From afed6e629fd9bc413049077437c38a0a3779045b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 11 Jun 2024 20:37:02 +0200 Subject: [PATCH] auto-update docs for EasyBuild v4.9.2 --- docs/version-specific/easyblocks.md | 6 + docs/version-specific/easyconfig-constants.md | 2 +- .../version-specific/easyconfig-parameters.md | 1 + docs/version-specific/supported-software.md | 1709 ++++++++++++++--- 4 files changed, 1400 insertions(+), 318 deletions(-) diff --git a/docs/version-specific/easyblocks.md b/docs/version-specific/easyblocks.md index 67ddb9c66..cc341ef65 100644 --- a/docs/version-specific/easyblocks.md +++ b/docs/version-specific/easyblocks.md @@ -22,6 +22,7 @@ - EB_TensorRT - JAR - PackedBinary + - EB_AEDT - EB_ANSYS - EB_ant - EB_AOCC @@ -37,6 +38,7 @@ - EB_MCR - EB_MotionCor2 - EB_NVHPC + - EB_optiSLang - EB_ORCA - EB_PGI - EB_Samcef @@ -87,6 +89,7 @@ - EB_OpenBabel - EB_OpenCV - EB_PSI + - EB_QuantumESPRESSOcmake - EB_ROOT - EB_ScaLAPACK - EB_SuperLU @@ -199,6 +202,7 @@ - EB_BLAT - EB_Bowtie2 - EB_BWISE + - EB_MetalWalls - EB_MSM - EB_mutil - EB_MXNet @@ -332,6 +336,7 @@ - EB_scipy - ModuleRC - PackedBinary + - EB_AEDT - EB_ANSYS - EB_ant - EB_AOCC @@ -347,6 +352,7 @@ - EB_MCR - EB_MotionCor2 - EB_NVHPC + - EB_optiSLang - EB_ORCA - EB_PGI - EB_Samcef diff --git a/docs/version-specific/easyconfig-constants.md b/docs/version-specific/easyconfig-constants.md index f09f085c0..961efad38 100644 --- a/docs/version-specific/easyconfig-constants.md +++ b/docs/version-specific/easyconfig-constants.md @@ -14,6 +14,6 @@ Constant name |Constant value ``OS_TYPE`` |``Darwin`` |System type (e.g. 'Linux' or 'Darwin') ``OS_VERSION`` |``UNKNOWN`` |System version ``SYSTEM`` |``{'name': 'system', 'version': 'system'}`` |System toolchain -``SYS_PYTHON_VERSION``|``3.9.6`` |System Python version (platform.python_version()) +``SYS_PYTHON_VERSION``|``3.12.3`` |System Python version (platform.python_version()) *(see also* ``eb --avail-easyconfig-constants`` *)* diff --git a/docs/version-specific/easyconfig-parameters.md b/docs/version-specific/easyconfig-parameters.md index d2a56d135..2ed5e4d7f 100644 --- a/docs/version-specific/easyconfig-parameters.md +++ b/docs/version-specific/easyconfig-parameters.md @@ -42,6 +42,7 @@ `hidden` |Install module file as 'hidden' by prefixing its version with '.' |`False` `installopts` |Extra options for installation |`""` `maxparallel` |Max degree of parallelism |`None` +`module_only` |Only generate module file |`False` `parallel` |Degree of parallelism for e.g. make (default: based on the number of cores, active cpuset and restrictions in ulimit) |`None` `patches` |List of patches to apply |`[]` `postinstallcmds` |Commands to run after the install step. |`[]` diff --git a/docs/version-specific/supported-software.md b/docs/version-specific/supported-software.md index d77f6b67b..dfaf8ecaa 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 3470 different software packages (incl. toolchains, bundles): +EasyBuild supports 3552 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) @@ -49,14 +49,15 @@ A software package for algebraic, geometric and combinatorial problems on linear *homepage*: -version |toolchain ----------|----------------------------------------------------- -``1.6.9``|``GCC/11.3.0``, ``GCC/8.2.0-2.31.1``, ``intel/2018b`` +version |toolchain +----------|----------------------------------------------------- +``1.6.9`` |``GCC/11.3.0``, ``GCC/8.2.0-2.31.1``, ``intel/2018b`` +``1.6.10``|``GCC/13.2.0`` ## A -[ABAQUS](#abaqus) - [ABINIT](#abinit) - [ABRA2](#abra2) - [ABRicate](#abricate) - [Abseil](#abseil) - [abTEM](#abtem) - [ABySS](#abyss) - [ack](#ack) - [ACTC](#actc) - [ada](#ada) - [AdapterRemoval](#adapterremoval) - [ADDA](#adda) - [ADF](#adf) - [ADIOS](#adios) - [adjustText](#adjusttext) - [ADMIXTURE](#admixture) - [ADOL-C](#adol-c) - [Advisor](#advisor) - [affinity](#affinity) - [AFNI](#afni) - [AGAT](#agat) - [AGeNT](#agent) - [AGFusion](#agfusion) - [AICSImageIO](#aicsimageio) - [AIMAll](#aimall) - [aiohttp](#aiohttp) - [ALADIN](#aladin) - [ALAMODE](#alamode) - [Albacore](#albacore) - [Albumentations](#albumentations) - [alevin-fry](#alevin-fry) - [ALFA](#alfa) - [Alfred](#alfred) - [ALL](#all) - [alleleCount](#allelecount) - [alleleIntegrator](#alleleintegrator) - [Allinea](#allinea) - [ALLPATHS-LG](#allpaths-lg) - [almosthere](#almosthere) - [Alpha](#alpha) - [AlphaFold](#alphafold) - [AlphaPulldown](#alphapulldown) - [ALPS](#alps) - [alsa-lib](#alsa-lib) - [AMAPVox](#amapvox) - [Amara](#amara) - [amask](#amask) - [Amber](#amber) - [AmberMini](#ambermini) - [AmberTools](#ambertools) - [AMD-LibM](#amd-libm) - [AMD-RNG](#amd-rng) - [AMD-SecureRNG](#amd-securerng) - [AMD-uProf](#amd-uprof) - [AMICA](#amica) - [AMOS](#amos) - [AMPHORA2](#amphora2) - [AMPL-MP](#ampl-mp) - [amplimap](#amplimap) - [AMPtk](#amptk) - [AMRFinderPlus](#amrfinderplus) - [AmrPlusPlus](#amrplusplus) - [AMS](#ams) - [Anaconda2](#anaconda2) - [Anaconda3](#anaconda3) - [anadama2](#anadama2) - [aNCI](#anci) - [andi](#andi) - [ANGEL](#angel) - [angsd](#angsd) - [ANIcalculator](#anicalculator) - [anndata](#anndata) - [Annif](#annif) - [Annocript](#annocript) - [annovar](#annovar) - [ANSYS](#ansys) - [ANSYS_CFD](#ansys_cfd) - [ant](#ant) - [ANTIC](#antic) - [antiSMASH](#antismash) - [ANTLR](#antlr) - [ANTs](#ants) - [anvio](#anvio) - [any2fasta](#any2fasta) - [AOCC](#aocc) - [AOFlagger](#aoflagger) - [AOMP](#aomp) - [APBS](#apbs) - [apex](#apex) - [APR](#apr) - [APR-util](#apr-util) - [AptaSUITE](#aptasuite) - [ARAGORN](#aragorn) - [Arb](#arb) - [Arcade-Learning-Environment](#arcade-learning-environment) - [arcasHLA](#arcashla) - [ARCH](#arch) - [Archive-Zip](#archive-zip) - [ArchR](#archr) - [archspec](#archspec) - [AreTomo2](#aretomo2) - [ARGoS](#argos) - [argtable](#argtable) - [aria2](#aria2) - [Arlequin](#arlequin) - [Armadillo](#armadillo) - [arosics](#arosics) - [ARPACK++](#arpack++) - [arpack-ng](#arpack-ng) - [ArrayFire](#arrayfire) - [Arriba](#arriba) - [Arrow](#arrow) - [arrow-R](#arrow-r) - [ART](#art) - [Artemis](#artemis) - [artic-ncov2019](#artic-ncov2019) - [ARTS](#arts) - [ArviZ](#arviz) - [ARWEN](#arwen) - [ASAP](#asap) - [ASAP3](#asap3) - [ASCAT](#ascat) - [ASE](#ase) - [ASF-SearchAPI](#asf-searchapi) - [ASHS](#ashs) - [Aspera-CLI](#aspera-cli) - [Aspera-Connect](#aspera-connect) - [assimp](#assimp) - [Assimulo](#assimulo) - [ASTRID](#astrid) - [astro-tulips](#astro-tulips) - [astropy](#astropy) - [at-spi2-atk](#at-spi2-atk) - [at-spi2-core](#at-spi2-core) - [ATAT](#atat) - [ATK](#atk) - [ATLAS](#atlas) - [atomate](#atomate) - [AtomPAW](#atompaw) - [atools](#atools) - [atropos](#atropos) - [ATSAS](#atsas) - [attr](#attr) - [attrdict](#attrdict) - [attrdict3](#attrdict3) - [augur](#augur) - [AUGUSTUS](#augustus) - [Austin](#austin) - [AUTO-07p](#auto-07p) - [Autoconf](#autoconf) - [Autoconf-archive](#autoconf-archive) - [AutoDock](#autodock) - [AutoDock-GPU](#autodock-gpu) - [AutoDock-Vina](#autodock-vina) - [AutoDockSuite](#autodocksuite) - [AutoGeneS](#autogenes) - [AutoGrid](#autogrid) - [Automake](#automake) - [AutoMap](#automap) - [autopep8](#autopep8) - [Autotools](#autotools) - [Avogadro2](#avogadro2) - [avro-cpp](#avro-cpp) - [awscli](#awscli) - [Ax](#ax) - [axel](#axel) +[ABAQUS](#abaqus) - [ABINIT](#abinit) - [ABRA2](#abra2) - [ABRicate](#abricate) - [Abseil](#abseil) - [abTEM](#abtem) - [ABySS](#abyss) - [ack](#ack) - [ACTC](#actc) - [ada](#ada) - [AdapterRemoval](#adapterremoval) - [ADDA](#adda) - [ADF](#adf) - [ADIOS](#adios) - [adjustText](#adjusttext) - [ADMIXTURE](#admixture) - [ADOL-C](#adol-c) - [Advisor](#advisor) - [AEDT](#aedt) - [affinity](#affinity) - [AFNI](#afni) - [AGAT](#agat) - [AGeNT](#agent) - [AGFusion](#agfusion) - [AICSImageIO](#aicsimageio) - [AIMAll](#aimall) - [aiohttp](#aiohttp) - [ALADIN](#aladin) - [ALAMODE](#alamode) - [Albacore](#albacore) - [Albumentations](#albumentations) - [alevin-fry](#alevin-fry) - [ALFA](#alfa) - [Alfred](#alfred) - [ALL](#all) - [alleleCount](#allelecount) - [alleleIntegrator](#alleleintegrator) - [Allinea](#allinea) - [ALLPATHS-LG](#allpaths-lg) - [almosthere](#almosthere) - [Alpha](#alpha) - [AlphaFold](#alphafold) - [AlphaPulldown](#alphapulldown) - [ALPS](#alps) - [alsa-lib](#alsa-lib) - [AMAPVox](#amapvox) - [Amara](#amara) - [amask](#amask) - [Amber](#amber) - [AmberMini](#ambermini) - [AmberTools](#ambertools) - [AMD-LibM](#amd-libm) - [AMD-RNG](#amd-rng) - [AMD-SecureRNG](#amd-securerng) - [AMD-uProf](#amd-uprof) - [amdahl](#amdahl) - [AMGX](#amgx) - [AMICA](#amica) - [AMOS](#amos) - [AMPHORA2](#amphora2) - [AMPL-MP](#ampl-mp) - [amplimap](#amplimap) - [AMPtk](#amptk) - [AMRFinderPlus](#amrfinderplus) - [AmrPlusPlus](#amrplusplus) - [AMS](#ams) - [Anaconda2](#anaconda2) - [Anaconda3](#anaconda3) - [anadama2](#anadama2) - [aNCI](#anci) - [andi](#andi) - [ANGEL](#angel) - [angsd](#angsd) - [ANIcalculator](#anicalculator) - [anndata](#anndata) - [Annif](#annif) - [Annocript](#annocript) - [annovar](#annovar) - [ANSYS](#ansys) - [ANSYS_CFD](#ansys_cfd) - [ant](#ant) - [ANTIC](#antic) - [antiSMASH](#antismash) - [ANTLR](#antlr) - [ANTs](#ants) - [anvio](#anvio) - [any2fasta](#any2fasta) - [AOCC](#aocc) - [AOFlagger](#aoflagger) - [AOMP](#aomp) - [APBS](#apbs) - [apex](#apex) - [APR](#apr) - [APR-util](#apr-util) - [AptaSUITE](#aptasuite) - [ARAGORN](#aragorn) - [Arb](#arb) - [Arcade-Learning-Environment](#arcade-learning-environment) - [arcasHLA](#arcashla) - [ARCH](#arch) - [Archive-Zip](#archive-zip) - [ArchR](#archr) - [archspec](#archspec) - [AreTomo2](#aretomo2) - [ARGoS](#argos) - [argtable](#argtable) - [aria2](#aria2) - [Arlequin](#arlequin) - [Armadillo](#armadillo) - [arosics](#arosics) - [ARPACK++](#arpack++) - [arpack-ng](#arpack-ng) - [ArrayFire](#arrayfire) - [Arriba](#arriba) - [Arrow](#arrow) - [arrow-R](#arrow-r) - [ART](#art) - [Artemis](#artemis) - [artic-ncov2019](#artic-ncov2019) - [ARTS](#arts) - [ArviZ](#arviz) - [ARWEN](#arwen) - [ASAP](#asap) - [ASAP3](#asap3) - [ASCAT](#ascat) - [ASE](#ase) - [ASF-SearchAPI](#asf-searchapi) - [ASHS](#ashs) - [Aspera-CLI](#aspera-cli) - [Aspera-Connect](#aspera-connect) - [assembly-stats](#assembly-stats) - [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 @@ -255,10 +256,11 @@ A small library for automatically adjustment of text position in matplotlib plot *homepage*: version |versionsuffix |toolchain ----------|-----------------|--------------- -``0.7.3``| |``foss/2021b`` +---------|-----------------|------------------------------ +``0.7.3``| |``foss/2021b``, ``foss/2023a`` ``0.7.3``|``-Python-3.6.6``|``foss/2018b`` ``0.7.3``|``-Python-3.7.2``|``intel/2019a`` +``1.1.1``| |``foss/2023a`` ### ADMIXTURE @@ -302,6 +304,16 @@ version |toolchain ``2023.0.0`` |``system`` ``2023.2.0`` |``system`` +### AEDT + +The Ansys Electronics Desktop (AEDT) is a platform that enables true electronics system design. AEDT provides access to the Ansys gold-standard electromagnetics simulation solutions such as Ansys HFSS, Ansys Maxwell, Ansys Q3D Extractor, Ansys SIwave, and Ansys Icepak using electrical CAD (ECAD) and mechanical CAD (MCAD) workflows. + +*homepage*: + +version |toolchain +----------|---------- +``2024R1``|``system`` + ### affinity A small C++ wrapper for managing Linux CPU sets and CPU affinity. It also includes a tool to report binding, which is useful for testing different binding options @@ -323,6 +335,7 @@ version |versionsuffix |toolchain ``18.1.09`` |``-Python-3.6.4`` |``intel/2018a`` ``18.3.00`` |``-Python-3.6.6`` |``foss/2018b`` ``19.0.01`` |``-Python-2.7.14``|``foss/2017b``, ``intel/2017b`` +``24.0.02`` | |``foss/2023a`` ``20160329``|``-Python-2.7.11``|``intel/2016a`` ### AGAT @@ -388,6 +401,7 @@ version |versionsuffix |toolchain ``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`` +``3.9.5``| |``GCCcore/13.2.0`` ### ALADIN @@ -442,6 +456,7 @@ version |toolchain ---------|------------------ ``0.4.3``|``GCCcore/11.2.0`` ``0.6.0``|``GCCcore/10.3.0`` +``0.9.0``|``GCCcore/13.2.0`` ### ALFA @@ -594,6 +609,7 @@ version |toolchain ---------|---------------------------------------------------------- ``1.2.4``|``GCCcore/9.3.0`` ``1.2.8``|``GCCcore/10.2.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``1.2.9``|``GCCcore/12.3.0`` ### AMAPVox @@ -719,6 +735,26 @@ version |toolchain ``3.5.671``|``system`` ``4.1.424``|``system`` +### amdahl + +This Python module contains a pseudo-application that can be used as a black box to reproduce Amdahl's Law. It does not do real calculations, nor any real communication, so can easily be overloaded. + +*homepage*: + +version |toolchain +---------|--------------- +``0.3.1``|``gompi/2023a`` + +### AMGX + +Distributed multigrid linear solver library on GPU + +*homepage*: + +version |versionsuffix |toolchain +---------|----------------|-------------- +``2.4.0``|``-CUDA-12.1.1``|``foss/2023a`` + ### AMICA Code for AMICA: Adaptive Mixture ICA with shared components @@ -933,9 +969,9 @@ anndata is a Python package for handling annotated data matrices in memory and o *homepage*: version |toolchain -----------------|-------------- +----------------|------------------------------ ``0.8.0`` |``foss/2022a`` -``0.9.2`` |``foss/2021a`` +``0.9.2`` |``foss/2021a``, ``foss/2021b`` ``0.10.5.post1``|``foss/2023a`` ### Annif @@ -1269,6 +1305,7 @@ ArchR is a full-featured R package for processing and analyzing single-cell ATAC version |versionsuffix|toolchain ---------|-------------|-------------- ``1.0.1``|``-R-4.1.2`` |``foss/2021b`` +``1.0.2``|``-R-4.2.2`` |``foss/2022b`` ``1.0.2``|``-R-4.3.2`` |``foss/2023a`` ### archspec @@ -1459,7 +1496,7 @@ version |versionsuffix|toolchain ``6.0.0.2`` |``-R-4.2.0`` |``foss/2021b`` ``8.0.0`` |``-R-4.2.1`` |``foss/2022a`` ``11.0.0.3``|``-R-4.2.2`` |``foss/2022b`` -``14.0.0.2``|``-R-4.3.2`` |``foss/2023a`` +``14.0.1`` |``-R-4.3.2`` |``foss/2023a`` ### ART @@ -1648,6 +1685,16 @@ version |toolchain ``3.6.1``|``system`` ``3.9.6``|``system`` +### assembly-stats + +Get assembly statistics from FASTA and FASTQ files. + +*homepage*: + +version |toolchain +---------|------------------ +``1.0.1``|``GCCcore/11.3.0`` + ### assimp Open Asset Import Library (assimp) is a library to import and export various 3d-model-formats including scene-post-processing to generate missing render data. @@ -1705,7 +1752,7 @@ version |versionsuffix |toolchain ``4.2.1`` | |``foss/2020b``, ``intel/2020b``, ``intelcuda/2020b`` ``4.3.1`` | |``foss/2021a``, ``foss/2021b``, ``intel/2021a`` ``5.0.4`` | |``foss/2021a`` -``5.1.1`` | |``foss/2022a`` +``5.1.1`` | |``foss/2022a``, ``intel/2022a`` ``5.2.2`` | |``gfbf/2022b`` ### at-spi2-atk @@ -1818,13 +1865,14 @@ version |versionsuffix |toolchain ### atropos -Atropos is tool for specific, sensitive, and speedy trimming of NGS reads. +Atropos is tool for specific, sensitive, and speedy trimming of NGS reads. *homepage*: version |versionsuffix |toolchain ----------|-----------------|--------------- ``1.1.21``|``-Python-3.6.6``|``intel/2018b`` +``1.1.32``| |``gompi/2023a`` ### ATSAS @@ -1867,8 +1915,8 @@ AttrDict is a Python library that provides mapping objects that allow their elem *homepage*: version |toolchain ----------|-------------------------------------- -``2.0.2``|``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +---------|---------------------------------------------------------- +``2.0.2``|``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.3.0`` ### augur @@ -1920,7 +1968,7 @@ version |toolchain ### Autoconf -Autoconf is an extensible package of M4 macros that produce shell scripts to automatically configure software source code packages. These scripts can adapt the packages to many kinds of UNIX-like systems without manual user intervention. Autoconf creates a configuration script for a package from a template file that lists the operating system features that the package can use, in the form of M4 macro calls. +Autoconf is an extensible package of M4 macros that produce shell scripts to automatically configure software source code packages. These scripts can adapt the packages to many kinds of UNIX-like systems without manual user intervention. Autoconf creates a configuration script for a package from a template file that lists the operating system features that the package can use, in the form of M4 macro calls. *homepage*: @@ -1929,6 +1977,7 @@ 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``, ``GCCcore/13.2.0``, ``system`` +``2.72``|``GCCcore/13.3.0`` ### Autoconf-archive @@ -2022,7 +2071,7 @@ 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``, ``GCCcore/13.2.0``, ``system`` +``1.16.5``|``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``GCCcore/13.2.0``, ``GCCcore/13.3.0``, ``system`` ### AutoMap @@ -2044,6 +2093,7 @@ version |versionsuffix |toolchain ---------|-----------------|--------------- ``1.4.4``|``-Python-3.6.4``|``intel/2018a`` ``2.0.4``| |``foss/2022a`` +``2.2.0``| |``foss/2023a`` ### Autotools @@ -2061,6 +2111,7 @@ version |toolchain ``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``, ``GCCcore/13.2.0``, ``system`` +``20231222``|``GCCcore/13.3.0`` ### Avogadro2 @@ -2122,7 +2173,7 @@ 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) - [bases2fastq](#bases2fastq) - [Bash](#bash) - [bashplotlib](#bashplotlib) - [bat](#bat) - [batchgenerators](#batchgenerators) - [BatMeth2](#batmeth2) - [BayesAss](#bayesass) - [BayesAss3-SNPs](#bayesass3-snps) - [BayeScan](#bayescan) - [BayeScEnv](#bayescenv) - [BayesPrism](#bayesprism) - [BayesTraits](#bayestraits) - [Bazel](#bazel) - [bbcp](#bbcp) - [bbFTP](#bbftp) - [BBMap](#bbmap) - [bc](#bc) - [BCALM](#bcalm) - [bcbio-gff](#bcbio-gff) - [BCEL](#bcel) - [BCFtools](#bcftools) - [bcgTree](#bcgtree) - [bcl-convert](#bcl-convert) - [bcl2fastq2](#bcl2fastq2) - [bcolz](#bcolz) - [bcrypt](#bcrypt) - [BDBag](#bdbag) - [Beagle](#beagle) - [beagle-lib](#beagle-lib) - [Beast](#beast) - [BeautifulSoup](#beautifulsoup) - [BEDOPS](#bedops) - [BEDTools](#bedtools) - [BEEF](#beef) - [behave](#behave) - [bench](#bench) - [BerkeleyGW](#berkeleygw) - [BFAST](#bfast) - [BFC](#bfc) - [BGC-Bayesian-genomic-clines](#bgc-bayesian-genomic-clines) - [BgeeCall](#bgeecall) - [BgeeDB](#bgeedb) - [bgen](#bgen) - [bgen-reader](#bgen-reader) - [BiasAdjustCXX](#biasadjustcxx) - [bibtexparser](#bibtexparser) - [BiG-SCAPE](#big-scape) - [BigDFT](#bigdft) - [BinSanity](#binsanity) - [binutils](#binutils) - [Bio-DB-HTS](#bio-db-hts) - [Bio-EUtilities](#bio-eutilities) - [Bio-SamTools](#bio-samtools) - [Bio-SearchIO-hmmer](#bio-searchio-hmmer) - [bioawk](#bioawk) - [biobakery-workflows](#biobakery-workflows) - [biobambam2](#biobambam2) - [biogeme](#biogeme) - [biom-format](#biom-format) - [biomart-perl](#biomart-perl) - [BioPerl](#bioperl) - [BioPP](#biopp) - [Biopython](#biopython) - [BioServices](#bioservices) - [BirdNET](#birdnet) - [biscuit](#biscuit) - [Bismark](#bismark) - [Bison](#bison) - [bitarray](#bitarray) - [BLACS](#blacs) - [BLASR](#blasr) - [blasr_libcpp](#blasr_libcpp) - [BLAST](#blast) - [BLAST+](#blast+) - [BLAT](#blat) - [Blender](#blender) - [BLIS](#blis) - [Blitz++](#blitz++) - [BlobTools](#blobtools) - [Block](#block) - [Blosc](#blosc) - [Blosc2](#blosc2) - [BLT](#blt) - [bmtagger](#bmtagger) - [BMTK](#bmtk) - [bnpy](#bnpy) - [BOINC](#boinc) - [bokeh](#bokeh) - [BoltzTraP](#boltztrap) - [BoltzTraP2](#boltztrap2) - [Bonito](#bonito) - [Bonmin](#bonmin) - [Bonnie++](#bonnie++) - [Boost](#boost) - [Boost.MPI](#boost.mpi) - [Boost.Python](#boost.python) - [Boost.Python-NumPy](#boost.python-numpy) - [boost_histogram](#boost_histogram) - [BOPTEST](#boptest) - [boto3](#boto3) - [Bottleneck](#bottleneck) - [Bowtie](#bowtie) - [Bowtie2](#bowtie2) - [Bpipe](#bpipe) - [bpp](#bpp) - [bpytop](#bpytop) - [Bracken](#bracken) - [Braindecode](#braindecode) - [BRAKER](#braker) - [BreakDancer](#breakdancer) - [breseq](#breseq) - [BRiAl](#brial) - [Brotli](#brotli) - [Brotli-python](#brotli-python) - [Brunsli](#brunsli) - [bsddb3](#bsddb3) - [BSMAPz](#bsmapz) - [Bsoft](#bsoft) - [BSseeker2](#bsseeker2) - [btllib](#btllib) - [BuDDy](#buddy) - [BUFRLIB](#bufrlib) - [build](#build) - [buildenv](#buildenv) - [buildingspy](#buildingspy) - [Bullet](#bullet) - [BUSCO](#busco) - [BUStools](#bustools) - [BWA](#bwa) - [bwa-mem2](#bwa-mem2) - [bwa-meth](#bwa-meth) - [bwakit](#bwakit) - [bwidget](#bwidget) - [BWISE](#bwise) - [bx-python](#bx-python) - [BXH_XCEDE_TOOLS](#bxh_xcede_tools) - [byacc](#byacc) - [byobu](#byobu) - [bzip2](#bzip2) +[BA3-SNPS-autotune](#ba3-snps-autotune) - [BabelStream](#babelstream) - [babl](#babl) - [Bader](#bader) - [BAGEL](#bagel) - [BAli-Phy](#bali-phy) - [bam-readcount](#bam-readcount) - [Bambi](#bambi) - [bamFilters](#bamfilters) - [BAMM](#bamm) - [BAMSurgeon](#bamsurgeon) - [bamtofastq](#bamtofastq) - [BamTools](#bamtools) - [BamUtil](#bamutil) - [Bandage](#bandage) - [barrnap](#barrnap) - [basemap](#basemap) - [bases2fastq](#bases2fastq) - [Bash](#bash) - [bashplotlib](#bashplotlib) - [bat](#bat) - [batchgenerators](#batchgenerators) - [BatMeth2](#batmeth2) - [BayesAss](#bayesass) - [BayesAss3-SNPs](#bayesass3-snps) - [BayeScan](#bayescan) - [BayeScEnv](#bayescenv) - [BayesPrism](#bayesprism) - [BayesTraits](#bayestraits) - [Bazel](#bazel) - [bbcp](#bbcp) - [bbFTP](#bbftp) - [BBMap](#bbmap) - [bc](#bc) - [BCALM](#bcalm) - [bcbio-gff](#bcbio-gff) - [BCEL](#bcel) - [BCFtools](#bcftools) - [bcgTree](#bcgtree) - [bcl-convert](#bcl-convert) - [bcl2fastq2](#bcl2fastq2) - [bcolz](#bcolz) - [bcrypt](#bcrypt) - [BDBag](#bdbag) - [Beagle](#beagle) - [beagle-lib](#beagle-lib) - [Beast](#beast) - [BeautifulSoup](#beautifulsoup) - [BEDOPS](#bedops) - [BEDTools](#bedtools) - [BEEF](#beef) - [behave](#behave) - [bench](#bench) - [BerkeleyGW](#berkeleygw) - [BFAST](#bfast) - [BFC](#bfc) - [BGC-Bayesian-genomic-clines](#bgc-bayesian-genomic-clines) - [BgeeCall](#bgeecall) - [BgeeDB](#bgeedb) - [bgen](#bgen) - [bgen-reader](#bgen-reader) - [BiasAdjustCXX](#biasadjustcxx) - [bibtexparser](#bibtexparser) - [BiG-SCAPE](#big-scape) - [BigDFT](#bigdft) - [BinSanity](#binsanity) - [binutils](#binutils) - [Bio-DB-HTS](#bio-db-hts) - [Bio-EUtilities](#bio-eutilities) - [Bio-FeatureIO](#bio-featureio) - [Bio-SamTools](#bio-samtools) - [Bio-SearchIO-hmmer](#bio-searchio-hmmer) - [bioawk](#bioawk) - [biobakery-workflows](#biobakery-workflows) - [biobambam2](#biobambam2) - [biogeme](#biogeme) - [biom-format](#biom-format) - [biomart-perl](#biomart-perl) - [BioPerl](#bioperl) - [BioPP](#biopp) - [Biopython](#biopython) - [BioServices](#bioservices) - [BirdNET](#birdnet) - [biscuit](#biscuit) - [Bismark](#bismark) - [Bison](#bison) - [bitarray](#bitarray) - [bitshuffle](#bitshuffle) - [BLACS](#blacs) - [BLASR](#blasr) - [blasr_libcpp](#blasr_libcpp) - [BLAST](#blast) - [BLAST+](#blast+) - [BLAT](#blat) - [Blender](#blender) - [BLIS](#blis) - [Blitz++](#blitz++) - [BlobTools](#blobtools) - [Block](#block) - [Blosc](#blosc) - [Blosc2](#blosc2) - [BLT](#blt) - [bmtagger](#bmtagger) - [BMTK](#bmtk) - [bnpy](#bnpy) - [BOINC](#boinc) - [bokeh](#bokeh) - [BoltzTraP](#boltztrap) - [BoltzTraP2](#boltztrap2) - [Bonito](#bonito) - [Bonmin](#bonmin) - [Bonnie++](#bonnie++) - [Boost](#boost) - [Boost.MPI](#boost.mpi) - [Boost.Python](#boost.python) - [Boost.Python-NumPy](#boost.python-numpy) - [boost_histogram](#boost_histogram) - [BOPTEST](#boptest) - [boto3](#boto3) - [Bottleneck](#bottleneck) - [Bowtie](#bowtie) - [Bowtie2](#bowtie2) - [Bpipe](#bpipe) - [bpp](#bpp) - [bpytop](#bpytop) - [Bracken](#bracken) - [Braindecode](#braindecode) - [BRAKER](#braker) - [BreakDancer](#breakdancer) - [breseq](#breseq) - [BRiAl](#brial) - [Brotli](#brotli) - [Brotli-python](#brotli-python) - [Brunsli](#brunsli) - [bsddb3](#bsddb3) - [BSMAPz](#bsmapz) - [Bsoft](#bsoft) - [BSseeker2](#bsseeker2) - [btllib](#btllib) - [BuDDy](#buddy) - [BUFRLIB](#bufrlib) - [build](#build) - [buildenv](#buildenv) - [buildingspy](#buildingspy) - [Bullet](#bullet) - [BUSCO](#busco) - [BUStools](#bustools) - [BWA](#bwa) - [bwa-mem2](#bwa-mem2) - [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 @@ -2463,6 +2514,7 @@ 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`` +``6.1.0`` | |``GCCcore/12.3.0`` ``6.3.1`` | |``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### bbcp @@ -2568,6 +2620,7 @@ version |toolchain ``1.15.1``|``GCC/11.3.0`` ``1.17`` |``GCC/12.2.0`` ``1.18`` |``GCC/12.3.0`` +``1.19`` |``GCC/13.2.0`` ### bcgTree @@ -2624,6 +2677,7 @@ Acceptable password hashing for your software and your servers (but you should r version |toolchain ---------|------------------ ``4.0.1``|``GCCcore/12.3.0`` +``4.1.3``|``GCCcore/13.2.0`` ### BDBag @@ -2930,6 +2984,7 @@ version |toolchain ``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``, ``GCCcore/13.2.0``, ``system`` +``2.42`` |``GCCcore/13.3.0``, ``GCCcore/14.1.0``, ``system`` ### Bio-DB-HTS @@ -2955,6 +3010,16 @@ version |toolchain --------|----------------- ``1.76``|``GCCcore/8.3.0`` +### Bio-FeatureIO + +An I/O iterator subsystem for genomic sequence features + +*homepage*: + +version |toolchain +-----------|------------------ +``1.6.905``|``GCCcore/12.3.0`` + ### Bio-SamTools This is a Perl interface to the SAMtools sequence alignment interface. @@ -3026,11 +3091,11 @@ The BIOM file format (canonically pronounced biome) is designed to be a general *homepage*: 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`` +``2.1.15``| |``foss/2022b``, ``foss/2023a`` ### biomart-perl @@ -3168,7 +3233,7 @@ 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/13.2.0``, ``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/13.3.0``, ``GCCcore/14.1.0``, ``GCCcore/9.5.0``, ``system`` ### bitarray @@ -3183,6 +3248,16 @@ version |versionsuffix |toolchain ``1.2.1``|``-Python-3.7.4`` |``foss/2019b`` ``1.5.3``|``-Python-2.7.16``|``GCC/8.3.0`` +### bitshuffle + +Filter for improving compression of typed binary data. Bitshuffle is an algorithm that rearranges typed, binary data for improving compression, as well as a python/C package that implements this algorithm within the Numpy framework. The library can be used along side HDF5 to compress and decompress datasets and is integrated through the dynamically loaded filters framework. Bitshuffle is HDF5 filter number 32008. + +*homepage*: + +version |toolchain +---------|-------------- +``0.5.1``|``foss/2023a`` + ### BLACS The BLACS (Basic Linear Algebra Communication Subprograms) project is an ongoing investigation whose purpose is to create a linear algebra oriented message passing interface that may be implemented efficiently and uniformly across a large range of distributed memory platforms. @@ -3299,6 +3374,7 @@ version |versionsuffix|toolchain ``0.8.0``| |``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ``0.8.1``| |``GCC/10.3.0``, ``GCC/11.2.0``, ``GCCcore/10.3.0`` ``0.9.0``| |``GCC/11.3.0``, ``GCC/12.2.0``, ``GCC/12.3.0``, ``GCC/13.2.0``, ``intel-compilers/2022.1.0`` +``1.0`` | |``GCC/13.2.0``, ``GCC/13.3.0`` ``1.2`` |``-amd`` |``GCC/7.3.0-2.30`` ``2.2`` |``-amd`` |``GCCcore/9.3.0`` ``3.0`` |``-amd`` |``GCCcore/10.3.0`` @@ -3441,6 +3517,7 @@ version |versionsuffix |toolchain ``2.4.3`` | |``foss/2022a`` ``3.2.1`` | |``foss/2022b`` ``3.2.2`` | |``foss/2023a`` +``3.4.1`` | |``gfbf/2023b`` ### BoltzTraP @@ -3550,7 +3627,7 @@ version |versionsuffix |toolchain ``1.71.0``| |``gompi/2019b``, ``gompic/2019b``, ``iimpi/2019b``, ``iimpic/2019b`` ``1.72.0``| |``gompi/2020a``, ``gompic/2020a``, ``iimpi/2020a`` ``1.72.0``|``-no_mpi`` |``GCCcore/9.3.0`` -``1.74.0``| |``GCC/10.2.0``, ``iccifort/2020.4.304`` +``1.74.0``| |``GCC/10.2.0``, ``GCC/12.3.0``, ``iccifort/2020.4.304`` ``1.75.0``| |``GCC/11.2.0`` ``1.76.0``| |``GCC/10.3.0``, ``intel-compilers/2021.2.0`` ``1.77.0``| |``GCC/11.2.0``, ``intel-compilers/2021.4.0`` @@ -3558,6 +3635,7 @@ version |versionsuffix |toolchain ``1.81.0``| |``GCC/12.2.0`` ``1.82.0``| |``GCC/12.3.0`` ``1.83.0``| |``GCC/13.2.0`` +``1.85.0``| |``GCC/13.3.0`` ### Boost.MPI @@ -3746,6 +3824,7 @@ version |versionsuffix |toolchain ``0.7`` |``-PyTorch-1.10.0`` |``foss/2021a`` ``0.7`` |``-PyTorch-1.10.0-CUDA-11.3.1``|``foss/2021a`` ``0.8.1``|``-PyTorch-2.1.2`` |``foss/2023a`` +``0.8.1``|``-PyTorch-2.1.2-CUDA-12.1.1`` |``foss/2023a`` ### BRAKER @@ -3801,7 +3880,7 @@ Brotli is a generic-purpose lossless compression algorithm that compresses data version |toolchain ---------|----------------------------------------------------------------------------------------------------------------------------------------- ``1.0.9``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/8.3.0`` -``1.1.0``|``GCCcore/13.2.0`` +``1.1.0``|``GCCcore/13.2.0``, ``GCCcore/13.3.0`` ### Brotli-python @@ -3810,8 +3889,8 @@ Brotli is a generic-purpose lossless compression algorithm that compresses data *homepage*: version |toolchain ----------|------------------------------------------------------------------------------ -``1.0.9``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +---------|-------------------------------------------------------------------------------------------------- +``1.0.9``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ``1.1.0``|``GCCcore/13.2.0`` ### Brunsli @@ -3976,7 +4055,7 @@ version |toolchain ### BWA -Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. +Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. *homepage*: @@ -3988,6 +4067,7 @@ version |toolchain ``0.7.16a`` |``foss/2016b``, ``intel/2017a`` ``0.7.17`` |``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``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/2018a``, ``intel/2018b`` ``0.7.17-20220923``|``GCCcore/12.3.0`` +``0.7.18`` |``GCCcore/12.3.0`` ### bwa-mem2 @@ -4103,12 +4183,12 @@ bzip2 is a freely available, patent free, high-quality data compressor. It typi version |toolchain ---------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ ``1.0.6``|``GCC/4.8.1``, ``GCC/4.8.2``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.3-2.25``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GNU/4.9.3-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``gimkl/2017a``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` -``1.0.8``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``GCCcore/13.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``system`` +``1.0.8``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``GCCcore/13.2.0``, ``GCCcore/13.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``system`` ## C -[c-ares](#c-ares) - [C3D](#c3d) - [cadaver](#cadaver) - [CaDiCaL](#cadical) - [CAFE5](#cafe5) - [Caffe](#caffe) - [cairo](#cairo) - [cairomm](#cairomm) - [Calcam](#calcam) - [CalculiX-CrunchiX](#calculix-crunchix) - [Calendrical](#calendrical) - [Calib](#calib) - [CAMPARI](#campari) - [Cantera](#cantera) - [canu](#canu) - [Canvas](#canvas) - [CAP3](#cap3) - [CapnProto](#capnproto) - [captum](#captum) - [Cargo](#cargo) - [Carma](#carma) - [carputils](#carputils) - [Cartopy](#cartopy) - [CASA](#casa) - [casacore](#casacore) - [Casanovo](#casanovo) - [CaSpER](#casper) - [CASPR](#caspr) - [CASTEP](#castep) - [castor](#castor) - [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) - [CellBender](#cellbender) - [CellChat](#cellchat) - [CellMix](#cellmix) - [CellOracle](#celloracle) - [Cellpose](#cellpose) - [CellRanger](#cellranger) - [CellRanger-ARC](#cellranger-arc) - [CellRanger-ATAC](#cellranger-atac) - [CellRank](#cellrank) - [CellTypist](#celltypist) - [CENSO](#censo) - [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) - [Circlator](#circlator) - [Circos](#circos) - [Circuitscape](#circuitscape) - [CIRI](#ciri) - [CIRI-long](#ciri-long) - [CIRIquant](#ciriquant) - [cisTEM](#cistem) - [CITE-seq-Count](#cite-seq-count) - [Clair3](#clair3) - [Clang](#clang) - [Clang-AOMP](#clang-aomp) - [Clang-Python-bindings](#clang-python-bindings) - [CLAPACK](#clapack) - [Clarabel.rs](#clarabel.rs) - [CLEAR](#clear) - [CLEASE](#clease) - [CLHEP](#clhep) - [CliMetLab](#climetlab) - [CLIP](#clip) - [cliquer](#cliquer) - [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-cli](#code-cli) - [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) - [Concorde](#concorde) - [ConcurrentVersionsSystem](#concurrentversionssystem) - [configparser](#configparser) - [configurable-http-proxy](#configurable-http-proxy) - [CONN](#conn) - [connected-components-3d](#connected-components-3d) - [ConnectomeWorkbench](#connectomeworkbench) - [contextily](#contextily) - [Control-FREEC](#control-freec) - [cooler](#cooler) - [CoordgenLibs](#coordgenlibs) - [Coot](#coot) - [CopyKAT](#copykat) - [core-counter](#core-counter) - [Coreutils](#coreutils) - [corner](#corner) - [CoSymLib](#cosymlib) - [coverage](#coverage) - [cowsay](#cowsay) - [CP2K](#cp2k) - [CPB](#cpb) - [CPC2](#cpc2) - [cpio](#cpio) - [CPLEX](#cplex) - [CPMD](#cpmd) - [CPPE](#cppe) - [CppHeaderParser](#cppheaderparser) - [CppUnit](#cppunit) - [cppy](#cppy) - [cppyy](#cppyy) - [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) - [CUDD](#cudd) - [cuDNN](#cudnn) - [Cufflinks](#cufflinks) - [CUnit](#cunit) - [CuPy](#cupy) - [cURL](#curl) - [cuSPARSELt](#cusparselt) - [custodian](#custodian) - [cutadapt](#cutadapt) - [cuTENSOR](#cutensor) - [cuteSV](#cutesv) - [CUTLASS](#cutlass) - [CVglasso](#cvglasso) - [CVXOPT](#cvxopt) - [CVXPY](#cvxpy) - [CWIPI](#cwipi) - [cwltool](#cwltool) - [cxxopts](#cxxopts) - [cysignals](#cysignals) - [Cython](#cython) - [cython-blis](#cython-blis) - [cytoolz](#cytoolz) - [Cytoscape](#cytoscape) - [cytosim](#cytosim) - [cyvcf2](#cyvcf2) +[c-ares](#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) - [Cassiopeia](#cassiopeia) - [CASTEP](#castep) - [castor](#castor) - [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) - [CCCL](#cccl) - [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) - [CellBender](#cellbender) - [CellChat](#cellchat) - [CellMix](#cellmix) - [CellOracle](#celloracle) - [Cellpose](#cellpose) - [CellRanger](#cellranger) - [CellRanger-ARC](#cellranger-arc) - [CellRanger-ATAC](#cellranger-atac) - [CellRank](#cellrank) - [CellTypist](#celltypist) - [CENSO](#censo) - [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) - [charm-gems](#charm-gems) - [CHASE](#chase) - [Check](#check) - [CheckM](#checkm) - [CheckM-Database](#checkm-database) - [CheckM2](#checkm2) - [Cheetah](#cheetah) - [Chemaxon-Marvin](#chemaxon-marvin) - [chemprop](#chemprop) - [CheMPS2](#chemps2) - [CHERAB](#cherab) - [chewBBACA](#chewbbaca) - [chi2comb](#chi2comb) - [Chimera](#chimera) - [ChimPipe](#chimpipe) - [ChIPseeker](#chipseeker) - [Chromaprint](#chromaprint) - [chromVARmotifs](#chromvarmotifs) - [cicero](#cicero) - [CIF2Cell](#cif2cell) - [cimfomfa](#cimfomfa) - [CIRCexplorer](#circexplorer) - [CIRCexplorer2](#circexplorer2) - [Circlator](#circlator) - [Circos](#circos) - [Circuitscape](#circuitscape) - [CIRI](#ciri) - [CIRI-long](#ciri-long) - [CIRIquant](#ciriquant) - [cisTEM](#cistem) - [CITE-seq-Count](#cite-seq-count) - [Clair3](#clair3) - [Clang](#clang) - [Clang-AOMP](#clang-aomp) - [Clang-Python-bindings](#clang-python-bindings) - [CLAPACK](#clapack) - [Clarabel.rs](#clarabel.rs) - [CLEAR](#clear) - [CLEASE](#clease) - [CLHEP](#clhep) - [CliMetLab](#climetlab) - [CLIP](#clip) - [cliquer](#cliquer) - [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) - [cmph](#cmph) - [CMSeq](#cmseq) - [CNT-ILP](#cnt-ilp) - [CNVkit](#cnvkit) - [CNVnator](#cnvnator) - [Co-phylog](#co-phylog) - [COBRApy](#cobrapy) - [CoCoALib](#cocoalib) - [CodAn](#codan) - [code-cli](#code-cli) - [code-server](#code-server) - [CODEX2](#codex2) - [CodingQuarry](#codingquarry) - [Cogent](#cogent) - [Coin](#coin) - [CoinUtils](#coinutils) - [ColabFold](#colabfold) - [colossalai](#colossalai) - [COMEBin](#comebin) - [Commet](#commet) - [CompareM](#comparem) - [Compass](#compass) - [Compress-Raw-Zlib](#compress-raw-zlib) - [COMSOL](#comsol) - [Con3F](#con3f) - [conan](#conan) - [CONCOCT](#concoct) - [Concorde](#concorde) - [ConcurrentVersionsSystem](#concurrentversionssystem) - [configparser](#configparser) - [configurable-http-proxy](#configurable-http-proxy) - [CONN](#conn) - [connected-components-3d](#connected-components-3d) - [ConnectomeWorkbench](#connectomeworkbench) - [contextily](#contextily) - [Control-FREEC](#control-freec) - [cooler](#cooler) - [CoordgenLibs](#coordgenlibs) - [Coot](#coot) - [CopyKAT](#copykat) - [core-counter](#core-counter) - [Coreutils](#coreutils) - [corner](#corner) - [CoSymLib](#cosymlib) - [coverage](#coverage) - [cowsay](#cowsay) - [CP2K](#cp2k) - [CPB](#cpb) - [CPC2](#cpc2) - [cpio](#cpio) - [CPLEX](#cplex) - [CPMD](#cpmd) - [CPPE](#cppe) - [CppHeaderParser](#cppheaderparser) - [CppUnit](#cppunit) - [cppy](#cppy) - [cppyy](#cppyy) - [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) - [ctffind5](#ctffind5) - [CTPL](#ctpl) - [Cube](#cube) - [CubeGUI](#cubegui) - [CubeLib](#cubelib) - [CubeWriter](#cubewriter) - [CuCLARK](#cuclark) - [CUDA](#cuda) - [CUDA-Samples](#cuda-samples) - [CUDAcompat](#cudacompat) - [CUDAcore](#cudacore) - [CUDD](#cudd) - [cuDNN](#cudnn) - [Cufflinks](#cufflinks) - [CUnit](#cunit) - [CuPy](#cupy) - [cURL](#curl) - [currentNe](#currentne) - [cuSPARSELt](#cusparselt) - [custodian](#custodian) - [cutadapt](#cutadapt) - [cuTENSOR](#cutensor) - [cuteSV](#cutesv) - [CUTLASS](#cutlass) - [CVglasso](#cvglasso) - [CVX](#cvx) - [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 @@ -4256,8 +4336,8 @@ CAMPARI is a joint package for performing and analyzing molecular simulations, i *homepage*: version|toolchain --------|--------------- -``4.0``|``intel/2020b`` +-------|-------------------------------- +``4.0``|``intel/2020b``, ``intel/2023a`` ### Cantera @@ -4442,6 +4522,16 @@ version |toolchain ------------|-------------- ``20200730``|``foss/2022a`` +### Cassiopeia + +A Package for Cas9-Enabled Single Cell Lineage Tracing Tree Reconstruction. + +*homepage*: + +version |toolchain +---------|-------------- +``2.0.0``|``foss/2023a`` + ### CASTEP CASTEP is an electronic structure materials modelling code based on density functional theory (DFT), with functionality including geometry optimization molecular dynamics, phonons, NMR chemical shifts and much more. @@ -4623,6 +4713,16 @@ version |versionsuffix|toolchain ``4.8.3`` | |``system`` ``4.9`` | |``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0`` +### CCCL + +CUDA C++ Core Libraries (header only) + +*homepage*: + +version |versionsuffix |toolchain +---------|----------------|------------------ +``2.3.0``|``-CUDA-12.1.1``|``GCCcore/12.3.0`` + ### CCfits CCfits is an object oriented interface to the cfitsio library. It is designed to make the capabilities of cfitsio available to programmers working in C++. @@ -4729,10 +4829,10 @@ An efficient implementation of the Double Description Method *homepage*: version |toolchain ----------|------------------ +---------|-------------------------------------- ``0.94i``|``GCCcore/8.2.0`` ``0.94j``|``GCCcore/8.3.0`` -``0.94m``|``GCCcore/11.3.0`` +``0.94m``|``GCCcore/11.3.0``, ``GCCcore/13.2.0`` ### CDFlib @@ -4820,8 +4920,8 @@ version |versionsuffix |toolchain ---------|----------------|-------------- ``0.2.1``|``-CUDA-11.3.1``|``foss/2021a`` ``0.2.2``| |``foss/2022a`` -``0.3.1``| |``foss/2022a`` -``0.3.1``|``-CUDA-11.7.0``|``foss/2022a`` +``0.3.0``| |``foss/2023a`` +``0.3.0``|``-CUDA-12.1.1``|``foss/2023a`` ### CellChat @@ -4886,6 +4986,8 @@ version |toolchain ``7.0.0``|``system`` ``7.1.0``|``system`` ``7.2.0``|``system`` +``8.0.0``|``system`` +``8.0.1``|``system`` ### CellRanger-ARC @@ -4898,6 +5000,7 @@ version |toolchain ``1.0.1``|``system`` ``2.0.0``|``system`` ``2.0.1``|``system`` +``2.0.2``|``system`` ### CellRanger-ATAC @@ -4920,6 +5023,7 @@ CellRank is a toolkit to uncover cellular dynamics based on Markov state modeli version |toolchain ---------|-------------- ``1.4.0``|``foss/2021a`` +``2.0.2``|``foss/2023a`` ### CellTypist @@ -5004,6 +5108,7 @@ C Foreign Function Interface for Python. Interact with almost any C code from Py version |toolchain ----------|---------------------------------------------------------- ``1.15.1``|``GCCcore/11.3.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0`` +``1.16.0``|``GCCcore/13.3.0`` ### CFITSIO @@ -5063,8 +5168,10 @@ version |versionsuffix |toolchain ``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`` +``5.4`` | |``GCCcore/12.3.0`` ``5.5.2`` | |``GCCcore/12.2.0`` ``5.6`` | |``GCCcore/12.3.0`` +``5.6.1`` | |``GCCcore/13.2.0`` ### cget @@ -5117,13 +5224,23 @@ CharLS is a C++ implementation of the JPEG-LS standard for lossless and near-los *homepage*: version |toolchain ----------|------------------------------------ +---------|-------------------------------------- ``2.0.0``|``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``2.1.0``|``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``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`` +``2.4.2``|``GCCcore/12.2.0``, ``GCCcore/12.3.0`` + +### charm-gems + +This repository contains the gems C++ code and python bindings used in Freesurfer's Sequence-Adaptive Multimodal SEGmentation (SAMSEG) and in SimNIBS 4.0 Complete Head Anatomy Reconstruction Method (CHARM) to create individualized head models for electric field simulations. + +*homepage*: + +version |toolchain +---------|-------------- +``1.3.3``|``foss/2023a`` ### CHASE @@ -5142,9 +5259,9 @@ Check is a unit testing framework for C. It features a simple interface for defi *homepage*: version |toolchain -----------|--------------------------------------------------------------------------------------------------------------------- +----------|------------------------------------------------------------------------------------------------------------------------------------------------------------- ``0.12.0``|``GCCcore/6.4.0`` -``0.15.2``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/13.2.0``, ``GCCcore/9.3.0`` +``0.15.2``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0``, ``GCCcore/9.3.0`` ### CheckM @@ -5174,6 +5291,16 @@ version |toolchain --------------|---------- ``2015_01_16``|``system`` +### CheckM2 + +Assessing the quality of metagenome-derived genome bins using machine learning + +*homepage*: + +version |toolchain +---------|-------------- +``1.0.2``|``foss/2022b`` + ### Cheetah Cheetah is an open source template engine and code generation tool. @@ -5298,6 +5425,16 @@ version |toolchain ---------|----------------- ``1.4.3``|``GCCcore/8.2.0`` +### chromVARmotifs + +The goal of chromVARmotifs is to make it easy to use several different motif collections in R, particularly for use with motifmatchr and chromVAR packages. + +*homepage*: + +version |versionsuffix|toolchain +---------|-------------|-------------- +``0.2.0``|``-R-4.3.2`` |``foss/2023a`` + ### cicero Cicero is an R package that provides tools for analyzing single-cell chromatin accessibility experiments. @@ -5488,6 +5625,7 @@ version |versionsuffix |toolchain ``16.0.4``| |``GCCcore/12.2.0`` ``16.0.6``| |``GCCcore/12.3.0`` ``16.0.6``|``-CUDA-12.1.1`` |``GCCcore/12.3.0`` +``17.0.6``| |``GCCcore/13.2.0`` ### Clang-AOMP @@ -5601,8 +5739,8 @@ Cliquer is a set of C routines for finding cliques in an arbitrary weighted grap *homepage*: version |toolchain ---------|------------------ -``1.21``|``GCCcore/11.3.0`` +--------|-------------------------------------- +``1.21``|``GCCcore/11.3.0``, ``GCCcore/13.2.0`` ### CLISP @@ -5750,6 +5888,7 @@ version |toolchain ``3.24.3``|``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ``3.26.3``|``GCCcore/12.3.0``, ``GCCcore/13.1.0`` ``3.27.6``|``GCCcore/13.2.0`` +``3.29.3``|``GCCcore/13.3.0`` ### CMAverse @@ -5783,6 +5922,16 @@ version|toolchain -------|-------------- ``2.0``|``foss/2022a`` +### cmph + +Cmph is a free minimal perfect hash C library, providing several algorithms in the literature in a consistent, ease to use, API. + +*homepage*: + +version|toolchain +-------|------------------ +``2.0``|``GCCcore/12.3.0`` + ### CMSeq CMSeq is a set of commands to provide an interface to .bam files for coverage and sequence consensus. @@ -5860,6 +6009,7 @@ version |toolchain ``0.99601``|``GCC/8.2.0-2.31.1`` ``0.99700``|``GCC/8.3.0`` ``0.99818``|``GCC/11.3.0`` +``0.99850``|``GCC/13.2.0`` ### CodAn @@ -5894,6 +6044,7 @@ version |toolchain ``4.16.1``|``system`` ``4.21.1``|``system`` ``4.22.1``|``system`` +``4.89.1``|``system`` ### CODEX2 @@ -5970,6 +6121,16 @@ version |versionsuffix |toolchain ---------|----------------|-------------- ``0.1.8``|``-CUDA-11.3.1``|``foss/2021a`` +### COMEBin + +Effective binning of metagenomic contigs using COntrastive Multi-viEw representation learning + +*homepage*: + +version |toolchain +------------------|-------------- +``1.0.3-20240310``|``foss/2022a`` + ### Commet COMMET ("COmpare Multiple METagenomes") provides a global similarity overview between all datasets of a large metagenomic project. @@ -5991,6 +6152,16 @@ version |versionsuffix |toolchain ``0.0.23``|``-Python-2.7.15``|``foss/2018b`` ``0.1.2`` | |``foss/2021b`` +### Compass + +In-Silico Modeling of Metabolic Heterogeneity using Single-Cell Transcriptomes. + +*homepage*: + +version |toolchain +-----------|-------------- +``2024.04``|``foss/2021b`` + ### Compress-Raw-Zlib Low-Level Interface to zlib or zlib-ng compression library @@ -6095,6 +6266,7 @@ version |versionsuffix |toolchain ``4.5.3``| |``GCCcore/11.3.0`` ``4.5.5``| |``GCCcore/12.2.0`` ``4.5.6``| |``GCCcore/12.3.0`` +``4.6.1``| |``GCCcore/13.2.0`` ### CONN @@ -6253,6 +6425,7 @@ version |versionsuffix |toolchain ``5.5`` | |``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ``7.2.3``| |``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ``7.2.7``| |``GCCcore/11.3.0`` +``7.4.4``| |``GCCcore/13.2.0`` ### cowsay @@ -6313,8 +6486,9 @@ The cpio package contains tools for archiving. *homepage*: version |toolchain ---------|------------------ +--------|------------------------------------------------------------------------------ ``2.14``|``GCCcore/11.3.0`` +``2.15``|``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0``, ``GCCcore/13.3.0`` ### CPLEX @@ -6365,9 +6539,9 @@ CppUnit is the C++ port of the famous JUnit framework for unit testing. *homepage*: version |toolchain -----------|-------------------------------------------------------------------------------------------------------------------- +----------|---------------------------------------------------------------------------------------------------------------------------------------- ``1.12.1``|``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``foss/2016a`` -``1.15.1``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.3.0``, ``GCCcore/12.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``1.15.1``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ### cppy @@ -6389,6 +6563,7 @@ cppyy is an automatic, run-time, Python-C++ bindings generator, for calling C++ version |toolchain ---------|------------------ ``3.0.0``|``GCCcore/11.3.0`` +``3.1.2``|``GCCcore/13.2.0`` ### cppzmq @@ -6488,11 +6663,13 @@ CREST is an utility/driver program for the xtb program. Originally it was design *homepage*: -version |toolchain -----------|------------------------------- -``2.11`` |``intel/2021a`` -``2.11.2``|``intel/2021a`` -``2.12`` |``gfbf/2023a``, ``intel/2022a`` +version |toolchain +------------|------------------------------- +``2.11`` |``intel/2021a`` +``2.11.2`` |``intel/2021a`` +``2.12`` |``gfbf/2023a``, ``intel/2022a`` +``3.0.1`` |``gfbf/2022b`` +``20240319``|``gfbf/2023a`` ### CRF++ @@ -6718,6 +6895,16 @@ version |versionsuffix |toolchain ``4.1.14``| |``foss/2019b``, ``foss/2021b``, ``foss/2022a``, ``foss/2022b``, ``foss/2023a``, ``fosscuda/2019b``, ``fosscuda/2020b`` ``4.1.14``|``-CUDA-11.3.1``|``foss/2021a`` +### ctffind5 + +Program for finding CTFs of electron micrographs. + +*homepage*: + +version |toolchain +---------|-------------- +``5.0.2``|``foss/2023a`` + ### CTPL Modern and efficient C++ Thread Pool Library @@ -6924,6 +7111,7 @@ version |versionsuffix |toolchain ``8.4.1.50`` |``-CUDA-11.5.2`` |``system`` ``8.4.1.50`` |``-CUDA-11.6.0`` |``system`` ``8.4.1.50`` |``-CUDA-11.7.0`` |``system`` +``8.5.0.96`` |``-CUDA-11.7.0`` |``system`` ``8.6.0.163``|``-CUDA-11.8.0`` |``system`` ``8.7.0.84`` |``-CUDA-11.8.0`` |``system`` ``8.8.0.121``|``-CUDA-12.0.0`` |``system`` @@ -6949,8 +7137,8 @@ Automated testing framework for C. *homepage*: version |toolchain ----------|--------------------------------------------------------- -``2.1-3``|``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/6.4.0`` +---------|----------------------------------------------------------------------------- +``2.1-3``|``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.3.0``, ``GCCcore/6.4.0`` ### CuPy @@ -7000,6 +7188,17 @@ version |toolchain ``7.86.0``|``GCCcore/12.2.0`` ``8.0.1`` |``GCCcore/12.3.0``, ``GCCcore/13.1.0`` ``8.3.0`` |``GCCcore/13.2.0`` +``8.7.1`` |``GCCcore/13.3.0`` + +### currentNe + +Estimation of current effective population using artificial neural networks. + +*homepage*: + +version |toolchain +---------|------------------ +``1.0.0``|``GCCcore/12.3.0`` ### cuSPARSELt @@ -7099,6 +7298,16 @@ version|versionsuffix|toolchain -------|-------------|-------------- ``1.0``|``-R-4.2.1`` |``foss/2022a`` +### CVX + +CVX is a Matlab-based modeling system for convex optimization. CVX turns Matlab into a modeling language, allowing constraints and objectives to be specified using standard Matlab expression syntax. + +*homepage*: + +version|versionsuffix |toolchain +-------|-----------------|---------- +``2.2``|``-MATLAB-2023a``|``system`` + ### CVXOPT CVXOPT is a free software package for convex optimization based on the Python programming language. Its main purpose is to make the development of software for convex optimization applications straightforward by building on Python's extensive standard library and on the strengths of Python as a high-level programming language. @@ -7170,6 +7379,7 @@ version |versionsuffix |toolchain ``1.10.2``|``-Python-2.7.14``|``foss/2017b``, ``intel/2017b`` ``1.10.2``|``-Python-3.6.3`` |``foss/2017b``, ``intel/2017b`` ``1.11.2``| |``GCCcore/11.3.0`` +``1.11.4``| |``GCCcore/13.2.0`` ### Cython @@ -7178,7 +7388,7 @@ Cython is an optimising static compiler for both the Python programming language *homepage*: version |versionsuffix |toolchain ------------|------------------|-------------------------------------- +-----------|------------------|---------------------------------------------------------- ``0.23.4`` |``-Python-2.7.10``|``gimkl/2.11.5`` ``0.24.1`` |``-Python-2.7.11``|``foss/2016a`` ``0.25.2`` |``-Python-2.7.12``|``foss/2016b`` @@ -7189,7 +7399,8 @@ version |versionsuffix |toolchain ``0.29.22``| |``GCCcore/10.2.0`` ``0.29.33``| |``GCCcore/11.3.0`` ``3.0.7`` | |``GCCcore/12.3.0`` -``3.0.8`` | |``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +``3.0.8`` | |``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` +``3.0.10`` | |``GCCcore/13.2.0`` ``3.0a5`` | |``GCCcore/10.2.0`` ### cython-blis @@ -7247,7 +7458,7 @@ 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) - [datalad](#datalad) - [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) - [DeepLoc](#deeploc) - [deepmedic](#deepmedic) - [DeepMod2](#deepmod2) - [DeepSurv](#deepsurv) - [deepTools](#deeptools) - [DEICODE](#deicode) - [Delft3D](#delft3d) - [Delly](#delly) - [DeltaLake](#deltalake) - [DeMixT](#demixt) - [Demystify](#demystify) - [DendroPy](#dendropy) - [denseweight](#denseweight) - [DensPart](#denspart) - [Deprecated](#deprecated) - [desktop-file-utils](#desktop-file-utils) - [destiny](#destiny) - [Detectron2](#detectron2) - [DETONATE](#detonate) - [devbio-napari](#devbio-napari) - [Devito](#devito) - [DFA](#dfa) - [DFT-D3](#dft-d3) - [DFT-D4](#dft-d4) - [DFTB+](#dftb+) - [dftd3-lib](#dftd3-lib) - [dftd4](#dftd4) - [DGL](#dgl) - [DIA-NN](#dia-nn) - [DIAL](#dial) - [dialog](#dialog) - [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) - [DjVuLibre](#djvulibre) - [DL_POLY_4](#dl_poly_4) - [DL_POLY_Classic](#dl_poly_classic) - [dlb](#dlb) - [dlib](#dlib) - [DLPack](#dlpack) - [dm-haiku](#dm-haiku) - [dm-reverb](#dm-reverb) - [dm-tree](#dm-tree) - [DMCfun](#dmcfun) - [DMLC-Core](#dmlc-core) - [DMTCP](#dmtcp) - [DOLFIN](#dolfin) - [dominate](#dominate) - [dorado](#dorado) - [Doris](#doris) - [DosageConvertor](#dosageconvertor) - [dotNET-Core-Runtime](#dotnet-core-runtime) - [dotNET-SDK](#dotnet-sdk) - [double-conversion](#double-conversion) - [DoubletFinder](#doubletfinder) - [Doxygen](#doxygen) - [DP3](#dp3) - [DRAGMAP](#dragmap) - [Drake](#drake) - [dRep](#drep) - [drmaa-python](#drmaa-python) - [DROP](#drop) - [dropEst](#dropest) - [DSA](#dsa) - [dSFMT](#dsfmt) - [DSRC](#dsrc) - [Dsuite](#dsuite) - [dtcmp](#dtcmp) - [dtcwt](#dtcwt) - [DualSPHysics](#dualsphysics) - [DUBStepR](#dubstepr) - [dune-core](#dune-core) - [dune-fem](#dune-fem) - [duplex-tools](#duplex-tools) - [dx-toolkit](#dx-toolkit) - [dxpy](#dxpy) - [DyMat](#dymat) - [dynesty](#dynesty) +[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) - [datalad](#datalad) - [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) - [deepfold](#deepfold) - [DeepLabCut](#deeplabcut) - [DeepLoc](#deeploc) - [deepmedic](#deepmedic) - [DeepMod2](#deepmod2) - [DeepSurv](#deepsurv) - [deepTools](#deeptools) - [DEICODE](#deicode) - [Delft3D](#delft3d) - [Delly](#delly) - [DeltaLake](#deltalake) - [DeMixT](#demixt) - [Demystify](#demystify) - [DendroPy](#dendropy) - [denseweight](#denseweight) - [DensPart](#denspart) - [Deprecated](#deprecated) - [desktop-file-utils](#desktop-file-utils) - [destiny](#destiny) - [Detectron2](#detectron2) - [DETONATE](#detonate) - [devbio-napari](#devbio-napari) - [Devito](#devito) - [DFA](#dfa) - [DFT-D3](#dft-d3) - [DFT-D4](#dft-d4) - [DFTB+](#dftb+) - [dftd3-lib](#dftd3-lib) - [dftd4](#dftd4) - [DGL](#dgl) - [DIA-NN](#dia-nn) - [DIAL](#dial) - [dialog](#dialog) - [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) - [DjVuLibre](#djvulibre) - [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](#dotnet-core) - [dotNET-Core-Runtime](#dotnet-core-runtime) - [dotNET-SDK](#dotnet-sdk) - [double-conversion](#double-conversion) - [DoubletFinder](#doubletfinder) - [Doxygen](#doxygen) - [DP3](#dp3) - [DRAGMAP](#dragmap) - [Drake](#drake) - [dRep](#drep) - [drmaa-python](#drmaa-python) - [DROP](#drop) - [dropEst](#dropest) - [DSA](#dsa) - [dSFMT](#dsfmt) - [DSRC](#dsrc) - [Dsuite](#dsuite) - [dtcmp](#dtcmp) - [dtcwt](#dtcwt) - [DualSPHysics](#dualsphysics) - [DUBStepR](#dubstepr) - [dune-core](#dune-core) - [dune-fem](#dune-fem) - [duplex-tools](#duplex-tools) - [dx-toolkit](#dx-toolkit) - [dxpy](#dxpy) - [DyMat](#dymat) - [dynesty](#dynesty) ### dadi @@ -7356,7 +7567,7 @@ version |versionsuffix |toolchain ### dask -Dask natively scales Python. Dask provides advanced parallelism for analytics, enabling performance at scale for the tools you love. +Dask natively scales Python. Dask provides advanced parallelism for analytics, enabling performance at scale for the tools you love. *homepage*: @@ -7387,6 +7598,7 @@ version |versionsuffix |toolchain ``2023.7.1`` | |``foss/2022b`` ``2023.9.2`` | |``foss/2023a`` ``2023.12.1``| |``foss/2023a`` +``2024.5.1`` | |``gfbf/2023b`` ### dask-labextension @@ -7395,8 +7607,9 @@ This package provides a JupyterLab extension to manage Dask clusters, as well as *homepage*: version |toolchain ----------|-------------- +---------|------------------------------ ``6.0.0``|``foss/2022a`` +``7.0.0``|``foss/2023a``, ``gfbf/2023b`` ### datalad @@ -7597,6 +7810,7 @@ version |toolchain ---------|------------------------------- ``9.1.1``|``foss/2019a``, ``intel/2019a`` ``9.3.3``|``foss/2021a`` +``9.5.2``|``foss/2023a`` ### deap @@ -7654,6 +7868,16 @@ version |versionsuffix |toolchain ``5.8.1``| |``GCCcore/11.3.0`` ``6.7.1``| |``GCCcore/12.2.0``, ``GCCcore/12.3.0`` +### deepfold + +This package provides an implementation of DeepFold, a trainable, Transformer-based deep protein folding model. We modified the open-source code of DeepMind AlphaFold v2.0 and Uni-Fold-jax. Pretrained models can be found in environment variable $DEEPFOLD_PARAMETERS + +*homepage*: + +version |versionsuffix |toolchain +------------|----------------|-------------- +``20240308``|``-CUDA-11.7.0``|``foss/2022a`` + ### DeepLabCut Markerless tracking of user-defined features with deep learning @@ -8231,6 +8455,7 @@ version |versionsuffix |toolchain ---------|----------------|-------------- ``0.0.9``| |``foss/2022a`` ``0.0.9``|``-CUDA-11.3.1``|``foss/2021a`` +``0.0.9``|``-CUDA-11.7.0``|``foss/2022a`` ### dm-reverb @@ -8324,6 +8549,7 @@ version |versionsuffix |toolchain ``0.3.0``|``-CUDA-11.7.0``|``foss/2022a`` ``0.3.1``|``-CUDA-11.7.0``|``foss/2022a`` ``0.5.1``|``-CUDA-11.7.0``|``foss/2022a`` +``0.5.3``|``-CUDA-11.7.0``|``foss/2022a`` ### Doris @@ -8347,6 +8573,19 @@ version |toolchain ---------|-------------- ``1.0.4``|``GCC/10.2.0`` +### dotNET-Core + +.NET is a free, cross-platform, open source developer platform for building many different types of applications. With .NET, you can use multiple languages, editors, and libraries to build for web, mobile, desktop, gaming, and IoT. Contains the SDK and the Runtime. + +*homepage*: + +version |toolchain +-----------|---------- +``6.0`` |``system`` +``6.0.420``|``system`` +``8.0`` |``system`` +``8.0.203``|``system`` + ### dotNET-Core-Runtime .NET is a free, cross-platform, open source developer platform for building many different types of applications. @@ -8419,6 +8658,7 @@ version |toolchain ``1.9.5`` |``GCCcore/12.2.0`` ``1.9.7`` |``GCCcore/12.3.0`` ``1.9.8`` |``GCCcore/13.2.0`` +``1.11.0`` |``GCCcore/13.3.0`` ### DP3 @@ -8653,7 +8893,7 @@ version |toolchain ## E -[E-ANTIC](#e-antic) - [e3nn](#e3nn) - [ea-utils](#ea-utils) - [earthengine-api](#earthengine-api) - [easel](#easel) - [EasyBuild](#easybuild) - [EasyQC](#easyqc) - [ebGSEA](#ebgsea) - [ecBuild](#ecbuild) - [ecCodes](#eccodes) - [eccodes-python](#eccodes-python) - [ecFlow](#ecflow) - [ECL](#ecl) - [eclib](#eclib) - [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) - [Elmer](#elmer) - [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) - [EnergyPlus](#energyplus) - [EnsEMBLCoreAPI](#ensemblcoreapi) - [entrypoints](#entrypoints) - [epct](#epct) - [EPD](#epd) - [EPIC](#epic) - [epiScanpy](#episcanpy) - [EpiSCORE](#episcore) - [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) - [EUKulele](#eukulele) - [Evcxr-REPL](#evcxr-repl) - [EveryBeam](#everybeam) - [EvidentialGene](#evidentialgene) - [evince](#evince) - [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) - [ExpressBetaDiversity](#expressbetadiversity) - [Extrae](#extrae) - [ExtremeLy](#extremely) - [EZC3D](#ezc3d) +[E-ANTIC](#e-antic) - [e3nn](#e3nn) - [ea-utils](#ea-utils) - [earthengine-api](#earthengine-api) - [easel](#easel) - [EasyBuild](#easybuild) - [EasyMocap](#easymocap) - [EasyQC](#easyqc) - [ebGSEA](#ebgsea) - [ecBuild](#ecbuild) - [ecCodes](#eccodes) - [eccodes-python](#eccodes-python) - [ecFlow](#ecflow) - [ECL](#ecl) - [eclib](#eclib) - [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) - [Elmer](#elmer) - [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) - [EnergyPlus](#energyplus) - [EnsEMBLCoreAPI](#ensemblcoreapi) - [ensmallen](#ensmallen) - [entrypoints](#entrypoints) - [epct](#epct) - [EPD](#epd) - [EPIC](#epic) - [epiScanpy](#episcanpy) - [EpiSCORE](#episcore) - [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) - [EUKulele](#eukulele) - [EVcouplings](#evcouplings) - [Evcxr-REPL](#evcxr-repl) - [EveryBeam](#everybeam) - [EvidentialGene](#evidentialgene) - [evince](#evince) - [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) - [ExpressBetaDiversity](#expressbetadiversity) - [Extrae](#extrae) - [ExtremeLy](#extremely) - [EZC3D](#ezc3d) ### E-ANTIC @@ -8667,6 +8907,7 @@ version |toolchain ``0.1.2``|``GCC/8.2.0-2.31.1`` ``0.1.5``|``GCC/8.3.0`` ``1.3.0``|``gfbf/2022a`` +``2.0.2``|``gfbf/2023b`` ### e3nn @@ -8674,10 +8915,12 @@ Euclidean neural networks (e3nn) is a python library based on pytorch to create *homepage*: -version |versionsuffix |toolchain ----------|----------------|-------------- -``0.3.3``| |``foss/2022a`` -``0.3.3``|``-CUDA-11.7.0``|``foss/2022a`` +version |versionsuffix |toolchain +---------|-------------------------------|-------------- +``0.3.3``| |``foss/2022a`` +``0.3.3``|``-CUDA-11.7.0`` |``foss/2022a`` +``0.3.3``|``-CUDA-12.1.1`` |``foss/2023a`` +``0.3.3``|``-PyTorch-1.13.1-CUDA-11.7.0``|``foss/2022a`` ### ea-utils @@ -8817,6 +9060,18 @@ version |toolchain ``4.8.1`` |``system`` ``4.8.2`` |``system`` ``4.9.0`` |``system`` +``4.9.1`` |``system`` + +### EasyMocap + +EasyMoCap is an open-source toolbox designed for markerless human motion capture from RGB videos. This project offers a wide range of motion capture methods across various settings. + +*homepage*: + +version|versionsuffix |toolchain +-------|----------------|-------------- +``0.2``| |``foss/2022a`` +``0.2``|``-CUDA-11.7.0``|``foss/2022a`` ### EasyQC @@ -8899,9 +9154,10 @@ ECL (Embeddable Common-Lisp) is an interpreter of the Common-Lisp language as d *homepage*: -version |toolchain -----------|------------------ -``23.9.9``|``GCCcore/11.3.0`` +version |toolchain +-----------|------------------ +``23.9.9`` |``GCCcore/11.3.0`` +``24.5.10``|``GCCcore/13.2.0`` ### eclib @@ -8912,6 +9168,7 @@ The eclib package includes mwrank (for 2-descent on elliptic curves over Q) and version |toolchain ------------|-------------- ``20230424``|``GCC/11.3.0`` +``20240408``|``GCC/13.2.0`` ### ED2 @@ -9001,7 +9258,7 @@ Eigen is a C++ template library for linear algebra: matrices, vectors, numerical *homepage*: version |toolchain -----------|---------------------------------------------------------------------------------------------------------------------- +----------|------------------------------------------------------------------------------------------------------------------------------------------ ``3.2.3`` |``foss/2016a``, ``foss/2016b`` ``3.2.5`` |``system`` ``3.2.6`` |``system`` @@ -9016,7 +9273,7 @@ version |toolchain ``3.3.7`` |``GCCcore/9.3.0``, ``system`` ``3.3.8`` |``GCCcore/10.2.0`` ``3.3.9`` |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``3.4.0`` |``GCCcore/10.2.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0`` +``3.4.0`` |``GCCcore/10.2.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0``, ``GCCcore/13.3.0`` ### EigenExa @@ -9324,6 +9581,16 @@ version |versionsuffix |toolchain ------------------|----------------|-------------- ``96.0-r20190601``|``-Perl-5.28.1``|``foss/2019a`` +### ensmallen + +ensmallen is a high-quality C++ library for non-linear numerical optimization + +*homepage*: + +version |toolchain +----------|-------------- +``2.21.1``|``foss/2023a`` + ### entrypoints Entry points are a way for Python packages to advertise objects with some common interface. @@ -9428,6 +9695,7 @@ version |versionsuffix |toolchain ---------|----------------|------------------------------ ``2.0.0``| |``foss/2021a``, ``foss/2022b`` ``2.0.0``|``-CUDA-11.3.1``|``foss/2021a`` +``2.0.0``|``-CUDA-12.1.1``|``foss/2023a`` ### ESMF @@ -9493,6 +9761,7 @@ version |versionsuffix |toolchain ``4.2.1``| |``foss/2021a``, ``foss/2022a``, ``foss/2023a`` ``4.2.1``|``-CUDA-11.3.1``|``foss/2021a`` ``4.2.1``|``-CUDA-11.8.0``|``foss/2022a`` +``4.2.2``| |``foss/2023a`` ### Essentia @@ -9551,6 +9820,16 @@ version |toolchain ---------|-------------- ``2.0.6``|``foss/2022a`` +### EVcouplings + +Predict protein structure, function and mutations using evolutionary sequence covariation. + +*homepage*: + +version |toolchain +---------|-------------- +``0.1.1``|``foss/2023a`` + ### Evcxr-REPL A Rust REPL (Read-Eval-Print loop) built using the evcxr evaluation context. @@ -9684,6 +9963,7 @@ version |toolchain ``2.4.8``|``GCCcore/11.3.0``, ``GCCcore/12.1.0`` ``2.4.9``|``GCCcore/12.2.0`` ``2.5.0``|``GCCcore/12.3.0``, ``GCCcore/13.2.0`` +``2.6.2``|``GCCcore/13.3.0`` ### expect @@ -9764,7 +10044,7 @@ version |toolchain ## F -[f90cache](#f90cache) - [f90nml](#f90nml) - [f90wrap](#f90wrap) - [Faber](#faber) - [FabIO](#fabio) - [FACE](#face) - [faceswap](#faceswap) - [FALCON](#falcon) - [FANN](#fann) - [fast5](#fast5) - [FASTA](#fasta) - [fasta-reader](#fasta-reader) - [fastahack](#fastahack) - [fastai](#fastai) - [FastaIndex](#fastaindex) - [FastANI](#fastani) - [Fastaq](#fastaq) - [FastFold](#fastfold) - [fastjet](#fastjet) - [fastjet-contrib](#fastjet-contrib) - [FastME](#fastme) - [fastml](#fastml) - [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) - [FFAVES](#ffaves) - [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) - [forbear](#forbear) - [FORD](#ford) - [foss](#foss) - [fosscuda](#fosscuda) - [FoX](#fox) - [FOX-Toolkit](#fox-toolkit) - [fplll](#fplll) - [FPM](#fpm) - [fpocket](#fpocket) - [fpylll](#fpylll) - [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) - [ftfy](#ftfy) - [FTGL](#ftgl) - [fugue](#fugue) - [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) - [f90nml](#f90nml) - [f90wrap](#f90wrap) - [Faber](#faber) - [FabIO](#fabio) - [FACE](#face) - [faceswap](#faceswap) - [Faiss](#faiss) - [FALCON](#falcon) - [FANN](#fann) - [fast5](#fast5) - [FASTA](#fasta) - [fasta-reader](#fasta-reader) - [fastahack](#fastahack) - [fastai](#fastai) - [FastaIndex](#fastaindex) - [FastANI](#fastani) - [Fastaq](#fastaq) - [FastFold](#fastfold) - [fastjet](#fastjet) - [fastjet-contrib](#fastjet-contrib) - [FastME](#fastme) - [fastml](#fastml) - [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) - [FDMNES](#fdmnes) - [FDS](#fds) - [fdstools](#fdstools) - [FDTD_Solutions](#fdtd_solutions) - [feh](#feh) - [FEniCS](#fenics) - [fermi-lite](#fermi-lite) - [Ferret](#ferret) - [festival](#festival) - [fetchMG](#fetchmg) - [FFAVES](#ffaves) - [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) - [forbear](#forbear) - [FORD](#ford) - [foss](#foss) - [fosscuda](#fosscuda) - [FoX](#fox) - [FOX-Toolkit](#fox-toolkit) - [fplll](#fplll) - [FPM](#fpm) - [fpocket](#fpocket) - [fpylll](#fpylll) - [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) - [ftfy](#ftfy) - [FTGL](#ftgl) - [fugue](#fugue) - [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 @@ -9797,6 +10077,7 @@ version |toolchain ----------|-------------- ``0.2.8`` |``foss/2021a`` ``0.2.11``|``foss/2022a`` +``0.2.13``|``foss/2023a`` ### Faber @@ -9840,6 +10121,16 @@ version |versionsuffix |toolchain ------------|-----------------|-------------- ``20180212``|``-Python-3.6.3``|``foss/2017b`` +### Faiss + +Faiss is a library for efficient similarity search and clustering of dense vectors. It contains algorithms that search in sets of vectors of any size, up to ones that possibly do not fit in RAM. It also contains supporting code for evaluation and parameter tuning. Faiss is written in C++ with complete wrappers for Python/numpy. Some of the most useful algorithms are implemented on the GPU. It is developed primarily at Meta's Fundamental AI Research group. + +*homepage*: + +version |versionsuffix |toolchain +---------|----------------|-------------- +``1.7.4``|``-CUDA-12.1.1``|``foss/2023a`` + ### FALCON Falcon: a set of tools for fast aligning long reads for consensus and assembly @@ -10240,6 +10531,16 @@ version |toolchain ---------|----------------------------------------------------------------------------------------------------------------------------------- ``0.8.0``|``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``iccifort/2020.4.304``, ``intel-compilers/2021.2.0``, ``intel-compilers/2021.4.0`` +### FDMNES + +X-ray spectroscopies are techniques which probe the electronic and structural properties of the materials. Most often performed at synchrotron, they are extensively used to analyse all classes of materials. The advances on the experimental side need the complementary progress on the theoretical side to extract confidentely all the information the data can furnish. In this context, the purpose of our FDMNES project is to supply to the community a user friendly ab initio code to simulate X-ray absorption and emission spectroscopies as well as resonant x-ray scattering and x-ray Raman spectroscopies, among other techniques. FDMNES, for Finite Difference Method Near Edge Structure, uses the density functional theory (DFT). It is thus specially devoted to the simulation of the K edges of all the chemical elements and of the L23 edges of the heavy ones. For the other edges, it includes advances by the use of the time dependent DFT (TD-DFT). + +*homepage*: + +version |toolchain +--------------|--------------- +``2024-02-29``|``gomkl/2023a`` + ### FDS Fire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-speed flows, with an emphasis on smoke and heat transport from fires. @@ -10373,9 +10674,9 @@ Finite Field Linear Algebra Subroutines / Package *homepage*: version |toolchain ----------|-------------- +---------|------------------------------ ``2.2.0``|``foss/2016a`` -``2.5.0``|``gfbf/2022a`` +``2.5.0``|``gfbf/2022a``, ``gfbf/2023b`` ### FFmpeg @@ -10471,7 +10772,7 @@ version |versionsuffix|toolchain ``3.3.8`` |``-amd`` |``gompi/2020a`` ``3.3.8`` |``-serial`` |``GCC/9.3.0`` ``3.3.9`` | |``gompi/2021a``, ``intel/2021a`` -``3.3.10``| |``GCC/11.3.0``, ``GCC/12.2.0``, ``GCC/12.3.0``, ``GCC/13.2.0``, ``NVHPC/22.7-CUDA-11.7.0``, ``gompi/2021b``, ``iimpi/2021b``, ``iimpi/2022a``, ``iimpi/2022b`` +``3.3.10``| |``GCC/11.3.0``, ``GCC/12.2.0``, ``GCC/12.3.0``, ``GCC/13.2.0``, ``GCC/13.3.0``, ``NVHPC/22.7-CUDA-11.7.0``, ``gompi/2021b``, ``iimpi/2021b``, ``iimpi/2022a``, ``iimpi/2022b`` ### FFTW.MPI @@ -10480,8 +10781,8 @@ FFTW is a C subroutine library for computing the discrete Fourier transform (DFT *homepage*: version |toolchain -----------|----------------------------------------------------------------------------------------------------------------------------------------------- -``3.3.10``|``gompi/2022.05``, ``gompi/2022.10``, ``gompi/2022a``, ``gompi/2022b``, ``gompi/2023.09``, ``gompi/2023a``, ``gompi/2023b``, ``nvompi/2022.07`` +----------|------------------------------------------------------------------------------------------------------------------------------------------------------------------ +``3.3.10``|``gompi/2022.05``, ``gompi/2022.10``, ``gompi/2022a``, ``gompi/2022b``, ``gompi/2023.09``, ``gompi/2023a``, ``gompi/2023b``, ``gompi/2024.05``, ``nvompi/2022.07`` ### fgbio @@ -10489,9 +10790,10 @@ A set of tools to analyze genomic data with a focus on Next Generation Sequencin *homepage*: -version |toolchain ----------|---------- -``1.3.0``|``system`` +version |versionsuffix|toolchain +---------|-------------|---------- +``1.3.0``| |``system`` +``2.2.1``|``-Java-8`` |``system`` ### FGSL @@ -10567,7 +10869,7 @@ The file command is 'a file type guesser', that is, a command-line tool that te *homepage*: version |toolchain ---------|-------------------------------------- +--------|---------------------------------------------------------- ``5.17``|``GCC/4.8.2`` ``5.25``|``intel/2016a`` ``5.28``|``foss/2016b`` @@ -10578,7 +10880,7 @@ version |toolchain ``5.39``|``GCCcore/10.2.0`` ``5.40``|``GCCcore/10.3.0`` ``5.41``|``GCCcore/11.2.0`` -``5.43``|``GCCcore/11.3.0``, ``GCCcore/12.3.0`` +``5.43``|``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### filevercmp @@ -10874,14 +11176,14 @@ 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/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`` +``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/13.3.0``, ``GCCcore/14.1.0``, ``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`` ### Flexbar @@ -10906,6 +11208,7 @@ version |toolchain ``3.2.0``|``GCC/11.3.0``, ``NVHPC/22.7-CUDA-11.7.0`` ``3.2.1``|``GCC/12.2.0`` ``3.3.1``|``GCC/12.3.0``, ``GCC/13.2.0`` +``3.4.4``|``GCC/13.3.0`` ### FlexiDot @@ -10985,6 +11288,7 @@ version |toolchain ``1.3.6``|``GCCcore/10.3.0`` ``1.3.7``|``GCCcore/11.2.0`` ``1.3.8``|``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` +``1.3.9``|``GCCcore/13.2.0`` ### FLUENT @@ -11042,6 +11346,7 @@ Flatiron Institute Fast Multipole Libraries: a set of libraries to compute N-bod version |toolchain ------------|-------------- +``1.0.4`` |``foss/2023a`` ``20211018``|``foss/2020b`` ### FMPy @@ -11140,6 +11445,7 @@ version |versionsuffix |toolchain ``2.14.0`` | |``GCCcore/11.3.0`` ``2.14.1`` | |``GCCcore/12.2.0`` ``2.14.2`` | |``GCCcore/12.3.0``, ``GCCcore/13.2.0`` +``2.15.0`` | |``GCCcore/13.3.0`` ### fontsproto @@ -11205,6 +11511,7 @@ version |toolchain ``2023.09``|``system`` ``2023a`` |``system`` ``2023b`` |``system`` +``2024.05``|``system`` ### fosscuda @@ -11476,7 +11783,7 @@ version |versionsuffix |toolchain ``2.11.0``| |``GCCcore/11.2.0`` ``2.12.1``| |``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ``2.13.0``| |``GCCcore/12.3.0`` -``2.13.2``| |``GCCcore/13.2.0`` +``2.13.2``| |``GCCcore/13.2.0``, ``GCCcore/13.3.0`` ### freetype-py @@ -11485,8 +11792,9 @@ Python binding for the freetype library *homepage*: version |versionsuffix |toolchain ----------|-----------------|----------------- +---------|-----------------|------------------ ``2.2.0``|``-Python-3.7.4``|``GCCcore/8.3.0`` +``2.4.0``| |``GCCcore/11.3.0`` ### FreeXL @@ -11773,7 +12081,7 @@ version|toolchain ## G -[G-PhoCS](#g-phocs) - [g2clib](#g2clib) - [g2lib](#g2lib) - [g2log](#g2log) - [Gaia](#gaia) - [GAMESS-US](#gamess-us) - [gap](#gap) - [GapCloser](#gapcloser) - [GapFiller](#gapfiller) - [gappa](#gappa) - [GAPPadder](#gappadder) - [GARLI](#garli) - [garnett](#garnett) - [GAT](#gat) - [GATB-Core](#gatb-core) - [GATE](#gate) - [GATK](#gatk) - [Gaussian](#gaussian) - [gawk](#gawk) - [gbasis](#gbasis) - [Gblocks](#gblocks) - [GBprocesS](#gbprocess) - [gbs2ploidy](#gbs2ploidy) - [gc](#gc) - [GC3Pie](#gc3pie) - [GCC](#gcc) - [GCCcore](#gcccore) - [gcccuda](#gcccuda) - [gcloud](#gcloud) - [GConf](#gconf) - [gcsfs](#gcsfs) - [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) - [Gdspy](#gdspy) - [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) - [GenomeComb](#genomecomb) - [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) - [GFF3-toolkit](#gff3-toolkit) - [GffCompare](#gffcompare) - [gffread](#gffread) - [gffutils](#gffutils) - [gflags](#gflags) - [GFOLD](#gfold) - [gh](#gh) - [GHC](#ghc) - [Ghostscript](#ghostscript) - [GI-DocGen](#gi-docgen) - [giac](#giac) - [Gibbs2](#gibbs2) - [giflib](#giflib) - [gifsicle](#gifsicle) - [GIMIC](#gimic) - [gimkl](#gimkl) - [GimmeMotifs](#gimmemotifs) - [GIMP](#gimp) - [gimpi](#gimpi) - [gimpic](#gimpic) - [GIMPS](#gimps) - [giolf](#giolf) - [giolfc](#giolfc) - [Giotto-Suite](#giotto-suite) - [git](#git) - [git-annex](#git-annex) - [git-extras](#git-extras) - [git-lfs](#git-lfs) - [GitPython](#gitpython) - [Givaro](#givaro) - [Giza](#giza) - [GKeyll](#gkeyll) - [GKlib-METIS](#gklib-metis) - [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) - [GMP-ECM](#gmp-ecm) - [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) - [GRASP-suite](#grasp-suite) - [GRASS](#grass) - [Greenlet](#greenlet) - [Grep](#grep) - [gretl](#gretl) - [grib_api](#grib_api) - [grid](#grid) - [GRIDSS](#gridss) - [GRIT](#grit) - [GRNBoost](#grnboost) - [groff](#groff) - [GroIMP](#groimp) - [GROMACS](#gromacs) - [GromacsWrapper](#gromacswrapper) - [Groovy](#groovy) - [gRPC](#grpc) - [GSD](#gsd) - [GSEA](#gsea) - [gsettings-desktop-schemas](#gsettings-desktop-schemas) - [GSL](#gsl) - [gSOAP](#gsoap) - [gspell](#gspell) - [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) - [GUIDANCE](#guidance) - [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) - [gcsfs](#gcsfs) - [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) - [Gdspy](#gdspy) - [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) - [GenomeComb](#genomecomb) - [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) - [GFF3-toolkit](#gff3-toolkit) - [GffCompare](#gffcompare) - [gffread](#gffread) - [gffutils](#gffutils) - [gflags](#gflags) - [GFOLD](#gfold) - [gh](#gh) - [GHC](#ghc) - [Ghostscript](#ghostscript) - [GI-DocGen](#gi-docgen) - [giac](#giac) - [Gibbs2](#gibbs2) - [giflib](#giflib) - [gifsicle](#gifsicle) - [GIMIC](#gimic) - [gimkl](#gimkl) - [GimmeMotifs](#gimmemotifs) - [GIMP](#gimp) - [gimpi](#gimpi) - [gimpic](#gimpic) - [GIMPS](#gimps) - [giolf](#giolf) - [giolfc](#giolfc) - [Giotto-Suite](#giotto-suite) - [git](#git) - [git-annex](#git-annex) - [git-extras](#git-extras) - [git-lfs](#git-lfs) - [GitPython](#gitpython) - [Givaro](#givaro) - [Giza](#giza) - [GKeyll](#gkeyll) - [GKlib-METIS](#gklib-metis) - [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) - [GMP-ECM](#gmp-ecm) - [gmpich](#gmpich) - [gmpolf](#gmpolf) - [gmpy2](#gmpy2) - [gmsh](#gmsh) - [GMT](#gmt) - [gmvapich2](#gmvapich2) - [gmvolf](#gmvolf) - [GNU](#gnu) - [gnupg-bundle](#gnupg-bundle) - [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) - [GRASP-suite](#grasp-suite) - [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) - [grpcio](#grpcio) - [GSD](#gsd) - [GSEA](#gsea) - [gsettings-desktop-schemas](#gsettings-desktop-schemas) - [GSL](#gsl) - [gSOAP](#gsoap) - [gspell](#gspell) - [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) - [GUIDANCE](#guidance) - [Guile](#guile) - [GULP](#gulp) - [Gurobi](#gurobi) - [GUSHR](#gushr) - [gzip](#gzip) ### G-PhoCS @@ -11832,17 +12140,19 @@ version |versionsuffix |toolchain ### GAMESS-US -The General Atomic and Molecular Electronic Structure System (GAMESS) is a general ab initio quantum chemistry package. +The General Atomic and Molecular Electronic Structure System (GAMESS) is a general ab initio quantum chemistry package. This module can be used on a maximum of 1 nodes and 1024 CPUs per node. -*homepage*: +*homepage*: version |versionsuffix|toolchain ----------------|-------------|--------------- +---------------|-------------|--------------------------------------------- ``20141205-R1``| |``intel/2016a`` ``20170420-R1``| |``intel/2016b`` ``20170420-R1``|``-sockets`` |``intel/2016b`` ``20180214-R1``| |``foss/2016b`` ``20180214-R1``|``-sockets`` |``foss/2016b`` +``20220930-R2``| |``gompi/2022a`` +``20230930-R2``| |``gompi/2022a``, ``intel-compilers/2022.1.0`` ### gap @@ -12088,6 +12398,7 @@ version |toolchain ``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`` +``8.2.6`` |``GCCcore/13.2.0`` ### GC3Pie @@ -12174,6 +12485,8 @@ version |versionsuffix |toolchain ``12.3.0``| |``system`` ``13.1.0``| |``system`` ``13.2.0``| |``system`` +``13.3.0``| |``system`` +``14.1.0``| |``system`` ``system``| |``system`` ``system``|``-2.29`` |``system`` @@ -12221,6 +12534,8 @@ version |toolchain ``12.3.0``|``system`` ``13.1.0``|``system`` ``13.2.0``|``system`` +``13.3.0``|``system`` +``14.1.0``|``system`` ``system``|``system`` ### gcccuda @@ -12249,6 +12564,7 @@ Libraries and tools for interacting with Google Cloud products and services. version |toolchain -----------|---------- ``382.0.0``|``system`` +``472.0.0``|``system`` ### GConf @@ -12369,6 +12685,7 @@ version |versionsuffix |toolchain ``11.1`` | |``GCCcore/11.2.0`` ``12.1`` | |``GCCcore/11.3.0`` ``13.2`` | |``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0`` +``14.2`` | |``GCCcore/13.3.0`` ### gdbgui @@ -12489,6 +12806,7 @@ version |versionsuffix |toolchain ``2.3`` | |``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ``2.3.1``| |``GCCcore/12.3.0`` ``2.4`` | |``GCCcore/13.2.0`` +``2.4.1``| |``GCCcore/13.3.0`` ### Gdspy @@ -12599,13 +12917,14 @@ version |toolchain ### gemmi -Gemmi is a library, accompanied by a set of programs, developed primarily for use in macromolecular crystallography (MX). For working with: macromolecular models (content of PDB, PDBx/mmCIF and mmJSON files), refinement restraints (CIF files), reflection data (MTZ and mmCIF formats), data on a 3D grid (electron density maps, masks, MRC/CCP4 format) crystallographic symmetry. Parts of this library can be useful in structural bioinformatics (for symmetry- aware analysis of protein models), and in other molecular-structure sciences that use CIF files (we have the fastest open-source CIF parser). +Gemmi is a library, accompanied by a set of programs, developed primarily for use in macromolecular crystallography (MX). For working with: macromolecular models (content of PDB, PDBx/mmCIF and mmJSON files), refinement restraints (CIF files), reflection data (MTZ and mmCIF formats), data on a 3D grid (electron density maps, masks, MRC/CCP4 format) crystallographic symmetry. Parts of this library can be useful in structural bioinformatics (for symmetry- aware analysis of protein models), and in other molecular-structure sciences that use CIF files (we have the fastest open-source CIF parser). *homepage*: version |toolchain ---------|------------------ ``0.4.5``|``GCCcore/10.2.0`` +``0.6.5``|``GCCcore/12.3.0`` ### gencore_variant_detection @@ -12647,8 +12966,8 @@ Gengetopt is a tool to write command line option parsing code for C programs. *homepage*: version |toolchain ---------|----------------------------------------------------------------------------- -``2.23``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.3.0``, ``GCCcore/9.3.0`` +--------|------------------------------------------------------------------------------------------------- +``2.23``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.3.0``, ``GCCcore/13.2.0``, ``GCCcore/9.3.0`` ### GenMap @@ -12920,6 +13239,7 @@ version |versionsuffix |toolchain ``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`` +``0.22.5`` | |``GCCcore/13.3.0``, ``system`` ### gexiv2 @@ -12944,6 +13264,7 @@ version |toolchain ``2023.09``|``system`` ``2023a`` |``system`` ``2023b`` |``system`` +``2024.05``|``system`` ### GFF3-toolkit @@ -13075,13 +13396,14 @@ version |toolchain ### giac -Giac is a C++ library, it is the CAS computing kernel. It may be used inside other C++ programs, and also Python, Java and Javascript programs. +Giac is a C++ library, it is the CAS computing kernel. It may be used inside other C++ programs, and also Python, Java and Javascript programs. *homepage*: version |toolchain ------------|-------------- ``1.9.0-69``|``gfbf/2022a`` +``1.9.0-99``|``gfbf/2023b`` ### Gibbs2 @@ -13253,6 +13575,7 @@ version |versionsuffix|toolchain ``2.38.1`` |``-nodocs`` |``GCCcore/12.2.0`` ``2.41.0`` |``-nodocs`` |``GCCcore/12.3.0`` ``2.42.0`` | |``GCCcore/13.2.0`` +``2.45.1`` | |``GCCcore/13.3.0`` ### git-annex @@ -13318,19 +13641,20 @@ C++ library for arithmetic and algebraic computations *homepage*: version |toolchain ----------|------------------ +---------|-------------------------------------- ``4.0.1``|``foss/2016a`` -``4.2.0``|``GCCcore/11.3.0`` +``4.2.0``|``GCCcore/11.3.0``, ``GCCcore/13.2.0`` ### Giza -Giza is an open, lightweight scientific plotting library built on top of cairo that provides uniform output to multiple devices. +Giza is an open, lightweight scientific plotting library built on top of cairo that provides uniform output to multiple devices. *homepage*: version |toolchain ----------|-------------- +---------|------------------ ``1.1.0``|``foss/2018b`` +``1.4.1``|``GCCcore/13.2.0`` ### GKeyll @@ -13369,11 +13693,11 @@ GL2PS: an OpenGL to PostScript printing library *homepage*: version |versionsuffix |toolchain ----------|----------------|------------------------------------------------------------------------------------------------------------------------------------ +---------|----------------|----------------------------------------------------------------------------------------------------------------------------------------- ``1.3.9``| |``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` ``1.3.9``|``-Mesa-11.2.1``|``foss/2016a``, ``intel/2016a`` ``1.4.0``| |``GCCcore/8.3.0``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``foss/2019a``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` -``1.4.2``| |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/9.3.0`` +``1.4.2``| |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/9.3.0`` ### Glade @@ -13397,9 +13721,9 @@ The OpenGL Extension Wrangler Library (GLEW) is a cross-platform open-source C/C version |versionsuffix|toolchain ---------|-------------|--------------------------------------------------------------------------------------------------------------- ``2.1.0``| |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2018b`` -``2.2.0``|``-egl`` |``GCCcore/10.2.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``2.2.0``|``-egl`` |``GCCcore/10.2.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.3.0`` ``2.2.0``|``-glx`` |``GCCcore/10.2.0``, ``GCCcore/11.2.0`` -``2.2.0``|``-osmesa`` |``GCCcore/10.2.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``2.2.0``|``-osmesa`` |``GCCcore/10.2.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.3.0`` ### GLFW @@ -13414,7 +13738,7 @@ version |toolchain ``3.3.3``|``GCCcore/10.2.0`` ``3.3.4``|``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``3.3.8``|``GCCcore/11.3.0`` -``3.4`` |``GCCcore/12.2.0`` +``3.4`` |``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### GLI @@ -13665,7 +13989,7 @@ version |toolchain ``6.1.2`` |``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2016b`` ``6.2.0`` |``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ``6.2.1`` |``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` -``6.3.0`` |``GCCcore/13.2.0`` +``6.3.0`` |``GCCcore/13.2.0``, ``GCCcore/13.3.0`` ### GMP-ECM @@ -13674,8 +13998,8 @@ Yet another implementation of the Elliptic Curve Method. *homepage*: version |toolchain ----------|------------------ -``7.0.5``|``GCCcore/11.3.0`` +---------|-------------------------------------- +``7.0.5``|``GCCcore/11.3.0``, ``GCCcore/13.2.0`` ### gmpich @@ -13734,6 +14058,7 @@ version |versionsuffix |toolchain ``4.8.4`` |``-Python-3.6.4`` |``foss/2018a`` ``4.9.0`` | |``foss/2021a`` ``4.11.1``| |``foss/2022a`` +``4.12.2``| |``foss/2023a`` ### GMT @@ -13783,6 +14108,16 @@ version |toolchain ``4.9.3-2.25``|``system`` ``5.1.0-2.25``|``system`` +### gnupg-bundle + +GnuPG — The Universal Crypto Engine + +*homepage*: + +version |toolchain +------------|------------------ +``20240306``|``GCCcore/13.2.0`` + ### gnuplot Portable interactive, function plotting utility @@ -13811,13 +14146,13 @@ GnuTLS is a secure communications library implementing the SSL, TLS and DTLS pr *homepage*: version |toolchain -----------|------------------ +----------|-------------------------------------- ``3.3.21``|``intel/2016a`` ``3.4.7`` |``GNU/4.9.3-2.25`` ``3.4.11``|``foss/2016a`` ``3.7.2`` |``GCCcore/10.3.0`` ``3.7.3`` |``GCCcore/11.2.0`` -``3.7.8`` |``GCCcore/11.3.0`` +``3.7.8`` |``GCCcore/11.3.0``, ``GCCcore/12.3.0`` ### Go @@ -13870,6 +14205,7 @@ version |toolchain ---------|------------------------------ ``1.1.6``|``foss/2020b`` ``1.3.1``|``foss/2021b``, ``foss/2022a`` +``1.4.5``|``foss/2023a`` ### gobff @@ -14014,6 +14350,7 @@ version |versionsuffix|toolchain ``2023.09``| |``system`` ``2023a`` | |``system`` ``2023b`` | |``system`` +``2024.05``| |``system`` ``system`` |``-2.29`` |``system`` ### gompic @@ -14120,9 +14457,9 @@ GNU gperf is a perfect hash function generator. For a given list of strings, it *homepage*: version |toolchain ----------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +---------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ``3.0.4``|``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` -``3.1`` |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``3.1`` |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0``, ``GCCcore/13.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ### gperftools @@ -14575,6 +14912,16 @@ version |toolchain ``1.57.0``|``GCCcore/12.3.0`` ``1.62.1``|``GCCcore/13.2.0`` +### grpcio + +gRPC is a modern, open source, high-performance remote procedure call (RPC) framework that can run anywhere. gRPC enables client and server applications to communicate transparently, and simplifies the building of connected systems. + +*homepage*: + +version |toolchain +----------|------------------ +``1.57.0``|``GCCcore/12.3.0`` + ### GSD The GSD file format is the native file format for HOOMD-blue. GSD files store trajectories of the HOOMD-blue system state in a binary file with efficient random access to frames. GSD allows all particle and topology properties to vary from one frame to the next. Use the GSD Python API to specify the initial condition for a HOOMD-blue simulation or analyze trajectory output with a script. Read a GSD trajectory with a visualization tool to explore the behavior of the simulation. @@ -14712,6 +15059,7 @@ gsutil is a Python application that lets you access Cloud Storage from the comma version |toolchain --------|------------------ ``5.10``|``GCCcore/11.2.0`` +``5.29``|``GCCcore/13.2.0`` ### gsw @@ -14740,6 +15088,7 @@ version |versionsuffix |toolchain ``2.0.0``| |``foss/2021a``, ``intel/2021b`` ``2.1.1``| |``foss/2021b`` ``2.3.2``| |``foss/2022a``, ``foss/2023a`` +``2.4.0``| |``foss/2023a`` ### GTK+ @@ -14937,12 +15286,12 @@ version |toolchain ``1.9`` |``GCCcore/7.3.0`` ``1.10``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``1.12``|``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` -``1.13``|``GCCcore/13.2.0`` +``1.13``|``GCCcore/13.2.0``, ``GCCcore/13.3.0`` ## H -[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) - [hdWGCNA](#hdwgcna) - [HEALPix](#healpix) - [Health-GPS](#health-gps) - [heaptrack](#heaptrack) - [hector](#hector) - [HeFFTe](#heffte) - [Hello](#hello) - [help2man](#help2man) - [HepMC](#hepmc) - [HepMC3](#hepmc3) - [HF-Datasets](#hf-datasets) - [HH-suite](#hh-suite) - [HiC-Pro](#hic-pro) - [hic-straw](#hic-straw) - [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) - [HPCC](#hpcc) - [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](#h4toh5) - [H5hut](#h5hut) - [h5netcdf](#h5netcdf) - [h5py](#h5py) - [Hadoop](#hadoop) - [HAL](#hal) - [hampel](#hampel) - [hanythingondemand](#hanythingondemand) - [HAPGEN2](#hapgen2) - [HarfBuzz](#harfbuzz) - [Harminv](#harminv) - [harmony](#harmony) - [hatch-jupyter-builder](#hatch-jupyter-builder) - [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) - [hdWGCNA](#hdwgcna) - [HEALPix](#healpix) - [Health-GPS](#health-gps) - [heaptrack](#heaptrack) - [hector](#hector) - [HeFFTe](#heffte) - [Hello](#hello) - [help2man](#help2man) - [HepMC](#hepmc) - [HepMC3](#hepmc3) - [hevea](#hevea) - [HF-Datasets](#hf-datasets) - [HH-suite](#hh-suite) - [HiC-Pro](#hic-pro) - [hic-straw](#hic-straw) - [HiCExplorer](#hicexplorer) - [HiCMatrix](#hicmatrix) - [hierfstat](#hierfstat) - [hifiasm](#hifiasm) - [HighFive](#highfive) - [HiGHS](#highs) - [Highway](#highway) - [HIP](#hip) - [hipify-clang](#hipify-clang) - [HIPS](#hips) - [hipSYCL](#hipsycl) - [hiredis](#hiredis) - [HISAT2](#hisat2) - [histolab](#histolab) - [hivtrace](#hivtrace) - [hl7apy](#hl7apy) - [HLAminer](#hlaminer) - [hmmcopy_utils](#hmmcopy_utils) - [HMMER](#hmmer) - [HMMER2](#hmmer2) - [hmmlearn](#hmmlearn) - [HOME](#home) - [HOMER](#homer) - [HOOMD-blue](#hoomd-blue) - [Horovod](#horovod) - [horton](#horton) - [how_are_we_stranded_here](#how_are_we_stranded_here) - [HPCC](#hpcc) - [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 @@ -15024,6 +15373,7 @@ version |versionsuffix |toolchain ``3.7.0`` | |``foss/2022a``, ``intel/2022a`` ``3.8.0`` | |``foss/2022b`` ``3.9.0`` | |``foss/2023a`` +``3.11.0``| |``foss/2023b`` ### Hadoop @@ -15149,6 +15499,16 @@ version |versionsuffix|toolchain ``0.1.0-20210528``|``-R-4.0.3`` |``foss/2020b`` ``1.0.0-20200224``|``-R-4.0.0`` |``foss/2020a`` +### hatch-jupyter-builder + +Hatch Jupyter Builder is a plugin for the hatchling Python build backend. It is primarily targeted for package authors who are providing JavaScript as part of their Python packages. Typical use cases are Jupyter Lab Extensions and Jupyter Widgets. + +*homepage*: + +version |toolchain +---------|------------------ +``0.9.1``|``GCCcore/13.2.0`` + ### hatchling Extensible, standards compliant build backend used by Hatch, a modern, extensible Python project manager. @@ -15196,13 +15556,14 @@ version |versionsuffix |toolchain HDDM is a Python toolbox for hierarchical Bayesian parameter estimation of the Drift Diffusion Model (via PyMC). -*homepage*: +*homepage*: version |versionsuffix |toolchain ----------|------------------|--------------- +---------|------------------|------------------------------- ``0.6.1``|``-Python-3.6.6`` |``intel/2018b`` ``0.7.5``|``-Python-2.7.16``|``intel/2019b`` ``0.7.5``|``-Python-3.7.4`` |``intel/2019b`` +``0.9.9``| |``foss/2021b``, ``intel/2021b`` ### HDF @@ -15400,7 +15761,7 @@ 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``, ``GCCcore/13.2.0`` +``1.49.3`` |``GCCcore/11.4.0``, ``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``GCCcore/13.2.0``, ``GCCcore/13.3.0``, ``GCCcore/14.1.0`` ### HepMC @@ -15423,6 +15784,16 @@ version |toolchain ``3.2.5``|``GCC/11.3.0`` ``3.2.6``|``GCC/12.3.0`` +### hevea + +A quite complete and fast LATEX to HTML translator + +*homepage*: + +version |toolchain +--------|-------------- +``2.36``|``GCC/13.2.0`` + ### HF-Datasets The largest hub of ready-to-use datasets for ML models with fast, easy-to-use and efficient data manipulation tools. @@ -15440,10 +15811,10 @@ The HH-suite is an open-source software package for sensitive protein sequence *homepage*: version |versionsuffix |toolchain ---------------|-----------------|---------------------------------------------------------------------------------------------------- +--------------|-----------------|--------------------------------------------------------------------------------------------------------------------- ``3.0-beta.3``| |``intel/2018a`` ``3.2.0`` | |``foss/2019b``, ``fosscuda/2019b`` -``3.3.0`` | |``foss/2020a``, ``gompi/2020b``, ``gompi/2021a``, ``gompi/2021b``, ``gompi/2022a``, ``gompic/2020b`` +``3.3.0`` | |``foss/2020a``, ``gompi/2020b``, ``gompi/2021a``, ``gompi/2021b``, ``gompi/2022a``, ``gompi/2023a``, ``gompic/2020b`` ``3.3.0`` |``-Python-3.7.4``|``gompic/2019b`` ### HiC-Pro @@ -15522,6 +15893,16 @@ version |toolchain ``2.6.2``|``gompi/2021a``, ``gompi/2022a`` ``2.7.1``|``gompi/2023a`` +### HiGHS + +Open source serial and parallel solvers for large-scale sparse linear programming (LP), mixed-integer programming (MIP), and quadratic programming (QP) models. + +*homepage*: + +version |toolchain +---------|-------------- +``1.7.0``|``gfbf/2023b`` + ### Highway Highway is a C++ library for SIMD (Single Instruction, Multiple Data), i.e. applying the same operation to 'lanes'. @@ -15593,13 +15974,13 @@ HISAT2 is a fast and sensitive alignment program for mapping next-generation seq *homepage*: version |toolchain ---------------|-------------------------------------------------------------------------------------------------- +--------------|------------------------------------------------------------------------------------------------------------------- ``2.0.3-beta``|``intel/2016a`` ``2.0.4`` |``foss/2016b`` ``2.0.5`` |``intel/2017a`` ``2.1.0`` |``foss/2017b``, ``foss/2018b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` ``2.2.0`` |``foss/2018b`` -``2.2.1`` |``foss/2019b``, ``foss/2020a``, ``gompi/2020b``, ``gompi/2021a``, ``gompi/2021b``, ``gompi/2022a`` +``2.2.1`` |``foss/2019b``, ``foss/2020a``, ``gompi/2020b``, ``gompi/2021a``, ``gompi/2021b``, ``gompi/2022a``, ``gompi/2022b`` ### histolab @@ -15641,6 +16022,16 @@ version|versionsuffix |toolchain -------|----------------|-------------- ``1.4``|``-Perl-5.28.0``|``foss/2018b`` +### hmmcopy_utils + +Tools for extracting read counts and gc and mappability statistics in preparation for running HMMCopy. + +*homepage*: + +version |toolchain +------------|------------------ +``20210728``|``GCCcore/12.3.0`` + ### HMMER HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). Compared to BLAST, FASTA, and other sequence alignment and database search tools based on older scoring methodology, HMMER aims to be significantly more accurate and more able to detect remote homologs because of the strength of its underlying mathematical models. In the past, this strength came at significant computational expense, but in the new HMMER3 project, HMMER is now essentially as fast as BLAST. @@ -15687,6 +16078,16 @@ version|versionsuffix |toolchain -------|------------------|-------------- ``0.9``|``-Python-2.7.13``|``foss/2017a`` +### HOMER + +HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis. It is a collection of command line programs for unix-style operating systems written in Perl and C++. HOMER was primarily written as a de novo motif discovery algorithm and is well suited for finding 8-20 bp motifs in large scale genomics data. HOMER contains many useful tools for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets. + +*homepage*: + +version |versionsuffix|toolchain +--------|-------------|-------------- +``4.11``|``-R-4.3.2`` |``foss/2023a`` + ### HOOMD-blue HOOMD-blue is a general-purpose particle simulation toolkit, implementing molecular dynamics and hard particle Monte Carlo optimized for fast execution on both GPUs and CPUs. @@ -15810,11 +16211,11 @@ HPL is a software package that solves a (random) dense linear system in double p *homepage*: version |versionsuffix |toolchain -----------|----------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +----------|----------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ``2.0.15``|``-CUDA-11.7.0``|``intel/2022a`` ``2.1`` | |``foss/2016.04``, ``foss/2016.06``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``gmpolf/2016a``, ``gmvolf/1.7.20``, ``gmvolf/2016a``, ``intel/2016.00``, ``intel/2016.01``, ``intel/2016.02-GCC-4.9``, ``intel/2016.02-GCC-5.3``, ``intel/2016.03-GCC-4.9``, ``intel/2016.03-GCC-5.3``, ``intel/2016.03-GCC-5.4``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``pomkl/2016.03``, ``pomkl/2016.04``, ``pomkl/2016.09`` ``2.2`` | |``foss/2016.07``, ``foss/2016.09``, ``foss/2017a``, ``foss/2017b``, ``foss/2018.08``, ``foss/2018a``, ``foss/2018b``, ``fosscuda/2017b``, ``fosscuda/2018a``, ``fosscuda/2018b``, ``gimkl/2018b``, ``giolf/2017b``, ``giolf/2018a``, ``giolfc/2017b``, ``gmpolf/2017.10``, ``goblf/2018b``, ``gomkl/2018b``, ``intel/2017.00``, ``intel/2017.01``, ``intel/2017.02``, ``intel/2017.09``, ``intel/2017a``, ``intel/2017b``, ``intel/2018.00``, ``intel/2018.01``, ``intel/2018.02``, ``intel/2018.04``, ``intel/2018a``, ``intel/2018b``, ``intel/2019.00``, ``intel/2019.01``, ``intelcuda/2016.10``, ``intelcuda/2017b``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``iomkl/2016.09-GCC-5.4.0-2.26``, ``iomkl/2017.01``, ``iomkl/2017a``, ``iomkl/2017b``, ``iomkl/2018.02``, ``iomkl/2018a``, ``iomkl/2018b``, ``pomkl/2016.09`` -``2.3`` | |``CrayCCE/19.06``, ``CrayGNU/19.06``, ``CrayIntel/19.06``, ``Fujitsu/21.05``, ``foss/2019a``, ``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``foss/2022.05``, ``foss/2022.10``, ``foss/2022a``, ``foss/2022b``, ``foss/2023.09``, ``foss/2023a``, ``foss/2023b``, ``fosscuda/2019b``, ``fosscuda/2020a``, ``gobff/2020.06-amd``, ``gobff/2020.11``, ``gobff/2020b``, ``gobff/2021a``, ``goblf/2020b``, ``gomkl/2019a``, ``gomkl/2020b``, ``gomkl/2021a``, ``gomkl/2022a``, ``iibff/2020b``, ``intel/2019.02``, ``intel/2019.03``, ``intel/2019a``, ``intel/2019b``, ``intel/2020.00``, ``intel/2020.06-impi-18.5``, ``intel/2020.12``, ``intel/2020a``, ``intel/2020b``, ``intel/2021a``, ``intel/2021b``, ``intel/2022.00``, ``intel/2022.09``, ``intel/2022.11``, ``intel/2022.12``, ``intel/2022a``, ``intel/2022b``, ``intel/2023.03``, ``intel/2023.07``, ``intel/2023a``, ``intel/2023b``, ``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/2023.09``, ``foss/2023a``, ``foss/2023b``, ``foss/2024.05``, ``fosscuda/2019b``, ``fosscuda/2020a``, ``gobff/2020.06-amd``, ``gobff/2020.11``, ``gobff/2020b``, ``gobff/2021a``, ``goblf/2020b``, ``gomkl/2019a``, ``gomkl/2020b``, ``gomkl/2021a``, ``gomkl/2022a``, ``iibff/2020b``, ``intel/2019.02``, ``intel/2019.03``, ``intel/2019a``, ``intel/2019b``, ``intel/2020.00``, ``intel/2020.06-impi-18.5``, ``intel/2020.12``, ``intel/2020a``, ``intel/2020b``, ``intel/2021a``, ``intel/2021b``, ``intel/2022.00``, ``intel/2022.09``, ``intel/2022.11``, ``intel/2022.12``, ``intel/2022a``, ``intel/2022b``, ``intel/2023.03``, ``intel/2023.07``, ``intel/2023a``, ``intel/2023b``, ``intelcuda/2019b``, ``intelcuda/2020a``, ``iomkl/2019.01``, ``iomkl/2021a``, ``iomkl/2021b`` ### htop @@ -15876,6 +16277,7 @@ version |versionsuffix|toolchain ``1.15.1`` | |``GCC/11.3.0`` ``1.17`` | |``GCC/12.2.0`` ``1.18`` | |``GCC/12.3.0`` +``1.19.1`` | |``GCC/13.2.0`` ``20160107``|``-PacBio`` |``intel/2017a`` ### HTSplotter @@ -15957,6 +16359,7 @@ version |toolchain ``2.8.0`` |``GCCcore/12.2.0`` ``2.9.1`` |``GCCcore/12.3.0`` ``2.9.2`` |``GCCcore/13.2.0`` +``2.10.0`` |``GCCcore/13.3.0`` ### Hybpiper @@ -16024,6 +16427,7 @@ version |toolchain ``2.3.13``|``foss/2016b`` ``2.5.1`` |``gompi/2019a`` ``2.5.33``|``gompi/2021a`` +``2.5.60``|``gompi/2022a`` ### HyPo @@ -16082,7 +16486,7 @@ version |toolchain ## I -[i-cisTarget](#i-cistarget) - [i-PI](#i-pi) - [I-TASSER](#i-tasser) - [i7z](#i7z) - [ICA-AROMA](#ica-aroma) - [icc](#icc) - [iccifort](#iccifort) - [iccifortcuda](#iccifortcuda) - [iced](#iced) - [ichorCNA](#ichorcna) - [icmake](#icmake) - [iCount](#icount) - [ICU](#icu) - [IDBA-UD](#idba-ud) - [idemux](#idemux) - [IDG](#idg) - [ieeg-cli](#ieeg-cli) - [ifort](#ifort) - [IgBLAST](#igblast) - [IGMPlot](#igmplot) - [igraph](#igraph) - [IGV](#igv) - [igv-reports](#igv-reports) - [igvShiny](#igvshiny) - [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) - [IML](#iml) - [Imlib2](#imlib2) - [immunedeconv](#immunedeconv) - [IMOD](#imod) - [impi](#impi) - [IMPUTE2](#impute2) - [imutils](#imutils) - [InChI](#inchi) - [indicators](#indicators) - [Inelastica](#inelastica) - [inferCNV](#infercnv) - [infercnvpy](#infercnvpy) - [Inferelator](#inferelator) - [Infernal](#infernal) - [inflection](#inflection) - [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) - [InterOp](#interop) - [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) - [IonQuant](#ionquant) - [IOR](#ior) - [IOzone](#iozone) - [iperf](#iperf) - [IPM](#ipm) - [Ipopt](#ipopt) - [ipp](#ipp) - [IPy](#ipy) - [ipympl](#ipympl) - [ipyparallel](#ipyparallel) - [ipyrad](#ipyrad) - [IPython](#ipython) - [IQ-TREE](#iq-tree) - [Iris](#iris) - [IRkernel](#irkernel) - [irodsfs](#irodsfs) - [IronPython](#ironpython) - [ISA-L](#isa-l) - [ISL](#isl) - [isoCirc](#isocirc) - [IsoformSwitchAnalyzeR](#isoformswitchanalyzer) - [IsoNet](#isonet) - [IsoQuant](#isoquant) - [IsoSeq](#isoseq) - [ispc](#ispc) - [itac](#itac) - [ITK](#itk) - [itpp](#itpp) - [ITSTool](#itstool) - [ITSx](#itsx) - [iVar](#ivar) +[i-cisTarget](#i-cistarget) - [i-PI](#i-pi) - [I-TASSER](#i-tasser) - [i7z](#i7z) - [ICA-AROMA](#ica-aroma) - [icc](#icc) - [iccifort](#iccifort) - [iccifortcuda](#iccifortcuda) - [iced](#iced) - [ichorCNA](#ichorcna) - [icmake](#icmake) - [ICON](#icon) - [iCount](#icount) - [ICU](#icu) - [IDBA-UD](#idba-ud) - [idemux](#idemux) - [IDG](#idg) - [ieeg-cli](#ieeg-cli) - [ifort](#ifort) - [IgBLAST](#igblast) - [IGMPlot](#igmplot) - [igraph](#igraph) - [IGV](#igv) - [igv-reports](#igv-reports) - [igvShiny](#igvshiny) - [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) - [IML](#iml) - [Imlib2](#imlib2) - [immunedeconv](#immunedeconv) - [IMOD](#imod) - [impi](#impi) - [IMPUTE2](#impute2) - [imutils](#imutils) - [InChI](#inchi) - [indicators](#indicators) - [Inelastica](#inelastica) - [inferCNV](#infercnv) - [infercnvpy](#infercnvpy) - [Inferelator](#inferelator) - [Infernal](#infernal) - [inflection](#inflection) - [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) - [InterOp](#interop) - [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) - [IonQuant](#ionquant) - [IOR](#ior) - [IOzone](#iozone) - [iperf](#iperf) - [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 @@ -16257,6 +16661,16 @@ version |toolchain -----------|-------------- ``7.23.02``|``foss/2016a`` +### ICON + +ICON is a flexible, scalable, high-performance modelling framework for weather, climate and environmental prediction that provides actionable information for society and advances our understanding of the Earth's climate system. + +*homepage*: + +version |toolchain +-----------|-------------- +``2024.01``|``foss/2023a`` + ### iCount iCount: protein-RNA interaction analysis is a Python module and associated command-line interface (CLI), which provides all the commands needed to process iCLIP data on protein-RNA interactions. @@ -16285,6 +16699,7 @@ version |toolchain ``72.1``|``GCCcore/12.2.0`` ``73.2``|``GCCcore/12.3.0`` ``74.1``|``GCCcore/13.2.0`` +``75.1``|``GCCcore/13.3.0`` ### IDBA-UD @@ -16599,6 +17014,7 @@ version |toolchain -------------|------------------------------ ``2021.8.26``|``foss/2020b`` ``2022.9.26``|``foss/2021a``, ``foss/2022a`` +``2024.1.1`` |``foss/2023a`` ### imageio @@ -16731,6 +17147,7 @@ version |versionsuffix |toolchain ``0.4.0``|``-CUDA-11.4.1`` |``foss/2021b`` ``0.4.0``|``-CUDA-11.7.0`` |``foss/2022a`` ``0.4.0``|``-Python-3.7.4``|``foss/2019b`` +``0.4.1``|``-CUDA-12.1.1`` |``foss/2023a`` ### imkl @@ -16802,8 +17219,8 @@ IML is a free library of C source code which implements algorithms for computing *homepage*: version |toolchain ----------|-------------- -``1.0.5``|``gfbf/2022a`` +---------|------------------------------ +``1.0.5``|``gfbf/2022a``, ``gfbf/2023b`` ### Imlib2 @@ -17404,6 +17821,7 @@ version |versionsuffix|toolchain ``3.0.1``|``-mpiio`` |``foss/2016a`` ``3.2.1``| |``gompi/2019b`` ``3.3.0``| |``gompi/2020b``, ``gompi/2021a``, ``gompi/2022a`` +``4.0.0``| |``gompi/2023b`` ### IOzone @@ -17479,7 +17897,8 @@ Leveraging the Jupyter interactive widgets framework, ipympl enables the interac version |toolchain ---------|------------------------------ -``0.9.3``|``foss/2022a``, ``foss/2023a`` +``0.9.3``|``foss/2022a``, ``gfbf/2023a`` +``0.9.4``|``gfbf/2023b`` ### ipyparallel @@ -17580,6 +17999,7 @@ version |versionsuffix |toolchain ``1.2`` |``-R-4.1.0`` |``foss/2021a`` ``1.3`` |``-R-4.2.0`` |``foss/2021b`` ``1.3.2`` |``-R-4.2.1`` |``foss/2022a`` +``1.3.2`` |``-R-4.3.2`` |``gfbf/2023a`` ### irodsfs @@ -17621,14 +18041,14 @@ isl is a library for manipulating sets and relations of integer points bounded b *homepage*: version |toolchain ---------|---------------------------------------------------------- +--------|------------------------------------------------------------------------------ ``0.14``|``GCC/4.9.2`` ``0.15``|``GCC/4.9.3-2.25``, ``GNU/4.9.3-2.25``, ``foss/2016a`` ``0.16``|``GCC/4.9.3-2.25`` ``0.17``|``foss/2016a`` ``0.23``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` ``0.24``|``GCCcore/11.2.0``, ``GCCcore/11.3.0`` -``0.26``|``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0`` +``0.26``|``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0``, ``GCCcore/13.3.0`` ### isoCirc @@ -17787,7 +18207,7 @@ version |toolchain ## J -[JAGS](#jags) - [Jansson](#jansson) - [Jasmine](#jasmine) - [JasPer](#jasper) - [Java](#java) - [JavaFX](#javafx) - [jax](#jax) - [JAXFrontCE](#jaxfrontce) - [jbigkit](#jbigkit) - [Jblob](#jblob) - [jedi](#jedi) - [jedi-language-server](#jedi-language-server) - [Jellyfish](#jellyfish) - [jemalloc](#jemalloc) - [jhbuild](#jhbuild) - [JiTCODE](#jitcode) - [jModelTest](#jmodeltest) - [Jmol](#jmol) - [Jorg](#jorg) - [joypy](#joypy) - [jq](#jq) - [json-c](#json-c) - [json-fortran](#json-fortran) - [JSON-GLib](#json-glib) - [JsonCpp](#jsoncpp) - [JUBE](#jube) - [Judy](#judy) - [Julia](#julia) - [JUnit](#junit) - [Jupyter-bundle](#jupyter-bundle) - [jupyter-contrib-nbextensions](#jupyter-contrib-nbextensions) - [jupyter-matlab-proxy](#jupyter-matlab-proxy) - [jupyter-resource-usage](#jupyter-resource-usage) - [jupyter-rsession-proxy](#jupyter-rsession-proxy) - [jupyter-server](#jupyter-server) - [jupyter-server-proxy](#jupyter-server-proxy) - [JupyterHub](#jupyterhub) - [JupyterLab](#jupyterlab) - [jupyterlab-lmod](#jupyterlab-lmod) - [jupyterlmod](#jupyterlmod) - [JupyterNotebook](#jupyternotebook) - [JWM](#jwm) - [jxrlib](#jxrlib) +[JAGS](#jags) - [Jansson](#jansson) - [Jasmine](#jasmine) - [JasPer](#jasper) - [Java](#java) - [JavaFX](#javafx) - [jax](#jax) - [JAXFrontCE](#jaxfrontce) - [jbigkit](#jbigkit) - [Jblob](#jblob) - [jedi](#jedi) - [jedi-language-server](#jedi-language-server) - [Jellyfish](#jellyfish) - [jemalloc](#jemalloc) - [jhbuild](#jhbuild) - [JiTCODE](#jitcode) - [jiter](#jiter) - [jModelTest](#jmodeltest) - [Jmol](#jmol) - [Jorg](#jorg) - [joypy](#joypy) - [jq](#jq) - [json-c](#json-c) - [json-fortran](#json-fortran) - [JSON-GLib](#json-glib) - [JsonCpp](#jsoncpp) - [JUBE](#jube) - [Judy](#judy) - [Julia](#julia) - [JUnit](#junit) - [Jupyter-bundle](#jupyter-bundle) - [jupyter-contrib-nbextensions](#jupyter-contrib-nbextensions) - [jupyter-matlab-proxy](#jupyter-matlab-proxy) - [jupyter-resource-usage](#jupyter-resource-usage) - [jupyter-rsession-proxy](#jupyter-rsession-proxy) - [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 @@ -17801,7 +18221,7 @@ version |toolchain ``4.2.0``|``foss/2016a``, ``intel/2016a``, ``intel/2017a`` ``4.3.0``|``foss/2017b``, ``foss/2018b``, ``foss/2019a``, ``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``fosscuda/2020b``, ``intel/2017b`` ``4.3.1``|``foss/2022a`` -``4.3.2``|``foss/2022b`` +``4.3.2``|``foss/2022b``, ``foss/2023a`` ### Jansson @@ -17813,7 +18233,7 @@ version |toolchain ----------|------------------------------ ``2.6`` |``GCC/4.8.3`` ``2.13.1``|``GCC/10.2.0``, ``GCC/11.2.0`` -``2.14`` |``GCC/11.3.0`` +``2.14`` |``GCC/11.3.0``, ``GCC/12.3.0`` ### Jasmine @@ -17973,8 +18393,8 @@ JBIG-KIT is a software implementation of the JBIG1 data compression standard (I *homepage*: version|toolchain --------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -``2.1``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +-------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ +``2.1``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0``, ``GCCcore/13.3.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ### Jblob @@ -18014,12 +18434,12 @@ Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. *homepage*: version |toolchain -----------|--------------------------------------------------------------------------------------------------- +----------|------------------------------------------------------------------------------------------------------------------- ``1.1.11``|``foss/2016a``, ``foss/2016b`` ``1.1.12``|``foss/2018b``, ``intel/2018a`` ``2.2.6`` |``foss/2016b``, ``intel/2017a`` ``2.2.10``|``foss/2018b``, ``intel/2018a`` -``2.3.0`` |``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0``, ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0`` +``2.3.0`` |``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0``, ``GCC/12.2.0``, ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0`` ### jemalloc @@ -18037,7 +18457,7 @@ version |toolchain ``5.1.0``|``GCCcore/7.3.0`` ``5.2.0``|``GCCcore/8.2.0`` ``5.2.1``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``5.3.0``|``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +``5.3.0``|``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### jhbuild @@ -18060,6 +18480,16 @@ version |versionsuffix |toolchain ``1.3.2``|``-Python-3.6.4``|``intel/2018a`` ``1.4.0``|``-Python-3.7.2``|``foss/2019a`` +### jiter + +Fast iterable JSON parser + +*homepage*: + +version |toolchain +---------|------------------ +``0.4.1``|``GCCcore/12.3.0`` + ### jModelTest jModelTest is a tool to carry out statistical selection of best-fit models of nucleotide substitution. @@ -18253,6 +18683,7 @@ This bundle collects a range of Jupyter interfaces (Lab, Notebook and nbclassic) version |toolchain ------------|------------------ ``20230823``|``GCCcore/12.3.0`` +``20240522``|``GCCcore/13.2.0`` ### jupyter-contrib-nbextensions @@ -18261,8 +18692,8 @@ A collection of various notebook extensions for Jupyter *homepage*: version |toolchain ----------|------------------ -``0.7.0``|``GCCcore/11.3.0`` +---------|-------------------------------------- +``0.7.0``|``GCCcore/11.3.0``, ``GCCcore/12.3.0`` ### jupyter-matlab-proxy @@ -18270,10 +18701,11 @@ MATLAB Integration for Jupyter *homepage*: -version |toolchain ----------|------------------ -``0.3.4``|``GCCcore/10.3.0`` -``0.5.0``|``GCCcore/11.3.0`` +version |toolchain +----------|------------------ +``0.3.4`` |``GCCcore/10.3.0`` +``0.5.0`` |``GCCcore/11.3.0`` +``0.12.2``|``GCCcore/12.3.0`` ### jupyter-resource-usage @@ -18287,6 +18719,7 @@ version |toolchain ``0.6.2``|``GCCcore/10.3.0`` ``0.6.3``|``GCCcore/11.3.0`` ``1.0.0``|``GCCcore/12.3.0`` +``1.0.2``|``GCCcore/13.2.0`` ### jupyter-rsession-proxy @@ -18297,6 +18730,7 @@ Jupyter extensions for running an RStudio rsession proxy version |toolchain ---------|------------------ ``2.1.0``|``GCCcore/11.3.0`` +``2.2.0``|``GCCcore/12.3.0`` ### jupyter-server @@ -18309,6 +18743,7 @@ version |toolchain ``1.21.0``|``GCCcore/11.3.0`` ``2.7.0`` |``GCCcore/12.2.0`` ``2.7.2`` |``GCCcore/12.3.0`` +``2.14.0``|``GCCcore/13.2.0`` ### jupyter-server-proxy @@ -18321,6 +18756,7 @@ version |toolchain ``3.2.1``|``GCCcore/10.3.0`` ``3.2.2``|``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ``4.0.0``|``GCCcore/12.3.0`` +``4.1.2``|``GCCcore/13.2.0`` ### JupyterHub @@ -18337,6 +18773,7 @@ version |versionsuffix |toolchain ``3.0.0``| |``GCCcore/11.3.0`` ``4.0.1``| |``GCCcore/12.2.0`` ``4.0.2``| |``GCCcore/12.3.0`` +``4.1.5``| |``GCCcore/13.2.0`` ### JupyterLab @@ -18354,6 +18791,7 @@ version |versionsuffix |toolchain ``3.5.0`` | |``GCCcore/11.3.0`` ``4.0.3`` | |``GCCcore/12.2.0`` ``4.0.5`` | |``GCCcore/12.3.0`` +``4.2.0`` | |``GCCcore/13.2.0`` ### jupyterlab-lmod @@ -18386,6 +18824,7 @@ version |toolchain ---------|------------------ ``7.0.2``|``GCCcore/12.3.0`` ``7.0.3``|``GCCcore/12.2.0`` +``7.2.0``|``GCCcore/13.2.0`` ### JWM @@ -18404,8 +18843,8 @@ Open source implementation of jpegxr *homepage*: version|toolchain --------|---------------------------------------------------------- -``1.1``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.3.0`` +-------|------------------------------------------------------------------------------ +``1.1``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.3.0``, ``GCCcore/12.3.0`` ## K @@ -18459,6 +18898,7 @@ version |toolchain ``3.3.1``|``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ``3.3.2``|``GCCcore/11.2.0`` ``3.3.5``|``GCCcore/11.3.0`` +``3.4.0``|``GCCcore/12.3.0`` ### kallisto @@ -18478,6 +18918,7 @@ version |toolchain ``0.46.1``|``foss/2019b``, ``iimpi/2020a``, ``iimpi/2020b`` ``0.46.2``|``foss/2020b`` ``0.48.0``|``gompi/2021a``, ``gompi/2021b``, ``gompi/2022a`` +``0.50.1``|``gompi/2022b`` ### KAT @@ -18752,6 +19193,7 @@ KrakenUniq: confident and fast metagenomics classification using unique k-mer co version |toolchain ---------|-------------- ``1.0.3``|``GCC/11.3.0`` +``1.0.4``|``GCC/12.2.0`` ### Kratos @@ -18830,7 +19272,7 @@ version |toolchain ## L -[L_RNA_scaffolder](#l_rna_scaffolder) - [Lab-Streaming-Layer](#lab-streaming-layer) - [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++) - [lcalc](#lcalc) - [LCov](#lcov) - [LDC](#ldc) - [lDDT](#lddt) - [LeadIT](#leadit) - [leafcutter](#leafcutter) - [leidenalg](#leidenalg) - [LEMON](#lemon) - [Leptonica](#leptonica) - [LERC](#lerc) - [less](#less) - [LevelDB](#leveldb) - [Levenshtein](#levenshtein) - [lftp](#lftp) - [LHAPDF](#lhapdf) - [LIANA](#liana) - [libaec](#libaec) - [libaed2](#libaed2) - [libaio](#libaio) - [libarchive](#libarchive) - [libav](#libav) - [libavif](#libavif) - [libbaseencode](#libbaseencode) - [libBigWig](#libbigwig) - [libbitmask](#libbitmask) - [libcdms](#libcdms) - [libcerf](#libcerf) - [libcint](#libcint) - [libcircle](#libcircle) - [libcmaes](#libcmaes) - [libconfig](#libconfig) - [libcotp](#libcotp) - [libcpuset](#libcpuset) - [libcroco](#libcroco) - [libctl](#libctl) - [libdap](#libdap) - [libde265](#libde265) - [libdeflate](#libdeflate) - [libdivsufsort](#libdivsufsort) - [libdrm](#libdrm) - [libdrs](#libdrs) - [libdwarf](#libdwarf) - [libedit](#libedit) - [libelf](#libelf) - [libemf](#libemf) - [libepoxy](#libepoxy) - [libev](#libev) - [libevent](#libevent) - [libexif](#libexif) - [libfabric](#libfabric) - [libfdf](#libfdf) - [libffcall](#libffcall) - [libffi](#libffi) - [libFLAME](#libflame) - [libfontenc](#libfontenc) - [libfyaml](#libfyaml) - [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) - [libgxps](#libgxps) - [libhandy](#libhandy) - [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) - [libspectre](#libspectre) - [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) - [lit](#lit) - [LittleCMS](#littlecms) - [LLDB](#lldb) - [LLVM](#llvm) - [LMDB](#lmdb) - [LMfit](#lmfit) - [Lmod](#lmod) - [lmoments3](#lmoments3) - [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) - [LoopTools](#looptools) - [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) - [Lab-Streaming-Layer](#lab-streaming-layer) - [Lace](#lace) - [LADR](#ladr) - [lagrangian-filtering](#lagrangian-filtering) - [LAME](#lame) - [LAMMPS](#lammps) - [lancet](#lancet) - [LangChain](#langchain) - [langchain-anthropic](#langchain-anthropic) - [LAPACK](#lapack) - [LASSO-Python](#lasso-python) - [LAST](#last) - [LASTZ](#lastz) - [lavaan](#lavaan) - [LayoutParser](#layoutparser) - [LBFGS++](#lbfgs++) - [lcalc](#lcalc) - [LCov](#lcov) - [LDC](#ldc) - [lDDT](#lddt) - [LeadIT](#leadit) - [leafcutter](#leafcutter) - [leidenalg](#leidenalg) - [LEMON](#lemon) - [Leptonica](#leptonica) - [LERC](#lerc) - [less](#less) - [LevelDB](#leveldb) - [Levenshtein](#levenshtein) - [lftp](#lftp) - [LHAPDF](#lhapdf) - [LIANA](#liana) - [libabigail](#libabigail) - [libaec](#libaec) - [libaed2](#libaed2) - [libaio](#libaio) - [libarchive](#libarchive) - [libav](#libav) - [libavif](#libavif) - [libbaseencode](#libbaseencode) - [libBigWig](#libbigwig) - [libbitmask](#libbitmask) - [libbraiding](#libbraiding) - [libcdms](#libcdms) - [libcerf](#libcerf) - [libcint](#libcint) - [libcircle](#libcircle) - [libcmaes](#libcmaes) - [libconfig](#libconfig) - [libcotp](#libcotp) - [libcpuset](#libcpuset) - [libcroco](#libcroco) - [libctl](#libctl) - [libdap](#libdap) - [libde265](#libde265) - [libdeflate](#libdeflate) - [libdivsufsort](#libdivsufsort) - [libdrm](#libdrm) - [libdrs](#libdrs) - [libdwarf](#libdwarf) - [libedit](#libedit) - [libelf](#libelf) - [libemf](#libemf) - [libepoxy](#libepoxy) - [libev](#libev) - [libevent](#libevent) - [libexif](#libexif) - [libfabric](#libfabric) - [libfdf](#libfdf) - [libffcall](#libffcall) - [libffi](#libffi) - [libFLAME](#libflame) - [libfontenc](#libfontenc) - [libfyaml](#libfyaml) - [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) - [libgxps](#libgxps) - [libhandy](#libhandy) - [libharu](#libharu) - [libheif](#libheif) - [libhomfly](#libhomfly) - [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) - [libspectre](#libspectre) - [libssh](#libssh) - [libStatGen](#libstatgen) - [libsupermesh](#libsupermesh) - [LIBSVM](#libsvm) - [LIBSVM-MATLAB](#libsvm-matlab) - [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) - [Lightning](#lightning) - [liknorm](#liknorm) - [likwid](#likwid) - [lil-aretomo](#lil-aretomo) - [limix](#limix) - [LinBox](#linbox) - [line_profiler](#line_profiler) - [Lingeling](#lingeling) - [LISFLOOD-FP](#lisflood-fp) - [lit](#lit) - [LittleCMS](#littlecms) - [LLDB](#lldb) - [LLVM](#llvm) - [LMDB](#lmdb) - [LMfit](#lmfit) - [Lmod](#lmod) - [lmoments3](#lmoments3) - [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) - [LoopTools](#looptools) - [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 @@ -18923,6 +19365,26 @@ version |toolchain ---------|----------------------- ``1.1.0``|``iccifort/2019.5.281`` +### LangChain + +LangChain is a framework for developing applications powered by large language models (LLMs). + +*homepage*: + +version |toolchain +---------|-------------- +``0.2.1``|``foss/2023a`` + +### langchain-anthropic + +This package contains the LangChain integration for Anthropic's generative models. + +*homepage*: + +version |toolchain +----------|-------------- +``0.1.15``|``foss/2023a`` + ### LAPACK LAPACK is written in Fortran90 and provides routines for solving systems of simultaneous linear equations, least-squares solutions of linear systems of equations, eigenvalue problems, and singular value problems. @@ -18934,6 +19396,7 @@ version |toolchain ``3.8.0`` |``GCC/7.3.0-2.30`` ``3.9.1`` |``GCC/10.2.0`` ``3.10.1``|``GCC/11.2.0``, ``GCC/11.3.0`` +``3.12.0``|``GCC/12.3.0``, ``GCC/13.2.0`` ### LASSO-Python @@ -19010,8 +19473,8 @@ Lcalc is a package for working with L-functions. *homepage*: version |toolchain ----------|------------------ -``2.0.5``|``GCCcore/11.3.0`` +---------|-------------------------------------- +``2.0.5``|``GCCcore/11.3.0``, ``GCCcore/13.2.0`` ### LCov @@ -19183,6 +19646,16 @@ version |versionsuffix|toolchain ----------|-------------|-------------- ``0.1.11``|``-R-4.2.1`` |``foss/2022a`` +### libabigail + +ABIGAIL stands for the Application Binary Interface Generic Analysis and Instrumentation Library. It’s a framework which aims at helping developers and software distributors to spot some ABI-related issues like interface incompatibility in ELF shared libraries by performing a static analysis of the ELF binaries at hand. The type of interface incompatibilities that Abigail focuses on is related to changes on the exported ELF functions and variables symbols, as well as layout and size changes of data types of the functions and variables exported by shared libraries. In other words, if the return type of a function exported by a shared library changes in an incompatible way from one version of a given shared library to another, we want Abigail to help people catch that. + +*homepage*: + +version|toolchain +-------|------------------ +``2.5``|``GCCcore/13.2.0`` + ### libaec Libaec provides fast lossless compression of 1 up to 32 bit wide signed or unsigned integers (samples). The library achieves best results for low entropy data as often encountered in space imaging instrument data or numerical model output from weather or climate simulations. While floating point representations are not directly supported, they can also be efficiently coded by grouping exponents and mantissa. @@ -19213,7 +19686,7 @@ 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``, ``GCCcore/12.3.0`` +``0.3.113``|``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0`` ### libarchive @@ -19230,6 +19703,7 @@ version |toolchain ``3.6.1``|``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ``3.6.2``|``GCCcore/12.3.0``, ``GCCcore/13.1.0`` ``3.7.2``|``GCCcore/13.2.0`` +``3.7.4``|``GCCcore/13.3.0`` ### libav @@ -19248,9 +19722,10 @@ 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``|``GCCcore/11.3.0``, ``foss/2021a``, ``foss/2022a`` +``0.11.1``|``GCCcore/10.3.0``, ``GCCcore/11.3.0`` +``1.0.4`` |``GCCcore/12.3.0`` ### libbaseencode @@ -19283,6 +19758,16 @@ version|toolchain -------|---------- ``2.0``|``system`` +### libbraiding + +This is a project to expose the functionalitis of the Braiding program as a shared library. The original goal is to include it as a component of SageMath, but it can be used in any other c++ program. + +*homepage*: + +version|toolchain +-------|------------------ +``1.2``|``GCCcore/13.2.0`` + ### libcdms Climate Data Management System Library. @@ -19431,6 +19916,7 @@ version |toolchain ----------|------------------------------ ``1.0.8`` |``GCC/10.3.0``, ``GCC/11.2.0`` ``1.0.11``|``GCC/11.3.0`` +``1.0.15``|``GCC/12.3.0`` ### libdeflate @@ -19447,6 +19933,7 @@ version |toolchain ``1.15``|``GCCcore/12.2.0`` ``1.18``|``GCCcore/12.3.0`` ``1.19``|``GCCcore/13.2.0`` +``1.20``|``GCCcore/13.3.0`` ### libdivsufsort @@ -19504,6 +19991,7 @@ version |toolchain ------------|--------------------------------------------------- ``0.4.1`` |``GCCcore/11.3.0`` ``0.7.0`` |``GCCcore/12.3.0`` +``0.9.2`` |``GCCcore/13.2.0`` ``20140805``|``GCC/4.9.2`` ``20150310``|``GCC/4.9.2``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0`` ``20190529``|``GCCcore/8.2.0`` @@ -19521,7 +20009,7 @@ version |toolchain ------------|-------------------------------------- ``20150325``|``GNU/4.9.3-2.25`` ``20180525``|``GCCcore/6.4.0`` -``20191231``|``GCCcore/9.3.0`` +``20191231``|``GCCcore/12.3.0``, ``GCCcore/9.3.0`` ``20210910``|``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ### libelf @@ -19565,8 +20053,8 @@ A full-featured and high-performance (see benchmark) event loop that is loosely *homepage*: version |toolchain ---------|------------------------------ -``4.33``|``GCC/11.2.0``, ``GCC/11.3.0`` +--------|---------------------------------------------- +``4.33``|``GCC/11.2.0``, ``GCC/11.3.0``, ``GCC/12.3.0`` ### libevent @@ -19575,11 +20063,11 @@ 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``, ``GCCcore/13.2.0``, ``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``, ``GCCcore/13.3.0``, ``system`` ### libexif @@ -19610,6 +20098,7 @@ version |toolchain ``1.16.1``|``GCCcore/12.2.0`` ``1.18.0``|``GCCcore/12.3.0`` ``1.19.0``|``GCCcore/13.2.0`` +``1.21.0``|``GCCcore/13.3.0`` ### libfdf @@ -19646,6 +20135,7 @@ version |toolchain ``3.3`` |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` ``3.4.2``|``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ``3.4.4``|``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``GCCcore/13.2.0`` +``3.4.5``|``GCCcore/13.3.0`` ### libFLAME @@ -19676,8 +20166,8 @@ Fully feature complete YAML parser and emitter, supporting the latest YAML spec *homepage*: version|toolchain --------|------------------ -``0.9``|``GCCcore/12.2.0`` +-------|-------------------------------------- +``0.9``|``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### libgcrypt @@ -19693,6 +20183,7 @@ version |toolchain ``1.9.2`` |``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ``1.9.3`` |``GCCcore/11.2.0`` ``1.10.1``|``GCCcore/11.3.0`` +``1.10.3``|``GCCcore/12.3.0`` ### libgd @@ -19708,7 +20199,7 @@ 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``, ``GCCcore/12.3.0`` +``2.3.3``|``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0`` ### libgdiplus @@ -19814,6 +20305,7 @@ version |toolchain ``1.41``|``GCCcore/10.2.0`` ``1.42``|``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``1.46``|``GCCcore/11.3.0`` +``1.48``|``GCCcore/12.3.0`` ### libgpuarray @@ -19892,6 +20384,17 @@ version |toolchain ----------|------------------------------ ``1.12.0``|``GCC/10.3.0``, ``GCC/11.2.0`` ``1.16.2``|``GCC/11.3.0`` +``1.17.6``|``GCC/12.3.0`` + +### libhomfly + +This is basically a conversion of the program written by Robert J Jenkins Jr into a shared library. It accepts as entry a character string, formatted in the same way as the input files that the original code used (see below). The returned value is the string that the original program would print on screen. + +*homepage*: + +version |toolchain +----------|------------------ +``1.02r6``|``GCCcore/13.2.0`` ### libibmad @@ -19933,7 +20436,7 @@ version |toolchain --------|------------------------------------------------------------------------------------------------------------------- ``1.15``|``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0`` ``1.16``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``1.17``|``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0`` +``1.17``|``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0``, ``GCCcore/13.3.0`` ### libidn @@ -19960,6 +20463,7 @@ version |toolchain ---------|------------------------------------------------------------------------------------------------------------------------------------- ``2.3.0``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``2.3.2``|``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/13.2.0`` +``2.3.7``|``GCCcore/12.3.0`` ### Libint @@ -20011,7 +20515,7 @@ version |versionsuffix |toolchain ``2.1.3`` | |``GCCcore/11.3.0`` ``2.1.4`` | |``GCCcore/12.2.0`` ``2.1.5.1``| |``GCCcore/12.3.0`` -``3.0.1`` | |``GCCcore/13.2.0`` +``3.0.1`` | |``GCCcore/13.2.0``, ``GCCcore/13.3.0`` ### libjxl @@ -20020,11 +20524,11 @@ JPEG XL image format reference implementation *homepage*: version |toolchain ----------|------------------ +---------|-------------------------------------- ``0.5`` |``GCCcore/10.3.0`` ``0.6.1``|``GCCcore/10.2.0`` ``0.8.1``|``foss/2022a`` -``0.8.2``|``GCCcore/13.2.0`` +``0.8.2``|``GCCcore/12.3.0``, ``GCCcore/13.2.0`` ### libleidenalg @@ -20043,9 +20547,9 @@ LibLZF is a very small data compression library. It consists of only two .c and *homepage*: version|toolchain --------|-------------------------------------- +-------|---------------------------------------------------------- ``3.4``|``GCCcore/10.2.0`` -``3.6``|``GCCcore/10.3.0``, ``GCCcore/11.3.0`` +``3.6``|``GCCcore/10.3.0``, ``GCCcore/11.3.0``, ``GCCcore/12.3.0`` ### libmad @@ -20054,8 +20558,8 @@ MAD is a high-quality MPEG audio decoder. *homepage*: version |toolchain ------------|------------------ -``0.15.1b``|``GCCcore/11.3.0`` +-----------|-------------------------------------- +``0.15.1b``|``GCCcore/11.3.0``, ``GCCcore/12.3.0`` ### libmatheval @@ -20140,6 +20644,7 @@ version |toolchain ---------|-------------------------------------- ``1.3.0``|``GCCcore/10.3.0`` ``2.0.0``|``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +``2.0.1``|``GCCcore/12.3.0`` ### libobjcryst @@ -20207,6 +20712,7 @@ version |toolchain ``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``, ``GCCcore/13.2.0`` +``0.18.1``|``GCCcore/13.3.0`` ### libplinkio @@ -20243,6 +20749,7 @@ version |toolchain ``1.6.38``|``GCCcore/12.2.0`` ``1.6.39``|``GCCcore/12.3.0`` ``1.6.40``|``GCCcore/13.2.0`` +``1.6.43``|``GCCcore/13.3.0`` ### libpsl @@ -20327,7 +20834,7 @@ version |toolchain ``8.0`` |``GCCcore/10.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``system`` ``8.1`` |``FCC/4.5.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ``8.1.2``|``GCCcore/11.3.0``, ``GCCcore/12.1.0`` -``8.2`` |``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``GCCcore/13.2.0`` +``8.2`` |``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``GCCcore/13.2.0``, ``GCCcore/13.3.0`` ### libRmath @@ -20507,9 +21014,9 @@ C++ implementation of R*-tree, an MVR-tree and a TPR-tree with C API *homepage*: version |toolchain ----------|-------------------------------------------------------------------------------------- +---------|-------------------------------------------------------------------------------------------------- ``1.8.5``|``GCCcore/6.4.0``, ``GCCcore/8.2.0``, ``foss/2016b``, ``intel/2016b``, ``intel/2018a`` -``1.9.3``|``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/13.2.0`` +``1.9.3``|``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0`` ### libspatialite @@ -20555,6 +21062,16 @@ version |toolchain ``1.0.15`` |``GCCcore/10.2.0`` ``20190330``|``GCCcore/6.4.0`` +### libsupermesh + +libsupermesh parallel supermeshing library. + +*homepage*: + +version |toolchain +--------------|-------------- +``2025-01-25``|``foss/2023a`` + ### LIBSVM LIBSVM is an integrated software for support vector classification, (C-SVC, nu-SVC), regression (epsilon-SVR, nu-SVR) and distribution estimation (one-class SVM). It supports multi-class classification. @@ -20569,6 +21086,16 @@ version |toolchain ``3.25``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``3.30``|``GCCcore/11.3.0`` +### LIBSVM-MATLAB + +MATLAB interface of LIBSVM, an integrated software for support vector classification, (C-SVC, nu-SVC), regression (epsilon-SVR, nu-SVR) and distribution estimation (one-class SVM). It supports multi-class classification. + +*homepage*: + +version |versionsuffix |toolchain +--------|--------------------|------------------ +``3.30``|``-MATLAB-2022b-r5``|``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". @@ -20603,7 +21130,7 @@ version |toolchain ``4.16.0``|``GCCcore/10.2.0``, ``GCCcore/8.3.0`` ``4.17.0``|``GCCcore/10.3.0`` ``4.18.0``|``GCCcore/11.2.0`` -``4.19.0``|``GCCcore/11.3.0`` +``4.19.0``|``GCCcore/11.3.0``, ``GCCcore/12.3.0`` ### libtecla @@ -20633,7 +21160,7 @@ version |toolchain ``4.3.0`` |``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ``4.4.0`` |``GCCcore/12.2.0`` ``4.5.0`` |``GCCcore/12.3.0`` -``4.6.0`` |``GCCcore/13.2.0`` +``4.6.0`` |``GCCcore/13.2.0``, ``GCCcore/13.3.0`` ### libtirpc @@ -20661,7 +21188,7 @@ 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``, ``GCCcore/13.2.0``, ``system`` +``2.4.7``|``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``GCCcore/13.2.0``, ``GCCcore/13.3.0``, ``system`` ### libtree @@ -20731,8 +21258,9 @@ libuv is a multi-platform support library with a focus on asynchronous I/O. *homepage*: version |toolchain -----------|----------------- +----------|------------------ ``1.37.0``|``GCCcore/8.3.0`` +``1.48.0``|``GCCcore/12.3.0`` ### libvdwxc @@ -20996,6 +21524,7 @@ version |versionsuffix |toolchain ``2.10.3``| |``GCCcore/12.2.0`` ``2.11.4``| |``GCCcore/12.3.0`` ``2.11.5``| |``GCCcore/13.2.0`` +``2.12.7``| |``GCCcore/13.3.0`` ### libxml2-python @@ -21124,12 +21653,12 @@ LibYAML is a YAML parser and emitter written in C. *homepage*: version |toolchain ----------|------------------------------------------------------------------------------------------------------------------------------------------ +---------|-------------------------------------------------------------------------------------------------------------------------------------------------------------- ``0.1.6``|``GCCcore/6.4.0``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` ``0.1.7``|``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``system`` ``0.2.1``|``GCCcore/7.3.0``, ``system`` ``0.2.2``|``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``0.2.5``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0`` +``0.2.5``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0``, ``GCCcore/13.3.0`` ### libzeep @@ -21186,6 +21715,16 @@ version |toolchain ``1.1.1``|``foss/2018a`` ``1.1.2``|``GCC/11.2.0``, ``foss/2018b`` +### Lightning + +The deep learning framework to pretrain, finetune and deploy AI models. Lightning has 4 core packages: PyTorch Lightning: Train and deploy PyTorch at scale. Lightning Fabric: Expert control. Lightning Data: Blazing fast, distributed streaming of training data from cloud storage. Lightning Apps: Build AI products and ML workflows. + +*homepage*: + +version |versionsuffix |toolchain +---------|----------------|-------------- +``2.2.1``|``-CUDA-12.1.1``|``foss/2023a`` + ### liknorm Moments of the product of an exponential-family likelihood with a Normal distribution. @@ -21212,8 +21751,18 @@ version |toolchain ``5.1.0``|``GCCcore/9.3.0`` ``5.2.0``|``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``iccifort/2020.4.304``, ``intel-compilers/2021.2.0`` ``5.2.1``|``GCC/11.2.0`` -``5.2.2``|``GCC/11.3.0`` -``5.3.0``|``GCC/12.3.0`` +``5.2.2``|``GCC/11.3.0``, ``GCC/12.3.0`` +``5.3.0``|``GCC/12.3.0``, ``GCC/13.2.0`` + +### lil-aretomo + +A lightweight Python API for AreTomo. + +*homepage*: + +version |toolchain +---------|-------------- +``0.1.1``|``foss/2023a`` ### limix @@ -21232,9 +21781,9 @@ C++ library for exact, high-performance linear algebra *homepage*: version |toolchain ----------|-------------- +---------|------------------------------ ``1.4.0``|``foss/2016a`` -``1.7.0``|``gfbf/2022a`` +``1.7.0``|``gfbf/2022a``, ``gfbf/2023b`` ### line_profiler @@ -21248,6 +21797,7 @@ version |versionsuffix |toolchain ``3.5.1``| |``foss/2021b`` ``4.0.0``| |``foss/2022a`` ``4.1.1``| |``GCCcore/12.2.0`` +``4.1.2``| |``GCCcore/13.2.0`` ### Lingeling @@ -21593,10 +22143,10 @@ lrslib is a self-contained ANSI C implementation of the reverse search algorithm *homepage*: version |toolchain ---------|--------------- +--------|-------------------------------- ``6.2`` |``intel/2018b`` ``7.0a``|``gompi/2019a`` -``7.2`` |``gompi/2022a`` +``7.2`` |``gompi/2022a``, ``gompi/2023b`` ### LS-PrePost @@ -21791,13 +22341,13 @@ LZ4 is lossless compression algorithm, providing compression speed at 400 MB/s p *homepage*: version |toolchain ----------|---------------------------------------------------------- +---------|------------------------------------------------------------------------------ ``1.8.2``|``GCCcore/5.4.0``, ``GCCcore/6.4.0`` ``1.9.0``|``GCCcore/7.3.0`` ``1.9.1``|``GCCcore/8.2.0`` ``1.9.2``|``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``1.9.3``|``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` -``1.9.4``|``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0`` +``1.9.4``|``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0``, ``GCCcore/13.3.0`` ### LZO @@ -21813,7 +22363,7 @@ version |toolchain ## M -[M1QN3](#m1qn3) - [M3GNet](#m3gnet) - [M4](#m4) - [m4ri](#m4ri) - [m4rie](#m4rie) - [MACH](#mach) - [MACS2](#macs2) - [MACS3](#macs3) - [MACSE](#macse) - [maeparser](#maeparser) - [MAFFT](#mafft) - [MAGeCK](#mageck) - [magick](#magick) - [Magics](#magics) - [magma](#magma) - [MAGMA-gene-analysis](#magma-gene-analysis) - [MagresPython](#magrespython) - [mahotas](#mahotas) - [MAJIQ](#majiq) - [make](#make) - [makedepend](#makedepend) - [makedepf90](#makedepf90) - [makeinfo](#makeinfo) - [MAKER](#maker) - [Mako](#mako) - [Mamba](#mamba) - [mandrake](#mandrake) - [mannkendall](#mannkendall) - [manta](#manta) - [mapDamage](#mapdamage) - [Maple](#maple) - [MapSplice](#mapsplice) - [Maq](#maq) - [MariaDB](#mariadb) - [MariaDB-connector-c](#mariadb-connector-c) - [Markdown](#markdown) - [MARS](#mars) - [Mash](#mash) - [Mashtree](#mashtree) - [MaSuRCA](#masurca) - [Mathematica](#mathematica) - [MathGL](#mathgl) - [MATIO](#matio) - [MATLAB](#matlab) - [MATLAB-Engine](#matlab-engine) - [matlab-proxy](#matlab-proxy) - [matplotlib](#matplotlib) - [matplotlib-inline](#matplotlib-inline) - [MATSim](#matsim) - [maturin](#maturin) - [Maude](#maude) - [mauveAligner](#mauvealigner) - [Maven](#maven) - [mawk](#mawk) - [MaxBin](#maxbin) - [MaxQuant](#maxquant) - [mayavi](#mayavi) - [maze](#maze) - [MbedTLS](#mbedtls) - [MBROLA](#mbrola) - [mbuffer](#mbuffer) - [mc](#mc) - [MCL](#mcl) - [MCR](#mcr) - [mctc-lib](#mctc-lib) - [mcu](#mcu) - [MDAnalysis](#mdanalysis) - [MDBM](#mdbm) - [MDI](#mdi) - [MDSplus](#mdsplus) - [MDSplus-Java](#mdsplus-java) - [MDSplus-Python](#mdsplus-python) - [mdtest](#mdtest) - [MDTraj](#mdtraj) - [mdust](#mdust) - [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) - [MetaDecoder](#metadecoder) - [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) - [mfqe](#mfqe) - [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) - [Miniforge3](#miniforge3) - [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) - [MitoHiFi](#mitohifi) - [MitoZ](#mitoz) - [MiXCR](#mixcr) - [MixMHC2pred](#mixmhc2pred) - [mkl-dnn](#mkl-dnn) - [mkl-service](#mkl-service) - [mkl_fft](#mkl_fft) - [MLC](#mlc) - [MLflow](#mlflow) - [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) - [MODFLOW](#modflow) - [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) - [morphosamplers](#morphosamplers) - [mosdepth](#mosdepth) - [Mothur](#mothur) - [motif](#motif) - [MotionCor2](#motioncor2) - [MotionCor3](#motioncor3) - [motionSegmentation](#motionsegmentation) - [MoviePy](#moviepy) - [mpath](#mpath) - [MPB](#mpb) - [MPC](#mpc) - [MPFI](#mpfi) - [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) - [MSFragger](#msfragger) - [msgpack-c](#msgpack-c) - [MSM](#msm) - [MSPC](#mspc) - [msprime](#msprime) - [mstore](#mstore) - [MTL4](#mtl4) - [MuJoCo](#mujoco) - [mujoco-py](#mujoco-py) - [multicharge](#multicharge) - [multichoose](#multichoose) - [MultilevelEstimators](#multilevelestimators) - [MultiNest](#multinest) - [multiprocess](#multiprocess) - [MultiQC](#multiqc) - [Multiwfn](#multiwfn) - [muMerge](#mumerge) - [MUMmer](#mummer) - [MUMPS](#mumps) - [muParser](#muparser) - [muparserx](#muparserx) - [MuPeXI](#mupexi) - [MUSCLE](#muscle) - [MUSCLE3](#muscle3) - [MuSiC](#music) - [MUST](#must) - [MuTect](#mutect) - [mutil](#mutil) - [MVAPICH2](#mvapich2) - [MView](#mview) - [mxml](#mxml) - [mxmlplus](#mxmlplus) - [MXNet](#mxnet) - [MyCC](#mycc) - [mygene](#mygene) - [MyMediaLite](#mymedialite) - [mympingpong](#mympingpong) - [Myokit](#myokit) - [mypy](#mypy) - [MySQL](#mysql) - [MySQL-python](#mysql-python) - [mysqlclient](#mysqlclient) +[M1QN3](#m1qn3) - [M3GNet](#m3gnet) - [M4](#m4) - [m4ri](#m4ri) - [m4rie](#m4rie) - [MACH](#mach) - [MACS2](#macs2) - [MACS3](#macs3) - [MACSE](#macse) - [maeparser](#maeparser) - [MAFFT](#mafft) - [MAGeCK](#mageck) - [magick](#magick) - [Magics](#magics) - [magma](#magma) - [MAGMA-gene-analysis](#magma-gene-analysis) - [MagresPython](#magrespython) - [mahotas](#mahotas) - [MAJIQ](#majiq) - [make](#make) - [makedepend](#makedepend) - [makedepf90](#makedepf90) - [makefun](#makefun) - [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) - [Markdown](#markdown) - [MARS](#mars) - [Mash](#mash) - [Mashtree](#mashtree) - [MaSuRCA](#masurca) - [Mathematica](#mathematica) - [MathGL](#mathgl) - [MATIO](#matio) - [MATLAB](#matlab) - [MATLAB-Engine](#matlab-engine) - [matlab-proxy](#matlab-proxy) - [matplotlib](#matplotlib) - [matplotlib-inline](#matplotlib-inline) - [MATSim](#matsim) - [maturin](#maturin) - [Maude](#maude) - [mauveAligner](#mauvealigner) - [Maven](#maven) - [mawk](#mawk) - [MaxBin](#maxbin) - [MaxQuant](#maxquant) - [mayavi](#mayavi) - [maze](#maze) - [MbedTLS](#mbedtls) - [MBROLA](#mbrola) - [mbuffer](#mbuffer) - [mc](#mc) - [MCL](#mcl) - [MCR](#mcr) - [mctc-lib](#mctc-lib) - [mcu](#mcu) - [MDAnalysis](#mdanalysis) - [MDBM](#mdbm) - [MDI](#mdi) - [MDSplus](#mdsplus) - [MDSplus-Java](#mdsplus-java) - [MDSplus-Python](#mdsplus-python) - [mdtest](#mdtest) - [MDTraj](#mdtraj) - [mdust](#mdust) - [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) - [MetaDecoder](#metadecoder) - [metaerg](#metaerg) - [MetaEuk](#metaeuk) - [MetaGeneAnnotator](#metageneannotator) - [Metagenome-Atlas](#metagenome-atlas) - [Metal](#metal) - [MetalWalls](#metalwalls) - [MetaMorpheus](#metamorpheus) - [MetaPhlAn](#metaphlan) - [MetaPhlAn2](#metaphlan2) - [metaWRAP](#metawrap) - [Metaxa2](#metaxa2) - [methylartist](#methylartist) - [MethylDackel](#methyldackel) - [methylpy](#methylpy) - [METIS](#metis) - [mfqe](#mfqe) - [mgen](#mgen) - [mgltools](#mgltools) - [mhcflurry](#mhcflurry) - [mhcnuggets](#mhcnuggets) - [MICOM](#micom) - [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) - [Miniforge3](#miniforge3) - [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) - [MitoHiFi](#mitohifi) - [MitoZ](#mitoz) - [MiXCR](#mixcr) - [MixMHC2pred](#mixmhc2pred) - [mkl-dnn](#mkl-dnn) - [mkl-service](#mkl-service) - [mkl_fft](#mkl_fft) - [ml-collections](#ml-collections) - [ml_dtypes](#ml_dtypes) - [MLC](#mlc) - [MLflow](#mlflow) - [mlpack](#mlpack) - [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) - [MODFLOW](#modflow) - [modred](#modred) - [MOFA2](#mofa2) - [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) - [morphosamplers](#morphosamplers) - [mosdepth](#mosdepth) - [Mothur](#mothur) - [motif](#motif) - [MotionCor2](#motioncor2) - [MotionCor3](#motioncor3) - [motionSegmentation](#motionsegmentation) - [MoviePy](#moviepy) - [mpath](#mpath) - [MPB](#mpb) - [MPC](#mpc) - [MPFI](#mpfi) - [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) - [MSFragger](#msfragger) - [msgpack-c](#msgpack-c) - [MSM](#msm) - [MSPC](#mspc) - [msprime](#msprime) - [mstore](#mstore) - [MTL4](#mtl4) - [MuJoCo](#mujoco) - [mujoco-py](#mujoco-py) - [multicharge](#multicharge) - [multichoose](#multichoose) - [MultilevelEstimators](#multilevelestimators) - [MultiNest](#multinest) - [multiprocess](#multiprocess) - [MultiQC](#multiqc) - [Multiwfn](#multiwfn) - [muMerge](#mumerge) - [MUMmer](#mummer) - [mumott](#mumott) - [MUMPS](#mumps) - [muParser](#muparser) - [muparserx](#muparserx) - [MuPeXI](#mupexi) - [MUSCLE](#muscle) - [MUSCLE3](#muscle3) - [MuSiC](#music) - [MUST](#must) - [MuTect](#mutect) - [mutil](#mutil) - [MVAPICH2](#mvapich2) - [MView](#mview) - [mxml](#mxml) - [mxmlplus](#mxmlplus) - [MXNet](#mxnet) - [MyCC](#mycc) - [mygene](#mygene) - [MyMediaLite](#mymedialite) - [mympingpong](#mympingpong) - [Myokit](#myokit) - [mypy](#mypy) - [MySQL](#mysql) - [MySQL-python](#mysql-python) - [mysqlclient](#mysqlclient) ### M1QN3 @@ -21847,7 +22397,7 @@ 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/13.2.0``, ``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/13.3.0``, ``GCCcore/14.1.0``, ``GCCcore/9.4.0``, ``GCCcore/9.5.0``, ``system`` ### m4ri @@ -21856,8 +22406,8 @@ M4RI is a library for fast arithmetic with dense matrices over F2. *homepage*: version |toolchain -------------|-------------- -``20200125``|``GCC/11.3.0`` +------------|------------------------------ +``20200125``|``GCC/11.3.0``, ``GCC/13.2.0`` ### m4rie @@ -21866,8 +22416,8 @@ M4RIE is a library for fast arithmetic with dense matrices. *homepage*: version |toolchain -------------|-------------- -``20200125``|``GCC/11.3.0`` +------------|------------------------------ +``20200125``|``GCC/11.3.0``, ``GCC/13.2.0`` ### MACH @@ -21886,13 +22436,13 @@ Model Based Analysis for ChIP-Seq data *homepage*: version |versionsuffix |toolchain -------------------|------------------|------------------------------- +------------------|------------------|---------------------------------------------- ``2.1.1.20160309``|``-Python-2.7.14``|``intel/2017b`` ``2.1.2.1`` |``-Python-2.7.14``|``foss/2017b``, ``intel/2017b`` ``2.1.2.1`` |``-Python-2.7.15``|``intel/2019a`` ``2.2.5`` |``-Python-3.6.6`` |``foss/2018b`` ``2.2.7.1`` | |``foss/2021a``, ``foss/2021b`` -``2.2.9.1`` | |``foss/2022a``, ``foss/2022b`` +``2.2.9.1`` | |``foss/2022a``, ``foss/2022b``, ``foss/2023a`` ### MACS3 @@ -21901,10 +22451,10 @@ Model Based Analysis for ChIP-Seq data *homepage*: version |toolchain ------------|-------------- +-----------|------------------------------ ``3.0.0`` |``foss/2022b`` ``3.0.0b2``|``foss/2022b`` -``3.0.1`` |``gfbf/2023a`` +``3.0.1`` |``foss/2022b``, ``gfbf/2023a`` ### MACSE @@ -21998,6 +22548,7 @@ 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-11.7.0``|``foss/2022b`` ``2.7.1``|``-CUDA-12.0.0``|``foss/2022b`` ``2.7.2``|``-CUDA-12.1.1``|``foss/2023a`` ``2.7.2``|``-CUDA-12.4.0``|``foss/2023b`` @@ -22057,7 +22608,7 @@ version |toolchain ``4.1`` |``GCC/4.9.2`` ``4.2.1``|``GCC/7.3.0-2.30``, ``GCCcore/8.3.0`` ``4.3`` |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/9.3.0`` -``4.4.1``|``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0`` +``4.4.1``|``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0``, ``GCCcore/13.3.0`` ### makedepend @@ -22081,6 +22632,16 @@ version |toolchain ---------|-------------- ``2.8.8``|``foss/2017a`` +### makefun + +Small library to dynamically create python functions. makefun helps you create functions dynamically, with the signature of your choice. It was largely inspired by decorator and functools, and created mainly to cover some of their limitations. + +*homepage*: + +version |toolchain +----------|------------------ +``1.15.2``|``GCCcore/12.3.0`` + ### makeinfo makeinfo is part of the Texinfo project, the official documentation format of the GNU project. @@ -22093,7 +22654,7 @@ version |versionsuffix|toolchain ``6.7`` |``-minimal`` |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``6.8`` | |``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ``7.0.3``| |``GCCcore/12.2.0``, ``GCCcore/12.3.0`` -``7.1`` | |``GCCcore/13.2.0`` +``7.1`` | |``GCCcore/13.2.0``, ``GCCcore/13.3.0`` ### MAKER @@ -22126,6 +22687,7 @@ version |versionsuffix |toolchain ``1.1.4``| |``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``1.2.0``| |``GCCcore/11.3.0`` ``1.2.4``| |``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0`` +``1.3.5``| |``GCCcore/13.3.0`` ### Mamba @@ -22262,8 +22824,8 @@ This is a Python implementation of John Gruber's Markdown. It is almost complete *homepage*: version|toolchain --------|-------------------------------------- -``3.6``|``GCCcore/12.2.0``, ``GCCcore/13.2.0`` +-------|---------------------------------------------------------- +``3.6``|``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0`` ### MARS @@ -22409,9 +22971,10 @@ A Python package which enables you to launch MATLAB and access it from a web bro *homepage*: -version |toolchain ----------|------------------ -``0.5.4``|``GCCcore/11.3.0`` +version |toolchain +----------|------------------ +``0.5.4`` |``GCCcore/11.3.0`` +``0.18.1``|``GCCcore/12.3.0`` ### matplotlib @@ -22486,6 +23049,7 @@ version |versionsuffix |toolchain ---------|-------------------|------------------------------ ``0.8.1``|``-Java-1.8.0_112``|``intel/2016b`` ``14.0`` |``-Java-11`` |``GCCcore/11.2.0``, ``system`` +``15.0`` |``-Java-17`` |``GCCcore/12.3.0``, ``system`` ### maturin @@ -22796,6 +23360,7 @@ version |versionsuffix |toolchain ``1.9.4``|``-Python-3.8.2``|``foss/2020a``, ``intel/2020a`` ``1.9.5``| |``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` ``1.9.7``| |``foss/2021a``, ``foss/2021b``, ``foss/2022a``, ``intel/2021b``, ``intel/2022a`` +``1.9.9``| |``gfbf/2023a`` ### mdust @@ -23146,6 +23711,7 @@ version |versionsuffix |toolchain ``1.1.1`` | |``GCCcore/12.3.0`` ``1.2.3`` | |``GCCcore/13.2.0`` ``1.3.1`` | |``GCCcore/12.3.0`` +``1.4.0`` | |``GCCcore/13.3.0`` ### meson-python @@ -23166,8 +23732,8 @@ Mesh-Quality Improvement Library *homepage*: version |toolchain ----------|------------------------------------------------------------------------------------------------------------ -``2.3.0``|``GCCcore/10.2.0``, ``GCCcore/6.4.0``, ``GCCcore/8.3.0``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2017a`` +---------|-------------------------------------------------------------------------------------------------------------------------------- +``2.3.0``|``GCCcore/10.2.0``, ``GCCcore/12.3.0``, ``GCCcore/6.4.0``, ``GCCcore/8.3.0``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2017a`` ### MESS @@ -23265,6 +23831,16 @@ version |toolchain ``2011-03-25``|``foss/2016a`` ``2020-05-05``|``GCC/10.2.0`` +### MetalWalls + +MetalWalls (MW) is a molecular dynamics code dedicated to the modelling of electrochemical systems. Its main originality is the inclusion of a series of methods allowing to apply a constant potential within the electrode materials. + +*homepage*: + +version |toolchain +-----------|-------------- +``21.06.1``|``foss/2023a`` + ### MetaMorpheus MetaMorpheus is a bottom-up proteomics database search software with integrated post-translational modification (PTM) discovery capability. This program combines features of Morpheus and G-PTM-D in a single tool. @@ -23274,6 +23850,7 @@ MetaMorpheus is a bottom-up proteomics database search software with integrated version |toolchain -----------|------------------ ``0.0.320``|``GCCcore/10.3.0`` +``1.0.5`` |``system`` ### MetaPhlAn @@ -23360,9 +23937,9 @@ METIS is a set of serial programs for partitioning graphs, partitioning finite e *homepage*: version |versionsuffix|toolchain ----------|-------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +---------|-------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ ``5.0.2``| |``gimkl/2.11.5`` -``5.1.0``| |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/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``| |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``foss/2018b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` ``5.1.0``|``-32bitIDX``|``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` ``5.1.0``|``-int64`` |``GCCcore/11.3.0`` @@ -23417,6 +23994,16 @@ version|versionsuffix |toolchain ``2.3``| |``foss/2020b``, ``fosscuda/2020b`` ``2.3``|``-Python-3.7.2``|``foss/2019a``, ``fosscuda/2019a`` +### MICOM + +Python package to study microbial communities using metabolic modeling. + +*homepage*: + +version |toolchain +----------|-------------- +``0.33.2``|``foss/2023b`` + ### MicrobeAnnotator Easy-to-use pipeline for the comprehensive metabolic annotation of microbial genomes. @@ -23834,6 +24421,26 @@ version |versionsuffix |toolchain ----------|-----------------|--------------- ``1.0.14``|``-Python-3.6.6``|``intel/2018b`` +### ml-collections + +ML Collections is a library of Python Collections designed for ML use cases. + +*homepage*: + +version |toolchain +---------|-------------- +``0.1.1``|``foss/2022a`` + +### ml_dtypes + +ml_dtypes is a stand-alone implementation of several NumPy dtype extensions used in machine learning libraries, including: bfloat16: an alternative to the standard float16 format float8_*: several experimental 8-bit floating point representations including: float8_e4m3b11fnuz float8_e4m3fn float8_e4m3fnuz float8_e5m2 float8_e5m2fnuz + +*homepage*: + +version |toolchain +---------|-------------- +``0.3.2``|``gfbf/2023a`` + ### MLC Intel Memory Latency Checker (Intel MLC) is a tool used to measure memory latencies and b/w, and how they change with increasing load on the system. @@ -23854,6 +24461,16 @@ version |toolchain ----------|-------------- ``2.10.2``|``gfbf/2023a`` +### mlpack + +mlpack is a fast, header-only C++ machine learning library written in C++ and built on the Armadillo linear algebra library, the ensmallen numerical optimization library, and the cereal serialization library. + +*homepage*: + +version |toolchain +---------|-------------- +``4.3.0``|``foss/2023a`` + ### MLxtend Mlxtend (machine learning extensions) is a Python library of useful tools for the day-to-day data science tasks. @@ -23997,6 +24614,16 @@ version |versionsuffix |toolchain ---------|-----------------|-------------- ``2.0.2``|``-Python-3.5.2``|``foss/2016b`` +### MOFA2 + +MOFA is a factor analysis model that provides a general framework for the integration of multi-omic data sets in an unsupervised fashion. Intuitively, MOFA can be viewed as a versatile and statistically rigorous generalization of principal component analysis to multi-omics data. Given several data matrices with measurements of multiple -omics data types on the same or on overlapping sets of samples, MOFA infers an interpretable low-dimensional representation in terms of a few latent factors. These learnt factors represent the driving sources of variation across data modalities, thus facilitating the identification of cellular states or disease subgroups. + +*homepage*: + +version |versionsuffix|toolchain +----------|-------------|-------------- +``1.14.0``|``-R-4.3.2`` |``foss/2023a`` + ### Molcas Molcas is an ab initio quantum chemistry software package developed by scientists to be used by scientists. The basic philosophy is is to be able to treat general electronic structures for molecules consisting of atoms from most of the periodic table. As such, the primary focus of the package is on multiconfigurational methods with applications typically connected to the treatment of highly degenerate states. @@ -24024,6 +24651,7 @@ version |toolchain ``1.7.1`` |``GCCcore/12.2.0`` ``1.11.0``|``GCCcore/12.3.0`` ``2.3.1`` |``GCCcore/13.2.0`` +``2.31.0``|``GCCcore/13.3.0`` ### Molden @@ -24087,12 +24715,14 @@ Molpro is a complete system of ab initio programs for molecular electronic struc *homepage*: -version |versionsuffix |toolchain --------------|------------------------|---------- -``2010.1.23``|``.Linux_x86_64`` |``system`` -``2015.1.0`` |``.linux_x86_64_intel`` |``system`` -``2015.1.3`` |``.linux_x86_64_openmp``|``system`` -``2015.1.10``|``.linux_x86_64_openmp``|``system`` +version |versionsuffix |toolchain +-------------|-------------------------|---------- +``2010.1.23``|``.Linux_x86_64`` |``system`` +``2015.1.0`` |``.linux_x86_64_intel`` |``system`` +``2015.1.3`` |``.linux_x86_64_openmp`` |``system`` +``2015.1.10``|``.linux_x86_64_openmp`` |``system`` +``2024.1.0`` |``.linux_x86_64_mpipr`` |``system`` +``2024.1.0`` |``.linux_x86_64_sockets``|``system`` ### MONA @@ -24117,6 +24747,7 @@ version |versionsuffix |toolchain ``1.0.1``| |``foss/2022a`` ``1.0.1``|``-CUDA-11.7.0``|``foss/2022a`` ``1.3.0``| |``foss/2023a`` +``1.3.0``|``-CUDA-12.1.1``|``foss/2023a`` ### MONAI-Label @@ -24338,7 +24969,7 @@ 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/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0`` +``1.3.1``| |``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0``, ``GCCcore/13.3.0`` ### MPFI @@ -24347,8 +24978,8 @@ MPFI stands for Multiple Precision Floating-point Interval library. *homepage*: version |toolchain ----------|------------------ -``1.5.4``|``GCCcore/11.3.0`` +---------|-------------------------------------- +``1.5.4``|``GCCcore/11.3.0``, ``GCCcore/13.2.0`` ### MPFR @@ -24366,7 +24997,7 @@ version |toolchain ``4.0.2``|``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``4.1.0``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ``4.2.0``|``GCCcore/12.2.0``, ``GCCcore/12.3.0`` -``4.2.1``|``GCCcore/13.2.0`` +``4.2.1``|``GCCcore/13.2.0``, ``GCCcore/13.3.0`` ### mpi4py @@ -24457,6 +25088,7 @@ version |versionsuffix |toolchain ``1.0.0``|``-Python-2.7.15``|``foss/2018b`` ``1.1.0``|``-Python-3.8.2`` |``GCCcore/9.3.0`` ``1.2.1``| |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``1.3.0``| |``GCCcore/12.3.0`` ### MrBayes @@ -24626,6 +25258,7 @@ version |toolchain ---------|------------------ ``2.1.1``|``GCCcore/11.2.0`` ``2.2.2``|``GCCcore/11.3.0`` +``3.1.4``|``GCCcore/12.3.0`` ### mujoco-py @@ -24744,9 +25377,19 @@ version |toolchain ``4.0.0beta2``|``GCCcore/10.2.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0``, ``foss/2018b`` ``4.0.0rc1`` |``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` +### mumott + +mumott is a Python library for the analysis of multi-modal tensor tomography data. + +*homepage*: + +version|toolchain +-------|-------------- +``2.1``|``foss/2022b`` + ### MUMPS -A parallel sparse direct solver +A parallel sparse direct solver. This module is for its sequential variant. *homepage*: @@ -24761,6 +25404,7 @@ version |versionsuffix |toolchain ``5.5.0``|``-metis`` |``foss/2021a`` ``5.5.1``|``-metis`` |``foss/2022a`` ``5.6.1``|``-metis`` |``foss/2022b``, ``foss/2023a`` +``5.6.1``|``-metis-seq``|``gomkl/2023a`` ### muParser @@ -25020,7 +25664,7 @@ version |versionsuffix |toolchain ## N -[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](#nf-core) - [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) - [noise](#noise) - [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](#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](#nf-core) - [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) - [noise](#noise) - [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) - [nvitop](#nvitop) - [nvofbf](#nvofbf) - [nvompi](#nvompi) - [NVSHMEM](#nvshmem) - [nvtop](#nvtop) - [NWChem](#nwchem) - [NxTrim](#nxtrim) ### n2v @@ -25160,10 +25804,11 @@ Functions to extract information from Oxford Nanopore sequencing data and alignm *homepage*: version |versionsuffix |toolchain -----------|-----------------|------------------------------ +----------|-----------------|---------------------------------------------- ``1.12.1``|``-Python-3.7.4``|``intel/2019b`` ``1.15.0``| |``intel/2020b`` -``1.18.1``| |``foss/2021a``, ``foss/2022a`` +``1.18.1``| |``foss/2021a``, ``foss/2022a``, ``foss/2022b`` +``1.19.1``| |``foss/2022a`` ### NanoLyse @@ -25177,16 +25822,16 @@ version |toolchain ### nanomath -A few simple math function for other Oxford Nanopore processing scripts +A few simple math functions for other Oxford Nanopore processing scripts *homepage*: version |versionsuffix |toolchain -----------|-----------------|--------------- +----------|-----------------|------------------------------ ``0.23.1``|``-Python-3.7.4``|``intel/2019b`` ``1.2.0`` | |``intel/2020b`` ``1.2.1`` | |``foss/2021a`` -``1.3.0`` | |``foss/2022a`` +``1.3.0`` | |``foss/2022a``, ``foss/2022b`` ### nanomax-analysis-utils @@ -25220,6 +25865,7 @@ version |versionsuffix |toolchain ----------|-----------------|------------------------------- ``1.28.4``|``-Python-3.7.4``|``intel/2019b`` ``1.33.0``| |``foss/2021a``, ``intel/2020b`` +``1.42.0``| |``foss/2022a`` ### nanopolish @@ -25258,14 +25904,15 @@ version |toolchain ### napari -napari is a fast, interactive, multi-dimensional image viewer for Python. It's designed for browsing, annotating, and analyzing large multi-dimensional images. It's built on top of Qt (for the GUI), vispy (for performant GPU-based rendering), and the scientific Python stack (numpy, scipy). +napari is a fast, interactive, multi-dimensional image viewer for Python. It's designed for browsing, annotating, and analyzing large multi-dimensional images. It's built on top of Qt (for the GUI), vispy (for performant GPU-based rendering), and the scientific Python stack (numpy, scipy). *homepage*: -version |toolchain -----------|------------------------------ -``0.4.15``|``foss/2021b`` -``0.4.18``|``foss/2022a``, ``foss/2023a`` +version |toolchain +----------------|------------------------------ +``0.4.15`` |``foss/2021b`` +``0.4.18`` |``foss/2022a``, ``foss/2023a`` +``0.4.19.post1``|``foss/2023a`` ### NASM @@ -25283,6 +25930,7 @@ version |toolchain ``2.14.02``|``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``2.15.05``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ``2.16.01``|``GCCcore/12.3.0``, ``GCCcore/13.2.0`` +``2.16.03``|``GCCcore/13.3.0`` ### nauty @@ -25296,6 +25944,7 @@ version |toolchain ``2.7rc2``|``GCC/8.2.0-2.31.1`` ``2.7rc5``|``GCC/8.3.0`` ``2.8.6`` |``GCC/11.3.0`` +``2.8.8`` |``GCC/13.2.0`` ### nbclassic @@ -25304,8 +25953,8 @@ NbClassic provides a backwards compatible Jupyter Notebook interface that you c *homepage*: version |toolchain ----------|------------------ -``1.0.0``|``GCCcore/12.3.0`` +---------|-------------------------------------- +``1.0.0``|``GCCcore/12.3.0``, ``GCCcore/13.2.0`` ### NBO @@ -25372,6 +26021,7 @@ version |versionsuffix |toolchain ``2.10.3`` |``-CUDA-11.5.2`` |``GCCcore/11.2.0`` ``2.11.4`` | |``gcccuda/2019b`` ``2.12.12``|``-CUDA-11.7.0`` |``GCCcore/11.3.0`` +``2.16.2`` |``-CUDA-11.7.0`` |``GCCcore/12.2.0`` ``2.16.2`` |``-CUDA-12.0.0`` |``GCCcore/12.2.0`` ``2.18.3`` |``-CUDA-12.1.1`` |``GCCcore/12.3.0`` ``2.20.5`` |``-CUDA-12.4.0`` |``GCCcore/13.2.0`` @@ -25503,6 +26153,7 @@ version|toolchain ``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``, ``GCCcore/13.2.0``, ``system`` +``6.5``|``GCCcore/13.3.0``, ``system`` ### ncview @@ -25910,6 +26561,7 @@ version |toolchain ``22.10.6``|``system`` ``23.04.2``|``system`` ``23.10.0``|``system`` +``24.04.2``|``system`` ### NextGenMap @@ -25974,6 +26626,7 @@ This is an implementation of the Hypertext Transfer Protocol version 2 in C. Th version |toolchain ----------|------------------------------ ``1.48.0``|``GCC/11.2.0``, ``GCC/11.3.0`` +``1.58.0``|``GCC/12.3.0`` ### nghttp3 @@ -25984,6 +26637,7 @@ nghttp3 is an implementation of RFC 9114 HTTP/3 mapping over QUIC and RFC 9204 version |toolchain ---------|-------------------------------------- ``0.6.0``|``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``1.3.0``|``GCCcore/12.3.0`` ### NGLess @@ -26006,6 +26660,7 @@ version |versionsuffix |toolchain ``2.7.0``|``-Python-3.7.2``|``intel/2019a`` ``2.7.7``|``-Python-3.8.2``|``intel/2020a`` ``3.0.3``| |``foss/2021a``, ``foss/2022a`` +``3.1.2``| |``foss/2023a`` ### NGS @@ -26081,6 +26736,7 @@ version|toolchain version |toolchain ---------|------------------------------ ``0.7.0``|``GCC/11.2.0``, ``GCC/11.3.0`` +``1.2.0``|``GCC/12.3.0`` ### NiBabel @@ -26191,6 +26847,7 @@ version |toolchain ``1.10.1``|``GCCcore/10.2.0`` ``1.10.2``|``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ``1.11.1``|``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0`` +``1.12.1``|``GCCcore/13.3.0`` ### Nipype @@ -26302,6 +26959,7 @@ version |toolchain ``18.12.1``|``GCCcore/12.2.0`` ``18.17.1``|``GCCcore/12.3.0`` ``20.9.0`` |``GCCcore/13.2.0`` +``20.13.1``|``GCCcore/13.3.0`` ### noise @@ -26549,6 +27207,7 @@ version |toolchain ``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``, ``GCCcore/13.2.0`` +``2.0.18``|``GCCcore/13.3.0`` ### numba @@ -26656,6 +27315,16 @@ version |versionsuffix |toolchain ``23.7`` |``-CUDA-12.2.0``|``system`` ``24.1`` |``-CUDA-12.3.0``|``system`` +### nvitop + +An interactive NVIDIA-GPU process viewer and beyond, the one-stop solution for GPU process management. + +*homepage*: + +version |versionsuffix |toolchain +---------|----------------|------------------ +``1.3.2``|``-CUDA-12.3.0``|``GCCcore/12.3.0`` + ### nvofbf NVHPC based toolchain, including OpenMPI for MPI support, OpenBLAS (via FlexiBLAS for BLAS and LAPACK support), FFTW and ScaLAPACK. @@ -26703,6 +27372,7 @@ version |toolchain ``1.2.2``|``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ``2.0.2``|``GCCcore/11.3.0`` ``3.0.1``|``GCCcore/12.2.0`` +``3.1.0``|``GCCcore/12.3.0`` ### NWChem @@ -26733,7 +27403,7 @@ 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) - [OMERO.insight](#omero.insight) - [OMERO.py](#omero.py) - [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) - [OpenMEEG](#openmeeg) - [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-Java](#openslide-java) - [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](#oases) - [OBITools](#obitools) - [OBITools3](#obitools3) - [OCaml](#ocaml) - [ocamlbuild](#ocamlbuild) - [occt](#occt) - [oceanspy](#oceanspy) - [OCNet](#ocnet) - [Octave](#octave) - [Octopus-vcf](#octopus-vcf) - [OGDF](#ogdf) - [olaFlow](#olaflow) - [olego](#olego) - [OMA](#oma) - [OmegaFold](#omegafold) - [OMERO.insight](#omero.insight) - [OMERO.py](#omero.py) - [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) - [OpenMEEG](#openmeeg) - [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-Java](#openslide-java) - [openslide-python](#openslide-python) - [OpenSSL](#openssl) - [OpenStackClient](#openstackclient) - [OPERA](#opera) - [OPERA-MS](#opera-ms) - [OptaDOS](#optados) - [Optax](#optax) - [optiSLang](#optislang) - [OptiType](#optitype) - [OptiX](#optix) - [Optuna](#optuna) - [OR-Tools](#or-tools) - [ORCA](#orca) - [ORFfinder](#orffinder) - [OrfM](#orfm) - [orthAgogue](#orthagogue) - [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 @@ -26781,6 +27451,17 @@ version |toolchain ``4.02.3``|``foss/2016a`` ``4.07.1``|``foss/2018b`` ``4.14.0``|``GCC/11.3.0`` +``5.1.1`` |``GCC/13.2.0`` + +### ocamlbuild + +OCamlbuild is a generic build tool, that has built-in rules for building OCaml library and programs. + +*homepage*: + +version |toolchain +----------|-------------- +``0.14.3``|``GCC/13.2.0`` ### occt @@ -26943,9 +27624,9 @@ Open Neural Network Exchange (ONNX) is an open ecosystem that empowers AI develo *homepage*: version |toolchain -----------|-------------- +----------|------------------------------ ``1.11.0``|``foss/2021a`` -``1.15.0``|``foss/2022b`` +``1.15.0``|``foss/2022b``, ``gfbf/2023a`` ### ONNX-Runtime @@ -27095,9 +27776,11 @@ version |versionsuffix |toolchain ``0.3.17``| |``GCC/10.3.0``, ``GCC/11.2.0`` ``0.3.18``| |``GCC/11.2.0`` ``0.3.20``| |``GCC/11.2.0``, ``GCC/11.3.0``, ``NVHPC/22.7-CUDA-11.7.0`` +``0.3.20``|``-int8`` |``GCC/11.3.0`` ``0.3.21``| |``GCC/12.2.0`` ``0.3.23``| |``GCC/12.3.0`` ``0.3.24``| |``GCC/13.2.0`` +``0.3.27``| |``GCC/13.3.0`` ### openCARP @@ -27177,6 +27860,7 @@ version |versionsuffix |toolchain ``4.6.0`` |``-CUDA-11.7.0-contrib`` |``foss/2022a`` ``4.6.0`` |``-contrib`` |``foss/2022a`` ``4.8.0`` |``-contrib`` |``foss/2022b`` +``4.8.1`` |``-CUDA-12.1.1-contrib`` |``foss/2023a`` ``4.8.1`` |``-contrib`` |``foss/2023a`` ### OpenEXR @@ -27475,6 +28159,7 @@ version |versionsuffix |toolchain ``4.1.4`` | |``GCC/11.3.0``, ``GCC/12.2.0``, ``NVHPC/22.7-CUDA-11.7.0`` ``4.1.5`` | |``GCC/12.2.0``, ``GCC/12.3.0``, ``intel-compilers/2023.1.0`` ``4.1.6`` | |``GCC/13.2.0`` +``5.0.3`` | |``GCC/13.3.0`` ``system``| |``GCC/system-2.29`` ### OpenMS @@ -27674,9 +28359,20 @@ Optax is a gradient processing and optimization library for JAX. *homepage*: -version |toolchain ----------|-------------- -``0.1.7``|``foss/2022a`` +version |versionsuffix |toolchain +---------|----------------|-------------- +``0.1.7``| |``foss/2022a`` +``0.1.7``|``-CUDA-11.7.0``|``foss/2022a`` + +### optiSLang + +Ansys optiSLang is a constantly evolving, leading-edge answer to the challenges posed by CAE-based Robust Design Optimization (RDO). Its state-of-the-art algorithms efficiently and automatically search for the most robust design configuration, eliminating the slow, manual process that used to define RDO. + +*homepage*: + +version |toolchain +----------|---------- +``2024R1``|``system`` ### OptiType @@ -27769,6 +28465,16 @@ version |toolchain ``0.6.1``|``foss/2016b`` ``0.7.1``|``GCC/12.3.0``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` +### orthAgogue + +orthAgogue: a tool for high speed estimation of homology relations within and between species in massive data sets. orthAgogue is easy to use and offers flexibility through a range of optional parameters. + +*homepage*: + +version |toolchain +------------|--------------- +``20141105``|``gompi/2023a`` + ### OrthoFinder OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics @@ -27845,6 +28551,7 @@ version |versionsuffix |toolchain ``7.1-1``| |``gompi/2023a``, ``iimpi/2023a`` ``7.2`` | |``gompi/2023.09``, ``gompi/2023b`` ``7.2`` |``-CUDA-12.1.1``|``gompi/2023a`` +``7.4`` | |``gompi/2024.05`` ### OTF2 @@ -27905,7 +28612,7 @@ version |versionsuffix |toolchain ## P -[p11-kit](#p11-kit) - [p4-phylogenetics](#p4-phylogenetics) - [p4est](#p4est) - [p4vasp](#p4vasp) - [p7zip](#p7zip) - [packmol](#packmol) - [PAGAN2](#pagan2) - [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) - [PASA](#pasa) - [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) - [pblat](#pblat) - [pbmm2](#pbmm2) - [pbs_python](#pbs_python) - [PBSuite](#pbsuite) - [PBZIP2](#pbzip2) - [PCAngsd](#pcangsd) - [PCC](#pcc) - [PCL](#pcl) - [PCMSolver](#pcmsolver) - [PCRaster](#pcraster) - [PCRE](#pcre) - [PCRE2](#pcre2) - [PDM](#pdm) - [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) - [PFFT](#pfft) - [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) - [Philosopher](#philosopher) - [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) - [phyluce](#phyluce) - [PhyML](#phyml) - [phyx](#phyx) - [picard](#picard) - [PICI-LIGGGHTS](#pici-liggghts) - [PICRUSt2](#picrust2) - [pigz](#pigz) - [PIL](#pil) - [PileOMeth](#pileometh) - [Pillow](#pillow) - [Pillow-SIMD](#pillow-simd) - [Pilon](#pilon) - [PIMS](#pims) - [Pindel](#pindel) - [Pingouin](#pingouin) - [Pint](#pint) - [pip](#pip) - [PIPITS](#pipits) - [PIRATE](#pirate) - [pIRS](#pirs) - [Pisces](#pisces) - [piSvM](#pisvm) - [piSvM-JSC](#pisvm-jsc) - [pixman](#pixman) - [pizzly](#pizzly) - [pkg-config](#pkg-config) - [pkgconf](#pkgconf) - [pkgconfig](#pkgconfig) - [PLAMS](#plams) - [plantcv](#plantcv) - [PlaScope](#plascope) - [PlasmaPy](#plasmapy) - [PLAST](#plast) - [Platanus](#platanus) - [Platypus](#platypus) - [Platypus-Opt](#platypus-opt) - [plc](#plc) - [PLINK](#plink) - [plinkliftover](#plinkliftover) - [plinkQC](#plinkqc) - [PLINKSEQ](#plinkseq) - [plot1cell](#plot1cell) - [Ploticus](#ploticus) - [plotly](#plotly) - [plotly-orca](#plotly-orca) - [plotly.py](#plotly.py) - [plotutils](#plotutils) - [PLplot](#plplot) - [PLUMED](#plumed) - [PLY](#ply) - [PMIx](#pmix) - [pmt](#pmt) - [pmx](#pmx) - [PnetCDF](#pnetcdf) - [pocl](#pocl) - [pod5-file-format](#pod5-file-format) - [poetry](#poetry) - [polars](#polars) - [polymake](#polymake) - [pomkl](#pomkl) - [pompi](#pompi) - [poppler](#poppler) - [poppunk](#poppunk) - [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) - [primecount](#primecount) - [primecountpy](#primecountpy) - [Primer3](#primer3) - [PRINSEQ](#prinseq) - [printproto](#printproto) - [PRISMS-PF](#prisms-pf) - [ProbABEL](#probabel) - [ProBiS](#probis) - [prodigal](#prodigal) - [ProFit](#profit) - [PROJ](#proj) - [ProjectQ](#projectq) - [prokka](#prokka) - [prompt-toolkit](#prompt-toolkit) - [proovread](#proovread) - [propy](#propy) - [Proteinortho](#proteinortho) - [ProtHint](#prothint) - [protobuf](#protobuf) - [protobuf-python](#protobuf-python) - [protozero](#protozero) - [PRSice](#prsice) - [PSASS](#psass) - [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) - [psycopg](#psycopg) - [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) - [PyAV](#pyav) - [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) - [pycubescd](#pycubescd) - [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) - [PyInstaller](#pyinstaller) - [pyiron](#pyiron) - [Pyke3](#pyke3) - [pylift](#pylift) - [Pylint](#pylint) - [pylipid](#pylipid) - [pyMannKendall](#pymannkendall) - [pymatgen](#pymatgen) - [pymatgen-db](#pymatgen-db) - [pymbar](#pymbar) - [PyMC](#pymc) - [PyMC3](#pymc3) - [pymca](#pymca) - [pymemcache](#pymemcache) - [PyMOL](#pymol) - [PyNAST](#pynast) - [pyobjcryst](#pyobjcryst) - [PyOD](#pyod) - [pyodbc](#pyodbc) - [Pyomo](#pyomo) - [PyOpenCL](#pyopencl) - [PyOpenGL](#pyopengl) - [pyparsing](#pyparsing) - [pyperf](#pyperf) - [pyplusplus](#pyplusplus) - [pypmt](#pypmt) - [PYPOWER](#pypower) - [pyproj](#pyproj) - [PyPSA](#pypsa) - [PyPy](#pypy) - [pyqstem](#pyqstem) - [PyQt](#pyqt) - [PyQt-builder](#pyqt-builder) - [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) - [PySINDy](#pysindy) - [pyslim](#pyslim) - [pysndfx](#pysndfx) - [Pysolar](#pysolar) - [pyspoa](#pyspoa) - [pysqlite](#pysqlite) - [PyStan](#pystan) - [pysteps](#pysteps) - [pystran](#pystran) - [PyTables](#pytables) - [PyTensor](#pytensor) - [pytesseract](#pytesseract) - [pytest](#pytest) - [pytest-benchmark](#pytest-benchmark) - [pytest-cpp](#pytest-cpp) - [pytest-flakefinder](#pytest-flakefinder) - [pytest-rerunfailures](#pytest-rerunfailures) - [pytest-shard](#pytest-shard) - [pytest-workflow](#pytest-workflow) - [pytest-xdist](#pytest-xdist) - [pythermalcomfort](#pythermalcomfort) - [PYTHIA](#pythia) - [Python](#python) - [Python-bundle](#python-bundle) - [Python-bundle-PyPI](#python-bundle-pypi) - [python-casacore](#python-casacore) - [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-3dunet](#pytorch-3dunet) - [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) - [PyTorchVideo](#pytorchvideo) - [PyVCF](#pyvcf) - [PyVCF3](#pyvcf3) - [pyWannier90](#pywannier90) - [PyWavelets](#pywavelets) - [PyWBGT](#pywbgt) - [pyXDF](#pyxdf) - [PyYAML](#pyyaml) - [PyZMQ](#pyzmq) +[p11-kit](#p11-kit) - [p4-phylogenetics](#p4-phylogenetics) - [p4est](#p4est) - [p4vasp](#p4vasp) - [p7zip](#p7zip) - [packmol](#packmol) - [PAGAN2](#pagan2) - [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) - [PASA](#pasa) - [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) - [pblat](#pblat) - [pbmm2](#pbmm2) - [pbs_python](#pbs_python) - [PBSuite](#pbsuite) - [PBZIP2](#pbzip2) - [PCAngsd](#pcangsd) - [PCC](#pcc) - [PCL](#pcl) - [PCMSolver](#pcmsolver) - [PCRaster](#pcraster) - [PCRE](#pcre) - [PCRE2](#pcre2) - [pdf2docx](#pdf2docx) - [PDM](#pdm) - [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) - [PFFT](#pfft) - [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) - [Philosopher](#philosopher) - [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) - [phyluce](#phyluce) - [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) - [planarity](#planarity) - [plantcv](#plantcv) - [plantri](#plantri) - [PlaScope](#plascope) - [PlasmaPy](#plasmapy) - [PLAST](#plast) - [Platanus](#platanus) - [Platypus](#platypus) - [Platypus-Opt](#platypus-opt) - [plc](#plc) - [PLINK](#plink) - [plinkliftover](#plinkliftover) - [plinkQC](#plinkqc) - [PLINKSEQ](#plinkseq) - [plmc](#plmc) - [plot1cell](#plot1cell) - [Ploticus](#ploticus) - [plotly](#plotly) - [plotly-orca](#plotly-orca) - [plotly.py](#plotly.py) - [plotutils](#plotutils) - [PLplot](#plplot) - [PLUMED](#plumed) - [PLY](#ply) - [PMIx](#pmix) - [pmt](#pmt) - [pmx](#pmx) - [PnetCDF](#pnetcdf) - [pocl](#pocl) - [pod5-file-format](#pod5-file-format) - [poetry](#poetry) - [polars](#polars) - [polymake](#polymake) - [pomkl](#pomkl) - [pompi](#pompi) - [poppler](#poppler) - [poppunk](#poppunk) - [popscle](#popscle) - [popt](#popt) - [Porechop](#porechop) - [porefoam](#porefoam) - [poretools](#poretools) - [PortAudio](#portaudio) - [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) - [premailer](#premailer) - [PREQUAL](#prequal) - [preseq](#preseq) - [presto](#presto) - [pretty-yaml](#pretty-yaml) - [primecount](#primecount) - [primecountpy](#primecountpy) - [Primer3](#primer3) - [PRINSEQ](#prinseq) - [printproto](#printproto) - [PRISMS-PF](#prisms-pf) - [ProbABEL](#probabel) - [ProBiS](#probis) - [prodigal](#prodigal) - [ProFit](#profit) - [PROJ](#proj) - [ProjectQ](#projectq) - [prokka](#prokka) - [prompt-toolkit](#prompt-toolkit) - [proovread](#proovread) - [propy](#propy) - [ProteinMPNN](#proteinmpnn) - [Proteinortho](#proteinortho) - [ProtHint](#prothint) - [protobuf](#protobuf) - [protobuf-python](#protobuf-python) - [protozero](#protozero) - [PRRTE](#prrte) - [PRSice](#prsice) - [PSASS](#psass) - [pscom](#pscom) - [PSI](#psi) - [PSI4](#psi4) - [PsiCLASS](#psiclass) - [PSIPRED](#psipred) - [PSM2](#psm2) - [psmc](#psmc) - [psmpi](#psmpi) - [psmpi2](#psmpi2) - [PSolver](#psolver) - [PSORTb](#psortb) - [psrecord](#psrecord) - [pstoedit](#pstoedit) - [psutil](#psutil) - [psycopg](#psycopg) - [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) - [PyAEDT](#pyaedt) - [PyAMG](#pyamg) - [PyAPS3](#pyaps3) - [PyAV](#pyav) - [pybedtools](#pybedtools) - [PyBerny](#pyberny) - [pyBigWig](#pybigwig) - [pybind11](#pybind11) - [pybind11-stubgen](#pybind11-stubgen) - [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) - [pycubescd](#pycubescd) - [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) - [PyEXR](#pyexr) - [pyFAI](#pyfai) - [pyfaidx](#pyfaidx) - [pyfasta](#pyfasta) - [PyFFmpeg](#pyffmpeg) - [pyFFTW](#pyfftw) - [pyfits](#pyfits) - [PyFMI](#pyfmi) - [PyFoam](#pyfoam) - [PyFR](#pyfr) - [PyFrag](#pyfrag) - [pyGAM](#pygam) - [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) - [PyHMMER](#pyhmmer) - [PyImageJ](#pyimagej) - [PyInstaller](#pyinstaller) - [pyiron](#pyiron) - [Pyke3](#pyke3) - [pylift](#pylift) - [Pylint](#pylint) - [pylipid](#pylipid) - [pyMannKendall](#pymannkendall) - [pymatgen](#pymatgen) - [pymatgen-db](#pymatgen-db) - [pymbar](#pymbar) - [PyMC](#pymc) - [PyMC3](#pymc3) - [pymca](#pymca) - [pymemcache](#pymemcache) - [PyMOL](#pymol) - [PyNAST](#pynast) - [pyobjcryst](#pyobjcryst) - [PyOD](#pyod) - [pyodbc](#pyodbc) - [Pyomo](#pyomo) - [PyOpenCL](#pyopencl) - [PyOpenGL](#pyopengl) - [pyparsing](#pyparsing) - [pyperf](#pyperf) - [pyplusplus](#pyplusplus) - [pypmt](#pypmt) - [PYPOWER](#pypower) - [pyproj](#pyproj) - [PyPSA](#pypsa) - [PyPy](#pypy) - [pyqstem](#pyqstem) - [PyQt](#pyqt) - [PyQt-builder](#pyqt-builder) - [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) - [pyseer](#pyseer) - [pysheds](#pysheds) - [pyshp](#pyshp) - [PySide2](#pyside2) - [PySINDy](#pysindy) - [pyslim](#pyslim) - [pysndfx](#pysndfx) - [Pysolar](#pysolar) - [pyspoa](#pyspoa) - [pysqlite](#pysqlite) - [PyStan](#pystan) - [pysteps](#pysteps) - [pystran](#pystran) - [PyTables](#pytables) - [PyTensor](#pytensor) - [pytesseract](#pytesseract) - [pytest](#pytest) - [pytest-benchmark](#pytest-benchmark) - [pytest-cpp](#pytest-cpp) - [pytest-flakefinder](#pytest-flakefinder) - [pytest-rerunfailures](#pytest-rerunfailures) - [pytest-shard](#pytest-shard) - [pytest-workflow](#pytest-workflow) - [pytest-xdist](#pytest-xdist) - [pythermalcomfort](#pythermalcomfort) - [PYTHIA](#pythia) - [Python](#python) - [Python-bundle](#python-bundle) - [Python-bundle-PyPI](#python-bundle-pypi) - [python-casacore](#python-casacore) - [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-3dunet](#pytorch-3dunet) - [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) - [PyTorchVideo](#pytorchvideo) - [PyVCF](#pyvcf) - [PyVCF3](#pyvcf3) - [PyVista](#pyvista) - [pyWannier90](#pywannier90) - [PyWavelets](#pywavelets) - [PyWBGT](#pywbgt) - [pyXDF](#pyxdf) - [PyYAML](#pyyaml) - [PyZMQ](#pyzmq) ### p11-kit @@ -27919,6 +28626,7 @@ version |toolchain ``0.23.2``|``GCCcore/5.4.0``, ``GNU/4.9.3-2.25``, ``foss/2016a``, ``intel/2016a`` ``0.24.0``|``GCCcore/10.3.0`` ``0.24.1``|``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``0.25.3``|``GCCcore/12.3.0`` ### p4-phylogenetics @@ -27936,10 +28644,11 @@ p4est is a C library to manage a collection (a forest) of multiple connected ada *homepage*: -version|toolchain --------|------------------------------- -``2.2``|``foss/2019a``, ``intel/2019a`` -``2.8``|``foss/2021a`` +version |toolchain +---------|------------------------------- +``2.2`` |``foss/2019a``, ``intel/2019a`` +``2.8`` |``foss/2021a`` +``2.8.6``|``foss/2023a`` ### p4vasp @@ -28235,6 +28944,7 @@ version |toolchain ``20210722``|``GCCcore/11.2.0`` ``20220722``|``GCCcore/11.3.0`` ``20230722``|``GCCcore/12.2.0``, ``GCCcore/12.3.0`` +``20240322``|``GCCcore/13.2.0`` ### parallel-fastq-dump @@ -28369,6 +29079,7 @@ version |toolchain ----------|------------------ ``2.7.6`` |``foss/2016a`` ``2.15.4``|``GCCcore/11.3.0`` +``2.15.5``|``GCCcore/13.2.0`` ### ParmEd @@ -28480,7 +29191,7 @@ PatchELF is a small utility to modify the dynamic linker and RPATH of ELF execut *homepage*: version |toolchain -----------|--------------------------------------------------------- +----------|---------------------------------------------------------- ``0.8`` |``GNU/4.9.3-2.25`` ``0.9`` |``GCCcore/6.4.0``, ``foss/2016a`` ``0.10`` |``GCCcore/7.2.0``, ``GCCcore/8.3.0`` @@ -28488,7 +29199,7 @@ version |toolchain ``0.13`` |``GCCcore/11.2.0`` ``0.15.0``|``GCCcore/11.3.0`` ``0.17.2``|``GCCcore/12.2.0`` -``0.18.0``|``GCCcore/12.3.0``, ``GCCcore/13.2.0`` +``0.18.0``|``GCCcore/12.3.0``, ``GCCcore/13.2.0``, ``GCCcore/13.3.0`` ### path.py @@ -28522,8 +29233,8 @@ Tools for plotting Oxford Nanopore and other long-read data *homepage*: version |versionsuffix |toolchain -----------|-----------------|--------------- -``0.2.3`` | |``foss/2021a`` +----------|-----------------|-------------------------------------------------------------- +``0.2.3`` | |``foss/2021a``, ``foss/2022a``, ``foss/2022b``, ``foss/2023a`` ``0.1923``|``-Python-3.7.4``|``intel/2019b`` ``0.1924``| |``intel/2020b`` @@ -28711,6 +29422,17 @@ version |toolchain ``10.37``|``GCCcore/11.2.0`` ``10.40``|``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ``10.42``|``GCCcore/12.3.0``, ``GCCcore/13.2.0`` +``10.43``|``GCCcore/13.3.0`` + +### pdf2docx + +Open source Python library converting pdf to docx. + +*homepage*: + +version |toolchain +---------|-------------- +``0.5.8``|``foss/2023a`` ### PDM @@ -28836,6 +29558,7 @@ version |versionsuffix|toolchain ``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``, ``system`` +``5.38.2``| |``GCCcore/13.3.0`` ### perl-app-cpanminus @@ -28925,6 +29648,7 @@ version |versionsuffix |toolchain ``3.9.1`` |``-Python-3.6.4``|``foss/2018a`` ``3.12.0``|``-Python-3.7.4``|``foss/2019b`` ``3.15.0``| |``foss/2021a`` +``3.20.3``| |``foss/2023a`` ### PfamScan @@ -29260,7 +29984,7 @@ version |toolchain ### PhyML -Phylogenetic estimation using (Maximum) Likelihood +PhyML is a software package that uses modern statistical approaches to analyse alignments of nucleotide or amino acid sequences in a phylogenetic framework. *homepage*: @@ -29268,6 +29992,7 @@ version |toolchain ----------------|-------------- ``3.3.20190321``|``foss/2018b`` ``3.3.20200621``|``foss/2020b`` +``3.3.20220408``|``foss/2023a`` ### phyx @@ -29351,7 +30076,7 @@ version |toolchain ``2.4`` |``GCCcore/10.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2018a`` ``2.6`` |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``2.7`` |``GCCcore/11.3.0``, ``GCCcore/12.2.0`` -``2.8`` |``GCCcore/12.3.0`` +``2.8`` |``GCCcore/12.3.0``, ``GCCcore/13.2.0`` ### PIL @@ -29617,6 +30342,7 @@ version |toolchain ``1.9.4``|``GCCcore/13.1.0`` ``1.9.5``|``GCCcore/12.3.0`` ``2.0.3``|``GCCcore/13.2.0`` +``2.2.0``|``GCCcore/13.3.0``, ``system`` ### pkgconfig @@ -29654,6 +30380,16 @@ version |toolchain ---------|--------------- ``1.5.1``|``intel/2022a`` +### planarity + +A library for implementing graph algorithms + +*homepage*: + +version |toolchain +-----------|-------------- +``3.0.2.0``|``GCC/13.2.0`` + ### plantcv PlantCV: Plant phenotyping using computer vision. @@ -29664,6 +30400,16 @@ version |versionsuffix |toolchain ---------|-----------------|-------------- ``3.8.0``|``-Python-3.8.2``|``foss/2020a`` +### plantri + +Plantri is a program that generates certain types of graphs that are imbedded on the sphere. Exactly one member of each isomorphism class is output, using an amount of memory almost independent of the number of graphs produced. This, together with the exceptionally fast operation and careful validation, makes the program suitable for processing very large numbers of graphs. Isomorphisms are defined with respect to the embeddings, so in some cases outputs may be isomorphic as abstract graphs. + +*homepage*: + +version|toolchain +-------|------------------ +``5.4``|``GCCcore/13.2.0`` + ### PlaScope Plasmid exploration of bacterial genomes @@ -29729,12 +30475,13 @@ version |toolchain 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). -*homepage*: +*homepage*: version |versionsuffix |toolchain ---------|------------------|------------------------------- ``3.0.1``|``-Python-2.7.15``|``foss/2019a``, ``intel/2018b`` ``3.0.1``|``-Python-3.7.4`` |``foss/2019b`` +``3.10`` | |``intel/2022a`` ### PLINK @@ -29789,6 +30536,16 @@ version |toolchain --------|---------------------------------------------------------- ``0.10``|``GCC/6.4.0-2.28``, ``iccifort/2017.4.196-GCC-6.4.0-2.28`` +### plmc + +Inference of couplings in proteins and RNAs from sequence variation. + +*homepage*: + +version |versionsuffix|toolchain +------------|-------------|------------------ +``20230121``|``-32bit`` |``GCCcore/12.3.0`` + ### plot1cell plot1cell: a package for advanced single cell data visualization @@ -29940,6 +30697,7 @@ version |toolchain ``4.2.2``|``GCCcore/12.2.0`` ``4.2.4``|``GCCcore/12.3.0`` ``4.2.6``|``GCCcore/13.2.0`` +``5.0.2``|``GCCcore/13.3.0`` ### pmt @@ -29978,6 +30736,7 @@ version |toolchain ``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``, ``gompi/2023a``, ``iimpi/2022a`` +``1.13.0``|``iimpi/2023a`` ### pocl @@ -30023,13 +30782,14 @@ version |versionsuffix |toolchain ### polars -Lightning-fast DataFrame library for Rust and Python. +Polars is a blazingly fast DataFrame library for manipulating structured data. The core is written in Rust and this module provides its interface for Python. *homepage*: version |toolchain ----------|-------------- ``0.15.6``|``foss/2022a`` +``0.20.2``|``gfbf/2023a`` ### polymake @@ -30080,6 +30840,7 @@ version |toolchain ``22.01.0``|``GCC/11.2.0`` ``22.12.0``|``GCC/11.3.0`` ``23.09.0``|``GCC/12.3.0`` +``24.04.0``|``GCC/13.2.0`` ### poppunk @@ -30146,6 +30907,16 @@ version |versionsuffix |toolchain ---------|------------------|--------------- ``0.6.0``|``-Python-2.7.14``|``intel/2018a`` +### PortAudio + +PortAudio is a free, cross-platform, open-source, audio I/O library. It lets you write simple audio programs in 'C' or C++ that will compile and run on many platforms including Windows, Macintosh OS X, and Unix (OSS/ALSA). It is intended to promote the exchange of audio software between developers on different platforms. Many applications use PortAudio for Audio I/O. + +*homepage*: + +version |toolchain +----------|-------------- +``19.7.0``|``foss/2022a`` + ### Portcullis Portcullis stands for PORTable CULLing of Invalid Splice junctions from pre-aligned RNA-seq data. It is known that RNAseq mapping tools generate many invalid junction predictions, particularly in deep datasets with high coverage over splice sites. In order to address this, instead for creating a new RNAseq mapper, with a focus on SJ accuracy we created a tool that takes in a BAM file generated by an RNAseq mapper of the user's own choice (e.g. Tophat2, Gsnap, STAR2 or HISAT2) as input (i.e. it's portable). It then, analyses and quantifies all splice junctions in the file before, filtering (culling) those which are unlikely to be genuine. Portcullis output's junctions in a variety of formats making it suitable for downstream analysis (such as differential splicing analysis and gene modelling) without additional work. Portcullis can also filter the original BAM file removing alignments associated with bad junctions. @@ -30163,8 +30934,8 @@ PortMidi is a library for software developers. It supports real-time input and o *homepage*: version |toolchain ----------|------------------ -``2.0.4``|``GCCcore/11.3.0`` +---------|-------------------------------------- +``2.0.4``|``GCCcore/11.3.0``, ``GCCcore/12.3.0`` ### Postgres-XL @@ -30223,7 +30994,7 @@ version |toolchain ``3.7.0.0`` |``intel/2016b`` ``3.7.0.7`` |``foss/2017b``, ``foss/2018b``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` ``3.7.0.8`` |``GCC/10.2.0``, ``iccifort/2020.4.304`` -``3.7.0.10``|``GCC/11.3.0`` +``3.7.0.10``|``GCC/11.3.0``, ``GCC/12.3.0`` ### powerlaw @@ -30329,6 +31100,16 @@ version |versionsuffix |toolchain ``2.2.0``|``-Python-3.8.2``|``foss/2020a``, ``intel/2020a`` ``2.5.0``| |``foss/2022a`` +### premailer + +CSS blocks into inline style attributes for HTML emails + +*homepage*: + +version |toolchain +----------|------------------ +``3.10.0``|``GCCcore/12.3.0`` + ### PREQUAL A program to identify and mask regions with non-homologous adjacent characters in FASTA files. @@ -30350,7 +31131,7 @@ version |toolchain ``2.0.2``|``foss/2016b`` ``2.0.3``|``foss/2018b``, ``intel/2018a`` ``3.1.2``|``GCC/10.3.0``, ``GCC/11.2.0`` -``3.2.0``|``GCC/11.3.0`` +``3.2.0``|``GCC/11.3.0``, ``GCC/12.2.0`` ### presto @@ -30362,6 +31143,7 @@ version |versionsuffix|toolchain ------------------|-------------|-------------- ``1.0.0-20200718``|``-R-4.1.2`` |``foss/2021b`` ``1.0.0-20230113``|``-R-4.2.1`` |``foss/2022a`` +``1.0.0-20230501``|``-R-4.2.2`` |``foss/2022b`` ``1.0.0-20230501``|``-R-4.3.2`` |``foss/2023a`` ### pretty-yaml @@ -30565,6 +31347,16 @@ version|versionsuffix |toolchain -------|------------------|-------------- ``1.0``|``-Python-2.7.13``|``foss/2017a`` +### ProteinMPNN + +A deep learning based protein sequence design method is described that is widely applicable to current design challenges and shows outstanding performance in both in silico and experimental tests. + +*homepage*: + +version |versionsuffix |toolchain +------------------|----------------|-------------- +``1.0.1-20230627``|``-CUDA-11.7.0``|``foss/2022a`` + ### Proteinortho Proteinortho is a tool to detect orthologous genes within different species. @@ -30657,6 +31449,16 @@ version |toolchain ``1.6.8``|``GCCcore/7.3.0`` ``1.7.0``|``GCCcore/8.3.0`` +### PRRTE + +PRRTE is the PMIx Reference RunTime Environment + +*homepage*: + +version |toolchain +---------|------------------ +``3.0.5``|``GCCcore/13.3.0`` + ### PRSice PRSice (pronounced 'precise') is a Polygenic Risk Score software for calculating, applying, evaluating and plotting the results of polygenic risk scores (PRS) analyses. @@ -30735,8 +31537,18 @@ Accurate protein secondary structure prediction *homepage*: version |toolchain ---------|------------- -``4.02``|``GCC/8.3.0`` +--------|----------------------------- +``4.02``|``GCC/12.3.0``, ``GCC/8.3.0`` + +### PSM2 + +Low-level user-space communications interface for the Intel(R) OPA family of products. + +*homepage*: + +version |toolchain +----------|------------------------------------------------------------------------------------------------------------------------------------------ +``12.0.1``|``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0``, ``GCCcore/13.3.0`` ### psmc @@ -30835,6 +31647,7 @@ version |versionsuffix |toolchain ``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`` +``5.9.8``| |``GCCcore/12.3.0`` ### psycopg @@ -31007,6 +31820,7 @@ A simple IPython/Jupyter widget to embed an interactive 3Dmol.js viewer in a not version |toolchain ---------------|------------------ ``2.0.1.post1``|``GCCcore/11.3.0`` +``2.1.0`` |``GCCcore/12.3.0`` ### pyABC @@ -31018,6 +31832,16 @@ version |versionsuffix |toolchain ----------|-----------------|-------------- ``0.10.4``|``-Python-3.7.4``|``foss/2019b`` +### PyAEDT + +PyAEDT is a Python library that interacts directly with the Ansys Electronics Desktop (AEDT) API, enabling straightforward and efficient automation in your workflow. + +*homepage*: + +version |toolchain +---------|------------------ +``0.8.7``|``GCCcore/12.3.0`` + ### PyAMG PyAMG is a library of Algebraic Multigrid (AMG) solvers with a convenient Python interface. @@ -31029,6 +31853,7 @@ version |versionsuffix |toolchain ``3.0.1``|``-Python-2.7.11``|``intel/2016a`` ``4.0.0``| |``foss/2020b``, ``intel/2020b`` ``4.2.3``| |``foss/2021a`` +``5.1.0``| |``foss/2023a`` ### PyAPS3 @@ -31065,6 +31890,7 @@ version |versionsuffix |toolchain ``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``, ``GCC/11.2.0`` ``0.9.0`` | |``GCC/11.3.0``, ``GCC/12.2.0`` +``0.9.1`` | |``foss/2023a`` ### PyBerny @@ -31088,7 +31914,7 @@ 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`` +``0.3.22``| |``foss/2022b``, ``foss/2023a`` ### pybind11 @@ -31110,6 +31936,16 @@ version |versionsuffix |toolchain ``2.10.3``| |``GCCcore/12.2.0`` ``2.11.1``| |``GCCcore/12.3.0``, ``GCCcore/13.2.0`` +### pybind11-stubgen + +Static analysis tools and IDE usually struggle to understand python binary extensions. pybind11-stubgen generates stubs for python extensions to make them less opaque. While the CLI tool includes tweaks to target modules compiled specifically with pybind11 but it should work well with modules built with other libraries. + +*homepage*: + +version |toolchain +---------|------------------ +``2.5.1``|``GCCcore/12.3.0`` + ### pybinding Pybinding is a Python package for numerical tight-binding calculations in solid state physics. @@ -31259,9 +32095,9 @@ pycodestyle is a tool to check your Python code against some of the style conven *homepage*: version |versionsuffix |toolchain -----------|-----------------|--------------- +----------|-----------------|------------------------------ ``2.5.0`` |``-Python-3.6.4``|``intel/2018a`` -``2.11.1``| |``foss/2022a`` +``2.11.1``| |``foss/2022a``, ``foss/2023a`` ### PyCogent @@ -31320,6 +32156,7 @@ version |versionsuffix |toolchain ------------|-----------------|---------------------------------------------------------- ``7.43.0.5``|``-Python-3.7.4``|``GCCcore/8.3.0`` ``7.45.2`` | |``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` +``7.45.3`` | |``GCCcore/13.2.0`` ### PyDamage @@ -31441,6 +32278,16 @@ version |toolchain ``1.4.1``|``foss/2021b`` ``2.0.0``|``foss/2021b`` +### PyEXR + +A simple EXR IO-library for Python that simplifies the use of OpenEXR. + +*homepage*: + +version |toolchain +----------|-------------- +``0.3.10``|``gfbf/2023a`` + ### pyFAI Python implementation of fast azimuthal integration. @@ -31555,6 +32402,16 @@ version |versionsuffix|toolchain ``2019-20220216`` |``-ASA`` |``intel/2020b`` ``2023-dev.20240220``|``-ASA`` |``intel/2022a`` +### pyGAM + +pyGAM is a package for building Generalized Additive Models in Python, with an emphasis on modularity and performance. The API will be immediately familiar to anyone with experience of scikit-learn or scipy. + +*homepage*: + +version |toolchain +---------|-------------- +``0.9.1``|``gfbf/2023a`` + ### 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. @@ -31564,6 +32421,7 @@ Pygame is a set of Python modules designed for writing video games. Pygame adds version |toolchain ---------|------------------ ``2.1.0``|``GCCcore/11.3.0`` +``2.5.2``|``GCCcore/12.3.0`` ### pygccxml @@ -31594,11 +32452,11 @@ PyGEOS is a C/Python library with vectorized geometry functions. The geometry op *homepage*: version |versionsuffix |toolchain -----------|-----------------|--------------- +----------|-----------------|------------------------------ ``0.7.1`` |``-Python-3.7.4``|``foss/2019b`` ``0.8`` |``-Python-3.8.2``|``foss/2020a`` ``0.10.2``| |``intel/2020b`` -``0.14`` | |``gfbf/2022b`` +``0.14`` | |``gfbf/2022b``, ``gfbf/2023a`` ### pyGIMLi @@ -31724,6 +32582,16 @@ version |toolchain ----------|-------------- ``0.10.1``|``foss/2019a`` +### PyHMMER + +HMMER is a biological sequence analysis tool that uses profile hidden Markov models to search for sequence homologs. HMMER3 is developed and maintained by the Eddy/Rivas Laboratory at Harvard University. pyhmmer is a Python package, implemented using the Cython language, that provides bindings to HMMER3. It directly interacts with the HMMER internals, which has the following advantages over CLI wrappers (like hmmer-py) + +*homepage*: + +version |toolchain +----------|--------------- +``0.10.6``|``gompi/2023a`` + ### PyImageJ PyImageJ provides a set of wrapper functions for integration between ImageJ2 and Python. It also supports the original ImageJ API and data structures. A major advantage of this approach is the ability to combine ImageJ and ImageJ2 with other tools available from the Python software ecosystem, including NumPy, SciPy, scikit-image, CellProfiler, OpenCV, ITK and many more. @@ -31754,6 +32622,7 @@ version |versionsuffix |toolchain ---------|-----------------|--------------- ``0.2.5``|``-Python-3.7.2``|``intel/2019a`` ``0.3.0``|``-Python-3.8.2``|``intel/2020a`` +``0.5.1``| |``foss/2023a`` ### Pyke3 @@ -31856,7 +32725,8 @@ PyMC is a probabilistic programming library for Python that allows users to buil *homepage*: version |toolchain ----------|-------------- +---------|------------------------------- +``2.3.8``|``foss/2021b``, ``intel/2021b`` ``5.9.0``|``foss/2023a`` ### PyMC3 @@ -32160,6 +33030,7 @@ version |versionsuffix |toolchain ``0.11.1``| |``foss/2020b``, ``fosscuda/2020b`` ``0.12.3``| |``foss/2021a`` ``0.13.3``| |``foss/2022a`` +``0.13.7``| |``foss/2023a`` ### pyradiomics @@ -32226,6 +33097,8 @@ version |versionsuffix |toolchain ``1.8.0``|``-CUDA-11.3.1``|``foss/2021a`` ``1.8.4``| |``foss/2022a`` ``1.8.4``|``-CUDA-11.7.0``|``foss/2022a`` +``1.9.0``| |``foss/2023a`` +``1.9.0``|``-CUDA-12.1.1``|``foss/2023a`` ### Pyro4 @@ -32280,7 +33153,7 @@ version |versionsuffix |toolchain ``0.19.1`` | |``GCC/11.3.0`` ``0.20.0`` | |``GCC/11.3.0`` ``0.21.0`` | |``GCC/12.2.0`` -``0.22.0`` | |``GCC/12.3.0`` +``0.22.0`` | |``GCC/12.3.0``, ``GCC/13.2.0`` ### pysamstats @@ -32338,6 +33211,16 @@ version |versionsuffix |toolchain ``2.1.1``| |``foss/2022a`` ``2.4.0``| |``foss/2022b`` +### pyseer + +pyseer was first written a python reimplementation of seer, which was written in C++. pyseer uses linear models with fixed or mixed effects to estimate the effect of genetic variation in a bacterial population on a phenotype of interest, while accounting for potentially very strong confounding population structure. This allows for genome-wide association studies (GWAS) to be performed in clonal organisms such as bacteria and viruses. + +*homepage*: + +version |toolchain +----------|-------------- +``1.3.11``|``foss/2022b`` + ### pysheds Simple and fast watershed delineation in python. @@ -32493,7 +33376,7 @@ version |versionsuffix |toolchain ``3.6.1`` | |``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``fosscuda/2020b``, ``intel/2020b`` ``3.6.1`` |``-Python-3.7.4`` |``foss/2019b``, ``fosscuda/2019b`` ``3.6.1`` |``-Python-3.8.2`` |``foss/2020a``, ``intel/2020a`` -``3.8.0`` | |``foss/2022a``, ``foss/2022b`` +``3.8.0`` | |``foss/2022a``, ``foss/2022b``, ``foss/2023a`` ``3.9.2`` | |``foss/2023b`` ### PyTensor @@ -32686,6 +33569,7 @@ version |versionsuffix |toolchain ``3.11.2``|``-bare`` |``GCCcore/12.2.0`` ``3.11.3``| |``GCCcore/12.3.0`` ``3.11.5``| |``GCCcore/13.2.0`` +``3.12.3``| |``GCCcore/13.3.0`` ### Python-bundle @@ -32799,9 +33683,9 @@ LibSBML Python API. *homepage*: version |toolchain -----------|-------------- +----------|------------------------------ ``5.19.7``|``foss/2021a`` -``5.20.2``|``foss/2023b`` +``5.20.2``|``foss/2021b``, ``foss/2023b`` ### python-louvain @@ -32810,9 +33694,9 @@ Louvain algorithm for community detection *homepage*: version |toolchain ---------|-------------- +--------|------------------------------ ``0.15``|``foss/2021b`` -``0.16``|``foss/2022a`` +``0.16``|``foss/2022a``, ``foss/2023a`` ### python-mujoco @@ -32823,6 +33707,7 @@ This package is the canonical Python bindings for the MuJoCo physics engine. The version |toolchain ---------|-------------- ``2.2.2``|``foss/2022a`` +``3.1.4``|``foss/2023a`` ### python-parasail @@ -32868,11 +33753,11 @@ xxhash is a Python binding for the xxHash library by Yann Collet. *homepage*: version |toolchain ----------|------------------ +---------|-------------------------------------- ``2.0.2``|``GCCcore/10.2.0`` ``3.1.0``|``GCCcore/11.3.0`` ``3.2.0``|``GCCcore/12.2.0`` -``3.4.1``|``GCCcore/12.3.0`` +``3.4.1``|``GCCcore/12.3.0``, ``GCCcore/13.2.0`` ### pythran @@ -32922,7 +33807,7 @@ version |versionsuffix |toolchain ``1.12.1``|``-CUDA-11.5.2`` |``foss/2021b`` ``1.12.1``|``-CUDA-11.7.0`` |``foss/2022a`` ``1.13.1``| |``foss/2022a``, ``foss/2022b`` -``1.13.1``|``-CUDA-11.7.0`` |``foss/2022a`` +``1.13.1``|``-CUDA-11.7.0`` |``foss/2022a``, ``foss/2022b`` ``2.0.1`` | |``foss/2022a``, ``foss/2022b`` ``2.1.2`` | |``foss/2022a``, ``foss/2022b``, ``foss/2023a``, ``foss/2023b`` ``2.1.2`` |``-CUDA-12.1.1`` |``foss/2023a`` @@ -32947,6 +33832,8 @@ version |versionsuffix |toolchain ----------|----------------|-------------- ``1.12.1``|``-CUDA-11.7.0``|``foss/2022a`` ``1.13.1``|``-CUDA-11.7.0``|``foss/2022a`` +``2.1.2`` | |``foss/2023a`` +``2.1.2`` |``-CUDA-12.1.1``|``foss/2023a`` ### pytorch-CycleGAN-pix2pix @@ -32974,6 +33861,7 @@ version |versionsuffix |toolchain ``2.1.0``|``-PyTorch-1.12.0`` |``foss/2022a`` ``2.1.0``|``-PyTorch-1.12.0-CUDA-11.7.0``|``foss/2022a`` ``2.1.0``|``-PyTorch-1.12.1-CUDA-11.3.1``|``foss/2021a`` +``2.5.0``|``-PyTorch-2.1.2-CUDA-12.1.1`` |``foss/2023a`` ### PyTorch-Ignite @@ -33058,6 +33946,16 @@ version |toolchain ---------|------------------ ``1.0.3``|``GCCcore/11.3.0`` +### PyVista + +3D plotting and mesh analysis through a streamlined interface for the Visualization Toolkit (VTK) + +*homepage*: + +version |toolchain +----------|-------------- +``0.43.8``|``foss/2023a`` + ### pyWannier90 A Wannier90 Python interface for VASP and PySCF @@ -33159,7 +34057,7 @@ version |versionsuffix |toolchain ## Q -[q2-krona](#q2-krona) - [Q6](#q6) - [QCA](#qca) - [qcat](#qcat) - [QCG-PilotJob](#qcg-pilotjob) - [qcint](#qcint) - [QCxMS](#qcxms) - [QD](#qd) - [QDD](#qdd) - [QEMU](#qemu) - [qforce](#qforce) - [QGIS](#qgis) - [Qhull](#qhull) - [QIIME](#qiime) - [QIIME2](#qiime2) - [Qiskit](#qiskit) - [QJson](#qjson) - [QML](#qml) - [qnorm](#qnorm) - [qpth](#qpth) - [qrupdate](#qrupdate) - [QScintilla](#qscintilla) - [Qt](#qt) - [Qt5](#qt5) - [Qt5Webkit](#qt5webkit) - [Qt6](#qt6) - [Qtconsole](#qtconsole) - [QtKeychain](#qtkeychain) - [QTLtools](#qtltools) - [qtop](#qtop) - [QtPy](#qtpy) - [Qualimap](#qualimap) - [Quandl](#quandl) - [QuantumESPRESSO](#quantumespresso) - [QUAST](#quast) - [QuaZIP](#quazip) - [QuickFF](#quickff) - [QuickPIC](#quickpic) - [QuickTree](#quicktree) - [Quip](#quip) - [Quorum](#quorum) - [QuPath](#qupath) - [QuTiP](#qutip) - [Qwt](#qwt) - [QwtPolar](#qwtpolar) +[q2-krona](#q2-krona) - [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) - [qmflows](#qmflows) - [QML](#qml) - [qnorm](#qnorm) - [qpth](#qpth) - [qrupdate](#qrupdate) - [QScintilla](#qscintilla) - [Qt](#qt) - [Qt5](#qt5) - [Qt5Webkit](#qt5webkit) - [Qt6](#qt6) - [Qtconsole](#qtconsole) - [QtKeychain](#qtkeychain) - [QTLtools](#qtltools) - [qtop](#qtop) - [QtPy](#qtpy) - [Qualimap](#qualimap) - [Quandl](#quandl) - [QuantumESPRESSO](#quantumespresso) - [QUAST](#quast) - [QuaZIP](#quazip) - [QuickFF](#quickff) - [QuickPIC](#quickpic) - [QuickTree](#quicktree) - [Quip](#quip) - [Quorum](#quorum) - [QuPath](#qupath) - [QuTiP](#qutip) - [Qwt](#qwt) - [QwtPolar](#qwtpolar) ### q2-krona @@ -33355,6 +34253,16 @@ version |toolchain ---------|---------------------------------------------------------------------- ``0.9.0``|``GCCcore/10.2.0``, ``GCCcore/8.2.0``, ``foss/2016b``, ``intel/2016b`` +### qmflows + +This library tackles the construction and efficient execution of computational chemistry workflows. This allows computational chemists to use the emerging massively parallel compute environments in an easy manner and focus on interpretation of scientific data rather than on tedious job submission procedures and manual data processing. + +*homepage*: + +version |toolchain +---------|-------------- +``1.0.0``|``foss/2022a`` + ### QML QML is a Python2/3-compatible toolkit for representation learning of properties of molecules and solids. @@ -33372,8 +34280,8 @@ Fast-ish (and correct!) quantile normalization in Python *homepage*: version |toolchain ----------|-------------- -``0.8.1``|``foss/2022a`` +---------|------------------------------ +``0.8.1``|``foss/2022a``, ``foss/2023a`` ### qpth @@ -33618,6 +34526,7 @@ version |versionsuffix |toolchain ``2.2.0``|``-Python-2.7.14``|``intel/2017b`` ``2.2.4``|``-Python-3.7.2`` |``intel/2019a`` ``2.2.4``|``-Python-3.8.2`` |``intel/2020a`` +``2.2.7``| |``foss/2023a`` ``2.2.7``|``-Python-3.8.2`` |``intel/2020a`` ### QuickPIC @@ -34102,6 +35011,7 @@ version |versionsuffix |toolchain ``8.2.11``|``-hybrid-avx`` |``foss/2017b``, ``intel/2017b`` ``8.2.11``|``-hybrid-avx2`` |``foss/2017b``, ``intel/2017b``, ``intel/2018a`` ``8.2.11``|``-hybrid-sse3`` |``foss/2017b``, ``intel/2017b`` +``8.2.12``|``-avx2`` |``gompi/2022b`` ``8.2.12``|``-hybrid-avx2`` |``gompi/2020a``, ``gompi/2020b``, ``gompi/2021a``, ``gompi/2021b``, ``iimpi/2019b``, ``intel/2018b``, ``intel/2019a`` ``8.2.12``|``-pthreads-avx2``|``GCC/10.2.0`` @@ -34118,7 +35028,7 @@ version |toolchain ``1.0.2``|``gompi/2020b`` ``1.0.3``|``GCC/10.2.0`` ``1.1.0``|``GCC/11.2.0`` -``1.2.0``|``GCC/12.3.0`` +``1.2.0``|``GCC/12.2.0``, ``GCC/12.3.0`` ### Ray-assembler @@ -35117,6 +36027,7 @@ version |versionsuffix |toolchain ``6.24.06`` | |``foss/2021b`` ``6.26.06`` | |``foss/2022a`` ``6.26.10`` | |``foss/2022b`` +``6.30.06`` | |``foss/2023a`` ``v5.34.34``|``-Python-2.7.11``|``intel/2016a`` ``v5.34.36``|``-Python-2.7.11``|``intel/2016a`` ``v6.06.02``|``-Python-2.7.12``|``intel/2016b`` @@ -35169,11 +36080,12 @@ version |toolchain Database interface and 'PostgreSQL' driver for 'R'. This package provides a Database Interface 'DBI' compliant driver for 'R' to access 'PostgreSQL' database systems. -*homepage*: +*homepage*: version |toolchain ---------|-------------- ``0.7-5``|``foss/2022a`` +``0.7-6``|``gfbf/2023a`` ### rpy2 @@ -35263,6 +36175,7 @@ version |versionsuffix |toolchain ``1.3.1093`` |``-Java-11-R-4.0.0``|``foss/2020a`` ``1.4.1717`` |``-Java-11-R-4.1.0``|``foss/2021a`` ``2022.07.2+576``|``-Java-11-R-4.2.1``|``foss/2022a`` +``2023.12.1+402``|``-Java-11-R-4.3.3``|``gfbf/2023b`` ### RTG-Tools @@ -35285,6 +36198,7 @@ version |versionsuffix |toolchain ---------|------------------|------------------ ``0.8.3``|``-Python-2.7.14``|``intel/2018a`` ``1.0.1``| |``GCCcore/12.2.0`` +``1.2.0``| |``GCCcore/12.3.0`` ### ruamel.yaml @@ -35381,6 +36295,7 @@ version |toolchain ``1.73.0``|``GCCcore/13.2.0`` ``1.75.0``|``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ``1.76.0``|``GCCcore/13.2.0`` +``1.78.0``|``GCCcore/13.3.0`` ### rustworkx @@ -35395,7 +36310,7 @@ version |toolchain ## S -[S-Lang](#s-lang) - [s3fs](#s3fs) - [S4](#s4) - [Sabre](#sabre) - [safestringlib](#safestringlib) - [Safetensors](#safetensors) - [SAGE](#sage) - [Sailfish](#sailfish) - [SALib](#salib) - [Salmon](#salmon) - [SALMON-TDDFT](#salmon-tddft) - [Sambamba](#sambamba) - [samblaster](#samblaster) - [Samcef](#samcef) - [samclip](#samclip) - [samplot](#samplot) - [SAMtools](#samtools) - [sansa](#sansa) - [SAP](#sap) - [SAS](#sas) - [Satsuma2](#satsuma2) - [savvy](#savvy) - [Saxon-HE](#saxon-he) - [SBCL](#sbcl) - [sbt](#sbt) - [ScaFaCoS](#scafacos) - [ScaLAPACK](#scalapack) - [Scalasca](#scalasca) - [SCALCE](#scalce) - [Scalene](#scalene) - [scanpy](#scanpy) - [scArches](#scarches) - [scCODA](#sccoda) - [sceasy](#sceasy) - [SCENIC](#scenic) - [scGeneFit](#scgenefit) - [SCGid](#scgid) - [scGSVA](#scgsva) - [scHiCExplorer](#schicexplorer) - [Schrodinger](#schrodinger) - [scib](#scib) - [scib-metrics](#scib-metrics) - [sciClone](#sciclone) - [ScientificPython](#scientificpython) - [scikit-allel](#scikit-allel) - [scikit-bio](#scikit-bio) - [scikit-build](#scikit-build) - [scikit-build-core](#scikit-build-core) - [scikit-cuda](#scikit-cuda) - [scikit-extremes](#scikit-extremes) - [scikit-image](#scikit-image) - [scikit-learn](#scikit-learn) - [scikit-lego](#scikit-lego) - [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) - [scrublet](#scrublet) - [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) - [SEACells](#seacells) - [SearchGUI](#searchgui) - [SeaView](#seaview) - [SECAPR](#secapr) - [Seeder](#seeder) - [segemehl](#segemehl) - [segment-anything](#segment-anything) - [segmentation-models](#segmentation-models) - [segmentation-models-pytorch](#segmentation-models-pytorch) - [SeisSol](#seissol) - [SelEstim](#selestim) - [SELFIES](#selfies) - [SemiBin](#semibin) - [semla](#semla) - [Sentence-Transformers](#sentence-transformers) - [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) - [simanneal](#simanneal) - [simint](#simint) - [SimNIBS](#simnibs) - [SimPEG](#simpeg) - [SIMPLE](#simple) - [Simple-DFTD3](#simple-dftd3) - [SimpleElastix](#simpleelastix) - [SimpleITK](#simpleitk) - [simpy](#simpy) - [Simstrat](#simstrat) - [SimVascular](#simvascular) - [SingleM](#singlem) - [Singular](#singular) - [sinto](#sinto) - [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) - [sktime](#sktime) - [SlamDunk](#slamdunk) - [SLATEC](#slatec) - [SLEPc](#slepc) - [slepc4py](#slepc4py) - [sleuth](#sleuth) - [slidingwindow](#slidingwindow) - [SLiM](#slim) - [slow5tools](#slow5tools) - [slurm-drmaa](#slurm-drmaa) - [smafa](#smafa) - [smallgenomeutilities](#smallgenomeutilities) - [SMAP](#smap) - [SMARTdenovo](#smartdenovo) - [SMC++](#smc++) - [smfishHmrf](#smfishhmrf) - [smithwaterman](#smithwaterman) - [Smoldyn](#smoldyn) - [smooth-topk](#smooth-topk) - [SMRT-Link](#smrt-link) - [SMV](#smv) - [snakemake](#snakemake) - [SNAP](#snap) - [SNAP-ESA](#snap-esa) - [SNAP-ESA-python](#snap-esa-python) - [SNAP-HMM](#snap-hmm) - [SNAPE-pooled](#snape-pooled) - [snaphu](#snaphu) - [snappy](#snappy) - [Sniffles](#sniffles) - [snippy](#snippy) - [snp-sites](#snp-sites) - [snpEff](#snpeff) - [SNPhylo](#snphylo) - [SNPomatic](#snpomatic) - [SOAPaligner](#soapaligner) - [SOAPdenovo-Trans](#soapdenovo-trans) - [SOAPdenovo2](#soapdenovo2) - [SOAPfuse](#soapfuse) - [socat](#socat) - [SOCI](#soci) - [SolexaQA++](#solexaqa++) - [solo](#solo) - [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) - [SPEI](#spei) - [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) - [SQLAlchemy](#sqlalchemy) - [SQLite](#sqlite) - [SqueezeMeta](#squeezemeta) - [Squidpy](#squidpy) - [SRA-Toolkit](#sra-toolkit) - [sradownloader](#sradownloader) - [SRPRISM](#srprism) - [SRST2](#srst2) - [SSAHA2](#ssaha2) - [SSN](#ssn) - [SSPACE_Basic](#sspace_basic) - [SSW](#ssw) - [STACEY](#stacey) - [Stack](#stack) - [Stacks](#stacks) - [STAMP](#stamp) - [StaMPS](#stamps) - [Stampy](#stampy) - [STAR](#star) - [STAR-CCM+](#star-ccm+) - [STAR-Fusion](#star-fusion) - [stardist](#stardist) - [starparser](#starparser) - [stars](#stars) - [Stata](#stata) - [Statistics-R](#statistics-r) - [statsmodels](#statsmodels) - [STEAK](#steak) - [STIR](#stir) - [stpipeline](#stpipeline) - [strace](#strace) - [Strainberry](#strainberry) - [STREAM](#stream) - [strelka](#strelka) - [StringTie](#stringtie) - [stripy](#stripy) - [STRique](#strique) - [Structure](#structure) - [Structure_threader](#structure_threader) - [STRUMPACK](#strumpack) - [suave](#suave) - [SuAVE-biomat](#suave-biomat) - [Subread](#subread) - [subset-bam](#subset-bam) - [Subversion](#subversion) - [suds](#suds) - [SuiteSparse](#suitesparse) - [SUMACLUST](#sumaclust) - [SUMATRA](#sumatra) - [SUMO](#sumo) - [SUNDIALS](#sundials) - [SunPy](#sunpy) - [SuperLU](#superlu) - [SuperLU_DIST](#superlu_dist) - [supermagic](#supermagic) - [supernova](#supernova) - [SUPPA](#suppa) - [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) - [SYMMETRICA](#symmetrica) - [SYMPHONY](#symphony) - [sympy](#sympy) - [synapseclient](#synapseclient) - [synthcity](#synthcity) - [SyRI](#syri) - [sysbench](#sysbench) - [Szip](#szip) +[S-Lang](#s-lang) - [s3fs](#s3fs) - [S4](#s4) - [Sabre](#sabre) - [safestringlib](#safestringlib) - [Safetensors](#safetensors) - [SAGE](#sage) - [Sailfish](#sailfish) - [SALib](#salib) - [Salmon](#salmon) - [SALMON-TDDFT](#salmon-tddft) - [Sambamba](#sambamba) - [samblaster](#samblaster) - [Samcef](#samcef) - [samclip](#samclip) - [samplot](#samplot) - [SAMtools](#samtools) - [sansa](#sansa) - [SAP](#sap) - [SAS](#sas) - [Satsuma2](#satsuma2) - [savvy](#savvy) - [Saxon-HE](#saxon-he) - [SBCL](#sbcl) - [sbt](#sbt) - [ScaFaCoS](#scafacos) - [ScaLAPACK](#scalapack) - [Scalasca](#scalasca) - [SCALCE](#scalce) - [Scalene](#scalene) - [scanpy](#scanpy) - [scArches](#scarches) - [scCODA](#sccoda) - [sceasy](#sceasy) - [SCENIC](#scenic) - [scGeneFit](#scgenefit) - [SCGid](#scgid) - [scGSVA](#scgsva) - [scHiCExplorer](#schicexplorer) - [Schrodinger](#schrodinger) - [scib](#scib) - [scib-metrics](#scib-metrics) - [sciClone](#sciclone) - [ScientificPython](#scientificpython) - [scikit-allel](#scikit-allel) - [scikit-bio](#scikit-bio) - [scikit-build](#scikit-build) - [scikit-build-core](#scikit-build-core) - [scikit-cuda](#scikit-cuda) - [scikit-extremes](#scikit-extremes) - [scikit-image](#scikit-image) - [scikit-learn](#scikit-learn) - [scikit-lego](#scikit-lego) - [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) - [SciTools-Iris](#scitools-iris) - [SCnorm](#scnorm) - [Scoary](#scoary) - [SCons](#scons) - [SCOOP](#scoop) - [SCopeLoomR](#scopeloomr) - [Score-P](#score-p) - [SCOTCH](#scotch) - [scp](#scp) - [scPred](#scpred) - [Scrappie](#scrappie) - [SCReadCounts](#screadcounts) - [scrublet](#scrublet) - [scVelo](#scvelo) - [scvi-tools](#scvi-tools) - [Scythe](#scythe) - [SDCC](#sdcc) - [SDL](#sdl) - [SDL2](#sdl2) - [SDL2_gfx](#sdl2_gfx) - [SDL2_image](#sdl2_image) - [SDL2_mixer](#sdl2_mixer) - [SDL2_ttf](#sdl2_ttf) - [SDL_image](#sdl_image) - [SDSL](#sdsl) - [Seaborn](#seaborn) - [SEACells](#seacells) - [SearchGUI](#searchgui) - [SeaView](#seaview) - [SECAPR](#secapr) - [Seeder](#seeder) - [segemehl](#segemehl) - [segment-anything](#segment-anything) - [segmentation-models](#segmentation-models) - [segmentation-models-pytorch](#segmentation-models-pytorch) - [SeisSol](#seissol) - [SelEstim](#selestim) - [SELFIES](#selfies) - [SemiBin](#semibin) - [semla](#semla) - [Sentence-Transformers](#sentence-transformers) - [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) - [simanneal](#simanneal) - [simint](#simint) - [SimNIBS](#simnibs) - [SimPEG](#simpeg) - [SIMPLE](#simple) - [Simple-DFTD3](#simple-dftd3) - [SimpleElastix](#simpleelastix) - [SimpleITK](#simpleitk) - [simpy](#simpy) - [Simstrat](#simstrat) - [SimVascular](#simvascular) - [SingleM](#singlem) - [Singular](#singular) - [sinto](#sinto) - [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) - [sktime](#sktime) - [SlamDunk](#slamdunk) - [SLATEC](#slatec) - [SLEPc](#slepc) - [slepc4py](#slepc4py) - [sleuth](#sleuth) - [slidingwindow](#slidingwindow) - [SLiM](#slim) - [slow5tools](#slow5tools) - [slurm-drmaa](#slurm-drmaa) - [smafa](#smafa) - [smallgenomeutilities](#smallgenomeutilities) - [SMAP](#smap) - [SMARTdenovo](#smartdenovo) - [SMC++](#smc++) - [smfishHmrf](#smfishhmrf) - [smithwaterman](#smithwaterman) - [Smoldyn](#smoldyn) - [smooth-topk](#smooth-topk) - [SMRT-Link](#smrt-link) - [SMV](#smv) - [snakemake](#snakemake) - [SNAP](#snap) - [SNAP-ESA](#snap-esa) - [SNAP-ESA-python](#snap-esa-python) - [SNAP-HMM](#snap-hmm) - [SNAPE-pooled](#snape-pooled) - [snaphu](#snaphu) - [snappy](#snappy) - [Sniffles](#sniffles) - [snippy](#snippy) - [snp-sites](#snp-sites) - [snpEff](#snpeff) - [SNPhylo](#snphylo) - [SNPomatic](#snpomatic) - [SOAPaligner](#soapaligner) - [SOAPdenovo-Trans](#soapdenovo-trans) - [SOAPdenovo2](#soapdenovo2) - [SOAPfuse](#soapfuse) - [socat](#socat) - [SOCI](#soci) - [SolexaQA++](#solexaqa++) - [solo](#solo) - [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) - [SPEI](#spei) - [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) - [SQLAlchemy](#sqlalchemy) - [SQLite](#sqlite) - [SqueezeMeta](#squeezemeta) - [Squidpy](#squidpy) - [SRA-Toolkit](#sra-toolkit) - [sradownloader](#sradownloader) - [SRPRISM](#srprism) - [SRST2](#srst2) - [SSAHA2](#ssaha2) - [SSN](#ssn) - [SSPACE_Basic](#sspace_basic) - [SSW](#ssw) - [STACEY](#stacey) - [Stack](#stack) - [Stacks](#stacks) - [STAMP](#stamp) - [StaMPS](#stamps) - [Stampy](#stampy) - [STAR](#star) - [STAR-CCM+](#star-ccm+) - [STAR-Fusion](#star-fusion) - [stardist](#stardist) - [starparser](#starparser) - [stars](#stars) - [Stata](#stata) - [Statistics-R](#statistics-r) - [statsmodels](#statsmodels) - [STEAK](#steak) - [STIR](#stir) - [stpipeline](#stpipeline) - [strace](#strace) - [Strainberry](#strainberry) - [STREAM](#stream) - [strelka](#strelka) - [StringTie](#stringtie) - [stripy](#stripy) - [STRique](#strique) - [Structure](#structure) - [Structure_threader](#structure_threader) - [STRUMPACK](#strumpack) - [suave](#suave) - [SuAVE-biomat](#suave-biomat) - [Subread](#subread) - [subset-bam](#subset-bam) - [subunit](#subunit) - [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) - [SUPPA](#suppa) - [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) - [SYMMETRICA](#symmetrica) - [SYMPHONY](#symphony) - [sympy](#sympy) - [synapseclient](#synapseclient) - [synthcity](#synthcity) - [SyRI](#syri) - [sysbench](#sysbench) - [Szip](#szip) ### S-Lang @@ -35611,6 +36526,7 @@ version |versionsuffix |toolchain ``1.16.1``| |``GCC/11.2.0``, ``GCC/11.3.0`` ``1.17`` | |``GCC/12.2.0`` ``1.18`` | |``GCC/12.3.0`` +``1.19.2``| |``GCC/13.2.0`` ### sansa @@ -35698,6 +36614,8 @@ version |versionsuffix |toolchain ----------|-------------------|---------- ``1.0.2`` |``-Java-1.8.0_152``|``system`` ``1.3.13``|``-Java-1.8`` |``system`` +``1.3.13``|``-Java-8`` |``system`` +``1.6.2`` |``-Java-8`` |``system`` ### ScaFaCoS @@ -35717,7 +36635,7 @@ The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines *homepage*: version |versionsuffix |toolchain ----------|---------------------------------|----------------------------------------------------------------------------------------------------------------------------------------------- +---------|---------------------------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------ ``2.0.2``| |``gompi/2019b``, ``gompic/2019b`` ``2.0.2``|``-BLIS-0.3.2`` |``gompi/2018b`` ``2.0.2``|``-OpenBLAS-0.2.13-LAPACK-3.5.0``|``gmvapich2/1.7.20`` @@ -35735,7 +36653,7 @@ version |versionsuffix |toolchain ``2.1.0``|``-bl`` |``gompi/2020b`` ``2.1.0``|``-fb`` |``gompi/2021a``, ``gompi/2021b`` ``2.2`` |``-amd`` |``gompi/2020a`` -``2.2.0``|``-fb`` |``gompi/2022.05``, ``gompi/2022.10``, ``gompi/2022a``, ``gompi/2022b``, ``gompi/2023.09``, ``gompi/2023a``, ``gompi/2023b``, ``nvompi/2022.07`` +``2.2.0``|``-fb`` |``gompi/2022.05``, ``gompi/2022.10``, ``gompi/2022a``, ``gompi/2022b``, ``gompi/2023.09``, ``gompi/2023a``, ``gompi/2023b``, ``gompi/2024.05``, ``nvompi/2022.07`` ### Scalasca @@ -35949,7 +36867,7 @@ version |versionsuffix |toolchain ---------|-----------------|-------------------------------------------------------------- ``0.5.6``|``-Python-3.8.2``|``foss/2020a`` ``0.5.7``| |``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``foss/2022a`` -``0.5.9``| |``foss/2023a`` +``0.6.0``| |``foss/2023a`` ### scikit-build @@ -35975,6 +36893,7 @@ Scikit-build-core is a complete ground-up rewrite of scikit-build on top of mode version |toolchain ---------|------------------ ``0.5.0``|``GCCcore/12.3.0`` +``0.9.3``|``GCCcore/13.2.0`` ### scikit-cuda @@ -36068,6 +36987,7 @@ version |versionsuffix |toolchain ``1.3.1`` | |``gfbf/2023a``, ``iimkl/2023a`` ``1.3.2`` | |``gfbf/2023b`` ``1.4.0`` | |``gfbf/2023b`` +``1.4.2`` | |``gfbf/2023a`` ### scikit-lego @@ -36191,6 +37111,17 @@ version |versionsuffix |toolchain ``2023.07``| |``gfbf/2023a``, ``iimkl/2023a`` ``2023.11``| |``gfbf/2023.09``, ``gfbf/2023b`` +### SciTools-Iris + +A powerful, format-agnostic, community-driven Python package for analysing and visualising Earth science data. + +*homepage*: + +version |toolchain +---------|-------------- +``3.2.1``|``foss/2022a`` +``3.9.0``|``foss/2023a`` + ### SCnorm This package implements SCnorm — a method to normalize single-cell RNA-seq data. @@ -36308,6 +37239,7 @@ version |versionsuffix|toolchain ``7.0.1`` | |``gompi/2022a``, ``iimpi/2022a`` ``7.0.1`` |``-int64`` |``gompi/2022a`` ``7.0.3`` | |``gompi/2022b``, ``gompi/2023a`` +``7.0.4`` | |``gompi/2023b`` ### scp @@ -36341,6 +37273,16 @@ version |toolchain ---------|--------------- ``1.3.2``|``intel/2018a`` +### SCReadCounts + +SCReadCounts is a computational tool for a cell-level assessment of the read counts bearing a particular nucleotide at genomic positions of interest from single cell RNA sequencing (scRNA-seq) data. + +*homepage*: + +version |toolchain +---------|-------------- +``1.4.0``|``foss/2023b`` + ### scrublet Single-Cell Remover of Doublets - Python code for identifying doublets in single-cell RNA-seq data @@ -36423,6 +37365,16 @@ version |toolchain ``2.28.2``|``GCCcore/12.3.0`` ``2.28.5``|``GCCcore/13.2.0`` +### SDL2_gfx + +Graphics drawing primitives library for SDL2 + +*homepage*: + +version |toolchain +---------|------------------ +``1.0.4``|``GCCcore/11.3.0`` + ### SDL2_image 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.) @@ -36433,6 +37385,7 @@ version |toolchain ---------|------------------ ``2.0.3``|``GCCcore/6.4.0`` ``2.6.3``|``GCCcore/11.3.0`` +``2.8.2``|``GCCcore/12.3.0`` ### SDL2_mixer @@ -36443,6 +37396,7 @@ Due to popular demand, here is a simple multi-channel audio mixer. It supports version |toolchain ---------|------------------ ``2.6.3``|``GCCcore/11.3.0`` +``2.8.0``|``GCCcore/12.3.0`` ### SDL2_ttf @@ -36453,6 +37407,7 @@ This library is a wrapper around the FreeType and Harfbuzz libraries, allowing y version |toolchain ----------|------------------ ``2.20.2``|``GCCcore/11.3.0`` +``2.22.0``|``GCCcore/12.3.0`` ### SDL_image @@ -36497,10 +37452,10 @@ version |versionsuffix |toolchain ``0.10.1``| |``intel/2020b`` ``0.10.1``|``-Python-3.8.2`` |``foss/2020a``, ``intel/2020a`` ``0.11.1``| |``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` -``0.11.2``| |``foss/2021a``, ``foss/2021b`` +``0.11.2``| |``foss/2021a``, ``foss/2021b``, ``intel/2021b`` ``0.12.1``| |``foss/2022a`` ``0.12.2``| |``foss/2022b`` -``0.13.2``| |``gfbf/2023a`` +``0.13.2``| |``gfbf/2023a``, ``gfbf/2023b`` ### SEACells @@ -36668,6 +37623,7 @@ version |versionsuffix |toolchain ``0.1.96``| |``GCC/10.2.0``, ``GCC/10.3.0`` ``0.1.97``| |``GCC/11.3.0`` ``0.1.99``| |``GCC/12.2.0`` +``0.2.0`` | |``GCC/12.3.0`` ### sentinelsat @@ -36858,6 +37814,7 @@ version |versionsuffix|toolchain ``4.3.0`` |``-R-4.2.1`` |``foss/2022a`` ``4.4.0`` |``-R-4.2.2`` |``foss/2022b`` ``5.0.1`` |``-R-4.2.2`` |``foss/2022b`` +``5.1.0`` |``-R-4.3.2`` |``foss/2023a`` ### SeuratData @@ -36878,6 +37835,7 @@ Interfaces for HDF5-based Single Cell File Formats version |versionsuffix|toolchain --------------|-------------|-------------- ``0.0.0.9020``|``-R-4.2.1`` |``foss/2022a`` +``20231104`` |``-R-4.3.2`` |``foss/2023a`` ### SeuratWrappers @@ -37183,13 +38141,14 @@ version|versionsuffix |toolchain ### SimNIBS -SimNIBS is a free and open source software package for the Simulation of Non-invasive Brain Stimulation. +SimNIBS is a free and open source software package for the Simulation of Non-invasive Brain Stimulation *homepage*: version |toolchain ---------|-------------- ``3.2.4``|``foss/2020b`` +``4.0.1``|``foss/2023a`` ### SimPEG @@ -37304,6 +38263,7 @@ version |toolchain ------------|-------------------------------- ``4.1.2`` |``GCC/8.2.0-2.31.1``, ``system`` ``4.3.2p10``|``gfbf/2022a`` +``4.4.0`` |``gfbf/2023b`` ### sinto @@ -37454,6 +38414,7 @@ version |versionsuffix |toolchain ``0.11.0``|``-PyTorch-1.10.0`` |``foss/2021a`` ``0.11.0``|``-PyTorch-1.10.0-CUDA-11.3.1``|``foss/2021a`` ``0.15.0``|``-PyTorch-2.1.2`` |``foss/2023a`` +``0.15.0``|``-PyTorch-2.1.2-CUDA-12.1.1`` |``foss/2023a`` ### sktime @@ -37916,10 +38877,10 @@ SOCI is a database access library for C++ that makes the illusion of embedding S *homepage*: version |toolchain ----------|---------------------------------------------- +---------|-------------------------------------------------------------- ``4.0.1``|``GCC/10.2.0``, ``GCCcore/9.3.0`` ``4.0.2``|``GCC/10.3.0`` -``4.0.3``|``GCC/11.2.0``, ``GCC/11.3.0``, ``GCC/12.2.0`` +``4.0.3``|``GCC/11.2.0``, ``GCC/11.3.0``, ``GCC/12.2.0``, ``GCC/13.2.0`` ### SolexaQA++ @@ -37998,8 +38959,8 @@ Sound eXchange, the Swiss Army knife of audio manipulation *homepage*: version |toolchain -----------|--------------------------------- -``14.4.2``|``GCC/8.3.0``, ``GCCcore/11.3.0`` +----------|----------------------------------------------------- +``14.4.2``|``GCC/8.3.0``, ``GCCcore/11.3.0``, ``GCCcore/12.3.0`` ### SoXt @@ -38041,6 +39002,7 @@ version |toolchain ``0.16.2``|``system`` ``0.17.0``|``system`` ``0.17.2``|``system`` +``0.21.2``|``system`` ### spaCy @@ -38477,6 +39439,7 @@ version |toolchain ``3.41.2`` |``GCCcore/13.1.0`` ``3.42.0`` |``GCCcore/12.3.0`` ``3.43.1`` |``GCCcore/13.2.0`` +``3.45.3`` |``GCCcore/13.3.0`` ### SqueezeMeta @@ -38499,6 +39462,7 @@ Squidpy is a tool for the analysis and visualization of spatial molecular data. version |toolchain ---------|-------------- ``1.2.2``|``foss/2021b`` +``1.4.1``|``foss/2023a`` ### SRA-Toolkit @@ -38507,7 +39471,7 @@ The SRA Toolkit, and the source-code SRA System Development Kit (SDK), will all *homepage*: version |versionsuffix |toolchain ------------|-------------------|--------------- +-----------|-------------------|-------------------------------- ``2.3.5`` |``-centos_linux64``|``system`` ``2.5.4-1``|``-centos_linux64``|``system`` ``2.5.7`` |``-centos_linux64``|``system`` @@ -38523,7 +39487,7 @@ version |versionsuffix |toolchain ``3.0.0`` | |``gompi/2021b`` ``3.0.0`` |``-centos_linux64``|``system`` ``3.0.3`` | |``gompi/2022a`` -``3.0.5`` | |``gompi/2021a`` +``3.0.5`` | |``gompi/2021a``, ``gompi/2022b`` ``3.0.10`` | |``gompi/2023a`` ### sradownloader @@ -38715,7 +39679,7 @@ version |toolchain ``2.7.10a_alpha_220601``|``GCC/10.3.0`` ``2.7.10b`` |``GCC/11.3.0``, ``GCC/12.2.0`` ``2.7.11a`` |``GCC/12.2.0``, ``GCC/12.3.0`` -``2.7.11b`` |``GCC/12.3.0`` +``2.7.11b`` |``GCC/12.3.0``, ``GCC/13.2.0`` ### STAR-CCM+ @@ -39023,6 +39987,16 @@ version |toolchain ---------|------------------ ``1.1.0``|``GCCcore/10.3.0`` +### subunit + +Subunit is a streaming protocol for test results. + +*homepage*: + +version |toolchain +---------|------------------ +``1.4.3``|``GCCcore/12.2.0`` + ### Subversion Subversion is an open source version control system. @@ -39261,8 +40235,8 @@ Svist4get is a simple bioinformatics tool for visualization of genomic signal t *homepage*: version |toolchain ----------|-------------- -``1.3.1``|``foss/2020b`` +---------|------------------------------ +``1.3.1``|``foss/2020b``, ``foss/2023a`` ### swarm @@ -39333,6 +40307,7 @@ version |versionsuffix |toolchain ``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``, ``GCCcore/13.2.0`` +``4.2.1`` | |``GCCcore/13.3.0`` ### SWIPE @@ -39360,11 +40335,12 @@ SymEngine is a standalone fast C++ symbolic manipulation library *homepage*: -version |versionsuffix|toolchain ----------|-------------|-------------------- -``0.3.0``|``-20181006``|``intel/2018a`` -``0.4.0``| |``GCC/8.2.0-2.31.1`` -``0.7.0``| |``GCC/10.3.0`` +version |versionsuffix|toolchain +----------|-------------|-------------------- +``0.3.0`` |``-20181006``|``intel/2018a`` +``0.4.0`` | |``GCC/8.2.0-2.31.1`` +``0.7.0`` | |``GCC/10.3.0`` +``0.11.2``| |``gfbf/2023b`` ### SymEngine-python @@ -39372,9 +40348,10 @@ Python wrappers to the C++ library SymEngine, a fast C++ symbolic manipulation l *homepage*: -version |toolchain ----------|-------------- -``0.7.2``|``GCC/10.3.0`` +version |toolchain +----------|-------------- +``0.7.2`` |``GCC/10.3.0`` +``0.11.0``|``gfbf/2023b`` ### SYMMETRICA @@ -39383,8 +40360,8 @@ Symmetrica is a Collection of C routines for representation theory. *homepage*: version|toolchain --------|------------------ -``2.0``|``GCCcore/11.3.0`` +-------|-------------------------------------- +``2.0``|``GCCcore/11.3.0``, ``GCCcore/13.2.0`` ### SYMPHONY @@ -39473,7 +40450,7 @@ version |toolchain ## T -[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) - [tiny-cuda-nn](#tiny-cuda-nn) - [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) - [tox](#tox) - [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) - [Triton](#triton) - [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](#t-coffee) - [t-SNE-CUDA](#t-sne-cuda) - [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) - [TF-COMB](#tf-comb) - [TFEA](#tfea) - [Theano](#theano) - [ThemisPy](#themispy) - [THetA](#theta) - [thirdorder](#thirdorder) - [thurstonianIRT](#thurstonianirt) - [TiCCutils](#ticcutils) - [tidybayes](#tidybayes) - [tidymodels](#tidymodels) - [Tika](#tika) - [tiktoken](#tiktoken) - [TiMBL](#timbl) - [time](#time) - [timm](#timm) - [TINKER](#tinker) - [tiny-cuda-nn](#tiny-cuda-nn) - [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) - [TorchIO](#torchio) - [torchsampler](#torchsampler) - [torchtext](#torchtext) - [torchvf](#torchvf) - [torchvision](#torchvision) - [tornado](#tornado) - [TotalView](#totalview) - [tox](#tox) - [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) - [Triton](#triton) - [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 @@ -39487,6 +40464,16 @@ version |toolchain ``13.45.61.3c310a9``|``system`` ``13.46.0.919e8c6b``|``system`` +### t-SNE-CUDA + +GPU Accelerated t-SNE for CUDA with Python bindings + +*homepage*: + +version |versionsuffix |toolchain +---------|----------------|-------------- +``3.0.1``|``-CUDA-12.1.1``|``foss/2023a`` + ### tabix Generic indexer for TAB-delimited genome position files @@ -39575,10 +40562,10 @@ TAMkin is a post-processing toolkit for normal mode analysis, thermochemistry a *homepage*: version |versionsuffix |toolchain ----------|------------------|---------------------------------------------- +---------|------------------|-------------------------------------------------------------- ``1.0.9``|``-Python-2.7.11``|``intel/2016a`` ``1.2.4``|``-Python-2.7.14``|``intel/2017b`` -``1.2.6``| |``foss/2020b``, ``foss/2021a``, ``foss/2021b`` +``1.2.6``| |``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``foss/2023a`` ``1.2.6``|``-Python-3.7.2`` |``intel/2019a`` ``1.2.6``|``-Python-3.8.2`` |``foss/2020a``, ``intel/2020a`` @@ -39639,7 +40626,7 @@ Intel Threading Building Blocks (Intel TBB) is a widely used, award-winning C++ *homepage*: version |toolchain ---------------|---------------------------------------------------------- +--------------|------------------------------------------------------------------------------ ``4.0.0.233`` |``system`` ``4.0.5.339`` |``system`` ``4.3.6.211`` |``system`` @@ -39655,9 +40642,9 @@ version |toolchain ``2018_U5`` |``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``2019_U4`` |``GCCcore/8.2.0`` ``2019_U9`` |``GCCcore/8.3.0`` -``2020.1`` |``GCCcore/9.3.0`` +``2020.1`` |``GCCcore/12.3.0``, ``GCCcore/9.3.0`` ``2020.2`` |``GCCcore/8.3.0`` -``2020.3`` |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``2020.3`` |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/12.3.0`` ``2021.4.0`` |``GCCcore/11.2.0`` ``2021.5.0`` |``GCCcore/11.3.0`` ``2021.10.0`` |``GCCcore/12.2.0`` @@ -39707,6 +40694,7 @@ version |toolchain ``8.6.11``|``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``8.6.12``|``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ``8.6.13``|``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``GCCcore/13.2.0`` +``8.6.14``|``GCCcore/13.3.0`` ### TCLAP @@ -39874,6 +40862,7 @@ version |versionsuffix |toolchain ``2.11.0``| |``foss/2022a`` ``2.11.0``|``-CUDA-11.7.0`` |``foss/2022a`` ``2.13.0``| |``foss/2022b``, ``foss/2023a`` +``2.15.1``| |``foss/2023a`` ### tensorflow-compression @@ -40044,11 +41033,11 @@ TeX is a typesetting language. Instead of visually formatting your text, you ent *homepage*: version |toolchain -------------|------------------------------ +------------|---------------------------------------------- ``20200406``|``GCCcore/8.3.0`` ``20210324``|``GCC/10.3.0``, ``GCC/11.2.0`` ``20220321``|``GCC/11.2.0`` -``20230313``|``GCC/11.3.0``, ``GCC/12.3.0`` +``20230313``|``GCC/11.3.0``, ``GCC/12.3.0``, ``GCC/13.2.0`` ### Text-CSV @@ -40060,6 +41049,16 @@ version |versionsuffix |toolchain --------|----------------|-------------- ``1.33``|``-Perl-5.22.1``|``foss/2016a`` +### TF-COMB + +Transcription Factor Co-Occurrence using Market Basket analysis. + +*homepage*: + +version|toolchain +-------|-------------- +``1.1``|``foss/2023a`` + ### TFEA Transcription Factor Enrichment Analysis @@ -40180,6 +41179,16 @@ version |toolchain --------|---------- ``1.16``|``system`` +### tiktoken + +tiktoken is a fast BPE tokeniser for use with OpenAI's models + +*homepage*: + +version |toolchain +---------|------------------ +``0.6.0``|``GCCcore/12.3.0`` + ### TiMBL TiMBL (Tilburg Memory Based Learner) is an open source software package implementing several memory-based learning algorithms, among which IB1-IG, an implementation of k-nearest neighbor classification with feature weighting suitable for symbolic feature spaces, and IGTree, a decision-tree approximation of IB1-IG. All implemented algorithms have in common that they store some representation of the training set explicitly in memory. During testing, new cases are classified by extrapolation from the most similar stored cases. @@ -40354,6 +41363,7 @@ version |toolchain ``3.2`` |``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ``3.2a``|``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``system`` ``3.3a``|``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``system`` +``3.4`` |``GCCcore/13.2.0``, ``GCCcore/13.3.0``, ``system`` ### TN93 @@ -40375,6 +41385,7 @@ version |toolchain -----------|-------------- ``0.12.12``|``foss/2021b`` ``0.14.0`` |``foss/2020b`` +``0.16.1`` |``foss/2023a`` ### ToFu @@ -40421,6 +41432,7 @@ version |toolchain ----------|------------------ ``0.12.1``|``GCCcore/10.3.0`` ``0.13.3``|``GCCcore/12.2.0`` +``0.15.2``|``GCCcore/12.3.0`` ### Tombo @@ -40456,7 +41468,7 @@ version|toolchain ### topaz -Particle picking software for single particle cryo-electron microscopy using convolutional neural networks and positive-unlabeled learning. Includes methods for micrograph denoising. +Particle picking software for single particle cryo-electron microscopy using convolutional neural networks and positive-unlabeled learning. Includes methods for micrograph denoising. *homepage*: @@ -40465,6 +41477,7 @@ version |versionsuffix |toolchain ``0.2.5`` | |``foss/2021a`` ``0.2.5`` |``-CUDA-11.3.1``|``foss/2021a`` ``0.2.5.20230926``|``-CUDA-11.7.0``|``foss/2022a`` +``0.2.5.20231120``|``-CUDA-12.1.1``|``foss/2023a`` ### TopHat @@ -40511,6 +41524,16 @@ version |versionsuffix |toolchain ---------|------------------|---------------------------------- ``1.5.2``|``-PyTorch-1.7.1``|``foss/2020b``, ``fosscuda/2020b`` +### TorchIO + +TorchIO is an open-source Python library for efficient loading, preprocessing, augmentation and patch-based sampling of 3D medical images in deep learning, following the design of PyTorch. It includes multiple intensity and spatial transforms for data augmentation and preprocessing. These transforms include typical computer vision operations such as random affine transformations and also domain-specific ones such as simulation of intensity artifacts due to MRI magnetic field inhomogeneity (bias) or k-space motion artifacts. + +*homepage*: + +version |versionsuffix |toolchain +----------|----------------|-------------- +``0.19.6``|``-CUDA-12.1.1``|``foss/2023a`` + ### torchsampler A (PyTorch) imbalanced dataset sampler for oversampling low classes and undersampling high frequent ones. @@ -40579,6 +41602,7 @@ version |versionsuffix |toolchain ``0.13.1``|``-CUDA-11.7.0`` |``foss/2022a`` ``0.14.1``| |``foss/2022b`` ``0.16.0``| |``foss/2023a`` +``0.16.0``|``-CUDA-12.1.1`` |``foss/2023a`` ### tornado @@ -40589,6 +41613,7 @@ Tornado is a Python web framework and asynchronous networking library. version |toolchain ---------|------------------ ``6.3.2``|``GCCcore/12.3.0`` +``6.4`` |``GCCcore/13.2.0`` ### TotalView @@ -40683,6 +41708,7 @@ version |versionsuffix |toolchain ``4.24.0``| |``foss/2022a`` ``4.29.2``| |``foss/2022a`` ``4.30.2``| |``foss/2022b`` +``4.39.3``| |``gfbf/2023a`` ### Transrate @@ -41142,6 +42168,7 @@ version |toolchain ``1.0.0``|``GCCcore/11.3.0`` ``1.1.0``|``GCCcore/12.2.0`` ``1.2.0``|``GCCcore/12.3.0``, ``GCCcore/13.2.0`` +``1.3.0``|``GCCcore/13.3.0`` ### UCC-CUDA @@ -41191,6 +42218,7 @@ version |versionsuffix |toolchain ``1.14.0`` | |``GCCcore/12.2.0`` ``1.14.1`` | |``GCCcore/12.3.0`` ``1.15.0`` | |``GCCcore/13.2.0`` +``1.16.0`` | |``GCCcore/13.2.0``, ``GCCcore/13.3.0`` ``1.16.0-rc4``| |``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0`` ### UCX-CUDA @@ -41206,6 +42234,7 @@ version |versionsuffix |toolchain ``1.11.2``|``-CUDA-11.4.1``|``GCCcore/11.2.0`` ``1.11.2``|``-CUDA-11.5.2``|``GCCcore/11.2.0`` ``1.12.1``|``-CUDA-11.7.0``|``GCCcore/11.3.0`` +``1.13.1``|``-CUDA-11.7.0``|``GCCcore/12.2.0`` ``1.13.1``|``-CUDA-12.0.0``|``GCCcore/12.2.0`` ``1.14.1``|``-CUDA-12.1.1``|``GCCcore/12.3.0`` ``1.15.0``|``-CUDA-12.4.0``|``GCCcore/13.2.0`` @@ -41455,8 +42484,8 @@ UnZip is an extraction utility for archives compressed in .zip format (also call *homepage*: version|toolchain --------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -``6.0``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``GCCcore/13.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``system`` +-------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +``6.0``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``GCCcore/13.2.0``, ``GCCcore/13.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``system`` ### UQTk @@ -41544,11 +42573,12 @@ version |toolchain ``2.38`` |``GCCcore/11.3.0`` ``2.38.1``|``GCCcore/12.2.0`` ``2.39`` |``GCCcore/12.3.0``, ``GCCcore/13.2.0`` +``2.40`` |``GCCcore/13.3.0`` ## V -[V8](#v8) - [vaeda](#vaeda) - [Vala](#vala) - [Valgrind](#valgrind) - [Vamb](#vamb) - [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) - [VSCode](#vscode) - [VSEARCH](#vsearch) - [vt](#vt) - [VTK](#vtk) - [VTune](#vtune) - [VV](#vv) - [VXL](#vxl) +[V8](#v8) - [vaeda](#vaeda) - [Vala](#vala) - [Valgrind](#valgrind) - [Vamb](#vamb) - [Vampir](#vampir) - [Vampire](#vampire) - [VAMPIRE-ASM](#vampire-asm) - [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) - [VSCode](#vscode) - [VSEARCH](#vsearch) - [vt](#vt) - [VTK](#vtk) - [VTune](#vtune) - [VV](#vv) - [VXL](#vxl) ### V8 @@ -41602,6 +42632,7 @@ version |toolchain ``3.19.0``|``gompi/2022a`` ``3.20.0``|``gompi/2022a`` ``3.21.0``|``gompi/2022b``, ``gompi/2023a`` +``3.23.0``|``gompi/2023b`` ### Vamb @@ -41634,6 +42665,16 @@ version |toolchain ---------|------------------ ``4.5.1``|``GCCcore/10.2.0`` +### VAMPIRE-ASM + +Vampire is designed from the ground-up to be an easy to use, fast, open-source and extensible software package capable of modelling almost any magnetic material with atomic resolution. + +*homepage*: + +version|toolchain +-------|-------------- +``6.0``|``foss/2022b`` + ### VarDict VarDict is an ultra sensitive variant caller for both single and paired sample variant calling from BAM files. @@ -41986,6 +43027,7 @@ version |toolchain ----------|------------------------------- ``0.6.6`` |``foss/2020b``, ``intel/2020b`` ``0.12.2``|``foss/2022a``, ``gfbf/2023a`` +``0.14.1``|``foss/2023a`` ### vitessce-python @@ -42171,6 +43213,7 @@ Visual Studio Code is a lightweight but powerful source code editor which r version |toolchain ----------|---------- ``1.85.0``|``system`` +``1.88.1``|``system`` ### VSEARCH @@ -42228,7 +43271,7 @@ version |versionsuffix |toolchain ``9.2.0.rc2``| |``foss/2022a`` ``9.2.2`` | |``foss/2022a`` ``9.2.6`` | |``foss/2022b`` -``9.3.0`` | |``foss/2023a`` +``9.3.0`` | |``foss/2023a``, ``foss/2023b`` ### VTune @@ -42286,7 +43329,7 @@ version |toolchain ## W -[waLBerla](#walberla) - [wandb](#wandb) - [Wannier90](#wannier90) - [WannierTools](#wanniertools) - [Wayland](#wayland) - [Waylandpp](#waylandpp) - [WCSLIB](#wcslib) - [WCT](#wct) - [wcwidth](#wcwidth) - [webin-cli](#webin-cli) - [WebKitGTK+](#webkitgtk+) - [WebSocket++](#websocket++) - [WEKA](#weka) - [WFA2](#wfa2) - [wget](#wget) - [wgsim](#wgsim) - [WHAM](#wham) - [WhatsHap](#whatshap) - [wheel](#wheel) - [WIEN2k](#wien2k) - [WildMagic](#wildmagic) - [Winnowmap](#winnowmap) - [WisecondorX](#wisecondorx) - [WISExome](#wisexome) - [wkhtmltopdf](#wkhtmltopdf) - [worker](#worker) - [wpebackend-fdo](#wpebackend-fdo) - [WPS](#wps) - [wrapt](#wrapt) - [WRF](#wrf) - [WRF-Fire](#wrf-fire) - [wrf-python](#wrf-python) - [WSClean](#wsclean) - [wtdbg2](#wtdbg2) - [wxPropertyGrid](#wxpropertygrid) - [wxPython](#wxpython) - [wxWidgets](#wxwidgets) +[waLBerla](#walberla) - [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) - [wfdb](#wfdb) - [WGDgc](#wgdgc) - [wget](#wget) - [wgsim](#wgsim) - [WHAM](#wham) - [WhatsHap](#whatshap) - [wheel](#wheel) - [WIEN2k](#wien2k) - [WildMagic](#wildmagic) - [Winnowmap](#winnowmap) - [WisecondorX](#wisecondorx) - [WISExome](#wisexome) - [wkhtmltopdf](#wkhtmltopdf) - [worker](#worker) - [wpebackend-fdo](#wpebackend-fdo) - [WPS](#wps) - [wrapt](#wrapt) - [WRF](#wrf) - [WRF-Fire](#wrf-fire) - [wrf-python](#wrf-python) - [WSClean](#wsclean) - [wtdbg2](#wtdbg2) - [wxPropertyGrid](#wxpropertygrid) - [wxPython](#wxpython) - [wxWidgets](#wxwidgets) ### waLBerla @@ -42319,13 +43362,13 @@ A tool for obtaining maximally-localised Wannier functions *homepage*: version |versionsuffix|toolchain ------------|-------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +-----------|-------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ``1.2`` | |``intel/2016.02-GCC-4.9`` ``2.0.1`` | |``intel/2016.02-GCC-4.9``, ``intel/2016a`` ``2.0.1.1``|``-abinit`` |``intel/2018b`` ``2.1.0`` | |``foss/2017b``, ``intel/2017a``, ``intel/2017b`` ``3.0.0`` | |``intel/2018b`` -``3.1.0`` | |``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``foss/2022a``, ``foss/2023a``, ``gomkl/2021a``, ``gomkl/2023a``, ``intel/2020a``, ``intel/2020b``, ``intel/2021a``, ``intel/2021b``, ``intel/2022a``, ``intel/2022b``, ``intel/2023a`` +``3.1.0`` | |``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``foss/2022a``, ``foss/2023a``, ``gomkl/2021a``, ``gomkl/2022a``, ``gomkl/2023a``, ``intel/2020a``, ``intel/2020b``, ``intel/2021a``, ``intel/2021b``, ``intel/2022a``, ``intel/2022b``, ``intel/2023a`` ### WannierTools @@ -42448,6 +43491,26 @@ version |toolchain ``2.3.3``|``GCCcore/11.3.0`` ``2.3.4``|``GCCcore/12.3.0`` +### wfdb + +The native Python waveform-database (WFDB) package. A library of tools for reading, writing, and processing WFDB signals and annotations. + +*homepage*: + +version |toolchain +---------|-------------- +``4.1.2``|``foss/2022a`` + +### WGDgc + +Analysis of whole genome duplications (WGD) and triplications (WGT) using comparative gene count data + +*homepage*: + +version|versionsuffix|toolchain +-------|-------------|-------------- +``1.3``|``-R-4.3.2`` |``foss/2023a`` + ### 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. @@ -42464,6 +43527,7 @@ version |toolchain ``1.21.2``|``GCCcore/11.2.0`` ``1.21.3``|``GCCcore/11.3.0`` ``1.21.4``|``GCCcore/13.2.0`` +``1.24.5``|``GCCcore/12.3.0`` ### wgsim @@ -43273,6 +44337,7 @@ version |toolchain ``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``, ``GCCcore/13.2.0`` +``1.20.1``|``GCCcore/13.3.0`` ### xpdf @@ -43308,6 +44373,7 @@ version |versionsuffix |toolchain ``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``, ``GCCcore/12.2.0`` ``1.2.6``| |``GCCcore/12.3.0`` +``1.2.7``| |``GCCcore/13.2.0`` ### xproto @@ -43355,7 +44421,8 @@ version |versionsuffix |toolchain ``6.5.0`` | |``foss/2021b`` ``6.5.1`` | |``foss/2022a`` ``6.6.0`` | |``foss/2022a``, ``intel/2022a`` -``6.6.1`` | |``gfbf/2023a`` +``6.6.1`` | |``gfbf/2022b``, ``gfbf/2023a`` +``6.7.0`` | |``gfbf/2023a`` ### xtensor @@ -43405,6 +44472,7 @@ 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`` ``9.0.2112``|``GCCcore/12.3.0`` +``9.1.0307``|``GCCcore/13.2.0`` ### xxHash @@ -43416,7 +44484,7 @@ version |toolchain ---------|---------------------------------------------------------- ``0.8.0``|``GCCcore/11.2.0`` ``0.8.1``|``GCCcore/10.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` -``0.8.2``|``GCCcore/12.3.0`` +``0.8.2``|``GCCcore/12.3.0``, ``GCCcore/13.2.0`` ### XZ @@ -43436,6 +44504,7 @@ version |versionsuffix |toolchain ``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`` +``5.4.5``| |``GCCcore/13.3.0`` ## Y @@ -43450,8 +44519,8 @@ YACS was created as a lightweight library to define and manage system configurat *homepage*: version |toolchain ----------|------------------------------------------------------------------------------------------------- -``0.1.8``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/8.3.0`` +---------|--------------------------------------------------------------------------------------------------------------------- +``0.1.8``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.3.0``, ``GCCcore/8.3.0`` ### Yade @@ -43509,6 +44578,7 @@ version |toolchain ---------|---------------------------------------------------------- ``0.6.3``|``GCCcore/8.3.0`` ``0.7.0``|``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` +``0.8.0``|``GCCcore/13.2.0`` ### YANK @@ -43633,6 +44703,7 @@ version |versionsuffix |toolchain ``2.10.1``| |``foss/2021a`` ``2.13.3``| |``foss/2021b``, ``foss/2022a`` ``2.16.0``| |``foss/2022b`` +``2.17.1``| |``foss/2023a`` ### Zeo++ @@ -43682,6 +44753,7 @@ version |toolchain ---------|--------------------------------------------------------- ``0.5.5``|``GCCcore/10.2.0`` ``1.0.0``|``GCCcore/10.3.0``, ``GCCcore/11.3.0``, ``GCCcore/9.3.0`` +``1.0.1``|``GCCcore/12.3.0`` ### Zgoubi @@ -43720,14 +44792,14 @@ Zip is a compression and file packaging/archive utility. Although highly compati *homepage*: version|toolchain --------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -``3.0``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +-------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ +``3.0``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0``, ``GCCcore/13.3.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ### zlib -zlib is designed to be a free, general-purpose, legally unencumbered -- that is, not covered by any patents -- lossless data-compression library for use on virtually any computer hardware and operating system. +zlib is designed to be a free, general-purpose, legally unencumbered -- that is, not covered by any patents -- lossless data-compression library for use on virtually any computer hardware and operating system. -*homepage*: +*homepage*: version |toolchain ----------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- @@ -43737,6 +44809,7 @@ version |toolchain ``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``, ``GCCcore/13.2.0``, ``system`` +``1.3.1`` |``GCCcore/13.3.0``, ``GCCcore/14.1.0``, ``system`` ### zlib-ng @@ -43749,6 +44822,7 @@ version |toolchain ``2.0.5``|``GCCcore/10.2.0`` ``2.0.6``|``GCCcore/10.3.0`` ``2.0.7``|``GCCcore/11.3.0`` +``2.1.6``|``GCCcore/12.3.0`` ### zlibbioc @@ -43768,8 +44842,8 @@ Zopfli Compression Algorithm is a compression library programmed in C to perform *homepage*: version |toolchain ----------|---------------------------------------------------------- -``1.0.3``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.3.0`` +---------|------------------------------------------------------------------------------ +``1.0.3``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.3.0``, ``GCCcore/12.3.0`` ### ZPAQ @@ -43810,6 +44884,7 @@ version |toolchain ``1.5.0``|``GCCcore/11.2.0`` ``1.5.2``|``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ``1.5.5``|``GCCcore/12.3.0``, ``GCCcore/13.2.0`` +``1.5.6``|``GCCcore/13.3.0`` ### zUMIs