diff --git a/docs/version-specific/easyblocks.md b/docs/version-specific/easyblocks.md index cfa43fc88..61a2ead38 100644 --- a/docs/version-specific/easyblocks.md +++ b/docs/version-specific/easyblocks.md @@ -258,6 +258,7 @@ - EB_python_minus_meep - EB_PyTorch - EB_PyZMQ + - EB_scipy - EB_SEPP - EB_TensorFlow - EB_TensorRT @@ -314,6 +315,7 @@ - MesonNinja - CMakeNinja - EB_Mesa + - EB_scipy - ModuleRC - PackedBinary - EB_ANSYS @@ -367,6 +369,7 @@ - EB_python_minus_meep - EB_PyTorch - EB_PyZMQ + - EB_scipy - EB_SEPP - EB_TensorFlow - EB_TensorRT diff --git a/docs/version-specific/easyconfig-parameters.md b/docs/version-specific/easyconfig-parameters.md index cb2e7ae6d..f9d3bfc9e 100644 --- a/docs/version-specific/easyconfig-parameters.md +++ b/docs/version-specific/easyconfig-parameters.md @@ -54,7 +54,7 @@ `required_linked_shared_libs`|List of shared libraries (names, file names, or paths) which must be linked in all installed binaries/libraries |`[]` `runtest` |Indicates if a test should be run after make; should specify argument after make (for e.g.,"test" for make test) |`None` `sanity_check_commands` |format: [(name, options)] e.g. [('gzip','-h')]. Using a non-tuple is equivalent to (name, '-h') |`[]` -`sanity_check_paths` |List of files and directories to check (format: {'files':<list>, 'dirs':<list>}) |`{}` +`sanity_check_paths` |List of files and directories to check (format: {'files':<list>, 'dirs':<list>}) |`{}` `skip` |Skip existing software |`False` `skipsteps` |Skip these steps |`[]` `source_urls` |List of URLs for source files |`[]` @@ -81,16 +81,16 @@ ## Dependencies parameters -**Parameter name** |**Description** |**Default value** --------------------------|---------------------------------------------------------------------|----------------- -`allow_system_deps` |Allow listed system dependencies (format: (<name>, <version>)) |`[]` -`builddependencies` |List of build dependencies |`[]` -`dependencies` |List of dependencies |`[]` -`hiddendependencies` |List of dependencies available as hidden modules |`[]` -`moddependpaths` |Absolute path(s) to prepend to MODULEPATH before loading dependencies|`None` -`multi_deps` |Dict of lists of dependency versions over which to iterate |`{}` -`multi_deps_load_default`|Load module for first version listed in multi_deps by default |`True` -`osdependencies` |OS dependencies that should be present on the system |`[]` +**Parameter name** |**Description** |**Default value** +-------------------------|--------------------------------------------------------------------------|----------------- +`allow_system_deps` |Allow listed system dependencies (format: (<name>, <version>))|`[]` +`builddependencies` |List of build dependencies |`[]` +`dependencies` |List of dependencies |`[]` +`hiddendependencies` |List of dependencies available as hidden modules |`[]` +`moddependpaths` |Absolute path(s) to prepend to MODULEPATH before loading dependencies |`None` +`multi_deps` |Dict of lists of dependency versions over which to iterate |`{}` +`multi_deps_load_default`|Load module for first version listed in multi_deps by default |`True` +`osdependencies` |OS dependencies that should be present on the system |`[]` ## License parameters @@ -134,6 +134,7 @@ `moduleclass` |Module class to be used for this software |`"base"` `moduleforceunload` |Force unload of all modules when loading the extension |`False` `moduleloadnoconflict` |Don't check for conflicts, unload other versions instead |`False` +`modunloadmsg` |Message that should be printed when generated module is unloaded |`{}` `recursive_module_unload` |Recursive unload of all dependencies when unloading module (True/False to hard enable/disable; None implies honoring the --recursive-module-unload EasyBuild configuration setting|`None` `site_contacts` |String/list of strings with site contacts for the software |`None` `upstream_contacts` |String/list of strings with upstream contact addresses (e.g., support e-mail, mailing list, bugtracker) |`None` diff --git a/docs/version-specific/easyconfig-templates.md b/docs/version-specific/easyconfig-templates.md index 516f0f12a..888c34734 100644 --- a/docs/version-specific/easyconfig-templates.md +++ b/docs/version-specific/easyconfig-templates.md @@ -49,9 +49,10 @@ Template name |Template value ## Template values set outside EasyBlock runstep Template name |Template value -------------------|---------------------- +------------------|------------------------------------------- ``%(builddir)s`` |Build directory ``%(installdir)s``|Installation directory +``%(start_dir)s`` |Directory in which the build process begins ## Template values which are defined dynamically diff --git a/docs/version-specific/eb-help.md b/docs/version-specific/eb-help.md index 504feaf2a..36336bcad 100644 --- a/docs/version-specific/eb-help.md +++ b/docs/version-specific/eb-help.md @@ -31,8 +31,8 @@ Option flag |Option description ## Configfile options Option flag |Option description ------------------------------------------|--------------------------------------------------------------------- -``--configfiles=CONFIGFILES`` |Parse (additional) configfiles (type comma-separated list; default: ) +-----------------------------------------|---------------------------------------------------------- +``--configfiles=CONFIGFILES`` |Parse (additional) configfiles (type comma-separated list) ``--ignoreconfigfiles=IGNORECONFIGFILES``|Ignore configfiles (type comma-separated list) ## Basic options @@ -51,9 +51,9 @@ Option flag |Option description ``-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; default: ) +``-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; default: ) +``--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) @@ -71,9 +71,9 @@ Option flag |Option descrip ``--external-modules-metadata=EXTERNAL-MODULES-METADATA`` |List of (glob patterns for) paths to files specifying metadata for external modules (INI format) (type comma-separated list) ``--hooks=HOOKS`` |Location of Python module with hook implementations (type str) ``--ignore-dirs=IGNORE-DIRS`` |Directory names to ignore when searching for files/dirs (type comma-separated list; default: .git,.svn) -``--include-easyblocks=INCLUDE-EASYBLOCKS`` |Location(s) of extra or customized easyblocks (type comma-separated list; default: ) -``--include-module-naming-schemes=INCLUDE-MODULE-NAMING-SCHEMES``|Location(s) of extra or customized module naming schemes (type comma-separated list; default: ) -``--include-toolchains=INCLUDE-TOOLCHAINS`` |Location(s) of extra or customized toolchains or toolchain components (type comma-separated list; default: ) +``--include-easyblocks=INCLUDE-EASYBLOCKS`` |Location(s) of extra or customized easyblocks (type comma-separated list) +``--include-module-naming-schemes=INCLUDE-MODULE-NAMING-SCHEMES``|Location(s) of extra or customized module naming schemes (type comma-separated list) +``--include-toolchains=INCLUDE-TOOLCHAINS`` |Location(s) of extra or customized toolchains or toolchain components (type comma-separated list) ``--installpath=INSTALLPATH`` |Install path for software and modules (default: /home/example/.local/easybuild) ``--installpath-modules=INSTALLPATH-MODULES`` |Install path for modules (if None, combine --installpath and --subdir-modules) ``--installpath-software=INSTALLPATH-SOFTWARE`` |Install path for software (if None, combine --installpath and --subdir-software) @@ -87,7 +87,7 @@ Option flag |Option descrip ``--modules-footer=PATH`` |Path to file containing footer to be added to all generated module files ``--modules-header=PATH`` |Path to file containing header to be added to all generated module files ``--modules-tool=MODULES-TOOL`` |Modules tool to use (type choice; default: Lmod) (choices: EnvironmentModules, EnvironmentModulesC, EnvironmentModulesTcl, Lmod) -``--package-naming-scheme=PACKAGE-NAMING-SCHEME`` |Packaging naming scheme choice (type choice; default: EasyBuildPNS) (choices: EasyBuildPNS) +``--package-naming-scheme=PACKAGE-NAMING-SCHEME`` |Packaging naming scheme choice (type choice; default: EasyBuildPNS) (choices: EasyBuildDebFriendlyPNS, EasyBuildPNS) ``--packagepath=PACKAGEPATH`` |The destination path for the packages built by package-tool (default: /home/example/.local/easybuild/packages) ``--prefix=PREFIX`` |Change prefix for buildpath, installpath, sourcepath and repositorypath (used prefix for defaults /home/example/.local/easybuild) ``--recursive-module-unload`` |Enable generating of modules that unload recursively. (default: False) @@ -139,11 +139,11 @@ Option flag |Option description ``--close-pr-msg=CLOSE-PR-MSG`` |Custom close message for pull request closed with --close-pr; (type ) ``--close-pr-reasons=CLOSE-PR-REASONS`` |Close reason for pull request closed with --close-pr; supported values: archived, inactive, obsolete, retest (type ) ``--dump-test-report=DUMP-TEST-REPORT`` |Dump test report to specified path (default: test_report.md) -``--from-pr=PR#`` |Obtain easyconfigs from specified PR (type comma-separated list; default: ) +``--from-pr=PR#`` |Obtain easyconfigs from specified PR (type comma-separated list) ``--git-working-dirs-path=GIT-WORKING-DIRS-PATH`` |Path to Git working directories for EasyBuild repositories (type ) ``--github-org=GITHUB-ORG`` |GitHub organization (type ) ``--github-user=GITHUB-USER`` |GitHub username (type ) -``--include-easyblocks-from-pr=PR#`` |Include easyblocks from specified PR (type comma-separated list; default: ) +``--include-easyblocks-from-pr=PR#`` |Include easyblocks from specified PR (type comma-separated list) ``--install-github-token`` |Install GitHub token (requires --github-user) (default: False) ``--list-prs=STATE,ORDER,DIRECTION`` |List pull requests (type ; default: open,created,desc) ``--merge-pr=PR#`` |Merge pull request (type ) @@ -218,8 +218,8 @@ Option flag |Option description Option flag |Option description -------------------------------------------------------------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -``--accept-eula=ACCEPT-EULA`` |Accept EULA for specified software [DEPRECATED, use --accept-eula-for instead!] (type comma-separated list; default: ) -``--accept-eula-for=ACCEPT-EULA-FOR`` |Accept EULA for specified software (type comma-separated list; default: ) +``--accept-eula=ACCEPT-EULA`` |Accept EULA for specified software [DEPRECATED, use --accept-eula-for instead!] (type comma-separated list) +``--accept-eula-for=ACCEPT-EULA-FOR`` |Accept EULA for specified software (type comma-separated list) ``--add-dummy-to-minimal-toolchains`` |Include dummy toolchain in minimal toolchain searches [DEPRECATED, use --add-system-to-minimal-toolchains instead!] (default: False) ``--add-system-to-minimal-toolchains`` |Include system toolchain in minimal toolchain searches (default: False) ``--allow-loaded-modules=ALLOW-LOADED-MODULES`` |List of software names for which to allow loaded modules in initial environment (type comma-separated list; default: EasyBuild) @@ -297,7 +297,7 @@ Option flag |Option ``--set-default-module`` |Set the generated module as default (default: False) ``--set-gid-bit`` |Set group ID bit on newly created directories (default: False) ``--show-progress-bar`` |Show progress bar in terminal output (default: True; disable with --disable-show-progress-bar) -``--silence-deprecation-warnings=SILENCE-DEPRECATION-WARNINGS`` |Silence specified deprecation warnings (type comma-separated list) +``--silence-deprecation-warnings=SILENCE-DEPRECATION-WARNINGS`` |Silence specified deprecation warnings out of (python2, Lmod6, easyconfig, toolchain) (type comma-separated list) ``--skip-extensions`` |Skip installation of extensions (default: False) ``-t, --skip-test-cases`` |Skip running test cases (default: False) ``--skip-test-step`` |Skip running the test step (e.g. unit tests) (default: False) diff --git a/docs/version-specific/generic-easyblocks.md b/docs/version-specific/generic-easyblocks.md index 084078cf9..82542edf0 100644 --- a/docs/version-specific/generic-easyblocks.md +++ b/docs/version-specific/generic-easyblocks.md @@ -354,6 +354,7 @@ easyconfig parameter |description ``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"`` +``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 |``[]`` ``use_pip`` |Install using '%(python)s -m pip install --prefix=%(prefix)s %(installopts)s %(loc)s' |``None`` @@ -542,6 +543,7 @@ easyconfig parameter |description ``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"`` +``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 |``[]`` ``use_pip`` |Install using '%(python)s -m pip install --prefix=%(prefix)s %(installopts)s %(loc)s' |``None`` @@ -638,6 +640,7 @@ easyconfig parameter |description ``runtest`` |Run unit tests. |``True`` ``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']`` +``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 |``[]`` ``use_pip`` |Install using '%(python)s -m pip install --prefix=%(prefix)s %(installopts)s %(loc)s' |``None`` @@ -814,6 +817,7 @@ Support for building and installing software with 'meson' and 'ninja'. easyconfig parameter |description |default value ----------------------|-------------------------------------|------------- +``configure_cmd`` |Configure command to use |``"meson"`` ``separate_build_dir``|Perform build in a separate directory|``True`` ### Customised steps in ``MesonNinja`` easyblock @@ -957,6 +961,7 @@ easyconfig parameter |description ``sanity_check_components`` |List of components for which to run sanity checks |``[]`` ``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']`` +``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 |``[]`` ``use_pip`` |Install using '%(python)s -m pip install --prefix=%(prefix)s %(installopts)s %(loc)s' |``None`` @@ -989,6 +994,7 @@ easyconfig parameter |description ``runtest`` |Run unit tests. |``True`` ``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']`` +``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 |``[]`` ``use_pip`` |Install using '%(python)s -m pip install --prefix=%(prefix)s %(installopts)s %(loc)s' |``None`` @@ -1279,6 +1285,7 @@ easyconfig parameter |description ``runtest`` |Run unit tests. |``True`` ``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']`` +``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 |``[]`` ``use_pip`` |Install using '%(python)s -m pip install --prefix=%(prefix)s %(installopts)s %(loc)s' |``None`` @@ -1311,6 +1318,7 @@ easyconfig parameter |description ``runtest`` |Run unit tests. |``True`` ``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']`` +``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 |``[]`` ``use_pip`` |Install using '%(python)s -m pip install --prefix=%(prefix)s %(installopts)s %(loc)s' |``None`` diff --git a/docs/version-specific/supported-software.md b/docs/version-specific/supported-software.md index d5a1c939c..b6494c5af 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 2906 different software packages (incl. toolchains, bundles): +EasyBuild supports 2995 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) @@ -46,7 +46,7 @@ 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) - [AFNI](#afni) - [AGAT](#agat) - [AGFusion](#agfusion) - [aiohttp](#aiohttp) - [ALADIN](#aladin) - [Albacore](#albacore) - [Albumentations](#albumentations) - [alevin-fry](#alevin-fry) - [ALFA](#alfa) - [Alfred](#alfred) - [alleleCount](#allelecount) - [Allinea](#allinea) - [ALLPATHS-LG](#allpaths-lg) - [almosthere](#almosthere) - [Alpha](#alpha) - [AlphaFold](#alphafold) - [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) - [AmrPlusPlus](#amrplusplus) - [AMS](#ams) - [Anaconda2](#anaconda2) - [Anaconda3](#anaconda3) - [aNCI](#anci) - [andi](#andi) - [ANGEL](#angel) - [angsd](#angsd) - [ANIcalculator](#anicalculator) - [Annif](#annif) - [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) - [ASE](#ase) - [ASHS](#ashs) - [Aspera-CLI](#aspera-cli) - [Aspera-Connect](#aspera-connect) - [assimp](#assimp) - [Assimulo](#assimulo) - [ASTRID](#astrid) - [astropy](#astropy) - [at-spi2-atk](#at-spi2-atk) - [at-spi2-core](#at-spi2-core) - [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) - [AutoGeneS](#autogenes) - [AutoGrid](#autogrid) - [Automake](#automake) - [AutoMap](#automap) - [autopep8](#autopep8) - [Autotools](#autotools) - [Avogadro2](#avogadro2) - [awscli](#awscli) +[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) - [AFNI](#afni) - [AGAT](#agat) - [AGFusion](#agfusion) - [aiohttp](#aiohttp) - [ALADIN](#aladin) - [Albacore](#albacore) - [Albumentations](#albumentations) - [alevin-fry](#alevin-fry) - [ALFA](#alfa) - [Alfred](#alfred) - [alleleCount](#allelecount) - [Allinea](#allinea) - [ALLPATHS-LG](#allpaths-lg) - [almosthere](#almosthere) - [Alpha](#alpha) - [AlphaFold](#alphafold) - [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) - [AmrPlusPlus](#amrplusplus) - [AMS](#ams) - [Anaconda2](#anaconda2) - [Anaconda3](#anaconda3) - [aNCI](#anci) - [andi](#andi) - [ANGEL](#angel) - [angsd](#angsd) - [ANIcalculator](#anicalculator) - [Annif](#annif) - [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) - [ASE](#ase) - [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) - [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) - [AutoGeneS](#autogenes) - [AutoGrid](#autogrid) - [Automake](#automake) - [AutoMap](#automap) - [autopep8](#autopep8) - [Autotools](#autotools) - [Avogadro2](#avogadro2) - [awscli](#awscli) ### ABAQUS @@ -475,6 +475,7 @@ version |versionsuffix |toolchain ``2.1.2``|``-TensorFlow-2.5.0``|``foss/2020b``, ``fosscuda/2020b`` ``2.2.2``| |``foss/2021a`` ``2.2.2``|``-CUDA-11.3.1`` |``foss/2021a`` +``2.3.0``|``-CUDA-11.4.1`` |``foss/2021b`` ### ALPS @@ -495,9 +496,9 @@ The Advanced Linux Sound Architecture (ALSA) provides audio and MIDI functionali *homepage*: version |toolchain ----------|-------------------------------------- +---------|---------------------------------------------------------- ``1.2.4``|``GCCcore/9.3.0`` -``1.2.8``|``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``1.2.8``|``GCCcore/10.2.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ### AMAPVox @@ -735,6 +736,7 @@ version |toolchain ``2021.05``|``system`` ``2021.11``|``system`` ``2022.05``|``system`` +``2022.10``|``system`` ### aNCI @@ -779,6 +781,7 @@ version |toolchain ``0.925``|``foss/2018b`` ``0.933``|``GCC/8.3.0``, ``iccifort/2019.5.281`` ``0.935``|``GCC/10.2.0`` +``0.940``|``GCC/11.2.0`` ### ANIcalculator @@ -787,8 +790,8 @@ This tool will calculate the bidirectional average nucleotide identity (gANI) an *homepage*: version|toolchain --------|------------------ -``1.0``|``GCCcore/10.3.0`` +-------|-------------------------------------- +``1.0``|``GCCcore/10.3.0``, ``GCCcore/11.3.0`` ### Annif @@ -1096,6 +1099,7 @@ version |versionsuffix |toolchain ``0.1.2``| |``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ``0.1.3``| |``GCCcore/11.2.0`` ``0.1.4``| |``GCCcore/11.3.0`` +``0.2.0``| |``GCCcore/12.2.0`` ### ARGoS @@ -1158,6 +1162,7 @@ version |versionsuffix |toolchain ``9.900.1``| |``foss/2019b``, ``foss/2020a`` ``10.5.3`` | |``foss/2020b`` ``10.7.5`` | |``foss/2021a`` +``11.4.3`` | |``foss/2022b`` ### arosics @@ -1192,7 +1197,7 @@ version |toolchain ``3.5.0``|``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``intel/2017a``, ``intel/2017b`` ``3.6.2``|``intel/2018a`` ``3.7.0``|``foss/2019a``, ``foss/2019b``, ``foss/2020a``, ``intel/2019b``, ``intel/2020a`` -``3.8.0``|``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``foss/2022a`` +``3.8.0``|``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``foss/2022a``, ``foss/2022b`` ### ArrayFire @@ -1431,6 +1436,16 @@ version |toolchain ---------|--------------- ``2.2.1``|``gompi/2019a`` +### astro-tulips + +tulips creates diagrams of the structure and evolution of stars. It creates plots and movies based on output from the MESA stellar evolution code + +*homepage*: + +version |toolchain +---------|-------------- +``1.0.1``|``foss/2022a`` + ### astropy The Astropy Project is a community effort to develop a common core package for Astronomy in Python and foster an ecosystem of interoperable astronomy packages. The Astropy community is committed to supporting diversity and inclusion. @@ -1624,6 +1639,7 @@ version |versionsuffix |toolchain ``3.3.2``|``-Python-2.7.15``|``intel/2018b`` ``3.3.3``| |``foss/2019b``, ``intel/2019b`` ``3.4.0``| |``foss/2020a``, ``foss/2020b``, ``foss/2021a``, ``foss/2021b`` +``3.5.0``| |``foss/2022a`` ### Austin @@ -1774,7 +1790,7 @@ version |toolchain ``20200321``|``GCCcore/10.2.0`` ``20210128``|``FCC/4.5.0``, ``GCCcore/10.3.0`` ``20210726``|``GCCcore/11.2.0`` -``20220317``|``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +``20220317``|``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``system`` ### Avogadro2 @@ -1804,8 +1820,18 @@ version |versionsuffix |toolchain ## B -[BabelStream](#babelstream) - [babl](#babl) - [Bader](#bader) - [BAGEL](#bagel) - [BAli-Phy](#bali-phy) - [bam-readcount](#bam-readcount) - [Bambi](#bambi) - [bamFilters](#bamfilters) - [BAMM](#bamm) - [BamM](#bamm) - [BAMSurgeon](#bamsurgeon) - [bamtofastq](#bamtofastq) - [BamTools](#bamtools) - [BamUtil](#bamutil) - [Bandage](#bandage) - [barrnap](#barrnap) - [basemap](#basemap) - [Bash](#bash) - [bashplotlib](#bashplotlib) - [bat](#bat) - [BatMeth2](#batmeth2) - [BayesAss](#bayesass) - [BayeScan](#bayescan) - [BayeScEnv](#bayescenv) - [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) - [BDBag](#bdbag) - [Beagle](#beagle) - [beagle-lib](#beagle-lib) - [Beast](#beast) - [BeautifulSoup](#beautifulsoup) - [BEDOPS](#bedops) - [BEDTools](#bedtools) - [BEEF](#beef) - [behave](#behave) - [BerkeleyGW](#berkeleygw) - [BFAST](#bfast) - [BFC](#bfc) - [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) - [Blosc](#blosc) - [Blosc2](#blosc2) - [BLT](#blt) - [bmtagger](#bmtagger) - [bnpy](#bnpy) - [BOINC](#boinc) - [bokeh](#bokeh) - [BoltzTraP](#boltztrap) - [Bonito](#bonito) - [Bonmin](#bonmin) - [Bonnie++](#bonnie++) - [Boost](#boost) - [Boost.MPI](#boost.mpi) - [Boost.Python](#boost.python) - [boost_histogram](#boost_histogram) - [boto3](#boto3) - [Bottleneck](#bottleneck) - [Bowtie](#bowtie) - [Bowtie2](#bowtie2) - [Bpipe](#bpipe) - [bpp](#bpp) - [bpytop](#bpytop) - [Bracken](#bracken) - [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) - [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) - [BAMSurgeon](#bamsurgeon) - [bamtofastq](#bamtofastq) - [BamTools](#bamtools) - [BamUtil](#bamutil) - [Bandage](#bandage) - [barrnap](#barrnap) - [basemap](#basemap) - [Bash](#bash) - [bashplotlib](#bashplotlib) - [bat](#bat) - [BatMeth2](#batmeth2) - [BayesAss](#bayesass) - [BayesAss3-SNPs](#bayesass3-snps) - [BayeScan](#bayescan) - [BayeScEnv](#bayescenv) - [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) - [BDBag](#bdbag) - [Beagle](#beagle) - [beagle-lib](#beagle-lib) - [Beast](#beast) - [BeautifulSoup](#beautifulsoup) - [BEDOPS](#bedops) - [BEDTools](#bedtools) - [BEEF](#beef) - [behave](#behave) - [BerkeleyGW](#berkeleygw) - [BFAST](#bfast) - [BFC](#bfc) - [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) - [Bonito](#bonito) - [Bonmin](#bonmin) - [Bonnie++](#bonnie++) - [Boost](#boost) - [Boost.MPI](#boost.mpi) - [Boost.Python](#boost.python) - [boost_histogram](#boost_histogram) - [boto3](#boto3) - [Bottleneck](#bottleneck) - [Bowtie](#bowtie) - [Bowtie2](#bowtie2) - [Bpipe](#bpipe) - [bpp](#bpp) - [bpytop](#bpytop) - [Bracken](#bracken) - [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) - [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 +This program will automatically tune mixing parameters for BA3-SNPs by implementing a binary search algorithm and conducting short exploratory runs of BA3-SNPS. + +*homepage*: + +version |toolchain +---------|-------------- +``2.1.2``|``GCC/11.3.0`` ### BabelStream @@ -1889,27 +1915,6 @@ version |toolchain --------------|-------------- ``2022-06-30``|``GCC/11.3.0`` -### BAMM - -BAMM is oriented entirely towards detecting and quantifying heterogeneity in evolutionary rates. It uses reversible jump Markov chain Monte Carlo to automatically explore a vast universe of candidate models of lineage diversification and trait evolution. - -*homepage*: - -version |toolchain ----------|-------------- -``2.5.0``|``foss/2016b`` - -### BamM - -BamM is a c library, wrapped in python, that parses BAM files - -*homepage*: - -version |versionsuffix |toolchain ----------|------------------|-------------- -``1.7.3``|``-Python-2.7.12``|``foss/2016b`` -``1.7.3``|``-Python-2.7.14``|``foss/2018a`` - ### BAMSurgeon Tools for adding mutations to existing .bam files, used for testing mutation callers @@ -2042,6 +2047,16 @@ version |toolchain ---------|-------------- ``3.0.4``|``foss/2016a`` +### BayesAss3-SNPs + +Modification of BayesAss 3.0.4 to allow handling of large SNP datasets generated via methods such as RADseq protocols. + +*homepage*: + +version|toolchain +-------|-------------- +``1.1``|``GCC/11.3.0`` + ### BayeScan BayeScan aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. @@ -2173,6 +2188,7 @@ version |versionsuffix |toolchain ---------|-----------------|-------------- ``0.6.6``|``-Python-3.8.2``|``foss/2020a`` ``0.6.7``| |``foss/2021a`` +``0.7.0``| |``foss/2022a`` ### BCEL @@ -2203,6 +2219,7 @@ version |toolchain ``1.12`` |``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/9.3.0`` ``1.14`` |``GCC/11.2.0`` ``1.15.1``|``GCC/11.3.0`` +``1.17`` |``GCC/12.2.0`` ### bcgTree @@ -2232,9 +2249,9 @@ bcl2fastq Conversion Software both demultiplexes data and converts BCL files gen *homepage*: version |versionsuffix |toolchain -----------|------------------|------------------------------------------------------------------------------------------------------------- +----------|------------------|----------------------------------------------------------------------------------------------------------------------------- ``2.19.1``|``-Python-2.7.12``|``foss/2016b`` -``2.20.0``| |``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``foss/2018b``, ``intel/2019a`` +``2.20.0``| |``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``foss/2018b``, ``intel/2019a`` ``2.20.0``|``-Python-2.7.12``|``foss/2016b`` ``2.20.0``|``-Python-2.7.14``|``intel/2017b`` @@ -2285,12 +2302,13 @@ version |versionsuffix |toolchain ``3.0.2``| |``foss/2018b`` ``3.0.2``|``-CUDA-9.2.88``|``foss/2018b`` ``3.1.2``| |``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/8.2.0-2.31.1``, ``GCC/9.3.0``, ``gcccuda/2019b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` +``4.0.0``| |``GCC/11.3.0`` ### Beast BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. -*homepage*: +*homepage*: version |toolchain ----------|------------------------------------ @@ -2305,6 +2323,7 @@ version |toolchain ``2.6.3`` |``gcccuda/2019b`` ``2.6.4`` |``GCC/10.2.0`` ``2.6.7`` |``GCC/10.3.0`` +``2.7.3`` |``GCC/11.3.0`` ### BeautifulSoup @@ -2322,6 +2341,7 @@ version |versionsuffix |toolchain ``4.9.1`` |``-Python-3.8.2``|``GCCcore/9.3.0`` ``4.9.3`` | |``GCCcore/10.2.0`` ``4.10.0``| |``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``4.11.1``| |``GCCcore/12.2.0`` ### BEDOPS @@ -2538,8 +2558,8 @@ Code to parse output from hmmsearch, hmmscan, phmmer and nhmmer, compatible with *homepage*: version |toolchain ----------|------------------------------ -``1.7.3``|``GCC/10.2.0``, ``GCC/10.3.0`` +---------|---------------------------------------------- +``1.7.3``|``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0`` ### bioawk @@ -2654,6 +2674,7 @@ version |versionsuffix |toolchain ``1.78``| |``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` ``1.78``|``-Python-3.8.2`` |``foss/2020a``, ``intel/2020a`` ``1.79``| |``foss/2021a``, ``foss/2021b``, ``foss/2022a``, ``intel/2021b`` +``1.81``| |``foss/2022b`` ### BioServices @@ -2802,13 +2823,14 @@ version |versionsuffix |toolchain ### BLAT -BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more. +BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more. -*homepage*: +*homepage*: 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/11.3.0`` ### Blender @@ -2827,6 +2849,7 @@ version |versionsuffix |toolchain ``3.1.2``|``-linux-x64`` |``system`` ``3.2.2``|``-linux-x64`` |``system`` ``3.3.1``|``-linux-x86_64-CUDA-11.7.0``|``system`` +``3.4.1``|``-linux-x86_64-CUDA-11.7.0``|``system`` ### BLIS @@ -2854,9 +2877,9 @@ Blitz++ is a (LGPLv3+) licensed meta-template library for array manipulation in *homepage*: version |toolchain ----------|--------------------------------------------------------- +---------|----------------------------------------------------------------------------- ``0.10`` |``GCCcore/6.4.0``, ``foss/2016a`` -``1.0.2``|``GCCcore/10.2.0``, ``GCCcore/11.3.0``, ``GCCcore/9.3.0`` +``1.0.2``|``GCCcore/10.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/9.3.0`` ### BlobTools @@ -2868,6 +2891,16 @@ version |versionsuffix |toolchain ------------|------------------|-------------- ``20180528``|``-Python-2.7.15``|``foss/2018b`` +### Block + +Block implements the density matrix renormalization group (DMRG) algorithm for quantum chemistry. + +*homepage*: + +version |toolchain +------------------|-------------- +``1.5.3-20200525``|``foss/2022a`` + ### Blosc Blosc, an extremely fast, multi-threaded, meta-compressor library @@ -2897,6 +2930,7 @@ version |toolchain ``2.0.3``|``GCCcore/10.2.0`` ``2.0.4``|``GCCcore/10.3.0`` ``2.4.3``|``GCCcore/11.3.0`` +``2.6.1``|``GCCcore/11.3.0`` ### BLT @@ -3061,6 +3095,7 @@ version |versionsuffix |toolchain ``1.76.0``| |``GCC/10.3.0``, ``intel-compilers/2021.2.0`` ``1.77.0``| |``GCC/11.2.0``, ``intel-compilers/2021.4.0`` ``1.79.0``| |``GCC/11.2.0``, ``GCC/11.3.0`` +``1.81.0``| |``GCC/12.2.0`` ### Boost.MPI @@ -3126,6 +3161,7 @@ version |versionsuffix |toolchain ---------|-----------------|--------------- ``1.2.1``|``-Python-3.6.4``|``intel/2018a`` ``1.3.2``|``-Python-3.8.2``|``foss/2020a`` +``1.3.6``| |``foss/2022a`` ### Bowtie @@ -3140,7 +3176,7 @@ 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`` +``1.3.1`` |``GCC/11.2.0``, ``GCC/11.3.0`` ### Bowtie2 @@ -3215,10 +3251,10 @@ BRAKER is a pipeline for fully automated prediction of protein coding genes with *homepage*: version |versionsuffix |toolchain ----------|-----------------|--------------- +---------|-----------------|------------------------------ ``2.1.2``| |``intel/2019a`` ``2.1.5``|``-Python-3.7.4``|``intel/2019b`` -``2.1.6``| |``foss/2021b`` +``2.1.6``| |``foss/2021b``, ``foss/2022a`` ### BreakDancer @@ -3259,8 +3295,8 @@ Brotli is a generic-purpose lossless compression algorithm that compresses data *homepage*: version |toolchain ----------|------------------ -``1.0.9``|``GCCcore/10.3.0`` +---------|------------------------------------------------------------------------------ +``1.0.9``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ### Brunsli @@ -3269,8 +3305,8 @@ Brunsli is a lossless JPEG repacking library. *homepage*: version|toolchain --------|-------------------------------------- -``0.1``|``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +-------|------------------------------------------------------------------------------ +``0.1``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ### bsddb3 @@ -3385,6 +3421,7 @@ version |versionsuffix |toolchain ``5.1.2``| |``foss/2020b`` ``5.4.2``| |``foss/2021a`` ``5.4.3``| |``foss/2021b`` +``5.4.5``| |``foss/2022a`` ### BUStools @@ -3469,6 +3506,7 @@ version |versionsuffix |toolchain ``0.8.9`` |``-Python-3.8.2`` |``foss/2020a`` ``0.8.11``| |``foss/2021a`` ``0.8.13``| |``foss/2021b`` +``0.9.0`` | |``foss/2022a`` ### BXH_XCEDE_TOOLS @@ -3516,7 +3554,7 @@ version |toolchain ## C -[c-ares](#c-ares) - [C3D](#c3d) - [cadaver](#cadaver) - [CaDiCaL](#cadical) - [CAFE5](#cafe5) - [Caffe](#caffe) - [cairo](#cairo) - [cairomm](#cairomm) - [Calcam](#calcam) - [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) - [CaSpER](#casper) - [CASTEP](#castep) - [CastXML](#castxml) - [CAT-BAT](#cat-bat) - [Catch2](#catch2) - [category_encoders](#category_encoders) - [CatMAP](#catmap) - [causallift](#causallift) - [causalml](#causalml) - [CaVEMan](#caveman) - [CAVIAR](#caviar) - [Cbc](#cbc) - [CBLAS](#cblas) - [ccache](#ccache) - [CCfits](#ccfits) - [CCL](#ccl) - [cclib](#cclib) - [cctools](#cctools) - [CD-HIT](#cd-hit) - [CDAT](#cdat) - [cdbfasta](#cdbfasta) - [CDBtools](#cdbtools) - [cddlib](#cddlib) - [cDNA_Cupcake](#cdna_cupcake) - [CDO](#cdo) - [cdo-bindings](#cdo-bindings) - [cdsapi](#cdsapi) - [cell2location](#cell2location) - [CellMix](#cellmix) - [CellRanger](#cellranger) - [CellRanger-ARC](#cellranger-arc) - [CellRanger-ATAC](#cellranger-atac) - [CellRank](#cellrank) - [CellTypist](#celltypist) - [Centrifuge](#centrifuge) - [Cereal](#cereal) - [CESM-deps](#cesm-deps) - [CFDEMcoupling](#cfdemcoupling) - [CFITSIO](#cfitsio) - [cftime](#cftime) - [CGAL](#cgal) - [cget](#cget) - [Cgl](#cgl) - [CGmapTools](#cgmaptools) - [CGNS](#cgns) - [CharLS](#charls) - [CHARMM](#charmm) - [charmm](#charmm) - [CHASE](#chase) - [Check](#check) - [check](#check) - [CheckM](#checkm) - [Cheetah](#cheetah) - [Chemaxon-Marvin](#chemaxon-marvin) - [CheMPS2](#chemps2) - [CHERAB](#cherab) - [chewBBACA](#chewbbaca) - [chi2comb](#chi2comb) - [Chimera](#chimera) - [ChimPipe](#chimpipe) - [Chromaprint](#chromaprint) - [cicero](#cicero) - [CIF2Cell](#cif2cell) - [CIRCexplorer](#circexplorer) - [CIRCexplorer2](#circexplorer2) - [Circos](#circos) - [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) - [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) - [Cogent](#cogent) - [Coin](#coin) - [CoinUtils](#coinutils) - [colossalai](#colossalai) - [Commet](#commet) - [CompareM](#comparem) - [Compress-Raw-Zlib](#compress-raw-zlib) - [COMSOL](#comsol) - [Con3F](#con3f) - [CONCOCT](#concoct) - [configparser](#configparser) - [configurable-http-proxy](#configurable-http-proxy) - [CONN](#conn) - [ConnectomeWorkbench](#connectomeworkbench) - [Control-FREEC](#control-freec) - [CoordgenLibs](#coordgenlibs) - [Coot](#coot) - [core-counter](#core-counter) - [Coreutils](#coreutils) - [corner](#corner) - [CoSymLib](#cosymlib) - [coverage](#coverage) - [cowsay](#cowsay) - [CP2K](#cp2k) - [CPB](#cpb) - [CPLEX](#cplex) - [CPPE](#cppe) - [CppUnit](#cppunit) - [cppy](#cppy) - [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) - [CrossMap](#crossmap) - [CrossTalkZ](#crosstalkz) - [CRPropa](#crpropa) - [Crumble](#crumble) - [cryoCARE](#cryocare) - [cryoDRGN](#cryodrgn) - [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) - [CUDA](#cuda) - [CUDA-Samples](#cuda-samples) - [CUDAcompat](#cudacompat) - [CUDAcore](#cudacore) - [cuDNN](#cudnn) - [Cufflinks](#cufflinks) - [CUnit](#cunit) - [CuPy](#cupy) - [cURL](#curl) - [custodian](#custodian) - [cutadapt](#cutadapt) - [cuTENSOR](#cutensor) - [CVS](#cvs) - [CVXOPT](#cvxopt) - [CVXPY](#cvxpy) - [CWIPI](#cwipi) - [cwltool](#cwltool) - [cxxopts](#cxxopts) - [cysignals](#cysignals) - [Cython](#cython) - [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) - [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) - [CaSpER](#casper) - [CASTEP](#castep) - [CastXML](#castxml) - [CAT-BAT](#cat-bat) - [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) - [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) - [CellMix](#cellmix) - [Cellpose](#cellpose) - [CellRanger](#cellranger) - [CellRanger-ARC](#cellranger-arc) - [CellRanger-ATAC](#cellranger-atac) - [CellRank](#cellrank) - [CellTypist](#celltypist) - [Centrifuge](#centrifuge) - [Cereal](#cereal) - [CESM-deps](#cesm-deps) - [CFDEMcoupling](#cfdemcoupling) - [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) - [Chromaprint](#chromaprint) - [cicero](#cicero) - [CIF2Cell](#cif2cell) - [cimfomfa](#cimfomfa) - [CIRCexplorer](#circexplorer) - [CIRCexplorer2](#circexplorer2) - [Circos](#circos) - [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) - [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) - [Cogent](#cogent) - [Coin](#coin) - [CoinUtils](#coinutils) - [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) - [ConnectomeWorkbench](#connectomeworkbench) - [Control-FREEC](#control-freec) - [cooler](#cooler) - [CoordgenLibs](#coordgenlibs) - [Coot](#coot) - [core-counter](#core-counter) - [Coreutils](#coreutils) - [corner](#corner) - [CoSymLib](#cosymlib) - [coverage](#coverage) - [cowsay](#cowsay) - [CP2K](#cp2k) - [CPB](#cpb) - [CPLEX](#cplex) - [CPPE](#cppe) - [CppUnit](#cppunit) - [cppy](#cppy) - [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) - [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) - [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) - [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 @@ -3673,7 +3711,7 @@ Canu is a fork of the Celera Assembler designed for high-noise single-molecule s *homepage*: version |versionsuffix |toolchain ----------|----------------|-------------------------------------- +---------|----------------|---------------------------------------------------------- ``1.4`` | |``foss/2016b`` ``1.7`` | |``intel/2018a`` ``1.8`` |``-Perl-5.26.0``|``foss/2017b``, ``intel/2017b`` @@ -3682,7 +3720,7 @@ version |versionsuffix |toolchain ``1.9`` |``-Java-11`` |``GCCcore/8.3.0`` ``2.1.1``| |``GCCcore/10.2.0`` ``2.1.1``|``-Java-11`` |``GCCcore/9.3.0`` -``2.2`` | |``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``2.2`` | |``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ``2.2`` |``-Java-11`` |``GCCcore/10.3.0`` ### Canvas @@ -3841,15 +3879,26 @@ version |toolchain ---------|-------------- ``2.4.1``|``foss/2021b`` +### CatLearn + +An environment for atomistic machine learning in Python for applications in catalysis + +*homepage*: + +version |toolchain +---------|--------------- +``0.6.2``|``intel/2022a`` + ### CatMAP Catalyst Micro-kinetic Analysis Package for automated creation of micro-kinetic models used in catalyst screening. -*homepage*: +*homepage*: version |versionsuffix |toolchain ------------|------------------|--------------- ``20170927``|``-Python-2.7.14``|``intel/2017b`` +``20220519``| |``foss/2022a`` ### causallift @@ -3981,11 +4030,11 @@ CD-HIT is a very widely used program for clustering and comparing protein or nu *homepage*: version |versionsuffix |toolchain ----------|--------------|--------------------------------------------------------------------------------------------------------------------- +---------|--------------|------------------------------------------------------------------------------------------------------------------------------------- ``4.6.4``|``-2015-0603``|``GNU/4.9.3-2.25`` ``4.6.6``| |``foss/2016b`` ``4.6.8``| |``foss/2018b``, ``intel/2017a``, ``intel/2018a`` -``4.8.1``| |``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``foss/2018b``, ``iccifort/2019.5.281`` +``4.8.1``| |``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``foss/2018b``, ``iccifort/2019.5.281`` ### CDAT @@ -4028,6 +4077,16 @@ version |toolchain ``0.94i``|``GCCcore/8.2.0`` ``0.94j``|``GCCcore/8.3.0`` +### CDFlib + +cdflib is a python module to read/write CDF (Common Data Format .cdf) files without needing to install the CDF NASA library. + +*homepage*: + +version |toolchain +---------|-------------- +``0.4.9``|``foss/2022a`` + ### cDNA_Cupcake cDNA_Cupcake is a miscellaneous collection of Python and R scripts used for analyzing sequencing data. @@ -4102,6 +4161,16 @@ version |versionsuffix|toolchain ---------|-------------|-------------- ``1.6.2``|``-R-3.5.1`` |``foss/2018b`` +### Cellpose + +a generalist algorithm for cellular segmentation + +*homepage*: + +version |toolchain +---------|---------------------------------- +``0.6.5``|``foss/2020b``, ``fosscuda/2020b`` + ### CellRanger Cell Ranger is a set of analysis pipelines that process Chromium single-cell RNA-seq output to align reads, generate gene-cell matrices and perform clustering and gene expression analysis. @@ -4121,6 +4190,7 @@ version |toolchain ``6.0.2``|``system`` ``6.1.2``|``system`` ``7.0.0``|``system`` +``7.1.0``|``system`` ### CellRanger-ARC @@ -4187,6 +4257,7 @@ cereal is a header-only C++11 serialization library. cereal takes arbitrary data version |toolchain ---------|---------- ``1.3.0``|``system`` +``1.3.2``|``system`` ### CESM-deps @@ -4214,15 +4285,16 @@ CFITSIO is a library of C and Fortran subroutines for reading and writing data f *homepage*: -version |toolchain ---------|---------------------------------------------------------- -``3.38``|``foss/2016a``, ``intel/2016a`` -``3.41``|``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``intel/2016b`` -``3.42``|``GCCcore/6.4.0``, ``intel/2017b`` -``3.45``|``GCCcore/7.3.0``, ``intel/2018b`` -``3.47``|``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``3.48``|``GCCcore/9.3.0`` -``3.49``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +version |toolchain +---------|---------------------------------------------------------- +``3.38`` |``foss/2016a``, ``intel/2016a`` +``3.41`` |``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``intel/2016b`` +``3.42`` |``GCCcore/6.4.0``, ``intel/2017b`` +``3.45`` |``GCCcore/7.3.0``, ``intel/2018b`` +``3.47`` |``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``3.48`` |``GCCcore/9.3.0`` +``3.49`` |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``4.2.0``|``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ### cftime @@ -4319,26 +4391,6 @@ version |toolchain ``2.3.4``|``GCCcore/10.3.0`` ``2.4.1``|``GCCcore/11.3.0`` -### CHARMM - -CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a versatile and widely used molecular simulation program with broad application to many-particle systems. - -*homepage*: - -version |toolchain ---------|------------------------------- -``37b2``|``foss/2016a``, ``intel/2016a`` - -### charmm - -CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a versatile and widely used molecular simulation program with broad application to many-particle systems. charmm provides all the functionality of CHARMM except its performance enhancements. - -*homepage*: - -version |toolchain ---------|------------------------------- -``43b2``|``foss/2017b``, ``intel/2017b`` - ### CHASE Case-control HAplotype Sharing analyses. Haplotype sharing analyses for genome-wide association studies. @@ -4357,17 +4409,8 @@ Check is a unit testing framework for C. It features a simple interface for defi version |toolchain ----------|----------------------------------------------------------------------------- -``0.15.2``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` - -### check - -Check is a unit testing framework for C. It features a simple interface for defining unit tests, putting little in the way of the developer. Tests are run in a separate address space, so both assertion failures and code errors that cause segmentation faults or other signals can be caught. Test results are reportable in the following: Subunit, TAP, XML, and a generic logging format. - -*homepage*: - -version |toolchain -----------|----------------- ``0.12.0``|``GCCcore/6.4.0`` +``0.15.2``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` ### CheckM @@ -4385,6 +4428,17 @@ version |versionsuffix |toolchain ``1.1.2`` |``-Python-3.7.4`` |``foss/2019b``, ``intel/2019b`` ``1.1.3`` | |``foss/2021a``, ``foss/2021b`` ``1.1.3`` |``-Python-3.8.2`` |``intel/2020a`` +``1.2.2`` | |``foss/2022a`` + +### CheckM-Database + +CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. This is the corresponding database. + +*homepage*: + +version |toolchain +--------------|---------- +``2015_01_16``|``system`` ### Cheetah @@ -4406,6 +4460,17 @@ version |toolchain ---------|---------- ``21.14``|``system`` +### chemprop + +Message Passing Neural Networks for Molecule Property Prediction + +*homepage*: + +version |versionsuffix |toolchain +---------|----------------|-------------- +``1.5.2``| |``foss/2022a`` +``1.5.2``|``-CUDA-11.7.0``|``foss/2022a`` + ### CheMPS2 CheMPS2 is a scientific library which contains a spin-adapted implementation of the density matrix renormalization group (DMRG) for ab initio quantum chemistry. @@ -4507,6 +4572,16 @@ version |versionsuffix |toolchain ----------|------------------|----------------- ``1.2.10``|``-Python-2.7.16``|``GCCcore/8.3.0`` +### cimfomfa + +This library supports both MCL, a cluster algorithm for graphs, and zoem, a macro/DSL language. It supplies abstractions for memory management, I/O, associative arrays, strings, heaps, and a few other things. The string library has had heavy testing as part of zoem. Both understandably and regrettably I chose long ago to make it C-string-compatible, hence nul bytes may not be part of a string. At some point I hope to rectify this, perhaps unrealistically. + +*homepage*: + +version |toolchain +----------|------------------ +``22.273``|``GCCcore/11.3.0`` + ### CIRCexplorer CIRCexplorer2 is a comprehensive and integrative circular RNA analysis toolset. @@ -4957,6 +5032,7 @@ Run VS Code on any machine anywhere and access it in the browser. version |toolchain ---------|---------- ``3.7.3``|``system`` +``4.9.1``|``system`` ### CODEX2 @@ -5061,6 +5137,16 @@ version |versionsuffix |toolchain ----------------|-----------------|--------------- ``1.0-20190329``|``-Python-3.7.2``|``intel/2019a`` +### conan + +Decentralized, open-source (MIT), C/C++ package manager. + +*homepage*: + +version |toolchain +----------|------------------ +``1.58.0``|``GCCcore/11.3.0`` + ### CONCOCT Clustering cONtigs with COverage and ComposiTion (CONCOCT) is a program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads. @@ -5100,6 +5186,7 @@ version |versionsuffix |toolchain ``3.1.1``|``-nodejs-8.9.4``|``foss/2017a`` ``4.2.1``| |``GCCcore/10.2.0`` ``4.4.0``| |``GCCcore/10.3.0`` +``4.5.3``| |``GCCcore/11.3.0`` ### CONN @@ -5135,6 +5222,16 @@ version |toolchain ``11.5``|``GCC/7.3.0-2.30``, ``GCC/8.2.0-2.31.1`` ``11.6``|``GCC/10.2.0`` +### cooler + +Cooler is a support library for a storage format, also called cooler, used to store genomic interaction data of any size, such as Hi-C contact matrices. + +*homepage*: + +version |toolchain +---------|-------------- +``0.9.1``|``foss/2022a`` + ### CoordgenLibs Schrodinger-developed 2D Coordinate Generation @@ -5292,7 +5389,7 @@ A small C++ header library which makes it easier to write Python extension modul version |toolchain ---------|-------------------------------------- ``1.1.0``|``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``1.2.1``|``GCCcore/11.3.0`` +``1.2.1``|``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ### cpu_features @@ -5428,6 +5525,16 @@ version|versionsuffix|toolchain -------|-------------|---------- ``56`` |``-Java-11`` |``system`` +### crossguid + +CrossGuid is a minimal, cross platform, C++ GUID library. It uses the best native GUID/UUID generator on the given platform and has a generic class for parsing, stringifying, and comparing IDs. The guid generation technique is determined by your platform: + +*homepage*: + +version |toolchain +------------|------------------ +``20190529``|``GCCcore/11.3.0`` + ### CrossMap CrossMap is a program for genome coordinates conversion between different assemblies (such as hg18 (NCBI36) <=> hg19 (GRCh37)). It supports commonly used file formats including BAM, CRAM, SAM, Wiggle, BigWig, BED, GFF, GTF and VCF. @@ -5558,9 +5665,10 @@ csvkit is a suite of command-line tools for converting to and working with CSV, *homepage*: version |versionsuffix |toolchain ----------|-----------------|----------------- +---------|-----------------|------------------ ``1.0.4``| |``GCCcore/8.2.0`` ``1.0.5``|``-Python-3.7.4``|``GCCcore/8.3.0`` +``1.1.0``| |``GCCcore/11.3.0`` ### ctags @@ -5626,7 +5734,7 @@ version |toolchain ---------|------------------------------------------------------- ``4.4.4``|``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``4.6`` |``GCCcore/10.2.0``, ``GCCcore/10.3.0`` -``4.8`` |``GCCcore/11.3.0`` +``4.8`` |``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ### CubeWriter @@ -5638,7 +5746,7 @@ version |toolchain ---------|--------------------------------------------------------------------------- ``4.4.3``|``GCCcore/10.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``4.6`` |``GCCcore/10.2.0``, ``GCCcore/10.3.0`` -``4.8`` |``GCCcore/11.3.0`` +``4.8`` |``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ### CUDA @@ -5676,6 +5784,7 @@ version |toolchain ``11.7.0`` |``system`` ``11.8.0`` |``system`` ``12.0.0`` |``system`` +``12.1.0`` |``system`` ### CUDA-Samples @@ -5757,6 +5866,7 @@ version |versionsuffix |toolchain ``8.4.1.50`` |``-CUDA-11.7.0`` |``system`` ``8.6.0.163``|``-CUDA-11.8.0`` |``system`` ``8.7.0.84`` |``-CUDA-11.8.0`` |``system`` +``8.8.0.121``|``-CUDA-12.0.0`` |``system`` ### Cufflinks @@ -5823,6 +5933,16 @@ version |toolchain ``7.84.0``|``GCCcore/12.1.0`` ``7.86.0``|``GCCcore/12.2.0`` +### cuSPARSELt + +NVIDIA cuSPARSELt is a high-performance CUDA library dedicated to general matrix-matrix operations in which at least one operand is a sparse matrix + +*homepage*: + +version |versionsuffix |toolchain +-----------|----------------|---------- +``0.3.0.3``|``-CUDA-11.4.1``|``system`` + ### custodian A simple JIT job management framework in Python. @@ -5872,6 +5992,7 @@ version |versionsuffix |toolchain ``1.2.2.5``| |``gcccuda/2019b`` ``1.2.2.5``|``-CUDA-11.1.1``|``system`` ``1.6.0.3``|``-CUDA-11.3.1``|``system`` +``1.6.1.5``|``-CUDA-11.4.1``|``system`` ``1.6.1.5``|``-CUDA-11.7.0``|``system`` ### CVS @@ -5928,6 +6049,7 @@ Common workflow language (CWL) reference implementation. version |toolchain ----------------------|-------------- +``3.1.20221008225030``|``foss/2021a`` ``3.1.20221018083734``|``foss/2021a`` ### cxxopts @@ -5967,8 +6089,19 @@ version |versionsuffix |toolchain ``0.29.10``|``-Python-2.7.14``|``foss/2017b``, ``intel/2017b`` ``0.29.10``|``-Python-3.6.3`` |``foss/2017b``, ``intel/2017b`` ``0.29.22``| |``GCCcore/10.2.0`` +``0.29.33``| |``GCCcore/11.3.0`` ``3.0a5`` | |``GCCcore/10.2.0`` +### cython-blis + +Fast BLAS-like operations from Python and Cython, without the tears. Provides the Blis linear algebra routines as a self-contained Python C-extension. + +*homepage*: + +version |toolchain +---------|-------------- +``0.9.1``|``foss/2022a`` + ### cytoolz Cython implementation of the toolz package, which provides high performance utility functions for iterables, functions, and dictionaries. @@ -6014,7 +6147,7 @@ version |versionsuffix |toolchain ## D -[dadi](#dadi) - [dagitty](#dagitty) - [Dakota](#dakota) - [Dalton](#dalton) - [damageproto](#damageproto) - [dammit](#dammit) - [DANPOS2](#danpos2) - [DAS_Tool](#das_tool) - [dask](#dask) - [datamash](#datamash) - [davix](#davix) - [DB](#db) - [DB_File](#db_file) - [DBD-mysql](#dbd-mysql) - [DBG2OLC](#dbg2olc) - [DBus](#dbus) - [dbus-glib](#dbus-glib) - [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) - [Delly](#delly) - [DeMixT](#demixt) - [DendroPy](#dendropy) - [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) - [DIAMOND](#diamond) - [Dice](#dice) - [dicom2nifti](#dicom2nifti) - [DicomBrowser](#dicombrowser) - [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) - [dm-reverb](#dm-reverb) - [dm-tree](#dm-tree) - [DMCfun](#dmcfun) - [DMTCP](#dmtcp) - [DOLFIN](#dolfin) - [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) - [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) - [dxpy](#dxpy) - [DyMat](#dymat) +[dadi](#dadi) - [dagitty](#dagitty) - [Dakota](#dakota) - [Dalton](#dalton) - [damageproto](#damageproto) - [dammit](#dammit) - [DANPOS2](#danpos2) - [DAS_Tool](#das_tool) - [dask](#dask) - [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) - [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) - [DIAMOND](#diamond) - [Dice](#dice) - [dicom2nifti](#dicom2nifti) - [DicomBrowser](#dicombrowser) - [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-reverb](#dm-reverb) - [dm-tree](#dm-tree) - [DMCfun](#dmcfun) - [DMLC-Core](#dmlc-core) - [DMTCP](#dmtcp) - [DOLFIN](#dolfin) - [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) - [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) - [dxpy](#dxpy) - [DyMat](#dymat) ### dadi @@ -6184,6 +6317,16 @@ version |versionsuffix |toolchain ``1.857``| |``GCCcore/11.2.0`` ``1.858``| |``GCCcore/11.3.0`` +### DBCSR + +DBCSR stands for Distributed Blocked Compressed Sparse Row. DBCSR is a library designed to efficiently perform sparse matrix-matrix multiplication, among other operations. + +*homepage*: + +version |toolchain +---------|-------------- +``2.5.0``|``foss/2021b`` + ### DBD-mysql Perl binding for MySQL @@ -6245,6 +6388,16 @@ version |toolchain ``0.110``|``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``intel/2017b`` ``0.112``|``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +### dclone + +Low level functions for implementing maximum likelihood estimating procedures for complex models using data cloning and Bayesian Markov chain Monte Carlo methods + +*homepage*: + +version |versionsuffix|toolchain +---------|-------------|-------------- +``2.3-0``|``-R-4.2.1`` |``foss/2022a`` + ### dcm2niix dcm2niix is designed to convert neuroimaging data from the DICOM format to the NIfTI format. @@ -6440,6 +6593,26 @@ version |versionsuffix |toolchain ``4.5.2``| |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ``4.5.2``|``-Python-2.7.18``|``GCCcore/10.2.0`` +### DensPart + +Atoms-in-molecules density partitioning schemes based on stockholder recipe + +*homepage*: + +version |toolchain +------------|--------------- +``20220603``|``intel/2022a`` + +### Deprecated + +If you need to mark a function or a method as deprecated, you can use the @deprecated decorator. + +*homepage*: + +version |toolchain +----------|-------------- +``1.2.13``|``foss/2022a`` + ### destiny R packages to create and plot diffusion maps. @@ -6496,11 +6669,11 @@ version |versionsuffix |toolchain DFT-D3 implements a dispersion correction for density functionals, Hartree-Fock and semi-empirical quantum chemical methods. -*homepage*: +*homepage*: version |toolchain ----------|------------------------------------------------------------------------------------- -``3.2.0``|``GCC/8.3.0``, ``iccifort/2020.4.304``, ``intel-compilers/2021.2.0``, ``intel/2019a`` +---------|------------------------------------------------------------------------------------------------------------------- +``3.2.0``|``GCC/8.3.0``, ``iccifort/2020.4.304``, ``intel-compilers/2021.2.0``, ``intel-compilers/2021.4.0``, ``intel/2019a`` ### DFT-D4 @@ -6545,6 +6718,7 @@ DGL is an easy-to-use, high performance and scalable Python package for deep lea version |versionsuffix |toolchain ---------|-------------------------------|------------------ ``0.6.1``|``-Python-3.7.4-PyTorch-1.8.1``|``fosscuda/2019b`` +``0.9.1``|``-CUDA-11.3.1`` |``foss/2021a`` ### DIAL @@ -6573,6 +6747,7 @@ version |toolchain ``2.0.7`` |``GCC/10.2.0`` ``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`` ### Dice @@ -6636,6 +6811,7 @@ version |toolchain ``0.3.0``|``GCCcore/8.2.0`` ``0.3.3``|``GCCcore/10.2.0``, ``GCCcore/8.3.0`` ``0.3.4``|``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``0.3.6``|``GCCcore/11.3.0`` ### DIRAC @@ -6648,6 +6824,9 @@ 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/2022b``, ``intel/2022b`` +``23.0``|``-int64`` |``intel/2022b`` ### distributed @@ -6714,6 +6893,16 @@ version |versionsuffix |toolchain ``19.22``| |``foss/2021a`` ``19.22``|``-CUDA-11.3.1``|``foss/2021a`` +### DLPack + +DLPack is a stable in-memory data structure for an ndarray system to interact with a variety of frameworks. + +*homepage*: + +version|toolchain +-------|-------------- +``0.3``|``GCC/10.3.0`` + ### dm-reverb Reverb is an efficient and easy-to-use data storage and transport system designed for machine learning research. Reverb is primarily used as an experience replay system for distributed reinforcement learning algorithms but the system also supports multiple data structure representations such as FIFO, LIFO, and priority queues. @@ -6736,6 +6925,7 @@ version |toolchain ``0.1.1``|``GCCcore/8.3.0`` ``0.1.5``|``GCCcore/10.2.0`` ``0.1.6``|``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``0.1.8``|``GCCcore/11.3.0`` ### DMCfun @@ -6747,6 +6937,16 @@ version |versionsuffix|toolchain ---------|-------------|-------------- ``1.3.0``|``-R-3.6.2`` |``foss/2019b`` +### DMLC-Core + +DMLC-Core is the backbone library to support all DMLC projects, offers the bricks to build efficient and scalable distributed machine learning libraries. + +*homepage*: + +version|toolchain +-------|-------------- +``0.5``|``GCC/10.3.0`` + ### DMTCP DMTCP is a tool to transparently checkpoint the state of multiple simultaneous applications, including multi-threaded and distributed applications. It operates directly on the user binary executable, without any Linux kernel modules or other kernel modifications. @@ -6772,6 +6972,16 @@ version |versionsuffix |toolchain ``2018.1.0.post1``|``-Python-3.6.4``|``foss/2018a`` ``2019.1.0.post0``|``-Python-3.7.4``|``foss/2019b`` +### dorado + +Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads. + +*homepage*: + +version |versionsuffix |toolchain +---------|----------------|-------------- +``0.1.1``|``-CUDA-11.7.0``|``foss/2022a`` + ### Doris Delft object-oriented radar interferometric software @@ -6837,9 +7047,10 @@ R package for detecting doublets in single-cell RNA sequencing data *homepage*: -version |versionsuffix|toolchain ----------|-------------|-------------- -``2.0.3``|``-R-4.0.0`` |``foss/2020a`` +version |versionsuffix|toolchain +------------------|-------------|-------------- +``2.0.3`` |``-R-4.0.0`` |``foss/2020a`` +``2.0.3-20230131``|``-R-4.2.1`` |``foss/2022a`` ### Doxygen @@ -6891,6 +7102,7 @@ dRep is a python program which performs rapid pair-wise comparison of genome set version |toolchain ---------|-------------- ``3.0.0``|``foss/2021a`` +``3.4.2``|``foss/2022a`` ### DROP @@ -7018,6 +7230,16 @@ version |toolchain -----------|-------------- ``2.8.0.6``|``foss/2020b`` +### duplex-tools + +Duplex Tools contains a set of utilities for dealing with Duplex sequencing data. Tools are provided to identify and prepare duplex pairs for basecalling by Dorado (recommended) and Guppy, and for recovering simplex basecalls from incorrectly concatenated pairs. + +*homepage*: + +version |toolchain +---------|-------------- +``0.3.1``|``foss/2022a`` + ### dxpy DNAnexus Platform API bindings for Python @@ -7041,7 +7263,7 @@ version|versionsuffix |toolchain ## E -[E-ANTIC](#e-antic) - [ea-utils](#ea-utils) - [earthengine-api](#earthengine-api) - [EasyBuild](#easybuild) - [EasyQC](#easyqc) - [ecBuild](#ecbuild) - [ecCodes](#eccodes) - [eccodes-python](#eccodes-python) - [ED2](#ed2) - [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) - [EricScript](#ericscript) - [ESL-Bundle](#esl-bundle) - [ESM-2](#esm-2) - [ESMF](#esmf) - [ESMPy](#esmpy) - [ESMValTool](#esmvaltool) - [eSpeak-NG](#espeak-ng) - [Essentia](#essentia) - [ETE](#ete) - [ETSF_IO](#etsf_io) - [eudev](#eudev) - [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) +[E-ANTIC](#e-antic) - [ea-utils](#ea-utils) - [earthengine-api](#earthengine-api) - [EasyBuild](#easybuild) - [EasyQC](#easyqc) - [ecBuild](#ecbuild) - [ecCodes](#eccodes) - [eccodes-python](#eccodes-python) - [ED2](#ed2) - [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) - [Essentia](#essentia) - [ETE](#ete) - [ETSF_IO](#etsf_io) - [eudev](#eudev) - [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) ### E-ANTIC @@ -7176,6 +7398,7 @@ version |toolchain ``4.6.0`` |``system`` ``4.6.1`` |``system`` ``4.6.2`` |``system`` +``4.7.0`` |``system`` ### EasyQC @@ -7248,11 +7471,11 @@ Lightweight, super fast library for sequence alignment using edit (Levenshtein) *homepage*: version |versionsuffix |toolchain ----------------|-----------------|---------------------------------------------- +---------------|-----------------|-------------------------------------------------------------- ``1.3.8.post1``|``-Python-3.7.4``|``GCC/8.3.0``, ``iccifort/2019.5.281`` ``1.3.8.post1``|``-Python-3.8.2``|``GCC/9.3.0`` ``1.3.8.post2``|``-Python-3.8.2``|``iccifort/2020.1.217`` -``1.3.9`` | |``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0`` +``1.3.9`` | |``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0`` ### EggLib @@ -7270,11 +7493,12 @@ EggNOG-mapper is a tool for fast functional annotation of novel sequences. It us *homepage*: -version |versionsuffix |toolchain ----------|------------------|--------------- -``1.0.3``|``-Python-2.7.14``|``intel/2018a`` -``2.1.4``| |``foss/2020b`` -``2.1.7``| |``foss/2021b`` +version |versionsuffix |toolchain +----------|------------------|--------------- +``1.0.3`` |``-Python-2.7.14``|``intel/2018a`` +``2.1.4`` | |``foss/2020b`` +``2.1.7`` | |``foss/2021b`` +``2.1.10``| |``foss/2020b`` ### EGTtools @@ -7304,7 +7528,7 @@ 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`` @@ -7319,7 +7543,7 @@ 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`` +``3.4.0`` |``GCCcore/10.2.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ### EigenExa @@ -7397,6 +7621,7 @@ version |toolchain ``0.183``|``GCCcore/10.2.0`` ``0.185``|``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``0.187``|``GCCcore/11.3.0`` +``0.189``|``GCCcore/12.2.0`` ### Elk @@ -7419,20 +7644,22 @@ Eigenvalue SoLvers for Petaflop-Applications. *homepage*: -version |toolchain --------------------|--------------------------------------------------------------------------------- -``2015.02.002`` |``foss/2018a``, ``gimkl/2017a``, ``intel/2018a`` -``2016.05.004`` |``intel/2016b``, ``intel/2017a`` -``2016.11.001.pre``|``foss/2018b``, ``intel/2018b`` -``2017.11.001`` |``foss/2018b``, ``intel/2018a``, ``intel/2018b`` -``2018.05.001`` |``foss/2018b``, ``intel/2018b`` -``2018.11.001`` |``intel/2019a`` -``2019.11.001`` |``foss/2019b``, ``foss/2020a``, ``intel/2019b``, ``intel/2020a``, ``iomkl/2019b`` -``2020.05.001`` |``intel/2020a`` -``2020.11.001`` |``foss/2020b``, ``intel/2020b`` -``2021.05.001`` |``foss/2021a``, ``foss/2021b``, ``intel/2021a``, ``intel/2021b`` -``2021.05.002`` |``intel/2020b`` -``2021.11.001`` |``foss/2021b``, ``foss/2022a``, ``intel/2021b``, ``intel/2022a`` +version |versionsuffix |toolchain +-------------------|----------------|--------------------------------------------------------------------------------- +``2015.02.002`` | |``foss/2018a``, ``gimkl/2017a``, ``intel/2018a`` +``2016.05.004`` | |``intel/2016b``, ``intel/2017a`` +``2016.11.001.pre``| |``foss/2018b``, ``intel/2018b`` +``2017.11.001`` | |``foss/2018b``, ``intel/2018a``, ``intel/2018b`` +``2018.05.001`` | |``foss/2018b``, ``intel/2018b`` +``2018.11.001`` | |``intel/2019a`` +``2019.11.001`` | |``foss/2019b``, ``foss/2020a``, ``intel/2019b``, ``intel/2020a``, ``iomkl/2019b`` +``2020.05.001`` | |``intel/2020a`` +``2020.11.001`` | |``foss/2020b``, ``intel/2020b`` +``2021.05.001`` | |``foss/2021a``, ``foss/2021b``, ``intel/2021a``, ``intel/2021b`` +``2021.05.002`` | |``intel/2020b`` +``2021.11.001`` | |``foss/2021b``, ``foss/2022a``, ``intel/2021b``, ``intel/2022a`` +``2022.05.001`` | |``foss/2022a``, ``intel/2022a`` +``2022.05.001`` |``-CUDA-11.7.0``|``foss/2022a`` ### ELPH @@ -7637,6 +7864,17 @@ EpiScanpy is a toolkit to analyse single-cell open chromatin (scATAC-seq) and si version |toolchain ---------|-------------- ``0.3.1``|``foss/2021a`` +``0.4.0``|``foss/2022a`` + +### eQuilibrator + +Calculation of standard thermodynamic potentials of biochemical reactions. + +*homepage*: + +version |toolchain +---------|-------------- +``0.4.7``|``foss/2021a`` ### EricScript @@ -7844,8 +8082,8 @@ Exonerate is a generic tool for pairwise sequence comparison. It allows you to *homepage*: version |toolchain ----------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -``2.4.0``|``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/6.4.0-2.28``, ``GCC/8.3.0``, ``foss/2016a``, ``foss/2016b``, ``iccifort/2017.4.196-GCC-6.4.0-2.28``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281``, ``intel/2017a`` +---------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +``2.4.0``|``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0``, ``GCC/6.4.0-2.28``, ``GCC/8.3.0``, ``foss/2016a``, ``foss/2016b``, ``iccifort/2017.4.196-GCC-6.4.0-2.28``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281``, ``intel/2017a`` ### expat @@ -7913,7 +8151,7 @@ version |toolchain ## F -[f90cache](#f90cache) - [f90wrap](#f90wrap) - [Faber](#faber) - [FabIO](#fabio) - [faceswap](#faceswap) - [FALCON](#falcon) - [FANN](#fann) - [fast5](#fast5) - [FASTA](#fasta) - [fastahack](#fastahack) - [FastaIndex](#fastaindex) - [FastANI](#fastani) - [Fastaq](#fastaq) - [FastFold](#fastfold) - [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) - [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) - [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) - [flook](#flook) - [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) - [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) - [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) - [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) - [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) - [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) - [FUNWAVE-TVD](#funwave-tvd) - [FUSE](#fuse) - [FuSeq](#fuseq) - [FusionCatcher](#fusioncatcher) - [futhark](#futhark) - [futile](#futile) - [future](#future) - [fxtract](#fxtract) ### f90cache @@ -7956,6 +8194,7 @@ version |versionsuffix |toolchain ----------|-----------------|---------------------------------- ``0.10.2``|``-Python-3.7.4``|``foss/2019b``, ``fosscuda/2019b`` ``0.11.0``| |``foss/2020b``, ``fosscuda/2020b`` +``0.14.0``| |``foss/2021b`` ### faceswap @@ -8018,6 +8257,17 @@ version |toolchain ---------|----------------------------------------------------------------------------- ``1.0.0``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` +### fastai + +The fastai deep learning library. + +*homepage*: + +version |versionsuffix |toolchain +----------|----------------|-------------- +``2.7.10``| |``foss/2022a`` +``2.7.10``|``-CUDA-11.7.0``|``foss/2022a`` + ### FastaIndex FastA index (.fai) handler compatible with samtools faidx @@ -8035,12 +8285,12 @@ FastANI is developed for fast alignment-free computation of whole-genome Averag *homepage*: version |toolchain ---------|----------------------------------------------------------------------------------------------------- +--------|--------------------------------------------------------------------------------------------------------------------- ``1.1`` |``foss/2018b``, ``intel/2018b`` ``1.2`` |``GCC/8.2.0-2.31.1``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` ``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``, ``iccifort/2020.4.304``, ``intel-compilers/2021.4.0`` +``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`` ### Fastaq @@ -8062,6 +8312,26 @@ version |versionsuffix |toolchain ------------|----------------|-------------- ``20220729``|``-CUDA-11.3.1``|``foss/2021a`` +### fastjet + +A software package for jet finding in pp and e+e- collisions + +*homepage*: + +version |toolchain +---------|--------------- +``3.4.0``|``gompi/2022a`` + +### fastjet-contrib + +3rd party extensions of FastJet + +*homepage*: + +version |toolchain +---------|--------------- +``1.049``|``gompi/2022a`` + ### FastME FastME: a comprehensive, accurate and fast distance-based phylogeny inference program. @@ -8139,6 +8409,7 @@ version |versionsuffix |toolchain ``0.11.4``|``-Perl-5.24.0``|``foss/2016b`` ``0.12.0``|``-Perl-5.26.1``|``intel/2018a`` ``0.13.0``|``-Perl-5.28.0``|``foss/2018b`` +``0.14.0``| |``GCC/11.3.0`` ### FastQC @@ -8460,6 +8731,7 @@ version |toolchain ``4.3.2`` |``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``4.4.2`` |``GCCcore/11.3.0`` ``5.0.1`` |``GCCcore/11.3.0`` +``5.1.2`` |``GCCcore/12.2.0`` ### ffmpi @@ -8481,6 +8753,16 @@ version |versionsuffix |toolchain ---------|------------------|--------------- ``0.8.3``|``-Python-2.7.11``|``intel/2016a`` +### ffnvcodec + +FFmpeg nvidia headers. Adds support for nvenc and nvdec. Requires Nvidia GPU and drivers to be present (picked up dynamically). + +*homepage*: + +version |toolchain +------------|---------- +``11.1.5.2``|``system`` + ### fftlib A library that intercepts FFTW calls and adds features on top of it. In particular, it enables FFT plan reuse when there are multiple calls for the same geometry. @@ -8498,7 +8780,7 @@ FFTW is a C subroutine library for computing the discrete Fourier transform (DFT *homepage*: version |versionsuffix|toolchain -----------|-------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +----------|-------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ``1.0.0`` |``-fujitsu`` |``FCC/4.5.0`` ``2.1.5`` | |``intel/2016b``, ``intel/2017a``, ``intel/2018b`` ``3.3.4`` | |``gmpich/2016a``, ``gmvapich2/1.7.20``, ``gmvapich2/2016a``, ``gompi/2016.04``, ``gompi/2016.06``, ``gompi/2016.07``, ``gompi/2016a``, ``gompi/2016b``, ``intel/2016a``, ``intel/2016b`` @@ -8506,7 +8788,7 @@ version |versionsuffix|toolchain ``3.3.6`` | |``gimpi/2017b``, ``gimpic/2017b``, ``gompi/2017a``, ``gompi/2017b``, ``gompic/2017b``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intelcuda/2017b`` ``3.3.7`` | |``gimkl/2017a``, ``gimpi/2018a``, ``gmpich/2017.08``, ``gompi/2018a``, ``gompic/2018a``, ``intel/2017b``, ``intel/2018.00``, ``intel/2018.01``, ``intel/2018a``, ``iomkl/2018a`` ``3.3.7`` |``-serial`` |``GCC/6.4.0-2.28`` -``3.3.8`` | |``gompi/2018.08``, ``gompi/2018b``, ``gompi/2019a``, ``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b``, ``gompic/2018b``, ``gompic/2019a``, ``gompic/2019b``, ``gompic/2020a``, ``gompic/2020b``, ``iimpi/2020b``, ``intel/2018b``, ``intel/2019a``, ``intel/2019b``, ``intel/2020a``, ``intel/2020b``, ``iomkl/2018b`` +``3.3.8`` | |``gompi/2018.08``, ``gompi/2018b``, ``gompi/2019a``, ``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b``, ``gompic/2018b``, ``gompic/2019a``, ``gompic/2019b``, ``gompic/2020a``, ``gompic/2020b``, ``iimpi/2020b``, ``intel/2018b``, ``intel/2019a``, ``intel/2019b``, ``intel/2020a``, ``intel/2020b``, ``iomkl/2018b``, ``iomkl/2020b`` ``3.3.8`` |``-amd`` |``gompi/2020a`` ``3.3.8`` |``-serial`` |``GCC/9.3.0`` ``3.3.9`` | |``gompi/2021a``, ``intel/2021a`` @@ -8650,6 +8932,16 @@ version |versionsuffix |toolchain ----------------|------------------|--------------- ``1.2-20170228``|``-Python-2.7.14``|``intel/2017b`` +### finder + +finder is a gene annotator pipeline which automates the process of downloading short reads, aligning them and using the assembled transcripts to generate gene annotations. + +*homepage*: + +version |toolchain +---------|-------------- +``1.1.0``|``foss/2021b`` + ### findhap Find haplotypes and impute genotypes using multiple chip sets and sequence data @@ -8785,6 +9077,7 @@ version |toolchain ---------|---------------------------------------------------------- ``1.3.3``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``1.3.4``|``GCCcore/11.3.0`` +``1.4.2``|``GCCcore/12.2.0`` ### FLAIR @@ -8858,6 +9151,8 @@ version |toolchain ----------|---------------------------------------------------------- ``1.12.0``|``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``2.0.0`` |``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``2.0.7`` |``GCCcore/11.3.0`` +``23.1.4``|``GCCcore/12.2.0`` ### flatbuffers-python @@ -8951,6 +9246,7 @@ version |toolchain ``2.5.2``|``GCC/7.3.0-2.30``, ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``iccifort/2018.3.222-GCC-7.3.0-2.30`` ``2.7.1``|``GCC/10.3.0`` ``2.8.4``|``GCC/11.2.0`` +``2.9.0``|``GCC/11.3.0`` ### flook @@ -8962,6 +9258,16 @@ version |toolchain ---------|----------------------------------------------------------------------------------------------------------------------------------- ``0.8.1``|``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``iccifort/2020.4.304``, ``intel-compilers/2021.2.0``, ``intel-compilers/2021.4.0`` +### flowFDA + +R package for analysing flow cytometry experiments with model based clustering, functional principal component analysis + +*homepage*: + +version |versionsuffix|toolchain +-----------------|-------------|-------------- +``0.99-20220602``|``-R-4.2.1`` |``foss/2022a`` + ### FLTK FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL and its built-in GLUT emulation. @@ -9658,7 +9964,7 @@ 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) - [GARLI](#garli) - [garnett](#garnett) - [GAT](#gat) - [GATE](#gate) - [GATK](#gatk) - [Gaussian](#gaussian) - [gawk](#gawk) - [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-library](#gem-library) - [GEMMA](#gemma) - [gemmi](#gemmi) - [gencore_variant_detection](#gencore_variant_detection) - [GeneMark-ET](#genemark-et) - [gengetopt](#gengetopt) - [Genome_Profiler](#genome_profiler) - [GenomeMapper](#genomemapper) - [GenomeTester4](#genometester4) - [GenomeThreader](#genomethreader) - [GenomeTools](#genometools) - [GenomeWorks](#genomeworks) - [GenotypeHarmonizer](#genotypeharmonizer) - [genozip](#genozip) - [gensim](#gensim) - [geocube](#geocube) - [geopandas](#geopandas) - [geopy](#geopy) - [georges](#georges) - [GEOS](#geos) - [Gerris](#gerris) - [GETORB](#getorb) - [GetOrganelle](#getorganelle) - [gettext](#gettext) - [gexiv2](#gexiv2) - [gfbf](#gfbf) - [GffCompare](#gffcompare) - [gffread](#gffread) - [gflags](#gflags) - [GFOLD](#gfold) - [gh](#gh) - [GHC](#ghc) - [Ghostscript](#ghostscript) - [Gibbs2](#gibbs2) - [giflib](#giflib) - [gifsicle](#gifsicle) - [GIMIC](#gimic) - [gimkl](#gimkl) - [GIMP](#gimp) - [gimpi](#gimpi) - [gimpic](#gimpic) - [GIMPS](#gimps) - [giolf](#giolf) - [giolfc](#giolfc) - [git](#git) - [git-extras](#git-extras) - [git-lfs](#git-lfs) - [GitPython](#gitpython) - [Givaro](#givaro) - [Giza](#giza) - [GL2PS](#gl2ps) - [Glade](#glade) - [glew](#glew) - [GLFW](#glfw) - [GLib](#glib) - [glib-networking](#glib-networking) - [glibc](#glibc) - [GLibmm](#glibmm) - [GLIMMER](#glimmer) - [GlimmerHMM](#glimmerhmm) - [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) - [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) - [Graphene](#graphene) - [GraphicsMagick](#graphicsmagick) - [graphite2](#graphite2) - [GraPhlAn](#graphlan) - [GraphMap](#graphmap) - [GraphMap2](#graphmap2) - [Graphviz](#graphviz) - [graphviz](#graphviz) - [GRASP](#grasp) - [GRASS](#grass) - [Greenlet](#greenlet) - [Grep](#grep) - [gretl](#gretl) - [grib_api](#grib_api) - [GRIT](#grit) - [GRNBoost](#grnboost) - [groff](#groff) - [GroIMP](#groimp) - [GROMACS](#gromacs) - [GromacsWrapper](#gromacswrapper) - [GroopM](#groopm) - [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) - [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) - [GARLI](#garli) - [garnett](#garnett) - [GAT](#gat) - [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-library](#gem-library) - [GEMMA](#gemma) - [gemmi](#gemmi) - [gencore_variant_detection](#gencore_variant_detection) - [GeneMark-ET](#genemark-et) - [gengetopt](#gengetopt) - [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) - [Gerris](#gerris) - [GETORB](#getorb) - [GetOrganelle](#getorganelle) - [gettext](#gettext) - [gexiv2](#gexiv2) - [gfbf](#gfbf) - [GffCompare](#gffcompare) - [gffread](#gffread) - [gflags](#gflags) - [GFOLD](#gfold) - [gh](#gh) - [GHC](#ghc) - [Ghostscript](#ghostscript) - [Gibbs2](#gibbs2) - [giflib](#giflib) - [gifsicle](#gifsicle) - [GIMIC](#gimic) - [gimkl](#gimkl) - [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) - [GL2PS](#gl2ps) - [Glade](#glade) - [glew](#glew) - [GLFW](#glfw) - [GLib](#glib) - [glib-networking](#glib-networking) - [glibc](#glibc) - [GLibmm](#glibmm) - [GLIMMER](#glimmer) - [GlimmerHMM](#glimmerhmm) - [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) - [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) - [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 @@ -9890,6 +10196,16 @@ version |toolchain ``5.1.0``|``GCC/10.2.0`` ``5.1.1``|``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0`` +### gbasis + +Python library for analytical evaluation and integration of Gaussian-type basis functions and related quantities. + +*homepage*: + +version |toolchain +------------|--------------- +``20210904``|``intel/2022a`` + ### Gblocks Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis @@ -10161,6 +10477,7 @@ version |versionsuffix |toolchain ``2.2.3``|``-Python-3.6.3`` |``foss/2017b`` ``2.2.3``|``-Python-3.6.4`` |``foss/2018a``, ``intel/2018a``, ``iomkl/2018a`` ``2.2.3``|``-Python-3.6.6`` |``foss/2018b``, ``intel/2018b`` +``2.4.4``| |``foss/2021b``, ``intel/2021b`` ``3.0.0``|``-Python-2.7.15`` |``foss/2019a``, ``intel/2019a`` ``3.0.0``|``-Python-3.7.2`` |``foss/2019a``, ``intel/2019a`` ``3.0.2``|``-Python-3.7.4`` |``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` @@ -10169,6 +10486,7 @@ version |versionsuffix |toolchain ``3.3.0``| |``foss/2021a`` ``3.3.2``| |``foss/2021b`` ``3.5.0``| |``foss/2022a`` +``3.6.2``| |``foss/2022b`` ### GDB @@ -10261,9 +10579,10 @@ GDGraph is a Perl package to generate charts *homepage*: version |versionsuffix |toolchain ---------|----------------|--------------- +--------|----------------|------------------ ``1.54``|``-Perl-5.26.1``|``intel/2018a`` ``1.54``|``-Perl-5.28.0``|``foss/2018b`` +``1.56``| |``GCCcore/11.3.0`` ### gdist @@ -10413,11 +10732,11 @@ Eukaryotic gene prediction suite with automatic training *homepage*: version |toolchain ---------|------------------ +--------|-------------------------------------- ``4.38``|``GCCcore/8.2.0`` ``4.57``|``GCCcore/8.3.0`` ``4.65``|``GCCcore/10.2.0`` -``4.71``|``GCCcore/11.2.0`` +``4.71``|``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ### gengetopt @@ -10449,6 +10768,16 @@ version |toolchain ---------|-------------- ``0.4.4``|``foss/2016a`` +### genomepy + +genomepy is designed to provide a simple and straightforward way to download and use genomic data + +*homepage*: + +version |toolchain +----------|-------------- +``0.15.0``|``foss/2022a`` + ### GenomeTester4 A toolkit for performing set operations - union, intersection and complement - on k-mer lists. @@ -10463,7 +10792,7 @@ version|toolchain GenomeThreader is a software tool to compute gene structure predictions. -*homepage*: +*homepage*: version |versionsuffix |toolchain ---------|-----------------------|---------- @@ -10482,7 +10811,7 @@ version |versionsuffix |toolchain ``1.5.10``|``-Python-2.7.15``|``foss/2018b`` ``1.6.1`` | |``GCC/10.2.0``, ``GCC/8.3.0``, ``GCC/9.3.0`` ``1.6.1`` |``-Python-2.7.16``|``GCC/8.3.0`` -``1.6.2`` | |``GCC/10.3.0`` +``1.6.2`` | |``GCC/10.3.0``, ``GCC/11.3.0`` ### GenomeWorks @@ -10581,7 +10910,7 @@ GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (J *homepage*: version |versionsuffix |toolchain -----------|------------------|----------------------------------------------------------------------- +----------|------------------|----------------------------------------------------------------------------------------------------- ``3.5.0`` |``-Python-2.7.11``|``intel/2016a`` ``3.5.0`` |``-Python-2.7.12``|``intel/2016b`` ``3.6.1`` |``-Python-2.7.12``|``foss/2016b``, ``intel/2016b`` @@ -10598,8 +10927,9 @@ version |versionsuffix |toolchain ``3.8.0`` | |``GCC/8.3.0`` ``3.8.0`` |``-Python-3.7.4`` |``GCC/8.3.0``, ``iccifort/2019.5.281`` ``3.8.1`` |``-Python-3.8.2`` |``GCC/9.3.0``, ``iccifort/2020.1.217`` -``3.9.1`` | |``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``iccifort/2020.4.304`` +``3.9.1`` | |``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``iccifort/2020.4.304``, ``intel-compilers/2021.4.0`` ``3.10.3``| |``GCC/11.3.0`` +``3.11.1``| |``GCC/12.2.0`` ### Gerris @@ -10785,9 +11115,9 @@ 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/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/8.3.0``, ``GCCcore/9.3.0`` ### gifsicle @@ -10888,6 +11218,16 @@ version |toolchain ---------|---------- ``2017b``|``system`` +### Giotto-Suite + +Giotto Suite is focused on building a modular platform for analyzing spatial-omics technologies and strives to be interoperable with other popular spatial analysis tools and classes. Using established packages optimized for large(r) data, Giotto Suite adopts fast and memory efficient methods to create an interactive analysis. + +*homepage*: + +version |versionsuffix|toolchain +---------|-------------|-------------- +``3.0.1``|``-R-4.2.1`` |``foss/2022a`` + ### git Git is a free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency. @@ -10977,6 +11317,16 @@ version |toolchain ---------|-------------- ``1.1.0``|``foss/2018b`` +### GKeyll + +Gkeyll v2.0 (pronounced as in the book “The Strange Case of Dr. Jekyll and Mr. Hyde”) is a computational plasma physics code mostly written in C/C++ and LuaJIT. Gkeyll contains solvers for gyrokinetic equations, Vlasov-Maxwell equations, and multi-fluid equations. Gkeyll contains ab-initio and novel implementations of a number of algorithms, and perhaps is unique in using a JIT compiled typeless dynamic language for as its main implementation language. + +*homepage*: + +version |versionsuffix |toolchain +------------|-----------------|-------------- +``20220803``|``-Python-3.8.2``|``foss/2020a`` + ### GL2PS GL2PS: an OpenGL to PostScript printing library @@ -11188,7 +11538,7 @@ version |toolchain ### GLPK -The GLPK (GNU Linear Programming Kit) package is intended for solving large-scale linear programming (LP), mixed integer programming (MIP), and other related problems. It is a set of routines written in ANSI C and organized in the form of a callable library. +The GLPK (GNU Linear Programming Kit) package is intended for solving large-scale linear programming (LP), mixed integer programming (MIP), and other related problems. It is a set of routines written in ANSI C and organized in the form of a callable library. *homepage*: @@ -11198,7 +11548,7 @@ version |toolchain ``4.60``|``GCCcore/5.4.0``, ``intel/2016b`` ``4.61``|``intel/2017a`` ``4.65``|``GCCcore/10.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``5.0`` |``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``5.0`` |``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ### glproto @@ -11236,6 +11586,7 @@ version |toolchain ``2019-09-12``|``GCC/8.3.0`` ``2020-12-17``|``GCC/9.3.0`` ``2021-21-17``|``GCC/11.2.0`` +``2023-02-17``|``GCC/11.3.0`` ### GMP @@ -11292,7 +11643,7 @@ version |versionsuffix |toolchain ``2.1.0b1``|``-Python-3.6.3`` |``foss/2017b``, ``intel/2017b`` ``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`` +``2.1.2`` | |``GCC/11.2.0``, ``GCC/11.3.0``, ``intel-compilers/2022.1.0`` ### gmsh @@ -11300,16 +11651,17 @@ Gmsh is a 3D finite element grid generator with a build-in CAD engine and post-p *homepage*: -version |versionsuffix |toolchain ----------|------------------|------------------------------- -``3.0.6``|``-Python-2.7.14``|``foss/2017b`` -``3.0.6``|``-Python-3.6.6`` |``foss/2018b`` -``4.2.2``|``-Python-3.6.6`` |``foss/2018b`` -``4.5.6``|``-Python-2.7.16``|``intel/2019b`` -``4.5.6``|``-Python-3.7.4`` |``foss/2019b`` -``4.7.1``|``-Python-3.8.2`` |``foss/2020a``, ``intel/2020a`` -``4.8.4``|``-Python-3.6.4`` |``foss/2018a`` -``4.9.0``| |``foss/2021a`` +version |versionsuffix |toolchain +----------|------------------|------------------------------- +``3.0.6`` |``-Python-2.7.14``|``foss/2017b`` +``3.0.6`` |``-Python-3.6.6`` |``foss/2018b`` +``4.2.2`` |``-Python-3.6.6`` |``foss/2018b`` +``4.5.6`` |``-Python-2.7.16``|``intel/2019b`` +``4.5.6`` |``-Python-3.7.4`` |``foss/2019b`` +``4.7.1`` |``-Python-3.8.2`` |``foss/2020a``, ``intel/2020a`` +``4.8.4`` |``-Python-3.6.4`` |``foss/2018a`` +``4.9.0`` | |``foss/2021a`` +``4.11.1``| |``foss/2022a`` ### GMT @@ -11377,6 +11729,7 @@ version |toolchain ``5.4.1``|``GCCcore/10.2.0`` ``5.4.2``|``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``5.4.4``|``GCCcore/11.3.0`` +``5.4.6``|``GCCcore/12.2.0`` ### GnuTLS @@ -11438,6 +11791,7 @@ A Python library for Gene Ontology analyses version |toolchain ---------|-------------- ``1.1.6``|``foss/2020b`` +``1.3.1``|``foss/2022a`` ### gobff @@ -11534,6 +11888,8 @@ version |toolchain ``2020a``|``system`` ``2020b``|``system`` ``2021a``|``system`` +``2021b``|``system`` +``2022a``|``system`` ### gompi @@ -11604,6 +11960,7 @@ version |toolchain ``1.8.1`` |``GCCcore/8.2.0`` ``1.10.0``|``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``1.11.0``|``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``1.12.1``|``GCCcore/12.2.0`` ### gotree @@ -11722,9 +12079,10 @@ GPyTorch is a Gaussian process library implemented using PyTorch. *homepage*: -version |toolchain ----------|-------------- -``1.3.0``|``foss/2020b`` +version |versionsuffix |toolchain +---------|----------------|-------------- +``1.3.0``| |``foss/2020b`` +``1.9.1``|``-CUDA-11.3.1``|``foss/2021a`` ### Grace @@ -11772,6 +12130,16 @@ version |versionsuffix |toolchain ``2.26``|``-Python-3.6.3``|``foss/2017b`` ``2.27``|``-Python-3.6.6``|``foss/2018b`` +### GraphDB + +GraphDB is an enterprise ready Semantic Graph Database, compliant with W3C Standards. Semantic graph databases (also called RDF triplestores) provide the core infrastructure for solutions where modelling agility, data integration, relationship exploration and cross-enterprise data publishing and consumption are important. + +*homepage*: + +version |toolchain +----------|---------- +``10.1.5``|``system`` + ### Graphene Graphene is a a thin layer of types for graphic libraries @@ -11779,9 +12147,9 @@ Graphene is a a thin layer of types for graphic libraries *homepage*: version |toolchain -----------|------------------ +----------|-------------------------------------- ``1.6.0`` |``intel/2017a`` -``1.10.8``|``GCCcore/11.3.0`` +``1.10.8``|``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ### GraphicsMagick @@ -11859,17 +12227,18 @@ version |versionsuffix |toolchain ``2.50.0``| |``GCCcore/11.2.0`` ``5.0.0`` | |``GCCcore/11.3.0`` -### graphviz +### graphviz-python Simple Python interface for Graphviz *homepage*: -version |versionsuffix |toolchain ----------|------------------|------------------------------- -``0.5.1``|``-Python-2.7.12``|``foss/2016b``, ``intel/2016b`` -``0.5.1``|``-Python-3.5.2`` |``intel/2016b`` -``0.8.2``|``-Python-3.6.4`` |``intel/2018a`` +version |versionsuffix |toolchain +----------|------------------|------------------------------- +``0.5.1`` |``-Python-2.7.12``|``foss/2016b``, ``intel/2016b`` +``0.5.1`` |``-Python-3.5.2`` |``intel/2016b`` +``0.8.2`` |``-Python-3.6.4`` |``intel/2018a`` +``0.20.1``| |``GCCcore/11.3.0`` ### GRASP @@ -11905,6 +12274,7 @@ version |versionsuffix |toolchain ``0.4.9`` |``-Python-3.5.1`` |``intel/2016a`` ``0.4.11``|``-Python-2.7.12``|``intel/2016b`` ``0.4.12``|``-Python-2.7.14``|``intel/2017b`` +``2.0.2`` | |``foss/2022a`` ### Grep @@ -11938,6 +12308,16 @@ version |toolchain ``1.21.0``|``foss/2017a`` ``1.24.0``|``foss/2017b``, ``intel/2017a``, ``intel/2017b`` +### grid + +Grid is a free and open-source Python library for numerical integration, interpolation and differentiation of interest for the quantum chemistry community. + +*homepage*: + +version |toolchain +------------|--------------- +``20220610``|``intel/2022a`` + ### GRIT GRIT - A tool for the integrative analysis of RNA-seq type assays @@ -12035,16 +12415,6 @@ version |versionsuffix |toolchain ---------|-----------------|------------------ ``0.8.0``|``-Python-3.7.2``|``fosscuda/2019a`` -### GroopM - -GroopM is a metagenomic binning toolset. It leverages spatio-temporal dynamics (differential coverage) to accurately (and almost automatically) extract population genomes from multi-sample metagenomic datasets. - -*homepage*: - -version |versionsuffix |toolchain ----------|------------------|-------------- -``0.3.4``|``-Python-2.7.12``|``foss/2016b`` - ### Groovy Groovy is a powerful, optionally typed and dynamic language, with static-typing and static compilation capabilities, for the Java platform aimed at improving developer productivity thanks to a concise, familiar and easy to learn syntax. @@ -12093,7 +12463,7 @@ The GNU Scientific Library (GSL) is a numerical library for C and C++ programmer *homepage*: version |toolchain ----------|---------------------------------------------------------------------------------------------------------------------------- +---------|---------------------------------------------------------------------------------------------------------------------------------------------- ``1.16`` |``foss/2016a``, ``intel/2016a`` ``2.1`` |``GCC/5.4.0-2.26``, ``foss/2016a``, ``foss/2016b``, ``iccifort/2016.3.210-GCC-5.4.0-2.26``, ``intel/2016a``, ``intel/2016b`` ``2.2.1``|``intel/2016a``, ``intel/2016b`` @@ -12101,7 +12471,7 @@ version |toolchain ``2.4`` |``GCCcore/6.4.0`` ``2.5`` |``GCC/7.3.0-2.30``, ``GCC/8.2.0-2.31.1``, ``iccifort/2018.3.222-GCC-7.3.0-2.30``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` ``2.6`` |``GCC/10.2.0``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2019.5.281``, ``iccifort/2020.1.217``, ``iccifort/2020.4.304`` -``2.7`` |``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0``, ``intel-compilers/2021.2.0``, ``intel-compilers/2021.4.0`` +``2.7`` |``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0``, ``GCC/12.2.0``, ``GCCcore/12.2.0``, ``intel-compilers/2021.2.0``, ``intel-compilers/2021.4.0`` ### gSOAP @@ -12150,6 +12520,7 @@ version |toolchain ``1.18.4`` |``GCC/10.2.0``, ``GCC/10.3.0`` ``1.18.5`` |``GCC/11.2.0`` ``1.20.2`` |``GCC/11.3.0`` +``1.22.1`` |``GCCcore/12.2.0`` ### GStreamer @@ -12168,6 +12539,7 @@ version |toolchain ``1.18.4`` |``GCC/10.2.0``, ``GCC/10.3.0`` ``1.18.5`` |``GCC/11.2.0`` ``1.20.2`` |``GCC/11.3.0`` +``1.22.1`` |``GCCcore/12.2.0`` ### gsutil @@ -12204,6 +12576,7 @@ version |versionsuffix |toolchain ``1.5.0``| |``intel/2020b`` ``1.7.0``| |``foss/2020b``, ``foss/2021a``, ``intel/2020b`` ``2.0.0``| |``foss/2021a``, ``intel/2021b`` +``2.1.1``| |``foss/2021b`` ### GTK+ @@ -12362,6 +12735,16 @@ version |versionsuffix |toolchain ``9.5.0``| |``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``9.5.2``| |``GCCcore/11.3.0`` +### GUSHR + +Assembly-free construction of UTRs from short read RNA-Seq data on the basis of coding sequence annotation. + +*homepage*: + +version |toolchain +--------------|-------------- +``2020-09-28``|``foss/2021b`` + ### gzip gzip (GNU zip) is a popular data compression program as a replacement for compress @@ -12378,7 +12761,7 @@ version |toolchain ## H -[h4toh5](#h4toh5) - [H5hut](#h5hut) - [h5py](#h5py) - [Hadoop](#hadoop) - [HAL](#hal) - [hanythingondemand](#hanythingondemand) - [HAPGEN2](#hapgen2) - [HarfBuzz](#harfbuzz) - [Harminv](#harminv) - [harmony](#harmony) - [HBase](#hbase) - [HDBSCAN](#hdbscan) - [HDDM](#hddm) - [HDF](#hdf) - [HDF-EOS](#hdf-eos) - [HDF-EOS5](#hdf-eos5) - [HDF5](#hdf5) - [hdf5storage](#hdf5storage) - [HDFView](#hdfview) - [HEALPix](#healpix) - [heaptrack](#heaptrack) - [hector](#hector) - [HeFFTe](#heffte) - [Hello](#hello) - [help2man](#help2man) - [HH-suite](#hh-suite) - [HiC-Pro](#hic-pro) - [HiCExplorer](#hicexplorer) - [hierfstat](#hierfstat) - [hifiasm](#hifiasm) - [HighFive](#highfive) - [Highway](#highway) - [HIP](#hip) - [hipify-clang](#hipify-clang) - [HIPS](#hips) - [hipSYCL](#hipsycl) - [hiredis](#hiredis) - [HISAT2](#hisat2) - [histolab](#histolab) - [hivtrace](#hivtrace) - [hl7apy](#hl7apy) - [HLAminer](#hlaminer) - [HMMER](#hmmer) - [HMMER2](#hmmer2) - [hmmlearn](#hmmlearn) - [HOME](#home) - [Horovod](#horovod) - [horton](#horton) - [how_are_we_stranded_here](#how_are_we_stranded_here) - [HPCG](#hpcg) - [HPCX](#hpcx) - [HPDBSCAN](#hpdbscan) - [HPL](#hpl) - [htop](#htop) - [HTSeq](#htseq) - [HTSlib](#htslib) - [hub](#hub) - [humann](#humann) - [hunspell](#hunspell) - [hwloc](#hwloc) - [Hydra](#hydra) - [Hyperopt](#hyperopt) - [HyperQueue](#hyperqueue) - [hyperspy](#hyperspy) - [HyPhy](#hyphy) - [HyPo](#hypo) - [hypothesis](#hypothesis) - [Hypre](#hypre) +[h4toh5](#h4toh5) - [H5hut](#h5hut) - [h5py](#h5py) - [Hadoop](#hadoop) - [HAL](#hal) - [hanythingondemand](#hanythingondemand) - [HAPGEN2](#hapgen2) - [HarfBuzz](#harfbuzz) - [Harminv](#harminv) - [harmony](#harmony) - [HBase](#hbase) - [HDBSCAN](#hdbscan) - [HDDM](#hddm) - [HDF](#hdf) - [HDF-EOS](#hdf-eos) - [HDF-EOS5](#hdf-eos5) - [HDF5](#hdf5) - [hdf5storage](#hdf5storage) - [HDFView](#hdfview) - [HEALPix](#healpix) - [Health-GPS](#health-gps) - [heaptrack](#heaptrack) - [hector](#hector) - [HeFFTe](#heffte) - [Hello](#hello) - [help2man](#help2man) - [HepMC3](#hepmc3) - [HH-suite](#hh-suite) - [HiC-Pro](#hic-pro) - [HiCExplorer](#hicexplorer) - [HiCMatrix](#hicmatrix) - [hierfstat](#hierfstat) - [hifiasm](#hifiasm) - [HighFive](#highfive) - [Highway](#highway) - [HIP](#hip) - [hipify-clang](#hipify-clang) - [HIPS](#hips) - [hipSYCL](#hipsycl) - [hiredis](#hiredis) - [HISAT2](#hisat2) - [histolab](#histolab) - [hivtrace](#hivtrace) - [hl7apy](#hl7apy) - [HLAminer](#hlaminer) - [HMMER](#hmmer) - [HMMER2](#hmmer2) - [hmmlearn](#hmmlearn) - [HOME](#home) - [Horovod](#horovod) - [horton](#horton) - [how_are_we_stranded_here](#how_are_we_stranded_here) - [HPCG](#hpcg) - [HPCX](#hpcx) - [HPDBSCAN](#hpdbscan) - [HPL](#hpl) - [htop](#htop) - [HTSeq](#htseq) - [HTSlib](#htslib) - [hub](#hub) - [humann](#humann) - [hunspell](#hunspell) - [hwloc](#hwloc) - [Hydra](#hydra) - [Hyperopt](#hyperopt) - [HyperQueue](#hyperqueue) - [hyperspy](#hyperspy) - [HyPhy](#hyphy) - [HyPo](#hypo) - [hypothesis](#hypothesis) - [Hypre](#hypre) ### h4toh5 @@ -12445,7 +12828,8 @@ version |versionsuffix |toolchain ``3.1.0`` | |``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b``, ``intelcuda/2020b`` ``3.2.1`` | |``foss/2021a``, ``gomkl/2021a`` ``3.6.0`` | |``foss/2021b``, ``intel/2021b`` -``3.7.0`` | |``foss/2022a`` +``3.7.0`` | |``foss/2022a``, ``intel/2022a`` +``3.8.0`` | |``foss/2022b`` ### Hadoop @@ -12578,6 +12962,7 @@ version |versionsuffix |toolchain ----------|-----------------|-------------- ``0.8.24``|``-Python-3.7.4``|``foss/2019b`` ``0.8.27``| |``foss/2021a`` +``0.8.29``| |``foss/2022a`` ### HDDM @@ -12598,13 +12983,13 @@ 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/9.3.0`` +``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`` ### HDF-EOS @@ -12650,16 +13035,17 @@ version |versionsuffix|toolchain ``1.10.1`` | |``foss/2017a``, ``foss/2017b``, ``foss/2018a``, ``fosscuda/2017b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018.00``, ``intel/2018.01``, ``intel/2018a``, ``intelcuda/2017b``, ``iomkl/2017b``, ``iomkl/2018a`` ``1.10.2`` | |``PGI/18.4-GCC-6.4.0-2.28``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b``, ``iomkl/2018b`` ``1.10.5`` | |``gompi/2019a``, ``gompi/2019b``, ``gompic/2019a``, ``gompic/2019b``, ``iimpi/2019a``, ``iimpi/2019b``, ``iimpic/2019a``, ``iimpic/2019b``, ``iompi/2019b`` -``1.10.5`` |``-serial`` |``GCCcore/8.3.0`` +``1.10.5`` |``-serial`` |``GCC/8.3.0`` ``1.10.6`` | |``gompi/2020a``, ``gompic/2020a``, ``iimpi/2020a``, ``iimpic/2020a`` ``1.10.7`` | |``gompi/2020b``, ``gompi/2021a``, ``gompic/2020b``, ``iimpi/2020b``, ``iimpi/2021a``, ``iimpic/2020b`` ``1.10.8`` | |``gompi/2021b``, ``gompi/2022a`` ``1.12.0`` | |``gompi/2020a``, ``iimpi/2020a`` ``1.12.1`` | |``gompi/2021a``, ``gompi/2021b``, ``iimpi/2021b`` ``1.12.2`` | |``gompi/2022a``, ``iimpi/2022a`` -``1.12.2`` |``-serial`` |``GCCcore/11.3.0`` +``1.12.2`` |``-serial`` |``GCC/11.3.0`` ``1.13.1`` | |``gompi/2022a``, ``iimpi/2022a`` -``1.13.1`` |``-serial`` |``GCCcore/11.3.0`` +``1.13.1`` |``-serial`` |``GCC/11.3.0`` +``1.14.0`` | |``gompi/2022b``, ``iimpi/2022b`` ### hdf5storage @@ -12692,6 +13078,17 @@ version |toolchain --------|------------------------------------ ``3.50``|``GCCcore/7.3.0``, ``GCCcore/8.2.0`` +### Health-GPS + +Health-GPS microsimulation is part of the STOP project, and supports researchers and policy makers in the analysis of the health and economic impacts of alternative measures to tackle chronic diseases and obesity in children. The model reproduces the characteristics of a population and simulates key individual event histories associated with key components of relevant behaviours, such as physical activity, and diseases such as diabetes or cancer. To run the test-jobs with HealthGPS.Tests the data-directory, found in your installation folder, must be in the current path. + +*homepage*: + +version |toolchain +-----------|------------------ +``1.1.3.0``|``GCCcore/11.3.0`` +``1.2.2.0``|``GCCcore/11.3.0`` + ### heaptrack A heap memory profiler for Linux. @@ -12752,6 +13149,16 @@ version |toolchain ``1.48.3`` |``FCC/4.5.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0``, ``GCCcore/11.2.0``, ``GCCcore/9.4.0`` ``1.49.2`` |``GCCcore/11.3.0``, ``GCCcore/12.1.0``, ``GCCcore/12.2.0``, ``GCCcore/9.5.0`` +### HepMC3 + +HepMC is a standard for storing Monte Carlo event data. + +*homepage*: + +version |toolchain +---------|-------------- +``3.2.5``|``GCC/11.3.0`` + ### HH-suite The HH-suite is an open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs). @@ -12784,6 +13191,17 @@ HiCexplorer addresses the common tasks of Hi-C analysis from processing to visua version |versionsuffix |toolchain ---------|-----------------|-------------- ``2.1.1``|``-Python-3.6.4``|``foss/2018a`` +``3.7.2``| |``foss/2022a`` + +### HiCMatrix + +This library implements the central class of HiCExplorer to manage Hi-C interaction matrices. + +*homepage*: + +version|toolchain +-------|-------------- +``17`` |``foss/2022a`` ### hierfstat @@ -12813,8 +13231,8 @@ HighFive is a modern header-only C++11 friendly interface for libhdf5. *homepage*: version |toolchain ----------|--------------- -``2.6.2``|``gompi/2021a`` +---------|-------------------------------- +``2.6.2``|``gompi/2021a``, ``gompi/2022a`` ### Highway @@ -12825,6 +13243,7 @@ Highway is a C++ library for SIMD (Single Instruction, Multiple Data), i.e. appl version |toolchain ----------|-------------------------------------- ``0.12.2``|``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +``1.0.3`` |``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ### HIP @@ -12889,7 +13308,7 @@ version |toolchain ``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`` +``2.2.1`` |``foss/2019b``, ``foss/2020a``, ``gompi/2020b``, ``gompi/2021b``, ``gompi/2022a`` ### histolab @@ -12938,11 +13357,11 @@ HMMER is used for searching sequence databases for homologs of protein sequence *homepage*: version |toolchain ----------|-------------------------------------------------------------------------------------------------------------------------------------------- +---------|-------------------------------------------------------------------------------------------------------------------------------------------------------- ``3.1b2``|``GCC/6.4.0-2.28``, ``foss/2016a``, ``foss/2016b``, ``foss/2018a``, ``iccifort/2017.4.196-GCC-6.4.0-2.28``, ``intel/2017a``, ``intel/2018a`` ``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``, ``gompic/2020b``, ``iimpi/2020b``, ``iimpi/2021b`` +``3.3.2``|``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b``, ``gompi/2021a``, ``gompi/2021b``, ``gompi/2022a``, ``gompic/2020b``, ``iimpi/2020b``, ``iimpi/2021b`` ### HMMER2 @@ -13063,10 +13482,10 @@ 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``, ``fosscuda/2019b``, ``fosscuda/2020a``, ``gobff/2020.06-amd``, ``gobff/2020.11``, ``gobff/2020b``, ``gobff/2021a``, ``goblf/2020b``, ``gomkl/2019a``, ``gomkl/2020b``, ``gomkl/2021a``, ``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/2022b``, ``intelcuda/2019b``, ``intelcuda/2020a``, ``iomkl/2019.01``, ``iomkl/2021a`` +``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``, ``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/2022b``, ``intelcuda/2019b``, ``intelcuda/2020a``, ``iomkl/2019.01``, ``iomkl/2021a``, ``iomkl/2021b`` ### htop @@ -13125,6 +13544,7 @@ version |versionsuffix|toolchain ``1.12`` | |``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/9.3.0`` ``1.14`` | |``GCC/11.2.0`` ``1.15.1`` | |``GCC/11.3.0`` +``1.17`` | |``GCC/12.2.0`` ``20160107``|``-PacBio`` |``intel/2017a`` ### hub @@ -13210,12 +13630,12 @@ hyperopt is a Python library for optimizing over awkward search spaces with real *homepage*: version |versionsuffix |toolchain ----------|--------------------------|------------------ +---------|--------------------------|------------------------------ ``0.1`` |``-Python-2.7.14`` |``intel/2017b`` ``0.1.1``|``-Python-3.6.6`` |``intel/2018b`` ``0.2.4``|``-Python-3.7.4-Java-1.8``|``intel/2019b`` ``0.2.5``| |``fosscuda/2020b`` -``0.2.7``| |``foss/2021a`` +``0.2.7``| |``foss/2021a``, ``foss/2022a`` ### HyperQueue @@ -13280,6 +13700,7 @@ version |versionsuffix |toolchain ``6.13.1``| |``GCCcore/10.3.0`` ``6.14.6``| |``GCCcore/11.2.0`` ``6.46.7``| |``GCCcore/11.3.0`` +``6.68.2``| |``GCCcore/12.2.0`` ### Hypre @@ -13297,11 +13718,12 @@ version |toolchain ``2.21.0``|``foss/2021a``, ``fosscuda/2020b`` ``2.24.0``|``intel/2021b`` ``2.25.0``|``foss/2022a`` +``2.27.0``|``foss/2022b`` ## 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) - [Infernal](#infernal) - [Infomap](#infomap) - [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) - [iomkl](#iomkl) - [iompi](#iompi) - [IOR](#ior) - [IOzone](#iozone) - [IPM](#ipm) - [Ipopt](#ipopt) - [ipp](#ipp) - [IPy](#ipy) - [ipyparallel](#ipyparallel) - [ipyrad](#ipyrad) - [IPython](#ipython) - [IQ-TREE](#iq-tree) - [Iris](#iris) - [IRkernel](#irkernel) - [IronPython](#ironpython) - [ISA-L](#isa-l) - [ISL](#isl) - [isoCirc](#isocirc) - [IsoNet](#isonet) - [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) - [InChI](#inchi) - [indicators](#indicators) - [Inelastica](#inelastica) - [inferCNV](#infercnv) - [infercnvpy](#infercnvpy) - [Inferelator](#inferelator) - [Infernal](#infernal) - [Infomap](#infomap) - [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) - [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) - [IsoNet](#isonet) - [ispc](#ispc) - [itac](#itac) - [ITK](#itk) - [itpp](#itpp) - [ITSTool](#itstool) - [ITSx](#itsx) - [iVar](#ivar) ### i-cisTarget @@ -13586,15 +14008,16 @@ igraph is a collection of network analysis tools with the emphasis on efficiency *homepage*: -version |toolchain ----------|------------------------------------------------ -``0.7.1``|``foss/2018b``, ``intel/2016b``, ``intel/2017b`` -``0.8.0``|``foss/2019b`` -``0.8.2``|``foss/2020a`` -``0.8.5``|``foss/2020b`` -``0.9.1``|``foss/2020b``, ``fosscuda/2020b`` -``0.9.4``|``foss/2021a`` -``0.9.5``|``foss/2021b`` +version |toolchain +----------|------------------------------------------------ +``0.7.1`` |``foss/2018b``, ``intel/2016b``, ``intel/2017b`` +``0.8.0`` |``foss/2019b`` +``0.8.2`` |``foss/2020a`` +``0.8.5`` |``foss/2020b`` +``0.9.1`` |``foss/2020b``, ``fosscuda/2020b`` +``0.9.4`` |``foss/2021a`` +``0.9.5`` |``foss/2021b`` +``0.10.3``|``foss/2022a`` ### IGV @@ -13610,6 +14033,7 @@ version |versionsuffix |toolchain ``2.8.0`` |``-Java-11`` |``system`` ``2.9.4`` |``-Java-11`` |``system`` ``2.12.3``|``-Java-11`` |``system`` +``2.16.0``|``-Java-11`` |``system`` ### igv-reports @@ -13701,6 +14125,7 @@ version |versionsuffix |toolchain ``2022.05`` | |``system`` ``2022.09`` | |``system`` ``2022.11`` | |``system`` +``2022.12`` | |``system`` ``2022a`` | |``system`` ``2022b`` | |``system`` ``system`` |``-GCC-system-2.29``|``system`` @@ -13729,6 +14154,7 @@ Julia kernel for Jupyter version |versionsuffix |toolchain ----------|----------------|---------- ``1.23.3``|``-Julia-1.6.7``|``system`` +``1.24.0``|``-Julia-1.8.5``|``system`` ### ILAMB @@ -13853,6 +14279,7 @@ Imath is a C++ and python library of 2D and 3D vector, matrix, and math operatio version |toolchain ---------|------------------ ``3.1.5``|``GCCcore/11.3.0`` +``3.1.6``|``GCCcore/12.2.0`` ### IMB @@ -13861,11 +14288,11 @@ The Intel MPI Benchmarks perform a set of MPI performance measurements for point *homepage*: version |toolchain -----------|------------------------------------------------------------------ +----------|----------------------------------------------------------------------------------- ``4.1`` |``foss/2016a``, ``foss/2017a``, ``intel/2017.02``, ``intel/2017a`` ``2018.1``|``intel/2017a`` ``2019.3``|``gompi/2019a``, ``iimpi/2019a`` -``2021.3``|``gompi/2021b`` +``2021.3``|``gompi/2021b``, ``gompi/2022a``, ``gompi/2022b``, ``iimpi/2022a``, ``iimpi/2022b`` ### imbalanced-learn @@ -13873,14 +14300,15 @@ imbalanced-learn is a Python package offering a number of re-sampling techniques *homepage*: -version |versionsuffix |toolchain ----------|------------------|--------------- -``0.2.1``|``-Python-2.7.12``|``intel/2016b`` -``0.2.1``|``-Python-3.5.2`` |``intel/2016b`` -``0.3.3``|``-Python-3.6.4`` |``foss/2018a`` -``0.4.3``|``-Python-3.6.6`` |``foss/2018b`` -``0.7.0``| |``foss/2020b`` -``0.9.0``| |``foss/2021b`` +version |versionsuffix |toolchain +----------|------------------|--------------- +``0.2.1`` |``-Python-2.7.12``|``intel/2016b`` +``0.2.1`` |``-Python-3.5.2`` |``intel/2016b`` +``0.3.3`` |``-Python-3.6.4`` |``foss/2018a`` +``0.4.3`` |``-Python-3.6.6`` |``foss/2018b`` +``0.7.0`` | |``foss/2020b`` +``0.9.0`` | |``foss/2021b`` +``0.10.1``| |``foss/2022a`` ### imgaug @@ -13932,11 +14360,12 @@ version |versionsuffix|toolchain ``2021.1.1`` | |``iimpi/2020.12`` ``2021.2.0`` | |``gompi/2021a``, ``iimpi/2021a``, ``iompi/2021a`` ``2021.3.0`` | |``gompi/2021a`` -``2021.4.0`` | |``system`` +``2021.4.0`` | |``iompi/2021b``, ``system`` ``2022.0.1`` | |``system`` -``2022.1.0`` | |``system`` +``2022.1.0`` | |``gompi/2022a``, ``system`` ``2022.2.0`` | |``system`` ``2022.2.1`` | |``system`` +``2023.0.0`` | |``system`` ### imkl-FFTW @@ -13951,6 +14380,7 @@ version |toolchain ``2022.1.0``|``iimpi/2022.05``, ``iimpi/2022a`` ``2022.2.0``|``iimpi/2022.09`` ``2022.2.1``|``iimpi/2022.11``, ``iimpi/2022b`` +``2023.0.0``|``iimpi/2022.12`` ### Imlib2 @@ -14032,6 +14462,7 @@ version |versionsuffix|toolchain ``2021.6.0`` | |``intel-compilers/2022.1.0`` ``2021.7.0`` | |``intel-compilers/2022.2.0`` ``2021.7.1`` | |``intel-compilers/2022.2.1`` +``2021.8.0`` | |``intel-compilers/2023.0.0`` ``system`` | |``iccifort/system-GCC-system-2.29`` ### IMPUTE2 @@ -14101,6 +14532,16 @@ version |toolchain ---------|-------------- ``0.4.0``|``foss/2021b`` +### Inferelator + +Inferelator 3.0 is a package for gene regulatory network inference that is based on regularized regression. + +*homepage*: + +version |toolchain +---------|-------------- +``0.6.1``|``foss/2022a`` + ### Infernal Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities. @@ -14251,6 +14692,7 @@ version |versionsuffix|toolchain ``2022.05`` | |``system`` ``2022.09`` | |``system`` ``2022.11`` | |``system`` +``2022.12`` | |``system`` ``2022a`` | |``system`` ``2022b`` | |``system`` @@ -14271,6 +14713,7 @@ version |toolchain ``2022.1.0``|``system`` ``2022.2.0``|``system`` ``2022.2.1``|``system`` +``2023.0.0``|``system`` ### IntelClusterChecker @@ -14401,6 +14844,16 @@ version |versionsuffix|toolchain ---------------|-------------|--------------- ``3.2-2020111``|``-nocpl`` |``gompi/2019b`` +### iodata + +Python library for reading, writing, and converting computational chemistry file formats and generating input files. + +*homepage*: + +version |toolchain +-----------|--------------- +``1.0.0a2``|``intel/2022a`` + ### iomkl Compiler toolchain including Intel compilers, Open MPI and Intel Math Kernel Library (MKL). @@ -14423,6 +14876,7 @@ version |toolchain ``2020a`` |``system`` ``2020b`` |``system`` ``2021a`` |``system`` +``2021b`` |``system`` ### iompi @@ -14446,6 +14900,7 @@ version |toolchain ``2020a`` |``system`` ``2020b`` |``system`` ``2021a`` |``system`` +``2021b`` |``system`` ### IOR @@ -14606,6 +15061,19 @@ version |versionsuffix |toolchain ``1.2`` |``-R-4.0.0-Python-3.8.2`` |``foss/2020a`` ``1.2`` |``-R-4.1.0`` |``foss/2021a`` ``1.3`` |``-R-4.2.0`` |``foss/2021b`` +``1.3.2`` |``-R-4.2.1`` |``foss/2022a`` + +### irodsfs + +FUSE implementation of iRODS Client written in Golang. + +*homepage*: + +version |versionsuffix |toolchain +----------|----------------|---------- +``0.8.9`` |``-linux-amd64``|``system`` +``0.8.11``|``-linux-amd64``|``system`` +``0.8.12``|``-linux-amd64``|``system`` ### IronPython @@ -14765,12 +15233,12 @@ 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-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) - [JWM](#jwm) - [jxrlib](#jxrlib) +[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-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) - [JWM](#jwm) - [jxrlib](#jxrlib) ### JAGS -JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation +JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation *homepage*: @@ -14778,6 +15246,7 @@ version |toolchain ---------|------------------------------------------------------------------------------------------------------------------------------------------------------------------- ``4.2.0``|``foss/2016a``, ``intel/2016a``, ``intel/2017a`` ``4.3.0``|``foss/2017b``, ``foss/2018b``, ``foss/2019a``, ``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``fosscuda/2020b``, ``intel/2017b`` +``4.3.1``|``foss/2022a`` ### Jansson @@ -14918,6 +15387,8 @@ version |versionsuffix |toolchain ``0.3.14``|``-CUDA-11.7.0``|``foss/2022a`` ``0.3.23``| |``foss/2022a`` ``0.3.23``|``-CUDA-11.4.1``|``foss/2021b`` +``0.4.4`` | |``foss/2022a`` +``0.4.4`` |``-CUDA-11.7.0``|``foss/2022a`` ### JAXFrontCE @@ -14946,12 +15417,12 @@ Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. *homepage*: version |toolchain -----------|------------------------------------------------------------------- +----------|--------------------------------------------------------------------------------------------------- ``1.1.11``|``foss/2016a``, ``foss/2016b`` ``1.1.12``|``foss/2018b``, ``intel/2018a`` ``2.2.6`` |``foss/2016b``, ``intel/2017a`` ``2.2.10``|``foss/2018b``, ``intel/2018a`` -``2.3.0`` |``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0`` +``2.3.0`` |``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0``, ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0`` ### jemalloc @@ -14960,7 +15431,7 @@ jemalloc is a general purpose malloc(3) implementation that emphasizes fragmenta *homepage*: version |toolchain ----------|------------------------------------------------------------------------------------------------ +---------|-------------------------------------------------------------------------------------------------------------------- ``4.1.0``|``intel/2016a`` ``4.2.0``|``foss/2016a``, ``intel/2016a`` ``4.2.1``|``intel/2016b`` @@ -14968,7 +15439,7 @@ version |toolchain ``5.0.1``|``GCCcore/6.4.0`` ``5.1.0``|``GCCcore/7.3.0`` ``5.2.0``|``GCCcore/8.2.0`` -``5.2.1``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``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/8.3.0``, ``GCCcore/9.3.0`` ``5.3.0``|``GCCcore/11.3.0`` ### jhbuild @@ -15043,7 +15514,7 @@ JSON-C implements a reference counting object model that allows you to easily co version |toolchain --------|---------------------------------------------------------- ``0.15``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``0.16``|``GCCcore/11.3.0`` +``0.16``|``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ### json-fortran @@ -15131,6 +15602,7 @@ version |versionsuffix |toolchain ``1.7.3``|``-linux-x86_64``|``system`` ``1.8.0``|``-linux-x86_64``|``system`` ``1.8.2``|``-linux-x86_64``|``system`` +``1.8.5``|``-linux-x86_64``|``system`` ### JUnit @@ -15159,6 +15631,16 @@ version |versionsuffix |toolchain ``4.12``|``-Java-1.8.0_77`` |``system`` ``4.12``|``-Java-1.8.0_92`` |``system`` +### jupyter-contrib-nbextensions + +A collection of various notebook extensions for Jupyter + +*homepage*: + +version |toolchain +---------|------------------ +``0.7.0``|``GCCcore/11.3.0`` + ### jupyter-matlab-proxy MATLAB Integration for Jupyter @@ -15168,6 +15650,7 @@ MATLAB Integration for Jupyter version |toolchain ---------|------------------ ``0.3.4``|``GCCcore/10.3.0`` +``0.5.0``|``GCCcore/11.3.0`` ### jupyter-resource-usage @@ -15178,6 +15661,7 @@ Jupyter Notebook Extension for monitoring your own Resource Usage (memory and/or version |toolchain ---------|------------------ ``0.6.1``|``GCCcore/10.3.0`` +``0.6.3``|``GCCcore/11.3.0`` ### jupyter-server @@ -15198,6 +15682,7 @@ Jupyter Server Proxy lets you run arbitrary external processes (such as RStudio, version |toolchain ---------|------------------ ``3.2.1``|``GCCcore/10.3.0`` +``3.2.2``|``GCCcore/11.3.0`` ### JupyterHub @@ -15211,6 +15696,7 @@ version |versionsuffix |toolchain ``0.8.1``|``-Python-3.6.4``|``foss/2017a`` ``1.1.0``| |``GCCcore/10.2.0`` ``1.4.1``| |``GCCcore/10.3.0`` +``3.0.0``| |``GCCcore/11.3.0`` ### JupyterLab @@ -15227,6 +15713,26 @@ version |versionsuffix |toolchain ``3.2.8`` | |``GCCcore/10.3.0`` ``3.5.0`` | |``GCCcore/11.3.0`` +### jupyterlab-lmod + +JupyterLab extension that allows user to interact with environment modules before launching kernels. The extension use Lmod's Python interface to accomplish module related task like loading, unloading, saving collection, etc. + +*homepage*: + +version |toolchain +---------|------------------ +``1.0.2``|``GCCcore/11.3.0`` + +### jupyterlmod + +Jupyter interactive notebook server extension that allows user to interact with environment modules before launching kernels. The extension use Lmod's Python interface to accomplish module related task like loading, unloading, saving collection, etc. + +*homepage*: + +version |toolchain +---------|------------------ +``3.0.0``|``GCCcore/11.3.0`` + ### JWM JWM is a light-weight window manager for the X11 Window System. @@ -15250,7 +15756,7 @@ version|toolchain ## K -[KaHIP](#kahip) - [Kaiju](#kaiju) - [Kaleido](#kaleido) - [Kalign](#kalign) - [kallisto](#kallisto) - [KAT](#kat) - [kbproto](#kbproto) - [kedro](#kedro) - [Kent_tools](#kent_tools) - [Keras](#keras) - [khmer](#khmer) - [kim-api](#kim-api) - [king](#king) - [KITE](#kite) - [kma](#kma) - [KMC](#kmc) - [KmerGenie](#kmergenie) - [KNIME](#knime) - [kpcalg](#kpcalg) - [Kraken](#kraken) - [Kraken2](#kraken2) - [Kratos](#kratos) - [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) - [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) - [Kratos](#kratos) - [krbalancing](#krbalancing) - [KronaTools](#kronatools) - [kwant](#kwant) - [KWIML](#kwiml) - [kWIP](#kwip) - [KyotoCabinet](#kyotocabinet) ### KaHIP @@ -15260,8 +15766,8 @@ The graph partitioning framework KaHIP -- Karlsruhe High Quality Partitioning. *homepage*: version |toolchain ---------|--------------- -``3.14``|``gompi/2022a`` +--------|-------------------------------- +``3.14``|``gompi/2022a``, ``gompi/2022b`` ### Kaiju @@ -15282,9 +15788,9 @@ 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`` +``0.2.1``|``GCCcore/10.3.0``, ``GCCcore/11.3.0`` ### Kalign @@ -15315,7 +15821,7 @@ 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`` +``0.48.0``|``gompi/2021b``, ``gompi/2022a`` ### KAT @@ -15328,6 +15834,16 @@ version |versionsuffix |toolchain ``2.4.2``|``-Python-3.6.4``|``foss/2018a`` ``2.4.2``|``-Python-3.7.2``|``foss/2019a`` +### kb-python + +kallisto | bustools is a workflow for pre-processing single-cell RNA-seq data. Pre-processing single-cell RNA-seq involves: (1) association of reads with their cells of origin, (2) collapsing of reads according to unique molecular identifiers (UMIs), and (3) generation of gene or feature counts from the reads to generate a cell x gene matrix. + +*homepage*: + +version |toolchain +----------|-------------- +``0.27.3``|``foss/2021b`` + ### kbproto X.org KBProto protocol headers. @@ -15360,6 +15876,7 @@ version |versionsuffix |toolchain ``411`` | |``GCC/10.2.0`` ``418`` | |``GCC/10.3.0`` ``422`` | |``GCC/11.2.0`` +``442`` | |``GCC/11.3.0`` ``20130806``|``-linux.x86_64``|``system`` ``20171107``|``-linux.x86_64``|``system`` ``20180716``|``-linux.x86_64``|``system`` @@ -15419,6 +15936,16 @@ version |toolchain ``2.2.1``|``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ``2.3.0``|``GCCcore/11.2.0`` +### kineto + +A CPU+GPU Profiling library that provides access to timeline traces and hardware performance counters + +*homepage*: + +version |toolchain +---------|-------------- +``0.4.0``|``GCC/11.3.0`` + ### king KING is a toolset that makes use of high-throughput SNP data typically seen in a genome-wide association study (GWAS) or a sequencing project. Applications of KING include family relationship inference and pedigree error checking, quality control, population substructure identification, forensics, gene mapping, etc. @@ -15463,6 +15990,16 @@ version |versionsuffix |toolchain ``3.1.2rc1``|``-Python-3.7.4``|``GCC/8.3.0`` ``3.2.1`` | |``GCC/11.2.0`` +### KMCP + +KMCP: accurate metagenomic profiling of both prokaryotic and viral populations by pseudo-mapping + +*homepage*: + +version |toolchain +---------|---------- +``0.9.1``|``system`` + ### KmerGenie KmerGenie estimates the best k-mer length for genome de novo assembly. @@ -15501,12 +16038,12 @@ Kraken is a system for assigning taxonomic labels to short DNA sequences, usual *homepage*: version |versionsuffix |toolchain ----------------|----------------|--------------------------------------------------------- +---------------|----------------|----------------------------------------------------------------------------- ``0.10.5-beta``|``-Perl-5.22.1``|``foss/2016a`` ``0.10.5-beta``|``-Perl-5.24.0``|``foss/2016b`` ``1.0`` |``-Perl-5.26.1``|``intel/2018a`` ``1.1`` |``-Perl-5.28.0``|``foss/2018b`` -``1.1.1`` | |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` +``1.1.1`` | |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.3.0``, ``GCCcore/9.3.0`` ``1.1.1`` |``-Perl-5.28.1``|``GCCcore/8.2.0`` ### Kraken2 @@ -15535,6 +16072,16 @@ version|versionsuffix |toolchain -------|-----------------|------------------------------- ``6.0``|``-Python-3.6.4``|``foss/2018a``, ``intel/2018a`` +### krbalancing + +A C++ extension for Python which computes K.R. balanced matrices. + +*homepage*: + +version |toolchain +-----------|------------------ +``0.5.0b0``|``GCCcore/11.3.0`` + ### KronaTools Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files. @@ -15591,7 +16138,7 @@ version |toolchain ## L -[L_RNA_scaffolder](#l_rna_scaffolder) - [LADR](#ladr) - [lagrangian-filtering](#lagrangian-filtering) - [LAME](#lame) - [LAMMPS](#lammps) - [lancet](#lancet) - [LAPACK](#lapack) - [LAST](#last) - [LASTZ](#lastz) - [lavaan](#lavaan) - [LBFGS++](#lbfgs++) - [LCov](#lcov) - [LDC](#ldc) - [lDDT](#lddt) - [LeadIT](#leadit) - [leidenalg](#leidenalg) - [LEMON](#lemon) - [Leptonica](#leptonica) - [LERC](#lerc) - [less](#less) - [LevelDB](#leveldb) - [lftp](#lftp) - [LHAPDF](#lhapdf) - [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) - [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) - [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) - [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) - [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) - [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) - [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) - [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) - [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) - [LBFGS++](#lbfgs++) - [LCov](#lcov) - [LDC](#ldc) - [lDDT](#lddt) - [LeadIT](#leadit) - [leidenalg](#leidenalg) - [LEMON](#lemon) - [Leptonica](#leptonica) - [LERC](#lerc) - [less](#less) - [LevelDB](#leveldb) - [lftp](#lftp) - [LHAPDF](#lhapdf) - [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) - [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) - [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) - [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) - [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) - [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) - [Lucene-Geo-Gazetteer](#lucene-geo-gazetteer) - [LUMPY](#lumpy) - [LUSCUS](#luscus) - [lwgrp](#lwgrp) - [lxml](#lxml) - [lynx](#lynx) - [lz4](#lz4) - [LZO](#lzo) ### L_RNA_scaffolder @@ -15604,6 +16151,16 @@ version |versionsuffix |toolchain ------------|----------------|--------------- ``20141124``|``-Perl-5.24.0``|``intel/2016b`` +### Lace + +Building SuperTranscripts: A linear representation of transcriptome data + +*homepage*: + +version |toolchain +----------|-------------- +``1.14.1``|``foss/2022a`` + ### LADR Prover9, Mace4, and several related programs come packaged in a system called LADR (Library for Automated Deduction Research). @@ -15631,9 +16188,9 @@ LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGP *homepage*: version |toolchain -----------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +----------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ ``3.99.5``|``foss/2016b``, ``intel/2017a`` -``3.100`` |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``intel/2017b`` +``3.100`` |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``intel/2017b`` ### LAMMPS @@ -15673,6 +16230,16 @@ version |toolchain ``3.9.1`` |``GCC/10.2.0`` ``3.10.1``|``GCC/11.2.0``, ``GCC/11.3.0`` +### LASSO-Python + +This python library is designed for general purpose usage in the field of Computer Aided Engineering (CAE). It's name originates from the original initiator and donator of the project Lasso GmbH. The library is now maintained by an open-source community. + +*homepage*: + +version |toolchain +---------|-------------- +``2.0.0``|``foss/2022b`` + ### LAST LAST finds similar regions between sequences. @@ -15775,6 +16342,7 @@ version |versionsuffix |toolchain ``0.8.3``| |``foss/2020b``, ``fosscuda/2020b`` ``0.8.7``| |``foss/2021a`` ``0.8.8``| |``foss/2021b`` +``0.9.1``| |``foss/2022a`` ### LEMON @@ -15805,9 +16373,10 @@ LERC is an open-source image or raster format which supports rapid encoding and *homepage*: -version|toolchain --------|-------------------------------------- -``3.0``|``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +version |toolchain +---------|-------------------------------------- +``3.0`` |``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +``4.0.0``|``GCCcore/12.2.0`` ### less @@ -15957,6 +16526,7 @@ version |toolchain ``1.15``|``GCCcore/10.3.0`` ``1.17``|``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``2.1`` |``GCCcore/11.3.0`` +``2.3`` |``GCCcore/12.2.0`` ### libcint @@ -16161,6 +16731,16 @@ version |toolchain ----------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ``0.8.13``|``GCC/4.8.3``, ``GCC/4.9.2``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/8.2.0``, ``GCCcore/9.3.0`` +### libemf + +Library implementation of ECMA-234 API for the generation of enhanced metafiles. + +*homepage*: + +version |toolchain +----------|------------------ +``1.0.13``|``GCCcore/11.3.0`` + ### libepoxy Epoxy is a library for handling OpenGL function pointer management for you @@ -16311,7 +16891,7 @@ version |toolchain ``2.2.5``|``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``intel/2017b``, ``intel/2018a`` ``2.3.0``|``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ``2.3.1``|``GCCcore/10.3.0`` -``2.3.3``|``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``2.3.3``|``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ### libgdiplus @@ -16345,7 +16925,7 @@ version |toolchain ``1.5.1``|``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``1.6.0``|``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ``1.7.0``|``GCCcore/11.2.0`` -``1.7.1``|``GCCcore/11.3.0`` +``1.7.1``|``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ### libgit2 @@ -16359,6 +16939,7 @@ version |toolchain ``1.1.0``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` ``1.1.1``|``GCCcore/11.2.0`` ``1.4.3``|``GCCcore/11.3.0`` +``1.5.0``|``GCCcore/12.2.0`` ### libglade @@ -16699,6 +17280,7 @@ The libnsl package contains the public client interface for NIS(YP). version |toolchain ---------|------------------ ``1.3.0``|``GCCcore/10.3.0`` +``2.0.0``|``GCCcore/11.3.0`` ### libobjcryst @@ -16718,9 +17300,9 @@ Ogg is a multimedia container format, and the native file and stream format for *homepage*: version |toolchain ----------|-------------------------------------- +---------|---------------------------------------------------------- ``1.3.4``|``GCCcore/10.2.0``, ``GCCcore/10.3.0`` -``1.3.5``|``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``1.3.5``|``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ### libopus @@ -16729,8 +17311,8 @@ Opus is a totally open, royalty-free, highly versatile audio codec. Opus is unma *homepage*: version |toolchain ----------|------------------ -``1.3.1``|``GCCcore/11.3.0`` +---------|-------------------------------------- +``1.3.1``|``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ### libosmium @@ -16818,19 +17400,10 @@ A library to handle PSML, the pseudopotential markup language. *homepage*: -version |toolchain ----------|----------------------- -``1.1.8``|``iccifort/2019.5.281`` - -### libpsml - -LibPSML provides a Fortran API to parse files in the PSeudopotential Markup Language (PSML) format. - -*homepage*: - version |toolchain ----------|----------------------------------------------------------------------------------------------------------------------------------- ``1.1.7`` |``foss/2016b``, ``foss/2017a`` +``1.1.8`` |``iccifort/2019.5.281`` ``1.1.10``|``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``iccifort/2020.4.304``, ``intel-compilers/2021.2.0``, ``intel-compilers/2021.4.0`` ### libpsortb @@ -17021,6 +17594,7 @@ version |toolchain ``1.0.28``|``GCCcore/10.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``intel/2017a`` ``1.0.31``|``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``1.1.0`` |``GCCcore/11.3.0`` +``1.2.0`` |``GCCcore/12.2.0`` ### libsodium @@ -17179,6 +17753,7 @@ version |toolchain ``1.2.6``|``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``1.3.1``|``GCCcore/10.2.0`` ``1.3.2``|``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``1.3.3``|``GCCcore/12.2.0`` ### libtool @@ -17281,8 +17856,8 @@ Ogg Vorbis is a fully open, non-proprietary, patent-and-royalty-free, general-pu *homepage*: version |toolchain ----------|------------------------------------------------------------------------------ -``1.3.7``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +---------|-------------------------------------------------------------------------------------------------- +``1.3.7``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ### libwebp @@ -17577,6 +18152,7 @@ version |versionsuffix |toolchain ``1.1.32``| |``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``1.1.33``| |``GCCcore/8.2.0`` ``1.1.34``| |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``1.1.37``| |``GCCcore/12.2.0`` ### libxsmm @@ -17969,6 +18545,7 @@ version |toolchain ``0.3.4``|``GCCcore/8.2.0`` ``0.4.1``|``GCC/7.3.0-2.30``, ``GCCcore/8.3.0`` ``0.4.3``|``GCCcore/10.2.0`` +``0.4.5``|``GCCcore/11.3.0`` ### loompy @@ -17977,9 +18554,19 @@ Python implementation of the Loom file format, an efficient file format for larg *homepage*: version |toolchain ----------|------------------------------- +---------|----------------------------------------------- ``3.0.6``|``intel/2020b`` -``3.0.7``|``foss/2021b``, ``intel/2021b`` +``3.0.7``|``foss/2021a``, ``foss/2021b``, ``intel/2021b`` + +### loomR + +An R interface for loom files + +*homepage*: + +version |versionsuffix|toolchain +------------------|-------------|-------------- +``0.2.0-20180425``|``-R-4.2.1`` |``foss/2022a`` ### LPeg @@ -18010,7 +18597,7 @@ Mixed Integer Linear Programming (MILP) solver version |toolchain ------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ``5.5.2.5`` |``GCC/6.4.0-2.28``, ``GCC/8.3.0``, ``foss/2018a``, ``iccifort/2017.4.196-GCC-6.4.0-2.28``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281``, ``intel/2017a``, ``intel/2018b`` -``5.5.2.11``|``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/9.3.0`` +``5.5.2.11``|``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0``, ``GCC/9.3.0`` ### lrslib @@ -18066,8 +18653,8 @@ LTR_retriever is a highly accurate and sensitive program for identification of *homepage*: version |toolchain ----------|-------------- -``2.9.0``|``foss/2020b`` +---------|------------------------------ +``2.9.0``|``foss/2020b``, ``foss/2022a`` ### LtrDetector @@ -18095,7 +18682,7 @@ version |toolchain ``5.3.5`` |``GCCcore/10.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``system`` ``5.4.2`` |``GCCcore/10.2.0`` ``5.4.3`` |``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``5.4.4`` |``GCCcore/11.3.0`` +``5.4.4`` |``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ### LuaJIT @@ -18222,7 +18809,7 @@ version |toolchain ## M -[M1QN3](#m1qn3) - [M4](#m4) - [MACH](#mach) - [MACS2](#macs2) - [MACSE](#macse) - [maeparser](#maeparser) - [MAFFT](#mafft) - [MAGeCK](#mageck) - [magick](#magick) - [Magics](#magics) - [MAGMA](#magma) - [magma](#magma) - [MagresPython](#magrespython) - [mahotas](#mahotas) - [MAJIQ](#majiq) - [make](#make) - [makedepend](#makedepend) - [makedepf90](#makedepf90) - [makeinfo](#makeinfo) - [Mako](#mako) - [Mamba](#mamba) - [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) - [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) - [mcu](#mcu) - [MDAnalysis](#mdanalysis) - [MDBM](#mdbm) - [MDSplus](#mdsplus) - [MDSplus-Java](#mdsplus-java) - [MDSplus-Python](#mdsplus-python) - [mdtest](#mdtest) - [MDTraj](#mdtraj) - [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) - [MethylDackel](#methyldackel) - [methylpy](#methylpy) - [METIS](#metis) - [mgltools](#mgltools) - [mhcflurry](#mhcflurry) - [mhcnuggets](#mhcnuggets) - [MicrobeAnnotator](#microbeannotator) - [microctools](#microctools) - [MiGEC](#migec) - [MIGRATE-N](#migrate-n) - [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) - [MOABS](#moabs) - [ModelTest-NG](#modeltest-ng) - [modred](#modred) - [Molcas](#molcas) - [mold](#mold) - [Molden](#molden) - [Molekel](#molekel) - [molmod](#molmod) - [Molpro](#molpro) - [MONA](#mona) - [MONAI](#monai) - [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) - [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) - [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) - [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) - [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) - [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) - [mcu](#mcu) - [MDAnalysis](#mdanalysis) - [MDBM](#mdbm) - [MDSplus](#mdsplus) - [MDSplus-Java](#mdsplus-java) - [MDSplus-Python](#mdsplus-python) - [mdtest](#mdtest) - [MDTraj](#mdtraj) - [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) - [mgltools](#mgltools) - [mhcflurry](#mhcflurry) - [mhcnuggets](#mhcnuggets) - [MicrobeAnnotator](#microbeannotator) - [microctools](#microctools) - [MiGEC](#migec) - [MIGRATE-N](#migrate-n) - [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) - [MOABS](#moabs) - [ModelTest-NG](#modeltest-ng) - [modred](#modred) - [Molcas](#molcas) - [mold](#mold) - [Molden](#molden) - [Molekel](#molekel) - [molmod](#molmod) - [Molpro](#molpro) - [MONA](#mona) - [MONAI](#monai) - [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) - [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) - [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 @@ -18295,9 +18882,9 @@ version |toolchain ### MAFFT -MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <~200 sequences), FFT-NS-2 (fast; for alignment of <~30,000 sequences), etc. +MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences), FFT-NS-2 (fast; for alignment of <∼30,000 sequences), etc. -*homepage*: +*homepage*: version |versionsuffix |toolchain ---------|--------------------|--------------------------------------------------------------------------------------- @@ -18311,6 +18898,7 @@ version |versionsuffix |toolchain ``7.475``|``-with-extensions``|``GCC/10.2.0``, ``gompi/2020b`` ``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`` ### MAGeCK @@ -18342,18 +18930,6 @@ version |toolchain ----------|--------------- ``4.13.0``|``gompi/2022a`` -### MAGMA - -MAGMA is a tool for gene analysis and generalized gene-set analysis of GWAS data. It can be used to analyse both raw genotype data as well as summary SNP p-values from a previous GWAS or meta-analysis. - -*homepage*: - -version |toolchain -----------|-------------- -``1.07b`` |``foss/2018b`` -``1.07bb``|``GCC/8.3.0`` -``1.09b`` |``GCC/11.2.0`` - ### magma The MAGMA project aims to develop a dense linear algebra library similar to LAPACK but for heterogeneous/hybrid architectures, starting with current Multicore+GPU systems. @@ -18372,6 +18948,18 @@ version |versionsuffix |toolchain ``2.6.2``|``-CUDA-11.4.1``|``foss/2021b`` ``2.6.2``|``-CUDA-11.7.0``|``foss/2022a`` +### MAGMA-gene-analysis + +MAGMA is a tool for gene analysis and generalized gene-set analysis of GWAS data. It can be used to analyse both raw genotype data as well as summary SNP p-values from a previous GWAS or meta-analysis. + +*homepage*: + +version |toolchain +----------|-------------- +``1.07b`` |``foss/2018b`` +``1.07bb``|``GCC/8.3.0`` +``1.09b`` |``GCC/11.2.0`` + ### MagresPython MagresPython is a Python library for parsing the CCP-NC ab-initio magnetic resonance file format. This is used in the latest version of the CASTEP and Quantum ESPRESSO (PWSCF) codes. @@ -18449,6 +19037,16 @@ version|versionsuffix|toolchain ``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`` +### MAKER + +MAKER is a portable and easily configurable genome annotation pipeline. Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. + +*homepage*: + +version |toolchain +-----------|-------------- +``3.01.04``|``foss/2022a`` + ### Mako A super-fast templating language that borrows the best ideas from the existing templating languages @@ -18516,6 +19114,7 @@ version |toolchain ----------|---------- ``15`` |``system`` ``2017.2``|``system`` +``2022.1``|``system`` ### MapSplice @@ -18592,11 +19191,11 @@ 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``, ``intel-compilers/2021.4.0`` +``2.3``|``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0``, ``intel-compilers/2021.4.0`` ### MaSuRCA @@ -18613,6 +19212,7 @@ version |versionsuffix |toolchain ``3.3.1``|``-Perl-5.28.0``|``foss/2018b`` ``4.0.1``|``-Perl-5.30.2``|``foss/2020a`` ``4.0.9``|``-Perl-5.32.1``|``foss/2021a`` +``4.1.0``| |``GCC/11.3.0`` ### Mathematica @@ -18632,6 +19232,7 @@ version |toolchain ``12.0.0``|``system`` ``12.1.1``|``system`` ``13.0.0``|``system`` +``13.1.0``|``system`` ### MathGL @@ -18657,6 +19258,7 @@ version |toolchain ``1.5.17``|``GCCcore/8.3.0`` ``1.5.19``|``GCCcore/9.3.0`` ``1.5.21``|``GCCcore/10.2.0`` +``1.5.23``|``GCCcore/11.3.0`` ### MATLAB @@ -18664,19 +19266,22 @@ MATLAB is a high-level language and interactive environment that enables you to *homepage*: -version |toolchain ----------|---------- -``2012b``|``system`` -``2013b``|``system`` -``2015a``|``system`` -``2016a``|``system`` -``2017a``|``system`` -``2018b``|``system`` -``2019b``|``system`` -``2020a``|``system`` -``2020b``|``system`` -``2021a``|``system`` -``2021b``|``system`` +version |versionsuffix|toolchain +---------|-------------|---------- +``2012b``| |``system`` +``2013b``| |``system`` +``2015a``| |``system`` +``2016a``| |``system`` +``2017a``| |``system`` +``2018b``| |``system`` +``2019b``| |``system`` +``2020a``| |``system`` +``2020b``| |``system`` +``2021a``| |``system`` +``2021b``| |``system`` +``2022a``| |``system`` +``2022a``|``-r3`` |``system`` +``2022b``| |``system`` ### MATLAB-Engine @@ -18751,6 +19356,7 @@ version |versionsuffix |toolchain ``3.4.3``| |``foss/2021b``, ``intel/2021b`` ``3.5.1``| |``foss/2020b``, ``intel/2020b`` ``3.5.2``| |``foss/2021b``, ``foss/2022a``, ``intel/2022a`` +``3.7.0``| |``gfbf/2022b`` ### matplotlib-inline @@ -18842,6 +19448,7 @@ version |toolchain -------------|------------------ ``1.6.10.43``|``foss/2018b`` ``2.0.3.0`` |``GCCcore/11.2.0`` +``2.2.0.0`` |``GCCcore/11.2.0`` ### mayavi @@ -18911,14 +19518,15 @@ version |toolchain The MCL algorithm is short for the Markov Cluster Algorithm, a fast and scalable unsupervised cluster algorithm for graphs (also known as networks) based on simulation of (stochastic) flow in graphs. -*homepage*: +*homepage*: version |versionsuffix |toolchain -----------|----------------|------------------------------------------------------------------------------------------------------------- +----------|----------------|--------------------------------------------------------------------------------------------------------------------------------- ``02.063``| |``intel/2016b`` -``14.137``| |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``intel/2016b`` +``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`` ### MCR @@ -18972,6 +19580,7 @@ version |versionsuffix |toolchain ``1.1.1`` | |``foss/2020b`` ``2.0.0`` | |``foss/2021a``, ``foss/2021b``, ``intel/2021b`` ``2.2.0`` | |``foss/2022a`` +``2.4.2`` | |``foss/2022b`` ### MDBM @@ -19122,14 +19731,14 @@ An ultra-fast single-node solution for large and complex metagenomics assembly *homepage*: version |versionsuffix |toolchain ----------|------------------|------------------------------------------------------------------------- +---------|------------------|--------------------------------------------------------------------------------------------- ``1.1.2``|``-Python-2.7.14``|``foss/2018a`` ``1.1.3``|``-Python-2.7.14``|``foss/2017b``, ``foss/2018a`` ``1.1.3``|``-Python-3.6.3`` |``foss/2017b`` ``1.1.4``|``-Python-2.7.15``|``foss/2018b`` ``1.1.4``|``-Python-3.6.6`` |``foss/2018b`` ``1.2.8``| |``GCCcore/8.2.0`` -``1.2.9``| |``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0``, ``foss/2018b`` +``1.2.9``| |``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/9.3.0``, ``foss/2018b`` ``1.2.9``|``-Python-2.7.18``|``GCCcore/10.2.0`` ### Megalodon @@ -19395,10 +20004,10 @@ An efficient tool for accurately reconstructing single genomes from complex micr *homepage*: version |versionsuffix |toolchain -----------|------------------|-------------------------------- +----------|------------------|------------------------------------------------ ``2.12.1``|``-Python-2.7.15``|``foss/2018b`` ``2.14`` | |``gompi/2019a`` -``2.15`` | |``gompi/2021a``, ``gompi/2021b`` +``2.15`` | |``GCC/11.2.0``, ``gompi/2021a``, ``gompi/2021b`` ``2.15`` |``-Python-2.7.18``|``gompi/2020b`` ### MetaboAnalystR @@ -19428,10 +20037,10 @@ MetaEuk is a modular toolkit designed for large-scale gene discovery and annotat *homepage*: version|toolchain --------|-------------- +-------|------------------------------ ``4`` |``GCC/10.2.0`` ``5`` |``GCC/10.3.0`` -``6`` |``GCC/11.2.0`` +``6`` |``GCC/11.2.0``, ``GCC/11.3.0`` ### MetaGeneAnnotator @@ -19518,6 +20127,16 @@ version|toolchain -------|--------------- ``2.2``|``gompi/2019a`` +### methylartist + +Tools for plotting methylation data in various ways + +*homepage*: + +version |toolchain +---------|-------------- +``1.2.6``|``foss/2021b`` + ### MethylDackel A (mostly) universal methylation extractor for BS-seq experiments. @@ -19548,9 +20167,9 @@ METIS is a set of serial programs for partitioning graphs, partitioning finite e *homepage*: version |versionsuffix|toolchain ----------|-------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ +---------|-------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ``5.0.2``| |``gimkl/2.11.5`` -``5.1.0``| |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``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/2018b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` +``5.1.0``| |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``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/2018b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` ``5.1.0``|``-32bitIDX``|``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` ### mgltools @@ -19729,15 +20348,16 @@ Miniconda is a free minimal installer for conda. It is a small, bootstrap versi *homepage*: -version |toolchain -----------|---------- -``4.4.10``|``system`` -``4.5.12``|``system`` -``4.6.14``|``system`` -``4.7.10``|``system`` -``4.8.3`` |``system`` -``4.9.2`` |``system`` -``4.12.0``|``system`` +version |toolchain +-------------|---------- +``4.4.10`` |``system`` +``4.5.12`` |``system`` +``4.6.14`` |``system`` +``4.7.10`` |``system`` +``4.8.3`` |``system`` +``4.9.2`` |``system`` +``4.12.0`` |``system`` +``22.11.1-1``|``system`` ### minieigen @@ -19779,7 +20399,7 @@ version |toolchain ``2.18`` |``GCCcore/10.2.0`` ``2.20`` |``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ``2.22`` |``GCCcore/11.2.0`` -``2.24`` |``GCCcore/11.2.0`` +``2.24`` |``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ### Minipolish @@ -19988,13 +20608,14 @@ version |versionsuffix |toolchain ### mm-common -The mm-common module provides the build infrastructure and utilities shared among the GNOME C++ binding libraries. +The mm-common module provides the build infrastructure and utilities shared among the GNOME C++ binding libraries. *homepage*: version |toolchain ---------|------------------ ``1.0.4``|``GCCcore/10.3.0`` +``1.0.5``|``GCCcore/11.3.0`` ### Mmg @@ -20304,10 +20925,10 @@ 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/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/8.3.0``, ``GCCcore/9.3.0``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``foss/2019a``, ``intel/2017b``, ``intel/2018a``, ``intel/2019a`` ### MotionCor2 @@ -20383,12 +21004,13 @@ version |toolchain ``4.0.1``|``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``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`` ### mpi4py MPI for Python (mpi4py) provides bindings of the Message Passing Interface (MPI) standard for the Python programming language, allowing any Python program to exploit multiple processors. -*homepage*: +*homepage*: version |versionsuffix |toolchain ---------|---------------------------------|-------------------------------- @@ -20400,6 +21022,7 @@ version |versionsuffix |toolchain ``3.0.0``|``-Python-3.6.3`` |``intel/2017b`` ``3.0.1``|``-Python-3.6.6`` |``intel/2018b`` ``3.0.2``|``-timed-pingpong`` |``gompi/2019a``, ``iimpi/2019a`` +``3.1.4``| |``gompi/2022b`` ### MPICH @@ -20464,11 +21087,12 @@ mpmath can be used as an arbitrary-precision substitute for Python's float/compl *homepage*: version |versionsuffix |toolchain ----------|------------------|------------------------------- +---------|------------------|------------------------------------------------------------------------------ ``0.19`` |``-Python-2.7.11``|``foss/2016a``, ``intel/2016a`` ``1.0.0``|``-Python-2.7.14``|``intel/2018a`` ``1.0.0``|``-Python-2.7.15``|``foss/2018b`` ``1.1.0``|``-Python-3.8.2`` |``GCCcore/9.3.0`` +``1.2.1``| |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ### MrBayes @@ -20477,9 +21101,9 @@ MrBayes is a program for Bayesian inference and model choice across a wide rang *homepage*: version |toolchain -----------|----------------------------------------------- +----------|-------------------------------------------------- ``3.2.6`` |``foss/2016a``, ``foss/2017a``, ``gompi/2020b`` -``3.2.7`` |``gompi/2020b``, ``gompic/2019b`` +``3.2.7`` |``gompi/2020b``, ``gompi/2022a``, ``gompic/2019b`` ``3.2.7a``|``foss/2020a``, ``iimpi/2019a`` ### mrcfile @@ -20581,6 +21205,7 @@ msprime is a coalescent simulator and library for processing tree-based genetic version |versionsuffix |toolchain ---------|-----------------|--------------- ``0.7.0``|``-Python-3.7.2``|``intel/2019a`` +``1.2.0``| |``foss/2021b`` ### mstore @@ -20675,6 +21300,7 @@ version |versionsuffix |toolchain ``1.10.1``| |``foss/2020b`` ``1.11`` | |``foss/2021a`` ``1.12`` | |``foss/2021b`` +``1.14`` | |``foss/2022a`` ### Multiwfn @@ -20701,13 +21327,13 @@ version |toolchain MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. AMOS makes use of it. -*homepage*: +*homepage*: version |toolchain --------------|------------------------------------------------------------------------- ``3.23`` |``GCCcore/10.3.0``, ``GCCcore/9.3.0``, ``foss/2016b`` ``4.0.0beta2``|``GCCcore/10.2.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0``, ``foss/2018b`` -``4.0.0rc1`` |``GCCcore/11.2.0`` +``4.0.0rc1`` |``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ### MUMPS @@ -20852,7 +21478,7 @@ version |toolchain Flexible and Efficient Library for Deep Learning -*homepage*: +*homepage*: version |versionsuffix |toolchain ---------|--------------------------|-------------- @@ -20877,6 +21503,7 @@ Python Client for MyGene.Info services. version |toolchain ---------|--------------- ``3.1.0``|``intel/2019a`` +``3.2.2``|``foss/2022a`` ### MyMediaLite @@ -20959,7 +21586,7 @@ version |versionsuffix |toolchain ## N -[n2v](#n2v) - [NAG](#nag) - [NAGfor](#nagfor) - [NAMD](#namd) - [namedlist](#namedlist) - [nano](#nano) - [NanoComp](#nanocomp) - [nanocompore](#nanocompore) - [NanoFilt](#nanofilt) - [nanofilt](#nanofilt) - [nanoget](#nanoget) - [NanoLyse](#nanolyse) - [nanomath](#nanomath) - [nanomax-analysis-utils](#nanomax-analysis-utils) - [nanonet](#nanonet) - [NanoPlot](#nanoplot) - [nanopolish](#nanopolish) - [NanopolishComp](#nanopolishcomp) - [napari](#napari) - [NASM](#nasm) - [nauty](#nauty) - [NBO](#nbo) - [NCBI-Toolkit](#ncbi-toolkit) - [ncbi-vdb](#ncbi-vdb) - [NCCL](#nccl) - [NCCL-tests](#nccl-tests) - [ncdf4](#ncdf4) - [ncdu](#ncdu) - [NCIPLOT](#nciplot) - [NCL](#ncl) - [ncl](#ncl) - [NCO](#nco) - [ncompress](#ncompress) - [ncurses](#ncurses) - [ncview](#ncview) - [nd2reader](#nd2reader) - [ne](#ne) - [NECI](#neci) - [NEdit](#nedit) - [Nek5000](#nek5000) - [Nektar++](#nektar++) - [neon](#neon) - [neptune-client](#neptune-client) - [Net-core](#net-core) - [netCDF](#netcdf) - [netCDF-C++](#netcdf-c++) - [netCDF-C++4](#netcdf-c++4) - [netCDF-Fortran](#netcdf-fortran) - [netcdf4-python](#netcdf4-python) - [netloc](#netloc) - [NetLogo](#netlogo) - [netMHC](#netmhc) - [netMHCIIpan](#netmhciipan) - [netMHCpan](#netmhcpan) - [NetPIPE](#netpipe) - [NetPyNE](#netpyne) - [nettle](#nettle) - [networkTools](#networktools) - [networkx](#networkx) - [NeuroKit](#neurokit) - [NEURON](#neuron) - [NewHybrids](#newhybrids) - [Nextflow](#nextflow) - [NextGenMap](#nextgenmap) - [nf-core-mag](#nf-core-mag) - [NFFT](#nfft) - [nghttp2](#nghttp2) - [nghttp3](#nghttp3) - [NGLess](#ngless) - [nglview](#nglview) - [NGS](#ngs) - [NGS-Python](#ngs-python) - [NGSadmix](#ngsadmix) - [NGSpeciesID](#ngspeciesid) - [ngspice](#ngspice) - [ngtcp2](#ngtcp2) - [NiBabel](#nibabel) - [NIfTI](#nifti) - [nifti2dicom](#nifti2dicom) - [Nilearn](#nilearn) - [Nim](#nim) - [NIMBLE](#nimble) - [Ninja](#ninja) - [Nipype](#nipype) - [NLMpy](#nlmpy) - [nlohmann_json](#nlohmann_json) - [NLopt](#nlopt) - [NLTK](#nltk) - [nnU-Net](#nnu-net) - [Node-RED](#node-red) - [nodejs](#nodejs) - [Normaliz](#normaliz) - [nose-parameterized](#nose-parameterized) - [novoalign](#novoalign) - [NOVOPlasty](#novoplasty) - [npstat](#npstat) - [NRGLjubljana](#nrgljubljana) - [Nsight-Compute](#nsight-compute) - [Nsight-Systems](#nsight-systems) - [NSPR](#nspr) - [NSS](#nss) - [nsync](#nsync) - [ntCard](#ntcard) - [ntEdit](#ntedit) - [ntHits](#nthits) - [NTL](#ntl) - [NTPoly](#ntpoly) - [num2words](#num2words) - [numactl](#numactl) - [numba](#numba) - [numdiff](#numdiff) - [numexpr](#numexpr) - [numpy](#numpy) - [NVHPC](#nvhpc) - [nvofbf](#nvofbf) - [nvompi](#nvompi) - [NVSHMEM](#nvshmem) - [nvtop](#nvtop) - [NWChem](#nwchem) - [NxTrim](#nxtrim) +[n2v](#n2v) - [NAG](#nag) - [NAGfor](#nagfor) - [NAMD](#namd) - [namedlist](#namedlist) - [nano](#nano) - [NanoComp](#nanocomp) - [nanocompore](#nanocompore) - [NanoFilt](#nanofilt) - [nanoflann](#nanoflann) - [nanoget](#nanoget) - [NanoLyse](#nanolyse) - [nanomath](#nanomath) - [nanomax-analysis-utils](#nanomax-analysis-utils) - [nanonet](#nanonet) - [NanoPlot](#nanoplot) - [nanopolish](#nanopolish) - [NanopolishComp](#nanopolishcomp) - [napari](#napari) - [NASM](#nasm) - [nauty](#nauty) - [NBO](#nbo) - [NCBI-Toolkit](#ncbi-toolkit) - [ncbi-vdb](#ncbi-vdb) - [NCCL](#nccl) - [NCCL-tests](#nccl-tests) - [ncdf4](#ncdf4) - [ncdu](#ncdu) - [NCIPLOT](#nciplot) - [NCL](#ncl) - [NCO](#nco) - [ncompress](#ncompress) - [ncurses](#ncurses) - [ncview](#ncview) - [nd2reader](#nd2reader) - [ne](#ne) - [NECI](#neci) - [NEdit](#nedit) - [Nek5000](#nek5000) - [Nektar++](#nektar++) - [neon](#neon) - [neptune-client](#neptune-client) - [Net-core](#net-core) - [netCDF](#netcdf) - [netCDF-C++](#netcdf-c++) - [netCDF-C++4](#netcdf-c++4) - [netCDF-Fortran](#netcdf-fortran) - [netcdf4-python](#netcdf4-python) - [netloc](#netloc) - [NetLogo](#netlogo) - [netMHC](#netmhc) - [netMHCII](#netmhcii) - [netMHCIIpan](#netmhciipan) - [netMHCpan](#netmhcpan) - [NetPIPE](#netpipe) - [NetPyNE](#netpyne) - [nettle](#nettle) - [networkTools](#networktools) - [networkx](#networkx) - [NeuroKit](#neurokit) - [NEURON](#neuron) - [NewHybrids](#newhybrids) - [Nextflow](#nextflow) - [NextGenMap](#nextgenmap) - [NEXUS-CL](#nexus-cl) - [nf-core-mag](#nf-core-mag) - [NFFT](#nfft) - [nghttp2](#nghttp2) - [nghttp3](#nghttp3) - [NGLess](#ngless) - [nglview](#nglview) - [NGS](#ngs) - [NGS-Python](#ngs-python) - [NGSadmix](#ngsadmix) - [NGSpeciesID](#ngspeciesid) - [ngspice](#ngspice) - [ngtcp2](#ngtcp2) - [NiBabel](#nibabel) - [nichenetr](#nichenetr) - [NIfTI](#nifti) - [nifti2dicom](#nifti2dicom) - [Nilearn](#nilearn) - [Nim](#nim) - [NIMBLE](#nimble) - [Ninja](#ninja) - [Nipype](#nipype) - [NLMpy](#nlmpy) - [nlohmann_json](#nlohmann_json) - [NLopt](#nlopt) - [NLTK](#nltk) - [nnU-Net](#nnu-net) - [Node-RED](#node-red) - [nodejs](#nodejs) - [Normaliz](#normaliz) - [nose-parameterized](#nose-parameterized) - [novoalign](#novoalign) - [NOVOPlasty](#novoplasty) - [npstat](#npstat) - [NRGLjubljana](#nrgljubljana) - [Nsight-Compute](#nsight-compute) - [Nsight-Systems](#nsight-systems) - [NSPR](#nspr) - [NSS](#nss) - [nsync](#nsync) - [ntCard](#ntcard) - [ntEdit](#ntedit) - [ntHits](#nthits) - [NTL](#ntl) - [NTPoly](#ntpoly) - [num2words](#num2words) - [numactl](#numactl) - [numba](#numba) - [numdiff](#numdiff) - [numexpr](#numexpr) - [numpy](#numpy) - [NVHPC](#nvhpc) - [nvofbf](#nvofbf) - [nvompi](#nvompi) - [NVSHMEM](#nvshmem) - [nvtop](#nvtop) - [NWChem](#nwchem) - [NxTrim](#nxtrim) ### n2v @@ -21006,9 +21633,9 @@ version |versionsuffix |toolchain ``2.12``|``-mpi`` |``foss/2017a``, ``foss/2017b``, ``intel/2017a``, ``intel/2017b`` ``2.13``| |``fosscuda/2018b`` ``2.13``|``-mpi`` |``foss/2018b``, ``foss/2019b``, ``intel/2018b`` -``2.14``| |``fosscuda/2019b`` +``2.14``| |``fosscuda/2019b``, ``fosscuda/2020b`` ``2.14``|``-CUDA-11.3.1``|``foss/2021a`` -``2.14``|``-mpi`` |``foss/2019b``, ``foss/2020a``, ``intel/2020a`` +``2.14``|``-mpi`` |``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``intel/2020a`` ### namedlist @@ -21030,6 +21657,7 @@ version|toolchain -------|------------------ ``6.4``|``GCCcore/11.3.0`` ``7.0``|``GCCcore/11.3.0`` +``7.1``|``GCCcore/12.2.0`` ### NanoComp @@ -21059,21 +21687,21 @@ Filtering and trimming of long read sequencing data. *homepage*: version |versionsuffix |toolchain ----------|-----------------|--------------- -``2.6.0``|``-Python-3.7.4``|``intel/2019b`` +---------|-----------------|------------------------------- +``2.5.0``|``-Python-3.6.6``|``foss/2018b`` +``2.6.0``|``-Python-3.7.4``|``foss/2019b``, ``intel/2019b`` +``2.6.0``|``-Python-3.8.2``|``intel/2020a`` ``2.8.0``| |``foss/2021b`` -### nanofilt +### nanoflann -Filtering and trimming of long read sequencing data. +nanoflann is a C++11 header-only library for building KD-Trees of datasets with different topologies. -*homepage*: +*homepage*: -version |versionsuffix |toolchain ----------|-----------------|--------------- -``2.5.0``|``-Python-3.6.6``|``foss/2018b`` -``2.6.0``|``-Python-3.7.4``|``foss/2019b`` -``2.6.0``|``-Python-3.8.2``|``intel/2020a`` +version |toolchain +---------|------------------ +``1.4.0``|``GCCcore/10.3.0`` ### nanoget @@ -21119,6 +21747,7 @@ version |versionsuffix |toolchain ---------|-----------------|---------------------------------- ``0.4`` |``-Python-3.7.4``|``foss/2019b``, ``fosscuda/2019b`` ``0.4.3``| |``foss/2020b``, ``fosscuda/2020b`` +``0.4.4``| |``foss/2021b`` ### nanonet @@ -21241,7 +21870,8 @@ version |toolchain ``2.10.7`` |``gompi/2020a`` ``2.10.9`` |``gompi/2020b``, ``gompi/2021a`` ``2.11.2`` |``gompi/2021b`` -``3.0.0`` |``gompi/2022a`` +``3.0.0`` |``gompi/2021b``, ``gompi/2022a`` +``3.0.2`` |``gompi/2022a`` ### NCCL @@ -21332,16 +21962,6 @@ version |toolchain ``6.5.0``|``intel/2018a`` ``6.6.2``|``foss/2018b``, ``foss/2020a``, ``foss/2020b``, ``foss/2021a``, ``intel/2018b``, ``intel/2019b``, ``intel/2020a`` -### ncl - -The NEXUS Class Library is a C++ library for parsing NEXUS files. - -*homepage*: - -version |toolchain -----------|-------------------- -``2.1.18``|``GCC/8.2.0-2.31.1`` - ### NCO The NCO toolkit manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5. @@ -21363,7 +21983,7 @@ version |toolchain ``5.0.1``|``foss/2021a`` ``5.0.3``|``foss/2021b``, ``intel/2021b`` ``5.1.0``|``foss/2022a`` -``5.1.3``|``foss/2021a`` +``5.1.3``|``foss/2021a``, ``foss/2022a`` ### ncompress @@ -21517,7 +22137,7 @@ version |versionsuffix |toolchain ``4.7.4`` | |``gompi/2020a``, ``gompi/2020b``, ``gompic/2020a``, ``gompic/2020b``, ``iimpi/2020a``, ``iimpi/2020b``, ``iimpic/2020b`` ``4.8.0`` | |``gompi/2021a``, ``iimpi/2021a`` ``4.8.1`` | |``gompi/2021b``, ``iimpi/2021b`` -``4.9.0`` | |``gompi/2022a``, ``iimpi/2022a`` +``4.9.0`` | |``gompi/2022a``, ``gompi/2022b``, ``iimpi/2022a``, ``iimpi/2022b`` ### netCDF-C++ @@ -21607,17 +22227,29 @@ version |versionsuffix|toolchain ``5.3.1``|``-64`` |``system`` ``6.0.4``|``-64`` |``system`` ``6.2.0``|``-64`` |``system`` +``6.2.2``|``-64`` |``system`` +``6.3.0``|``-64`` |``system`` ### netMHC -NetMHC 4.0 software predicts binding of peptides to a number of different HLA alleles using artificial neural networks (ANN). +NetMHC 4.0 predicts binding of peptides to a number of different HLA alleles using artificial neural networks (ANN). -*homepage*: +*homepage*: version |toolchain --------|---------- ``4.0a``|``system`` +### netMHCII + +NetMHCII 2.3 server predicts binding of peptides to HLA-DR, HLA-DQ, HLA-DP and mouse MHC class II alleles using articial neuron networks. Predictions can be obtained for 25 HLA-DR alleles, 20 HLA-DQ, 9 HLA-DP, and 7 mouse H2 class II alleles. + +*homepage*: + +version|toolchain +-------|---------- +``2.3``|``system`` + ### netMHCIIpan NetMHCIIpan 3.2 server predicts binding of peptides to MHC class II molecules. The predictions are available for the three human MHC class II isotypes HLA-DR, HLA-DP and HLA-DQ, as well as mouse molecules (H-2). @@ -21630,9 +22262,9 @@ version|toolchain ### netMHCpan -The NetMHCpan software predicts binding of peptides to any known MHC molecule using artificial neural networks (ANNs). +The NetMHCpan software predicts binding of peptides to any known MHC molecule using artificial neural networks (ANNs). -*homepage*: +*homepage*: version |toolchain --------|---------- @@ -21677,6 +22309,7 @@ version |toolchain ``3.7.2``|``GCCcore/10.3.0`` ``3.7.3``|``GCCcore/11.2.0`` ``3.8`` |``GCCcore/11.3.0`` +``3.8.1``|``GCCcore/12.2.0`` ### networkTools @@ -21713,7 +22346,8 @@ version |versionsuffix |toolchain ``2.5.1``| |``foss/2021a`` ``2.6.2``| |``foss/2020b`` ``2.6.3``| |``foss/2021a``, ``foss/2021b``, ``intel/2021b`` -``2.8.4``| |``foss/2022a`` +``2.8.4``| |``foss/2022a``, ``intel/2022a`` +``3.0`` | |``foss/2022b`` ### NeuroKit @@ -21767,6 +22401,8 @@ version |toolchain ``22.04.0``|``system`` ``22.10.0``|``system`` ``22.10.1``|``system`` +``22.10.5``|``system`` +``22.10.6``|``system`` ### NextGenMap @@ -21778,6 +22414,16 @@ version |toolchain ---------|------------------------------ ``0.5.5``|``GCC/11.2.0``, ``foss/2016b`` +### NEXUS-CL + +The NEXUS Class Library is a C++ library for parsing NEXUS files. + +*homepage*: + +version |toolchain +----------|-------------------- +``2.1.18``|``GCC/8.2.0-2.31.1`` + ### nf-core-mag The Nextflow pipeline 'mag' ported to EasyBuild/EESSI. @@ -21939,6 +22585,16 @@ version |versionsuffix |toolchain ``3.2.2``| |``foss/2021b`` ``4.0.2``| |``foss/2022a`` +### nichenetr + +R implementation of the NicheNet method, to predict active ligand-target links between interacting cells + +*homepage*: + +version |versionsuffix|toolchain +------------------|-------------|-------------- +``1.1.1-20230223``|``-R-4.2.1`` |``foss/2022a`` + ### NIfTI Niftilib is a set of i/o libraries for reading and writing files in the nifti-1 data format. @@ -22047,6 +22703,7 @@ version |toolchain ``3.10.0``|``GCCcore/10.3.0`` ``3.10.4``|``GCCcore/11.2.0`` ``3.10.5``|``GCCcore/11.3.0`` +``3.11.2``|``GCCcore/12.2.0`` ### NLopt @@ -22060,7 +22717,7 @@ version |toolchain ``2.6.1``|``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``2.6.2``|``GCCcore/10.2.0`` ``2.7.0``|``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``2.7.1``|``GCCcore/11.3.0`` +``2.7.1``|``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ### NLTK @@ -22354,6 +23011,8 @@ version |versionsuffix |toolchain ``0.53.1``| |``foss/2020b``, ``foss/2021a``, ``fosscuda/2020b`` ``0.54.1``| |``foss/2021b``, ``intel/2021b`` ``0.54.1``|``-CUDA-11.4.1`` |``foss/2021b`` +``0.56.4``| |``foss/2022a`` +``0.56.4``|``-CUDA-11.7.0`` |``foss/2022a`` ### numdiff @@ -22424,6 +23083,9 @@ version |versionsuffix |toolchain ``21.9`` | |``system`` ``21.11``| |``system`` ``22.7`` |``-CUDA-11.7.0``|``system`` +``22.9`` |``-CUDA-11.7.0``|``system`` +``22.11``|``-CUDA-11.7.0``|``system`` +``23.1`` |``-CUDA-12.0.0``|``system`` ### nvofbf @@ -22456,6 +23118,7 @@ version |versionsuffix |toolchain ``2.4.1``|``-CUDA-11.4.1``|``gompi/2021b`` ``2.5.0``|``-CUDA-11.7.0``|``gompi/2022a`` ``2.7.0``|``-CUDA-11.7.0``|``gompi/2022a`` +``2.8.0``|``-CUDA-11.7.0``|``gompi/2022a`` ### nvtop @@ -22552,9 +23215,9 @@ Open CASCADE Technology (OCCT) is an object-oriented C++ class library designed *homepage*: version |toolchain ------------|-------------- +-----------|------------------------------ ``7.3.0p4``|``foss/2019b`` -``7.5.0p1``|``foss/2021a`` +``7.5.0p1``|``foss/2021a``, ``foss/2022a`` ### oceanspy @@ -22734,7 +23397,7 @@ version |toolchain ``2.0`` |``foss/2016a`` ``2.0.5``|``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``2.0.6``|``GCCcore/10.2.0``, ``GCCcore/10.3.0`` -``2.0.7``|``GCCcore/11.3.0`` +``2.0.7``|``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ### Open-Data-Cube-Core @@ -22894,7 +23557,7 @@ OpenEXR is a high dynamic-range (HDR) image file format developed by Industrial *homepage*: version |toolchain ----------|-------------------------------- +---------|-------------------------------------- ``2.2.0``|``intel/2016b``, ``intel/2017a`` ``2.3.0``|``foss/2018b``, ``intel/2018b`` ``2.4.0``|``GCCcore/8.3.0`` @@ -22902,7 +23565,7 @@ version |toolchain ``2.5.5``|``GCCcore/10.2.0`` ``3.0.1``|``GCCcore/10.3.0`` ``3.1.1``|``GCCcore/11.2.0`` -``3.1.5``|``GCCcore/11.3.0`` +``3.1.5``|``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ### OpenFace @@ -23057,17 +23720,18 @@ OpenMM is a toolkit for molecular simulation. *homepage*: -version |versionsuffix |toolchain ----------|-------------------|--------------------------------------------------- -``7.1.1``|``-Python-3.6.3`` |``intel/2017b`` -``7.4.1``|``-Python-3.7.4`` |``foss/2019b``, ``intel/2019b`` -``7.4.2``|``-Python-3.8.2`` |``intel/2020a`` -``7.5.0``| |``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` -``7.5.0``|``-Python-3.8.2`` |``fosscuda/2020a``, ``intel/2020a`` -``7.5.1``| |``foss/2020b``, ``fosscuda/2020b`` -``7.5.1``|``-DeepMind-patch``|``foss/2021a`` -``7.7.0``| |``foss/2021a``, ``foss/2022a`` -``7.7.0``|``-CUDA-11.3.1`` |``foss/2021a`` +version |versionsuffix |toolchain +---------|-------------------------------|--------------------------------------------------- +``7.1.1``|``-Python-3.6.3`` |``intel/2017b`` +``7.4.1``|``-Python-3.7.4`` |``foss/2019b``, ``intel/2019b`` +``7.4.2``|``-Python-3.8.2`` |``intel/2020a`` +``7.5.0``| |``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` +``7.5.0``|``-Python-3.8.2`` |``fosscuda/2020a``, ``intel/2020a`` +``7.5.1``| |``foss/2020b``, ``fosscuda/2020b`` +``7.5.1``|``-CUDA-11.3.1-DeepMind-patch``|``foss/2021a`` +``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`` ### OpenMM-PLUMED @@ -23150,9 +23814,10 @@ version |versionsuffix |toolchain ``4.0.6`` | |``GCC/10.3.0`` ``4.0.7`` | |``GCC/10.3.0`` ``4.1.0`` | |``GCC/10.2.0`` -``4.1.1`` | |``GCC/10.3.0``, ``GCC/11.2.0``, ``intel-compilers/2021.2.0`` +``4.1.1`` | |``GCC/10.3.0``, ``GCC/11.2.0``, ``intel-compilers/2021.2.0``, ``intel-compilers/2021.4.0`` ``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`` ``system``| |``GCC/system-2.29`` ### OpenMS @@ -23267,7 +23932,7 @@ version |toolchain ### OpenSSL -The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) protocols as well as a full-strength general purpose cryptography library. +The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) protocols as well as a full-strength general purpose cryptography library. *homepage*: @@ -23357,6 +24022,7 @@ version |toolchain ----------|-------------- ``2.9.1`` |``foss/2021a`` ``2.10.0``|``foss/2021b`` +``3.1.0`` |``foss/2022a`` ### OR-Tools @@ -23389,6 +24055,7 @@ version |versionsuffix |toolchain ``5.0.2`` | |``gompi/2021a``, ``gompi/2021b`` ``5.0.2`` |``-static`` |``gompi/2021a``, ``gompi/2021b`` ``5.0.3`` | |``gompi/2021b`` +``5.0.4`` | |``gompi/2022a`` ### ORFfinder @@ -23474,7 +24141,7 @@ version |versionsuffix |toolchain ``5.7.1``| |``ffmpi/4.5.0``, ``gompi/2021a``, ``gompi/2021b``, ``iimpi/2021a``, ``iompi/2021a`` ``5.7.1``|``-CUDA-11.3.1``|``gompi/2021a`` ``5.8`` | |``iimpi/2021b`` -``5.9`` | |``gompi/2022.05``, ``gompi/2022a`` +``5.9`` | |``gompi/2022.05``, ``gompi/2022a``, ``iimpi/2022a`` ``5.9`` |``-CUDA-11.3.1``|``gompi/2021a`` ``5.9`` |``-CUDA-11.4.1``|``gompi/2021b`` ``5.9`` |``-CUDA-11.7.0``|``gompi/2022a`` @@ -23493,7 +24160,7 @@ version |toolchain ``2.2`` |``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``2.3`` |``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ``3.0`` |``GCCcore/11.3.0`` -``3.0.2``|``GCCcore/11.3.0`` +``3.0.2``|``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ### OVITO @@ -23529,7 +24196,7 @@ 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) - [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) - [ParallelIO](#parallelio) - [parameterized](#parameterized) - [parasail](#parasail) - [Paraver](#paraver) - [ParaView](#paraview) - [Parcels](#parcels) - [PARI-GP](#pari-gp) - [ParmEd](#parmed) - [ParMETIS](#parmetis) - [ParMGridGen](#parmgridgen) - [PartitionFinder](#partitionfinder) - [pasta](#pasta) - [PaStiX](#pastix) - [patch](#patch) - [patchelf](#patchelf) - [path.py](#path.py) - [PAUP](#paup) - [pauvre](#pauvre) - [pbbam](#pbbam) - [pbcopper](#pbcopper) - [pbdagcon](#pbdagcon) - [pbmm2](#pbmm2) - [pbs_python](#pbs_python) - [PBSuite](#pbsuite) - [PCAngsd](#pcangsd) - [PCC](#pcc) - [PCL](#pcl) - [PCMSolver](#pcmsolver) - [PCRaster](#pcraster) - [PCRE](#pcre) - [PCRE2](#pcre2) - [PDT](#pdt) - [PEAR](#pear) - [PennCNV](#penncnv) - [PEPT](#pept) - [Percolator](#percolator) - [Perl](#perl) - [perl-app-cpanminus](#perl-app-cpanminus) - [Perl4-CoreLibs](#perl4-corelibs) - [PEST++](#pest++) - [PETSc](#petsc) - [petsc4py](#petsc4py) - [pfind](#pfind) - [pftoolsV3](#pftoolsv3) - [pFUnit](#pfunit) - [PGDSpider](#pgdspider) - [PGI](#pgi) - [PHANOTATE](#phanotate) - [Phantompeakqualtools](#phantompeakqualtools) - [PHASE](#phase) - [PHAST](#phast) - [PheWAS](#phewas) - [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) - [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) - [pIRS](#pirs) - [Pisces](#pisces) - [piSvM](#pisvm) - [piSvM-JSC](#pisvm-jsc) - [pixman](#pixman) - [pizzly](#pizzly) - [pkg-config](#pkg-config) - [pkgconf](#pkgconf) - [pkgconfig](#pkgconfig) - [plantcv](#plantcv) - [PlaScope](#plascope) - [PlasmaPy](#plasmapy) - [PLAST](#plast) - [Platanus](#platanus) - [Platypus](#platypus) - [plc](#plc) - [PLINK](#plink) - [plinkQC](#plinkqc) - [PLINKSEQ](#plinkseq) - [Ploticus](#ploticus) - [plotly](#plotly) - [plotly-orca](#plotly-orca) - [plotly.py](#plotly.py) - [PLplot](#plplot) - [PLUMED](#plumed) - [PLY](#ply) - [PMIx](#pmix) - [pmx](#pmx) - [PnetCDF](#pnetcdf) - [pocl](#pocl) - [poetry](#poetry) - [polars](#polars) - [polymake](#polymake) - [pomkl](#pomkl) - [pompi](#pompi) - [poppler](#poppler) - [popscle](#popscle) - [popt](#popt) - [Porechop](#porechop) - [porefoam](#porefoam) - [poretools](#poretools) - [Portcullis](#portcullis) - [Postgres-XL](#postgres-xl) - [PostgreSQL](#postgresql) - [POT](#pot) - [POV-Ray](#pov-ray) - [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) - [py](#py) - [py-aiger](#py-aiger) - [py-aiger-bdd](#py-aiger-bdd) - [py-cpuinfo](#py-cpuinfo) - [pyABC](#pyabc) - [PyAMG](#pyamg) - [PyAPS3](#pyaps3) - [pybedtools](#pybedtools) - [PyBerny](#pyberny) - [pyBigWig](#pybigwig) - [pybind11](#pybind11) - [PyCairo](#pycairo) - [PyCalib](#pycalib) - [pyccel](#pyccel) - [PyCharm](#pycharm) - [PyCheMPS2](#pychemps2) - [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) - [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) - [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) - [pymatgen](#pymatgen) - [pymatgen-db](#pymatgen-db) - [pymbar](#pymbar) - [PyMC3](#pymc3) - [pymca](#pymca) - [pymemcache](#pymemcache) - [PyMOL](#pymol) - [PyNAST](#pynast) - [pyobjcryst](#pyobjcryst) - [PyOD](#pyod) - [Pyomo](#pyomo) - [PyOpenCL](#pyopencl) - [PyOpenGL](#pyopengl) - [pyparsing](#pyparsing) - [pyplusplus](#pyplusplus) - [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) - [pysndfx](#pysndfx) - [Pysolar](#pysolar) - [pyspoa](#pyspoa) - [pysqlite](#pysqlite) - [PyStan](#pystan) - [pysteps](#pysteps) - [pystran](#pystran) - [PyTables](#pytables) - [pytest](#pytest) - [pytest-benchmark](#pytest-benchmark) - [pytest-xdist](#pytest-xdist) - [PYTHIA](#pythia) - [Python](#python) - [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-parasail](#python-parasail) - [python-telegram-bot](#python-telegram-bot) - [python-weka-wrapper3](#python-weka-wrapper3) - [pythran](#pythran) - [PyTorch](#pytorch) - [PyTorch-Geometric](#pytorch-geometric) - [PyTorch-Lightning](#pytorch-lightning) - [PyTorch3D](#pytorch3d) - [PyVCF](#pyvcf) - [pyWannier90](#pywannier90) - [PyWavelets](#pywavelets) - [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) - [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) - [parasail](#parasail) - [Paraver](#paraver) - [ParaView](#paraview) - [Parcels](#parcels) - [PARI-GP](#pari-gp) - [ParmEd](#parmed) - [ParMETIS](#parmetis) - [ParMGridGen](#parmgridgen) - [PartitionFinder](#partitionfinder) - [pasta](#pasta) - [PaStiX](#pastix) - [patch](#patch) - [patchelf](#patchelf) - [path.py](#path.py) - [PAUP](#paup) - [pauvre](#pauvre) - [pbbam](#pbbam) - [pbcopper](#pbcopper) - [pbdagcon](#pbdagcon) - [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) - [PEAR](#pear) - [PennCNV](#penncnv) - [PEPT](#pept) - [Percolator](#percolator) - [Perl](#perl) - [perl-app-cpanminus](#perl-app-cpanminus) - [Perl4-CoreLibs](#perl4-corelibs) - [Perseus](#perseus) - [PEST++](#pest++) - [PETSc](#petsc) - [petsc4py](#petsc4py) - [PfamScan](#pfamscan) - [pfind](#pfind) - [pftoolsV3](#pftoolsv3) - [pFUnit](#pfunit) - [PGDSpider](#pgdspider) - [PGI](#pgi) - [PHANOTATE](#phanotate) - [Phantompeakqualtools](#phantompeakqualtools) - [PHASE](#phase) - [PHAST](#phast) - [Phenoflow](#phenoflow) - [PheWAS](#phewas) - [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) - [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) - [plc](#plc) - [PLINK](#plink) - [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) - [pmx](#pmx) - [PnetCDF](#pnetcdf) - [pocl](#pocl) - [poetry](#poetry) - [polars](#polars) - [polymake](#polymake) - [pomkl](#pomkl) - [pompi](#pompi) - [poppler](#poppler) - [popscle](#popscle) - [popt](#popt) - [Porechop](#porechop) - [porefoam](#porefoam) - [poretools](#poretools) - [Portcullis](#portcullis) - [Postgres-XL](#postgres-xl) - [PostgreSQL](#postgresql) - [POT](#pot) - [POV-Ray](#pov-ray) - [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) - [py](#py) - [py-aiger](#py-aiger) - [py-aiger-bdd](#py-aiger-bdd) - [py-cpuinfo](#py-cpuinfo) - [pyABC](#pyabc) - [PyAMG](#pyamg) - [PyAPS3](#pyaps3) - [pybedtools](#pybedtools) - [PyBerny](#pyberny) - [pyBigWig](#pybigwig) - [pybind11](#pybind11) - [pybinding](#pybinding) - [PyCairo](#pycairo) - [PyCalib](#pycalib) - [pyccel](#pyccel) - [PyCharm](#pycharm) - [PyCheMPS2](#pychemps2) - [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) - [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) - [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) - [pymatgen](#pymatgen) - [pymatgen-db](#pymatgen-db) - [pymbar](#pymbar) - [PyMC3](#pymc3) - [pymca](#pymca) - [pymemcache](#pymemcache) - [PyMOL](#pymol) - [PyNAST](#pynast) - [pyobjcryst](#pyobjcryst) - [PyOD](#pyod) - [Pyomo](#pyomo) - [PyOpenCL](#pyopencl) - [PyOpenGL](#pyopengl) - [pyparsing](#pyparsing) - [pyperf](#pyperf) - [pyplusplus](#pyplusplus) - [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) - [pytest](#pytest) - [pytest-benchmark](#pytest-benchmark) - [pytest-rerunfailures](#pytest-rerunfailures) - [pytest-shard](#pytest-shard) - [pytest-xdist](#pytest-xdist) - [PYTHIA](#pythia) - [Python](#python) - [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-parasail](#python-parasail) - [python-telegram-bot](#python-telegram-bot) - [python-weka-wrapper3](#python-weka-wrapper3) - [pythran](#pythran) - [PyTorch](#pytorch) - [PyTorch-Geometric](#pytorch-geometric) - [PyTorch-Ignite](#pytorch-ignite) - [PyTorch-Lightning](#pytorch-lightning) - [PyTorch3D](#pytorch3d) - [PyVCF](#pyvcf) - [PyVCF3](#pyvcf3) - [pyWannier90](#pywannier90) - [PyWavelets](#pywavelets) - [PyYAML](#pyyaml) - [PyZMQ](#pyzmq) ### p11-kit @@ -23650,10 +24317,11 @@ PAML is a package of programs for phylogenetic analyses of DNA or protein sequ *homepage*: -version |toolchain ---------|----------------------------------------------------------------------------- -``4.9i``|``GCC/6.4.0-2.28``, ``iccifort/2017.4.196-GCC-6.4.0-2.28`` -``4.9j``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` +version |toolchain +----------|----------------------------------------------------------------------------- +``4.9i`` |``GCC/6.4.0-2.28``, ``iccifort/2017.4.196-GCC-6.4.0-2.28`` +``4.9j`` |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` +``4.10.5``|``GCCcore/11.3.0`` ### panaroo @@ -23665,6 +24333,7 @@ version |toolchain ---------|-------------- ``1.2.8``|``foss/2020b`` ``1.2.9``|``foss/2021a`` +``1.3.2``|``foss/2021b`` ### pandapower @@ -23839,10 +24508,20 @@ parallel fastq-dump wrapper *homepage*: version |versionsuffix |toolchain ----------|-----------------|----------------- +---------|-----------------|-------------------------------- ``0.6.5``|``-Python-3.7.2``|``GCCcore/8.2.0`` ``0.6.6``|``-Python-3.8.2``|``GCCcore/9.3.0`` -``0.6.7``| |``gompi/2020b`` +``0.6.7``| |``gompi/2020b``, ``gompi/2022a`` + +### Parallel-Hashmap + +Parallel Hashmap is built on a modified version of Abseil's flat_hash_map. Parallel Hashmap has lower space requirements, is nearly as fast as the underlying flat_hash_map, and can be used from multiple threads with high levels of concurrency. + +*homepage*: + +version |toolchain +--------|------------------ +``1.33``|``GCCcore/10.3.0`` ### ParallelIO @@ -23851,8 +24530,9 @@ A high-level Parallel I/O Library for structured grid applications *homepage*: version |toolchain -----------|--------------- +----------|-------------------------------- ``2.2.2a``|``intel/2017a`` +``2.5.10``|``gompi/2022a``, ``iimpi/2022a`` ### parameterized @@ -23878,6 +24558,7 @@ version |toolchain ``2.4.2``|``GCC/9.3.0``, ``iccifort/2020.1.217`` ``2.4.3``|``GCC/10.2.0``, ``GCC/10.3.0`` ``2.5`` |``GCC/11.2.0`` +``2.6`` |``GCC/11.3.0`` ### Paraver @@ -23950,8 +24631,8 @@ ParMETIS is an MPI-based parallel library that implements a variety of algorithm *homepage*: version |toolchain ----------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -``4.0.3``|``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``gimkl/2.11.5``, ``gompi/2019a``, ``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b``, ``gompi/2021a``, ``gompi/2021b``, ``gompi/2022a``, ``iimpi/2019a``, ``iimpi/2019b``, ``iimpi/2020a``, ``iimpi/2020b``, ``iimpi/2021a``, ``iimpi/2021b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` +---------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +``4.0.3``|``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``gimkl/2.11.5``, ``gompi/2019a``, ``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b``, ``gompi/2021a``, ``gompi/2021b``, ``gompi/2022a``, ``gompi/2022b``, ``iimpi/2019a``, ``iimpi/2019b``, ``iimpi/2020a``, ``iimpi/2020b``, ``iimpi/2021a``, ``iimpi/2021b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` ### ParMGridGen @@ -24189,7 +24870,7 @@ version |toolchain ``8.42``|``GCCcore/6.4.0`` ``8.43``|``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``8.44``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` -``8.45``|``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``8.45``|``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ### PCRE2 @@ -24208,6 +24889,16 @@ version |toolchain ``10.37``|``GCCcore/11.2.0`` ``10.40``|``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +### pdsh + +A high performance, parallel remote shell utility + +*homepage*: + +version |toolchain +--------|-------------------------------------- +``2.34``|``GCCcore/11.3.0``, ``GCCcore/12.2.0`` + ### PDT Program Database Toolkit (PDT) is a framework for analyzing source code written in several programming languages and for making rich program knowledge accessible to developers of static and dynamic analysis tools. PDT implements a standard program representation, the program database (PDB), that can be accessed in a uniform way through a class library supporting common PDB operations. @@ -24215,10 +24906,10 @@ Program Database Toolkit (PDT) is a framework for analyzing source code written *homepage*: version |toolchain -----------|--------------------------------------------------------- +----------|----------------------------------------------------------------------------- ``3.22`` |``foss/2016a`` ``3.25`` |``GCCcore/10.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``3.25.1``|``GCCcore/10.3.0``, ``GCCcore/11.3.0``, ``GCCcore/9.3.0`` +``3.25.1``|``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/9.3.0`` ### PEAR @@ -24298,6 +24989,7 @@ version |versionsuffix|toolchain ``5.34.1``| |``GCCcore/11.3.0`` ``5.34.1``|``-minimal`` |``GCCcore/11.3.0`` ``5.36.0``| |``GCCcore/12.1.0``, ``GCCcore/12.2.0`` +``5.36.0``|``-minimal`` |``GCCcore/12.2.0`` ### perl-app-cpanminus @@ -24319,6 +25011,16 @@ version |versionsuffix |toolchain ---------|----------------|--------------- ``0.003``|``-Perl-5.24.1``|``intel/2017a`` +### Perseus + +The Perseus software platform supports biological and biomedical researchers in interpreting protein quantification, interaction and post-translational modification data. + +*homepage*: + +version |toolchain +-----------|------------------ +``2.0.7.0``|``GCCcore/11.2.0`` + ### PEST++ PEST++ is a software suite aimed at supporting complex numerical models in the decision-support context. Much focus has been devoted to supporting environmental models (groundwater, surface water, etc) but these tools are readily applicable to any computer model. @@ -24364,6 +25066,16 @@ version |versionsuffix |toolchain ``3.12.0``|``-Python-3.7.4``|``foss/2019b`` ``3.15.0``| |``foss/2021a`` +### PfamScan + +PfamScan is used to search a FASTA sequence against a library of Pfam HMM. + +*homepage*: + +version|toolchain +-------|--------------- +``1.6``|``gompi/2022a`` + ### pfind Drop-in replacement for find, implemented for using parallel access and MPI. @@ -24477,6 +25189,16 @@ version|toolchain ``1.4``|``intel/2017a`` ``1.5``|``GCC/6.4.0-2.28``, ``iccifort/2017.4.196-GCC-6.4.0-2.28`` +### Phenoflow + +R package offering functionality for the advanced analysis of microbial flow cytometry data + +*homepage*: + +version |versionsuffix|toolchain +------------------|-------------|-------------- +``1.1.2-20200917``|``-R-4.2.1`` |``foss/2022a`` + ### PheWAS Provides an accessible R interface to the phenome wide association study. @@ -24752,6 +25474,7 @@ version |versionsuffix |toolchain ``9.1.0``| |``GCCcore/10.3.0`` ``9.1.1``| |``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ``9.2.0``| |``GCCcore/10.2.0`` +``9.4.0``| |``GCCcore/12.2.0`` ### Pillow-SIMD @@ -24848,6 +25571,17 @@ version|versionsuffix |toolchain -------|-----------------|-------------- ``2.7``|``-Python-3.8.2``|``foss/2020a`` ``2.8``| |``foss/2021a`` +``3.0``| |``foss/2021a`` + +### PIRATE + +A toolbox for pangenome analysis and threshold evaluation. + +*homepage*: + +version |versionsuffix|toolchain +---------|-------------|-------------- +``1.0.5``|``-R-4.2.1`` |``foss/2022a`` ### pIRS @@ -24944,7 +25678,7 @@ pkgconfig is a Python module to interface with the pkg-config command line tool *homepage*: version |versionsuffix |toolchain ----------|------------------|--------------------------------------------------- +---------|------------------|---------------------------------------------------------- ``1.1.0``|``-Python-2.7.11``|``foss/2016a``, ``intel/2016a`` ``1.1.0``|``-Python-2.7.12``|``foss/2016b``, ``intel/2016b`` ``1.1.0``|``-Python-3.5.1`` |``foss/2016a`` @@ -24961,7 +25695,17 @@ version |versionsuffix |toolchain ``1.5.1``|``-Python-3.8.2`` |``GCCcore/9.3.0`` ``1.5.1``|``-python`` |``GCCcore/10.2.0``, ``GCCcore/8.2.0`` ``1.5.4``|``-python`` |``GCCcore/10.3.0`` -``1.5.5``|``-python`` |``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``1.5.5``|``-python`` |``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` + +### PLAMS + +The Python Library for Automating Molecular Simulation (PLAMS) is powerful and flexible Python tool interfaced to the Amsterdam Modeling Suite engines ADF, BAND, DFTB, MOPAC, ReaxFF, and UFF. + +*homepage*: + +version |toolchain +---------|--------------- +``1.5.1``|``intel/2022a`` ### plantcv @@ -25037,7 +25781,7 @@ version |versionsuffix |toolchain ### PLINK -Whole-genome association analysis toolset +PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. *homepage*: @@ -25056,6 +25800,7 @@ version |toolchain ``2.00a2.3_x86_64`` |``system`` ``2.00a3.1`` |``GCC/11.2.0`` ``2.00a3.6`` |``GCC/11.3.0`` +``2.00a3.7`` |``foss/2022a`` ### plinkQC @@ -25077,6 +25822,16 @@ version |toolchain --------|---------------------------------------------------------- ``0.10``|``GCC/6.4.0-2.28``, ``iccifort/2017.4.196-GCC-6.4.0-2.28`` +### plot1cell + +plot1cell: a package for advanced single cell data visualization + +*homepage*: + +version |versionsuffix|toolchain +---------|-------------|-------------- +``0.0.1``|``-R-4.2.1`` |``foss/2022a`` + ### Ploticus Ploticus is a free GPL software utility that can produce various types of plots and graphs @@ -25123,6 +25878,8 @@ version |toolchain ``4.14.3``|``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ``5.1.0`` |``GCCcore/10.3.0`` ``5.4.0`` |``GCCcore/11.2.0`` +``5.12.0``|``GCCcore/11.3.0`` +``5.13.1``|``GCCcore/12.2.0`` ### PLplot @@ -25164,6 +25921,7 @@ version |versionsuffix |toolchain ``2.7.2``| |``foss/2021a``, ``intel/2021a`` ``2.7.3``| |``foss/2021b`` ``2.8.0``| |``foss/2021b`` +``2.8.1``| |``foss/2022a`` ### PLY @@ -25221,7 +25979,7 @@ version |toolchain ``1.10.0``|``foss/2018b``, ``intel/2018b`` ``1.12.1``|``gompi/2019b``, ``gompi/2020a``, ``gompic/2019b``, ``gompic/2020a``, ``iimpi/2020a`` ``1.12.2``|``gompi/2020b``, ``gompi/2021a``, ``gompic/2020b``, ``iimpi/2021a`` -``1.12.3``|``gompi/2021b``, ``gompi/2022a`` +``1.12.3``|``gompi/2021b``, ``gompi/2022a``, ``iimpi/2022a`` ### pocl @@ -25240,13 +25998,14 @@ version|toolchain ### poetry -Python packaging and dependency management made easy +Python packaging and dependency management made easy. Poetry helps you declare, manage and install dependencies of Python projects, ensuring you have the right stack everywhere. -*homepage*: +*homepage*: version |versionsuffix |toolchain ----------|-----------------|----------------- +---------|-----------------|------------------ ``1.0.9``|``-Python-3.8.2``|``GCCcore/9.3.0`` +``1.2.2``| |``GCCcore/11.3.0`` ### polars @@ -25267,6 +26026,7 @@ polymake is open source software for research in polyhedral geometry. It deals w version |toolchain ---------|-------------- ``4.0r1``|``foss/2019b`` +``4.8`` |``GCC/11.3.0`` ### pomkl @@ -25484,8 +26244,8 @@ PRANK is a probabilistic multiple alignment program for DNA, codon and amino-a *homepage*: version |toolchain -----------|------------------------------------------------------------------------------ -``170427``|``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/9.3.0``, ``intel/2018a`` +----------|---------------------------------------------------------------------------------------------- +``170427``|``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0``, ``GCC/9.3.0``, ``intel/2018a`` ### PRC @@ -25529,6 +26289,7 @@ version |toolchain ``2.0.2``|``foss/2016b`` ``2.0.3``|``foss/2018b``, ``intel/2018a`` ``3.1.2``|``GCC/10.3.0``, ``GCC/11.2.0`` +``3.2.0``|``GCC/11.3.0`` ### presto @@ -25539,6 +26300,7 @@ Presto performs a fast Wilcoxon rank sum test and auROC analysis. version |versionsuffix|toolchain ------------------|-------------|-------------- ``1.0.0-20200718``|``-R-4.1.2`` |``foss/2021b`` +``1.0.0-20230113``|``-R-4.2.1`` |``foss/2022a`` ### pretty-yaml @@ -25614,9 +26376,9 @@ Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbi *homepage*: version |toolchain ----------|--------------------------------------------------------------------------------------------------------------------------------------------------------- +---------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ``2.6.2``|``GCC/4.9.3-binutils-2.25`` -``2.6.3``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``2.6.3``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ### ProFit @@ -25646,6 +26408,7 @@ version |toolchain ``8.0.1``|``GCCcore/10.3.0`` ``8.1.0``|``GCCcore/11.2.0`` ``9.0.0``|``GCCcore/11.3.0`` +``9.1.1``|``GCCcore/12.2.0`` ### ProjectQ @@ -25664,12 +26427,12 @@ Prokka is a software tool for the rapid annotation of prokaryotic genomes. *homepage*: version |versionsuffix |toolchain -----------|------------------|------------------------------------------------------------------ +----------|------------------|----------------------------------------------------------------------------------- ``1.11`` |``-BioPerl-1.7.0``|``foss/2016b`` ``1.13`` |``-BioPerl-1.7.2``|``intel/2018a`` ``1.13.4``| |``foss/2018b`` ``1.13.7``| |``gompi/2019a`` -``1.14.5``| |``gompi/2019a``, ``gompi/2019b``, ``gompi/2020b``, ``gompi/2021a`` +``1.14.5``| |``gompi/2019a``, ``gompi/2019b``, ``gompi/2020b``, ``gompi/2021a``, ``gompi/2021b`` ### prompt-toolkit @@ -25750,6 +26513,7 @@ version |toolchain ``3.14.0`` |``GCCcore/10.2.0`` ``3.17.3`` |``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``3.19.4`` |``GCCcore/11.3.0`` +``3.21.9`` |``GCCcore/10.3.0`` ### protobuf-python @@ -25957,13 +26721,14 @@ version |versionsuffix |toolchain Psycopg is the most popular PostgreSQL adapter for the Python programming language. -*homepage*: +*homepage*: version |versionsuffix |toolchain ---------|------------------|------------------------------- ``2.7`` |``-Python-2.7.12``|``foss/2016b``, ``intel/2016b`` ``2.8.3``|``-Python-3.7.2`` |``foss/2019a`` ``2.8.6``|``-Python-3.8.2`` |``GCCcore/9.3.0`` +``2.9.5``| |``GCCcore/11.2.0`` ### ptemcee @@ -26075,8 +26840,10 @@ py-cpuinfo gets CPU info with pure Python. *homepage*: version |toolchain ----------|---------- +---------|-------------------------------------- ``5.0.0``|``system`` +``8.0.0``|``GCCcore/11.2.0`` +``9.0.0``|``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ### pyABC @@ -26144,10 +26911,10 @@ A python extension, written in C, for quick access to bigBed files and access t *homepage*: version |versionsuffix |toolchain -----------|-----------------|-------------------------------------------------- +----------|-----------------|------------------------------------------------------------------ ``0.3.13``|``-Python-3.6.6``|``foss/2018b`` ``0.3.17``| |``GCCcore/8.2.0``, ``GCCcore/9.3.0`` -``0.3.18``| |``GCCcore/10.2.0``, ``foss/2021a``, ``foss/2021b`` +``0.3.18``| |``GCCcore/10.2.0``, ``foss/2021a``, ``foss/2021b``, ``foss/2022a`` ### pybind11 @@ -26155,17 +26922,28 @@ pybind11 is a lightweight header-only library that exposes C++ types in Python a *homepage*: -version |versionsuffix |toolchain ----------|------------------|------------------ -``2.2.4``|``-Python-3.6.4`` |``foss/2018a`` -``2.2.4``|``-Python-3.6.6`` |``intel/2018b`` -``2.4.3``|``-Python-3.7.4`` |``GCCcore/8.3.0`` -``2.4.3``|``-Python-3.8.2`` |``GCCcore/9.3.0`` -``2.6.0``| |``GCCcore/10.2.0`` -``2.6.2``| |``GCCcore/10.3.0`` -``2.7.1``| |``GCCcore/11.2.0`` -``2.7.1``|``-Python-2.7.18``|``GCCcore/11.2.0`` -``2.9.2``| |``GCCcore/11.3.0`` +version |versionsuffix |toolchain +----------|------------------|------------------ +``2.2.4`` |``-Python-3.6.4`` |``foss/2018a`` +``2.2.4`` |``-Python-3.6.6`` |``intel/2018b`` +``2.4.3`` |``-Python-3.7.4`` |``GCCcore/8.3.0`` +``2.4.3`` |``-Python-3.8.2`` |``GCCcore/9.3.0`` +``2.6.0`` | |``GCCcore/10.2.0`` +``2.6.2`` | |``GCCcore/10.3.0`` +``2.7.1`` | |``GCCcore/11.2.0`` +``2.7.1`` |``-Python-2.7.18``|``GCCcore/11.2.0`` +``2.9.2`` | |``GCCcore/11.3.0`` +``2.10.3``| |``GCCcore/12.2.0`` + +### pybinding + +Pybinding is a Python package for numerical tight-binding calculations in solid state physics. + +*homepage*: + +version |toolchain +---------|-------------- +``0.9.5``|``foss/2022a`` ### PyCairo @@ -26219,6 +26997,7 @@ version |toolchain ``2019.3.1``|``system`` ``2021.1.1``|``system`` ``2022.2.2``|``system`` +``2022.3.2``|``system`` ### PyCheMPS2 @@ -26395,9 +27174,9 @@ Python interface to Graphviz's Dot language. *homepage*: version |toolchain ----------|-------------------------------------- +---------|---------------------------------------------------------- ``1.4.1``|``GCCcore/9.3.0``, ``foss/2019b`` -``1.4.2``|``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +``1.4.2``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.3.0`` ### pyEGA3 @@ -26443,6 +27222,7 @@ version |versionsuffix |toolchain ----------|-----------------|---------------------------------- ``0.19.0``|``-Python-3.7.4``|``foss/2019b``, ``fosscuda/2019b`` ``0.20.0``| |``foss/2020b``, ``fosscuda/2020b`` +``0.21.3``| |``foss/2021b`` ### pyfaidx @@ -26456,6 +27236,7 @@ version |versionsuffix |toolchain ``0.5.9.5``|``-Python-3.7.4``|``GCCcore/8.3.0`` ``0.6.3.1``| |``GCCcore/10.3.0`` ``0.7.0`` | |``GCCcore/11.2.0`` +``0.7.1`` | |``GCCcore/11.3.0`` ### pyfasta @@ -26561,6 +27342,7 @@ pyGenomeTracks aims to produce high-quality genome browser tracks that are highl version|toolchain -------|-------------- ``3.7``|``foss/2021b`` +``3.8``|``foss/2022a`` ### PyGEOS @@ -26630,10 +27412,11 @@ PyGraphviz is a Python interface to the Graphviz graph layout and visualization *homepage*: -version|toolchain --------|------------------------------ -``1.5``|``foss/2019b`` -``1.7``|``foss/2020b``, ``foss/2021a`` +version |toolchain +--------|------------------------------ +``1.5`` |``foss/2019b`` +``1.7`` |``foss/2020b``, ``foss/2021a`` +``1.10``|``GCCcore/11.3.0`` ### pygrib @@ -26806,6 +27589,7 @@ version |versionsuffix |toolchain ---------|-----------------|---------------------------------- ``5.6.3``| |``foss/2020b``, ``fosscuda/2020b`` ``5.6.3``|``-Python-3.7.4``|``foss/2019b``, ``fosscuda/2019b`` +``5.7.6``| |``foss/2021b`` ### pymemcache @@ -26911,6 +27695,16 @@ version |versionsuffix |toolchain ---------|------------------|----------------- ``2.4.6``|``-Python-2.7.16``|``GCCcore/8.3.0`` +### pyperf + +The Python pyperf module is a toolkit to write, run and analyze benchmarks + +*homepage*: + +version |toolchain +---------|------------------ +``2.5.0``|``GCCcore/11.3.0`` + ### pyplusplus Py++ is a code generator for Boost.Python that simplifies writing Python bindings of a C/C++ library The tool is implemented as a Python module which is controlled by a user script. @@ -27134,6 +27928,7 @@ version |versionsuffix |toolchain ``0.17.0`` | |``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`` ### pysamstats @@ -27186,6 +27981,7 @@ version |versionsuffix |toolchain ---------|-----------------|----------------------------------------------- ``1.6.3``|``-Python-3.7.2``|``foss/2019a`` ``1.7.6``| |``foss/2020b``, ``foss/2021a``, ``gomkl/2021a`` +``2.1.1``| |``foss/2022a`` ### pysheds @@ -27218,6 +28014,16 @@ version |toolchain ------------|------------------ ``5.14.2.3``|``GCCcore/10.2.0`` +### pyslim + +A Python API for reading and modifying tskit tree sequence files produced by SLiM, or modifying files produced by other programs (e.g., msprime, fwdpy11, and tsinfer) for use in SLiM. + +*homepage*: + +version |toolchain +---------|-------------- +``1.0.1``|``foss/2021b`` + ### pysndfx A lightweight Python wrapper for SoX - Sound eXchange. Supported effects range from EQ and compression to phasers, reverb and pitch shifters. @@ -27296,7 +28102,7 @@ version |versionsuffix |toolchain ### PyTables -PyTables is a package for managing hierarchical datasets and designed to efficiently and easily cope with extremely large amounts of data. PyTables is built on top of the HDF5 library, using the Python language and the NumPy package. It features an object-oriented interface that, combined with C extensions for the performance-critical parts of the code (generated using Cython), makes it a fast, yet extremely easy to use tool for interactively browse, process and search very large amounts of data. One important feature of PyTables is that it optimizes memory and disk resources so that data takes much less space (specially if on-flight compression is used) than other solutions such as relational or object oriented databases. +PyTables is a package for managing hierarchical datasets and designed to efficiently and easily cope with extremely large amounts of data. PyTables is built on top of the HDF5 library, using the Python language and the NumPy package. It features an object-oriented interface that, combined with C extensions for the performance-critical parts of the code (generated using Cython), makes it a fast, yet extremely easy to use tool for interactively browsing, processing and searching very large amounts of data. One important feature of PyTables is that it optimizes memory and disk resources so that data takes much less space (specially if on-flight compression is used) than other solutions such as relational or object oriented databases. *homepage*: @@ -27320,6 +28126,7 @@ version |versionsuffix |toolchain ``3.6.1`` | |``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``fosscuda/2020b``, ``intel/2020b`` ``3.6.1`` |``-Python-3.7.4`` |``foss/2019b``, ``fosscuda/2019b`` ``3.6.1`` |``-Python-3.8.2`` |``foss/2020a``, ``intel/2020a`` +``3.8.0`` | |``foss/2022a`` ### pytest @@ -27352,6 +28159,26 @@ version |toolchain ---------|------------------ ``3.4.1``|``GCCcore/10.2.0`` +### pytest-rerunfailures + +pytest plugin to re-run tests to eliminate flaky failures. + +*homepage*: + +version |toolchain +--------|------------------ +``11.1``|``GCCcore/11.3.0`` + +### pytest-shard + +pytest plugin to support parallelism across multiple machines. Shards tests based on a hash of their test name enabling easy parallelism across machines, suitable for a wide variety of continuous integration services. Tests are split at the finest level of granularity, individual test cases, enabling parallelism even if all of your tests are in a single file (or even single parameterized test method). + +*homepage*: + +version |toolchain +---------|------------------ +``0.1.2``|``GCCcore/11.3.0`` + ### pytest-xdist xdist: pytest distributed testing plugin The pytest-xdist plugin extends pytest with some unique test execution modes: * test run parallelization: if you have multiple CPUs or hosts you can use those for a combined test run. This allows to speed up development or to use special resources of remote machines. * --looponfail: run your tests repeatedly in a subprocess. After each run pytest waits until a file in your project changes and then re-runs the previously failing tests. This is repeated until all tests pass after which again a full run is performed. * Multi-Platform coverage: you can specify different Python interpreters or different platforms and run tests in parallel on all of them. Before running tests remotely, pytest efficiently “rsyncs” your program source code to the remote place. All test results are reported back and displayed to your local terminal. You may specify different Python versions and interpreters. @@ -27421,6 +28248,7 @@ version |versionsuffix |toolchain ``3.10.4``|``-bare`` |``GCCcore/11.3.0`` ``3.10.8``| |``GCCcore/12.2.0`` ``3.10.8``|``-bare`` |``GCCcore/12.2.0`` +``3.11.2``|``-bare`` |``GCCcore/12.2.0`` ### python-docx @@ -27456,6 +28284,7 @@ version |versionsuffix |toolchain ``0.9.0`` | |``foss/2020b``, ``fosscuda/2020b`` ``0.9.6`` | |``foss/2021a`` ``0.9.8`` | |``foss/2021b`` +``0.10.3`` | |``foss/2022a`` ### python-irodsclient @@ -27501,6 +28330,16 @@ version |toolchain ----------|-------------- ``5.19.7``|``foss/2021a`` +### python-louvain + +Louvain algorithm for community detection + +*homepage*: + +version |toolchain +--------|-------------- +``0.16``|``foss/2022a`` + ### python-parasail Python Bindings for the Parasail C Library @@ -27515,6 +28354,7 @@ version |versionsuffix |toolchain ``1.2.2`` |``-Python-3.8.2`` |``intel/2020a`` ``1.2.3`` |``-Python-3.8.2`` |``foss/2020a`` ``1.2.4`` | |``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``fosscuda/2020b`` +``1.3.3`` | |``foss/2022a`` ### python-telegram-bot @@ -27598,6 +28438,16 @@ version |versionsuffix |toolchain ``2.0.1``|``-PyTorch-1.9.0`` |``fosscuda/2020b`` ``2.1.0``|``-PyTorch-1.12.1-CUDA-11.3.1``|``foss/2021a`` +### PyTorch-Ignite + +Ignite is a high-level library to help with training and evaluating neural networks in PyTorch flexibly and transparently. + +*homepage*: + +version |versionsuffix |toolchain +---------|----------------|-------------- +``0.4.9``|``-CUDA-11.3.1``|``foss/2021a`` + ### PyTorch-Lightning PyTorch Lightning is the lightweight PyTorch wrapper for ML researchers. @@ -27633,6 +28483,16 @@ version |versionsuffix |toolchain ---------|------------------|------------- ``0.6.8``|``-Python-2.7.16``|``GCC/8.3.0`` +### PyVCF3 + +A VCFv4.0 and 4.1 parser for Python. The intent of this module is to mimic the csv module in the Python stdlib, as opposed to more flexible serialization formats like JSON or YAML. vcf will attempt to parse the content of each record based on the data types specified in the meta-information lines -- specifically the ##INFO and ##FORMAT lines. If these lines are missing or incomplete, it will check against the reserved types mentioned in the spec. Failing that, it will just return strings. PyVCF3 has been created because the Official PyVCF repository is no longer maintained and do not accept any pull requests. This fork is for python 3 only and has been published on pyPI as PyVCF3. + +*homepage*: + +version |toolchain +---------|------------------ +``1.0.3``|``GCCcore/11.3.0`` + ### pyWannier90 A Wannier90 Python interface for VASP and PySCF @@ -27703,6 +28563,7 @@ version |versionsuffix |toolchain ``17.0.0``|``-Python-3.6.4-zmq4`` |``foss/2018a`` ``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`` ## Q @@ -27752,6 +28613,7 @@ A python service for easy execution of many tasks inside a single allocation. version |toolchain ----------|-------------- ``0.12.3``|``foss/2021a`` +``0.13.1``|``foss/2022a`` ### qcint @@ -27827,7 +28689,7 @@ version |toolchain ----------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ``2015.2``|``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` ``2019.1``|``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``2020.2``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``2020.2``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ### QIIME @@ -27855,6 +28717,7 @@ version |toolchain ``2020.11``|``system`` ``2021.8`` |``system`` ``2022.8`` |``system`` +``2022.11``|``system`` ### Qiskit @@ -27965,9 +28828,9 @@ Qt Port of WebKit. WebKit is an open source web browser engine. *homepage*: version |toolchain -------------------|-------------------------------------- +------------------|---------------------------------------------------------- ``5.212.0-alpha3``|``GCCcore/8.2.0`` -``5.212.0-alpha4``|``GCCcore/10.2.0``, ``GCCcore/11.2.0`` +``5.212.0-alpha4``|``GCCcore/10.2.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ### Qtconsole @@ -28015,7 +28878,7 @@ version|versionsuffix|toolchain ### QtPy -QtPy is a small abstraction layer that lets you write applications using a single API call to either PyQt or PySide. It provides support for PyQt5, PyQt4, PySide2 and PySide. +QtPy is a small abstraction layer that lets you write applications using a single API call to either PyQt or PySide. It provides support for PyQt5, PyQt4, PySide2 and PySide. *homepage*: @@ -28024,6 +28887,7 @@ version |versionsuffix |toolchain ``1.9.0``| |``GCCcore/10.2.0`` ``1.9.0``|``-Python-3.7.4``|``GCCcore/8.3.0`` ``2.2.1``| |``GCCcore/11.2.0`` +``2.3.0``| |``GCCcore/11.3.0`` ### Qualimap @@ -28088,6 +28952,7 @@ version |versionsuffix |toolchain ``5.0.2``|``-Python-2.7.18``|``foss/2020b`` ``5.0.2``|``-Python-3.7.2`` |``foss/2019a`` ``5.0.2``|``-Python-3.8.2`` |``foss/2020a`` +``5.2.0``| |``foss/2022a`` ### QuaZIP @@ -28181,7 +29046,7 @@ version |toolchain ## R -[R](#r) - [R-bundle-Bioconductor](#r-bundle-bioconductor) - [R-INLA](#r-inla) - [R-keras](#r-keras) - [R-opencv](#r-opencv) - [R-tesseract](#r-tesseract) - [Racon](#racon) - [radeontop](#radeontop) - [RaGOO](#ragoo) - [Ragout](#ragout) - [RagTag](#ragtag) - [rampart](#rampart) - [randfold](#randfold) - [randrproto](#randrproto) - [RapidJSON](#rapidjson) - [rapidtide](#rapidtide) - [RAPSearch2](#rapsearch2) - [Rascaf](#rascaf) - [RASPA2](#raspa2) - [rasterio](#rasterio) - [rasterstats](#rasterstats) - [Ratatosk](#ratatosk) - [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) - [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) - [rgdal](#rgdal) - [rgeos](#rgeos) - [Rgurobi](#rgurobi) - [rhdf5](#rhdf5) - [RheoTool](#rheotool) - [rickflow](#rickflow) - [RInChI](#rinchi) - [rioxarray](#rioxarray) - [rising](#rising) - [rjags](#rjags) - [RLCard](#rlcard) - [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) - [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) - [Rust](#rust) +[R](#r) - [R-bundle-Bioconductor](#r-bundle-bioconductor) - [R-INLA](#r-inla) - [R-keras](#r-keras) - [R-opencv](#r-opencv) - [R-tesseract](#r-tesseract) - [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) - [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) - [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) - [rgdal](#rgdal) - [rgeos](#rgeos) - [Rgurobi](#rgurobi) - [rhdf5](#rhdf5) - [RheoTool](#rheotool) - [rickflow](#rickflow) - [RInChI](#rinchi) - [rioxarray](#rioxarray) - [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) - [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) - [Rust](#rust) ### R @@ -28218,6 +29083,7 @@ version |versionsuffix |toolchain ``4.1.2``| |``foss/2021b`` ``4.2.0``| |``foss/2021b`` ``4.2.1``| |``foss/2022a`` +``4.2.2``| |``foss/2022b`` ### R-bundle-Bioconductor @@ -28287,6 +29153,16 @@ version|versionsuffix|toolchain -------|-------------|-------------- ``4.0``|``-R-3.5.1`` |``foss/2018b`` +### R2jags + +Providing wrapper functions to implement Bayesian analysis in JAGS. + +*homepage*: + +version |versionsuffix|toolchain +---------|-------------|-------------- +``0.7-1``|``-R-4.2.1`` |``foss/2022a`` + ### Racon Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. @@ -28374,6 +29250,16 @@ version |toolchain ---------|------------------------------- ``1.5.0``|``foss/2016a``, ``intel/2016a`` +### rapidcsv + +Rapidcsv is a C++ header-only library for CSV parsing. While the name admittedly was inspired by the rapidjson project, the objectives are not the same. The goal of rapidcsv is to be an easy-to-use CSV library enabling rapid development. For optimal performance (be it CPU or memory usage) a CSV parser implemented for the specific use-case is likely to be more performant. + +*homepage*: + +version |toolchain +--------|------------------ +``8.64``|``GCCcore/11.3.0`` + ### RapidJSON A fast JSON parser/generator for C++ with both SAX/DOM style API @@ -28384,6 +29270,16 @@ version |toolchain ---------|--------------------------------------------------------------------------------------------------------------------------------------- ``1.1.0``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +### rapidNJ + +RapidNJ is an algorithmic engineered implementation of canonical neighbour-joining. It uses an efficient search heuristic to speed-up the core computations of the neighbour-joining method that enables RapidNJ to outperform other state-of-the-art neighbour-joining implementations. + +*homepage*: + +version |toolchain +---------|------------------ +``2.3.3``|``GCCcore/11.3.0`` + ### rapidtide Rapidtide is a suite of python programs used to perform time delay analysis on functional imaging data to find time lagged correlations between the voxelwise time series and other time series. @@ -28501,9 +29397,9 @@ version |toolchain ### Ray-project -Ray is an open source project that makes it simple to scale any compute-intensive Python workload — from deep learning to production model serving. With a rich set of libraries and integrations built on a flexible distributed execution framework, Ray makes distributed computing easy and accessible to every engineer. +Ray is a fast and simple framework for building and running distributed applications. -*homepage*: +*homepage*: version |versionsuffix |toolchain ----------|-----------------|------------------------------ @@ -28511,6 +29407,7 @@ version |versionsuffix |toolchain ``1.0.1`` |``-Python-3.7.4``|``fosscuda/2019b`` ``1.9.2`` | |``foss/2021b`` ``1.13.0``| |``foss/2021a``, ``foss/2021b`` +``2.2.0`` | |``foss/2022a`` ### Raysect @@ -28604,6 +29501,7 @@ version |versionsuffix |toolchain ``2020.09.3``|``-Python-3.7.4``|``foss/2019b`` ``2021.03.4``| |``foss/2021a`` ``2022.03.5``| |``foss/2021b`` +``2022.09.4``| |``foss/2022a`` ### RDP-Classifier @@ -28674,8 +29572,8 @@ Patched version of RECON to be used with RepeatModeler. *homepage*: version |toolchain ---------|-------------- -``1.08``|``GCC/10.2.0`` +--------|------------------------------ +``1.08``|``GCC/10.2.0``, ``GCC/11.3.0`` ### Red @@ -28696,6 +29594,7 @@ Redis is an open source (BSD licensed), in-memory data structure store, used as version |toolchain ---------|------------------------------ ``6.2.6``|``GCC/10.3.0``, ``GCC/11.2.0`` +``7.0.8``|``GCC/11.3.0`` ### redis-py @@ -28707,6 +29606,7 @@ version |toolchain ---------|-------------- ``4.3.1``|``foss/2021a`` ``4.3.3``|``foss/2021b`` +``4.5.1``|``foss/2022a`` ### Redundans @@ -28722,7 +29622,7 @@ version |toolchain ReFrame is a framework for writing regression tests for HPC systems. -*homepage*: +*homepage*: version |toolchain ----------|---------- @@ -28748,6 +29648,8 @@ version |toolchain ``3.11.1``|``system`` ``3.11.2``|``system`` ``3.12.0``|``system`` +``4.0.1`` |``system`` +``4.0.5`` |``system`` ### regionmask @@ -28850,6 +29752,7 @@ version |versionsuffix |toolchain ``4.0.8`` |``-Perl-5.28.0-HMMER``|``intel/2018b`` ``4.0.9-p2``|``-HMMER`` |``gompi/2019b`` ``4.1.2-p1``| |``foss/2020b`` +``4.1.4`` | |``foss/2022a`` ### RepeatModeler @@ -28860,6 +29763,7 @@ RepeatModeler is a de novo transposable element (TE) family identification and m version |toolchain ----------|-------------- ``2.0.2a``|``foss/2020b`` +``2.0.4`` |``foss/2022a`` ### RepeatScout @@ -28868,8 +29772,8 @@ De Novo Repeat Finder, Price A.L., Jones N.C. and Pevzner P.A. Developed and te *homepage*: version |toolchain ----------|-------------- -``1.0.6``|``GCC/10.2.0`` +---------|------------------------------ +``1.0.6``|``GCC/10.2.0``, ``GCC/11.3.0`` ### request @@ -29042,6 +29946,16 @@ version |versionsuffix |toolchain ``0.2.2``|``-CUDA-11.3.1``|``foss/2021a`` ``0.2.2``|``-CUDA-11.7.0``|``foss/2022a`` +### Rivet + +Rivet toolkit (Robust Independent Validation of Experiment and Theory) To use your own analysis you must append the path to `RIVET_ANALYSIS_PATH`. + +*homepage*: + +version |versionsuffix |toolchain +---------|-----------------|--------------- +``3.1.7``|``-HepMC3-3.2.5``|``gompi/2022a`` + ### rjags The rjags package is an interface to the JAGS library. @@ -29061,6 +29975,7 @@ version |versionsuffix|toolchain ``4-10``|``-R-4.0.5`` |``foss/2020b``, ``fosscuda/2020b`` ``4-10``|``-R-4.1.0`` |``foss/2021a`` ``4-12``|``-R-4.1.2`` |``foss/2021b`` +``4-13``|``-R-4.2.1`` |``foss/2022a`` ### RLCard @@ -29072,6 +29987,16 @@ version |toolchain ---------|-------------- ``1.0.9``|``foss/2022a`` +### rmarkdown + +Convert R Markdown documents into a variety of formats. + +*homepage*: + +version |versionsuffix|toolchain +--------|-------------|-------------- +``2.20``|``-R-4.1.0`` |``foss/2021a`` + ### Rmath Rmath is the standalone version of the R math library. Rmath can be used in your own C/C++ routines. @@ -29105,6 +30030,7 @@ version |versionsuffix |toolchain ``2.9.0`` | |``gompi/2019b`` ``2.10.0``| |``gompi/2019b`` ``2.11.0``| |``gompi/2020b`` +``2.13.0``| |``gompi/2022a`` ### RNA-Bloom @@ -29210,10 +30136,10 @@ Rapid large-scale prokaryote pan genome analysis *homepage*: version |versionsuffix |toolchain -----------|----------------|------------------------------ +----------|----------------|---------------------------------------------- ``3.12.0``| |``system`` ``3.12.0``|``-Perl-5.26.1``|``intel/2018a`` -``3.13.0``| |``foss/2020a``, ``foss/2021a`` +``3.13.0``| |``foss/2020a``, ``foss/2021a``, ``foss/2022a`` ### ROCm @@ -29319,6 +30245,7 @@ version |versionsuffix |toolchain ``6.14.06`` |``-Python-2.7.15``|``foss/2018b`` ``6.14.06`` |``-Python-3.6.6`` |``foss/2018b`` ``6.20.04`` |``-Python-3.7.4`` |``foss/2019b`` +``6.22.08`` | |``foss/2020b`` ``6.24.06`` | |``foss/2021b`` ``v5.34.34``|``-Python-2.7.11``|``intel/2016a`` ``v5.34.36``|``-Python-2.7.11``|``intel/2016a`` @@ -29404,7 +30331,7 @@ version |toolchain ``1.3.0`` |``foss/2016b``, ``intel/2017a`` ``1.3.1`` |``foss/2017b``, ``intel/2017b``, ``intel/2018a`` ``1.3.2`` |``foss/2018b`` -``1.3.3`` |``foss/2019b`` +``1.3.3`` |``foss/2019b``, ``foss/2022a`` ### RSeQC @@ -29557,7 +30484,7 @@ version |toolchain ## S -[S-Lang](#s-lang) - [S4](#s4) - [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) - [scanpy](#scanpy) - [SCENIC](#scenic) - [scGeneFit](#scgenefit) - [SCGid](#scgid) - [Schrodinger](#schrodinger) - [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-uplift](#scikit-uplift) - [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) - [SDL_image](#sdl_image) - [SDSL](#sdsl) - [Seaborn](#seaborn) - [SearchGUI](#searchgui) - [SECAPR](#secapr) - [Seeder](#seeder) - [segemehl](#segemehl) - [segmentation-models](#segmentation-models) - [SeisSol](#seissol) - [SelEstim](#selestim) - [SELFIES](#selfies) - [SentencePiece](#sentencepiece) - [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) - [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) - [silx](#silx) - [simint](#simint) - [SimNIBS](#simnibs) - [SimPEG](#simpeg) - [SIMPLE](#simple) - [SimpleElastix](#simpleelastix) - [SimpleITK](#simpleitk) - [simpy](#simpy) - [SimVascular](#simvascular) - [SingleM](#singlem) - [Singular](#singular) - [SiNVICT](#sinvict) - [SIONlib](#sionlib) - [SIP](#sip) - [SISSO](#sisso) - [SISSO++](#sisso++) - [SKESA](#skesa) - [sketchmap](#sketchmap) - [skewer](#skewer) - [sklearn-pandas](#sklearn-pandas) - [sklearn-som](#sklearn-som) - [skorch](#skorch) - [SlamDunk](#slamdunk) - [slamdunk](#slamdunk) - [SLATEC](#slatec) - [SLEPc](#slepc) - [slepc4py](#slepc4py) - [sleuth](#sleuth) - [slidingwindow](#slidingwindow) - [SLiM](#slim) - [slow5tools](#slow5tools) - [smafa](#smafa) - [smallgenomeutilities](#smallgenomeutilities) - [SMARTdenovo](#smartdenovo) - [SMC++](#smc++) - [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) - [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) - [SoQt](#soqt) - [SortMeRNA](#sortmerna) - [SoX](#sox) - [SoXt](#soxt) - [SpaceRanger](#spaceranger) - [Spack](#spack) - [spaCy](#spacy) - [SPAdes](#spades) - [spaln](#spaln) - [Spark](#spark) - [sparsehash](#sparsehash) - [spatialreg](#spatialreg) - [spdlog](#spdlog) - [SpectrA](#spectra) - [spectral.methods](#spectral.methods) - [speech_tools](#speech_tools) - [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) - [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) - [stars](#stars) - [Stata](#stata) - [Statistics-R](#statistics-r) - [statsmodels](#statsmodels) - [STEAK](#steak) - [STIR](#stir) - [stpipeline](#stpipeline) - [STREAM](#stream) - [strelka](#strelka) - [StringTie](#stringtie) - [stripy](#stripy) - [STRique](#strique) - [Structure](#structure) - [STRUMPACK](#strumpack) - [suave](#suave) - [Subread](#subread) - [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) - [SVDetect](#svdetect) - [SVDquest](#svdquest) - [SVG](#svg) - [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) - [SyRI](#syri) - [Szip](#szip) +[S-Lang](#s-lang) - [S4](#s4) - [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) - [scanpy](#scanpy) - [scArches](#scarches) - [SCENIC](#scenic) - [scGeneFit](#scgenefit) - [SCGid](#scgid) - [scHiCExplorer](#schicexplorer) - [Schrodinger](#schrodinger) - [scib](#scib) - [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-uplift](#scikit-uplift) - [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) - [SDL_image](#sdl_image) - [SDSL](#sdsl) - [Seaborn](#seaborn) - [SearchGUI](#searchgui) - [SeaView](#seaview) - [SECAPR](#secapr) - [Seeder](#seeder) - [segemehl](#segemehl) - [segmentation-models](#segmentation-models) - [SeisSol](#seissol) - [SelEstim](#selestim) - [SELFIES](#selfies) - [SentencePiece](#sentencepiece) - [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) - [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) - [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) - [smafa](#smafa) - [smallgenomeutilities](#smallgenomeutilities) - [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) - [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) - [SoQt](#soqt) - [SortMeRNA](#sortmerna) - [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) - [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) - [Strainberry](#strainberry) - [STREAM](#stream) - [strelka](#strelka) - [StringTie](#stringtie) - [stripy](#stripy) - [STRique](#strique) - [Structure](#structure) - [STRUMPACK](#strumpack) - [suave](#suave) - [Subread](#subread) - [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) - [SVDetect](#svdetect) - [SVDquest](#svdquest) - [SVG](#svg) - [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) - [SyRI](#syri) - [Szip](#szip) ### S-Lang @@ -29631,6 +30558,7 @@ version |versionsuffix |toolchain ``1.2.0`` | |``gompi/2019b`` ``1.3.0`` | |``gompi/2020a`` ``1.4.0`` | |``GCC/11.2.0``, ``gompi/2020b`` +``1.9.0`` | |``GCC/11.3.0`` ### SALMON-TDDFT @@ -29727,6 +30655,7 @@ version |versionsuffix |toolchain ``1.15`` | |``GCC/11.2.0`` ``1.15.1``| |``GCC/11.2.0``, ``GCC/11.3.0`` ``1.16.1``| |``GCC/11.2.0``, ``GCC/11.3.0`` +``1.17`` | |``GCC/12.2.0`` ### sansa @@ -29855,11 +30784,12 @@ Scalasca is a software tool that supports the performance optimization of paral *homepage*: -version|toolchain --------|--------------------------------- -``2.3``|``foss/2016a`` -``2.5``|``gompi/2019a``, ``gompi/2020a`` -``2.6``|``gompi/2021a``, ``gompic/2020b`` +version |toolchain +---------|--------------------------------- +``2.3`` |``foss/2016a`` +``2.5`` |``gompi/2019a``, ``gompi/2020a`` +``2.6`` |``gompi/2021a``, ``gompic/2020b`` +``2.6.1``|``gompi/2022a`` ### SCALCE @@ -29882,7 +30812,17 @@ version |toolchain ``1.7.2``|``foss/2020b`` ``1.8.1``|``foss/2020b``, ``foss/2021a`` ``1.8.2``|``foss/2021b`` -``1.9.1``|``foss/2021b`` +``1.9.1``|``foss/2021b``, ``foss/2022a`` + +### scArches + +Single-cell architecture surgery (scArches) is a package for reference-based analysis of single-cell data. + +*homepage*: + +version |toolchain +---------|-------------- +``0.5.6``|``foss/2021a`` ### SCENIC @@ -29914,6 +30854,16 @@ version |toolchain ---------|-------------- ``0.9b0``|``foss/2021b`` +### scHiCExplorer + +The scHiCExplorer is a software to demultiplex, process, correct, normalize, manipulate, analyse and visualize single-cell Hi-C data. + +*homepage*: + +version|toolchain +-------|-------------- +``7`` |``foss/2022a`` + ### Schrodinger Schrodinger aims to provide integrated software solutions and services that truly meet its customers needs. We want to empower researchers around the world to achieve their goals of improving human health and quality of life through advanced computational techniques that transform the way chemists design compounds and materials. @@ -29928,6 +30878,16 @@ version |toolchain ``2022-2``|``system`` ``2022-3``|``system`` +### scib + +Benchmarking atlas-level data integration in single-cell genomics. + +*homepage*: + +version |toolchain +---------|-------------- +``1.1.1``|``foss/2022a`` + ### sciClone An R package for inferring the subclonal architecture of tumors @@ -30061,6 +31021,7 @@ version |versionsuffix |toolchain ``1.0.1`` | |``foss/2021b``, ``intel/2021b`` ``1.0.2`` | |``foss/2021b`` ``1.1.2`` | |``foss/2022a``, ``intel/2022a`` +``1.2.1`` | |``gfbf/2022b`` ### scikit-misc @@ -30069,8 +31030,8 @@ Miscellaneous tools for data analysis and scientific computing *homepage*: version |toolchain ----------|-------------- -``0.1.4``|``foss/2021a`` +---------|------------------------------ +``0.1.4``|``foss/2021a``, ``foss/2022a`` ### scikit-multilearn @@ -30148,6 +31109,7 @@ version |versionsuffix |toolchain ``2021.10``| |``foss/2021b``, ``intel/2021b`` ``2021.10``|``-Python-2.7.18``|``foss/2021b`` ``2022.05``| |``foss/2022.05``, ``foss/2022a``, ``intel/2022.05``, ``intel/2022a`` +``2023.02``| |``gfbf/2022b`` ### SCnorm @@ -30230,12 +31192,14 @@ The Score-P measurement infrastructure is a highly scalable and easy-to-use too *homepage*: version |versionsuffix |toolchain ----------|----------------|-------------------------------------------------- +---------|----------------|------------------------------------------------------------------------------------------------------- ``2.0.1``| |``foss/2016a`` -``6.0`` | |``gompi/2019a``, ``gompi/2020a``, ``gompic/2019b`` -``7.0`` | |``gompi/2021a``, ``gompic/2020b`` +``6.0`` | |``gompi/2019a``, ``gompi/2019b``, ``gompi/2020a``, ``gompic/2019a``, ``gompic/2019b``, ``gompic/2020a`` +``7.0`` | |``gompi/2020b``, ``gompi/2021a``, ``gompic/2020b`` ``7.1`` |``-CUDA-11.3.1``|``gompi/2021a`` -``8.0`` | |``gompi/2022a`` +``8.0`` | |``gompi/2021b``, ``gompi/2022a`` +``8.0`` |``-CUDA-11.4.1``|``gompi/2021b`` +``8.0`` |``-CUDA-11.7.0``|``gompi/2022a`` ### SCOTCH @@ -30342,7 +31306,7 @@ version |toolchain SDL: Simple DirectMedia Layer, a cross-platform multimedia library -*homepage*: +*homepage*: version |toolchain ----------|---------------------------------------------------------------------- @@ -30353,6 +31317,7 @@ version |toolchain ``2.0.14``|``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ``2.0.20``|``GCCcore/11.2.0`` ``2.0.22``|``GCCcore/11.3.0`` +``2.26.3``|``GCCcore/12.2.0`` ### SDL2_image @@ -30420,6 +31385,16 @@ version |versionsuffix |toolchain ---------|-------------------|---------- ``3.3.3``|``-Java-1.8.0_152``|``system`` +### SeaView + +SeaView is a multiplatform, graphical user interface for multiple sequence alignment and molecular phylogeny. + +*homepage*: + +version |toolchain +---------|------------------ +``5.0.5``|``GCCcore/11.2.0`` + ### SECAPR SECAPR is a bioinformatics pipeline for the rapid and user-friendly processing of targeted enriched Illumina sequences, from raw reads to alignments @@ -30521,12 +31496,12 @@ SATe-enabled Phylogenetic Placement - addresses the problem of phylogenetic plac *homepage*: version |versionsuffix |toolchain -----------|-----------------|-------------- +----------|-----------------|------------------------------ ``4.3.10``|``-Python-3.7.4``|``foss/2019b`` ``4.3.10``|``-Python-3.8.2``|``foss/2020a`` ``4.4.0`` | |``foss/2020b`` ``4.5.0`` | |``foss/2021a`` -``4.5.1`` | |``foss/2021b`` +``4.5.1`` | |``foss/2021b``, ``foss/2022a`` ### Seq-Gen @@ -30583,6 +31558,7 @@ version |toolchain ``0.13.2``|``system`` ``2.1.0`` |``system`` ``2.2.0`` |``system`` +``2.3.1`` |``system`` ### SeqLib @@ -30938,6 +31914,16 @@ version |versionsuffix |toolchain ``6.0g``|``-fast`` |``foss/2022a`` ``6.0g``|``-fast-CUDA-11.7.0``|``foss/2022a`` +### silhouetteRank + +silhouetteRank is a tool for finding spatially variable genes based on computing silhouette coefficient from binarized spatial gene expression data + +*homepage*: + +version |toolchain +------------|-------------- +``1.0.5.13``|``foss/2022a`` + ### silx The silx project provides a collection of Python packages to support the development of data assessment, reduction and analysis applications at synchrotron radiation facilities. @@ -30948,6 +31934,7 @@ version |versionsuffix |toolchain ----------|-----------------|---------------------------------- ``0.13.2``|``-Python-3.7.4``|``foss/2019b``, ``fosscuda/2019b`` ``0.14.0``| |``foss/2020b``, ``fosscuda/2020b`` +``1.0.0`` | |``foss/2021b`` ### simint @@ -31085,7 +32072,7 @@ version |versionsuffix|toolchain ``1.7.1``|``-tools`` |``foss/2017a`` ``1.7.4``|``-tools`` |``GCCcore/8.2.0`` ``1.7.6``|``-tools`` |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``1.7.7``|``-tools`` |``GCCcore/11.3.0`` +``1.7.7``|``-tools`` |``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ### SIP @@ -31104,6 +32091,16 @@ version |versionsuffix |toolchain ``4.19.8`` |``-Python-3.6.4`` |``foss/2018a``, ``intel/2018a`` ``4.19.13``|``-Python-2.7.15``|``fosscuda/2018b`` +### siscone + +Hadron Seedless Infrared-Safe Cone jet algorithm + +*homepage*: + +version |toolchain +---------|------------------ +``3.0.5``|``GCCcore/11.3.0`` + ### SISSO A data-driven method combining symbolic regression and compressed sensing toward accurate & interpretable models. @@ -31197,16 +32194,6 @@ version |toolchain ---------|-------------- ``0.4.3``|``foss/2021b`` -### slamdunk - -SlamDunk is a novel, fully automated software tool for automated, robust, scalable and reproducible SLAMseq data analysis. - -*homepage*: - -version |toolchain ----------|-------------- -``0.4.3``|``foss/2021b`` - ### SLATEC SLATEC Common Mathematical Library, a comprehensive software library containing over 1400 general purpose mathematical and statistical routines written in Fortran 77. @@ -31329,6 +32316,16 @@ version |toolchain ----------|-------------- ``1.15.4``|``foss/2022a`` +### smfishHmrf + +smFish spatial pattern mining and cell type prediction + +*homepage*: + +version |toolchain +---------|-------------- +``1.3.3``|``foss/2022a`` + ### smithwaterman smith-waterman-gotoh alignment algorithm. @@ -31396,6 +32393,8 @@ version |versionsuffix |toolchain ``6.1.0`` | |``foss/2020b`` ``6.6.1`` | |``foss/2021a`` ``6.10.0``| |``foss/2021b`` +``7.18.2``| |``foss/2021b`` +``7.22.0``| |``foss/2022a`` ### SNAP @@ -31404,13 +32403,13 @@ Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for h *homepage*: version |toolchain ---------------|--------------- +--------------|------------------------------ ``1.0beta.23``|``intel/2017b`` -``2.0.1`` |``GCC/12.2.0`` +``2.0.1`` |``GCC/11.3.0``, ``GCC/12.2.0`` ### 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. +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. *homepage*: @@ -31418,6 +32417,7 @@ version |toolchain --------------|------------------------------------------------------------------------- ``2013-11-29``|``GCC/6.4.0-2.28``, ``GCC/8.3.0``, ``iccifort/2017.4.196-GCC-6.4.0-2.28`` ``20190603`` |``GCC/10.2.0`` +``20221022`` |``GCC/11.3.0`` ### SNAPE-pooled @@ -31651,6 +32651,7 @@ version |toolchain ``1.3.0``|``GCC/10.3.0`` ``1.3.1``|``GCC/11.2.0`` ``2.0.0``|``GCC/11.2.0`` +``2.0.1``|``GCC/11.3.0`` ### Spack @@ -31697,6 +32698,7 @@ version |versionsuffix |toolchain ``3.15.2``| |``GCC/10.2.0`` ``3.15.2``|``-Python-2.7.18``|``GCC/10.2.0`` ``3.15.3``| |``GCC/10.3.0``, ``GCC/11.2.0`` +``3.15.5``| |``GCC/11.3.0`` ### spaln @@ -31704,11 +32706,12 @@ Spaln (space-efficient spliced alignment) is a stand-alone program that maps an *homepage*: -version |toolchain -----------|---------------------------------------- -``2.3.3c``|``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` -``2.4.03``|``iccifort/2019.5.281`` -``2.4.12``|``GCC/10.2.0``, ``GCC/11.2.0`` +version |toolchain +-----------|---------------------------------------- +``2.3.3c`` |``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` +``2.4.03`` |``iccifort/2019.5.281`` +``2.4.12`` |``GCC/10.2.0``, ``GCC/11.2.0`` +``2.4.13f``|``GCC/11.3.0`` ### Spark @@ -31738,6 +32741,17 @@ version |versionsuffix |toolchain ``3.1.1``| |``foss/2020b``, ``fosscuda/2020b`` ``3.1.1``|``-Python-3.8.2`` |``foss/2020a`` ``3.2.1``| |``foss/2021b`` +``3.3.1``| |``foss/2022a`` + +### sparse-neighbors-search + +A Python/C++ implementation of an approximate nearest neighbor search for sparse data structures based on the idea of local sensitive hash functions. + +*homepage*: + +version|toolchain +-------|-------------- +``0.7``|``foss/2022a`` ### sparsehash @@ -31749,7 +32763,17 @@ version |toolchain ---------|------------------------------------------------------------------------------------------------------------------------------ ``2.0.2``|``foss/2016a`` ``2.0.3``|``GCCcore/5.4.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2016b``, ``intel/2017a`` -``2.0.4``|``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +``2.0.4``|``GCCcore/10.2.0``, ``GCCcore/11.3.0``, ``GCCcore/9.3.0`` + +### SpatialDE + +SpatialDE is a method to identify genes which significantly depend on spatial coordinates in non-linear and non-parametric ways. The intended applications are spatially resolved RNA-sequencing from e.g. Spatial Transcriptomics, or in situ gene expression measurements from e.g. SeqFISH or MERFISH. + +*homepage*: + +version |toolchain +---------|-------------- +``1.1.3``|``foss/2022a`` ### spatialreg @@ -32061,7 +33085,7 @@ version |toolchain The SRA Toolkit, and the source-code SRA System Development Kit (SDK), will allow you to programmatically access data housed within SRA and convert it from the SRA format -*homepage*: +*homepage*: version |versionsuffix |toolchain -----------|-------------------|--------------- @@ -32077,7 +33101,19 @@ version |versionsuffix |toolchain ``2.10.5`` |``-centos_linux64``|``system`` ``2.10.8`` | |``gompi/2020a`` ``2.10.9`` | |``gompi/2020b`` +``3.0.0`` | |``gompi/2021b`` ``3.0.0`` |``-centos_linux64``|``system`` +``3.0.3`` | |``gompi/2022a`` + +### sradownloader + +SRAdownloader takes the annotation table from the SRA run selector tool and retrieves the raw fastq files for the selected samples + +*homepage*: + +version|toolchain +-------|------------------ +``3.9``|``GCCcore/11.3.0`` ### SRPRISM @@ -32140,9 +33176,10 @@ SSW is a fast implementation of the Smith-Waterman algorithm, which uses the Si *homepage*: -version|toolchain --------|----------------------------------------------------------------------------- -``1.1``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` +version |toolchain +---------|----------------------------------------------------------------------------- +``1.1`` |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` +``1.2.4``|``GCCcore/10.3.0`` ### STACEY @@ -32253,6 +33290,7 @@ version |toolchain ``2.7.8a`` |``GCC/10.2.0`` ``2.7.9a`` |``GCC/10.3.0``, ``GCC/11.2.0`` ``2.7.10a_alpha_220601``|``GCC/10.3.0`` +``2.7.10b`` |``GCC/11.3.0`` ### STAR-CCM+ @@ -32269,6 +33307,8 @@ version |versionsuffix|toolchain ``17.04.008``|``-r8`` |``system`` ``17.06.007``| |``system`` ``17.06.007``|``-r8`` |``system`` +``18.02.008``| |``system`` +``18.02.008``|``-r8`` |``system`` ### STAR-Fusion @@ -32282,6 +33322,16 @@ version |versionsuffix |toolchain ``1.6.0``|``-Perl-5.28.1-Python-3.7.2``|``GCC/8.2.0-2.31.1`` ``1.8.1``|``-Python-3.7.4`` |``foss/2019b`` +### stardist + +Object Detection with Star-convex Shapes. + +*homepage*: + +version |toolchain +---------|-------------- +``0.8.3``|``foss/2021b`` + ### 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. @@ -32369,6 +33419,16 @@ version |versionsuffix |toolchain ``1.7.6``|``-Python-3.7.2`` |``foss/2019a`` ``1.7.6``|``-Python-3.7.4`` |``foss/2019b`` +### Strainberry + +Strainberry is a method that performs strain separation in low-complexity metagenomes using error-prone long-read technologies. It exploits state-of-the-art tools for variant calling, haplotype phasing, and genome assembly, in order to achieve single-sample assembly of strains with higher quality than other state-of-the-art long-read assemblers. + +*homepage*: + +version|toolchain +-------|-------------- +``1.1``|``foss/2022a`` + ### STREAM The STREAM benchmark is a simple synthetic benchmark program that measures sustainable memory bandwidth (in MB/s) and the corresponding computation rate for simple vector kernels. @@ -32376,8 +33436,8 @@ The STREAM benchmark is a simple synthetic benchmark program that measures susta *homepage*: version |toolchain ---------|------------------------------------------------------------------------------------------------------------------ -``5.10``|``GCC/7.3.0-2.30``, ``GCC/8.2.0-2.31.1``, ``GCC/9.3.0``, ``iccifort/2020.1.217``, ``intel/2016b``, ``intel/2018b`` +--------|---------------------------------------------------------------------------------------------------------------------------------------------------------------- +``5.10``|``GCC/11.3.0``, ``GCC/7.3.0-2.30``, ``GCC/8.2.0-2.31.1``, ``GCC/9.3.0``, ``iccifort/2020.1.217``, ``intel-compilers/2022.2.1``, ``intel/2016b``, ``intel/2018b`` ### strelka @@ -32668,6 +33728,7 @@ Perl binding for SVG version |versionsuffix |toolchain --------|----------------|-------------- ``2.84``|``-Perl-5.30.0``|``foss/2019b`` +``2.87``| |``GCC/11.3.0`` ### svist4get @@ -32819,8 +33880,8 @@ version |versionsuffix |toolchain ``1.7.1`` | |``foss/2020b``, ``intel/2020b`` ``1.8`` | |``foss/2021a`` ``1.9`` | |``foss/2021b`` -``1.10.1``| |``foss/2022a`` -``1.11.1``| |``foss/2022a`` +``1.10.1``| |``foss/2022a``, ``intel/2022a`` +``1.11.1``| |``foss/2022a``, ``intel/2022a`` ### SyRI @@ -32841,12 +33902,12 @@ Szip compression software, providing lossless compression of scientific data version |toolchain ---------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ``2.1`` |``GCC/4.8.1``, ``GCCcore/5.4.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``gimkl/2.11.5``, ``gimkl/2017a``, ``gmpolf/2017.10``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``intel/2017.01``, ``intel/2017a``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25`` -``2.1.1``|``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/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``2.1.1``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ## T -[tabix](#tabix) - [tabixpp](#tabixpp) - [taco](#taco) - [TagDust](#tagdust) - [TagLib](#taglib) - [Taiyaki](#taiyaki) - [TALON](#talon) - [TALYS](#talys) - [TAMkin](#tamkin) - [task-spooler](#task-spooler) - [taxator-tk](#taxator-tk) - [TBA](#tba) - [tbb](#tbb) - [tbl2asn](#tbl2asn) - [TCC](#tcc) - [Tcl](#tcl) - [TCLAP](#tclap) - [tcsh](#tcsh) - [tecplot360ex](#tecplot360ex) - [TELEMAC-MASCARET](#telemac-mascaret) - [Telescope](#telescope) - [Teneto](#teneto) - [tensorboard](#tensorboard) - [tensorboardX](#tensorboardx) - [TensorFlow](#tensorflow) - [TensorFlow-Datasets](#tensorflow-datasets) - [tensorflow-probability](#tensorflow-probability) - [TensorRT](#tensorrt) - [terastructure](#terastructure) - [termcolor](#termcolor) - [Tesla-Deployment-Kit](#tesla-deployment-kit) - [tesseract](#tesseract) - [testpath](#testpath) - [TetGen](#tetgen) - [TEToolkit](#tetoolkit) - [TEtranscripts](#tetranscripts) - [texinfo](#texinfo) - [texlive](#texlive) - [Text-CSV](#text-csv) - [TFEA](#tfea) - [Theano](#theano) - [ThemisPy](#themispy) - [THetA](#theta) - [thurstonianIRT](#thurstonianirt) - [TiCCutils](#ticcutils) - [tidybayes](#tidybayes) - [tidymodels](#tidymodels) - [Tika](#tika) - [TiMBL](#timbl) - [time](#time) - [TINKER](#tinker) - [TinyDB](#tinydb) - [TinyXML](#tinyxml) - [Tk](#tk) - [Tkinter](#tkinter) - [TM-align](#tm-align) - [tMAE](#tmae) - [tmap](#tmap) - [tmux](#tmux) - [TN93](#tn93) - [TOBIAS](#tobias) - [ToFu](#tofu) - [Togl](#togl) - [tokenizers](#tokenizers) - [Tombo](#tombo) - [TOML-Fortran](#toml-fortran) - [topaz](#topaz) - [TopHat](#tophat) - [torchaudio](#torchaudio) - [torchdata](#torchdata) - [torchinfo](#torchinfo) - [torchsampler](#torchsampler) - [torchtext](#torchtext) - [torchvision](#torchvision) - [TotalView](#totalview) - [tqdm](#tqdm) - [Tracer](#tracer) - [TranscriptClean](#transcriptclean) - [TransDecoder](#transdecoder) - [Transformers](#transformers) - [Transrate](#transrate) - [travis](#travis) - [TRAVIS-Analyzer](#travis-analyzer) - [treatSens](#treatsens) - [TreeMix](#treemix) - [TreeShrink](#treeshrink) - [TRF](#trf) - [Triangle](#triangle) - [Trilinos](#trilinos) - [Trim_Galore](#trim_galore) - [trimAl](#trimal) - [trimesh](#trimesh) - [Trimmomatic](#trimmomatic) - [Trinity](#trinity) - [TRIQS](#triqs) - [TRIQS-cthyb](#triqs-cthyb) - [TRIQS-dft_tools](#triqs-dft_tools) - [TRIQS-tprf](#triqs-tprf) - [TRUST](#trust) - [TRUST4](#trust4) - [Trycycler](#trycycler) - [tsne](#tsne) - [TurboVNC](#turbovnc) - [TVB](#tvb) - [tvb-data](#tvb-data) - [TVB-deps](#tvb-deps) - [tvb-framework](#tvb-framework) - [tvb-library](#tvb-library) - [TWL-NINJA](#twl-ninja) - [typing-extensions](#typing-extensions) +[tabix](#tabix) - [tabixpp](#tabixpp) - [taco](#taco) - [TagDust](#tagdust) - [TagLib](#taglib) - [Taiyaki](#taiyaki) - [TALON](#talon) - [TALYS](#talys) - [TAMkin](#tamkin) - [task-spooler](#task-spooler) - [taxator-tk](#taxator-tk) - [TBA](#tba) - [tbb](#tbb) - [tbl2asn](#tbl2asn) - [TCC](#tcc) - [Tcl](#tcl) - [TCLAP](#tclap) - [tcsh](#tcsh) - [tecplot360ex](#tecplot360ex) - [TELEMAC-MASCARET](#telemac-mascaret) - [Telescope](#telescope) - [Teneto](#teneto) - [tensorboard](#tensorboard) - [tensorboardX](#tensorboardx) - [TensorFlow](#tensorflow) - [TensorFlow-Datasets](#tensorflow-datasets) - [tensorflow-probability](#tensorflow-probability) - [TensorRT](#tensorrt) - [terastructure](#terastructure) - [termcolor](#termcolor) - [Tesla-Deployment-Kit](#tesla-deployment-kit) - [tesseract](#tesseract) - [testpath](#testpath) - [TetGen](#tetgen) - [TEToolkit](#tetoolkit) - [TEtranscripts](#tetranscripts) - [texinfo](#texinfo) - [texlive](#texlive) - [Text-CSV](#text-csv) - [TFEA](#tfea) - [Theano](#theano) - [ThemisPy](#themispy) - [THetA](#theta) - [thurstonianIRT](#thurstonianirt) - [TiCCutils](#ticcutils) - [tidybayes](#tidybayes) - [tidymodels](#tidymodels) - [Tika](#tika) - [TiMBL](#timbl) - [time](#time) - [TINKER](#tinker) - [TinyDB](#tinydb) - [TinyXML](#tinyxml) - [Tk](#tk) - [Tkinter](#tkinter) - [TM-align](#tm-align) - [tMAE](#tmae) - [tmap](#tmap) - [tmux](#tmux) - [TN93](#tn93) - [TOBIAS](#tobias) - [ToFu](#tofu) - [Togl](#togl) - [toil](#toil) - [tokenizers](#tokenizers) - [Tombo](#tombo) - [TOML-Fortran](#toml-fortran) - [topaz](#topaz) - [TopHat](#tophat) - [torchaudio](#torchaudio) - [torchdata](#torchdata) - [torchinfo](#torchinfo) - [torchsampler](#torchsampler) - [torchtext](#torchtext) - [torchvision](#torchvision) - [TotalView](#totalview) - [tqdm](#tqdm) - [Tracer](#tracer) - [TranscriptClean](#transcriptclean) - [TransDecoder](#transdecoder) - [Transformers](#transformers) - [Transrate](#transrate) - [travis](#travis) - [TRAVIS-Analyzer](#travis-analyzer) - [treatSens](#treatsens) - [TreeMix](#treemix) - [TreeShrink](#treeshrink) - [TRF](#trf) - [Triangle](#triangle) - [Trilinos](#trilinos) - [Trim_Galore](#trim_galore) - [trimAl](#trimal) - [trimesh](#trimesh) - [Trimmomatic](#trimmomatic) - [Trinity](#trinity) - [TRIQS](#triqs) - [TRIQS-cthyb](#triqs-cthyb) - [TRIQS-dft_tools](#triqs-dft_tools) - [TRIQS-tprf](#triqs-tprf) - [TRUST](#trust) - [TRUST4](#trust4) - [Trycycler](#trycycler) - [tsne](#tsne) - [TurboVNC](#turbovnc) - [TVB](#tvb) - [tvb-data](#tvb-data) - [TVB-deps](#tvb-deps) - [tvb-framework](#tvb-framework) - [tvb-library](#tvb-library) - [TWL-NINJA](#twl-ninja) - [typing-extensions](#typing-extensions) ### tabix @@ -33200,6 +34261,8 @@ version |versionsuffix |toolchain ``2.7.1`` | |``foss/2021b`` ``2.7.1`` |``-CUDA-11.4.1`` |``foss/2021b`` ``2.8.4`` | |``foss/2021b`` +``2.11.0``| |``foss/2022a`` +``2.11.0``|``-CUDA-11.7.0`` |``foss/2022a`` ### TensorFlow-Datasets @@ -33210,6 +34273,7 @@ TensorFlow Datasets is a collection of datasets ready to use, with TensorFlow or version |versionsuffix |toolchain ---------|----------------|-------------- ``4.7.0``|``-CUDA-11.3.1``|``foss/2021a`` +``4.8.3``|``-CUDA-11.4.1``|``foss/2021b`` ### tensorflow-probability @@ -33334,6 +34398,7 @@ version |toolchain ``6.6`` |``GCCcore/8.2.0`` ``6.7`` |``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``6.8`` |``GCCcore/11.2.0`` +``7.0.2``|``GCCcore/11.3.0`` ### texlive @@ -33539,7 +34604,7 @@ version |versionsuffix |toolchain ``8.6.9`` | |``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``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`` +``8.6.12``| |``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ### Tkinter @@ -33567,6 +34632,7 @@ version |versionsuffix |toolchain ``3.9.5`` | |``GCCcore/10.3.0`` ``3.9.6`` | |``GCCcore/11.2.0`` ``3.10.4``| |``GCCcore/11.3.0`` +``3.10.8``| |``GCCcore/12.2.0`` ### TM-align @@ -33662,6 +34728,16 @@ version|toolchain -------|--------------------------------------------------------- ``2.0``|``GCCcore/10.2.0``, ``GCCcore/11.3.0``, ``GCCcore/8.3.0`` +### toil + +A scalable, efficient, cross-platform (Linux/macOS) and easy-to-use workflow engine in pure Python. + +*homepage*: + +version |toolchain +---------|-------------- +``5.8.0``|``foss/2021a`` + ### tokenizers Fast State-of-the-Art Tokenizers optimized for Research and Production @@ -33715,7 +34791,7 @@ 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`` +``2.1.2``|``-Python-2.7.18``|``GCC/10.2.0``, ``GCC/11.3.0`` ### torchaudio @@ -33836,6 +34912,7 @@ version |versionsuffix |toolchain ``4.61.2``| |``GCCcore/10.3.0`` ``4.62.3``| |``GCCcore/11.2.0`` ``4.64.0``| |``GCCcore/11.3.0`` +``4.64.1``| |``GCCcore/12.2.0`` ### Tracer @@ -33948,9 +35025,9 @@ Tandem Repeats Finder: a program to analyze DNA sequences. *homepage*: version |versionsuffix|toolchain -----------|-------------|------------------------------------------------------------------------- +----------|-------------|--------------------------------------------------------------------------------------------- ``4.09`` |``-linux64`` |``system`` -``4.09.1``| |``GCC/10.3.0``, ``GCCcore/10.2.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` +``4.09.1``| |``GCC/10.3.0``, ``GCCcore/10.2.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/9.3.0`` ### Triangle @@ -33973,6 +35050,7 @@ version |versionsuffix |toolchain ``12.12.1``|``-Python-2.7.14``|``foss/2017b``, ``intel/2017b`` ``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`` ### Trim_Galore @@ -33980,23 +35058,24 @@ Trim Galore! is a wrapper script to automate quality and adapter trimming as wel *homepage*: -version |versionsuffix |toolchain ----------|-------------------------|------------------------------- -``0.4.2``| |``foss/2016b`` -``0.4.4``| |``foss/2016b``, ``intel/2017a`` -``0.5.0``| |``foss/2018b`` -``0.5.0``|``-Python-3.6.6`` |``intel/2018b`` -``0.6.0``|``-Python-2.7.15`` |``foss/2018b`` -``0.6.0``|``-Python-3.6.6`` |``foss/2018b`` -``0.6.1``|``-Python-2.7.15`` |``foss/2018b`` -``0.6.1``|``-Python-3.6.6`` |``foss/2018b`` -``0.6.2``|``-Java-11`` |``GCCcore/8.2.0`` -``0.6.2``|``-Python-2.7.15`` |``foss/2018b`` -``0.6.2``|``-Python-3.6.6`` |``foss/2018b`` -``0.6.5``|``-Java-11-Python-3.7.4``|``GCCcore/8.3.0`` -``0.6.6``|``-Python-2.7.18`` |``GCC/10.2.0`` -``0.6.6``|``-Python-3.8.2`` |``GCCcore/9.3.0`` -``0.6.7``| |``GCCcore/10.3.0`` +version |versionsuffix |toolchain +----------|-------------------------|------------------------------- +``0.4.2`` | |``foss/2016b`` +``0.4.4`` | |``foss/2016b``, ``intel/2017a`` +``0.5.0`` | |``foss/2018b`` +``0.5.0`` |``-Python-3.6.6`` |``intel/2018b`` +``0.6.0`` |``-Python-2.7.15`` |``foss/2018b`` +``0.6.0`` |``-Python-3.6.6`` |``foss/2018b`` +``0.6.1`` |``-Python-2.7.15`` |``foss/2018b`` +``0.6.1`` |``-Python-3.6.6`` |``foss/2018b`` +``0.6.2`` |``-Java-11`` |``GCCcore/8.2.0`` +``0.6.2`` |``-Python-2.7.15`` |``foss/2018b`` +``0.6.2`` |``-Python-3.6.6`` |``foss/2018b`` +``0.6.5`` |``-Java-11-Python-3.7.4``|``GCCcore/8.3.0`` +``0.6.6`` |``-Python-2.7.18`` |``GCC/10.2.0`` +``0.6.6`` |``-Python-3.8.2`` |``GCCcore/9.3.0`` +``0.6.7`` | |``GCCcore/10.3.0`` +``0.6.10``| |``GCCcore/11.2.0`` ### trimAl @@ -34052,6 +35131,7 @@ version |versionsuffix |toolchain ``2.9.1`` |``-Python-2.7.16``|``foss/2019b`` ``2.9.1`` |``-Python-3.7.4`` |``foss/2019b`` ``2.10.0``|``-Python-3.7.4`` |``foss/2019b`` +``2.15.1``| |``foss/2022a`` ### TRIQS @@ -34220,6 +35300,7 @@ Nearly Infinite Neighbor Joining Application. version |toolchain ---------------------|-------------- ``0.97-cluster_only``|``GCC/10.2.0`` +``0.98-cluster_only``|``GCC/11.3.0`` ### typing-extensions @@ -34355,7 +35436,7 @@ version |toolchain ``2.2.24``|``intel/2017a`` ``2.2.25``|``foss/2017b``, ``intel/2017b`` ``2.2.26``|``GCCcore/10.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2018a``, ``foss/2018b``, ``foss/2020a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b``, ``iomkl/2018b`` -``2.2.28``|``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``2.2.28``|``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ### UFL @@ -34375,9 +35456,9 @@ Uniform Manifold Approximation and Projection (UMAP) is a dimension reduction te *homepage*: version |toolchain ----------|------------------------------ -``0.4.6``|``fosscuda/2020b`` -``0.5.3``|``foss/2021a``, ``foss/2021b`` +---------|-------------------------------------------------------------- +``0.4.6``|``foss/2020b``, ``fosscuda/2020b`` +``0.5.3``|``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``foss/2022a`` ### UMI-tools @@ -34451,8 +35532,9 @@ Python library for lossy ASCII transliterations of Unicode text (port of Text::U *homepage*: version |versionsuffix |toolchain ----------|-----------------|----------------- +---------|-----------------|------------------ ``1.1.1``|``-Python-3.7.4``|``GCCcore/8.3.0`` +``1.3.6``| |``GCCcore/11.3.0`` ### unimap @@ -34594,7 +35676,7 @@ version |toolchain ## V -[V8](#v8) - [Vala](#vala) - [Valgrind](#valgrind) - [Vampir](#vampir) - [Vampire](#vampire) - [VarDict](#vardict) - [variant_tools](#variant_tools) - [VariantMetaCaller](#variantmetacaller) - [VarScan](#varscan) - [vartools](#vartools) - [VASP](#vasp) - [VAtools](#vatools) - [vawk](#vawk) - [VBZ-Compression](#vbz-compression) - [VCF-kit](#vcf-kit) - [vcflib](#vcflib) - [vcfnp](#vcfnp) - [VCFtools](#vcftools) - [VEGAS](#vegas) - [velocyto](#velocyto) - [Velvet](#velvet) - [VEP](#vep) - [verifyBamID](#verifybamid) - [VERSE](#verse) - [VESTA](#vesta) - [ViennaRNA](#viennarna) - [Vim](#vim) - [VirSorter](#virsorter) - [VirtualGL](#virtualgl) - [Virtuoso-opensource](#virtuoso-opensource) - [VisPy](#vispy) - [VMD](#vmd) - [VMTK](#vmtk) - [voltools](#voltools) - [vorbis-tools](#vorbis-tools) - [Voro++](#voro++) - [vsc-base](#vsc-base) - [vsc-install](#vsc-install) - [vsc-mympirun](#vsc-mympirun) - [vsc-mympirun-scoop](#vsc-mympirun-scoop) - [vsc-processcontrol](#vsc-processcontrol) - [VSEARCH](#vsearch) - [vt](#vt) - [VTK](#vtk) - [VTune](#vtune) - [VV](#vv) - [VXL](#vxl) +[V8](#v8) - [Vala](#vala) - [Valgrind](#valgrind) - [Vampir](#vampir) - [Vampire](#vampire) - [VarDict](#vardict) - [variant_tools](#variant_tools) - [VariantMetaCaller](#variantmetacaller) - [VarScan](#varscan) - [vartools](#vartools) - [VASP](#vasp) - [VAtools](#vatools) - [vawk](#vawk) - [VBZ-Compression](#vbz-compression) - [VCF-kit](#vcf-kit) - [vcflib](#vcflib) - [vcfnp](#vcfnp) - [VCFtools](#vcftools) - [vConTACT2](#vcontact2) - [VEGAS](#vegas) - [velocyto](#velocyto) - [Velvet](#velvet) - [VEP](#vep) - [verifyBamID](#verifybamid) - [VERSE](#verse) - [VESTA](#vesta) - [ViennaRNA](#viennarna) - [Vim](#vim) - [VirSorter](#virsorter) - [VirSorter2](#virsorter2) - [VirtualGL](#virtualgl) - [Virtuoso-opensource](#virtuoso-opensource) - [VisPy](#vispy) - [vitessce-python](#vitessce-python) - [vitessceR](#vitesscer) - [VMD](#vmd) - [VMTK](#vmtk) - [voltools](#voltools) - [vorbis-tools](#vorbis-tools) - [Voro++](#voro++) - [vsc-base](#vsc-base) - [vsc-install](#vsc-install) - [vsc-mympirun](#vsc-mympirun) - [vsc-mympirun-scoop](#vsc-mympirun-scoop) - [vsc-processcontrol](#vsc-processcontrol) - [VSEARCH](#vsearch) - [vt](#vt) - [VTK](#vtk) - [VTune](#vtune) - [VV](#vv) - [VXL](#vxl) ### V8 @@ -34799,6 +35881,16 @@ version |versionsuffix |toolchain ``0.1.16``| |``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2019.5.281`` ``0.1.16``|``-Perl-5.28.0``|``foss/2018b``, ``intel/2018b`` +### vConTACT2 + +vConTACT2 is a tool to perform guilt-by-contig-association classification of viral genomic sequence data. + +*homepage*: + +version |toolchain +----------|-------------- +``0.11.3``|``foss/2022a`` + ### VEGAS VEGAS (Versatile Gene-based Association Study) is a free program for performing gene-based tests for association using the results from genetic association studies @@ -34816,8 +35908,8 @@ Velocyto is a library for the analysis of RNA velocity. *homepage*: version |versionsuffix |toolchain ------------|-----------------|--------------- -``0.17.17``| |``foss/2021a`` +-----------|-----------------|------------------------------ +``0.17.17``| |``foss/2021a``, ``foss/2022a`` ``0.17.17``|``-Python-3.8.2``|``intel/2020a`` ### Velvet @@ -34918,6 +36010,16 @@ version |versionsuffix |toolchain ------------|----------------|-------------- ``20160601``|``-Perl-5.22.1``|``foss/2016a`` +### VirSorter2 + +VirSorter2 applies a multi-classifier, expert-guided approach to detect diverse DNA and RNA virus genomes. + +*homepage*: + +version |toolchain +---------|-------------- +``2.2.4``|``foss/2022a`` + ### VirtualGL VirtualGL is an open source toolkit that gives any Linux or Unix remote display software the ability to run OpenGL applications with full hardware acceleration. @@ -34950,6 +36052,26 @@ version |toolchain ---------|------------------------------- ``0.6.6``|``foss/2020b``, ``intel/2020b`` +### vitessce-python + +Python API and Jupyter widget facilitating interactive visualization of spatial single-cell data with Vitessce. + +*homepage*: + +version |toolchain +------------|-------------- +``20230222``|``foss/2022a`` + +### vitessceR + +Vitessce is a visual integration tool for exploration of spatial single-cell experiments. + +*homepage*: + +version |versionsuffix|toolchain +-------------------|-------------|-------------- +``0.99.0-20230110``|``-R-4.2.1`` |``foss/2022a`` + ### VMD VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. @@ -35080,6 +36202,7 @@ version |versionsuffix |toolchain ``5.2.9`` | |``system`` ``5.2.10`` | |``system`` ``5.2.11`` | |``system`` +``5.3.0`` | |``system`` ### vsc-mympirun-scoop @@ -35115,6 +36238,7 @@ version |toolchain ``2.15.0``|``GCC/9.3.0`` ``2.18.0``|``GCC/10.2.0`` ``2.21.1``|``GCC/10.3.0`` +``2.22.1``|``GCC/11.3.0`` ### vt @@ -35352,6 +36476,7 @@ version |toolchain ``1.20.3``|``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ``1.21.1``|``GCCcore/10.3.0`` ``1.21.2``|``GCCcore/11.2.0`` +``1.21.3``|``GCCcore/11.3.0`` ### wgsim @@ -35562,9 +36687,9 @@ Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio *homepage*: version|toolchain --------|------------------------------------- +-------|--------------------------------------------------------- ``2.3``|``GCC/7.3.0-2.30`` -``2.5``|``GCCcore/11.2.0``, ``GCCcore/9.3.0`` +``2.5``|``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/9.3.0`` ### wxPropertyGrid @@ -35601,15 +36726,16 @@ wxWidgets is a C++ library that lets developers create applications for Windows, *homepage*: -version |toolchain ----------|------------------------------ -``3.0.3``|``foss/2018a`` -``3.0.4``|``GCC/8.2.0-2.31.1`` -``3.1.3``|``GCC/8.3.0`` -``3.1.4``|``GCC/10.2.0`` -``3.1.5``|``GCC/10.3.0``, ``GCC/11.2.0`` -``3.2.0``|``GCC/11.2.0`` -``3.2.1``|``GCC/11.3.0`` +version |toolchain +-----------|------------------------------ +``3.0.3`` |``foss/2018a`` +``3.0.4`` |``GCC/8.2.0-2.31.1`` +``3.1.3`` |``GCC/8.3.0`` +``3.1.4`` |``GCC/10.2.0`` +``3.1.5`` |``GCC/10.3.0``, ``GCC/11.2.0`` +``3.2.0`` |``GCC/11.2.0`` +``3.2.1`` |``GCC/11.3.0`` +``3.2.2.1``|``GCCcore/12.2.0`` ## X @@ -35675,6 +36801,7 @@ version |toolchain ``20210414``|``GCCcore/10.3.0`` ``20210613``|``GCCcore/11.2.0`` ``20220620``|``GCCcore/11.3.0`` +``20230226``|``GCCcore/12.2.0`` ### x265 @@ -35683,7 +36810,7 @@ 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`` @@ -35692,7 +36819,7 @@ 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`` +``3.5``|``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ### XALT @@ -35848,6 +36975,7 @@ version |toolchain ``3.2.0``|``GCCcore/7.3.0`` ``3.2.2``|``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``3.2.3``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` +``3.2.4``|``GCCcore/12.2.0`` ### xESMF @@ -35940,6 +37068,7 @@ version |toolchain ``1.4.0``|``GCCcore/10.2.0`` ``1.4.4``|``GCCcore/10.3.0`` ``3.0.2``|``GCCcore/11.2.0`` +``3.0.8``|``GCCcore/11.3.0`` ### XMDS2 @@ -36132,7 +37261,7 @@ version |toolchain ### xtb -Semiempirical Extended Tight-Binding Program Package. +xtb - An extended tight-binding semi-empirical program package. *homepage*: @@ -36141,6 +37270,8 @@ version |versionsuffix |toolchain ``6.2.2-hotfix``|``-Python-3.6.3``|``intel/2017b`` ``6.2.3`` | |``foss/2019b`` ``6.4.1`` | |``foss/2021b``, ``intel/2021a`` +``6.5.0`` | |``foss/2021b`` +``6.5.1`` | |``foss/2022a`` ### xtensor @@ -36175,6 +37306,7 @@ version |toolchain ``1.20.11``|``GCCcore/10.3.0`` ``1.20.13``|``GCCcore/11.2.0`` ``21.1.3`` |``GCCcore/11.3.0`` +``21.1.6`` |``GCCcore/12.2.0`` ### xxd @@ -36183,8 +37315,8 @@ xxd is part of the VIM package and this will only install xxd, not vim! xxd conv *homepage*: version |toolchain -------------|---------------------------------------------------------- -``8.2.4220``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +------------|------------------------------------------------------------------------------ +``8.2.4220``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ### xxHash @@ -36216,7 +37348,7 @@ version |versionsuffix |toolchain ## Y -[YACS](#yacs) - [Yade](#yade) - [yaff](#yaff) - [Yambo](#yambo) - [yaml-cpp](#yaml-cpp) - [YANK](#yank) - [YAPS](#yaps) - [Yasm](#yasm) - [YAXT](#yaxt) - [Yices](#yices) +[YACS](#yacs) - [Yade](#yade) - [yaff](#yaff) - [Yambo](#yambo) - [yaml-cpp](#yaml-cpp) - [YANK](#yank) - [YAPS](#yaps) - [Yasm](#yasm) - [YAXT](#yaxt) - [Yices](#yices) - [YODA](#yoda) ### YACS @@ -36313,8 +37445,8 @@ 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/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/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 @@ -36342,6 +37474,16 @@ version |toolchain ---------|------------------ ``2.6.2``|``GCCcore/10.2.0`` +### YODA + +Yet more Objects for (High Energy Physics) Data Analysis + +*homepage*: + +version |toolchain +---------|-------------- +``1.9.7``|``GCC/11.3.0`` + ## Z