diff --git a/docs/version-specific/easyblocks.md b/docs/version-specific/easyblocks.md index bfa627766..c1d7da071 100644 --- a/docs/version-specific/easyblocks.md +++ b/docs/version-specific/easyblocks.md @@ -265,7 +265,9 @@ - EB_PyZMQ - EB_scipy - EB_SEPP + - EB_sympy - EB_TensorFlow + - EB_tensorflow_minus_compression - EB_TensorRT - EB_torchvision - EB_VSC_minus_tools @@ -379,7 +381,9 @@ - EB_PyZMQ - EB_scipy - EB_SEPP + - EB_sympy - EB_TensorFlow + - EB_tensorflow_minus_compression - EB_TensorRT - EB_torchvision - EB_VSC_minus_tools diff --git a/docs/version-specific/easyconfig-parameters.md b/docs/version-specific/easyconfig-parameters.md index f9d3bfc9e..5f0f4bbf3 100644 --- a/docs/version-specific/easyconfig-parameters.md +++ b/docs/version-specific/easyconfig-parameters.md @@ -146,6 +146,7 @@ **Parameter name**|**Description** |**Default value** ------------------|---------------------------------------------------------------------------------------------------------------------------|----------------- `block` |List of other 'block' sections on which this block depends (only relevant in easyconfigs with subblocks) |`None` +`build_info_msg` |String with information to be printed to stdout and logged during the building of the easyconfig |`None` `buildstats` |A list of dicts with build statistics |`None` `deprecated` |String specifying reason why this easyconfig file is deprecated and will be archived in the next major release of EasyBuild|`False` diff --git a/docs/version-specific/eb-help.md b/docs/version-specific/eb-help.md index b89d065f9..228b571e6 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: /home/example/.config/easybuild/config.cfg) +-----------------------------------------|---------------------------------------------------------- +``--configfiles=CONFIGFILES`` |Parse (additional) configfiles (type comma-separated list) ``--ignoreconfigfiles=IGNORECONFIGFILES``|Ignore configfiles (type comma-separated list) ## Basic options @@ -298,6 +298,7 @@ Option flag |Option ``--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 out of (python2, Lmod6, easyconfig, toolchain) (type comma-separated list) +``--silence-hook-trigger`` |Suppress printing of debug message every time a hook is triggered (default: False) ``--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 ffd79de33..91c8e57c5 100644 --- a/docs/version-specific/generic-easyblocks.md +++ b/docs/version-specific/generic-easyblocks.md @@ -278,11 +278,12 @@ Support for configuring with CMake, building and installing with MesonNinja. ### Extra easyconfig parameters specific to ``CMakeNinja`` easyblock easyconfig parameter |description |default value ---------------------------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|------------------ +--------------------------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|------------- ``abs_path_compilers`` |Specify compilers via absolute file path (not via command names) |``False`` ``allow_system_boost`` |Always allow CMake to pick up on Boost installed in OS (even if Boost is included as a dependency) |``False`` -``build_cmd`` |Build command to use |``"make"`` +``build_cmd`` |Build command to use |``"ninja"`` ``build_cmd_targets`` |Target name (string) or list of target names to build |``""`` +``build_dir`` |build_dir to pass to meson |``None`` ``build_shared_libs`` |Build shared library (instead of static library)None can be used to add no flag (usually results in static library) |``None`` ``build_type`` |Build type for CMake, e.g. Release.Defaults to 'Release' or 'Debug' depending on toolchainopts[debug] |``None`` ``configure_cmd`` |Configure command to use |``"cmake"`` @@ -290,7 +291,7 @@ easyconfig parameter |description ``configure_without_installdir``|Avoid passing an install directory to the configure command (such as via --prefix) |``False`` ``generator`` |Build file generator to use. None to use CMakes default |``"Ninja"`` ``host_type`` |Value to provide to --host option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script)|``None`` -``install_cmd`` |Install command to use |``"make install"`` +``install_cmd`` |Install command to use |``"ninja"`` ``install_target_subdir`` |Subdirectory to use as installation target |``None`` ``prefix_opt`` |Prefix command line option for configure script ('--prefix=' if None) |``None`` ``separate_build_dir`` |Perform build in a separate directory |``True`` @@ -886,7 +887,10 @@ Support for building and installing software with 'meson' and 'ninja'. easyconfig parameter |description |default value ----------------------|-------------------------------------|------------- +``build_cmd`` |Build command to use |``"ninja"`` +``build_dir`` |build_dir to pass to meson |``None`` ``configure_cmd`` |Configure command to use |``"meson"`` +``install_cmd`` |Install command to use |``"ninja"`` ``separate_build_dir``|Perform build in a separate directory|``True`` ### Customised steps in ``MesonNinja`` easyblock @@ -994,6 +998,7 @@ easyconfig parameter |description ``default_component_specs`` |Default specs to use for every component |``{}`` ``default_easyblock`` |Default easyblock to use for components |``None`` ``options`` |Dictionary with extension options. |``{}`` +``prefix_opt`` |String to use for option to set installation prefix (default is 'PREFIX') |``None`` ``runtest`` |Run unit tests. |``"test"`` ``sanity_check_all_components``|Enable sanity checks for all components |``False`` ``sanity_check_components`` |List of components for which to run sanity checks |``[]`` @@ -1006,10 +1011,11 @@ Builds and installs a Perl module, and can provide a dedicated module file. ### Extra easyconfig parameters specific to ``PerlModule`` easyblock -easyconfig parameter|description |default value ---------------------|----------------------------------|------------- -``options`` |Dictionary with extension options.|``{}`` -``runtest`` |Run unit tests. |``"test"`` +easyconfig parameter|description |default value +--------------------|-------------------------------------------------------------------------|------------- +``options`` |Dictionary with extension options. |``{}`` +``prefix_opt`` |String to use for option to set installation prefix (default is 'PREFIX')|``None`` +``runtest`` |Run unit tests. |``"test"`` ### Customised steps in ``PerlModule`` easyblock diff --git a/docs/version-specific/supported-software.md b/docs/version-specific/supported-software.md index 2a08950d1..0da9e33bf 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 3161 different software packages (incl. toolchains, bundles): +EasyBuild supports 3244 different software packages (incl. toolchains, bundles): [a](#a) - [b](#b) - [c](#c) - [d](#d) - [e](#e) - [f](#f) - [g](#g) - [h](#h) - [i](#i) - [j](#j) - [k](#k) - [l](#l) - [m](#m) - [n](#n) - [o](#o) - [p](#p) - [q](#q) - [r](#r) - [s](#s) - [t](#t) - [u](#u) - [v](#v) - [w](#w) - [x](#x) - [y](#y) - [z](#z) @@ -56,7 +56,7 @@ version |toolchain ## A -[ABAQUS](#abaqus) - [ABINIT](#abinit) - [ABRA2](#abra2) - [ABRicate](#abricate) - [Abseil](#abseil) - [abTEM](#abtem) - [ABySS](#abyss) - [ack](#ack) - [ACT](#act) - [ACTC](#actc) - [ada](#ada) - [AdapterRemoval](#adapterremoval) - [ADDA](#adda) - [ADF](#adf) - [ADIOS](#adios) - [adjustText](#adjusttext) - [ADMIXTURE](#admixture) - [ADOL-C](#adol-c) - [Advisor](#advisor) - [affinity](#affinity) - [AFNI](#afni) - [AGAT](#agat) - [AGeNT](#agent) - [AGFusion](#agfusion) - [AIMAll](#aimall) - [aiohttp](#aiohttp) - [ALADIN](#aladin) - [Albacore](#albacore) - [Albumentations](#albumentations) - [alevin-fry](#alevin-fry) - [ALFA](#alfa) - [Alfred](#alfred) - [alleleCount](#allelecount) - [alleleIntegrator](#alleleintegrator) - [Allinea](#allinea) - [ALLPATHS-LG](#allpaths-lg) - [almosthere](#almosthere) - [Alpha](#alpha) - [AlphaFold](#alphafold) - [AlphaPulldown](#alphapulldown) - [ALPS](#alps) - [alsa-lib](#alsa-lib) - [AMAPVox](#amapvox) - [Amara](#amara) - [amask](#amask) - [Amber](#amber) - [AmberMini](#ambermini) - [AmberTools](#ambertools) - [AMD-LibM](#amd-libm) - [AMD-RNG](#amd-rng) - [AMD-SecureRNG](#amd-securerng) - [AMD-uProf](#amd-uprof) - [AMOS](#amos) - [AMPHORA2](#amphora2) - [AMPL-MP](#ampl-mp) - [amplimap](#amplimap) - [AMPtk](#amptk) - [AmrPlusPlus](#amrplusplus) - [AMS](#ams) - [Anaconda2](#anaconda2) - [Anaconda3](#anaconda3) - [aNCI](#anci) - [andi](#andi) - [ANGEL](#angel) - [angsd](#angsd) - [ANIcalculator](#anicalculator) - [anndata](#anndata) - [Annif](#annif) - [Annocript](#annocript) - [annovar](#annovar) - [ANSYS](#ansys) - [ANSYS_CFD](#ansys_cfd) - [ant](#ant) - [antiSMASH](#antismash) - [ANTLR](#antlr) - [ANTs](#ants) - [anvio](#anvio) - [any2fasta](#any2fasta) - [AOCC](#aocc) - [AOMP](#aomp) - [APBS](#apbs) - [apex](#apex) - [APR](#apr) - [APR-util](#apr-util) - [AptaSUITE](#aptasuite) - [ARAGORN](#aragorn) - [Arb](#arb) - [Arcade-Learning-Environment](#arcade-learning-environment) - [arcasHLA](#arcashla) - [ARCH](#arch) - [Archive-Zip](#archive-zip) - [ArchR](#archr) - [archspec](#archspec) - [ARGoS](#argos) - [argtable](#argtable) - [aria2](#aria2) - [Arlequin](#arlequin) - [Armadillo](#armadillo) - [arosics](#arosics) - [ARPACK++](#arpack++) - [arpack-ng](#arpack-ng) - [ArrayFire](#arrayfire) - [Arriba](#arriba) - [Arrow](#arrow) - [arrow-R](#arrow-r) - [ART](#art) - [artic-ncov2019](#artic-ncov2019) - [ARTS](#arts) - [ArviZ](#arviz) - [ARWEN](#arwen) - [ASAP](#asap) - [ASAP3](#asap3) - [ASCAT](#ascat) - [ASE](#ase) - [ASF-SearchAPI](#asf-searchapi) - [ASHS](#ashs) - [Aspera-CLI](#aspera-cli) - [Aspera-Connect](#aspera-connect) - [assimp](#assimp) - [Assimulo](#assimulo) - [ASTRID](#astrid) - [astro-tulips](#astro-tulips) - [astropy](#astropy) - [at-spi2-atk](#at-spi2-atk) - [at-spi2-core](#at-spi2-core) - [ATAT](#atat) - [ATK](#atk) - [ATLAS](#atlas) - [atomate](#atomate) - [AtomPAW](#atompaw) - [atools](#atools) - [atropos](#atropos) - [ATSAS](#atsas) - [attr](#attr) - [attrdict](#attrdict) - [attrdict3](#attrdict3) - [augur](#augur) - [AUGUSTUS](#augustus) - [Austin](#austin) - [AUTO-07p](#auto-07p) - [Autoconf](#autoconf) - [Autoconf-archive](#autoconf-archive) - [AutoDock](#autodock) - [AutoDock-GPU](#autodock-gpu) - [AutoDock-Vina](#autodock-vina) - [AutoDockSuite](#autodocksuite) - [AutoGeneS](#autogenes) - [AutoGrid](#autogrid) - [Automake](#automake) - [AutoMap](#automap) - [autopep8](#autopep8) - [Autotools](#autotools) - [Avogadro2](#avogadro2) - [avro-cpp](#avro-cpp) - [awscli](#awscli) - [axel](#axel) +[ABAQUS](#abaqus) - [ABINIT](#abinit) - [ABRA2](#abra2) - [ABRicate](#abricate) - [Abseil](#abseil) - [abTEM](#abtem) - [ABySS](#abyss) - [ack](#ack) - [ACT](#act) - [ACTC](#actc) - [ada](#ada) - [AdapterRemoval](#adapterremoval) - [ADDA](#adda) - [ADF](#adf) - [ADIOS](#adios) - [adjustText](#adjusttext) - [ADMIXTURE](#admixture) - [ADOL-C](#adol-c) - [Advisor](#advisor) - [affinity](#affinity) - [AFNI](#afni) - [AGAT](#agat) - [AGeNT](#agent) - [AGFusion](#agfusion) - [AIMAll](#aimall) - [aiohttp](#aiohttp) - [ALADIN](#aladin) - [ALAMODE](#alamode) - [Albacore](#albacore) - [Albumentations](#albumentations) - [alevin-fry](#alevin-fry) - [ALFA](#alfa) - [Alfred](#alfred) - [alleleCount](#allelecount) - [alleleIntegrator](#alleleintegrator) - [Allinea](#allinea) - [ALLPATHS-LG](#allpaths-lg) - [almosthere](#almosthere) - [Alpha](#alpha) - [AlphaFold](#alphafold) - [AlphaPulldown](#alphapulldown) - [ALPS](#alps) - [alsa-lib](#alsa-lib) - [AMAPVox](#amapvox) - [Amara](#amara) - [amask](#amask) - [Amber](#amber) - [AmberMini](#ambermini) - [AmberTools](#ambertools) - [AMD-LibM](#amd-libm) - [AMD-RNG](#amd-rng) - [AMD-SecureRNG](#amd-securerng) - [AMD-uProf](#amd-uprof) - [AMOS](#amos) - [AMPHORA2](#amphora2) - [AMPL-MP](#ampl-mp) - [amplimap](#amplimap) - [AMPtk](#amptk) - [AMRFinderPlus](#amrfinderplus) - [AmrPlusPlus](#amrplusplus) - [AMS](#ams) - [Anaconda2](#anaconda2) - [Anaconda3](#anaconda3) - [aNCI](#anci) - [andi](#andi) - [ANGEL](#angel) - [angsd](#angsd) - [ANIcalculator](#anicalculator) - [anndata](#anndata) - [Annif](#annif) - [Annocript](#annocript) - [annovar](#annovar) - [ANSYS](#ansys) - [ANSYS_CFD](#ansys_cfd) - [ant](#ant) - [antiSMASH](#antismash) - [ANTLR](#antlr) - [ANTs](#ants) - [anvio](#anvio) - [any2fasta](#any2fasta) - [AOCC](#aocc) - [AOMP](#aomp) - [APBS](#apbs) - [apex](#apex) - [APR](#apr) - [APR-util](#apr-util) - [AptaSUITE](#aptasuite) - [ARAGORN](#aragorn) - [Arb](#arb) - [Arcade-Learning-Environment](#arcade-learning-environment) - [arcasHLA](#arcashla) - [ARCH](#arch) - [Archive-Zip](#archive-zip) - [ArchR](#archr) - [archspec](#archspec) - [ARGoS](#argos) - [argtable](#argtable) - [aria2](#aria2) - [Arlequin](#arlequin) - [Armadillo](#armadillo) - [arosics](#arosics) - [ARPACK++](#arpack++) - [arpack-ng](#arpack-ng) - [ArrayFire](#arrayfire) - [Arriba](#arriba) - [Arrow](#arrow) - [arrow-R](#arrow-r) - [ART](#art) - [artic-ncov2019](#artic-ncov2019) - [ARTS](#arts) - [ArviZ](#arviz) - [ARWEN](#arwen) - [ASAP](#asap) - [ASAP3](#asap3) - [ASCAT](#ascat) - [ASE](#ase) - [ASF-SearchAPI](#asf-searchapi) - [ASHS](#ashs) - [Aspera-CLI](#aspera-cli) - [Aspera-Connect](#aspera-connect) - [assimp](#assimp) - [Assimulo](#assimulo) - [ASTRID](#astrid) - [astro-tulips](#astro-tulips) - [astropy](#astropy) - [at-spi2-atk](#at-spi2-atk) - [at-spi2-core](#at-spi2-core) - [ATAT](#atat) - [ATK](#atk) - [ATLAS](#atlas) - [atomate](#atomate) - [AtomPAW](#atompaw) - [atools](#atools) - [atropos](#atropos) - [ATSAS](#atsas) - [attr](#attr) - [attrdict](#attrdict) - [attrdict3](#attrdict3) - [augur](#augur) - [AUGUSTUS](#augustus) - [Austin](#austin) - [AUTO-07p](#auto-07p) - [Autoconf](#autoconf) - [Autoconf-archive](#autoconf-archive) - [AutoDock](#autodock) - [AutoDock-GPU](#autodock-gpu) - [AutoDock-Vina](#autodock-vina) - [AutoDockSuite](#autodocksuite) - [AutoGeneS](#autogenes) - [AutoGrid](#autogrid) - [Automake](#automake) - [AutoMap](#automap) - [autopep8](#autopep8) - [Autotools](#autotools) - [Avogadro2](#avogadro2) - [avro-cpp](#avro-cpp) - [awscli](#awscli) - [Ax](#ax) - [axel](#axel) ### ABAQUS @@ -102,6 +102,7 @@ version |versionsuffix |toolchain ``9.4.1`` | |``foss/2020b``, ``intel/2020a``, ``intel/2020b`` ``9.4.2`` | |``foss/2021a``, ``intel/2021a`` ``9.6.2`` | |``foss/2022a``, ``intel/2021a``, ``intel/2021b``, ``intel/2022a`` +``9.10.3``| |``intel/2022a`` ### ABRA2 @@ -307,6 +308,8 @@ version |toolchain ``2021.2.0`` |``system`` ``2021.4.0`` |``system`` ``2022.1.0`` |``system`` +``2023.0.0`` |``system`` +``2023.2.0`` |``system`` ### affinity @@ -383,6 +386,7 @@ version |versionsuffix |toolchain ``3.5.4``|``-Python-3.6.6``|``foss/2018b`` ``3.8.1``| |``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``3.8.3``| |``GCCcore/11.3.0`` +``3.8.5``| |``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### ALADIN @@ -394,6 +398,16 @@ version |toolchain ---------------|--------------- ``36t1_op2bf1``|``intel/2016a`` +### ALAMODE + +ALAMODE is an open source software designed for analyzing lattice anharmonicity and lattice thermal conductivity of solids. By using an external DFT package such as VASP and Quantum ESPRESSO, you can extract harmonic and anharmonic force constants straightforwardly with ALAMODE. Using the calculated anharmonic force constants, you can also estimate lattice thermal conductivity, phonon linewidth, and other anharmonic phonon properties from first principles. + +*homepage*: + +version |toolchain +---------|-------------- +``1.4.2``|``foss/2022b`` + ### Albacore Albacore is a software project that provides an entry point to the Oxford Nanopore basecalling algorithms. @@ -689,6 +703,7 @@ version |toolchain -----------|---------- ``3.4.502``|``system`` ``3.5.671``|``system`` +``4.1.424``|``system`` ### AMOS @@ -740,6 +755,16 @@ version |toolchain ---------|-------------- ``1.5.4``|``foss/2021b`` +### AMRFinderPlus + +This software and the accompanying database are designed to find acquired antimicrobial resistance genes and some point mutations in protein or assembled nucleotide sequences. + +*homepage*: + +version |toolchain +-----------|-------------------------------- +``3.11.18``|``gompi/2021b``, ``gompi/2022b`` + ### AmrPlusPlus AmrPlusPlus v2.0 can process the raw data from the sequencer, identify the fragments of DNA, and count them. It also provides a count of the polymorphisms that occur in each DNA fragment with respect to the reference database. @@ -807,6 +832,7 @@ version |toolchain ``2022.05`` |``system`` ``2022.10`` |``system`` ``2023.03-1``|``system`` +``2023.07-2``|``system`` ### aNCI @@ -872,6 +898,7 @@ anndata is a Python package for handling annotated data matrices in memory and o version |toolchain ---------|-------------- ``0.8.0``|``foss/2022a`` +``0.9.2``|``foss/2021a`` ### Annif @@ -1039,7 +1066,7 @@ version |toolchain ``3.0.0``|``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ``3.1.0``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``3.2.0``|``GCCcore/11.2.0``, ``GCCcore/11.3.0`` -``4.0.0``|``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +``4.0.0``|``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### AOMP @@ -1082,16 +1109,18 @@ version |toolchain ---------|-------------------------------------------------------------------------------------------------------------------- ``1.6.3``|``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``iomkl/2018a`` ``1.7.0``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/8.2.0``, ``GCCcore/9.3.0`` +``1.7.4``|``GCCcore/12.3.0`` ### APR-util Apache Portable Runtime (APR) util libraries. -*homepage*: +*homepage*: version |toolchain ---------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ``1.6.1``|``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/9.3.0``, ``iomkl/2018a`` +``1.6.3``|``GCCcore/12.3.0`` ### AptaSUITE @@ -1137,6 +1166,7 @@ The Arcade Learning Environment (ALE) is a simple framework that allows research version |toolchain ---------|-------------- ``0.7.3``|``foss/2021b`` +``0.8.1``|``foss/2022a`` ### arcasHLA @@ -1192,6 +1222,7 @@ version |versionsuffix |toolchain ``0.1.3``| |``GCCcore/11.2.0`` ``0.1.4``| |``GCCcore/11.3.0`` ``0.2.0``| |``GCCcore/12.2.0`` +``0.2.1``| |``GCCcore/12.3.0`` ### ARGoS @@ -1255,6 +1286,7 @@ version |versionsuffix |toolchain ``10.5.3`` | |``foss/2020b`` ``10.7.5`` | |``foss/2021a`` ``11.4.3`` | |``foss/2022a``, ``foss/2022b`` +``12.6.2`` | |``foss/2023a`` ### arosics @@ -1290,6 +1322,7 @@ version |toolchain ``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``, ``foss/2022b`` +``3.9.0``|``foss/2023a`` ### ArrayFire @@ -1527,8 +1560,9 @@ Open Asset Import Library (assimp) is a library to import and export various 3d *homepage*: version |toolchain ----------|----------------- +---------|------------------ ``5.0.1``|``GCCcore/8.3.0`` +``5.2.5``|``GCCcore/12.3.0`` ### Assimulo @@ -1585,12 +1619,12 @@ AT-SPI 2 toolkit bridge *homepage*: version |toolchain -----------|-------------------------------------------------------------------------------------------------- +----------|---------------------------------------------------------------------------------------------------------------------- ``2.26.3``|``fosscuda/2018b`` ``2.32.0``|``GCCcore/8.2.0`` ``2.34.1``|``GCCcore/8.3.0`` ``2.34.2``|``GCCcore/9.3.0`` -``2.38.0``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +``2.38.0``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### at-spi2-core @@ -1598,17 +1632,18 @@ Assistive Technology Service Provider Interface. *homepage*: -version |toolchain -----------|------------------ -``2.26.3``|``fosscuda/2018b`` -``2.32.0``|``GCCcore/8.2.0`` -``2.34.0``|``GCCcore/8.3.0`` -``2.36.0``|``GCCcore/9.3.0`` -``2.38.0``|``GCCcore/10.2.0`` -``2.40.2``|``GCCcore/10.3.0`` -``2.40.3``|``GCCcore/11.2.0`` -``2.44.1``|``GCCcore/11.3.0`` -``2.46.0``|``GCCcore/12.2.0`` +version |toolchain +-----------|------------------ +``2.26.3`` |``fosscuda/2018b`` +``2.32.0`` |``GCCcore/8.2.0`` +``2.34.0`` |``GCCcore/8.3.0`` +``2.36.0`` |``GCCcore/9.3.0`` +``2.38.0`` |``GCCcore/10.2.0`` +``2.40.2`` |``GCCcore/10.3.0`` +``2.40.3`` |``GCCcore/11.2.0`` +``2.44.1`` |``GCCcore/11.3.0`` +``2.46.0`` |``GCCcore/12.2.0`` +``2.49.91``|``GCCcore/12.3.0`` ### ATAT @@ -1638,7 +1673,7 @@ version |toolchain ``2.32.0``|``GCCcore/8.2.0`` ``2.34.1``|``GCCcore/8.3.0`` ``2.36.0``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` -``2.38.0``|``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +``2.38.0``|``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### ATLAS @@ -1735,8 +1770,8 @@ AttrDict is a Python library that provides mapping objects that allow their elem *homepage*: version |toolchain ----------|------------------ -``2.0.2``|``GCCcore/11.2.0`` +---------|-------------------------------------- +``2.0.2``|``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ### augur @@ -1796,7 +1831,7 @@ version |toolchain --------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ``2.68``|``foss/2016b`` ``2.69``|``GCC/4.8.2``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/5.2.0``, ``GCC/5.4.0-2.26``, ``GCCcore/10.2.0``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GNU/4.9.2-2.25``, ``GNU/4.9.3-2.25``, ``GNU/5.1.0-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` -``2.71``|``FCC/4.5.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``system`` +``2.71``|``FCC/4.5.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``GCCcore/13.2.0``, ``system`` ### Autoconf-archive @@ -1889,7 +1924,7 @@ version |toolchain ``1.16.2``|``GCCcore/10.2.0`` ``1.16.3``|``FCC/4.5.0``, ``GCCcore/10.3.0`` ``1.16.4``|``GCCcore/11.2.0`` -``1.16.5``|``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``system`` +``1.16.5``|``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``GCCcore/13.2.0``, ``system`` ### AutoMap @@ -1926,7 +1961,7 @@ 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``, ``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``system`` +``20220317``|``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``GCCcore/13.2.0``, ``system`` ### Avogadro2 @@ -1964,6 +1999,16 @@ version |versionsuffix |toolchain ``2.0.55`` |``-Python-3.8.2`` |``GCCcore/9.3.0`` ``2.11.21`` | |``GCCcore/11.3.0`` +### Ax + +Ax is an accessible, general-purpose platform for understanding, managing, deploying, and automating adaptive experiments. Adaptive experimentation is the machine-learning guided process of iteratively exploring a (possibly infinite) parameter space in order to identify optimal configurations in a resource-efficient manner. Ax currently supports Bayesian optimization and bandit optimization as exploration strategies. Bayesian optimization in Ax is powered by BoTorch, a modern library for Bayesian optimization research built on PyTorch. + +*homepage*: + +version |toolchain +---------|-------------- +``0.3.3``|``foss/2022a`` + ### axel Lightweight CLI download accelerator @@ -1977,7 +2022,7 @@ version |toolchain ## B -[BA3-SNPS-autotune](#ba3-snps-autotune) - [BabelStream](#babelstream) - [babl](#babl) - [Bader](#bader) - [BAGEL](#bagel) - [BAli-Phy](#bali-phy) - [bam-readcount](#bam-readcount) - [Bambi](#bambi) - [bamFilters](#bamfilters) - [BAMM](#bamm) - [BAMSurgeon](#bamsurgeon) - [bamtofastq](#bamtofastq) - [BamTools](#bamtools) - [BamUtil](#bamutil) - [Bandage](#bandage) - [barrnap](#barrnap) - [basemap](#basemap) - [Bash](#bash) - [bashplotlib](#bashplotlib) - [bat](#bat) - [batchgenerators](#batchgenerators) - [BatMeth2](#batmeth2) - [BayesAss](#bayesass) - [BayesAss3-SNPs](#bayesass3-snps) - [BayeScan](#bayescan) - [BayeScEnv](#bayescenv) - [BayesPrism](#bayesprism) - [BayesTraits](#bayestraits) - [Bazel](#bazel) - [bbcp](#bbcp) - [bbFTP](#bbftp) - [BBMap](#bbmap) - [bc](#bc) - [BCALM](#bcalm) - [bcbio-gff](#bcbio-gff) - [BCEL](#bcel) - [BCFtools](#bcftools) - [bcgTree](#bcgtree) - [bcl-convert](#bcl-convert) - [bcl2fastq2](#bcl2fastq2) - [bcolz](#bcolz) - [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) - [BGC-Bayesian-genomic-clines](#bgc-bayesian-genomic-clines) - [bgen](#bgen) - [bgen-reader](#bgen-reader) - [bibtexparser](#bibtexparser) - [BiG-SCAPE](#big-scape) - [BigDFT](#bigdft) - [BinSanity](#binsanity) - [binutils](#binutils) - [Bio-DB-HTS](#bio-db-hts) - [Bio-EUtilities](#bio-eutilities) - [Bio-SamTools](#bio-samtools) - [Bio-SearchIO-hmmer](#bio-searchio-hmmer) - [bioawk](#bioawk) - [biobambam2](#biobambam2) - [biogeme](#biogeme) - [biom-format](#biom-format) - [biomart-perl](#biomart-perl) - [BioPerl](#bioperl) - [BioPP](#biopp) - [Biopython](#biopython) - [BioServices](#bioservices) - [BirdNET](#birdnet) - [biscuit](#biscuit) - [Bismark](#bismark) - [Bison](#bison) - [bitarray](#bitarray) - [BLACS](#blacs) - [BLASR](#blasr) - [blasr_libcpp](#blasr_libcpp) - [BLAST](#blast) - [BLAST+](#blast+) - [BLAT](#blat) - [Blender](#blender) - [BLIS](#blis) - [Blitz++](#blitz++) - [BlobTools](#blobtools) - [Block](#block) - [Blosc](#blosc) - [Blosc2](#blosc2) - [BLT](#blt) - [bmtagger](#bmtagger) - [bnpy](#bnpy) - [BOINC](#boinc) - [bokeh](#bokeh) - [BoltzTraP](#boltztrap) - [BoltzTraP2](#boltztrap2) - [Bonito](#bonito) - [Bonmin](#bonmin) - [Bonnie++](#bonnie++) - [Boost](#boost) - [Boost.MPI](#boost.mpi) - [Boost.Python](#boost.python) - [boost_histogram](#boost_histogram) - [boto3](#boto3) - [Bottleneck](#bottleneck) - [Bowtie](#bowtie) - [Bowtie2](#bowtie2) - [Bpipe](#bpipe) - [bpp](#bpp) - [bpytop](#bpytop) - [Bracken](#bracken) - [Braindecode](#braindecode) - [BRAKER](#braker) - [BreakDancer](#breakdancer) - [breseq](#breseq) - [Brotli](#brotli) - [Brotli-python](#brotli-python) - [Brunsli](#brunsli) - [bsddb3](#bsddb3) - [BSMAPz](#bsmapz) - [Bsoft](#bsoft) - [BSseeker2](#bsseeker2) - [BuDDy](#buddy) - [BUFRLIB](#bufrlib) - [build](#build) - [buildenv](#buildenv) - [buildingspy](#buildingspy) - [Bullet](#bullet) - [BUSCO](#busco) - [BUStools](#bustools) - [BWA](#bwa) - [bwa-meth](#bwa-meth) - [bwakit](#bwakit) - [bwidget](#bwidget) - [BWISE](#bwise) - [bx-python](#bx-python) - [BXH_XCEDE_TOOLS](#bxh_xcede_tools) - [byacc](#byacc) - [byobu](#byobu) - [bzip2](#bzip2) +[BA3-SNPS-autotune](#ba3-snps-autotune) - [BabelStream](#babelstream) - [babl](#babl) - [Bader](#bader) - [BAGEL](#bagel) - [BAli-Phy](#bali-phy) - [bam-readcount](#bam-readcount) - [Bambi](#bambi) - [bamFilters](#bamfilters) - [BAMM](#bamm) - [BAMSurgeon](#bamsurgeon) - [bamtofastq](#bamtofastq) - [BamTools](#bamtools) - [BamUtil](#bamutil) - [Bandage](#bandage) - [barrnap](#barrnap) - [basemap](#basemap) - [Bash](#bash) - [bashplotlib](#bashplotlib) - [bat](#bat) - [batchgenerators](#batchgenerators) - [BatMeth2](#batmeth2) - [BayesAss](#bayesass) - [BayesAss3-SNPs](#bayesass3-snps) - [BayeScan](#bayescan) - [BayeScEnv](#bayescenv) - [BayesPrism](#bayesprism) - [BayesTraits](#bayestraits) - [Bazel](#bazel) - [bbcp](#bbcp) - [bbFTP](#bbftp) - [BBMap](#bbmap) - [bc](#bc) - [BCALM](#bcalm) - [bcbio-gff](#bcbio-gff) - [BCEL](#bcel) - [BCFtools](#bcftools) - [bcgTree](#bcgtree) - [bcl-convert](#bcl-convert) - [bcl2fastq2](#bcl2fastq2) - [bcolz](#bcolz) - [bcrypt](#bcrypt) - [BDBag](#bdbag) - [Beagle](#beagle) - [beagle-lib](#beagle-lib) - [Beast](#beast) - [BeautifulSoup](#beautifulsoup) - [BEDOPS](#bedops) - [BEDTools](#bedtools) - [BEEF](#beef) - [behave](#behave) - [bench](#bench) - [BerkeleyGW](#berkeleygw) - [BFAST](#bfast) - [BFC](#bfc) - [BGC-Bayesian-genomic-clines](#bgc-bayesian-genomic-clines) - [BgeeDB](#bgeedb) - [bgen](#bgen) - [bgen-reader](#bgen-reader) - [bibtexparser](#bibtexparser) - [BiG-SCAPE](#big-scape) - [BigDFT](#bigdft) - [BinSanity](#binsanity) - [binutils](#binutils) - [Bio-DB-HTS](#bio-db-hts) - [Bio-EUtilities](#bio-eutilities) - [Bio-SamTools](#bio-samtools) - [Bio-SearchIO-hmmer](#bio-searchio-hmmer) - [bioawk](#bioawk) - [biobambam2](#biobambam2) - [biogeme](#biogeme) - [biom-format](#biom-format) - [biomart-perl](#biomart-perl) - [BioPerl](#bioperl) - [BioPP](#biopp) - [Biopython](#biopython) - [BioServices](#bioservices) - [BirdNET](#birdnet) - [biscuit](#biscuit) - [Bismark](#bismark) - [Bison](#bison) - [bitarray](#bitarray) - [BLACS](#blacs) - [BLASR](#blasr) - [blasr_libcpp](#blasr_libcpp) - [BLAST](#blast) - [BLAST+](#blast+) - [BLAT](#blat) - [Blender](#blender) - [BLIS](#blis) - [Blitz++](#blitz++) - [BlobTools](#blobtools) - [Block](#block) - [Blosc](#blosc) - [Blosc2](#blosc2) - [BLT](#blt) - [bmtagger](#bmtagger) - [bnpy](#bnpy) - [BOINC](#boinc) - [bokeh](#bokeh) - [BoltzTraP](#boltztrap) - [BoltzTraP2](#boltztrap2) - [Bonito](#bonito) - [Bonmin](#bonmin) - [Bonnie++](#bonnie++) - [Boost](#boost) - [Boost.MPI](#boost.mpi) - [Boost.Python](#boost.python) - [Boost.Python-NumPy](#boost.python-numpy) - [boost_histogram](#boost_histogram) - [boto3](#boto3) - [Bottleneck](#bottleneck) - [Bowtie](#bowtie) - [Bowtie2](#bowtie2) - [Bpipe](#bpipe) - [bpp](#bpp) - [bpytop](#bpytop) - [Bracken](#bracken) - [Braindecode](#braindecode) - [BRAKER](#braker) - [BreakDancer](#breakdancer) - [breseq](#breseq) - [Brotli](#brotli) - [Brotli-python](#brotli-python) - [Brunsli](#brunsli) - [bsddb3](#bsddb3) - [BSMAPz](#bsmapz) - [Bsoft](#bsoft) - [BSseeker2](#bsseeker2) - [BuDDy](#buddy) - [BUFRLIB](#bufrlib) - [build](#build) - [buildenv](#buildenv) - [buildingspy](#buildingspy) - [Bullet](#bullet) - [BUSCO](#busco) - [BUStools](#bustools) - [BWA](#bwa) - [bwa-meth](#bwa-meth) - [bwakit](#bwakit) - [bwidget](#bwidget) - [BWISE](#bwise) - [bx-python](#bx-python) - [BXH_XCEDE_TOOLS](#bxh_xcede_tools) - [byacc](#byacc) - [byobu](#byobu) - [bzip2](#bzip2) ### BA3-SNPS-autotune @@ -2024,13 +2069,14 @@ version |toolchain ### BAGEL -BAGEL (Brilliantly Advanced General Electronic-structure Library) is a parallel electronic-structure program. +BAGEL (Brilliantly Advanced General Electronic-structure Library) is a parallel electronic-structure program. *homepage*: version |toolchain ---------|--------------- ``1.1.1``|``intel/2016b`` +``1.2.2``|``foss/2021a`` ### BAli-Phy @@ -2051,6 +2097,7 @@ Count DNA sequence reads in BAM files version |toolchain ---------|--------------------------------------------- ``0.8.0``|``GCC/11.2.0``, ``GCC/9.3.0``, ``foss/2018b`` +``1.0.1``|``GCC/12.2.0`` ### Bambi @@ -2114,7 +2161,7 @@ version |toolchain ``2.4.1``|``intel/2017a`` ``2.5.0``|``foss/2016b``, ``intel/2017b`` ``2.5.1``|``GCC/10.2.0``, ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281``, ``iccifort/2020.4.304``, ``intel/2017b``, ``intel/2018b`` -``2.5.2``|``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0``, ``GCC/12.2.0`` +``2.5.2``|``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0``, ``GCC/12.2.0``, ``GCC/12.3.0`` ### BamUtil @@ -2305,6 +2352,7 @@ version |versionsuffix|toolchain ``3.7.2`` | |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.3.0`` ``4.2.2`` | |``GCCcore/11.2.0`` ``5.1.1`` | |``GCCcore/11.3.0`` +``6.3.1`` | |``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### bbcp @@ -2333,14 +2381,14 @@ BBMap short read aligner, and other bioinformatic tools. *homepage*: version |versionsuffix |toolchain -----------|-------------------|------------------------------- +----------|-------------------|--------------------------------------------- ``36.62`` |``-Java-1.8.0_112``|``intel/2016b`` ``37.93`` | |``foss/2018a``, ``intel/2018a`` ``38.26`` | |``foss/2018b`` ``38.50b``| |``GCC/8.2.0-2.31.1`` ``38.76`` | |``GCC/8.2.0-2.31.1`` ``38.79`` | |``GCC/8.3.0`` -``38.87`` | |``iccifort/2020.1.217`` +``38.87`` | |``GCC/8.2.0-2.31.1``, ``iccifort/2020.1.217`` ``38.90`` | |``GCC/10.2.0``, ``GCC/9.3.0`` ``38.96`` | |``GCC/10.3.0`` ``38.98`` | |``GCC/11.2.0`` @@ -2408,6 +2456,7 @@ version |toolchain ``1.14`` |``GCC/11.2.0`` ``1.15.1``|``GCC/11.3.0`` ``1.17`` |``GCC/12.2.0`` +``1.18`` |``GCC/12.3.0`` ### bcgTree @@ -2437,9 +2486,9 @@ 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/11.3.0``, ``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/12.2.0``, ``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`` @@ -2455,6 +2504,16 @@ version |versionsuffix |toolchain ``1.2.1``| |``foss/2020b`` ``1.2.1``|``-Python-3.8.2`` |``foss/2020a`` +### bcrypt + +Acceptable password hashing for your software and your servers (but you should really use argon2id or scrypt) + +*homepage*: + +version |toolchain +---------|------------------ +``4.0.1``|``GCCcore/12.3.0`` + ### BDBag The bdbag utilities are a collection of software programs for working with BagIt packages that conform to the Bagit and Bagit/RO profiles. @@ -2530,6 +2589,7 @@ version |versionsuffix |toolchain ``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`` +``4.12.2``| |``GCCcore/12.3.0`` ### BEDOPS @@ -2562,6 +2622,7 @@ version |toolchain ``2.28.0``|``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` ``2.29.2``|``GCC/8.3.0``, ``GCC/9.3.0`` ``2.30.0``|``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0``, ``GCC/12.2.0``, ``iccifort/2020.4.304`` +``2.31.0``|``GCC/12.3.0`` ### BEEF @@ -2584,6 +2645,16 @@ version |versionsuffix |toolchain ``1.2.5``|``-Python-2.7.12``|``foss/2016b`` ``1.2.6``|``-Python-3.6.4`` |``intel/2018a`` +### bench + +Tools to accurately benchmark and analyze execution times for R expressions. + +*homepage*: + +version |versionsuffix|toolchain +---------|-------------|-------------- +``1.1.2``|``-R-4.2.1`` |``foss/2022a`` + ### BerkeleyGW The BerkeleyGW Package is a set of computer codes that calculates the quasiparticle properties and the optical responses of a large variety of materials from bulk periodic crystals to nanostructures such as slabs, wires and molecules. @@ -2629,6 +2700,16 @@ version |toolchain --------|--------------- ``1.03``|``gompi/2021a`` +### BgeeDB + +Annotation and gene expression data retrieval from Bgee database. TopAnat, an anatomical entities Enrichment Analysis tool for UBERON ontology. + +*homepage*: + +version |versionsuffix |toolchain +----------|---------------|-------------- +``2.26.0``|``-R-%(rver)s``|``foss/2021a`` + ### bgen A BGEN file format reader. It fully supports the BGEN format specifications 1.2 and 1.3. @@ -2714,7 +2795,7 @@ version |toolchain ``2.37`` |``GCCcore/11.2.0``, ``system`` ``2.38`` |``GCCcore/11.3.0``, ``GCCcore/12.1.0``, ``GCCcore/9.5.0``, ``system`` ``2.39`` |``GCCcore/12.2.0``, ``system`` -``2.40`` |``GCCcore/11.4.0``, ``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``system`` +``2.40`` |``GCCcore/11.4.0``, ``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``GCCcore/13.2.0``, ``system`` ### Bio-DB-HTS @@ -2757,8 +2838,8 @@ 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``, ``GCC/11.2.0``, ``GCC/11.3.0`` +---------|------------------------------------------------------------------------------ +``1.7.3``|``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0``, ``GCC/12.2.0`` ### bioawk @@ -2804,6 +2885,7 @@ version |versionsuffix |toolchain ``2.1.10``|``-Python-3.8.2``|``foss/2020a`` ``2.1.12``| |``foss/2021b`` ``2.1.14``| |``foss/2022a`` +``2.1.15``| |``foss/2022b`` ### biomart-perl @@ -2870,7 +2952,7 @@ version |versionsuffix |toolchain ``1.74``| |``foss/2019a`` ``1.75``|``-Python-2.7.16``|``foss/2019b`` ``1.75``|``-Python-3.7.4`` |``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` -``1.76``|``-Python-2.7.18``|``foss/2020b`` +``1.76``|``-Python-2.7.18``|``foss/2020b``, ``foss/2021b`` ``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`` @@ -2940,7 +3022,7 @@ version |toolchain ``3.6.1``|``GCCcore/10.1.0`` ``3.7.1``|``GCCcore/10.2.0``, ``system`` ``3.7.6``|``FCC/4.5.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0``, ``GCCcore/11.2.0``, ``GCCcore/9.4.0``, ``system`` -``3.8.2``|``GCCcore/11.3.0``, ``GCCcore/11.4.0``, ``GCCcore/12.1.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``GCCcore/9.5.0``, ``system`` +``3.8.2``|``GCCcore/11.3.0``, ``GCCcore/11.4.0``, ``GCCcore/12.1.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``GCCcore/13.2.0``, ``GCCcore/9.5.0``, ``system`` ### bitarray @@ -3196,6 +3278,7 @@ version |versionsuffix |toolchain ``2.4.1`` | |``foss/2021a`` ``2.4.2`` | |``foss/2021b`` ``2.4.3`` | |``foss/2022a`` +``3.2.1`` | |``foss/2022b`` ### BoltzTraP @@ -3311,6 +3394,7 @@ version |versionsuffix |toolchain ``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`` +``1.82.0``| |``GCC/12.3.0`` ### Boost.MPI @@ -3346,6 +3430,16 @@ version |versionsuffix |toolchain ``1.77.0``| |``GCC/11.2.0`` ``1.79.0``| |``GCC/11.3.0`` +### Boost.Python-NumPy + +Boost.Python is a C++ library which enables seamless interoperability between C++ and the Python programming language. + +*homepage*: + +version |toolchain +----------|-------------- +``1.79.0``|``foss/2022a`` + ### boost_histogram Boost-histogram is a Python package providing Python bindings for Boost.Histogram. @@ -3798,7 +3892,7 @@ version |toolchain ## C -[c-ares](#c-ares) - [C3D](#c3d) - [cadaver](#cadaver) - [CaDiCaL](#cadical) - [CAFE5](#cafe5) - [Caffe](#caffe) - [cairo](#cairo) - [cairomm](#cairomm) - [Calcam](#calcam) - [CalculiX-CrunchiX](#calculix-crunchix) - [Calendrical](#calendrical) - [Calib](#calib) - [CAMPARI](#campari) - [Cantera](#cantera) - [canu](#canu) - [Canvas](#canvas) - [CAP3](#cap3) - [CapnProto](#capnproto) - [captum](#captum) - [Cargo](#cargo) - [Carma](#carma) - [carputils](#carputils) - [Cartopy](#cartopy) - [CASA](#casa) - [casacore](#casacore) - [Casanovo](#casanovo) - [CaSpER](#casper) - [CASPR](#caspr) - [CASTEP](#castep) - [CastXML](#castxml) - [CAT-BAT](#cat-bat) - [Catch2](#catch2) - [category_encoders](#category_encoders) - [CatLearn](#catlearn) - [CatMAP](#catmap) - [causallift](#causallift) - [causalml](#causalml) - [CaVEMan](#caveman) - [CAVIAR](#caviar) - [Cbc](#cbc) - [CBLAS](#cblas) - [ccache](#ccache) - [CCfits](#ccfits) - [CCL](#ccl) - [cclib](#cclib) - [cctbx-base](#cctbx-base) - [cctools](#cctools) - [CD-HIT](#cd-hit) - [CDAT](#cdat) - [cdbfasta](#cdbfasta) - [CDBtools](#cdbtools) - [cddlib](#cddlib) - [CDFlib](#cdflib) - [cDNA_Cupcake](#cdna_cupcake) - [CDO](#cdo) - [cdo-bindings](#cdo-bindings) - [cdsapi](#cdsapi) - [cell2location](#cell2location) - [CellChat](#cellchat) - [CellMix](#cellmix) - [CellOracle](#celloracle) - [Cellpose](#cellpose) - [CellRanger](#cellranger) - [CellRanger-ARC](#cellranger-arc) - [CellRanger-ATAC](#cellranger-atac) - [CellRank](#cellrank) - [CellTypist](#celltypist) - [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) - [Circuitscape](#circuitscape) - [CIRI](#ciri) - [CIRI-long](#ciri-long) - [cisTEM](#cistem) - [CITE-seq-Count](#cite-seq-count) - [Clang](#clang) - [Clang-AOMP](#clang-aomp) - [Clang-Python-bindings](#clang-python-bindings) - [CLAPACK](#clapack) - [CLEASE](#clease) - [CLHEP](#clhep) - [CliMetLab](#climetlab) - [CLIP](#clip) - [CLISP](#clisp) - [ClonalFrameML](#clonalframeml) - [CLooG](#cloog) - [CloudCompare](#cloudcompare) - [Clp](#clp) - [Clustal-Omega](#clustal-omega) - [ClustalW2](#clustalw2) - [Cluster-Buster](#cluster-buster) - [ClusterShell](#clustershell) - [CMake](#cmake) - [CMAverse](#cmaverse) - [CmdStanR](#cmdstanr) - [cmocean](#cmocean) - [CMSeq](#cmseq) - [CNT-ILP](#cnt-ilp) - [CNVkit](#cnvkit) - [CNVnator](#cnvnator) - [Co-phylog](#co-phylog) - [COBRApy](#cobrapy) - [CoCoALib](#cocoalib) - [CodAn](#codan) - [code-server](#code-server) - [CODEX2](#codex2) - [CodingQuarry](#codingquarry) - [Cogent](#cogent) - [Coin](#coin) - [CoinUtils](#coinutils) - [ColabFold](#colabfold) - [colossalai](#colossalai) - [Commet](#commet) - [CompareM](#comparem) - [Compress-Raw-Zlib](#compress-raw-zlib) - [COMSOL](#comsol) - [Con3F](#con3f) - [conan](#conan) - [CONCOCT](#concoct) - [configparser](#configparser) - [configurable-http-proxy](#configurable-http-proxy) - [CONN](#conn) - [ConnectomeWorkbench](#connectomeworkbench) - [Control-FREEC](#control-freec) - [cooler](#cooler) - [CoordgenLibs](#coordgenlibs) - [Coot](#coot) - [CopyKAT](#copykat) - [core-counter](#core-counter) - [Coreutils](#coreutils) - [corner](#corner) - [CoSymLib](#cosymlib) - [coverage](#coverage) - [cowsay](#cowsay) - [CP2K](#cp2k) - [CPB](#cpb) - [CPC2](#cpc2) - [CPLEX](#cplex) - [CPPE](#cppe) - [CppHeaderParser](#cppheaderparser) - [CppUnit](#cppunit) - [cppy](#cppy) - [cppzmq](#cppzmq) - [cpu_features](#cpu_features) - [cram](#cram) - [cramtools](#cramtools) - [CrayCCE](#craycce) - [CrayGNU](#craygnu) - [CrayIntel](#crayintel) - [CrayPGI](#craypgi) - [crb-blast](#crb-blast) - [CREST](#crest) - [CRF++](#crf++) - [CRISPR-DAV](#crispr-dav) - [CRISPResso2](#crispresso2) - [cromwell](#cromwell) - [crossguid](#crossguid) - [CrossMap](#crossmap) - [CrossTalkZ](#crosstalkz) - [CRPropa](#crpropa) - [Crumble](#crumble) - [cryoCARE](#cryocare) - [cryoDRGN](#cryodrgn) - [CryptoMiniSat](#cryptominisat) - [CrystFEL](#crystfel) - [CSB](#csb) - [CSBDeep](#csbdeep) - [CSBLAST](#csblast) - [cscope](#cscope) - [csvkit](#csvkit) - [ctags](#ctags) - [ctffind](#ctffind) - [CTPL](#ctpl) - [Cube](#cube) - [CubeGUI](#cubegui) - [CubeLib](#cubelib) - [CubeWriter](#cubewriter) - [CuCLARK](#cuclark) - [CUDA](#cuda) - [CUDA-Samples](#cuda-samples) - [CUDAcompat](#cudacompat) - [CUDAcore](#cudacore) - [cuDNN](#cudnn) - [Cufflinks](#cufflinks) - [CUnit](#cunit) - [CuPy](#cupy) - [cURL](#curl) - [cuSPARSELt](#cusparselt) - [custodian](#custodian) - [cutadapt](#cutadapt) - [cuTENSOR](#cutensor) - [cuteSV](#cutesv) - [CVS](#cvs) - [CVXOPT](#cvxopt) - [CVXPY](#cvxpy) - [CWIPI](#cwipi) - [cwltool](#cwltool) - [cxxopts](#cxxopts) - [cysignals](#cysignals) - [Cython](#cython) - [cython-blis](#cython-blis) - [cytoolz](#cytoolz) - [Cytoscape](#cytoscape) - [cytosim](#cytosim) - [cyvcf2](#cyvcf2) +[c-ares](#c-ares) - [C3D](#c3d) - [cadaver](#cadaver) - [CaDiCaL](#cadical) - [CAFE5](#cafe5) - [Caffe](#caffe) - [cairo](#cairo) - [cairomm](#cairomm) - [Calcam](#calcam) - [CalculiX-CrunchiX](#calculix-crunchix) - [Calendrical](#calendrical) - [Calib](#calib) - [CAMPARI](#campari) - [Cantera](#cantera) - [canu](#canu) - [Canvas](#canvas) - [CAP3](#cap3) - [CapnProto](#capnproto) - [captum](#captum) - [Cargo](#cargo) - [Carma](#carma) - [carputils](#carputils) - [Cartopy](#cartopy) - [CASA](#casa) - [casacore](#casacore) - [Casanovo](#casanovo) - [CaSpER](#casper) - [CASPR](#caspr) - [CASTEP](#castep) - [CastXML](#castxml) - [CAT-BAT](#cat-bat) - [CatBoost](#catboost) - [Catch2](#catch2) - [category_encoders](#category_encoders) - [CatLearn](#catlearn) - [CatMAP](#catmap) - [causallift](#causallift) - [causalml](#causalml) - [CaVEMan](#caveman) - [CAVIAR](#caviar) - [Cbc](#cbc) - [CBLAS](#cblas) - [ccache](#ccache) - [CCfits](#ccfits) - [CCL](#ccl) - [cclib](#cclib) - [cctbx-base](#cctbx-base) - [cctools](#cctools) - [CD-HIT](#cd-hit) - [CDAT](#cdat) - [cdbfasta](#cdbfasta) - [CDBtools](#cdbtools) - [cddlib](#cddlib) - [CDFlib](#cdflib) - [cDNA_Cupcake](#cdna_cupcake) - [CDO](#cdo) - [cdo-bindings](#cdo-bindings) - [cdsapi](#cdsapi) - [cell2location](#cell2location) - [CellChat](#cellchat) - [CellMix](#cellmix) - [CellOracle](#celloracle) - [Cellpose](#cellpose) - [CellRanger](#cellranger) - [CellRanger-ARC](#cellranger-arc) - [CellRanger-ATAC](#cellranger-atac) - [CellRank](#cellrank) - [CellTypist](#celltypist) - [centerline](#centerline) - [Centrifuge](#centrifuge) - [Cereal](#cereal) - [CESM-deps](#cesm-deps) - [CFDEMcoupling](#cfdemcoupling) - [cffi](#cffi) - [CFITSIO](#cfitsio) - [cftime](#cftime) - [CGAL](#cgal) - [cget](#cget) - [Cgl](#cgl) - [CGmapTools](#cgmaptools) - [CGNS](#cgns) - [CharLS](#charls) - [CHASE](#chase) - [Check](#check) - [CheckM](#checkm) - [CheckM-Database](#checkm-database) - [Cheetah](#cheetah) - [Chemaxon-Marvin](#chemaxon-marvin) - [chemprop](#chemprop) - [CheMPS2](#chemps2) - [CHERAB](#cherab) - [chewBBACA](#chewbbaca) - [chi2comb](#chi2comb) - [Chimera](#chimera) - [ChimPipe](#chimpipe) - [ChIPseeker](#chipseeker) - [Chromaprint](#chromaprint) - [cicero](#cicero) - [CIF2Cell](#cif2cell) - [cimfomfa](#cimfomfa) - [CIRCexplorer](#circexplorer) - [CIRCexplorer2](#circexplorer2) - [Circos](#circos) - [Circuitscape](#circuitscape) - [CIRI](#ciri) - [CIRI-long](#ciri-long) - [cisTEM](#cistem) - [CITE-seq-Count](#cite-seq-count) - [Clang](#clang) - [Clang-AOMP](#clang-aomp) - [Clang-Python-bindings](#clang-python-bindings) - [CLAPACK](#clapack) - [CLEASE](#clease) - [CLHEP](#clhep) - [CliMetLab](#climetlab) - [CLIP](#clip) - [CLISP](#clisp) - [ClonalFrameML](#clonalframeml) - [CLooG](#cloog) - [CloudCompare](#cloudcompare) - [Clp](#clp) - [Clustal-Omega](#clustal-omega) - [ClustalW2](#clustalw2) - [Cluster-Buster](#cluster-buster) - [ClusterShell](#clustershell) - [CMake](#cmake) - [CMAverse](#cmaverse) - [CmdStanR](#cmdstanr) - [cmocean](#cmocean) - [CMSeq](#cmseq) - [CNT-ILP](#cnt-ilp) - [CNVkit](#cnvkit) - [CNVnator](#cnvnator) - [Co-phylog](#co-phylog) - [COBRApy](#cobrapy) - [CoCoALib](#cocoalib) - [CodAn](#codan) - [code-server](#code-server) - [CODEX2](#codex2) - [CodingQuarry](#codingquarry) - [Cogent](#cogent) - [Coin](#coin) - [CoinUtils](#coinutils) - [ColabFold](#colabfold) - [colossalai](#colossalai) - [Commet](#commet) - [CompareM](#comparem) - [Compress-Raw-Zlib](#compress-raw-zlib) - [COMSOL](#comsol) - [Con3F](#con3f) - [conan](#conan) - [CONCOCT](#concoct) - [configparser](#configparser) - [configurable-http-proxy](#configurable-http-proxy) - [CONN](#conn) - [connected-components-3d](#connected-components-3d) - [ConnectomeWorkbench](#connectomeworkbench) - [Control-FREEC](#control-freec) - [cooler](#cooler) - [CoordgenLibs](#coordgenlibs) - [Coot](#coot) - [CopyKAT](#copykat) - [core-counter](#core-counter) - [Coreutils](#coreutils) - [corner](#corner) - [CoSymLib](#cosymlib) - [coverage](#coverage) - [cowsay](#cowsay) - [CP2K](#cp2k) - [CPB](#cpb) - [CPC2](#cpc2) - [CPLEX](#cplex) - [CPPE](#cppe) - [CppHeaderParser](#cppheaderparser) - [CppUnit](#cppunit) - [cppy](#cppy) - [cppzmq](#cppzmq) - [cpu_features](#cpu_features) - [cram](#cram) - [cramtools](#cramtools) - [CrayCCE](#craycce) - [CrayGNU](#craygnu) - [CrayIntel](#crayintel) - [CrayPGI](#craypgi) - [crb-blast](#crb-blast) - [CREST](#crest) - [CRF++](#crf++) - [CRISPR-DAV](#crispr-dav) - [CRISPResso2](#crispresso2) - [cromwell](#cromwell) - [crossguid](#crossguid) - [CrossMap](#crossmap) - [CrossTalkZ](#crosstalkz) - [CRPropa](#crpropa) - [Crumble](#crumble) - [cryoCARE](#cryocare) - [cryoDRGN](#cryodrgn) - [cryptography](#cryptography) - [CryptoMiniSat](#cryptominisat) - [CrystFEL](#crystfel) - [CSB](#csb) - [CSBDeep](#csbdeep) - [CSBLAST](#csblast) - [cscope](#cscope) - [csvkit](#csvkit) - [ctags](#ctags) - [ctffind](#ctffind) - [CTPL](#ctpl) - [Cube](#cube) - [CubeGUI](#cubegui) - [CubeLib](#cubelib) - [CubeWriter](#cubewriter) - [CuCLARK](#cuclark) - [CUDA](#cuda) - [CUDA-Samples](#cuda-samples) - [CUDAcompat](#cudacompat) - [CUDAcore](#cudacore) - [cuDNN](#cudnn) - [Cufflinks](#cufflinks) - [CUnit](#cunit) - [CuPy](#cupy) - [cURL](#curl) - [cuSPARSELt](#cusparselt) - [custodian](#custodian) - [cutadapt](#cutadapt) - [cuTENSOR](#cutensor) - [cuteSV](#cutesv) - [CVglasso](#cvglasso) - [CVS](#cvs) - [CVXOPT](#cvxopt) - [CVXPY](#cvxpy) - [CWIPI](#cwipi) - [cwltool](#cwltool) - [cxxopts](#cxxopts) - [cysignals](#cysignals) - [Cython](#cython) - [cython-blis](#cython-blis) - [cytoolz](#cytoolz) - [Cytoscape](#cytoscape) - [cytosim](#cytosim) - [cyvcf2](#cyvcf2) ### c-ares @@ -3811,6 +3905,7 @@ version |toolchain ----------|-------------------------------------- ``1.17.2``|``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ``1.18.1``|``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``1.19.1``|``GCCcore/12.3.0`` ### C3D @@ -3880,6 +3975,7 @@ version |versionsuffix |toolchain ``1.14.12``| |``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``1.16.0`` | |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``1.17.4`` | |``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +``1.17.8`` | |``GCCcore/12.3.0`` ### cairomm @@ -3909,8 +4005,8 @@ A Free Software Three-Dimensional Structural Finite Element Program *homepage*: version |toolchain ---------|-------------- -``2.20``|``foss/2021a`` +--------|------------------------------ +``2.20``|``foss/2021a``, ``foss/2022b`` ### Calendrical @@ -3966,7 +4062,7 @@ 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`` @@ -3975,7 +4071,7 @@ 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``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +``2.2`` | |``GCC/12.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ``2.2`` |``-Java-11`` |``GCCcore/10.3.0`` ### Canvas @@ -4155,6 +4251,16 @@ version |toolchain ---------|-------------- ``5.2.3``|``GCC/10.3.0`` +### CatBoost + +CatBoost is a high-performance open source library for gradient boosting on decision trees + +*homepage*: + +version|toolchain +-------|-------------- +``1.2``|``gfbf/2023a`` + ### Catch2 A modern, C++-native, header-only, test framework for unit-tests, TDD and BDD - using C++11, C++14, C++17 and later (or C++03 on the Catch1.x branch) @@ -4246,9 +4352,9 @@ Cbc (Coin-or branch and cut) is an open-source mixed integer linear programming *homepage*: version |toolchain -----------|------------------------------ +----------|---------------------------------------------- ``2.10.3``|``foss/2018b`` -``2.10.5``|``foss/2020b``, ``foss/2021a`` +``2.10.5``|``foss/2020b``, ``foss/2021a``, ``foss/2022b`` ### CBLAS @@ -4276,6 +4382,8 @@ version |versionsuffix|toolchain ``4.2.1`` | |``system`` ``4.6.1`` | |``GCCcore/11.2.0`` ``4.6.3`` | |``GCCcore/11.3.0``, ``system`` +``4.7.5`` | |``system`` +``4.8.3`` | |``system`` ### CCfits @@ -4425,6 +4533,7 @@ version |toolchain ``2.0.5`` |``gompi/2021b`` ``2.0.6`` |``gompi/2022a`` ``2.1.1`` |``gompi/2021a`` +``2.2.2`` |``gompi/2023a`` ### cdo-bindings @@ -4566,6 +4675,16 @@ version |toolchain ---------|-------------- ``1.0.0``|``foss/2021b`` +### centerline + +Roads, rivers and similar linear structures are often represented by long and complex polygons. Since one of the most important attributes of a linear structure is its length, extracting that attribute from a polygon can prove to be more or less difficult. This library tries to solve this problem by creating the the polygon's centerline using the Voronoi diagram. For more info on how to use this package, see the official documentation. + +*homepage*: + +version |toolchain +---------|-------------- +``1.0.1``|``foss/2022a`` + ### Centrifuge Classifier for metagenomic sequences @@ -4606,14 +4725,24 @@ CFDEMcoupling is an open source CFD-DEM engine. It provides the possibility to c *homepage*: version |toolchain ----------|-------------- -``3.8.0``|``foss/2018a`` +---------|------------------------------ +``3.8.0``|``foss/2018a``, ``foss/2019b`` + +### cffi + +C Foreign Function Interface for Python. Interact with almost any C code from Python, based on C-like declarations that you can often copy-paste from header files or documentation. + +*homepage*: + +version |toolchain +----------|------------------ +``1.15.1``|``GCCcore/12.3.0`` ### CFITSIO -CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format. +CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format. -*homepage*: +*homepage*: version |toolchain ---------|---------------------------------------------------------- @@ -4625,6 +4754,7 @@ version |toolchain ``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`` +``4.3.0``|``GCCcore/12.3.0`` ### cftime @@ -4660,10 +4790,12 @@ version |versionsuffix |toolchain ``4.11.1``|``-Python-3.6.4`` |``foss/2018a`` ``4.11.1``|``-Python-3.6.6`` |``foss/2018b`` ``4.14`` |``-Python-3.7.2`` |``foss/2019a``, ``intel/2019a`` +``4.14.1``|``-Python-2.7.16``|``foss/2019b`` ``4.14.1``|``-Python-3.7.4`` |``foss/2019b``, ``intel/2019b`` ``4.14.3``| |``gompi/2021a``, ``gompi/2021b``, ``gompi/2022a``, ``iimpi/2021a`` ``4.14.3``|``-Python-3.8.2`` |``gompi/2020a``, ``iimpi/2020a`` ``5.2`` | |``gompi/2020b`` +``5.5.2`` | |``GCCcore/12.2.0`` ### cget @@ -4685,6 +4817,7 @@ version |toolchain ----------|------------------------------ ``0.60.2``|``foss/2018b`` ``0.60.3``|``foss/2020b``, ``foss/2021a`` +``0.60.7``|``foss/2022b`` ### CGmapTools @@ -4720,6 +4853,7 @@ version |toolchain ``2.2.0``|``GCCcore/10.2.0`` ``2.3.4``|``GCCcore/10.3.0`` ``2.4.1``|``GCCcore/11.3.0`` +``2.4.2``|``GCCcore/12.2.0`` ### CHASE @@ -4873,6 +5007,16 @@ version |versionsuffix |toolchain ``0.9.5``| |``foss/2018b`` ``0.9.5``|``-Python-2.7.12``|``foss/2016b`` +### ChIPseeker + +This package implements functions to retrieve the nearest genes around the peak, annotate genomic region of the peak, statstical methods for estimate the significance of overlap among ChIP peak data sets, and incorporate GEO database for user to compare the own dataset with those deposited in database. + +*homepage*: + +version |versionsuffix|toolchain +----------|-------------|-------------- +``1.32.1``|``-R-4.2.1`` |``foss/2022a`` + ### Chromaprint Chromaprint is the core component of the AcoustID project. It's a client-side library that implements a custom algorithm for extracting fingerprints from any audio source. @@ -4892,6 +5036,7 @@ Cicero is an R package that provides tools for analyzing single-cell chromatin a version |versionsuffix |toolchain ------------|---------------------|-------------- ``1.3.4.11``|``-R-4.0.3-Monocle3``|``foss/2020b`` +``1.3.8`` |``-R-4.2.1-Monocle3``|``foss/2022a`` ### CIF2Cell @@ -5037,6 +5182,8 @@ version |versionsuffix |toolchain ``13.0.1``| |``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ``13.0.1``|``-CUDA-11.4.1`` |``GCCcore/11.2.0`` ``15.0.5``| |``GCCcore/11.3.0`` +``16.0.4``| |``GCCcore/12.2.0`` +``16.0.6``| |``GCCcore/12.3.0`` ### Clang-AOMP @@ -5173,6 +5320,7 @@ version |toolchain ``1.17.3``|``foss/2018b`` ``1.17.6``|``foss/2020b``, ``foss/2021a`` ``1.17.7``|``foss/2021b`` +``1.17.8``|``foss/2022b`` ### Clustal-Omega @@ -5197,13 +5345,14 @@ version|toolchain ### Cluster-Buster -Cluster-Buster: Finding dense clusters of motifs in DNA sequences +Cluster-Buster is a program for finding interesting functional regions, such as transcriptional enhancers, in DNA sequences. -*homepage*: +*homepage*: version |toolchain ------------|--------------- ``20160106``|``intel/2016a`` +``20200507``|``GCC/12.2.0`` ### ClusterShell @@ -5251,7 +5400,7 @@ version |toolchain ``3.10.2``|``GCCcore/6.4.0``, ``GCCcore/7.2.0`` ``3.10.3``|``GCCcore/6.4.0``, ``GCCcore/7.2.0`` ``3.11.1``|``GCCcore/6.4.0`` -``3.11.4``|``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``3.11.4``|``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0`` ``3.12.1``|``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``system`` ``3.13.3``|``GCCcore/8.2.0`` ``3.15.1``|``system`` @@ -5444,6 +5593,7 @@ version |toolchain ``2.11.3``|``GCCcore/7.3.0``, ``foss/2018b`` ``2.11.4``|``GCC/10.3.0``, ``GCCcore/10.2.0`` ``2.11.6``|``GCC/11.2.0`` +``2.11.9``|``GCC/12.2.0`` ### ColabFold @@ -5526,6 +5676,7 @@ Decentralized, open-source (MIT), C/C++ package manager. version |toolchain ----------|------------------ ``1.58.0``|``GCCcore/11.3.0`` +``1.60.2``|``GCCcore/12.3.0`` ### CONCOCT @@ -5567,6 +5718,8 @@ version |versionsuffix |toolchain ``4.2.1``| |``GCCcore/10.2.0`` ``4.4.0``| |``GCCcore/10.3.0`` ``4.5.3``| |``GCCcore/11.3.0`` +``4.5.5``| |``GCCcore/12.2.0`` +``4.5.6``| |``GCCcore/12.3.0`` ### CONN @@ -5578,6 +5731,16 @@ version|versionsuffix |toolchain -------|-----------------|---------- ``21a``|``-MATLAB-2021a``|``system`` +### connected-components-3d + +cc3d is an implementation of connected components in three dimensions using a 26, 18, or 6-connected neighborhood in 3D or 4 and 8-connected in 2D. + +*homepage*: + +version |toolchain +----------|-------------- +``3.12.1``|``foss/2022b`` + ### ConnectomeWorkbench Connectome Workbench is an open source, freely available visualization and discovery tool used to map neuroimaging data, especially data generated by the Human Connectome Project. @@ -5700,6 +5863,7 @@ version |versionsuffix |toolchain ``4.5.1``|``-Python-2.7.14``|``intel/2017b`` ``5.5`` | |``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ``7.2.3``| |``GCCcore/12.2.0`` +``7.2.7``| |``GCCcore/11.3.0`` ### cowsay @@ -5731,6 +5895,7 @@ version |versionsuffix|toolchain ``8.2`` | |``foss/2021a``, ``intel/2021a`` ``9.1`` | |``foss/2022a`` ``2022.1``| |``foss/2022a`` +``2023.1``| |``foss/2022b`` ### CPB @@ -5802,9 +5967,9 @@ A small C++ header library which makes it easier to write Python extension modul *homepage*: version |toolchain ----------|-------------------------------------- +---------|---------------------------------------------------------- ``1.1.0``|``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``1.2.1``|``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +``1.2.1``|``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### cppzmq @@ -6024,6 +6189,16 @@ version |versionsuffix |toolchain ``0.3.5`` |``-CUDA-11.3.1``|``foss/2021a`` ``1.0.0-beta``|``-CUDA-11.3.1``|``foss/2021a`` +### cryptography + +cryptography is a package designed to expose cryptographic primitives and recipes to Python developers. + +*homepage*: + +version |toolchain +----------|------------------ +``41.0.1``|``GCCcore/12.3.0`` + ### CryptoMiniSat CryptoMiniSat is an advanced SAT solver @@ -6161,6 +6336,7 @@ 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/11.2.0``, ``GCCcore/11.3.0`` +``4.8.1``|``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### CubeWriter @@ -6173,6 +6349,7 @@ 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/11.2.0``, ``GCCcore/11.3.0`` +``4.8.1``|``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### CuCLARK @@ -6224,6 +6401,7 @@ version |toolchain ``12.1.0`` |``system`` ``12.1.1`` |``system`` ``12.2.0`` |``system`` +``12.2.2`` |``system`` ### CUDA-Samples @@ -6451,6 +6629,16 @@ version |toolchain ---------|-------------- ``2.0.3``|``foss/2022a`` +### CVglasso + +CVglasso is an R package that estimates a lasso-penalized precision matrix via block-wise coordinate descent – also known as the graphical lasso (glasso) algorithm. + +*homepage*: + +version|versionsuffix|toolchain +-------|-------------|-------------- +``1.0``|``-R-4.2.1`` |``foss/2022a`` + ### CVS CVS is a version control system, an important component of Source Configuration Management (SCM). @@ -6604,7 +6792,7 @@ version |versionsuffix |toolchain ## D -[dadi](#dadi) - [dagitty](#dagitty) - [Dakota](#dakota) - [DALI](#dali) - [DaliLite](#dalilite) - [Dalton](#dalton) - [damageproto](#damageproto) - [dammit](#dammit) - [DANPOS2](#danpos2) - [DAS_Tool](#das_tool) - [dask](#dask) - [dask-labextension](#dask-labextension) - [datamash](#datamash) - [davix](#davix) - [DB](#db) - [DB_File](#db_file) - [DBCSR](#dbcsr) - [DBD-mysql](#dbd-mysql) - [DBG2OLC](#dbg2olc) - [DBus](#dbus) - [dbus-glib](#dbus-glib) - [dclone](#dclone) - [dcm2niix](#dcm2niix) - [DCMTK](#dcmtk) - [dd](#dd) - [deal.II](#deal.ii) - [deap](#deap) - [decona](#decona) - [deconf](#deconf) - [DeconICA](#deconica) - [deepdiff](#deepdiff) - [DeepLabCut](#deeplabcut) - [deepmedic](#deepmedic) - [DeepMod2](#deepmod2) - [DeepSurv](#deepsurv) - [deepTools](#deeptools) - [DEICODE](#deicode) - [Delly](#delly) - [DeMixT](#demixt) - [DendroPy](#dendropy) - [DensPart](#denspart) - [Deprecated](#deprecated) - [destiny](#destiny) - [Detectron2](#detectron2) - [detonate](#detonate) - [Devito](#devito) - [DFA](#dfa) - [DFT-D3](#dft-d3) - [DFT-D4](#dft-d4) - [DFTB+](#dftb+) - [dftd3-lib](#dftd3-lib) - [DGL](#dgl) - [DIAL](#dial) - [DIALOGUE](#dialogue) - [DIAMOND](#diamond) - [Dice](#dice) - [DiCE-ML](#dice-ml) - [dicom2nifti](#dicom2nifti) - [DicomBrowser](#dicombrowser) - [Diffutils](#diffutils) - [dijitso](#dijitso) - [dill](#dill) - [DIRAC](#dirac) - [distributed](#distributed) - [DistributedStream](#distributedstream) - [DL_POLY_4](#dl_poly_4) - [DL_POLY_Classic](#dl_poly_classic) - [dlb](#dlb) - [dlib](#dlib) - [DLPack](#dlpack) - [dm-haiku](#dm-haiku) - [dm-reverb](#dm-reverb) - [dm-tree](#dm-tree) - [DMCfun](#dmcfun) - [DMLC-Core](#dmlc-core) - [DMTCP](#dmtcp) - [DOLFIN](#dolfin) - [dominate](#dominate) - [dorado](#dorado) - [Doris](#doris) - [DosageConvertor](#dosageconvertor) - [dotNET-Core-Runtime](#dotnet-core-runtime) - [dotNET-SDK](#dotnet-sdk) - [double-conversion](#double-conversion) - [DoubletFinder](#doubletfinder) - [Doxygen](#doxygen) - [DRAGMAP](#dragmap) - [Drake](#drake) - [dRep](#drep) - [DROP](#drop) - [dropEst](#dropest) - [DSA](#dsa) - [dSFMT](#dsfmt) - [DSRC](#dsrc) - [Dsuite](#dsuite) - [dtcmp](#dtcmp) - [dtcwt](#dtcwt) - [DualSPHysics](#dualsphysics) - [DUBStepR](#dubstepr) - [dune-core](#dune-core) - [dune-fem](#dune-fem) - [duplex-tools](#duplex-tools) - [dx-toolkit](#dx-toolkit) - [dxpy](#dxpy) - [DyMat](#dymat) +[dadi](#dadi) - [dagitty](#dagitty) - [Dakota](#dakota) - [DALI](#dali) - [DaliLite](#dalilite) - [Dalton](#dalton) - [damageproto](#damageproto) - [dammit](#dammit) - [DANPOS2](#danpos2) - [DAS_Tool](#das_tool) - [dask](#dask) - [dask-labextension](#dask-labextension) - [datamash](#datamash) - [davix](#davix) - [DB](#db) - [DB_File](#db_file) - [DBCSR](#dbcsr) - [DBD-mysql](#dbd-mysql) - [DBG2OLC](#dbg2olc) - [DBus](#dbus) - [dbus-glib](#dbus-glib) - [dclone](#dclone) - [dcm2niix](#dcm2niix) - [DCMTK](#dcmtk) - [dd](#dd) - [deal.II](#deal.ii) - [deap](#deap) - [decona](#decona) - [deconf](#deconf) - [DeconICA](#deconica) - [deepdiff](#deepdiff) - [DeepLabCut](#deeplabcut) - [deepmedic](#deepmedic) - [DeepMod2](#deepmod2) - [DeepSurv](#deepsurv) - [deepTools](#deeptools) - [DEICODE](#deicode) - [Delly](#delly) - [DeMixT](#demixt) - [DendroPy](#dendropy) - [DensPart](#denspart) - [Deprecated](#deprecated) - [destiny](#destiny) - [Detectron2](#detectron2) - [detonate](#detonate) - [Devito](#devito) - [DFA](#dfa) - [DFT-D3](#dft-d3) - [DFT-D4](#dft-d4) - [DFTB+](#dftb+) - [dftd3-lib](#dftd3-lib) - [DGL](#dgl) - [DIAL](#dial) - [DIALOGUE](#dialogue) - [DIAMOND](#diamond) - [Dice](#dice) - [DiCE-ML](#dice-ml) - [dicom2nifti](#dicom2nifti) - [DicomBrowser](#dicombrowser) - [DiffBind](#diffbind) - [Diffutils](#diffutils) - [dijitso](#dijitso) - [dill](#dill) - [DIRAC](#dirac) - [distributed](#distributed) - [DistributedStream](#distributedstream) - [DL_POLY_4](#dl_poly_4) - [DL_POLY_Classic](#dl_poly_classic) - [dlb](#dlb) - [dlib](#dlib) - [DLPack](#dlpack) - [dm-haiku](#dm-haiku) - [dm-reverb](#dm-reverb) - [dm-tree](#dm-tree) - [DMCfun](#dmcfun) - [DMLC-Core](#dmlc-core) - [DMTCP](#dmtcp) - [DOLFIN](#dolfin) - [dominate](#dominate) - [dorado](#dorado) - [Doris](#doris) - [DosageConvertor](#dosageconvertor) - [dotNET-Core-Runtime](#dotnet-core-runtime) - [dotNET-SDK](#dotnet-sdk) - [double-conversion](#double-conversion) - [DoubletFinder](#doubletfinder) - [Doxygen](#doxygen) - [DRAGMAP](#dragmap) - [Drake](#drake) - [dRep](#drep) - [drmaa-python](#drmaa-python) - [DROP](#drop) - [dropEst](#dropest) - [DSA](#dsa) - [dSFMT](#dsfmt) - [DSRC](#dsrc) - [Dsuite](#dsuite) - [dtcmp](#dtcmp) - [dtcwt](#dtcwt) - [DualSPHysics](#dualsphysics) - [DUBStepR](#dubstepr) - [dune-core](#dune-core) - [dune-fem](#dune-fem) - [duplex-tools](#duplex-tools) - [dx-toolkit](#dx-toolkit) - [dxpy](#dxpy) - [DyMat](#dymat) ### dadi @@ -6741,6 +6929,7 @@ version |versionsuffix |toolchain ``2021.9.1`` | |``foss/2021a`` ``2022.1.0`` | |``foss/2021b`` ``2022.10.0``| |``foss/2022a`` +``2023.7.1`` | |``foss/2022b`` ### dask-labextension @@ -6903,6 +7092,7 @@ version |toolchain ``1.0.20201102``|``GCCcore/8.3.0`` ``1.0.20211006``|``GCCcore/10.3.0`` ``1.0.20220720``|``GCCcore/11.3.0`` +``1.0.20230411``|``GCCcore/12.2.0`` ### DCMTK @@ -7071,6 +7261,7 @@ version |versionsuffix |toolchain ``0.7.8``|``-linux_x86_64``|``system`` ``0.8.7``| |``gompi/2020b`` ``1.1.5``| |``GCC/11.3.0`` +``1.1.6``| |``GCC/12.2.0`` ### DeMixT @@ -7260,7 +7451,7 @@ version |toolchain ``2.0.11``|``GCC/10.3.0`` ``2.0.13``|``GCC/10.3.0``, ``GCC/11.2.0`` ``2.1.0`` |``GCC/11.3.0`` -``2.1.8`` |``GCC/10.3.0`` +``2.1.8`` |``GCC/10.3.0``, ``GCC/12.2.0`` ### Dice @@ -7303,6 +7494,16 @@ version |versionsuffix |toolchain -----------|------------------|---------- ``1.7.0b5``|``-Java-1.7.0_80``|``system`` +### DiffBind + +Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions. + +*homepage*: + +version |versionsuffix|toolchain +---------|-------------|-------------- +``3.6.5``|``-R-4.2.1`` |``foss/2022a`` + ### Diffutils Diffutils: GNU diff utilities - find the differences between files @@ -7335,6 +7536,7 @@ version |toolchain ``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`` +``0.3.7``|``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### DIRAC @@ -7435,6 +7637,7 @@ Haiku is a simple neural network library for JAX developed by some of the author version |versionsuffix |toolchain ---------|----------------|-------------- +``0.0.9``| |``foss/2022a`` ``0.0.9``|``-CUDA-11.3.1``|``foss/2021a`` ### dm-reverb @@ -7653,6 +7856,16 @@ version |toolchain ``3.0.0``|``foss/2021a`` ``3.4.2``|``foss/2022a`` +### drmaa-python + +Distributed Resource Management Application API (DRMAA) bindings for Python. + +*homepage*: + +version |versionsuffix|toolchain +---------|-------------|------------------ +``0.7.9``|``-slurm`` |``GCCcore/12.2.0`` + ### DROP Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders @@ -7824,7 +8037,7 @@ version|versionsuffix |toolchain ## E -[E-ANTIC](#e-antic) - [ea-utils](#ea-utils) - [earthengine-api](#earthengine-api) - [easel](#easel) - [EasyBuild](#easybuild) - [EasyQC](#easyqc) - [ecBuild](#ecbuild) - [ecCodes](#eccodes) - [eccodes-python](#eccodes-python) - [ecFlow](#ecflow) - [ED2](#ed2) - [EDirect](#edirect) - [edlib](#edlib) - [EggLib](#egglib) - [eggnog-mapper](#eggnog-mapper) - [EGTtools](#egttools) - [eht-imaging](#eht-imaging) - [Eigen](#eigen) - [EigenExa](#eigenexa) - [EIGENSOFT](#eigensoft) - [einops](#einops) - [elastix](#elastix) - [elbencho](#elbencho) - [ELFIO](#elfio) - [elfutils](#elfutils) - [Elk](#elk) - [ELPA](#elpa) - [ELPH](#elph) - [elprep](#elprep) - [ELSI](#elsi) - [ELSI-RCI](#elsi-rci) - [Emacs](#emacs) - [EMAN2](#eman2) - [EMBOSS](#emboss) - [Embree](#embree) - [emcee](#emcee) - [EMU](#emu) - [enaBrowserTool](#enabrowsertool) - [enchant](#enchant) - [enchant-2](#enchant-2) - [EnsEMBLCoreAPI](#ensemblcoreapi) - [entrypoints](#entrypoints) - [EPD](#epd) - [EPIC](#epic) - [epiScanpy](#episcanpy) - [eQuilibrator](#equilibrator) - [EricScript](#ericscript) - [ESL-Bundle](#esl-bundle) - [ESM-2](#esm-2) - [ESMF](#esmf) - [ESMPy](#esmpy) - [ESMValTool](#esmvaltool) - [eSpeak-NG](#espeak-ng) - [ESPResSo](#espresso) - [Essentia](#essentia) - [ETE](#ete) - [ETSF_IO](#etsf_io) - [eudev](#eudev) - [Evcxr-REPL](#evcxr-repl) - [EvidentialGene](#evidentialgene) - [evmix](#evmix) - [ExaBayes](#exabayes) - [ExaML](#examl) - [Excel-Writer-XLSX](#excel-writer-xlsx) - [ExifTool](#exiftool) - [exiv2](#exiv2) - [Exonerate](#exonerate) - [expat](#expat) - [expect](#expect) - [expecttest](#expecttest) - [eXpress](#express) - [Extrae](#extrae) - [EZC3D](#ezc3d) +[E-ANTIC](#e-antic) - [e3nn](#e3nn) - [ea-utils](#ea-utils) - [earthengine-api](#earthengine-api) - [easel](#easel) - [EasyBuild](#easybuild) - [EasyQC](#easyqc) - [ecBuild](#ecbuild) - [ecCodes](#eccodes) - [eccodes-python](#eccodes-python) - [ecFlow](#ecflow) - [ED2](#ed2) - [EDirect](#edirect) - [edlib](#edlib) - [EggLib](#egglib) - [eggnog-mapper](#eggnog-mapper) - [EGTtools](#egttools) - [eht-imaging](#eht-imaging) - [Eigen](#eigen) - [EigenExa](#eigenexa) - [EIGENSOFT](#eigensoft) - [einops](#einops) - [elastix](#elastix) - [elbencho](#elbencho) - [ELFIO](#elfio) - [elfutils](#elfutils) - [Elk](#elk) - [ELPA](#elpa) - [ELPH](#elph) - [elprep](#elprep) - [ELSI](#elsi) - [ELSI-RCI](#elsi-rci) - [Emacs](#emacs) - [EMAN2](#eman2) - [EMBOSS](#emboss) - [Embree](#embree) - [emcee](#emcee) - [EMU](#emu) - [enaBrowserTool](#enabrowsertool) - [enchant](#enchant) - [enchant-2](#enchant-2) - [EnsEMBLCoreAPI](#ensemblcoreapi) - [entrypoints](#entrypoints) - [EPD](#epd) - [EPIC](#epic) - [epiScanpy](#episcanpy) - [eQuilibrator](#equilibrator) - [EricScript](#ericscript) - [ESL-Bundle](#esl-bundle) - [ESM-2](#esm-2) - [ESMF](#esmf) - [ESMPy](#esmpy) - [ESMValTool](#esmvaltool) - [eSpeak-NG](#espeak-ng) - [ESPResSo](#espresso) - [Essentia](#essentia) - [ETE](#ete) - [ETSF_IO](#etsf_io) - [eudev](#eudev) - [Evcxr-REPL](#evcxr-repl) - [EvidentialGene](#evidentialgene) - [evmix](#evmix) - [ExaBayes](#exabayes) - [ExaML](#examl) - [Excel-Writer-XLSX](#excel-writer-xlsx) - [ExifTool](#exiftool) - [exiv2](#exiv2) - [Exonerate](#exonerate) - [expat](#expat) - [expect](#expect) - [expecttest](#expecttest) - [eXpress](#express) - [Extrae](#extrae) - [EZC3D](#ezc3d) ### E-ANTIC @@ -7838,6 +8051,16 @@ version |toolchain ``0.1.2``|``GCC/8.2.0-2.31.1`` ``0.1.5``|``GCC/8.3.0`` +### e3nn + +Euclidean neural networks (e3nn) is a python library based on pytorch to create equivariant neural networks for the group O(3). + +*homepage*: + +version |toolchain +---------|-------------- +``0.3.3``|``foss/2022a`` + ### ea-utils Command-line tools for processing biological sequencing data. Barcode demultiplexing, adapter trimming, etc. Primarily written to support an Illumina based pipeline - but should work with any FASTQs. @@ -7972,6 +8195,7 @@ version |toolchain ``4.7.0`` |``system`` ``4.7.1`` |``system`` ``4.7.2`` |``system`` +``4.8.0`` |``system`` ### EasyQC @@ -7992,6 +8216,7 @@ A CMake-based build system, consisting of a collection of CMake macros and funct version |toolchain ---------|---------- ``3.7.0``|``system`` +``3.8.0``|``system`` ### ecCodes @@ -8013,6 +8238,7 @@ version |versionsuffix |toolchain ``2.22.1``| |``gompi/2021a`` ``2.24.2``| |``gompi/2021b``, ``iimpi/2021b`` ``2.27.0``| |``gompi/2022a`` +``2.31.0``| |``gompi/2023a`` ### eccodes-python @@ -8256,6 +8482,7 @@ version |versionsuffix |toolchain ``2022.05.001`` | |``foss/2022a``, ``foss/2022b``, ``intel/2022a``, ``intel/2022b`` ``2022.05.001`` |``-CUDA-11.7.0``|``foss/2022a`` ``2022.05.001`` |``-CUDA-12.0.0``|``foss/2022b`` +``2023.05.001`` | |``foss/2023a`` ### ELPH @@ -8563,8 +8790,10 @@ A software package for performing and analyzing scientific Molecular Dynamics si *homepage*: version |versionsuffix |toolchain ----------|----------------|-------------- +---------|----------------|------------------------------ +``4.2.1``| |``foss/2021a``, ``foss/2022a`` ``4.2.1``|``-CUDA-11.3.1``|``foss/2021a`` +``4.2.1``|``-CUDA-11.8.0``|``foss/2022a`` ### Essentia @@ -8685,14 +8914,15 @@ version |toolchain ### exiv2 -Exiv2 is a Cross-platform C++ library and a command line utility to manage image metadata. +Exiv2 is a C++ library and a command line utility to manage image metadata. It provides fast and easy read and write access to the Exif, IPTC and XMP metadata of digital images in various formats. Exiv2 is available as free software and with a commercial license, and is used in many projects. -*homepage*: +*homepage*: version |toolchain ----------|------------------ ``0.27.4``|``GCCcore/10.3.0`` ``0.27.5``|``GCCcore/11.2.0`` +``0.28.0``|``GCCcore/12.3.0`` ### Exonerate @@ -8742,8 +8972,9 @@ This library implements expect tests (also known as "golden" tests). Expect test *homepage*: version |toolchain ----------|------------------------------------------------------------------------------ -``0.1.3``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +---------|-------------------------------------------------------------------------------------------------- +``0.1.3``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +``0.1.5``|``GCCcore/12.3.0`` ### eXpress @@ -8782,7 +9013,7 @@ version |toolchain ## F -[f90cache](#f90cache) - [f90wrap](#f90wrap) - [Faber](#faber) - [FabIO](#fabio) - [faceswap](#faceswap) - [FALCON](#falcon) - [FANN](#fann) - [fast5](#fast5) - [FASTA](#fasta) - [fastahack](#fastahack) - [fastai](#fastai) - [FastaIndex](#fastaindex) - [FastANI](#fastani) - [Fastaq](#fastaq) - [FastFold](#fastfold) - [fastjet](#fastjet) - [fastjet-contrib](#fastjet-contrib) - [FastME](#fastme) - [fastp](#fastp) - [fastparquet](#fastparquet) - [fastPHASE](#fastphase) - [fastq-pair](#fastq-pair) - [fastq-tools](#fastq-tools) - [FastQ_Screen](#fastq_screen) - [FastQC](#fastqc) - [fastqsplitter](#fastqsplitter) - [FastQTL](#fastqtl) - [fastqz](#fastqz) - [FastRFS](#fastrfs) - [fastStructure](#faststructure) - [FastTree](#fasttree) - [FastViromeExplorer](#fastviromeexplorer) - [FASTX-Toolkit](#fastx-toolkit) - [fatslim](#fatslim) - [fbm](#fbm) - [FBPIC](#fbpic) - [FCC](#fcc) - [FCM](#fcm) - [fdict](#fdict) - [FDS](#fds) - [fdstools](#fdstools) - [FDTD_Solutions](#fdtd_solutions) - [feh](#feh) - [FEniCS](#fenics) - [fermi-lite](#fermi-lite) - [Ferret](#ferret) - [festival](#festival) - [fetchMG](#fetchmg) - [FFC](#ffc) - [FFLAS-FFPACK](#fflas-ffpack) - [FFmpeg](#ffmpeg) - [ffmpi](#ffmpi) - [ffnet](#ffnet) - [ffnvcodec](#ffnvcodec) - [fftlib](#fftlib) - [FFTW](#fftw) - [FFTW.MPI](#fftw.mpi) - [fgbio](#fgbio) - [FGSL](#fgsl) - [FHI-aims](#fhi-aims) - [FIAT](#fiat) - [FIGARO](#figaro) - [FigureGen](#figuregen) - [Fiji](#fiji) - [file](#file) - [filevercmp](#filevercmp) - [Filtlong](#filtlong) - [find_circ](#find_circ) - [finder](#finder) - [findhap](#findhap) - [findutils](#findutils) - [fineRADstructure](#fineradstructure) - [fineSTRUCTURE](#finestructure) - [fio](#fio) - [Fiona](#fiona) - [Firefox](#firefox) - [FIRESTARTER](#firestarter) - [FireWorks](#fireworks) - [FIt-SNE](#fit-sne) - [FIX](#fix) - [fixesproto](#fixesproto) - [FLAC](#flac) - [FLAIR](#flair) - [flair-NLP](#flair-nlp) - [FLANN](#flann) - [FLASH](#flash) - [Flask](#flask) - [flatbuffers](#flatbuffers) - [flatbuffers-python](#flatbuffers-python) - [FLEUR](#fleur) - [flex](#flex) - [Flexbar](#flexbar) - [FlexiBLAS](#flexiblas) - [FlexiDot](#flexidot) - [Flink](#flink) - [FLINT](#flint) - [flook](#flook) - [flowFDA](#flowfda) - [FLTK](#fltk) - [FLUENT](#fluent) - [Flye](#flye) - [FMILibrary](#fmilibrary) - [FMM3D](#fmm3d) - [FMPy](#fmpy) - [FMRIprep](#fmriprep) - [FMS](#fms) - [fmt](#fmt) - [FoBiS](#fobis) - [FoldX](#foldx) - [fontconfig](#fontconfig) - [fontsproto](#fontsproto) - [FORD](#ford) - [foss](#foss) - [fosscuda](#fosscuda) - [FoX](#fox) - [FOX-Toolkit](#fox-toolkit) - [FPM](#fpm) - [fpocket](#fpocket) - [fqtrim](#fqtrim) - [fqzcomp](#fqzcomp) - [FragGeneScan](#fraggenescan) - [FragPipe](#fragpipe) - [FRANz](#franz) - [FreeBarcodes](#freebarcodes) - [freebayes](#freebayes) - [FreeFEM](#freefem) - [FreeFem++](#freefem++) - [freeglut](#freeglut) - [FreeImage](#freeimage) - [FreeSASA](#freesasa) - [FreeSurfer](#freesurfer) - [FreeTDS](#freetds) - [freetype](#freetype) - [freetype-py](#freetype-py) - [FreeXL](#freexl) - [freud-analysis](#freud-analysis) - [FriBidi](#fribidi) - [FRUIT](#fruit) - [FRUIT_processor](#fruit_processor) - [FSL](#fsl) - [FSLeyes](#fsleyes) - [fsom](#fsom) - [FSON](#fson) - [FTGL](#ftgl) - [Fujitsu](#fujitsu) - [fullrmc](#fullrmc) - [fumi_tools](#fumi_tools) - [funannotate](#funannotate) - [FunGAP](#fungap) - [FUNWAVE-TVD](#funwave-tvd) - [FUSE](#fuse) - [FuSeq](#fuseq) - [FusionCatcher](#fusioncatcher) - [futhark](#futhark) - [futile](#futile) - [future](#future) - [fxtract](#fxtract) +[f90cache](#f90cache) - [f90wrap](#f90wrap) - [Faber](#faber) - [FabIO](#fabio) - [faceswap](#faceswap) - [FALCON](#falcon) - [FANN](#fann) - [fast5](#fast5) - [FASTA](#fasta) - [fastahack](#fastahack) - [fastai](#fastai) - [FastaIndex](#fastaindex) - [FastANI](#fastani) - [Fastaq](#fastaq) - [FastFold](#fastfold) - [fastjet](#fastjet) - [fastjet-contrib](#fastjet-contrib) - [FastME](#fastme) - [fastp](#fastp) - [fastparquet](#fastparquet) - [fastPHASE](#fastphase) - [fastq-pair](#fastq-pair) - [fastq-tools](#fastq-tools) - [FastQ_Screen](#fastq_screen) - [FastQC](#fastqc) - [fastqsplitter](#fastqsplitter) - [FastQTL](#fastqtl) - [fastqz](#fastqz) - [FastRFS](#fastrfs) - [fastStructure](#faststructure) - [FastTree](#fasttree) - [FastViromeExplorer](#fastviromeexplorer) - [FASTX-Toolkit](#fastx-toolkit) - [fatslim](#fatslim) - [fbm](#fbm) - [FBPIC](#fbpic) - [FCC](#fcc) - [FCM](#fcm) - [fdict](#fdict) - [FDS](#fds) - [fdstools](#fdstools) - [FDTD_Solutions](#fdtd_solutions) - [feh](#feh) - [FEniCS](#fenics) - [fermi-lite](#fermi-lite) - [Ferret](#ferret) - [festival](#festival) - [fetchMG](#fetchmg) - [FFC](#ffc) - [FFLAS-FFPACK](#fflas-ffpack) - [FFmpeg](#ffmpeg) - [ffmpi](#ffmpi) - [ffnet](#ffnet) - [ffnvcodec](#ffnvcodec) - [fftlib](#fftlib) - [FFTW](#fftw) - [FFTW.MPI](#fftw.mpi) - [fgbio](#fgbio) - [FGSL](#fgsl) - [FHI-aims](#fhi-aims) - [FIAT](#fiat) - [FIGARO](#figaro) - [FigureGen](#figuregen) - [Fiji](#fiji) - [file](#file) - [filevercmp](#filevercmp) - [Filtlong](#filtlong) - [find_circ](#find_circ) - [finder](#finder) - [findhap](#findhap) - [findutils](#findutils) - [fineRADstructure](#fineradstructure) - [fineSTRUCTURE](#finestructure) - [fio](#fio) - [Fiona](#fiona) - [Firefox](#firefox) - [FIRESTARTER](#firestarter) - [FireWorks](#fireworks) - [FIt-SNE](#fit-sne) - [FIX](#fix) - [fixesproto](#fixesproto) - [FLAC](#flac) - [FLAIR](#flair) - [flair-NLP](#flair-nlp) - [FLANN](#flann) - [FLASH](#flash) - [Flask](#flask) - [flatbuffers](#flatbuffers) - [flatbuffers-python](#flatbuffers-python) - [FLEUR](#fleur) - [flex](#flex) - [Flexbar](#flexbar) - [FlexiBLAS](#flexiblas) - [FlexiDot](#flexidot) - [Flink](#flink) - [FLINT](#flint) - [flit](#flit) - [flook](#flook) - [flowFDA](#flowfda) - [FLTK](#fltk) - [FLUENT](#fluent) - [Flye](#flye) - [FMILibrary](#fmilibrary) - [FMM3D](#fmm3d) - [FMPy](#fmpy) - [FMRIprep](#fmriprep) - [FMS](#fms) - [fmt](#fmt) - [FoBiS](#fobis) - [FoldX](#foldx) - [fontconfig](#fontconfig) - [fontsproto](#fontsproto) - [FORD](#ford) - [foss](#foss) - [fosscuda](#fosscuda) - [FoX](#fox) - [FOX-Toolkit](#fox-toolkit) - [FPM](#fpm) - [fpocket](#fpocket) - [fqtrim](#fqtrim) - [fqzcomp](#fqzcomp) - [FragGeneScan](#fraggenescan) - [FragPipe](#fragpipe) - [FRANz](#franz) - [FreeBarcodes](#freebarcodes) - [freebayes](#freebayes) - [FreeFEM](#freefem) - [FreeFem++](#freefem++) - [freeglut](#freeglut) - [FreeImage](#freeimage) - [FreeSASA](#freesasa) - [FreeSurfer](#freesurfer) - [FreeTDS](#freetds) - [freetype](#freetype) - [freetype-py](#freetype-py) - [FreeXL](#freexl) - [freud-analysis](#freud-analysis) - [FriBidi](#fribidi) - [FRUIT](#fruit) - [FRUIT_processor](#fruit_processor) - [FSL](#fsl) - [FSLeyes](#fsleyes) - [fsom](#fsom) - [FSON](#fson) - [FTGL](#ftgl) - [Fujitsu](#fujitsu) - [fullrmc](#fullrmc) - [fumi_tools](#fumi_tools) - [funannotate](#funannotate) - [FunGAP](#fungap) - [FUNWAVE-TVD](#funwave-tvd) - [FUSE](#fuse) - [FuSeq](#fuseq) - [FusionCatcher](#fusioncatcher) - [futhark](#futhark) - [futile](#futile) - [future](#future) - [fxtract](#fxtract) ### f90cache @@ -8886,8 +9117,8 @@ Utilities for indexing and sequence extraction from FASTA files. *homepage*: version |toolchain ----------|----------------------------------------------------------------------------- -``1.0.0``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` +---------|------------------------------------------------------------------------------------------------- +``1.0.0``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/9.3.0`` ### fastai @@ -8995,10 +9226,11 @@ fastparquet is a python implementation of the parquet format, aiming to integrat *homepage*: -version |toolchain ----------|-------------- -``0.7.2``|``foss/2021a`` -``0.8.0``|``foss/2021b`` +version |toolchain +------------|-------------- +``0.7.2`` |``foss/2021a`` +``0.8.0`` |``foss/2021b`` +``2023.4.0``|``gfbf/2022b`` ### fastPHASE @@ -9366,6 +9598,7 @@ version |toolchain ``4.4.2`` |``GCCcore/11.3.0`` ``5.0.1`` |``GCCcore/11.3.0`` ``5.1.2`` |``GCCcore/12.2.0`` +``6.0`` |``GCCcore/12.3.0`` ### ffmpi @@ -9393,9 +9626,10 @@ FFmpeg nvidia headers. Adds support for nvenc and nvdec. Requires Nvidia GPU and *homepage*: -version |toolchain -------------|---------- -``11.1.5.2``|``system`` +version |toolchain +-------------|---------- +``11.1.5.2`` |``system`` +``12.0.16.0``|``system`` ### fftlib @@ -9414,7 +9648,7 @@ 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`` @@ -9422,7 +9656,7 @@ 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``, ``iomkl/2020b`` +``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``, ``iompi/2020b`` ``3.3.8`` |``-amd`` |``gompi/2020a`` ``3.3.8`` |``-serial`` |``GCC/9.3.0`` ``3.3.9`` | |``gompi/2021a``, ``intel/2021a`` @@ -9542,9 +9776,9 @@ filevercmp function as in sort --version-sort. *homepage*: version |toolchain -------------|---------------------------------------------------------- +------------|------------------------------------------------------------------------------ ``20141119``|``GCCcore/9.3.0`` -``20191210``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``20191210``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ### Filtlong @@ -9785,12 +10019,13 @@ FlatBuffers: Memory Efficient Serialization Library *homepage*: -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`` +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`` +``23.5.26``|``GCCcore/12.3.0`` ### flatbuffers-python @@ -9798,11 +10033,13 @@ Python Flatbuffers runtime library. *homepage*: -version |versionsuffix |toolchain ---------|-----------------|---------------------------------------------------------- -``1.12``| |``GCCcore/10.2.0`` -``1.12``|``-Python-3.7.4``|``GCCcore/8.3.0`` -``2.0`` | |``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +version |versionsuffix |toolchain +-----------|-----------------|---------------------------------------------------------- +``1.12`` | |``GCCcore/10.2.0`` +``1.12`` |``-Python-3.7.4``|``GCCcore/8.3.0`` +``2.0`` | |``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``23.1.4`` | |``GCCcore/12.2.0`` +``23.5.26``| |``GCCcore/12.3.0`` ### FLEUR @@ -9821,14 +10058,14 @@ Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, some *homepage*: version |toolchain -----------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +----------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ ``2.5.35``|``system`` ``2.5.38``|``GCC/4.8.2`` ``2.5.39``|``GCC/4.9.2``, ``GCC/4.9.2-binutils-2.25``, ``GCC/4.9.3``, ``GCC/4.9.3-binutils-2.25``, ``GCC/5.1.0-binutils-2.25``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GNU/4.9.3-2.25``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``system`` ``2.6.0`` |``GCC/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/4.9.4``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` ``2.6.2`` |``intel/2016b`` ``2.6.3`` |``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/7.1.0``, ``gimkl/2017a``, ``system`` -``2.6.4`` |``FCC/4.5.0``, ``GCCcore/10.1.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/11.4.0``, ``GCCcore/12.1.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/7.4.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/8.4.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GCCcore/9.4.0``, ``GCCcore/9.5.0``, ``GCCcore/system``, ``system`` +``2.6.4`` |``FCC/4.5.0``, ``GCCcore/10.1.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/11.4.0``, ``GCCcore/12.1.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``GCCcore/13.2.0``, ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/7.4.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/8.4.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GCCcore/9.4.0``, ``GCCcore/9.5.0``, ``GCCcore/system``, ``system`` ### Flexbar @@ -9887,6 +10124,16 @@ version |toolchain ``2.8.4``|``foss/2021b`` ``2.9.0``|``gfbf/2022a`` +### flit + +A simple packaging tool for simple packages. + +*homepage*: + +version |toolchain +---------|------------------ +``3.9.0``|``GCCcore/12.3.0`` + ### flook The fortran-Lua-hook library. @@ -9920,7 +10167,7 @@ version |toolchain ``1.3.5``|``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ``1.3.6``|``GCCcore/10.3.0`` ``1.3.7``|``GCCcore/11.2.0`` -``1.3.8``|``GCCcore/11.3.0`` +``1.3.8``|``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ### FLUENT @@ -10298,8 +10545,8 @@ FreeImage is an Open Source library project for developers who would like to sup *homepage*: version |toolchain -----------|--------------------------------------------------------------------------------------------------------------------------------------- -``3.18.0``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +----------|----------------------------------------------------------------------------------------------------------------------------------------------------------- +``3.18.0``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ### FreeSASA @@ -10334,6 +10581,10 @@ version |versionsuffix |toolchain ``7.4.0``|``-centos8_x86_64``|``system`` ``7.4.0``|``-ubuntu20_amd64``|``system`` ``7.4.0``|``-ubuntu22_amd64``|``system`` +``7.4.1``|``-centos7_x86_64``|``system`` +``7.4.1``|``-centos8_x86_64``|``system`` +``7.4.1``|``-ubuntu20_amd64``|``system`` +``7.4.1``|``-ubuntu22_amd64``|``system`` ### FreeTDS @@ -10416,7 +10667,7 @@ version |toolchain ``1.0.5`` |``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``1.0.9`` |``GCCcore/9.3.0`` ``1.0.10``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``1.0.12``|``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +``1.0.12``|``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### FRUIT @@ -10480,6 +10731,7 @@ A tiny C library for managing SOM (Self-Organizing Maps) neural networks. version |toolchain ------------|----------------------------------------------------------------------------- ``20141119``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` +``20151117``|``GCCcore/11.3.0`` ### FSON @@ -10643,7 +10895,7 @@ 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) - [GATB-Core](#gatb-core) - [GATE](#gate) - [GATK](#gatk) - [Gaussian](#gaussian) - [gawk](#gawk) - [gbasis](#gbasis) - [Gblocks](#gblocks) - [GBprocesS](#gbprocess) - [gbs2ploidy](#gbs2ploidy) - [gc](#gc) - [GC3Pie](#gc3pie) - [GCC](#gcc) - [GCCcore](#gcccore) - [gcccuda](#gcccuda) - [gcloud](#gcloud) - [GConf](#gconf) - [GCTA](#gcta) - [Gctf](#gctf) - [GD](#gd) - [GDAL](#gdal) - [GDB](#gdb) - [gdbgui](#gdbgui) - [gdbm](#gdbm) - [gdc-client](#gdc-client) - [GDCHART](#gdchart) - [GDCM](#gdcm) - [GDGraph](#gdgraph) - [gdist](#gdist) - [Gdk-Pixbuf](#gdk-pixbuf) - [GDRCopy](#gdrcopy) - [Geant4](#geant4) - [Geant4-data](#geant4-data) - [gearshifft](#gearshifft) - [GEGL](#gegl) - [GEM](#gem) - [GEM-library](#gem-library) - [gemelli](#gemelli) - [GEMMA](#gemma) - [gemmi](#gemmi) - [gencore_variant_detection](#gencore_variant_detection) - [GeneMark-ET](#genemark-et) - [gengetopt](#gengetopt) - [GenMap](#genmap) - [Genome_Profiler](#genome_profiler) - [GenomeMapper](#genomemapper) - [genomepy](#genomepy) - [GenomeTester4](#genometester4) - [GenomeThreader](#genomethreader) - [GenomeTools](#genometools) - [GenomeWorks](#genomeworks) - [GenotypeHarmonizer](#genotypeharmonizer) - [genozip](#genozip) - [gensim](#gensim) - [geocube](#geocube) - [geopandas](#geopandas) - [geopy](#geopy) - [georges](#georges) - [GEOS](#geos) - [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) - [GimmeMotifs](#gimmemotifs) - [GIMP](#gimp) - [gimpi](#gimpi) - [gimpic](#gimpic) - [GIMPS](#gimps) - [giolf](#giolf) - [giolfc](#giolfc) - [Giotto-Suite](#giotto-suite) - [git](#git) - [git-extras](#git-extras) - [git-lfs](#git-lfs) - [GitPython](#gitpython) - [Givaro](#givaro) - [Giza](#giza) - [GKeyll](#gkeyll) - [GL2PS](#gl2ps) - [Glade](#glade) - [glew](#glew) - [GLFW](#glfw) - [GLI](#gli) - [GLib](#glib) - [glib-networking](#glib-networking) - [glibc](#glibc) - [GLibmm](#glibmm) - [GLIMMER](#glimmer) - [GlimmerHMM](#glimmerhmm) - [GLIMPSE](#glimpse) - [GLM](#glm) - [GLM-AED](#glm-aed) - [GlobalArrays](#globalarrays) - [Globus-CLI](#globus-cli) - [GlobusConnectPersonal](#globusconnectpersonal) - [glog](#glog) - [GLPK](#glpk) - [glproto](#glproto) - [Glucose](#glucose) - [GMAP-GSNAP](#gmap-gsnap) - [GMP](#gmp) - [gmpich](#gmpich) - [gmpolf](#gmpolf) - [gmpy2](#gmpy2) - [gmsh](#gmsh) - [GMT](#gmt) - [gmvapich2](#gmvapich2) - [gmvolf](#gmvolf) - [GNU](#gnu) - [gnuplot](#gnuplot) - [GnuTLS](#gnutls) - [Go](#go) - [goalign](#goalign) - [GOATOOLS](#goatools) - [gobff](#gobff) - [GObject-Introspection](#gobject-introspection) - [goblf](#goblf) - [GOBNILP](#gobnilp) - [Godon](#godon) - [gofasta](#gofasta) - [golf](#golf) - [gomkl](#gomkl) - [gompi](#gompi) - [gompic](#gompic) - [google-java-format](#google-java-format) - [googletest](#googletest) - [gotree](#gotree) - [GP2C](#gp2c) - [GPAW](#gpaw) - [GPAW-setups](#gpaw-setups) - [gperf](#gperf) - [gperftools](#gperftools) - [gpustat](#gpustat) - [GPy](#gpy) - [GPyOpt](#gpyopt) - [GPyTorch](#gpytorch) - [Grace](#grace) - [Gradle](#gradle) - [gradunwarp](#gradunwarp) - [graph-tool](#graph-tool) - [GraphDB](#graphdb) - [Graphene](#graphene) - [GraphicsMagick](#graphicsmagick) - [graphite2](#graphite2) - [GraPhlAn](#graphlan) - [GraphMap](#graphmap) - [GraphMap2](#graphmap2) - [Graphviz](#graphviz) - [graphviz-python](#graphviz-python) - [GRASP](#grasp) - [GRASS](#grass) - [Greenlet](#greenlet) - [Grep](#grep) - [gretl](#gretl) - [grib_api](#grib_api) - [grid](#grid) - [GRIDSS](#gridss) - [GRIT](#grit) - [GRNBoost](#grnboost) - [groff](#groff) - [GroIMP](#groimp) - [GROMACS](#gromacs) - [GromacsWrapper](#gromacswrapper) - [Groovy](#groovy) - [gRPC](#grpc) - [GSEA](#gsea) - [gsettings-desktop-schemas](#gsettings-desktop-schemas) - [GSL](#gsl) - [gSOAP](#gsoap) - [gsport](#gsport) - [GST-plugins-bad](#gst-plugins-bad) - [GST-plugins-base](#gst-plugins-base) - [GStreamer](#gstreamer) - [gsutil](#gsutil) - [gsw](#gsw) - [GTDB-Tk](#gtdb-tk) - [GTK+](#gtk+) - [GTK2](#gtk2) - [GTK3](#gtk3) - [GTK4](#gtk4) - [GtkSourceView](#gtksourceview) - [GTOOL](#gtool) - [GTS](#gts) - [gubbins](#gubbins) - [guenomu](#guenomu) - [Guile](#guile) - [GULP](#gulp) - [Gurobi](#gurobi) - [GUSHR](#gushr) - [gzip](#gzip) +[G-PhoCS](#g-phocs) - [g2clib](#g2clib) - [g2lib](#g2lib) - [g2log](#g2log) - [Gaia](#gaia) - [GAMESS-US](#gamess-us) - [gap](#gap) - [GapCloser](#gapcloser) - [GapFiller](#gapfiller) - [gappa](#gappa) - [GAPPadder](#gappadder) - [GARLI](#garli) - [garnett](#garnett) - [GAT](#gat) - [GATB-Core](#gatb-core) - [GATE](#gate) - [GATK](#gatk) - [Gaussian](#gaussian) - [gawk](#gawk) - [gbasis](#gbasis) - [Gblocks](#gblocks) - [GBprocesS](#gbprocess) - [gbs2ploidy](#gbs2ploidy) - [gc](#gc) - [GC3Pie](#gc3pie) - [GCC](#gcc) - [GCCcore](#gcccore) - [gcccuda](#gcccuda) - [gcloud](#gcloud) - [GConf](#gconf) - [GCTA](#gcta) - [Gctf](#gctf) - [GD](#gd) - [GDAL](#gdal) - [GDB](#gdb) - [gdbgui](#gdbgui) - [gdbm](#gdbm) - [gdc-client](#gdc-client) - [GDCHART](#gdchart) - [GDCM](#gdcm) - [GDGraph](#gdgraph) - [gdist](#gdist) - [Gdk-Pixbuf](#gdk-pixbuf) - [GDRCopy](#gdrcopy) - [Geant4](#geant4) - [Geant4-data](#geant4-data) - [gearshifft](#gearshifft) - [GEGL](#gegl) - [GEM](#gem) - [GEM-library](#gem-library) - [gemelli](#gemelli) - [GEMMA](#gemma) - [gemmi](#gemmi) - [gencore_variant_detection](#gencore_variant_detection) - [GeneMark-ET](#genemark-et) - [GenerativeModels](#generativemodels) - [gengetopt](#gengetopt) - [GenMap](#genmap) - [Genome_Profiler](#genome_profiler) - [GenomeMapper](#genomemapper) - [genomepy](#genomepy) - [GenomeTester4](#genometester4) - [GenomeThreader](#genomethreader) - [GenomeTools](#genometools) - [GenomeWorks](#genomeworks) - [GenotypeHarmonizer](#genotypeharmonizer) - [genozip](#genozip) - [gensim](#gensim) - [geocube](#geocube) - [geopandas](#geopandas) - [geopy](#geopy) - [georges](#georges) - [GEOS](#geos) - [geosphere](#geosphere) - [Gerris](#gerris) - [GETORB](#getorb) - [GetOrganelle](#getorganelle) - [gettext](#gettext) - [gexiv2](#gexiv2) - [gfbf](#gfbf) - [GffCompare](#gffcompare) - [gffread](#gffread) - [gffutils](#gffutils) - [gflags](#gflags) - [GFOLD](#gfold) - [gh](#gh) - [GHC](#ghc) - [Ghostscript](#ghostscript) - [Gibbs2](#gibbs2) - [giflib](#giflib) - [gifsicle](#gifsicle) - [GIMIC](#gimic) - [gimkl](#gimkl) - [GimmeMotifs](#gimmemotifs) - [GIMP](#gimp) - [gimpi](#gimpi) - [gimpic](#gimpic) - [GIMPS](#gimps) - [giolf](#giolf) - [giolfc](#giolfc) - [Giotto-Suite](#giotto-suite) - [git](#git) - [git-extras](#git-extras) - [git-lfs](#git-lfs) - [GitPython](#gitpython) - [Givaro](#givaro) - [Giza](#giza) - [GKeyll](#gkeyll) - [gkmSVM](#gkmsvm) - [GL2PS](#gl2ps) - [Glade](#glade) - [glew](#glew) - [GLFW](#glfw) - [GLI](#gli) - [GLib](#glib) - [glib-networking](#glib-networking) - [glibc](#glibc) - [GLibmm](#glibmm) - [GLIMMER](#glimmer) - [GlimmerHMM](#glimmerhmm) - [GLIMPSE](#glimpse) - [GLM](#glm) - [GLM-AED](#glm-aed) - [GlobalArrays](#globalarrays) - [Globus-CLI](#globus-cli) - [GlobusConnectPersonal](#globusconnectpersonal) - [glog](#glog) - [GLPK](#glpk) - [glproto](#glproto) - [Glucose](#glucose) - [GMAP-GSNAP](#gmap-gsnap) - [GMP](#gmp) - [gmpich](#gmpich) - [gmpolf](#gmpolf) - [gmpy2](#gmpy2) - [gmsh](#gmsh) - [GMT](#gmt) - [gmvapich2](#gmvapich2) - [gmvolf](#gmvolf) - [GNU](#gnu) - [gnuplot](#gnuplot) - [GnuTLS](#gnutls) - [Go](#go) - [goalign](#goalign) - [GOATOOLS](#goatools) - [gobff](#gobff) - [GObject-Introspection](#gobject-introspection) - [goblf](#goblf) - [GOBNILP](#gobnilp) - [Godon](#godon) - [gofasta](#gofasta) - [golf](#golf) - [gomkl](#gomkl) - [gompi](#gompi) - [gompic](#gompic) - [google-java-format](#google-java-format) - [googletest](#googletest) - [gotree](#gotree) - [GP2C](#gp2c) - [GPAW](#gpaw) - [GPAW-setups](#gpaw-setups) - [gperf](#gperf) - [gperftools](#gperftools) - [gpustat](#gpustat) - [GPy](#gpy) - [GPyOpt](#gpyopt) - [GPyTorch](#gpytorch) - [Grace](#grace) - [Gradle](#gradle) - [gradunwarp](#gradunwarp) - [graph-tool](#graph-tool) - [GraphDB](#graphdb) - [Graphene](#graphene) - [GraphicsMagick](#graphicsmagick) - [graphite2](#graphite2) - [GraPhlAn](#graphlan) - [GraphMap](#graphmap) - [GraphMap2](#graphmap2) - [Graphviz](#graphviz) - [graphviz-python](#graphviz-python) - [GRASP](#grasp) - [GRASS](#grass) - [Greenlet](#greenlet) - [Grep](#grep) - [gretl](#gretl) - [grib_api](#grib_api) - [grid](#grid) - [GRIDSS](#gridss) - [GRIT](#grit) - [GRNBoost](#grnboost) - [groff](#groff) - [GroIMP](#groimp) - [GROMACS](#gromacs) - [GromacsWrapper](#gromacswrapper) - [Groovy](#groovy) - [gRPC](#grpc) - [GSEA](#gsea) - [gsettings-desktop-schemas](#gsettings-desktop-schemas) - [GSL](#gsl) - [gSOAP](#gsoap) - [gsport](#gsport) - [GST-plugins-bad](#gst-plugins-bad) - [GST-plugins-base](#gst-plugins-base) - [GStreamer](#gstreamer) - [gsutil](#gsutil) - [gsw](#gsw) - [GTDB-Tk](#gtdb-tk) - [GTK+](#gtk+) - [GTK2](#gtk2) - [GTK3](#gtk3) - [GTK4](#gtk4) - [GtkSourceView](#gtksourceview) - [GTOOL](#gtool) - [GTS](#gts) - [gubbins](#gubbins) - [guenomu](#guenomu) - [Guile](#guile) - [GULP](#gulp) - [Gurobi](#gurobi) - [GUSHR](#gushr) - [gzip](#gzip) ### G-PhoCS @@ -10756,6 +11008,16 @@ version |toolchain ---------|-------------- ``0.7.1``|``GCC/10.3.0`` +### GAPPadder + +GAPPadder is tool for closing gaps on draft genomes with short sequencing data + +*homepage*: + +version |versionsuffix |toolchain +------------|------------------|-------------- +``20170601``|``-Python-2.7.18``|``foss/2021b`` + ### GARLI GARLI, Genetic Algorithm for Rapid Likelihood Inference is a program for inferring phylogenetic trees. Using an approach similar to a classical genetic algorithm, it rapidly searches the space of evolutionary trees and model parameters to find the solution maximizing the likelihood score. It implements nucleotide, amino acid and codon-based models of sequence evolution, and runs on all platforms. @@ -10944,6 +11206,7 @@ version |toolchain ``8.0.4`` |``GCCcore/10.3.0`` ``8.2.0`` |``GCCcore/11.2.0`` ``8.2.2`` |``GCCcore/10.2.0``, ``GCCcore/11.3.0`` +``8.2.4`` |``GCCcore/12.3.0`` ### GC3Pie @@ -11029,6 +11292,7 @@ version |versionsuffix |toolchain ``12.2.0``| |``system`` ``12.3.0``| |``system`` ``13.1.0``| |``system`` +``13.2.0``| |``system`` ``system``| |``system`` ``system``|``-2.29`` |``system`` @@ -11075,6 +11339,7 @@ version |toolchain ``12.2.0``|``system`` ``12.3.0``|``system`` ``13.1.0``|``system`` +``13.2.0``|``system`` ``system``|``system`` ### gcccuda @@ -11111,8 +11376,8 @@ GConf is a system for storing application preferences. It is intended for user *homepage*: version |toolchain ----------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -``3.2.6``|``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2016a``, ``foss/2018b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b`` +---------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +``3.2.6``|``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2016a``, ``foss/2018b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b`` ### GCTA @@ -11211,6 +11476,7 @@ version |versionsuffix |toolchain ``10.2`` |``-Python-3.8.2`` |``GCCcore/9.3.0`` ``11.1`` | |``GCCcore/11.2.0`` ``12.1`` | |``GCCcore/11.3.0`` +``13.2`` | |``GCCcore/12.3.0`` ### gdbgui @@ -11314,7 +11580,7 @@ version |toolchain ``2.40.0`` |``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ``2.42.6`` |``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``2.42.8`` |``GCCcore/11.3.0`` -``2.42.10``|``GCCcore/12.2.0`` +``2.42.10``|``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### GDRCopy @@ -11461,6 +11727,16 @@ version |toolchain ``4.65``|``GCCcore/10.2.0`` ``4.71``|``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +### GenerativeModels + + + +*homepage*: + +version |versionsuffix |toolchain +---------|----------------|-------------- +``0.2.1``|``-CUDA-11.7.0``|``foss/2022a`` + ### gengetopt Gengetopt is a tool to write command line option parsing code for C programs. @@ -11663,6 +11939,17 @@ version |versionsuffix |toolchain ``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`` +``3.12.0``| |``GCC/12.3.0`` + +### geosphere + +Spherical trigonometry for geographic applications. That is, compute distances and related measures for angular (longitude/latitude) locations. + +*homepage*: + +version |versionsuffix|toolchain +----------|-------------|-------------- +``1.5-18``|``-R-4.2.1`` |``foss/2022a`` ### Gerris @@ -11716,6 +12003,7 @@ version |versionsuffix |toolchain ``0.20.1`` | |``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``system`` ``0.21`` | |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``system`` ``0.21.1`` | |``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``system`` +``0.22`` | |``GCCcore/13.2.0``, ``system`` ### gexiv2 @@ -11766,6 +12054,16 @@ version |toolchain ``0.11.6``|``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``0.12.7``|``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/12.2.0`` +### gffutils + +Gffutils is a Python package for working with and manipulating the GFF and GTF format files typically used for genomic annotations. + +*homepage*: + +version |toolchain +--------|-------------- +``0.12``|``foss/2022b`` + ### gflags The gflags package contains a C++ library that implements commandline flags processing. It includes built-in support for standard types such as string and the ability to define flags in the source file in which they are used. @@ -11809,6 +12107,7 @@ version |versionsuffix|toolchain ----------|-------------|---------- ``6.12.3``| |``system`` ``8.6.5`` |``-x86_64`` |``system`` +``9.2.2`` |``-x86_64`` |``system`` ### Ghostscript @@ -11816,22 +12115,23 @@ Ghostscript is a versatile processor for PostScript data with the ability to ren *homepage*: -version |versionsuffix |toolchain -----------|------------------|-------------------------------------------------- -``9.19`` | |``intel/2016a``, ``intel/2016b`` -``9.20`` | |``foss/2016b``, ``intel/2016b`` -``9.21`` | |``intel/2017a`` -``9.22`` | |``GCCcore/6.4.0``, ``foss/2017b``, ``intel/2017b`` -``9.22`` |``-cairo-1.14.12``|``GCCcore/6.4.0`` -``9.23`` | |``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``9.23`` |``-cairo-1.14.12``|``GCCcore/6.4.0`` -``9.27`` | |``GCCcore/8.2.0`` -``9.50`` | |``GCCcore/8.3.0`` -``9.52`` | |``GCCcore/9.3.0`` -``9.53.3``| |``GCCcore/10.2.0`` -``9.54.0``| |``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``9.56.1``| |``GCCcore/11.3.0`` -``10.0.0``| |``GCCcore/12.2.0`` +version |versionsuffix |toolchain +-----------|------------------|-------------------------------------------------- +``9.19`` | |``intel/2016a``, ``intel/2016b`` +``9.20`` | |``foss/2016b``, ``intel/2016b`` +``9.21`` | |``intel/2017a`` +``9.22`` | |``GCCcore/6.4.0``, ``foss/2017b``, ``intel/2017b`` +``9.22`` |``-cairo-1.14.12``|``GCCcore/6.4.0`` +``9.23`` | |``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``9.23`` |``-cairo-1.14.12``|``GCCcore/6.4.0`` +``9.27`` | |``GCCcore/8.2.0`` +``9.50`` | |``GCCcore/8.3.0`` +``9.52`` | |``GCCcore/9.3.0`` +``9.53.3`` | |``GCCcore/10.2.0`` +``9.54.0`` | |``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``9.56.1`` | |``GCCcore/11.3.0`` +``10.0.0`` | |``GCCcore/12.2.0`` +``10.01.2``| |``GCCcore/12.3.0`` ### Gibbs2 @@ -11850,9 +12150,9 @@ giflib is a library for reading and writing gif images. It is API and ABI compat *homepage*: version |toolchain ----------|---------------------------------------------------------------------------------------------------------------------------------------- +---------|------------------------------------------------------------------------------------------------------------------------------------------------------------ ``5.1.4``|``GCCcore/7.3.0``, ``GCCcore/8.2.0`` -``5.2.1``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``5.2.1``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ### gifsicle @@ -12074,6 +12374,16 @@ version |versionsuffix |toolchain ------------|-----------------|-------------- ``20220803``|``-Python-3.8.2``|``foss/2020a`` +### gkmSVM + +Gapped-Kmer Support Vector Machine. + +*homepage*: + +version |versionsuffix|toolchain +----------|-------------|-------------- +``0.82.0``|``-R-4.2.1`` |``foss/2022a`` + ### GL2PS GL2PS: an OpenGL to PostScript printing library @@ -12162,6 +12472,7 @@ version |toolchain ``2.69.1``|``GCCcore/11.2.0`` ``2.72.1``|``GCCcore/11.3.0`` ``2.75.0``|``GCCcore/12.2.0`` +``2.77.1``|``GCCcore/12.3.0`` ### glib-networking @@ -12235,11 +12546,11 @@ OpenGL Mathematics (GLM) is a header only C++ mathematics library for graphics s *homepage*: version |toolchain ------------|------------------------------------------------------------------------------------------------- +-----------|----------------------------------------------------------------------------------------------------------------------------------------- ``0.9.7.6``|``intel/2016a`` ``0.9.8.3``|``GCCcore/5.4.0``, ``GCCcore/7.3.0`` ``0.9.9.0``|``GCCcore/6.4.0`` -``0.9.9.8``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/8.3.0`` +``0.9.9.8``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/8.3.0`` ### GLM-AED @@ -12315,7 +12626,7 @@ 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``, ``GCCcore/12.2.0`` +``5.0`` |``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### glproto @@ -12403,7 +12714,7 @@ GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x *homepage*: version |versionsuffix |toolchain ------------|------------------|---------------------------------------------------------------------- +-----------|------------------|------------------------------------------------------------------------------------------ ``2.0.8`` |``-Python-2.7.13``|``intel/2017a`` ``2.0.8`` |``-Python-2.7.14``|``foss/2017b``, ``intel/2017b`` ``2.0.8`` |``-Python-3.6.3`` |``foss/2017b``, ``intel/2017b`` @@ -12411,7 +12722,8 @@ 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``, ``intel-compilers/2022.1.0`` +``2.1.2`` | |``GCC/11.2.0``, ``GCC/11.3.0``, ``intel-compilers/2021.4.0``, ``intel-compilers/2022.1.0`` +``2.1.5`` | |``GCC/12.3.0`` ### gmsh @@ -12498,6 +12810,7 @@ version |toolchain ``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`` +``5.4.8``|``GCCcore/12.3.0`` ### GnuTLS @@ -12601,6 +12914,7 @@ version |versionsuffix |toolchain ``1.68.0``| |``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``1.72.0``| |``GCCcore/11.3.0`` ``1.74.0``| |``GCCcore/12.2.0`` +``1.76.1``| |``GCCcore/12.3.0`` ### goblf @@ -12820,6 +13134,7 @@ version |toolchain ``2.8`` |``GCCcore/9.3.0`` ``2.9.1`` |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``2.10`` |``GCCcore/11.3.0`` +``2.12`` |``GCCcore/12.3.0`` ### gpustat @@ -12929,9 +13244,9 @@ 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``, ``GCCcore/12.2.0`` +``1.10.8``|``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### GraphicsMagick @@ -12995,7 +13310,7 @@ Graphviz is open source graph visualization software. Graph visualization is a *homepage*: version |versionsuffix |toolchain -----------|-------------------------|------------------------------- +----------|-------------------------|-------------------------------------- ``2.38.0``| |``foss/2016b``, ``intel/2016b`` ``2.40.1``| |``foss/2018b``, ``intel/2018a`` ``2.40.1``|``-Python-2.7.15`` |``foss/2018b`` @@ -13008,6 +13323,7 @@ version |versionsuffix |toolchain ``2.47.2``| |``GCCcore/10.3.0`` ``2.50.0``| |``GCCcore/11.2.0`` ``5.0.0`` | |``GCCcore/11.3.0`` +``8.1.0`` | |``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### graphviz-python @@ -13016,11 +13332,11 @@ 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`` -``0.20.1``| |``GCCcore/11.3.0`` +``0.20.1``| |``GCCcore/11.3.0``, ``GCCcore/12.3.0`` ### GRASP @@ -13051,12 +13367,12 @@ The greenlet package is a spin-off of Stackless, a version of CPython that suppo *homepage*: version |versionsuffix |toolchain -----------|------------------|--------------- +----------|------------------|------------------------------ ``0.4.9`` |``-Python-2.7.11``|``intel/2016a`` ``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`` +``2.0.2`` | |``foss/2022a``, ``foss/2022b`` ### Grep @@ -13230,6 +13546,7 @@ gRPC is a modern, open source, high-performance remote procedure call (RPC) fram version |toolchain ----------|------------------ ``1.44.0``|``GCCcore/11.2.0`` +``1.57.0``|``GCCcore/12.3.0`` ### GSEA @@ -13258,7 +13575,7 @@ 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`` @@ -13266,7 +13583,7 @@ 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``, ``GCC/12.2.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``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``, ``GCC/12.3.0``, ``intel-compilers/2021.2.0``, ``intel-compilers/2021.4.0`` ### gSOAP @@ -13298,6 +13615,7 @@ GStreamer is a library for constructing graphs of media-handling components. Th version |toolchain ----------|-------------- ``1.20.2``|``GCC/11.3.0`` +``1.22.5``|``GCC/12.2.0`` ### GST-plugins-base @@ -13315,7 +13633,8 @@ 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`` +``1.22.1`` |``GCC/12.2.0`` +``1.22.5`` |``GCC/12.3.0`` ### GStreamer @@ -13334,7 +13653,8 @@ 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`` +``1.22.1`` |``GCC/12.2.0`` +``1.22.5`` |``GCC/12.3.0`` ### gsutil @@ -13414,6 +13734,7 @@ version |toolchain ``3.24.31``|``GCCcore/11.2.0`` ``3.24.33``|``GCCcore/11.3.0`` ``3.24.35``|``GCCcore/12.2.0`` +``3.24.37``|``GCCcore/12.3.0`` ### GTK4 @@ -13421,9 +13742,10 @@ GTK+ is the primary library used to construct user interfaces in GNOME. It prov *homepage*: -version |toolchain ----------|-------------- -``4.7.0``|``GCC/11.3.0`` +version |toolchain +----------|-------------- +``4.7.0`` |``GCC/11.3.0`` +``4.11.3``|``GCC/12.2.0`` ### GtkSourceView @@ -13453,8 +13775,8 @@ GTS stands for the GNU Triangulated Surface Library. It is an Open Source Free *homepage*: version |toolchain -------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -``0.7.6`` |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2018b``, ``foss/2019b``, ``foss/2020a``, ``intel/2016a``, ``intel/2016b``, ``intel/2018a`` +------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +``0.7.6`` |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2018b``, ``foss/2019b``, ``foss/2020a``, ``intel/2016a``, ``intel/2016b``, ``intel/2018a`` ``20121130``|``foss/2017b`` ### gubbins @@ -13492,7 +13814,7 @@ version |toolchain ``2.2.7`` |``GCCcore/10.3.0`` ``3.0.7`` |``GCCcore/11.2.0`` ``3.0.8`` |``GCCcore/11.3.0`` -``3.0.9`` |``GCCcore/10.2.0`` +``3.0.9`` |``GCCcore/10.2.0``, ``GCCcore/12.3.0`` ### GULP @@ -13558,7 +13880,7 @@ version |toolchain ## H -[h4toh5](#h4toh5) - [H5hut](#h5hut) - [h5netcdf](#h5netcdf) - [h5py](#h5py) - [Hadoop](#hadoop) - [HAL](#hal) - [hanythingondemand](#hanythingondemand) - [HAPGEN2](#hapgen2) - [HarfBuzz](#harfbuzz) - [Harminv](#harminv) - [harmony](#harmony) - [HBase](#hbase) - [HD-BET](#hd-bet) - [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) - [HOOMD-blue](#hoomd-blue) - [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) - [HTSplotter](#htsplotter) - [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) - [h5netcdf](#h5netcdf) - [h5py](#h5py) - [Hadoop](#hadoop) - [HAL](#hal) - [hampel](#hampel) - [hanythingondemand](#hanythingondemand) - [HAPGEN2](#hapgen2) - [HarfBuzz](#harfbuzz) - [Harminv](#harminv) - [harmony](#harmony) - [hatchling](#hatchling) - [HBase](#hbase) - [HD-BET](#hd-bet) - [HDBSCAN](#hdbscan) - [HDDM](#hddm) - [HDF](#hdf) - [HDF-EOS](#hdf-eos) - [HDF-EOS2](#hdf-eos2) - [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) - [HOOMD-blue](#hoomd-blue) - [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) - [HTSplotter](#htsplotter) - [hub](#hub) - [humann](#humann) - [hunspell](#hunspell) - [hwloc](#hwloc) - [Hybpiper](#hybpiper) - [Hydra](#hydra) - [Hyperopt](#hyperopt) - [HyperQueue](#hyperqueue) - [hyperspy](#hyperspy) - [HyPhy](#hyphy) - [HyPo](#hypo) - [hypothesis](#hypothesis) - [Hypre](#hypre) ### h4toh5 @@ -13571,6 +13893,7 @@ version |versionsuffix |toolchain ---------|------------------------|------------------------------------------------ ``2.2.2``|``-linux-x86_64-static``|``system`` ``2.2.3``| |``foss/2018b``, ``gompi/2019b``, ``gompi/2020b`` +``2.2.5``| |``gompi/2022a`` ### H5hut @@ -13591,6 +13914,7 @@ A Python interface for the netCDF4 file-format that reads and writes local or re version |toolchain ---------|-------------- ``1.1.0``|``foss/2021b`` +``1.2.0``|``foss/2022a`` ### h5py @@ -13637,6 +13961,7 @@ version |versionsuffix |toolchain ``3.6.0`` | |``foss/2021b``, ``intel/2021b`` ``3.7.0`` | |``foss/2022a``, ``intel/2022a`` ``3.8.0`` | |``foss/2022b`` +``3.9.0`` | |``foss/2023a`` ### Hadoop @@ -13666,6 +13991,16 @@ version|toolchain -------|-------------- ``2.1``|``foss/2020b`` +### hampel + +The Hampel filter is generally used to detect anomalies in data with a timeseries structure. It basically consists of a sliding window of a parameterizable size. For each window, each observation will be compared with the Median Absolute Deviation (MAD). The observation will be considered an outlier in the case in which it exceeds the MAD by n times (the parameter n is also parameterizable). + +*homepage*: + +version |toolchain +---------|-------------- +``0.0.5``|``foss/2022a`` + ### hanythingondemand HanythingOnDemand (HOD) is a system for provisioning virtual Hadoop clusters over a large physical cluster. It uses the Torque resource manager to do node allocation. @@ -13726,7 +14061,7 @@ version |toolchain ``2.8.1``|``GCCcore/10.3.0`` ``2.8.2``|``GCCcore/11.2.0`` ``4.2.1``|``GCCcore/11.3.0`` -``5.3.1``|``GCCcore/12.2.0`` +``5.3.1``|``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### Harminv @@ -13750,6 +14085,16 @@ version |versionsuffix|toolchain ------------------|-------------|-------------- ``1.0.0-20200224``|``-R-4.0.0`` |``foss/2020a`` +### hatchling + +Extensible, standards compliant build backend used by Hatch, a modern, extensible Python project manager. + +*homepage*: + +version |toolchain +----------|------------------ +``1.18.0``|``GCCcore/12.3.0`` + ### HBase Apache HBase. is the Hadoop database, a distributed, scalable, big data store. @@ -13820,6 +14165,16 @@ version |toolchain --------|-------------------------------------------------------- ``2.20``|``GCCcore/10.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0`` +### HDF-EOS2 + +HDF-EOS libraries are software libraries built on HDF libraries. It supports three data structures for remote sensing data: Grid, Point and Swath. + +*homepage*: + +version|toolchain +-------|------------------ +``3.0``|``GCCcore/11.3.0`` + ### HDF-EOS5 HDF-EOS libraries are software libraries built on HDF libraries. It supports three data structures for remote sensing data: Grid, Point and Swath. @@ -13864,7 +14219,7 @@ version |versionsuffix|toolchain ``1.12.2`` |``-serial`` |``GCC/11.3.0``, ``NVHPC/22.7-CUDA-11.7.0`` ``1.13.1`` | |``gompi/2022a``, ``iimpi/2022a`` ``1.13.1`` |``-serial`` |``GCC/11.3.0`` -``1.14.0`` | |``gompi/2022b``, ``iimpi/2022b`` +``1.14.0`` | |``gompi/2022b``, ``gompi/2023a``, ``iimpi/2022b``, ``iimpi/2023a`` ### hdf5storage @@ -13967,7 +14322,7 @@ version |toolchain ``1.47.16``|``GCCcore/10.2.0`` ``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`` -``1.49.3`` |``GCCcore/11.4.0``, ``GCCcore/12.3.0``, ``GCCcore/13.1.0`` +``1.49.3`` |``GCCcore/11.4.0``, ``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``GCCcore/13.2.0`` ### HepMC3 @@ -14116,6 +14471,7 @@ Hiredis is a minimalistic C client library for the Redis database. It is minima version |toolchain ---------|-------------------------------------- ``1.0.2``|``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``1.2.0``|``GCCcore/12.3.0`` ### HISAT2 @@ -14222,9 +14578,10 @@ HOOMD-blue is a general-purpose particle simulation toolkit, implementing molecu *homepage*: -version |toolchain ----------|-------------- -``4.0.1``|``foss/2022a`` +version |versionsuffix |toolchain +---------|----------------|-------------- +``4.0.1``| |``foss/2022a`` +``4.0.1``|``-CUDA-11.7.0``|``foss/2022a`` ### Horovod @@ -14248,12 +14605,23 @@ version |versionsuffix |toolchain ``0.21.3``|``-PyTorch-1.7.1`` |``fosscuda/2020b`` ``0.21.3``|``-TensorFlow-2.3.1-Python-3.8.2`` |``foss/2020a``, ``fosscuda/2020a`` ``0.22.0``|``-PyTorch-1.8.1`` |``fosscuda/2020b`` +``0.22.1``|``-CUDA-11.3.1-TensorFlow-2.5.3`` |``foss/2021a`` ``0.22.1``|``-CUDA-11.3.1-TensorFlow-2.6.0`` |``foss/2021a`` ``0.22.1``|``-TensorFlow-2.5.0`` |``fosscuda/2020b`` ``0.22.1``|``-TensorFlow-2.5.0-Python-3.7.4`` |``fosscuda/2019b`` ``0.23.0``|``-CUDA-11.3.1-PyTorch-1.10.0`` |``foss/2021a`` ``0.23.0``|``-TensorFlow-2.5.0`` |``fosscuda/2020b`` ``0.25.0``|``-CUDA-11.3.1-PyTorch-1.10.0`` |``foss/2021a`` +``0.28.1``|``-CUDA-11.3.1-PyTorch-1.11.0`` |``foss/2021a`` +``0.28.1``|``-CUDA-11.3.1-PyTorch-1.12.1`` |``foss/2021a`` +``0.28.1``|``-CUDA-11.4.1-TensorFlow-2.7.1`` |``foss/2021b`` +``0.28.1``|``-CUDA-11.4.1-TensorFlow-2.8.4`` |``foss/2021b`` +``0.28.1``|``-CUDA-11.5.2-PyTorch-1.12.1`` |``foss/2021b`` +``0.28.1``|``-CUDA-11.7.0-PyTorch-1.12.0`` |``foss/2022a`` +``0.28.1``|``-CUDA-11.7.0-PyTorch-1.12.1`` |``foss/2022a`` +``0.28.1``|``-CUDA-11.7.0-TensorFlow-2.11.0`` |``foss/2022a`` +``0.28.1``|``-CUDA-11.7.0-TensorFlow-2.9.1`` |``foss/2022a`` +``0.28.1``|``-PyTorch-1.9.0`` |``fosscuda/2020b`` ### horton @@ -14315,10 +14683,10 @@ 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``, ``foss/2023a``, ``fosscuda/2019b``, ``fosscuda/2020a``, ``gobff/2020.06-amd``, ``gobff/2020.11``, ``gobff/2020b``, ``gobff/2021a``, ``goblf/2020b``, ``gomkl/2019a``, ``gomkl/2020b``, ``gomkl/2021a``, ``gomkl/2022a``, ``iibff/2020b``, ``intel/2019.02``, ``intel/2019.03``, ``intel/2019a``, ``intel/2019b``, ``intel/2020.00``, ``intel/2020.06-impi-18.5``, ``intel/2020.12``, ``intel/2020a``, ``intel/2020b``, ``intel/2021a``, ``intel/2021b``, ``intel/2022.00``, ``intel/2022.09``, ``intel/2022.11``, ``intel/2022.12``, ``intel/2022b``, ``intel/2023.03``, ``intel/2023a``, ``intelcuda/2019b``, ``intelcuda/2020a``, ``iomkl/2019.01``, ``iomkl/2021a``, ``iomkl/2021b`` +``2.3``|``CrayCCE/19.06``, ``CrayGNU/19.06``, ``CrayIntel/19.06``, ``Fujitsu/21.05``, ``foss/2019a``, ``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``foss/2022.05``, ``foss/2022.10``, ``foss/2022a``, ``foss/2022b``, ``foss/2023a``, ``fosscuda/2019b``, ``fosscuda/2020a``, ``gobff/2020.06-amd``, ``gobff/2020.11``, ``gobff/2020b``, ``gobff/2021a``, ``goblf/2020b``, ``gomkl/2019a``, ``gomkl/2020b``, ``gomkl/2021a``, ``gomkl/2022a``, ``iibff/2020b``, ``intel/2019.02``, ``intel/2019.03``, ``intel/2019a``, ``intel/2019b``, ``intel/2020.00``, ``intel/2020.06-impi-18.5``, ``intel/2020.12``, ``intel/2020a``, ``intel/2020b``, ``intel/2021a``, ``intel/2021b``, ``intel/2022.00``, ``intel/2022.09``, ``intel/2022.11``, ``intel/2022.12``, ``intel/2022a``, ``intel/2022b``, ``intel/2023.03``, ``intel/2023a``, ``intelcuda/2019b``, ``intelcuda/2020a``, ``iomkl/2019.01``, ``iomkl/2021a``, ``iomkl/2021b`` ### htop @@ -14327,10 +14695,11 @@ An interactive process viewer for Unix *homepage*: version |toolchain ----------|---------- +---------|------------------ ``2.0.0``|``system`` ``2.0.1``|``system`` ``3.2.1``|``system`` +``3.2.2``|``GCCcore/11.3.0`` ### HTSeq @@ -14378,6 +14747,7 @@ version |versionsuffix|toolchain ``1.14`` | |``GCC/11.2.0`` ``1.15.1`` | |``GCC/11.3.0`` ``1.17`` | |``GCC/12.2.0`` +``1.18`` | |``GCC/12.3.0`` ``20160107``|``-PacBio`` |``intel/2017a`` ### HTSplotter @@ -14457,16 +14827,28 @@ version |toolchain ``2.7.1`` |``GCCcore/11.3.0`` ``2.8.0`` |``GCCcore/12.2.0`` ``2.9.1`` |``GCCcore/12.3.0`` +``2.9.2`` |``GCCcore/13.2.0`` + +### Hybpiper + +HybPiper was designed for targeted sequence capture, in which DNA sequencing libraries are enriched for gene regions of interest, especially for phylogenetics. HybPiper is a suite of Python scripts/modules that wrap and connect bioinformatics tools in order to extract target sequences from high-throughput DNA sequencing reads. + +*homepage*: + +version |toolchain +---------|-------------- +``2.1.6``|``foss/2022b`` ### Hydra -Hydra is an open-source Python framework that simplifies the development of research and other complex applications. The key feature is the ability to dynamically create a hierarchical configuration by composition and override it through config files and the command line. The name Hydra comes from its ability to run multiple similar jobs - much like a Hydra with multiple heads. +Hydra is an open-source Python framework that simplifies the development of research and other complex applications. The key feature is the ability to dynamically create a hierarchical configuration by composition and override it through config files and the command line. The name Hydra comes from its ability to run multiple similar jobs - much like a Hydra with multiple heads. *homepage*: version |toolchain ---------|------------------ ``1.1.1``|``GCCcore/10.3.0`` +``1.3.2``|``GCCcore/11.3.0`` ### Hyperopt @@ -14546,6 +14928,7 @@ version |versionsuffix |toolchain ``6.14.6``| |``GCCcore/11.2.0`` ``6.46.7``| |``GCCcore/11.3.0`` ``6.68.2``| |``GCCcore/12.2.0`` +``6.82.0``| |``GCCcore/12.3.0`` ### Hypre @@ -14564,11 +14947,12 @@ version |toolchain ``2.24.0``|``intel/2021b`` ``2.25.0``|``foss/2022a`` ``2.27.0``|``foss/2022b`` +``2.29.0``|``foss/2023a`` ## I -[i-cisTarget](#i-cistarget) - [i-PI](#i-pi) - [I-TASSER](#i-tasser) - [i7z](#i7z) - [ICA-AROMA](#ica-aroma) - [icc](#icc) - [iccifort](#iccifort) - [iccifortcuda](#iccifortcuda) - [ichorCNA](#ichorcna) - [icmake](#icmake) - [iCount](#icount) - [ICU](#icu) - [IDBA-UD](#idba-ud) - [idemux](#idemux) - [ieeg-cli](#ieeg-cli) - [ifort](#ifort) - [IgBLAST](#igblast) - [IGMPlot](#igmplot) - [igraph](#igraph) - [IGV](#igv) - [igv-reports](#igv-reports) - [IGVTools](#igvtools) - [iibff](#iibff) - [iimkl](#iimkl) - [iimpi](#iimpi) - [iimpic](#iimpic) - [IJulia](#ijulia) - [ILAMB](#ilamb) - [IMa2](#ima2) - [IMa2p](#ima2p) - [imagecodecs](#imagecodecs) - [imageio](#imageio) - [ImageJ](#imagej) - [ImageMagick](#imagemagick) - [imake](#imake) - [Imath](#imath) - [IMB](#imb) - [imbalanced-learn](#imbalanced-learn) - [imgaug](#imgaug) - [imkl](#imkl) - [imkl-FFTW](#imkl-fftw) - [Imlib2](#imlib2) - [immunedeconv](#immunedeconv) - [IMOD](#imod) - [impi](#impi) - [IMPUTE2](#impute2) - [InChI](#inchi) - [indicators](#indicators) - [Inelastica](#inelastica) - [inferCNV](#infercnv) - [infercnvpy](#infercnvpy) - [Inferelator](#inferelator) - [Infernal](#infernal) - [Infomap](#infomap) - [inline](#inline) - [InParanoid](#inparanoid) - [inputproto](#inputproto) - [Inspector](#inspector) - [IntaRNA](#intarna) - [INTEGRATE](#integrate) - [INTEGRATE-Neo](#integrate-neo) - [intel](#intel) - [intel-compilers](#intel-compilers) - [IntelClusterChecker](#intelclusterchecker) - [intelcuda](#intelcuda) - [IntelDAAL](#inteldaal) - [IntelPython](#intelpython) - [InterProScan](#interproscan) - [InterProScan_data](#interproscan_data) - [intervaltree](#intervaltree) - [intervaltree-python](#intervaltree-python) - [intltool](#intltool) - [io_lib](#io_lib) - [ioapi](#ioapi) - [iodata](#iodata) - [iomkl](#iomkl) - [iompi](#iompi) - [IOR](#ior) - [IOzone](#iozone) - [IPM](#ipm) - [Ipopt](#ipopt) - [ipp](#ipp) - [IPy](#ipy) - [ipympl](#ipympl) - [ipyparallel](#ipyparallel) - [ipyrad](#ipyrad) - [IPython](#ipython) - [IQ-TREE](#iq-tree) - [Iris](#iris) - [IRkernel](#irkernel) - [irodsfs](#irodsfs) - [IronPython](#ironpython) - [ISA-L](#isa-l) - [ISL](#isl) - [isoCirc](#isocirc) - [IsoNet](#isonet) - [IsoSeq](#isoseq) - [ispc](#ispc) - [itac](#itac) - [ITK](#itk) - [itpp](#itpp) - [ITSTool](#itstool) - [ITSx](#itsx) - [iVar](#ivar) +[i-cisTarget](#i-cistarget) - [i-PI](#i-pi) - [I-TASSER](#i-tasser) - [i7z](#i7z) - [ICA-AROMA](#ica-aroma) - [icc](#icc) - [iccifort](#iccifort) - [iccifortcuda](#iccifortcuda) - [ichorCNA](#ichorcna) - [icmake](#icmake) - [iCount](#icount) - [ICU](#icu) - [IDBA-UD](#idba-ud) - [idemux](#idemux) - [ieeg-cli](#ieeg-cli) - [ifort](#ifort) - [IgBLAST](#igblast) - [IGMPlot](#igmplot) - [igraph](#igraph) - [IGV](#igv) - [igv-reports](#igv-reports) - [IGVTools](#igvtools) - [iibff](#iibff) - [iimkl](#iimkl) - [iimpi](#iimpi) - [iimpic](#iimpic) - [IJulia](#ijulia) - [ILAMB](#ilamb) - [IMa2](#ima2) - [IMa2p](#ima2p) - [imagecodecs](#imagecodecs) - [imageio](#imageio) - [ImageJ](#imagej) - [ImageMagick](#imagemagick) - [imake](#imake) - [Imath](#imath) - [IMB](#imb) - [imbalanced-learn](#imbalanced-learn) - [imgaug](#imgaug) - [imkl](#imkl) - [imkl-FFTW](#imkl-fftw) - [Imlib2](#imlib2) - [immunedeconv](#immunedeconv) - [IMOD](#imod) - [impi](#impi) - [IMPUTE2](#impute2) - [InChI](#inchi) - [indicators](#indicators) - [Inelastica](#inelastica) - [inferCNV](#infercnv) - [infercnvpy](#infercnvpy) - [Inferelator](#inferelator) - [Infernal](#infernal) - [Infomap](#infomap) - [inih](#inih) - [inline](#inline) - [InParanoid](#inparanoid) - [inputproto](#inputproto) - [Inspector](#inspector) - [IntaRNA](#intarna) - [INTEGRATE](#integrate) - [INTEGRATE-Neo](#integrate-neo) - [intel](#intel) - [intel-compilers](#intel-compilers) - [IntelClusterChecker](#intelclusterchecker) - [intelcuda](#intelcuda) - [IntelDAAL](#inteldaal) - [IntelPython](#intelpython) - [InterProScan](#interproscan) - [InterProScan_data](#interproscan_data) - [intervaltree](#intervaltree) - [intervaltree-python](#intervaltree-python) - [intltool](#intltool) - [io_lib](#io_lib) - [ioapi](#ioapi) - [iodata](#iodata) - [iomkl](#iomkl) - [iompi](#iompi) - [IOR](#ior) - [IOzone](#iozone) - [IPM](#ipm) - [Ipopt](#ipopt) - [ipp](#ipp) - [IPy](#ipy) - [ipympl](#ipympl) - [ipyparallel](#ipyparallel) - [ipyrad](#ipyrad) - [IPython](#ipython) - [IQ-TREE](#iq-tree) - [Iris](#iris) - [IRkernel](#irkernel) - [irodsfs](#irodsfs) - [IronPython](#ironpython) - [ISA-L](#isa-l) - [ISL](#isl) - [isoCirc](#isocirc) - [IsoformSwitchAnalyzeR](#isoformswitchanalyzer) - [IsoNet](#isonet) - [IsoQuant](#isoquant) - [IsoSeq](#isoseq) - [ispc](#ispc) - [itac](#itac) - [ITK](#itk) - [itpp](#itpp) - [ITSTool](#itstool) - [ITSx](#itsx) - [iVar](#ivar) ### i-cisTarget @@ -14759,6 +15143,7 @@ version |toolchain ``69.1``|``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``71.1``|``GCCcore/11.3.0`` ``72.1``|``GCCcore/12.2.0`` +``73.2``|``GCCcore/12.3.0`` ### IDBA-UD @@ -14864,6 +15249,7 @@ version |toolchain ``0.9.4`` |``foss/2021a`` ``0.9.5`` |``foss/2021b`` ``0.10.3``|``foss/2022a`` +``0.10.6``|``foss/2022b`` ### IGV @@ -14924,6 +15310,7 @@ version |toolchain ---------|---------- ``2018a``|``system`` ``2022b``|``system`` +``2023a``|``system`` ### iimpi @@ -15061,6 +15448,7 @@ version |versionsuffix |toolchain ``2.10.5``| |``foss/2021a`` ``2.13.5``| |``foss/2021b`` ``2.22.2``| |``foss/2022a`` +``2.31.1``| |``foss/2022b`` ### ImageJ @@ -15106,6 +15494,7 @@ version |versionsuffix |toolchain ``7.1.0-4`` | |``GCCcore/11.2.0`` ``7.1.0-37`` | |``GCCcore/11.3.0`` ``7.1.0-53`` | |``GCCcore/12.2.0`` +``7.1.1-15`` | |``GCCcore/12.3.0`` ### imake @@ -15373,6 +15762,8 @@ version |versionsuffix |toolchain ``1.3.3`` | |``foss/2020b``, ``foss/2021a`` ``1.3.3`` |``-Python-3.8.2`` |``foss/2020a`` ``1.10.1``|``-R-4.1.2`` |``foss/2021b`` +``1.12.0``|``-R-4.2.1`` |``foss/2022a`` +``1.14.2``|``-R-4.2.2`` |``foss/2022b`` ### infercnvpy @@ -15416,6 +15807,16 @@ version |toolchain ------------|-------------------- ``20190308``|``GCC/8.2.0-2.31.1`` +### inih + +Direct Rendering Manager runtime library. + +*homepage*: + +version|toolchain +-------|------------------ +``57`` |``GCCcore/12.3.0`` + ### inline Functionality to dynamically define R functions and S4 methods with 'inlined' C, C++ or Fortran code supporting the .C and .Call calling conventions. @@ -15650,8 +16051,8 @@ An interval tree can be used to efficiently find a set of numeric intervals ove *homepage*: version|toolchain --------|----------------------------------------------------------------------------- -``0.1``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` +-------|------------------------------------------------------------------------------------------------- +``0.1``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/9.3.0`` ### intervaltree-python @@ -15660,9 +16061,9 @@ A mutable, self-balancing interval tree. Queries may be by point, by range over *homepage*: version |versionsuffix |toolchain ----------|-----------------|-------------------------------------- +---------|-----------------|---------------------------------------------------------- ``3.0.2``|``-Python-3.6.6``|``foss/2018b`` -``3.1.0``| |``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``3.1.0``| |``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ### intltool @@ -15888,6 +16289,7 @@ version |versionsuffix |toolchain ``7.25.0``| |``GCCcore/10.3.0`` ``7.26.0``| |``GCCcore/11.2.0`` ``8.5.0`` | |``GCCcore/11.3.0`` +``8.14.0``| |``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### IQ-TREE @@ -15968,7 +16370,7 @@ version |toolchain isl is a library for manipulating sets and relations of integer points bounded by linear constraints. -*homepage*: +*homepage*: version |toolchain --------|--------------------------------------------------------- @@ -15978,6 +16380,7 @@ version |toolchain ``0.17``|``foss/2016a`` ``0.23``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` ``0.24``|``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``0.26``|``GCCcore/12.3.0`` ### isoCirc @@ -15989,6 +16392,16 @@ version |toolchain ---------|-------------- ``1.0.4``|``foss/2020b`` +### IsoformSwitchAnalyzeR + +Analysis of alternative splicing and isoform switches with predicted functional consequences (e.g. gain/loss of protein domains etc.) from quantification of all types of RNASeq by tools such as Kallisto, Salmon, StringTie, Cufflinks/Cuffdiff etc. + +*homepage*: + +version |versionsuffix|toolchain +----------|-------------|-------------- +``1.18.0``|``-R-4.2.1`` |``foss/2022a`` + ### IsoNet IsoNet stands for for ISOtropic reconstructioN of Electron Tomography. It trains deep convolutional neural networks to reconstruct meaningful contents in the mis sing wedge for electron tomography, and to increase signal-to-noise ratio, using the information learned from the original tomogram. The software requires tomograms as input. Observing at about 30A resolution, the IsoNet generated tomograms are largely isotropic. @@ -15999,6 +16412,16 @@ version |toolchain ---------------------------|------------------ ``0.1_20210822_04_674f67f``|``fosscuda/2020b`` +### IsoQuant + +IsoQuant is a tool for the genome-based analysis of long RNA reads, such as PacBio or Oxford Nanopores. IsoQuant allows to reconstruct and quantify transcript models with high precision and decent recall. If the reference annotation is given, IsoQuant also assigns reads to the annotated isoforms based on their intron and exon structure. IsoQuant further performs annotated gene, isoform, exon and intron quantification. If reads are grouped (e.g. according to cell type), counts are reported according to the provided grouping. + +*homepage*: + +version |toolchain +---------|-------------- +``3.3.0``|``foss/2022b`` + ### IsoSeq IsoSeq v3 contains the newest tools to identify transcripts in PacBio single-molecule sequencing data. Starting in SMRT Link v6.0.0, those tools power the IsoSeq GUI-based analysis application. A composable workflow of existing tools and algorithms, combined with a new clustering technique, allows to process the ever-increasing yield of PacBio machines with similar performance to IsoSeq versions 1 and 2. Starting with version 3.4, support for UMI and cell barcode based deduplication has been added. @@ -16113,7 +16536,7 @@ version |toolchain ## J -[JAGS](#jags) - [Jansson](#jansson) - [Jasmine](#jasmine) - [JasPer](#jasper) - [Java](#java) - [JavaFX](#javafx) - [jax](#jax) - [JAXFrontCE](#jaxfrontce) - [jbigkit](#jbigkit) - [Jellyfish](#jellyfish) - [jemalloc](#jemalloc) - [jhbuild](#jhbuild) - [JiTCODE](#jitcode) - [jModelTest](#jmodeltest) - [Jorg](#jorg) - [joypy](#joypy) - [jq](#jq) - [json-c](#json-c) - [json-fortran](#json-fortran) - [JSON-GLib](#json-glib) - [JsonCpp](#jsoncpp) - [JUBE](#jube) - [Judy](#judy) - [Julia](#julia) - [JUnit](#junit) - [jupyter-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) - [Jansson](#jansson) - [Jasmine](#jasmine) - [JasPer](#jasper) - [Java](#java) - [JavaFX](#javafx) - [jax](#jax) - [JAXFrontCE](#jaxfrontce) - [jbigkit](#jbigkit) - [Jellyfish](#jellyfish) - [jemalloc](#jemalloc) - [jhbuild](#jhbuild) - [JiTCODE](#jitcode) - [jModelTest](#jmodeltest) - [Jorg](#jorg) - [joypy](#joypy) - [jq](#jq) - [json-c](#json-c) - [json-fortran](#json-fortran) - [JSON-GLib](#json-glib) - [JsonCpp](#jsoncpp) - [JUBE](#jube) - [Judy](#judy) - [Julia](#julia) - [JUnit](#junit) - [Jupyter-bundle](#jupyter-bundle) - [jupyter-contrib-nbextensions](#jupyter-contrib-nbextensions) - [jupyter-matlab-proxy](#jupyter-matlab-proxy) - [jupyter-resource-usage](#jupyter-resource-usage) - [jupyter-server](#jupyter-server) - [jupyter-server-proxy](#jupyter-server-proxy) - [JupyterHub](#jupyterhub) - [JupyterLab](#jupyterlab) - [jupyterlab-lmod](#jupyterlab-lmod) - [jupyterlmod](#jupyterlmod) - [JupyterNotebook](#jupyternotebook) - [JWM](#jwm) - [jxrlib](#jxrlib) ### JAGS @@ -16232,6 +16655,7 @@ version |versionsuffix |toolchain ``11.0.8`` |``-aarch64`` |``system`` ``11.0.16`` | |``system`` ``11.0.18`` | |``system`` +``11.0.20`` | |``system`` ``13`` | |``system`` ``13.0.2`` | |``system`` ``15`` | |``system`` @@ -16387,9 +16811,9 @@ jq is a lightweight and flexible command-line JSON processor. *homepage*: version|toolchain --------|---------------------------------------------------------- +-------|------------------------------------------------------------------------------ ``1.5``|``GCCcore/10.2.0``, ``GCCcore/6.4.0`` -``1.6``|``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +``1.6``|``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### json-c @@ -16409,8 +16833,8 @@ JSON-Fortran: A Modern Fortran JSON API *homepage*: version |toolchain ----------|------------------ -``8.3.0``|``GCCcore/11.2.0`` +---------|-------------------------------------- +``8.3.0``|``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ### JSON-GLib @@ -16433,7 +16857,7 @@ version |toolchain ``0.10.7``|``GCCcore/8.2.0`` ``1.9.3`` |``GCCcore/8.3.0`` ``1.9.4`` |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` -``1.9.5`` |``GCCcore/11.3.0`` +``1.9.5`` |``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### JUBE @@ -16490,6 +16914,8 @@ version |versionsuffix |toolchain ``1.8.2``|``-linux-x86_64``|``system`` ``1.8.5``|``-linux-x86_64``|``system`` ``1.9.0``|``-linux-x86_64``|``system`` +``1.9.2``|``-linux-x86_64``|``system`` +``1.9.3``|``-linux-x86_64``|``system`` ### JUnit @@ -16518,6 +16944,16 @@ version |versionsuffix |toolchain ``4.12``|``-Java-1.8.0_77`` |``system`` ``4.12``|``-Java-1.8.0_92`` |``system`` +### Jupyter-bundle + +This bundle collects a range of Jupyter interfaces (Lab, Notebook and nbclassic), extensions (Jupyter Server Proxy, Jupyter Resource Monitor, Jupyter Lmod) and the JupyterHub. + +*homepage*: + +version |toolchain +------------|------------------ +``20230823``|``GCCcore/12.3.0`` + ### jupyter-contrib-nbextensions A collection of various notebook extensions for Jupyter @@ -16550,6 +16986,7 @@ version |toolchain ``0.6.1``|``GCCcore/10.3.0`` ``0.6.2``|``GCCcore/10.3.0`` ``0.6.3``|``GCCcore/11.3.0`` +``1.0.0``|``GCCcore/12.3.0`` ### jupyter-server @@ -16560,6 +16997,8 @@ The Jupyter Server provides the backend (i.e. the core services, APIs, and REST version |toolchain ----------|------------------ ``1.21.0``|``GCCcore/11.3.0`` +``2.7.0`` |``GCCcore/12.2.0`` +``2.7.2`` |``GCCcore/12.3.0`` ### jupyter-server-proxy @@ -16568,9 +17007,10 @@ Jupyter Server Proxy lets you run arbitrary external processes (such as RStudio, *homepage*: version |toolchain ----------|------------------ +---------|-------------------------------------- ``3.2.1``|``GCCcore/10.3.0`` -``3.2.2``|``GCCcore/11.3.0`` +``3.2.2``|``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +``4.0.0``|``GCCcore/12.3.0`` ### JupyterHub @@ -16585,6 +17025,8 @@ version |versionsuffix |toolchain ``1.1.0``| |``GCCcore/10.2.0`` ``1.4.1``| |``GCCcore/10.3.0`` ``3.0.0``| |``GCCcore/11.3.0`` +``4.0.1``| |``GCCcore/12.2.0`` +``4.0.2``| |``GCCcore/12.3.0`` ### JupyterLab @@ -16600,6 +17042,8 @@ version |versionsuffix |toolchain ``3.1.6`` | |``GCCcore/11.2.0`` ``3.2.8`` | |``GCCcore/10.3.0`` ``3.5.0`` | |``GCCcore/11.3.0`` +``4.0.3`` | |``GCCcore/12.2.0`` +``4.0.5`` | |``GCCcore/12.3.0`` ### jupyterlab-lmod @@ -16618,9 +17062,19 @@ Jupyter interactive notebook server extension that allows users to interact with *homepage*: version |toolchain ----------|------------------ +---------|-------------------------------------- ``3.0.0``|``GCCcore/11.3.0`` -``4.0.3``|``GCCcore/11.3.0`` +``4.0.3``|``GCCcore/11.3.0``, ``GCCcore/12.3.0`` + +### JupyterNotebook + +The Jupyter Notebook is the original web application for creating and sharing computational documents. It offers a simple, streamlined, document-centric experience. + +*homepage*: + +version |toolchain +---------|------------------ +``7.0.2``|``GCCcore/12.3.0`` ### JWM @@ -16731,8 +17185,8 @@ kallisto | bustools is a workflow for pre-processing single-cell RNA-seq data. *homepage*: version |toolchain -----------|-------------- -``0.27.3``|``foss/2021b`` +----------|------------------------------ +``0.27.3``|``foss/2021b``, ``foss/2022a`` ### kbproto @@ -16874,9 +17328,10 @@ KMA is a mapping method designed to map raw reads directly against redundant dat *homepage*: -version |toolchain -----------|--------------- -``1.2.22``|``intel/2019b`` +version |toolchain +-----------|--------------- +``1.2.22`` |``intel/2019b`` +``1.4.12a``|``GCC/12.2.0`` ### KMC @@ -16884,12 +17339,14 @@ KMC is a disk-based programm for counting k-mers from (possibly gzipped) FASTQ/F *homepage*: -version |versionsuffix |toolchain -------------|-----------------|------------------------------ -``3.1.0`` | |``foss/2018a``, ``foss/2018b`` -``3.1.1`` |``-Python-3.7.2``|``GCC/8.2.0-2.31.1`` -``3.1.2rc1``|``-Python-3.7.4``|``GCC/8.3.0`` -``3.2.1`` | |``GCC/11.2.0`` +version |versionsuffix |toolchain +------------|------------------|------------------------------ +``3.1.0`` | |``foss/2018a``, ``foss/2018b`` +``3.1.1`` |``-Python-3.7.2`` |``GCC/8.2.0-2.31.1`` +``3.1.2rc1``|``-Python-3.7.4`` |``GCC/8.3.0`` +``3.2.1`` | |``GCC/11.2.0`` +``3.2.1`` |``-Python-2.7.18``|``GCC/11.2.0`` +``3.2.2`` | |``GCC/12.2.0`` ### KMCP @@ -17049,7 +17506,7 @@ version |toolchain ## L -[L_RNA_scaffolder](#l_rna_scaffolder) - [Lace](#lace) - [LADR](#ladr) - [lagrangian-filtering](#lagrangian-filtering) - [LAME](#lame) - [LAMMPS](#lammps) - [lancet](#lancet) - [LAPACK](#lapack) - [LASSO-Python](#lasso-python) - [LAST](#last) - [LASTZ](#lastz) - [lavaan](#lavaan) - [LayoutParser](#layoutparser) - [LBFGS++](#lbfgs++) - [LCov](#lcov) - [LDC](#ldc) - [lDDT](#lddt) - [LeadIT](#leadit) - [leidenalg](#leidenalg) - [LEMON](#lemon) - [Leptonica](#leptonica) - [LERC](#lerc) - [less](#less) - [LevelDB](#leveldb) - [lftp](#lftp) - [LHAPDF](#lhapdf) - [LIANA](#liana) - [libaec](#libaec) - [libaio](#libaio) - [libarchive](#libarchive) - [libav](#libav) - [libavif](#libavif) - [libBigWig](#libbigwig) - [libbitmask](#libbitmask) - [libcdms](#libcdms) - [libcerf](#libcerf) - [libcint](#libcint) - [libcircle](#libcircle) - [libcmaes](#libcmaes) - [libconfig](#libconfig) - [libcpuset](#libcpuset) - [libcroco](#libcroco) - [libctl](#libctl) - [libdap](#libdap) - [libde265](#libde265) - [libdeflate](#libdeflate) - [libdivsufsort](#libdivsufsort) - [libdrm](#libdrm) - [libdrs](#libdrs) - [libdwarf](#libdwarf) - [libedit](#libedit) - [libelf](#libelf) - [libemf](#libemf) - [libepoxy](#libepoxy) - [libev](#libev) - [libevent](#libevent) - [libexif](#libexif) - [libfabric](#libfabric) - [libfdf](#libfdf) - [libffcall](#libffcall) - [libffi](#libffi) - [libFLAME](#libflame) - [libfontenc](#libfontenc) - [libgcrypt](#libgcrypt) - [libgd](#libgd) - [libgdiplus](#libgdiplus) - [libGDSII](#libgdsii) - [libgeotiff](#libgeotiff) - [libgit2](#libgit2) - [libglade](#libglade) - [libGLU](#libglu) - [libglvnd](#libglvnd) - [libgpg-error](#libgpg-error) - [libgpuarray](#libgpuarray) - [libGridXC](#libgridxc) - [libgtextutils](#libgtextutils) - [libharu](#libharu) - [libheif](#libheif) - [libibmad](#libibmad) - [libibumad](#libibumad) - [libICE](#libice) - [libiconv](#libiconv) - [libidn](#libidn) - [libidn2](#libidn2) - [Libint](#libint) - [LiBis](#libis) - [libjpeg-turbo](#libjpeg-turbo) - [libjxl](#libjxl) - [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) - [libWallModelledLES](#libwallmodelledles) - [libwebp](#libwebp) - [libwpe](#libwpe) - [libX11](#libx11) - [libXau](#libxau) - [libxc](#libxc) - [libxcb](#libxcb) - [libXcursor](#libxcursor) - [libXdamage](#libxdamage) - [libXdmcp](#libxdmcp) - [libXext](#libxext) - [libXfixes](#libxfixes) - [libXfont](#libxfont) - [libXft](#libxft) - [libXi](#libxi) - [libXinerama](#libxinerama) - [libxkbcommon](#libxkbcommon) - [libxml++](#libxml++) - [libxml2](#libxml2) - [libxml2-python](#libxml2-python) - [libXmu](#libxmu) - [libXp](#libxp) - [libXpm](#libxpm) - [libXrandr](#libxrandr) - [libXrender](#libxrender) - [libxslt](#libxslt) - [libxsmm](#libxsmm) - [libXt](#libxt) - [libXxf86vm](#libxxf86vm) - [libyaml](#libyaml) - [libzeep](#libzeep) - [libzip](#libzip) - [lie_learn](#lie_learn) - [lifelines](#lifelines) - [Lighter](#lighter) - [liknorm](#liknorm) - [likwid](#likwid) - [limix](#limix) - [LinBox](#linbox) - [line_profiler](#line_profiler) - [Lingeling](#lingeling) - [LISFLOOD-FP](#lisflood-fp) - [LittleCMS](#littlecms) - [LLDB](#lldb) - [LLVM](#llvm) - [LMDB](#lmdb) - [LMfit](#lmfit) - [Lmod](#lmod) - [LncLOOM](#lncloom) - [LocARNA](#locarna) - [LoFreq](#lofreq) - [Log-Log4perl](#log-log4perl) - [logaddexp](#logaddexp) - [LOHHLA](#lohhla) - [Loki](#loki) - [longestrunsubsequence](#longestrunsubsequence) - [longread_umi](#longread_umi) - [Longshot](#longshot) - [loompy](#loompy) - [loomR](#loomr) - [LoRDEC](#lordec) - [LPeg](#lpeg) - [LPJmL](#lpjml) - [lpsolve](#lpsolve) - [lrslib](#lrslib) - [LS-PrePost](#ls-prepost) - [LSD2](#lsd2) - [LSMS](#lsms) - [LTR_retriever](#ltr_retriever) - [LtrDetector](#ltrdetector) - [Lua](#lua) - [LuaJIT](#luajit) - [LuaJIT2-OpenResty](#luajit2-openresty) - [LuaRocks](#luarocks) - [Lucene-Geo-Gazetteer](#lucene-geo-gazetteer) - [LUMPY](#lumpy) - [LUSCUS](#luscus) - [lwgrp](#lwgrp) - [lxml](#lxml) - [lynx](#lynx) - [lz4](#lz4) - [LZO](#lzo) +[L_RNA_scaffolder](#l_rna_scaffolder) - [Lace](#lace) - [LADR](#ladr) - [lagrangian-filtering](#lagrangian-filtering) - [LAME](#lame) - [LAMMPS](#lammps) - [lancet](#lancet) - [LAPACK](#lapack) - [LASSO-Python](#lasso-python) - [LAST](#last) - [LASTZ](#lastz) - [lavaan](#lavaan) - [LayoutParser](#layoutparser) - [LBFGS++](#lbfgs++) - [LCov](#lcov) - [LDC](#ldc) - [lDDT](#lddt) - [LeadIT](#leadit) - [leafcutter](#leafcutter) - [leidenalg](#leidenalg) - [LEMON](#lemon) - [Leptonica](#leptonica) - [LERC](#lerc) - [less](#less) - [LevelDB](#leveldb) - [lftp](#lftp) - [LHAPDF](#lhapdf) - [LIANA](#liana) - [libaec](#libaec) - [libaio](#libaio) - [libarchive](#libarchive) - [libav](#libav) - [libavif](#libavif) - [libBigWig](#libbigwig) - [libbitmask](#libbitmask) - [libcdms](#libcdms) - [libcerf](#libcerf) - [libcint](#libcint) - [libcircle](#libcircle) - [libcmaes](#libcmaes) - [libconfig](#libconfig) - [libcpuset](#libcpuset) - [libcroco](#libcroco) - [libctl](#libctl) - [libdap](#libdap) - [libde265](#libde265) - [libdeflate](#libdeflate) - [libdivsufsort](#libdivsufsort) - [libdrm](#libdrm) - [libdrs](#libdrs) - [libdwarf](#libdwarf) - [libedit](#libedit) - [libelf](#libelf) - [libemf](#libemf) - [libepoxy](#libepoxy) - [libev](#libev) - [libevent](#libevent) - [libexif](#libexif) - [libfabric](#libfabric) - [libfdf](#libfdf) - [libffcall](#libffcall) - [libffi](#libffi) - [libFLAME](#libflame) - [libfontenc](#libfontenc) - [libgcrypt](#libgcrypt) - [libgd](#libgd) - [libgdiplus](#libgdiplus) - [libGDSII](#libgdsii) - [libgeotiff](#libgeotiff) - [libgit2](#libgit2) - [libglade](#libglade) - [libGLU](#libglu) - [libglvnd](#libglvnd) - [libgpg-error](#libgpg-error) - [libgpuarray](#libgpuarray) - [libGridXC](#libgridxc) - [libgtextutils](#libgtextutils) - [libharu](#libharu) - [libheif](#libheif) - [libibmad](#libibmad) - [libibumad](#libibumad) - [libICE](#libice) - [libiconv](#libiconv) - [libidn](#libidn) - [libidn2](#libidn2) - [Libint](#libint) - [LiBis](#libis) - [libjpeg-turbo](#libjpeg-turbo) - [libjxl](#libjxl) - [libleidenalg](#libleidenalg) - [LibLZF](#liblzf) - [libmad](#libmad) - [libmatheval](#libmatheval) - [libmaus2](#libmaus2) - [libmbd](#libmbd) - [libMemcached](#libmemcached) - [libmicrohttpd](#libmicrohttpd) - [libmo_unpack](#libmo_unpack) - [libmypaint](#libmypaint) - [libnsl](#libnsl) - [libobjcryst](#libobjcryst) - [libogg](#libogg) - [libopus](#libopus) - [libosmium](#libosmium) - [libpci](#libpci) - [libpciaccess](#libpciaccess) - [libplinkio](#libplinkio) - [libpng](#libpng) - [libpsl](#libpsl) - [libPSML](#libpsml) - [libpsortb](#libpsortb) - [libpspio](#libpspio) - [libpthread-stubs](#libpthread-stubs) - [libQGLViewer](#libqglviewer) - [libreadline](#libreadline) - [libRmath](#librmath) - [librosa](#librosa) - [librsb](#librsb) - [librsvg](#librsvg) - [librttopo](#librttopo) - [libsamplerate](#libsamplerate) - [libSBML](#libsbml) - [libsigc++](#libsigc++) - [libsigsegv](#libsigsegv) - [libSM](#libsm) - [libsndfile](#libsndfile) - [libsodium](#libsodium) - [LibSoup](#libsoup) - [libspatialindex](#libspatialindex) - [libspatialite](#libspatialite) - [libssh](#libssh) - [libStatGen](#libstatgen) - [LIBSVM](#libsvm) - [LIBSVM-Python](#libsvm-python) - [libtar](#libtar) - [libtasn1](#libtasn1) - [libtecla](#libtecla) - [LibTIFF](#libtiff) - [libtirpc](#libtirpc) - [libtool](#libtool) - [libtree](#libtree) - [libunistring](#libunistring) - [libunwind](#libunwind) - [libutempter](#libutempter) - [LibUUID](#libuuid) - [libuv](#libuv) - [libvdwxc](#libvdwxc) - [libvorbis](#libvorbis) - [libvori](#libvori) - [libWallModelledLES](#libwallmodelledles) - [libwebp](#libwebp) - [libwpe](#libwpe) - [libX11](#libx11) - [libXau](#libxau) - [libxc](#libxc) - [libxcb](#libxcb) - [libXcursor](#libxcursor) - [libXdamage](#libxdamage) - [libXdmcp](#libxdmcp) - [libXext](#libxext) - [libXfixes](#libxfixes) - [libXfont](#libxfont) - [libXft](#libxft) - [libXi](#libxi) - [libXinerama](#libxinerama) - [libxkbcommon](#libxkbcommon) - [libxml++](#libxml++) - [libxml2](#libxml2) - [libxml2-python](#libxml2-python) - [libXmu](#libxmu) - [libXp](#libxp) - [libXpm](#libxpm) - [libXrandr](#libxrandr) - [libXrender](#libxrender) - [libxslt](#libxslt) - [libxsmm](#libxsmm) - [libXt](#libxt) - [libXxf86vm](#libxxf86vm) - [libyaml](#libyaml) - [libzeep](#libzeep) - [libzip](#libzip) - [lie_learn](#lie_learn) - [lifelines](#lifelines) - [Lighter](#lighter) - [liknorm](#liknorm) - [likwid](#likwid) - [limix](#limix) - [LinBox](#linbox) - [line_profiler](#line_profiler) - [Lingeling](#lingeling) - [LISFLOOD-FP](#lisflood-fp) - [LittleCMS](#littlecms) - [LLDB](#lldb) - [LLVM](#llvm) - [LMDB](#lmdb) - [LMfit](#lmfit) - [Lmod](#lmod) - [LncLOOM](#lncloom) - [LocARNA](#locarna) - [LoFreq](#lofreq) - [Log-Log4perl](#log-log4perl) - [logaddexp](#logaddexp) - [LOHHLA](#lohhla) - [Loki](#loki) - [longestrunsubsequence](#longestrunsubsequence) - [longread_umi](#longread_umi) - [Longshot](#longshot) - [loompy](#loompy) - [loomR](#loomr) - [LoRDEC](#lordec) - [LPeg](#lpeg) - [LPJmL](#lpjml) - [lpsolve](#lpsolve) - [lrslib](#lrslib) - [LS-PrePost](#ls-prepost) - [LSD2](#lsd2) - [LSMS](#lsms) - [LTR_retriever](#ltr_retriever) - [LtrDetector](#ltrdetector) - [Lua](#lua) - [LuaJIT](#luajit) - [LuaJIT2-OpenResty](#luajit2-openresty) - [LuaRocks](#luarocks) - [Lucene-Geo-Gazetteer](#lucene-geo-gazetteer) - [LUMPY](#lumpy) - [LUSCUS](#luscus) - [lwgrp](#lwgrp) - [lxml](#lxml) - [lynx](#lynx) - [lz4](#lz4) - [LZO](#lzo) ### L_RNA_scaffolder @@ -17100,9 +17557,9 @@ 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/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`` +``3.100`` |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``intel/2017b`` ### LAMMPS @@ -17253,19 +17710,30 @@ version |toolchain ---------|---------- ``2.1.9``|``system`` +### leafcutter + +Leafcutter quantifies RNA splicing variation using short-read RNA-seq data. The core idea is to leverage spliced reads (reads that span an intron) to quantify (differential) intron usage across samples. The advantages of this approach include: easy detection of novel introns, modeling of more complex splicing events than exonic PSI, avoiding the challenge of isoform abundance estimation, simple, computationally efficient algorithms scaling to 100s or even 1000s of samples. For details please see our bioRxiv preprint and corresponding Nature Genetics publication. + +*homepage*: + +version |versionsuffix|toolchain +---------|-------------|-------------- +``0.2.9``|``-R-4.2.2`` |``foss/2022b`` + ### leidenalg Implementation of the Leiden algorithm for various quality functions to be used with igraph in Python. *homepage*: -version |versionsuffix |toolchain ----------|-----------------|---------------------------------- -``0.8.2``|``-Python-3.8.2``|``foss/2020a`` -``0.8.3``| |``foss/2020b``, ``fosscuda/2020b`` -``0.8.7``| |``foss/2021a`` -``0.8.8``| |``foss/2021b`` -``0.9.1``| |``foss/2022a`` +version |versionsuffix |toolchain +----------|-----------------|---------------------------------- +``0.8.2`` |``-Python-3.8.2``|``foss/2020a`` +``0.8.3`` | |``foss/2020b``, ``fosscuda/2020b`` +``0.8.7`` | |``foss/2021a`` +``0.8.8`` | |``foss/2021b`` +``0.9.1`` | |``foss/2022a`` +``0.10.1``| |``foss/2022b`` ### LEMON @@ -17297,9 +17765,9 @@ 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`` -``4.0.0``|``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +``4.0.0``|``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### less @@ -17362,8 +17830,8 @@ Libaec provides fast lossless compression of 1 up to 32 bit wide signed or unsig *homepage*: version |toolchain ----------|------------------------------------------------------------------------------ -``1.0.6``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +---------|-------------------------------------------------------------------------------------------------- +``1.0.6``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.3.0`` ### libaio @@ -17375,7 +17843,7 @@ version |toolchain -----------|------------------------------------------------------------------------------ ``0.3.111``|``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``0.3.112``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` -``0.3.113``|``GCCcore/12.2.0`` +``0.3.113``|``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### libarchive @@ -17409,9 +17877,9 @@ This library aims to be a friendly, portable C implementation of the AV1 Image F *homepage*: version |toolchain -----------|------------------------------ +----------|-------------------------------------------------- ``0.9.0`` |``foss/2020b`` -``0.11.1``|``foss/2021a``, ``foss/2022a`` +``0.11.1``|``GCCcore/11.3.0``, ``foss/2021a``, ``foss/2022a`` ### libBigWig @@ -17461,7 +17929,7 @@ 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`` +``2.3`` |``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### libcint @@ -17619,6 +18087,7 @@ version |toolchain ``2.4.107``|``GCCcore/11.2.0`` ``2.4.110``|``GCCcore/11.3.0`` ``2.4.114``|``GCCcore/12.2.0`` +``2.4.115``|``GCCcore/12.3.0`` ### libdrs @@ -17639,6 +18108,7 @@ The DWARF Debugging Information Format is of interest to programmers working on version |toolchain ------------|--------------------------------------------------- ``0.4.1`` |``GCCcore/11.3.0`` +``0.7.0`` |``GCCcore/12.3.0`` ``20140805``|``GCC/4.9.2`` ``20150310``|``GCC/4.9.2``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0`` ``20190529``|``GCCcore/8.2.0`` @@ -17686,12 +18156,12 @@ Epoxy is a library for handling OpenGL function pointer management for you *homepage*: version |toolchain -----------|-------------------------------------------------------- +----------|---------------------------------------------------------- ``1.5.2`` |``foss/2018a`` ``1.5.3`` |``GCCcore/8.2.0``, ``fosscuda/2018b`` ``1.5.4`` |``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``1.5.8`` |``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``1.5.10``|``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +``1.5.10``|``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### libev @@ -17710,11 +18180,11 @@ The libevent API provides a mechanism to execute a callback function when a spec *homepage*: version |toolchain -----------|---------------------------------------------------------------------------------------------------------------------------------- +----------|------------------------------------------------------------------------------------------------------------------------------------------------------ ``2.0.22``|``GCC/4.9.2``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.3``, ``GNU/4.9.3-2.25`` ``2.1.8`` |``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``system`` ``2.1.11``|``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``2.1.12``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``system`` +``2.1.12``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0``, ``system`` ### libexif @@ -17744,6 +18214,7 @@ version |toolchain ``1.15.1``|``GCCcore/11.3.0`` ``1.16.1``|``GCCcore/12.2.0`` ``1.18.0``|``GCCcore/12.3.0`` +``1.19.0``|``GCCcore/13.2.0`` ### libfdf @@ -17831,7 +18302,7 @@ 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``, ``GCCcore/12.2.0`` +``2.3.3``|``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### libgdiplus @@ -17880,6 +18351,7 @@ version |toolchain ``1.1.1``|``GCCcore/11.2.0`` ``1.4.3``|``GCCcore/11.3.0`` ``1.5.0``|``GCCcore/12.2.0`` +``1.7.1``|``GCCcore/12.3.0`` ### libglade @@ -17903,6 +18375,7 @@ version |versionsuffix |toolchain ``9.0.0``|``-Mesa-11.2.1``|``foss/2016a``, ``intel/2016a`` ``9.0.1``| |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``9.0.2``| |``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +``9.0.3``| |``GCCcore/12.3.0`` ### libglvnd @@ -17916,7 +18389,7 @@ version |toolchain ``1.3.2``|``GCCcore/10.2.0`` ``1.3.3``|``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``1.4.0``|``GCCcore/11.3.0`` -``1.6.0``|``GCCcore/12.2.0`` +``1.6.0``|``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### libgpg-error @@ -18075,7 +18548,7 @@ version |versionsuffix |toolchain ``2.4.2``| |``intel/2018a`` ``2.5.0``| |``gompi/2019a``, ``iimpi/2019a`` ``2.6.0``|``-lmax-6-cp2k``|``GCC/10.2.0``, ``GCC/10.3.0``, ``gompi/2020a``, ``iccifort/2020.4.304``, ``iimpi/2020a``, ``iimpi/2021a`` -``2.7.2``|``-lmax-6-cp2k``|``GCC/11.3.0`` +``2.7.2``|``-lmax-6-cp2k``|``GCC/11.3.0``, ``GCC/12.2.0`` ### LiBis @@ -18123,6 +18596,16 @@ version |toolchain ``0.6.1``|``GCCcore/10.2.0`` ``0.8.1``|``foss/2022a`` +### libleidenalg + +Implements the Leiden algorithm in C++ + +*homepage*: + +version |toolchain +----------|-------------- +``0.11.1``|``foss/2022b`` + ### LibLZF LibLZF is a very small data compression library. It consists of only two .c and two .h files and is very easy to incorporate into your own programs. The compression algorithm is very, very fast, yet still written in portable C. @@ -18223,9 +18706,9 @@ The libnsl package contains the public client interface for NIS(YP). *homepage*: version |toolchain ----------|------------------ +---------|-------------------------------------- ``1.3.0``|``GCCcore/10.3.0`` -``2.0.0``|``GCCcore/11.3.0`` +``2.0.0``|``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ### libobjcryst @@ -18292,7 +18775,7 @@ version |toolchain ``0.13.4``|``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b`` ``0.14`` |``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``0.16`` |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0`` -``0.17`` |``GCCcore/12.2.0``, ``GCCcore/12.3.0`` +``0.17`` |``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0`` ### libplinkio @@ -18545,6 +19028,7 @@ version |toolchain ``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`` +``1.2.2`` |``GCCcore/12.3.0`` ### libsodium @@ -18553,7 +19037,7 @@ Sodium is a modern, easy-to-use software library for encryption, decryption, sig *homepage*: version |toolchain -----------|---------------------------------------------------------------------------------------------------------------------------------------- +----------|------------------------------------------------------------------------------------------------------------------------------------------------------------ ``1.0.6`` |``intel/2016a`` ``1.0.8`` |``foss/2016a`` ``1.0.11``|``foss/2016b``, ``intel/2016b`` @@ -18561,7 +19045,7 @@ version |toolchain ``1.0.13``|``GCCcore/6.4.0``, ``foss/2017a`` ``1.0.16``|``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``1.0.17``|``GCCcore/8.2.0`` -``1.0.18``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``1.0.18``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ### LibSoup @@ -18637,6 +19121,16 @@ version |toolchain ``3.25``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``3.30``|``GCCcore/11.3.0`` +### LIBSVM-Python + +This tool provides a simple Python interface to LIBSVM, a library for support vector machines (http://www.csie.ntu.edu.tw/~cjlin/libsvm). The interface is very easy to use as the usage is the same as that of LIBSVM. The interface is developed with the built-in Python library "ctypes". + +*homepage*: + +version |toolchain +--------|-------------- +``3.30``|``foss/2022a`` + ### libtar C library for manipulating POSIX tar files @@ -18717,7 +19211,7 @@ version |toolchain ``2.4.2``|``GCC/4.8.2``, ``GCC/4.9.2`` ``2.4.5``|``GCC/4.8.4``, ``GCC/4.9.2`` ``2.4.6``|``FCC/4.5.0``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/5.2.0``, ``GCC/5.4.0-2.26``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GNU/4.9.2-2.25``, ``GNU/4.9.3-2.25``, ``GNU/5.1.0-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` -``2.4.7``|``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``system`` +``2.4.7``|``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``GCCcore/13.2.0``, ``system`` ### libtree @@ -18743,7 +19237,7 @@ version |toolchain ``0.9.7`` |``GCCcore/6.4.0`` ``0.9.10``|``GCCcore/10.3.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``1.0`` |``GCCcore/11.2.0``, ``GCCcore/11.3.0`` -``1.1`` |``GCCcore/10.2.0`` +``1.1`` |``GCCcore/10.2.0``, ``GCCcore/12.3.0`` ### libunwind @@ -18811,6 +19305,16 @@ version |toolchain ---------|---------------------------------------------------------------------------------------------------------------------- ``1.3.7``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` +### libvori + +C++ library implementing the Voronoi integration as well as the compressed bqb file format. The present version of libvori is a very early development version, which is hard-coded to work with the CP2k program package. + +*homepage*: + +version |toolchain +----------|-------------------------------------- +``220621``|``GCCcore/11.3.0``, ``GCCcore/12.2.0`` + ### libWallModelledLES libWallModelledLES is a library based on OpenFOAM® technology, extending the capabilities of OpenFOAM in the area of wall-modelled LES (WMLES). This is a turbulence modelling methodology, which allows to make LES cheaper by not resolving the inner region of turbulent boundary layers. @@ -18834,6 +19338,7 @@ version |toolchain ``1.1.0``|``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``1.2.0``|``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``1.2.4``|``GCCcore/11.3.0`` +``1.3.1``|``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### libwpe @@ -18844,6 +19349,7 @@ WPE is the reference WebKit port for embedded and low-consumption computer devic version |toolchain ----------|------------------ ``1.13.3``|``GCCcore/11.2.0`` +``1.14.1``|``GCCcore/11.3.0`` ### libX11 @@ -19037,6 +19543,7 @@ version |versionsuffix |toolchain ``2.9.13``| |``GCCcore/11.3.0`` ``2.10.3``| |``GCCcore/12.2.0`` ``2.11.4``| |``GCCcore/12.3.0`` +``2.11.5``| |``GCCcore/13.2.0`` ### libxml2-python @@ -19135,7 +19642,7 @@ version |toolchain ``1.10`` |``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2018b`` ``1.16.1``|``GCC/10.2.0``, ``GCC/9.3.0``, ``iccifort/2020.1.217``, ``iccifort/2020.4.304`` ``1.16.2``|``GCC/10.3.0``, ``intel-compilers/2021.2.0`` -``1.17`` |``GCC/11.2.0``, ``GCC/11.3.0`` +``1.17`` |``GCC/11.2.0``, ``GCC/11.3.0``, ``GCC/12.2.0`` ### libXt @@ -19322,6 +19829,7 @@ version |toolchain ``2.12`` |``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``2.13.1``|``GCCcore/11.3.0`` ``2.14`` |``GCCcore/12.2.0`` +``2.15`` |``GCCcore/12.3.0`` ### LLDB @@ -19363,6 +19871,7 @@ version |toolchain ``12.0.1``|``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``14.0.3``|``GCCcore/11.3.0`` ``15.0.5``|``GCCcore/12.2.0`` +``16.0.6``|``GCCcore/12.3.0`` ### LMDB @@ -19672,6 +20181,7 @@ version |toolchain ``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``, ``GCCcore/12.2.0`` +``5.4.6`` |``GCCcore/12.3.0`` ### LuaJIT @@ -19811,7 +20321,7 @@ version |toolchain ## M -[M1QN3](#m1qn3) - [M3GNet](#m3gnet) - [M4](#m4) - [MACH](#mach) - [MACS2](#macs2) - [MACSE](#macse) - [maeparser](#maeparser) - [MAFFT](#mafft) - [MAGeCK](#mageck) - [magick](#magick) - [Magics](#magics) - [magma](#magma) - [MAGMA-gene-analysis](#magma-gene-analysis) - [MagresPython](#magrespython) - [mahotas](#mahotas) - [MAJIQ](#majiq) - [make](#make) - [makedepend](#makedepend) - [makedepf90](#makedepf90) - [makeinfo](#makeinfo) - [MAKER](#maker) - [Mako](#mako) - [Mamba](#mamba) - [mandrake](#mandrake) - [mannkendall](#mannkendall) - [manta](#manta) - [mapDamage](#mapdamage) - [Maple](#maple) - [MapSplice](#mapsplice) - [Maq](#maq) - [MariaDB](#mariadb) - [MariaDB-connector-c](#mariadb-connector-c) - [MARS](#mars) - [Mash](#mash) - [MaSuRCA](#masurca) - [Mathematica](#mathematica) - [MathGL](#mathgl) - [MATIO](#matio) - [MATLAB](#matlab) - [MATLAB-Engine](#matlab-engine) - [matlab-proxy](#matlab-proxy) - [matplotlib](#matplotlib) - [matplotlib-inline](#matplotlib-inline) - [MATSim](#matsim) - [Maude](#maude) - [mauveAligner](#mauvealigner) - [Maven](#maven) - [mawk](#mawk) - [MaxBin](#maxbin) - [MaxQuant](#maxquant) - [mayavi](#mayavi) - [maze](#maze) - [MbedTLS](#mbedtls) - [MBROLA](#mbrola) - [mbuffer](#mbuffer) - [mc](#mc) - [MCL](#mcl) - [MCR](#mcr) - [mctc-lib](#mctc-lib) - [mcu](#mcu) - [MDAnalysis](#mdanalysis) - [MDBM](#mdbm) - [MDSplus](#mdsplus) - [MDSplus-Java](#mdsplus-java) - [MDSplus-Python](#mdsplus-python) - [mdtest](#mdtest) - [MDTraj](#mdtraj) - [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) - [MOABB](#moabb) - [MOABS](#moabs) - [MOB-suite](#mob-suite) - [ModelTest-NG](#modeltest-ng) - [modred](#modred) - [Molcas](#molcas) - [mold](#mold) - [Molden](#molden) - [molecularGSM](#moleculargsm) - [Molekel](#molekel) - [molmod](#molmod) - [Molpro](#molpro) - [MONA](#mona) - [MONAI](#monai) - [MONAI-Label](#monai-label) - [mongolite](#mongolite) - [Mono](#mono) - [Monocle3](#monocle3) - [moonjit](#moonjit) - [MOOSE](#moose) - [mordecai](#mordecai) - [MoreRONN](#moreronn) - [mosdepth](#mosdepth) - [Mothur](#mothur) - [motif](#motif) - [MotionCor2](#motioncor2) - [motionSegmentation](#motionsegmentation) - [MoviePy](#moviepy) - [MPB](#mpb) - [MPC](#mpc) - [MPFR](#mpfr) - [mpi4py](#mpi4py) - [MPICH](#mpich) - [MPICH2](#mpich2) - [mpifileutils](#mpifileutils) - [mpiP](#mpip) - [MPJ-Express](#mpj-express) - [mpmath](#mpmath) - [MrBayes](#mrbayes) - [mrcfile](#mrcfile) - [MRChem](#mrchem) - [MRCPP](#mrcpp) - [MRIcron](#mricron) - [MRPRESSO](#mrpresso) - [MRtrix](#mrtrix) - [msgpack-c](#msgpack-c) - [MSM](#msm) - [MSPC](#mspc) - [msprime](#msprime) - [mstore](#mstore) - [MTL4](#mtl4) - [MuJoCo](#mujoco) - [mujoco-py](#mujoco-py) - [multichoose](#multichoose) - [MultilevelEstimators](#multilevelestimators) - [MultiNest](#multinest) - [MultiQC](#multiqc) - [Multiwfn](#multiwfn) - [muMerge](#mumerge) - [MUMmer](#mummer) - [MUMPS](#mumps) - [muParser](#muparser) - [muparserx](#muparserx) - [MuPeXI](#mupexi) - [MUSCLE](#muscle) - [MuSiC](#music) - [MUST](#must) - [MuTect](#mutect) - [mutil](#mutil) - [MVAPICH2](#mvapich2) - [MView](#mview) - [mxml](#mxml) - [mxmlplus](#mxmlplus) - [MXNet](#mxnet) - [MyCC](#mycc) - [mygene](#mygene) - [MyMediaLite](#mymedialite) - [mympingpong](#mympingpong) - [Myokit](#myokit) - [mypy](#mypy) - [MySQL](#mysql) - [MySQL-python](#mysql-python) - [mysqlclient](#mysqlclient) +[M1QN3](#m1qn3) - [M3GNet](#m3gnet) - [M4](#m4) - [MACH](#mach) - [MACS2](#macs2) - [MACSE](#macse) - [maeparser](#maeparser) - [MAFFT](#mafft) - [MAGeCK](#mageck) - [magick](#magick) - [Magics](#magics) - [magma](#magma) - [MAGMA-gene-analysis](#magma-gene-analysis) - [MagresPython](#magrespython) - [mahotas](#mahotas) - [MAJIQ](#majiq) - [make](#make) - [makedepend](#makedepend) - [makedepf90](#makedepf90) - [makeinfo](#makeinfo) - [MAKER](#maker) - [Mako](#mako) - [Mamba](#mamba) - [mandrake](#mandrake) - [mannkendall](#mannkendall) - [manta](#manta) - [mapDamage](#mapdamage) - [Maple](#maple) - [MapSplice](#mapsplice) - [Maq](#maq) - [MariaDB](#mariadb) - [MariaDB-connector-c](#mariadb-connector-c) - [MARS](#mars) - [Mash](#mash) - [MaSuRCA](#masurca) - [Mathematica](#mathematica) - [MathGL](#mathgl) - [MATIO](#matio) - [MATLAB](#matlab) - [MATLAB-Engine](#matlab-engine) - [matlab-proxy](#matlab-proxy) - [matplotlib](#matplotlib) - [matplotlib-inline](#matplotlib-inline) - [MATSim](#matsim) - [maturin](#maturin) - [Maude](#maude) - [mauveAligner](#mauvealigner) - [Maven](#maven) - [mawk](#mawk) - [MaxBin](#maxbin) - [MaxQuant](#maxquant) - [mayavi](#mayavi) - [maze](#maze) - [MbedTLS](#mbedtls) - [MBROLA](#mbrola) - [mbuffer](#mbuffer) - [mc](#mc) - [MCL](#mcl) - [MCR](#mcr) - [mctc-lib](#mctc-lib) - [mcu](#mcu) - [MDAnalysis](#mdanalysis) - [MDBM](#mdbm) - [MDSplus](#mdsplus) - [MDSplus-Java](#mdsplus-java) - [MDSplus-Python](#mdsplus-python) - [mdtest](#mdtest) - [MDTraj](#mdtraj) - [meboot](#meboot) - [medaka](#medaka) - [medImgProc](#medimgproc) - [MedPy](#medpy) - [Meep](#meep) - [MEGA](#mega) - [MEGACC](#megacc) - [MEGAHIT](#megahit) - [Megalodon](#megalodon) - [MEGAN](#megan) - [Meld](#meld) - [MEM](#mem) - [MEME](#meme) - [memkind](#memkind) - [memory-profiler](#memory-profiler) - [MEMOTE](#memote) - [memtester](#memtester) - [meRanTK](#merantk) - [MERCKX](#merckx) - [Mercurial](#mercurial) - [Mesa](#mesa) - [Mesa-demos](#mesa-demos) - [meshalyzer](#meshalyzer) - [meshio](#meshio) - [meshtool](#meshtool) - [Meson](#meson) - [meson-python](#meson-python) - [Mesquite](#mesquite) - [MESS](#mess) - [MetaBAT](#metabat) - [MetaboAnalystR](#metaboanalystr) - [metaerg](#metaerg) - [MetaEuk](#metaeuk) - [MetaGeneAnnotator](#metageneannotator) - [Metagenome-Atlas](#metagenome-atlas) - [Metal](#metal) - [MetaMorpheus](#metamorpheus) - [MetaPhlAn](#metaphlan) - [MetaPhlAn2](#metaphlan2) - [metaWRAP](#metawrap) - [Metaxa2](#metaxa2) - [methylartist](#methylartist) - [MethylDackel](#methyldackel) - [methylpy](#methylpy) - [METIS](#metis) - [mgen](#mgen) - [mgltools](#mgltools) - [mhcflurry](#mhcflurry) - [mhcnuggets](#mhcnuggets) - [MicrobeAnnotator](#microbeannotator) - [microctools](#microctools) - [MiGEC](#migec) - [MIGRATE-N](#migrate-n) - [Mikado](#mikado) - [Miller](#miller) - [mimalloc](#mimalloc) - [MINC](#minc) - [MinCED](#minced) - [Mini-XML](#mini-xml) - [miniasm](#miniasm) - [minibar](#minibar) - [MiniCARD](#minicard) - [Miniconda2](#miniconda2) - [Miniconda3](#miniconda3) - [minieigen](#minieigen) - [Minimac4](#minimac4) - [minimap2](#minimap2) - [Minipolish](#minipolish) - [MiniSat](#minisat) - [minizip](#minizip) - [MINPACK](#minpack) - [MinPath](#minpath) - [MIRA](#mira) - [miRDeep2](#mirdeep2) - [Mish-Cuda](#mish-cuda) - [misha](#misha) - [MITgcmutils](#mitgcmutils) - [MITObim](#mitobim) - [MitoZ](#mitoz) - [MiXCR](#mixcr) - [MixMHC2pred](#mixmhc2pred) - [mkl-dnn](#mkl-dnn) - [mkl-service](#mkl-service) - [mkl_fft](#mkl_fft) - [MLC](#mlc) - [MLxtend](#mlxtend) - [mm-common](#mm-common) - [Mmg](#mmg) - [MMSEQ](#mmseq) - [MMseqs2](#mmseqs2) - [mmtf-cpp](#mmtf-cpp) - [MNE-Python](#mne-python) - [MOABB](#moabb) - [MOABS](#moabs) - [MOB-suite](#mob-suite) - [ModelTest-NG](#modeltest-ng) - [modred](#modred) - [Molcas](#molcas) - [mold](#mold) - [Molden](#molden) - [molecularGSM](#moleculargsm) - [Molekel](#molekel) - [molmod](#molmod) - [Molpro](#molpro) - [MONA](#mona) - [MONAI](#monai) - [MONAI-Label](#monai-label) - [mongolite](#mongolite) - [Mono](#mono) - [Monocle3](#monocle3) - [moonjit](#moonjit) - [MOOSE](#moose) - [mordecai](#mordecai) - [MoreRONN](#moreronn) - [mosdepth](#mosdepth) - [Mothur](#mothur) - [motif](#motif) - [MotionCor2](#motioncor2) - [motionSegmentation](#motionsegmentation) - [MoviePy](#moviepy) - [MPB](#mpb) - [MPC](#mpc) - [MPFR](#mpfr) - [mpi4py](#mpi4py) - [MPICH](#mpich) - [MPICH2](#mpich2) - [mpifileutils](#mpifileutils) - [mpiP](#mpip) - [MPJ-Express](#mpj-express) - [mpmath](#mpmath) - [MrBayes](#mrbayes) - [mrcfile](#mrcfile) - [MRChem](#mrchem) - [MRCPP](#mrcpp) - [MRIcron](#mricron) - [MRPRESSO](#mrpresso) - [MRtrix](#mrtrix) - [msgpack-c](#msgpack-c) - [MSM](#msm) - [MSPC](#mspc) - [msprime](#msprime) - [mstore](#mstore) - [MTL4](#mtl4) - [MuJoCo](#mujoco) - [mujoco-py](#mujoco-py) - [multichoose](#multichoose) - [MultilevelEstimators](#multilevelestimators) - [MultiNest](#multinest) - [MultiQC](#multiqc) - [Multiwfn](#multiwfn) - [muMerge](#mumerge) - [MUMmer](#mummer) - [MUMPS](#mumps) - [muParser](#muparser) - [muparserx](#muparserx) - [MuPeXI](#mupexi) - [MUSCLE](#muscle) - [MuSiC](#music) - [MUST](#must) - [MuTect](#mutect) - [mutil](#mutil) - [MVAPICH2](#mvapich2) - [MView](#mview) - [mxml](#mxml) - [mxmlplus](#mxmlplus) - [MXNet](#mxnet) - [MyCC](#mycc) - [mygene](#mygene) - [MyMediaLite](#mymedialite) - [mympingpong](#mympingpong) - [Myokit](#myokit) - [mypy](#mypy) - [MySQL](#mysql) - [MySQL-python](#mysql-python) - [mysqlclient](#mysqlclient) ### M1QN3 @@ -19845,7 +20355,7 @@ version |toolchain ``1.4.16``|``GCC/4.8.1``, ``GCC/4.8.2``, ``system`` ``1.4.17``|``GCC/4.8.2``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.2-binutils-2.25``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/4.9.3-binutils-2.25``, ``GCC/5.1.0-binutils-2.25``, ``GCC/5.2.0``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/4.9.4``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GNU/4.9.2-2.25``, ``GNU/4.9.3-2.25``, ``GNU/5.1.0-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` ``1.4.18``|``FCC/4.5.0``, ``GCCcore/10.1.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.1.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/7.4.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/8.4.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GCCcore/system``, ``system`` -``1.4.19``|``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/11.4.0``, ``GCCcore/12.1.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``GCCcore/9.4.0``, ``GCCcore/9.5.0``, ``system`` +``1.4.19``|``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/11.4.0``, ``GCCcore/12.1.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``GCCcore/13.2.0``, ``GCCcore/9.4.0``, ``GCCcore/9.5.0``, ``system`` ### MACH @@ -19870,6 +20380,7 @@ version |versionsuffix |toolchain ``2.1.2.1`` |``-Python-2.7.15``|``intel/2019a`` ``2.2.5`` |``-Python-3.6.6`` |``foss/2018b`` ``2.2.7.1`` | |``foss/2021b`` +``2.2.9.1`` | |``foss/2022b`` ### MACSE @@ -19961,6 +20472,7 @@ version |versionsuffix |toolchain ``2.6.2``|``-CUDA-11.4.1``|``foss/2021b`` ``2.6.2``|``-CUDA-11.5.2``|``foss/2021b`` ``2.6.2``|``-CUDA-11.7.0``|``foss/2022a`` +``2.7.1``|``-CUDA-12.0.0``|``foss/2022b`` ### MAGMA-gene-analysis @@ -19990,9 +20502,10 @@ Mahotas is a computer vision and image processing library for Python *homepage*: -version |versionsuffix |toolchain ----------|------------------|--------------- -``1.4.3``|``-Python-2.7.12``|``intel/2016b`` +version |versionsuffix |toolchain +----------|------------------|--------------- +``1.4.3`` |``-Python-2.7.12``|``intel/2016b`` +``1.4.13``| |``foss/2022a`` ### MAJIQ @@ -20046,11 +20559,12 @@ makeinfo is part of the Texinfo project, the official documentation format of th *homepage*: -version|versionsuffix|toolchain --------|-------------|------------------------------------------------------------------------------------------- -``6.7``| |``FCC/4.5.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``6.7``|``-minimal`` |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``6.8``| |``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +version |versionsuffix|toolchain +---------|-------------|------------------------------------------------------------------------------------------- +``6.7`` | |``FCC/4.5.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``6.7`` |``-minimal`` |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``6.8`` | |``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``7.0.3``| |``GCCcore/12.3.0`` ### MAKER @@ -20082,7 +20596,7 @@ version |versionsuffix |toolchain ``1.1.3``| |``GCCcore/10.2.0`` ``1.1.4``| |``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``1.2.0``| |``GCCcore/11.3.0`` -``1.2.4``| |``GCCcore/12.2.0`` +``1.2.4``| |``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### Mamba @@ -20093,6 +20607,7 @@ Mamba is a fast, robust, and cross-platform package manager. It runs on Windows, version |toolchain ------------|---------- ``4.14.0-0``|``system`` +``23.1.0-4``|``system`` ### mandrake @@ -20287,14 +20802,14 @@ matio is an C library for reading and writing Matlab MAT files. *homepage*: version |toolchain -----------|------------------ +----------|-------------------------------------- ``1.5.9`` |``GCCcore/5.4.0`` ``1.5.11``|``foss/2017b`` ``1.5.12``|``GCCcore/6.4.0`` ``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`` +``1.5.23``|``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ### MATLAB @@ -20395,6 +20910,7 @@ version |versionsuffix |toolchain ``3.5.1``| |``foss/2020b``, ``intel/2020b`` ``3.5.2``| |``foss/2021b``, ``foss/2022a``, ``intel/2022a`` ``3.7.0``| |``gfbf/2022b`` +``3.7.2``| |``gfbf/2023a`` ### matplotlib-inline @@ -20417,6 +20933,16 @@ version |versionsuffix |toolchain ``0.8.1``|``-Java-1.8.0_112``|``intel/2016b`` ``14.0`` |``-Java-11`` |``GCCcore/11.2.0``, ``system`` +### maturin + +This project is meant as a zero configuration replacement for setuptools-rust and milksnake. It supports building wheels for python 3.5+ on windows, linux, mac and freebsd, can upload them to pypi and has basic pypy and graalpy support. + +*homepage*: + +version |toolchain +---------|-------------------------------------- +``1.1.0``|``GCCcore/12.2.0``, ``GCCcore/12.3.0`` + ### Maude Maude is a high-performance reflective language and system supporting both equational and rewriting logic specification and programming for a wide range of applications. Maude has been influenced in important ways by the OBJ3 language, which can be regarded as an equational logic sublanguage. Besides supporting equational specification and programming, Maude also supports rewriting logic computation. @@ -20700,6 +21226,16 @@ version |versionsuffix |toolchain ``1.9.5``| |``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` ``1.9.7``| |``foss/2021a``, ``foss/2022a``, ``intel/2021b``, ``intel/2022a`` +### meboot + +Maximum entropy density based dependent data bootstrap. An algorithm is provided to create a population of time series (ensemble) without assuming stationarity. + +*homepage*: + +version |versionsuffix|toolchain +-----------|-------------|-------------- +``1.4-9.2``|``-R-4.2.1`` |``foss/2022a`` + ### medaka medaka is a tool to create a consensus sequence from nanopore sequencing data. @@ -20718,6 +21254,8 @@ version |versionsuffix |toolchain ``1.4.3`` |``-Python-3.7.4``|``foss/2019b`` ``1.5.0`` | |``foss/2021a`` ``1.6.0`` | |``foss/2021b`` +``1.8.1`` | |``foss/2022a`` +``1.9.1`` | |``foss/2022a`` ### medImgProc @@ -20923,6 +21461,7 @@ version |versionsuffix |toolchain ``5.7.1``|``-Python-3.8.2`` |``GCCcore/9.3.0`` ``5.8`` | |``GCCcore/10.3.0`` ``6.2`` | |``GCCcore/11.3.0`` +``6.4.5``| |``GCCcore/12.3.0`` ### Mesa @@ -20949,6 +21488,7 @@ version |toolchain ``21.1.7``|``GCCcore/11.2.0`` ``22.0.3``|``GCCcore/11.3.0`` ``22.2.4``|``GCCcore/12.2.0`` +``23.1.4``|``GCCcore/12.3.0`` ### Mesa-demos @@ -21029,6 +21569,7 @@ Python build backend (PEP 517) for Meson projects version |toolchain ----------|------------------ ``0.11.0``|``GCCcore/12.2.0`` +``0.13.2``|``GCCcore/12.3.0`` ### Mesquite @@ -21226,6 +21767,16 @@ version |versionsuffix|toolchain ``5.1.0``| |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``foss/2018b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` ``5.1.0``|``-32bitIDX``|``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` +### mgen + +Convenient matrix generation functions + +*homepage*: + +version |toolchain +---------|-------------- +``1.2.1``|``foss/2022a`` + ### mgltools The MGLTools software suite can be used for visualization and analysis of molecular structures and comprises the Python Molecular Viewer (PMV, a general purpose molecular viewer), AutoDockTools (ADT, a set of PMV commands specifically developed to support AutoDock users) and Vision (a visual programming environment). @@ -21300,6 +21851,16 @@ version |toolchain ``4.2.14``|``foss/2018a`` ``5.0.4`` |``foss/2021b`` +### Mikado + +Mikado is a lightweight Python3 pipeline to identify the most useful or “best” set of transcripts from multiple transcript assemblies. Our approach leverages transcript assemblies generated by multiple methods to define expressed loci, assign a representative transcript and return a set of gene models that selects against transcripts that are chimeric, fragmented or with short or disrupted CDS. + +*homepage*: + +version |toolchain +---------|-------------- +``2.3.4``|``foss/2022b`` + ### Miller Miller is like awk, sed, cut, join, and sort for name-indexed data such as CSV, TSV, and tabular JSON @@ -21412,6 +21973,7 @@ version |toolchain ``4.9.2`` |``system`` ``4.12.0`` |``system`` ``22.11.1-1``|``system`` +``23.5.2-0`` |``system`` ### minieigen @@ -21950,6 +22512,7 @@ version |versionsuffix |toolchain ---------|-------------------------|-------------- ``0.2.0``|``-Python-3.7.2-R-3.6.0``|``foss/2019a`` ``0.2.3``|``-R-4.0.3`` |``foss/2020b`` +``1.3.1``|``-R-4.2.1`` |``foss/2022a`` ### moonjit @@ -22087,6 +22650,7 @@ version |versionsuffix |toolchain ``1.0.3``|``-MPFR-3.1.6``|``foss/2017b``, ``intel/2017b`` ``1.1.0``| |``GCC/8.3.0``, ``GCC/9.3.0``, ``GCCcore/9.3.0`` ``1.2.1``| |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``1.3.1``| |``GCCcore/12.3.0`` ### MPFR @@ -22121,7 +22685,7 @@ 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`` +``3.1.4``| |``gompi/2022b``, ``gompi/2023a`` ### MPICH @@ -22273,6 +22837,7 @@ version |versionsuffix |toolchain ``3.0-rc-20191217``|``-Python-3.7.4`` |``foss/2019b`` ``3.0.0`` |``-Python-3.8.2`` |``foss/2020a`` ``3.0.3`` | |``foss/2021a`` +``3.0.4`` | |``foss/2022b`` ``3.0_RC2`` |``-Python-2.7.13``|``foss/2017a`` ``3.0_RC3`` |``-Python-2.7.14``|``intel/2018a`` @@ -22366,8 +22931,8 @@ generate multiset combinations (n multichoose k). *homepage*: version |toolchain ----------|----------------------------------------------------------------------------- -``1.0.3``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` +---------|------------------------------------------------------------------------------------------------- +``1.0.3``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/9.3.0`` ### MultilevelEstimators @@ -22462,6 +23027,7 @@ version |versionsuffix |toolchain ``5.4.1``|``-metis`` |``foss/2021b``, ``intel/2021b`` ``5.5.0``|``-metis`` |``foss/2021a`` ``5.5.1``|``-metis`` |``foss/2022a`` +``5.6.1``|``-metis`` |``foss/2022b``, ``foss/2023a`` ### muParser @@ -22607,6 +23173,7 @@ Flexible and Efficient Library for Deep Learning version |versionsuffix |toolchain ---------|--------------------------|-------------- ``0.9.3``|``-Python-2.7.12-R-3.3.3``|``foss/2016b`` +``1.9.1``| |``foss/2022a`` ### MyCC @@ -22710,7 +23277,7 @@ version |versionsuffix |toolchain ## N -[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) - [NanoStat](#nanostat) - [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](#n2v) - [NAG](#nag) - [NAGfor](#nagfor) - [NAMD](#namd) - [namedlist](#namedlist) - [nano](#nano) - [NanoCaller](#nanocaller) - [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) - [NanoStat](#nanostat) - [napari](#napari) - [NASM](#nasm) - [nauty](#nauty) - [nbclassic](#nbclassic) - [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) - [ncolor](#ncolor) - [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) - [nose3](#nose3) - [novaSTA](#novasta) - [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 @@ -22761,6 +23328,7 @@ version |versionsuffix |toolchain ``2.13``|``-mpi`` |``foss/2018b``, ``foss/2019b``, ``intel/2018b`` ``2.14``| |``fosscuda/2019b``, ``fosscuda/2020b`` ``2.14``|``-CUDA-11.3.1``|``foss/2021a`` +``2.14``|``-CUDA-11.7.0``|``foss/2022a`` ``2.14``|``-mpi`` |``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``foss/2022a``, ``intel/2020a`` ### namedlist @@ -22786,6 +23354,16 @@ version|toolchain ``7.1``|``GCCcore/12.2.0`` ``7.2``|``GCCcore/12.2.0`` +### NanoCaller + +NanoCaller is a computational method that integrates long reads in deep convolutional neural network for the detection of SNPs/indels from long-read sequencing data. + +*homepage*: + +version |toolchain +---------|-------------- +``3.4.1``|``foss/2022a`` + ### NanoComp Comparing runs of Oxford Nanopore sequencing data and alignments @@ -22941,6 +23519,7 @@ napari is a fast, interactive, multi-dimensional image viewer for Python. It's version |toolchain ----------|-------------- ``0.4.15``|``foss/2021b`` +``0.4.18``|``foss/2022a`` ### NASM @@ -22971,6 +23550,16 @@ version |toolchain ``2.7rc2``|``GCC/8.2.0-2.31.1`` ``2.7rc5``|``GCC/8.3.0`` +### nbclassic + +NbClassic provides a backwards compatible Jupyter Notebook interface that you can install side-by-side with the latest versions: That way, you can fearlessly upgrade without worrying about your classic extensions and customizations breaking. + +*homepage*: + +version |toolchain +---------|------------------ +``1.0.0``|``GCCcore/12.3.0`` + ### NBO The Natural Bond Orbital (NBO) program is a discovery tool for chemical insights from complex wavefunctions. @@ -23079,6 +23668,7 @@ version |toolchain ``1.15.1``|``GCCcore/9.3.0`` ``1.16`` |``GCC/10.3.0``, ``GCC/11.2.0`` ``1.17`` |``GCC/11.3.0`` +``1.18`` |``GCC/12.3.0`` ### NCIPLOT @@ -23128,6 +23718,16 @@ version |toolchain ``5.1.0``|``foss/2022a`` ``5.1.3``|``foss/2021a``, ``foss/2022a`` +### ncolor + +Fast remapping of instance labels 1,2,3,...,M to a smaller set of repeating, disjoint labels, 1,2,...,N. + +*homepage*: + +version |toolchain +---------|-------------- +``1.2.1``|``foss/2022a`` + ### ncompress Compress is a fast, simple LZW file compressor. Compress does not have the highest compression rate, but it is one of the fastest programs to compress data. Compress is the defacto standard in the UNIX community for compressing files. @@ -23151,7 +23751,7 @@ version|toolchain ``6.1``|``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``system`` ``6.2``|``FCC/4.5.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0``, ``system`` ``6.3``|``GCCcore/11.3.0``, ``GCCcore/12.1.0``, ``GCCcore/12.2.0``, ``system`` -``6.4``|``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``system`` +``6.4``|``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``GCCcore/13.2.0``, ``system`` ### ncview @@ -23162,7 +23762,7 @@ Ncview is a visual browser for netCDF format files. Typically you would use ncv version |toolchain ---------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ``2.1.7``|``foss/2017b``, ``foss/2018b``, ``foss/2019b``, ``gompi/2019a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b``, ``intel/2019b``, ``iomkl/2018b`` -``2.1.8``|``gompi/2020a``, ``gompi/2021a``, ``gompi/2021b``, ``gompi/2022a`` +``2.1.8``|``gompi/2020a``, ``gompi/2021a``, ``gompi/2021b``, ``gompi/2022a``, ``gompi/2023a`` ### nd2reader @@ -23282,6 +23882,7 @@ version |versionsuffix |toolchain ``4.8.0`` | |``gompi/2021a``, ``iimpi/2021a`` ``4.8.1`` | |``gompi/2021b``, ``iimpi/2021b`` ``4.9.0`` | |``gompi/2022a``, ``gompi/2022b``, ``iimpi/2022a``, ``iimpi/2022b`` +``4.9.2`` | |``gompi/2023a``, ``iimpi/2023a`` ### netCDF-C++ @@ -23300,11 +23901,11 @@ NetCDF (network Common Data Form) is a set of software libraries and machine-in *homepage*: version |versionsuffix |toolchain ----------|----------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +---------|----------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ``4.3.0``| |``foss/2018b``, ``gompi/2019a``, ``iimpi/2019a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2018a``, ``intel/2018b``, ``iomkl/2018b`` ``4.3.0``|``-HDF5-1.8.18``|``intel/2017a`` ``4.3.0``|``-HDF5-1.8.19``|``intel/2017b`` -``4.3.1``| |``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b``, ``gompi/2021a``, ``gompi/2021b``, ``gompi/2022a``, ``iimpi/2019b``, ``iimpi/2020a``, ``iimpi/2020b``, ``iimpi/2021a``, ``iimpi/2021b``, ``iimpi/2022a`` +``4.3.1``| |``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b``, ``gompi/2021a``, ``gompi/2021b``, ``gompi/2022a``, ``gompi/2023a``, ``iimpi/2019b``, ``iimpi/2020a``, ``iimpi/2020b``, ``iimpi/2021a``, ``iimpi/2021b``, ``iimpi/2022a`` ### netCDF-Fortran @@ -23324,6 +23925,7 @@ version |versionsuffix |toolchain ``4.5.2``| |``gompi/2019b``, ``gompi/2020a``, ``gompic/2019b``, ``gompic/2020a``, ``iimpi/2019b``, ``iimpi/2020a``, ``iimpic/2019b`` ``4.5.3``| |``gompi/2020b``, ``gompi/2021a``, ``gompi/2021b``, ``gompic/2020b``, ``iimpi/2020b``, ``iimpi/2021a``, ``iimpi/2021b`` ``4.6.0``| |``gompi/2022a``, ``gompi/2022b``, ``iimpi/2022a`` +``4.6.1``| |``gompi/2023a`` ### netcdf4-python @@ -23455,6 +24057,7 @@ version |toolchain ``3.7.3``|``GCCcore/11.2.0`` ``3.8`` |``GCCcore/11.3.0`` ``3.8.1``|``GCCcore/12.2.0`` +``3.9.1``|``GCCcore/12.3.0`` ### networkTools @@ -23494,6 +24097,7 @@ version |versionsuffix |toolchain ``2.8.4``| |``foss/2022a``, ``intel/2022a`` ``2.8.8``| |``gfbf/2022b`` ``3.0`` | |``gfbf/2022b`` +``3.1`` | |``gfbf/2023a`` ### NeuroKit @@ -23865,7 +24469,7 @@ 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``, ``GCCcore/12.2.0`` +``2.7.1``|``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### NLTK @@ -23922,6 +24526,7 @@ version |toolchain ``14.17.6``|``GCCcore/11.2.0`` ``16.15.1``|``GCCcore/11.3.0`` ``18.12.1``|``GCCcore/12.2.0`` +``18.17.1``|``GCCcore/12.3.0`` ### Normaliz @@ -23948,6 +24553,26 @@ version |versionsuffix |toolchain ``0.5.0``|``-Python-3.5.2`` |``intel/2016b`` ``0.6.0``|``-Python-3.6.1`` |``intel/2017a`` +### nose3 + +Nose extends unittest to make testing easier. + +*homepage*: + +version |toolchain +---------|------------------ +``1.3.8``|``GCCcore/11.3.0`` + +### novaSTA + +C++ version of subtomogram averaging (SA) scripts from TOM/AV3 package https://doi.org/10.1073/pnas.0409178102. Both CPU and GPU parallelization is supported although the latter performs significantly worse in terms of processing time (the code is not well optimized) and is thus not recommended for larger datasets. + +*homepage*: + +version|versionsuffix |toolchain +-------|----------------|-------------- +``1.1``|``-CUDA-11.7.0``|``foss/2022a`` + ### novoalign NovoCraft is a software bundle. NovoAlign: Market’s leading aligner with fully packed features designed for mapping of short reads onto a reference genome from Illumina, Ion Torrent, 454, and Color Spance NGS platforms. NovoAlignCS: Leading aligner packed with features designed to fully support reads from ABI SOLiD Color Space. NovoSort: Custom designed multi-threaded sort/merge tools for BAM files. NovoMethyl: It can analyse a set of alignments to identify methylated cytosine’s. WARNING! You can only use the sofware without a license (with some features disabled) if you are a non-profit organisation and use is for your own research or for use by students as part of their course. A license is required for use where these programs are part of a service where a third party is billed. @@ -24056,6 +24681,7 @@ version |toolchain ----------|------------------------------------------------------------------------------------------------ ``1.24.0``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``1.25.0``|``GCCcore/11.3.0`` +``1.26.0``|``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### ntCard @@ -24134,7 +24760,7 @@ version |toolchain ``2.0.12``|``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``2.0.13``|``GCCcore/10.2.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0`` ``2.0.14``|``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` -``2.0.16``|``GCCcore/12.2.0``, ``GCCcore/12.3.0`` +``2.0.16``|``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0`` ### numba @@ -24237,6 +24863,7 @@ version |versionsuffix |toolchain ``22.9`` |``-CUDA-11.7.0``|``system`` ``22.11``|``-CUDA-11.7.0``|``system`` ``23.1`` |``-CUDA-12.0.0``|``system`` +``23.7`` |``-CUDA-12.1.1``|``system`` ### nvofbf @@ -24314,7 +24941,7 @@ version |toolchain ## O -[Oases](#oases) - [OBITools](#obitools) - [OBITools3](#obitools3) - [OCaml](#ocaml) - [occt](#occt) - [oceanspy](#oceanspy) - [OCNet](#ocnet) - [Octave](#octave) - [Octopus-vcf](#octopus-vcf) - [OGDF](#ogdf) - [olaFlow](#olaflow) - [olego](#olego) - [OMA](#oma) - [OmegaFold](#omegafold) - [onedrive](#onedrive) - [ONNX](#onnx) - [ONNX-Runtime](#onnx-runtime) - [ont-fast5-api](#ont-fast5-api) - [ont-guppy](#ont-guppy) - [ont-remora](#ont-remora) - [OOMPA](#oompa) - [OPARI2](#opari2) - [Open-Data-Cube-Core](#open-data-cube-core) - [OpenAI-Gym](#openai-gym) - [OpenBabel](#openbabel) - [OpenBLAS](#openblas) - [openCARP](#opencarp) - [OpenCensus-python](#opencensus-python) - [OpenCoarrays](#opencoarrays) - [OpenColorIO](#opencolorio) - [OpenCV](#opencv) - [OpenEXR](#openexr) - [OpenFace](#openface) - [OpenFAST](#openfast) - [OpenFOAM](#openfoam) - [OpenFOAM-Extend](#openfoam-extend) - [OpenFold](#openfold) - [OpenForceField](#openforcefield) - [OpenImageIO](#openimageio) - [OpenJPEG](#openjpeg) - [OpenKIM-API](#openkim-api) - [openkim-models](#openkim-models) - [OpenMM](#openmm) - [OpenMM-PLUMED](#openmm-plumed) - [OpenMMTools](#openmmtools) - [OpenMolcas](#openmolcas) - [OpenMPI](#openmpi) - [OpenMS](#openms) - [OpenNLP](#opennlp) - [OpenPGM](#openpgm) - [OpenPIV](#openpiv) - [openpyxl](#openpyxl) - [OpenRefine](#openrefine) - [OpenSceneGraph](#openscenegraph) - [OpenSees](#opensees) - [OpenSlide](#openslide) - [openslide-python](#openslide-python) - [OpenSSL](#openssl) - [OpenStackClient](#openstackclient) - [OPERA](#opera) - [OPERA-MS](#opera-ms) - [OptaDOS](#optados) - [OptiType](#optitype) - [OptiX](#optix) - [Optuna](#optuna) - [OR-Tools](#or-tools) - [ORCA](#orca) - [ORFfinder](#orffinder) - [OrfM](#orfm) - [OrthoFinder](#orthofinder) - [OrthoMCL](#orthomcl) - [Osi](#osi) - [OSPRay](#ospray) - [OSU-Micro-Benchmarks](#osu-micro-benchmarks) - [OTF2](#otf2) - [OVITO](#ovito) - [ownCloud](#owncloud) - [oxDNA](#oxdna) - [oxford_asl](#oxford_asl) +[Oases](#oases) - [OBITools](#obitools) - [OBITools3](#obitools3) - [OCaml](#ocaml) - [occt](#occt) - [oceanspy](#oceanspy) - [OCNet](#ocnet) - [Octave](#octave) - [Octopus-vcf](#octopus-vcf) - [OGDF](#ogdf) - [olaFlow](#olaflow) - [olego](#olego) - [OMA](#oma) - [OmegaFold](#omegafold) - [Omnipose](#omnipose) - [onedrive](#onedrive) - [ONNX](#onnx) - [ONNX-Runtime](#onnx-runtime) - [ont-fast5-api](#ont-fast5-api) - [ont-guppy](#ont-guppy) - [ont-remora](#ont-remora) - [OOMPA](#oompa) - [OPARI2](#opari2) - [Open-Data-Cube-Core](#open-data-cube-core) - [OpenAI-Gym](#openai-gym) - [OpenBabel](#openbabel) - [OpenBLAS](#openblas) - [openCARP](#opencarp) - [OpenCensus-python](#opencensus-python) - [OpenCoarrays](#opencoarrays) - [OpenColorIO](#opencolorio) - [OpenCV](#opencv) - [OpenEXR](#openexr) - [OpenFace](#openface) - [OpenFAST](#openfast) - [OpenFOAM](#openfoam) - [OpenFOAM-Extend](#openfoam-extend) - [OpenFold](#openfold) - [OpenForceField](#openforcefield) - [OpenImageIO](#openimageio) - [OpenJPEG](#openjpeg) - [OpenKIM-API](#openkim-api) - [openkim-models](#openkim-models) - [OpenMM](#openmm) - [OpenMM-PLUMED](#openmm-plumed) - [OpenMMTools](#openmmtools) - [OpenMolcas](#openmolcas) - [OpenMPI](#openmpi) - [OpenMS](#openms) - [OpenNLP](#opennlp) - [OpenPGM](#openpgm) - [OpenPIV](#openpiv) - [openpyxl](#openpyxl) - [OpenRefine](#openrefine) - [OpenSceneGraph](#openscenegraph) - [OpenSees](#opensees) - [OpenSlide](#openslide) - [openslide-python](#openslide-python) - [OpenSSL](#openssl) - [OpenStackClient](#openstackclient) - [OPERA](#opera) - [OPERA-MS](#opera-ms) - [OptaDOS](#optados) - [Optax](#optax) - [OptiType](#optitype) - [OptiX](#optix) - [Optuna](#optuna) - [OR-Tools](#or-tools) - [ORCA](#orca) - [ORFfinder](#orffinder) - [OrfM](#orfm) - [OrthoFinder](#orthofinder) - [OrthoMCL](#orthomcl) - [Osi](#osi) - [OSPRay](#ospray) - [OSU-Micro-Benchmarks](#osu-micro-benchmarks) - [OTF2](#otf2) - [OVITO](#ovito) - [ownCloud](#owncloud) - [oxDNA](#oxdna) - [oxford_asl](#oxford_asl) ### Oases @@ -24470,6 +25097,17 @@ version |versionsuffix |toolchain ---------|----------------|-------------- ``1.1.0``|``-CUDA-11.7.0``|``foss/2022a`` +### Omnipose + +Omnipose is a general image segmentation tool that builds on Cellpose in a number of ways described in our paper. It works for both 2D and 3D images and on any imaging modality or cell shape, so long as you train it on representative images. + +*homepage*: + +version |versionsuffix |toolchain +---------|----------------|-------------- +``0.4.4``| |``foss/2022a`` +``0.4.4``|``-CUDA-11.7.0``|``foss/2022a`` + ### onedrive A free Microsoft OneDrive Client which supports OneDrive Personal, OneDrive for Business, OneDrive for Office365 and SharePoint. @@ -24514,7 +25152,7 @@ version |versionsuffix |toolchain ``3.3.0``|``-Python-3.7.4``|``foss/2019b`` ``4.0.0``| |``foss/2021a`` ``4.0.2``| |``foss/2021a``, ``foss/2021b`` -``4.1.1``| |``foss/2022b`` +``4.1.1``| |``foss/2022a``, ``foss/2022b`` ### ont-guppy @@ -24558,11 +25196,11 @@ OPARI2, the successor of Forschungszentrum Juelich's OPARI, is a source-to-sour *homepage*: 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/11.2.0``, ``GCCcore/11.3.0`` +``2.0.7``|``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### Open-Data-Cube-Core @@ -24584,6 +25222,7 @@ version |versionsuffix |toolchain ----------|-----------------|-------------- ``0.17.1``|``-Python-3.7.4``|``foss/2019b`` ``0.21.0``| |``foss/2021b`` +``0.26.2``| |``foss/2022a`` ### OpenBabel @@ -24715,6 +25354,7 @@ version |versionsuffix |toolchain ``4.5.5`` |``-contrib`` |``foss/2021b`` ``4.6.0`` |``-CUDA-11.7.0-contrib`` |``foss/2022a`` ``4.6.0`` |``-contrib`` |``foss/2022a`` +``4.8.0`` |``-contrib`` |``foss/2022b`` ### OpenEXR @@ -24774,6 +25414,7 @@ version |versionsuffix|toolchain ``4.x-20170904``| |``intel/2016b`` ``5.0`` | |``foss/2017b``, ``intel/2017a``, ``intel/2017b`` ``5.0-20180108``| |``foss/2018a``, ``intel/2017b``, ``intel/2018a`` +``5.0-20180606``| |``foss/2019b`` ``6`` | |``foss/2018b``, ``foss/2019b``, ``intel/2018a`` ``7`` | |``foss/2019b`` ``7`` |``-20200508``|``foss/2019b`` @@ -24782,6 +25423,7 @@ version |versionsuffix|toolchain ``9`` | |``foss/2021a``, ``intel/2021a`` ``10`` | |``foss/2022a`` ``10`` |``-20230119``|``foss/2022a`` +``11`` | |``foss/2022a`` ``v1606+`` | |``foss/2018b`` ``v1612+`` | |``foss/2018b`` ``v1712`` | |``foss/2017b``, ``intel/2017b`` @@ -24845,6 +25487,7 @@ version |toolchain ``2.0.12`` |``gompi/2019b``, ``iimpi/2019b`` ``2.1.12.0``|``gompi/2020a``, ``iimpi/2020a`` ``2.3.17.0``|``GCC/11.3.0`` +``2.4.14.0``|``GCC/12.3.0`` ### OpenJPEG @@ -24988,7 +25631,7 @@ version |versionsuffix |toolchain ``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``, ``GCC/12.3.0`` +``4.1.5`` | |``GCC/12.2.0``, ``GCC/12.3.0``, ``intel-compilers/2023.1.0`` ``system``| |``GCC/system-2.29`` ### OpenMS @@ -25018,8 +25661,8 @@ OpenPGM is an open source implementation of the Pragmatic General Multicast (PGM *homepage*: version |toolchain ------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -``5.2.122``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` +-----------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ +``5.2.122``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` ### OpenPIV @@ -25170,6 +25813,16 @@ version |toolchain -----------|-------------- ``1.2.380``|``GCC/11.3.0`` +### Optax + +Optax is a gradient processing and optimization library for JAX. + +*homepage*: + +version |toolchain +---------|-------------- +``0.1.7``|``foss/2022a`` + ### OptiType OptiType is a novel HLA genotyping algorithm based on integer linear programming, capable of producing accurate 4-digit HLA genotyping predictions from NGS data by simultaneously selecting all major and minor HLA Class I alleles. @@ -25297,6 +25950,7 @@ version |toolchain ``0.108.5``|``GCCcore/7.3.0``, ``foss/2018b`` ``0.108.6``|``GCC/10.3.0``, ``GCCcore/10.2.0`` ``0.108.7``|``GCC/11.2.0`` +``0.108.8``|``GCC/12.2.0`` ### OSPRay @@ -25329,7 +25983,7 @@ version |versionsuffix |toolchain ``5.9`` |``-CUDA-11.7.0``|``gompi/2022a`` ``5.9`` |``-ROCm-4.5.0`` |``gompi/2021b`` ``6.2`` | |``gompi/2022.10``, ``gompi/2022b`` -``7.1-1``| |``gompi/2023a`` +``7.1-1``| |``gompi/2023a``, ``iimpi/2023a`` ### OTF2 @@ -25344,6 +25998,7 @@ version |toolchain ``2.3`` |``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ``3.0`` |``GCCcore/11.3.0`` ``3.0.2``|``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``3.0.3``|``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### OVITO @@ -25389,7 +26044,7 @@ version |versionsuffix |toolchain ## P -[p11-kit](#p11-kit) - [p4-phylogenetics](#p4-phylogenetics) - [p4est](#p4est) - [p4vasp](#p4vasp) - [p7zip](#p7zip) - [packmol](#packmol) - [pagmo](#pagmo) - [pairsnp](#pairsnp) - [PAL2NAL](#pal2nal) - [paladin](#paladin) - [PALEOMIX](#paleomix) - [PAML](#paml) - [panaroo](#panaroo) - [pandapower](#pandapower) - [pandas](#pandas) - [pandas-datareader](#pandas-datareader) - [PANDAseq](#pandaseq) - [Pandoc](#pandoc) - [Panedr](#panedr) - [Pango](#pango) - [pangolin](#pangolin) - [panito](#panito) - [PAPI](#papi) - [parallel](#parallel) - [parallel-fastq-dump](#parallel-fastq-dump) - [Parallel-Hashmap](#parallel-hashmap) - [ParallelIO](#parallelio) - [parameterized](#parameterized) - [parasail](#parasail) - [Paraver](#paraver) - [ParaView](#paraview) - [Parcels](#parcels) - [PARI-GP](#pari-gp) - [ParmEd](#parmed) - [ParMETIS](#parmetis) - [ParMGridGen](#parmgridgen) - [PartitionFinder](#partitionfinder) - [pasta](#pasta) - [PaStiX](#pastix) - [pastml](#pastml) - [patch](#patch) - [patchelf](#patchelf) - [path.py](#path.py) - [PAUP](#paup) - [pauvre](#pauvre) - [pbbam](#pbbam) - [pbcopper](#pbcopper) - [pbdagcon](#pbdagcon) - [pbipa](#pbipa) - [pbmm2](#pbmm2) - [pbs_python](#pbs_python) - [PBSuite](#pbsuite) - [PCAngsd](#pcangsd) - [PCC](#pcc) - [PCL](#pcl) - [PCMSolver](#pcmsolver) - [PCRaster](#pcraster) - [PCRE](#pcre) - [PCRE2](#pcre2) - [pdsh](#pdsh) - [PDT](#pdt) - [PEAR](#pear) - [PennCNV](#penncnv) - [PEPT](#pept) - [Percolator](#percolator) - [Perl](#perl) - [perl-app-cpanminus](#perl-app-cpanminus) - [Perl-bundle-CPAN](#perl-bundle-cpan) - [Perl4-CoreLibs](#perl4-corelibs) - [Perseus](#perseus) - [PEST++](#pest++) - [PETSc](#petsc) - [petsc4py](#petsc4py) - [PfamScan](#pfamscan) - [pfind](#pfind) - [pftoolsV3](#pftoolsv3) - [pFUnit](#pfunit) - [PGDSpider](#pgdspider) - [PGI](#pgi) - [PGPLOT](#pgplot) - [PHANOTATE](#phanotate) - [Phantompeakqualtools](#phantompeakqualtools) - [PHASE](#phase) - [PHAST](#phast) - [Phenoflow](#phenoflow) - [PheWAS](#phewas) - [PheWeb](#pheweb) - [PhiPack](#phipack) - [PHLAT](#phlat) - [phonemizer](#phonemizer) - [phono3py](#phono3py) - [phonopy](#phonopy) - [photontorch](#photontorch) - [phototonic](#phototonic) - [PHYLIP](#phylip) - [PhyloBayes-MPI](#phylobayes-mpi) - [phylokit](#phylokit) - [phylonaut](#phylonaut) - [PhyloPhlAn](#phylophlan) - [PhyML](#phyml) - [phyx](#phyx) - [picard](#picard) - [PICI-LIGGGHTS](#pici-liggghts) - [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) - [plinkliftover](#plinkliftover) - [plinkQC](#plinkqc) - [PLINKSEQ](#plinkseq) - [plot1cell](#plot1cell) - [Ploticus](#ploticus) - [plotly](#plotly) - [plotly-orca](#plotly-orca) - [plotly.py](#plotly.py) - [PLplot](#plplot) - [PLUMED](#plumed) - [PLY](#ply) - [PMIx](#pmix) - [pmt](#pmt) - [pmx](#pmx) - [PnetCDF](#pnetcdf) - [pocl](#pocl) - [pod5-file-format](#pod5-file-format) - [poetry](#poetry) - [polars](#polars) - [polymake](#polymake) - [pomkl](#pomkl) - [pompi](#pompi) - [poppler](#poppler) - [popscle](#popscle) - [popt](#popt) - [Porechop](#porechop) - [porefoam](#porefoam) - [poretools](#poretools) - [Portcullis](#portcullis) - [Postgres-XL](#postgres-xl) - [PostgreSQL](#postgresql) - [POT](#pot) - [POV-Ray](#pov-ray) - [powerlaw](#powerlaw) - [pp-sketchlib](#pp-sketchlib) - [PPanGGOLiN](#ppanggolin) - [PPfold](#ppfold) - [ppl](#ppl) - [pplacer](#pplacer) - [pplpy](#pplpy) - [PRANK](#prank) - [PRC](#prc) - [preCICE](#precice) - [PREQUAL](#prequal) - [preseq](#preseq) - [presto](#presto) - [pretty-yaml](#pretty-yaml) - [Primer3](#primer3) - [PRINSEQ](#prinseq) - [printproto](#printproto) - [PRISMS-PF](#prisms-pf) - [ProbABEL](#probabel) - [prodigal](#prodigal) - [ProFit](#profit) - [PROJ](#proj) - [ProjectQ](#projectq) - [prokka](#prokka) - [prompt-toolkit](#prompt-toolkit) - [proovread](#proovread) - [propy](#propy) - [Proteinortho](#proteinortho) - [ProtHint](#prothint) - [protobuf](#protobuf) - [protobuf-python](#protobuf-python) - [protozero](#protozero) - [PRSice](#prsice) - [pscom](#pscom) - [PSI](#psi) - [PSI4](#psi4) - [PsiCLASS](#psiclass) - [PSIPRED](#psipred) - [psmc](#psmc) - [psmpi](#psmpi) - [psmpi2](#psmpi2) - [PSolver](#psolver) - [PSORTb](#psortb) - [psrecord](#psrecord) - [pstoedit](#pstoedit) - [psutil](#psutil) - [psycopg2](#psycopg2) - [ptemcee](#ptemcee) - [PTESFinder](#ptesfinder) - [pubtcrs](#pubtcrs) - [pugixml](#pugixml) - [pullseq](#pullseq) - [PuLP](#pulp) - [purge_dups](#purge_dups) - [py](#py) - [py-aiger](#py-aiger) - [py-aiger-bdd](#py-aiger-bdd) - [py-cpuinfo](#py-cpuinfo) - [py3Dmol](#py3dmol) - [pyABC](#pyabc) - [PyAMG](#pyamg) - [PyAPS3](#pyaps3) - [pybedtools](#pybedtools) - [PyBerny](#pyberny) - [pyBigWig](#pybigwig) - [pybind11](#pybind11) - [pybinding](#pybinding) - [PyBioLib](#pybiolib) - [PyCairo](#pycairo) - [PyCalib](#pycalib) - [pyccel](#pyccel) - [PyCharm](#pycharm) - [PyCheMPS2](#pychemps2) - [Pychopper](#pychopper) - [PyCifRW](#pycifrw) - [PyClone](#pyclone) - [pycma](#pycma) - [pycocotools](#pycocotools) - [pycodestyle](#pycodestyle) - [PyCogent](#pycogent) - [pycoQC](#pycoqc) - [PyCUDA](#pycuda) - [PycURL](#pycurl) - [PyDamage](#pydamage) - [pydantic](#pydantic) - [PyDatastream](#pydatastream) - [pydicom](#pydicom) - [pydicom-seg](#pydicom-seg) - [pydlpoly](#pydlpoly) - [pydot](#pydot) - [pyEGA3](#pyega3) - [pyenchant](#pyenchant) - [PyEVTK](#pyevtk) - [pyFAI](#pyfai) - [pyfaidx](#pyfaidx) - [pyfasta](#pyfasta) - [PyFFmpeg](#pyffmpeg) - [pyFFTW](#pyfftw) - [pyfits](#pyfits) - [PyFMI](#pyfmi) - [PyFoam](#pyfoam) - [PyFR](#pyfr) - [PyFrag](#pyfrag) - [pygccxml](#pygccxml) - [pyGenomeTracks](#pygenometracks) - [PyGEOS](#pygeos) - [pyGIMLi](#pygimli) - [Pygments](#pygments) - [pygmo](#pygmo) - [PyGObject](#pygobject) - [pygraphviz](#pygraphviz) - [pygrib](#pygrib) - [PyGTK](#pygtk) - [PyGTS](#pygts) - [PyGWAS](#pygwas) - [pyhdf](#pyhdf) - [PyImageJ](#pyimagej) - [pyiron](#pyiron) - [Pyke3](#pyke3) - [pylift](#pylift) - [Pylint](#pylint) - [pyMannKendall](#pymannkendall) - [pymatgen](#pymatgen) - [pymatgen-db](#pymatgen-db) - [pymbar](#pymbar) - [PyMC3](#pymc3) - [pymca](#pymca) - [pymemcache](#pymemcache) - [PyMOL](#pymol) - [PyNAST](#pynast) - [pyobjcryst](#pyobjcryst) - [PyOD](#pyod) - [Pyomo](#pyomo) - [PyOpenCL](#pyopencl) - [PyOpenGL](#pyopengl) - [pyparsing](#pyparsing) - [pyperf](#pyperf) - [pyplusplus](#pyplusplus) - [pypmt](#pypmt) - [PYPOWER](#pypower) - [pyproj](#pyproj) - [PyPSA](#pypsa) - [pyqstem](#pyqstem) - [PyQt](#pyqt) - [PyQt5](#pyqt5) - [PyQtGraph](#pyqtgraph) - [pyradiomics](#pyradiomics) - [PyRe](#pyre) - [PyRETIS](#pyretis) - [pyringe](#pyringe) - [pyro-api](#pyro-api) - [pyro-ppl](#pyro-ppl) - [Pyro4](#pyro4) - [PyRosetta](#pyrosetta) - [Pysam](#pysam) - [pysamstats](#pysamstats) - [PySAT](#pysat) - [pyScaf](#pyscaf) - [pySCENIC](#pyscenic) - [PySCF](#pyscf) - [pysheds](#pysheds) - [pyshp](#pyshp) - [PySide2](#pyside2) - [pyslim](#pyslim) - [pysndfx](#pysndfx) - [Pysolar](#pysolar) - [pyspoa](#pyspoa) - [pysqlite](#pysqlite) - [PyStan](#pystan) - [pysteps](#pysteps) - [pystran](#pystran) - [PyTables](#pytables) - [pytesseract](#pytesseract) - [pytest](#pytest) - [pytest-benchmark](#pytest-benchmark) - [pytest-cpp](#pytest-cpp) - [pytest-flakefinder](#pytest-flakefinder) - [pytest-rerunfailures](#pytest-rerunfailures) - [pytest-shard](#pytest-shard) - [pytest-xdist](#pytest-xdist) - [PYTHIA](#pythia) - [Python](#python) - [Python-bundle](#python-bundle) - [python-docx](#python-docx) - [python-hl7](#python-hl7) - [python-igraph](#python-igraph) - [python-irodsclient](#python-irodsclient) - [python-isal](#python-isal) - [python-Levenshtein](#python-levenshtein) - [python-libsbml](#python-libsbml) - [python-louvain](#python-louvain) - [python-mujoco](#python-mujoco) - [python-parasail](#python-parasail) - [python-telegram-bot](#python-telegram-bot) - [python-weka-wrapper3](#python-weka-wrapper3) - [python-xxhash](#python-xxhash) - [pythran](#pythran) - [PyTorch](#pytorch) - [PyTorch-bundle](#pytorch-bundle) - [pytorch-CycleGAN-pix2pix](#pytorch-cyclegan-pix2pix) - [PyTorch-Geometric](#pytorch-geometric) - [PyTorch-Ignite](#pytorch-ignite) - [PyTorch-Image-Models](#pytorch-image-models) - [PyTorch-Lightning](#pytorch-lightning) - [PyTorch3D](#pytorch3d) - [PyVCF](#pyvcf) - [PyVCF3](#pyvcf3) - [pyWannier90](#pywannier90) - [PyWavelets](#pywavelets) - [PyWBGT](#pywbgt) - [PyYAML](#pyyaml) - [PyZMQ](#pyzmq) +[p11-kit](#p11-kit) - [p4-phylogenetics](#p4-phylogenetics) - [p4est](#p4est) - [p4vasp](#p4vasp) - [p7zip](#p7zip) - [packmol](#packmol) - [pagmo](#pagmo) - [pairsnp](#pairsnp) - [PAL2NAL](#pal2nal) - [paladin](#paladin) - [PALEOMIX](#paleomix) - [PAML](#paml) - [panaroo](#panaroo) - [pandapower](#pandapower) - [pandas](#pandas) - [pandas-datareader](#pandas-datareader) - [PANDAseq](#pandaseq) - [Pandoc](#pandoc) - [Panedr](#panedr) - [Pango](#pango) - [pangolin](#pangolin) - [panito](#panito) - [PAPI](#papi) - [parallel](#parallel) - [parallel-fastq-dump](#parallel-fastq-dump) - [Parallel-Hashmap](#parallel-hashmap) - [ParallelIO](#parallelio) - [parameterized](#parameterized) - [paramiko](#paramiko) - [parasail](#parasail) - [Paraver](#paraver) - [ParaView](#paraview) - [Parcels](#parcels) - [PARI-GP](#pari-gp) - [ParmEd](#parmed) - [ParMETIS](#parmetis) - [ParMGridGen](#parmgridgen) - [Parsl](#parsl) - [PartitionFinder](#partitionfinder) - [pasta](#pasta) - [PaStiX](#pastix) - [pastml](#pastml) - [patch](#patch) - [patchelf](#patchelf) - [path.py](#path.py) - [PAUP](#paup) - [pauvre](#pauvre) - [pbbam](#pbbam) - [pbcopper](#pbcopper) - [pbdagcon](#pbdagcon) - [pbipa](#pbipa) - [pbmm2](#pbmm2) - [pbs_python](#pbs_python) - [PBSuite](#pbsuite) - [PCAngsd](#pcangsd) - [PCC](#pcc) - [PCL](#pcl) - [PCMSolver](#pcmsolver) - [PCRaster](#pcraster) - [PCRE](#pcre) - [PCRE2](#pcre2) - [pdsh](#pdsh) - [PDT](#pdt) - [peakdetect](#peakdetect) - [PEAR](#pear) - [PennCNV](#penncnv) - [PEPT](#pept) - [Percolator](#percolator) - [Perl](#perl) - [perl-app-cpanminus](#perl-app-cpanminus) - [Perl-bundle-CPAN](#perl-bundle-cpan) - [Perl4-CoreLibs](#perl4-corelibs) - [Perseus](#perseus) - [PEST++](#pest++) - [PETSc](#petsc) - [petsc4py](#petsc4py) - [PfamScan](#pfamscan) - [pfind](#pfind) - [pftoolsV3](#pftoolsv3) - [pFUnit](#pfunit) - [PGDSpider](#pgdspider) - [PGI](#pgi) - [PGPLOT](#pgplot) - [PHANOTATE](#phanotate) - [Phantompeakqualtools](#phantompeakqualtools) - [PHASE](#phase) - [PHAST](#phast) - [Phenoflow](#phenoflow) - [PheWAS](#phewas) - [PheWeb](#pheweb) - [PhiPack](#phipack) - [PHLAT](#phlat) - [phonemizer](#phonemizer) - [phono3py](#phono3py) - [phonopy](#phonopy) - [photontorch](#photontorch) - [phototonic](#phototonic) - [PHYLIP](#phylip) - [PhyloBayes-MPI](#phylobayes-mpi) - [phylokit](#phylokit) - [phylonaut](#phylonaut) - [PhyloPhlAn](#phylophlan) - [PhyML](#phyml) - [phyx](#phyx) - [picard](#picard) - [PICI-LIGGGHTS](#pici-liggghts) - [PICRUSt2](#picrust2) - [pigz](#pigz) - [PIL](#pil) - [PileOMeth](#pileometh) - [Pillow](#pillow) - [Pillow-SIMD](#pillow-simd) - [Pilon](#pilon) - [PIMS](#pims) - [Pindel](#pindel) - [Pingouin](#pingouin) - [Pint](#pint) - [pip](#pip) - [PIPITS](#pipits) - [PIRATE](#pirate) - [pIRS](#pirs) - [Pisces](#pisces) - [piSvM](#pisvm) - [piSvM-JSC](#pisvm-jsc) - [pixman](#pixman) - [pizzly](#pizzly) - [pkg-config](#pkg-config) - [pkgconf](#pkgconf) - [pkgconfig](#pkgconfig) - [PLAMS](#plams) - [plantcv](#plantcv) - [PlaScope](#plascope) - [PlasmaPy](#plasmapy) - [PLAST](#plast) - [Platanus](#platanus) - [Platypus](#platypus) - [Platypus-Opt](#platypus-opt) - [plc](#plc) - [PLINK](#plink) - [plinkliftover](#plinkliftover) - [plinkQC](#plinkqc) - [PLINKSEQ](#plinkseq) - [plot1cell](#plot1cell) - [Ploticus](#ploticus) - [plotly](#plotly) - [plotly-orca](#plotly-orca) - [plotly.py](#plotly.py) - [PLplot](#plplot) - [PLUMED](#plumed) - [PLY](#ply) - [PMIx](#pmix) - [pmt](#pmt) - [pmx](#pmx) - [PnetCDF](#pnetcdf) - [pocl](#pocl) - [pod5-file-format](#pod5-file-format) - [poetry](#poetry) - [polars](#polars) - [polymake](#polymake) - [pomkl](#pomkl) - [pompi](#pompi) - [poppler](#poppler) - [popscle](#popscle) - [popt](#popt) - [Porechop](#porechop) - [porefoam](#porefoam) - [poretools](#poretools) - [Portcullis](#portcullis) - [PortMidi](#portmidi) - [Postgres-XL](#postgres-xl) - [PostgreSQL](#postgresql) - [POT](#pot) - [POV-Ray](#pov-ray) - [powerlaw](#powerlaw) - [pp-sketchlib](#pp-sketchlib) - [PPanGGOLiN](#ppanggolin) - [PPfold](#ppfold) - [ppl](#ppl) - [pplacer](#pplacer) - [pplpy](#pplpy) - [PRANK](#prank) - [PRC](#prc) - [preCICE](#precice) - [PREQUAL](#prequal) - [preseq](#preseq) - [presto](#presto) - [pretty-yaml](#pretty-yaml) - [Primer3](#primer3) - [PRINSEQ](#prinseq) - [printproto](#printproto) - [PRISMS-PF](#prisms-pf) - [ProbABEL](#probabel) - [prodigal](#prodigal) - [ProFit](#profit) - [PROJ](#proj) - [ProjectQ](#projectq) - [prokka](#prokka) - [prompt-toolkit](#prompt-toolkit) - [proovread](#proovread) - [propy](#propy) - [Proteinortho](#proteinortho) - [ProtHint](#prothint) - [protobuf](#protobuf) - [protobuf-python](#protobuf-python) - [protozero](#protozero) - [PRSice](#prsice) - [pscom](#pscom) - [PSI](#psi) - [PSI4](#psi4) - [PsiCLASS](#psiclass) - [PSIPRED](#psipred) - [psmc](#psmc) - [psmpi](#psmpi) - [psmpi2](#psmpi2) - [PSolver](#psolver) - [PSORTb](#psortb) - [psrecord](#psrecord) - [pstoedit](#pstoedit) - [psutil](#psutil) - [psycopg2](#psycopg2) - [ptemcee](#ptemcee) - [PTESFinder](#ptesfinder) - [pubtcrs](#pubtcrs) - [pugixml](#pugixml) - [pullseq](#pullseq) - [PuLP](#pulp) - [purge_dups](#purge_dups) - [pv](#pv) - [py](#py) - [py-aiger](#py-aiger) - [py-aiger-bdd](#py-aiger-bdd) - [py-c3d](#py-c3d) - [py-cpuinfo](#py-cpuinfo) - [py3Dmol](#py3dmol) - [pyABC](#pyabc) - [PyAMG](#pyamg) - [PyAPS3](#pyaps3) - [pybedtools](#pybedtools) - [PyBerny](#pyberny) - [pyBigWig](#pybigwig) - [pybind11](#pybind11) - [pybinding](#pybinding) - [PyBioLib](#pybiolib) - [PyCairo](#pycairo) - [PyCalib](#pycalib) - [pyccel](#pyccel) - [PyCharm](#pycharm) - [PyCheMPS2](#pychemps2) - [Pychopper](#pychopper) - [PyCifRW](#pycifrw) - [PyClone](#pyclone) - [pycma](#pycma) - [pycocotools](#pycocotools) - [pycodestyle](#pycodestyle) - [PyCogent](#pycogent) - [pycoQC](#pycoqc) - [PyCUDA](#pycuda) - [PycURL](#pycurl) - [PyDamage](#pydamage) - [pydantic](#pydantic) - [PyDatastream](#pydatastream) - [pydicom](#pydicom) - [pydicom-seg](#pydicom-seg) - [pydlpoly](#pydlpoly) - [pydot](#pydot) - [pyEGA3](#pyega3) - [pyenchant](#pyenchant) - [PyEVTK](#pyevtk) - [pyFAI](#pyfai) - [pyfaidx](#pyfaidx) - [pyfasta](#pyfasta) - [PyFFmpeg](#pyffmpeg) - [pyFFTW](#pyfftw) - [pyfits](#pyfits) - [PyFMI](#pyfmi) - [PyFoam](#pyfoam) - [PyFR](#pyfr) - [PyFrag](#pyfrag) - [pygame](#pygame) - [pygccxml](#pygccxml) - [pyGenomeTracks](#pygenometracks) - [PyGEOS](#pygeos) - [pyGIMLi](#pygimli) - [Pygments](#pygments) - [pygmo](#pygmo) - [PyGObject](#pygobject) - [pygraphviz](#pygraphviz) - [pygrib](#pygrib) - [PyGTK](#pygtk) - [PyGTS](#pygts) - [PyGWAS](#pygwas) - [pyhdf](#pyhdf) - [PyImageJ](#pyimagej) - [pyiron](#pyiron) - [Pyke3](#pyke3) - [pylift](#pylift) - [Pylint](#pylint) - [pyMannKendall](#pymannkendall) - [pymatgen](#pymatgen) - [pymatgen-db](#pymatgen-db) - [pymbar](#pymbar) - [PyMC3](#pymc3) - [pymca](#pymca) - [pymemcache](#pymemcache) - [PyMOL](#pymol) - [PyNAST](#pynast) - [pyobjcryst](#pyobjcryst) - [PyOD](#pyod) - [pyodbc](#pyodbc) - [Pyomo](#pyomo) - [PyOpenCL](#pyopencl) - [PyOpenGL](#pyopengl) - [pyparsing](#pyparsing) - [pyperf](#pyperf) - [pyplusplus](#pyplusplus) - [pypmt](#pypmt) - [PYPOWER](#pypower) - [pyproj](#pyproj) - [PyPSA](#pypsa) - [pyqstem](#pyqstem) - [PyQt](#pyqt) - [PyQt5](#pyqt5) - [PyQtGraph](#pyqtgraph) - [pyradiomics](#pyradiomics) - [PyRe](#pyre) - [PyRETIS](#pyretis) - [pyringe](#pyringe) - [pyro-api](#pyro-api) - [pyro-ppl](#pyro-ppl) - [Pyro4](#pyro4) - [PyRosetta](#pyrosetta) - [Pysam](#pysam) - [pysamstats](#pysamstats) - [PySAT](#pysat) - [pyScaf](#pyscaf) - [pySCENIC](#pyscenic) - [PySCF](#pyscf) - [pysheds](#pysheds) - [pyshp](#pyshp) - [PySide2](#pyside2) - [pyslim](#pyslim) - [pysndfx](#pysndfx) - [Pysolar](#pysolar) - [pyspoa](#pyspoa) - [pysqlite](#pysqlite) - [PyStan](#pystan) - [pysteps](#pysteps) - [pystran](#pystran) - [PyTables](#pytables) - [pytesseract](#pytesseract) - [pytest](#pytest) - [pytest-benchmark](#pytest-benchmark) - [pytest-cpp](#pytest-cpp) - [pytest-flakefinder](#pytest-flakefinder) - [pytest-rerunfailures](#pytest-rerunfailures) - [pytest-shard](#pytest-shard) - [pytest-xdist](#pytest-xdist) - [PYTHIA](#pythia) - [Python](#python) - [Python-bundle](#python-bundle) - [Python-bundle-PyPI](#python-bundle-pypi) - [python-docx](#python-docx) - [python-hl7](#python-hl7) - [python-igraph](#python-igraph) - [python-irodsclient](#python-irodsclient) - [python-isal](#python-isal) - [python-Levenshtein](#python-levenshtein) - [python-libsbml](#python-libsbml) - [python-louvain](#python-louvain) - [python-mujoco](#python-mujoco) - [python-parasail](#python-parasail) - [python-telegram-bot](#python-telegram-bot) - [python-weka-wrapper3](#python-weka-wrapper3) - [python-xxhash](#python-xxhash) - [pythran](#pythran) - [PyTorch](#pytorch) - [PyTorch-bundle](#pytorch-bundle) - [pytorch-CycleGAN-pix2pix](#pytorch-cyclegan-pix2pix) - [PyTorch-Geometric](#pytorch-geometric) - [PyTorch-Ignite](#pytorch-ignite) - [PyTorch-Image-Models](#pytorch-image-models) - [PyTorch-Lightning](#pytorch-lightning) - [PyTorch3D](#pytorch3d) - [PyVCF](#pyvcf) - [PyVCF3](#pyvcf3) - [pyWannier90](#pywannier90) - [PyWavelets](#pywavelets) - [PyWBGT](#pywbgt) - [PyYAML](#pyyaml) - [PyZMQ](#pyzmq) ### p11-kit @@ -25638,6 +26293,7 @@ version |toolchain ``1.48.8`` |``GCCcore/11.2.0`` ``1.50.7`` |``GCCcore/11.3.0`` ``1.50.12``|``GCCcore/12.2.0`` +``1.50.14``|``GCCcore/12.3.0`` ### pangolin @@ -25676,6 +26332,7 @@ version |toolchain ``6.0.0`` |``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``6.0.0.1``|``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``7.0.0`` |``GCCcore/11.3.0`` +``7.0.1`` |``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### parallel @@ -25684,7 +26341,7 @@ parallel: Build and execute shell commands in parallel *homepage*: version |toolchain -------------|------------------------------- +------------|-------------------------------------- ``20141122``|``GCC/4.9.2`` ``20150322``|``GCC/4.9.2`` ``20150822``|``GCC/4.9.2`` @@ -25704,6 +26361,7 @@ version |toolchain ``20210622``|``GCCcore/10.3.0`` ``20210722``|``GCCcore/11.2.0`` ``20220722``|``GCCcore/11.3.0`` +``20230722``|``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### parallel-fastq-dump @@ -25748,6 +26406,16 @@ version |toolchain ---------|------------------ ``0.8.1``|``GCCcore/10.3.0`` +### paramiko + +Paramiko is a pure-Python (3.6+) implementation of the SSHv2 protocol, providing both client and server functionality. It provides the foundation for the high-level SSH library Fabric, which is what we recommend you use for common client use-cases such as running remote shell commands or transferring files. + +*homepage*: + +version |toolchain +---------|------------------ +``3.2.0``|``GCCcore/12.3.0`` + ### parasail parasail is a SIMD C (C99) library containing implementations of the Smith-Waterman (local), Needleman-Wunsch (global), and semi-global pairwise sequence alignment algorithms. @@ -25790,6 +26458,7 @@ version |versionsuffix |toolchain ``5.1.2`` |``-mpi`` |``foss/2016b``, ``intel/2016b`` ``5.2.0`` |``-mpi`` |``foss/2016b``, ``intel/2017a`` ``5.3.0`` |``-mpi`` |``foss/2016b`` +``5.4.1`` |``-Python-2.7.16-mpi``|``foss/2019b`` ``5.4.1`` |``-mpi`` |``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` ``5.5.2`` |``-Python-2.7.15-mpi``|``foss/2018b`` ``5.6.2`` |``-Python-3.7.4-mpi`` |``foss/2019b``, ``intel/2019b`` @@ -25852,6 +26521,16 @@ version|toolchain -------|---------------------------------------------------------------------------------------------------------------------- ``1.0``|``gimkl/2.11.5``, ``gompi/2019b``, ``gompi/2020a``, ``iimpi/2019b``, ``iimpi/2020a``, ``intel/2016a``, ``intel/2017a`` +### Parsl + +Parsl extends parallelism in Python beyond a single computer. You can use Parsl just like Python's parallel executors but across multiple cores and nodes. However, the real power of Parsl is in expressing multi-step workflows of functions. Parsl lets you chain functions together and will launch each function as inputs and computing resources are available. + +*homepage*: + +version |toolchain +-------------|------------------ +``2023.7.17``|``GCCcore/11.3.0`` + ### PartitionFinder PartitionFinder 2 is a Python program for simultaneously choosing partitioning schemes and models of molecular evolution for phylogenetic analyses of DNA, protein, and morphological data. You can PartitionFinder 2 before running a phylogenetic analysis, in order to decide how to divide up your sequence data into separate blocks before analysis, and to simultaneously perform model selection on each of those blocks. @@ -25861,6 +26540,7 @@ PartitionFinder 2 is a Python program for simultaneously choosing partitioning s version |versionsuffix |toolchain ---------|------------------|--------------- ``2.1.1``|``-Python-2.7.16``|``intel/2019b`` +``2.1.1``|``-Python-2.7.18``|``foss/2020b`` ### pasta @@ -25916,6 +26596,7 @@ version |toolchain ``0.12`` |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` ``0.13`` |``GCCcore/11.2.0`` ``0.15.0``|``GCCcore/11.3.0`` +``0.17.2``|``GCCcore/12.2.0`` ``0.18.0``|``GCCcore/12.3.0`` ### path.py @@ -26126,8 +26807,8 @@ A high performance, parallel remote shell utility *homepage*: version |toolchain ---------|-------------------------------------- -``2.34``|``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +--------|---------------------------------------------------------- +``2.34``|``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### PDT @@ -26136,10 +26817,20 @@ 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/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/9.3.0`` +``3.25.1``|``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/9.3.0`` + +### peakdetect + +Simple peak detection library for Python based on Billauer's work and this gist. + +*homepage*: + +version|toolchain +-------|-------------- +``1.2``|``foss/2022a`` ### PEAR @@ -26221,6 +26912,7 @@ version |versionsuffix|toolchain ``5.36.0``| |``GCCcore/12.1.0``, ``GCCcore/12.2.0`` ``5.36.0``|``-minimal`` |``GCCcore/12.2.0`` ``5.36.1``| |``GCCcore/12.3.0``, ``GCCcore/13.1.0`` +``5.38.0``| |``GCCcore/13.2.0`` ### perl-app-cpanminus @@ -26350,6 +27042,7 @@ version |toolchain ---------|--------------- ``3.2.9``|``gompi/2018b`` ``4.2.0``|``gompi/2020b`` +``4.7.3``|``gompi/2022a`` ### PGDSpider @@ -26676,6 +27369,16 @@ version |toolchain ---------|-------------- ``3.8.1``|``foss/2022a`` +### PICRUSt2 + +PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences. + +*homepage*: + +version |toolchain +---------|-------------- +``2.5.2``|``foss/2022b`` + ### pigz pigz, which stands for parallel implementation of gzip, is a fully functional replacement for gzip that exploits multiple processors and multiple cores to the hilt when compressing data. pigz was written by Mark Adler, and uses the zlib and pthread libraries. @@ -26720,36 +27423,37 @@ Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Py *homepage*: -version |versionsuffix |toolchain ----------|---------------------------------|--------------------------------------------------- -``3.2.0``|``-Python-2.7.11`` |``intel/2016a`` -``3.2.0``|``-Python-2.7.11-freetype-2.6.3``|``foss/2016a``, ``intel/2016a`` -``3.4.2``|``-Python-2.7.12`` |``intel/2016b`` -``3.4.2``|``-Python-3.5.2`` |``foss/2016b``, ``intel/2016b`` -``3.4.2``|``-Python-3.5.2-freetype-2.6.5`` |``intel/2016b`` -``4.1.0``|``-Python-2.7.13`` |``intel/2017a`` -``4.1.1``|``-Python-3.6.1`` |``intel/2017a`` -``4.2.1``|``-Python-3.6.1`` |``intel/2017a`` -``4.3.0``|``-Python-2.7.13`` |``intel/2017a`` -``4.3.0``|``-Python-2.7.14`` |``intel/2017b`` -``4.3.0``|``-Python-3.6.3`` |``foss/2017b`` -``5.0.0``|``-Python-2.7.14`` |``foss/2017b``, ``intel/2017b``, ``intel/2018a`` -``5.0.0``|``-Python-3.6.3`` |``foss/2017b``, ``intel/2017b`` -``5.0.0``|``-Python-3.6.4`` |``foss/2018a``, ``intel/2018a`` -``5.3.0``|``-Python-2.7.15`` |``foss/2018b`` -``5.3.0``|``-Python-3.6.6`` |``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` -``6.0.0``| |``GCCcore/8.2.0`` -``6.2.1``| |``GCCcore/8.3.0`` -``6.2.2``|``-Python-2.7.18`` |``foss/2020b`` -``7.0.0``|``-Python-3.8.2`` |``GCCcore/9.3.0`` -``8.0.1``| |``GCCcore/10.2.0`` -``8.2.0``| |``GCCcore/10.3.0`` -``8.3.1``| |``GCCcore/11.2.0`` -``8.3.2``| |``GCCcore/11.2.0`` -``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`` +version |versionsuffix |toolchain +----------|---------------------------------|--------------------------------------------------- +``3.2.0`` |``-Python-2.7.11`` |``intel/2016a`` +``3.2.0`` |``-Python-2.7.11-freetype-2.6.3``|``foss/2016a``, ``intel/2016a`` +``3.4.2`` |``-Python-2.7.12`` |``intel/2016b`` +``3.4.2`` |``-Python-3.5.2`` |``foss/2016b``, ``intel/2016b`` +``3.4.2`` |``-Python-3.5.2-freetype-2.6.5`` |``intel/2016b`` +``4.1.0`` |``-Python-2.7.13`` |``intel/2017a`` +``4.1.1`` |``-Python-3.6.1`` |``intel/2017a`` +``4.2.1`` |``-Python-3.6.1`` |``intel/2017a`` +``4.3.0`` |``-Python-2.7.13`` |``intel/2017a`` +``4.3.0`` |``-Python-2.7.14`` |``intel/2017b`` +``4.3.0`` |``-Python-3.6.3`` |``foss/2017b`` +``5.0.0`` |``-Python-2.7.14`` |``foss/2017b``, ``intel/2017b``, ``intel/2018a`` +``5.0.0`` |``-Python-3.6.3`` |``foss/2017b``, ``intel/2017b`` +``5.0.0`` |``-Python-3.6.4`` |``foss/2018a``, ``intel/2018a`` +``5.3.0`` |``-Python-2.7.15`` |``foss/2018b`` +``5.3.0`` |``-Python-3.6.6`` |``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` +``6.0.0`` | |``GCCcore/8.2.0`` +``6.2.1`` | |``GCCcore/8.3.0`` +``6.2.2`` |``-Python-2.7.18`` |``foss/2020b`` +``7.0.0`` |``-Python-3.8.2`` |``GCCcore/9.3.0`` +``8.0.1`` | |``GCCcore/10.2.0`` +``8.2.0`` | |``GCCcore/10.3.0`` +``8.3.1`` | |``GCCcore/11.2.0`` +``8.3.2`` | |``GCCcore/11.2.0`` +``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`` +``10.0.0``| |``GCCcore/12.3.0`` ### Pillow-SIMD @@ -26768,6 +27472,7 @@ version |versionsuffix |toolchain ``8.3.1`` | |``GCCcore/11.2.0`` ``8.3.2`` | |``GCCcore/11.2.0`` ``9.2.0`` | |``GCCcore/11.3.0`` +``9.5.0`` | |``GCCcore/12.3.0`` ### Pilon @@ -26824,6 +27529,7 @@ version |versionsuffix |toolchain ``0.14`` |``-Python-3.7.4``|``GCCcore/8.3.0`` ``0.19.2``| |``GCCcore/11.2.0`` ``0.20.1``| |``GCCcore/10.3.0`` +``0.22`` | |``GCCcore/11.3.0`` ### pip @@ -26911,7 +27617,7 @@ version |toolchain ``0.38.0``|``GCCcore/8.2.0`` ``0.38.4``|``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``0.40.0``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` -``0.42.2``|``GCCcore/12.2.0`` +``0.42.2``|``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### pizzly @@ -26948,6 +27654,7 @@ version |toolchain ``1.9.3``|``GCCcore/12.2.0`` ``1.9.4``|``GCCcore/13.1.0`` ``1.9.5``|``GCCcore/12.3.0`` +``2.0.3``|``GCCcore/13.2.0`` ### pkgconfig @@ -26956,7 +27663,7 @@ 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`` @@ -26973,7 +27680,7 @@ 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``, ``GCCcore/12.2.0`` +``1.5.5``|``-python`` |``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### PLAMS @@ -27046,6 +27753,16 @@ version |versionsuffix |toolchain ---------|------------------|--------------- ``0.8.1``|``-Python-2.7.11``|``intel/2016a`` +### Platypus-Opt + +Platypus is a framework for evolutionary computing in Python with a focus on multiobjective evolutionary algorithms (MOEAs). + +*homepage*: + +version |toolchain +---------|-------------- +``1.1.0``|``foss/2022a`` + ### plc plc is the public Planck Likelihood Code. It provides C and Fortran libraries that allow users to compute the log likelihoods of the temperature, polarization, and lensing maps. Optionally, it also provides a python version of this library, as well as tools to modify the predetermined options for some likelihoods (e.g. changing the high-ell and low-ell lmin and lmax values of the temperature). @@ -27168,6 +27885,7 @@ version |toolchain ``5.4.0`` |``GCCcore/11.2.0`` ``5.12.0``|``GCCcore/11.3.0`` ``5.13.1``|``GCCcore/12.2.0`` +``5.16.0``|``GCCcore/12.3.0`` ### PLplot @@ -27211,6 +27929,7 @@ version |versionsuffix |toolchain ``2.7.3``| |``foss/2021b`` ``2.8.0``| |``foss/2021b`` ``2.8.1``| |``foss/2022a`` +``2.9.0``| |``foss/2022b`` ### PLY @@ -27219,7 +27938,8 @@ PLY is yet another implementation of lex and yacc for Python. *homepage*: version |versionsuffix |toolchain ---------|-----------------|----------------- +--------|-----------------|------------------ +``3.11``| |``GCCcore/12.2.0`` ``3.11``|``-Python-3.6.4``|``foss/2018a`` ``3.11``|``-Python-3.7.4``|``GCCcore/8.3.0`` @@ -27279,11 +27999,11 @@ 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``, ``iimpi/2022a`` +``1.12.3``|``gompi/2021b``, ``gompi/2022a``, ``gompi/2023a``, ``iimpi/2022a`` ### pocl -Pocl is a portable open source (MIT-licensed) implementation of the OpenCL standard +PoCL is a portable open source (MIT-licensed) implementation of the OpenCL standard (1.2 with some 2.0 features supported). *homepage*: @@ -27295,6 +28015,7 @@ version|toolchain ``1.5``|``GCC/9.3.0`` ``1.6``|``GCC/10.2.0``, ``gcccuda/2020b``, ``iccifort/2020.4.304`` ``1.8``|``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0`` +``4.0``|``GCC/12.3.0`` ### pod5-file-format @@ -27316,6 +28037,7 @@ version |versionsuffix |toolchain ---------|-----------------|------------------ ``1.0.9``|``-Python-3.8.2``|``GCCcore/9.3.0`` ``1.2.2``| |``GCCcore/11.3.0`` +``1.5.1``| |``GCCcore/12.3.0`` ### polars @@ -27441,6 +28163,16 @@ version |versionsuffix |toolchain ---------|-----------------|-------------- ``1.2.2``|``-Python-3.7.4``|``foss/2019b`` +### PortMidi + +PortMidi is a library for software developers. It supports real-time input and output of MIDI data using a system-independent interface. PortMidi runs on Windows (using MME), Macintosh (using CoreMIDI), and Linux (using ALSA). + +*homepage*: + +version |toolchain +---------|------------------ +``2.0.4``|``GCCcore/11.3.0`` + ### Postgres-XL Postgres-XL is a horizontally scalable open source SQL database cluster, flexible enough to handle varying database workloads: @@ -27736,6 +28468,7 @@ version |toolchain ``5.0.0``|``foss/2018a``, ``foss/2018b``, ``intel/2018a``, ``intel/2018b``, ``iomkl/2018a`` ``6.0.0``|``GCCcore/8.2.0`` ``6.2.1``|``GCCcore/8.3.0`` +``6.3.1``|``GCCcore/10.3.0`` ``7.0.0``|``GCCcore/9.3.0`` ``7.2.1``|``GCCcore/10.2.0`` ``8.0.1``|``GCCcore/10.3.0`` @@ -27761,12 +28494,12 @@ 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``, ``gompi/2021b``, ``gompi/2022a`` +``1.14.5``| |``gompi/2019a``, ``gompi/2019b``, ``gompi/2020b``, ``gompi/2021a``, ``gompi/2021b``, ``gompi/2022a``, ``gompi/2022b`` ### prompt-toolkit @@ -27850,6 +28583,7 @@ version |toolchain ``3.19.4`` |``GCCcore/11.3.0`` ``3.21.9`` |``GCCcore/10.3.0`` ``23.0`` |``GCCcore/12.2.0`` +``24.0`` |``GCCcore/12.3.0`` ### protobuf-python @@ -27878,6 +28612,7 @@ version |versionsuffix |toolchain ``3.17.3``| |``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``3.19.4``| |``GCCcore/11.3.0`` ``4.23.0``| |``GCCcore/12.2.0`` +``4.24.0``| |``GCCcore/12.3.0`` ### protozero @@ -28055,6 +28790,7 @@ version |versionsuffix |toolchain ``5.6.3``| |``GCCcore/8.2.0`` ``5.9.3``| |``GCCcore/10.2.0``, ``GCCcore/11.3.0`` ``5.9.4``| |``GCCcore/11.2.0`` +``5.9.5``| |``GCCcore/12.2.0`` ### psycopg2 @@ -28130,6 +28866,7 @@ PuLP is an LP modeler written in Python. PuLP can generate MPS or LP files and c version |toolchain ---------|-------------- ``2.5.1``|``foss/2021a`` +``2.7.0``|``foss/2022b`` ### purge_dups @@ -28141,6 +28878,16 @@ version |toolchain ---------|-------------- ``1.2.5``|``foss/2021b`` +### pv + +Pipe Viewer - monitor the progress of data through a pipe + +*homepage*: + +version |toolchain +----------|------------------ +``1.7.24``|``GCCcore/12.3.0`` + ### py library with cross-python path, ini-parsing, io, code, log facilities @@ -28173,6 +28920,16 @@ version |versionsuffix |toolchain ---------|-----------------|-------------- ``3.0.0``|``-Python-3.8.2``|``foss/2020a`` +### py-c3d + +This is a small library for reading and writing C3D binary files. C3D files are a standard format for recording 3-dimensional time sequence data, especially data recorded by a 3D motion tracking apparatus. + +*homepage*: + +version |toolchain +---------|-------------- +``0.5.2``|``foss/2022a`` + ### py-cpuinfo py-cpuinfo gets CPU info with pure Python. @@ -28241,7 +28998,7 @@ version |versionsuffix |toolchain ``0.8.1`` | |``foss/2019b`` ``0.8.2`` | |``GCC/10.2.0``, ``GCC/11.2.0``, ``iccifort/2020.4.304`` ``0.8.2`` |``-Python-2.7.18``|``GCC/10.2.0`` -``0.9.0`` | |``GCC/11.3.0`` +``0.9.0`` | |``GCC/11.3.0``, ``GCC/12.2.0`` ### PyBerny @@ -28265,6 +29022,7 @@ 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``, ``foss/2022a`` +``0.3.22``| |``foss/2022b`` ### pybind11 @@ -28284,6 +29042,7 @@ version |versionsuffix |toolchain ``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`` +``2.11.1``| |``GCCcore/12.3.0`` ### pybinding @@ -28324,6 +29083,7 @@ version |versionsuffix |toolchain ``1.20.0``| |``GCCcore/10.2.0`` ``1.20.1``| |``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``1.21.0``| |``GCCcore/11.3.0`` +``1.24.0``| |``GCCcore/12.2.0`` ### PyCalib @@ -28478,9 +29238,9 @@ PycURL is a Python interface to libcurl. PycURL can be used to fetch objects ide *homepage*: version |versionsuffix |toolchain -------------|-----------------|------------------ +------------|-----------------|---------------------------------------------------------- ``7.43.0.5``|``-Python-3.7.4``|``GCCcore/8.3.0`` -``7.45.2`` | |``GCCcore/11.3.0`` +``7.45.2`` | |``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### PyDamage @@ -28708,6 +29468,16 @@ version |versionsuffix|toolchain -----------------|-------------|--------------- ``2019-20220216``|``-ASA`` |``intel/2020b`` +### pygame + +Pygame is a set of Python modules designed for writing video games. Pygame adds functionality on top of the excellent SDL library. This allows you to create fully featured games and multimedia programs in the python language. + +*homepage*: + +version |toolchain +---------|------------------ +``2.1.0``|``GCCcore/11.3.0`` + ### pygccxml Python package for easy C++ declarations navigation. @@ -28792,6 +29562,7 @@ version |versionsuffix |toolchain ``3.34.0``|``-Python-3.7.2`` |``GCCcore/8.2.0`` ``3.34.0``|``-Python-3.7.4`` |``GCCcore/8.3.0`` ``3.42.1``| |``GCCcore/11.3.0`` +``3.44.1``| |``GCCcore/12.2.0`` ### pygraphviz @@ -28912,12 +29683,13 @@ Pylint is a tool that checks for errors in Python code, tries to enforce a codi *homepage*: -version |versionsuffix |toolchain ----------|------------------|------------------------------------------------ -``1.9.3``|``-Python-2.7.15``|``foss/2018b``, ``intel/2018b``, ``iomkl/2018b`` -``1.9.5``|``-Python-2.7.15``|``GCCcore/8.2.0`` -``1.9.5``|``-Python-2.7.16``|``GCCcore/8.3.0`` -``2.7.4``| |``GCCcore/10.2.0`` +version |versionsuffix |toolchain +----------|------------------|------------------------------------------------ +``1.9.3`` |``-Python-2.7.15``|``foss/2018b``, ``intel/2018b``, ``iomkl/2018b`` +``1.9.5`` |``-Python-2.7.15``|``GCCcore/8.2.0`` +``1.9.5`` |``-Python-2.7.16``|``GCCcore/8.3.0`` +``2.7.4`` | |``GCCcore/10.2.0`` +``2.17.4``| |``GCCcore/12.2.0`` ### pyMannKendall @@ -29042,6 +29814,16 @@ version |toolchain ---------|------------------------------- ``0.8.7``|``foss/2020b``, ``intel/2020b`` +### pyodbc + +pyodbc is an open source Python module that makes accessing ODBC databases simple. It implements the DB API 2.0 specification but is packed with even more Pythonic convenience. + +*homepage*: + +version |toolchain +----------|-------------- +``4.0.39``|``foss/2022b`` + ### Pyomo Pyomo is a Python-based open-source software package that supports a diverse set of optimization capabilities for formulating and analyzing optimization models. @@ -29126,8 +29908,8 @@ PMT is a high-level software library capable of collecting power consumptio *homepage*: version |toolchain ----------|-------------- -``1.1.0``|``foss/2022a`` +---------|------------------------------ +``1.1.0``|``foss/2022a``, ``gfbf/2023a`` ### PYPOWER @@ -29155,6 +29937,7 @@ version |versionsuffix |toolchain ``3.3.1`` | |``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ``3.4.0`` | |``GCCcore/11.3.0`` ``3.5.0`` | |``GCCcore/12.2.0`` +``3.6.0`` | |``GCCcore/12.3.0`` ### PyPSA @@ -29292,6 +30075,7 @@ Pyro is a flexible, scalable deep probabilistic programming library built on PyT version |toolchain ---------|------------------ ``1.5.2``|``fosscuda/2020b`` +``1.8.4``|``foss/2022a`` ### Pyro4 @@ -29675,7 +30459,7 @@ version |versionsuffix |toolchain ``2.7.15``|``-bare`` |``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` ``2.7.16``| |``GCCcore/8.3.0`` ``2.7.16``|``-bare`` |``GCCcore/8.3.0`` -``2.7.18``| |``GCCcore/10.2.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` +``2.7.18``| |``GCCcore/10.2.0``, ``GCCcore/11.2.0``, ``GCCcore/12.3.0``, ``GCCcore/9.3.0`` ``2.7.18``|``-bare`` |``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/9.3.0`` ``3.5.1`` | |``foss/2016a``, ``intel/2016a`` ``3.5.2`` | |``foss/2016.04``, ``foss/2016b``, ``intel/2016b`` @@ -29711,6 +30495,16 @@ version |toolchain ----------|-------------- ``3.10.4``|``foss/2022a`` +### Python-bundle-PyPI + +Bundle of Python packages from PyPI + +*homepage*: + +version |toolchain +-----------|------------------ +``2023.06``|``GCCcore/12.3.0`` + ### python-docx python-docx is a Python library for creating and updating Microsoft Word (.docx) files @@ -29746,6 +30540,7 @@ version |versionsuffix |toolchain ``0.9.6`` | |``foss/2021a`` ``0.9.8`` | |``foss/2021b`` ``0.10.3`` | |``foss/2022a`` +``0.10.6`` | |``foss/2022b`` ### python-irodsclient @@ -30090,11 +30885,12 @@ version |versionsuffix |toolchain ``18.1.1``|``-Python-3.7.4`` |``GCCcore/8.3.0`` ``22.3.0``| |``GCCcore/10.3.0`` ``24.0.1``| |``GCCcore/11.3.0`` +``25.1.1``| |``GCCcore/12.3.0`` ## Q -[Q6](#q6) - [QCA](#qca) - [qcat](#qcat) - [QCG-PilotJob](#qcg-pilotjob) - [qcint](#qcint) - [QCxMS](#qcxms) - [QD](#qd) - [QDD](#qdd) - [QEMU](#qemu) - [QGIS](#qgis) - [Qhull](#qhull) - [QIIME](#qiime) - [QIIME2](#qiime2) - [Qiskit](#qiskit) - [QJson](#qjson) - [QML](#qml) - [qnorm](#qnorm) - [qpth](#qpth) - [qrupdate](#qrupdate) - [QScintilla](#qscintilla) - [Qt](#qt) - [Qt5](#qt5) - [Qt5Webkit](#qt5webkit) - [Qtconsole](#qtconsole) - [QtKeychain](#qtkeychain) - [QTLtools](#qtltools) - [qtop](#qtop) - [QtPy](#qtpy) - [Qualimap](#qualimap) - [Quandl](#quandl) - [QuantumESPRESSO](#quantumespresso) - [QUAST](#quast) - [QuaZIP](#quazip) - [QuickFF](#quickff) - [QuickPIC](#quickpic) - [Quip](#quip) - [Quorum](#quorum) - [QuTiP](#qutip) - [Qwt](#qwt) - [QwtPolar](#qwtpolar) +[Q6](#q6) - [QCA](#qca) - [qcat](#qcat) - [QCG-PilotJob](#qcg-pilotjob) - [qcint](#qcint) - [QCxMS](#qcxms) - [QD](#qd) - [QDD](#qdd) - [QEMU](#qemu) - [qforce](#qforce) - [QGIS](#qgis) - [Qhull](#qhull) - [QIIME](#qiime) - [QIIME2](#qiime2) - [Qiskit](#qiskit) - [QJson](#qjson) - [QML](#qml) - [qnorm](#qnorm) - [qpth](#qpth) - [qrupdate](#qrupdate) - [QScintilla](#qscintilla) - [Qt](#qt) - [Qt5](#qt5) - [Qt5Webkit](#qt5webkit) - [Qtconsole](#qtconsole) - [QtKeychain](#qtkeychain) - [QTLtools](#qtltools) - [qtop](#qtop) - [QtPy](#qtpy) - [Qualimap](#qualimap) - [Quandl](#quandl) - [QuantumESPRESSO](#quantumespresso) - [QUAST](#quast) - [QuaZIP](#quazip) - [QuickFF](#quickff) - [QuickPIC](#quickpic) - [Quip](#quip) - [Quorum](#quorum) - [QuTiP](#qutip) - [Qwt](#qwt) - [QwtPolar](#qwtpolar) ### Q6 @@ -30193,6 +30989,16 @@ version |toolchain ----------|--------------- ``2.10.1``|``intel/2017b`` +### qforce + +Quantum Mechanically augmented molecular force fields. Q-Force is a software package for deriving all-atom force fields from quantum mechanical calculations in an automated manner. + +*homepage*: + +version |toolchain +----------|-------------- +``0.6.11``|``foss/2022a`` + ### QGIS QGIS is a user friendly Open Source Geographic Information System (GIS) @@ -30216,7 +31022,7 @@ 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``, ``GCCcore/12.2.0`` +``2020.2``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### QIIME @@ -30230,21 +31036,22 @@ version |toolchain ### QIIME2 -QIIME is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data. +QIIME 2 is a powerful, extensible, and decentralized microbiome bioinformatics platform that is free, open source, and community developed. -*homepage*: +*homepage*: -version |toolchain ------------|---------- -``2017.10``|``system`` -``2018.2`` |``system`` -``2019.4`` |``system`` -``2019.7`` |``system`` -``2020.8`` |``system`` -``2020.11``|``system`` -``2021.8`` |``system`` -``2022.8`` |``system`` -``2022.11``|``system`` +version |toolchain +------------|-------------- +``2017.10`` |``system`` +``2018.2`` |``system`` +``2019.4`` |``system`` +``2019.7`` |``system`` +``2020.8`` |``system`` +``2020.11`` |``system`` +``2021.8`` |``system`` +``2022.8`` |``system`` +``2022.11`` |``system`` +``2023.5.1``|``foss/2022a`` ### Qiskit @@ -30340,23 +31147,24 @@ Qt is a comprehensive cross-platform C++ application framework. *homepage*: -version |toolchain -----------|------------------------------------------------------------------------------------ -``5.6.0`` |``foss/2016a``, ``intel/2016a`` -``5.7.0`` |``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` -``5.7.1`` |``intel/2016b`` -``5.8.0`` |``foss/2017a``, ``foss/2017b``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b`` -``5.9.3`` |``foss/2017b`` -``5.9.8`` |``fosscuda/2018b`` -``5.10.1``|``foss/2018a``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018a``, ``intel/2018b`` -``5.11.2``|``foss/2018b`` -``5.12.3``|``GCCcore/8.2.0`` -``5.13.1``|``GCCcore/8.3.0`` -``5.14.1``|``GCCcore/9.3.0`` -``5.14.2``|``GCCcore/10.2.0`` -``5.15.2``|``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``5.15.5``|``GCCcore/11.3.0`` -``5.15.7``|``GCCcore/12.2.0`` +version |toolchain +-----------|------------------------------------------------------------------------------------ +``5.6.0`` |``foss/2016a``, ``intel/2016a`` +``5.7.0`` |``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` +``5.7.1`` |``intel/2016b`` +``5.8.0`` |``foss/2017a``, ``foss/2017b``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b`` +``5.9.3`` |``foss/2017b`` +``5.9.8`` |``fosscuda/2018b`` +``5.10.1`` |``foss/2018a``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018a``, ``intel/2018b`` +``5.11.2`` |``foss/2018b`` +``5.12.3`` |``GCCcore/8.2.0`` +``5.13.1`` |``GCCcore/8.3.0`` +``5.14.1`` |``GCCcore/9.3.0`` +``5.14.2`` |``GCCcore/10.2.0`` +``5.15.2`` |``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``5.15.5`` |``GCCcore/11.3.0`` +``5.15.7`` |``GCCcore/12.2.0`` +``5.15.10``|``GCCcore/12.3.0`` ### Qt5Webkit @@ -30474,6 +31282,7 @@ version |versionsuffix|toolchain ``6.8`` | |``foss/2021a``, ``foss/2021b``, ``intel/2021a`` ``7.0`` | |``foss/2021b``, ``intel/2021b`` ``7.1`` | |``foss/2022a``, ``intel/2022a`` +``7.2`` | |``foss/2022b``, ``intel/2022b`` ### QUAST @@ -30584,7 +31393,7 @@ version |toolchain ## R -[R](#r) - [R-bundle-Bioconductor](#r-bundle-bioconductor) - [R-INLA](#r-inla) - [R-keras](#r-keras) - [R-MXM](#r-mxm) - [R-opencv](#r-opencv) - [R-tesseract](#r-tesseract) - [R-transport](#r-transport) - [R2jags](#r2jags) - [Racon](#racon) - [radeontop](#radeontop) - [RaGOO](#ragoo) - [Ragout](#ragout) - [RagTag](#ragtag) - [rampart](#rampart) - [randfold](#randfold) - [randrproto](#randrproto) - [rapidcsv](#rapidcsv) - [RapidJSON](#rapidjson) - [rapidNJ](#rapidnj) - [rapidtide](#rapidtide) - [RAPSearch2](#rapsearch2) - [Rascaf](#rascaf) - [RASPA2](#raspa2) - [rasterio](#rasterio) - [rasterstats](#rasterstats) - [Ratatosk](#ratatosk) - [Raven](#raven) - [RAxML](#raxml) - [RAxML-NG](#raxml-ng) - [Ray-assembler](#ray-assembler) - [Ray-project](#ray-project) - [Raysect](#raysect) - [RBFOpt](#rbfopt) - [rclone](#rclone) - [Rcorrector](#rcorrector) - [RcppGSL](#rcppgsl) - [rCUDA](#rcuda) - [RDFlib](#rdflib) - [RDKit](#rdkit) - [RDP-Classifier](#rdp-classifier) - [RE2](#re2) - [re2c](#re2c) - [Reads2snp](#reads2snp) - [Reapr](#reapr) - [ReaxFF](#reaxff) - [RECON](#recon) - [Red](#red) - [Redis](#redis) - [redis-py](#redis-py) - [Redundans](#redundans) - [ReFrame](#reframe) - [regionmask](#regionmask) - [RegTools](#regtools) - [Relate](#relate) - [RELION](#relion) - [ReMatCh](#rematch) - [REMORA](#remora) - [renderproto](#renderproto) - [RepastHPC](#repasthpc) - [RepeatMasker](#repeatmasker) - [RepeatModeler](#repeatmodeler) - [RepeatScout](#repeatscout) - [request](#request) - [requests](#requests) - [RERconverge](#rerconverge) - [resolos](#resolos) - [retworkx](#retworkx) - [RevBayes](#revbayes) - [rgdal](#rgdal) - [rgeos](#rgeos) - [Rgurobi](#rgurobi) - [rhdf5](#rhdf5) - [RheoTool](#rheotool) - [rickflow](#rickflow) - [RInChI](#rinchi) - [rioxarray](#rioxarray) - [ripunzip](#ripunzip) - [rising](#rising) - [Rivet](#rivet) - [rjags](#rjags) - [RLCard](#rlcard) - [rmarkdown](#rmarkdown) - [Rmath](#rmath) - [rMATS-turbo](#rmats-turbo) - [RMBlast](#rmblast) - [RNA-Bloom](#rna-bloom) - [RNA-SeQC](#rna-seqc) - [RNAclust](#rnaclust) - [RNAcode](#rnacode) - [RNAIndel](#rnaindel) - [RNAmmer](#rnammer) - [rnaQUAST](#rnaquast) - [RNAz](#rnaz) - [RnBeads](#rnbeads) - [Roary](#roary) - [ROCm](#rocm) - [rocm-cmake](#rocm-cmake) - [ROCm-CompilerSupport](#rocm-compilersupport) - [rocm-smi](#rocm-smi) - [rocminfo](#rocminfo) - [ROCR-Runtime](#rocr-runtime) - [ROCT-Thunk-Interface](#roct-thunk-interface) - [ROI_PAC](#roi_pac) - [ROME](#rome) - [ROOT](#root) - [root_numpy](#root_numpy) - [rootpy](#rootpy) - [Rosetta](#rosetta) - [rpmrebuild](#rpmrebuild) - [RPostgreSQL](#rpostgresql) - [rpy2](#rpy2) - [RQGIS3](#rqgis3) - [RSEM](#rsem) - [RSeQC](#rseqc) - [RStan](#rstan) - [rstanarm](#rstanarm) - [RStudio-Server](#rstudio-server) - [RTG-Tools](#rtg-tools) - [Rtree](#rtree) - [ruamel.yaml](#ruamel.yaml) - [Ruby](#ruby) - [Ruby-Tk](#ruby-tk) - [ruffus](#ruffus) - [Rust](#rust) - [rustworkx](#rustworkx) +[R](#r) - [R-bundle-Bioconductor](#r-bundle-bioconductor) - [R-INLA](#r-inla) - [R-keras](#r-keras) - [R-MXM](#r-mxm) - [R-opencv](#r-opencv) - [R-tesseract](#r-tesseract) - [R-transport](#r-transport) - [R2jags](#r2jags) - [Racon](#racon) - [radeontop](#radeontop) - [RaGOO](#ragoo) - [Ragout](#ragout) - [RagTag](#ragtag) - [rampart](#rampart) - [randfold](#randfold) - [randrproto](#randrproto) - [rapidcsv](#rapidcsv) - [RapidJSON](#rapidjson) - [rapidNJ](#rapidnj) - [rapidtide](#rapidtide) - [RAPSearch2](#rapsearch2) - [Rascaf](#rascaf) - [RASPA2](#raspa2) - [rasterio](#rasterio) - [rasterstats](#rasterstats) - [Ratatosk](#ratatosk) - [Raven](#raven) - [RAxML](#raxml) - [RAxML-NG](#raxml-ng) - [Ray-assembler](#ray-assembler) - [Ray-project](#ray-project) - [Raysect](#raysect) - [RBFOpt](#rbfopt) - [rclone](#rclone) - [Rcorrector](#rcorrector) - [RcppGSL](#rcppgsl) - [rCUDA](#rcuda) - [RDFlib](#rdflib) - [RDKit](#rdkit) - [RDP-Classifier](#rdp-classifier) - [RE2](#re2) - [re2c](#re2c) - [Reads2snp](#reads2snp) - [Reapr](#reapr) - [ReaxFF](#reaxff) - [RECON](#recon) - [Red](#red) - [Redis](#redis) - [redis-py](#redis-py) - [Redundans](#redundans) - [ReFrame](#reframe) - [regionmask](#regionmask) - [RegTools](#regtools) - [Relate](#relate) - [RELION](#relion) - [ReMatCh](#rematch) - [REMORA](#remora) - [renderproto](#renderproto) - [RepastHPC](#repasthpc) - [RepeatMasker](#repeatmasker) - [RepeatModeler](#repeatmodeler) - [RepeatScout](#repeatscout) - [request](#request) - [requests](#requests) - [RERconverge](#rerconverge) - [resolos](#resolos) - [retworkx](#retworkx) - [RevBayes](#revbayes) - [RFdiffusion](#rfdiffusion) - [rgdal](#rgdal) - [rgeos](#rgeos) - [Rgurobi](#rgurobi) - [rhdf5](#rhdf5) - [RheoTool](#rheotool) - [Rhodium](#rhodium) - [rickflow](#rickflow) - [RInChI](#rinchi) - [rioxarray](#rioxarray) - [ripunzip](#ripunzip) - [rising](#rising) - [Rivet](#rivet) - [rjags](#rjags) - [RLCard](#rlcard) - [rmarkdown](#rmarkdown) - [Rmath](#rmath) - [rMATS-turbo](#rmats-turbo) - [RMBlast](#rmblast) - [RNA-Bloom](#rna-bloom) - [RNA-SeQC](#rna-seqc) - [RNAclust](#rnaclust) - [RNAcode](#rnacode) - [RNAIndel](#rnaindel) - [RNAmmer](#rnammer) - [rnaQUAST](#rnaquast) - [RNAz](#rnaz) - [RnBeads](#rnbeads) - [Roary](#roary) - [ROCm](#rocm) - [rocm-cmake](#rocm-cmake) - [ROCm-CompilerSupport](#rocm-compilersupport) - [rocm-smi](#rocm-smi) - [rocminfo](#rocminfo) - [ROCR-Runtime](#rocr-runtime) - [ROCT-Thunk-Interface](#roct-thunk-interface) - [ROI_PAC](#roi_pac) - [ROME](#rome) - [ROOT](#root) - [root_numpy](#root_numpy) - [rootpy](#rootpy) - [Rosetta](#rosetta) - [rpmrebuild](#rpmrebuild) - [RPostgreSQL](#rpostgresql) - [rpy2](#rpy2) - [RQGIS3](#rqgis3) - [RSEM](#rsem) - [RSeQC](#rseqc) - [RStan](#rstan) - [rstanarm](#rstanarm) - [RStudio-Server](#rstudio-server) - [RTG-Tools](#rtg-tools) - [Rtree](#rtree) - [ruamel.yaml](#ruamel.yaml) - [Ruby](#ruby) - [Ruby-Tk](#ruby-tk) - [ruffus](#ruffus) - [ruptures](#ruptures) - [Rust](#rust) - [rustworkx](#rustworkx) ### R @@ -30736,7 +31545,7 @@ version |toolchain ``1.4.10``|``GCC/7.3.0-2.30`` ``1.4.13``|``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``1.4.21``|``GCCcore/10.2.0``, ``GCCcore/10.3.0`` -``1.5.0`` |``GCCcore/11.2.0`` +``1.5.0`` |``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ### radeontop @@ -31006,7 +31815,7 @@ version |versionsuffix |toolchain Rclone is a command line program to sync files and directories to and from a variety of online storage services -*homepage*: +*homepage*: version |versionsuffix|toolchain ----------|-------------|---------- @@ -31014,6 +31823,7 @@ version |versionsuffix|toolchain ``1.54.1``|``-amd64`` |``system`` ``1.56.0``|``-amd64`` |``system`` ``1.57.0``| |``system`` +``1.63.1``|``-amd64`` |``system`` ### Rcorrector @@ -31100,6 +31910,7 @@ version |toolchain ``2022-02-01``|``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``2022-06-01``|``GCCcore/11.3.0`` ``2023-03-01``|``GCCcore/12.2.0`` +``2023-08-01``|``GCCcore/12.3.0`` ### re2c @@ -31116,6 +31927,7 @@ version |toolchain ``2.1.1``|``GCCcore/10.3.0`` ``2.2`` |``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ``3.0`` |``GCCcore/12.2.0`` +``3.1`` |``GCCcore/12.3.0`` ### Reads2snp @@ -31256,6 +32068,7 @@ version |toolchain ---------|------------------------------ ``0.4.2``|``foss/2020b`` ``0.5.2``|``foss/2020b``, ``foss/2021b`` +``1.0.0``|``foss/2022b`` ### Relate @@ -31425,6 +32238,16 @@ version |toolchain ``1.1.1``|``GCC/10.2.0``, ``GCC/11.2.0`` ``1.2.1``|``gompi/2022a`` +### RFdiffusion + +RFdiffusion is an open source method for structure generation, with or without conditional information (a motif, target etc). It can perform a whole range of protein design challenges as we have outlined in the RFdiffusion paper. + +*homepage*: + +version |toolchain +---------|-------------- +``1.1.0``|``foss/2022a`` + ### rgdal Provides bindings to the 'Geospatial' Data Abstraction Library ('GDAL') (>= 1.11.4 and <= 2.5.0) and access to projection/transformation operations from the 'PROJ.4' library. @@ -31487,6 +32310,16 @@ version|toolchain -------|-------------- ``5.0``|``foss/2019b`` +### Rhodium + +Rhodium is an open source Python library for robust decision making (RDM) and multiobjective robust decision making (MORDM), and exploratory modelling (EM). + +*homepage*: + +version |toolchain +---------|-------------- +``1.2.0``|``foss/2022a`` + ### rickflow Running and Analyzing OpenMM Jobs @@ -31574,6 +32407,7 @@ version |versionsuffix|toolchain ``4-10``|``-R-4.1.0`` |``foss/2021a`` ``4-12``|``-R-4.1.2`` |``foss/2021b`` ``4-13``|``-R-4.2.1`` |``foss/2022a`` +``4-13``|``-R-4.2.2`` |``foss/2022b`` ### RLCard @@ -31724,9 +32558,10 @@ RnBeads is an R package for comprehensive analysis of DNA methylation data obtai *homepage*: -version |versionsuffix|toolchain ----------|-------------|-------------- -``2.6.0``|``-R-4.0.0`` |``foss/2020a`` +version |versionsuffix|toolchain +----------|-------------|-------------- +``2.6.0`` |``-R-4.0.0`` |``foss/2020a`` +``2.14.0``|``-R-4.2.1`` |``foss/2022a`` ### Roary @@ -32001,9 +32836,10 @@ RTG Tools contains utilities to easily manipulate and accurately compare multipl *homepage*: -version |versionsuffix|toolchain ----------|-------------|---------- -``3.9.1``|``-Java-1.8``|``system`` +version |versionsuffix|toolchain +----------|-------------|---------- +``3.9.1`` |``-Java-1.8``|``system`` +``3.12.1``|``-Java-11`` |``system`` ### Rtree @@ -32070,6 +32906,16 @@ version |toolchain ---------|---------------------------------- ``2.8.4``|``GCCcore/11.3.0``, ``foss/2021b`` +### ruptures + +ruptures is a Python library for off-line change point detection. This package provides methods for the analysis and segmentation of non-stationary signals. Implemented algorithms include exact and approximate detection for various parametric and non-parametric models. ruptures focuses on ease of use by providing a well-documented and consistent interface. In addition, thanks to its modular structure, different algorithms and models can be connected and extended within this package. + +*homepage*: + +version |toolchain +---------|-------------- +``1.1.8``|``foss/2022a`` + ### Rust Rust is a systems programming language that runs blazingly fast, prevents segfaults, and guarantees thread safety. @@ -32109,7 +32955,7 @@ version |toolchain ## S -[S-Lang](#s-lang) - [S4](#s4) - [Safetensors](#safetensors) - [SAGE](#sage) - [Sailfish](#sailfish) - [SALib](#salib) - [Salmon](#salmon) - [SALMON-TDDFT](#salmon-tddft) - [Sambamba](#sambamba) - [samblaster](#samblaster) - [Samcef](#samcef) - [samclip](#samclip) - [samplot](#samplot) - [SAMtools](#samtools) - [sansa](#sansa) - [SAP](#sap) - [SAS](#sas) - [Satsuma2](#satsuma2) - [savvy](#savvy) - [Saxon-HE](#saxon-he) - [SBCL](#sbcl) - [sbt](#sbt) - [ScaFaCoS](#scafacos) - [ScaLAPACK](#scalapack) - [Scalasca](#scalasca) - [SCALCE](#scalce) - [Scalene](#scalene) - [scanpy](#scanpy) - [scArches](#scarches) - [sceasy](#sceasy) - [SCENIC](#scenic) - [scGeneFit](#scgenefit) - [SCGid](#scgid) - [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) - [SCIP](#scip) - [SCIPhI](#sciphi) - [scipy](#scipy) - [SciPy-bundle](#scipy-bundle) - [SCnorm](#scnorm) - [Scoary](#scoary) - [SCons](#scons) - [SCOOP](#scoop) - [SCopeLoomR](#scopeloomr) - [Score-P](#score-p) - [SCOTCH](#scotch) - [scp](#scp) - [scPred](#scpred) - [Scrappie](#scrappie) - [scVelo](#scvelo) - [scvi-tools](#scvi-tools) - [Scythe](#scythe) - [SDCC](#sdcc) - [SDL](#sdl) - [SDL2](#sdl2) - [SDL2_image](#sdl2_image) - [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) - [Simple-DFTD3](#simple-dftd3) - [SimpleElastix](#simpleelastix) - [SimpleITK](#simpleitk) - [simpy](#simpy) - [SimVascular](#simvascular) - [SingleM](#singlem) - [Singular](#singular) - [SiNVICT](#sinvict) - [SIONlib](#sionlib) - [SIP](#sip) - [siscone](#siscone) - [SISSO](#sisso) - [SISSO++](#sisso++) - [SKESA](#skesa) - [sketchmap](#sketchmap) - [skewer](#skewer) - [sklearn-pandas](#sklearn-pandas) - [sklearn-som](#sklearn-som) - [skorch](#skorch) - [SlamDunk](#slamdunk) - [SLATEC](#slatec) - [SLEPc](#slepc) - [slepc4py](#slepc4py) - [sleuth](#sleuth) - [slidingwindow](#slidingwindow) - [SLiM](#slim) - [slow5tools](#slow5tools) - [smafa](#smafa) - [smallgenomeutilities](#smallgenomeutilities) - [SMAP](#smap) - [SMARTdenovo](#smartdenovo) - [SMC++](#smc++) - [smfishHmrf](#smfishhmrf) - [smithwaterman](#smithwaterman) - [Smoldyn](#smoldyn) - [smooth-topk](#smooth-topk) - [SMRT-Link](#smrt-link) - [SMV](#smv) - [snakemake](#snakemake) - [SNAP](#snap) - [SNAP-HMM](#snap-hmm) - [SNAPE-pooled](#snape-pooled) - [snaphu](#snaphu) - [snappy](#snappy) - [Sniffles](#sniffles) - [snippy](#snippy) - [snp-sites](#snp-sites) - [snpEff](#snpeff) - [SNPhylo](#snphylo) - [SNPomatic](#snpomatic) - [SOAPaligner](#soapaligner) - [SOAPdenovo-Trans](#soapdenovo-trans) - [SOAPdenovo2](#soapdenovo2) - [SOAPfuse](#soapfuse) - [socat](#socat) - [SOCI](#soci) - [SolexaQA++](#solexaqa++) - [sonic](#sonic) - [SoPlex](#soplex) - [SoQt](#soqt) - [SortMeRNA](#sortmerna) - [SoupX](#soupx) - [SoX](#sox) - [SoXt](#soxt) - [SpaceRanger](#spaceranger) - [Spack](#spack) - [spaCy](#spacy) - [SPAdes](#spades) - [spaln](#spaln) - [Spark](#spark) - [sparse-neighbors-search](#sparse-neighbors-search) - [sparsehash](#sparsehash) - [SpatialDE](#spatialde) - [spatialreg](#spatialreg) - [spdlog](#spdlog) - [SpectrA](#spectra) - [spectral.methods](#spectral.methods) - [speech_tools](#speech_tools) - [spektral](#spektral) - [spglib](#spglib) - [spglib-python](#spglib-python) - [Sphinx](#sphinx) - [Sphinx-RTD-Theme](#sphinx-rtd-theme) - [SpiceyPy](#spiceypy) - [SpiecEasi](#spieceasi) - [SplAdder](#spladder) - [SPLASH](#splash) - [SpliceMap](#splicemap) - [split-seq](#split-seq) - [splitRef](#splitref) - [SPM](#spm) - [spoa](#spoa) - [SPOOLES](#spooles) - [SPOTPY](#spotpy) - [SPRNG](#sprng) - [Spyder](#spyder) - [SQLite](#sqlite) - [SqueezeMeta](#squeezemeta) - [Squidpy](#squidpy) - [SRA-Toolkit](#sra-toolkit) - [sradownloader](#sradownloader) - [SRPRISM](#srprism) - [SRST2](#srst2) - [SSAHA2](#ssaha2) - [SSN](#ssn) - [SSPACE_Basic](#sspace_basic) - [SSW](#ssw) - [STACEY](#stacey) - [Stack](#stack) - [Stacks](#stacks) - [STAMP](#stamp) - [StaMPS](#stamps) - [Stampy](#stampy) - [STAR](#star) - [STAR-CCM+](#star-ccm+) - [STAR-Fusion](#star-fusion) - [stardist](#stardist) - [stars](#stars) - [Stata](#stata) - [Statistics-R](#statistics-r) - [statsmodels](#statsmodels) - [STEAK](#steak) - [STIR](#stir) - [stpipeline](#stpipeline) - [strace](#strace) - [Strainberry](#strainberry) - [STREAM](#stream) - [strelka](#strelka) - [StringTie](#stringtie) - [stripy](#stripy) - [STRique](#strique) - [Structure](#structure) - [Structure_threader](#structure_threader) - [STRUMPACK](#strumpack) - [suave](#suave) - [Subread](#subread) - [subset-bam](#subset-bam) - [Subversion](#subversion) - [suds](#suds) - [SuiteSparse](#suitesparse) - [SUMACLUST](#sumaclust) - [SUMATRA](#sumatra) - [SUMO](#sumo) - [SUNDIALS](#sundials) - [SunPy](#sunpy) - [SuperLU](#superlu) - [SuperLU_DIST](#superlu_dist) - [supermagic](#supermagic) - [supernova](#supernova) - [SURVIVOR](#survivor) - [SVclone](#svclone) - [SVDetect](#svdetect) - [SVDquest](#svdquest) - [SVG](#svg) - [SVIM](#svim) - [svist4get](#svist4get) - [swarm](#swarm) - [SWASH](#swash) - [SWAT+](#swat+) - [swifter](#swifter) - [SWIG](#swig) - [SWIPE](#swipe) - [swissknife](#swissknife) - [SymEngine](#symengine) - [SymEngine-python](#symengine-python) - [SYMPHONY](#symphony) - [sympy](#sympy) - [synthcity](#synthcity) - [SyRI](#syri) - [sysbench](#sysbench) - [Szip](#szip) +[S-Lang](#s-lang) - [S4](#s4) - [Sabre](#sabre) - [Safetensors](#safetensors) - [SAGE](#sage) - [Sailfish](#sailfish) - [SALib](#salib) - [Salmon](#salmon) - [SALMON-TDDFT](#salmon-tddft) - [Sambamba](#sambamba) - [samblaster](#samblaster) - [Samcef](#samcef) - [samclip](#samclip) - [samplot](#samplot) - [SAMtools](#samtools) - [sansa](#sansa) - [SAP](#sap) - [SAS](#sas) - [Satsuma2](#satsuma2) - [savvy](#savvy) - [Saxon-HE](#saxon-he) - [SBCL](#sbcl) - [sbt](#sbt) - [ScaFaCoS](#scafacos) - [ScaLAPACK](#scalapack) - [Scalasca](#scalasca) - [SCALCE](#scalce) - [Scalene](#scalene) - [scanpy](#scanpy) - [scArches](#scarches) - [sceasy](#sceasy) - [SCENIC](#scenic) - [scGeneFit](#scgenefit) - [SCGid](#scgid) - [scGSVA](#scgsva) - [scHiCExplorer](#schicexplorer) - [Schrodinger](#schrodinger) - [scib](#scib) - [scib-metrics](#scib-metrics) - [sciClone](#sciclone) - [ScientificPython](#scientificpython) - [scikit-allel](#scikit-allel) - [scikit-bio](#scikit-bio) - [scikit-build](#scikit-build) - [scikit-cuda](#scikit-cuda) - [scikit-image](#scikit-image) - [scikit-learn](#scikit-learn) - [scikit-misc](#scikit-misc) - [scikit-multilearn](#scikit-multilearn) - [scikit-optimize](#scikit-optimize) - [scikit-plot](#scikit-plot) - [scikit-uplift](#scikit-uplift) - [SCIP](#scip) - [SCIPhI](#sciphi) - [scipy](#scipy) - [SciPy-bundle](#scipy-bundle) - [SCnorm](#scnorm) - [Scoary](#scoary) - [SCons](#scons) - [SCOOP](#scoop) - [SCopeLoomR](#scopeloomr) - [Score-P](#score-p) - [SCOTCH](#scotch) - [scp](#scp) - [scPred](#scpred) - [Scrappie](#scrappie) - [scVelo](#scvelo) - [scvi-tools](#scvi-tools) - [Scythe](#scythe) - [SDCC](#sdcc) - [SDL](#sdl) - [SDL2](#sdl2) - [SDL2_image](#sdl2_image) - [SDL2_mixer](#sdl2_mixer) - [SDL2_ttf](#sdl2_ttf) - [SDL_image](#sdl_image) - [SDSL](#sdsl) - [Seaborn](#seaborn) - [SearchGUI](#searchgui) - [SeaView](#seaview) - [SECAPR](#secapr) - [Seeder](#seeder) - [segemehl](#segemehl) - [segment-anything](#segment-anything) - [segmentation-models](#segmentation-models) - [SeisSol](#seissol) - [SelEstim](#selestim) - [SELFIES](#selfies) - [SentencePiece](#sentencepiece) - [sentinelsat](#sentinelsat) - [sep](#sep) - [SEPP](#sepp) - [Seq-Gen](#seq-gen) - [seq2HLA](#seq2hla) - [SeqAn](#seqan) - [SeqAn3](#seqan3) - [SeqKit](#seqkit) - [SeqLib](#seqlib) - [Seqmagick](#seqmagick) - [SeqPrep](#seqprep) - [seqtk](#seqtk) - [Serf](#serf) - [setuptools](#setuptools) - [setuptools-rust](#setuptools-rust) - [Seurat](#seurat) - [SeuratData](#seuratdata) - [SeuratDisk](#seuratdisk) - [SeuratWrappers](#seuratwrappers) - [sf](#sf) - [sfftk](#sfftk) - [Shannon](#shannon) - [SHAP](#shap) - [shapAAR](#shapaar) - [SHAPEIT](#shapeit) - [SHAPEIT4](#shapeit4) - [Shapely](#shapely) - [sharutils](#sharutils) - [Shasta](#shasta) - [ShengBTE](#shengbte) - [shift](#shift) - [SHORE](#shore) - [Short-Pair](#short-pair) - [shovill](#shovill) - [shrinkwrap](#shrinkwrap) - [SHTns](#shtns) - [Sibelia](#sibelia) - [SICER2](#sicer2) - [sickle](#sickle) - [Siesta](#siesta) - [SignalP](#signalp) - [silhouetteRank](#silhouetterank) - [silx](#silx) - [simint](#simint) - [SimNIBS](#simnibs) - [SimPEG](#simpeg) - [SIMPLE](#simple) - [Simple-DFTD3](#simple-dftd3) - [SimpleElastix](#simpleelastix) - [SimpleITK](#simpleitk) - [simpy](#simpy) - [SimVascular](#simvascular) - [SingleM](#singlem) - [Singular](#singular) - [SiNVICT](#sinvict) - [SIONlib](#sionlib) - [SIP](#sip) - [siscone](#siscone) - [SISSO](#sisso) - [SISSO++](#sisso++) - [SKESA](#skesa) - [sketchmap](#sketchmap) - [skewer](#skewer) - [sklearn-pandas](#sklearn-pandas) - [sklearn-som](#sklearn-som) - [skorch](#skorch) - [SlamDunk](#slamdunk) - [SLATEC](#slatec) - [SLEPc](#slepc) - [slepc4py](#slepc4py) - [sleuth](#sleuth) - [slidingwindow](#slidingwindow) - [SLiM](#slim) - [slow5tools](#slow5tools) - [slurm-drmaa](#slurm-drmaa) - [smafa](#smafa) - [smallgenomeutilities](#smallgenomeutilities) - [SMAP](#smap) - [SMARTdenovo](#smartdenovo) - [SMC++](#smc++) - [smfishHmrf](#smfishhmrf) - [smithwaterman](#smithwaterman) - [Smoldyn](#smoldyn) - [smooth-topk](#smooth-topk) - [SMRT-Link](#smrt-link) - [SMV](#smv) - [snakemake](#snakemake) - [SNAP](#snap) - [SNAP-HMM](#snap-hmm) - [SNAPE-pooled](#snape-pooled) - [snaphu](#snaphu) - [snappy](#snappy) - [Sniffles](#sniffles) - [snippy](#snippy) - [snp-sites](#snp-sites) - [snpEff](#snpeff) - [SNPhylo](#snphylo) - [SNPomatic](#snpomatic) - [SOAPaligner](#soapaligner) - [SOAPdenovo-Trans](#soapdenovo-trans) - [SOAPdenovo2](#soapdenovo2) - [SOAPfuse](#soapfuse) - [socat](#socat) - [SOCI](#soci) - [SolexaQA++](#solexaqa++) - [sonic](#sonic) - [SoPlex](#soplex) - [SoQt](#soqt) - [SortMeRNA](#sortmerna) - [SoupX](#soupx) - [SoX](#sox) - [SoXt](#soxt) - [SpaceRanger](#spaceranger) - [Spack](#spack) - [spaCy](#spacy) - [SPAdes](#spades) - [spaln](#spaln) - [Spark](#spark) - [sparse-neighbors-search](#sparse-neighbors-search) - [sparsehash](#sparsehash) - [SpatialDE](#spatialde) - [spatialreg](#spatialreg) - [spdlog](#spdlog) - [SpectrA](#spectra) - [spectral.methods](#spectral.methods) - [speech_tools](#speech_tools) - [spektral](#spektral) - [spglib](#spglib) - [spglib-python](#spglib-python) - [Sphinx](#sphinx) - [Sphinx-RTD-Theme](#sphinx-rtd-theme) - [SpiceyPy](#spiceypy) - [SpiecEasi](#spieceasi) - [SplAdder](#spladder) - [SPLASH](#splash) - [SpliceMap](#splicemap) - [split-seq](#split-seq) - [splitRef](#splitref) - [SPM](#spm) - [spoa](#spoa) - [SPOOLES](#spooles) - [SPOTPY](#spotpy) - [SPRNG](#sprng) - [Spyder](#spyder) - [SQLite](#sqlite) - [SqueezeMeta](#squeezemeta) - [Squidpy](#squidpy) - [SRA-Toolkit](#sra-toolkit) - [sradownloader](#sradownloader) - [SRPRISM](#srprism) - [SRST2](#srst2) - [SSAHA2](#ssaha2) - [SSN](#ssn) - [SSPACE_Basic](#sspace_basic) - [SSW](#ssw) - [STACEY](#stacey) - [Stack](#stack) - [Stacks](#stacks) - [STAMP](#stamp) - [StaMPS](#stamps) - [Stampy](#stampy) - [STAR](#star) - [STAR-CCM+](#star-ccm+) - [STAR-Fusion](#star-fusion) - [stardist](#stardist) - [stars](#stars) - [Stata](#stata) - [Statistics-R](#statistics-r) - [statsmodels](#statsmodels) - [STEAK](#steak) - [STIR](#stir) - [stpipeline](#stpipeline) - [strace](#strace) - [Strainberry](#strainberry) - [STREAM](#stream) - [strelka](#strelka) - [StringTie](#stringtie) - [stripy](#stripy) - [STRique](#strique) - [Structure](#structure) - [Structure_threader](#structure_threader) - [STRUMPACK](#strumpack) - [suave](#suave) - [SuAVE-biomat](#suave-biomat) - [Subread](#subread) - [subset-bam](#subset-bam) - [Subversion](#subversion) - [suds](#suds) - [SuiteSparse](#suitesparse) - [SUMACLUST](#sumaclust) - [SUMATRA](#sumatra) - [SUMO](#sumo) - [SUNDIALS](#sundials) - [SunPy](#sunpy) - [SuperLU](#superlu) - [SuperLU_DIST](#superlu_dist) - [supermagic](#supermagic) - [supernova](#supernova) - [SURVIVOR](#survivor) - [SVclone](#svclone) - [SVDetect](#svdetect) - [SVDquest](#svdquest) - [SVG](#svg) - [SVIM](#svim) - [svist4get](#svist4get) - [swarm](#swarm) - [SWASH](#swash) - [SWAT+](#swat+) - [swifter](#swifter) - [SWIG](#swig) - [SWIPE](#swipe) - [swissknife](#swissknife) - [SymEngine](#symengine) - [SymEngine-python](#symengine-python) - [SYMPHONY](#symphony) - [sympy](#sympy) - [synthcity](#synthcity) - [SyRI](#syri) - [sysbench](#sysbench) - [Szip](#szip) ### S-Lang @@ -32132,6 +32978,16 @@ version |toolchain ------------------|-------------- ``1.1.1-20180610``|``foss/2017b`` +### Sabre + +Sabre is a tool that will demultiplex barcoded reads into separate files. It will work on both single-end and paired-end data in fastq format. It simply compares the provided barcodes with each read and separates the read into its appropriate barcode file, after stripping the barcode from the read (and also stripping the quality values of the barcode bases). + +*homepage*: + +version |toolchain +--------------|-------------- +``2013-09-28``|``GCC/12.2.0`` + ### Safetensors Safetensors is a new simple format for storing tensors safely (as opposed to pickle) and that is still fast (zero-copy). Safetensors is really fast. @@ -32292,6 +33148,7 @@ version |versionsuffix |toolchain ``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`` +``1.18`` | |``GCC/12.3.0`` ### sansa @@ -32447,6 +33304,7 @@ Scalene is a high-performance CPU, GPU and memory profiler for Python that does version |toolchain ----------|------------------ ``1.5.13``|``GCCcore/11.2.0`` +``1.5.26``|``GCCcore/12.3.0`` ### scanpy @@ -32512,6 +33370,16 @@ version |toolchain ---------|-------------- ``0.9b0``|``foss/2021b`` +### scGSVA + +scGSVA provides wrap functions to do GSVA analysis for single cell data. And scGSVA includes functions to build annotation for almost all species. scGSVA also provides function to generate figures based on the GSVA results. + +*homepage*: + +version |versionsuffix|toolchain +----------|-------------|-------------- +``0.0.14``|``-R-4.2.1`` |``foss/2022a`` + ### scHiCExplorer The scHiCExplorer is a software to demultiplex, process, correct, normalize, manipulate, analyse and visualize single-cell Hi-C data. @@ -32547,6 +33415,16 @@ version |toolchain ``1.1.1``|``foss/2022a`` ``1.1.3``|``foss/2021a`` +### scib-metrics + +Accelerated and Python-only metrics for benchmarking single-cell integration outputs + +*homepage*: + +version |toolchain +---------|-------------- +``0.3.3``|``foss/2021a`` + ### sciClone An R package for inferring the subclonal architecture of tumors @@ -32604,6 +33482,7 @@ version |versionsuffix |toolchain ``0.11.1``| |``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b``, ``intelcuda/2020b`` ``0.15.0``| |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ``0.17.2``| |``GCCcore/12.2.0`` +``0.17.6``| |``GCCcore/12.3.0`` ### scikit-cuda @@ -32641,6 +33520,7 @@ version |versionsuffix |toolchain ``0.18.3``| |``foss/2021a`` ``0.19.1``| |``foss/2021b`` ``0.19.3``| |``foss/2022a`` +``0.21.0``| |``foss/2022b`` ### scikit-learn @@ -32716,6 +33596,16 @@ version |versionsuffix |toolchain ``0.8.1``|``-Python-3.8.2``|``foss/2020a`` ``0.9.0``| |``foss/2021a`` +### scikit-plot + +Scikit-plot is the result of an unartistic data scientist's dreadful realization that *visualization is one of the most crucial components in the data science process, not just a mere afterthought*. + +*homepage*: + +version |toolchain +---------|-------------- +``0.3.7``|``foss/2022b`` + ### scikit-uplift scikit-uplift is a Python module for classic approaches for uplift modeling built on top of scikit-learn. Uplift prediction aims to estimate the causal impact of a treatment at the individual level. @@ -32780,6 +33670,7 @@ version |versionsuffix |toolchain ``2021.10``|``-Python-2.7.18``|``foss/2021b`` ``2022.05``| |``foss/2022.05``, ``foss/2022a``, ``intel/2022.05``, ``intel/2022a`` ``2023.02``| |``gfbf/2022b`` +``2023.07``| |``gfbf/2023a`` ### SCnorm @@ -32870,6 +33761,8 @@ version |versionsuffix |toolchain ``8.0`` | |``gompi/2021b``, ``gompi/2022a`` ``8.0`` |``-CUDA-11.4.1``|``gompi/2021b`` ``8.0`` |``-CUDA-11.7.0``|``gompi/2022a`` +``8.1`` | |``gompi/2022b``, ``gompi/2023a`` +``8.1`` |``-CUDA-12.0.0``|``gompi/2022b`` ### SCOTCH @@ -32887,6 +33780,7 @@ version |versionsuffix|toolchain ``6.1.0`` | |``gompi/2020b``, ``gompi/2021a``, ``iimpi/2020b``, ``iimpi/2021a`` ``6.1.2`` | |``gompi/2021b``, ``iimpi/2021b`` ``7.0.1`` | |``gompi/2022a``, ``iimpi/2022a`` +``7.0.3`` | |``gompi/2022b``, ``gompi/2023a`` ### scp @@ -32988,16 +33882,38 @@ version |toolchain ``2.0.20``|``GCCcore/11.2.0`` ``2.0.22``|``GCCcore/11.3.0`` ``2.26.3``|``GCCcore/12.2.0`` +``2.28.2``|``GCCcore/12.3.0`` ### SDL2_image -SDL_image is an image file loading library. +This is a simple library to load images of various formats as SDL surfaces. It can load BMP, GIF, JPEG, LBM, PCX, PNG, PNM (PPM/PGM/PBM), QOI, TGA, XCF, XPM, and simple SVG format images. It can also load AVIF, JPEG-XL, TIFF, and WebP images, depending on build options (see the note below for details.) -*homepage*: +*homepage*: version |toolchain ----------|----------------- +---------|------------------ ``2.0.3``|``GCCcore/6.4.0`` +``2.6.3``|``GCCcore/11.3.0`` + +### SDL2_mixer + +Due to popular demand, here is a simple multi-channel audio mixer. It supports 8 channels of 16 bit stereo audio, plus a single channel of music. It can load FLAC, MP3, Ogg, VOC, and WAV format audio. It can also load MIDI, MOD, and Opus audio, depending on build options (see the note below for details.) + +*homepage*: + +version |toolchain +---------|------------------ +``2.6.3``|``GCCcore/11.3.0`` + +### SDL2_ttf + +This library is a wrapper around the FreeType and Harfbuzz libraries, allowing you to use TrueType fonts to render text in SDL applications. + +*homepage*: + +version |toolchain +----------|------------------ +``2.20.2``|``GCCcore/11.3.0`` ### SDL_image @@ -33097,6 +34013,16 @@ version |toolchain ``0.2.0``|``foss/2016b``, ``intel/2017b``, ``intel/2018a`` ``0.3.4``|``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/8.3.0``, ``foss/2018b``, ``iccifort/2020.4.304`` +### segment-anything + +The Segment Anything Model (SAM) produces high quality object masks from input prompts such as points or boxes, and it can be used to generate masks for all objects in an image. It has been trained on a dataset of 11 million images and 1.1 billion masks, and has strong zero-shot performance on a variety of segmentation tasks. + +*homepage*: + +version|toolchain +-------|-------------- +``1.0``|``foss/2022a`` + ### segmentation-models Python library with Neural Networks for Image Segmentation based on Keras and TensorFlow. @@ -33150,6 +34076,16 @@ version |versionsuffix |toolchain ``0.1.96``| |``GCC/10.2.0``, ``GCC/10.3.0`` ``0.1.97``| |``GCC/11.3.0`` +### sentinelsat + +Sentinelsat makes searching, downloading and retrieving the metadata of Sentinel satellite images from the Copernicus Open Access Hub easy. + +*homepage*: + +version |toolchain +---------|------------------ +``1.2.1``|``GCCcore/11.3.0`` + ### sep Python and C library for Source Extraction and Photometry. (this easyconfig provides python library only) @@ -33291,9 +34227,20 @@ Easily download, build, install, upgrade, and uninstall Python packages *homepage*: version |versionsuffix|toolchain -----------|-------------|---------- +----------|-------------|------------------ ``1.4.2`` | |``system`` ``41.0.1``|``-py3`` |``system`` +``64.0.3``| |``GCCcore/12.2.0`` + +### setuptools-rust + +setuptools-rust is a plugin for setuptools to build Rust Python extensions implemented with PyO3 or rust-cpython. + +*homepage*: + +version |toolchain +---------|------------------ +``1.6.0``|``GCCcore/12.3.0`` ### Seurat @@ -33310,6 +34257,7 @@ version |versionsuffix|toolchain ``3.1.5`` |``-R-4.0.0`` |``foss/2020a`` ``4.0.1`` |``-R-4.0.3`` |``foss/2020b`` ``4.0.3`` |``-R-4.0.3`` |``foss/2020b`` +``4.1.0`` |``-R-4.1.0`` |``foss/2021a`` ``4.2.0`` |``-R-4.2.1`` |``foss/2022a`` ``4.3.0`` |``-R-4.1.2`` |``foss/2021b`` ``4.3.0`` |``-R-4.2.1`` |``foss/2022a`` @@ -33343,6 +34291,7 @@ SeuratWrappers is a collection of community-provided methods and extensions for version |versionsuffix|toolchain ------------|-------------|-------------- ``20210528``|``-R-4.0.3`` |``foss/2020b`` +``20221022``|``-R-4.2.1`` |``foss/2022a`` ### sf @@ -33432,7 +34381,7 @@ version |versionsuffix |toolchain ``1.8.1.post1``| |``GCC/11.2.0`` ``1.8.2`` | |``foss/2021b``, ``foss/2022a`` ``1.8a1`` | |``GCC/10.2.0``, ``GCC/10.3.0``, ``iccifort/2020.4.304`` -``2.0.1`` | |``foss/2022b`` +``2.0.1`` | |``foss/2022b``, ``gfbf/2023a`` ### sharutils @@ -33751,14 +34700,14 @@ SIONlib is a scalable I/O library for parallel access to task-local files. The *homepage*: version |versionsuffix|toolchain ----------|-------------|---------------------------------------------------------------------------- +---------|-------------|------------------------------------------------------------------------------ ``1.6.1``| |``foss/2016a`` ``1.6.1``|``-tools`` |``foss/2016a`` ``1.7.1``| |``foss/2017a`` ``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/11.2.0``, ``GCCcore/11.3.0`` +``1.7.7``|``-tools`` |``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### SIP @@ -33966,6 +34915,16 @@ version |toolchain ---------|--------------- ``0.4.0``|``gompi/2021b`` +### slurm-drmaa + +DRMAA for Slurm Workload Manager (Slurm) is an implementation of Open Grid Forum Distributed Resource Management Application API (DRMAA) version 1 for submission and control of jobs to Slurm. Using DRMAA, grid applications builders, portal developers and ISVs can use the same high-level API to link their software with different cluster/resource management systems. + +*homepage*: + +version |toolchain +---------|------------------ +``1.1.3``|``GCCcore/12.2.0`` + ### smafa Smafa attempts to align or cluster pre-aligned biological sequences, handling sequences which are all the same length. @@ -34033,8 +34992,8 @@ smith-waterman-gotoh alignment algorithm. *homepage*: version |toolchain -------------|----------------------------------------------------------------------------- -``20160702``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` +------------|------------------------------------------------------------------------------------------------- +``20160702``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/9.3.0`` ### Smoldyn @@ -34095,6 +35054,7 @@ version |versionsuffix |toolchain ``6.10.0``| |``foss/2021b`` ``7.18.2``| |``foss/2021b`` ``7.22.0``| |``foss/2022a`` +``7.32.3``| |``foss/2022b`` ### SNAP @@ -34376,13 +35336,14 @@ Space Ranger is a set of analysis pipelines that process Visium spatial RNA-seq *homepage*: version |toolchain ----------|-------------- +---------|------------------------------ ``1.1.0``|``GCC/9.3.0`` ``1.2.2``|``GCC/9.3.0`` ``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`` +``2.1.0``|``GCC/11.3.0``, ``GCC/12.2.0`` ### Spack @@ -34527,6 +35488,7 @@ Very fast, header-only/compiled, C++ logging library. version |toolchain ----------|-------------------------------------- ``1.9.2`` |``GCCcore/10.3.0`` +``1.10.0``|``GCCcore/11.2.0`` ``1.11.0``|``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### SpectrA @@ -34578,12 +35540,12 @@ Spglib is a C library for finding and handling crystal symmetries. *homepage*: version |toolchain -----------|------------------------- +----------|-------------------------------------- ``1.9.2`` |``intel/2016.02-GCC-4.9`` ``1.9.9`` |``intel/2017b`` ``1.16.1``|``GCCcore/10.2.0`` ``1.16.2``|``GCCcore/10.3.0`` -``2.0.2`` |``GCCcore/11.3.0`` +``2.0.2`` |``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ### spglib-python @@ -34656,6 +35618,7 @@ Sparse InversE Covariance estimation for Ecological Association and Statistical version |versionsuffix|toolchain ------------|-------------|--------------- ``1.0.0`` |``-R-3.4.4`` |``intel/2018a`` +``1.1.1`` |``-R-4.2.1`` |``foss/2022a`` ``20160830``|``-R-3.3.1`` |``intel/2016b`` ### SplAdder @@ -34739,8 +35702,8 @@ SPOOLES is a library for solving sparse real and complex linear systems of equa *homepage*: version|toolchain --------|--------------- -``2.2``|``gompi/2021a`` +-------|-------------------------------- +``2.2``|``gompi/2021a``, ``gompi/2022b`` ### SPOTPY @@ -34945,9 +35908,10 @@ Stack is a cross-platform program for developing Haskell projects. It is intende *homepage*: -version |versionsuffix|toolchain ----------|-------------|---------- -``2.3.3``|``-x86_64`` |``system`` +version |versionsuffix|toolchain +----------|-------------|---------- +``2.3.3`` |``-x86_64`` |``system`` +``2.11.1``|``-x86_64`` |``system`` ### Stacks @@ -35039,6 +36003,7 @@ version |toolchain ``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``, ``GCC/12.2.0`` +``2.7.11a`` |``GCC/12.3.0`` ### STAR-CCM+ @@ -35258,8 +36223,8 @@ The program structure is a free software package for using multi-locus genotype *homepage*: version |toolchain ----------|----------------------------------------------------------------------------------------------------- -``2.3.4``|``GCC/12.2.0``, ``GCC/8.2.0-2.31.1``, ``iccifort/2019.3.199-GCC-8.3.0-2.32``, ``iccifort/2019.5.281`` +---------|--------------------------------------------------------------------------------------------------------------------- +``2.3.4``|``GCC/11.3.0``, ``GCC/12.2.0``, ``GCC/8.2.0-2.31.1``, ``iccifort/2019.3.199-GCC-8.3.0-2.32``, ``iccifort/2019.5.281`` ### Structure_threader @@ -35291,6 +36256,16 @@ version |toolchain ------------|-------------- ``20160529``|``foss/2020b`` +### SuAVE-biomat + +Surface Assessment via Grid Evaluation (SuAVE) for Every Surface Curvature and Cavity Shape + +*homepage*: + +version |toolchain +------------------|--------------- +``2.0.0-20230815``|``intel/2023a`` + ### Subread High performance read alignment, quantification and mutation discovery @@ -35416,6 +36391,7 @@ version |toolchain ``6.2.0``|``foss/2020b``, ``intel/2020b`` ``6.3.0``|``foss/2021b``, ``foss/2022a`` ``6.5.1``|``foss/2022a`` +``6.6.0``|``foss/2022b`` ### SunPy @@ -35451,6 +36427,7 @@ version |versionsuffix |toolchain ``5.4.0``|``-trisolve-merge``|``intel/2020a`` ``6.4.0``| |``foss/2020a``, ``intel/2020a`` ``8.1.0``| |``foss/2022a`` +``8.1.2``| |``foss/2022b`` ### supermagic @@ -35612,6 +36589,7 @@ version |versionsuffix |toolchain ``3.0.12``|``-Python-3.7.2`` |``GCCcore/8.2.0`` ``4.0.1`` | |``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``4.0.2`` | |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``4.1.1`` | |``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### SWIPE @@ -35683,9 +36661,10 @@ version |versionsuffix |toolchain ``1.6.2`` |``-Python-3.8.2`` |``foss/2020a`` ``1.7.1`` | |``foss/2020b``, ``intel/2020b`` ``1.8`` | |``foss/2021a`` -``1.9`` | |``foss/2021b`` +``1.9`` | |``foss/2021b``, ``intel/2021b`` ``1.10.1``| |``foss/2022a``, ``intel/2022a`` ``1.11.1``| |``foss/2022a``, ``intel/2022a`` +``1.12`` | |``gfbf/2023a`` ### synthcity @@ -35731,8 +36710,19 @@ version |toolchain ## T -[tabix](#tabix) - [tabixpp](#tabixpp) - [taco](#taco) - [TagDust](#tagdust) - [TagLib](#taglib) - [Taiyaki](#taiyaki) - [TALON](#talon) - [TALYS](#talys) - [TAMkin](#tamkin) - [tantan](#tantan) - [Tapenade](#tapenade) - [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-Graphics](#tensorflow-graphics) - [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) - [thirdorder](#thirdorder) - [thurstonianIRT](#thurstonianirt) - [TiCCutils](#ticcutils) - [tidybayes](#tidybayes) - [tidymodels](#tidymodels) - [Tika](#tika) - [TiMBL](#timbl) - [time](#time) - [timm](#timm) - [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) - [TOPAS](#topas) - [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) - [Trinotate](#trinotate) - [Triplexator](#triplexator) - [TRIQS](#triqs) - [TRIQS-cthyb](#triqs-cthyb) - [TRIQS-dft_tools](#triqs-dft_tools) - [TRIQS-tprf](#triqs-tprf) - [tRNAscan-SE](#trnascan-se) - [TRUST](#trust) - [TRUST4](#trust4) - [Trycycler](#trycycler) - [tsne](#tsne) - [turbinesFoam](#turbinesfoam) - [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) +[T-Coffee](#t-coffee) - [tabix](#tabix) - [tabixpp](#tabixpp) - [taco](#taco) - [TagDust](#tagdust) - [TagLib](#taglib) - [Taiyaki](#taiyaki) - [TALON](#talon) - [TALYS](#talys) - [TAMkin](#tamkin) - [tantan](#tantan) - [Tapenade](#tapenade) - [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-compression](#tensorflow-compression) - [TensorFlow-Datasets](#tensorflow-datasets) - [TensorFlow-Graphics](#tensorflow-graphics) - [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) - [thirdorder](#thirdorder) - [thurstonianIRT](#thurstonianirt) - [TiCCutils](#ticcutils) - [tidybayes](#tidybayes) - [tidymodels](#tidymodels) - [Tika](#tika) - [TiMBL](#timbl) - [time](#time) - [timm](#timm) - [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) - [TOPAS](#topas) - [topaz](#topaz) - [TopHat](#tophat) - [torchaudio](#torchaudio) - [torchdata](#torchdata) - [torchinfo](#torchinfo) - [torchsampler](#torchsampler) - [torchtext](#torchtext) - [torchvf](#torchvf) - [torchvision](#torchvision) - [tornado](#tornado) - [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) - [Trinotate](#trinotate) - [Triplexator](#triplexator) - [TRIQS](#triqs) - [TRIQS-cthyb](#triqs-cthyb) - [TRIQS-dft_tools](#triqs-dft_tools) - [TRIQS-tprf](#triqs-tprf) - [tRNAscan-SE](#trnascan-se) - [TRUST](#trust) - [TRUST4](#trust4) - [Trycycler](#trycycler) - [tseriesEntropy](#tseriesentropy) - [tsne](#tsne) - [turbinesFoam](#turbinesfoam) - [TurboVNC](#turbovnc) - [TVB](#tvb) - [tvb-data](#tvb-data) - [TVB-deps](#tvb-deps) - [tvb-framework](#tvb-framework) - [tvb-library](#tvb-library) - [TWL-NINJA](#twl-ninja) - [TXR](#txr) - [typing-extensions](#typing-extensions) + +### T-Coffee + +A collection of tools for Computing, Evaluating and Manipulating Multiple Alignments of DNA, RNA, Protein Sequences and Structures + +*homepage*: + +version |toolchain +--------------------|---------- +``13.45.61.3c310a9``|``system`` +``13.46.0.919e8c6b``|``system`` ### tabix @@ -35753,6 +36743,7 @@ C++ wrapper to tabix indexer version |toolchain ---------|------------------------------------------------------------- ``1.1.0``|``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/9.3.0`` +``1.1.2``|``GCC/11.3.0`` ### taco @@ -35905,6 +36896,7 @@ version |toolchain ``2020.3`` |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``2021.4.0`` |``GCCcore/11.2.0`` ``2021.5.0`` |``GCCcore/11.3.0`` +``2021.10.0`` |``GCCcore/12.2.0`` ### tbl2asn @@ -35918,6 +36910,7 @@ version |versionsuffix|toolchain ``20180227``|``-linux64`` |``system`` ``20200302``|``-linux64`` |``system`` ``20220427``|``-linux64`` |``system`` +``20230713``|``-linux64`` |``system`` ### TCC @@ -35977,6 +36970,7 @@ version |toolchain ``6.22.04``|``GCCcore/10.3.0`` ``6.24.01``|``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ``6.24.07``|``GCCcore/12.2.0`` +``6.24.10``|``GCCcore/12.3.0`` ### tecplot360ex @@ -36112,6 +37106,17 @@ version |versionsuffix |toolchain ``2.9.1`` |``-CUDA-11.7.0`` |``foss/2022a`` ``2.11.0``| |``foss/2022a`` ``2.11.0``|``-CUDA-11.7.0`` |``foss/2022a`` +``2.13.0``| |``foss/2022b``, ``foss/2023a`` + +### tensorflow-compression + +TensorFlow Compression (TFC) contains data compression tools for TensorFlow. + +*homepage*: + +version |versionsuffix |toolchain +----------|----------------|-------------- +``2.11.0``|``-CUDA-11.7.0``|``foss/2022a`` ### TensorFlow-Datasets @@ -36145,6 +37150,7 @@ version |versionsuffix |toolchain ``0.9.0`` |``-Python-3.7.4``|``foss/2019b`` ``0.12.1``| |``foss/2020b``, ``fosscuda/2020b`` ``0.16.0``| |``foss/2021b`` +``0.19.0``|``-CUDA-11.7.0`` |``foss/2022a`` ### TensorRT @@ -36419,9 +37425,9 @@ The `time' command runs another program, then displays information about the res *homepage*: version|toolchain --------|----------------------------------------------------------------------------------------------------------------------------------------------------------- +-------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ``1.7``|``system`` -``1.9``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``1.9``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ### timm @@ -36485,6 +37491,7 @@ version |versionsuffix |toolchain ``8.6.10``| |``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ``8.6.11``| |``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``8.6.12``| |``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +``8.6.13``| |``GCCcore/12.3.0`` ### Tkinter @@ -36513,6 +37520,7 @@ version |versionsuffix |toolchain ``3.9.6`` | |``GCCcore/11.2.0`` ``3.10.4``| |``GCCcore/11.3.0`` ``3.10.8``| |``GCCcore/12.2.0`` +``3.11.3``| |``GCCcore/12.3.0`` ### TM-align @@ -36742,6 +37750,17 @@ version |versionsuffix |toolchain ``0.10.0``|``-PyTorch-1.9.0`` |``fosscuda/2020b`` ``0.14.1``|``-PyTorch-1.12.0`` |``foss/2022a`` +### torchvf + +TorchVF is a unifying Python library for using vector fields for efficient proposal-free instance segmentation. + +*homepage*: + +version |versionsuffix |toolchain +---------|----------------|-------------- +``0.1.3``| |``foss/2022a`` +``0.1.3``|``-CUDA-11.7.0``|``foss/2022a`` + ### torchvision Datasets, Transforms and Models specific to Computer Vision @@ -36772,6 +37791,16 @@ version |versionsuffix |toolchain ``0.13.1``| |``foss/2022a`` ``0.13.1``|``-CUDA-11.7.0`` |``foss/2022a`` +### tornado + +Tornado is a Python web framework and asynchronous networking library. + +*homepage*: + +version |toolchain +---------|------------------ +``6.3.2``|``GCCcore/12.3.0`` + ### TotalView TotalView is a GUI-based source code defect analysis tool that gives you unprecedented control over processes and thread execution and visibility into program state and variables. It allows you to debug one or many processes and/or threads in a single window with complete control over program execution. This allows you to set breakpoints, stepping line by line through the code on a single thread, or with coordinated groups of processes or threads, and run or halt arbitrary sets of processes or threads. You can reproduce and troubleshoot difficult problems that can occur in concurrent programs that take advantage of threads, OpenMP, MPI, GPUs or coprocessors. @@ -36807,6 +37836,7 @@ version |versionsuffix |toolchain ``4.62.3``| |``GCCcore/11.2.0`` ``4.64.0``| |``GCCcore/11.3.0`` ``4.64.1``| |``GCCcore/12.2.0`` +``4.66.1``| |``GCCcore/12.3.0`` ### Tracer @@ -37145,6 +38175,16 @@ version |versionsuffix |toolchain ``0.5.2``| |``foss/2021a`` ``0.5.3``| |``foss/2021b`` +### tseriesEntropy + +Implements an Entropy measure of dependence based on the Bhattacharya-Hellinger-Matusita distance. Can be used as a (nonlinear) autocorrelation/crosscorrelation function for continuous and categorical time series. The package includes tests for serial dependence and nonlinearity based on it. Some routines have a parallel version that can be used in a multicore/cluster environment. The package makes use of S4 classes. + +*homepage*: + +version |versionsuffix|toolchain +---------|-------------|-------------- +``0.6-0``|``-R-4.2.1`` |``foss/2022a`` + ### tsne Python library containing T-SNE algorithms. @@ -37241,6 +38281,16 @@ version |toolchain ``0.97-cluster_only``|``GCC/10.2.0`` ``0.98-cluster_only``|``GCC/11.3.0`` +### TXR + +TXR is a pragmatic, convenient tool ready to take on your daily hacking challenges with its dual personality: its whole-document pattern matching and extraction language for scraping information from arbitrary text sources, and its powerful data-processing language to slice through problems like a hot knife through butter. Many tasks can be accomplished with TXR "one liners" directly from your system prompt. + +*homepage*: + +version|toolchain +-------|------------------ +``291``|``GCCcore/12.2.0`` + ### typing-extensions Typing Extensions - Backported and Experimental Type Hints for Python @@ -37260,7 +38310,7 @@ version |versionsuffix |toolchain ## U -[UCC](#ucc) - [UCC-CUDA](#ucc-cuda) - [UCLUST](#uclust) - [UCX](#ucx) - [UCX-CUDA](#ucx-cuda) - [ucx-py](#ucx-py) - [UCX-ROCm](#ucx-rocm) - [udocker](#udocker) - [UDUNITS](#udunits) - [UFL](#ufl) - [Ultralytics](#ultralytics) - [umap-learn](#umap-learn) - [UMI-tools](#umi-tools) - [umi4cPackage](#umi4cpackage) - [umis](#umis) - [UNAFold](#unafold) - [uncertainty-calibration](#uncertainty-calibration) - [unicore-uftp](#unicore-uftp) - [Unicycler](#unicycler) - [Unidecode](#unidecode) - [unimap](#unimap) - [units](#units) - [unixODBC](#unixodbc) - [unrar](#unrar) - [UnZip](#unzip) - [UQTk](#uqtk) - [USEARCH](#usearch) - [UShER](#usher) - [USPEX](#uspex) - [utf8proc](#utf8proc) - [util-linux](#util-linux) +[UCC](#ucc) - [UCC-CUDA](#ucc-cuda) - [UCLUST](#uclust) - [UCX](#ucx) - [UCX-CUDA](#ucx-cuda) - [ucx-py](#ucx-py) - [UCX-ROCm](#ucx-rocm) - [udocker](#udocker) - [UDUNITS](#udunits) - [UFL](#ufl) - [Ultralytics](#ultralytics) - [umap-learn](#umap-learn) - [UMI-tools](#umi-tools) - [umi4cPackage](#umi4cpackage) - [umis](#umis) - [UNAFold](#unafold) - [uncertainty-calibration](#uncertainty-calibration) - [unicore-uftp](#unicore-uftp) - [Unicycler](#unicycler) - [Unidecode](#unidecode) - [unifdef](#unifdef) - [UniFrac](#unifrac) - [unimap](#unimap) - [units](#units) - [unixODBC](#unixodbc) - [unrar](#unrar) - [UnZip](#unzip) - [UQTk](#uqtk) - [USEARCH](#usearch) - [UShER](#usher) - [USPEX](#uspex) - [utf8proc](#utf8proc) - [util-linux](#util-linux) ### UCC @@ -37502,6 +38552,26 @@ version |versionsuffix |toolchain ``1.1.1``|``-Python-3.7.4``|``GCCcore/8.3.0`` ``1.3.6``| |``GCCcore/11.3.0`` +### unifdef + +unifdef - selectively remove C preprocessor conditionals The unifdef utility selectively processes conditional C preprocessor and the additional text that they delimit, while otherwise leaving the file alone. + +*homepage*: + +version |toolchain +--------|------------------ +``2.12``|``GCCcore/11.3.0`` + +### UniFrac + +UniFrac is the de facto repository for high-performance phylogenetic diversity calculations. The methods in this repository are based on an implementation of the Strided State UniFrac algorithm which is faster, and uses less memory than Fast UniFrac. Strided State UniFrac supports Unweighted UniFrac, Weighted UniFrac, Generalized UniFrac, Variance Adjusted UniFrac and meta UniFrac, in both double and single precision (fp32). This repository also includes Stacked Faith (manuscript in preparation), a method for calculating Faith's PD that is faster and uses less memory than the Fast UniFrac-based reference implementation. + +*homepage*: + +version |toolchain +---------|-------------- +``1.3.2``|``foss/2022a`` + ### unimap Unimap is a fork of minimap2 optimized for assembly-to-reference alignment. It integrates the minigraph chaining algorithm and can align through long INDELs (up to 100kb by default) much faster than minimap2. Unimap is a better fit for resolving segmental duplications and is recommended over minimap2 for alignment between high-quality assemblies. Unimap does not replace minimap2 for other types of alignment. It drops the support of multi-part index and short-read mapping. Its long-read alignment is different from minimap2 but is not necessarily better. Unimap is more of a specialized minimap2 at the moment. @@ -37528,9 +38598,10 @@ unixODBC provides a uniform interface between application and database driver *homepage*: -version |toolchain ----------|-------------- -``2.3.7``|``foss/2018b`` +version |toolchain +----------|-------------- +``2.3.7`` |``foss/2018b`` +``2.3.11``|``foss/2022b`` ### unrar @@ -37644,7 +38715,7 @@ 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) - [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) - [visdom](#visdom) - [vispr](#vispr) - [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](#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) - [virtualenv](#virtualenv) - [VirtualGL](#virtualgl) - [Virtuoso-opensource](#virtuoso-opensource) - [visdom](#visdom) - [vispr](#vispr) - [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 @@ -37686,6 +38757,7 @@ version |toolchain ``3.18.1``|``gompi/2021b``, ``iimpi/2021b`` ``3.19.0``|``gompi/2022a`` ``3.20.0``|``gompi/2022a`` +``3.21.0``|``gompi/2022b``, ``gompi/2023a`` ### Vampir @@ -37824,6 +38896,7 @@ version |versionsuffix |toolchain ``1.0.2``|``-Python-3.8.2``|``GCC/9.3.0`` ``1.0.3``|``-R-4.1.0`` |``foss/2021a`` ``1.0.3``|``-R-4.1.2`` |``foss/2021b`` +``1.0.9``|``-R-4.2.1`` |``foss/2022a`` ### vcfnp @@ -37990,6 +39063,16 @@ version |toolchain ---------|-------------- ``2.2.4``|``foss/2022a`` +### virtualenv + +A tool for creating isolated virtual python environments. + +*homepage*: + +version |toolchain +-----------|------------------ +``20.23.1``|``GCCcore/12.3.0`` + ### 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. @@ -38001,6 +39084,7 @@ version |toolchain ``2.6.1``|``foss/2018b`` ``2.6.2``|``GCCcore/9.3.0`` ``3.0`` |``GCC/11.2.0`` +``3.1`` |``GCC/12.3.0`` ### Virtuoso-opensource @@ -38038,9 +39122,10 @@ VisPy is a high-performance interactive 2D/3D data visualization library levera *homepage*: -version |toolchain ----------|------------------------------- -``0.6.6``|``foss/2020b``, ``intel/2020b`` +version |toolchain +----------|------------------------------- +``0.6.6`` |``foss/2020b``, ``intel/2020b`` +``0.12.2``|``foss/2022a`` ### vitessce-python @@ -38262,6 +39347,7 @@ version |versionsuffix |toolchain ``8.1.1`` |``-Python-3.6.6`` |``foss/2018b``, ``fosscuda/2018b`` ``8.2.0`` | |``foss/2021a`` ``8.2.0`` |``-Python-2.7.15``|``foss/2019a`` +``8.2.0`` |``-Python-2.7.16``|``foss/2019b`` ``8.2.0`` |``-Python-3.7.2`` |``foss/2019a``, ``intel/2019a`` ``8.2.0`` |``-Python-3.7.4`` |``foss/2019b`` ``8.2.0`` |``-Python-3.8.2`` |``foss/2020a``, ``fosscuda/2020a``, ``intel/2020a`` @@ -38326,7 +39412,7 @@ version |toolchain ## W -[wandb](#wandb) - [Wannier90](#wannier90) - [WannierTools](#wanniertools) - [Wayland](#wayland) - [Waylandpp](#waylandpp) - [WCSLIB](#wcslib) - [WCT](#wct) - [wcwidth](#wcwidth) - [webin-cli](#webin-cli) - [WebKitGTK+](#webkitgtk+) - [WebSocket++](#websocket++) - [WEKA](#weka) - [wget](#wget) - [wgsim](#wgsim) - [WHAM](#wham) - [WhatsHap](#whatshap) - [wheel](#wheel) - [WIEN2k](#wien2k) - [WildMagic](#wildmagic) - [Winnowmap](#winnowmap) - [WisecondorX](#wisecondorx) - [WISExome](#wisexome) - [wkhtmltopdf](#wkhtmltopdf) - [worker](#worker) - [wpebackend-fdo](#wpebackend-fdo) - [WPS](#wps) - [wrapt](#wrapt) - [WRF](#wrf) - [WRF-Fire](#wrf-fire) - [wrf-python](#wrf-python) - [wtdbg2](#wtdbg2) - [wxPropertyGrid](#wxpropertygrid) - [wxPython](#wxpython) - [wxWidgets](#wxwidgets) +[wandb](#wandb) - [Wannier90](#wannier90) - [WannierTools](#wanniertools) - [Wayland](#wayland) - [Waylandpp](#waylandpp) - [WCSLIB](#wcslib) - [WCT](#wct) - [wcwidth](#wcwidth) - [webin-cli](#webin-cli) - [WebKitGTK+](#webkitgtk+) - [WebSocket++](#websocket++) - [WEKA](#weka) - [WFA2](#wfa2) - [wget](#wget) - [wgsim](#wgsim) - [WHAM](#wham) - [WhatsHap](#whatshap) - [wheel](#wheel) - [WIEN2k](#wien2k) - [WildMagic](#wildmagic) - [Winnowmap](#winnowmap) - [WisecondorX](#wisecondorx) - [WISExome](#wisexome) - [wkhtmltopdf](#wkhtmltopdf) - [worker](#worker) - [wpebackend-fdo](#wpebackend-fdo) - [WPS](#wps) - [wrapt](#wrapt) - [WRF](#wrf) - [WRF-Fire](#wrf-fire) - [wrf-python](#wrf-python) - [wtdbg2](#wtdbg2) - [wxPropertyGrid](#wxpropertygrid) - [wxPython](#wxpython) - [wxWidgets](#wxwidgets) ### wandb @@ -38377,6 +39463,7 @@ version |toolchain ----------|-------------------------------------- ``1.20.0``|``GCCcore/11.3.0`` ``1.21.0``|``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``1.22.0``|``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### Waylandpp @@ -38442,6 +39529,7 @@ version |toolchain ``2.24.1``|``GCC/8.2.0-2.31.1`` ``2.27.4``|``GCC/10.3.0``, ``GCC/8.3.0`` ``2.37.1``|``GCC/11.2.0`` +``2.40.4``|``GCC/11.3.0`` ### WebSocket++ @@ -38464,6 +39552,16 @@ version |versionsuffix |toolchain ``3.6.12``|``-Java-1.7.0_80``|``system`` ``3.7.0`` |``-Java-1.7.0_80``|``system`` +### WFA2 + +The wavefront alignment (WFA) algorithm is an exact gap-affine algorithm that takes advantage of homologous regions between the sequences to accelerate the alignment process. + +*homepage*: + +version |toolchain +---------|------------------ +``2.3.3``|``GCCcore/11.3.0`` + ### wget GNU Wget is a free software package for retrieving files using HTTP, HTTPS and FTP, the most widely-used Internet protocols. It is a non-interactive commandline tool, so it may easily be called from scripts, cron jobs, terminals without X-Windows support, etc. @@ -38619,13 +39717,14 @@ version |versionsuffix |toolchain ### wpebackend-fdo -WPE WebKit allows embedders to create simple and performant systems based on Web platform technologies. It is a WebKit port designed with flexibility and hardware acceleration in mind, leveraging common 3D graphics APIs for best performance. +WPE WebKit allows embedders to create simple and performant systems based on Web platform technologies. It is a WebKit port designed with flexibility and hardware acceleration in mind, leveraging common 3D graphics APIs for best performance. *homepage*: version |toolchain ----------|------------------ ``1.13.1``|``GCCcore/11.2.0`` +``1.14.1``|``GCCcore/11.3.0`` ### WPS @@ -38651,8 +39750,8 @@ The aim of the wrapt module is to provide a transparent object proxy for Python, *homepage*: version |toolchain -----------|------------------------------- -``1.15.0``|``foss/2022a``, ``intel/2022a`` +----------|----------------------------------------------- +``1.15.0``|``foss/2022a``, ``gfbf/2022b``, ``intel/2022a`` ### WRF @@ -38733,6 +39832,7 @@ version |versionsuffix |toolchain ``4.0.7.post2``|``-Python-3.7.4`` |``GCC/8.3.0`` ``4.1.1`` | |``foss/2021a`` ``4.2.0`` | |``foss/2021b`` +``4.2.1`` | |``foss/2022a`` ### wxWidgets @@ -38749,7 +39849,7 @@ version |toolchain ``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`` +``3.2.2.1``|``GCC/12.2.0``, ``GCC/12.3.0`` ## X @@ -38798,7 +39898,7 @@ x264 is a free software library and application for encoding video streams into *homepage*: version |toolchain -------------|--------------------------------- +------------|-------------------------------------- ``20160114``|``gimkl/2.11.5``, ``intel/2016a`` ``20160430``|``foss/2016a``, ``intel/2016a`` ``20160614``|``foss/2016b``, ``intel/2016b`` @@ -38816,7 +39916,7 @@ version |toolchain ``20210414``|``GCCcore/10.3.0`` ``20210613``|``GCCcore/11.2.0`` ``20220620``|``GCCcore/11.3.0`` -``20230226``|``GCCcore/12.2.0`` +``20230226``|``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### x265 @@ -38825,7 +39925,7 @@ 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`` @@ -38834,7 +39934,7 @@ version|toolchain ``3.0``|``GCCcore/8.2.0`` ``3.2``|``GCCcore/8.3.0`` ``3.3``|``GCCcore/10.2.0``, ``GCCcore/9.3.0`` -``3.5``|``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +``3.5``|``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### XALT @@ -39242,7 +40342,7 @@ version |toolchain ``1.19.1``|``GCCcore/6.3.0``, ``GCCcore/6.4.0`` ``1.19.2``|``GCCcore/10.2.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0`` ``1.19.3``|``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` -``1.20.0``|``GCCcore/12.3.0`` +``1.20.0``|``GCCcore/12.3.0``, ``GCCcore/13.2.0`` ### XPLOR-NIH @@ -39266,7 +40366,7 @@ version |versionsuffix |toolchain ``1.2.2``|``-X11-20180131``|``GCCcore/6.4.0`` ``1.2.3``| |``GCCcore/7.3.0`` ``1.2.4``| |``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``1.2.5``| |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``1.2.5``| |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ### xproto @@ -39348,6 +40448,7 @@ version |toolchain ``1.20.13``|``GCCcore/11.2.0`` ``21.1.3`` |``GCCcore/11.3.0`` ``21.1.6`` |``GCCcore/12.2.0`` +``21.1.8`` |``GCCcore/12.3.0`` ### xxd @@ -39358,6 +40459,7 @@ xxd is part of the VIM package and this will only install xxd, not vim! xxd conv version |toolchain ------------|------------------------------------------------------------------------------ ``8.2.4220``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``9.0.1696``|``GCCcore/12.2.0`` ### xxHash @@ -39387,6 +40489,7 @@ version |versionsuffix |toolchain ``5.2.5``| |``GCCcore/10.1.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/9.3.0`` ``5.2.7``| |``GCCcore/12.2.0`` ``5.4.2``| |``GCCcore/12.3.0``, ``GCCcore/13.1.0`` +``5.4.4``| |``GCCcore/13.2.0`` ## Y @@ -39448,6 +40551,7 @@ version |toolchain ---------|------------------------- ``3.4.2``|``intel/2016.02-GCC-4.9`` ``5.0.4``|``intel/2021a`` +``5.1.2``|``intel/2021b`` ### yaml-cpp @@ -39539,14 +40643,20 @@ Z3 is a theorem prover from Microsoft Research. *homepage*: -version |toolchain -----------|------------------------------------ -``4.8.9`` |``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``4.8.10``|``GCCcore/10.2.0`` -``4.8.11``|``GCCcore/10.3.0`` -``4.8.12``|``GCCcore/11.2.0`` -``4.8.16``|``GCCcore/11.3.0`` -``4.10.2``|``GCCcore/11.3.0`` +version |versionsuffix |toolchain +----------|------------------|-------------------------------------- +``4.8.9`` | |``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``4.8.10``| |``GCCcore/10.2.0`` +``4.8.10``|``-Python-3.8.6`` |``GCCcore/10.2.0`` +``4.8.11``| |``GCCcore/10.3.0`` +``4.8.11``|``-Python-3.9.5`` |``GCCcore/10.3.0`` +``4.8.12``| |``GCCcore/11.2.0`` +``4.8.12``|``-Python-3.9.6`` |``GCCcore/11.2.0`` +``4.8.16``| |``GCCcore/11.3.0`` +``4.8.16``|``-Python-3.10.4``|``GCCcore/11.3.0`` +``4.10.2``| |``GCCcore/11.3.0`` +``4.10.2``|``-Python-3.10.4``|``GCCcore/11.3.0`` +``4.12.2``| |``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### zarr @@ -39561,6 +40671,7 @@ version |versionsuffix |toolchain ``2.8.1`` | |``foss/2020b`` ``2.10.1``| |``foss/2021a`` ``2.13.3``| |``foss/2021b``, ``foss/2022a`` +``2.16.0``| |``foss/2022b`` ### ZeroMQ @@ -39577,7 +40688,7 @@ version |toolchain ``4.2.5``|``foss/2018a``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018a``, ``intel/2018b`` ``4.3.2``|``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``4.3.3``|``GCCcore/10.2.0`` -``4.3.4``|``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +``4.3.4``|``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### zfp @@ -39643,7 +40754,7 @@ version |toolchain ``1.2.10``|``system`` ``1.2.11``|``FCC/4.5.0``, ``GCCcore/10.1.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0``, ``GCCcore/11.2.0``, ``GCCcore/5.4.0``, ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.1.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/7.4.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/8.4.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GCCcore/9.4.0``, ``GCCcore/system``, ``gimkl/2017a``, ``system`` ``1.2.12``|``GCCcore/11.3.0``, ``GCCcore/12.1.0``, ``GCCcore/12.2.0``, ``GCCcore/9.5.0``, ``system`` -``1.2.13``|``GCCcore/11.4.0``, ``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``system`` +``1.2.13``|``GCCcore/11.4.0``, ``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``GCCcore/13.2.0``, ``system`` ### zlib-ng diff --git a/docs/version-specific/toolchain-opts.md b/docs/version-specific/toolchain-opts.md index c5514657b..52afd923a 100644 --- a/docs/version-specific/toolchain-opts.md +++ b/docs/version-specific/toolchain-opts.md @@ -2,7 +2,7 @@ *(see also* ``eb --avail-toolchain-opts `` *)* -[cgmpich](#cgmpich) - [cgmpolf](#cgmpolf) - [cgmvapich2](#cgmvapich2) - [cgmvolf](#cgmvolf) - [cgompi](#cgompi) - [cgoolf](#cgoolf) - [ClangGCC](#clanggcc) - [CrayCCE](#craycce) - [CrayGNU](#craygnu) - [CrayIntel](#crayintel) - [CrayPGI](#craypgi) - [FCC](#fcc) - [ffmpi](#ffmpi) - [foss](#foss) - [fosscuda](#fosscuda) - [Fujitsu](#fujitsu) - [GCC](#gcc) - [GCCcore](#gcccore) - [gcccuda](#gcccuda) - [gfbf](#gfbf) - [gimkl](#gimkl) - [gimpi](#gimpi) - [gimpic](#gimpic) - [giolf](#giolf) - [giolfc](#giolfc) - [gmacml](#gmacml) - [gmkl](#gmkl) - [gmklc](#gmklc) - [gmpich2](#gmpich2) - [gmpich](#gmpich) - [gmpit](#gmpit) - [gmpolf](#gmpolf) - [gmvapich2](#gmvapich2) - [gmvolf](#gmvolf) - [GNU](#gnu) - [goalf](#goalf) - [gobff](#gobff) - [goblf](#goblf) - [gofbf](#gofbf) - [golf](#golf) - [golfc](#golfc) - [gomkl](#gomkl) - [gomklc](#gomklc) - [gompi](#gompi) - [gompic](#gompic) - [goolf](#goolf) - [goolfc](#goolfc) - [gpsmpi](#gpsmpi) - [gpsolf](#gpsolf) - [gqacml](#gqacml) - [gsmpi](#gsmpi) - [gsolf](#gsolf) - [iccifort](#iccifort) - [iccifortcuda](#iccifortcuda) - [ictce](#ictce) - [iibff](#iibff) - [iimkl](#iimkl) - [iimklc](#iimklc) - [iimpi](#iimpi) - [iimpic](#iimpic) - [iiqmpi](#iiqmpi) - [impich](#impich) - [impmkl](#impmkl) - [intel-compilers](#intel-compilers) - [intel-para](#intel-para) - [intel](#intel) - [intelcuda](#intelcuda) - [iomkl](#iomkl) - [iomklc](#iomklc) - [iompi](#iompi) - [iompic](#iompic) - [ipsmpi](#ipsmpi) - [iqacml](#iqacml) - [ismkl](#ismkl) - [NVHPC](#nvhpc) - [nvofbf](#nvofbf) - [nvompi](#nvompi) - [nvompic](#nvompic) - [nvpsmpi](#nvpsmpi) - [nvpsmpic](#nvpsmpic) - [PGI](#pgi) - [pmkl](#pmkl) - [pomkl](#pomkl) - [pompi](#pompi) - [system](#system) - [xlcxlf](#xlcxlf) - [xlmpich2](#xlmpich2) - [xlmpich](#xlmpich) - [xlmvapich2](#xlmvapich2) - [xlompi](#xlompi) +[cgmpich](#cgmpich) - [cgmpolf](#cgmpolf) - [cgmvapich2](#cgmvapich2) - [cgmvolf](#cgmvolf) - [cgompi](#cgompi) - [cgoolf](#cgoolf) - [ClangGCC](#clanggcc) - [CrayCCE](#craycce) - [CrayGNU](#craygnu) - [CrayIntel](#crayintel) - [CrayPGI](#craypgi) - [FCC](#fcc) - [ffmpi](#ffmpi) - [foss](#foss) - [fosscuda](#fosscuda) - [Fujitsu](#fujitsu) - [GCC](#gcc) - [GCCcore](#gcccore) - [gcccuda](#gcccuda) - [gfbf](#gfbf) - [gimkl](#gimkl) - [gimpi](#gimpi) - [gimpic](#gimpic) - [giolf](#giolf) - [giolfc](#giolfc) - [gmacml](#gmacml) - [gmkl](#gmkl) - [gmklc](#gmklc) - [gmpich2](#gmpich2) - [gmpich](#gmpich) - [gmpit](#gmpit) - [gmpolf](#gmpolf) - [gmvapich2](#gmvapich2) - [gmvolf](#gmvolf) - [GNU](#gnu) - [goalf](#goalf) - [gobff](#gobff) - [goblf](#goblf) - [gofbf](#gofbf) - [golf](#golf) - [golfc](#golfc) - [gomkl](#gomkl) - [gomklc](#gomklc) - [gompi](#gompi) - [gompic](#gompic) - [goolf](#goolf) - [goolfc](#goolfc) - [gpsmpi](#gpsmpi) - [gpsolf](#gpsolf) - [gqacml](#gqacml) - [gsmpi](#gsmpi) - [gsolf](#gsolf) - [iccifort](#iccifort) - [iccifortcuda](#iccifortcuda) - [ictce](#ictce) - [ifbf](#ifbf) - [iibff](#iibff) - [iimkl](#iimkl) - [iimklc](#iimklc) - [iimpi](#iimpi) - [iimpic](#iimpic) - [iiqmpi](#iiqmpi) - [impich](#impich) - [impmkl](#impmkl) - [intel-compilers](#intel-compilers) - [intel-para](#intel-para) - [intel](#intel) - [intelcuda](#intelcuda) - [iofbf](#iofbf) - [iomkl](#iomkl) - [iomklc](#iomklc) - [iompi](#iompi) - [iompic](#iompic) - [ipsmpi](#ipsmpi) - [iqacml](#iqacml) - [ismkl](#ismkl) - [NVHPC](#nvhpc) - [nvofbf](#nvofbf) - [nvompi](#nvompi) - [nvompic](#nvompic) - [nvpsmpi](#nvpsmpi) - [nvpsmpic](#nvpsmpic) - [PGI](#pgi) - [pmkl](#pmkl) - [pomkl](#pomkl) - [pompi](#pompi) - [system](#system) - [xlcxlf](#xlcxlf) - [xlmpich2](#xlmpich2) - [xlmpich](#xlmpich) - [xlmvapich2](#xlmvapich2) - [xlompi](#xlompi) ## cgmpich @@ -2284,6 +2284,50 @@ option |description ``verbose`` |Verbose output |``False`` ``veryloose`` |Very loose precision |``False`` +## ifbf + +### Available options for ifbf toolchain + +option |description |default +-------------------------|------------------------------------------------------------------------------------------------------------------------------------------|--------- +``32bit`` |Compile 32bit target |``False`` +``cciscxx`` |Use CC as CXX |``False`` +``cstd`` |Specify C standard |``None`` +``debug`` |Enable debug |``False`` +``defaultopt`` |Default compiler optimizations |``False`` +``defaultprec`` |Default precision |``False`` +``error-unknown-option`` |Error instead of warning for unknown options |``False`` +``extra_cflags`` |Specify extra CFLAGS options. |``None`` +``extra_cxxflags`` |Specify extra CXXFLAGS options. |``None`` +``extra_f90flags`` |Specify extra F90FLAGS options. |``None`` +``extra_fcflags`` |Specify extra FCFLAGS options. |``None`` +``extra_fflags`` |Specify extra FFLAGS options. |``None`` +``i8`` |Integers are 8 byte integers |``False`` +``ieee`` |Adhere to IEEE-754 rules |``False`` +``intel-static`` |Link Intel provided libraries statically |``False`` +``loose`` |Loose precision |``False`` +``lowopt`` |Low compiler optimizations |``False`` +``no-icc`` |Don't set Intel specific macros |``False`` +``noopt`` |Disable compiler optimizations |``False`` +``oneapi`` |Use oneAPI compilers icx/icpx/ifx instead of classic compilers |``None`` +``oneapi_c_cxx`` |Use oneAPI C/C++ compilers icx/icpx instead of classic Intel C/C++ compilers (auto-enabled for Intel compilers version 2022.2.0, or newer)|``None`` +``oneapi_fortran`` |Use oneAPI Fortran compiler ifx instead of classic Intel Fortran compiler |``False`` +``openmp`` |Enable OpenMP |``False`` +``opt`` |High compiler optimizations |``False`` +``optarch`` |Enable architecture optimizations |``True`` +``packed-linker-options``|Pack the linker options as comma separated list |``False`` +``pic`` |Use PIC |``False`` +``precise`` |High precision |``False`` +``r8`` |Real is 8 byte real |``False`` +``rpath`` |Use RPATH wrappers when --rpath is enabled in EasyBuild configuration |``True`` +``shared`` |Build shared library |``False`` +``static`` |Build static library |``False`` +``strict`` |Strict (highest) precision |``False`` +``unroll`` |Unroll loops |``False`` +``vectorize`` |Enable compiler auto-vectorization, default except for noopt and lowopt |``None`` +``verbose`` |Verbose output |``False`` +``veryloose`` |Very loose precision |``False`` + ## iibff ### Available options for iibff toolchain @@ -2803,6 +2847,51 @@ option |description ``verbose`` |Verbose output |``False`` ``veryloose`` |Very loose precision |``False`` +## iofbf + +### Available options for iofbf toolchain + +option |description |default +-------------------------|------------------------------------------------------------------------------------------------------------------------------------------|--------- +``32bit`` |Compile 32bit target |``False`` +``cciscxx`` |Use CC as CXX |``False`` +``cstd`` |Specify C standard |``None`` +``debug`` |Enable debug |``False`` +``defaultopt`` |Default compiler optimizations |``False`` +``defaultprec`` |Default precision |``False`` +``error-unknown-option`` |Error instead of warning for unknown options |``False`` +``extra_cflags`` |Specify extra CFLAGS options. |``None`` +``extra_cxxflags`` |Specify extra CXXFLAGS options. |``None`` +``extra_f90flags`` |Specify extra F90FLAGS options. |``None`` +``extra_fcflags`` |Specify extra FCFLAGS options. |``None`` +``extra_fflags`` |Specify extra FFLAGS options. |``None`` +``i8`` |Integers are 8 byte integers |``False`` +``ieee`` |Adhere to IEEE-754 rules |``False`` +``intel-static`` |Link Intel provided libraries statically |``False`` +``loose`` |Loose precision |``False`` +``lowopt`` |Low compiler optimizations |``False`` +``no-icc`` |Don't set Intel specific macros |``False`` +``noopt`` |Disable compiler optimizations |``False`` +``oneapi`` |Use oneAPI compilers icx/icpx/ifx instead of classic compilers |``None`` +``oneapi_c_cxx`` |Use oneAPI C/C++ compilers icx/icpx instead of classic Intel C/C++ compilers (auto-enabled for Intel compilers version 2022.2.0, or newer)|``None`` +``oneapi_fortran`` |Use oneAPI Fortran compiler ifx instead of classic Intel Fortran compiler |``False`` +``openmp`` |Enable OpenMP |``False`` +``opt`` |High compiler optimizations |``False`` +``optarch`` |Enable architecture optimizations |``True`` +``packed-linker-options``|Pack the linker options as comma separated list |``False`` +``pic`` |Use PIC |``False`` +``precise`` |High precision |``False`` +``r8`` |Real is 8 byte real |``False`` +``rpath`` |Use RPATH wrappers when --rpath is enabled in EasyBuild configuration |``True`` +``shared`` |Build shared library |``False`` +``static`` |Build static library |``False`` +``strict`` |Strict (highest) precision |``False`` +``unroll`` |Unroll loops |``False`` +``usempi`` |Use MPI compiler as default compiler |``False`` +``vectorize`` |Enable compiler auto-vectorization, default except for noopt and lowopt |``None`` +``verbose`` |Verbose output |``False`` +``veryloose`` |Very loose precision |``False`` + ## iomkl ### Available options for iomkl toolchain diff --git a/docs/version-specific/toolchains.md b/docs/version-specific/toolchains.md index 649b4960d..ae399fd0e 100644 --- a/docs/version-specific/toolchains.md +++ b/docs/version-specific/toolchains.md @@ -57,6 +57,7 @@ Name |Compiler(s) |MPI |Linear algebra |FFT **iccifort** |icc, ifort |*(none)* |*(none)* |*(none)* **iccifortcuda** |icc, ifort, CUDA|*(none)* |*(none)* |*(none)* **ictce** |icc, ifort |impi |imkl |imkl +**ifbf** |intel-compilers |*(none)* |FlexiBLAS |FFTW **iibff** |icc, ifort |impi |BLIS, libFLAME, ScaLAPACK|FFTW **iimkl** |icc, ifort |*(none)* |imkl |imkl **iimklc** |icc, ifort |*(none)* |imkl |imkl @@ -69,6 +70,7 @@ Name |Compiler(s) |MPI |Linear algebra |FFT **intel-compilers**|intel-compilers |*(none)* |*(none)* |*(none)* **intel-para** |icc, ifort |psmpi |imkl |imkl **intelcuda** |icc, ifort, CUDA|impi |imkl |imkl +**iofbf** |icc, ifort |OpenMPI |FlexiBLAS, ScaLAPACK |FFTW **iomkl** |icc, ifort |OpenMPI |imkl |imkl **iomklc** |icc, ifort, CUDA|OpenMPI |imkl |imkl **iompi** |icc, ifort |OpenMPI |*(none)* |*(none)*