igraph, r-magrittr

Description:

Creates 'D3' 'JavaScript' network, tree, dendrogram, and Sankey graphs from 'R'.

r-nleqslv¶

Homepage:

https://cran.r-project.org/package=nleqslv

Spack package:

r-nleqslv/package.py

Versions:

3.3.2

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

nleqslv: Solve Systems of Nonlinear Equations

r-nlme¶

Homepage:

https://cran.r-project.org/package=nlme

Spack package:

r-nlme/package.py

Versions:

3.1-131, 3.1-130, 3.1-128

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Fit and compare Gaussian linear and nonlinear mixed-effects models.

r-nloptr¶

Homepage:

https://cran.r-project.org/package=nloptr

Spack package:

r-nloptr/package.py

Versions:

1.0.4

Build Dependencies:

r, r-testthat, nlopt

Link Dependencies:

r, nlopt

Run Dependencies:

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:

http://renozao.github.io/NMF

Spack package:

r-nmf/package.py

Versions:

0.20.6

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:

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-nnet¶

Homepage:

http://www.stats.ox.ac.uk/pub/MASS4/

Spack package:

r-nnet/package.py

Versions:

7.3-12

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Software for feed-forward neural networks with a single hidden layer, and for multinomial log-linear models.

r-nnls¶

Homepage:

https://cran.r-project.org/package=nnls

Spack package:

r-nnls/package.py

Versions:

1.4

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

https://CRAN.R-project.org/package=nor1mix

Spack package:

r-nor1mix/package.py

Versions:

1.2-3

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

https://cran.r-project.org/package=nortest

Spack package:

r-nortest/package.py

Versions:

1.0-4

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

nortest: Tests for Normality Five omnibus tests for testing the composite hypothesis of normality.

r-np¶

Homepage:

https://github.com/JeffreyRacine/R-Package-np/

Spack package:

r-np/package.py

Versions:

0.60-2

Build Dependencies:

r, r-boot, r-cubature

Link Dependencies:

Run Dependencies:

r, r-boot, r-cubature

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-numderiv¶

Homepage:

https://cran.r-project.org/package=numDeriv

Spack package:

r-numderiv/package.py

Versions:

2016.8-1

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Methods for calculating (usually) accurate numerical first and second order derivatives.

r-oligoclasses¶

Homepage:

https://www.bioconductor.org/packages/oligoClasses/

Spack package:

r-oligoclasses/package.py

Versions:

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

Link Dependencies:

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

Description:

This package contains class definitions, validity checks, and initialization methods for classes used by the oligo and crlmm packages.

r-oo¶

Homepage:

https://github.com/HenrikBengtsson/R.oo

Spack package:

r-oo/package.py

Versions:

1.21.0

Build Dependencies:

r, r-methodss3

Link Dependencies:

Run Dependencies:

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-openssl¶

Homepage:

https://CRAN.R-project.org/package=openssl

Spack package:

r-openssl/package.py

Versions:

0.9.7, 0.9.6, 0.9.4

Build Dependencies:

r, openssl

Link Dependencies:

r, openssl

Run Dependencies:

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-optparse¶

Homepage:

https://cran.r-project.org/package=optparse

Spack package:

r-optparse/package.py

Versions:

1.6.0

Build Dependencies:

r, r-getopt

Link Dependencies:

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-org-hs-eg-db¶

Homepage:

https://bioconductor.org/packages/org.Hs.eg.db/

Spack package:

r-org-hs-eg-db/package.py

Versions:

3.4.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Genome wide annotation for Human, primarily based on mapping using Entrez Gene identifiers.

r-organismdbi¶

Homepage:

https://bioconductor.org/packages/OrganismDbi/

Spack package:

r-organismdbi/package.py

Versions:

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

Link Dependencies:

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

Description:

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:

https://github.com/rstudio/packrat/

Spack package:

r-packrat/package.py

Versions:

0.4.8-1, 0.4.7-1

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Manage the R packages your project depends on in an isolated, portable, and reproducible way.

r-pacman¶

Homepage:

https://cran.r-project.org/package=pacman

Spack package:

r-pacman/package.py

Versions:

0.4.1

Build Dependencies:

r, r-devtools

Link Dependencies:

Run Dependencies:

r, r-devtools

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:

https://github.com/dwbapst/paleotree

Spack package:

r-paleotree/package.py

Versions:

3.1.3

Build Dependencies:

r, r-ape, r-phangorn, r-phytools

Link Dependencies:

Run Dependencies:

r, r-ape, r-phangorn, r-phytools

Description:

Provides tools for transforming, a posteriori time-scaling, and modifying phylogenies containing extinct (i.e. fossil) lineages

r-pamr¶

Homepage:

https://cran.r-project.org/package=pamr

Spack package:

r-pamr/package.py

Versions:

1.55

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Some functions for sample classification in microarrays.

r-pan¶

Homepage:

https://cran.r-project.org/package=pan

Spack package:

r-pan/package.py

Versions:

1.4

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Multiple imputation for multivariate panel or clustered data.

r-parallelmap¶

Homepage:

https://github.com/berndbischl/parallelMap

Spack package:

r-parallelmap/package.py

Versions:

1.3

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

https://github.com/berndbischl/ParamHelpers

Spack package:

r-paramhelpers/package.py

Versions:

1.10

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

https://cran.r-project.org/web/packages/party/index.html

Spack package:

r-party/package.py

Versions:

1.1-2

Build Dependencies:

r, r-mvtnorm, r-modeltools, r-strucchange, r-survival, r-coin, r-zoo, r-sandwich

Link Dependencies:

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:

http://partykit.r-forge.r-project.org/partykit

Spack package:

r-partykit/package.py

Versions:

1.1-1

Build Dependencies:

r, r-survival, r-formula

Link Dependencies:

Run Dependencies:

r, r-survival, r-formula

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:

https://www.bioconductor.org/packages/pathview/

Spack package:

r-pathview/package.py

Versions:

1.16.7

Build Dependencies:

r, r-keggrest, r-png, r-annotationdbi, r-graph, r-rgraphviz, r-xml, r-kegggraph, r-org-hs-eg-db

Link Dependencies:

Run Dependencies:

r, r-keggrest, r-png, r-annotationdbi, r-graph, r-rgraphviz, r-xml, r-kegggraph, r-org-hs-eg-db

Description:

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:

https://cran.r-project.org/web/packages/pbapply/index.html

Spack package:

r-pbapply/package.py

Versions:

1.3-3, 1.3-2, 1.3-1, 1.3-0, 1.2-2

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

A lightweight package that adds progress bar to vectorized R apply functions.

r-pbdzmq¶

Homepage:

http://r-pbd.org/

Spack package:

r-pbdzmq/package.py

Versions:

0.2-4

Build Dependencies:

r, r-r6, zeromq

Link Dependencies:

r, zeromq

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:

http://people.math.aau.dk/~sorenh/software/pbkrtest/

Spack package:

r-pbkrtest/package.py

Versions:

0.4-6, 0.4-4

Build Dependencies:

r, r-lme4, r-matrix, r-mass

Link Dependencies:

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:

http://bioconductor.org/packages/pcaMethods/

Spack package:

r-pcamethods/package.py

Versions:

1.68.0

Build Dependencies:

r, r-biobase, r-biocgenerics, r-rcpp, r-mass

Link Dependencies:

Run Dependencies:

r, r-biobase, r-biocgenerics, r-rcpp, r-mass

Description:

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:

https://cran.r-project.org/web/packages/pcaPP/index.html

Spack package:

r-pcapp/package.py

Versions:

1.9-72, 1.9-70, 1.9-61, 1.9-60, 1.9-50

Build Dependencies:

r, r-mvtnorm

Link Dependencies:

Run Dependencies:

r, r-mvtnorm

Description:

Provides functions for robust PCA by projection pursuit.

r-permute¶

Homepage:

https://github.com/gavinsimpson/permute

Spack package:

r-permute/package.py

Versions:

0.9-4

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

https://www.bioconductor.org/packages/PFAM.db/

Spack package:

r-pfam-db/package.py

Versions:

3.4.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

A set of protein ID mappings for PFAM assembled using data from public repositories.

r-phangorn¶

Homepage:

https://cran.r-project.org/package=phangorn

Spack package:

r-phangorn/package.py

Versions:

2.3.1

Build Dependencies:

r, r-ape, r-quadprog, r-igraph, r-matrix, r-fastmatch, r-magrittr, r-rcpp

Link Dependencies:

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:

https://github.com/kundajelab/phantompeakqualtools

Spack package:

r-phantompeakqualtools/package.py

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-phyloseq¶

Homepage:

https://www.bioconductor.org/packages/phyloseq/

Spack package:

r-phyloseq/package.py

Versions:

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:

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:

phyloseq provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data.

r-phylostratr¶

Homepage:

https://github.com/arenasee/phylostratr

Spack package:

r-phylostratr/package.py

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:

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:

http://github.com/liamrevell/phytools

Spack package:

r-phytools/package.py

Versions:

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

Link Dependencies:

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

Description:

Phylogenetic Tools for Comparative Biology (and Other Things)

r-picante¶

Homepage:

https://cran.r-project.org/package=picante

Spack package:

r-picante/package.py

Versions:

1.6-2, 1.6-1

Build Dependencies:

r, r-ape, r-nlme, r-vegan

Link Dependencies:

Run Dependencies:

r, r-ape, r-nlme, r-vegan

Description:

R tools for integrating phylogenies and ecology

r-pillar¶

Homepage:

https://cran.r-project.org/package=pillar

Spack package:

r-pillar/package.py

Versions:

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

Link Dependencies:

Run Dependencies:

r, r-cli, r-crayon, r-fansi, r-rlang, r-utf8

Description:

Provides a 'pillar' generic designed for formatting columns of data using the full range of colours provided by modern terminals.

r-pkgbuild¶

Homepage:

https://cran.r-project.org/package=pkgbuild

Spack package:

r-pkgbuild/package.py

Versions:

1.0.3

Build Dependencies:

r, r-callr, r-cli, r-crayon, r-desc, r-prettyunits, r-r6, r-rprojroot, r-withr

Link Dependencies:

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:

https://cran.rstudio.com/web/packages/pkgconfig/index.html

Spack package:

r-pkgconfig/package.py

Versions:

2.0.2, 2.0.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

https://cran.r-project.org/package=pkgload

Spack package:

r-pkgload/package.py

Versions:

1.0.2

Build Dependencies:

r, r-desc, r-pkgbuild, r-rlang, r-rprojroot, r-rstudioapi, r-withr

Link Dependencies:

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:

https://renozao.github.io/pkgmaker

Spack package:

r-pkgmaker/package.py

Versions:

0.27, 0.22

Build Dependencies:

r, r-registry, r-codetools, r-digest, r-stringi, r-magrittr, r-stringr, r-xtable, r-withr, r-bibtex, r-devtools, r-roxygen2, r-runit, r-testthat, r-knitr, r-rmarkdown, r-yaml, r-biobase

Link Dependencies:

Run Dependencies:

r, r-registry, r-codetools, r-digest, r-stringi, r-magrittr, r-stringr, r-xtable, r-withr, r-bibtex, r-devtools, r-roxygen2, r-runit, r-testthat, r-knitr, r-rmarkdown, r-yaml, r-biobase

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:

https://cran.r-project.org/package=plogr

Spack package:

r-plogr/package.py

Versions:

0.2.0, 0.1-1

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

https://CRAN.R-project.org/package=plot3D

Spack package:

r-plot3d/package.py

Versions:

1.1.1

Build Dependencies:

r, r-misc3d

Link Dependencies:

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:

https://cran.r-project.org/web/packages/plotly/index.html

Spack package:

r-plotly/package.py

Versions:

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

Link Dependencies:

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

Description:

Easily translate 'ggplot2' graphs to an interactive web-based version and/or create custom web-based visualizations directly from R.

r-plotrix¶

Homepage:

https://cran.r-project.org/package=plotrix

Spack package:

r-plotrix/package.py

Versions:

3.6-4, 3.6-3

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Lots of plots, various labeling, axis and color scaling functions.

r-pls¶

Homepage:

https://cran.r-project.org/package=pls

Spack package:

r-pls/package.py

Versions:

2.6-0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Multivariate regression methods Partial Least Squares Regression (PLSR), Principal Component Regression (PCR) and Canonical Powered Partial Least Squares (CPPLS).

r-plyr¶

Homepage:

http://had.co.nz/plyr

Spack package:

r-plyr/package.py

Versions:

1.8.4

Build Dependencies:

r, r-rcpp

Link Dependencies:

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:

https://cran.r-project.org/package=PMCMR

Spack package:

r-pmcmr/package.py

Versions:

4.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

http://www.rforge.net/png/

Spack package:

r-png/package.py

Versions:

0.1-7

Build Dependencies:

r, libpng

Link Dependencies:

r, libpng

Run Dependencies:

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-popgenome¶

Homepage:

https://popgenome.weebly.com

Spack package:

r-popgenome/package.py

Versions:

2.6.1

Build Dependencies:

r, r-ff

Link Dependencies:

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:

https://cran.r-project.org/package=PopVar

Spack package:

r-popvar/package.py

Versions:

1.2.1

Build Dependencies:

r, r-bglr, r-qtl, r-rrblup

Link Dependencies:

Run Dependencies:

r, r-bglr, r-qtl, r-rrblup

Description:

PopVar: Genomic Breeding Tools: Genetic Variance Prediction andCross- Validation

r-powerlaw¶

Homepage:

https://github.com/csgillespie/poweRlaw

Spack package:

r-powerlaw/package.py

Versions:

0.70.1

Build Dependencies:

r, r-vgam

Link Dependencies:

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:

http://www.homepages.ucl.ac.uk/~ucakche

Spack package:

r-prabclus/package.py

Versions:

2.2-6

Build Dependencies:

r, r-mclust

Link Dependencies:

Run Dependencies:

r, r-mclust

Description:

prabclus: Functions for Clustering of Presence-Absence, Abundance and Multilocus Genetic Data

r-praise¶

Homepage:

https://github.com/gaborcsardi/praise

Spack package:

r-praise/package.py

Versions:

1.0.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

https://bioconductor.org/packages/preprocessCore/

Spack package:

r-preprocesscore/package.py

Versions:

1.44.0, 1.38.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

A library of core preprocessing routines

r-prettyunits¶

Homepage:

https://cran.r-project.org/package=prettyunits

Spack package:

r-prettyunits/package.py

Versions:

1.0.2

Build Dependencies:

r, r-magrittr, r-assertthat

Link Dependencies:

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:

https://github.com/r-lib/processx

Spack package:

r-processx/package.py

Versions:

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-utils

Link Dependencies:

Run Dependencies:

r, r-assertthat, r-crayon, r-ps, r-r6, r-utils

Description:

Tools to run system processes in the background

r-prodlim¶

Homepage:

https://cran.r-project.org/package=prodlim

Spack package:

r-prodlim/package.py

Versions:

1.5.9

Build Dependencies:

r, r-rcpp, r-survival, r-kernsmooth, r-lava

Link Dependencies:

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:

https://cran.r-project.org/package=progress

Spack package:

r-progress/package.py

Versions:

1.1.2

Build Dependencies:

r, r-r6, r-prettyunits

Link Dependencies:

Run Dependencies:

r, r-r6, r-prettyunits

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-protgenerics¶

Homepage:

https://bioconductor.org/packages/ProtGenerics/

Spack package:

r-protgenerics/package.py

Versions:

1.8.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

S4 generic functions needed by Bioconductor proteomics packages.

r-proto¶

Homepage:

http://r-proto.googlecode.com/

Spack package:

r-proto/package.py

Versions:

1.0.0, 0.3-10

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

An object oriented system using object-based, also called prototype- based, rather than class-based object oriented ideas.

r-proxy¶

Homepage:

https://cran.r-project.org/package=proxy

Spack package:

r-proxy/package.py

Versions:

0.4-19

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

https://github.com/hadley/pryr

Spack package:

r-pryr/package.py

Versions:

0.1.2

Build Dependencies:

r, r-stringr, r-rcpp

Link Dependencies:

Run Dependencies:

r, r-stringr, r-rcpp

Description:

Useful tools to pry back the covers of R and understand the language at a deeper level.

r-ps¶

Homepage:

https://github.com/r-lib/ps

Spack package:

r-ps/package.py

Versions:

1.1.0, 1.0.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Manipulate processes on Windows, Linux and MacOS

r-psych¶

Homepage:

http://personality-project.org/r/psych

Spack package:

r-psych/package.py

Versions:

1.7.8

Build Dependencies:

r, r-mnormt, r-foreign, r-lattice, r-nlme

Link Dependencies:

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:

https://cran.r-project.org/package=ptw

Spack package:

r-ptw/package.py

Versions:

1.9-12

Build Dependencies:

r, r-nloptr

Link Dependencies:

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:

http://purrr.tidyverse.org/

Spack package:

r-purrr/package.py

Versions:

0.2.4

Build Dependencies:

r, r-magrittr, r-rlang, r-tibble

Link Dependencies:

Run Dependencies:

r, r-magrittr, r-rlang, r-tibble

Description:

A complete and consistent functional programming toolkit for R.

r-qtl¶

Homepage:

http://rqtl.org

Spack package:

r-qtl/package.py

Versions:

1.44-9

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

qtl: Tools for Analyzing QTL Experiments

r-quadprog¶

Homepage:

https://cran.r-project.org/web/packages/quadprog/index.html

Spack package:

r-quadprog/package.py

Versions:

1.5-5

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

This package contains routines and documentation for solving quadratic programming problems.

r-quantmod¶

Homepage:

http://www.quantmod.com/

Spack package:

r-quantmod/package.py

Versions:

0.4-10, 0.4-5

Build Dependencies:

r, r-xts, r-zoo, r-ttr, r-curl

Link Dependencies:

Run Dependencies:

r, r-xts, r-zoo, r-ttr, r-curl

Description:

Specify, build, trade, and analyse quantitative financial trading strategies.

r-quantreg¶

Homepage:

https://cran.r-project.org/package=quantreg

Spack package:

r-quantreg/package.py

Versions:

5.29, 5.26

Build Dependencies:

r, r-sparsem, r-matrix, r-matrixmodels

Link Dependencies:

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:

https://www.bioconductor.org/packages/quantro/

Spack package:

r-quantro/package.py

Versions:

1.10.0

Build Dependencies:

r, r-biobase, r-minfi, r-doparallel, r-foreach, r-iterators, r-ggplot2, r-rcolorbrewer

Link Dependencies:

Run Dependencies:

r, r-biobase, r-minfi, r-doparallel, r-foreach, r-iterators, r-ggplot2, r-rcolorbrewer

Description:

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:

https://www.bioconductor.org/packages/qvalue/

Spack package:

r-qvalue/package.py

Versions:

2.12.0, 2.8.0

Build Dependencies:

r, r-ggplot2, r-reshape2

Link Dependencies:

Run Dependencies:

r, r-ggplot2, r-reshape2

Description:

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-r6¶

Homepage:

https://github.com/wch/R6/

Spack package:

r-r6/package.py

Versions:

2.2.2, 2.2.0, 2.1.2

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

https://cran.r-project.org/web/packages/RandomFields

Spack package:

r-randomfields/package.py

Versions:

3.1.50

Build Dependencies:

r, r-sp, r-randomfieldsutils

Link Dependencies:

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:

https://cran.r-project.org/web/packages/RandomFieldsUtils

Spack package:

r-randomfieldsutils/package.py

Versions:

0.3.25

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

https://www.stat.berkeley.edu/~breiman/RandomForests/

Spack package:

r-randomforest/package.py

Versions:

4.6-12

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Classification and regression based on a forest of trees using random inputs.

r-ranger¶

Homepage:

https://cran.r-project.org/web/packages/ranger/index.html

Spack package:

r-ranger/package.py

Versions:

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:

Run Dependencies:

r, r-matrix, r-rcpp, r-rcppeigen

Description:

A fast implementation of Random Forests, particularly suited for high dimensional data.

r-rappdirs¶

Homepage:

https://cran.r-project.org/package=rappdirs

Spack package:

r-rappdirs/package.py

Versions:

0.3.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

http://cran.r-project.org/package=raster

Spack package:

r-raster/package.py

Versions:

2.5-8

Build Dependencies:

r, r-sp, r-rcpp

Link Dependencies:

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:

https://www.bioconductor.org/packages/RBGL/

Spack package:

r-rbgl/package.py

Versions:

1.52.0

Build Dependencies:

r, r-graph

Link Dependencies:

Run Dependencies:

r, r-graph

Description:

A fairly extensive and comprehensive interface to the graph algorithms contained in the BOOST library.

r-rbokeh¶

Homepage:

https://hafen.github.io/rbokeh

Spack package:

r-rbokeh/package.py

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:

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-rcolorbrewer¶

Homepage:

http://colorbrewer2.org

Spack package:

r-rcolorbrewer/package.py

Versions:

1.1-2

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Provides color schemes for maps (and other graphics) designed by Cynthia Brewer as described at http://colorbrewer2.org

r-rcpp¶

Homepage:

http://dirk.eddelbuettel.com/code/rcpp.html

Spack package:

r-rcpp/package.py

Versions:

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:

Link Dependencies:

Run Dependencies:

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-rcpparmadillo¶

Homepage:

https://cran.r-project.org/package=RcppArmadillo

Spack package:

r-rcpparmadillo/package.py

Versions:

0.8.100.1.0

Build Dependencies:

r, r-rcpp

Link Dependencies:

Run Dependencies:

r, r-rcpp

Description:

'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra Library.

r-rcppblaze¶

Homepage:

https://github.com/Chingchuan-chen/RcppBlaze

Spack package:

r-rcppblaze/package.py

Versions:

0.2.2

Build Dependencies:

r, r-rcpp, r-matrix, r-bh

Link Dependencies:

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:

https://github.com/eddelbuettel/rcppcctz

Spack package:

r-rcppcctz/package.py

Versions:

0.2.3

Build Dependencies:

r, r-rcpp

Link Dependencies:

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:

https://github.com/eddelbuettel/rcppcnpy

Spack package:

r-rcppcnpy/package.py

Versions:

0.2.9

Build Dependencies:

r, cnpy, r-rcpp

Link Dependencies:

r, cnpy

Run Dependencies:

r, r-rcpp

Description:

Rcpp bindings for NumPy files.

r-rcppeigen¶

Homepage:

http://eigen.tuxfamily.org/

Spack package:

r-rcppeigen/package.py

Versions:

0.3.3.3.1, 0.3.2.9.0, 0.3.2.8.1

Build Dependencies:

r, r-matrix, r-rcpp

Link Dependencies:

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-rcppprogress¶

Homepage:

https://cran.r-project.org/web/packages/RcppProgress/index.html

Spack package:

r-rcppprogress/package.py

Versions:

0.3, 0.2.1, 0.2, 0.1

Build Dependencies:

r, r-rcpp

Link Dependencies:

Run Dependencies:

r, r-rcpp

Description:

r-rcurl¶

Homepage:

https://cran.rstudio.com/web/packages/RCurl/index.html

Spack package:

r-rcurl/package.py

Versions:

1.95-4.8

Build Dependencies:

r, r-bitops, curl

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:

https://cran.r-project.org/web/packages/rda/index.html

Spack package:

r-rda/package.py

Versions:

1.0.2-1

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Shrunken Centroids Regularized Discriminant Analysis for the classification purpose in high dimensional data.

r-readr¶

Homepage:

https://cran.rstudio.com/web/packages/readr/index.html

Spack package:

r-readr/package.py

Versions:

1.1.1

Build Dependencies:

r, r-rcpp, r-tibble, r-hms, r-r6, r-bh

Link Dependencies:

Run Dependencies:

r, r-rcpp, r-tibble, r-hms, r-r6, r-bh

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:

http://readxl.tidyverse.org/

Spack package:

r-readxl/package.py

Versions:

1.1.0, 1.0.0

Build Dependencies:

r, r-tibble, r-rcpp, r-cellranger

Link Dependencies:

Run Dependencies:

r, r-tibble, r-rcpp, r-cellranger

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-registry¶

Homepage:

https://cran.r-project.org/web/packages/registry/index.html

Spack package:

r-registry/package.py

Versions:

0.3

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Provides a generic infrastructure for creating and using registries.

r-rematch¶

Homepage:

https://cran.r-project.org/package=rematch

Spack package:

r-rematch/package.py

Versions:

1.0.1

Build Dependencies:

r, r-covr, r-testthat

Link Dependencies:

Run Dependencies:

r, r-covr, r-testthat

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-reordercluster¶

Homepage:

https://cran.r-project.org/package=ReorderCluster

Spack package:

r-reordercluster/package.py

Versions:

1.0

Build Dependencies:

r, r-gplots, r-rcpp

Link Dependencies:

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:

https://bioconductor.org/packages/ReportingTools/

Spack package:

r-reportingtools/package.py

Versions:

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-utils, r-deseq2, r-ggplot2, r-ggbio, r-iranges

Link Dependencies:

Run Dependencies:

Description:

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:

https://github.com/IRkernel/repr

Spack package:

r-repr/package.py

Versions:

0.9

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

String and binary representations of objects for several formats and mime types.

r-reprex¶

Homepage:

https://github.com/jennybc/reprex

Spack package:

r-reprex/package.py

Versions:

0.1.1

Build Dependencies:

r, r-callr, r-clipr, r-knitr, r-rmarkdown, r-whisker

Link Dependencies:

Run Dependencies:

r, r-callr, r-clipr, r-knitr, r-rmarkdown, r-whisker

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:

https://cran.r-project.org/package=reshape

Spack package:

r-reshape/package.py

Versions:

0.8.7

Build Dependencies:

r, r-plyr

Link Dependencies:

Run Dependencies:

r, r-plyr

Description:

Flexibly restructure and aggregate data using just two functions: melt and cast.

r-reshape2¶

Homepage:

https://github.com/hadley/reshape

Spack package:

r-reshape2/package.py

Versions:

1.4.2, 1.4.1

Build Dependencies:

r, r-plyr, r-stringr, r-rcpp

Link Dependencies:

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-rex¶

Homepage:

https://cran.r-project.org/package=rex

Spack package:

r-rex/package.py

Versions:

1.1.2

Build Dependencies:

r, r-lazyeval, r-magrittr

Link Dependencies:

Run Dependencies:

r, r-lazyeval, r-magrittr

Description:

A friendly interface for the construction of regular expressions.

r-rgdal¶

Homepage:

https://cran.r-project.org/package=rgdal

Spack package:

r-rgdal/package.py

Versions:

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:

http://sekhon.berkeley.edu/rgenoud/

Spack package:

r-rgenoud/package.py

Versions:

5.8-1.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

A genetic algorithm plus derivative optimizer.

r-rgeos¶

Homepage:

https://cran.r-project.org/package=rgeos

Spack package:

r-rgeos/package.py

Versions:

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-rgl¶

Homepage:

https://r-forge.r-project.org/projects/rgl

Spack package:

r-rgl/package.py

Versions:

0.99.16, 0.98.1

Build Dependencies:

r, libx11, gl, glu, r-htmlwidgets, r-htmltools, r-knitr, r-jsonlite, r-shiny, r-magrittr, r-crosstalk, r-manipulatewidget

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:

https://cran.r-project.org/package=RgoogleMaps

Spack package:

r-rgooglemaps/package.py

Versions:

1.2.0.7

Build Dependencies:

r, r-png, r-rjsonio

Link Dependencies:

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:

http://bioconductor.org/packages/Rgraphviz/

Spack package:

r-rgraphviz/package.py

Versions:

2.20.0

Build Dependencies:

r, r-graph

Link Dependencies:

Run Dependencies:

r, r-graph

Description:

Interfaces R with the AT and T graphviz library for plotting R graph objects from the graph package.

r-rhdf5¶

Homepage:

https://www.bioconductor.org/packages/rhdf5/

Spack package:

r-rhdf5/package.py

Versions:

2.20.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

This R/Bioconductor 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-rhmmer¶

Homepage:

https://cran.r-project.org/package=rhmmer

Spack package:

r-rhmmer/package.py

Versions:

0.1.0

Build Dependencies:

r, r-magrittr, r-readr, r-dplyr, r-tidyr, r-rlang, r-testthat, r-covr

Link Dependencies:

Run Dependencies:

r, r-magrittr, r-readr, r-dplyr, r-tidyr, r-rlang, r-testthat, r-covr

Description:

rhmmer: Utilities Parsing 'HMMER' Results

r-rhtslib¶

Homepage:

https://www.bioconductor.org/packages/Rhtslib/

Spack package:

r-rhtslib/package.py

Versions:

1.8.0

Build Dependencies:

r, r-zlibbioc, autoconf

Link Dependencies:

Run Dependencies:

Description:

This package provides version 1.1 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:

http://dirk.eddelbuettel.com/code/rinside.html

Spack package:

r-rinside/package.py

Versions:

0.2.15, 0.2.14, 0.2.13

Build Dependencies:

r, r-rcpp

Link Dependencies:

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-rjags¶

Homepage:

https://cran.r-project.org/web/packages/rjags/index.html

Spack package:

r-rjags/package.py

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:

http://www.rforge.net/rJava/

Spack package:

r-rjava/package.py

Versions:

0.9-11, 0.9-8

Build Dependencies:

r, java

Link Dependencies:

r, java

Run Dependencies:

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:

https://cran.r-project.org/package=rjson

Spack package:

r-rjson/package.py

Versions:

0.2.15

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Converts R object into JSON objects and vice-versa.

r-rjsonio¶

Homepage:

https://cran.r-project.org/package=RJSONIO

Spack package:

r-rjsonio/package.py

Versions:

1.3-0

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

https://cran.r-project.org/package=rlang

Spack package:

r-rlang/package.py

Versions:

0.3.1, 0.3.0.1, 0.3.0, 0.2.2, 0.1.4, 0.1.2, 0.1.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

A toolbox for working with base types, core R features like the condition system, and core 'Tidyverse' features like tidy evaluation.

r-rmarkdown¶

Homepage:

http://rmarkdown.rstudio.com/

Spack package:

r-rmarkdown/package.py

Versions:

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

Link Dependencies:

Run Dependencies:

r, r-knitr, r-yaml, r-htmltools, r-evaluate, r-base64enc, r-jsonlite, r-rprojroot, r-mime, r-stringr, r-catools

Description:

Convert R Markdown documents into a variety of formats.

r-rminer¶

Homepage:

http://www3.dsi.uminho.pt/pcortez/rminer.html

Spack package:

r-rminer/package.py

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:

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:

http://rmpfr.r-forge.r-project.org

Spack package:

r-rmpfr/package.py

Versions:

0.6-1

Build Dependencies:

r, r-gmp, mpfr

Link Dependencies:

r, mpfr

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:

http://www.stats.uwo.ca/faculty/yu/Rmpi

Spack package:

r-rmpi/package.py

Versions:

0.6-6

Build Dependencies:

r, mpi

Link Dependencies:

r, mpi

Run Dependencies:

Description:

An interface (wrapper) to MPI APIs. It also provides interactive R manager and worker environment.

r-rmysql¶

Homepage:

https://github.com/rstats-db/rmysql

Spack package:

r-rmysql/package.py

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-rngtools¶

Homepage:

https://renozao.github.io/rngtools

Spack package:

r-rngtools/package.py

Versions:

1.3.1, 1.2.4

Build Dependencies:

r, r-pkgmaker, r-stringr, r-digest

Link Dependencies:

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:

https://github.com/ropensci/rnoaa

Spack package:

r-rnoaa/package.py

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:

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:

https://cran.r-project.org/package=robust

Spack package:

r-robust/package.py

Versions:

0.4-18

Build Dependencies:

r, r-lattice, r-mass, r-robustbase, r-rrcov, r-fit-models

Link Dependencies:

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:

https://robustbase.r-forge.r-project.org

Spack package:

r-robustbase/package.py

Versions:

0.92-7

Build Dependencies:

r, r-deoptimr

Link Dependencies:

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-rocr¶

Homepage:

https://cran.r-project.org/package=ROCR

Spack package:

r-rocr/package.py

Versions:

1.0-7

Build Dependencies:

r, r-gplots

Link Dependencies:

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:

https://cran.rstudio.com/web/packages/RODBC/

Spack package:

r-rodbc/package.py

Versions:

1.3-13

Build Dependencies:

r, unixodbc

Link Dependencies:

r, unixodbc

Run Dependencies:

Description:

An ODBC database interface.

r-rots¶

Homepage:

https://bioconductor.org/packages/release/bioc/html/ROTS.html

Spack package:

r-rots/package.py

Versions:

1.8.0

Build Dependencies:

r, r-rcpp, r-biobase

Link Dependencies:

Run Dependencies:

r, r-rcpp, r-biobase

Description:

Calculates the Reproducibility-Optimized Test Statistic (ROTS) for differential testing in omics data.

r-roxygen2¶

Homepage:

https://github.com/klutometis/roxygen

Spack package:

r-roxygen2/package.py

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:

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:

https://cran.r-project.org/package=rpart

Spack package:

r-rpart/package.py

Versions:

4.1-11, 4.1-10

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Recursive partitioning for classification, regression and survival trees.

r-rpart-plot¶

Homepage:

https://cran.r-project.org/package=rpart.plot

Spack package:

r-rpart-plot/package.py

Versions:

2.1.0

Build Dependencies:

r, r-rpart

Link Dependencies:

Run Dependencies:

r, r-rpart

Description:

Plot 'rpart' models. Extends plot.rpart() and text.rpart() in the 'rpart' package.

r-rpostgresql¶

Homepage:

https://code.google.com/p/rpostgresql/

Spack package:

r-rpostgresql/package.py

Versions:

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:

https://cran.r-project.org/package=rprojroot

Spack package:

r-rprojroot/package.py

Versions:

1.2

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

http://potatobreeding.cals.wisc.edu/software

Spack package:

r-rrblup/package.py

Versions:

4.6

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

rrBLUP: Ridge Regression and Other Kernels for Genomic Selection

r-rrcov¶

Homepage:

https://cran.r-project.org/package=rrcov

Spack package:

r-rrcov/package.py

Versions:

1.4-7

Build Dependencies:

r, r-robustbase, r-mvtnorm, r-lattice, r-cluster, r-pcapp, r-mass, r-ellipse

Link Dependencies:

Run Dependencies:

r, r-robustbase, r-mvtnorm, r-lattice, r-cluster, r-pcapp, r-mass, r-ellipse

Description:

rrcov: Scalable Robust Estimators with High Breakdown Point

r-rrpp¶

Homepage:

https://github.com/mlcollyer/RRPP

Spack package:

r-rrpp/package.py

Versions:

0.3.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

https://bioconductor.org/packages/Rsamtools/

Spack package:

r-rsamtools/package.py

Versions:

1.32.2, 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

Link Dependencies:

Run Dependencies:

r, r-genomeinfodb, r-genomicranges, r-biostrings, r-biocgenerics, r-s4vectors, r-iranges, r-xvector, r-zlibbioc, r-bitops, r-biocparallel

Description:

This package provides an interface to the 'samtools', 'bcftools', and 'tabix' utilities (see 'LICENCE') for manipulating SAM (Sequence Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed tab-delimited (tabix) files.

r-rsnns¶

Homepage:

http://sci2s.ugr.es/dicits/software/RSNNS

Spack package:

r-rsnns/package.py

Versions:

0.4-7

Build Dependencies:

r, r-rcpp

Link Dependencies:

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:

https://cran.r-project.org/package=Rsolnp

Spack package:

r-rsolnp/package.py

Versions:

1.16

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

General Non-linear Optimization Using Augmented Lagrange Multiplier Method.

r-rsqlite¶

Homepage:

https://cran.rstudio.com/web/packages/RSQLite/index.html

Spack package:

r-rsqlite/package.py

Versions:

2.0

Build Dependencies:

r, r-dbi, r-bit64, r-blob, r-memoise, r-pkgconfig, r-rcpp, r-bh, r-plogr

Link Dependencies:

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:

http://mc-stan.org/

Spack package:

r-rstan/package.py

Versions:

2.18.2, 2.17.2, 2.10.1

Build Dependencies:

r, r-ggplot2, r-stanheaders, r-inline, r-gridextra, r-rcpp, r-rcppeigen, r-bh, r-loo, r-pkgbuild

Link Dependencies:

Run Dependencies:

r, r-ggplot2, r-stanheaders, r-inline, r-gridextra, r-rcpp, r-rcppeigen, r-bh, r-loo, r-pkgbuild

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:

http://discourse.mc-stan.org/

Spack package:

r-rstantools/package.py

Versions:

1.5.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

rstantools: Tools for Developing R Packages Interfacing with 'Stan'

r-rstudioapi¶

Homepage:

https://cran.r-project.org/web/packages/rstudioapi/index.html

Spack package:

r-rstudioapi/package.py

Versions:

0.7, 0.6, 0.5

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Access the RStudio API (if available) and provide informative error messages when it's not.

r-rtracklayer¶

Homepage:

http://bioconductor.org/packages/rtracklayer/

Spack package:

r-rtracklayer/package.py

Versions:

1.40.5, 1.36.6

Build Dependencies:

r, r-xml, r-biocgenerics, r-s4vectors, r-iranges, r-xvector, r-genomeinfodb, r-biostrings, r-zlibbioc, r-rcurl, r-rsamtools, r-genomicalignments, r-genomicranges

Link Dependencies:

Run Dependencies:

r, r-xml, r-biocgenerics, r-s4vectors, r-iranges, r-xvector, r-genomeinfodb, r-biostrings, r-zlibbioc, r-rcurl, r-rsamtools, r-genomicalignments, r-genomicranges

Description:

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:

https://CRAN.R-project.org/package=Rtsne

Spack package:

r-rtsne/package.py

Versions:

0.13, 0.11, 0.10

Build Dependencies:

r, r-rcpp

Link Dependencies:

Run Dependencies:

r, r-rcpp

Description:

An R wrapper around the fast T-distributed Stochastic Neighbor Embedding implementation.

r-runit¶

Homepage:

https://cran.r-project.org/package=RUnit

Spack package:

r-runit/package.py

Versions:

0.4.32

Build Dependencies:

r, r-xml

Link Dependencies:

Run Dependencies:

r, r-xml

Description:

RUnit: R Unit Test Framework

r-rvcheck¶

Homepage:

https://cran.r-project.org/package=rvcheck

Spack package:

r-rvcheck/package.py

Versions:

0.0.9

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Check latest release version of R and R package (both in 'CRAN', 'Bioconductor' or 'Github').

r-rvest¶

Homepage:

https://github.com/hadley/rvest

Spack package:

r-rvest/package.py

Versions:

0.3.2

Build Dependencies:

r, r-xml2, r-httr, r-selectr, r-magrittr

Link Dependencies:

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:

http://github.com/armstrtw/rzmq

Spack package:

r-rzmq/package.py

Versions:

0.7.7

Build Dependencies:

r, zeromq

Link Dependencies:

r, zeromq

Run Dependencies:

Description:

Interface to the ZeroMQ lightweight messaging kernel.

r-s4vectors¶

Homepage:

https://bioconductor.org/packages/S4Vectors/

Spack package:

r-s4vectors/package.py

Versions:

0.18.3, 0.16.0, 0.14.7

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

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:

https://cran.r-project.org/package=samr

Spack package:

r-samr/package.py

Versions:

2.0

Build Dependencies:

r, r-impute, r-matrixstats

Link Dependencies:

Run Dependencies:

r, r-impute, r-matrixstats

Description:

Significance Analysis of Microarrays.

r-sandwich¶

Homepage:

https://cran.r-project.org/package=sandwich

Spack package:

r-sandwich/package.py

Versions:

2.3-4

Build Dependencies:

r, r-zoo

Link Dependencies:

Run Dependencies:

r, r-zoo

Description:

Model-robust standard error estimators for cross-sectional, time series, and longitudinal data.

r-scales¶

Homepage:

https://github.com/hadley/scales

Spack package:

r-scales/package.py

Versions:

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:

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:

https://CRAN.R-project.org/package=scatterplot3d

Spack package:

r-scatterplot3d/package.py

Versions:

0.3-40

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

scatterplot3d: 3D Scatter Plot

r-sdmtools¶

Homepage:

https://cran.r-project.org/web/packages/SDMTools/index.html

Spack package:

r-sdmtools/package.py

Versions:

1.1-221, 1.1-20, 1.1-13, 1.1-12, 1.1-11

Build Dependencies:

r, r-utils

Link Dependencies:

Run Dependencies:

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:

https://CRAN.R-project.org/package=segmented

Spack package:

r-segmented/package.py

Versions:

0.5-2.2, 0.5-1.4

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

https://sjp.co.nz/projects/selectr

Spack package:

r-selectr/package.py

Versions:

0.3-1

Build Dependencies:

r, r-testthat, r-stringr, r-xml, r-xml2

Link Dependencies:

Run Dependencies:

r, r-testthat, r-stringr, r-xml, r-xml2

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:

http://seqinr.r-forge.r-project.org

Spack package:

r-seqinr/package.py

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-seqlogo¶

Homepage:

https://bioconductor.org/packages/seqLogo/

Spack package:

r-seqlogo/package.py

Versions:

1.44.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

seqLogo takes the position weight matrix of a DNA sequence motif and plots the corresponding sequence logo as introduced by Schneider and Stephens (1990).

r-seurat¶

Homepage:

http://satijalab.org/seurat/

Spack package:

r-seurat/package.py

Versions:

2.1.0, 2.0.1

Build Dependencies:

r, r-ggplot2, r-gplots, r-reshape2, r-ape, r-tidyr, r-caret, r-gdata, r-glue, r-pkgconfig, r-plogr, 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

Link Dependencies:

Run Dependencies:

Description:

Seurat is an R package designed for QC, analysis, and exploration of single cell RNA-seq data.

r-sf¶

Homepage:

https://github.com/r-spatial/sf/

Spack package:

r-sf/package.py

Versions:

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:

https://cran.r-project.org/web/packages/sfsmisc/index.html

Spack package:

r-sfsmisc/package.py

Versions:

1.1-0

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

https://cran.r-project.org/package=shape

Spack package:

r-shape/package.py

Versions:

1.4.3, 1.4.2

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Functions for plotting graphical shapes such as ellipses, circles, cylinders, arrows, ...

r-shiny¶

Homepage:

http://shiny.rstudio.com/

Spack package:

r-shiny/package.py

Versions:

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

Link Dependencies:

Run Dependencies:

r, r-httpuv, r-mime, r-jsonlite, r-xtable, r-digest, r-htmltools, r-r6, r-sourcetools

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:

https://cran.r-project.org/package=shinydashboard

Spack package:

r-shinydashboard/package.py

Versions:

0.7.0, 0.6.1

Build Dependencies:

r, r-htmltools, r-shiny

Link Dependencies:

Run Dependencies:

r, r-htmltools, r-shiny

Description:

Create Dashboards with 'Shiny'

r-shortread¶

Homepage:

https://www.bioconductor.org/packages/ShortRead/

Spack package:

r-shortread/package.py

Versions:

1.34.2

Build Dependencies:

r, r-latticeextra, r-lattice, r-zlibbioc, r-hwriter, r-genomicranges, r-genomeinfodb, r-iranges, r-s4vectors, r-biobase, r-genomicalignments, r-rsamtools, r-biostrings, r-biocparallel, r-biocgenerics

Link Dependencies:

Run Dependencies:

r, r-latticeextra, r-lattice, r-zlibbioc, r-hwriter, r-genomicranges, r-genomeinfodb, r-iranges, r-s4vectors, r-biobase, r-genomicalignments, r-rsamtools, r-biostrings, r-biocparallel, r-biocgenerics

Description:

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:

http://bioconductor.org/packages/siggenes/

Spack package:

r-siggenes/package.py

Versions:

1.50.0

Build Dependencies:

r, r-biobase, r-multtest

Link Dependencies:

Run Dependencies:

r, r-biobase, r-multtest

Description:

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:

http://bioconductor.org/packages/simpleaffy/

Spack package:

r-simpleaffy/package.py

Versions:

2.52.0

Build Dependencies:

r, r-biocgenerics, r-biobase, r-affy, r-genefilter, r-gcrma

Link Dependencies:

Run Dependencies:

r, r-biocgenerics, r-biobase, r-affy, r-genefilter, r-gcrma

Description:

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-sm¶

Homepage:

http://www.stats.gla.ac.uk/~adrian/sm

Spack package:

r-sm/package.py

Versions:

2.2-5.5

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

http://github.com/jakobbossek/smoof

Spack package:

r-smoof/package.py

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:

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:

https://cran.r-project.org/web/packages/sn/index.html

Spack package:

r-sn/package.py

Versions:

1.5-0, 1.4-0, 1.3-0, 1.2-4, 1.2-3

Build Dependencies:

r, r-mnormt, r-numderiv

Link Dependencies:

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-snow¶

Homepage:

https://cran.r-project.org/web/packages/snow/index.html

Spack package:

r-snow/package.py

Versions:

0.4-2

Build Dependencies:

Link Dependencies:

Run Dependencies:

r, r-rmpi

Description:

Support for simple parallel computing in R.

r-snowfall¶

Homepage:

https://cran.r-project.org/web/packages/snowfall/index.html

Spack package:

r-snowfall/package.py

Versions:

1.84-6.1

Build Dependencies:

r, r-snow

Link Dependencies:

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:

https://bioconductor.org/packages/SNPRelate

Spack package:

r-snprelate/package.py

Versions:

1.12.2

Build Dependencies:

r, r-gdsfmt

Link Dependencies:

Run Dependencies:

r, r-gdsfmt

Description:

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-som¶

Homepage:

https://cran.r-project.org/web/packages/som/index.html

Spack package:

r-som/package.py

Versions:

0.3-5.1, 0.3-5, 0.3-4, 0.3-3, 0.3-2

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Self-Organizing Map (with application in gene clustering).

r-somaticsignatures¶

Homepage:

https://bioconductor.org/packages/SomaticSignatures/

Spack package:

r-somaticsignatures/package.py

Versions:

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:

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:

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:

https://cran.r-project.org/package=sourcetools

Spack package:

r-sourcetools/package.py

Versions:

0.1.6, 0.1.5

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Tools for Reading, Tokenizing and Parsing R Code.

r-sp¶

Homepage:

https://github.com/edzer/sp/

Spack package:

r-sp/package.py

Versions:

1.2-3

Build Dependencies:

Link Dependencies:

Run Dependencies:

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-sparsem¶

Homepage:

http://www.econ.uiuc.edu/~roger/research/sparse/sparse.html

Spack package:

r-sparsem/package.py

Versions:

1.74, 1.7

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

https://cran.r-project.org/package=spatial

Spack package:

r-spatial/package.py

Versions:

7.3-11

Build Dependencies:

r, r-mass

Link Dependencies:

Run Dependencies:

r, r-mass

Description:

spatial: Functions for Kriging and Point Pattern Analysis

r-spdep¶

Homepage:

https://r-forge.r-project.org/projects/spdep

Spack package:

r-spdep/package.py

Versions:

0.6-13

Build Dependencies:

r, r-sp, r-learnbayes, r-deldir, r-coda, r-gmodels, r-expm

Link Dependencies:

Run Dependencies:

r, r-sp, r-learnbayes, r-deldir, r-coda, r-gmodels, r-expm

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:

https://cran.r-project.org/package=speedglm

Spack package:

r-speedglm/package.py

Versions:

0.3-2

Build Dependencies:

r, r-mass, r-matrix

Link Dependencies:

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:

https://bioconductor.org/packages/SPEM/

Spack package:

r-spem/package.py

Versions:

1.18.0

Build Dependencies:

r, r-rsolnp, r-biobase

Link Dependencies:

Run Dependencies:

r, r-rsolnp, r-biobase

Description:

This package can optimize the parameter in S-system models given time series data

r-splancs¶

Homepage:

https://cran.r-project.org/web/packages/splancs/index.html

Spack package:

r-splancs/package.py

Versions:

2.01-40

Build Dependencies:

r, r-sp

Link Dependencies:

Run Dependencies:

r, r-sp

Description:

Spatial and Space-Time Point Pattern Analysis

r-splitstackshape¶

Homepage:

http://github.com/mrdwab/splitstackshape

Spack package:

r-splitstackshape/package.py

Versions:

1.4.4

Build Dependencies:

r, r-data-table

Link Dependencies:

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:

https://cran.r-project.org/package=sqldf

Spack package:

r-sqldf/package.py

Versions:

0.4-11

Build Dependencies:

r, r-gsubfn, r-proto, r-rsqlite, r-dbi, r-chron

Link Dependencies:

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-squash¶

Homepage:

https://cran.r-project.org/package=squash

Spack package:

r-squash/package.py

Versions:

1.0.8, 1.0.7

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Color-Based Plots for Multivariate Visualization

r-sseq¶

Homepage:

https://www.bioconductor.org/packages/sSeq/

Spack package:

r-sseq/package.py

Versions:

1.20.0

Build Dependencies:

r, r-catools, r-rcolorbrewer

Link Dependencies:

Run Dependencies:

r, r-catools, r-rcolorbrewer

Description:

Shrinkage estimation of dispersion in Negative Binomial models for RNA- seq experiments with small sample size

r-stanheaders¶

Homepage:

http://mc-stan.org/

Spack package:

r-stanheaders/package.py

Versions:

2.18.1, 2.17.1, 2.10.0-2

Build Dependencies:

Link Dependencies:

Run Dependencies:

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-statmod¶

Homepage:

https://cran.r-project.org/package=statmod

Spack package:

r-statmod/package.py

Versions:

1.4.30

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

http://www.statnet.org

Spack package:

r-statnet-common/package.py

Versions:

3.3.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Non-statistical utilities used by the software developed by the Statnet Project. They may also be of use to others.

r-stringi¶

Homepage:

http://www.gagolewski.com/software/stringi/

Spack package:

r-stringi/package.py

Versions:

1.1.5, 1.1.3, 1.1.2, 1.1.1

Build Dependencies:

r, icu4c

Link Dependencies:

r, icu4c

Run Dependencies:

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:

https://cran.r-project.org/web/packages/stringr/index.html

Spack package:

r-stringr/package.py

Versions:

1.2.0, 1.1.0, 1.0.0

Build Dependencies:

r, r-stringi, r-magrittr

Link Dependencies:

Run Dependencies:

r, r-stringi, r-magrittr

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:

https://cran.r-project.org/package=strucchange

Spack package:

r-strucchange/package.py

Versions:

1.5-1

Build Dependencies:

r, r-zoo, r-sandwich

Link Dependencies:

Run Dependencies:

r, r-zoo, r-sandwich

Description:

Testing, monitoring and dating structural changes in (linear) regression models.

r-subplex¶

Homepage:

https://cran.r-project.org/package=subplex

Spack package:

r-subplex/package.py

Versions:

1.4-1

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Unconstrained Optimization using the Subplex Algorithm

r-summarizedexperiment¶

Homepage:

https://bioconductor.org/packages/SummarizedExperiment/

Spack package:

r-summarizedexperiment/package.py

Versions:

1.10.0, 1.8.1, 1.6.5

Build Dependencies:

r, r-genomicranges, r-biobase, r-delayedarray, r-matrix, r-s4vectors, r-iranges, r-genomeinfodb, r-biocgenerics

Link Dependencies:

Run Dependencies:

r, r-genomicranges, r-biobase, r-delayedarray, r-matrix, r-s4vectors, r-iranges, r-genomeinfodb, r-biocgenerics

Description:

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-survey¶

Homepage:

http://r-survey.r-forge.r-project.org/survey/

Spack package:

r-survey/package.py

Versions:

3.30-3

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

https://cran.r-project.org/package=survival

Spack package:

r-survival/package.py

Versions:

2.41-3, 2.40-1, 2.39-5

Build Dependencies:

r, r-matrix

Link Dependencies:

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:

https://www.bioconductor.org/packages/sva/

Spack package:

r-sva/package.py

Versions:

3.24.4

Build Dependencies:

r, r-mgcv, r-genefilter, r-biocparallel, r-matrixstats, r-limma

Link Dependencies:

Run Dependencies:

r, r-mgcv, r-genefilter, r-biocparallel, r-matrixstats, r-limma

Description:

Surrogate Variable Analysis.

r-tarifx¶

Homepage:

https://cran.r-project.org/package=taRifx

Spack package:

r-tarifx/package.py

Versions:

1.0.6

Build Dependencies:

r, r-reshape2, r-plyr

Link Dependencies:

Run Dependencies:

r, r-reshape2, r-plyr

Description:

A collection of various utility and convenience functions.

r-taxizedb¶

Homepage:

https://cran.r-project.org/package=taxizedb

Spack package:

r-taxizedb/package.py

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, r-roxygen2, r-testthat

Link Dependencies:

Run Dependencies:

r, r-curl, r-dbi, r-rpostgresql, r-rmysql, r-rsqlite, r-dplyr, r-dbplyr, r-magrittr, r-hoardr, r-roxygen2, r-testthat

Description:

taxizedb: Tools for Working with 'Taxonomic' Databases

r-tclust¶

Homepage:

https://cran.r-project.org/web/packages/tclust/index.html

Spack package:

r-tclust/package.py

Versions:

1.3-1, 1.2-7, 1.2-3, 1.1-03, 1.1-02

Build Dependencies:

r, r-cluster, r-mclust, r-mvtnorm, r-sn

Link Dependencies:

Run Dependencies:

r, r-cluster, r-mclust, r-mvtnorm, r-sn

Description:

Provides functions for robust trimmed clustering.

r-tensora¶

Homepage:

https://cran.r-project.org/web/packages/tensorA/index.html

Spack package:

r-tensora/package.py

Versions:

0.36

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

https://cran.r-project.org/package=testit

Spack package:

r-testit/package.py

Versions:

0.7, 0.5

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Provides two convenience functions assert() and test_pkg() to facilitate testing R packages.

r-testthat¶

Homepage:

https://github.com/hadley/testthat

Spack package:

r-testthat/package.py

Versions:

1.0.2

Build Dependencies:

r, r-digest, r-crayon, r-praise, r-magrittr, r-r6

Link Dependencies:

Run Dependencies:

r, r-digest, r-crayon, r-praise, r-magrittr, r-r6

Description:

A unit testing system designed to be fun, flexible and easy to set up.

r-tfbstools¶

Homepage:

http://bioconductor.org/packages/TFBSTools/

Spack package:

r-tfbstools/package.py

Versions:

1.16.0

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:

Run Dependencies:

Description:

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. 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:

https://github.com/ge11232002/TFMPvalue

Spack package:

r-tfmpvalue/package.py

Versions:

0.0.6

Build Dependencies:

r, r-rcpp

Link Dependencies:

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:

https://cran.r-project.org/package=TH.data

Spack package:

r-th-data/package.py

Versions:

1.0-8, 1.0-7

Build Dependencies:

r, r-survival, r-mass

Link Dependencies:

Run Dependencies:

r, r-survival, r-mass

Description:

Contains data sets used in other packages Torsten Hothorn maintains.

r-threejs¶

Homepage:

http://bwlewis.github.io/rthreejs

Spack package:

r-threejs/package.py

Versions:

0.2.2

Build Dependencies:

r, r-htmlwidgets, r-base64enc, r-matrix, r-jsonlite

Link Dependencies:

Run Dependencies:

r, r-htmlwidgets, r-base64enc, r-matrix, r-jsonlite

Description:

Create interactive 3D scatter plots, network plots, and globes using the 'three.js' visualization library ("http://threejs.org").

r-tibble¶

Homepage:

https://github.com/tidyverse/tibble

Spack package:

r-tibble/package.py

Versions:

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

Link Dependencies:

Run Dependencies:

r, r-assertthat, r-lazyeval, r-rcpp, r-rlang, r-cli, r-crayon, r-pillar, r-pkgconfig

Description:

Provides a 'tbl_df' class that offers better checking and printing capabilities than traditional data frames.

r-tidycensus¶

Homepage:

https://cran.r-project.org/package=tidycensus

Spack package:

r-tidycensus/package.py

Versions:

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:

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-tidyr¶

Homepage:

https://github.com/hadley/tidyr

Spack package:

r-tidyr/package.py

Versions:

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:

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:

https://cran.r-project.org/package=tidyselect

Spack package:

r-tidyselect/package.py

Versions:

0.2.3

Build Dependencies:

r, r-glue, r-purrr, r-rlang, r-rcpp

Link Dependencies:

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:

http://tidyverse.tidyverse.org/

Spack package:

r-tidyverse/package.py

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:

Run Dependencies:

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:

http://www.rforge.net/tiff/

Spack package:

r-tiff/package.py

Versions:

0.1-5

Build Dependencies:

r, libjpeg, libtiff

Link Dependencies:

r, libjpeg, libtiff

Run Dependencies:

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:

https://cran.r-project.org/package=tigris

Spack package:

r-tigris/package.py

Versions:

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:

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:

https://cran.r-project.org/package=timeDate

Spack package:

r-timedate/package.py

Versions:

3012.100

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Environment for teaching "Financial Engineering and Computational Finance". Managing chronological and calendar objects.

r-tmixclust¶

Homepage:

https://bioconductor.org/packages/TMixClust/

Spack package:

r-tmixclust/package.py

Versions:

1.0.1

Build Dependencies:

r, r-gss, r-mvtnorm, r-zoo, r-cluster, r-biocparallel, r-flexclust, r-biobase, r-spem

Link Dependencies:

Run Dependencies:

r, r-gss, r-mvtnorm, r-zoo, r-cluster, r-biocparallel, r-flexclust, r-biobase, r-spem

Description:

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:

https://www.bioconductor.org/packages/topGO/

Spack package:

r-topgo/package.py

Versions:

2.30.1, 2.28.0

Build Dependencies:

r, r-dbi, r-matrixstats, r-lattice, r-sparsem, r-annotationdbi, r-go-db, r-biobase, r-graph, r-biocgenerics

Link Dependencies:

Run Dependencies:

r, r-dbi, r-matrixstats, r-lattice, r-sparsem, r-annotationdbi, r-go-db, r-biobase, r-graph, r-biocgenerics

Description:

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:

https://github.com/Ironholds/triebeard/

Spack package:

r-triebeard/package.py

Versions:

0.3.0

Build Dependencies:

r, r-rcpp

Link Dependencies:

Run Dependencies:

r, r-rcpp

Description:

triebeard: 'Radix' Trees in 'Rcpp'

r-trimcluster¶

Homepage:

http://www.homepages.ucl.ac.uk/~ucakche

Spack package:

r-trimcluster/package.py

Versions:

0.1-2

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

trimcluster: Cluster analysis with trimming

r-truncnorm¶

Homepage:

https://cran.r-project.org/package=truncnorm

Spack package:

r-truncnorm/package.py

Versions:

1.0-8

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Density, probability, quantile and random number generation functions for the truncated normal distribution.

r-trust¶

Homepage:

http://www.stat.umn.edu/geyer/trust

Spack package:

r-trust/package.py

Versions:

0.1-7

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Does local optimization using two derivatives and trust regions. Guaranteed to converge to local minimum of objective function.

r-tseries¶

Homepage:

https://cran.r-project.org/package=tseries

Spack package:

r-tseries/package.py

Versions:

0.10-42

Build Dependencies:

r, r-quadprog, r-zoo, r-quantmod

Link Dependencies:

Run Dependencies:

r, r-quadprog, r-zoo, r-quantmod

Description:

Time series analysis and computational finance.

r-tsne¶

Homepage:

https://cran.r-project.org/web/packages/tsne/index.html

Spack package:

r-tsne/package.py

Versions:

0.1-3, 0.1-2, 0.1-1

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

A "pure R" implementation of the t-SNE algorithm.

r-ttr¶

Homepage:

https://github.com/joshuaulrich/TTR

Spack package:

r-ttr/package.py

Versions:

0.23-1

Build Dependencies:

r, r-xts, r-zoo

Link Dependencies:

Run Dependencies:

r, r-xts, r-zoo

Description:

Functions and data to construct technical trading rules with R.

r-udunits2¶

Homepage:

https://github.com/pacificclimate/Rudunits2

Spack package:

r-udunits2/package.py

Versions:

0.13

Build Dependencies:

r, udunits2

Link Dependencies:

r, udunits2

Run Dependencies:

Description:

Provides simple bindings to Unidata's udunits library.

r-units¶

Homepage:

https://github.com/edzer/units/

Spack package:

r-units/package.py

Versions:

0.4-6

Build Dependencies:

r, r-udunits2

Link Dependencies:

Run Dependencies:

r, r-udunits2

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-urltools¶

Homepage:

https://github.com/Ironholds/urltools/

Spack package:

r-urltools/package.py

Versions:

1.7.3

Build Dependencies:

r, r-rcpp, r-triebeard

Link Dependencies:

Run Dependencies:

r, r-rcpp, r-triebeard

Description:

urltools: Vectorised Tools for URL Handling and Parsing

r-utf8¶

Homepage:

https://cran.r-project.org/package=utf8

Spack package:

r-utf8/package.py

Versions:

1.1.3, 1.1.2, 1.1.1, 1.1.0, 1.0.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Process and print 'UTF-8' encoded international text (Unicode). Input, validate, normalize, encode, format, and display.

r-utils¶

Homepage:

https://github.com/HenrikBengtsson/R.utils

Spack package:

r-utils/package.py

Versions:

2.5.0

Build Dependencies:

r, r-oo

Link Dependencies:

Run Dependencies:

r, r-oo

Description:

Utility functions useful when programming and developing R packages.

r-uuid¶

Homepage:

http://www.rforge.net/uuid

Spack package:

r-uuid/package.py

Versions:

0.1-2

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Tools for generating and handling of UUIDs (Universally Unique Identifiers).

r-variantannotation¶

Homepage:

https://www.bioconductor.org/packages/VariantAnnotation/

Spack package:

r-variantannotation/package.py

Versions:

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

Link Dependencies:

Run Dependencies:

Description:

Annotate variants, compute amino acid coding changes, predict coding outcomes.

r-varselrf¶

Homepage:

http://ligarto.org/rdiaz/Software/Software.html

Spack package:

r-varselrf/package.py

Versions:

0.7-8

Build Dependencies:

r, r-randomforest

Link Dependencies:

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:

https://cran.r-project.org/package=vcd

Spack package:

r-vcd/package.py

Versions:

1.4-1

Build Dependencies:

r, r-mass, r-colorspace, r-lmtest

Link Dependencies:

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-vegan¶

Homepage:

https://github.com/vegandevs/vegan

Spack package:

r-vegan/package.py

Versions:

2.4-3

Build Dependencies:

r, r-permute

Link Dependencies:

Run Dependencies:

r, r-permute

Description:

Ordination methods, diversity analysis and other functions for community and vegetation ecologists.

r-vfs¶

Homepage:

https://cran.r-project.org/package=VFS

Spack package:

r-vfs/package.py

Versions:

1.0.2

Build Dependencies:

r, r-e1071, r-nleqslv, r-knitr, r-rmarkdown, r-testthat

Link Dependencies:

Run Dependencies:

r, r-e1071, r-nleqslv, r-knitr, r-rmarkdown, r-testthat

Description:

VFS: Vegetated Filter Strip and Erosion Model

r-vgam¶

Homepage:

https://cran.r-project.org/web/packages/VGAM/index.html

Spack package:

r-vgam/package.py

Versions:

1.0-4, 1.0-3, 1.0-2, 1.0-1, 1.0-0

Build Dependencies:

r, r-mass, r-mgcv

Link Dependencies:

Run Dependencies:

r, r-mass, r-mgcv

Description:

An implementation of about 6 major classes of statistical regression models.

r-vipor¶

Homepage:

https://cran.r-project.org/package=vipor

Spack package:

r-vipor/package.py

Versions:

0.4.5, 0.4.4

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Plot Categorical Data Using Quasirandom Noise and Density Estimates

r-viridis¶

Homepage:

https://github.com/sjmgarnier/viridis

Spack package:

r-viridis/package.py

Versions:

0.4.0

Build Dependencies:

r, r-viridislite, r-ggplot2, r-gridextra

Link Dependencies:

Run Dependencies:

r, r-viridislite, r-ggplot2, r-gridextra

Description:

viridis: Default Color Maps from 'matplotlib'

r-viridislite¶

Homepage:

https://github.com/sjmgarnier/viridisLite

Spack package:

r-viridislite/package.py

Versions:

0.2.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

viridisLite: Default Color Maps from 'matplotlib' (Lite Version)

r-visnetwork¶

Homepage:

https://github.com/datastorm-open/visNetwork

Spack package:

r-visnetwork/package.py

Versions:

1.0.1

Build Dependencies:

r, r-htmlwidgets, r-htmltools, r-jsonlite, r-magrittr

Link Dependencies:

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:

https://www.bioconductor.org/packages/vsn/

Spack package:

r-vsn/package.py

Versions:

3.44.0

Build Dependencies:

r, r-biobase, r-affy, r-limma, r-lattice, r-ggplot2, r-hexbin

Link Dependencies:

Run Dependencies:

r, r-biobase, r-affy, r-limma, r-lattice, r-ggplot2, r-hexbin

Description:

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-webshot¶

Homepage:

https://github.com/wch/webshot/

Spack package:

r-webshot/package.py

Versions:

0.5.1

Build Dependencies:

r, r-magrittr, r-jsonlite, r-callr

Link Dependencies:

Run Dependencies:

r, r-magrittr, r-jsonlite, r-callr

Description:

webshot: Take Screenshots of Web Pages

r-wgcna¶

Homepage:

https://cran.r-project.org/package=WGCNA

Spack package:

r-wgcna/package.py

Versions:

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:

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:

http://github.com/edwindj/whisker

Spack package:

r-whisker/package.py

Versions:

0.3-2

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

logicless templating, reuse templates in many programming languages including R

r-withr¶

Homepage:

http://github.com/jimhester/withr

Spack package:

r-withr/package.py

Versions:

2.1.2, 1.0.2, 1.0.1

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

https://www.bioconductor.org/packages/XDE/

Spack package:

r-xde/package.py

Versions:

2.22.0

Build Dependencies:

r, r-biobase, r-biocgenerics, r-genefilter, r-gtools, r-mergemaid, r-mvtnorm

Link Dependencies:

Run Dependencies:

r, r-biobase, r-biocgenerics, r-genefilter, r-gtools, r-mergemaid, r-mvtnorm

Description:

Multi-level model for cross-study detection of differential gene expression.

r-xgboost¶

Homepage:

https://github.com/dmlc/xgboost

Spack package:

r-xgboost/package.py

Versions:

0.6-4, 0.4-4

Build Dependencies:

r, r-matrix, r-data-table, r-magrittr, r-stringi, r-stringr

Link Dependencies:

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:

http://miraisolutions.wordpress.com/

Spack package:

r-xlconnect/package.py

Versions:

0.2-12, 0.2-11

Build Dependencies:

r, r-xlconnectjars, r-rjava

Link Dependencies:

Run Dependencies:

r, r-xlconnectjars, r-rjava

Description:

Provides comprehensive functionality to read, write and format Excel data.

r-xlconnectjars¶

Homepage:

http://miraisolutions.wordpress.com/

Spack package:

r-xlconnectjars/package.py

Versions:

0.2-12, 0.2-9

Build Dependencies:

r, r-rjava

Link Dependencies:

Run Dependencies:

r, r-rjava

Description:

Provides external JAR dependencies for the XLConnect package.

r-xlsx¶

Homepage:

http://code.google.com/p/rexcel/

Spack package:

r-xlsx/package.py

Versions:

0.5.7

Build Dependencies:

r, r-rjava, r-xlsxjars

Link Dependencies:

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:

https://cran.rstudio.com/web/packages/xlsxjars/index.html

Spack package:

r-xlsxjars/package.py

Versions:

0.6.1

Build Dependencies:

r, r-rjava

Link Dependencies:

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:

https://www.bioconductor.org/packages/xmapbridge/

Spack package:

r-xmapbridge/package.py

Versions:

1.34.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

xmapBridge can plot graphs in the X:Map genome browser. This package exports plotting files in a suitable format.

r-xml¶

Homepage:

https://cran.r-project.org/web/packages/XML/index.html

Spack package:

r-xml/package.py

Versions:

3.98-1.9, 3.98-1.5, 3.98-1.4

Build Dependencies:

r, libxml2

Link Dependencies:

r, libxml2

Run Dependencies:

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:

https://cran.r-project.org/package=xml2

Spack package:

r-xml2/package.py

Versions:

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:

https://cran.r-project.org/package=XNomial

Spack package:

r-xnomial/package.py

Versions:

1.0.4

Build Dependencies:

r, r-knitr

Link Dependencies:

Run Dependencies:

r, r-knitr

Description:

XNomial: Exact Goodness-of-Fit Test for Multinomial Data with Fixed Probabilities

r-xtable¶

Homepage:

http://xtable.r-forge.r-project.org/

Spack package:

r-xtable/package.py

Versions:

1.8-2

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

Coerce data to LaTeX and HTML tables.

r-xts¶

Homepage:

http://r-forge.r-project.org/projects/xts/

Spack package:

r-xts/package.py

Versions:

0.11-2, 0.9-7

Build Dependencies:

r, r-zoo

Link Dependencies:

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:

https://bioconductor.org/packages/XVector/

Spack package:

r-xvector/package.py

Versions:

0.20.0, 0.16.0

Build Dependencies:

r, r-biocgenerics, r-s4vectors, r-iranges, r-zlibbioc

Link Dependencies:

Run Dependencies:

r, r-biocgenerics, r-s4vectors, r-iranges, r-zlibbioc

Description:

Memory efficient S4 classes for storing sequences "externally" (behind an R external pointer, or on disk).

r-yaml¶

Homepage:

https://cran.r-project.org/web/packages/yaml/index.html

Spack package:

r-yaml/package.py

Versions:

2.1.14, 2.1.13

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

This package implements the libyaml YAML 1.1 parser and emitter (http://pyyaml.org/wiki/LibYAML) for R.

r-yapsa¶

Homepage:

http://bioconductor.org/packages/YAPSA/

Spack package:

r-yapsa/package.py

Versions:

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-gtrellis, r-pmcmr, r-complexheatmap, r-keggrest

Link Dependencies:

Run Dependencies:

Description:

r-yaqcaffy¶

Homepage:

http://bioconductor.org/packages/yaqcaffy/

Spack package:

r-yaqcaffy/package.py

Versions:

1.36.0

Build Dependencies:

r, r-simpleaffy

Link Dependencies:

Run Dependencies:

r, r-simpleaffy

Description:

Quality control of Affymetrix GeneChip expression data and reproducibility analysis of human whole genome chips with the MAQC reference datasets.

r-yarn¶

Homepage:

https://bioconductor.org/packages/yarn/

Spack package:

r-yarn/package.py

Versions:

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:

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:

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-zlibbioc¶

Homepage:

http://bioconductor.org/packages/release/bioc/html/zlibbioc.html

Spack package:

r-zlibbioc/package.py

Versions:

1.26.0, 1.22.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

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:

http://zoo.r-forge.r-project.org/

Spack package:

r-zoo/package.py

Versions:

1.7-14, 1.7-13

Build Dependencies:

Link Dependencies:

Run Dependencies:

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:

https://github.com/devonmpowell/r3d

Spack package:

r3d/package.py

Versions:

2018-12-19

Description:

Fast, robust polyhedral intersections, analytic integration, and conservative voxelization.

racon¶

Homepage:

https://github.com/isovic/racon

Spack package:

racon/package.py

Versions:

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:

https://bitbucket.org/gill_martinez/raft_aps

Spack package:

raft/package.py

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:

http://www.colm.net/open-source/ragel

Spack package:

ragel/package.py

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:

http://software.llnl.gov/RAJA/

Spack package:

raja/package.py

Versions:

develop, master, 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:

http://bioinformatics.psb.ugent.be/supplementary_data/erbon/nov2003/

Spack package:

randfold/package.py

Versions:

2.0.1

Build Dependencies:

squid

Link Dependencies:

squid

Description:

Minimum free energy of folding randomization test software

random123¶

Homepage:

http://www.deshawresearch.com/resources_random123.html

Spack package:

random123/package.py

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:

http://cgit.freedesktop.org/xorg/proto/randrproto

Spack package:

randrproto/package.py

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:

https://github.com/ericniebler/range-v3

Spack package:

range-v3/package.py

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

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:

https://github.com/ECP-VeloC/rankstr

Spack package:

rankstr/package.py

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:

http://rapidjson.org

Spack package:

rapidjson/package.py

Versions:

1.1.0, 1.0.2, 1.0.1, 1.0.0

Build Dependencies:

Description:

A fast JSON parser/generator for C++ with both SAX/DOM style API

ravel¶

Homepage:

https://github.com/llnl/ravel

Spack package:

ravel/package.py

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:

https://sco.h-its.org/exelixis/web/software/raxml

Spack package:

raxml/package.py

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:

http://denovoassembler.sourceforge.net/

Spack package:

ray/package.py

Versions:

2.3.1

Build Dependencies:

cmake, mpi

Link Dependencies:

mpi

Description:

Parallel genome assemblies for parallel DNA sequencing

rclone¶

Homepage:

http://rclone.org

Spack package:

rclone/package.py

Versions:

1.43

Build Dependencies:

Description:

Rclone is a command line program to sync files and directories to and from various cloud storage providers

rdma-core¶

Homepage:

https://github.com/linux-rdma/rdma-core

Spack package:

rdma-core/package.py

Versions:

20, 17.1, 13

Build Dependencies:

cmake, pkgconfig, libnl

Link Dependencies:

libnl

Description:

RDMA core userspace libraries and daemons

rdp-classifier¶

Homepage:

http://rdp.cme.msu.edu/

Spack package:

rdp-classifier/package.py

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.

re2c¶

Homepage:

http://re2c.org/index.html

Spack package:

re2c/package.py

Versions:

1.0.3

Description:

re2c: a free and open-source lexer generator for C and C++

readfq¶

Homepage:

https://github.com/lh3/readfq

Spack package:

readfq/package.py

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:

http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html

Spack package:

readline/package.py

Versions:

7.0, 6.3

Build Dependencies:

Link Dependencies:

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:

http://eddylab.org/software/recon/

Spack package:

recon/package.py

Versions:

1.05

Run Dependencies:

perl

Description:

RECON: a package for automated de novo identification of repeat families from genomic sequences.

recordproto¶

Homepage:

http://cgit.freedesktop.org/xorg/proto/recordproto

Spack package:

recordproto/package.py

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:

https://redis.io

Spack package:

redis/package.py

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:

https://github.com/ECP-VeloC/redset

Spack package:

redset/package.py

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:

https://github.com/Gabaldonlab/redundans

Spack package:

redundans/package.py

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.

regcm¶

Homepage:

https://gforge.ictp.it/gf/project/regcm/

Spack package:

regcm/package.py

Versions:

4.7.0

Build Dependencies:

netcdf, netcdf-fortran, hdf5, mpi

Link Dependencies:

netcdf, netcdf-fortran, hdf5, mpi

Description:

RegCM, ICTP Regional Climate Model (https://ictp.it).

relax¶

Homepage:

https://twiki.cern.ch/twiki/bin/view/LCG/RELAX

Spack package:

relax/package.py

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:

http://http://www2.mrc-lmb.cam.ac.uk/relion

Spack package:

relion/package.py

Versions:

develop, 3.0_beta, 2.1, 2.0.3

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:

https://github.com/PRUNERS/ReMPI

Spack package:

rempi/package.py

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:

http://plasmasturm.org/code/rename

Spack package:

rename/package.py

Versions:

1.600

Build Dependencies:

perl

Run Dependencies:

perl

Description:

Perl-powered file rename script with many helpful built-ins.

rendercheck¶

Homepage:

http://cgit.freedesktop.org/xorg/app/rendercheck

Spack package:

rendercheck/package.py

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:

http://cgit.freedesktop.org/xorg/proto/renderproto

Spack package:

renderproto/package.py

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:

http://www.repeatmasker.org

Spack package:

repeatmasker/package.py

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:

http://www.repeatmasker.org/RepeatModeler/

Spack package:

repeatmodeler/package.py

Versions:

1.0.11

Build Dependencies:

perl, perl-json, perl-uri, perl-lwp

Run Dependencies:

perl, perl-json, perl-uri, perl-lwp, repeatmasker, recon, repeatscout, trf, nseg, ncbi-rmblastn

Description:

RepeatModeler is a de-novo repeat family identification and modeling package.

repeatscout¶

Homepage:

http://www.repeatmasker.org/RepeatModeler/

Spack package:

repeatscout/package.py

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:

http://cgit.freedesktop.org/xorg/proto/resourceproto

Spack package:

resourceproto/package.py

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:

https://revbayes.github.io

Spack package:

revbayes/package.py

Versions:

1.0.10, 1.0.4

Build Dependencies:

cmake, boost, mpi

Link Dependencies:

boost, mpi

Description:

Bayesian phylogenetic inference using probabilistic graphical models and an interpreted language.

rgb¶

Homepage:

http://cgit.freedesktop.org/xorg/app/rgb

Spack package:

rgb/package.py

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:

https://sourceforge.net/projects/rhash/

Spack package:

rhash/package.py

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:

https://github.com/hanslub42/rlwrap

Spack package:

rlwrap/package.py

Versions:

0.43

Build Dependencies:

Link Dependencies:

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:

https://rnaseq-mats.sourceforge.net/index.html

Spack package:

rmats/package.py

Versions:

4.0.2

Build Dependencies:

py-numpy, openblas

Link Dependencies:

openblas

Run Dependencies:

Description:

MATS is a computational tool to detect differential alternative splicing events from RNA-Seq data.

rmlab¶

Homepage:

https://github.com/ax3l/lines-are-beautiful

Spack package:

rmlab/package.py

Versions:

develop

Build Dependencies:

cmake, pngwriter

Link Dependencies:

pngwriter

Description:

C++ File API for the reMarkable tablet

rna-seqc¶

Homepage:

http://archive.broadinstitute.org/cancer/cga/rna-seqc

Spack package:

rna-seqc/package.py

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.

rngstreams¶

Homepage:

http://statmath.wu.ac.at/software/RngStreams

Spack package:

rngstreams/package.py

Versions:

1.0.1

Description:

Multiple independent streams of pseudo-random numbers.

rocksdb¶

Homepage:

https://github.com/facebook/rocksdb

Spack package:

rocksdb/package.py

Versions:

develop, 5.17.2, 5.16.6, 5.15.10

Build Dependencies:

bzip2, gflags, lz4, snappy, zlib, zstd

Link Dependencies:

bzip2, gflags, lz4, snappy, zlib, zstd

Description:

RocksDB: A Persistent Key-Value Store for Flash and RAM Storage

rockstar¶

Homepage:

https://bitbucket.org/gfcstanford/rockstar

Spack package:

rockstar/package.py

Versions:

develop, yt

Build Dependencies:

hdf5

Link Dependencies:

hdf5

Description:

The Rockstar Halo Finder

root¶

Homepage:

https://root.cern.ch

Spack package:

root/package.py

Versions:

master, 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, 5.34.38

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, avahi, davix, cfitsio, fftw, graphviz, gsl, http, jemalloc, kerberos, ldap, libcxx, mysql-client, odbc, openssl, postgresql, pythia6, python, r, r-cpp, r-inside, shadow, sqlite, tbb, unuran, vc, veccore, 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, avahi, davix, cfitsio, fftw, graphviz, gsl, http, jemalloc, kerberos, ldap, libcxx, mysql-client, odbc, openssl, postgresql, pythia6, shadow, sqlite, tbb, unuran, vc, veccore, vdt, libxml2, xrootd

Run Dependencies:

python, r, r-cpp, r-inside

Description:

ROOT is a data analysis framework.

rose¶

Homepage:

http://rosecompiler.org/

Spack package:

rose/package.py

Versions:

master, 0.9.7

Build Dependencies:

autoconf, automake, libtool, boost, libgcrypt, java, z3

Link Dependencies:

boost, java, z3

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:

http://ross-org.github.io

Spack package:

ross/package.py

Versions:

develop, 7.0.1, 7.0.0, 6.0.0

Build Dependencies:

cmake, mpi

Link Dependencies:

mpi

Description:

Rensselaer Optimistic Simulation System

routino¶

Homepage:

https://www.routino.org

Spack package:

routino/package.py

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:

https://github.com/thkukuk/rpcsvc-proto

Spack package:

rpcsvc-proto/package.py

Versions:

1.4

Build Dependencies:

gettext

Link Dependencies:

gettext

Description:

rpcsvc protocol definitions from glibc.

rr¶

Homepage:

http://rr-project.org/

Spack package:

rr/package.py

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:

https://github.com/ANL-CESAR/RSBench

Spack package:

rsbench/package.py

Versions:

2, 0

Description:

A mini-app to represent the multipole resonance representation lookup cross section algorithm.

rsem¶

Homepage:

http://deweylab.github.io/RSEM/

Spack package:

rsem/package.py

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:

http://cgit.freedesktop.org/xorg/app/rstart

Spack package:

rstart/package.py

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:

https://rsync.samba.org

Spack package:

rsync/package.py

Versions:

3.1.3, 3.1.2, 3.1.1

Description:

An open source utility that provides fast incremental file transfer.

rtags¶

Homepage:

https://github.com/Andersbakken/rtags/

Spack package:

rtags/package.py

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:

https://github.com/davidsoergel/rtax

Spack package:

rtax/package.py

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:

https://www.ruby-lang.org/

Spack package:

ruby/package.py

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:

https://rubygems.org/gems/gnuplot/versions/2.6.2

Spack package:

ruby-gnuplot/package.py

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:

https://rubygems.org/gems/narray

Spack package:

ruby-narray/package.py

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:

https://rubygems.org/gems/ronn

Spack package:

ruby-ronn/package.py

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:

https://rubygems.org/gems/RubyInline

Spack package:

ruby-rubyinline/package.py

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:

https://github.com/nirvdrum/svn2git/

Spack package:

ruby-svn2git/package.py

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:

https://rubygems.org/gems/terminal-table

Spack package:

ruby-terminal-table/package.py

Versions:

1.8.0

Build Dependencies:

ruby

Link Dependencies:

ruby

Description:

Simple, feature rich ascii table generation library

rust¶

Homepage:

http://www.rust-lang.org

Spack package:

rust/package.py

Versions:

develop, 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:

http://www.rust-lang.org

Spack package:

rust-bindgen/package.py

Versions:

0.20.5

Build Dependencies:

rust, llvm

Link Dependencies:

rust, llvm

Description:

The rust programming language toolchain

sabre¶

Homepage:

https://github.com/najoshi/sabre

Spack package:

sabre/package.py

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:

http://saga-gis.org/

Spack package:

saga-gis/package.py

Versions:

develop, 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, python, wx, gdal, proj, unixodbc, swig

Link Dependencies:

python, wx, gdal, proj, unixodbc

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:

http://www.cs.cmu.edu/~ckingsf/software/sailfish

Spack package:

sailfish/package.py

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:

http://combine-lab.github.io/salmon/

Spack package:

salmon/package.py

Versions:

0.12.0, 0.9.1, 0.8.2

Build Dependencies:

cmake, tbb, boost

Link Dependencies:

tbb, boost

Description:

Salmon is a tool for quantifying the expression of transcripts using RNA-seq data.

sambamba¶

Homepage:

http://lomereiter.github.io/sambamba/

Spack package:

sambamba/package.py

Versions:

0.6.6

Build Dependencies:

ldc, python

Link Dependencies:

ldc

Description:

Sambamba: process your BAM data faster (bioinformatics)

samblaster¶

Homepage:

https://github.com/GregoryFaust/samblaster

Spack package:

samblaster/package.py

Versions:

0.1.24, 0.1.23

Description:

A tool to mark duplicates and extract discordant and split reads from sam files.

samrai¶

Homepage:

https://computation.llnl.gov/projects/samrai

Spack package:

samrai/package.py

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:

www.htslib.org

Spack package:

samtools/package.py

Versions:

1.9, 1.8, 1.7, 1.6, 1.5, 1.4, 1.3.1, 1.2

Build Dependencies:

ncurses, htslib, zlib, bzip2

Link Dependencies:

ncurses, htslib, zlib, bzip2

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:

https://www.gentoo.org/proj/en/portage/sandbox/

Spack package:

sandbox/package.py

Versions:

2.12

Description:

sandbox'd LD_PRELOAD hack by Gentoo Linux

sas¶

Homepage:

https://github.com/dpiparo/SAS

Spack package:

sas/package.py

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:

https://github.com/bioinfologics/satsuma2

Spack package:

satsuma2/package.py

Versions:

2016-11-22

Build Dependencies:

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:

https://github.com/CODARcode/savanna

Spack package:

savanna/package.py

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:

https://bitbucket.org/saws/saws/wiki/Home

Spack package:

saws/package.py

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:

http://www.scala-sbt.org

Spack package:

sbt/package.py

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:

https://www.scala-lang.org/

Spack package:

scala/package.py

Versions:

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:

http://www.scalasca.org

Spack package:

scalasca/package.py

Versions:

2.4, 2.3.1, 2.2.2, 2.1

Build Dependencies:

mpi, cubew, cube, otf2

Link Dependencies:

mpi, cubew, cube, otf2

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:

https://github.com/Kingsford-Group/scallop

Spack package:

scallop/package.py

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:

http://scalpel.sourceforge.net/index.html

Spack package:

scalpel/package.py

Versions:

0.5.3

Build Dependencies:

cmake, perl

Link Dependencies:

cmake, 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:

http://blog.theseed.org/servers/2010/07/scan-for-matches.html

Spack package:

scan-for-matches/package.py

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:

http://scons.org

Spack package:

scons/package.py

Versions:

3.0.4, 3.0.1, 2.5.1, 2.5.0

Build Dependencies:

Link Dependencies:

Run Dependencies:

Description:

SCons is a software construction tool

scorec-core¶

Homepage:

https://www.scorec.rpi.edu/

Spack package:

scorec-core/package.py

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:

http://www.vi-hps.org/projects/score-p

Spack package:

scorep/package.py

Versions:

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:

http://www.labri.fr/perso/pelegrin/scotch/

Spack package:

scotch/package.py

Versions:

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:

http://computation.llnl.gov/projects/scalable-checkpoint-restart-for-mpi

Spack package:

scr/package.py

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:

https://www.gnu.org/software/screen/

Spack package:

screen/package.py

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:

Link Dependencies:

Description:

Screen is a full-screen window manager that multiplexes a physical terminal between several processes, typically interactive shells.

scripts¶

Homepage:

http://cgit.freedesktop.org/xorg/app/scripts

Spack package:

scripts/package.py

Versions:

1.0.1

Build Dependencies:

libx11, pkgconfig, util-macros

Link Dependencies:

Description:

Various X related scripts.

scrnsaverproto¶

Homepage:

http://cgit.freedesktop.org/xorg/proto/scrnsaverproto

Spack package:

scrnsaverproto/package.py

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.

sctk¶

Homepage:

https://www.nist.gov/itl/iad/mig/tools

Spack package:

sctk/package.py

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:

https://wiki.libsdl.org/FrontPage

Spack package:

sdl2/package.py

Versions:

2.0.5

Build Dependencies:

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:

http://sdl.beuc.net/sdl.wiki/SDL_image

Spack package:

sdl2-image/package.py

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:

https://github.com/simongog/sdsl-lite

Spack package:

sdsl-lite/package.py

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:

http://gsjaardema.github.io/seacas/

Spack package:

seacas/package.py

Versions:

master

Build Dependencies:

cmake, netcdf, cgns, matio, metis, parmetis, mpi

Link Dependencies:

netcdf, cgns, 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:

http://www.gnu.org/software/sed/

Spack package:

sed/package.py

Versions:

4.2.2

Description:

GNU implementation of the famous stream editor.

sentieon-genomics¶

Homepage:

https://www.sentieon.com/

Spack package:

sentieon-genomics/package.py

Versions:

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:

https://www.seqan.de

Spack package:

seqan/package.py

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

seqprep¶

Homepage:

https://github.com/jstjohn/SeqPrep

Spack package:

seqprep/package.py

Versions:

1.3.2

Description:

SeqPrep is a program to merge paired end Illumina reads that are overlapping into a single longer read.

seqtk¶

Homepage:

https://github.com/lh3/seqtk

Spack package:

seqtk/package.py

Versions:

1.3, 1.2, 1.1

Build Dependencies:

zlib

Link Dependencies:

zlib

Description:

Toolkit for processing sequences in FASTA/Q formats.

serf¶

Homepage:

https://serf.apache.org/

Spack package:

serf/package.py

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:

http://cgit.freedesktop.org/xorg/app/sessreg

Spack package:

sessreg/package.py

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:

http://cgit.freedesktop.org/xorg/app/setxkbmap

Spack package:

setxkbmap/package.py

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.

sga¶

Homepage:

https://www.msi.umn.edu/sw/sga

Spack package:

sga/package.py

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.

shapeit¶

Homepage:

https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html

Spack package:

shapeit/package.py

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:

https://freedesktop.org/wiki/Software/shared-mime-info

Spack package:

shared-mime-info/package.py

Versions:

1.9, 1.8

Build Dependencies:

glib, libxml2, intltool, gettext, pkgconfig

Link Dependencies:

Description:

Database of common MIME types.

shiny-server¶

Homepage:

https://www.rstudio.com/products/shiny/shiny-server/

Spack package:

shiny-server/package.py

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:

https://github.com/MG-RAST/Shock

Spack package:

shocklibs/package.py

Versions:

0.9.24

Description:

The lib for shock: An object store for scientific data.

shoremap¶

Homepage:

http://bioinfo.mpipz.mpg.de/shoremap/

Spack package:

shoremap/package.py

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:

https://huttenhower.sph.harvard.edu/shortbred

Spack package:

shortbred/package.py

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:

http://sites.psu.edu/axtell/software/shortstack/

Spack package:

shortstack/package.py

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:

http://cgit.freedesktop.org/xorg/app/showfont

Spack package:

showfont/package.py

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.

shuffile¶

Homepage:

https://github.com/ECP-VeloC/shuffile

Spack package:

shuffile/package.py

Versions:

master, 0.0.3

Build Dependencies:

cmake, mpi, kvtree

Link Dependencies:

mpi, kvtree

Description:

Shuffle files between MPI ranks

sickle¶

Homepage:

https://github.com/najoshi/sickle

Spack package:

sickle/package.py

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:

https://departments.icmab.es/leem/siesta/

Spack package:

siesta/package.py

Versions:

4.0.1, 3.2-pl-5

Build Dependencies:

mpi, blas, lapack, scalapack, netcdf, netcdf-fortran

Link Dependencies:

mpi, blas, lapack, scalapack, netcdf, netcdf-fortran

Description:

SIESTA performs electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids.

signalp¶

Homepage:

http://www.cbs.dtu.dk/services/SignalP/

Spack package:

signalp/package.py

Versions:

4.1f

Build Dependencies:

perl, gnuplot

Link Dependencies:

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:

https://github.com/aperezdc/signify

Spack package:

signify/package.py

Versions:

Build Dependencies:

Link Dependencies:

Description:

OpenBSD tool to signs and verify signatures on files.

silo¶

Homepage:

http://wci.llnl.gov/simulation/computer-codes/silo

Spack package:

silo/package.py

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:

http://simgrid.org/

Spack package:

simgrid/package.py

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:

Link Dependencies:

Description:

To study the behavior of large-scale distributed systems such as Grids, Clouds, HPC or P2P systems.

simplemoc¶

Homepage:

https://github.com/ANL-CESAR/SimpleMOC/

Spack package:

simplemoc/package.py

Versions:

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:

https://github.com/LLNL/simul

Spack package:

simul/package.py

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:

https://github.com/eschnett/SimulationIO

Spack package:

simulationio/package.py

Versions:

develop, 1.0.0, 0.1.0

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:

https://www.sylabs.io/singularity/

Spack package:

singularity/package.py

Versions:

develop, 3.1.1

Build Dependencies:

go, libuuid, libgpg-error, git

Link Dependencies:

go, libuuid, libgpg-error, git

Run Dependencies:

squashfs

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 for details.

singularity-legacy¶

Homepage:

https://www.sylabs.io/singularity/

Spack package:

singularity-legacy/package.py

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:

https://github.com/electronic-structure/SIRIUS

Spack package:

sirius/package.py

Versions:

6.1.5

Build Dependencies:

cmake, python, mpi, gsl, lapack, fftw, libxc, spglib, hdf5, pkgconfig, elpa, libvdwxc, scalapack

Link Dependencies:

python, mpi, gsl, lapack, fftw, libxc, spglib, hdf5, elpa, libvdwxc, scalapack

Description:

Domain specific library for electronic structure calculations

skilion-onedrive¶

Homepage:

https://github.com/skilion/onedrive

Spack package:

skilion-onedrive/package.py

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.

sl¶

Homepage:

https://github.com/mtoyoda/sl

Spack package:

sl/package.py

Versions:

5.02

Build Dependencies:

Link Dependencies:

Description:

SL: Cure your bad habit of mistyping

slate¶

Homepage:

https://icl.utk.edu/slate/

Spack package:

slate/package.py

Versions:

develop

Build Dependencies:

cuda, intel-mkl, 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:

http://sleef.org

Spack package:

sleef/package.py

Versions:

3.2

Build Dependencies:

Description:

SIMD Library for Evaluating Elementary Functions, vectorized libm and DFT.

slepc¶

Homepage:

http://slepc.upv.es

Spack package:

slepc/package.py

Versions:

develop, 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:

https://slurm.schedmd.com

Spack package:

slurm/package.py

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:

http://www.sanger.ac.uk/science/tools/smalt-0

Spack package:

smalt/package.py

Versions:

0.7.6

Description:

SMALT aligns DNA sequencing reads with a reference genome.

smof¶

Homepage:

https://github.com/incertae-sedis/smof

Spack package:

smof/package.py

Versions:

2.13.1

Run Dependencies:

Description:

Explore and analyze biological sequence data

smproxy¶

Homepage:

http://cgit.freedesktop.org/xorg/app/smproxy

Spack package:

smproxy/package.py

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:

https://snakemake.readthedocs.io/en/stable/

Spack package:

snakemake/package.py

Versions:

3.11.2

Build Dependencies:

python, py-requests, py-setuptools, py-wrapt

Link Dependencies:

Run Dependencies:

python, py-requests, py-setuptools, py-wrapt

Description:

Snakemake is an MIT-licensed workflow management system.

snap¶

Homepage:

https://github.com/lanl/SNAP

Spack package:

snap/package.py

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:

http://snap.cs.berkeley.edu/

Spack package:

snap-berkeley/package.py

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:

http://korflab.ucdavis.edu/software.html

Spack package:

snap-korf/package.py

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:

https://github.com/google/snappy

Spack package:

snappy/package.py

Versions:

1.1.7

Build Dependencies:

Test Dependencies:

googletest

Description:

A fast compressor/decompressor: https://code.google.com/p/snappy

snbone¶

Homepage:

https://github.com/ANL-CESAR/

Spack package:

snbone/package.py

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:

https://github.com/fritzsedlazeck/Sniffles/wiki

Spack package:

sniffles/package.py

Versions:

1.0.7, 1.0.5

Build Dependencies:

Description:

Structural variation caller using third generation sequencing.

snpeff¶

Homepage:

http://snpeff.sourceforge.net/

Spack package:

snpeff/package.py

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:

http://chibba.pgml.uga.edu/snphylo/

Spack package:

snphylo/package.py

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:

https://mathgen.stats.ox.ac.uk/genetics_software/snptest/snptest.html

Spack package:

snptest/package.py

Versions:

2.5.2

Description:

SNPTEST is a program for the analysis of single SNP association in genome-wide studies.

soap2¶

Homepage:

http://soap.genomics.org.cn/soapaligner.html

Spack package:

soap2/package.py

Versions:

2.21

Description:

Software for short oligonucleotide alignment.

soapdenovo-trans¶

Homepage:

http://soap.genomics.org.cn/SOAPdenovo-Trans.html

Spack package:

soapdenovo-trans/package.py

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:

https://github.com/aquaskyline/SOAPdenovo2

Spack package:

soapdenovo2/package.py

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.

soapindel¶

Homepage:

http://soap.genomics.org.cn/soapindel.html

Spack package:

soapindel/package.py

Versions:

2.1.7.17

Build Dependencies:

perl

Run Dependencies:

perl

Description:

SOAPindel is focusing on calling indels from the next-generation paired- end sequencing data.

soapsnp¶

Homepage:

http://soap.genomics.org.cn/soapsnp.html

Spack package:

soapsnp/package.py

Versions:

1.03

Build Dependencies:

Link Dependencies:

Description:

SOAPsnp uses a method based on Bayes' theorem (the reverse probability model) to call consensus genotype by carefully considering the data quality, alignment, and recurring experimental errors.

sofa-c¶

Homepage:

http://www.iausofa.org/current_C.html

Spack package:

sofa-c/package.py

Versions:

20180130

Description:

Standards of Fundamental Astronomy (SOFA) library for ANSI C.

somatic-sniper¶

Homepage:

http://gmt.genome.wustl.edu/packages/somatic-sniper

Spack package:

somatic-sniper/package.py

Versions:

1.0.5.0

Build Dependencies:

cmake, ncurses

Link Dependencies:

Description:

A tool to call somatic single nucleotide variants.

sortmerna¶

Homepage:

https://github.com/biocore/sortmerna

Spack package:

sortmerna/package.py

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:

https://github.com/cdwdirect/sos_flow/wiki

Spack package:

sosflow/package.py

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:

http://www.mcs.anl.gov/petsc/index.html

Spack package:

sowing/package.py

Versions:

1.1.25-p1, 1.1.23-p1

Description:

Sowing generates Fortran interfaces and documentation for PETSc and MPICH.

sox¶

Homepage:

http://sox.sourceforge.net/Main/HomePage

Spack package:

sox/package.py

Versions:

14.4.2

Build Dependencies:

bzip2, flac, id3lib, libvorbis, opus

Link Dependencies:

bzip2, flac, id3lib, libvorbis, opus

Description:

SoX, the Swiss Army knife of sound processing programs.

spades¶

Homepage:

http://cab.spbu.ru/software/spades/

Spack package:

spades/package.py

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:

Description:

SPAdes - St. Petersburg genome assembler - is intended for both standard isolates and single-cell MDA bacteria assemblies.

span-lite¶

Homepage:

https://github.com/martinmoene/span-lite

Spack package:

span-lite/package.py

Versions:

0.5.0, 0.4.0, 0.3.0, 0.2.0, 0.1.0

Build Dependencies:

Description:

A single-file header-only version of a C++20-like span for C++98, C++11 and later

spark¶

Homepage:

http://spark.apache.org

Spack package:

spark/package.py

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:

https://github.com/sparsehash/sparsehash

Spack package:

sparsehash/package.py

Versions:

2.0.3

Description:

Sparse and dense hash-tables for C++ by Google

sparta¶

Homepage:

https://github.com/atulkakrana/sPARTA.github

Spack package:

sparta/package.py

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:

https://github.com/gabime/spdlog

Spack package:

spdlog/package.py

Versions:

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:

Description:

Very fast, header only, C++ logging library

spectrum-mpi¶

Homepage:

http://www-03.ibm.com/systems/spectrum-computing/products/mpi

Spack package:

spectrum-mpi/package.py

Description:

IBM MPI implementation from Spectrum MPI.

speex¶

Homepage:

https://speex.org

Spack package:

speex/package.py

Versions:

1.2.0

Description:

Speex is an Open Source/Free Software patent-free audio compression format designed for speech.

spglib¶

Homepage:

https://atztogo.github.io/spglib/

Spack package:

spglib/package.py

Versions:

1.10.3, 1.10.0

Build Dependencies:

Description:

C library for finding and handling crystal symmetries.

sph2pipe¶

Homepage:

https://www.ldc.upenn.edu/language-resources/tools/sphere-conversion-tools

Spack package:

sph2pipe/package.py

Versions:

2.5

Build Dependencies:

Description:

Sph2pipe is a portable tool for converting SPHERE files to other formats.

spherepack¶

Homepage:

https://www2.cisl.ucar.edu/resources/legacy/spherepack

Spack package:

spherepack/package.py

Versions:

3.2

Description:

SPHEREPACK - A Package for Modeling Geophysical Processes

spindle¶

Homepage:

https://computation.llnl.gov/project/spindle/

Spack package:

spindle/package.py

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:

https://www.fil.ion.ucl.ac.uk/spm/

Spack package:

spm/package.py

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:

https://spot.lrde.epita.fr/

Spack package:

spot/package.py

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:

https://www.sqlite.org

Spack package:

sqlite/package.py

Versions:

3.28.0, 3.27.2, 3.27.1, 3.27.0, 3.26.0

Build Dependencies:

Link Dependencies:

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:

https://sqlitebrowser.org

Spack package:

sqlitebrowser/package.py

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:

http://squashfs.sourceforge.net

Spack package:

squashfs/package.py

Versions:

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:

http://eddylab.org/software.html

Spack package:

squid/package.py

Versions:

1.9g

Description:

C function library for sequence analysis.

sra-toolkit¶

Homepage:

https://trace.ncbi.nlm.nih.gov/Traces/sra

Spack package:

sra-toolkit/package.py

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:

https://astro-informatics.github.io/ssht/

Spack package:

ssht/package.py

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:

https://www.baseclear.com/genomics/bioinformatics/basetools/SSPACE-longread

Spack package:

sspace-longread/package.py

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:

https://www.baseclear.com/genomics/bioinformatics/basetools/SSPACE

Spack package:

sspace-standard/package.py

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:

http://sst-simulator.org/

Spack package:

sst-core/package.py

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:

http://sst.sandia.gov/about_dumpi.html

Spack package:

sst-dumpi/package.py

Versions:

master, 6.1.0

Build Dependencies:

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:

http://sst.sandia.gov/about_sstmacro.html

Spack package:

sst-macro/package.py

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:

http://catchenlab.life.illinois.edu/stacks/

Spack package:

stacks/package.py

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:

http://staden.sourceforge.net/

Spack package:

staden-io-lib/package.py

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:

https://github.com/alexdobin/STAR

Spack package:

star/package.py

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:

http://mdx.plm.automation.siemens.com/star-ccm-plus

Spack package:

star-ccm-plus/package.py

Versions:

11.06.010_02

Description:

STAR-CCM+ (Computational Continuum Mechanics) CFD solver.

startup-notification¶

Homepage:

https://www.freedesktop.org/wiki/Software/startup-notification/

Spack package:

startup-notification/package.py

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:

http://paradyn.org/STAT/STAT.html

Spack package:

stat/package.py

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

Link Dependencies:

dyninst, fast-global-file-status, graphlib, graphviz, launchmon, mrnet, python, py-xdot, swig, mpi

Run Dependencies:

graphviz, py-pygtk, py-enum34

Description:

Library to create, manipulate, and export graphs Graphlib.

stata¶

Homepage:

https://www.stata.com/

Spack package:

stata/package.py

Versions:

Build Dependencies:

Link Dependencies:

Description:

STATA is a general-purpose statistical software package developed by StataCorp.

stc¶

Homepage:

http://swift-lang.org/Swift-T

Spack package:

stc/package.py

Versions:

develop, 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:

https://groups.oist.jp/cnu/software

Spack package:

steps/package.py

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

stow¶

Homepage:

https://www.gnu.org/software/stow/

Spack package:

stow/package.py

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:

https://strace.io

Spack package:

strace/package.py

Versions:

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:

https://www.cs.virginia.edu/stream/ref.html

Spack package:

stream/package.py

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:

https://github.com/Illumina/strelka

Spack package:

strelka/package.py

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:

https://people.seas.harvard.edu/~apw/stress/

Spack package:

stress/package.py

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:

https://github.com/martinmoene/string-view-lite

Spack package:

string-view-lite/package.py

Versions:

1.2.0, 1.1.0, 1.0.0, 0.2.0, 0.1.0

Build Dependencies:

Description:

A single-file header-only version of a C++17-like string_view for C++98, C++11 and later

stringtie¶

Homepage:

https://ccb.jhu.edu/software/stringtie

Spack package:

stringtie/package.py

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:

http://web.stanford.edu/group/pritchardlab/structure.html

Spack package:

structure/package.py

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:

http://portal.nersc.gov/project/sparse/strumpack

Spack package:

strumpack/package.py

Versions:

master, 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

Link Dependencies:

mpi, blas, lapack, scalapack, metis, parmetis, scotch

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:

http://www.sublimetext.com/

Spack package:

sublime-text/package.py

Versions:

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:

http://subread.sourceforge.net/

Spack package:

subread/package.py

Versions:

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:

https://subversion.apache.org/

Spack package:

subversion/package.py

Versions:

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, serf, perl, swig, perl-term-readkey

Link Dependencies:

apr, apr-util, zlib, sqlite, serf, perl, swig, perl-term-readkey

Description:

Apache Subversion - an open source version control system.

suite-sparse¶

Homepage:

http://faculty.cse.tamu.edu/davis/suitesparse.html

Spack package:

suite-sparse/package.py

Versions:

5.3.0, 5.2.0, 5.1.0, 4.5.5, 4.5.4, 4.5.3, 4.5.1

Build Dependencies:

blas, lapack, cmake, metis, tbb, cuda

Link Dependencies:

blas, lapack, metis, tbb, cuda

Description:

SuiteSparse is a suite of sparse matrix algorithms

sumaclust¶

Homepage:

https://git.metabarcoding.org/obitools/sumaclust

Spack package:

sumaclust/package.py

Versions:

1.0.20

Description:

Sumaclust aims to cluster sequences in a way that is fast and exact at the same time.

sundials¶

Homepage:

https://computation.llnl.gov/projects/sundials

Spack package:

sundials/package.py

Versions:

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, blas, lapack, suite-sparse, petsc, hypre, superlu-mt

Link Dependencies:

mpi, cuda, raja, blas, lapack, suite-sparse, petsc, hypre, superlu-mt

Description:

SUNDIALS (SUite of Nonlinear and DIfferential/ALgebraic equation Solvers)

superlu¶

Homepage:

http://crd-legacy.lbl.gov/~xiaoye/SuperLU/#superlu

Spack package:

superlu/package.py

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:

http://crd-legacy.lbl.gov/~xiaoye/SuperLU/

Spack package:

superlu-dist/package.py

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:

http://crd-legacy.lbl.gov/~xiaoye/SuperLU/#superlu_mt

Spack package:

superlu-mt/package.py

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:

https://support.10xgenomics.com/de-novo-assembly/software/overview/latest/welcome

Spack package:

supernova/package.py

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:

https://geodynamics.org/cig/software/sw4

Spack package:

sw4lite/package.py

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:

https://sourceforge.net/projects/swapassembler/

Spack package:

swap-assembler/package.py

Versions:

0.4

Build Dependencies:

mpich

Link Dependencies:

mpich

Description:

A scalable and fully parallelized genome assembler.

swarm¶

Homepage:

https://github.com/torognes/swarm

Spack package:

swarm/package.py

Versions:

2.1.13

Description:

A robust and fast clustering method for amplicon-based studies.

swfft¶

Homepage:

https://xgitlab.cels.anl.gov/hacc/SWFFT

Spack package:

swfft/package.py

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.

swiftsim¶

Homepage:

http://icc.dur.ac.uk/swift/

Spack package:

swiftsim/package.py

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:

http://www.swig.org

Spack package:

swig/package.py

Versions:

3.0.12, 3.0.11, 3.0.10, 3.0.8, 3.0.2, 2.0.12, 2.0.2, 1.3.40

Build Dependencies:

pcre

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.

symengine¶

Homepage:

https://github.com/symengine/symengine

Spack package:

symengine/package.py

Versions:

develop, 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:

http://www.math.uni-rostock.de/~rehn/software/sympol.html

Spack package:

sympol/package.py

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

sz¶

Homepage:

https://collab.cels.anl.gov/display/ESR/SZ

Spack package:

sz/package.py

Versions:

develop, 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:

https://github.com/samtools/tabix

Spack package:

tabix/package.py

Versions:

2013-12-16

Build Dependencies:

Run Dependencies:

Description:

Generic indexer for TAB-delimited genome position files

talass¶

Homepage:

http://www.cedmav.org/research/project/16-talass.html

Spack package:

talass/package.py

Versions:

2018-10-29

Build Dependencies:

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:

https://talloc.samba.org

Spack package:

talloc/package.py

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:

http://cbrc3.cbrc.jp/~martin/tantan

Spack package:

tantan/package.py

Versions:

Description:

tantan is a tool to mask simple regions (low complexity and short-period tandem repeats) in DNA, RNA, and protein sequences.

tar¶

Homepage:

https://www.gnu.org/software/tar/

Spack package:

tar/package.py

Versions:

1.31, 1.30, 1.29, 1.28

Description:

GNU Tar provides the ability to create tar archives, as well as various other kinds of manipulation.

targetp¶

Homepage:

http://www.cbs.dtu.dk/services/TargetP/

Spack package:

targetp/package.py

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:

http://www.taskwarrior.org

Spack package:

task/package.py

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:

http://www.taskwarrior.org

Spack package:

taskd/package.py

Versions:

1.1.0

Build Dependencies:

cmake, libuuid, gnutls

Link Dependencies:

libuuid, gnutls

Description:

TaskWarrior task synchronization daemon

tasmanian¶

Homepage:

http://tasmanian.ornl.gov

Spack package:

tasmanian/package.py

Versions:

develop, 6.0, 5.1, 5.0

Build Dependencies:

cmake, python, py-numpy, mpi, blas, cuda, magma

Link Dependencies:

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:

http://www.maizegenetics.net/tassel

Spack package:

tassel/package.py

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:

http://www.cs.uoregon.edu/research/tau

Spack package:

tau/package.py

Versions:

develop, 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, binutils, python, libunwind, mpi, cuda, gasnet

Link Dependencies:

pdt, scorep, otf2, likwid, papi, 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:

http://www.tcl.tk

Spack package:

tcl/package.py

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:

https://sourceforge.net/projects/incrtcl/

Spack package:

tcl-itcl/package.py

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:

http://www.tcl.tk/software/tcllib

Spack package:

tcl-tcllib/package.py

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:

http://tclxml.sourceforge.net/tclxml.html

Spack package:

tcl-tclxml/package.py

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:

http://tclap.sourceforge.net

Spack package:

tclap/package.py

Versions:

1.2.2, 1.2.1

Description:

Templatized C++ Command Line Parser

tcoffee¶

Homepage:

http://www.tcoffee.org/

Spack package:

tcoffee/package.py

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:

http://www.tcptrace.org/

Spack package:

tcptrace/package.py

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:

http://www.tcsh.org/

Spack package:

tcsh/package.py

Versions:

6.20.00

Build Dependencies:

Link Dependencies:

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:

http://uk-mac.github.io/TeaLeaf/

Spack package:

tealeaf/package.py

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.

templight¶

Homepage:

https://github.com/mikael-s-persson/templight

Spack package:

templight/package.py

Versions:

develop, 2019.01.09, 2018.07.20

Build Dependencies:

cmake, python, py-lit

Link Dependencies:

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:

https://github.com/mikael-s-persson/templight-tools

Spack package:

templight-tools/package.py

Versions:

develop

Build Dependencies:

Link Dependencies:

Description:

Supporting tools for the Templight Profiler

tetgen¶

Homepage:

http://wias-berlin.de/software/tetgen/

Spack package:

tetgen/package.py

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:

https://github.com/martemyev/tethex

Spack package:

tethex/package.py

Versions:

develop, 0.0.7

Build Dependencies:

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:

https://www.gnu.org/software/texinfo/

Spack package:

texinfo/package.py

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:

http://www.tug.org/texlive

Spack package:

texlive/package.py

Versions:

live

Build Dependencies:

perl

Description:

TeX Live is a free software distribution for the TeX typesetting system. Heads up, it's is not a reproducible installation.

tfel¶

Homepage:

http://tfel.sourceforge.net

Spack package:

tfel/package.py

Versions:

master, 3.2.1, 3.2.0, 3.1.4, 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, 2.0.4, 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:

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:

https://github.com/monochromegane/the_platinum_searcher

Spack package:

the-platinum-searcher/package.py

Versions:

head

Build Dependencies:

Link Dependencies:

Description:

Fast parallel recursive grep alternative

the-silver-searcher¶

Homepage:

http://geoff.greer.fm/ag/

Spack package:

the-silver-searcher/package.py

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:

https://sites.google.com/lbl.gov/exastar/home

Spack package:

thornado-mini/package.py

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:

http://thrift.apache.org

Spack package:

thrift/package.py

Versions:

0.11.0, 0.10.0, 0.9.3, 0.9.2

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:

https://thrust.github.io

Spack package:

thrust/package.py

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:

https://jonas.github.io/tig/

Spack package:

tig/package.py

Versions:

2.2.2

Build Dependencies:

Link Dependencies:

Description:

Text-mode interface for git

time¶

Homepage:

https://www.gnu.org/software/time/

Spack package:

time/package.py

Versions:

1.9

Description:

The time command runs another program, then displays information about the resources used by that program.

tinyxml¶

Homepage:

http://grinninglizard.com/tinyxml/

Spack package:

tinyxml/package.py

Versions:

2.6.2

Build Dependencies:

Description:

Simple, small, efficient, C++ XML parser

tinyxml2¶

Homepage:

http://grinninglizard.com/tinyxml2/

Spack package:

tinyxml2/package.py

Versions:

4.0.1, 4.0.0, 3.0.0, 2.2.0, 2.1.0, 2.0.2

Build Dependencies:

Description:

Simple, small, efficient, C++ XML parser

tioga¶

Homepage:

https://github.com/jsitaraman/tioga

Spack package:

tioga/package.py

Versions:

master

Build Dependencies:

cmake, mpi

Link Dependencies:

mpi

Description:

Topology Independent Overset Grid Assembly (TIOGA)

tk¶

Homepage:

http://www.tcl.tk

Spack package:

tk/package.py

Versions:

8.6.8, 8.6.6, 8.6.5, 8.6.3

Build Dependencies:

tcl, libx11

Link Dependencies:

tcl, libx11

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:

https://gitlab.com/miscripts/tldd

Spack package:

tldd/package.py

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:

http://zhanglab.ccmb.med.umich.edu/TM-align

Spack package:

tmalign/package.py

Versions:

2016-05-25

Description:

TM-align is an algorithm for sequence-order independent protein structure comparisons.

tmhmm¶

Homepage:

http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?tmhmm

Spack package:

tmhmm/package.py

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:

http://tmux.github.io

Spack package:

tmux/package.py

Versions:

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:

https://github.com/tmuxinator/tmuxinator

Spack package:

tmuxinator/package.py

Versions:

0.6.11

Build Dependencies:

ruby

Link Dependencies:

ruby

Description:

A session configuration creator and manager for tmux

tophat¶

Homepage:

http://ccb.jhu.edu/software/tophat/index.shtml

Spack package:

tophat/package.py

Versions:

2.1.2, 2.1.1

Build Dependencies:

autoconf, automake, libtool, m4, boost

Link Dependencies:

Run Dependencies:

bowtie2

Description:

Spliced read mapper for RNA-Seq.

tppred¶

Homepage:

https://tppred2.biocomp.unibo.it/tppred2/default/software

Spack package:

tppred/package.py

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:

https://tracer-codes.readthedocs.io

Spack package:

tracer/package.py

Versions:

develop, 2.2

Build Dependencies:

mpi, codes, otf2

Link Dependencies:

mpi, codes, otf2

Description:

Trace Replay and Network Simulation Framework

transabyss¶

Homepage:

http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss

Spack package:

transabyss/package.py

Versions:

1.5.5

Build Dependencies:

abyss, python, py-igraph, blat

Link Dependencies:

abyss, blat

Run Dependencies:

python, py-igraph

Description:

De novo assembly of RNAseq data using ABySS

transdecoder¶

Homepage:

http://transdecoder.github.io/

Spack package:

transdecoder/package.py

Versions:

5.5.0, 3.0.1

Build Dependencies:

perl

Run Dependencies:

perl, perl-uri-escape

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:

https://sestaton.github.io/Transposome/

Spack package:

transposome/package.py

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:

http://cgit.freedesktop.org/xorg/app/transset

Spack package:

transset/package.py

Versions:

1.0.1

Build Dependencies:

libx11, xproto, pkgconfig, util-macros

Link Dependencies:

Description:

transset is an utility for setting opacity property.

trapproto¶

Homepage:

https://cgit.freedesktop.org/xorg/proto/trapproto

Spack package:

trapproto/package.py

Versions:

3.4.3

Description:

X.org TrapProto protocol headers.

tree¶

Homepage:

http://mama.indstate.edu/users/ice/tree/

Spack package:

tree/package.py

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:

https:/github.com/tamuri/treesub

Spack package:

treesub/package.py

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:

https://tandem.bu.edu/trf/trf.html

Spack package:

trf/package.py

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:

http://www.cs.cmu.edu/~quake/triangle.html

Spack package:

triangle/package.py

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:

https://trilinos.org/

Spack package:

trilinos/package.py

Versions:

develop, master, 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, parallel-netcdf, parmetis, cgns, mumps, scalapack, superlu-dist, superlu, hypre, hdf5, python, py-numpy, swig

Link Dependencies:

blas, lapack, boost, matio, glm, metis, suite-sparse, zlib, mpi, netcdf, parallel-netcdf, parmetis, cgns, mumps, scalapack, superlu-dist, superlu, hypre, hdf5, python, swig

Run Dependencies:

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:

https://trilinos.org/

Spack package:

trilinos-catalyst-ioss-adapter/package.py

Versions:

develop, master

Build Dependencies:

cmake, bison, flex, paraview, py-numpy, netcdf

Link Dependencies:

paraview, netcdf

Run Dependencies:

Description:

Adapter for Trilinos Seacas Ioss and Paraview Catalyst

trimal¶

Homepage:

https://github.com/scapella/trimal

Spack package:

trimal/package.py

Versions:

1.4.1

Description:

A tool for automated alignment trimming in large-scale phylogenetic analyses

trimgalore¶

Homepage:

https://github.com/FelixKrueger/TrimGalore

Spack package:

trimgalore/package.py

Versions:

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:

http://www.usadellab.org/cms/?page=trimmomatic

Spack package:

trimmomatic/package.py

Versions:

0.38, 0.36, 0.33

Run Dependencies:

java

Description:

A flexible read trimming tool for Illumina NGS data.

trinity¶

Homepage:

http://trinityrnaseq.github.io/

Spack package:

trinity/package.py

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-dbfile, perl-uri-escape, 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:

https://trinotate.github.io/

Spack package:

trinotate/package.py

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:

http://lowelab.ucsc.edu/tRNAscan-SE/

Spack package:

trnascan-se/package.py

Versions:

2.0.0

Description:

Seaching for tRNA genes in genomic sequence

turbine¶

Homepage:

http://swift-lang.org/Swift-T

Spack package:

turbine/package.py

Versions:

develop, 1.2.3, 1.2.1, 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:

http://www.turbomole-gmbh.com/

Spack package:

turbomole/package.py

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:

http://mrzechonek.github.io/tut-framework/

Spack package:

tut/package.py

Versions:

2016-12-19

Build Dependencies:

Description:

TUT is a small and portable unit test framework for C++.

twm¶

Homepage:

http://cgit.freedesktop.org/xorg/app/twm

Spack package:

twm/package.py

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:

https://github.com/lanl/tycho2

Spack package:

tycho2/package.py

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:

https://github.com/UK-MAC/Typhon

Spack package:

typhon/package.py

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:

http://uk-mac.github.io/typhonio/

Spack package:

typhonio/package.py

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

uberftp¶

Homepage:

http://toolkit.globus.org/grid_software/data/uberftp.php

Spack package:

uberftp/package.py

Versions:

2_8, 2_7, 2_6

Build Dependencies:

globus-toolkit

Link Dependencies:

globus-toolkit

Description:

UberFTP is an interactive (text-based) client for GridFTP

ucx¶

Homepage:

http://www.openucx.org

Spack package:

ucx/package.py

Versions:

1.5.0, 1.4.0, 1.3.1, 1.3.0, 1.2.2, 1.2.1

Build Dependencies:

numactl, rdma-core

Link Dependencies:

numactl, rdma-core

Description:

a communication library implementing high-performance messaging for MPI/PGAS frameworks

udunits2¶

Homepage:

http://www.unidata.ucar.edu/software/udunits

Spack package:

udunits2/package.py

Versions:

2.2.24, 2.2.23, 2.2.21

Build Dependencies:

expat

Link Dependencies:

expat

Description:

Automated units conversion

ufo-core¶

Homepage:

https://ufo.kit.edu

Spack package:

ufo-core/package.py

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:

https://ufo.kit.edu

Spack package:

ufo-filters/package.py

Versions:

0.14.1

Build Dependencies:

cmake, ufo-core

Link Dependencies:

ufo-core

Description:

umpire¶

Homepage:

https://github.com/LLNL/Umpire

Spack package:

umpire/package.py

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:

http://grigoriefflab.janelia.org/unblur

Spack package:

unblur/package.py

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:

http://uncrustify.sourceforge.net/

Spack package:

uncrustify/package.py

Versions:

0.67, 0.61

Build Dependencies:

Description:

Source Code Beautifier for C, C++, C#, ObjectiveC, Java, and others.

unibilium¶

Homepage:

https://github.com/mauke/unibilium

Spack package:

unibilium/package.py

Versions:

1.2.0

Build Dependencies:

Description:

A terminfo parsing library

unifycr¶

Homepage:

https://github.com/LLNL/UnifyCR

Spack package:

unifycr/package.py

Versions:

develop, 0.2.0

Build Dependencies:

autoconf, automake, libtool, m4, pkgconfig, flatcc, gotcha, leveldb, margo, mpi, hdf5, numactl

Link Dependencies:

flatcc, gotcha, leveldb, margo, mpi, hdf5, numactl

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. UnifyCR is designed to support common I/O workloads, including checkpoint/restart. While primarily designed for N-N write/read, UnifyCR compliments its functionality with the support for N-1 write/read.

unison¶

Homepage:

https://www.cis.upenn.edu/~bcpierce/unison/

Spack package:

unison/package.py

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:

https://www.gnu.org/software/units/

Spack package:

units/package.py

Versions:

2.13

Build Dependencies:

Run Dependencies:

Description:

GNU units converts between different systems of units

unixodbc¶

Homepage:

http://www.unixodbc.org/

Spack package:

unixodbc/package.py

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.

unuran¶

Homepage:

http://statmath.wu.ac.at/unuran

Spack package:

unuran/package.py

Versions:

1.8.1

Build Dependencies:

gsl, rngstreams

Link Dependencies:

gsl, rngstreams

Description:

Universal Non-Uniform Random number generator.

unzip¶

Homepage:

http://www.info-zip.org/Zip.html

Spack package:

unzip/package.py

Versions:

6.0

Description:

Unzip is a compression and file packaging/archive utility.

usearch¶

Homepage:

http://www.drive5.com/usearch/

Spack package:

usearch/package.py

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

util-linux¶

Homepage:

http://freecode.com/projects/util-linux

Spack package:

util-linux/package.py

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:

http://cgit.freedesktop.org/xorg/util/macros/

Spack package:

util-macros/package.py

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:

http://www.ossp.org/pkg/lib/uuid

Spack package:

uuid/package.py

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:

https://github.com/skypjack/uvw

Spack package:

uvw/package.py

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:

http://valgrind.org/

Spack package:

valgrind/package.py

Versions:

develop, 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:

https://tu-dresden.de/zih/forschung/projekte/vampirtrace

Spack package:

vampirtrace/package.py

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:

https://github.com/AstraZeneca-NGS/VarDictJava

Spack package:

vardictjava/package.py

Versions:

1.5.1, 1.4.4

Run Dependencies:

java

Description:

VarDictJava is a variant discovery program written in Java. It is a partial Java port of VarDict variant caller.

varscan¶

Homepage:

http://dkoboldt.github.io/varscan/

Spack package:

varscan/package.py

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:

https://github.com/VcDevel/Vc

Spack package:

vc/package.py

Versions:

1.3.0, 1.2.0, 1.1.0

Build Dependencies:

Description:

SIMD Vector Classes for C++

vcftools¶

Homepage:

https://vcftools.github.io/

Spack package:

vcftools/package.py

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:

https://github.com/RichiH/vcsh

Spack package:

vcsh/package.py

Versions:

1.20151229-1, 1.20151229, 1.20150502, 1.20141026, 1.20141025

Run Dependencies:

git

Description:

config manager based on git

vdt¶

Homepage:

https://github.com/dpiparo/vdt

Spack package:

vdt/package.py

Versions:

0.4.3, 0.3.9, 0.3.8, 0.3.7, 0.3.6

Build Dependencies:

Description:

Vectorised math. A collection of fast and inline implementations of mathematical functions.

vecgeom¶

Homepage:

https://gitlab.cern.ch/VecGeom/VecGeom

Spack package:

vecgeom/package.py

Versions:

01.00.00, 00.05.00, 0.3.rc

Build Dependencies:

Description:

The vectorized geometry library for particle-detector simulation (toolkits).

veclibfort¶

Homepage:

https://github.com/mcg1969/vecLibFort

Spack package:

veclibfort/package.py

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:

https://vegas2.qimrberghofer.edu.au/

Spack package:

vegas2/package.py

Versions:

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:

https://github.com/ECP-VeloC/VELOC

Spack package:

veloc/package.py

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:

http://www.ebi.ac.uk/~zerbino/velvet/

Spack package:

velvet/package.py

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:

https://www.veripool.org/projects/verilator

Spack package:

verilator/package.py

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:

https://github.com/edf-hpc/verrou

Spack package:

verrou/package.py

Versions:

develop, 2.1.0, 2.0.0, 1.1.0

Build Dependencies:

autoconf, automake, libtool, m4, python

Link Dependencies:

Run Dependencies:

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.

videoproto¶

Homepage:

http://cgit.freedesktop.org/xorg/proto/videoproto

Spack package:

videoproto/package.py

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:

https://www.tbi.univie.ac.at/RNA/

Spack package:

viennarna/package.py

Versions:

2.4.3, 2.3.5

Build Dependencies:

perl, python, libsvm, gsl

Link Dependencies:

libsvm, gsl

Run Dependencies:

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:

http://cgit.freedesktop.org/xorg/app/viewres

Spack package:

viewres/package.py

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:

https://ukoethe.github.io/vigra/

Spack package:

vigra/package.py

Versions:

1.11.1

Build Dependencies:

cmake, libtiff, libpng, libjpeg, hdf5, fftw, openexr, py-numpy, boost, py-sphinx, doxygen, python, py-nose

Link Dependencies:

libtiff, libpng, libjpeg, hdf5, fftw, openexr, boost, python

Run Dependencies:

Test Dependencies:

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:

http://www.vim.org

Spack package:

vim/package.py

Versions:

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

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:

http://www.virtualgl.org/Main/HomePage

Spack package:

virtualgl/package.py

Versions:

2.5.2

Build Dependencies:

cmake, libjpeg-turbo, glu

Link Dependencies:

libjpeg-turbo, 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:

https://wci.llnl.gov/simulation/computer-codes/visit/

Spack package:

visit/package.py

Versions:

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

Link Dependencies:

vtk, qt, qwt, python, silo, hdf5, mpi

Description:

VisIt is an Open Source, interactive, scalable, visualization, animation and analysis tool.

vizglow¶

Homepage:

http://esgeetech.com/products/vizglow-plasma-modeling/

Spack package:

vizglow/package.py

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:

http://www.vmatch.de/

Spack package:

vmatch/package.py

Versions:

2.3.0

Description:

Vmatch is a versatile software tool for efficiently solving large scale sequence matching tasks

voropp¶

Homepage:

http://math.lbl.gov/voro++/about.html

Spack package:

voropp/package.py

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:

http://www.votca.org

Spack package:

votca-csg/package.py

Versions:

develop, 1.5, 1.4.1, 1.4

Build Dependencies:

cmake, votca-tools, gromacs, hdf5

Link Dependencies:

votca-tools, 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-ctp¶

Homepage:

http://www.votca.org

Spack package:

votca-ctp/package.py

Versions:

develop, 1.5

Build Dependencies:

cmake, votca-tools, votca-csg, gsl

Link Dependencies:

votca-tools, votca-csg, gsl

Description:

votca-tools¶

Homepage:

http://www.votca.org

Spack package:

votca-tools/package.py

Versions:

develop, 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:

votca-xtp¶

Homepage:

http://www.votca.org

Spack package:

votca-xtp/package.py

Versions:

develop, 1.5, 1.4.1

Build Dependencies:

cmake, votca-tools, votca-csg, votca-ctp, libxc, ceres-solver

Link Dependencies:

votca-tools, votca-csg, votca-ctp, libxc, ceres-solver

Description:

vpfft¶

Homepage:

http://www.exmatex.org/vpfft.html

Spack package:

vpfft/package.py

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:

https://github.com/lanl/vpic

Spack package:

vpic/package.py

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:

https://github.com/torognes/vsearch

Spack package:

vsearch/package.py

Versions:

2.4.3

Build Dependencies:

Description:

VSEARCH is a versatile open-source tool for metagenomics.

vt¶

Homepage:

http://genome.sph.umich.edu/wiki/vt

Spack package:

vt/package.py

Versions:

0.577

Build Dependencies:

zlib

Link Dependencies:

zlib

Description:

A tool set for short variant discovery in genetic sequence data.

vtk¶

Homepage:

http://www.vtk.org

Spack package:

vtk/package.py

Versions:

8.1.2, 8.1.1, 8.0.1, 7.1.0, 7.0.0, 6.3.0, 6.1.0

Build Dependencies:

cmake, python, gl, glx, mesa, qt, mpi, boost, ffmpeg, expat, freetype, glew, hdf5, libjpeg, jsoncpp, libxml2, lz4, netcdf, netcdf-cxx, libpng, libtiff, zlib

Link Dependencies:

python, gl, glx, mesa, qt, mpi, boost, ffmpeg, expat, freetype, glew, hdf5, libjpeg, jsoncpp, libxml2, lz4, netcdf, netcdf-cxx, libpng, libtiff, zlib

Run Dependencies:

py-mpi4py

Description:

The Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computer graphics, image processing and visualization.

vtkh¶

Homepage:

https://github.com/Alpine-DAV/vtk-h

Spack package:

vtkh/package.py

Versions:

develop, 0.1.0

Build Dependencies:

cmake, mpi, intel-tbb, cuda, vtkm

Link Dependencies:

mpi, intel-tbb, cuda, vtkm

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.

vtkm¶

Homepage:

https://m.vtk.org/

Spack package:

vtkm/package.py

Versions:

master, 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:

http://wannier.org

Spack package:

wannier90/package.py

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:

https://ecp-warpx.github.io/index.html

Spack package:

warpx/package.py

Versions:

master, dev

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.

wcslib¶

Homepage:

http://www.atnf.csiro.au/people/mcalabre/WCS/wcslib/

Spack package:

wcslib/package.py

Versions:

5.18

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:

http://www.gnu.org/software/wget/

Spack package:

wget/package.py

Versions:

1.20.3, 1.19.1, 1.17, 1.16

Build Dependencies:

gnutls, openssl, gettext, python, zlib, libpsl, pcre, perl, pkgconfig

Link Dependencies:

gnutls, openssl, zlib, libpsl, pcre

Test Dependencies:

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:

https://github.com/lh3/wgsim

Spack package:

wgsim/package.py

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.

windowswmproto¶

Homepage:

http://cgit.freedesktop.org/xorg/proto/windowswmproto

Spack package:

windowswmproto/package.py

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:

https://www.wireshark.org

Spack package:

wireshark/package.py

Versions:

2.6.0

Build Dependencies:

cmake, bison, cares, doxygen, flex, git, glib, gnutls, libgcrypt, libmaxminddb, libtool, libpcap, lua, krb5, pkgconfig, libsmi, libssh, nghttp2, portaudio, qt, gtkplus3, gtkplus, adwaita-icon-theme

Link Dependencies:

cares, glib, gnutls, libgcrypt, libmaxminddb, libpcap, lua, krb5, libsmi, libssh, nghttp2, portaudio, qt, gtkplus3, gtkplus, adwaita-icon-theme

Description:

Graphical network analyzer and capture tool

wordnet¶

Homepage:

https://wordnet.princeton.edu/

Spack package:

wordnet/package.py

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:

http://www.workrave.org/

Spack package:

workrave/package.py

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:

http://www.webtoolkit.eu/wt

Spack package:

wt/package.py

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:

https://github.com/ruanjue/wtdbg2

Spack package:

wtdbg2/package.py

Versions:

2.3

Build Dependencies:

zlib

Link Dependencies:

zlib

Description:

A fuzzy Bruijn graph approach to long noisy reads assembly

wx¶

Homepage:

http://www.wxwidgets.org/

Spack package:

wx/package.py

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.

wxpropgrid¶

Homepage:

http://wxpropgrid.sourceforge.net/

Spack package:

wxpropgrid/package.py

Versions:

1.4.15

Build Dependencies:

Link Dependencies:

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.

x11perf¶

Homepage:

http://cgit.freedesktop.org/xorg/app/x11perf

Spack package:

x11perf/package.py

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:

https://xapian.org

Spack package:

xapian-core/package.py

Versions:

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:

http://cgit.freedesktop.org/xorg/app/xauth

Spack package:

xauth/package.py

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:

http://cgit.freedesktop.org/xorg/app/xbacklight

Spack package:

xbacklight/package.py

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:

http://cgit.freedesktop.org/xorg/app/xbiff

Spack package:

xbiff/package.py

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:

https://cgit.freedesktop.org/xorg/data/bitmaps/

Spack package:

xbitmaps/package.py

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:

https://computation.llnl.gov/projects/parallel-time-integration-multigrid/software

Spack package:

xbraid/package.py

Versions:

2.2.0

Build Dependencies:

mpi

Link Dependencies:

mpi

Description:

XBraid: Parallel time integration with Multigrid

xcalc¶

Homepage:

http://cgit.freedesktop.org/xorg/app/xcalc

Spack package:

xcalc/package.py

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:

https://xcb.freedesktop.org/

Spack package:

xcb-demo/package.py

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:

http://xcb.freedesktop.org/

Spack package:

xcb-proto/package.py

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:

https://xcb.freedesktop.org/

Spack package:

xcb-util/package.py

Versions:

0.4.0

Build Dependencies:

libxcb, pkgconfig

Link Dependencies:

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:

https://xcb.freedesktop.org/

Spack package:

xcb-util-cursor/package.py

Versions:

0.1.3

Build Dependencies:

libxcb, xcb-util-renderutil, xcb-util-image, pkgconfig

Link Dependencies:

libxcb, xcb-util-renderutil, xcb-util-image

Description:

xcb-util-errors¶

Homepage:

https://xcb.freedesktop.org/

Spack package:

xcb-util-errors/package.py

Versions:

1.0

Build Dependencies:

libxcb, xcb-proto, pkgconfig

Link Dependencies:

Description:

xcb-util-image¶

Homepage:

https://xcb.freedesktop.org/

Spack package:

xcb-util-image/package.py

Versions:

0.4.0

Build Dependencies:

libxcb, xcb-util, xproto, pkgconfig

Link Dependencies:

libxcb, xcb-util

Description:

xcb-util-keysyms¶

Homepage:

https://xcb.freedesktop.org/

Spack package:

xcb-util-keysyms/package.py

Versions:

0.4.0

Build Dependencies:

libxcb, xproto, pkgconfig

Link Dependencies:

Description:

xcb-util-renderutil¶

Homepage:

https://xcb.freedesktop.org/

Spack package:

xcb-util-renderutil/package.py

Versions:

0.3.9

Build Dependencies:

libxcb, pkgconfig

Link Dependencies:

Description:

xcb-util-wm¶

Homepage:

https://xcb.freedesktop.org/

Spack package:

xcb-util-wm/package.py

Versions:

0.4.1

Build Dependencies:

m4, libxcb, pkgconfig

Link Dependencies:

Description:

xcb-util-xrm¶

Homepage:

https://github.com/Airblader/xcb-util-xrm

Spack package:

xcb-util-xrm/package.py

Versions:

1.2

Build Dependencies:

autoconf, automake, libtool, m4, pkgconfig, libxcb

Link Dependencies:

Description:

XCB util-xrm module provides the 'xrm' library, i.e. utility functions for the X resource manager.

xclip¶

Homepage:

https://github.com/astrand/xclip

Spack package:

xclip/package.py

Versions:

0.13

Build Dependencies:

libxmu, libx11, autoconf, automake, libtool, m4

Link Dependencies:

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:

http://cgit.freedesktop.org/xorg/app/xclipboard

Spack package:

xclipboard/package.py

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:

http://cgit.freedesktop.org/xorg/app/xclock

Spack package:

xclock/package.py

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:

http://cgit.freedesktop.org/xorg/proto/xcmiscproto

Spack package:

xcmiscproto/package.py

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:

http://cgit.freedesktop.org/xorg/app/xcmsdb

Spack package:

xcmsdb/package.py

Versions:

1.0.5

Build Dependencies:

libx11, pkgconfig, util-macros

Link Dependencies:

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:

http://cgit.freedesktop.org/xorg/app/xcompmgr

Spack package:

xcompmgr/package.py

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:

http://cgit.freedesktop.org/xorg/app/xconsole

Spack package:

xconsole/package.py

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:

http://cgit.freedesktop.org/xorg/data/cursors

Spack package:

xcursor-themes/package.py

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:

http://cgit.freedesktop.org/xorg/app/xcursorgen

Spack package:

xcursorgen/package.py

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:

http://cgit.freedesktop.org/xorg/app/xdbedizzy

Spack package:

xdbedizzy/package.py

Versions:

1.1.0

Build Dependencies:

libx11, libxext, pkgconfig, util-macros

Link Dependencies:

Description:

xdbedizzy is a demo of the X11 Double Buffer Extension (DBE) creating a double buffered spinning scene.

xditview¶

Homepage:

http://cgit.freedesktop.org/xorg/app/xditview

Spack package:

xditview/package.py

Versions:

1.0.4

Build Dependencies:

libxaw, libxmu, libxt, libx11, pkgconfig, util-macros

Link Dependencies:

Description:

xditview displays ditroff output on an X display.

xdm¶

Homepage:

http://cgit.freedesktop.org/xorg/app/xdm

Spack package:

xdm/package.py

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.

xdpyinfo¶

Homepage:

http://cgit.freedesktop.org/xorg/app/xdpyinfo

Spack package:

xdpyinfo/package.py

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:

http://cgit.freedesktop.org/xorg/app/xdriinfo

Spack package:

xdriinfo/package.py

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:

https://cgit.freedesktop.org/xorg/app/xedit

Spack package:

xedit/package.py

Versions:

1.2.2

Build Dependencies:

libxaw, libxmu, libxt, libx11, pkgconfig, util-macros

Link Dependencies:

Description:

Xedit is a simple text editor for X.

xerces-c¶

Homepage:

https://xerces.apache.org/xerces-c

Spack package:

xerces-c/package.py

Versions:

3.2.2, 3.2.1, 3.1.4

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:

https://xeus.readthedocs.io/en/latest/

Spack package:

xeus/package.py

Versions:

develop, 0.15.0, 0.14.1

Build Dependencies:

cmake, zeromq, cppzmq, cryptopp, xtl, nlohmann-json, libuuid

Link Dependencies:

zeromq, cppzmq, cryptopp, xtl, nlohmann-json, libuuid

Description:

QuantStack C++ implementation of Jupyter kernel protocol

xev¶

Homepage:

http://cgit.freedesktop.org/xorg/app/xev

Spack package:

xev/package.py

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:

http://cgit.freedesktop.org/xorg/proto/xextproto

Spack package:

xextproto/package.py

Versions:

7.3.0

Build Dependencies:

pkgconfig, util-macros

Description:

X Protocol Extensions.

xeyes¶

Homepage:

http://cgit.freedesktop.org/xorg/app/xeyes

Spack package:

xeyes/package.py

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:

https://cgit.freedesktop.org/xorg/proto/xf86bigfontproto

Spack package:

xf86bigfontproto/package.py

Versions:

1.2.0

Description:

X.org XF86BigFontProto protocol headers.

xf86dga¶

Homepage:

http://cgit.freedesktop.org/xorg/app/xf86dga

Spack package:

xf86dga/package.py

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:

https://cgit.freedesktop.org/xorg/proto/xf86dgaproto

Spack package:

xf86dgaproto/package.py

Versions:

2.1

Description:

X.org XF86DGAProto protocol headers.

xf86driproto¶

Homepage:

http://cgit.freedesktop.org/xorg/proto/xf86driproto

Spack package:

xf86driproto/package.py

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:

http://cgit.freedesktop.org/xorg/proto/xf86miscproto

Spack package:

xf86miscproto/package.py

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:

https://cgit.freedesktop.org/xorg/proto/xf86rushproto

Spack package:

xf86rushproto/package.py

Versions:

1.1.2

Description:

X.org XF86RushProto protocol headers.

xf86vidmodeproto¶

Homepage:

http://cgit.freedesktop.org/xorg/proto/xf86vidmodeproto

Spack package:

xf86vidmodeproto/package.py

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:

http://cgit.freedesktop.org/xorg/app/xfd

Spack package:

xfd/package.py

Versions:

1.1.2

Build Dependencies:

libxaw, fontconfig, libxft, libxrender, libxmu, libxt, xproto, pkgconfig, util-macros

Link Dependencies:

libxaw, fontconfig, libxft, libxrender, libxmu, libxt

Description:

xfd - display all the characters in a font using either the X11 core protocol or libXft2.

xfindproxy¶

Homepage:

http://cgit.freedesktop.org/xorg/app/xfindproxy

Spack package:

xfindproxy/package.py

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:

http://cgit.freedesktop.org/xorg/app/xfontsel

Spack package:

xfontsel/package.py

Versions:

1.0.5

Build Dependencies:

libxaw, libxmu, libxt, libx11, pkgconfig, util-macros

Link Dependencies:

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:

http://cgit.freedesktop.org/xorg/app/xfs

Spack package:

xfs/package.py

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:

http://cgit.freedesktop.org/xorg/app/xfsinfo

Spack package:

xfsinfo/package.py

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:

http://cgit.freedesktop.org/xorg/app/xfwp

Spack package:

xfwp/package.py

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:

http://cgit.freedesktop.org/xorg/app/xgamma

Spack package:

xgamma/package.py

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:

https://xgboost.ai/

Spack package:

xgboost/package.py

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:

http://cgit.freedesktop.org/xorg/app/xgc

Spack package:

xgc/package.py

Versions:

1.0.5

Build Dependencies:

libxaw, libxt, flex, bison, pkgconfig, util-macros

Link Dependencies:

Description:

xgc is an X11 graphics demo that shows various features of the X11 core protocol graphics primitives.

xhmm¶

Homepage:

http://atgu.mgh.harvard.edu/xhmm/index.shtml

Spack package:

xhmm/package.py

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:

http://cgit.freedesktop.org/xorg/app/xhost

Spack package:

xhost/package.py

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:

http://cgit.freedesktop.org/xorg/proto/xineramaproto

Spack package:

xineramaproto/package.py

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:

http://cgit.freedesktop.org/xorg/app/xinit

Spack package:

xinit/package.py

Versions:

1.3.4

Build Dependencies:

libx11, xproto, pkgconfig, util-macros

Link Dependencies:

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:

http://cgit.freedesktop.org/xorg/app/xinput

Spack package:

xinput/package.py

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:

https://forge.ipsl.jussieu.fr/ioserver/wiki

Spack package:

xios/package.py

Versions:

develop, 1.0

Build Dependencies:

netcdf, netcdf-fortran, hdf5, mpi, boost, blitz, perl, perl-uri-escape, gmake

Link Dependencies:

netcdf, netcdf-fortran, hdf5, mpi, boost, blitz

Description:

XML-IO-SERVER library for IO management of climate models.

xkbcomp¶

Homepage:

https://www.x.org/wiki/XKB/

Spack package:

xkbcomp/package.py

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:

https://www.x.org/wiki/XKB/

Spack package:

xkbdata/package.py

Versions:

1.0.1

Build Dependencies:

xkbcomp

Description:

The XKB data files for the various keyboard models, layouts, and locales.

xkbevd¶

Homepage:

http://cgit.freedesktop.org/xorg/app/xkbevd

Spack package:

xkbevd/package.py

Versions:

1.1.4

Build Dependencies:

libxkbfile, libx11, bison, pkgconfig, util-macros

Link Dependencies:

libxkbfile, libx11

Description:

XKB event daemon demo.

xkbprint¶

Homepage:

http://cgit.freedesktop.org/xorg/app/xkbprint

Spack package:

xkbprint/package.py

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:

http://cgit.freedesktop.org/xorg/app/xkbutils

Spack package:

xkbutils/package.py

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:

https://www.freedesktop.org/wiki/Software/XKeyboardConfig/

Spack package:

xkeyboard-config/package.py

Versions:

2.18

Build Dependencies:

libx11, libxslt, pkgconfig, intltool, xproto

Link Dependencies:

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:

http://cgit.freedesktop.org/xorg/app/xkill

Spack package:

xkill/package.py

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:

http://cgit.freedesktop.org/xorg/app/xload

Spack package:

xload/package.py

Versions:

1.1.2

Build Dependencies:

libxaw, libxmu, libxt, libx11, xproto, pkgconfig, util-macros

Link Dependencies:

Description:

xload displays a periodically updating histogram of the system load average.

xlogo¶

Homepage:

http://cgit.freedesktop.org/xorg/app/xlogo

Spack package:

xlogo/package.py

Versions:

1.0.4

Build Dependencies:

libsm, libxaw, libxmu, libxt, libxext, libx11, libxft, libxrender, pkgconfig, util-macros

Link Dependencies:

libsm, libxaw, libxmu, libxt, libxext, libx11, libxft, libxrender

Description:

The xlogo program simply displays the X Window System logo.

xlsatoms¶

Homepage:

http://cgit.freedesktop.org/xorg/app/xlsatoms

Spack package:

xlsatoms/package.py

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:

http://cgit.freedesktop.org/xorg/app/xlsclients

Spack package:

xlsclients/package.py

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:

http://cgit.freedesktop.org/xorg/app/xlsfonts

Spack package:

xlsfonts/package.py

Versions:

1.0.5

Build Dependencies:

libx11, xproto, pkgconfig, util-macros

Link Dependencies:

Description:

xlsfonts lists fonts available from an X server via the X11 core protocol.

xmag¶

Homepage:

http://cgit.freedesktop.org/xorg/app/xmag

Spack package:

xmag/package.py

Versions:

1.0.6

Build Dependencies:

libxaw, libxmu, libxt, libx11, pkgconfig, util-macros

Link Dependencies:

Description:

xmag displays a magnified snapshot of a portion of an X11 screen.

xman¶

Homepage:

http://cgit.freedesktop.org/xorg/app/xman

Spack package:

xman/package.py

Versions:

1.1.4

Build Dependencies:

libxaw, libxt, xproto, pkgconfig, util-macros

Link Dependencies:

Description:

xman is a graphical manual page browser using the Athena Widgets (Xaw) toolkit.

xmessage¶

Homepage:

http://cgit.freedesktop.org/xorg/app/xmessage

Spack package:

xmessage/package.py

Versions:

1.0.4

Build Dependencies:

libxaw, libxt, pkgconfig, util-macros

Link Dependencies:

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:

http://cgit.freedesktop.org/xorg/app/xmh

Spack package:

xmh/package.py

Versions:

1.0.3

Build Dependencies:

libxaw, libxmu, libxt, libx11, xbitmaps, pkgconfig, util-macros

Link Dependencies:

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:

https://launchpad.net/xmlf90

Spack package:

xmlf90/package.py

Versions:

1.5.2

Build Dependencies:

Description:

xmlf90 is a suite of libraries to handle XML in Fortran.

xmlto¶

Homepage:

https://pagure.io/xmlto

Spack package:

xmlto/package.py

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:

http://cgit.freedesktop.org/xorg/app/xmodmap

Spack package:

xmodmap/package.py

Versions:

1.0.9

Build Dependencies:

libx11, xproto, pkgconfig, util-macros

Link Dependencies:

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:

http://cgit.freedesktop.org/xorg/app/xmore

Spack package:

xmore/package.py

Versions:

1.0.2

Build Dependencies:

libxaw, libxt, pkgconfig, util-macros

Link Dependencies:

Description:

xmore - plain text display program for the X Window System.

xorg-cf-files¶

Homepage:

http://cgit.freedesktop.org/xorg/util/cf

Spack package:

xorg-cf-files/package.py

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:

http://cgit.freedesktop.org/xorg/doc/xorg-docs

Spack package:

xorg-docs/package.py

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:

https://people.freedesktop.org/~cndougla/xorg-gtest/

Spack package:

xorg-gtest/package.py

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-server¶

Homepage:

http://cgit.freedesktop.org/xorg/xserver

Spack package:

xorg-server/package.py

Versions:

1.18.99.901

Build Dependencies:

pixman, font-util, libxshmfence, libdrm, libx11, dri2proto, dri3proto, glproto, flex, bison, pkgconfig, util-macros, fixesproto, damageproto, xcmiscproto, xtrans, bigreqsproto, xproto, randrproto, renderproto, xextproto, inputproto, kbproto, fontsproto, videoproto, compositeproto, recordproto, scrnsaverproto, resourceproto, xf86driproto, presentproto, xineramaproto, libxkbfile, libxfont2, libxext, libxdamage, libxfixes, libepoxy

Link Dependencies:

pixman, font-util, libxshmfence, libdrm, libx11, glproto, fixesproto, damageproto, xcmiscproto, xtrans, bigreqsproto, xproto, randrproto, renderproto, xextproto, inputproto, kbproto, fontsproto, videoproto, compositeproto, recordproto, scrnsaverproto, resourceproto, xf86driproto, presentproto, xineramaproto, libxkbfile, libxfont2, libxext, libxdamage, libxfixes, libepoxy

Description:

X.Org Server is the free and open source implementation of the display server for the X Window System stewarded by the X.Org Foundation.

xorg-sgml-doctools¶

Homepage:

http://cgit.freedesktop.org/xorg/doc/xorg-sgml-doctools

Spack package:

xorg-sgml-doctools/package.py

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:

http://cgit.freedesktop.org/xorg/app/xphelloworld

Spack package:

xphelloworld/package.py

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:

https://nmr.cit.nih.gov/xplor-nih/

Spack package:

xplor-nih/package.py

Versions:

2.45

Build Dependencies:

Run Dependencies:

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:

http://cgit.freedesktop.org/xorg/app/xplsprinters

Spack package:

xplsprinters/package.py

Versions:

1.0.1

Build Dependencies:

libxp, libxprintutil, libx11, pkgconfig, util-macros

Link Dependencies:

libxp, libxprintutil, libx11

Description:

List Xprint printers.

xpr¶

Homepage:

http://cgit.freedesktop.org/xorg/app/xpr

Spack package:

xpr/package.py

Versions:

1.0.4

Build Dependencies:

libxmu, libx11, xproto, pkgconfig, util-macros

Link Dependencies:

Description:

xpr takes as input a window dump file produced by xwd and formats it for output on various types of printers.

xprehashprinterlist¶

Homepage:

http://cgit.freedesktop.org/xorg/app/xprehashprinterlist

Spack package:

xprehashprinterlist/package.py

Versions:

1.0.1

Build Dependencies:

libxp, libx11, pkgconfig, util-macros

Link Dependencies:

libxp, libx11

Description:

Rehash list of Xprint printers.

xprop¶

Homepage:

http://cgit.freedesktop.org/xorg/app/xprop

Spack package:

xprop/package.py

Versions:

1.2.2

Build Dependencies:

libx11, xproto, pkgconfig, util-macros

Link Dependencies:

Description:

xprop is a command line tool to display and/or set window and font properties of an X server.

xproto¶

Homepage:

http://cgit.freedesktop.org/xorg/proto/x11proto

Spack package:

xproto/package.py

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:

http://cgit.freedesktop.org/xorg/proto/pmproto

Spack package:

xproxymanagementprotocol/package.py

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:

http://xqilla.sourceforge.net/HomePage

Spack package:

xqilla/package.py

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:

http://cgit.freedesktop.org/xorg/app/xrandr

Spack package:

xrandr/package.py

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:

http://cgit.freedesktop.org/xorg/app/xrdb

Spack package:

xrdb/package.py

Versions:

1.1.0

Build Dependencies:

libxmu, libx11, xproto, pkgconfig, util-macros

Link Dependencies:

Description:

xrdb - X server resource database utility.

xrefresh¶

Homepage:

http://cgit.freedesktop.org/xorg/app/xrefresh

Spack package:

xrefresh/package.py

Versions:

1.0.5

Build Dependencies:

libx11, xproto, pkgconfig, util-macros

Link Dependencies:

Description:

xrefresh - refresh all or part of an X screen.

xrootd¶

Homepage:

http://xrootd.org

Spack package:

xrootd/package.py

Versions:

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:

http://cgit.freedesktop.org/xorg/app/xrx

Spack package:

xrx/package.py

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:

https://github.com/ANL-CESAR/XSBench/

Spack package:

xsbench/package.py

Versions:

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:

http://cgit.freedesktop.org/xorg/app/xscope

Spack package:

xscope/package.py

Versions:

1.4.1

Build Dependencies:

xproto, xtrans, pkgconfig, util-macros

Description:

XSCOPE -- a program to monitor X11/Client conversations.

xsd¶

Homepage:

https://www.codesynthesis.com

Spack package:

xsd/package.py

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:

http://xsdk.info

Spack package:

xsdk/package.py

Versions:

develop, 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

Link Dependencies:

hypre, mfem, superlu-dist, trilinos, petsc, dealii, pflotran, alquimia, sundials, plasma, magma, amrex, slepc, omega-h, strumpack, pumi, tasmanian, phist

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:

https://trilinos.org/

Spack package:

xsdktrilinos/package.py

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:

http://cgit.freedesktop.org/xorg/app/xset

Spack package:

xset/package.py

Versions:

1.2.3

Build Dependencies:

libxmu, libx11, xproto, pkgconfig, util-macros

Link Dependencies:

Description:

User preference utility for X.

xsetmode¶

Homepage:

http://cgit.freedesktop.org/xorg/app/xsetmode

Spack package:

xsetmode/package.py

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:

http://cgit.freedesktop.org/xorg/app/xsetpointer

Spack package:

xsetpointer/package.py

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:

http://cgit.freedesktop.org/xorg/app/xsetroot

Spack package:

xsetroot/package.py

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:

http://quantstack.net/xsimd

Spack package:

xsimd/package.py

Versions:

develop, 4.0.0, 3.1.0

Build Dependencies:

Test Dependencies:

googletest

Description:

C++ wrappers for SIMD intrinsics

xsm¶

Homepage:

http://cgit.freedesktop.org/xorg/app/xsm

Spack package:

xsm/package.py

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.

xstdcmap¶

Homepage:

http://cgit.freedesktop.org/xorg/app/xstdcmap

Spack package:

xstdcmap/package.py

Versions:

1.0.3

Build Dependencies:

libxmu, libx11, xproto, pkgconfig, util-macros

Link Dependencies:

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:

http://quantstack.net/xtensor

Spack package:

xtensor/package.py

Versions:

develop, 0.15.1, 0.13.1

Build Dependencies:

cmake, xtl, xsimd

Link Dependencies:

xtl, xsimd

Description:

Multi-dimensional arrays with broadcasting and lazy computing

xtensor-python¶

Homepage:

https://xtensor-python.readthedocs.io

Spack package:

xtensor-python/package.py

Versions:

develop, 0.17.0

Build Dependencies:

cmake, xtensor, xtl, py-pybind11, py-numpy, python

Link Dependencies:

xtensor, xtl, py-pybind11, py-numpy, python

Run Dependencies:

Description:

Python bindings for the xtensor C++ multi-dimensional array library

xterm¶

Homepage:

http://invisible-island.net/xterm/

Spack package:

xterm/package.py

Versions:

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:

https://github.com/QuantStack/xtl

Spack package:

xtl/package.py

Versions:

develop, 0.4.0, 0.3.4, 0.3.3

Build Dependencies:

Description:

QuantStack tools library

xtrans¶

Homepage:

http://cgit.freedesktop.org/xorg/lib/libxtrans

Spack package:

xtrans/package.py

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:

http://cgit.freedesktop.org/xorg/app/xtrap

Spack package:

xtrap/package.py

Versions:

1.0.2

Build Dependencies:

libx11, libxtrap, pkgconfig, util-macros

Link Dependencies:

libx11, libxtrap

Description:

XTrap sample clients.

xts¶

Homepage:

https://www.x.org/wiki/XorgTesting/

Spack package:

xts/package.py

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:

http://cgit.freedesktop.org/xorg/app/xvidtune

Spack package:

xvidtune/package.py

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:

http://cgit.freedesktop.org/xorg/app/xvinfo

Spack package:

xvinfo/package.py

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:

http://cgit.freedesktop.org/xorg/app/xwd

Spack package:

xwd/package.py

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:

http://cgit.freedesktop.org/xorg/app/xwininfo

Spack package:

xwininfo/package.py

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:

http://cgit.freedesktop.org/xorg/app/xwud

Spack package:

xwud/package.py

Versions:

1.0.4

Build Dependencies:

libx11, xproto, pkgconfig, util-macros

Link Dependencies:

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:

https://github.com/Cyan4973/xxHash

Spack package:

xxhash/package.py

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:

http://tukaani.org/xz/

Spack package:

xz/package.py

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:

http://lloyd.github.io/yajl/

Spack package:

yajl/package.py

Versions:

develop, 2.1.0

Build Dependencies:

Description:

Yet Another JSON Library (YAJL)

yambo¶

Homepage:

http://www.yambo-code.org/index.php

Spack package:

yambo/package.py

Versions:

4.2.2, 4.2.1, 4.2.0

Build Dependencies:

blas, lapack, mpi, netcdf, hdf5, fftw, scalapack, netcdf-fortran, libxc

Link Dependencies:

blas, lapack, mpi, netcdf, 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:

https://github.com/jbeder/yaml-cpp

Spack package:

yaml-cpp/package.py

Versions:

develop, 0.6.2, 0.5.3

Build Dependencies:

Link Dependencies:

Description:

A YAML parser and emitter in C++

yara¶

Homepage:

http://virustotal.github.io/yara/

Spack package:

yara/package.py

Versions:

3.9.0

Build Dependencies:

Description:

YARA is a tool aimed at (but not limited to) helping malware researchers to identify and classify malware samples

yasm¶

Homepage:

http://yasm.tortall.net

Spack package:

yasm/package.py

Versions:

develop, 1.3.0

Build Dependencies:

Link Dependencies:

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:

http://dhmunro.github.io/yorick-doc/

Spack package:

yorick/package.py

Versions:

master, 2.2.04, f90-plugin

Build Dependencies:

Link Dependencies:

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:

https://github.com/Z3Prover/z3/wiki

Spack package:

z3/package.py

Versions:

4.5.0, 4.4.1, 4.4.0

Build Dependencies:

Link Dependencies:

Description:

Z3 is a theorem prover from Microsoft Research. It is licensed under the MIT license.

zeromq¶

Homepage:

http://zguide.zeromq.org/

Spack package:

zeromq/package.py

Versions:

develop, 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

zfp¶

Homepage:

http://computation.llnl.gov/projects/floating-point-compression

Spack package:

zfp/package.py

Versions:

0.5.4, 0.5.2, 0.5.1, 0.5.0

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:

http://www.info-zip.org/Zip.html

Spack package:

zip/package.py

Versions:

3.0

Build Dependencies:

Link Dependencies: