From fde660ff179bbbab7bef740aa586e2461a95ca75 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 29 Oct 2023 16:05:11 +0100 Subject: [PATCH] auto-update docs for EasyBuild v4.8.2 --- docs/version-specific/easyconfig-templates.md | 7 + docs/version-specific/eb-help.md | 40 +- docs/version-specific/generic-easyblocks.md | 28 +- docs/version-specific/supported-software.md | 1277 +++++++++++++---- 4 files changed, 1014 insertions(+), 338 deletions(-) diff --git a/docs/version-specific/easyconfig-templates.md b/docs/version-specific/easyconfig-templates.md index 49f2a5f10..9c57296e7 100644 --- a/docs/version-specific/easyconfig-templates.md +++ b/docs/version-specific/easyconfig-templates.md @@ -16,16 +16,22 @@ Template name |Template value Template name |Template value --------------------|------------------------------------------------ +``%(cudamajver)s`` |major version for CUDA ``%(cudashortver)s``|short version for CUDA (``.``) ``%(cudaver)s`` |full version for CUDA +``%(cudamajver)s`` |major version for CUDAcore ``%(cudashortver)s``|short version for CUDAcore (``.``) ``%(cudaver)s`` |full version for CUDAcore +``%(javamajver)s`` |major version for Java ``%(javashortver)s``|short version for Java (``.``) ``%(javaver)s`` |full version for Java +``%(perlmajver)s`` |major version for Perl ``%(perlshortver)s``|short version for Perl (``.``) ``%(perlver)s`` |full version for Perl +``%(pymajver)s`` |major version for Python ``%(pyshortver)s`` |short version for Python (``.``) ``%(pyver)s`` |full version for Python +``%(rmajver)s`` |major version for R ``%(rshortver)s`` |short version for R (``.``) ``%(rver)s`` |full version for R @@ -59,6 +65,7 @@ Template name |Template value Template name |Template value ---------------------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ``%(arch)s`` |System architecture (e.g. x86_64, aarch64, ppc64le, ...) +``%(sysroot)s`` |Location root directory of system, prefix for standard paths like /usr/lib and /usr/includeas specify by the --sysroot configuration option ``%(mpi_cmd_prefix)s`` |Prefix command for running MPI programs (with default number of ranks) ``%(cuda_compute_capabilities)s``|Comma-separated list of CUDA compute capabilities, as specified via --cuda-compute-capabilities configuration option or via cuda_compute_capabilities easyconfig parameter ``%(cuda_cc_cmake)s`` |List of CUDA compute capabilities suitable for use with $CUDAARCHS in CMake 3.18+ diff --git a/docs/version-specific/eb-help.md b/docs/version-specific/eb-help.md index 12dc5bf82..5a2485bcf 100644 --- a/docs/version-specific/eb-help.md +++ b/docs/version-specific/eb-help.md @@ -37,26 +37,26 @@ Option flag |Option description ## Basic options -Option flag |Option description ----------------------------------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -``--dry-run`` |Print build overview incl. dependencies (full paths) (default: False) -``-D, --dry-run-short`` |Print build overview incl. dependencies (short paths) (default: False) -``-x, --extended-dry-run`` |Print build environment and (expected) build procedure that will be performed (default: False) -``--extended-dry-run-ignore-errors`` |Ignore errors that occur during dry run (default: True; disable with --disable-extended-dry-run-ignore-errors) -``-f, --force`` |Force to rebuild software even if it's already installed (i.e. if it can be found as module), and skipping check for OS dependencies (default: False) -``--ignore-locks`` |Ignore locks that prevent two identical installations running in parallel (default: False) -``--job`` |Submit the build as a job (default: False) -``--locks-dir=LOCKS-DIR`` |Directory to store lock files (should be on a shared filesystem); None implies .locks subdirectory of software installation directory -``-l, --logtostdout`` |Redirect main log to stdout (default: False) -``-M, --missing-modules`` |Print list of missing modules for dependencies of specified easyconfigs (default: False) -``-b BLOCKS, --only-blocks=BLOCKS`` |Only build listed blocks (type comma-separated list) -``--rebuild`` |Rebuild software, even if module already exists (don't skip OS dependencies checks) (default: False) -``-r PATH[:PATH], --robot=PATH[:PATH]``|Enable dependency resolution, using easyconfigs in specified paths (type pathsep-separated list) -``--robot-paths=PATH[:PATH]`` |Additional paths to consider by robot for easyconfigs (--robot paths get priority) (type pathsep-separated list; default: /home/example/work/easybuild-easyconfigs/easybuild/easyconfigs) -``--search-paths=PATH[:PATH]`` |Additional locations to consider in --search (next to --robot and --robot-paths paths) (type pathsep-separated list) -``-k, --skip`` |Skip existing software (useful for installing additional packages) (default: False) -``-s STOP, --stop=STOP`` |Stop the installation after certain step (type choice; default: source) (choices: fetch, ready, source, patch, prepare, configure, build, test, install, extensions, postiter, postproc, sanitycheck, cleanup, module, permissions, package, testcases) -``--strict=STRICT`` |Set strictness level (type choice; default: warn) (choices: ignore, warn, error) +Option flag |Option description +-------------------------------------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +``--dry-run`` |Print build overview incl. dependencies (full paths) (default: False) +``-D, --dry-run-short`` |Print build overview incl. dependencies (short paths) (default: False) +``-x, --extended-dry-run`` |Print build environment and (expected) build procedure that will be performed (default: False) +``--extended-dry-run-ignore-errors`` |Ignore errors that occur during dry run (default: True; disable with --disable-extended-dry-run-ignore-errors) +``-f, --force`` |Force to rebuild software even if it's already installed (i.e. if it can be found as module), and skipping check for OS dependencies (default: False) +``--ignore-locks`` |Ignore locks that prevent two identical installations running in parallel (default: False) +``--job`` |Submit the build as a job (default: False) +``--locks-dir=LOCKS-DIR`` |Directory to store lock files (should be on a shared filesystem); None implies .locks subdirectory of software installation directory +``-l, --logtostdout`` |Redirect main log to stdout (default: False) +``-M, --missing-modules`` |Print list of missing modules for dependencies of specified easyconfigs (default: False) +``-b BLOCKS, --only-blocks=BLOCKS`` |Only build listed blocks (type comma-separated list) +``--rebuild`` |Rebuild software, even if module already exists (don't skip OS dependencies checks) (default: False) +``-r [PATH[:PATH]], --robot=[PATH[:PATH]]``|Enable dependency resolution, optionally consider additional paths to search for easyconfigs (type pathsep-separated list) +``--robot-paths=PATH[:PATH]`` |Additional paths to consider by robot for easyconfigs (--robot paths get priority) (type pathsep-separated list; default: /home/example/work/easybuild-easyconfigs/easybuild/easyconfigs) +``--search-paths=PATH[:PATH]`` |Additional locations to consider in --search (next to --robot and --robot-paths paths) (type pathsep-separated list) +``-k, --skip`` |Skip existing software (useful for installing additional packages) (default: False) +``-s STOP, --stop=STOP`` |Stop the installation after certain step (type choice; default: source) (choices: fetch, ready, source, patch, prepare, configure, build, test, install, extensions, postiter, postproc, sanitycheck, cleanup, module, permissions, package, testcases) +``--strict=STRICT`` |Set strictness level (type choice; default: warn) (choices: ignore, warn, error) ## Configuration options diff --git a/docs/version-specific/generic-easyblocks.md b/docs/version-specific/generic-easyblocks.md index 91c8e57c5..ff47527e3 100644 --- a/docs/version-specific/generic-easyblocks.md +++ b/docs/version-specific/generic-easyblocks.md @@ -180,10 +180,11 @@ easyconfig parameter |description ``install_cmd`` |Install command to use |``"make install"`` ``install_target_subdir`` |Subdirectory to use as installation target |``None`` ``prefix_opt`` |Prefix command line option for configure script ('--prefix=' if None) |``None`` +``runtest`` |Make target to test build or True to use CTest |``None`` ``separate_build_dir`` |Perform build in a separate directory |``True`` ``srcdir`` |Source directory location to provide to cmake command |``None`` ``tar_config_opts`` |Override tar settings as determined by configure. |``False`` -``test_cmd`` |Test command to use ('runtest' value is appended) |``"make"`` +``test_cmd`` |Test command to use ('runtest' value is appended, default: 'make') |``None`` ### Customised steps in ``CMakeMake`` easyblock @@ -256,10 +257,11 @@ easyconfig parameter |description ``install_cmd`` |Install command to use |``"make install"`` ``install_target_subdir`` |Subdirectory to use as installation target |``None`` ``prefix_opt`` |Prefix command line option for configure script ('--prefix=' if None) |``None`` +``runtest`` |Make target to test build or True to use CTest |``None`` ``separate_build_dir`` |Perform build in a separate directory |``True`` ``srcdir`` |Source directory location to provide to cmake command |``None`` ``tar_config_opts`` |Override tar settings as determined by configure. |``False`` -``test_cmd`` |Test command to use ('runtest' value is appended) |``"make"`` +``test_cmd`` |Test command to use ('runtest' value is appended, default: 'make') |``None`` ``with_configure`` |Run configure script before building |``False`` ### Customised steps in ``CMakeMakeCp`` easyblock @@ -294,10 +296,11 @@ easyconfig parameter |description ``install_cmd`` |Install command to use |``"ninja"`` ``install_target_subdir`` |Subdirectory to use as installation target |``None`` ``prefix_opt`` |Prefix command line option for configure script ('--prefix=' if None) |``None`` +``runtest`` |Make target to test build or True to use CTest |``None`` ``separate_build_dir`` |Perform build in a separate directory |``True`` ``srcdir`` |Source directory location to provide to cmake command |``None`` ``tar_config_opts`` |Override tar settings as determined by configure. |``False`` -``test_cmd`` |Test command to use ('runtest' value is appended) |``"make"`` +``test_cmd`` |Test command to use ('runtest' value is appended, default: 'make') |``None`` ### Customised steps in ``CMakeNinja`` easyblock @@ -349,13 +352,13 @@ easyconfig parameter |description ``prefix_opt`` |Prefix command line option for configure script ('--prefix=' if None) |``None`` ``req_py_majver`` |Required major Python version (only relevant when using system Python) |``None`` ``req_py_minver`` |Required minor Python version (only relevant when using system Python) |``None`` -``runtest`` |Run unit tests. |``None`` +``runtest`` |Make target to test build or True to use CTest |``None`` ``sanity_pip_check`` |Run 'python -m pip check' to ensure all required Python packages are installed and check for any package with an invalid (0.0.0) version. |``False`` ``separate_build_dir`` |Perform build in a separate directory |``True`` ``source_urls`` |List of URLs for source files |``['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s']`` ``srcdir`` |Source directory location to provide to cmake command |``None`` ``tar_config_opts`` |Override tar settings as determined by configure. |``False`` -``test_cmd`` |Test command to use ('runtest' value is appended) |``"make"`` +``test_cmd`` |Test command to use ('runtest' value is appended, default: 'make') |``None`` ``testinstall`` |Install into temporary directory prior to running the tests. |``False`` ``unpack_sources`` |Unpack sources prior to build/install. Defaults to 'True' except for whl files |``None`` ``unversioned_packages`` |List of packages that don't have a version at all, i.e. show 0.0.0 |``[]`` @@ -464,7 +467,7 @@ easyconfig parameter |description ``install_cmd`` |Install command to use |``"make install"`` ``prefix_opt`` |Prefix command line option for configure script ('--prefix=' if None) |``None`` ``tar_config_opts`` |Override tar settings as determined by configure. |``False`` -``test_cmd`` |Test command to use ('runtest' value is appended) |``"make"`` +``test_cmd`` |Test command to use ('runtest' value is appended, default: 'make') |``None`` ``with_configure`` |Run configure script before building |``False`` ### Customised steps in ``CmdCp`` easyblock @@ -498,7 +501,8 @@ easyconfig parameter |description ### Customised steps in ``Conda`` easyblock -* ``install_step`` - Install software using 'conda env create' or 'conda create' & 'conda install'. +* ``install_step`` - Install software using 'conda env create' or 'conda create' & 'conda install' + (or the 'mamba', etc., equivalent). ## ``ConfigureMake`` @@ -523,7 +527,7 @@ easyconfig parameter |description ``install_cmd`` |Install command to use |``"make install"`` ``prefix_opt`` |Prefix command line option for configure script ('--prefix=' if None) |``None`` ``tar_config_opts`` |Override tar settings as determined by configure. |``False`` -``test_cmd`` |Test command to use ('runtest' value is appended) |``"make"`` +``test_cmd`` |Test command to use ('runtest' value is appended, default: 'make') |``None`` ### Commonly used easyconfig parameters with ``ConfigureMake`` easyblock @@ -611,7 +615,7 @@ easyconfig parameter |description ``sanity_pip_check`` |Run 'python -m pip check' to ensure all required Python packages are installed and check for any package with an invalid (0.0.0) version. |``False`` ``source_urls`` |List of URLs for source files |``['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s']`` ``tar_config_opts`` |Override tar settings as determined by configure. |``False`` -``test_cmd`` |Test command to use ('runtest' value is appended) |``"make"`` +``test_cmd`` |Test command to use ('runtest' value is appended, default: 'make') |``None`` ``testinstall`` |Install into temporary directory prior to running the tests. |``False`` ``unpack_sources`` |Unpack sources prior to build/install. Defaults to 'True' except for whl files |``None`` ``unversioned_packages`` |List of packages that don't have a version at all, i.e. show 0.0.0 |``[]`` @@ -865,7 +869,7 @@ easyconfig parameter |description ``install_cmd`` |Install command to use |``"make install"`` ``prefix_opt`` |Prefix command line option for configure script ('--prefix=' if None) |``None`` ``tar_config_opts`` |Override tar settings as determined by configure. |``False`` -``test_cmd`` |Test command to use ('runtest' value is appended) |``"make"`` +``test_cmd`` |Test command to use ('runtest' value is appended, default: 'make') |``None`` ``with_configure`` |Run configure script before building |``False`` ### Customised steps in ``MakeCp`` easyblock @@ -1257,7 +1261,7 @@ easyconfig parameter |description ``sanity_check_components`` |List of components for which to run sanity checks |``[]`` ``serial_number`` |Serial number for the product |``None`` ``tar_config_opts`` |Override tar settings as determined by configure. |``False`` -``test_cmd`` |Test command to use ('runtest' value is appended) |``"make"`` +``test_cmd`` |Test command to use ('runtest' value is appended, default: 'make') |``None`` ``use_gold_linker`` |Configure GCC to use GOLD as default linker (default: enable automatically for GCC < 11.3.0, except on RISC-V) |``None`` ``usetmppath`` |Use temporary path for installation |``False`` ``withamdgcn`` |Build GCC with AMD GCN offload support |``False`` @@ -1314,7 +1318,7 @@ easyconfig parameter |description ``set_mpi_wrappers_all`` |Set (default) compiler for all MPI wrapper commands |``False`` ``set_mpi_wrappers_compiler`` |Override default compiler used by MPI wrapper commands |``False`` ``tar_config_opts`` |Override tar settings as determined by configure. |``False`` -``test_cmd`` |Test command to use ('runtest' value is appended) |``"make"`` +``test_cmd`` |Test command to use ('runtest' value is appended, default: 'make') |``None`` ``usetmppath`` |Use temporary path for installation |``False`` ## ``Tarball`` diff --git a/docs/version-specific/supported-software.md b/docs/version-specific/supported-software.md index 0da9e33bf..10777c50b 100644 --- a/docs/version-specific/supported-software.md +++ b/docs/version-specific/supported-software.md @@ -5,7 +5,7 @@ This page contains a lot of information, it may take a while to load. -EasyBuild supports 3244 different software packages (incl. toolchains, bundles): +EasyBuild supports 3292 different software packages (incl. toolchains, bundles): [a](#a) - [b](#b) - [c](#c) - [d](#d) - [e](#e) - [f](#f) - [g](#g) - [h](#h) - [i](#i) - [j](#j) - [k](#k) - [l](#l) - [m](#m) - [n](#n) - [o](#o) - [p](#p) - [q](#q) - [r](#r) - [s](#s) - [t](#t) - [u](#u) - [v](#v) - [w](#w) - [x](#x) - [y](#y) - [z](#z) @@ -56,7 +56,7 @@ version |toolchain ## A -[ABAQUS](#abaqus) - [ABINIT](#abinit) - [ABRA2](#abra2) - [ABRicate](#abricate) - [Abseil](#abseil) - [abTEM](#abtem) - [ABySS](#abyss) - [ack](#ack) - [ACT](#act) - [ACTC](#actc) - [ada](#ada) - [AdapterRemoval](#adapterremoval) - [ADDA](#adda) - [ADF](#adf) - [ADIOS](#adios) - [adjustText](#adjusttext) - [ADMIXTURE](#admixture) - [ADOL-C](#adol-c) - [Advisor](#advisor) - [affinity](#affinity) - [AFNI](#afni) - [AGAT](#agat) - [AGeNT](#agent) - [AGFusion](#agfusion) - [AIMAll](#aimall) - [aiohttp](#aiohttp) - [ALADIN](#aladin) - [ALAMODE](#alamode) - [Albacore](#albacore) - [Albumentations](#albumentations) - [alevin-fry](#alevin-fry) - [ALFA](#alfa) - [Alfred](#alfred) - [alleleCount](#allelecount) - [alleleIntegrator](#alleleintegrator) - [Allinea](#allinea) - [ALLPATHS-LG](#allpaths-lg) - [almosthere](#almosthere) - [Alpha](#alpha) - [AlphaFold](#alphafold) - [AlphaPulldown](#alphapulldown) - [ALPS](#alps) - [alsa-lib](#alsa-lib) - [AMAPVox](#amapvox) - [Amara](#amara) - [amask](#amask) - [Amber](#amber) - [AmberMini](#ambermini) - [AmberTools](#ambertools) - [AMD-LibM](#amd-libm) - [AMD-RNG](#amd-rng) - [AMD-SecureRNG](#amd-securerng) - [AMD-uProf](#amd-uprof) - [AMOS](#amos) - [AMPHORA2](#amphora2) - [AMPL-MP](#ampl-mp) - [amplimap](#amplimap) - [AMPtk](#amptk) - [AMRFinderPlus](#amrfinderplus) - [AmrPlusPlus](#amrplusplus) - [AMS](#ams) - [Anaconda2](#anaconda2) - [Anaconda3](#anaconda3) - [aNCI](#anci) - [andi](#andi) - [ANGEL](#angel) - [angsd](#angsd) - [ANIcalculator](#anicalculator) - [anndata](#anndata) - [Annif](#annif) - [Annocript](#annocript) - [annovar](#annovar) - [ANSYS](#ansys) - [ANSYS_CFD](#ansys_cfd) - [ant](#ant) - [antiSMASH](#antismash) - [ANTLR](#antlr) - [ANTs](#ants) - [anvio](#anvio) - [any2fasta](#any2fasta) - [AOCC](#aocc) - [AOMP](#aomp) - [APBS](#apbs) - [apex](#apex) - [APR](#apr) - [APR-util](#apr-util) - [AptaSUITE](#aptasuite) - [ARAGORN](#aragorn) - [Arb](#arb) - [Arcade-Learning-Environment](#arcade-learning-environment) - [arcasHLA](#arcashla) - [ARCH](#arch) - [Archive-Zip](#archive-zip) - [ArchR](#archr) - [archspec](#archspec) - [ARGoS](#argos) - [argtable](#argtable) - [aria2](#aria2) - [Arlequin](#arlequin) - [Armadillo](#armadillo) - [arosics](#arosics) - [ARPACK++](#arpack++) - [arpack-ng](#arpack-ng) - [ArrayFire](#arrayfire) - [Arriba](#arriba) - [Arrow](#arrow) - [arrow-R](#arrow-r) - [ART](#art) - [artic-ncov2019](#artic-ncov2019) - [ARTS](#arts) - [ArviZ](#arviz) - [ARWEN](#arwen) - [ASAP](#asap) - [ASAP3](#asap3) - [ASCAT](#ascat) - [ASE](#ase) - [ASF-SearchAPI](#asf-searchapi) - [ASHS](#ashs) - [Aspera-CLI](#aspera-cli) - [Aspera-Connect](#aspera-connect) - [assimp](#assimp) - [Assimulo](#assimulo) - [ASTRID](#astrid) - [astro-tulips](#astro-tulips) - [astropy](#astropy) - [at-spi2-atk](#at-spi2-atk) - [at-spi2-core](#at-spi2-core) - [ATAT](#atat) - [ATK](#atk) - [ATLAS](#atlas) - [atomate](#atomate) - [AtomPAW](#atompaw) - [atools](#atools) - [atropos](#atropos) - [ATSAS](#atsas) - [attr](#attr) - [attrdict](#attrdict) - [attrdict3](#attrdict3) - [augur](#augur) - [AUGUSTUS](#augustus) - [Austin](#austin) - [AUTO-07p](#auto-07p) - [Autoconf](#autoconf) - [Autoconf-archive](#autoconf-archive) - [AutoDock](#autodock) - [AutoDock-GPU](#autodock-gpu) - [AutoDock-Vina](#autodock-vina) - [AutoDockSuite](#autodocksuite) - [AutoGeneS](#autogenes) - [AutoGrid](#autogrid) - [Automake](#automake) - [AutoMap](#automap) - [autopep8](#autopep8) - [Autotools](#autotools) - [Avogadro2](#avogadro2) - [avro-cpp](#avro-cpp) - [awscli](#awscli) - [Ax](#ax) - [axel](#axel) +[ABAQUS](#abaqus) - [ABINIT](#abinit) - [ABRA2](#abra2) - [ABRicate](#abricate) - [Abseil](#abseil) - [abTEM](#abtem) - [ABySS](#abyss) - [ack](#ack) - [ACTC](#actc) - [ada](#ada) - [AdapterRemoval](#adapterremoval) - [ADDA](#adda) - [ADF](#adf) - [ADIOS](#adios) - [adjustText](#adjusttext) - [ADMIXTURE](#admixture) - [ADOL-C](#adol-c) - [Advisor](#advisor) - [affinity](#affinity) - [AFNI](#afni) - [AGAT](#agat) - [AGeNT](#agent) - [AGFusion](#agfusion) - [AIMAll](#aimall) - [aiohttp](#aiohttp) - [ALADIN](#aladin) - [ALAMODE](#alamode) - [Albacore](#albacore) - [Albumentations](#albumentations) - [alevin-fry](#alevin-fry) - [ALFA](#alfa) - [Alfred](#alfred) - [ALL](#all) - [alleleCount](#allelecount) - [alleleIntegrator](#alleleintegrator) - [Allinea](#allinea) - [ALLPATHS-LG](#allpaths-lg) - [almosthere](#almosthere) - [Alpha](#alpha) - [AlphaFold](#alphafold) - [AlphaPulldown](#alphapulldown) - [ALPS](#alps) - [alsa-lib](#alsa-lib) - [AMAPVox](#amapvox) - [Amara](#amara) - [amask](#amask) - [Amber](#amber) - [AmberMini](#ambermini) - [AmberTools](#ambertools) - [AMD-LibM](#amd-libm) - [AMD-RNG](#amd-rng) - [AMD-SecureRNG](#amd-securerng) - [AMD-uProf](#amd-uprof) - [AMOS](#amos) - [AMPHORA2](#amphora2) - [AMPL-MP](#ampl-mp) - [amplimap](#amplimap) - [AMPtk](#amptk) - [AMRFinderPlus](#amrfinderplus) - [AmrPlusPlus](#amrplusplus) - [AMS](#ams) - [Anaconda2](#anaconda2) - [Anaconda3](#anaconda3) - [anadama2](#anadama2) - [aNCI](#anci) - [andi](#andi) - [ANGEL](#angel) - [angsd](#angsd) - [ANIcalculator](#anicalculator) - [anndata](#anndata) - [Annif](#annif) - [Annocript](#annocript) - [annovar](#annovar) - [ANSYS](#ansys) - [ANSYS_CFD](#ansys_cfd) - [ant](#ant) - [antiSMASH](#antismash) - [ANTLR](#antlr) - [ANTs](#ants) - [anvio](#anvio) - [any2fasta](#any2fasta) - [AOCC](#aocc) - [AOFlagger](#aoflagger) - [AOMP](#aomp) - [APBS](#apbs) - [apex](#apex) - [APR](#apr) - [APR-util](#apr-util) - [AptaSUITE](#aptasuite) - [ARAGORN](#aragorn) - [Arb](#arb) - [Arcade-Learning-Environment](#arcade-learning-environment) - [arcasHLA](#arcashla) - [ARCH](#arch) - [Archive-Zip](#archive-zip) - [ArchR](#archr) - [archspec](#archspec) - [ARGoS](#argos) - [argtable](#argtable) - [aria2](#aria2) - [Arlequin](#arlequin) - [Armadillo](#armadillo) - [arosics](#arosics) - [ARPACK++](#arpack++) - [arpack-ng](#arpack-ng) - [ArrayFire](#arrayfire) - [Arriba](#arriba) - [Arrow](#arrow) - [arrow-R](#arrow-r) - [ART](#art) - [Artemis](#artemis) - [artic-ncov2019](#artic-ncov2019) - [ARTS](#arts) - [ArviZ](#arviz) - [ARWEN](#arwen) - [ASAP](#asap) - [ASAP3](#asap3) - [ASCAT](#ascat) - [ASE](#ase) - [ASF-SearchAPI](#asf-searchapi) - [ASHS](#ashs) - [Aspera-CLI](#aspera-cli) - [Aspera-Connect](#aspera-connect) - [assimp](#assimp) - [Assimulo](#assimulo) - [ASTRID](#astrid) - [astro-tulips](#astro-tulips) - [astropy](#astropy) - [at-spi2-atk](#at-spi2-atk) - [at-spi2-core](#at-spi2-core) - [ATAT](#atat) - [ATK](#atk) - [ATLAS](#atlas) - [atomate](#atomate) - [AtomPAW](#atompaw) - [atools](#atools) - [atropos](#atropos) - [ATSAS](#atsas) - [attr](#attr) - [attrdict](#attrdict) - [attrdict3](#attrdict3) - [augur](#augur) - [AUGUSTUS](#augustus) - [Austin](#austin) - [AUTO-07p](#auto-07p) - [Autoconf](#autoconf) - [Autoconf-archive](#autoconf-archive) - [AutoDock](#autodock) - [AutoDock-GPU](#autodock-gpu) - [AutoDock-Vina](#autodock-vina) - [AutoDockSuite](#autodocksuite) - [AutoGeneS](#autogenes) - [AutoGrid](#autogrid) - [Automake](#automake) - [AutoMap](#automap) - [autopep8](#autopep8) - [Autotools](#autotools) - [Avogadro2](#avogadro2) - [avro-cpp](#avro-cpp) - [awscli](#awscli) - [Ax](#ax) - [axel](#axel) ### ABAQUS @@ -176,17 +176,6 @@ version |toolchain ``3.4.0``|``GCCcore/10.2.0`` ``3.5.0``|``GCCcore/10.3.0`` -### ACT - -ACT is a Java application for displaying pairwise comparisons between two or more DNA sequences. It can be used to identify and analyse regions of similarity and difference between genomes and to explore conservation of synteny, in the context of the entire sequences and their annotation. It can read complete EMBL, GENBANK and GFF entries or sequences in FASTA or raw format. - -*homepage*: - -version |versionsuffix|toolchain -----------|-------------|---------- -``18.0.2``|``-Java-11`` |``system`` -``18.0.3``|``-Java-11`` |``system`` - ### ACTC ACTC converts independent triangles into triangle strips or fans. @@ -462,6 +451,16 @@ version |toolchain ---------|-------------- ``0.2.6``|``GCC/11.2.0`` +### ALL + +A Load Balancing Library (ALL) aims to provide an easy way to include dynamic domain-based load balancing into particle based simulation codes. The library is developed in the Simulation Laboratory Molecular Systems of the Jülich Supercomputing Centre at Forschungszentrum Jülich. + +*homepage*: + +version |toolchain +---------|-------------- +``0.9.2``|``foss/2022b`` + ### alleleCount The alleleCount package primarily exists to prevent code duplication between some other projects, specifically AscatNGS and Battenberg. As of v4 the perl code wraps the C implementation of allele counting code for BAM/CRAM processing. @@ -472,6 +471,7 @@ version |toolchain ---------|----------------- ``4.0.0``|``GCCcore/6.4.0`` ``4.2.1``|``GCC/11.3.0`` +``4.3.0``|``GCC/12.2.0`` ### alleleIntegrator @@ -482,6 +482,7 @@ R package to generate allele specific counts for scRNA data and use it to identi version |versionsuffix|toolchain ---------|-------------|-------------- ``0.8.8``|``-R-4.2.1`` |``foss/2022a`` +``0.8.8``|``-R-4.2.2`` |``foss/2022b`` ### Allinea @@ -634,6 +635,7 @@ version |versionsuffix |toolchain ``20.11``|``-AmberTools-21.3`` |``foss/2020b``, ``fosscuda/2020b`` ``22.0`` |``-AmberTools-22.3`` |``foss/2021b`` ``22.0`` |``-AmberTools-22.3-CUDA-11.4.1`` |``foss/2021b`` +``22.4`` |``-AmberTools-22.5-CUDA-11.7.0`` |``foss/2022a`` ### AmberMini @@ -833,6 +835,17 @@ version |toolchain ``2022.10`` |``system`` ``2023.03-1``|``system`` ``2023.07-2``|``system`` +``2023.09-0``|``system`` + +### anadama2 + +AnADAMA2 is the next generation of AnADAMA (Another Automated Data Analysis Management Application). AnADAMA is a tool to create reproducible workflows and execute them efficiently. + +*homepage*: + +version |toolchain +----------|-------------- +``0.10.0``|``foss/2022a`` ### aNCI @@ -991,6 +1004,7 @@ version |versionsuffix |toolchain ``1.10.11``|``-Java-13`` |``system`` ``1.10.12``|``-Java-11`` |``system`` ``1.10.12``|``-Java-17`` |``system`` +``1.10.14``|``-Java-11`` |``system`` ### antiSMASH @@ -1068,6 +1082,16 @@ version |toolchain ``3.2.0``|``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ``4.0.0``|``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` +### AOFlagger + +The AOFlagger is a tool that can find and remove radio-frequency interference (RFI) in radio astronomical observations. It can make use of Lua scripts to make flagging strategies flexible, and the tools are applicable to a wide set of telescopes. + +*homepage*: + +version |toolchain +---------|-------------- +``3.4.0``|``foss/2022a`` + ### AOMP AMD fork of LLVM, setup for OpenMP offloading to Accelerators @@ -1364,7 +1388,7 @@ version |versionsuffix |toolchain ``0.17.1``|``-Python-3.8.2`` |``foss/2020a``, ``intel/2020a`` ``6.0.0`` | |``foss/2021a``, ``foss/2021b`` ``6.0.1`` | |``foss/2021a`` -``8.0.0`` | |``foss/2022.05``, ``foss/2022a`` +``8.0.0`` | |``foss/2021a``, ``foss/2022.05``, ``foss/2022a`` ``11.0.0``| |``gfbf/2022b`` ### arrow-R @@ -1392,6 +1416,18 @@ version |toolchain --------------|---------------------------------- ``2016.06.05``|``GCCcore/6.4.0``, ``intel/2016b`` +### Artemis + +The Artemis Software is a set of software tools for genome browsing and annotation. It includes: Artemis, Artemis Comparison Tool (ACT), BamView and DNAPlotter. + +*homepage*: + +version |versionsuffix|toolchain +----------|-------------|---------- +``18.0.2``|``-Java-11`` |``system`` +``18.0.3``|``-Java-11`` |``system`` +``18.2.0``|``-Java-11`` |``system`` + ### artic-ncov2019 Initial implementation of an ARTIC bioinformatics platform for nanopore sequencing of nCoV2019 novel coronavirus. @@ -1420,11 +1456,12 @@ Exploratory analysis of Bayesian models with Python *homepage*: version |versionsuffix |toolchain -----------|-----------------|------------------------------- +----------|-----------------|----------------------------------------------- ``0.7.0`` |``-Python-3.7.4``|``foss/2019b``, ``intel/2019b`` ``0.11.1``| |``intel/2020b`` ``0.11.4``| |``foss/2021b``, ``intel/2021b`` -``0.12.1``| |``foss/2022a``, ``intel/2022a`` +``0.12.1``| |``foss/2021a``, ``foss/2022a``, ``intel/2022a`` +``0.16.1``| |``foss/2023a`` ### ARWEN @@ -1464,6 +1501,7 @@ version |versionsuffix |toolchain ``3.11.10``|``-Python-3.7.2``|``foss/2019a``, ``intel/2019a`` ``3.12.2`` |``-ASE-3.21.1`` |``foss/2020b``, ``intel/2020b`` ``3.12.7`` |``-ASE-3.21.1`` |``foss/2020b``, ``intel/2020b`` +``3.13.2`` | |``foss/2023a`` ### ASCAT @@ -1474,6 +1512,7 @@ ASCAT is a method to derive copy number profiles of tumor cells, accounting for version |versionsuffix|toolchain ---------|-------------|-------------- ``3.1.2``|``-R-4.2.1`` |``foss/2022a`` +``3.1.2``|``-R-4.2.2`` |``foss/2022b`` ### ASE @@ -1482,7 +1521,7 @@ ASE is a python package providing an open source Atomic Simulation Environment *homepage*: version |versionsuffix |toolchain ---------------|------------------|------------------------------------------------------------------------------------------------- +--------------|------------------|----------------------------------------------------------------------------------------------------------------- ``3.9.1.4567``|``-Python-2.7.11``|``intel/2016a`` ``3.10.0`` |``-Python-2.7.11``|``intel/2016.02-GCC-4.9`` ``3.11.0`` |``-Python-2.7.12``|``intel/2016b`` @@ -1508,7 +1547,7 @@ version |versionsuffix |toolchain ``3.21.1`` | |``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` ``3.21.1`` |``-Python-3.8.2`` |``foss/2020a`` ``3.22.0`` | |``foss/2020b``, ``foss/2021a``, ``fosscuda/2020b``, ``intel/2020b``, ``intel/2021a`` -``3.22.1`` | |``foss/2021b``, ``foss/2022a``, ``gfbf/2022b``, ``gomkl/2021a``, ``intel/2021b``, ``intel/2022a`` +``3.22.1`` | |``foss/2021b``, ``foss/2022a``, ``gfbf/2022b``, ``gfbf/2023a``, ``gomkl/2021a``, ``intel/2021b``, ``intel/2022a`` ### ASF-SearchAPI @@ -1748,10 +1787,10 @@ Commands for Manipulating Filesystem Extended Attributes *homepage*: version |toolchain -----------|---------------------------------------------------------- +----------|------------------------------------------------------------------------------ ``2.4.47``|``GCCcore/8.2.0`` ``2.4.48``|``GCCcore/9.3.0`` -``2.5.1`` |``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``2.5.1`` |``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.3.0`` ### attrdict @@ -2022,7 +2061,7 @@ version |toolchain ## B -[BA3-SNPS-autotune](#ba3-snps-autotune) - [BabelStream](#babelstream) - [babl](#babl) - [Bader](#bader) - [BAGEL](#bagel) - [BAli-Phy](#bali-phy) - [bam-readcount](#bam-readcount) - [Bambi](#bambi) - [bamFilters](#bamfilters) - [BAMM](#bamm) - [BAMSurgeon](#bamsurgeon) - [bamtofastq](#bamtofastq) - [BamTools](#bamtools) - [BamUtil](#bamutil) - [Bandage](#bandage) - [barrnap](#barrnap) - [basemap](#basemap) - [Bash](#bash) - [bashplotlib](#bashplotlib) - [bat](#bat) - [batchgenerators](#batchgenerators) - [BatMeth2](#batmeth2) - [BayesAss](#bayesass) - [BayesAss3-SNPs](#bayesass3-snps) - [BayeScan](#bayescan) - [BayeScEnv](#bayescenv) - [BayesPrism](#bayesprism) - [BayesTraits](#bayestraits) - [Bazel](#bazel) - [bbcp](#bbcp) - [bbFTP](#bbftp) - [BBMap](#bbmap) - [bc](#bc) - [BCALM](#bcalm) - [bcbio-gff](#bcbio-gff) - [BCEL](#bcel) - [BCFtools](#bcftools) - [bcgTree](#bcgtree) - [bcl-convert](#bcl-convert) - [bcl2fastq2](#bcl2fastq2) - [bcolz](#bcolz) - [bcrypt](#bcrypt) - [BDBag](#bdbag) - [Beagle](#beagle) - [beagle-lib](#beagle-lib) - [Beast](#beast) - [BeautifulSoup](#beautifulsoup) - [BEDOPS](#bedops) - [BEDTools](#bedtools) - [BEEF](#beef) - [behave](#behave) - [bench](#bench) - [BerkeleyGW](#berkeleygw) - [BFAST](#bfast) - [BFC](#bfc) - [BGC-Bayesian-genomic-clines](#bgc-bayesian-genomic-clines) - [BgeeDB](#bgeedb) - [bgen](#bgen) - [bgen-reader](#bgen-reader) - [bibtexparser](#bibtexparser) - [BiG-SCAPE](#big-scape) - [BigDFT](#bigdft) - [BinSanity](#binsanity) - [binutils](#binutils) - [Bio-DB-HTS](#bio-db-hts) - [Bio-EUtilities](#bio-eutilities) - [Bio-SamTools](#bio-samtools) - [Bio-SearchIO-hmmer](#bio-searchio-hmmer) - [bioawk](#bioawk) - [biobambam2](#biobambam2) - [biogeme](#biogeme) - [biom-format](#biom-format) - [biomart-perl](#biomart-perl) - [BioPerl](#bioperl) - [BioPP](#biopp) - [Biopython](#biopython) - [BioServices](#bioservices) - [BirdNET](#birdnet) - [biscuit](#biscuit) - [Bismark](#bismark) - [Bison](#bison) - [bitarray](#bitarray) - [BLACS](#blacs) - [BLASR](#blasr) - [blasr_libcpp](#blasr_libcpp) - [BLAST](#blast) - [BLAST+](#blast+) - [BLAT](#blat) - [Blender](#blender) - [BLIS](#blis) - [Blitz++](#blitz++) - [BlobTools](#blobtools) - [Block](#block) - [Blosc](#blosc) - [Blosc2](#blosc2) - [BLT](#blt) - [bmtagger](#bmtagger) - [bnpy](#bnpy) - [BOINC](#boinc) - [bokeh](#bokeh) - [BoltzTraP](#boltztrap) - [BoltzTraP2](#boltztrap2) - [Bonito](#bonito) - [Bonmin](#bonmin) - [Bonnie++](#bonnie++) - [Boost](#boost) - [Boost.MPI](#boost.mpi) - [Boost.Python](#boost.python) - [Boost.Python-NumPy](#boost.python-numpy) - [boost_histogram](#boost_histogram) - [boto3](#boto3) - [Bottleneck](#bottleneck) - [Bowtie](#bowtie) - [Bowtie2](#bowtie2) - [Bpipe](#bpipe) - [bpp](#bpp) - [bpytop](#bpytop) - [Bracken](#bracken) - [Braindecode](#braindecode) - [BRAKER](#braker) - [BreakDancer](#breakdancer) - [breseq](#breseq) - [Brotli](#brotli) - [Brotli-python](#brotli-python) - [Brunsli](#brunsli) - [bsddb3](#bsddb3) - [BSMAPz](#bsmapz) - [Bsoft](#bsoft) - [BSseeker2](#bsseeker2) - [BuDDy](#buddy) - [BUFRLIB](#bufrlib) - [build](#build) - [buildenv](#buildenv) - [buildingspy](#buildingspy) - [Bullet](#bullet) - [BUSCO](#busco) - [BUStools](#bustools) - [BWA](#bwa) - [bwa-meth](#bwa-meth) - [bwakit](#bwakit) - [bwidget](#bwidget) - [BWISE](#bwise) - [bx-python](#bx-python) - [BXH_XCEDE_TOOLS](#bxh_xcede_tools) - [byacc](#byacc) - [byobu](#byobu) - [bzip2](#bzip2) +[BA3-SNPS-autotune](#ba3-snps-autotune) - [BabelStream](#babelstream) - [babl](#babl) - [Bader](#bader) - [BAGEL](#bagel) - [BAli-Phy](#bali-phy) - [bam-readcount](#bam-readcount) - [Bambi](#bambi) - [bamFilters](#bamfilters) - [BAMM](#bamm) - [BAMSurgeon](#bamsurgeon) - [bamtofastq](#bamtofastq) - [BamTools](#bamtools) - [BamUtil](#bamutil) - [Bandage](#bandage) - [barrnap](#barrnap) - [basemap](#basemap) - [bases2fastq](#bases2fastq) - [Bash](#bash) - [bashplotlib](#bashplotlib) - [bat](#bat) - [batchgenerators](#batchgenerators) - [BatMeth2](#batmeth2) - [BayesAss](#bayesass) - [BayesAss3-SNPs](#bayesass3-snps) - [BayeScan](#bayescan) - [BayeScEnv](#bayescenv) - [BayesPrism](#bayesprism) - [BayesTraits](#bayestraits) - [Bazel](#bazel) - [bbcp](#bbcp) - [bbFTP](#bbftp) - [BBMap](#bbmap) - [bc](#bc) - [BCALM](#bcalm) - [bcbio-gff](#bcbio-gff) - [BCEL](#bcel) - [BCFtools](#bcftools) - [bcgTree](#bcgtree) - [bcl-convert](#bcl-convert) - [bcl2fastq2](#bcl2fastq2) - [bcolz](#bcolz) - [bcrypt](#bcrypt) - [BDBag](#bdbag) - [Beagle](#beagle) - [beagle-lib](#beagle-lib) - [Beast](#beast) - [BeautifulSoup](#beautifulsoup) - [BEDOPS](#bedops) - [BEDTools](#bedtools) - [BEEF](#beef) - [behave](#behave) - [bench](#bench) - [BerkeleyGW](#berkeleygw) - [BFAST](#bfast) - [BFC](#bfc) - [BGC-Bayesian-genomic-clines](#bgc-bayesian-genomic-clines) - [BgeeCall](#bgeecall) - [BgeeDB](#bgeedb) - [bgen](#bgen) - [bgen-reader](#bgen-reader) - [bibtexparser](#bibtexparser) - [BiG-SCAPE](#big-scape) - [BigDFT](#bigdft) - [BinSanity](#binsanity) - [binutils](#binutils) - [Bio-DB-HTS](#bio-db-hts) - [Bio-EUtilities](#bio-eutilities) - [Bio-SamTools](#bio-samtools) - [Bio-SearchIO-hmmer](#bio-searchio-hmmer) - [bioawk](#bioawk) - [biobakery-workflows](#biobakery-workflows) - [biobambam2](#biobambam2) - [biogeme](#biogeme) - [biom-format](#biom-format) - [biomart-perl](#biomart-perl) - [BioPerl](#bioperl) - [BioPP](#biopp) - [Biopython](#biopython) - [BioServices](#bioservices) - [BirdNET](#birdnet) - [biscuit](#biscuit) - [Bismark](#bismark) - [Bison](#bison) - [bitarray](#bitarray) - [BLACS](#blacs) - [BLASR](#blasr) - [blasr_libcpp](#blasr_libcpp) - [BLAST](#blast) - [BLAST+](#blast+) - [BLAT](#blat) - [Blender](#blender) - [BLIS](#blis) - [Blitz++](#blitz++) - [BlobTools](#blobtools) - [Block](#block) - [Blosc](#blosc) - [Blosc2](#blosc2) - [BLT](#blt) - [bmtagger](#bmtagger) - [BMTK](#bmtk) - [bnpy](#bnpy) - [BOINC](#boinc) - [bokeh](#bokeh) - [BoltzTraP](#boltztrap) - [BoltzTraP2](#boltztrap2) - [Bonito](#bonito) - [Bonmin](#bonmin) - [Bonnie++](#bonnie++) - [Boost](#boost) - [Boost.MPI](#boost.mpi) - [Boost.Python](#boost.python) - [Boost.Python-NumPy](#boost.python-numpy) - [boost_histogram](#boost_histogram) - [boto3](#boto3) - [Bottleneck](#bottleneck) - [Bowtie](#bowtie) - [Bowtie2](#bowtie2) - [Bpipe](#bpipe) - [bpp](#bpp) - [bpytop](#bpytop) - [Bracken](#bracken) - [Braindecode](#braindecode) - [BRAKER](#braker) - [BreakDancer](#breakdancer) - [breseq](#breseq) - [Brotli](#brotli) - [Brotli-python](#brotli-python) - [Brunsli](#brunsli) - [bsddb3](#bsddb3) - [BSMAPz](#bsmapz) - [Bsoft](#bsoft) - [BSseeker2](#bsseeker2) - [BuDDy](#buddy) - [BUFRLIB](#bufrlib) - [build](#build) - [buildenv](#buildenv) - [buildingspy](#buildingspy) - [Bullet](#bullet) - [BUSCO](#busco) - [BUStools](#bustools) - [BWA](#bwa) - [bwa-meth](#bwa-meth) - [bwakit](#bwakit) - [bwidget](#bwidget) - [BWISE](#bwise) - [bx-python](#bx-python) - [BXH_XCEDE_TOOLS](#bxh_xcede_tools) - [byacc](#byacc) - [byobu](#byobu) - [bzip2](#bzip2) ### BA3-SNPS-autotune @@ -2211,6 +2250,16 @@ version |versionsuffix |toolchain ``1.2.2``|``-Python-3.8.2`` |``foss/2020a`` ``1.3.6``| |``foss/2022a`` +### bases2fastq + +Bases2Fastq Software demultiplexes sequencing data and converts base calls into FASTQ files for secondary analysis with the FASTQ-compatible software of your choice. The Element AVITI™ System records base calls, which are the main output of a sequencing run, with associated quality scores (Q-scores) in bases files. Bases files must be converted into the FASTQ file format for secondary analysis. To generate QC reports, also load BeautifulSoup and bokeh. + +*homepage*: + +version |toolchain +---------|---------- +``1.5.1``|``system`` + ### Bash Bash is an sh-compatible command language interpreter that executes commands read from the standard input or from a file. Bash also incorporates useful features from the Korn and C shells (ksh and csh). @@ -2700,6 +2749,16 @@ version |toolchain --------|--------------- ``1.03``|``gompi/2021a`` +### BgeeCall + +Automatic RNA-Seq present/absent gene expression calls generation + +*homepage*: + +version |versionsuffix |toolchain +----------|---------------|-------------- +``1.16.0``|``-R-%(rver)s``|``foss/2021a`` + ### BgeeDB Annotation and gene expression data retrieval from Bgee database. TopAnat, an anatomical entities Enrichment Analysis tool for UBERON ontology. @@ -2851,15 +2910,26 @@ version|toolchain -------|---------------------------------------------- ``1.0``|``GCC/10.3.0``, ``GCC/11.2.0``, ``foss/2018b`` +### biobakery-workflows + +bioBakery workflows is a collection of workflows and tasks for executing common microbial community analyses using standardized, validated tools and parameters. Quality control and statistical summary reports are automatically generated for most data types, which include 16S amplicons, metagenomes, and metatranscriptomes. Workflows are run directly from the command line and tasks can be imported to create your own custom workflows. The workflows and tasks are built with AnADAMA2 which allows for parallel task execution locally and in a grid compute environment. + +*homepage*: + +version|toolchain +-------|-------------- +``3.1``|``foss/2022a`` + ### biobambam2 Tools for processing BAM files *homepage*: -version |toolchain -----------|------------------------------- -``2.0.87``|``GCC/11.3.0``, ``intel/2018a`` +version |toolchain +-----------|------------------------------- +``2.0.87`` |``GCC/11.3.0``, ``intel/2018a`` +``2.0.185``|``GCC/12.3.0`` ### biogeme @@ -3105,6 +3175,7 @@ version |versionsuffix |toolchain ``2.12.0``| |``gompi/2021b`` ``2.13.0``| |``gompi/2022a`` ``2.14.0``| |``gompi/2022b`` +``2.14.1``| |``gompi/2023a`` ### BLAT @@ -3115,7 +3186,7 @@ BLAT on DNA is designed to quickly find sequences of 95% and greater similarity version|toolchain -------|-------------------------------------------------------------------------------------------------------------------- ``3.5``|``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``foss/2016b``, ``foss/2018b``, ``intel/2016b``, ``intel/2017a`` -``3.7``|``GCC/11.2.0``, ``GCC/11.3.0`` +``3.7``|``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0`` ### Blender @@ -3144,12 +3215,12 @@ AMD's fork of BLIS. BLIS is a portable software framework for instantiating high *homepage*: version |versionsuffix|toolchain ----------|-------------|---------------------------------------------------------------------------- +---------|-------------|-------------------------------------------------------------------------------------------- ``0.3.2``| |``GCC/7.3.0-2.30`` ``0.6.0``| |``GCC/8.3.0-2.32`` ``0.8.0``| |``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ``0.8.1``| |``GCC/10.3.0``, ``GCC/11.2.0``, ``GCCcore/10.3.0`` -``0.9.0``| |``GCC/11.3.0``, ``GCC/12.2.0``, ``GCC/12.3.0``, ``intel-compilers/2022.1.0`` +``0.9.0``| |``GCC/11.3.0``, ``GCC/12.2.0``, ``GCC/12.3.0``, ``GCC/13.2.0``, ``intel-compilers/2022.1.0`` ``1.2`` |``-amd`` |``GCC/7.3.0-2.30`` ``2.2`` |``-amd`` |``GCCcore/9.3.0`` ``3.0`` |``-amd`` |``GCCcore/10.3.0`` @@ -3239,6 +3310,16 @@ version |toolchain ---------|------------------------------------------------ ``3.101``|``foss/2018b``, ``gompi/2019a``, ``gompi/2020b`` +### BMTK + +The Brain Modeling Toolkit (BMTK) is a python-based software package for building, simulating and analyzing large-scale neural network models. It supports the building and simulation of models of varying levels-of-resolution; from multi-compartment biophysically detailed networks, to point-neuron models, to filter-based models, and even population-level firing rate models. + +*homepage*: + +version |toolchain +---------|-------------- +``1.0.8``|``foss/2021a`` + ### bnpy Bayesian nonparametric machine learning for python provides code for training popular clustering models on large datasets. The focus is on Bayesian nonparametric models based on the Dirichlet process, but it also provides parametric counterparts. @@ -3279,6 +3360,7 @@ version |versionsuffix |toolchain ``2.4.2`` | |``foss/2021b`` ``2.4.3`` | |``foss/2022a`` ``3.2.1`` | |``foss/2022b`` +``3.2.2`` | |``foss/2023a`` ### BoltzTraP @@ -3488,7 +3570,7 @@ version |toolchain ``1.2.2`` |``foss/2018b``, ``intel/2017b``, ``intel/2018a`` ``1.2.3`` |``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281`` ``1.3.0`` |``GCC/10.2.0``, ``GCC/9.3.0`` -``1.3.1`` |``GCC/11.2.0``, ``GCC/11.3.0`` +``1.3.1`` |``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0`` ### Bowtie2 @@ -3511,7 +3593,7 @@ version |toolchain ``2.4.2`` |``GCC/10.2.0``, ``GCC/9.3.0`` ``2.4.4`` |``GCC/10.3.0``, ``GCC/11.2.0`` ``2.4.5`` |``GCC/11.3.0`` -``2.5.1`` |``GCC/12.2.0`` +``2.5.1`` |``GCC/12.2.0``, ``GCC/12.3.0`` ### Bpipe @@ -3612,6 +3694,7 @@ Brotli is a generic-purpose lossless compression algorithm that compresses data version |toolchain ---------|----------------------------------------------------------------------------------------------------------------------------------------- ``1.0.9``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/8.3.0`` +``1.1.0``|``GCCcore/13.2.0`` ### Brotli-python @@ -3713,12 +3796,13 @@ This module sets a group of environment variables for compilers, linkers, maths *homepage*: version |versionsuffix |toolchain ------------|----------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -``default``| |``FCC/4.5.0``, ``Fujitsu/21.05``, ``foss/2017b``, ``foss/2018b``, ``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``foss/2022a``, ``foss/2022b``, ``fosscuda/2019b``, ``fosscuda/2020a``, ``fosscuda/2020b``, ``intel/2016b``, ``intel/2017a``, ``intel/2019b``, ``intel/2020a``, ``intel/2020b``, ``intel/2021a``, ``intel/2021b``, ``intel/2022a``, ``intel/2022b``, ``intelcuda/2019b``, ``intelcuda/2020a``, ``intelcuda/2020b`` +-----------|----------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +``default``| |``FCC/4.5.0``, ``Fujitsu/21.05``, ``foss/2017b``, ``foss/2018b``, ``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``foss/2022a``, ``foss/2022b``, ``foss/2023a``, ``fosscuda/2019b``, ``fosscuda/2020a``, ``fosscuda/2020b``, ``intel/2016b``, ``intel/2017a``, ``intel/2019b``, ``intel/2020a``, ``intel/2020b``, ``intel/2021a``, ``intel/2021b``, ``intel/2022a``, ``intel/2022b``, ``intel/2023a``, ``intelcuda/2019b``, ``intelcuda/2020a``, ``intelcuda/2020b``, ``nvompi/2022.07`` ``default``|``-CUDA-11.3.1``|``foss/2021a`` ``default``|``-CUDA-11.4.1``|``foss/2021b`` ``default``|``-CUDA-11.7.0``|``foss/2022a`` ``default``|``-CUDA-12.0.0``|``foss/2022b`` +``default``|``-CUDA-12.1.1``|``foss/2023a`` ### buildingspy @@ -3887,12 +3971,12 @@ bzip2 is a freely available, patent free, high-quality data compressor. It typi version |toolchain ---------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ ``1.0.6``|``GCC/4.8.1``, ``GCC/4.8.2``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.3-2.25``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GNU/4.9.3-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``gimkl/2017a``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` -``1.0.8``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``system`` +``1.0.8``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``GCCcore/13.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``system`` ## C -[c-ares](#c-ares) - [C3D](#c3d) - [cadaver](#cadaver) - [CaDiCaL](#cadical) - [CAFE5](#cafe5) - [Caffe](#caffe) - [cairo](#cairo) - [cairomm](#cairomm) - [Calcam](#calcam) - [CalculiX-CrunchiX](#calculix-crunchix) - [Calendrical](#calendrical) - [Calib](#calib) - [CAMPARI](#campari) - [Cantera](#cantera) - [canu](#canu) - [Canvas](#canvas) - [CAP3](#cap3) - [CapnProto](#capnproto) - [captum](#captum) - [Cargo](#cargo) - [Carma](#carma) - [carputils](#carputils) - [Cartopy](#cartopy) - [CASA](#casa) - [casacore](#casacore) - [Casanovo](#casanovo) - [CaSpER](#casper) - [CASPR](#caspr) - [CASTEP](#castep) - [CastXML](#castxml) - [CAT-BAT](#cat-bat) - [CatBoost](#catboost) - [Catch2](#catch2) - [category_encoders](#category_encoders) - [CatLearn](#catlearn) - [CatMAP](#catmap) - [causallift](#causallift) - [causalml](#causalml) - [CaVEMan](#caveman) - [CAVIAR](#caviar) - [Cbc](#cbc) - [CBLAS](#cblas) - [ccache](#ccache) - [CCfits](#ccfits) - [CCL](#ccl) - [cclib](#cclib) - [cctbx-base](#cctbx-base) - [cctools](#cctools) - [CD-HIT](#cd-hit) - [CDAT](#cdat) - [cdbfasta](#cdbfasta) - [CDBtools](#cdbtools) - [cddlib](#cddlib) - [CDFlib](#cdflib) - [cDNA_Cupcake](#cdna_cupcake) - [CDO](#cdo) - [cdo-bindings](#cdo-bindings) - [cdsapi](#cdsapi) - [cell2location](#cell2location) - [CellChat](#cellchat) - [CellMix](#cellmix) - [CellOracle](#celloracle) - [Cellpose](#cellpose) - [CellRanger](#cellranger) - [CellRanger-ARC](#cellranger-arc) - [CellRanger-ATAC](#cellranger-atac) - [CellRank](#cellrank) - [CellTypist](#celltypist) - [centerline](#centerline) - [Centrifuge](#centrifuge) - [Cereal](#cereal) - [CESM-deps](#cesm-deps) - [CFDEMcoupling](#cfdemcoupling) - [cffi](#cffi) - [CFITSIO](#cfitsio) - [cftime](#cftime) - [CGAL](#cgal) - [cget](#cget) - [Cgl](#cgl) - [CGmapTools](#cgmaptools) - [CGNS](#cgns) - [CharLS](#charls) - [CHASE](#chase) - [Check](#check) - [CheckM](#checkm) - [CheckM-Database](#checkm-database) - [Cheetah](#cheetah) - [Chemaxon-Marvin](#chemaxon-marvin) - [chemprop](#chemprop) - [CheMPS2](#chemps2) - [CHERAB](#cherab) - [chewBBACA](#chewbbaca) - [chi2comb](#chi2comb) - [Chimera](#chimera) - [ChimPipe](#chimpipe) - [ChIPseeker](#chipseeker) - [Chromaprint](#chromaprint) - [cicero](#cicero) - [CIF2Cell](#cif2cell) - [cimfomfa](#cimfomfa) - [CIRCexplorer](#circexplorer) - [CIRCexplorer2](#circexplorer2) - [Circos](#circos) - [Circuitscape](#circuitscape) - [CIRI](#ciri) - [CIRI-long](#ciri-long) - [cisTEM](#cistem) - [CITE-seq-Count](#cite-seq-count) - [Clang](#clang) - [Clang-AOMP](#clang-aomp) - [Clang-Python-bindings](#clang-python-bindings) - [CLAPACK](#clapack) - [CLEASE](#clease) - [CLHEP](#clhep) - [CliMetLab](#climetlab) - [CLIP](#clip) - [CLISP](#clisp) - [ClonalFrameML](#clonalframeml) - [CLooG](#cloog) - [CloudCompare](#cloudcompare) - [Clp](#clp) - [Clustal-Omega](#clustal-omega) - [ClustalW2](#clustalw2) - [Cluster-Buster](#cluster-buster) - [ClusterShell](#clustershell) - [CMake](#cmake) - [CMAverse](#cmaverse) - [CmdStanR](#cmdstanr) - [cmocean](#cmocean) - [CMSeq](#cmseq) - [CNT-ILP](#cnt-ilp) - [CNVkit](#cnvkit) - [CNVnator](#cnvnator) - [Co-phylog](#co-phylog) - [COBRApy](#cobrapy) - [CoCoALib](#cocoalib) - [CodAn](#codan) - [code-server](#code-server) - [CODEX2](#codex2) - [CodingQuarry](#codingquarry) - [Cogent](#cogent) - [Coin](#coin) - [CoinUtils](#coinutils) - [ColabFold](#colabfold) - [colossalai](#colossalai) - [Commet](#commet) - [CompareM](#comparem) - [Compress-Raw-Zlib](#compress-raw-zlib) - [COMSOL](#comsol) - [Con3F](#con3f) - [conan](#conan) - [CONCOCT](#concoct) - [configparser](#configparser) - [configurable-http-proxy](#configurable-http-proxy) - [CONN](#conn) - [connected-components-3d](#connected-components-3d) - [ConnectomeWorkbench](#connectomeworkbench) - [Control-FREEC](#control-freec) - [cooler](#cooler) - [CoordgenLibs](#coordgenlibs) - [Coot](#coot) - [CopyKAT](#copykat) - [core-counter](#core-counter) - [Coreutils](#coreutils) - [corner](#corner) - [CoSymLib](#cosymlib) - [coverage](#coverage) - [cowsay](#cowsay) - [CP2K](#cp2k) - [CPB](#cpb) - [CPC2](#cpc2) - [CPLEX](#cplex) - [CPPE](#cppe) - [CppHeaderParser](#cppheaderparser) - [CppUnit](#cppunit) - [cppy](#cppy) - [cppzmq](#cppzmq) - [cpu_features](#cpu_features) - [cram](#cram) - [cramtools](#cramtools) - [CrayCCE](#craycce) - [CrayGNU](#craygnu) - [CrayIntel](#crayintel) - [CrayPGI](#craypgi) - [crb-blast](#crb-blast) - [CREST](#crest) - [CRF++](#crf++) - [CRISPR-DAV](#crispr-dav) - [CRISPResso2](#crispresso2) - [cromwell](#cromwell) - [crossguid](#crossguid) - [CrossMap](#crossmap) - [CrossTalkZ](#crosstalkz) - [CRPropa](#crpropa) - [Crumble](#crumble) - [cryoCARE](#cryocare) - [cryoDRGN](#cryodrgn) - [cryptography](#cryptography) - [CryptoMiniSat](#cryptominisat) - [CrystFEL](#crystfel) - [CSB](#csb) - [CSBDeep](#csbdeep) - [CSBLAST](#csblast) - [cscope](#cscope) - [csvkit](#csvkit) - [ctags](#ctags) - [ctffind](#ctffind) - [CTPL](#ctpl) - [Cube](#cube) - [CubeGUI](#cubegui) - [CubeLib](#cubelib) - [CubeWriter](#cubewriter) - [CuCLARK](#cuclark) - [CUDA](#cuda) - [CUDA-Samples](#cuda-samples) - [CUDAcompat](#cudacompat) - [CUDAcore](#cudacore) - [cuDNN](#cudnn) - [Cufflinks](#cufflinks) - [CUnit](#cunit) - [CuPy](#cupy) - [cURL](#curl) - [cuSPARSELt](#cusparselt) - [custodian](#custodian) - [cutadapt](#cutadapt) - [cuTENSOR](#cutensor) - [cuteSV](#cutesv) - [CVglasso](#cvglasso) - [CVS](#cvs) - [CVXOPT](#cvxopt) - [CVXPY](#cvxpy) - [CWIPI](#cwipi) - [cwltool](#cwltool) - [cxxopts](#cxxopts) - [cysignals](#cysignals) - [Cython](#cython) - [cython-blis](#cython-blis) - [cytoolz](#cytoolz) - [Cytoscape](#cytoscape) - [cytosim](#cytosim) - [cyvcf2](#cyvcf2) +[c-ares](#c-ares) - [C3D](#c3d) - [cadaver](#cadaver) - [CaDiCaL](#cadical) - [CAFE5](#cafe5) - [Caffe](#caffe) - [cairo](#cairo) - [cairomm](#cairomm) - [Calcam](#calcam) - [CalculiX-CrunchiX](#calculix-crunchix) - [Calendrical](#calendrical) - [Calib](#calib) - [CAMPARI](#campari) - [Cantera](#cantera) - [canu](#canu) - [Canvas](#canvas) - [CAP3](#cap3) - [CapnProto](#capnproto) - [captum](#captum) - [Cargo](#cargo) - [Carma](#carma) - [carputils](#carputils) - [Cartopy](#cartopy) - [CASA](#casa) - [casacore](#casacore) - [Casanovo](#casanovo) - [CaSpER](#casper) - [CASPR](#caspr) - [CASTEP](#castep) - [CastXML](#castxml) - [CAT-BAT](#cat-bat) - [CatBoost](#catboost) - [Catch2](#catch2) - [category_encoders](#category_encoders) - [CatLearn](#catlearn) - [CatMAP](#catmap) - [causallift](#causallift) - [causalml](#causalml) - [CaVEMan](#caveman) - [CAVIAR](#caviar) - [Cbc](#cbc) - [CBLAS](#cblas) - [ccache](#ccache) - [CCfits](#ccfits) - [CCL](#ccl) - [cclib](#cclib) - [cctbx-base](#cctbx-base) - [cctools](#cctools) - [CD-HIT](#cd-hit) - [CDAT](#cdat) - [cdbfasta](#cdbfasta) - [CDBtools](#cdbtools) - [cddlib](#cddlib) - [CDFlib](#cdflib) - [cDNA_Cupcake](#cdna_cupcake) - [CDO](#cdo) - [cdo-bindings](#cdo-bindings) - [cdsapi](#cdsapi) - [cell2location](#cell2location) - [CellChat](#cellchat) - [CellMix](#cellmix) - [CellOracle](#celloracle) - [Cellpose](#cellpose) - [CellRanger](#cellranger) - [CellRanger-ARC](#cellranger-arc) - [CellRanger-ATAC](#cellranger-atac) - [CellRank](#cellrank) - [CellTypist](#celltypist) - [centerline](#centerline) - [Centrifuge](#centrifuge) - [Cereal](#cereal) - [CESM-deps](#cesm-deps) - [CFDEMcoupling](#cfdemcoupling) - [cffi](#cffi) - [CFITSIO](#cfitsio) - [cftime](#cftime) - [CGAL](#cgal) - [cget](#cget) - [Cgl](#cgl) - [CGmapTools](#cgmaptools) - [CGNS](#cgns) - [CharLS](#charls) - [CHASE](#chase) - [Check](#check) - [CheckM](#checkm) - [CheckM-Database](#checkm-database) - [Cheetah](#cheetah) - [Chemaxon-Marvin](#chemaxon-marvin) - [chemprop](#chemprop) - [CheMPS2](#chemps2) - [CHERAB](#cherab) - [chewBBACA](#chewbbaca) - [chi2comb](#chi2comb) - [Chimera](#chimera) - [ChimPipe](#chimpipe) - [ChIPseeker](#chipseeker) - [Chromaprint](#chromaprint) - [cicero](#cicero) - [CIF2Cell](#cif2cell) - [cimfomfa](#cimfomfa) - [CIRCexplorer](#circexplorer) - [CIRCexplorer2](#circexplorer2) - [Circos](#circos) - [Circuitscape](#circuitscape) - [CIRI](#ciri) - [CIRI-long](#ciri-long) - [CIRIquant](#ciriquant) - [cisTEM](#cistem) - [CITE-seq-Count](#cite-seq-count) - [Clair3](#clair3) - [Clang](#clang) - [Clang-AOMP](#clang-aomp) - [Clang-Python-bindings](#clang-python-bindings) - [CLAPACK](#clapack) - [CLEAR](#clear) - [CLEASE](#clease) - [CLHEP](#clhep) - [CliMetLab](#climetlab) - [CLIP](#clip) - [CLISP](#clisp) - [ClonalFrameML](#clonalframeml) - [CLooG](#cloog) - [CloudCompare](#cloudcompare) - [Clp](#clp) - [Clustal-Omega](#clustal-omega) - [ClustalW2](#clustalw2) - [Cluster-Buster](#cluster-buster) - [ClusterShell](#clustershell) - [CMake](#cmake) - [CMAverse](#cmaverse) - [CmdStanR](#cmdstanr) - [cmocean](#cmocean) - [CMSeq](#cmseq) - [CNT-ILP](#cnt-ilp) - [CNVkit](#cnvkit) - [CNVnator](#cnvnator) - [Co-phylog](#co-phylog) - [COBRApy](#cobrapy) - [CoCoALib](#cocoalib) - [CodAn](#codan) - [code-server](#code-server) - [CODEX2](#codex2) - [CodingQuarry](#codingquarry) - [Cogent](#cogent) - [Coin](#coin) - [CoinUtils](#coinutils) - [ColabFold](#colabfold) - [colossalai](#colossalai) - [Commet](#commet) - [CompareM](#comparem) - [Compress-Raw-Zlib](#compress-raw-zlib) - [COMSOL](#comsol) - [Con3F](#con3f) - [conan](#conan) - [CONCOCT](#concoct) - [ConcurrentVersionsSystem](#concurrentversionssystem) - [configparser](#configparser) - [configurable-http-proxy](#configurable-http-proxy) - [CONN](#conn) - [connected-components-3d](#connected-components-3d) - [ConnectomeWorkbench](#connectomeworkbench) - [Control-FREEC](#control-freec) - [cooler](#cooler) - [CoordgenLibs](#coordgenlibs) - [Coot](#coot) - [CopyKAT](#copykat) - [core-counter](#core-counter) - [Coreutils](#coreutils) - [corner](#corner) - [CoSymLib](#cosymlib) - [coverage](#coverage) - [cowsay](#cowsay) - [CP2K](#cp2k) - [CPB](#cpb) - [CPC2](#cpc2) - [cpio](#cpio) - [CPLEX](#cplex) - [CPPE](#cppe) - [CppHeaderParser](#cppheaderparser) - [CppUnit](#cppunit) - [cppy](#cppy) - [cppzmq](#cppzmq) - [cpu_features](#cpu_features) - [cram](#cram) - [cramtools](#cramtools) - [CrayCCE](#craycce) - [CrayGNU](#craygnu) - [CrayIntel](#crayintel) - [CrayPGI](#craypgi) - [crb-blast](#crb-blast) - [CREST](#crest) - [CRF++](#crf++) - [CRISPR-DAV](#crispr-dav) - [CRISPResso2](#crispresso2) - [cromwell](#cromwell) - [crossguid](#crossguid) - [CrossMap](#crossmap) - [CrossTalkZ](#crosstalkz) - [CRPropa](#crpropa) - [Crumble](#crumble) - [cryoCARE](#cryocare) - [cryoDRGN](#cryodrgn) - [cryptography](#cryptography) - [CryptoMiniSat](#cryptominisat) - [CrystFEL](#crystfel) - [CSB](#csb) - [CSBDeep](#csbdeep) - [CSBLAST](#csblast) - [cscope](#cscope) - [csvkit](#csvkit) - [ctags](#ctags) - [ctffind](#ctffind) - [CTPL](#ctpl) - [Cube](#cube) - [CubeGUI](#cubegui) - [CubeLib](#cubelib) - [CubeWriter](#cubewriter) - [CuCLARK](#cuclark) - [CUDA](#cuda) - [CUDA-Samples](#cuda-samples) - [CUDAcompat](#cudacompat) - [CUDAcore](#cudacore) - [cuDNN](#cudnn) - [Cufflinks](#cufflinks) - [CUnit](#cunit) - [CuPy](#cupy) - [cURL](#curl) - [cuSPARSELt](#cusparselt) - [custodian](#custodian) - [cutadapt](#cutadapt) - [cuTENSOR](#cutensor) - [cuteSV](#cutesv) - [CVglasso](#cvglasso) - [CVXOPT](#cvxopt) - [CVXPY](#cvxpy) - [CWIPI](#cwipi) - [cwltool](#cwltool) - [cxxopts](#cxxopts) - [cysignals](#cysignals) - [Cython](#cython) - [cython-blis](#cython-blis) - [cytoolz](#cytoolz) - [Cytoscape](#cytoscape) - [cytosim](#cytosim) - [cyvcf2](#cyvcf2) ### c-ares @@ -4054,6 +4138,7 @@ version |versionsuffix |toolchain ``2.3.0``|``-Python-2.7.14``|``foss/2017b``, ``intel/2017b``, ``intel/2018a`` ``2.4.0``|``-Python-2.7.14``|``intel/2018a`` ``2.6.0``| |``foss/2022a`` +``3.0.0``| |``foss/2023a`` ### canu @@ -4110,6 +4195,7 @@ version |toolchain ``0.9.1`` |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``0.10.2``|``GCCcore/11.3.0`` ``0.10.3``|``GCCcore/12.2.0`` +``1.0.1`` |``GCCcore/12.3.0`` ### captum @@ -4186,6 +4272,7 @@ A suite of C++ libraries for radio astronomy data processing. The ephemerides da version |toolchain ---------|-------------- ``3.4.0``|``foss/2021b`` +``3.5.0``|``foss/2022a`` ### Casanovo @@ -4272,6 +4359,7 @@ version |toolchain ``2.9.1`` |``system`` ``2.11.0``|``system`` ``2.13.4``|``system`` +``2.13.9``|``system`` ### category_encoders @@ -4704,9 +4792,9 @@ cereal is a header-only C++11 serialization library. cereal takes arbitrary data *homepage*: version |toolchain ----------|---------- +---------|------------------------------ ``1.3.0``|``system`` -``1.3.2``|``system`` +``1.3.2``|``GCCcore/12.2.0``, ``system`` ### CESM-deps @@ -4735,8 +4823,8 @@ C Foreign Function Interface for Python. Interact with almost any C code from Py *homepage*: version |toolchain -----------|------------------ -``1.15.1``|``GCCcore/12.3.0`` +----------|---------------------------------------------------------- +``1.15.1``|``GCCcore/11.3.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0`` ### CFITSIO @@ -4796,6 +4884,7 @@ version |versionsuffix |toolchain ``4.14.3``|``-Python-3.8.2`` |``gompi/2020a``, ``iimpi/2020a`` ``5.2`` | |``gompi/2020b`` ``5.5.2`` | |``GCCcore/12.2.0`` +``5.6`` | |``GCCcore/12.3.0`` ### cget @@ -4918,11 +5007,12 @@ version |versionsuffix |toolchain Marvin suite is a chemically intelligent desktop toolkit built to help you draw, edit, publish, render, import and export your chemical structures and as well as allowing you to convert between various chemical and graphical file formats. It is free for individual, academic and non-commercial use. -*homepage*: +*homepage*: version |toolchain ---------|---------- ``21.14``|``system`` +``23.9`` |``system`` ### chemprop @@ -5055,8 +5145,8 @@ This library supports both MCL, a cluster algorithm for graphs, and zoem, a macr *homepage*: version |toolchain -----------|------------------ -``22.273``|``GCCcore/11.3.0`` +----------|-------------------------------------- +``22.273``|``GCCcore/11.3.0``, ``GCCcore/12.3.0`` ### CIRCexplorer @@ -5075,10 +5165,10 @@ CIRCexplorer2 is a comprehensive and integrative circular RNA analysis toolset. *homepage*: version |versionsuffix |toolchain ----------|------------------|--------------- +---------|------------------|------------------------------ ``2.3.2``|``-Python-2.7.14``|``intel/2017b`` ``2.3.3``|``-Python-2.7.14``|``intel/2018a`` -``2.3.8``|``-Python-2.7.18``|``foss/2020b`` +``2.3.8``|``-Python-2.7.18``|``foss/2020b``, ``foss/2021b`` ### Circos @@ -5102,6 +5192,7 @@ Algorithms from circuit theory to predict connectivity in heterogeneous landscap version |versionsuffix |toolchain ----------|----------------|---------- ``5.12.3``|``-Julia-1.7.2``|``system`` +``5.12.3``|``-Julia-1.9.2``|``system`` ### CIRI @@ -5123,6 +5214,16 @@ version |toolchain ---------|-------------- ``1.0.2``|``foss/2020b`` +### CIRIquant + +CIRIquant is a comprehensive analysis pipeline for circRNA detection and quantification in RNA-Seq data + +*homepage*: + +version |versionsuffix |toolchain +------------------|------------------|-------------- +``1.1.2-20221201``|``-Python-2.7.18``|``foss/2021b`` + ### cisTEM cisTEM is user-friendly software to process cryo-EM images of macromolecular complexes and obtain high-resolution 3D reconstructions from them. @@ -5144,6 +5245,16 @@ version |versionsuffix |toolchain ``1.4.3``|``-Python-3.6.6``|``foss/2018b`` ``1.4.3``|``-Python-3.7.4``|``foss/2019b`` +### Clair3 + +Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories: pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall. Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration. + +*homepage*: + +version |toolchain +---------|-------------- +``1.0.4``|``foss/2022a`` + ### Clang C, C++, Objective-C compiler, based on LLVM. Does not include C++ standard library -- use libstdc++ from GCC. @@ -5217,6 +5328,16 @@ version |toolchain ---------|--------------------------------------------------------------------------- ``3.2.1``|``GCC/6.4.0-2.28``, ``iccifort/2017.4.196-GCC-6.4.0-2.28``, ``intel/2017a`` +### CLEAR + +Direct comparison of circular and linear RNA expression + +*homepage*: + +version |versionsuffix |toolchain +------------|------------------|-------------- +``20210117``|``-Python-2.7.18``|``foss/2021b`` + ### CLEASE CLuster Expansion in Atomic Simulation Environment (CLEASE) is a package that automates the cumbersome setup and construction procedure of cluster expansion (CE). It provides a comprehensive list of tools for specifying parameters for CE, generating training structures, fitting effective cluster interaction (ECI) values and running Monte Carlo simulations. @@ -5413,6 +5534,7 @@ version |toolchain ``3.23.1``|``GCCcore/11.3.0`` ``3.24.3``|``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ``3.26.3``|``GCCcore/12.3.0``, ``GCCcore/13.1.0`` +``3.27.6``|``GCCcore/13.2.0`` ### CMAverse @@ -5537,10 +5659,11 @@ Run VS Code on any machine anywhere and access it in the browser. *homepage*: -version |toolchain ----------|---------- -``3.7.3``|``system`` -``4.9.1``|``system`` +version |toolchain +----------|---------- +``3.7.3`` |``system`` +``4.9.1`` |``system`` +``4.16.1``|``system`` ### CODEX2 @@ -5692,6 +5815,16 @@ version |versionsuffix |toolchain ``1.1.0``|``-Python-2.7.15``|``foss/2019a`` ``1.1.0``|``-Python-2.7.18``|``foss/2020b`` +### ConcurrentVersionsSystem + +CVS is a version control system, an important component of Source Configuration Management (SCM). + +*homepage*: + +version |toolchain +-----------|----------------------------------------------------------------------- +``1.11.23``|``GCC/4.8.2``, ``GCCcore/11.2.0``, ``GCCcore/4.9.3``, ``GCCcore/6.4.0`` + ### configparser configparser is a Python library that brings the updated configparser from Python 3.5 to Python 2.6-3.5 @@ -5792,9 +5925,10 @@ Coot is for macromolecular model building, model completion and validation, par *homepage*: -version |versionsuffix |toolchain ----------|-------------------------------------------|---------- -``0.8.1``|``-binary-Linux-x86_64-rhel-6-python-gtk2``|``system`` +version |versionsuffix |toolchain +------------|---------------------------------------------------------|---------- +``0.8.1`` |``-binary-Linux-x86_64-rhel-6-python-gtk2`` |``system`` +``0.9.8.92``|``-binary-Linux-x86_64-scientific-linux-7.6-python-gtk2``|``system`` ### CopyKAT @@ -5805,6 +5939,7 @@ CopyKAT: Inference of genomic copy number and subclonal structure of human tumor version |versionsuffix|toolchain ---------|-------------|-------------- ``1.1.0``|``-R-4.2.1`` |``foss/2022a`` +``1.1.0``|``-R-4.2.2`` |``foss/2022b`` ### core-counter @@ -5917,6 +6052,16 @@ version |toolchain ---------|-------------- ``1.0.1``|``foss/2022a`` +### cpio + +The cpio package contains tools for archiving. + +*homepage*: + +version |toolchain +--------|------------------ +``2.14``|``GCCcore/11.3.0`` + ### CPLEX IBM ILOG CPLEX Optimizer's mathematical programming technology enables analytical decision support for improving efficiency, reducing costs, and increasing profitability. @@ -6123,8 +6268,8 @@ CrossGuid is a minimal, cross platform, C++ GUID library. It uses the best nati *homepage*: version |toolchain -------------|------------------ -``20190529``|``GCCcore/11.3.0`` +------------|-------------------------------------- +``20190529``|``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ### CrossMap @@ -6238,6 +6383,7 @@ CSBDeep is a toolbox for Content-aware Image Restoration (CARE). version |versionsuffix |toolchain ---------|-----------------|---------------------------------- ``0.4.1``|``-Python-3.7.2``|``foss/2019a``, ``fosscuda/2019a`` +``0.7.4``| |``foss/2022a`` ### CSBLAST @@ -6288,9 +6434,9 @@ Program for finding CTFs of electron micrographs. *homepage*: version |versionsuffix |toolchain -----------|----------------|-------------------------------------------------------------------------------------- +----------|----------------|------------------------------------------------------------------------------------------------------ ``4.1.13``| |``foss/2019a``, ``fosscuda/2019a``, ``fosscuda/2019b`` -``4.1.14``| |``foss/2019b``, ``foss/2021b``, ``foss/2022a``, ``fosscuda/2019b``, ``fosscuda/2020b`` +``4.1.14``| |``foss/2019b``, ``foss/2021b``, ``foss/2022a``, ``foss/2023a``, ``fosscuda/2019b``, ``fosscuda/2020b`` ``4.1.14``|``-CUDA-11.3.1``|``foss/2021a`` ### CTPL @@ -6412,6 +6558,8 @@ Samples for CUDA Developers which demonstrates features in CUDA Toolkit version |versionsuffix |toolchain --------|----------------|-------------- ``11.3``|``-CUDA-11.3.1``|``GCC/10.3.0`` +``11.6``|``-CUDA-11.7.0``|``GCC/11.3.0`` +``12.1``|``-CUDA-12.1.1``|``GCC/12.3.0`` ### CUDAcompat @@ -6486,6 +6634,7 @@ version |versionsuffix |toolchain ``8.7.0.84`` |``-CUDA-11.8.0`` |``system`` ``8.8.0.121``|``-CUDA-12.0.0`` |``system`` ``8.9.2.26`` |``-CUDA-12.1.1`` |``system`` +``8.9.2.26`` |``-CUDA-12.2.0`` |``system`` ### Cufflinks @@ -6519,6 +6668,7 @@ version |versionsuffix |toolchain ``8.2.0`` |``-Python-3.7.4``|``fosscuda/2019b`` ``8.5.0`` | |``fosscuda/2020b`` ``11.4.0``|``-CUDA-11.4.1`` |``foss/2021b`` +``12.1.0``|``-CUDA-12.0.0`` |``foss/2022b`` ### cURL @@ -6553,6 +6703,7 @@ version |toolchain ``7.84.0``|``GCCcore/12.1.0`` ``7.86.0``|``GCCcore/12.2.0`` ``8.0.1`` |``GCCcore/12.3.0``, ``GCCcore/13.1.0`` +``8.3.0`` |``GCCcore/13.2.0`` ### cuSPARSELt @@ -6639,16 +6790,6 @@ version|versionsuffix|toolchain -------|-------------|-------------- ``1.0``|``-R-4.2.1`` |``foss/2022a`` -### CVS - -CVS is a version control system, an important component of Source Configuration Management (SCM). - -*homepage*: - -version |toolchain ------------|----------------------------------------------------------------------- -``1.11.23``|``GCC/4.8.2``, ``GCCcore/11.2.0``, ``GCCcore/4.9.3``, ``GCCcore/6.4.0`` - ### CVXOPT CVXOPT is a free software package for convex optimization based on the Python programming language. Its main purpose is to make the development of software for convex optimization applications straightforward by building on Python's extensive standard library and on the strengths of Python as a high-level programming language. @@ -6792,7 +6933,7 @@ version |versionsuffix |toolchain ## D -[dadi](#dadi) - [dagitty](#dagitty) - [Dakota](#dakota) - [DALI](#dali) - [DaliLite](#dalilite) - [Dalton](#dalton) - [damageproto](#damageproto) - [dammit](#dammit) - [DANPOS2](#danpos2) - [DAS_Tool](#das_tool) - [dask](#dask) - [dask-labextension](#dask-labextension) - [datamash](#datamash) - [davix](#davix) - [DB](#db) - [DB_File](#db_file) - [DBCSR](#dbcsr) - [DBD-mysql](#dbd-mysql) - [DBG2OLC](#dbg2olc) - [DBus](#dbus) - [dbus-glib](#dbus-glib) - [dclone](#dclone) - [dcm2niix](#dcm2niix) - [DCMTK](#dcmtk) - [dd](#dd) - [deal.II](#deal.ii) - [deap](#deap) - [decona](#decona) - [deconf](#deconf) - [DeconICA](#deconica) - [deepdiff](#deepdiff) - [DeepLabCut](#deeplabcut) - [deepmedic](#deepmedic) - [DeepMod2](#deepmod2) - [DeepSurv](#deepsurv) - [deepTools](#deeptools) - [DEICODE](#deicode) - [Delly](#delly) - [DeMixT](#demixt) - [DendroPy](#dendropy) - [DensPart](#denspart) - [Deprecated](#deprecated) - [destiny](#destiny) - [Detectron2](#detectron2) - [detonate](#detonate) - [Devito](#devito) - [DFA](#dfa) - [DFT-D3](#dft-d3) - [DFT-D4](#dft-d4) - [DFTB+](#dftb+) - [dftd3-lib](#dftd3-lib) - [DGL](#dgl) - [DIAL](#dial) - [DIALOGUE](#dialogue) - [DIAMOND](#diamond) - [Dice](#dice) - [DiCE-ML](#dice-ml) - [dicom2nifti](#dicom2nifti) - [DicomBrowser](#dicombrowser) - [DiffBind](#diffbind) - [Diffutils](#diffutils) - [dijitso](#dijitso) - [dill](#dill) - [DIRAC](#dirac) - [distributed](#distributed) - [DistributedStream](#distributedstream) - [DL_POLY_4](#dl_poly_4) - [DL_POLY_Classic](#dl_poly_classic) - [dlb](#dlb) - [dlib](#dlib) - [DLPack](#dlpack) - [dm-haiku](#dm-haiku) - [dm-reverb](#dm-reverb) - [dm-tree](#dm-tree) - [DMCfun](#dmcfun) - [DMLC-Core](#dmlc-core) - [DMTCP](#dmtcp) - [DOLFIN](#dolfin) - [dominate](#dominate) - [dorado](#dorado) - [Doris](#doris) - [DosageConvertor](#dosageconvertor) - [dotNET-Core-Runtime](#dotnet-core-runtime) - [dotNET-SDK](#dotnet-sdk) - [double-conversion](#double-conversion) - [DoubletFinder](#doubletfinder) - [Doxygen](#doxygen) - [DRAGMAP](#dragmap) - [Drake](#drake) - [dRep](#drep) - [drmaa-python](#drmaa-python) - [DROP](#drop) - [dropEst](#dropest) - [DSA](#dsa) - [dSFMT](#dsfmt) - [DSRC](#dsrc) - [Dsuite](#dsuite) - [dtcmp](#dtcmp) - [dtcwt](#dtcwt) - [DualSPHysics](#dualsphysics) - [DUBStepR](#dubstepr) - [dune-core](#dune-core) - [dune-fem](#dune-fem) - [duplex-tools](#duplex-tools) - [dx-toolkit](#dx-toolkit) - [dxpy](#dxpy) - [DyMat](#dymat) +[dadi](#dadi) - [dagitty](#dagitty) - [Dakota](#dakota) - [DALI](#dali) - [DaliLite](#dalilite) - [Dalton](#dalton) - [damageproto](#damageproto) - [dammit](#dammit) - [DANPOS2](#danpos2) - [DAS_Tool](#das_tool) - [dask](#dask) - [dask-labextension](#dask-labextension) - [datamash](#datamash) - [davix](#davix) - [DB](#db) - [DB_File](#db_file) - [DBCSR](#dbcsr) - [DBD-mysql](#dbd-mysql) - [DBG2OLC](#dbg2olc) - [DBus](#dbus) - [dbus-glib](#dbus-glib) - [dclone](#dclone) - [dcm2niix](#dcm2niix) - [DCMTK](#dcmtk) - [dd](#dd) - [deal.II](#deal.ii) - [deap](#deap) - [decona](#decona) - [deconf](#deconf) - [DeconICA](#deconica) - [deepdiff](#deepdiff) - [DeepLabCut](#deeplabcut) - [deepmedic](#deepmedic) - [DeepMod2](#deepmod2) - [DeepSurv](#deepsurv) - [deepTools](#deeptools) - [DEICODE](#deicode) - [Delly](#delly) - [DeMixT](#demixt) - [DendroPy](#dendropy) - [DensPart](#denspart) - [Deprecated](#deprecated) - [destiny](#destiny) - [Detectron2](#detectron2) - [detonate](#detonate) - [Devito](#devito) - [DFA](#dfa) - [DFT-D3](#dft-d3) - [DFT-D4](#dft-d4) - [DFTB+](#dftb+) - [dftd3-lib](#dftd3-lib) - [DGL](#dgl) - [DIAL](#dial) - [DIALOGUE](#dialogue) - [DIAMOND](#diamond) - [Dice](#dice) - [DiCE-ML](#dice-ml) - [dicom2nifti](#dicom2nifti) - [DicomBrowser](#dicombrowser) - [DiffBind](#diffbind) - [Diffutils](#diffutils) - [dijitso](#dijitso) - [dill](#dill) - [DIRAC](#dirac) - [distributed](#distributed) - [DistributedStream](#distributedstream) - [DL_POLY_4](#dl_poly_4) - [DL_POLY_Classic](#dl_poly_classic) - [dlb](#dlb) - [dlib](#dlib) - [DLPack](#dlpack) - [dm-haiku](#dm-haiku) - [dm-reverb](#dm-reverb) - [dm-tree](#dm-tree) - [DMCfun](#dmcfun) - [DMLC-Core](#dmlc-core) - [DMTCP](#dmtcp) - [DOLFIN](#dolfin) - [dominate](#dominate) - [dorado](#dorado) - [Doris](#doris) - [DosageConvertor](#dosageconvertor) - [dotNET-Core-Runtime](#dotnet-core-runtime) - [dotNET-SDK](#dotnet-sdk) - [double-conversion](#double-conversion) - [DoubletFinder](#doubletfinder) - [Doxygen](#doxygen) - [DP3](#dp3) - [DRAGMAP](#dragmap) - [Drake](#drake) - [dRep](#drep) - [drmaa-python](#drmaa-python) - [DROP](#drop) - [dropEst](#dropest) - [DSA](#dsa) - [dSFMT](#dsfmt) - [DSRC](#dsrc) - [Dsuite](#dsuite) - [dtcmp](#dtcmp) - [dtcwt](#dtcwt) - [DualSPHysics](#dualsphysics) - [DUBStepR](#dubstepr) - [dune-core](#dune-core) - [dune-fem](#dune-fem) - [duplex-tools](#duplex-tools) - [dx-toolkit](#dx-toolkit) - [dxpy](#dxpy) - [DyMat](#dymat) ### dadi @@ -6930,6 +7071,7 @@ version |versionsuffix |toolchain ``2022.1.0`` | |``foss/2021b`` ``2022.10.0``| |``foss/2022a`` ``2023.7.1`` | |``foss/2022b`` +``2023.9.2`` | |``foss/2023a`` ### dask-labextension @@ -7451,7 +7593,7 @@ version |toolchain ``2.0.11``|``GCC/10.3.0`` ``2.0.13``|``GCC/10.3.0``, ``GCC/11.2.0`` ``2.1.0`` |``GCC/11.3.0`` -``2.1.8`` |``GCC/10.3.0``, ``GCC/12.2.0`` +``2.1.8`` |``GCC/10.3.0``, ``GCC/12.2.0``, ``GCC/12.3.0`` ### Dice @@ -7545,13 +7687,13 @@ DIRAC: Program for Atomic and Molecular Direct Iterative Relativistic All-electr *homepage*: version |versionsuffix |toolchain ---------|----------------------------|---------------------------------------------------------------- +--------|----------------------------|------------------------------------------------------------------------------------------------- ``19.0``|``-Python-2.7.18-int64`` |``intel/2020a`` ``19.0``|``-Python-2.7.18-mpi-int64``|``intel/2020a`` ``22.0``| |``foss/2021a``, ``intel/2021a`` ``22.0``|``-int64`` |``intel/2021a`` -``23.0``| |``foss/2022a``, ``foss/2022b``, ``intel/2022a``, ``intel/2022b`` -``23.0``|``-int64`` |``intel/2022b`` +``23.0``| |``foss/2022a``, ``foss/2022b``, ``foss/2023a``, ``intel/2022a``, ``intel/2022b``, ``intel/2023a`` +``23.0``|``-int64`` |``intel/2022b``, ``intel/2023a`` ### distributed @@ -7584,6 +7726,7 @@ DL_POLY is a general purpose classical molecular dynamics (MD) simulation softwa version |toolchain ---------|------------------------------- ``5.0.0``|``foss/2020b``, ``intel/2020b`` +``5.1.0``|``foss/2022b``, ``intel/2022b`` ### DL_POLY_Classic @@ -7802,6 +7945,7 @@ version |versionsuffix|toolchain ------------------|-------------|-------------- ``2.0.3`` |``-R-4.0.0`` |``foss/2020a`` ``2.0.3-20230131``|``-R-4.2.1`` |``foss/2022a`` +``2.0.3-20230819``|``-R-4.2.2`` |``foss/2022b`` ### Doxygen @@ -7824,6 +7968,17 @@ version |toolchain ``1.9.4`` |``GCCcore/11.3.0`` ``1.9.5`` |``GCCcore/12.2.0`` ``1.9.7`` |``GCCcore/12.3.0`` +``1.9.8`` |``GCCcore/13.2.0`` + +### DP3 + +DP3: streaming processing pipeline for radio interferometric data. + +*homepage*: + +version|toolchain +-------|-------------- +``6.0``|``foss/2022a`` ### DRAGMAP @@ -7939,7 +8094,7 @@ version |toolchain ---------|------------------------------------------------------------------ ``1.1.0``|``gompi/2019a``, ``gompi/2020a``, ``iimpi/2019a``, ``iimpi/2020a`` ``1.1.2``|``gompi/2020b`` -``1.1.4``|``gompi/2022a`` +``1.1.4``|``gompi/2022a``, ``gompi/2023a`` ### dtcwt @@ -8021,8 +8176,9 @@ DNAnexus Platform API bindings for Python *homepage*: version |versionsuffix |toolchain ------------|------------------|--------------- +-----------|------------------|------------------ ``0.266.1``|``-Python-2.7.14``|``intel/2018a`` +``0.345.0``| |``GCCcore/12.2.0`` ### DyMat @@ -8037,7 +8193,7 @@ version|versionsuffix |toolchain ## E -[E-ANTIC](#e-antic) - [e3nn](#e3nn) - [ea-utils](#ea-utils) - [earthengine-api](#earthengine-api) - [easel](#easel) - [EasyBuild](#easybuild) - [EasyQC](#easyqc) - [ecBuild](#ecbuild) - [ecCodes](#eccodes) - [eccodes-python](#eccodes-python) - [ecFlow](#ecflow) - [ED2](#ed2) - [EDirect](#edirect) - [edlib](#edlib) - [EggLib](#egglib) - [eggnog-mapper](#eggnog-mapper) - [EGTtools](#egttools) - [eht-imaging](#eht-imaging) - [Eigen](#eigen) - [EigenExa](#eigenexa) - [EIGENSOFT](#eigensoft) - [einops](#einops) - [elastix](#elastix) - [elbencho](#elbencho) - [ELFIO](#elfio) - [elfutils](#elfutils) - [Elk](#elk) - [ELPA](#elpa) - [ELPH](#elph) - [elprep](#elprep) - [ELSI](#elsi) - [ELSI-RCI](#elsi-rci) - [Emacs](#emacs) - [EMAN2](#eman2) - [EMBOSS](#emboss) - [Embree](#embree) - [emcee](#emcee) - [EMU](#emu) - [enaBrowserTool](#enabrowsertool) - [enchant](#enchant) - [enchant-2](#enchant-2) - [EnsEMBLCoreAPI](#ensemblcoreapi) - [entrypoints](#entrypoints) - [EPD](#epd) - [EPIC](#epic) - [epiScanpy](#episcanpy) - [eQuilibrator](#equilibrator) - [EricScript](#ericscript) - [ESL-Bundle](#esl-bundle) - [ESM-2](#esm-2) - [ESMF](#esmf) - [ESMPy](#esmpy) - [ESMValTool](#esmvaltool) - [eSpeak-NG](#espeak-ng) - [ESPResSo](#espresso) - [Essentia](#essentia) - [ETE](#ete) - [ETSF_IO](#etsf_io) - [eudev](#eudev) - [Evcxr-REPL](#evcxr-repl) - [EvidentialGene](#evidentialgene) - [evmix](#evmix) - [ExaBayes](#exabayes) - [ExaML](#examl) - [Excel-Writer-XLSX](#excel-writer-xlsx) - [ExifTool](#exiftool) - [exiv2](#exiv2) - [Exonerate](#exonerate) - [expat](#expat) - [expect](#expect) - [expecttest](#expecttest) - [eXpress](#express) - [Extrae](#extrae) - [EZC3D](#ezc3d) +[E-ANTIC](#e-antic) - [e3nn](#e3nn) - [ea-utils](#ea-utils) - [earthengine-api](#earthengine-api) - [easel](#easel) - [EasyBuild](#easybuild) - [EasyQC](#easyqc) - [ecBuild](#ecbuild) - [ecCodes](#eccodes) - [eccodes-python](#eccodes-python) - [ecFlow](#ecflow) - [ED2](#ed2) - [EDirect](#edirect) - [edlib](#edlib) - [EggLib](#egglib) - [eggnog-mapper](#eggnog-mapper) - [EGTtools](#egttools) - [eht-imaging](#eht-imaging) - [Eigen](#eigen) - [EigenExa](#eigenexa) - [EIGENSOFT](#eigensoft) - [einops](#einops) - [elastix](#elastix) - [elbencho](#elbencho) - [ELFIO](#elfio) - [elfutils](#elfutils) - [Elk](#elk) - [ELPA](#elpa) - [ELPH](#elph) - [elprep](#elprep) - [ELSI](#elsi) - [ELSI-RCI](#elsi-rci) - [Emacs](#emacs) - [EMAN2](#eman2) - [EMBOSS](#emboss) - [Embree](#embree) - [emcee](#emcee) - [EMU](#emu) - [enaBrowserTool](#enabrowsertool) - [enchant](#enchant) - [enchant-2](#enchant-2) - [EnsEMBLCoreAPI](#ensemblcoreapi) - [entrypoints](#entrypoints) - [EPD](#epd) - [EPIC](#epic) - [epiScanpy](#episcanpy) - [eQuilibrator](#equilibrator) - [EricScript](#ericscript) - [ESL-Bundle](#esl-bundle) - [ESM-2](#esm-2) - [ESMF](#esmf) - [ESMPy](#esmpy) - [ESMValTool](#esmvaltool) - [eSpeak-NG](#espeak-ng) - [ESPResSo](#espresso) - [Essentia](#essentia) - [ETE](#ete) - [ETSF_IO](#etsf_io) - [eudev](#eudev) - [Evcxr-REPL](#evcxr-repl) - [EveryBeam](#everybeam) - [EvidentialGene](#evidentialgene) - [evmix](#evmix) - [ExaBayes](#exabayes) - [ExaML](#examl) - [Excel-Writer-XLSX](#excel-writer-xlsx) - [ExifTool](#exiftool) - [exiv2](#exiv2) - [Exonerate](#exonerate) - [expat](#expat) - [expect](#expect) - [expecttest](#expecttest) - [eXpress](#express) - [Extrae](#extrae) - [EZC3D](#ezc3d) ### E-ANTIC @@ -8196,6 +8352,7 @@ version |toolchain ``4.7.1`` |``system`` ``4.7.2`` |``system`` ``4.8.0`` |``system`` +``4.8.1`` |``system`` ### EasyQC @@ -8282,6 +8439,7 @@ Entrez Direct (EDirect) provides access to the NCBI's suite of interconnected da version |toolchain -----------------|------------------ ``19.7.20230531``|``GCCcore/10.3.0`` +``20.5.20231006``|``GCCcore/12.3.0`` ### edlib @@ -8348,7 +8506,7 @@ Eigen is a C++ template library for linear algebra: matrices, vectors, numerical *homepage*: version |toolchain -----------|-------------------------------------------------------------------------------------------------- +----------|---------------------------------------------------------------------------------------------------------------------- ``3.2.3`` |``foss/2016a``, ``foss/2016b`` ``3.2.5`` |``system`` ``3.2.6`` |``system`` @@ -8363,7 +8521,7 @@ version |toolchain ``3.3.7`` |``GCCcore/9.3.0``, ``system`` ``3.3.8`` |``GCCcore/10.2.0`` ``3.3.9`` |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``3.4.0`` |``GCCcore/10.2.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` +``3.4.0`` |``GCCcore/10.2.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0`` ### EigenExa @@ -8482,7 +8640,7 @@ version |versionsuffix |toolchain ``2022.05.001`` | |``foss/2022a``, ``foss/2022b``, ``intel/2022a``, ``intel/2022b`` ``2022.05.001`` |``-CUDA-11.7.0``|``foss/2022a`` ``2022.05.001`` |``-CUDA-12.0.0``|``foss/2022b`` -``2023.05.001`` | |``foss/2023a`` +``2023.05.001`` | |``foss/2023a``, ``intel/2023a`` ### ELPH @@ -8594,7 +8752,7 @@ version |versionsuffix |toolchain ``2.2.1``| |``foss/2019a`` ``2.2.1``|``-Python-2.7.15``|``foss/2018b``, ``intel/2018b`` ``2.2.1``|``-Python-3.6.6`` |``foss/2018b``, ``intel/2018b`` -``3.1.4``| |``foss/2021b`` +``3.1.4``| |``foss/2021b``, ``foss/2022a`` ### EMU @@ -8851,6 +9009,16 @@ version |versionsuffix |toolchain ----------|----------------|------------------ ``0.14.2``|``-Rust-1.65.0``|``GCCcore/12.2.0`` +### EveryBeam + +Library that provides the antenna response pattern for several instruments, such as LOFAR (and LOBES), SKA (OSKAR), MWA, JVLA, etc. + +*homepage*: + +version |toolchain +---------|-------------- +``0.5.2``|``foss/2022a`` + ### EvidentialGene EvidentialGene is a genome informatics project for "Evidence Directed Gene Construction for Eukaryotes", for constructing high quality, accurate gene sets for animals and plants (any eukaryotes), being developed by Don Gilbert at Indiana University, gilbertd at indiana edu. @@ -8953,7 +9121,7 @@ version |toolchain ``2.4.1``|``GCCcore/11.2.0`` ``2.4.8``|``GCCcore/11.3.0``, ``GCCcore/12.1.0`` ``2.4.9``|``GCCcore/12.2.0`` -``2.5.0``|``GCCcore/12.3.0`` +``2.5.0``|``GCCcore/12.3.0``, ``GCCcore/13.2.0`` ### expect @@ -9013,7 +9181,7 @@ version |toolchain ## F -[f90cache](#f90cache) - [f90wrap](#f90wrap) - [Faber](#faber) - [FabIO](#fabio) - [faceswap](#faceswap) - [FALCON](#falcon) - [FANN](#fann) - [fast5](#fast5) - [FASTA](#fasta) - [fastahack](#fastahack) - [fastai](#fastai) - [FastaIndex](#fastaindex) - [FastANI](#fastani) - [Fastaq](#fastaq) - [FastFold](#fastfold) - [fastjet](#fastjet) - [fastjet-contrib](#fastjet-contrib) - [FastME](#fastme) - [fastp](#fastp) - [fastparquet](#fastparquet) - [fastPHASE](#fastphase) - [fastq-pair](#fastq-pair) - [fastq-tools](#fastq-tools) - [FastQ_Screen](#fastq_screen) - [FastQC](#fastqc) - [fastqsplitter](#fastqsplitter) - [FastQTL](#fastqtl) - [fastqz](#fastqz) - [FastRFS](#fastrfs) - [fastStructure](#faststructure) - [FastTree](#fasttree) - [FastViromeExplorer](#fastviromeexplorer) - [FASTX-Toolkit](#fastx-toolkit) - [fatslim](#fatslim) - [fbm](#fbm) - [FBPIC](#fbpic) - [FCC](#fcc) - [FCM](#fcm) - [fdict](#fdict) - [FDS](#fds) - [fdstools](#fdstools) - [FDTD_Solutions](#fdtd_solutions) - [feh](#feh) - [FEniCS](#fenics) - [fermi-lite](#fermi-lite) - [Ferret](#ferret) - [festival](#festival) - [fetchMG](#fetchmg) - [FFC](#ffc) - [FFLAS-FFPACK](#fflas-ffpack) - [FFmpeg](#ffmpeg) - [ffmpi](#ffmpi) - [ffnet](#ffnet) - [ffnvcodec](#ffnvcodec) - [fftlib](#fftlib) - [FFTW](#fftw) - [FFTW.MPI](#fftw.mpi) - [fgbio](#fgbio) - [FGSL](#fgsl) - [FHI-aims](#fhi-aims) - [FIAT](#fiat) - [FIGARO](#figaro) - [FigureGen](#figuregen) - [Fiji](#fiji) - [file](#file) - [filevercmp](#filevercmp) - [Filtlong](#filtlong) - [find_circ](#find_circ) - [finder](#finder) - [findhap](#findhap) - [findutils](#findutils) - [fineRADstructure](#fineradstructure) - [fineSTRUCTURE](#finestructure) - [fio](#fio) - [Fiona](#fiona) - [Firefox](#firefox) - [FIRESTARTER](#firestarter) - [FireWorks](#fireworks) - [FIt-SNE](#fit-sne) - [FIX](#fix) - [fixesproto](#fixesproto) - [FLAC](#flac) - [FLAIR](#flair) - [flair-NLP](#flair-nlp) - [FLANN](#flann) - [FLASH](#flash) - [Flask](#flask) - [flatbuffers](#flatbuffers) - [flatbuffers-python](#flatbuffers-python) - [FLEUR](#fleur) - [flex](#flex) - [Flexbar](#flexbar) - [FlexiBLAS](#flexiblas) - [FlexiDot](#flexidot) - [Flink](#flink) - [FLINT](#flint) - [flit](#flit) - [flook](#flook) - [flowFDA](#flowfda) - [FLTK](#fltk) - [FLUENT](#fluent) - [Flye](#flye) - [FMILibrary](#fmilibrary) - [FMM3D](#fmm3d) - [FMPy](#fmpy) - [FMRIprep](#fmriprep) - [FMS](#fms) - [fmt](#fmt) - [FoBiS](#fobis) - [FoldX](#foldx) - [fontconfig](#fontconfig) - [fontsproto](#fontsproto) - [FORD](#ford) - [foss](#foss) - [fosscuda](#fosscuda) - [FoX](#fox) - [FOX-Toolkit](#fox-toolkit) - [FPM](#fpm) - [fpocket](#fpocket) - [fqtrim](#fqtrim) - [fqzcomp](#fqzcomp) - [FragGeneScan](#fraggenescan) - [FragPipe](#fragpipe) - [FRANz](#franz) - [FreeBarcodes](#freebarcodes) - [freebayes](#freebayes) - [FreeFEM](#freefem) - [FreeFem++](#freefem++) - [freeglut](#freeglut) - [FreeImage](#freeimage) - [FreeSASA](#freesasa) - [FreeSurfer](#freesurfer) - [FreeTDS](#freetds) - [freetype](#freetype) - [freetype-py](#freetype-py) - [FreeXL](#freexl) - [freud-analysis](#freud-analysis) - [FriBidi](#fribidi) - [FRUIT](#fruit) - [FRUIT_processor](#fruit_processor) - [FSL](#fsl) - [FSLeyes](#fsleyes) - [fsom](#fsom) - [FSON](#fson) - [FTGL](#ftgl) - [Fujitsu](#fujitsu) - [fullrmc](#fullrmc) - [fumi_tools](#fumi_tools) - [funannotate](#funannotate) - [FunGAP](#fungap) - [FUNWAVE-TVD](#funwave-tvd) - [FUSE](#fuse) - [FuSeq](#fuseq) - [FusionCatcher](#fusioncatcher) - [futhark](#futhark) - [futile](#futile) - [future](#future) - [fxtract](#fxtract) +[f90cache](#f90cache) - [f90wrap](#f90wrap) - [Faber](#faber) - [FabIO](#fabio) - [faceswap](#faceswap) - [FALCON](#falcon) - [FANN](#fann) - [fast5](#fast5) - [FASTA](#fasta) - [fasta-reader](#fasta-reader) - [fastahack](#fastahack) - [fastai](#fastai) - [FastaIndex](#fastaindex) - [FastANI](#fastani) - [Fastaq](#fastaq) - [FastFold](#fastfold) - [fastjet](#fastjet) - [fastjet-contrib](#fastjet-contrib) - [FastME](#fastme) - [fastp](#fastp) - [fastparquet](#fastparquet) - [fastPHASE](#fastphase) - [fastq-pair](#fastq-pair) - [fastq-tools](#fastq-tools) - [FastQ_Screen](#fastq_screen) - [FastQC](#fastqc) - [fastqsplitter](#fastqsplitter) - [FastQTL](#fastqtl) - [fastqz](#fastqz) - [FastRFS](#fastrfs) - [fastStructure](#faststructure) - [FastTree](#fasttree) - [FastViromeExplorer](#fastviromeexplorer) - [FASTX-Toolkit](#fastx-toolkit) - [fatslim](#fatslim) - [fbm](#fbm) - [FBPIC](#fbpic) - [FCC](#fcc) - [FCM](#fcm) - [fdict](#fdict) - [FDS](#fds) - [fdstools](#fdstools) - [FDTD_Solutions](#fdtd_solutions) - [feh](#feh) - [FEniCS](#fenics) - [fermi-lite](#fermi-lite) - [Ferret](#ferret) - [festival](#festival) - [fetchMG](#fetchmg) - [FFC](#ffc) - [FFLAS-FFPACK](#fflas-ffpack) - [FFmpeg](#ffmpeg) - [ffmpi](#ffmpi) - [ffnet](#ffnet) - [ffnvcodec](#ffnvcodec) - [fftlib](#fftlib) - [FFTW](#fftw) - [FFTW.MPI](#fftw.mpi) - [fgbio](#fgbio) - [FGSL](#fgsl) - [FHI-aims](#fhi-aims) - [FIAT](#fiat) - [FIGARO](#figaro) - [FigureGen](#figuregen) - [Fiji](#fiji) - [file](#file) - [filevercmp](#filevercmp) - [Filtlong](#filtlong) - [find_circ](#find_circ) - [finder](#finder) - [findhap](#findhap) - [findutils](#findutils) - [fineRADstructure](#fineradstructure) - [fineSTRUCTURE](#finestructure) - [fio](#fio) - [Fiona](#fiona) - [Firefox](#firefox) - [FIRESTARTER](#firestarter) - [FireWorks](#fireworks) - [FIt-SNE](#fit-sne) - [FIX](#fix) - [fixesproto](#fixesproto) - [FLAC](#flac) - [FLAIR](#flair) - [flair-NLP](#flair-nlp) - [FLANN](#flann) - [FLASH](#flash) - [Flask](#flask) - [flatbuffers](#flatbuffers) - [flatbuffers-python](#flatbuffers-python) - [FLEUR](#fleur) - [flex](#flex) - [Flexbar](#flexbar) - [FlexiBLAS](#flexiblas) - [FlexiDot](#flexidot) - [Flink](#flink) - [FLINT](#flint) - [flit](#flit) - [flook](#flook) - [flowFDA](#flowfda) - [FLTK](#fltk) - [FLUENT](#fluent) - [Flye](#flye) - [FMILibrary](#fmilibrary) - [FMM3D](#fmm3d) - [FMPy](#fmpy) - [FMRIprep](#fmriprep) - [FMS](#fms) - [fmt](#fmt) - [FoBiS](#fobis) - [FoldX](#foldx) - [fontconfig](#fontconfig) - [fontsproto](#fontsproto) - [FORD](#ford) - [foss](#foss) - [fosscuda](#fosscuda) - [FoX](#fox) - [FOX-Toolkit](#fox-toolkit) - [FPM](#fpm) - [fpocket](#fpocket) - [fqtrim](#fqtrim) - [fqzcomp](#fqzcomp) - [FragGeneScan](#fraggenescan) - [FragPipe](#fragpipe) - [FRANz](#franz) - [FreeBarcodes](#freebarcodes) - [freebayes](#freebayes) - [FreeFEM](#freefem) - [FreeFem++](#freefem++) - [freeglut](#freeglut) - [FreeImage](#freeimage) - [FreeSASA](#freesasa) - [FreeSurfer](#freesurfer) - [FreeTDS](#freetds) - [freetype](#freetype) - [freetype-py](#freetype-py) - [FreeXL](#freexl) - [freud-analysis](#freud-analysis) - [FriBidi](#fribidi) - [FRUIT](#fruit) - [FRUIT_processor](#fruit_processor) - [FSL](#fsl) - [FSLeyes](#fsleyes) - [fsom](#fsom) - [FSON](#fson) - [FTGL](#ftgl) - [Fujitsu](#fujitsu) - [fullrmc](#fullrmc) - [fumi_tools](#fumi_tools) - [funannotate](#funannotate) - [FunGAP](#fungap) - [FUNWAVE-TVD](#funwave-tvd) - [FUSE](#fuse) - [FuSeq](#fuseq) - [FusionCatcher](#fusioncatcher) - [futhark](#futhark) - [futile](#futile) - [future](#future) - [fxtract](#fxtract) ### f90cache @@ -9110,6 +9278,16 @@ version |toolchain ``36.3.5e``|``foss/2016b`` ``36.3.8i``|``GCC/11.2.0``, ``GCC/12.2.0`` +### fasta-reader + +FASTA file reader + +*homepage*: + +version |toolchain +---------|-------------- +``3.0.2``|``GCC/12.3.0`` + ### fastahack Utilities for indexing and sequence extraction from FASTA files. @@ -9154,6 +9332,7 @@ version |toolchain ``1.3`` |``iccifort/2019.5.281`` ``1.31``|``iccifort/2020.1.217`` ``1.33``|``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0``, ``iccifort/2020.4.304``, ``intel-compilers/2021.4.0`` +``1.34``|``GCC/12.3.0`` ### Fastaq @@ -9205,6 +9384,7 @@ version |toolchain -----------|---------------------------------------------------------------------------------------- ``2.1.5`` |``foss/2016a`` ``2.1.6.1``|``GCC/10.2.0``, ``GCC/8.3.0``, ``iccifort/2019.5.281``, ``intel/2018a``, ``intel/2018b`` +``2.1.6.3``|``GCC/12.3.0`` ### fastp @@ -9660,7 +9840,7 @@ version |versionsuffix|toolchain ``3.3.8`` |``-amd`` |``gompi/2020a`` ``3.3.8`` |``-serial`` |``GCC/9.3.0`` ``3.3.9`` | |``gompi/2021a``, ``intel/2021a`` -``3.3.10``| |``GCC/11.3.0``, ``GCC/12.2.0``, ``GCC/12.3.0``, ``NVHPC/22.7-CUDA-11.7.0``, ``gompi/2021b``, ``iimpi/2021b``, ``iimpi/2022a``, ``iimpi/2022b`` +``3.3.10``| |``GCC/11.3.0``, ``GCC/12.2.0``, ``GCC/12.3.0``, ``GCC/13.2.0``, ``NVHPC/22.7-CUDA-11.7.0``, ``gompi/2021b``, ``iimpi/2021b``, ``iimpi/2022a``, ``iimpi/2022b`` ### FFTW.MPI @@ -9669,8 +9849,8 @@ FFTW is a C subroutine library for computing the discrete Fourier transform (DFT *homepage*: version |toolchain -----------|----------------------------------------------------------------------------------------------------------- -``3.3.10``|``gompi/2022.05``, ``gompi/2022.10``, ``gompi/2022a``, ``gompi/2022b``, ``gompi/2023a``, ``nvompi/2022.07`` +----------|------------------------------------------------------------------------------------------------------------------------------ +``3.3.10``|``gompi/2022.05``, ``gompi/2022.10``, ``gompi/2022a``, ``gompi/2022b``, ``gompi/2023.09``, ``gompi/2023a``, ``nvompi/2022.07`` ### fgbio @@ -10012,6 +10192,7 @@ version |versionsuffix |toolchain ``2.0.2``| |``GCCcore/11.2.0`` ``2.2.2``| |``GCCcore/11.3.0`` ``2.2.3``| |``GCCcore/12.2.0`` +``2.3.3``| |``GCCcore/12.3.0`` ### flatbuffers @@ -10089,7 +10270,7 @@ version |toolchain ``3.1.3``|``GCC/11.2.0`` ``3.2.0``|``GCC/11.3.0``, ``NVHPC/22.7-CUDA-11.7.0`` ``3.2.1``|``GCC/12.2.0`` -``3.3.1``|``GCC/12.3.0`` +``3.3.1``|``GCC/12.3.0``, ``GCC/13.2.0`` ### FlexiDot @@ -10204,6 +10385,7 @@ version |versionsuffix |toolchain ``2.8.3``| |``GCC/10.2.0``, ``iccifort/2020.4.304`` ``2.9`` | |``GCC/10.3.0``, ``intel-compilers/2021.2.0`` ``2.9.1``| |``GCC/11.2.0`` +``2.9.2``| |``GCC/11.3.0`` ### FMILibrary @@ -10270,8 +10452,10 @@ version |toolchain ``6.2.1`` |``GCCcore/9.3.0`` ``7.0.3`` |``GCCcore/9.3.0`` ``7.1.1`` |``GCCcore/11.2.0`` +``8.1.1`` |``GCCcore/11.2.0`` ``9.1.0`` |``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ``10.0.0``|``GCCcore/12.3.0`` +``10.1.0``|``GCCcore/12.3.0`` ### FoBiS @@ -10317,7 +10501,7 @@ version |versionsuffix |toolchain ``2.13.94``| |``GCCcore/11.2.0`` ``2.14.0`` | |``GCCcore/11.3.0`` ``2.14.1`` | |``GCCcore/12.2.0`` -``2.14.2`` | |``GCCcore/12.3.0`` +``2.14.2`` | |``GCCcore/12.3.0``, ``GCCcore/13.2.0`` ### fontsproto @@ -10370,6 +10554,7 @@ version |toolchain ``2022.10``|``system`` ``2022a`` |``system`` ``2022b`` |``system`` +``2023.09``|``system`` ``2023a`` |``system`` ### fosscuda @@ -10620,6 +10805,7 @@ version |versionsuffix |toolchain ``2.11.0``| |``GCCcore/11.2.0`` ``2.12.1``| |``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ``2.13.0``| |``GCCcore/12.3.0`` +``2.13.2``| |``GCCcore/13.2.0`` ### freetype-py @@ -10895,7 +11081,7 @@ version|toolchain ## G -[G-PhoCS](#g-phocs) - [g2clib](#g2clib) - [g2lib](#g2lib) - [g2log](#g2log) - [Gaia](#gaia) - [GAMESS-US](#gamess-us) - [gap](#gap) - [GapCloser](#gapcloser) - [GapFiller](#gapfiller) - [gappa](#gappa) - [GAPPadder](#gappadder) - [GARLI](#garli) - [garnett](#garnett) - [GAT](#gat) - [GATB-Core](#gatb-core) - [GATE](#gate) - [GATK](#gatk) - [Gaussian](#gaussian) - [gawk](#gawk) - [gbasis](#gbasis) - [Gblocks](#gblocks) - [GBprocesS](#gbprocess) - [gbs2ploidy](#gbs2ploidy) - [gc](#gc) - [GC3Pie](#gc3pie) - [GCC](#gcc) - [GCCcore](#gcccore) - [gcccuda](#gcccuda) - [gcloud](#gcloud) - [GConf](#gconf) - [GCTA](#gcta) - [Gctf](#gctf) - [GD](#gd) - [GDAL](#gdal) - [GDB](#gdb) - [gdbgui](#gdbgui) - [gdbm](#gdbm) - [gdc-client](#gdc-client) - [GDCHART](#gdchart) - [GDCM](#gdcm) - [GDGraph](#gdgraph) - [gdist](#gdist) - [Gdk-Pixbuf](#gdk-pixbuf) - [GDRCopy](#gdrcopy) - [Geant4](#geant4) - [Geant4-data](#geant4-data) - [gearshifft](#gearshifft) - [GEGL](#gegl) - [GEM](#gem) - [GEM-library](#gem-library) - [gemelli](#gemelli) - [GEMMA](#gemma) - [gemmi](#gemmi) - [gencore_variant_detection](#gencore_variant_detection) - [GeneMark-ET](#genemark-et) - [GenerativeModels](#generativemodels) - [gengetopt](#gengetopt) - [GenMap](#genmap) - [Genome_Profiler](#genome_profiler) - [GenomeMapper](#genomemapper) - [genomepy](#genomepy) - [GenomeTester4](#genometester4) - [GenomeThreader](#genomethreader) - [GenomeTools](#genometools) - [GenomeWorks](#genomeworks) - [GenotypeHarmonizer](#genotypeharmonizer) - [genozip](#genozip) - [gensim](#gensim) - [geocube](#geocube) - [geopandas](#geopandas) - [geopy](#geopy) - [georges](#georges) - [GEOS](#geos) - [geosphere](#geosphere) - [Gerris](#gerris) - [GETORB](#getorb) - [GetOrganelle](#getorganelle) - [gettext](#gettext) - [gexiv2](#gexiv2) - [gfbf](#gfbf) - [GffCompare](#gffcompare) - [gffread](#gffread) - [gffutils](#gffutils) - [gflags](#gflags) - [GFOLD](#gfold) - [gh](#gh) - [GHC](#ghc) - [Ghostscript](#ghostscript) - [Gibbs2](#gibbs2) - [giflib](#giflib) - [gifsicle](#gifsicle) - [GIMIC](#gimic) - [gimkl](#gimkl) - [GimmeMotifs](#gimmemotifs) - [GIMP](#gimp) - [gimpi](#gimpi) - [gimpic](#gimpic) - [GIMPS](#gimps) - [giolf](#giolf) - [giolfc](#giolfc) - [Giotto-Suite](#giotto-suite) - [git](#git) - [git-extras](#git-extras) - [git-lfs](#git-lfs) - [GitPython](#gitpython) - [Givaro](#givaro) - [Giza](#giza) - [GKeyll](#gkeyll) - [gkmSVM](#gkmsvm) - [GL2PS](#gl2ps) - [Glade](#glade) - [glew](#glew) - [GLFW](#glfw) - [GLI](#gli) - [GLib](#glib) - [glib-networking](#glib-networking) - [glibc](#glibc) - [GLibmm](#glibmm) - [GLIMMER](#glimmer) - [GlimmerHMM](#glimmerhmm) - [GLIMPSE](#glimpse) - [GLM](#glm) - [GLM-AED](#glm-aed) - [GlobalArrays](#globalarrays) - [Globus-CLI](#globus-cli) - [GlobusConnectPersonal](#globusconnectpersonal) - [glog](#glog) - [GLPK](#glpk) - [glproto](#glproto) - [Glucose](#glucose) - [GMAP-GSNAP](#gmap-gsnap) - [GMP](#gmp) - [gmpich](#gmpich) - [gmpolf](#gmpolf) - [gmpy2](#gmpy2) - [gmsh](#gmsh) - [GMT](#gmt) - [gmvapich2](#gmvapich2) - [gmvolf](#gmvolf) - [GNU](#gnu) - [gnuplot](#gnuplot) - [GnuTLS](#gnutls) - [Go](#go) - [goalign](#goalign) - [GOATOOLS](#goatools) - [gobff](#gobff) - [GObject-Introspection](#gobject-introspection) - [goblf](#goblf) - [GOBNILP](#gobnilp) - [Godon](#godon) - [gofasta](#gofasta) - [golf](#golf) - [gomkl](#gomkl) - [gompi](#gompi) - [gompic](#gompic) - [google-java-format](#google-java-format) - [googletest](#googletest) - [gotree](#gotree) - [GP2C](#gp2c) - [GPAW](#gpaw) - [GPAW-setups](#gpaw-setups) - [gperf](#gperf) - [gperftools](#gperftools) - [gpustat](#gpustat) - [GPy](#gpy) - [GPyOpt](#gpyopt) - [GPyTorch](#gpytorch) - [Grace](#grace) - [Gradle](#gradle) - [gradunwarp](#gradunwarp) - [graph-tool](#graph-tool) - [GraphDB](#graphdb) - [Graphene](#graphene) - [GraphicsMagick](#graphicsmagick) - [graphite2](#graphite2) - [GraPhlAn](#graphlan) - [GraphMap](#graphmap) - [GraphMap2](#graphmap2) - [Graphviz](#graphviz) - [graphviz-python](#graphviz-python) - [GRASP](#grasp) - [GRASS](#grass) - [Greenlet](#greenlet) - [Grep](#grep) - [gretl](#gretl) - [grib_api](#grib_api) - [grid](#grid) - [GRIDSS](#gridss) - [GRIT](#grit) - [GRNBoost](#grnboost) - [groff](#groff) - [GroIMP](#groimp) - [GROMACS](#gromacs) - [GromacsWrapper](#gromacswrapper) - [Groovy](#groovy) - [gRPC](#grpc) - [GSEA](#gsea) - [gsettings-desktop-schemas](#gsettings-desktop-schemas) - [GSL](#gsl) - [gSOAP](#gsoap) - [gsport](#gsport) - [GST-plugins-bad](#gst-plugins-bad) - [GST-plugins-base](#gst-plugins-base) - [GStreamer](#gstreamer) - [gsutil](#gsutil) - [gsw](#gsw) - [GTDB-Tk](#gtdb-tk) - [GTK+](#gtk+) - [GTK2](#gtk2) - [GTK3](#gtk3) - [GTK4](#gtk4) - [GtkSourceView](#gtksourceview) - [GTOOL](#gtool) - [GTS](#gts) - [gubbins](#gubbins) - [guenomu](#guenomu) - [Guile](#guile) - [GULP](#gulp) - [Gurobi](#gurobi) - [GUSHR](#gushr) - [gzip](#gzip) +[G-PhoCS](#g-phocs) - [g2clib](#g2clib) - [g2lib](#g2lib) - [g2log](#g2log) - [Gaia](#gaia) - [GAMESS-US](#gamess-us) - [gap](#gap) - [GapCloser](#gapcloser) - [GapFiller](#gapfiller) - [gappa](#gappa) - [GAPPadder](#gappadder) - [GARLI](#garli) - [garnett](#garnett) - [GAT](#gat) - [GATB-Core](#gatb-core) - [GATE](#gate) - [GATK](#gatk) - [Gaussian](#gaussian) - [gawk](#gawk) - [gbasis](#gbasis) - [Gblocks](#gblocks) - [GBprocesS](#gbprocess) - [gbs2ploidy](#gbs2ploidy) - [gc](#gc) - [GC3Pie](#gc3pie) - [GCC](#gcc) - [GCCcore](#gcccore) - [gcccuda](#gcccuda) - [gcloud](#gcloud) - [GConf](#gconf) - [GCTA](#gcta) - [Gctf](#gctf) - [GD](#gd) - [GDAL](#gdal) - [GDB](#gdb) - [gdbgui](#gdbgui) - [gdbm](#gdbm) - [gdc-client](#gdc-client) - [GDCHART](#gdchart) - [GDCM](#gdcm) - [GDGraph](#gdgraph) - [gdist](#gdist) - [Gdk-Pixbuf](#gdk-pixbuf) - [GDRCopy](#gdrcopy) - [Geant4](#geant4) - [Geant4-data](#geant4-data) - [gearshifft](#gearshifft) - [GEGL](#gegl) - [GEM](#gem) - [GEM-library](#gem-library) - [gemelli](#gemelli) - [GEMMA](#gemma) - [gemmi](#gemmi) - [gencore_variant_detection](#gencore_variant_detection) - [GeneMark-ET](#genemark-et) - [GenerativeModels](#generativemodels) - [gengetopt](#gengetopt) - [GenMap](#genmap) - [Genome_Profiler](#genome_profiler) - [GenomeMapper](#genomemapper) - [genomepy](#genomepy) - [GenomeTester4](#genometester4) - [GenomeThreader](#genomethreader) - [GenomeTools](#genometools) - [GenomeWorks](#genomeworks) - [GenotypeHarmonizer](#genotypeharmonizer) - [genozip](#genozip) - [gensim](#gensim) - [geocube](#geocube) - [geopandas](#geopandas) - [geopy](#geopy) - [georges](#georges) - [GEOS](#geos) - [geosphere](#geosphere) - [Gerris](#gerris) - [GETORB](#getorb) - [GetOrganelle](#getorganelle) - [gettext](#gettext) - [gexiv2](#gexiv2) - [gfbf](#gfbf) - [GffCompare](#gffcompare) - [gffread](#gffread) - [gffutils](#gffutils) - [gflags](#gflags) - [GFOLD](#gfold) - [gh](#gh) - [GHC](#ghc) - [Ghostscript](#ghostscript) - [Gibbs2](#gibbs2) - [giflib](#giflib) - [gifsicle](#gifsicle) - [GIMIC](#gimic) - [gimkl](#gimkl) - [GimmeMotifs](#gimmemotifs) - [GIMP](#gimp) - [gimpi](#gimpi) - [gimpic](#gimpic) - [GIMPS](#gimps) - [giolf](#giolf) - [giolfc](#giolfc) - [Giotto-Suite](#giotto-suite) - [git](#git) - [git-annex](#git-annex) - [git-extras](#git-extras) - [git-lfs](#git-lfs) - [GitPython](#gitpython) - [Givaro](#givaro) - [Giza](#giza) - [GKeyll](#gkeyll) - [gkmSVM](#gkmsvm) - [GL2PS](#gl2ps) - [Glade](#glade) - [glew](#glew) - [GLFW](#glfw) - [GLI](#gli) - [GLib](#glib) - [glib-networking](#glib-networking) - [glibc](#glibc) - [GLibmm](#glibmm) - [GLIMMER](#glimmer) - [GlimmerHMM](#glimmerhmm) - [GLIMPSE](#glimpse) - [GLM](#glm) - [GLM-AED](#glm-aed) - [GlobalArrays](#globalarrays) - [Globus-CLI](#globus-cli) - [GlobusConnectPersonal](#globusconnectpersonal) - [glog](#glog) - [GLPK](#glpk) - [glproto](#glproto) - [Glucose](#glucose) - [GMAP-GSNAP](#gmap-gsnap) - [GMP](#gmp) - [gmpich](#gmpich) - [gmpolf](#gmpolf) - [gmpy2](#gmpy2) - [gmsh](#gmsh) - [GMT](#gmt) - [gmvapich2](#gmvapich2) - [gmvolf](#gmvolf) - [GNU](#gnu) - [gnuplot](#gnuplot) - [GnuTLS](#gnutls) - [Go](#go) - [goalign](#goalign) - [GOATOOLS](#goatools) - [gobff](#gobff) - [GObject-Introspection](#gobject-introspection) - [goblf](#goblf) - [GOBNILP](#gobnilp) - [Godon](#godon) - [gofasta](#gofasta) - [golf](#golf) - [gomkl](#gomkl) - [gompi](#gompi) - [gompic](#gompic) - [google-java-format](#google-java-format) - [googletest](#googletest) - [gotree](#gotree) - [GP2C](#gp2c) - [GPAW](#gpaw) - [GPAW-setups](#gpaw-setups) - [gperf](#gperf) - [gperftools](#gperftools) - [gpustat](#gpustat) - [GPy](#gpy) - [GPyOpt](#gpyopt) - [GPyTorch](#gpytorch) - [Grace](#grace) - [Gradle](#gradle) - [gradunwarp](#gradunwarp) - [graph-tool](#graph-tool) - [GraphDB](#graphdb) - [Graphene](#graphene) - [GraphicsMagick](#graphicsmagick) - [graphite2](#graphite2) - [GraPhlAn](#graphlan) - [GraphMap](#graphmap) - [GraphMap2](#graphmap2) - [Graphviz](#graphviz) - [graphviz-python](#graphviz-python) - [GRASP](#grasp) - [GRASS](#grass) - [Greenlet](#greenlet) - [Grep](#grep) - [gretl](#gretl) - [grib_api](#grib_api) - [grid](#grid) - [GRIDSS](#gridss) - [GRIT](#grit) - [GRNBoost](#grnboost) - [groff](#groff) - [GroIMP](#groimp) - [GROMACS](#gromacs) - [GromacsWrapper](#gromacswrapper) - [Groovy](#groovy) - [gRPC](#grpc) - [GSD](#gsd) - [GSEA](#gsea) - [gsettings-desktop-schemas](#gsettings-desktop-schemas) - [GSL](#gsl) - [gSOAP](#gsoap) - [gsport](#gsport) - [GST-plugins-bad](#gst-plugins-bad) - [GST-plugins-base](#gst-plugins-base) - [GStreamer](#gstreamer) - [gsutil](#gsutil) - [gsw](#gsw) - [GTDB-Tk](#gtdb-tk) - [GTK+](#gtk+) - [GTK2](#gtk2) - [GTK3](#gtk3) - [GTK4](#gtk4) - [GtkSourceView](#gtksourceview) - [GTOOL](#gtool) - [GTS](#gts) - [gubbins](#gubbins) - [guenomu](#guenomu) - [Guile](#guile) - [GULP](#gulp) - [Gurobi](#gurobi) - [GUSHR](#gushr) - [gzip](#gzip) ### G-PhoCS @@ -11085,7 +11271,7 @@ The Genome Analysis Toolkit or GATK is a software package developed at the Broad *homepage*: version |versionsuffix |toolchain -------------|-------------------|------------------ +------------|-------------------|-------------------------------------- ``1.0.5083``| |``system`` ``2.5-2`` |``-Java-1.7.0_10`` |``system`` ``2.6-5`` |``-Java-1.7.0_10`` |``system`` @@ -11123,9 +11309,9 @@ version |versionsuffix |toolchain ``4.2.0.0`` |``-Java-11`` |``GCCcore/10.2.0`` ``4.2.3.0`` |``-Java-11`` |``GCCcore/11.2.0`` ``4.2.5.0`` |``-Java-11`` |``GCCcore/11.2.0`` -``4.2.6.1`` |``-Java-11`` |``GCCcore/11.2.0`` +``4.2.6.1`` |``-Java-11`` |``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``4.3.0.0`` |``-Java-11`` |``GCCcore/11.3.0`` -``4.4.0.0`` |``-Java-17`` |``GCCcore/12.2.0`` +``4.4.0.0`` |``-Java-17`` |``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### Gaussian @@ -11451,6 +11637,7 @@ version |versionsuffix |toolchain ``3.3.2``| |``foss/2021b`` ``3.5.0``| |``foss/2022a`` ``3.6.2``| |``foss/2022b`` +``3.7.1``| |``foss/2023a`` ### GDB @@ -11459,7 +11646,7 @@ The GNU Project Debugger *homepage*: version |versionsuffix |toolchain -----------|------------------|------------------------------- +----------|------------------|---------------------------------------------------------- ``7.8.2`` | |``GCC/4.9.2`` ``7.9`` | |``GCC/4.9.2`` ``7.10.1``|``-Python-2.7.11``|``foss/2016a``, ``intel/2016a`` @@ -11476,7 +11663,7 @@ version |versionsuffix |toolchain ``10.2`` |``-Python-3.8.2`` |``GCCcore/9.3.0`` ``11.1`` | |``GCCcore/11.2.0`` ``12.1`` | |``GCCcore/11.3.0`` -``13.2`` | |``GCCcore/12.3.0`` +``13.2`` | |``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0`` ### gdbgui @@ -11596,6 +11783,7 @@ version |versionsuffix |toolchain ``2.2`` | |``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ``2.3`` | |``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ``2.3.1``| |``GCCcore/12.3.0`` +``2.4`` | |``GCCcore/13.2.0`` ### Geant4 @@ -11689,10 +11877,10 @@ Genome-wide Efficient Mixed Model Association *homepage*: version |toolchain -----------|------------------------------ +----------|---------------------------------------------- ``0.97`` |``foss/2016b``, ``foss/2017a`` ``0.98.1``|``foss/2018b`` -``0.98.5``|``foss/2021b``, ``foss/2022b`` +``0.98.5``|``foss/2020a``, ``foss/2021b``, ``foss/2022b`` ### gemmi @@ -12021,11 +12209,12 @@ GNU Compiler Collection (GCC) based compiler toolchain, including FlexiBLAS (BL *homepage*: <(none)> -version |toolchain ----------|---------- -``2022a``|``system`` -``2022b``|``system`` -``2023a``|``system`` +version |toolchain +-----------|---------- +``2022a`` |``system`` +``2022b`` |``system`` +``2023.09``|``system`` +``2023a`` |``system`` ### GffCompare @@ -12150,9 +12339,9 @@ giflib is a library for reading and writing gif images. It is API and ABI compat *homepage*: version |toolchain ----------|------------------------------------------------------------------------------------------------------------------------------------------------------------ +---------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ``5.1.4``|``GCCcore/7.3.0``, ``GCCcore/8.2.0`` -``5.2.1``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``5.2.1``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ### gifsicle @@ -12301,6 +12490,17 @@ version |versionsuffix|toolchain ``2.36.0`` |``-nodocs`` |``GCCcore/11.3.0`` ``2.38.1`` |``-nodocs`` |``GCCcore/12.2.0`` ``2.41.0`` |``-nodocs`` |``GCCcore/12.3.0`` +``2.42.0`` | |``GCCcore/13.2.0`` + +### git-annex + +git-annex allows managing large files with git, without storing the file contents in git. It can sync, backup, and archive your data, offline and online. Checksums and encryption keep your data safe and secure. Bring the power and distributed nature of git to bear on your large files with git-annex. + +*homepage*: + +version |toolchain +---------------|------------------ +``10.20230802``|``GCCcore/12.2.0`` ### git-extras @@ -12576,7 +12776,7 @@ version |versionsuffix|toolchain ``5.7.2``|``-peigs`` |``intel/2019b`` ``5.8`` | |``intel/2020a``, ``intel/2021a``, ``iomkl/2021a`` ``5.8.1``| |``intel/2022a`` -``5.8.2``| |``intel/2022a`` +``5.8.2``| |``intel/2022a``, ``intel/2023a`` ### Globus-CLI @@ -12655,7 +12855,7 @@ GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences GSNAP: *homepage*: version |toolchain ---------------|--------------- +--------------|------------------------------ ``2016-05-01``|``foss/2016a`` ``2016-11-07``|``foss/2016b`` ``2018-05-11``|``intel/2018a`` @@ -12665,7 +12865,7 @@ version |toolchain ``2020-12-17``|``GCC/9.3.0`` ``2021-12-17``|``GCC/11.2.0`` ``2023-02-17``|``GCC/11.3.0`` -``2023-04-20``|``GCC/12.2.0`` +``2023-04-20``|``GCC/10.3.0``, ``GCC/12.2.0`` ### GMP @@ -12684,6 +12884,7 @@ version |toolchain ``6.1.2`` |``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2016b`` ``6.2.0`` |``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ``6.2.1`` |``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` +``6.3.0`` |``GCCcore/13.2.0`` ### gmpich @@ -12723,7 +12924,7 @@ version |versionsuffix |toolchain ``2.1.0b4``| |``GCC/8.3.0`` ``2.1.0b5``| |``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/9.3.0``, ``iccifort/2020.4.304`` ``2.1.2`` | |``GCC/11.2.0``, ``GCC/11.3.0``, ``intel-compilers/2021.4.0``, ``intel-compilers/2022.1.0`` -``2.1.5`` | |``GCC/12.3.0`` +``2.1.5`` | |``GCC/12.2.0``, ``GCC/12.3.0`` ### gmsh @@ -12853,6 +13054,8 @@ version |toolchain ``1.18.1``|``system`` ``1.18.3``|``system`` ``1.20.4``|``system`` +``1.21.1``|``system`` +``1.21.2``|``system`` ### goalign @@ -13013,6 +13216,7 @@ version |versionsuffix|toolchain ``2022.10``| |``system`` ``2022a`` | |``system`` ``2022b`` | |``system`` +``2023.09``| |``system`` ``2023a`` | |``system`` ``system`` |``-2.29`` |``system`` @@ -13056,6 +13260,7 @@ version |toolchain ``1.11.0``|``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ``1.12.1``|``GCCcore/12.2.0`` ``1.13.0``|``GCCcore/12.3.0`` +``1.14.0``|``GCCcore/13.2.0`` ### gotree @@ -13095,6 +13300,7 @@ version |versionsuffix |toolchain ``21.6.0`` | |``foss/2021a`` ``21.6.0`` |``-ASE-3.22.0`` |``foss/2020b``, ``intel/2020b`` ``22.8.0`` | |``foss/2021b``, ``foss/2022a``, ``intel/2021b``, ``intel/2022a`` +``23.9.1`` | |``foss/2022a``, ``foss/2023a``, ``intel/2022a`` ### GPAW-setups @@ -13116,9 +13322,9 @@ GNU gperf is a perfect hash function generator. For a given list of strings, it *homepage*: version |toolchain ----------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +---------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ``3.0.4``|``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` -``3.1`` |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``3.1`` |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ### gperftools @@ -13455,6 +13661,7 @@ Groff (GNU troff) is a typesetting system that reads plain text mixed with forma version |toolchain ----------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ``1.22.4``|``FCC/4.5.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.1.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``1.23.0``|``GCCcore/13.2.0`` ### GroIMP @@ -13548,6 +13755,16 @@ version |toolchain ``1.44.0``|``GCCcore/11.2.0`` ``1.57.0``|``GCCcore/12.3.0`` +### GSD + +The GSD file format is the native file format for HOOMD-blue. GSD files store trajectories of the HOOMD-blue system state in a binary file with efficient random access to frames. GSD allows all particle and topology properties to vary from one frame to the next. Use the GSD Python API to specify the initial condition for a HOOMD-blue simulation or analyze trajectory output with a script. Read a GSD trajectory with a visualization tool to explore the behavior of the simulation. + +*homepage*: + +version |toolchain +---------|-------------- +``3.2.0``|``foss/2022a`` + ### GSEA Gene Set Enrichment Analysis (GSEA) is a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states (e.g. phenotypes). @@ -13613,9 +13830,9 @@ GStreamer is a library for constructing graphs of media-handling components. Th *homepage*: version |toolchain -----------|-------------- +----------|------------------------------ ``1.20.2``|``GCC/11.3.0`` -``1.22.5``|``GCC/12.2.0`` +``1.22.5``|``GCC/12.2.0``, ``GCC/12.3.0`` ### GST-plugins-base @@ -13692,6 +13909,7 @@ version |versionsuffix |toolchain ``1.7.0``| |``foss/2020b``, ``foss/2021a``, ``intel/2020b`` ``2.0.0``| |``foss/2021a``, ``intel/2021b`` ``2.1.1``| |``foss/2021b`` +``2.3.2``| |``foss/2022a`` ### GTK+ @@ -13746,6 +13964,7 @@ version |toolchain ----------|-------------- ``4.7.0`` |``GCC/11.3.0`` ``4.11.3``|``GCC/12.2.0`` +``4.13.1``|``GCC/12.3.0`` ### GtkSourceView @@ -13876,6 +14095,7 @@ version |toolchain ``1.9`` |``GCCcore/7.3.0`` ``1.10``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``1.12``|``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` +``1.13``|``GCCcore/13.2.0`` ## H @@ -13912,9 +14132,9 @@ A Python interface for the netCDF4 file-format that reads and writes local or re *homepage*: version |toolchain ----------|-------------- +---------|------------------------------ ``1.1.0``|``foss/2021b`` -``1.2.0``|``foss/2022a`` +``1.2.0``|``foss/2022a``, ``foss/2023a`` ### h5py @@ -14083,6 +14303,7 @@ Harmony is a general-purpose R package with an efficient algorithm for integrati version |versionsuffix|toolchain ------------------|-------------|-------------- +``0.1.0-20210528``|``-R-4.0.3`` |``foss/2020b`` ``1.0.0-20200224``|``-R-4.0.0`` |``foss/2020a`` ### hatchling @@ -14146,14 +14367,16 @@ HDF (also known as HDF4) is a library and multi-object file format for storing *homepage*: -version |versionsuffix |toolchain -----------|--------------|--------------------------------------------------------------------------------------------------------------------- -``4.2.11``| |``intel/2016a`` -``4.2.12``| |``intel/2017a`` -``4.2.13``| |``GCCcore/6.4.0`` -``4.2.13``|``-no-netcdf``|``intel/2017a`` -``4.2.14``| |``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``4.2.15``| |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/9.3.0`` +version |versionsuffix |toolchain +------------|--------------|--------------------------------------------------------------------------------------------------------------------- +``4.2.11`` | |``intel/2016a`` +``4.2.12`` | |``intel/2017a`` +``4.2.13`` | |``GCCcore/6.4.0`` +``4.2.13`` |``-no-netcdf``|``intel/2017a`` +``4.2.14`` | |``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``4.2.15`` | |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/9.3.0`` +``4.2.16`` | |``GCCcore/12.3.0`` +``4.2.16-2``| |``GCCcore/12.3.0`` ### HDF-EOS @@ -14409,6 +14632,7 @@ HighFive is a modern header-only C++11 friendly interface for libhdf5. version |toolchain ---------|-------------------------------- ``2.6.2``|``gompi/2021a``, ``gompi/2022a`` +``2.7.1``|``gompi/2023a`` ### Highway @@ -14421,6 +14645,7 @@ version |toolchain ``0.12.2``|``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ``1.0.3`` |``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ``1.0.4`` |``GCCcore/11.3.0``, ``GCCcore/12.3.0`` +``1.0.7`` |``GCCcore/13.2.0`` ### HIP @@ -14480,13 +14705,13 @@ HISAT2 is a fast and sensitive alignment program for mapping next-generation seq *homepage*: version |toolchain ---------------|--------------------------------------------------------------------------------- +--------------|-------------------------------------------------------------------------------------------------- ``2.0.3-beta``|``intel/2016a`` ``2.0.4`` |``foss/2016b`` ``2.0.5`` |``intel/2017a`` ``2.1.0`` |``foss/2017b``, ``foss/2018b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` ``2.2.0`` |``foss/2018b`` -``2.2.1`` |``foss/2019b``, ``foss/2020a``, ``gompi/2020b``, ``gompi/2021b``, ``gompi/2022a`` +``2.2.1`` |``foss/2019b``, ``foss/2020a``, ``gompi/2020b``, ``gompi/2021a``, ``gompi/2021b``, ``gompi/2022a`` ### histolab @@ -14540,6 +14765,7 @@ version |toolchain ``3.2.1``|``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``gompi/2019b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iimpi/2019b``, ``intel/2018b`` ``3.3.1``|``gompi/2020a``, ``iimpi/2020a`` ``3.3.2``|``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b``, ``gompi/2021a``, ``gompi/2021b``, ``gompi/2022a``, ``gompi/2022b``, ``gompic/2020b``, ``iimpi/2020b``, ``iimpi/2021b`` +``3.4`` |``gompi/2023a`` ### HMMER2 @@ -14561,6 +14787,7 @@ version |versionsuffix |toolchain ---------|------------------|--------------- ``0.2.0``|``-Python-2.7.14``|``intel/2017b`` ``0.2.0``|``-Python-3.6.4`` |``intel/2018a`` +``0.3.0``| |``foss/2022b`` ### HOME @@ -14619,6 +14846,7 @@ version |versionsuffix |toolchain ``0.28.1``|``-CUDA-11.5.2-PyTorch-1.12.1`` |``foss/2021b`` ``0.28.1``|``-CUDA-11.7.0-PyTorch-1.12.0`` |``foss/2022a`` ``0.28.1``|``-CUDA-11.7.0-PyTorch-1.12.1`` |``foss/2022a`` +``0.28.1``|``-CUDA-11.7.0-PyTorch-1.13.1`` |``foss/2022a`` ``0.28.1``|``-CUDA-11.7.0-TensorFlow-2.11.0`` |``foss/2022a`` ``0.28.1``|``-CUDA-11.7.0-TensorFlow-2.9.1`` |``foss/2022a`` ``0.28.1``|``-PyTorch-1.9.0`` |``fosscuda/2020b`` @@ -14651,9 +14879,9 @@ The HPCG Benchmark project is an effort to create a more relevant metric for ran *homepage*: version|toolchain --------|------------------------------------------------------------------------------------------------- +-------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ``3.0``|``foss/2016b``, ``foss/2018b``, ``intel/2018b`` -``3.1``|``foss/2018b``, ``foss/2021a``, ``foss/2021b``, ``intel/2018b``, ``intel/2021a``, ``intel/2021b`` +``3.1``|``foss/2018b``, ``foss/2021a``, ``foss/2021b``, ``foss/2022a``, ``foss/2022b``, ``foss/2023a``, ``intel/2018b``, ``intel/2021a``, ``intel/2021b``, ``intel/2022a``, ``intel/2022b``, ``intel/2023a`` ### HPCX @@ -14682,11 +14910,12 @@ HPL is a software package that solves a (random) dense linear system in double p *homepage*: -version|toolchain --------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -``2.1``|``foss/2016.04``, ``foss/2016.06``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``gmpolf/2016a``, ``gmvolf/1.7.20``, ``gmvolf/2016a``, ``intel/2016.00``, ``intel/2016.01``, ``intel/2016.02-GCC-4.9``, ``intel/2016.02-GCC-5.3``, ``intel/2016.03-GCC-4.9``, ``intel/2016.03-GCC-5.3``, ``intel/2016.03-GCC-5.4``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``pomkl/2016.03``, ``pomkl/2016.04``, ``pomkl/2016.09`` -``2.2``|``foss/2016.07``, ``foss/2016.09``, ``foss/2017a``, ``foss/2017b``, ``foss/2018.08``, ``foss/2018a``, ``foss/2018b``, ``fosscuda/2017b``, ``fosscuda/2018a``, ``fosscuda/2018b``, ``gimkl/2018b``, ``giolf/2017b``, ``giolf/2018a``, ``giolfc/2017b``, ``gmpolf/2017.10``, ``goblf/2018b``, ``gomkl/2018b``, ``intel/2017.00``, ``intel/2017.01``, ``intel/2017.02``, ``intel/2017.09``, ``intel/2017a``, ``intel/2017b``, ``intel/2018.00``, ``intel/2018.01``, ``intel/2018.02``, ``intel/2018.04``, ``intel/2018a``, ``intel/2018b``, ``intel/2019.00``, ``intel/2019.01``, ``intelcuda/2016.10``, ``intelcuda/2017b``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``iomkl/2016.09-GCC-5.4.0-2.26``, ``iomkl/2017.01``, ``iomkl/2017a``, ``iomkl/2017b``, ``iomkl/2018.02``, ``iomkl/2018a``, ``iomkl/2018b``, ``pomkl/2016.09`` -``2.3``|``CrayCCE/19.06``, ``CrayGNU/19.06``, ``CrayIntel/19.06``, ``Fujitsu/21.05``, ``foss/2019a``, ``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``foss/2022.05``, ``foss/2022.10``, ``foss/2022a``, ``foss/2022b``, ``foss/2023a``, ``fosscuda/2019b``, ``fosscuda/2020a``, ``gobff/2020.06-amd``, ``gobff/2020.11``, ``gobff/2020b``, ``gobff/2021a``, ``goblf/2020b``, ``gomkl/2019a``, ``gomkl/2020b``, ``gomkl/2021a``, ``gomkl/2022a``, ``iibff/2020b``, ``intel/2019.02``, ``intel/2019.03``, ``intel/2019a``, ``intel/2019b``, ``intel/2020.00``, ``intel/2020.06-impi-18.5``, ``intel/2020.12``, ``intel/2020a``, ``intel/2020b``, ``intel/2021a``, ``intel/2021b``, ``intel/2022.00``, ``intel/2022.09``, ``intel/2022.11``, ``intel/2022.12``, ``intel/2022a``, ``intel/2022b``, ``intel/2023.03``, ``intel/2023a``, ``intelcuda/2019b``, ``intelcuda/2020a``, ``iomkl/2019.01``, ``iomkl/2021a``, ``iomkl/2021b`` +version |versionsuffix |toolchain +----------|----------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +``2.0.15``|``-CUDA-11.7.0``|``intel/2022a`` +``2.1`` | |``foss/2016.04``, ``foss/2016.06``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``gmpolf/2016a``, ``gmvolf/1.7.20``, ``gmvolf/2016a``, ``intel/2016.00``, ``intel/2016.01``, ``intel/2016.02-GCC-4.9``, ``intel/2016.02-GCC-5.3``, ``intel/2016.03-GCC-4.9``, ``intel/2016.03-GCC-5.3``, ``intel/2016.03-GCC-5.4``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``pomkl/2016.03``, ``pomkl/2016.04``, ``pomkl/2016.09`` +``2.2`` | |``foss/2016.07``, ``foss/2016.09``, ``foss/2017a``, ``foss/2017b``, ``foss/2018.08``, ``foss/2018a``, ``foss/2018b``, ``fosscuda/2017b``, ``fosscuda/2018a``, ``fosscuda/2018b``, ``gimkl/2018b``, ``giolf/2017b``, ``giolf/2018a``, ``giolfc/2017b``, ``gmpolf/2017.10``, ``goblf/2018b``, ``gomkl/2018b``, ``intel/2017.00``, ``intel/2017.01``, ``intel/2017.02``, ``intel/2017.09``, ``intel/2017a``, ``intel/2017b``, ``intel/2018.00``, ``intel/2018.01``, ``intel/2018.02``, ``intel/2018.04``, ``intel/2018a``, ``intel/2018b``, ``intel/2019.00``, ``intel/2019.01``, ``intelcuda/2016.10``, ``intelcuda/2017b``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``iomkl/2016.09-GCC-5.4.0-2.26``, ``iomkl/2017.01``, ``iomkl/2017a``, ``iomkl/2017b``, ``iomkl/2018.02``, ``iomkl/2018a``, ``iomkl/2018b``, ``pomkl/2016.09`` +``2.3`` | |``CrayCCE/19.06``, ``CrayGNU/19.06``, ``CrayIntel/19.06``, ``Fujitsu/21.05``, ``foss/2019a``, ``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``foss/2022.05``, ``foss/2022.10``, ``foss/2022a``, ``foss/2022b``, ``foss/2023.09``, ``foss/2023a``, ``fosscuda/2019b``, ``fosscuda/2020a``, ``gobff/2020.06-amd``, ``gobff/2020.11``, ``gobff/2020b``, ``gobff/2021a``, ``goblf/2020b``, ``gomkl/2019a``, ``gomkl/2020b``, ``gomkl/2021a``, ``gomkl/2022a``, ``iibff/2020b``, ``intel/2019.02``, ``intel/2019.03``, ``intel/2019a``, ``intel/2019b``, ``intel/2020.00``, ``intel/2020.06-impi-18.5``, ``intel/2020.12``, ``intel/2020a``, ``intel/2020b``, ``intel/2021a``, ``intel/2021b``, ``intel/2022.00``, ``intel/2022.09``, ``intel/2022.11``, ``intel/2022.12``, ``intel/2022a``, ``intel/2022b``, ``intel/2023.03``, ``intel/2023.07``, ``intel/2023a``, ``intelcuda/2019b``, ``intelcuda/2020a``, ``iomkl/2019.01``, ``iomkl/2021a``, ``iomkl/2021b`` ### htop @@ -14952,7 +15181,7 @@ version |toolchain ## I -[i-cisTarget](#i-cistarget) - [i-PI](#i-pi) - [I-TASSER](#i-tasser) - [i7z](#i7z) - [ICA-AROMA](#ica-aroma) - [icc](#icc) - [iccifort](#iccifort) - [iccifortcuda](#iccifortcuda) - [ichorCNA](#ichorcna) - [icmake](#icmake) - [iCount](#icount) - [ICU](#icu) - [IDBA-UD](#idba-ud) - [idemux](#idemux) - [ieeg-cli](#ieeg-cli) - [ifort](#ifort) - [IgBLAST](#igblast) - [IGMPlot](#igmplot) - [igraph](#igraph) - [IGV](#igv) - [igv-reports](#igv-reports) - [IGVTools](#igvtools) - [iibff](#iibff) - [iimkl](#iimkl) - [iimpi](#iimpi) - [iimpic](#iimpic) - [IJulia](#ijulia) - [ILAMB](#ilamb) - [IMa2](#ima2) - [IMa2p](#ima2p) - [imagecodecs](#imagecodecs) - [imageio](#imageio) - [ImageJ](#imagej) - [ImageMagick](#imagemagick) - [imake](#imake) - [Imath](#imath) - [IMB](#imb) - [imbalanced-learn](#imbalanced-learn) - [imgaug](#imgaug) - [imkl](#imkl) - [imkl-FFTW](#imkl-fftw) - [Imlib2](#imlib2) - [immunedeconv](#immunedeconv) - [IMOD](#imod) - [impi](#impi) - [IMPUTE2](#impute2) - [InChI](#inchi) - [indicators](#indicators) - [Inelastica](#inelastica) - [inferCNV](#infercnv) - [infercnvpy](#infercnvpy) - [Inferelator](#inferelator) - [Infernal](#infernal) - [Infomap](#infomap) - [inih](#inih) - [inline](#inline) - [InParanoid](#inparanoid) - [inputproto](#inputproto) - [Inspector](#inspector) - [IntaRNA](#intarna) - [INTEGRATE](#integrate) - [INTEGRATE-Neo](#integrate-neo) - [intel](#intel) - [intel-compilers](#intel-compilers) - [IntelClusterChecker](#intelclusterchecker) - [intelcuda](#intelcuda) - [IntelDAAL](#inteldaal) - [IntelPython](#intelpython) - [InterProScan](#interproscan) - [InterProScan_data](#interproscan_data) - [intervaltree](#intervaltree) - [intervaltree-python](#intervaltree-python) - [intltool](#intltool) - [io_lib](#io_lib) - [ioapi](#ioapi) - [iodata](#iodata) - [iomkl](#iomkl) - [iompi](#iompi) - [IOR](#ior) - [IOzone](#iozone) - [IPM](#ipm) - [Ipopt](#ipopt) - [ipp](#ipp) - [IPy](#ipy) - [ipympl](#ipympl) - [ipyparallel](#ipyparallel) - [ipyrad](#ipyrad) - [IPython](#ipython) - [IQ-TREE](#iq-tree) - [Iris](#iris) - [IRkernel](#irkernel) - [irodsfs](#irodsfs) - [IronPython](#ironpython) - [ISA-L](#isa-l) - [ISL](#isl) - [isoCirc](#isocirc) - [IsoformSwitchAnalyzeR](#isoformswitchanalyzer) - [IsoNet](#isonet) - [IsoQuant](#isoquant) - [IsoSeq](#isoseq) - [ispc](#ispc) - [itac](#itac) - [ITK](#itk) - [itpp](#itpp) - [ITSTool](#itstool) - [ITSx](#itsx) - [iVar](#ivar) +[i-cisTarget](#i-cistarget) - [i-PI](#i-pi) - [I-TASSER](#i-tasser) - [i7z](#i7z) - [ICA-AROMA](#ica-aroma) - [icc](#icc) - [iccifort](#iccifort) - [iccifortcuda](#iccifortcuda) - [ichorCNA](#ichorcna) - [icmake](#icmake) - [iCount](#icount) - [ICU](#icu) - [IDBA-UD](#idba-ud) - [idemux](#idemux) - [ieeg-cli](#ieeg-cli) - [ifort](#ifort) - [IgBLAST](#igblast) - [IGMPlot](#igmplot) - [igraph](#igraph) - [IGV](#igv) - [igv-reports](#igv-reports) - [IGVTools](#igvtools) - [iibff](#iibff) - [iimkl](#iimkl) - [iimpi](#iimpi) - [iimpic](#iimpic) - [IJulia](#ijulia) - [ILAMB](#ilamb) - [IMa2](#ima2) - [IMa2p](#ima2p) - [imagecodecs](#imagecodecs) - [imageio](#imageio) - [ImageJ](#imagej) - [ImageMagick](#imagemagick) - [imake](#imake) - [Imath](#imath) - [IMB](#imb) - [imbalanced-learn](#imbalanced-learn) - [imgaug](#imgaug) - [imkl](#imkl) - [imkl-FFTW](#imkl-fftw) - [Imlib2](#imlib2) - [immunedeconv](#immunedeconv) - [IMOD](#imod) - [impi](#impi) - [IMPUTE2](#impute2) - [imutils](#imutils) - [InChI](#inchi) - [indicators](#indicators) - [Inelastica](#inelastica) - [inferCNV](#infercnv) - [infercnvpy](#infercnvpy) - [Inferelator](#inferelator) - [Infernal](#infernal) - [Infomap](#infomap) - [inih](#inih) - [inline](#inline) - [InParanoid](#inparanoid) - [inputproto](#inputproto) - [Inspector](#inspector) - [IntaRNA](#intarna) - [INTEGRATE](#integrate) - [INTEGRATE-Neo](#integrate-neo) - [intel](#intel) - [intel-compilers](#intel-compilers) - [IntelClusterChecker](#intelclusterchecker) - [intelcuda](#intelcuda) - [IntelDAAL](#inteldaal) - [IntelPython](#intelpython) - [InterProScan](#interproscan) - [InterProScan_data](#interproscan_data) - [intervaltree](#intervaltree) - [intervaltree-python](#intervaltree-python) - [intltool](#intltool) - [io_lib](#io_lib) - [ioapi](#ioapi) - [iodata](#iodata) - [iomkl](#iomkl) - [iompi](#iompi) - [IOR](#ior) - [IOzone](#iozone) - [IPM](#ipm) - [Ipopt](#ipopt) - [ipp](#ipp) - [IPy](#ipy) - [ipympl](#ipympl) - [ipyparallel](#ipyparallel) - [ipyrad](#ipyrad) - [IPython](#ipython) - [IQ-TREE](#iq-tree) - [Iris](#iris) - [IRkernel](#irkernel) - [irodsfs](#irodsfs) - [IronPython](#ironpython) - [ISA-L](#isa-l) - [ISL](#isl) - [isoCirc](#isocirc) - [IsoformSwitchAnalyzeR](#isoformswitchanalyzer) - [IsoNet](#isonet) - [IsoQuant](#isoquant) - [IsoSeq](#isoseq) - [ispc](#ispc) - [itac](#itac) - [ITK](#itk) - [itpp](#itpp) - [ITSTool](#itstool) - [ITSx](#itsx) - [iVar](#ivar) ### i-cisTarget @@ -15362,6 +15591,7 @@ version |versionsuffix |toolchain ``2022a`` | |``system`` ``2022b`` | |``system`` ``2023.03`` | |``system`` +``2023.07`` | |``system`` ``2023a`` | |``system`` ``system`` |``-GCC-system-2.29``|``system`` @@ -15518,6 +15748,7 @@ version |toolchain ``3.1.5``|``GCCcore/11.3.0`` ``3.1.6``|``GCCcore/12.2.0`` ``3.1.7``|``GCCcore/12.3.0`` +``3.1.9``|``GCCcore/13.2.0`` ### IMB @@ -15605,6 +15836,7 @@ version |versionsuffix|toolchain ``2022.2.1`` | |``system`` ``2023.0.0`` | |``system`` ``2023.1.0`` | |``system`` +``2023.2.0`` | |``system`` ### imkl-FFTW @@ -15621,6 +15853,7 @@ version |toolchain ``2022.2.1``|``iimpi/2022.11``, ``iimpi/2022b`` ``2023.0.0``|``iimpi/2022.12`` ``2023.1.0``|``iimpi/2023.03``, ``iimpi/2023a`` +``2023.2.0``|``iimpi/2023.07`` ### Imlib2 @@ -15704,6 +15937,7 @@ version |versionsuffix|toolchain ``2021.7.1`` | |``intel-compilers/2022.2.1`` ``2021.8.0`` | |``intel-compilers/2023.0.0`` ``2021.9.0`` | |``intel-compilers/2023.1.0`` +``2021.10.0`` | |``intel-compilers/2023.2.1`` ``system`` | |``iccifort/system-GCC-system-2.29`` ### IMPUTE2 @@ -15719,6 +15953,16 @@ version |versionsuffix |toolchain ``2.3.2``|``_x86_64_dynamic``|``system`` ``2.3.2``|``_x86_64_static`` |``system`` +### imutils + +A series of convenience functions to make basic image processing operations such as translation, rotation, resizing, skeletonization, and displaying Matplotlib images easier with OpenCV and Python. + +*homepage*: + +version |toolchain +---------|------------------ +``0.5.4``|``fosscuda/2020b`` + ### InChI The IUPAC International Chemical Identifier (InChI TM) is a non-proprietary identifier for chemical substances that can be used in printed and electronic data sources thus enabling easier linking of diverse data compilations. @@ -15736,8 +15980,8 @@ version |toolchain *homepage*: version|toolchain --------|------------------ -``2.2``|``GCCcore/11.3.0`` +-------|-------------------------------------- +``2.2``|``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ### Inelastica @@ -15869,6 +16113,7 @@ version |toolchain ``2021.4.0`` |``system`` ``2022.0.0`` |``system`` ``2022.1.0`` |``system`` +``2023.2.0`` |``system`` ### IntaRNA @@ -15950,6 +16195,7 @@ version |versionsuffix|toolchain ``2022a`` | |``system`` ``2022b`` | |``system`` ``2023.03`` | |``system`` +``2023.07`` | |``system`` ``2023a`` | |``system`` ### intel-compilers @@ -15971,6 +16217,7 @@ version |toolchain ``2022.2.1``|``system`` ``2023.0.0``|``system`` ``2023.1.0``|``system`` +``2023.2.1``|``system`` ### IntelClusterChecker @@ -16072,8 +16319,8 @@ intltool is a set of tools to centralize translation of many different file for *homepage*: version |versionsuffix |toolchain -----------|----------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -``0.51.0``| |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +----------|----------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +``0.51.0``| |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``0.51.0``|``-Perl-5.20.3``|``intel/2016a`` ``0.51.0``|``-Perl-5.22.1``|``foss/2016a``, ``intel/2016a`` ``0.51.0``|``-Perl-5.24.0``|``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``foss/2016b``, ``gimkl/2017a``, ``intel/2016b`` @@ -16373,14 +16620,14 @@ isl is a library for manipulating sets and relations of integer points bounded b *homepage*: version |toolchain ---------|--------------------------------------------------------- +--------|---------------------------------------------------------- ``0.14``|``GCC/4.9.2`` ``0.15``|``GCC/4.9.3-2.25``, ``GNU/4.9.3-2.25``, ``foss/2016a`` ``0.16``|``GCC/4.9.3-2.25`` ``0.17``|``foss/2016a`` ``0.23``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` ``0.24``|``GCCcore/11.2.0``, ``GCCcore/11.3.0`` -``0.26``|``GCCcore/12.3.0`` +``0.26``|``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0`` ### isoCirc @@ -16424,13 +16671,14 @@ version |toolchain ### IsoSeq -IsoSeq v3 contains the newest tools to identify transcripts in PacBio single-molecule sequencing data. Starting in SMRT Link v6.0.0, those tools power the IsoSeq GUI-based analysis application. A composable workflow of existing tools and algorithms, combined with a new clustering technique, allows to process the ever-increasing yield of PacBio machines with similar performance to IsoSeq versions 1 and 2. Starting with version 3.4, support for UMI and cell barcode based deduplication has been added. +IsoSeq v3 contains the newest tools to identify transcripts in PacBio single-molecule sequencing data. Starting in SMRT Link v6.0.0, those tools power the IsoSeq GUI-based analysis application. A composable workflow of existing tools and algorithms, combined with a new clustering technique, allows to process the ever-increasing yield of PacBio machines with similar performance to IsoSeq versions 1 and 2. Starting with version 3.4, support for UMI and cell barcode based deduplication has been added. *homepage*: version |versionsuffix |toolchain ---------|-----------------|---------- ``3.8.2``|``-linux-x86_64``|``system`` +``4.0.0``|``-linux-x86_64``|``system`` ### ispc @@ -16464,6 +16712,7 @@ version |toolchain ``2021.2.0`` |``system`` ``2021.5.0`` |``system`` ``2021.6.0`` |``system`` +``2021.10.0`` |``system`` ### ITK @@ -16536,7 +16785,7 @@ version |toolchain ## J -[JAGS](#jags) - [Jansson](#jansson) - [Jasmine](#jasmine) - [JasPer](#jasper) - [Java](#java) - [JavaFX](#javafx) - [jax](#jax) - [JAXFrontCE](#jaxfrontce) - [jbigkit](#jbigkit) - [Jellyfish](#jellyfish) - [jemalloc](#jemalloc) - [jhbuild](#jhbuild) - [JiTCODE](#jitcode) - [jModelTest](#jmodeltest) - [Jorg](#jorg) - [joypy](#joypy) - [jq](#jq) - [json-c](#json-c) - [json-fortran](#json-fortran) - [JSON-GLib](#json-glib) - [JsonCpp](#jsoncpp) - [JUBE](#jube) - [Judy](#judy) - [Julia](#julia) - [JUnit](#junit) - [Jupyter-bundle](#jupyter-bundle) - [jupyter-contrib-nbextensions](#jupyter-contrib-nbextensions) - [jupyter-matlab-proxy](#jupyter-matlab-proxy) - [jupyter-resource-usage](#jupyter-resource-usage) - [jupyter-server](#jupyter-server) - [jupyter-server-proxy](#jupyter-server-proxy) - [JupyterHub](#jupyterhub) - [JupyterLab](#jupyterlab) - [jupyterlab-lmod](#jupyterlab-lmod) - [jupyterlmod](#jupyterlmod) - [JupyterNotebook](#jupyternotebook) - [JWM](#jwm) - [jxrlib](#jxrlib) +[JAGS](#jags) - [Jansson](#jansson) - [Jasmine](#jasmine) - [JasPer](#jasper) - [Java](#java) - [JavaFX](#javafx) - [jax](#jax) - [JAXFrontCE](#jaxfrontce) - [jbigkit](#jbigkit) - [Jblob](#jblob) - [Jellyfish](#jellyfish) - [jemalloc](#jemalloc) - [jhbuild](#jhbuild) - [JiTCODE](#jitcode) - [jModelTest](#jmodeltest) - [Jmol](#jmol) - [Jorg](#jorg) - [joypy](#joypy) - [jq](#jq) - [json-c](#json-c) - [json-fortran](#json-fortran) - [JSON-GLib](#json-glib) - [JsonCpp](#jsoncpp) - [JUBE](#jube) - [Judy](#judy) - [Julia](#julia) - [JUnit](#junit) - [Jupyter-bundle](#jupyter-bundle) - [jupyter-contrib-nbextensions](#jupyter-contrib-nbextensions) - [jupyter-matlab-proxy](#jupyter-matlab-proxy) - [jupyter-resource-usage](#jupyter-resource-usage) - [jupyter-server](#jupyter-server) - [jupyter-server-proxy](#jupyter-server-proxy) - [JupyterHub](#jupyterhub) - [JupyterLab](#jupyterlab) - [jupyterlab-lmod](#jupyterlab-lmod) - [jupyterlmod](#jupyterlmod) - [JupyterNotebook](#jupyternotebook) - [JWM](#jwm) - [jxrlib](#jxrlib) ### JAGS @@ -16717,8 +16966,18 @@ JBIG-KIT is a software implementation of the JBIG1 data compression standard (I *homepage*: version|toolchain --------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -``2.1``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +-------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +``2.1``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` + +### Jblob + +Jblob - WDC Climate dataset download + +*homepage*: + +version|toolchain +-------|---------- +``3.0``|``system`` ### Jellyfish @@ -16783,6 +17042,16 @@ version |versionsuffix |toolchain -------------------|------------------|---------- ``2.1.10r20160303``|``-Java-1.8.0_92``|``system`` +### Jmol + +Jmol: an open-source Java viewer for chemical structures in 3D + +*homepage*: + +version |versionsuffix|toolchain +-----------|-------------|---------- +``16.1.41``|``-Java-11`` |``system`` + ### Jorg A MAG Circularization Method By Lauren Lui, Torben Nielsen, and Adam Arkin @@ -17075,6 +17344,7 @@ The Jupyter Notebook is the original web application for creating and sharing c version |toolchain ---------|------------------ ``7.0.2``|``GCCcore/12.3.0`` +``7.0.3``|``GCCcore/12.2.0`` ### JWM @@ -17099,7 +17369,7 @@ version|toolchain ## K -[KaHIP](#kahip) - [Kaiju](#kaiju) - [Kaleido](#kaleido) - [Kalign](#kalign) - [kallisto](#kallisto) - [KAT](#kat) - [kb-python](#kb-python) - [kbproto](#kbproto) - [kedro](#kedro) - [Kent_tools](#kent_tools) - [Keras](#keras) - [KerasTuner](#kerastuner) - [khmer](#khmer) - [kim-api](#kim-api) - [kineto](#kineto) - [king](#king) - [KITE](#kite) - [kma](#kma) - [KMC](#kmc) - [KMCP](#kmcp) - [KmerGenie](#kmergenie) - [KNIME](#knime) - [kpcalg](#kpcalg) - [Kraken](#kraken) - [Kraken2](#kraken2) - [KrakenUniq](#krakenuniq) - [Kratos](#kratos) - [krbalancing](#krbalancing) - [KronaTools](#kronatools) - [kwant](#kwant) - [KWIML](#kwiml) - [kWIP](#kwip) - [KyotoCabinet](#kyotocabinet) +[KaHIP](#kahip) - [Kaiju](#kaiju) - [Kaleido](#kaleido) - [Kalign](#kalign) - [kallisto](#kallisto) - [KAT](#kat) - [kb-python](#kb-python) - [kbproto](#kbproto) - [kedro](#kedro) - [Kent_tools](#kent_tools) - [Keras](#keras) - [KerasTuner](#kerastuner) - [khmer](#khmer) - [kim-api](#kim-api) - [kineto](#kineto) - [king](#king) - [KITE](#kite) - [kma](#kma) - [KMC](#kmc) - [KMCP](#kmcp) - [KmerGenie](#kmergenie) - [kneaddata](#kneaddata) - [KNIME](#knime) - [kpcalg](#kpcalg) - [Kraken](#kraken) - [Kraken2](#kraken2) - [KrakenUniq](#krakenuniq) - [Kratos](#kratos) - [krbalancing](#krbalancing) - [KronaTools](#kronatools) - [kwant](#kwant) - [KWIML](#kwiml) - [kWIP](#kwip) - [KyotoCabinet](#kyotocabinet) ### KaHIP @@ -17131,9 +17401,9 @@ Fast static image export for web-based visualization libraries with zero depende *homepage*: version |toolchain ----------|-------------------------------------- +---------|---------------------------------------------------------- ``0.1.0``|``GCCcore/10.2.0`` -``0.2.1``|``GCCcore/10.3.0``, ``GCCcore/11.3.0`` +``0.2.1``|``GCCcore/10.3.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ### Kalign @@ -17155,7 +17425,7 @@ kallisto is a program for quantifying abundances of transcripts from RNA-Seq dat *homepage*: version |toolchain -----------|------------------------------------------------ +----------|------------------------------------------------- ``0.42.5``|``foss/2016a`` ``0.43.0``|``intel/2016b`` ``0.43.1``|``foss/2016b``, ``intel/2017a``, ``intel/2017b`` @@ -17165,7 +17435,7 @@ version |toolchain ``0.46.0``|``intel/2019a`` ``0.46.1``|``foss/2019b``, ``iimpi/2020a``, ``iimpi/2020b`` ``0.46.2``|``foss/2020b`` -``0.48.0``|``gompi/2021b``, ``gompi/2022a`` +``0.48.0``|``gompi/2021a``, ``gompi/2021b``, ``gompi/2022a`` ### KAT @@ -17289,7 +17559,7 @@ version |toolchain ``2.1.2``|``foss/2019a``, ``intel/2019a`` ``2.1.3``|``foss/2019b``, ``foss/2020a``, ``intel/2019b``, ``intel/2020a`` ``2.2.1``|``GCCcore/10.2.0``, ``GCCcore/10.3.0`` -``2.3.0``|``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``2.3.0``|``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.3.0`` ### kineto @@ -17369,6 +17639,16 @@ version |toolchain ``1.7044``|``intel/2017a`` ``1.7048``|``intel/2018a`` +### kneaddata + +KneadData is a tool designed to perform quality control on metagenomic and metatranscriptomic sequencing data, especially data from microbiome experiments. + +*homepage*: + +version |toolchain +----------|-------------- +``0.12.0``|``foss/2022a`` + ### KNIME KNIME Analytics Platform is the open source software for creating data science applications and services. KNIME stands for KoNstanz Information MinEr. @@ -17506,7 +17786,7 @@ version |toolchain ## L -[L_RNA_scaffolder](#l_rna_scaffolder) - [Lace](#lace) - [LADR](#ladr) - [lagrangian-filtering](#lagrangian-filtering) - [LAME](#lame) - [LAMMPS](#lammps) - [lancet](#lancet) - [LAPACK](#lapack) - [LASSO-Python](#lasso-python) - [LAST](#last) - [LASTZ](#lastz) - [lavaan](#lavaan) - [LayoutParser](#layoutparser) - [LBFGS++](#lbfgs++) - [LCov](#lcov) - [LDC](#ldc) - [lDDT](#lddt) - [LeadIT](#leadit) - [leafcutter](#leafcutter) - [leidenalg](#leidenalg) - [LEMON](#lemon) - [Leptonica](#leptonica) - [LERC](#lerc) - [less](#less) - [LevelDB](#leveldb) - [lftp](#lftp) - [LHAPDF](#lhapdf) - [LIANA](#liana) - [libaec](#libaec) - [libaio](#libaio) - [libarchive](#libarchive) - [libav](#libav) - [libavif](#libavif) - [libBigWig](#libbigwig) - [libbitmask](#libbitmask) - [libcdms](#libcdms) - [libcerf](#libcerf) - [libcint](#libcint) - [libcircle](#libcircle) - [libcmaes](#libcmaes) - [libconfig](#libconfig) - [libcpuset](#libcpuset) - [libcroco](#libcroco) - [libctl](#libctl) - [libdap](#libdap) - [libde265](#libde265) - [libdeflate](#libdeflate) - [libdivsufsort](#libdivsufsort) - [libdrm](#libdrm) - [libdrs](#libdrs) - [libdwarf](#libdwarf) - [libedit](#libedit) - [libelf](#libelf) - [libemf](#libemf) - [libepoxy](#libepoxy) - [libev](#libev) - [libevent](#libevent) - [libexif](#libexif) - [libfabric](#libfabric) - [libfdf](#libfdf) - [libffcall](#libffcall) - [libffi](#libffi) - [libFLAME](#libflame) - [libfontenc](#libfontenc) - [libgcrypt](#libgcrypt) - [libgd](#libgd) - [libgdiplus](#libgdiplus) - [libGDSII](#libgdsii) - [libgeotiff](#libgeotiff) - [libgit2](#libgit2) - [libglade](#libglade) - [libGLU](#libglu) - [libglvnd](#libglvnd) - [libgpg-error](#libgpg-error) - [libgpuarray](#libgpuarray) - [libGridXC](#libgridxc) - [libgtextutils](#libgtextutils) - [libharu](#libharu) - [libheif](#libheif) - [libibmad](#libibmad) - [libibumad](#libibumad) - [libICE](#libice) - [libiconv](#libiconv) - [libidn](#libidn) - [libidn2](#libidn2) - [Libint](#libint) - [LiBis](#libis) - [libjpeg-turbo](#libjpeg-turbo) - [libjxl](#libjxl) - [libleidenalg](#libleidenalg) - [LibLZF](#liblzf) - [libmad](#libmad) - [libmatheval](#libmatheval) - [libmaus2](#libmaus2) - [libmbd](#libmbd) - [libMemcached](#libmemcached) - [libmicrohttpd](#libmicrohttpd) - [libmo_unpack](#libmo_unpack) - [libmypaint](#libmypaint) - [libnsl](#libnsl) - [libobjcryst](#libobjcryst) - [libogg](#libogg) - [libopus](#libopus) - [libosmium](#libosmium) - [libpci](#libpci) - [libpciaccess](#libpciaccess) - [libplinkio](#libplinkio) - [libpng](#libpng) - [libpsl](#libpsl) - [libPSML](#libpsml) - [libpsortb](#libpsortb) - [libpspio](#libpspio) - [libpthread-stubs](#libpthread-stubs) - [libQGLViewer](#libqglviewer) - [libreadline](#libreadline) - [libRmath](#librmath) - [librosa](#librosa) - [librsb](#librsb) - [librsvg](#librsvg) - [librttopo](#librttopo) - [libsamplerate](#libsamplerate) - [libSBML](#libsbml) - [libsigc++](#libsigc++) - [libsigsegv](#libsigsegv) - [libSM](#libsm) - [libsndfile](#libsndfile) - [libsodium](#libsodium) - [LibSoup](#libsoup) - [libspatialindex](#libspatialindex) - [libspatialite](#libspatialite) - [libssh](#libssh) - [libStatGen](#libstatgen) - [LIBSVM](#libsvm) - [LIBSVM-Python](#libsvm-python) - [libtar](#libtar) - [libtasn1](#libtasn1) - [libtecla](#libtecla) - [LibTIFF](#libtiff) - [libtirpc](#libtirpc) - [libtool](#libtool) - [libtree](#libtree) - [libunistring](#libunistring) - [libunwind](#libunwind) - [libutempter](#libutempter) - [LibUUID](#libuuid) - [libuv](#libuv) - [libvdwxc](#libvdwxc) - [libvorbis](#libvorbis) - [libvori](#libvori) - [libWallModelledLES](#libwallmodelledles) - [libwebp](#libwebp) - [libwpe](#libwpe) - [libX11](#libx11) - [libXau](#libxau) - [libxc](#libxc) - [libxcb](#libxcb) - [libXcursor](#libxcursor) - [libXdamage](#libxdamage) - [libXdmcp](#libxdmcp) - [libXext](#libxext) - [libXfixes](#libxfixes) - [libXfont](#libxfont) - [libXft](#libxft) - [libXi](#libxi) - [libXinerama](#libxinerama) - [libxkbcommon](#libxkbcommon) - [libxml++](#libxml++) - [libxml2](#libxml2) - [libxml2-python](#libxml2-python) - [libXmu](#libxmu) - [libXp](#libxp) - [libXpm](#libxpm) - [libXrandr](#libxrandr) - [libXrender](#libxrender) - [libxslt](#libxslt) - [libxsmm](#libxsmm) - [libXt](#libxt) - [libXxf86vm](#libxxf86vm) - [libyaml](#libyaml) - [libzeep](#libzeep) - [libzip](#libzip) - [lie_learn](#lie_learn) - [lifelines](#lifelines) - [Lighter](#lighter) - [liknorm](#liknorm) - [likwid](#likwid) - [limix](#limix) - [LinBox](#linbox) - [line_profiler](#line_profiler) - [Lingeling](#lingeling) - [LISFLOOD-FP](#lisflood-fp) - [LittleCMS](#littlecms) - [LLDB](#lldb) - [LLVM](#llvm) - [LMDB](#lmdb) - [LMfit](#lmfit) - [Lmod](#lmod) - [LncLOOM](#lncloom) - [LocARNA](#locarna) - [LoFreq](#lofreq) - [Log-Log4perl](#log-log4perl) - [logaddexp](#logaddexp) - [LOHHLA](#lohhla) - [Loki](#loki) - [longestrunsubsequence](#longestrunsubsequence) - [longread_umi](#longread_umi) - [Longshot](#longshot) - [loompy](#loompy) - [loomR](#loomr) - [LoRDEC](#lordec) - [LPeg](#lpeg) - [LPJmL](#lpjml) - [lpsolve](#lpsolve) - [lrslib](#lrslib) - [LS-PrePost](#ls-prepost) - [LSD2](#lsd2) - [LSMS](#lsms) - [LTR_retriever](#ltr_retriever) - [LtrDetector](#ltrdetector) - [Lua](#lua) - [LuaJIT](#luajit) - [LuaJIT2-OpenResty](#luajit2-openresty) - [LuaRocks](#luarocks) - [Lucene-Geo-Gazetteer](#lucene-geo-gazetteer) - [LUMPY](#lumpy) - [LUSCUS](#luscus) - [lwgrp](#lwgrp) - [lxml](#lxml) - [lynx](#lynx) - [lz4](#lz4) - [LZO](#lzo) +[L_RNA_scaffolder](#l_rna_scaffolder) - [Lace](#lace) - [LADR](#ladr) - [lagrangian-filtering](#lagrangian-filtering) - [LAME](#lame) - [LAMMPS](#lammps) - [lancet](#lancet) - [LAPACK](#lapack) - [LASSO-Python](#lasso-python) - [LAST](#last) - [LASTZ](#lastz) - [lavaan](#lavaan) - [LayoutParser](#layoutparser) - [LBFGS++](#lbfgs++) - [LCov](#lcov) - [LDC](#ldc) - [lDDT](#lddt) - [LeadIT](#leadit) - [leafcutter](#leafcutter) - [leidenalg](#leidenalg) - [LEMON](#lemon) - [Leptonica](#leptonica) - [LERC](#lerc) - [less](#less) - [LevelDB](#leveldb) - [lftp](#lftp) - [LHAPDF](#lhapdf) - [LIANA](#liana) - [libaec](#libaec) - [libaio](#libaio) - [libarchive](#libarchive) - [libav](#libav) - [libavif](#libavif) - [libbaseencode](#libbaseencode) - [libBigWig](#libbigwig) - [libbitmask](#libbitmask) - [libcdms](#libcdms) - [libcerf](#libcerf) - [libcint](#libcint) - [libcircle](#libcircle) - [libcmaes](#libcmaes) - [libconfig](#libconfig) - [libcotp](#libcotp) - [libcpuset](#libcpuset) - [libcroco](#libcroco) - [libctl](#libctl) - [libdap](#libdap) - [libde265](#libde265) - [libdeflate](#libdeflate) - [libdivsufsort](#libdivsufsort) - [libdrm](#libdrm) - [libdrs](#libdrs) - [libdwarf](#libdwarf) - [libedit](#libedit) - [libelf](#libelf) - [libemf](#libemf) - [libepoxy](#libepoxy) - [libev](#libev) - [libevent](#libevent) - [libexif](#libexif) - [libfabric](#libfabric) - [libfdf](#libfdf) - [libffcall](#libffcall) - [libffi](#libffi) - [libFLAME](#libflame) - [libfontenc](#libfontenc) - [libgcrypt](#libgcrypt) - [libgd](#libgd) - [libgdiplus](#libgdiplus) - [libGDSII](#libgdsii) - [libgeotiff](#libgeotiff) - [libgit2](#libgit2) - [libglade](#libglade) - [libGLU](#libglu) - [libglvnd](#libglvnd) - [libgpg-error](#libgpg-error) - [libgpuarray](#libgpuarray) - [libGridXC](#libgridxc) - [libgtextutils](#libgtextutils) - [libharu](#libharu) - [libheif](#libheif) - [libibmad](#libibmad) - [libibumad](#libibumad) - [libICE](#libice) - [libiconv](#libiconv) - [libidn](#libidn) - [libidn2](#libidn2) - [Libint](#libint) - [LiBis](#libis) - [libjpeg-turbo](#libjpeg-turbo) - [libjxl](#libjxl) - [libleidenalg](#libleidenalg) - [LibLZF](#liblzf) - [libmad](#libmad) - [libmatheval](#libmatheval) - [libmaus2](#libmaus2) - [libmbd](#libmbd) - [libMemcached](#libmemcached) - [libmicrohttpd](#libmicrohttpd) - [libmo_unpack](#libmo_unpack) - [libmypaint](#libmypaint) - [libnsl](#libnsl) - [libobjcryst](#libobjcryst) - [libogg](#libogg) - [libopus](#libopus) - [libosmium](#libosmium) - [libpci](#libpci) - [libpciaccess](#libpciaccess) - [libplinkio](#libplinkio) - [libpng](#libpng) - [libpsl](#libpsl) - [libPSML](#libpsml) - [libpsortb](#libpsortb) - [libpspio](#libpspio) - [libpthread-stubs](#libpthread-stubs) - [libQGLViewer](#libqglviewer) - [libreadline](#libreadline) - [libRmath](#librmath) - [librosa](#librosa) - [librsb](#librsb) - [librsvg](#librsvg) - [librttopo](#librttopo) - [libsamplerate](#libsamplerate) - [libSBML](#libsbml) - [libsigc++](#libsigc++) - [libsigsegv](#libsigsegv) - [libSM](#libsm) - [libsndfile](#libsndfile) - [libsodium](#libsodium) - [LibSoup](#libsoup) - [libspatialindex](#libspatialindex) - [libspatialite](#libspatialite) - [libssh](#libssh) - [libStatGen](#libstatgen) - [LIBSVM](#libsvm) - [LIBSVM-Python](#libsvm-python) - [libtar](#libtar) - [libtasn1](#libtasn1) - [libtecla](#libtecla) - [LibTIFF](#libtiff) - [libtirpc](#libtirpc) - [libtool](#libtool) - [libtree](#libtree) - [libunistring](#libunistring) - [libunwind](#libunwind) - [libutempter](#libutempter) - [LibUUID](#libuuid) - [libuv](#libuv) - [libvdwxc](#libvdwxc) - [libvorbis](#libvorbis) - [libvori](#libvori) - [libWallModelledLES](#libwallmodelledles) - [libwebp](#libwebp) - [libwpe](#libwpe) - [libX11](#libx11) - [libXau](#libxau) - [libxc](#libxc) - [libxcb](#libxcb) - [libXcursor](#libxcursor) - [libXdamage](#libxdamage) - [libXdmcp](#libxdmcp) - [libXext](#libxext) - [libXfixes](#libxfixes) - [libXfont](#libxfont) - [libXft](#libxft) - [libXi](#libxi) - [libXinerama](#libxinerama) - [libxkbcommon](#libxkbcommon) - [libxml++](#libxml++) - [libxml2](#libxml2) - [libxml2-python](#libxml2-python) - [libXmu](#libxmu) - [libXp](#libxp) - [libXpm](#libxpm) - [libXrandr](#libxrandr) - [libXrender](#libxrender) - [libxslt](#libxslt) - [libxsmm](#libxsmm) - [libXt](#libxt) - [libXxf86vm](#libxxf86vm) - [libyaml](#libyaml) - [libzeep](#libzeep) - [libzip](#libzip) - [lie_learn](#lie_learn) - [lifelines](#lifelines) - [Lighter](#lighter) - [liknorm](#liknorm) - [likwid](#likwid) - [limix](#limix) - [LinBox](#linbox) - [line_profiler](#line_profiler) - [Lingeling](#lingeling) - [LISFLOOD-FP](#lisflood-fp) - [LittleCMS](#littlecms) - [LLDB](#lldb) - [LLVM](#llvm) - [LMDB](#lmdb) - [LMfit](#lmfit) - [Lmod](#lmod) - [LncLOOM](#lncloom) - [LocARNA](#locarna) - [LoFreq](#lofreq) - [Log-Log4perl](#log-log4perl) - [logaddexp](#logaddexp) - [LOHHLA](#lohhla) - [Loki](#loki) - [longestrunsubsequence](#longestrunsubsequence) - [longread_umi](#longread_umi) - [Longshot](#longshot) - [loompy](#loompy) - [loomR](#loomr) - [LoRDEC](#lordec) - [LPeg](#lpeg) - [LPJmL](#lpjml) - [lpsolve](#lpsolve) - [lrslib](#lrslib) - [LS-PrePost](#ls-prepost) - [LSD2](#lsd2) - [LSMS](#lsms) - [LTR_retriever](#ltr_retriever) - [LtrDetector](#ltrdetector) - [Lua](#lua) - [LuaJIT](#luajit) - [LuaJIT2-OpenResty](#luajit2-openresty) - [LuaRocks](#luarocks) - [Lucene-Geo-Gazetteer](#lucene-geo-gazetteer) - [LUMPY](#lumpy) - [LUSCUS](#luscus) - [lwgrp](#lwgrp) - [lxml](#lxml) - [lynx](#lynx) - [lz4](#lz4) - [LZO](#lzo) ### L_RNA_scaffolder @@ -17786,10 +18066,10 @@ LevelDB is a fast key-value storage library written at Google that provides an *homepage*: version |toolchain ---------|------------------------------------------------ +--------|-------------------------------------------------------- ``1.18``|``foss/2016a``, ``intel/2017a``, ``intel/2017b`` ``1.20``|``GCCcore/7.3.0`` -``1.22``|``GCCcore/8.2.0``, ``GCCcore/9.3.0`` +``1.22``|``GCCcore/11.3.0``, ``GCCcore/8.2.0``, ``GCCcore/9.3.0`` ### lftp @@ -17859,6 +18139,7 @@ version |toolchain ``3.5.1``|``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.3.0`` ``3.6.1``|``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ``3.6.2``|``GCCcore/12.3.0``, ``GCCcore/13.1.0`` +``3.7.2``|``GCCcore/13.2.0`` ### libav @@ -17881,6 +18162,16 @@ version |toolchain ``0.9.0`` |``foss/2020b`` ``0.11.1``|``GCCcore/11.3.0``, ``foss/2021a``, ``foss/2022a`` +### libbaseencode + +Library written in C for encoding and decoding data using base32 or base64 according to RFC-4648 + +*homepage*: + +version |toolchain +----------|------------------ +``1.0.11``|``GCCcore/10.2.0`` + ### libBigWig A C library for handling bigWig files @@ -17941,6 +18232,7 @@ version |toolchain ---------|----------------------------------------------- ``4.4.0``|``foss/2020b``, ``foss/2021a``, ``gomkl/2021a`` ``5.1.6``|``foss/2022a`` +``5.4.0``|``gfbf/2023a`` ### libcircle @@ -17949,9 +18241,9 @@ An API to provide an efficient distributed queue on a cluster. libcircle is an *homepage*: version |toolchain ---------------|------------------------------------------------------------------ +--------------|----------------------------------------------------------------------------------- ``0.2.1-rc.1``|``gompi/2019a``, ``iimpi/2019a`` -``0.3`` |``gompi/2020a``, ``gompi/2020b``, ``gompi/2022a``, ``iimpi/2020a`` +``0.3`` |``gompi/2020a``, ``gompi/2020b``, ``gompi/2022a``, ``gompi/2023a``, ``iimpi/2020a`` ### libcmaes @@ -17976,6 +18268,16 @@ version |toolchain ``1.7.2``|``GCCcore/7.3.0`` ``1.7.3``|``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +### libcotp + +C library that generates TOTP and HOTP according to RFC-6238 + +*homepage*: + +version |toolchain +---------|------------------ +``1.2.3``|``GCCcore/10.2.0`` + ### libcpuset libcpuset provides full access to cpuset capabilities @@ -18053,6 +18355,7 @@ version |toolchain ``1.10``|``GCCcore/11.3.0`` ``1.15``|``GCCcore/12.2.0`` ``1.18``|``GCCcore/12.3.0`` +``1.19``|``GCCcore/13.2.0`` ### libdivsufsort @@ -18088,6 +18391,7 @@ version |toolchain ``2.4.110``|``GCCcore/11.3.0`` ``2.4.114``|``GCCcore/12.2.0`` ``2.4.115``|``GCCcore/12.3.0`` +``2.4.117``|``GCCcore/13.2.0`` ### libdrs @@ -18123,11 +18427,11 @@ This BSD-style licensed command line editor library provides generic line editin *homepage*: version |toolchain -------------|------------------ +------------|-------------------------------------- ``20150325``|``GNU/4.9.3-2.25`` ``20180525``|``GCCcore/6.4.0`` ``20191231``|``GCCcore/9.3.0`` -``20210910``|``GCCcore/11.2.0`` +``20210910``|``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ### libelf @@ -18249,7 +18553,7 @@ version |toolchain ``3.2.1``|``GCC/4.9.2``, ``GCC/4.9.3-2.25``, ``GCC/5.4.0-2.26``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GNU/4.9.3-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``system`` ``3.3`` |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` ``3.4.2``|``GCCcore/11.2.0``, ``GCCcore/11.3.0`` -``3.4.4``|``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.1.0`` +``3.4.4``|``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``GCCcore/13.2.0`` ### libFLAME @@ -18375,7 +18679,7 @@ version |versionsuffix |toolchain ``9.0.0``|``-Mesa-11.2.1``|``foss/2016a``, ``intel/2016a`` ``9.0.1``| |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``9.0.2``| |``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` -``9.0.3``| |``GCCcore/12.3.0`` +``9.0.3``| |``GCCcore/12.3.0``, ``GCCcore/13.2.0`` ### libglvnd @@ -18390,6 +18694,7 @@ version |toolchain ``1.3.3``|``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``1.4.0``|``GCCcore/11.3.0`` ``1.6.0``|``GCCcore/12.2.0``, ``GCCcore/12.3.0`` +``1.7.0``|``GCCcore/13.2.0`` ### libgpg-error @@ -18505,7 +18810,7 @@ version |toolchain --------|------------------------------------------------------------------------------------------------------------------- ``1.15``|``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0`` ``1.16``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``1.17``|``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` +``1.17``|``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0`` ### libidn @@ -18583,6 +18888,7 @@ version |versionsuffix |toolchain ``2.1.3`` | |``GCCcore/11.3.0`` ``2.1.4`` | |``GCCcore/12.2.0`` ``2.1.5.1``| |``GCCcore/12.3.0`` +``3.0.1`` | |``GCCcore/13.2.0`` ### libjxl @@ -18647,6 +18953,7 @@ version |toolchain -----------|--------------- ``2.0.453``|``intel/2018a`` ``2.0.499``|``GCC/11.3.0`` +``2.0.813``|``GCC/12.3.0`` ### libmbd @@ -18811,6 +19118,7 @@ version |toolchain ``1.6.37``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``1.6.38``|``GCCcore/12.2.0`` ``1.6.39``|``GCCcore/12.3.0`` +``1.6.40``|``GCCcore/13.2.0`` ### libpsl @@ -18895,7 +19203,7 @@ version |toolchain ``8.0`` |``GCCcore/10.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``system`` ``8.1`` |``FCC/4.5.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ``8.1.2``|``GCCcore/11.3.0``, ``GCCcore/12.1.0`` -``8.2`` |``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.1.0`` +``8.2`` |``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``GCCcore/13.2.0`` ### libRmath @@ -18992,6 +19300,7 @@ version |toolchain ``2.10.1``|``GCCcore/7.3.0`` ``2.10.2``|``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``2.10.8``|``GCCcore/10.3.0`` +``2.12.1``|``GCCcore/11.3.0`` ``3.4.0`` |``GCCcore/11.3.0`` ### libsigsegv @@ -19046,6 +19355,7 @@ version |toolchain ``1.0.16``|``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``1.0.17``|``GCCcore/8.2.0`` ``1.0.18``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``1.0.19``|``GCCcore/13.2.0`` ### LibSoup @@ -19185,6 +19495,7 @@ version |toolchain ``4.3.0`` |``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ``4.4.0`` |``GCCcore/12.2.0`` ``4.5.0`` |``GCCcore/12.3.0`` +``4.6.0`` |``GCCcore/13.2.0`` ### libtirpc @@ -19246,13 +19557,13 @@ The primary goal of libunwind is to define a portable and efficient C programmin *homepage*: version |toolchain ----------|----------------------------------------------------------------------- +---------|------------------------------------------------------------------------------ ``1.1`` |``GCC/4.9.2``, ``foss/2016a``, ``intel/2016b`` ``1.2.1``|``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``foss/2016b`` ``1.3.1``|``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``1.4.0``|``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ``1.5.0``|``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``1.6.2``|``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` +``1.6.2``|``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0`` ### libutempter @@ -19291,9 +19602,9 @@ libvdwxc is a general library for evaluating energy and potential for exchange-c *homepage*: version |toolchain ----------|----------------------------------------------------------------------------------------------------------------------------------------------------------------- +---------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ``0.3.2``|``foss/2018b`` -``0.4.0``|``foss/2019a``, ``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``foss/2022a``, ``intel/2020b``, ``intel/2021a``, ``intel/2021b`` +``0.4.0``|``foss/2019a``, ``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``foss/2022a``, ``foss/2023a``, ``intel/2020b``, ``intel/2021a``, ``intel/2021b`` ### libvorbis @@ -19339,6 +19650,7 @@ version |toolchain ``1.2.0``|``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``1.2.4``|``GCCcore/11.3.0`` ``1.3.1``|``GCCcore/12.2.0``, ``GCCcore/12.3.0`` +``1.3.2``|``GCCcore/13.2.0`` ### libwpe @@ -19393,6 +19705,7 @@ version |toolchain ``5.1.6``|``GCC/11.2.0``, ``intel-compilers/2021.4.0`` ``5.2.3``|``GCC/11.3.0``, ``intel-compilers/2022.1.0`` ``6.1.0``|``GCC/12.2.0``, ``intel-compilers/2022.2.1`` +``6.2.2``|``GCC/12.3.0``, ``intel-compilers/2023.1.0`` ### libxcb @@ -19671,12 +19984,12 @@ LibYAML is a YAML parser and emitter written in C. *homepage*: version |toolchain ----------|---------------------------------------------------------------------------------------------------------------------- +---------|------------------------------------------------------------------------------------------------------------------------------------------ ``0.1.6``|``GCCcore/6.4.0``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` ``0.1.7``|``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``system`` ``0.2.1``|``GCCcore/7.3.0``, ``system`` ``0.2.2``|``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``0.2.5``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` +``0.2.5``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0`` ### libzeep @@ -19788,10 +20101,11 @@ line_profiler is a module for doing line-by-line profiling of functions. kernpro *homepage*: version |versionsuffix |toolchain ----------|-----------------|-------------- +---------|-----------------|------------------ ``3.1.0``|``-Python-3.8.2``|``foss/2020a`` ``3.5.1``| |``foss/2021b`` ``4.0.0``| |``foss/2022a`` +``4.1.1``| |``GCCcore/12.2.0`` ### Lingeling @@ -19871,7 +20185,7 @@ version |toolchain ``12.0.1``|``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``14.0.3``|``GCCcore/11.3.0`` ``15.0.5``|``GCCcore/12.2.0`` -``16.0.6``|``GCCcore/12.3.0`` +``16.0.6``|``GCCcore/12.3.0``, ``GCCcore/13.2.0`` ### LMDB @@ -19888,6 +20202,7 @@ version |toolchain ``0.9.24``|``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``0.9.28``|``GCCcore/10.3.0`` ``0.9.29``|``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +``0.9.31``|``GCCcore/12.3.0`` ### LMfit @@ -20054,6 +20369,7 @@ An R interface for loom files version |versionsuffix|toolchain ------------------|-------------|-------------- ``0.2.0-20180425``|``-R-4.2.1`` |``foss/2022a`` +``0.2.0-20180425``|``-R-4.2.2`` |``foss/2022b`` ### LoRDEC @@ -20255,7 +20571,7 @@ version |toolchain ---------|------------------------------------------------------------------ ``1.0.2``|``gompi/2019a``, ``gompi/2020a``, ``iimpi/2019a``, ``iimpi/2020a`` ``1.0.3``|``gompi/2020b`` -``1.0.5``|``gompi/2022a`` +``1.0.5``|``gompi/2022a``, ``gompi/2023a`` ### lxml @@ -20305,7 +20621,7 @@ version |toolchain ``1.9.1``|``GCCcore/8.2.0`` ``1.9.2``|``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``1.9.3``|``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` -``1.9.4``|``GCCcore/12.2.0``, ``GCCcore/12.3.0`` +``1.9.4``|``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0`` ### LZO @@ -20314,14 +20630,14 @@ Portable lossless data compression library *homepage*: version |toolchain ---------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ +--------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ``2.09``|``intel/2016b``, ``intel/2017b`` -``2.10``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``foss/2018a``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2017a`` +``2.10``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``foss/2018a``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2017a`` ## M -[M1QN3](#m1qn3) - [M3GNet](#m3gnet) - [M4](#m4) - [MACH](#mach) - [MACS2](#macs2) - [MACSE](#macse) - [maeparser](#maeparser) - [MAFFT](#mafft) - [MAGeCK](#mageck) - [magick](#magick) - [Magics](#magics) - [magma](#magma) - [MAGMA-gene-analysis](#magma-gene-analysis) - [MagresPython](#magrespython) - [mahotas](#mahotas) - [MAJIQ](#majiq) - [make](#make) - [makedepend](#makedepend) - [makedepf90](#makedepf90) - [makeinfo](#makeinfo) - [MAKER](#maker) - [Mako](#mako) - [Mamba](#mamba) - [mandrake](#mandrake) - [mannkendall](#mannkendall) - [manta](#manta) - [mapDamage](#mapdamage) - [Maple](#maple) - [MapSplice](#mapsplice) - [Maq](#maq) - [MariaDB](#mariadb) - [MariaDB-connector-c](#mariadb-connector-c) - [MARS](#mars) - [Mash](#mash) - [MaSuRCA](#masurca) - [Mathematica](#mathematica) - [MathGL](#mathgl) - [MATIO](#matio) - [MATLAB](#matlab) - [MATLAB-Engine](#matlab-engine) - [matlab-proxy](#matlab-proxy) - [matplotlib](#matplotlib) - [matplotlib-inline](#matplotlib-inline) - [MATSim](#matsim) - [maturin](#maturin) - [Maude](#maude) - [mauveAligner](#mauvealigner) - [Maven](#maven) - [mawk](#mawk) - [MaxBin](#maxbin) - [MaxQuant](#maxquant) - [mayavi](#mayavi) - [maze](#maze) - [MbedTLS](#mbedtls) - [MBROLA](#mbrola) - [mbuffer](#mbuffer) - [mc](#mc) - [MCL](#mcl) - [MCR](#mcr) - [mctc-lib](#mctc-lib) - [mcu](#mcu) - [MDAnalysis](#mdanalysis) - [MDBM](#mdbm) - [MDSplus](#mdsplus) - [MDSplus-Java](#mdsplus-java) - [MDSplus-Python](#mdsplus-python) - [mdtest](#mdtest) - [MDTraj](#mdtraj) - [meboot](#meboot) - [medaka](#medaka) - [medImgProc](#medimgproc) - [MedPy](#medpy) - [Meep](#meep) - [MEGA](#mega) - [MEGACC](#megacc) - [MEGAHIT](#megahit) - [Megalodon](#megalodon) - [MEGAN](#megan) - [Meld](#meld) - [MEM](#mem) - [MEME](#meme) - [memkind](#memkind) - [memory-profiler](#memory-profiler) - [MEMOTE](#memote) - [memtester](#memtester) - [meRanTK](#merantk) - [MERCKX](#merckx) - [Mercurial](#mercurial) - [Mesa](#mesa) - [Mesa-demos](#mesa-demos) - [meshalyzer](#meshalyzer) - [meshio](#meshio) - [meshtool](#meshtool) - [Meson](#meson) - [meson-python](#meson-python) - [Mesquite](#mesquite) - [MESS](#mess) - [MetaBAT](#metabat) - [MetaboAnalystR](#metaboanalystr) - [metaerg](#metaerg) - [MetaEuk](#metaeuk) - [MetaGeneAnnotator](#metageneannotator) - [Metagenome-Atlas](#metagenome-atlas) - [Metal](#metal) - [MetaMorpheus](#metamorpheus) - [MetaPhlAn](#metaphlan) - [MetaPhlAn2](#metaphlan2) - [metaWRAP](#metawrap) - [Metaxa2](#metaxa2) - [methylartist](#methylartist) - [MethylDackel](#methyldackel) - [methylpy](#methylpy) - [METIS](#metis) - [mgen](#mgen) - [mgltools](#mgltools) - [mhcflurry](#mhcflurry) - [mhcnuggets](#mhcnuggets) - [MicrobeAnnotator](#microbeannotator) - [microctools](#microctools) - [MiGEC](#migec) - [MIGRATE-N](#migrate-n) - [Mikado](#mikado) - [Miller](#miller) - [mimalloc](#mimalloc) - [MINC](#minc) - [MinCED](#minced) - [Mini-XML](#mini-xml) - [miniasm](#miniasm) - [minibar](#minibar) - [MiniCARD](#minicard) - [Miniconda2](#miniconda2) - [Miniconda3](#miniconda3) - [minieigen](#minieigen) - [Minimac4](#minimac4) - [minimap2](#minimap2) - [Minipolish](#minipolish) - [MiniSat](#minisat) - [minizip](#minizip) - [MINPACK](#minpack) - [MinPath](#minpath) - [MIRA](#mira) - [miRDeep2](#mirdeep2) - [Mish-Cuda](#mish-cuda) - [misha](#misha) - [MITgcmutils](#mitgcmutils) - [MITObim](#mitobim) - [MitoZ](#mitoz) - [MiXCR](#mixcr) - [MixMHC2pred](#mixmhc2pred) - [mkl-dnn](#mkl-dnn) - [mkl-service](#mkl-service) - [mkl_fft](#mkl_fft) - [MLC](#mlc) - [MLxtend](#mlxtend) - [mm-common](#mm-common) - [Mmg](#mmg) - [MMSEQ](#mmseq) - [MMseqs2](#mmseqs2) - [mmtf-cpp](#mmtf-cpp) - [MNE-Python](#mne-python) - [MOABB](#moabb) - [MOABS](#moabs) - [MOB-suite](#mob-suite) - [ModelTest-NG](#modeltest-ng) - [modred](#modred) - [Molcas](#molcas) - [mold](#mold) - [Molden](#molden) - [molecularGSM](#moleculargsm) - [Molekel](#molekel) - [molmod](#molmod) - [Molpro](#molpro) - [MONA](#mona) - [MONAI](#monai) - [MONAI-Label](#monai-label) - [mongolite](#mongolite) - [Mono](#mono) - [Monocle3](#monocle3) - [moonjit](#moonjit) - [MOOSE](#moose) - [mordecai](#mordecai) - [MoreRONN](#moreronn) - [mosdepth](#mosdepth) - [Mothur](#mothur) - [motif](#motif) - [MotionCor2](#motioncor2) - [motionSegmentation](#motionsegmentation) - [MoviePy](#moviepy) - [MPB](#mpb) - [MPC](#mpc) - [MPFR](#mpfr) - [mpi4py](#mpi4py) - [MPICH](#mpich) - [MPICH2](#mpich2) - [mpifileutils](#mpifileutils) - [mpiP](#mpip) - [MPJ-Express](#mpj-express) - [mpmath](#mpmath) - [MrBayes](#mrbayes) - [mrcfile](#mrcfile) - [MRChem](#mrchem) - [MRCPP](#mrcpp) - [MRIcron](#mricron) - [MRPRESSO](#mrpresso) - [MRtrix](#mrtrix) - [msgpack-c](#msgpack-c) - [MSM](#msm) - [MSPC](#mspc) - [msprime](#msprime) - [mstore](#mstore) - [MTL4](#mtl4) - [MuJoCo](#mujoco) - [mujoco-py](#mujoco-py) - [multichoose](#multichoose) - [MultilevelEstimators](#multilevelestimators) - [MultiNest](#multinest) - [MultiQC](#multiqc) - [Multiwfn](#multiwfn) - [muMerge](#mumerge) - [MUMmer](#mummer) - [MUMPS](#mumps) - [muParser](#muparser) - [muparserx](#muparserx) - [MuPeXI](#mupexi) - [MUSCLE](#muscle) - [MuSiC](#music) - [MUST](#must) - [MuTect](#mutect) - [mutil](#mutil) - [MVAPICH2](#mvapich2) - [MView](#mview) - [mxml](#mxml) - [mxmlplus](#mxmlplus) - [MXNet](#mxnet) - [MyCC](#mycc) - [mygene](#mygene) - [MyMediaLite](#mymedialite) - [mympingpong](#mympingpong) - [Myokit](#myokit) - [mypy](#mypy) - [MySQL](#mysql) - [MySQL-python](#mysql-python) - [mysqlclient](#mysqlclient) +[M1QN3](#m1qn3) - [M3GNet](#m3gnet) - [M4](#m4) - [MACH](#mach) - [MACS2](#macs2) - [MACS3](#macs3) - [MACSE](#macse) - [maeparser](#maeparser) - [MAFFT](#mafft) - [MAGeCK](#mageck) - [magick](#magick) - [Magics](#magics) - [magma](#magma) - [MAGMA-gene-analysis](#magma-gene-analysis) - [MagresPython](#magrespython) - [mahotas](#mahotas) - [MAJIQ](#majiq) - [make](#make) - [makedepend](#makedepend) - [makedepf90](#makedepf90) - [makeinfo](#makeinfo) - [MAKER](#maker) - [Mako](#mako) - [Mamba](#mamba) - [mandrake](#mandrake) - [mannkendall](#mannkendall) - [manta](#manta) - [mapDamage](#mapdamage) - [Maple](#maple) - [MapSplice](#mapsplice) - [Maq](#maq) - [MariaDB](#mariadb) - [MariaDB-connector-c](#mariadb-connector-c) - [MARS](#mars) - [Mash](#mash) - [Mashtree](#mashtree) - [MaSuRCA](#masurca) - [Mathematica](#mathematica) - [MathGL](#mathgl) - [MATIO](#matio) - [MATLAB](#matlab) - [MATLAB-Engine](#matlab-engine) - [matlab-proxy](#matlab-proxy) - [matplotlib](#matplotlib) - [matplotlib-inline](#matplotlib-inline) - [MATSim](#matsim) - [maturin](#maturin) - [Maude](#maude) - [mauveAligner](#mauvealigner) - [Maven](#maven) - [mawk](#mawk) - [MaxBin](#maxbin) - [MaxQuant](#maxquant) - [mayavi](#mayavi) - [maze](#maze) - [MbedTLS](#mbedtls) - [MBROLA](#mbrola) - [mbuffer](#mbuffer) - [mc](#mc) - [MCL](#mcl) - [MCR](#mcr) - [mctc-lib](#mctc-lib) - [mcu](#mcu) - [MDAnalysis](#mdanalysis) - [MDBM](#mdbm) - [MDSplus](#mdsplus) - [MDSplus-Java](#mdsplus-java) - [MDSplus-Python](#mdsplus-python) - [mdtest](#mdtest) - [MDTraj](#mdtraj) - [meboot](#meboot) - [medaka](#medaka) - [medImgProc](#medimgproc) - [MedPy](#medpy) - [Meep](#meep) - [MEGA](#mega) - [MEGACC](#megacc) - [MEGAHIT](#megahit) - [Megalodon](#megalodon) - [MEGAN](#megan) - [Meld](#meld) - [MEM](#mem) - [MEME](#meme) - [memkind](#memkind) - [memory-profiler](#memory-profiler) - [MEMOTE](#memote) - [memtester](#memtester) - [meRanTK](#merantk) - [MERCKX](#merckx) - [Mercurial](#mercurial) - [Mesa](#mesa) - [Mesa-demos](#mesa-demos) - [meshalyzer](#meshalyzer) - [meshio](#meshio) - [meshtool](#meshtool) - [Meson](#meson) - [meson-python](#meson-python) - [Mesquite](#mesquite) - [MESS](#mess) - [MetaBAT](#metabat) - [MetaboAnalystR](#metaboanalystr) - [metaerg](#metaerg) - [MetaEuk](#metaeuk) - [MetaGeneAnnotator](#metageneannotator) - [Metagenome-Atlas](#metagenome-atlas) - [Metal](#metal) - [MetaMorpheus](#metamorpheus) - [MetaPhlAn](#metaphlan) - [MetaPhlAn2](#metaphlan2) - [metaWRAP](#metawrap) - [Metaxa2](#metaxa2) - [methylartist](#methylartist) - [MethylDackel](#methyldackel) - [methylpy](#methylpy) - [METIS](#metis) - [mgen](#mgen) - [mgltools](#mgltools) - [mhcflurry](#mhcflurry) - [mhcnuggets](#mhcnuggets) - [MicrobeAnnotator](#microbeannotator) - [microctools](#microctools) - [MiGEC](#migec) - [MIGRATE-N](#migrate-n) - [Mikado](#mikado) - [Miller](#miller) - [mimalloc](#mimalloc) - [MINC](#minc) - [MinCED](#minced) - [Mini-XML](#mini-xml) - [miniasm](#miniasm) - [minibar](#minibar) - [MiniCARD](#minicard) - [Miniconda2](#miniconda2) - [Miniconda3](#miniconda3) - [minieigen](#minieigen) - [Minimac4](#minimac4) - [minimap2](#minimap2) - [Minipolish](#minipolish) - [MiniSat](#minisat) - [minizip](#minizip) - [MINPACK](#minpack) - [MinPath](#minpath) - [MIRA](#mira) - [miRDeep2](#mirdeep2) - [Mish-Cuda](#mish-cuda) - [misha](#misha) - [MITgcmutils](#mitgcmutils) - [MITObim](#mitobim) - [MitoZ](#mitoz) - [MiXCR](#mixcr) - [MixMHC2pred](#mixmhc2pred) - [mkl-dnn](#mkl-dnn) - [mkl-service](#mkl-service) - [mkl_fft](#mkl_fft) - [MLC](#mlc) - [MLxtend](#mlxtend) - [mm-common](#mm-common) - [Mmg](#mmg) - [MMSEQ](#mmseq) - [MMseqs2](#mmseqs2) - [mmtf-cpp](#mmtf-cpp) - [MNE-Python](#mne-python) - [MOABB](#moabb) - [MOABS](#moabs) - [MOB-suite](#mob-suite) - [ModelTest-NG](#modeltest-ng) - [modred](#modred) - [Molcas](#molcas) - [mold](#mold) - [Molden](#molden) - [molecularGSM](#moleculargsm) - [Molekel](#molekel) - [molmod](#molmod) - [Molpro](#molpro) - [MONA](#mona) - [MONAI](#monai) - [MONAI-Label](#monai-label) - [mongolite](#mongolite) - [Mono](#mono) - [Monocle3](#monocle3) - [moonjit](#moonjit) - [MOOSE](#moose) - [mordecai](#mordecai) - [MoreRONN](#moreronn) - [mosdepth](#mosdepth) - [Mothur](#mothur) - [motif](#motif) - [MotionCor2](#motioncor2) - [motionSegmentation](#motionsegmentation) - [MoviePy](#moviepy) - [mpath](#mpath) - [MPB](#mpb) - [MPC](#mpc) - [MPFR](#mpfr) - [mpi4py](#mpi4py) - [MPICH](#mpich) - [MPICH2](#mpich2) - [mpifileutils](#mpifileutils) - [mpiP](#mpip) - [MPJ-Express](#mpj-express) - [mpmath](#mpmath) - [MrBayes](#mrbayes) - [mrcfile](#mrcfile) - [MRChem](#mrchem) - [MRCPP](#mrcpp) - [MRIcron](#mricron) - [MRPRESSO](#mrpresso) - [MRtrix](#mrtrix) - [msgpack-c](#msgpack-c) - [MSM](#msm) - [MSPC](#mspc) - [msprime](#msprime) - [mstore](#mstore) - [MTL4](#mtl4) - [MuJoCo](#mujoco) - [mujoco-py](#mujoco-py) - [multichoose](#multichoose) - [MultilevelEstimators](#multilevelestimators) - [MultiNest](#multinest) - [MultiQC](#multiqc) - [Multiwfn](#multiwfn) - [muMerge](#mumerge) - [MUMmer](#mummer) - [MUMPS](#mumps) - [muParser](#muparser) - [muparserx](#muparserx) - [MuPeXI](#mupexi) - [MUSCLE](#muscle) - [MUSCLE3](#muscle3) - [MuSiC](#music) - [MUST](#must) - [MuTect](#mutect) - [mutil](#mutil) - [MVAPICH2](#mvapich2) - [MView](#mview) - [mxml](#mxml) - [mxmlplus](#mxmlplus) - [MXNet](#mxnet) - [MyCC](#mycc) - [mygene](#mygene) - [MyMediaLite](#mymedialite) - [mympingpong](#mympingpong) - [Myokit](#myokit) - [mypy](#mypy) - [MySQL](#mysql) - [MySQL-python](#mysql-python) - [mysqlclient](#mysqlclient) ### M1QN3 @@ -20379,9 +20695,19 @@ version |versionsuffix |toolchain ``2.1.2.1`` |``-Python-2.7.14``|``foss/2017b``, ``intel/2017b`` ``2.1.2.1`` |``-Python-2.7.15``|``intel/2019a`` ``2.2.5`` |``-Python-3.6.6`` |``foss/2018b`` -``2.2.7.1`` | |``foss/2021b`` +``2.2.7.1`` | |``foss/2021a``, ``foss/2021b`` ``2.2.9.1`` | |``foss/2022b`` +### MACS3 + +Model Based Analysis for ChIP-Seq data + +*homepage*: + +version |toolchain +-----------|-------------- +``3.0.0b2``|``foss/2022b`` + ### MACSE MACSE aligns coding NT sequences with respect to their AA translation while allowing NT sequences to contain multiple frameshifts and/or stop codons. MACSE is hence the first automatic solution to align protein-coding gene datasets containing non-functional sequences (pseudogenes) without disrupting the underlying codon structure. @@ -20422,6 +20748,7 @@ version |versionsuffix |toolchain ``7.487``|``-with-extensions``|``gompi/2021a`` ``7.490``|``-with-extensions``|``GCC/10.3.0``, ``GCC/11.2.0``, ``gompi/2021b`` ``7.505``|``-with-extensions``|``GCC/11.3.0``, ``GCC/12.2.0`` +``7.520``|``-with-extensions``|``GCC/12.3.0`` ### MAGeCK @@ -20529,7 +20856,7 @@ version |toolchain ``4.1`` |``GCC/4.9.2`` ``4.2.1``|``GCC/7.3.0-2.30``, ``GCCcore/8.3.0`` ``4.3`` |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/9.3.0`` -``4.4.1``|``GCCcore/12.2.0``, ``GCCcore/12.3.0`` +``4.4.1``|``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0`` ### makedepend @@ -20541,7 +20868,7 @@ version |toolchain ---------|----------------------------------------------------------------------------------------------- ``1.0.5``|``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` ``1.0.6``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``1.0.7``|``GCCcore/11.3.0`` +``1.0.7``|``GCCcore/11.3.0``, ``GCCcore/12.3.0`` ### makedepf90 @@ -20564,7 +20891,8 @@ version |versionsuffix|toolchain ``6.7`` | |``FCC/4.5.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``6.7`` |``-minimal`` |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``6.8`` | |``GCCcore/11.2.0``, ``GCCcore/11.3.0`` -``7.0.3``| |``GCCcore/12.3.0`` +``7.0.3``| |``GCCcore/12.2.0``, ``GCCcore/12.3.0`` +``7.1`` | |``GCCcore/13.2.0`` ### MAKER @@ -20596,7 +20924,7 @@ version |versionsuffix |toolchain ``1.1.3``| |``GCCcore/10.2.0`` ``1.1.4``| |``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``1.2.0``| |``GCCcore/11.3.0`` -``1.2.4``| |``GCCcore/12.2.0``, ``GCCcore/12.3.0`` +``1.2.4``| |``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0`` ### Mamba @@ -20742,11 +21070,21 @@ Fast genome and metagenome distance estimation using MinHash *homepage*: version|toolchain --------|---------------------------------------------------------------------------- +-------|------------------------------------------------------------------------------------------------------------ ``2.0``|``foss/2018a`` ``2.1``|``foss/2018b`` ``2.2``|``GCC/9.3.0`` -``2.3``|``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0``, ``intel-compilers/2021.4.0`` +``2.3``|``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0``, ``GCC/12.2.0``, ``GCC/12.3.0``, ``intel-compilers/2021.4.0`` + +### Mashtree + +Create a tree using Mash distances. + +*homepage*: + +version |toolchain +---------|-------------- +``1.4.6``|``GCC/12.2.0`` ### MaSuRCA @@ -20835,6 +21173,7 @@ version |versionsuffix|toolchain ``2022b``| |``system`` ``2022b``|``-r5`` |``system`` ``2023a``| |``system`` +``2023b``| |``system`` ### MATLAB-Engine @@ -21091,7 +21430,7 @@ version |versionsuffix |toolchain ``14.137``| |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``intel/2016b`` ``14.137``|``-Perl-5.26.1``|``GCCcore/6.4.0`` ``14.137``|``-Perl-5.28.0``|``GCCcore/7.3.0`` -``22.282``| |``GCCcore/11.3.0`` +``22.282``| |``GCCcore/11.3.0``, ``GCCcore/12.3.0`` ### MCR @@ -21351,6 +21690,7 @@ MEGAN is a comprehensive toolbox for interactively analyzing microbiome data version |versionsuffix|toolchain ----------|-------------|---------- ``6.22.0``|``-Java-17`` |``system`` +``6.25.3``|``-Java-17`` |``system`` ### Meld @@ -21489,6 +21829,7 @@ version |toolchain ``22.0.3``|``GCCcore/11.3.0`` ``22.2.4``|``GCCcore/12.2.0`` ``23.1.4``|``GCCcore/12.3.0`` +``23.1.9``|``GCCcore/13.2.0`` ### Mesa-demos @@ -21559,6 +21900,7 @@ version |versionsuffix |toolchain ``0.62.1``| |``GCCcore/11.3.0`` ``0.64.0``| |``GCCcore/12.2.0`` ``1.1.1`` | |``GCCcore/12.3.0`` +``1.2.3`` | |``GCCcore/13.2.0`` ### meson-python @@ -22271,7 +22613,7 @@ version |toolchain ``13-45111`` |``gompi/2020b``, ``gompi/2021a``, ``gompi/2021b`` ``13-45111-20211006``|``gompi/2020b`` ``13-45111-20211019``|``gompi/2020b`` -``14-7e284`` |``gompi/2022a`` +``14-7e284`` |``gompi/2022a``, ``gompi/2023a`` ### mmtf-cpp @@ -22369,6 +22711,7 @@ version |toolchain ``1.3.0`` |``GCCcore/11.3.0`` ``1.7.1`` |``GCCcore/12.2.0`` ``1.11.0``|``GCCcore/12.3.0`` +``2.3.1`` |``GCCcore/13.2.0`` ### Molden @@ -22513,6 +22856,7 @@ version |versionsuffix |toolchain ``0.2.0``|``-Python-3.7.2-R-3.6.0``|``foss/2019a`` ``0.2.3``|``-R-4.0.3`` |``foss/2020b`` ``1.3.1``|``-R-4.2.1`` |``foss/2022a`` +``1.3.1``|``-R-4.2.2`` |``foss/2022b`` ### moonjit @@ -22586,10 +22930,10 @@ Motif refers to both a graphical user interface (GUI) specification and the widg *homepage*: version |toolchain ----------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +---------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ``2.3.5``|``foss/2016a``, ``intel/2016a`` ``2.3.7``|``intel/2017a`` -``2.3.8``|``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``foss/2019a``, ``intel/2017b``, ``intel/2018a``, ``intel/2019a`` +``2.3.8``|``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``foss/2019a``, ``intel/2017b``, ``intel/2018a``, ``intel/2019a`` ### MotionCor2 @@ -22627,6 +22971,16 @@ version |versionsuffix |toolchain ``1.0.1``|``-Python-3.7.2``|``foss/2019a`` ``1.0.3``| |``foss/2021a``, ``foss/2021b`` +### mpath + +For now it's quit simple and get_path_info() method returns information about given path. It can be either a directory or a file path. + +*homepage*: + +version |toolchain +---------|------------------ +``1.1.3``|``GCCcore/11.3.0`` + ### MPB MPB is a free and open-source software package for computing the band structures, or dispersion relations, and electromagnetic modes of periodic dielectric structures, on both serial and parallel computers. MPB is an acronym for MIT Photonic Bands. @@ -22650,7 +23004,7 @@ version |versionsuffix |toolchain ``1.0.3``|``-MPFR-3.1.6``|``foss/2017b``, ``intel/2017b`` ``1.1.0``| |``GCC/8.3.0``, ``GCC/9.3.0``, ``GCCcore/9.3.0`` ``1.2.1``| |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` -``1.3.1``| |``GCCcore/12.3.0`` +``1.3.1``| |``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0`` ### MPFR @@ -22668,6 +23022,7 @@ version |toolchain ``4.0.2``|``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``4.1.0``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ``4.2.0``|``GCCcore/12.2.0``, ``GCCcore/12.3.0`` +``4.2.1``|``GCCcore/13.2.0`` ### mpi4py @@ -22722,7 +23077,7 @@ version |toolchain ``0.9.1`` |``gompi/2019a``, ``iimpi/2019a`` ``0.10`` |``gompi/2020a``, ``iimpi/2020a`` ``0.10.1``|``gompi/2020a`` -``0.11.1``|``gompi/2022a`` +``0.11.1``|``gompi/2022a``, ``gompi/2023a`` ### mpiP @@ -22850,6 +23205,7 @@ MessagePack is an efficient binary serialization format, which lets you exchange version |toolchain ---------|------------------ ``3.3.0``|``GCCcore/10.2.0`` +``6.0.0``|``GCC/12.2.0`` ### MSM @@ -23036,11 +23392,11 @@ muParser is an extensible high performance math expression parser library writt *homepage*: version |toolchain ----------|------------------------------------- +---------|-------------------------------------- ``2.2.5``|``GCCcore/6.4.0`` ``2.3.2``|``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ``2.3.3``|``GCCcore/10.3.0`` -``2.3.4``|``GCCcore/11.3.0`` +``2.3.4``|``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ### muparserx @@ -23077,6 +23433,16 @@ version |versionsuffix |toolchain ``5.1`` | |``GCCcore/11.2.0`` ``5.1.0`` | |``GCCcore/10.3.0``, ``GCCcore/11.3.0`` +### MUSCLE3 + +MUSCLE3 allows connecting multiple simulation models together into a multiscale simulation. Simulation models can be as simple as a single Python file, or as complex as a combination of multiple separate simulation codes written in C++ or Fortran, and running on an HPC machine. + +*homepage*: + +version |toolchain +---------|-------------- +``0.7.0``|``foss/2022b`` + ### MuSiC Multi-subject Single Cell deconvolution (MuSiC) is a deconvolution method that utilizes cross-subject scRNA-seq to estimate cell type proportions in bulk RNA-seq data. @@ -23282,12 +23648,13 @@ version |versionsuffix |toolchain ### n2v -Noise2Void - Learning Denoising from Single Noisy Images The field of image denoising is currently dominated by discriminative deep learning methods that are trained on pairs of noisy input and clean target images. Recently it has been shown that such methods can also be trained without clean targets. Instead, independent pairs of noisy images can be used, in an approach known as NOISE2NOISE (N2N). Here, we introduce NOISE2VOID (N2V), a training scheme that takes this idea one step further. It does not require noisy image pairs, nor clean target images. Consequently, N2V allows us to train directly on the body of data to be denoised and can therefore be applied when other methods cannot. Especially interesting is the application to biomedical image data, where the acquisition of training targets, clean or noisy, is frequently not possible. We compare the performance of N2V to approaches that have either clean target images and/or noisy image pairs available. Intuitively, N2V cannot be expected to outperform methods that have more information available during training. Still, we observe that the denoising performance of NOISE2VOID drops in moderation and compares favorably to training-free denoising methods. +Learning Denoising from Single Noisy Images *homepage*: version |versionsuffix |toolchain ---------|----------------|-------------- +``0.3.2``| |``foss/2022a`` ``0.3.2``|``-CUDA-11.3.1``|``foss/2021a`` ### NAG @@ -23489,6 +23856,7 @@ version |versionsuffix |toolchain ``0.13.1``|``-Python-3.6.6`` |``foss/2018b`` ``0.13.2``|``-Python-3.8.2`` |``foss/2020a`` ``0.13.3``| |``foss/2020b`` +``0.14.0``| |``foss/2022a`` ### NanopolishComp @@ -23536,7 +23904,7 @@ version |toolchain ``2.13.03``|``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``2.14.02``|``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``2.15.05``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` -``2.16.01``|``GCCcore/12.3.0`` +``2.16.01``|``GCCcore/12.3.0``, ``GCCcore/13.2.0`` ### nauty @@ -23566,10 +23934,11 @@ The Natural Bond Orbital (NBO) program is a discovery tool for chemical insights *homepage*: -version|toolchain --------|--------------- -``1.1``|``intel/2016a`` -``7.0``|``intel/2017b`` +version |toolchain +----------|--------------------------------------------------------------------------------------------- +``1.1`` |``intel/2016a`` +``7.0`` |``intel/2017b`` +``7.0.10``|``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/9.3.0``, ``gfbf/2022a``, ``gfbf/2022b`` ### NCBI-Toolkit @@ -23925,7 +24294,7 @@ version |versionsuffix |toolchain ``4.5.2``| |``gompi/2019b``, ``gompi/2020a``, ``gompic/2019b``, ``gompic/2020a``, ``iimpi/2019b``, ``iimpi/2020a``, ``iimpic/2019b`` ``4.5.3``| |``gompi/2020b``, ``gompi/2021a``, ``gompi/2021b``, ``gompic/2020b``, ``iimpi/2020b``, ``iimpi/2021a``, ``iimpi/2021b`` ``4.6.0``| |``gompi/2022a``, ``gompi/2022b``, ``iimpi/2022a`` -``4.6.1``| |``gompi/2023a`` +``4.6.1``| |``gompi/2023a``, ``iimpi/2023a`` ### netcdf4-python @@ -23952,6 +24321,7 @@ version |versionsuffix |toolchain ``1.5.7`` | |``foss/2021a``, ``foss/2021b``, ``intel/2021b`` ``1.6.1`` | |``foss/2022a``, ``intel/2022a`` ``1.6.3`` | |``foss/2022b`` +``1.6.4`` | |``foss/2023a`` ### netloc @@ -24419,7 +24789,7 @@ version |toolchain ``1.10.0``|``GCCcore/9.3.0`` ``1.10.1``|``GCCcore/10.2.0`` ``1.10.2``|``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` -``1.11.1``|``GCCcore/12.2.0``, ``GCCcore/12.3.0`` +``1.11.1``|``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0`` ### Nipype @@ -24720,9 +25090,9 @@ NTL is a high-performance, portable C++ library providing data structures and al *homepage*: version |toolchain -----------|------------------------------ +----------|---------------------------------------------- ``11.3.4``|``GCC/8.2.0-2.31.1`` -``11.5.1``|``GCC/11.2.0``, ``GCC/11.3.0`` +``11.5.1``|``GCC/11.2.0``, ``GCC/11.3.0``, ``GCC/12.2.0`` ### NTPoly @@ -24797,8 +25167,8 @@ Numdiff (which I will also write numdiff) is a little program that can be used t *homepage*: version |toolchain ----------|------------------ -``5.9.0``|``GCCcore/10.2.0`` +---------|-------------------------------------- +``5.9.0``|``GCCcore/10.2.0``, ``GCCcore/12.2.0`` ### numexpr @@ -25276,6 +25646,7 @@ version |versionsuffix |toolchain ``0.3.20``| |``GCC/11.2.0``, ``GCC/11.3.0``, ``NVHPC/22.7-CUDA-11.7.0`` ``0.3.21``| |``GCC/12.2.0`` ``0.3.23``| |``GCC/12.3.0`` +``0.3.24``| |``GCC/13.2.0`` ### openCARP @@ -25355,6 +25726,7 @@ version |versionsuffix |toolchain ``4.6.0`` |``-CUDA-11.7.0-contrib`` |``foss/2022a`` ``4.6.0`` |``-contrib`` |``foss/2022a`` ``4.8.0`` |``-contrib`` |``foss/2022b`` +``4.8.1`` |``-contrib`` |``foss/2023a`` ### OpenEXR @@ -25373,6 +25745,7 @@ version |toolchain ``3.1.1``|``GCCcore/11.2.0`` ``3.1.5``|``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ``3.1.7``|``GCCcore/12.3.0`` +``3.2.0``|``GCCcore/13.2.0`` ### OpenFace @@ -25421,7 +25794,7 @@ version |versionsuffix|toolchain ``8`` | |``foss/2020a``, ``foss/2020b`` ``8`` |``-20210316``|``foss/2020b`` ``9`` | |``foss/2021a``, ``intel/2021a`` -``10`` | |``foss/2022a`` +``10`` | |``foss/2022a``, ``foss/2023a`` ``10`` |``-20230119``|``foss/2022a`` ``11`` | |``foss/2022a`` ``v1606+`` | |``foss/2018b`` @@ -25496,12 +25869,12 @@ OpenJPEG is an open-source JPEG 2000 codec written in C language. It has been d *homepage*: version |toolchain ----------|----------------------------------------------------------------------------- +---------|------------------------------------------------------------------------------ ``2.1`` |``GCCcore/6.4.0`` ``2.3.0``|``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``2.3.1``|``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``2.4.0``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` -``2.5.0``|``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` +``2.5.0``|``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0`` ### OpenKIM-API @@ -25524,6 +25897,7 @@ version |toolchain ------------|------------------------------------------------------------------------------------ ``20190725``|``GCCcore/10.2.0``, ``foss/2019a``, ``foss/2019b``, ``intel/2019a``, ``intel/2019b`` ``20210128``|``GCCcore/10.2.0`` +``20210811``|``GCCcore/12.3.0`` ### OpenMM @@ -25544,7 +25918,7 @@ version |versionsuffix |toolchain ``7.5.1``|``-DeepMind-patch`` |``foss/2021a``, ``foss/2021b`` ``7.7.0``| |``foss/2021a``, ``foss/2022a`` ``7.7.0``|``-CUDA-11.3.1`` |``foss/2021a`` -``8.0.0``| |``foss/2022a`` +``8.0.0``| |``foss/2022a``, ``foss/2023a`` ``8.0.0``|``-CUDA-11.7.0`` |``foss/2022a`` ### OpenMM-PLUMED @@ -25582,6 +25956,7 @@ version |versionsuffix |toolchain ``22.06``| |``intel/2022a`` ``22.10``| |``intel/2022a`` ``22.10``|``-noGA`` |``intel/2022a`` +``23.06``| |``intel/2023a`` ### OpenMPI @@ -25632,6 +26007,7 @@ version |versionsuffix |toolchain ``4.1.2`` | |``GCC/10.2.0``, ``GCC/11.2.0`` ``4.1.4`` | |``GCC/11.3.0``, ``GCC/12.2.0``, ``NVHPC/22.7-CUDA-11.7.0`` ``4.1.5`` | |``GCC/12.2.0``, ``GCC/12.3.0``, ``intel-compilers/2023.1.0`` +``4.1.6`` | |``GCC/13.2.0`` ``system``| |``GCC/system-2.29`` ### OpenMS @@ -25661,8 +26037,8 @@ OpenPGM is an open source implementation of the Pragmatic General Multicast (PGM *homepage*: version |toolchain ------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ -``5.2.122``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` +-----------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +``5.2.122``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` ### OpenPIV @@ -25688,7 +26064,7 @@ version |versionsuffix |toolchain ``3.0.7`` | |``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ``3.0.9`` | |``GCCcore/11.2.0`` ``3.0.10``| |``GCCcore/11.3.0`` -``3.1.2`` | |``GCCcore/12.2.0`` +``3.1.2`` | |``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### OpenRefine @@ -25729,9 +26105,9 @@ OpenSlide is a C library that provides a simple interface to read whole-slide im *homepage*: version |versionsuffix |toolchain ----------|---------------|--------------------------------------------------------- +---------|---------------|----------------------------------------------------------------------------- ``3.4.1``| |``GCCcore/11.2.0``, ``GCCcore/8.2.0`` -``3.4.1``|``-largefiles``|``GCCcore/10.3.0``, ``GCCcore/11.3.0``, ``GCCcore/8.2.0`` +``3.4.1``|``-largefiles``|``GCCcore/10.3.0``, ``GCCcore/11.3.0``, ``GCCcore/12.3.0``, ``GCCcore/8.2.0`` ### openslide-python @@ -25744,6 +26120,7 @@ version |toolchain ``1.1.1``|``GCCcore/8.2.0`` ``1.1.2``|``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``1.2.0``|``GCCcore/11.3.0`` +``1.3.1``|``GCCcore/12.3.0`` ### OpenSSL @@ -25927,6 +26304,7 @@ version |versionsuffix |toolchain ``2.3.11``|``-Python-3.7.4`` |``intel/2019b`` ``2.5.2`` | |``foss/2020b`` ``2.5.4`` | |``foss/2020b`` +``2.5.5`` | |``foss/2023a`` ### OrthoMCL @@ -25982,8 +26360,11 @@ version |versionsuffix |toolchain ``5.9`` |``-CUDA-11.4.1``|``gompi/2021b`` ``5.9`` |``-CUDA-11.7.0``|``gompi/2022a`` ``5.9`` |``-ROCm-4.5.0`` |``gompi/2021b`` -``6.2`` | |``gompi/2022.10``, ``gompi/2022b`` +``6.2`` | |``gompi/2022.10``, ``gompi/2022b``, ``iimpi/2022b`` +``6.2`` |``-CUDA-12.0.0``|``gompi/2022b`` ``7.1-1``| |``gompi/2023a``, ``iimpi/2023a`` +``7.2`` | |``gompi/2023.09`` +``7.2`` |``-CUDA-12.1.1``|``gompi/2023a`` ### OTF2 @@ -26044,7 +26425,7 @@ version |versionsuffix |toolchain ## P -[p11-kit](#p11-kit) - [p4-phylogenetics](#p4-phylogenetics) - [p4est](#p4est) - [p4vasp](#p4vasp) - [p7zip](#p7zip) - [packmol](#packmol) - [pagmo](#pagmo) - [pairsnp](#pairsnp) - [PAL2NAL](#pal2nal) - [paladin](#paladin) - [PALEOMIX](#paleomix) - [PAML](#paml) - [panaroo](#panaroo) - [pandapower](#pandapower) - [pandas](#pandas) - [pandas-datareader](#pandas-datareader) - [PANDAseq](#pandaseq) - [Pandoc](#pandoc) - [Panedr](#panedr) - [Pango](#pango) - [pangolin](#pangolin) - [panito](#panito) - [PAPI](#papi) - [parallel](#parallel) - [parallel-fastq-dump](#parallel-fastq-dump) - [Parallel-Hashmap](#parallel-hashmap) - [ParallelIO](#parallelio) - [parameterized](#parameterized) - [paramiko](#paramiko) - [parasail](#parasail) - [Paraver](#paraver) - [ParaView](#paraview) - [Parcels](#parcels) - [PARI-GP](#pari-gp) - [ParmEd](#parmed) - [ParMETIS](#parmetis) - [ParMGridGen](#parmgridgen) - [Parsl](#parsl) - [PartitionFinder](#partitionfinder) - [pasta](#pasta) - [PaStiX](#pastix) - [pastml](#pastml) - [patch](#patch) - [patchelf](#patchelf) - [path.py](#path.py) - [PAUP](#paup) - [pauvre](#pauvre) - [pbbam](#pbbam) - [pbcopper](#pbcopper) - [pbdagcon](#pbdagcon) - [pbipa](#pbipa) - [pbmm2](#pbmm2) - [pbs_python](#pbs_python) - [PBSuite](#pbsuite) - [PCAngsd](#pcangsd) - [PCC](#pcc) - [PCL](#pcl) - [PCMSolver](#pcmsolver) - [PCRaster](#pcraster) - [PCRE](#pcre) - [PCRE2](#pcre2) - [pdsh](#pdsh) - [PDT](#pdt) - [peakdetect](#peakdetect) - [PEAR](#pear) - [PennCNV](#penncnv) - [PEPT](#pept) - [Percolator](#percolator) - [Perl](#perl) - [perl-app-cpanminus](#perl-app-cpanminus) - [Perl-bundle-CPAN](#perl-bundle-cpan) - [Perl4-CoreLibs](#perl4-corelibs) - [Perseus](#perseus) - [PEST++](#pest++) - [PETSc](#petsc) - [petsc4py](#petsc4py) - [PfamScan](#pfamscan) - [pfind](#pfind) - [pftoolsV3](#pftoolsv3) - [pFUnit](#pfunit) - [PGDSpider](#pgdspider) - [PGI](#pgi) - [PGPLOT](#pgplot) - [PHANOTATE](#phanotate) - [Phantompeakqualtools](#phantompeakqualtools) - [PHASE](#phase) - [PHAST](#phast) - [Phenoflow](#phenoflow) - [PheWAS](#phewas) - [PheWeb](#pheweb) - [PhiPack](#phipack) - [PHLAT](#phlat) - [phonemizer](#phonemizer) - [phono3py](#phono3py) - [phonopy](#phonopy) - [photontorch](#photontorch) - [phototonic](#phototonic) - [PHYLIP](#phylip) - [PhyloBayes-MPI](#phylobayes-mpi) - [phylokit](#phylokit) - [phylonaut](#phylonaut) - [PhyloPhlAn](#phylophlan) - [PhyML](#phyml) - [phyx](#phyx) - [picard](#picard) - [PICI-LIGGGHTS](#pici-liggghts) - [PICRUSt2](#picrust2) - [pigz](#pigz) - [PIL](#pil) - [PileOMeth](#pileometh) - [Pillow](#pillow) - [Pillow-SIMD](#pillow-simd) - [Pilon](#pilon) - [PIMS](#pims) - [Pindel](#pindel) - [Pingouin](#pingouin) - [Pint](#pint) - [pip](#pip) - [PIPITS](#pipits) - [PIRATE](#pirate) - [pIRS](#pirs) - [Pisces](#pisces) - [piSvM](#pisvm) - [piSvM-JSC](#pisvm-jsc) - [pixman](#pixman) - [pizzly](#pizzly) - [pkg-config](#pkg-config) - [pkgconf](#pkgconf) - [pkgconfig](#pkgconfig) - [PLAMS](#plams) - [plantcv](#plantcv) - [PlaScope](#plascope) - [PlasmaPy](#plasmapy) - [PLAST](#plast) - [Platanus](#platanus) - [Platypus](#platypus) - [Platypus-Opt](#platypus-opt) - [plc](#plc) - [PLINK](#plink) - [plinkliftover](#plinkliftover) - [plinkQC](#plinkqc) - [PLINKSEQ](#plinkseq) - [plot1cell](#plot1cell) - [Ploticus](#ploticus) - [plotly](#plotly) - [plotly-orca](#plotly-orca) - [plotly.py](#plotly.py) - [PLplot](#plplot) - [PLUMED](#plumed) - [PLY](#ply) - [PMIx](#pmix) - [pmt](#pmt) - [pmx](#pmx) - [PnetCDF](#pnetcdf) - [pocl](#pocl) - [pod5-file-format](#pod5-file-format) - [poetry](#poetry) - [polars](#polars) - [polymake](#polymake) - [pomkl](#pomkl) - [pompi](#pompi) - [poppler](#poppler) - [popscle](#popscle) - [popt](#popt) - [Porechop](#porechop) - [porefoam](#porefoam) - [poretools](#poretools) - [Portcullis](#portcullis) - [PortMidi](#portmidi) - [Postgres-XL](#postgres-xl) - [PostgreSQL](#postgresql) - [POT](#pot) - [POV-Ray](#pov-ray) - [powerlaw](#powerlaw) - [pp-sketchlib](#pp-sketchlib) - [PPanGGOLiN](#ppanggolin) - [PPfold](#ppfold) - [ppl](#ppl) - [pplacer](#pplacer) - [pplpy](#pplpy) - [PRANK](#prank) - [PRC](#prc) - [preCICE](#precice) - [PREQUAL](#prequal) - [preseq](#preseq) - [presto](#presto) - [pretty-yaml](#pretty-yaml) - [Primer3](#primer3) - [PRINSEQ](#prinseq) - [printproto](#printproto) - [PRISMS-PF](#prisms-pf) - [ProbABEL](#probabel) - [prodigal](#prodigal) - [ProFit](#profit) - [PROJ](#proj) - [ProjectQ](#projectq) - [prokka](#prokka) - [prompt-toolkit](#prompt-toolkit) - [proovread](#proovread) - [propy](#propy) - [Proteinortho](#proteinortho) - [ProtHint](#prothint) - [protobuf](#protobuf) - [protobuf-python](#protobuf-python) - [protozero](#protozero) - [PRSice](#prsice) - [pscom](#pscom) - [PSI](#psi) - [PSI4](#psi4) - [PsiCLASS](#psiclass) - [PSIPRED](#psipred) - [psmc](#psmc) - [psmpi](#psmpi) - [psmpi2](#psmpi2) - [PSolver](#psolver) - [PSORTb](#psortb) - [psrecord](#psrecord) - [pstoedit](#pstoedit) - [psutil](#psutil) - [psycopg2](#psycopg2) - [ptemcee](#ptemcee) - [PTESFinder](#ptesfinder) - [pubtcrs](#pubtcrs) - [pugixml](#pugixml) - [pullseq](#pullseq) - [PuLP](#pulp) - [purge_dups](#purge_dups) - [pv](#pv) - [py](#py) - [py-aiger](#py-aiger) - [py-aiger-bdd](#py-aiger-bdd) - [py-c3d](#py-c3d) - [py-cpuinfo](#py-cpuinfo) - [py3Dmol](#py3dmol) - [pyABC](#pyabc) - [PyAMG](#pyamg) - [PyAPS3](#pyaps3) - [pybedtools](#pybedtools) - [PyBerny](#pyberny) - [pyBigWig](#pybigwig) - [pybind11](#pybind11) - [pybinding](#pybinding) - [PyBioLib](#pybiolib) - [PyCairo](#pycairo) - [PyCalib](#pycalib) - [pyccel](#pyccel) - [PyCharm](#pycharm) - [PyCheMPS2](#pychemps2) - [Pychopper](#pychopper) - [PyCifRW](#pycifrw) - [PyClone](#pyclone) - [pycma](#pycma) - [pycocotools](#pycocotools) - [pycodestyle](#pycodestyle) - [PyCogent](#pycogent) - [pycoQC](#pycoqc) - [PyCUDA](#pycuda) - [PycURL](#pycurl) - [PyDamage](#pydamage) - [pydantic](#pydantic) - [PyDatastream](#pydatastream) - [pydicom](#pydicom) - [pydicom-seg](#pydicom-seg) - [pydlpoly](#pydlpoly) - [pydot](#pydot) - [pyEGA3](#pyega3) - [pyenchant](#pyenchant) - [PyEVTK](#pyevtk) - [pyFAI](#pyfai) - [pyfaidx](#pyfaidx) - [pyfasta](#pyfasta) - [PyFFmpeg](#pyffmpeg) - [pyFFTW](#pyfftw) - [pyfits](#pyfits) - [PyFMI](#pyfmi) - [PyFoam](#pyfoam) - [PyFR](#pyfr) - [PyFrag](#pyfrag) - [pygame](#pygame) - [pygccxml](#pygccxml) - [pyGenomeTracks](#pygenometracks) - [PyGEOS](#pygeos) - [pyGIMLi](#pygimli) - [Pygments](#pygments) - [pygmo](#pygmo) - [PyGObject](#pygobject) - [pygraphviz](#pygraphviz) - [pygrib](#pygrib) - [PyGTK](#pygtk) - [PyGTS](#pygts) - [PyGWAS](#pygwas) - [pyhdf](#pyhdf) - [PyImageJ](#pyimagej) - [pyiron](#pyiron) - [Pyke3](#pyke3) - [pylift](#pylift) - [Pylint](#pylint) - [pyMannKendall](#pymannkendall) - [pymatgen](#pymatgen) - [pymatgen-db](#pymatgen-db) - [pymbar](#pymbar) - [PyMC3](#pymc3) - [pymca](#pymca) - [pymemcache](#pymemcache) - [PyMOL](#pymol) - [PyNAST](#pynast) - [pyobjcryst](#pyobjcryst) - [PyOD](#pyod) - [pyodbc](#pyodbc) - [Pyomo](#pyomo) - [PyOpenCL](#pyopencl) - [PyOpenGL](#pyopengl) - [pyparsing](#pyparsing) - [pyperf](#pyperf) - [pyplusplus](#pyplusplus) - [pypmt](#pypmt) - [PYPOWER](#pypower) - [pyproj](#pyproj) - [PyPSA](#pypsa) - [pyqstem](#pyqstem) - [PyQt](#pyqt) - [PyQt5](#pyqt5) - [PyQtGraph](#pyqtgraph) - [pyradiomics](#pyradiomics) - [PyRe](#pyre) - [PyRETIS](#pyretis) - [pyringe](#pyringe) - [pyro-api](#pyro-api) - [pyro-ppl](#pyro-ppl) - [Pyro4](#pyro4) - [PyRosetta](#pyrosetta) - [Pysam](#pysam) - [pysamstats](#pysamstats) - [PySAT](#pysat) - [pyScaf](#pyscaf) - [pySCENIC](#pyscenic) - [PySCF](#pyscf) - [pysheds](#pysheds) - [pyshp](#pyshp) - [PySide2](#pyside2) - [pyslim](#pyslim) - [pysndfx](#pysndfx) - [Pysolar](#pysolar) - [pyspoa](#pyspoa) - [pysqlite](#pysqlite) - [PyStan](#pystan) - [pysteps](#pysteps) - [pystran](#pystran) - [PyTables](#pytables) - [pytesseract](#pytesseract) - [pytest](#pytest) - [pytest-benchmark](#pytest-benchmark) - [pytest-cpp](#pytest-cpp) - [pytest-flakefinder](#pytest-flakefinder) - [pytest-rerunfailures](#pytest-rerunfailures) - [pytest-shard](#pytest-shard) - [pytest-xdist](#pytest-xdist) - [PYTHIA](#pythia) - [Python](#python) - [Python-bundle](#python-bundle) - [Python-bundle-PyPI](#python-bundle-pypi) - [python-docx](#python-docx) - [python-hl7](#python-hl7) - [python-igraph](#python-igraph) - [python-irodsclient](#python-irodsclient) - [python-isal](#python-isal) - [python-Levenshtein](#python-levenshtein) - [python-libsbml](#python-libsbml) - [python-louvain](#python-louvain) - [python-mujoco](#python-mujoco) - [python-parasail](#python-parasail) - [python-telegram-bot](#python-telegram-bot) - [python-weka-wrapper3](#python-weka-wrapper3) - [python-xxhash](#python-xxhash) - [pythran](#pythran) - [PyTorch](#pytorch) - [PyTorch-bundle](#pytorch-bundle) - [pytorch-CycleGAN-pix2pix](#pytorch-cyclegan-pix2pix) - [PyTorch-Geometric](#pytorch-geometric) - [PyTorch-Ignite](#pytorch-ignite) - [PyTorch-Image-Models](#pytorch-image-models) - [PyTorch-Lightning](#pytorch-lightning) - [PyTorch3D](#pytorch3d) - [PyVCF](#pyvcf) - [PyVCF3](#pyvcf3) - [pyWannier90](#pywannier90) - [PyWavelets](#pywavelets) - [PyWBGT](#pywbgt) - [PyYAML](#pyyaml) - [PyZMQ](#pyzmq) +[p11-kit](#p11-kit) - [p4-phylogenetics](#p4-phylogenetics) - [p4est](#p4est) - [p4vasp](#p4vasp) - [p7zip](#p7zip) - [packmol](#packmol) - [pagmo](#pagmo) - [pairsnp](#pairsnp) - [PAL2NAL](#pal2nal) - [paladin](#paladin) - [PALEOMIX](#paleomix) - [PAML](#paml) - [panaroo](#panaroo) - [pandapower](#pandapower) - [pandas](#pandas) - [pandas-datareader](#pandas-datareader) - [PANDAseq](#pandaseq) - [Pandoc](#pandoc) - [Panedr](#panedr) - [Pango](#pango) - [pangolin](#pangolin) - [panito](#panito) - [PAPI](#papi) - [parallel](#parallel) - [parallel-fastq-dump](#parallel-fastq-dump) - [Parallel-Hashmap](#parallel-hashmap) - [ParallelIO](#parallelio) - [parameterized](#parameterized) - [paramiko](#paramiko) - [parasail](#parasail) - [Paraver](#paraver) - [ParaView](#paraview) - [Parcels](#parcels) - [PARI-GP](#pari-gp) - [ParmEd](#parmed) - [ParMETIS](#parmetis) - [ParMGridGen](#parmgridgen) - [Parsl](#parsl) - [PartitionFinder](#partitionfinder) - [pasta](#pasta) - [PaStiX](#pastix) - [pastml](#pastml) - [patch](#patch) - [patchelf](#patchelf) - [path.py](#path.py) - [PAUP](#paup) - [pauvre](#pauvre) - [pbbam](#pbbam) - [pbcopper](#pbcopper) - [pbdagcon](#pbdagcon) - [pbipa](#pbipa) - [pbmm2](#pbmm2) - [pbs_python](#pbs_python) - [PBSuite](#pbsuite) - [PCAngsd](#pcangsd) - [PCC](#pcc) - [PCL](#pcl) - [PCMSolver](#pcmsolver) - [PCRaster](#pcraster) - [PCRE](#pcre) - [PCRE2](#pcre2) - [pdsh](#pdsh) - [PDT](#pdt) - [peakdetect](#peakdetect) - [PEAR](#pear) - [PennCNV](#penncnv) - [PEPT](#pept) - [Percolator](#percolator) - [Perl](#perl) - [perl-app-cpanminus](#perl-app-cpanminus) - [Perl-bundle-CPAN](#perl-bundle-cpan) - [Perl4-CoreLibs](#perl4-corelibs) - [Perseus](#perseus) - [PEST++](#pest++) - [PETSc](#petsc) - [petsc4py](#petsc4py) - [PfamScan](#pfamscan) - [pfind](#pfind) - [pftoolsV3](#pftoolsv3) - [pFUnit](#pfunit) - [PGDSpider](#pgdspider) - [PGI](#pgi) - [PGPLOT](#pgplot) - [PHANOTATE](#phanotate) - [Phantompeakqualtools](#phantompeakqualtools) - [PHASE](#phase) - [PHAST](#phast) - [Phenoflow](#phenoflow) - [PheWAS](#phewas) - [PheWeb](#pheweb) - [PhiPack](#phipack) - [PHLAT](#phlat) - [phonemizer](#phonemizer) - [phono3py](#phono3py) - [phonopy](#phonopy) - [photontorch](#photontorch) - [phototonic](#phototonic) - [PHYLIP](#phylip) - [PhyloBayes-MPI](#phylobayes-mpi) - [phylokit](#phylokit) - [phylonaut](#phylonaut) - [PhyloPhlAn](#phylophlan) - [PhyML](#phyml) - [phyx](#phyx) - [picard](#picard) - [PICI-LIGGGHTS](#pici-liggghts) - [PICRUSt2](#picrust2) - [pigz](#pigz) - [PIL](#pil) - [PileOMeth](#pileometh) - [Pillow](#pillow) - [Pillow-SIMD](#pillow-simd) - [Pilon](#pilon) - [PIMS](#pims) - [Pindel](#pindel) - [Pingouin](#pingouin) - [Pint](#pint) - [pip](#pip) - [PIPITS](#pipits) - [PIRATE](#pirate) - [pIRS](#pirs) - [Pisces](#pisces) - [piSvM](#pisvm) - [piSvM-JSC](#pisvm-jsc) - [pixman](#pixman) - [pizzly](#pizzly) - [pkg-config](#pkg-config) - [pkgconf](#pkgconf) - [pkgconfig](#pkgconfig) - [PLAMS](#plams) - [plantcv](#plantcv) - [PlaScope](#plascope) - [PlasmaPy](#plasmapy) - [PLAST](#plast) - [Platanus](#platanus) - [Platypus](#platypus) - [Platypus-Opt](#platypus-opt) - [plc](#plc) - [PLINK](#plink) - [plinkliftover](#plinkliftover) - [plinkQC](#plinkqc) - [PLINKSEQ](#plinkseq) - [plot1cell](#plot1cell) - [Ploticus](#ploticus) - [plotly](#plotly) - [plotly-orca](#plotly-orca) - [plotly.py](#plotly.py) - [plotutils](#plotutils) - [PLplot](#plplot) - [PLUMED](#plumed) - [PLY](#ply) - [PMIx](#pmix) - [pmt](#pmt) - [pmx](#pmx) - [PnetCDF](#pnetcdf) - [pocl](#pocl) - [pod5-file-format](#pod5-file-format) - [poetry](#poetry) - [polars](#polars) - [polymake](#polymake) - [pomkl](#pomkl) - [pompi](#pompi) - [poppler](#poppler) - [popscle](#popscle) - [popt](#popt) - [Porechop](#porechop) - [porefoam](#porefoam) - [poretools](#poretools) - [Portcullis](#portcullis) - [PortMidi](#portmidi) - [Postgres-XL](#postgres-xl) - [PostgreSQL](#postgresql) - [POT](#pot) - [POV-Ray](#pov-ray) - [powerlaw](#powerlaw) - [pp-sketchlib](#pp-sketchlib) - [PPanGGOLiN](#ppanggolin) - [PPfold](#ppfold) - [ppl](#ppl) - [pplacer](#pplacer) - [pplpy](#pplpy) - [PRANK](#prank) - [PRC](#prc) - [preCICE](#precice) - [PREQUAL](#prequal) - [preseq](#preseq) - [presto](#presto) - [pretty-yaml](#pretty-yaml) - [Primer3](#primer3) - [PRINSEQ](#prinseq) - [printproto](#printproto) - [PRISMS-PF](#prisms-pf) - [ProbABEL](#probabel) - [ProBiS](#probis) - [prodigal](#prodigal) - [ProFit](#profit) - [PROJ](#proj) - [ProjectQ](#projectq) - [prokka](#prokka) - [prompt-toolkit](#prompt-toolkit) - [proovread](#proovread) - [propy](#propy) - [Proteinortho](#proteinortho) - [ProtHint](#prothint) - [protobuf](#protobuf) - [protobuf-python](#protobuf-python) - [protozero](#protozero) - [PRSice](#prsice) - [pscom](#pscom) - [PSI](#psi) - [PSI4](#psi4) - [PsiCLASS](#psiclass) - [PSIPRED](#psipred) - [psmc](#psmc) - [psmpi](#psmpi) - [psmpi2](#psmpi2) - [PSolver](#psolver) - [PSORTb](#psortb) - [psrecord](#psrecord) - [pstoedit](#pstoedit) - [psutil](#psutil) - [psycopg2](#psycopg2) - [ptemcee](#ptemcee) - [PTESFinder](#ptesfinder) - [pubtcrs](#pubtcrs) - [pugixml](#pugixml) - [pullseq](#pullseq) - [PuLP](#pulp) - [purge_dups](#purge_dups) - [pv](#pv) - [py](#py) - [py-aiger](#py-aiger) - [py-aiger-bdd](#py-aiger-bdd) - [py-c3d](#py-c3d) - [py-cpuinfo](#py-cpuinfo) - [py3Dmol](#py3dmol) - [pyABC](#pyabc) - [PyAMG](#pyamg) - [PyAPS3](#pyaps3) - [pybedtools](#pybedtools) - [PyBerny](#pyberny) - [pyBigWig](#pybigwig) - [pybind11](#pybind11) - [pybinding](#pybinding) - [PyBioLib](#pybiolib) - [PyCairo](#pycairo) - [PyCalib](#pycalib) - [pyccel](#pyccel) - [PyCharm](#pycharm) - [PyCheMPS2](#pychemps2) - [Pychopper](#pychopper) - [PyCifRW](#pycifrw) - [PyClone](#pyclone) - [pycma](#pycma) - [pycocotools](#pycocotools) - [pycodestyle](#pycodestyle) - [PyCogent](#pycogent) - [pycoQC](#pycoqc) - [PyCUDA](#pycuda) - [PycURL](#pycurl) - [PyDamage](#pydamage) - [pydantic](#pydantic) - [PyDatastream](#pydatastream) - [pydicom](#pydicom) - [pydicom-seg](#pydicom-seg) - [pydlpoly](#pydlpoly) - [pydot](#pydot) - [pyEGA3](#pyega3) - [pyenchant](#pyenchant) - [PyEVTK](#pyevtk) - [pyFAI](#pyfai) - [pyfaidx](#pyfaidx) - [pyfasta](#pyfasta) - [PyFFmpeg](#pyffmpeg) - [pyFFTW](#pyfftw) - [pyfits](#pyfits) - [PyFMI](#pyfmi) - [PyFoam](#pyfoam) - [PyFR](#pyfr) - [PyFrag](#pyfrag) - [pygame](#pygame) - [pygccxml](#pygccxml) - [pyGenomeTracks](#pygenometracks) - [PyGEOS](#pygeos) - [pyGIMLi](#pygimli) - [Pygments](#pygments) - [pygmo](#pygmo) - [PyGObject](#pygobject) - [pygraphviz](#pygraphviz) - [pygrib](#pygrib) - [PyGTK](#pygtk) - [PyGTS](#pygts) - [PyGWAS](#pygwas) - [pyhdf](#pyhdf) - [PyImageJ](#pyimagej) - [pyiron](#pyiron) - [Pyke3](#pyke3) - [pylift](#pylift) - [Pylint](#pylint) - [pyMannKendall](#pymannkendall) - [pymatgen](#pymatgen) - [pymatgen-db](#pymatgen-db) - [pymbar](#pymbar) - [PyMC](#pymc) - [PyMC3](#pymc3) - [pymca](#pymca) - [pymemcache](#pymemcache) - [PyMOL](#pymol) - [PyNAST](#pynast) - [pyobjcryst](#pyobjcryst) - [PyOD](#pyod) - [pyodbc](#pyodbc) - [Pyomo](#pyomo) - [PyOpenCL](#pyopencl) - [PyOpenGL](#pyopengl) - [pyparsing](#pyparsing) - [pyperf](#pyperf) - [pyplusplus](#pyplusplus) - [pypmt](#pypmt) - [PYPOWER](#pypower) - [pyproj](#pyproj) - [PyPSA](#pypsa) - [PyPy](#pypy) - [pyqstem](#pyqstem) - [PyQt](#pyqt) - [PyQt5](#pyqt5) - [PyQtGraph](#pyqtgraph) - [pyradiomics](#pyradiomics) - [PyRe](#pyre) - [PyRETIS](#pyretis) - [pyringe](#pyringe) - [pyro-api](#pyro-api) - [pyro-ppl](#pyro-ppl) - [Pyro4](#pyro4) - [PyRosetta](#pyrosetta) - [Pysam](#pysam) - [pysamstats](#pysamstats) - [PySAT](#pysat) - [pyScaf](#pyscaf) - [pySCENIC](#pyscenic) - [PySCF](#pyscf) - [pysheds](#pysheds) - [pyshp](#pyshp) - [PySide2](#pyside2) - [pyslim](#pyslim) - [pysndfx](#pysndfx) - [Pysolar](#pysolar) - [pyspoa](#pyspoa) - [pysqlite](#pysqlite) - [PyStan](#pystan) - [pysteps](#pysteps) - [pystran](#pystran) - [PyTables](#pytables) - [PyTensor](#pytensor) - [pytesseract](#pytesseract) - [pytest](#pytest) - [pytest-benchmark](#pytest-benchmark) - [pytest-cpp](#pytest-cpp) - [pytest-flakefinder](#pytest-flakefinder) - [pytest-rerunfailures](#pytest-rerunfailures) - [pytest-shard](#pytest-shard) - [pytest-xdist](#pytest-xdist) - [PYTHIA](#pythia) - [Python](#python) - [Python-bundle](#python-bundle) - [Python-bundle-PyPI](#python-bundle-pypi) - [python-docx](#python-docx) - [python-hl7](#python-hl7) - [python-igraph](#python-igraph) - [python-irodsclient](#python-irodsclient) - [python-isal](#python-isal) - [python-Levenshtein](#python-levenshtein) - [python-libsbml](#python-libsbml) - [python-louvain](#python-louvain) - [python-mujoco](#python-mujoco) - [python-parasail](#python-parasail) - [python-telegram-bot](#python-telegram-bot) - [python-weka-wrapper3](#python-weka-wrapper3) - [python-xxhash](#python-xxhash) - [pythran](#pythran) - [PyTorch](#pytorch) - [PyTorch-bundle](#pytorch-bundle) - [pytorch-CycleGAN-pix2pix](#pytorch-cyclegan-pix2pix) - [PyTorch-Geometric](#pytorch-geometric) - [PyTorch-Ignite](#pytorch-ignite) - [PyTorch-Image-Models](#pytorch-image-models) - [PyTorch-Lightning](#pytorch-lightning) - [PyTorch3D](#pytorch3d) - [PyVCF](#pyvcf) - [PyVCF3](#pyvcf3) - [pyWannier90](#pywannier90) - [PyWavelets](#pywavelets) - [PyWBGT](#pywbgt) - [PyYAML](#pyyaml) - [PyZMQ](#pyzmq) ### p11-kit @@ -26099,11 +26480,11 @@ p7zip is a quick port of 7z.exe and 7za.exe (command line version of 7zip) for U *homepage*: version |toolchain -----------|--------------------------------------------------------------------------- +----------|------------------------------------------------------------------------------ ``9.38.1``|``GCC/4.9.2``, ``system`` ``16.02`` |``GCC/6.4.0-2.28``, ``iccifort/2017.4.196-GCC-6.4.0-2.28``, ``intel/2018a`` ``17.03`` |``GCCcore/10.2.0`` -``17.04`` |``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``17.04`` |``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.3.0`` ### packmol @@ -26467,7 +26848,10 @@ version |versionsuffix |toolchain ``5.9.1`` |``-mpi`` |``foss/2021a``, ``foss/2021b``, ``intel/2021a`` ``5.10.1``|``-mpi`` |``foss/2022a`` ``5.11.0``|``-mpi`` |``foss/2022b`` +``5.11.1``| |``foss/2022b`` +``5.11.1``|``-CUDA-12.2.0`` |``foss/2022b`` ``5.11.1``|``-mpi`` |``foss/2022a`` +``5.11.2``| |``foss/2023a`` ### Parcels @@ -26597,7 +26981,7 @@ version |toolchain ``0.13`` |``GCCcore/11.2.0`` ``0.15.0``|``GCCcore/11.3.0`` ``0.17.2``|``GCCcore/12.2.0`` -``0.18.0``|``GCCcore/12.3.0`` +``0.18.0``|``GCCcore/12.3.0``, ``GCCcore/13.2.0`` ### path.py @@ -26798,7 +27182,7 @@ version |toolchain ``10.36``|``GCCcore/10.3.0`` ``10.37``|``GCCcore/11.2.0`` ``10.40``|``GCCcore/11.3.0``, ``GCCcore/12.2.0`` -``10.42``|``GCCcore/12.3.0`` +``10.42``|``GCCcore/12.3.0``, ``GCCcore/13.2.0`` ### pdsh @@ -26933,6 +27317,7 @@ A set of common packages from CPAN version |toolchain ----------|------------------ ``5.36.1``|``GCCcore/12.3.0`` +``5.38.0``|``GCCcore/13.2.0`` ### Perl4-CoreLibs @@ -26987,6 +27372,7 @@ version |versionsuffix |toolchain ``3.15.1``| |``foss/2021a``, ``intel/2021a`` ``3.17.4``| |``foss/2022a`` ``3.18.4``| |``intel/2021b`` +``3.19.2``| |``foss/2022b`` ### petsc4py @@ -27085,13 +27471,13 @@ version |versionsuffix |toolchain ### PGPLOT -The PGPLOT Graphics Subroutine Library is a Fortran- or C-callable, device-independent graphics package for making simple scientific graphs. It is intended for making graphical images of publication quality with minimum effort on the part of the user. For most applications, the program can be device-independent, and the output can be directed to the appropriate device at run time. +The PGPLOT Graphics Subroutine Library is a Fortran- or C-callable, device-independent graphics package for making simple scientific graphs. It is intended for making graphical images of publication quality with minimum effort on the part of the user. For most applications, the program can be device-independent, and the output can be directed to the appropriate device at run time. *homepage*: version |toolchain ----------|------------------ -``5.2.2``|``GCCcore/11.2.0`` +---------|-------------------------------------- +``5.2.2``|``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ### PHANOTATE @@ -27233,8 +27619,8 @@ Photontorch is a photonic simulator for highly parallel simulation and optimizat *homepage*: version |toolchain ----------|---------------------------------- -``0.4.1``|``foss/2020b``, ``fosscuda/2020b`` +---------|-------------------------------------------------- +``0.4.1``|``foss/2020b``, ``foss/2022a``, ``fosscuda/2020b`` ### phototonic @@ -27649,8 +28035,8 @@ pkgconf is a program which helps to configure compiler and linker flags for deve *homepage*: version |toolchain ----------|-------------------------------------------------- -``1.8.0``|``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``system`` +---------|---------------------------------------------------------------------- +``1.8.0``|``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``system`` ``1.9.3``|``GCCcore/12.2.0`` ``1.9.4``|``GCCcore/13.1.0`` ``1.9.5``|``GCCcore/12.3.0`` @@ -27836,6 +28222,7 @@ plot1cell: a package for advanced single cell data visualization version |versionsuffix|toolchain ---------|-------------|-------------- ``0.0.1``|``-R-4.2.1`` |``foss/2022a`` +``0.0.1``|``-R-4.2.2`` |``foss/2022b`` ### Ploticus @@ -27887,6 +28274,16 @@ version |toolchain ``5.13.1``|``GCCcore/12.2.0`` ``5.16.0``|``GCCcore/12.3.0`` +### plotutils + +The GNU plotutils package contains software for both programmers and technical users. Its centerpiece is libplot, a powerful C/C++ function library for exporting 2-D vector graphics in many file formats, both vector and bitmap. On the X Window System, it can also do 2-D vector graphics animations. libplot is device-independent, in the sense that its API (application programming interface) does not depend on the type of graphics file to be exported. A Postscript-like API is used both for file export and for graphics animations. A libplot programmer needs to learn only one API: not the details of many graphics file formats. + +*homepage*: + +version|toolchain +-------|-------------- +``2.6``|``GCC/11.3.0`` + ### PLplot PLplot is a cross-platform software package for creating scientific plots whose (UTF-8) plot symbols and text are limited in practice only by what Unicode-aware system fonts are installed on a user's computer. @@ -27965,6 +28362,7 @@ version |toolchain ``4.1.2``|``GCCcore/11.3.0`` ``4.2.2``|``GCCcore/12.2.0`` ``4.2.4``|``GCCcore/12.3.0`` +``4.2.6``|``GCCcore/13.2.0`` ### pmt @@ -28097,6 +28495,7 @@ version |toolchain ``21.06.1``|``GCC/10.2.0``, ``GCC/10.3.0`` ``22.01.0``|``GCC/11.2.0`` ``22.12.0``|``GCC/11.3.0`` +``23.09.0``|``GCC/12.3.0`` ### popscle @@ -28332,6 +28731,7 @@ version |versionsuffix |toolchain ---------|-----------------|------------------------------- ``2.1.1``|``-Python-3.8.2``|``foss/2020a`` ``2.2.0``|``-Python-3.8.2``|``foss/2020a``, ``intel/2020a`` +``2.5.0``| |``foss/2022a`` ### PREQUAL @@ -28369,7 +28769,7 @@ version |versionsuffix|toolchain ### pretty-yaml -PyYAML-based python module to produce pretty and readable YAML-serialized data. This module is for serialization only, see ruamel.yaml module for literate YAML parsing (keeping track of comments, spacing, line/column numbers of values, etc). +PyYAML-based python module to produce pretty and readable YAML-serialized data. This module is for serialization only, see ruamel.yaml module for literate YAML parsing (keeping track of comments, spacing, line/column numbers of values, etc). *homepage*: @@ -28378,6 +28778,7 @@ version |toolchain ``19.12.0``|``GCCcore/8.3.0`` ``20.4.0`` |``GCCcore/9.3.0`` ``21.10.1``|``GCCcore/10.3.0`` +``23.9.5`` |``GCCcore/11.3.0`` ### Primer3 @@ -28434,6 +28835,16 @@ version |toolchain ---------|----------------------------- ``0.5.0``|``GCCcore/9.3.0``, ``system`` +### ProBiS + +ProBiS algorithm aligns and superimposes complete protein surfaces, surface motifs, or protein binding sites. + +*homepage*: + +version |toolchain +------------|--------------- +``20230403``|``gompi/2022b`` + ### prodigal Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program developed at Oak Ridge National Laboratory and the University of Tennessee. @@ -28632,11 +29043,11 @@ PRSice (pronounced 'precise') is a Polygenic Risk Score software for calculatin *homepage*: version |toolchain -----------|------------------------------------- +----------|-------------------------------------- ``2.2.12``|``GCCcore/8.3.0`` ``2.3.1`` |``GCCcore/9.3.0`` ``2.3.3`` |``GCCcore/10.3.0``, ``GCCcore/9.3.0`` -``2.3.5`` |``GCCcore/11.3.0`` +``2.3.5`` |``GCCcore/11.3.0``, ``GCCcore/12.3.0`` ### pscom @@ -28997,7 +29408,7 @@ version |versionsuffix |toolchain ``0.8.0`` | |``foss/2019a``, ``intel/2019a`` ``0.8.1`` | |``foss/2019b`` ``0.8.2`` | |``GCC/10.2.0``, ``GCC/11.2.0``, ``iccifort/2020.4.304`` -``0.8.2`` |``-Python-2.7.18``|``GCC/10.2.0`` +``0.8.2`` |``-Python-2.7.18``|``GCC/10.2.0``, ``GCC/11.2.0`` ``0.9.0`` | |``GCC/11.3.0``, ``GCC/12.2.0`` ### PyBerny @@ -29084,6 +29495,7 @@ version |versionsuffix |toolchain ``1.20.1``| |``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``1.21.0``| |``GCCcore/11.3.0`` ``1.24.0``| |``GCCcore/12.2.0`` +``1.25.0``| |``GCCcore/12.3.0`` ### PyCalib @@ -29334,6 +29746,7 @@ version |versionsuffix |toolchain ``3.4.0`` |``-Python-3.7.4``|``GCCcore/8.3.0`` ``3.4.0`` |``-Python-3.8.2``|``GCCcore/9.3.0`` ``4.0.0`` | |``GCCcore/11.2.0`` +``5.0.2`` | |``GCCcore/12.3.0`` ### pyenchant @@ -29563,6 +29976,7 @@ version |versionsuffix |toolchain ``3.34.0``|``-Python-3.7.4`` |``GCCcore/8.3.0`` ``3.42.1``| |``GCCcore/11.3.0`` ``3.44.1``| |``GCCcore/12.2.0`` +``3.46.0``| |``GCCcore/12.3.0`` ### pygraphviz @@ -29575,6 +29989,7 @@ version |toolchain ``1.5`` |``foss/2019b`` ``1.7`` |``foss/2020b``, ``foss/2021a`` ``1.10``|``GCCcore/11.3.0`` +``1.11``|``GCCcore/12.3.0`` ### pygrib @@ -29739,6 +30154,16 @@ version |versionsuffix |toolchain ``3.0.3``|``-Python-3.6.3``|``intel/2017b`` ``3.0.3``|``-Python-3.8.2``|``intel/2020a`` +### PyMC + +PyMC is a probabilistic programming library for Python that allows users to build Bayesian models with a simple Python API and fit them using Markov chain Monte Carlo (MCMC) methods. + +*homepage*: + +version |toolchain +---------|-------------- +``5.9.0``|``foss/2023a`` + ### PyMC3 Probabilistic Programming in Python: Bayesian Modeling and Probabilistic Machine Learning with Theano @@ -29949,6 +30374,16 @@ version |toolchain ----------|-------------- ``0.17.1``|``foss/2020b`` +### PyPy + +A fast, compliant alternative implementation of Python + +*homepage*: + +version |versionsuffix|toolchain +----------|-------------|---------- +``7.3.12``|``-3.10`` |``system`` + ### pyqstem QSTEM is a program for quantitative image simulation in electron microscopy, including TEM, STEM and CBED image simulation. This project interfaces the QSTEM code with Python and the Atomic Simulation Environment (ASE) to provide a single environment for building models, simulating and analysing images. @@ -30072,10 +30507,11 @@ Pyro is a flexible, scalable deep probabilistic programming library built on PyT *homepage*: -version |toolchain ----------|------------------ -``1.5.2``|``fosscuda/2020b`` -``1.8.4``|``foss/2022a`` +version |versionsuffix |toolchain +---------|----------------|------------------ +``1.5.2``| |``fosscuda/2020b`` +``1.8.0``|``-CUDA-11.3.1``|``foss/2021a`` +``1.8.4``| |``foss/2022a`` ### Pyro4 @@ -30125,6 +30561,7 @@ version |versionsuffix |toolchain ``0.16.0.1``| |``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2020.1.217``, ``iccifort/2020.4.304`` ``0.16.0.1``|``-Python-2.7.18``|``GCC/10.2.0`` ``0.17.0`` | |``GCC/11.2.0`` +``0.17.0`` |``-Python-2.7.18``|``GCC/11.2.0`` ``0.18.0`` | |``GCC/11.2.0`` ``0.19.1`` | |``GCC/11.3.0`` ``0.20.0`` | |``GCC/11.3.0`` @@ -30330,6 +30767,16 @@ version |versionsuffix |toolchain ``3.6.1`` |``-Python-3.8.2`` |``foss/2020a``, ``intel/2020a`` ``3.8.0`` | |``foss/2022a``, ``foss/2022b`` +### PyTensor + +Optimizing compiler for evaluating mathematical expressions on CPUs and GPUs + +*homepage*: + +version |toolchain +----------|-------------- +``2.17.1``|``gfbf/2023a`` + ### pytesseract Python-tesseract is an optical character recognition (OCR) tool for python. That is, it will recognize and "read" the text embedded in images. Python-tesseract is a wrapper for Google's Tesseract-OCR Engine. It is also useful as a stand-alone invocation script to tesseract, as it can read all image types supported by the Pillow and Leptonica imaging libraries, including jpeg, png, gif, bmp, tiff, and others. Additionally, if used as a script, Python-tesseract will print the recognized text instead of writing it to a file. @@ -30399,8 +30846,9 @@ pytest plugin to re-run tests to eliminate flaky failures. *homepage*: version |toolchain ---------|------------------ +--------|-------------------------------------- ``11.1``|``GCCcore/11.3.0`` +``12.0``|``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### pytest-shard @@ -30409,8 +30857,8 @@ pytest plugin to support parallelism across multiple machines. Shards tests bas *homepage*: version |toolchain ----------|------------------ -``0.1.2``|``GCCcore/11.3.0`` +---------|-------------------------------------- +``0.1.2``|``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ### pytest-xdist @@ -30484,6 +30932,7 @@ version |versionsuffix |toolchain ``3.10.8``|``-bare`` |``GCCcore/12.2.0`` ``3.11.2``|``-bare`` |``GCCcore/12.2.0`` ``3.11.3``| |``GCCcore/12.3.0`` +``3.11.5``| |``GCCcore/13.2.0`` ### Python-bundle @@ -30700,7 +31149,9 @@ version |versionsuffix |toolchain ``1.12.1``|``-CUDA-11.3.1`` |``foss/2021a`` ``1.12.1``|``-CUDA-11.5.2`` |``foss/2021b`` ``1.12.1``|``-CUDA-11.7.0`` |``foss/2022a`` -``1.13.1``| |``foss/2022a`` +``1.13.1``| |``foss/2022a``, ``foss/2022b`` +``1.13.1``|``-CUDA-11.7.0`` |``foss/2022a`` +``2.0.1`` | |``foss/2022a`` ### PyTorch-bundle @@ -30711,6 +31162,7 @@ PyTorch with compatible versions of official Torch extensions. version |versionsuffix |toolchain ----------|----------------|-------------- ``1.12.1``|``-CUDA-11.7.0``|``foss/2022a`` +``1.13.1``|``-CUDA-11.7.0``|``foss/2022a`` ### pytorch-CycleGAN-pix2pix @@ -30744,9 +31196,11 @@ Ignite is a high-level library to help with training and evaluating neural netwo *homepage*: -version |versionsuffix |toolchain ----------|----------------|-------------- -``0.4.9``|``-CUDA-11.3.1``|``foss/2021a`` +version |versionsuffix |toolchain +----------|----------------|-------------- +``0.4.9`` |``-CUDA-11.3.1``|``foss/2021a`` +``0.4.12``| |``foss/2022a`` +``0.4.12``|``-CUDA-11.7.0``|``foss/2022a`` ### PyTorch-Image-Models @@ -30860,7 +31314,9 @@ version |versionsuffix |toolchain ``5.3`` | |``GCCcore/9.3.0`` ``5.3.1``| |``GCCcore/10.2.0`` ``5.4.1``| |``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``5.4.1``|``-Python-2.7.18``|``GCCcore/11.2.0`` ``6.0`` | |``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` +``6.0.1``| |``GCCcore/13.2.0`` ### PyZMQ @@ -30885,12 +31341,13 @@ version |versionsuffix |toolchain ``18.1.1``|``-Python-3.7.4`` |``GCCcore/8.3.0`` ``22.3.0``| |``GCCcore/10.3.0`` ``24.0.1``| |``GCCcore/11.3.0`` +``25.1.0``| |``GCCcore/12.2.0`` ``25.1.1``| |``GCCcore/12.3.0`` ## Q -[Q6](#q6) - [QCA](#qca) - [qcat](#qcat) - [QCG-PilotJob](#qcg-pilotjob) - [qcint](#qcint) - [QCxMS](#qcxms) - [QD](#qd) - [QDD](#qdd) - [QEMU](#qemu) - [qforce](#qforce) - [QGIS](#qgis) - [Qhull](#qhull) - [QIIME](#qiime) - [QIIME2](#qiime2) - [Qiskit](#qiskit) - [QJson](#qjson) - [QML](#qml) - [qnorm](#qnorm) - [qpth](#qpth) - [qrupdate](#qrupdate) - [QScintilla](#qscintilla) - [Qt](#qt) - [Qt5](#qt5) - [Qt5Webkit](#qt5webkit) - [Qtconsole](#qtconsole) - [QtKeychain](#qtkeychain) - [QTLtools](#qtltools) - [qtop](#qtop) - [QtPy](#qtpy) - [Qualimap](#qualimap) - [Quandl](#quandl) - [QuantumESPRESSO](#quantumespresso) - [QUAST](#quast) - [QuaZIP](#quazip) - [QuickFF](#quickff) - [QuickPIC](#quickpic) - [Quip](#quip) - [Quorum](#quorum) - [QuTiP](#qutip) - [Qwt](#qwt) - [QwtPolar](#qwtpolar) +[Q6](#q6) - [QCA](#qca) - [qcat](#qcat) - [QCG-PilotJob](#qcg-pilotjob) - [qcint](#qcint) - [QCxMS](#qcxms) - [QD](#qd) - [QDD](#qdd) - [QEMU](#qemu) - [qforce](#qforce) - [QGIS](#qgis) - [Qhull](#qhull) - [QIIME](#qiime) - [QIIME2](#qiime2) - [Qiskit](#qiskit) - [QJson](#qjson) - [QML](#qml) - [qnorm](#qnorm) - [qpth](#qpth) - [qrupdate](#qrupdate) - [QScintilla](#qscintilla) - [Qt](#qt) - [Qt5](#qt5) - [Qt5Webkit](#qt5webkit) - [Qt6](#qt6) - [Qtconsole](#qtconsole) - [QtKeychain](#qtkeychain) - [QTLtools](#qtltools) - [qtop](#qtop) - [QtPy](#qtpy) - [Qualimap](#qualimap) - [Quandl](#quandl) - [QuantumESPRESSO](#quantumespresso) - [QUAST](#quast) - [QuaZIP](#quazip) - [QuickFF](#quickff) - [QuickPIC](#quickpic) - [QuickTree](#quicktree) - [Quip](#quip) - [Quorum](#quorum) - [QuTiP](#qutip) - [Qwt](#qwt) - [QwtPolar](#qwtpolar) ### Q6 @@ -30934,9 +31391,9 @@ A python service for easy execution of many tasks inside a single allocation. *homepage*: version |toolchain -----------|-------------- +----------|------------------------------ ``0.12.3``|``foss/2021a`` -``0.13.1``|``foss/2022a`` +``0.13.1``|``foss/2022a``, ``gfbf/2022b`` ### qcint @@ -31177,6 +31634,16 @@ version |toolchain ``5.212.0-alpha3``|``GCCcore/8.2.0`` ``5.212.0-alpha4``|``GCCcore/10.2.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +### Qt6 + +Qt is a comprehensive cross-platform C++ application framework. + +*homepage*: + +version |toolchain +---------|------------------ +``6.5.2``|``GCCcore/12.3.0`` + ### Qtconsole A rich Qt-based console for working with Jupyter kernels, supporting rich media output, session export, and more. The Qtconsole is a very lightweight application that largely feels like a terminal, but provides a number of enhancements only possible in a GUI, such as inline figures, proper multiline editing with syntax highlighting, graphical calltips, and more. @@ -31282,7 +31749,7 @@ version |versionsuffix|toolchain ``6.8`` | |``foss/2021a``, ``foss/2021b``, ``intel/2021a`` ``7.0`` | |``foss/2021b``, ``intel/2021b`` ``7.1`` | |``foss/2022a``, ``intel/2022a`` -``7.2`` | |``foss/2022b``, ``intel/2022b`` +``7.2`` | |``foss/2022b``, ``foss/2023a``, ``intel/2022b`` ### QUAST @@ -31335,6 +31802,16 @@ version |toolchain ------------|--------------- ``20210224``|``gompi/2021b`` +### QuickTree + +QuickTree is an efficient implementation of the Neighbor-Joining algorithm (PMID: 3447015), capable of reconstructing phylogenies from huge alignments in time less than the age of the universe. + +*homepage*: + +version|toolchain +-------|-------------- +``2.5``|``GCC/12.2.0`` + ### Quip Quip compresses next-generation sequencing data with extreme prejudice. It supports input and output in the FASTQ and SAM/BAM formats, compressing large datasets to as little as 15% of their original size. @@ -31393,7 +31870,7 @@ version |toolchain ## R -[R](#r) - [R-bundle-Bioconductor](#r-bundle-bioconductor) - [R-INLA](#r-inla) - [R-keras](#r-keras) - [R-MXM](#r-mxm) - [R-opencv](#r-opencv) - [R-tesseract](#r-tesseract) - [R-transport](#r-transport) - [R2jags](#r2jags) - [Racon](#racon) - [radeontop](#radeontop) - [RaGOO](#ragoo) - [Ragout](#ragout) - [RagTag](#ragtag) - [rampart](#rampart) - [randfold](#randfold) - [randrproto](#randrproto) - [rapidcsv](#rapidcsv) - [RapidJSON](#rapidjson) - [rapidNJ](#rapidnj) - [rapidtide](#rapidtide) - [RAPSearch2](#rapsearch2) - [Rascaf](#rascaf) - [RASPA2](#raspa2) - [rasterio](#rasterio) - [rasterstats](#rasterstats) - [Ratatosk](#ratatosk) - [Raven](#raven) - [RAxML](#raxml) - [RAxML-NG](#raxml-ng) - [Ray-assembler](#ray-assembler) - [Ray-project](#ray-project) - [Raysect](#raysect) - [RBFOpt](#rbfopt) - [rclone](#rclone) - [Rcorrector](#rcorrector) - [RcppGSL](#rcppgsl) - [rCUDA](#rcuda) - [RDFlib](#rdflib) - [RDKit](#rdkit) - [RDP-Classifier](#rdp-classifier) - [RE2](#re2) - [re2c](#re2c) - [Reads2snp](#reads2snp) - [Reapr](#reapr) - [ReaxFF](#reaxff) - [RECON](#recon) - [Red](#red) - [Redis](#redis) - [redis-py](#redis-py) - [Redundans](#redundans) - [ReFrame](#reframe) - [regionmask](#regionmask) - [RegTools](#regtools) - [Relate](#relate) - [RELION](#relion) - [ReMatCh](#rematch) - [REMORA](#remora) - [renderproto](#renderproto) - [RepastHPC](#repasthpc) - [RepeatMasker](#repeatmasker) - [RepeatModeler](#repeatmodeler) - [RepeatScout](#repeatscout) - [request](#request) - [requests](#requests) - [RERconverge](#rerconverge) - [resolos](#resolos) - [retworkx](#retworkx) - [RevBayes](#revbayes) - [RFdiffusion](#rfdiffusion) - [rgdal](#rgdal) - [rgeos](#rgeos) - [Rgurobi](#rgurobi) - [rhdf5](#rhdf5) - [RheoTool](#rheotool) - [Rhodium](#rhodium) - [rickflow](#rickflow) - [RInChI](#rinchi) - [rioxarray](#rioxarray) - [ripunzip](#ripunzip) - [rising](#rising) - [Rivet](#rivet) - [rjags](#rjags) - [RLCard](#rlcard) - [rmarkdown](#rmarkdown) - [Rmath](#rmath) - [rMATS-turbo](#rmats-turbo) - [RMBlast](#rmblast) - [RNA-Bloom](#rna-bloom) - [RNA-SeQC](#rna-seqc) - [RNAclust](#rnaclust) - [RNAcode](#rnacode) - [RNAIndel](#rnaindel) - [RNAmmer](#rnammer) - [rnaQUAST](#rnaquast) - [RNAz](#rnaz) - [RnBeads](#rnbeads) - [Roary](#roary) - [ROCm](#rocm) - [rocm-cmake](#rocm-cmake) - [ROCm-CompilerSupport](#rocm-compilersupport) - [rocm-smi](#rocm-smi) - [rocminfo](#rocminfo) - [ROCR-Runtime](#rocr-runtime) - [ROCT-Thunk-Interface](#roct-thunk-interface) - [ROI_PAC](#roi_pac) - [ROME](#rome) - [ROOT](#root) - [root_numpy](#root_numpy) - [rootpy](#rootpy) - [Rosetta](#rosetta) - [rpmrebuild](#rpmrebuild) - [RPostgreSQL](#rpostgresql) - [rpy2](#rpy2) - [RQGIS3](#rqgis3) - [RSEM](#rsem) - [RSeQC](#rseqc) - [RStan](#rstan) - [rstanarm](#rstanarm) - [RStudio-Server](#rstudio-server) - [RTG-Tools](#rtg-tools) - [Rtree](#rtree) - [ruamel.yaml](#ruamel.yaml) - [Ruby](#ruby) - [Ruby-Tk](#ruby-tk) - [ruffus](#ruffus) - [ruptures](#ruptures) - [Rust](#rust) - [rustworkx](#rustworkx) +[R](#r) - [R-bundle-Bioconductor](#r-bundle-bioconductor) - [R-INLA](#r-inla) - [R-keras](#r-keras) - [R-MXM](#r-mxm) - [R-opencv](#r-opencv) - [R-tesseract](#r-tesseract) - [R-transport](#r-transport) - [R2jags](#r2jags) - [Racon](#racon) - [radeontop](#radeontop) - [RaGOO](#ragoo) - [Ragout](#ragout) - [RagTag](#ragtag) - [rampart](#rampart) - [randfold](#randfold) - [randrproto](#randrproto) - [rapidcsv](#rapidcsv) - [RapidJSON](#rapidjson) - [rapidNJ](#rapidnj) - [rapidtide](#rapidtide) - [RAPSearch2](#rapsearch2) - [Raptor](#raptor) - [Rascaf](#rascaf) - [RASPA2](#raspa2) - [rasterio](#rasterio) - [rasterstats](#rasterstats) - [Ratatosk](#ratatosk) - [Raven](#raven) - [RAxML](#raxml) - [RAxML-NG](#raxml-ng) - [Ray-assembler](#ray-assembler) - [Ray-project](#ray-project) - [Raysect](#raysect) - [RBFOpt](#rbfopt) - [RCall](#rcall) - [rclone](#rclone) - [Rcorrector](#rcorrector) - [RcppGSL](#rcppgsl) - [rCUDA](#rcuda) - [RDFlib](#rdflib) - [RDKit](#rdkit) - [RDP-Classifier](#rdp-classifier) - [RE2](#re2) - [re2c](#re2c) - [Reads2snp](#reads2snp) - [Reapr](#reapr) - [ReaxFF](#reaxff) - [RECON](#recon) - [Red](#red) - [Redis](#redis) - [redis-py](#redis-py) - [Redundans](#redundans) - [ReFrame](#reframe) - [regionmask](#regionmask) - [RegTools](#regtools) - [Relate](#relate) - [RELION](#relion) - [ReMatCh](#rematch) - [REMORA](#remora) - [renderproto](#renderproto) - [RepastHPC](#repasthpc) - [RepeatMasker](#repeatmasker) - [RepeatModeler](#repeatmodeler) - [RepeatScout](#repeatscout) - [request](#request) - [requests](#requests) - [RERconverge](#rerconverge) - [ResistanceGA](#resistancega) - [resolos](#resolos) - [retworkx](#retworkx) - [RevBayes](#revbayes) - [RFdiffusion](#rfdiffusion) - [rgdal](#rgdal) - [rgeos](#rgeos) - [Rgurobi](#rgurobi) - [rhdf5](#rhdf5) - [RheoTool](#rheotool) - [Rhodium](#rhodium) - [rickflow](#rickflow) - [RInChI](#rinchi) - [rioxarray](#rioxarray) - [ripunzip](#ripunzip) - [rising](#rising) - [Rivet](#rivet) - [rjags](#rjags) - [RLCard](#rlcard) - [rmarkdown](#rmarkdown) - [Rmath](#rmath) - [rMATS-turbo](#rmats-turbo) - [RMBlast](#rmblast) - [RNA-Bloom](#rna-bloom) - [RNA-SeQC](#rna-seqc) - [RNAclust](#rnaclust) - [RNAcode](#rnacode) - [RNAIndel](#rnaindel) - [RNAmmer](#rnammer) - [rnaQUAST](#rnaquast) - [RNAz](#rnaz) - [RnBeads](#rnbeads) - [Roary](#roary) - [ROCm](#rocm) - [rocm-cmake](#rocm-cmake) - [ROCm-CompilerSupport](#rocm-compilersupport) - [rocm-smi](#rocm-smi) - [rocminfo](#rocminfo) - [ROCR-Runtime](#rocr-runtime) - [ROCT-Thunk-Interface](#roct-thunk-interface) - [ROI_PAC](#roi_pac) - [ROME](#rome) - [ROOT](#root) - [root_numpy](#root_numpy) - [rootpy](#rootpy) - [Rosetta](#rosetta) - [rpmrebuild](#rpmrebuild) - [RPostgreSQL](#rpostgresql) - [rpy2](#rpy2) - [RQGIS3](#rqgis3) - [RSEM](#rsem) - [RSeQC](#rseqc) - [RStan](#rstan) - [rstanarm](#rstanarm) - [RStudio-Server](#rstudio-server) - [RTG-Tools](#rtg-tools) - [Rtree](#rtree) - [ruamel.yaml](#ruamel.yaml) - [Ruby](#ruby) - [Ruby-Tk](#ruby-tk) - [ruffus](#ruffus) - [ruptures](#ruptures) - [Rust](#rust) - [rustworkx](#rustworkx) ### R @@ -31587,6 +32064,7 @@ RagTag is a collection of software tools for scaffolding and improving modern ge version |toolchain ---------|-------------- ``2.0.1``|``foss/2020b`` +``2.1.0``|``foss/2022a`` ### rampart @@ -31627,6 +32105,7 @@ Rapidcsv is a C++ header-only library for CSV parsing. While the name admittedl version |toolchain --------|------------------ +``8.62``|``GCCcore/11.2.0`` ``8.64``|``GCCcore/11.3.0`` ### RapidJSON @@ -31669,6 +32148,16 @@ version |toolchain --------|------------- ``2.24``|``GCC/9.3.0`` +### Raptor + +Set of parsers and serializers that generate Resource Description Framework (RDF) triples by parsing syntaxes or serialize the triples into a syntax. + +*homepage*: + +version |toolchain +----------|------------------ +``2.0.16``|``GCCcore/10.3.0`` + ### Rascaf Rascaf (RnA-seq SCAFfolder) uses continuity and order information from paired-end RNA-seq reads to improve a draft assembly, particularly in the gene regions. @@ -31713,6 +32202,7 @@ rasterstats is a Python module for summarizing geospatial raster datasets based version |versionsuffix |toolchain ----------|-----------------|-------------- ``0.15.0``|``-Python-3.8.2``|``foss/2020a`` +``0.19.0``| |``foss/2022a`` ### Ratatosk @@ -31764,6 +32254,7 @@ version |toolchain ``1.0.2``|``gompi/2020b`` ``1.0.3``|``GCC/10.2.0`` ``1.1.0``|``GCC/11.2.0`` +``1.2.0``|``GCC/12.3.0`` ### Ray-assembler @@ -31811,6 +32302,16 @@ version |versionsuffix |toolchain ``4.1.1``| |``intel/2019a`` ``4.1.1``|``-Python-3.6.6``|``intel/2018b`` +### RCall + +This package facilitates communication between R and Julia and allows the user to call R packages from within Julia, providing the best of both worlds. + +*homepage*: + +version |versionsuffix |toolchain +-----------|------------------------|-------------- +``0.13.17``|``-R-4.2.1-Julia-1.9.2``|``foss/2022a`` + ### rclone Rclone is a command line program to sync files and directories to and from a variety of online storage services @@ -31867,6 +32368,7 @@ version |toolchain ``4.2.2``|``GCCcore/8.3.0``, ``foss/2019a`` ``5.0.0``|``GCCcore/10.2.0`` ``6.2.0``|``GCCcore/10.3.0``, ``GCCcore/11.3.0`` +``7.0.0``|``GCCcore/12.3.0`` ### RDKit @@ -31883,6 +32385,7 @@ version |versionsuffix |toolchain ``2021.03.4``| |``foss/2021a`` ``2022.03.5``| |``foss/2021b`` ``2022.09.4``| |``foss/2022a`` +``2023.03.3``| |``foss/2021a`` ### RDP-Classifier @@ -32045,6 +32548,8 @@ version |toolchain ``4.0.1`` |``system`` ``4.0.5`` |``system`` ``4.2.0`` |``system`` +``4.3.2`` |``system`` +``4.3.3`` |``system`` ### regionmask @@ -32150,7 +32655,7 @@ version |versionsuffix |toolchain ``4.0.9-p2``|``-HMMER`` |``gompi/2019b`` ``4.1.2-p1``| |``foss/2020b`` ``4.1.4`` | |``foss/2022a`` -``4.1.5`` | |``foss/2022a`` +``4.1.5`` | |``foss/2021a``, ``foss/2022a`` ### RepeatModeler @@ -32207,6 +32712,16 @@ version |versionsuffix|toolchain ---------|-------------|------------------------------- ``0.1.0``|``-R-3.4.3`` |``foss/2017b``, ``intel/2017b`` +### ResistanceGA + +An R package to optimize resistance surfaces using Genetic Algorithms. + +*homepage*: + +version |versionsuffix |toolchain +---------|------------------------|-------------- +``4.2-5``|``-R-4.2.1-Julia-1.9.2``|``foss/2022a`` + ### resolos Resolos is a toolkit written in Python for maintaining reproducible environments for scientific computations. It's main goal is to enable researchers to easily replicate environments through space (running code on HPC environment) and time (environment preservation for long term archival). For installation and detailed usage, check out the documentation. @@ -32463,6 +32978,7 @@ version |versionsuffix |toolchain ``2.10.0``| |``gompi/2019b`` ``2.11.0``| |``gompi/2020b`` ``2.13.0``| |``gompi/2022a`` +``2.14.0``| |``gompi/2021a`` ### RNA-Bloom @@ -32749,11 +33265,11 @@ rpy2 is an interface to R running embedded in a Python process. *homepage*: version |versionsuffix |toolchain ----------|------------------|--------------- +---------|------------------|------------------------------ ``2.7.9``|``-Python-2.7.12``|``foss/2016b`` ``2.8.2``|``-Python-2.7.13``|``intel/2017a`` ``3.2.6``|``-Python-3.7.4`` |``foss/2019b`` -``3.4.5``| |``foss/2021b`` +``3.4.5``| |``foss/2021a``, ``foss/2021b`` ### RQGIS3 @@ -32861,6 +33377,7 @@ ruamel.yaml is a YAML 1.2 loader/dumper package for Python. version |toolchain -----------|------------------------------------------------------------------------------ ``0.17.21``|``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +``0.17.32``|``GCCcore/12.3.0`` ### Ruby @@ -32941,6 +33458,7 @@ version |toolchain ``1.60.0``|``GCCcore/10.3.0``, ``GCCcore/11.3.0`` ``1.65.0``|``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ``1.70.0``|``GCCcore/12.3.0`` +``1.73.0``|``GCCcore/13.2.0`` ### rustworkx @@ -32955,7 +33473,7 @@ version |toolchain ## S -[S-Lang](#s-lang) - [S4](#s4) - [Sabre](#sabre) - [Safetensors](#safetensors) - [SAGE](#sage) - [Sailfish](#sailfish) - [SALib](#salib) - [Salmon](#salmon) - [SALMON-TDDFT](#salmon-tddft) - [Sambamba](#sambamba) - [samblaster](#samblaster) - [Samcef](#samcef) - [samclip](#samclip) - [samplot](#samplot) - [SAMtools](#samtools) - [sansa](#sansa) - [SAP](#sap) - [SAS](#sas) - [Satsuma2](#satsuma2) - [savvy](#savvy) - [Saxon-HE](#saxon-he) - [SBCL](#sbcl) - [sbt](#sbt) - [ScaFaCoS](#scafacos) - [ScaLAPACK](#scalapack) - [Scalasca](#scalasca) - [SCALCE](#scalce) - [Scalene](#scalene) - [scanpy](#scanpy) - [scArches](#scarches) - [sceasy](#sceasy) - [SCENIC](#scenic) - [scGeneFit](#scgenefit) - [SCGid](#scgid) - [scGSVA](#scgsva) - [scHiCExplorer](#schicexplorer) - [Schrodinger](#schrodinger) - [scib](#scib) - [scib-metrics](#scib-metrics) - [sciClone](#sciclone) - [ScientificPython](#scientificpython) - [scikit-allel](#scikit-allel) - [scikit-bio](#scikit-bio) - [scikit-build](#scikit-build) - [scikit-cuda](#scikit-cuda) - [scikit-image](#scikit-image) - [scikit-learn](#scikit-learn) - [scikit-misc](#scikit-misc) - [scikit-multilearn](#scikit-multilearn) - [scikit-optimize](#scikit-optimize) - [scikit-plot](#scikit-plot) - [scikit-uplift](#scikit-uplift) - [SCIP](#scip) - [SCIPhI](#sciphi) - [scipy](#scipy) - [SciPy-bundle](#scipy-bundle) - [SCnorm](#scnorm) - [Scoary](#scoary) - [SCons](#scons) - [SCOOP](#scoop) - [SCopeLoomR](#scopeloomr) - [Score-P](#score-p) - [SCOTCH](#scotch) - [scp](#scp) - [scPred](#scpred) - [Scrappie](#scrappie) - [scVelo](#scvelo) - [scvi-tools](#scvi-tools) - [Scythe](#scythe) - [SDCC](#sdcc) - [SDL](#sdl) - [SDL2](#sdl2) - [SDL2_image](#sdl2_image) - [SDL2_mixer](#sdl2_mixer) - [SDL2_ttf](#sdl2_ttf) - [SDL_image](#sdl_image) - [SDSL](#sdsl) - [Seaborn](#seaborn) - [SearchGUI](#searchgui) - [SeaView](#seaview) - [SECAPR](#secapr) - [Seeder](#seeder) - [segemehl](#segemehl) - [segment-anything](#segment-anything) - [segmentation-models](#segmentation-models) - [SeisSol](#seissol) - [SelEstim](#selestim) - [SELFIES](#selfies) - [SentencePiece](#sentencepiece) - [sentinelsat](#sentinelsat) - [sep](#sep) - [SEPP](#sepp) - [Seq-Gen](#seq-gen) - [seq2HLA](#seq2hla) - [SeqAn](#seqan) - [SeqAn3](#seqan3) - [SeqKit](#seqkit) - [SeqLib](#seqlib) - [Seqmagick](#seqmagick) - [SeqPrep](#seqprep) - [seqtk](#seqtk) - [Serf](#serf) - [setuptools](#setuptools) - [setuptools-rust](#setuptools-rust) - [Seurat](#seurat) - [SeuratData](#seuratdata) - [SeuratDisk](#seuratdisk) - [SeuratWrappers](#seuratwrappers) - [sf](#sf) - [sfftk](#sfftk) - [Shannon](#shannon) - [SHAP](#shap) - [shapAAR](#shapaar) - [SHAPEIT](#shapeit) - [SHAPEIT4](#shapeit4) - [Shapely](#shapely) - [sharutils](#sharutils) - [Shasta](#shasta) - [ShengBTE](#shengbte) - [shift](#shift) - [SHORE](#shore) - [Short-Pair](#short-pair) - [shovill](#shovill) - [shrinkwrap](#shrinkwrap) - [SHTns](#shtns) - [Sibelia](#sibelia) - [SICER2](#sicer2) - [sickle](#sickle) - [Siesta](#siesta) - [SignalP](#signalp) - [silhouetteRank](#silhouetterank) - [silx](#silx) - [simint](#simint) - [SimNIBS](#simnibs) - [SimPEG](#simpeg) - [SIMPLE](#simple) - [Simple-DFTD3](#simple-dftd3) - [SimpleElastix](#simpleelastix) - [SimpleITK](#simpleitk) - [simpy](#simpy) - [SimVascular](#simvascular) - [SingleM](#singlem) - [Singular](#singular) - [SiNVICT](#sinvict) - [SIONlib](#sionlib) - [SIP](#sip) - [siscone](#siscone) - [SISSO](#sisso) - [SISSO++](#sisso++) - [SKESA](#skesa) - [sketchmap](#sketchmap) - [skewer](#skewer) - [sklearn-pandas](#sklearn-pandas) - [sklearn-som](#sklearn-som) - [skorch](#skorch) - [SlamDunk](#slamdunk) - [SLATEC](#slatec) - [SLEPc](#slepc) - [slepc4py](#slepc4py) - [sleuth](#sleuth) - [slidingwindow](#slidingwindow) - [SLiM](#slim) - [slow5tools](#slow5tools) - [slurm-drmaa](#slurm-drmaa) - [smafa](#smafa) - [smallgenomeutilities](#smallgenomeutilities) - [SMAP](#smap) - [SMARTdenovo](#smartdenovo) - [SMC++](#smc++) - [smfishHmrf](#smfishhmrf) - [smithwaterman](#smithwaterman) - [Smoldyn](#smoldyn) - [smooth-topk](#smooth-topk) - [SMRT-Link](#smrt-link) - [SMV](#smv) - [snakemake](#snakemake) - [SNAP](#snap) - [SNAP-HMM](#snap-hmm) - [SNAPE-pooled](#snape-pooled) - [snaphu](#snaphu) - [snappy](#snappy) - [Sniffles](#sniffles) - [snippy](#snippy) - [snp-sites](#snp-sites) - [snpEff](#snpeff) - [SNPhylo](#snphylo) - [SNPomatic](#snpomatic) - [SOAPaligner](#soapaligner) - [SOAPdenovo-Trans](#soapdenovo-trans) - [SOAPdenovo2](#soapdenovo2) - [SOAPfuse](#soapfuse) - [socat](#socat) - [SOCI](#soci) - [SolexaQA++](#solexaqa++) - [sonic](#sonic) - [SoPlex](#soplex) - [SoQt](#soqt) - [SortMeRNA](#sortmerna) - [SoupX](#soupx) - [SoX](#sox) - [SoXt](#soxt) - [SpaceRanger](#spaceranger) - [Spack](#spack) - [spaCy](#spacy) - [SPAdes](#spades) - [spaln](#spaln) - [Spark](#spark) - [sparse-neighbors-search](#sparse-neighbors-search) - [sparsehash](#sparsehash) - [SpatialDE](#spatialde) - [spatialreg](#spatialreg) - [spdlog](#spdlog) - [SpectrA](#spectra) - [spectral.methods](#spectral.methods) - [speech_tools](#speech_tools) - [spektral](#spektral) - [spglib](#spglib) - [spglib-python](#spglib-python) - [Sphinx](#sphinx) - [Sphinx-RTD-Theme](#sphinx-rtd-theme) - [SpiceyPy](#spiceypy) - [SpiecEasi](#spieceasi) - [SplAdder](#spladder) - [SPLASH](#splash) - [SpliceMap](#splicemap) - [split-seq](#split-seq) - [splitRef](#splitref) - [SPM](#spm) - [spoa](#spoa) - [SPOOLES](#spooles) - [SPOTPY](#spotpy) - [SPRNG](#sprng) - [Spyder](#spyder) - [SQLite](#sqlite) - [SqueezeMeta](#squeezemeta) - [Squidpy](#squidpy) - [SRA-Toolkit](#sra-toolkit) - [sradownloader](#sradownloader) - [SRPRISM](#srprism) - [SRST2](#srst2) - [SSAHA2](#ssaha2) - [SSN](#ssn) - [SSPACE_Basic](#sspace_basic) - [SSW](#ssw) - [STACEY](#stacey) - [Stack](#stack) - [Stacks](#stacks) - [STAMP](#stamp) - [StaMPS](#stamps) - [Stampy](#stampy) - [STAR](#star) - [STAR-CCM+](#star-ccm+) - [STAR-Fusion](#star-fusion) - [stardist](#stardist) - [stars](#stars) - [Stata](#stata) - [Statistics-R](#statistics-r) - [statsmodels](#statsmodels) - [STEAK](#steak) - [STIR](#stir) - [stpipeline](#stpipeline) - [strace](#strace) - [Strainberry](#strainberry) - [STREAM](#stream) - [strelka](#strelka) - [StringTie](#stringtie) - [stripy](#stripy) - [STRique](#strique) - [Structure](#structure) - [Structure_threader](#structure_threader) - [STRUMPACK](#strumpack) - [suave](#suave) - [SuAVE-biomat](#suave-biomat) - [Subread](#subread) - [subset-bam](#subset-bam) - [Subversion](#subversion) - [suds](#suds) - [SuiteSparse](#suitesparse) - [SUMACLUST](#sumaclust) - [SUMATRA](#sumatra) - [SUMO](#sumo) - [SUNDIALS](#sundials) - [SunPy](#sunpy) - [SuperLU](#superlu) - [SuperLU_DIST](#superlu_dist) - [supermagic](#supermagic) - [supernova](#supernova) - [SURVIVOR](#survivor) - [SVclone](#svclone) - [SVDetect](#svdetect) - [SVDquest](#svdquest) - [SVG](#svg) - [SVIM](#svim) - [svist4get](#svist4get) - [swarm](#swarm) - [SWASH](#swash) - [SWAT+](#swat+) - [swifter](#swifter) - [SWIG](#swig) - [SWIPE](#swipe) - [swissknife](#swissknife) - [SymEngine](#symengine) - [SymEngine-python](#symengine-python) - [SYMPHONY](#symphony) - [sympy](#sympy) - [synthcity](#synthcity) - [SyRI](#syri) - [sysbench](#sysbench) - [Szip](#szip) +[S-Lang](#s-lang) - [S4](#s4) - [Sabre](#sabre) - [Safetensors](#safetensors) - [SAGE](#sage) - [Sailfish](#sailfish) - [SALib](#salib) - [Salmon](#salmon) - [SALMON-TDDFT](#salmon-tddft) - [Sambamba](#sambamba) - [samblaster](#samblaster) - [Samcef](#samcef) - [samclip](#samclip) - [samplot](#samplot) - [SAMtools](#samtools) - [sansa](#sansa) - [SAP](#sap) - [SAS](#sas) - [Satsuma2](#satsuma2) - [savvy](#savvy) - [Saxon-HE](#saxon-he) - [SBCL](#sbcl) - [sbt](#sbt) - [ScaFaCoS](#scafacos) - [ScaLAPACK](#scalapack) - [Scalasca](#scalasca) - [SCALCE](#scalce) - [Scalene](#scalene) - [scanpy](#scanpy) - [scArches](#scarches) - [scCODA](#sccoda) - [sceasy](#sceasy) - [SCENIC](#scenic) - [scGeneFit](#scgenefit) - [SCGid](#scgid) - [scGSVA](#scgsva) - [scHiCExplorer](#schicexplorer) - [Schrodinger](#schrodinger) - [scib](#scib) - [scib-metrics](#scib-metrics) - [sciClone](#sciclone) - [ScientificPython](#scientificpython) - [scikit-allel](#scikit-allel) - [scikit-bio](#scikit-bio) - [scikit-build](#scikit-build) - [scikit-build-core](#scikit-build-core) - [scikit-cuda](#scikit-cuda) - [scikit-image](#scikit-image) - [scikit-learn](#scikit-learn) - [scikit-misc](#scikit-misc) - [scikit-multilearn](#scikit-multilearn) - [scikit-optimize](#scikit-optimize) - [scikit-plot](#scikit-plot) - [scikit-uplift](#scikit-uplift) - [SCIP](#scip) - [SCIPhI](#sciphi) - [scipy](#scipy) - [SciPy-bundle](#scipy-bundle) - [SCnorm](#scnorm) - [Scoary](#scoary) - [SCons](#scons) - [SCOOP](#scoop) - [SCopeLoomR](#scopeloomr) - [Score-P](#score-p) - [SCOTCH](#scotch) - [scp](#scp) - [scPred](#scpred) - [Scrappie](#scrappie) - [scVelo](#scvelo) - [scvi-tools](#scvi-tools) - [Scythe](#scythe) - [SDCC](#sdcc) - [SDL](#sdl) - [SDL2](#sdl2) - [SDL2_image](#sdl2_image) - [SDL2_mixer](#sdl2_mixer) - [SDL2_ttf](#sdl2_ttf) - [SDL_image](#sdl_image) - [SDSL](#sdsl) - [Seaborn](#seaborn) - [SearchGUI](#searchgui) - [SeaView](#seaview) - [SECAPR](#secapr) - [Seeder](#seeder) - [segemehl](#segemehl) - [segment-anything](#segment-anything) - [segmentation-models](#segmentation-models) - [segmentation-models-pytorch](#segmentation-models-pytorch) - [SeisSol](#seissol) - [SelEstim](#selestim) - [SELFIES](#selfies) - [SentencePiece](#sentencepiece) - [sentinelsat](#sentinelsat) - [sep](#sep) - [SEPP](#sepp) - [Seq-Gen](#seq-gen) - [seq2HLA](#seq2hla) - [SeqAn](#seqan) - [SeqAn3](#seqan3) - [SeqKit](#seqkit) - [SeqLib](#seqlib) - [Seqmagick](#seqmagick) - [SeqPrep](#seqprep) - [seqtk](#seqtk) - [Serf](#serf) - [setuptools](#setuptools) - [setuptools-rust](#setuptools-rust) - [Seurat](#seurat) - [SeuratData](#seuratdata) - [SeuratDisk](#seuratdisk) - [SeuratWrappers](#seuratwrappers) - [sf](#sf) - [sfftk](#sfftk) - [Shannon](#shannon) - [SHAP](#shap) - [shapAAR](#shapaar) - [SHAPEIT](#shapeit) - [SHAPEIT4](#shapeit4) - [Shapely](#shapely) - [sharutils](#sharutils) - [Shasta](#shasta) - [ShengBTE](#shengbte) - [shift](#shift) - [SHORE](#shore) - [Short-Pair](#short-pair) - [shovill](#shovill) - [shrinkwrap](#shrinkwrap) - [SHTns](#shtns) - [Sibelia](#sibelia) - [SICER2](#sicer2) - [sickle](#sickle) - [Siesta](#siesta) - [SignalP](#signalp) - [silhouetteRank](#silhouetterank) - [silx](#silx) - [simint](#simint) - [SimNIBS](#simnibs) - [SimPEG](#simpeg) - [SIMPLE](#simple) - [Simple-DFTD3](#simple-dftd3) - [SimpleElastix](#simpleelastix) - [SimpleITK](#simpleitk) - [simpy](#simpy) - [SimVascular](#simvascular) - [SingleM](#singlem) - [Singular](#singular) - [SiNVICT](#sinvict) - [SIONlib](#sionlib) - [SIP](#sip) - [siscone](#siscone) - [SISSO](#sisso) - [SISSO++](#sisso++) - [SKESA](#skesa) - [sketchmap](#sketchmap) - [skewer](#skewer) - [sklearn-pandas](#sklearn-pandas) - [sklearn-som](#sklearn-som) - [skorch](#skorch) - [SlamDunk](#slamdunk) - [SLATEC](#slatec) - [SLEPc](#slepc) - [slepc4py](#slepc4py) - [sleuth](#sleuth) - [slidingwindow](#slidingwindow) - [SLiM](#slim) - [slow5tools](#slow5tools) - [slurm-drmaa](#slurm-drmaa) - [smafa](#smafa) - [smallgenomeutilities](#smallgenomeutilities) - [SMAP](#smap) - [SMARTdenovo](#smartdenovo) - [SMC++](#smc++) - [smfishHmrf](#smfishhmrf) - [smithwaterman](#smithwaterman) - [Smoldyn](#smoldyn) - [smooth-topk](#smooth-topk) - [SMRT-Link](#smrt-link) - [SMV](#smv) - [snakemake](#snakemake) - [SNAP](#snap) - [SNAP-ESA](#snap-esa) - [SNAP-ESA-python](#snap-esa-python) - [SNAP-HMM](#snap-hmm) - [SNAPE-pooled](#snape-pooled) - [snaphu](#snaphu) - [snappy](#snappy) - [Sniffles](#sniffles) - [snippy](#snippy) - [snp-sites](#snp-sites) - [snpEff](#snpeff) - [SNPhylo](#snphylo) - [SNPomatic](#snpomatic) - [SOAPaligner](#soapaligner) - [SOAPdenovo-Trans](#soapdenovo-trans) - [SOAPdenovo2](#soapdenovo2) - [SOAPfuse](#soapfuse) - [socat](#socat) - [SOCI](#soci) - [SolexaQA++](#solexaqa++) - [sonic](#sonic) - [SoPlex](#soplex) - [SoQt](#soqt) - [SortMeRNA](#sortmerna) - [SoupX](#soupx) - [SoX](#sox) - [SoXt](#soxt) - [SpaceRanger](#spaceranger) - [Spack](#spack) - [spaCy](#spacy) - [SPAdes](#spades) - [spaln](#spaln) - [Spark](#spark) - [sparse-neighbors-search](#sparse-neighbors-search) - [sparsehash](#sparsehash) - [SpatialDE](#spatialde) - [spatialreg](#spatialreg) - [spdlog](#spdlog) - [SpectrA](#spectra) - [spectral.methods](#spectral.methods) - [speech_tools](#speech_tools) - [spektral](#spektral) - [spglib](#spglib) - [spglib-python](#spglib-python) - [Sphinx](#sphinx) - [Sphinx-RTD-Theme](#sphinx-rtd-theme) - [SpiceyPy](#spiceypy) - [SpiecEasi](#spieceasi) - [SplAdder](#spladder) - [SPLASH](#splash) - [SpliceMap](#splicemap) - [split-seq](#split-seq) - [splitRef](#splitref) - [SPM](#spm) - [spoa](#spoa) - [SPOOLES](#spooles) - [SPOTPY](#spotpy) - [SPRNG](#sprng) - [Spyder](#spyder) - [SQLite](#sqlite) - [SqueezeMeta](#squeezemeta) - [Squidpy](#squidpy) - [SRA-Toolkit](#sra-toolkit) - [sradownloader](#sradownloader) - [SRPRISM](#srprism) - [SRST2](#srst2) - [SSAHA2](#ssaha2) - [SSN](#ssn) - [SSPACE_Basic](#sspace_basic) - [SSW](#ssw) - [STACEY](#stacey) - [Stack](#stack) - [Stacks](#stacks) - [STAMP](#stamp) - [StaMPS](#stamps) - [Stampy](#stampy) - [STAR](#star) - [STAR-CCM+](#star-ccm+) - [STAR-Fusion](#star-fusion) - [stardist](#stardist) - [starparser](#starparser) - [stars](#stars) - [Stata](#stata) - [Statistics-R](#statistics-r) - [statsmodels](#statsmodels) - [STEAK](#steak) - [STIR](#stir) - [stpipeline](#stpipeline) - [strace](#strace) - [Strainberry](#strainberry) - [STREAM](#stream) - [strelka](#strelka) - [StringTie](#stringtie) - [stripy](#stripy) - [STRique](#strique) - [Structure](#structure) - [Structure_threader](#structure_threader) - [STRUMPACK](#strumpack) - [suave](#suave) - [SuAVE-biomat](#suave-biomat) - [Subread](#subread) - [subset-bam](#subset-bam) - [Subversion](#subversion) - [suds](#suds) - [SuiteSparse](#suitesparse) - [SUMACLUST](#sumaclust) - [SUMATRA](#sumatra) - [SUMO](#sumo) - [SUNDIALS](#sundials) - [SunPy](#sunpy) - [SuperLU](#superlu) - [SuperLU_DIST](#superlu_dist) - [supermagic](#supermagic) - [supernova](#supernova) - [SURVIVOR](#survivor) - [SVclone](#svclone) - [SVDetect](#svdetect) - [SVDquest](#svdquest) - [SVG](#svg) - [SVIM](#svim) - [svist4get](#svist4get) - [swarm](#swarm) - [SWASH](#swash) - [SWAT+](#swat+) - [swifter](#swifter) - [SWIG](#swig) - [SWIPE](#swipe) - [swissknife](#swissknife) - [SymEngine](#symengine) - [SymEngine-python](#symengine-python) - [SYMPHONY](#symphony) - [sympy](#sympy) - [synapseclient](#synapseclient) - [synthcity](#synthcity) - [SyRI](#syri) - [sysbench](#sysbench) - [Szip](#szip) ### S-Lang @@ -33270,7 +33788,7 @@ version |versionsuffix |toolchain ``2.1.0``|``-bl`` |``gompi/2020b`` ``2.1.0``|``-fb`` |``gompi/2021a``, ``gompi/2021b`` ``2.2`` |``-amd`` |``gompi/2020a`` -``2.2.0``|``-fb`` |``gompi/2022.05``, ``gompi/2022.10``, ``gompi/2022a``, ``gompi/2022b``, ``gompi/2023a``, ``nvompi/2022.07`` +``2.2.0``|``-fb`` |``gompi/2022.05``, ``gompi/2022.10``, ``gompi/2022a``, ``gompi/2022b``, ``gompi/2023.09``, ``gompi/2023a``, ``nvompi/2022.07`` ### Scalasca @@ -33302,9 +33820,10 @@ Scalene is a high-performance CPU, GPU and memory profiler for Python that does *homepage*: version |toolchain -----------|------------------ +----------|-------------------------------------- ``1.5.13``|``GCCcore/11.2.0`` -``1.5.26``|``GCCcore/12.3.0`` +``1.5.20``|``GCCcore/11.3.0`` +``1.5.26``|``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### scanpy @@ -33330,6 +33849,16 @@ version |versionsuffix |toolchain ``0.5.6``| |``foss/2021a`` ``0.5.6``|``-CUDA-11.3.1``|``foss/2021a`` +### scCODA + +scCODA allows for identification of compositional changes in high-throughput sequencing count data, especially cell compositions from scRNA-seq. + +*homepage*: + +version |toolchain +---------|-------------- +``0.1.9``|``foss/2021a`` + ### sceasy sceasy is a package that helps easy conversion of different single-cell data formats to each other @@ -33465,9 +33994,9 @@ scikit-bio is an open-source, BSD-licensed Python 3 package providing data struc *homepage*: version |versionsuffix |toolchain ----------|-----------------|---------------------------------------------- +---------|-----------------|-------------------------------------------------------------- ``0.5.6``|``-Python-3.8.2``|``foss/2020a`` -``0.5.7``| |``foss/2020b``, ``foss/2021b``, ``foss/2022a`` +``0.5.7``| |``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``foss/2022a`` ### scikit-build @@ -33484,6 +34013,16 @@ version |versionsuffix |toolchain ``0.17.2``| |``GCCcore/12.2.0`` ``0.17.6``| |``GCCcore/12.3.0`` +### scikit-build-core + +Scikit-build-core is a complete ground-up rewrite of scikit-build on top of modern packaging APIs. It provides a bridge between CMake and the Python build system, allowing you to make Python modules with CMake. + +*homepage*: + +version |toolchain +---------|------------------ +``0.5.0``|``GCCcore/12.3.0`` + ### scikit-cuda SciKit-cuda, a.k.a. skcuda, provides Python interfaces to many of the functions in the CUDA device/runtime, CUBLAS, CUFFT, and CUSOLVER libraries distributed as part of NVIDIA's CUDA Programming Toolkit. @@ -33553,7 +34092,7 @@ version |versionsuffix |toolchain ``0.20.2``|``-Python-3.6.6`` |``foss/2018b`` ``0.20.3``| |``foss/2019a``, ``fosscuda/2019a``, ``intel/2019a`` ``0.20.4``|``-Python-2.7.16`` |``intel/2019b`` -``0.20.4``|``-Python-2.7.18`` |``foss/2020b`` +``0.20.4``|``-Python-2.7.18`` |``foss/2020b``, ``foss/2021b`` ``0.21.3``|``-Python-3.7.4`` |``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` ``0.23.1``|``-Python-3.8.2`` |``foss/2020a``, ``fosscuda/2020a``, ``intel/2020a``, ``intelcuda/2020a`` ``0.23.2``| |``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b``, ``intelcuda/2020b`` @@ -33562,6 +34101,7 @@ version |versionsuffix |toolchain ``1.0.2`` | |``foss/2021b`` ``1.1.2`` | |``foss/2022a``, ``intel/2022a`` ``1.2.1`` | |``gfbf/2022b`` +``1.3.1`` | |``gfbf/2023a`` ### scikit-misc @@ -33585,16 +34125,16 @@ version |versionsuffix |toolchain ### scikit-optimize -Scikit-Optimize, or skopt, is a simple and efficient library to minimize (very) expensive and noisy black-box functions. +Scikit-Optimize, or skopt, is a simple and efficient library to minimize (very) expensive and noisy black-box functions. *homepage*: version |versionsuffix |toolchain ----------|-----------------|--------------- +---------|-----------------|------------------------------ ``0.5.2``|``-Python-3.6.6``|``intel/2018b`` ``0.7.4``|``-Python-3.7.4``|``foss/2019b`` ``0.8.1``|``-Python-3.8.2``|``foss/2020a`` -``0.9.0``| |``foss/2021a`` +``0.9.0``| |``foss/2021a``, ``foss/2022a`` ### scikit-plot @@ -33697,7 +34237,7 @@ version |versionsuffix |toolchain SCons is a software construction tool. -*homepage*: +*homepage*: version |versionsuffix |toolchain ---------------|-----------------------|--------------------------------------------------------------------------------- @@ -33721,6 +34261,7 @@ version |versionsuffix |toolchain ``4.1.0.post1``| |``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ``4.2.0`` | |``GCCcore/11.2.0`` ``4.4.0`` | |``GCCcore/11.3.0`` +``4.5.2`` | |``GCCcore/12.3.0`` ### SCOOP @@ -34033,6 +34574,16 @@ version |versionsuffix |toolchain ---------|-----------------|---------------------------------- ``1.0.1``|``-Python-3.7.4``|``foss/2019b``, ``fosscuda/2019b`` +### segmentation-models-pytorch + +Python library with Neural Networks for Image Segmentation based on PyTorch. + +*homepage*: + +version |toolchain +---------|-------------- +``0.3.3``|``foss/2022a`` + ### SeisSol SeisSol is a software package for simulating wave propagation and dynamic rupture based on the arbitrary high-order accurate derivative discontinuous Galerkin method (ADER-DG). @@ -34333,6 +34884,8 @@ version |versionsuffix |toolchain ----------|-----------------|-------------- ``0.35.0``|``-Python-3.7.4``|``foss/2019b`` ``0.41.0``| |``foss/2022a`` +``0.42.1``| |``foss/2022a`` +``0.42.1``|``-Python-3.7.4``|``foss/2019b`` ### shapAAR @@ -34538,6 +35091,7 @@ version |versionsuffix |toolchain ``5.0b``|``-Linux`` |``system`` ``6.0g``|``-fast`` |``foss/2021b``, ``foss/2022a`` ``6.0g``|``-fast-CUDA-11.7.0``|``foss/2022a`` +``6.0h``|``-fast`` |``foss/2022b`` ### silhouetteRank @@ -35022,10 +35576,11 @@ PacBio’s open-source SMRT Analysis software suite is designed for use with Sin *homepage*: -version |versionsuffix |toolchain ----------------|-------------------|---------- -``5.1.0.26412``|``-cli-tools-only``|``system`` -``6.0.0.47841``|``-cli-tools-only``|``system`` +version |versionsuffix |toolchain +-----------------|-------------------|---------- +``5.1.0.26412`` |``-cli-tools-only``|``system`` +``6.0.0.47841`` |``-cli-tools-only``|``system`` +``12.0.0.177059``|``-cli-tools-only``|``system`` ### SMV @@ -35067,6 +35622,28 @@ version |toolchain ``1.0beta.23``|``intel/2017b`` ``2.0.1`` |``GCC/11.2.0``, ``GCC/11.3.0``, ``GCC/12.2.0`` +### SNAP-ESA + +The Sentinel Application Platform (SNAP) is a common architecture for all Sentinel Toolboxes being jointly developed by Brockmann Consult, SkyWatch and C-S. The SNAP architecture is ideal for Earth Observation processing and analysis due to the following technological innovations: Extensibility, Portability, Modular Rich Client Platform, Generic EO Data Abstraction, Tiled Memory Management, and a Graph Processing Framework. + +*homepage*: + +version |versionsuffix|toolchain +---------|-------------|---------- +``8.0`` |``-Java-1.8``|``system`` +``9.0.0``|``-Java-11`` |``system`` + +### SNAP-ESA-python + +Python interface to the Sentinel Application Platform (SNAP) API + +*homepage*: + +version |versionsuffix |toolchain +---------|---------------------------|------------------ +``8.0`` |``-Java-1.8-Python-2.7.18``|``GCCcore/10.2.0`` +``9.0.0``|``-Java-11-Python-2.7.18`` |``GCCcore/11.2.0`` + ### SNAP-HMM SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. SNAP is an acroynm for Semi-HMM-based Nucleic Acid Parser. @@ -35568,6 +36145,7 @@ version |versionsuffix |toolchain ``1.16.3`` | |``foss/2021b``, ``intel/2021b`` ``2.0.0`` | |``foss/2022a``, ``intel/2022a`` ``2.0.2`` | |``gfbf/2022b`` +``2.1.0`` | |``gfbf/2023a`` ### Sphinx @@ -35768,6 +36346,7 @@ version |toolchain ``3.39.4`` |``GCCcore/12.2.0`` ``3.41.2`` |``GCCcore/13.1.0`` ``3.42.0`` |``GCCcore/12.3.0`` +``3.43.1`` |``GCCcore/13.2.0`` ### SqueezeMeta @@ -36046,6 +36625,16 @@ version |versionsuffix |toolchain ``0.8.3``| |``foss/2021b`` ``0.8.3``|``-CUDA-11.4.1``|``foss/2021b`` +### starparser + +Use this package to manipulate Relion star files, including counting, modifying, plotting, and sifting the data. At the very least, this is a useful alternative to awk commands, which can get awkward. Below is a description of the command- line options with some examples. Alternatively, use starparser within Relion or load the modules in your own Python scripts. + +*homepage*: + +version |toolchain +--------|-------------- +``1.49``|``foss/2022a`` + ### stars Reading, manipulating, writing and plotting spatiotemporal arrays (raster and vector data cubes) in R, using GDAL bindings provided by sf, and NetCDF bindings by ncmeta and RNetCDF. @@ -36182,19 +36771,20 @@ StringTie is a fast and highly efficient assembler of RNA-Seq alignments into po *homepage*: -version |toolchain -----------|---------------------------------- -``1.3.0`` |``intel/2016b`` -``1.3.3`` |``GCCcore/6.4.0``, ``intel/2017a`` -``1.3.3b``|``foss/2016b`` -``1.3.5`` |``GCCcore/8.2.0``, ``foss/2018b`` -``2.0.3`` |``GCCcore/7.3.0`` -``2.1.0`` |``foss/2018b`` -``2.1.1`` |``GCC/8.3.0`` -``2.1.3`` |``GCC/8.3.0``, ``GCC/9.3.0`` -``2.1.4`` |``GCC/8.3.0``, ``GCC/9.3.0`` -``2.1.7`` |``GCC/10.3.0`` -``2.2.1`` |``GCC/11.2.0`` +version |versionsuffix |toolchain +----------|------------------|---------------------------------- +``1.3.0`` | |``intel/2016b`` +``1.3.3`` | |``GCCcore/6.4.0``, ``intel/2017a`` +``1.3.3b``| |``foss/2016b`` +``1.3.5`` | |``GCCcore/8.2.0``, ``foss/2018b`` +``2.0.3`` | |``GCCcore/7.3.0`` +``2.1.0`` | |``foss/2018b`` +``2.1.1`` | |``GCC/8.3.0`` +``2.1.3`` | |``GCC/8.3.0``, ``GCC/9.3.0`` +``2.1.4`` | |``GCC/8.3.0``, ``GCC/9.3.0`` +``2.1.7`` | |``GCC/10.3.0`` +``2.2.1`` | |``GCC/11.2.0`` +``2.2.1`` |``-Python-2.7.18``|``GCC/11.2.0`` ### stripy @@ -36391,7 +36981,7 @@ version |toolchain ``6.2.0``|``foss/2020b``, ``intel/2020b`` ``6.3.0``|``foss/2021b``, ``foss/2022a`` ``6.5.1``|``foss/2022a`` -``6.6.0``|``foss/2022b`` +``6.6.0``|``foss/2022b``, ``foss/2023a`` ### SunPy @@ -36497,9 +37087,9 @@ Perl binding for SVG *homepage*: version |versionsuffix |toolchain ---------|----------------|------------------------------ +--------|----------------|---------------------------------------------- ``2.84``|``-Perl-5.30.0``|``foss/2019b`` -``2.87``| |``GCC/11.2.0``, ``GCC/11.3.0`` +``2.87``| |``GCC/11.2.0``, ``GCC/11.3.0``, ``GCC/12.2.0`` ### SVIM @@ -36589,7 +37179,7 @@ version |versionsuffix |toolchain ``3.0.12``|``-Python-3.7.2`` |``GCCcore/8.2.0`` ``4.0.1`` | |``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``4.0.2`` | |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` -``4.1.1`` | |``GCCcore/12.2.0``, ``GCCcore/12.3.0`` +``4.1.1`` | |``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0`` ### SWIPE @@ -36664,7 +37254,17 @@ version |versionsuffix |toolchain ``1.9`` | |``foss/2021b``, ``intel/2021b`` ``1.10.1``| |``foss/2022a``, ``intel/2022a`` ``1.11.1``| |``foss/2022a``, ``intel/2022a`` -``1.12`` | |``gfbf/2023a`` +``1.12`` | |``gfbf/2022b``, ``gfbf/2023a`` + +### synapseclient + +The synapseclient package provides an interface to Synapse, a collaborative, open-source research platform that allows teams to share data, track analyses, and collaborate, providing support for: integrated presentation of data, code and text fine grained access control provenance tracking The synapseclient package lets you communicate with the cloud-hosted Synapse service to access data and create shared data analysis projects from within Python scripts or at the interactive Python console. Other Synapse clients exist for R, Java, and the web. The Python client can also be used from the command line. + +*homepage*: + +version |toolchain +---------|------------------ +``3.0.0``|``GCCcore/12.2.0`` ### synthcity @@ -36731,8 +37331,8 @@ Generic indexer for TAB-delimited genome position files *homepage*: version |toolchain ----------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------- -``0.2.6``|``GCCcore/10.2.0``, ``GCCcore/11.2.0``, ``GCCcore/5.4.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``foss/2016a``, ``intel/2016a``, ``intel/2016b`` +---------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +``0.2.6``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/5.4.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``foss/2016a``, ``intel/2016a``, ``intel/2016b`` ### tabixpp @@ -36941,7 +37541,7 @@ version |toolchain ``8.6.10``|``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ``8.6.11``|``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``8.6.12``|``GCCcore/11.3.0``, ``GCCcore/12.2.0`` -``8.6.13``|``GCCcore/12.3.0``, ``GCCcore/13.1.0`` +``8.6.13``|``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``GCCcore/13.2.0`` ### TCLAP @@ -37149,6 +37749,7 @@ version |versionsuffix |toolchain ----------|-----------------|---------------------------------- ``0.9.0`` |``-Python-3.7.4``|``foss/2019b`` ``0.12.1``| |``foss/2020b``, ``fosscuda/2020b`` +``0.14.0``| |``foss/2021a`` ``0.16.0``| |``foss/2021b`` ``0.19.0``|``-CUDA-11.7.0`` |``foss/2022a`` @@ -37161,6 +37762,7 @@ NVIDIA TensorRT is a platform for high-performance deep learning inference version |versionsuffix |toolchain -----------|------------------|------------------ ``4.0.1.6``|``-Python-2.7.15``|``fosscuda/2018b`` +``8.6.1`` |``-CUDA-11.7.0`` |``foss/2022a`` ### terastructure @@ -37276,6 +37878,7 @@ version |toolchain ``20200406``|``GCCcore/8.3.0`` ``20210324``|``GCC/10.3.0``, ``GCC/11.2.0`` ``20220321``|``GCC/11.2.0`` +``20230313``|``GCC/11.3.0`` ### Text-CSV @@ -37491,7 +38094,7 @@ version |versionsuffix |toolchain ``8.6.10``| |``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ``8.6.11``| |``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``8.6.12``| |``GCCcore/11.3.0``, ``GCCcore/12.2.0`` -``8.6.13``| |``GCCcore/12.3.0`` +``8.6.13``| |``GCCcore/12.3.0``, ``GCCcore/13.2.0`` ### Tkinter @@ -37521,6 +38124,7 @@ version |versionsuffix |toolchain ``3.10.4``| |``GCCcore/11.3.0`` ``3.10.8``| |``GCCcore/12.2.0`` ``3.11.3``| |``GCCcore/12.3.0`` +``3.11.5``| |``GCCcore/13.2.0`` ### TM-align @@ -37690,7 +38294,7 @@ version |versionsuffix |toolchain ``2.1.0``|``-Python-2.7.14``|``intel/2018a`` ``2.1.1``| |``foss/2016a``, ``foss/2016b``, ``foss/2017b``, ``intel/2017a``, ``intel/2017b`` ``2.1.2``| |``foss/2018b``, ``gompi/2019b``, ``iimpi/2019b`` -``2.1.2``|``-Python-2.7.18``|``GCC/10.2.0``, ``GCC/11.3.0``, ``gompi/2020a``, ``iimpi/2020a`` +``2.1.2``|``-Python-2.7.18``|``GCC/10.2.0``, ``GCC/11.2.0``, ``GCC/11.3.0``, ``gompi/2020a``, ``iimpi/2020a`` ### torchaudio @@ -37978,6 +38582,7 @@ version |versionsuffix |toolchain ``12.12.1``|``-Python-3.6.4`` |``foss/2018a``, ``intel/2018a`` ``12.12.1``|``-Python-3.7.4`` |``foss/2019b`` ``13.4.1`` | |``foss/2022a`` +``13.4.1`` |``-zoltan`` |``foss/2022a`` ### Trim_Galore @@ -38310,7 +38915,7 @@ version |versionsuffix |toolchain ## U -[UCC](#ucc) - [UCC-CUDA](#ucc-cuda) - [UCLUST](#uclust) - [UCX](#ucx) - [UCX-CUDA](#ucx-cuda) - [ucx-py](#ucx-py) - [UCX-ROCm](#ucx-rocm) - [udocker](#udocker) - [UDUNITS](#udunits) - [UFL](#ufl) - [Ultralytics](#ultralytics) - [umap-learn](#umap-learn) - [UMI-tools](#umi-tools) - [umi4cPackage](#umi4cpackage) - [umis](#umis) - [UNAFold](#unafold) - [uncertainty-calibration](#uncertainty-calibration) - [unicore-uftp](#unicore-uftp) - [Unicycler](#unicycler) - [Unidecode](#unidecode) - [unifdef](#unifdef) - [UniFrac](#unifrac) - [unimap](#unimap) - [units](#units) - [unixODBC](#unixodbc) - [unrar](#unrar) - [UnZip](#unzip) - [UQTk](#uqtk) - [USEARCH](#usearch) - [UShER](#usher) - [USPEX](#uspex) - [utf8proc](#utf8proc) - [util-linux](#util-linux) +[UCC](#ucc) - [UCC-CUDA](#ucc-cuda) - [UCLUST](#uclust) - [UCX](#ucx) - [UCX-CUDA](#ucx-cuda) - [ucx-py](#ucx-py) - [UCX-ROCm](#ucx-rocm) - [udocker](#udocker) - [UDUNITS](#udunits) - [UFL](#ufl) - [Ultralytics](#ultralytics) - [umap-learn](#umap-learn) - [UMI-tools](#umi-tools) - [umi4cPackage](#umi4cpackage) - [umis](#umis) - [UNAFold](#unafold) - [uncertainties](#uncertainties) - [uncertainty-calibration](#uncertainty-calibration) - [unicore-uftp](#unicore-uftp) - [Unicycler](#unicycler) - [Unidecode](#unidecode) - [unifdef](#unifdef) - [UniFrac](#unifrac) - [unimap](#unimap) - [units](#units) - [unixODBC](#unixodbc) - [unrar](#unrar) - [UnZip](#unzip) - [UQTk](#uqtk) - [USEARCH](#usearch) - [UShER](#usher) - [USPEX](#uspex) - [utf8proc](#utf8proc) - [util-linux](#util-linux) ### UCC @@ -38320,10 +38925,10 @@ UCC (Unified Collective Communication) is a collective communication operations *homepage*: version |toolchain ----------|------------------ +---------|-------------------------------------- ``1.0.0``|``GCCcore/11.3.0`` ``1.1.0``|``GCCcore/12.2.0`` -``1.2.0``|``GCCcore/12.3.0`` +``1.2.0``|``GCCcore/12.3.0``, ``GCCcore/13.2.0`` ### UCC-CUDA @@ -38372,6 +38977,7 @@ version |versionsuffix |toolchain ``1.13.1`` | |``GCCcore/12.2.0`` ``1.14.0`` | |``GCCcore/12.2.0`` ``1.14.1`` | |``GCCcore/12.3.0`` +``1.15.0`` | |``GCCcore/13.2.0`` ### UCX-CUDA @@ -38508,6 +39114,16 @@ version|versionsuffix |toolchain -------|----------------|--------------- ``3.8``|``-Perl-5.24.1``|``intel/2017a`` +### uncertainties + +Transparent calculations with uncertainties on the quantities involved (aka error propagation); fast calculation of derivatives + +*homepage*: + +version |toolchain +---------|-------------- +``3.1.7``|``foss/2021b`` + ### uncertainty-calibration Python library to measure the calibration error of models, including confidence intervals computed by Bootstrap resampling, and code to recalibrate models. @@ -38579,8 +39195,8 @@ Unimap is a fork of minimap2 optimized for assembly-to-reference alignment. It i *homepage*: version|toolchain --------|------------------ -``0.1``|``GCCcore/10.2.0`` +-------|-------------------------------------- +``0.1``|``GCCcore/10.2.0``, ``GCCcore/11.3.0`` ### units @@ -38622,8 +39238,8 @@ UnZip is an extraction utility for archives compressed in .zip format (also call *homepage*: version|toolchain --------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -``6.0``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``system`` +-------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +``6.0``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``GCCcore/13.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``system`` ### UQTk @@ -38710,7 +39326,7 @@ version |toolchain ``2.37`` |``GCCcore/11.2.0`` ``2.38`` |``GCCcore/11.3.0`` ``2.38.1``|``GCCcore/12.2.0`` -``2.39`` |``GCCcore/12.3.0`` +``2.39`` |``GCCcore/12.3.0``, ``GCCcore/13.2.0`` ## V @@ -38873,6 +39489,7 @@ VBZ compression HDF5 plugin for nanopolish version |toolchain ---------|--------------- ``1.0.1``|``gompi/2020b`` +``1.0.3``|``gompi/2022a`` ### VCF-kit @@ -38915,12 +39532,12 @@ The aim of VCFtools is to provide easily accessible methods for working with c *homepage*: version |versionsuffix |toolchain -----------|----------------|------------------------------------------------------------------------------------------------------------------------------------- +----------|----------------|----------------------------------------------------------------------------------------------------------------------------------------------------- ``0.1.14``|``-Perl-5.22.1``|``foss/2016a``, ``intel/2016a`` ``0.1.15``|``-Perl-5.24.0``|``foss/2016b`` ``0.1.15``|``-Perl-5.26.0``|``foss/2017b``, ``intel/2017b`` ``0.1.15``|``-Perl-5.26.1``|``foss/2018a`` -``0.1.16``| |``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0``, ``GCC/12.2.0``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2019.5.281`` +``0.1.16``| |``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0``, ``GCC/12.2.0``, ``GCC/12.3.0``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2019.5.281`` ``0.1.16``|``-Perl-5.28.0``|``foss/2018b``, ``intel/2018b`` ### vConTACT2 @@ -39388,6 +40005,7 @@ version |toolchain ``2022.0.0`` |``system`` ``2022.2.0`` |``system`` ``2022.3.0`` |``system`` +``2023.2.0`` |``system`` ### VV @@ -39412,7 +40030,7 @@ version |toolchain ## W -[wandb](#wandb) - [Wannier90](#wannier90) - [WannierTools](#wanniertools) - [Wayland](#wayland) - [Waylandpp](#waylandpp) - [WCSLIB](#wcslib) - [WCT](#wct) - [wcwidth](#wcwidth) - [webin-cli](#webin-cli) - [WebKitGTK+](#webkitgtk+) - [WebSocket++](#websocket++) - [WEKA](#weka) - [WFA2](#wfa2) - [wget](#wget) - [wgsim](#wgsim) - [WHAM](#wham) - [WhatsHap](#whatshap) - [wheel](#wheel) - [WIEN2k](#wien2k) - [WildMagic](#wildmagic) - [Winnowmap](#winnowmap) - [WisecondorX](#wisecondorx) - [WISExome](#wisexome) - [wkhtmltopdf](#wkhtmltopdf) - [worker](#worker) - [wpebackend-fdo](#wpebackend-fdo) - [WPS](#wps) - [wrapt](#wrapt) - [WRF](#wrf) - [WRF-Fire](#wrf-fire) - [wrf-python](#wrf-python) - [wtdbg2](#wtdbg2) - [wxPropertyGrid](#wxpropertygrid) - [wxPython](#wxpython) - [wxWidgets](#wxwidgets) +[wandb](#wandb) - [Wannier90](#wannier90) - [WannierTools](#wanniertools) - [Wayland](#wayland) - [Waylandpp](#waylandpp) - [WCSLIB](#wcslib) - [WCT](#wct) - [wcwidth](#wcwidth) - [webin-cli](#webin-cli) - [WebKitGTK+](#webkitgtk+) - [WebSocket++](#websocket++) - [WEKA](#weka) - [WFA2](#wfa2) - [wget](#wget) - [wgsim](#wgsim) - [WHAM](#wham) - [WhatsHap](#whatshap) - [wheel](#wheel) - [WIEN2k](#wien2k) - [WildMagic](#wildmagic) - [Winnowmap](#winnowmap) - [WisecondorX](#wisecondorx) - [WISExome](#wisexome) - [wkhtmltopdf](#wkhtmltopdf) - [worker](#worker) - [wpebackend-fdo](#wpebackend-fdo) - [WPS](#wps) - [wrapt](#wrapt) - [WRF](#wrf) - [WRF-Fire](#wrf-fire) - [wrf-python](#wrf-python) - [WSClean](#wsclean) - [wtdbg2](#wtdbg2) - [wxPropertyGrid](#wxpropertygrid) - [wxPython](#wxpython) - [wxWidgets](#wxwidgets) ### wandb @@ -39434,13 +40052,13 @@ A tool for obtaining maximally-localised Wannier functions *homepage*: version |versionsuffix|toolchain ------------|-------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------- +-----------|-------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ``1.2`` | |``intel/2016.02-GCC-4.9`` ``2.0.1`` | |``intel/2016.02-GCC-4.9``, ``intel/2016a`` ``2.0.1.1``|``-abinit`` |``intel/2018b`` ``2.1.0`` | |``foss/2017b``, ``intel/2017a``, ``intel/2017b`` ``3.0.0`` | |``intel/2018b`` -``3.1.0`` | |``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``foss/2022a``, ``gomkl/2021a``, ``intel/2020a``, ``intel/2020b``, ``intel/2021a``, ``intel/2021b``, ``intel/2022a`` +``3.1.0`` | |``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``foss/2022a``, ``foss/2023a``, ``gomkl/2021a``, ``intel/2020a``, ``intel/2020b``, ``intel/2021a``, ``intel/2021b``, ``intel/2022a``, ``intel/2023a`` ### WannierTools @@ -39477,13 +40095,13 @@ version |toolchain ### WCSLIB -The FITS "World Coordinate System" (WCS) standard defines keywords and usage that provide for the description of astronomical coordinate systems in a FITS image header. +The FITS "World Coordinate System" (WCS) standard defines keywords and usage that provide for the description of astronomical coordinate systems in a FITS image header. *homepage*: version |toolchain ---------|-------------- -``7.11``|``GCC/11.2.0`` +--------|------------------------------ +``7.11``|``GCC/11.2.0``, ``GCC/11.3.0`` ### WCT @@ -39702,7 +40320,7 @@ The Worker framework has been developed to help deal with parameter exploration *homepage*: version |versionsuffix |toolchain -----------|----------------|------------------------------ +----------|----------------|-------------------------------- ``1.6.4`` | |``intel/2016a`` ``1.6.5`` | |``intel/2016a`` ``1.6.6`` | |``intel/2016b`` @@ -39713,7 +40331,7 @@ version |versionsuffix |toolchain ``1.6.8`` |``-intel-2018b``|``system`` ``1.6.11``| |``intel/2019b`` ``1.6.12``| |``foss/2019a``, ``foss/2021b`` -``1.6.13``| |``iimpi/2021b`` +``1.6.13``| |``iimpi/2021b``, ``iimpi/2022b`` ### wpebackend-fdo @@ -39750,8 +40368,8 @@ The aim of the wrapt module is to provide a transparent object proxy for Python, *homepage*: version |toolchain -----------|----------------------------------------------- -``1.15.0``|``foss/2022a``, ``gfbf/2022b``, ``intel/2022a`` +----------|--------------------------------------------------------------- +``1.15.0``|``foss/2022a``, ``gfbf/2022b``, ``gfbf/2023a``, ``intel/2022a`` ### WRF @@ -39793,6 +40411,16 @@ version |versionsuffix |toolchain ``1.2.0``|``-Python-3.6.4``|``intel/2018a`` ``1.3.1``|``-Python-3.6.6``|``intel/2018b`` +### WSClean + +WSClean (w-stacking clean) is a fast generic widefield imager. It implements several gridding algorithms and offers fully-automated multi-scale multi-frequency deconvolution. + +*homepage*: + +version|toolchain +-------|-------------- +``3.4``|``foss/2022a`` + ### wtdbg2 Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. @@ -39854,7 +40482,7 @@ version |toolchain ## X -[X11](#x11) - [x13as](#x13as) - [x264](#x264) - [x265](#x265) - [XALT](#xalt) - [xarray](#xarray) - [xbitmaps](#xbitmaps) - [xcb-proto](#xcb-proto) - [xcb-util](#xcb-util) - [xcb-util-image](#xcb-util-image) - [xcb-util-keysyms](#xcb-util-keysyms) - [xcb-util-renderutil](#xcb-util-renderutil) - [xcb-util-wm](#xcb-util-wm) - [xCell](#xcell) - [XCFun](#xcfun) - [xclip](#xclip) - [XCrySDen](#xcrysden) - [xdotool](#xdotool) - [Xerces-C++](#xerces-c++) - [xESMF](#xesmf) - [xextproto](#xextproto) - [xf86vidmodeproto](#xf86vidmodeproto) - [XGBoost](#xgboost) - [XGrafix](#xgrafix) - [xineramaproto](#xineramaproto) - [XKeyboardConfig](#xkeyboardconfig) - [XlsxWriter](#xlsxwriter) - [XMDS2](#xmds2) - [Xmipp](#xmipp) - [xmitgcm](#xmitgcm) - [XML-Compile](#xml-compile) - [XML-LibXML](#xml-libxml) - [XML-Parser](#xml-parser) - [xmlf90](#xmlf90) - [XMLSec](#xmlsec) - [XMLStarlet](#xmlstarlet) - [xonsh](#xonsh) - [xorg-macros](#xorg-macros) - [XPLOR-NIH](#xplor-nih) - [xprop](#xprop) - [xproto](#xproto) - [XSD](#xsd) - [XTandem](#xtandem) - [xtb](#xtb) - [xtensor](#xtensor) - [xtrans](#xtrans) - [Xvfb](#xvfb) - [xxd](#xxd) - [xxHash](#xxhash) - [XZ](#xz) +[X11](#x11) - [x13as](#x13as) - [x264](#x264) - [x265](#x265) - [XALT](#xalt) - [xarray](#xarray) - [XBeach](#xbeach) - [xbitmaps](#xbitmaps) - [xcb-proto](#xcb-proto) - [xcb-util](#xcb-util) - [xcb-util-image](#xcb-util-image) - [xcb-util-keysyms](#xcb-util-keysyms) - [xcb-util-renderutil](#xcb-util-renderutil) - [xcb-util-wm](#xcb-util-wm) - [xCell](#xcell) - [XCFun](#xcfun) - [xclip](#xclip) - [XCrySDen](#xcrysden) - [xdotool](#xdotool) - [Xerces-C++](#xerces-c++) - [xESMF](#xesmf) - [xextproto](#xextproto) - [xf86vidmodeproto](#xf86vidmodeproto) - [XGBoost](#xgboost) - [XGrafix](#xgrafix) - [xineramaproto](#xineramaproto) - [XKeyboardConfig](#xkeyboardconfig) - [XlsxWriter](#xlsxwriter) - [XMDS2](#xmds2) - [Xmipp](#xmipp) - [xmitgcm](#xmitgcm) - [XML-Compile](#xml-compile) - [XML-LibXML](#xml-libxml) - [XML-Parser](#xml-parser) - [xmlf90](#xmlf90) - [XMLSec](#xmlsec) - [XMLStarlet](#xmlstarlet) - [xonsh](#xonsh) - [XOOPIC](#xoopic) - [xorg-macros](#xorg-macros) - [XPLOR-NIH](#xplor-nih) - [xprop](#xprop) - [xproto](#xproto) - [XSD](#xsd) - [XTandem](#xtandem) - [xtb](#xtb) - [xtensor](#xtensor) - [xtrans](#xtrans) - [Xvfb](#xvfb) - [xxd](#xxd) - [xxHash](#xxhash) - [XZ](#xz) ### X11 @@ -39880,6 +40508,7 @@ version |toolchain ``20220504``|``GCCcore/11.3.0`` ``20221110``|``GCCcore/12.2.0`` ``20230603``|``GCCcore/12.3.0`` +``20231019``|``GCCcore/13.2.0`` ### x13as @@ -39917,6 +40546,7 @@ version |toolchain ``20210613``|``GCCcore/11.2.0`` ``20220620``|``GCCcore/11.3.0`` ``20230226``|``GCCcore/12.2.0``, ``GCCcore/12.3.0`` +``20231019``|``GCCcore/13.2.0`` ### x265 @@ -39925,7 +40555,7 @@ x265 is a free software library and application for encoding video streams into *homepage*: version|toolchain --------|-------------------------------------------------------------------------------------------------- +-------|---------------------------------------------------------------------------------------------------------------------- ``2.4``|``foss/2016b`` ``2.5``|``intel/2017a`` ``2.6``|``GCCcore/6.4.0``, ``intel/2017b`` @@ -39934,7 +40564,7 @@ version|toolchain ``3.0``|``GCCcore/8.2.0`` ``3.2``|``GCCcore/8.3.0`` ``3.3``|``GCCcore/10.2.0``, ``GCCcore/9.3.0`` -``3.5``|``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` +``3.5``|``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0`` ### XALT @@ -39972,6 +40602,17 @@ version |versionsuffix |toolchain ``2022.6.0``| |``foss/2022a``, ``intel/2022a`` ``2022.9.0``| |``foss/2022a`` ``2023.4.2``| |``gfbf/2022b`` +``2023.9.0``| |``gfbf/2023a`` + +### XBeach + +XBeach is a two-dimensional model for wave propagation, long waves and mean flow, sediment transport and morphological changes of the nearshore area, beaches, dunes and backbarrier during storms. + +*homepage*: + +version |toolchain +------------|--------------- +``20230831``|``gompi/2022a`` ### xbitmaps @@ -40207,6 +40848,7 @@ version |toolchain ``3.0.2``|``GCCcore/11.2.0`` ``3.0.8``|``GCCcore/11.3.0`` ``3.1.2``|``GCCcore/12.2.0`` +``3.1.3``|``GCCcore/12.3.0`` ### XMDS2 @@ -40287,6 +40929,7 @@ version |versionsuffix |toolchain ``2.44_01``|``-Perl-5.28.0``|``GCCcore/7.3.0`` ``2.46`` |``-Perl-5.32.1``|``GCCcore/10.3.0`` ``2.46`` |``-Perl-5.34.1``|``GCCcore/11.3.0`` +``2.46`` |``-Perl-5.36.1``|``GCCcore/12.3.0`` ### xmlf90 @@ -40330,6 +40973,16 @@ version |toolchain ---------|--------------- ``0.3.2``|``intel/2016a`` +### XOOPIC + +XOOPIC is a two-dimensional 3-velocity particle-in-cell simulator. It can handle electrostatic and electromagnetic models, has a large variety of boundary conditions, supports multiple gasses and gas chemistry, and is easily reconfigurable via an input file. + +*homepage*: + +version |toolchain +------------|-------------- +``20210302``|``foss/2020a`` + ### xorg-macros X.org macros utilities. @@ -40375,10 +41028,10 @@ X protocol and ancillary headers *homepage*: version |toolchain -----------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +----------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ``7.0.28``|``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` ``7.0.29``|``intel/2016a`` -``7.0.31``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``7.0.31``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.3.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ### XSD @@ -40413,6 +41066,7 @@ version |versionsuffix |toolchain ``6.4.1`` | |``foss/2021b``, ``intel/2021a`` ``6.5.0`` | |``foss/2021b`` ``6.5.1`` | |``foss/2022a`` +``6.6.0`` | |``foss/2022a`` ### xtensor @@ -40592,8 +41246,8 @@ Yasm: Complete rewrite of the NASM assembler with BSD license *homepage*: version |toolchain ----------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -``1.3.0``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``gimkl/2.11.5``, ``gimkl/2017a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` +---------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +``1.3.0``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``gimkl/2.11.5``, ``gimkl/2017a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` ### YAXT @@ -40634,7 +41288,7 @@ version |toolchain ## Z -[Z3](#z3) - [zarr](#zarr) - [ZeroMQ](#zeromq) - [zfp](#zfp) - [Zgoubi](#zgoubi) - [ZIMPL](#zimpl) - [zingeR](#zinger) - [Zip](#zip) - [zlib](#zlib) - [zlib-ng](#zlib-ng) - [zlibbioc](#zlibbioc) - [Zopfli](#zopfli) - [ZPAQ](#zpaq) - [zsh](#zsh) - [zstd](#zstd) +[Z3](#z3) - [zarr](#zarr) - [ZeroMQ](#zeromq) - [zeus-mcmc](#zeus-mcmc) - [zfp](#zfp) - [Zgoubi](#zgoubi) - [ZIMPL](#zimpl) - [zingeR](#zinger) - [Zip](#zip) - [zlib](#zlib) - [zlib-ng](#zlib-ng) - [zlibbioc](#zlibbioc) - [Zopfli](#zopfli) - [ZPAQ](#zpaq) - [zsh](#zsh) - [zstd](#zstd) ### Z3 @@ -40689,6 +41343,17 @@ version |toolchain ``4.3.2``|``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``4.3.3``|``GCCcore/10.2.0`` ``4.3.4``|``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` +``4.3.5``|``GCCcore/13.2.0`` + +### zeus-mcmc + +Zeus is a Python implementation of the Ensemble Slice Sampling method. + +*homepage*: + +version |toolchain +---------|-------------- +``2.5.4``|``foss/2022a`` ### zfp @@ -40738,8 +41403,8 @@ Zip is a compression and file packaging/archive utility. Although highly compati *homepage*: version|toolchain --------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -``3.0``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +-------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +``3.0``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ### zlib @@ -40827,4 +41492,4 @@ version |toolchain ``1.4.9``|``GCCcore/10.3.0`` ``1.5.0``|``GCCcore/11.2.0`` ``1.5.2``|``GCCcore/11.3.0``, ``GCCcore/12.2.0`` -``1.5.5``|``GCCcore/12.3.0`` +``1.5.5``|``GCCcore/12.3.0``, ``GCCcore/13.2.0``