4ti2 ---- **Description** A software package for algebraic, geometric and combinatorial problems on linear spaces **More Information** https://4ti2.github.io/ **Available Versions**:: 1.6.10-GCC-13.2.0 1.6.9-GCC-11.3.0 ABINIT ------ **Description** ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave or wavelet basis. **More Information** https://www.abinit.org/ **Available Versions**:: 9.2.1-intel-2020a 10.2.5-intel-2023a ABRicate -------- **Description** Mass screening of contigs for antimicrobial and virulence genes **More Information** https://github.com/tseemann/abricate **Available Versions**:: 1.0.0-gompi-2021a ABySS ----- **Description** Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler **More Information** https://www.bcgsc.ca/platform/bioinfo/software/abyss **Available Versions**:: 2.1.5-foss-2019b ACTC ---- **Description** ACTC converts independent triangles into triangle strips or fans. **More Information** https://sourceforge.net/projects/actc **Available Versions**:: 1.1-GCCcore-8.3.0 1.1-GCCcore-10.2.0 ADMIXTURE --------- **Description** ADMIXTURE is a software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets. It uses the same statistical model as STRUCTURE but calculates estimates much more rapidly using a fast numerical optimization algorithm. **More Information** https://dalexander.github.io/admixture **Available Versions**:: 1.3.0 ADOL-C ------ **Description** The package ADOL-C (Automatic Differentiation by OverLoading in C++) facilitatesthe evaluation of first and higher derivatives of vector functions that are definedby computer programs written in C or C++. The resulting derivative evaluationroutines may be called from C/C++, Fortran, or any other language that can be linkedwith C. **More Information** https://projects.coin-or.org/ADOL-C **Available Versions**:: 2.7.2-gompi-2020a AMOS ---- **Description** The AMOS consortium is committed to the development of open-source whole genome assembly software **More Information** http://amos.sourceforge.net **Available Versions**:: 3.1.0-foss-2018b ANSYS ----- **Available Versions**:: 2022R1 2024R2 2024R1 2022R2 2023R2 2025R2 2023R1 2021R2 ANTIC ----- **Description** Antic is an algebraic number theory library. **More Information** https://github.com/flintlib/antic **Available Versions**:: 0.2.5-gfbf-2022a ANTLR ----- **Description** ANTLR, ANother Tool for Language Recognition, (formerly PCCTS) is a language tool that provides a framework for constructing recognizers, compilers, and translators from grammatical descriptions containing Java, C#, C++, or Python actions. **More Information** https://www.antlr2.org/ **Available Versions**:: 2.7.7-GCCcore-10.3.0-Java-11 2.7.7-GCCcore-10.2.0-Java-11 ANTs ---- **Description** ANTs extracts information from complex datasets that include imaging. ANTs is useful for managing, interpreting and visualizing multidimensional data. **More Information** https://stnava.github.io/ANTs/ **Available Versions**:: 2.5.0-foss-2022b AOCL-BLAS --------- **Description** AOCL-BLAS is AMD's optimized version of BLAS targeted for AMD EPYC and Ryzen CPUs. **More Information** https://github.com/amd/blis **Available Versions**:: 5.1-GCC-14.3.0 5.0-GCC-14.2.0 APR --- **Description** Apache Portable Runtime (APR) libraries. **More Information** https://apr.apache.org/ **Available Versions**:: 1.7.0-GCCcore-10.2.0 1.7.0-GCCcore-11.2.0 1.6.3-GCCcore-7.3.0 1.7.0-GCCcore-11.3.0 APR-util -------- **Description** Apache Portable Runtime (APR) util libraries. **More Information** https://apr.apache.org/ **Available Versions**:: 1.6.1-GCCcore-11.3.0 1.6.1-GCCcore-11.2.0 1.6.1-GCCcore-10.2.0 1.6.1-GCCcore-7.3.0 ASE --- **Description** ASE is a python package providing an open source Atomic Simulation Environment in the Python scripting language.From version 3.20.1 we also include the ase-ext package, it contains optional reimplementationsin C of functions in ASE. ASE uses it automatically when installed. **More Information** https://wiki.fysik.dtu.dk/ase **Available Versions**:: 3.22.1-intel-2022a 3.22.1-foss-2022a 3.24.0-gfbf-2024a ATK --- **Description** ATK provides the set of accessibility interfaces that are implemented by other toolkits and applications. Using the ATK interfaces, accessibility tools have full access to view and control running applications. **More Information** https://developer.gnome.org/atk/ **Available Versions**:: 2.38.0-GCCcore-12.2.0 2.38.0-GCCcore-11.3.0 2.36.0-GCCcore-10.2.0 2.36.0-GCCcore-9.3.0 2.32.0-GCCcore-8.2.0 2.36.0-GCCcore-11.2.0 2.34.1-GCCcore-8.3.0 2.38.0-GCCcore-13.2.0 2.38.0-GCCcore-12.3.0 AUGUSTUS -------- **Description** AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences **More Information** https://bioinf.uni-greifswald.de/augustus/ **Available Versions**:: 3.4.0-foss-2020b 3.3.3-foss-2019b Abaqus ------ **Description** Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit dynamics FEA. **More Information** https://www.simulia.com/products/abaqus_fea.html **Available Versions**:: 2022 Abseil ------ **Description** Abseil is an open-source collection of C++ library code designed to augment theC++ standard library. The Abseil library code is collected from Google's ownC++ code base, has been extensively tested and used in production, and is thesame code we depend on in our daily coding lives. **More Information** https://abseil.io/ **Available Versions**:: 20240116.1-GCCcore-13.2.0 20230125.3-GCCcore-12.3.0 20240722.0-GCCcore-13.3.0 AlphaFold --------- **Description** AlphaFold can predict protein structures with atomic accuracy even where no similar structure is known **More Information** https://deepmind.com/research/case-studies/alphafold **Available Versions**:: 2.3.1-foss-2022a-CUDA-11.7.0 2.3.4-foss-2022a-ColabFold 2.3.4-foss-2022a-CUDA-11.7.0-ColabFold 2.1.1-fosscuda-2020b 2.0.0-fosscuda-2020b 2.3.0-foss-2021b-CUDA-11.4.1 2.3.1-foss-2022a 2.2.2-foss-2021a-CUDA-11.3.1 Amber ----- **Description** Amber (originally Assisted Model Building with Energy Refinement) is software for performing molecular dynamics and structure prediction. **More Information** https://ambermd.org/amber.html **Available Versions**:: 22.0-foss-2021b-AmberTools-22.3 22.0-foss-2021b-AmberTools-22.0 22.4-foss-2022a-AmberTools-22.5-CUDA-11.7.0 AmberTools ---------- **Description** AmberTools consists of several independently developed packages that work well by themselves, and with Amber itself. The suite can also be used to carry out complete molecular dynamics simulations, with either explicit water or generalized Born solvent models. **More Information** https://ambermd.org/ **Available Versions**:: 22.3-foss-2021b Anaconda2 --------- **Description** Built to complement the rich, open source Python community,the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture. **More Information** https://www.anaconda.com **Available Versions**:: 2019.10 4.2.0 2019.03 Anaconda3 --------- **Description** Built to complement the rich, open source Python community,the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture. **More Information** https://www.anaconda.com **Available Versions**:: 2023.09-0 2022.10 2020.11 2021.05 2021.11 2022.05 2024.02-1 2024.06-1 2025.06-1 2020.02 Arb --- **Description** Arb is a C library for arbitrary-precision interval arithmetic. It has full support for both real and complex numbers. The library is thread-safe, portable, and extensively tested. **More Information** https://arblib.org/ **Available Versions**:: 2.23.0-gfbf-2022a Armadillo --------- **Description** Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions. **More Information** https://arma.sourceforge.net/ **Available Versions**:: 12.6.2-foss-2023a 12.8.0-foss-2023b 14.0.3-foss-2024a 9.900.1-foss-2020a Arriba ------ **Description** Arriba is a command-line tool for the detection of gene fusions from RNA-Seq data. It was developed for the use in a clinical research setting. Therefore, short runtimes and high sensitivity were important design criteria. **More Information** https://github.com/suhrig/arriba **Available Versions**:: 2.3.0-GCC-11.2.0 Arrow ----- **Description** Apache Arrow (incl. PyArrow Python bindings), a cross-language development platform for in-memory data. **More Information** https://arrow.apache.org **Available Versions**:: 8.0.0-foss-2022a 0.16.0-foss-2019b-Python-3.7.4 8.0.0-foss-2021b 6.0.0-foss-2021b 14.0.1-gfbf-2023a 17.0.0-gfbf-2024a Aspera-CLI ---------- **Description** IBM Aspera Command-Line Interface (the Aspera CLI) isa collection of Aspera tools for performing high-speed, secure datatransfers from the command line. The Aspera CLI is for users andorganizations who want to automate their transfer workflows. **More Information** https://asperasoft.com **Available Versions**:: 3.9.6.1467.159c5b1 Aspera-Connect -------------- **Description** Connect is an install-on-demand Web browser plug-in that facilitates high-speed uploads and downloads with an Aspera transfer server. **More Information** http://downloads.asperasoft.com/connect2/ **Available Versions**:: 3.9.6 AutoDock -------- **Description** AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. **More Information** http://autodock.scripps.edu/ **Available Versions**:: 4.2.6-GCC-9.3.0 AutoDock-GPU ------------ **Description** OpenCL and Cuda accelerated version of AutoDock. It leverages its embarrasinglyparallelizable LGA by processing ligand-receptor poses in parallel overmultiple compute units.AutoDock is a suite of automated docking tools. It is designed to predict howsmall molecules, such as substrates or drug candidates, bind to a receptor ofknown 3D structure. **More Information** https://github.com/ccsb-scripps/AutoDock-GPU **Available Versions**:: 1.5.3-GCC-11.3.0-CUDA-11.7.0 AutoDock-Vina ------------- **Description** AutoDock Vina is an open-source program for doing molecular docking. **More Information** https://vina.scripps.edu/ **Available Versions**:: 1.2.3-foss-2021b Autoconf -------- **Description** 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. **More Information** https://www.gnu.org/software/autoconf/ **Available Versions**:: 2.71-GCCcore-12.2.0 2.71-GCCcore-12.3.0 2.69-GCCcore-8.1.0 2.71-GCCcore-11.3.0 2.72-GCCcore-14.3.0 2.69-GCCcore-8.2.0 2.72-GCCcore-14.2.0 2.71 2.72-GCCcore-13.3.0 2.71-GCCcore-13.2.0 2.69-GCCcore-7.3.0 2.71-GCCcore-11.2.0 2.69 2.69-GCCcore-10.2.0 2.71-GCCcore-10.3.0 2.69-GCCcore-8.3.0 2.69-GCCcore-9.3.0 Automake -------- **Description** Automake: GNU Standards-compliant Makefile generator **More Information** https://www.gnu.org/software/automake/automake.html **Available Versions**:: 1.16.4-GCCcore-11.2.0 1.16.3-GCCcore-10.3.0 1.16.5-GCCcore-11.3.0 1.16.1-GCCcore-7.3.0 1.18-GCCcore-14.3.0 1.16.1-GCCcore-8.2.0 1.15.1-GCCcore-8.3.0 1.16.5-GCCcore-12.2.0 1.16.1-GCCcore-10.2.0 1.16.1-GCCcore-8.1.0 1.16.1-GCCcore-8.3.0 1.16.5-GCCcore-12.3.0 1.16.5 1.17-GCCcore-14.2.0 1.16.5-GCCcore-13.2.0 1.16.1-GCCcore-9.3.0 1.16.2-GCCcore-10.2.0 1.16.5-GCCcore-13.3.0 Autotools --------- **Description** This bundle collect the standard GNU build tools: Autoconf, Automake and libtool **More Information** https://autotools.io **Available Versions**:: 20210726-GCCcore-11.2.0 20180311-GCCcore-8.2.0 20240712-GCCcore-14.2.0 20180311-GCCcore-7.3.0 20180311-GCCcore-8.1.0 20210128-GCCcore-10.3.0 20220317-GCCcore-12.3.0 20220317-GCCcore-12.2.0 20231222-GCCcore-13.3.0 20220317-GCCcore-13.2.0 20250527-GCCcore-14.3.0 20220317 20180311-GCCcore-10.2.0 20180311-GCCcore-8.3.0 20200321-GCCcore-10.2.0 20180311-GCCcore-9.3.0 20220317-GCCcore-11.3.0 BAGEL ----- **Description** BAGEL (Brilliantly Advanced General Electronic-structure Library)is a parallel electronic-structure program. **More Information** http://www.nubakery.org **Available Versions**:: 1.2.2-foss-2023a 1.2.2-intel-2020a 1.2.2-foss-2019a BCFtools -------- **Description** Samtools is a suite of programs for interacting with high-throughput sequencing data. BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants **More Information** https://www.htslib.org/ **Available Versions**:: 1.11-GCC-10.2.0 1.10.2-GCC-8.3.0 1.14-GCC-11.2.0 1.9-foss-2018b 1.10.2-GCC-9.3.0 BEDTools -------- **Description** BEDTools: a powerful toolset for genome arithmetic.The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps andcomputing coverage.The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. **More Information** https://bedtools.readthedocs.io/ **Available Versions**:: 2.30.0-GCC-11.3.0 2.29.2-GCC-8.3.0 2.30.0-GCC-11.2.0 2.29.2-GCC-9.3.0 BLAST ----- **Description** Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences. **More Information** https://blast.ncbi.nlm.nih.gov/ **Available Versions**:: 2.11.0-Linux_x86_64 2.10.1-Linux_x86_64 BLAST+ ------ **Description** Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences. **More Information** https://blast.ncbi.nlm.nih.gov/ **Available Versions**:: 2.10.1-iimpi-2020a 2.9.0-gompi-2019b 2.7.1-foss-2018b 2.11.0-gompi-2020b 2.11.0-gompi-2021a 2.12.0-gompi-2021b 2.14.1-gompi-2023a 2.14.0-gompi-2022a 2.13.0-gompi-2022a BLAT ---- **Description** BLAT on DNA is designed to quickly find sequences of 95% andgreater similarity of length 25 bases or more. **More Information** https://genome.ucsc.edu/FAQ/FAQblat.html **Available Versions**:: 3.5-GCC-9.3.0 BLIS ---- **Description** BLIS is a portable software framework for instantiating high-performanceBLAS-like dense linear algebra libraries. **More Information** https://github.com/flame/blis/ **Available Versions**:: 0.8.1-GCC-10.3.0 0.9.0-GCC-12.3.0 1.0-GCC-13.3.0 2.0-GCC-14.3.0 0.8.1-GCC-11.2.0 0.9.0-GCC-12.2.0 1.1-GCC-14.2.0 0.9.0-GCC-11.3.0 0.9.0-GCC-13.2.0 BRAKER ------ **Description** BRAKER is a pipeline for fully automated prediction of protein coding genes with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes. **More Information** https://github.com/Gaius-Augustus/BRAKER **Available Versions**:: 2.1.6-foss-2019b-Python-3.7.4 BWA --- **Description** Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. **More Information** http://bio-bwa.sourceforge.net/ **Available Versions**:: 0.7.17-GCCcore-11.2.0 0.7.17-foss-2018b 0.7.18-GCCcore-13.3.0 0.7.17-GCCcore-11.3.0 0.7.17-GCC-9.3.0 BamTools -------- **Description** BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files. **More Information** https://github.com/pezmaster31/bamtools **Available Versions**:: 2.5.1-GCC-8.3.0 2.5.2-GCC-11.2.0 2.5.1-GCC-9.3.0 2.5.2-GCC-11.3.0 2.5.1-GCC-10.2.0 BayeScEnv --------- **Description** BayeScEnv is a Fst-based, genome-scan method that uses environmental variables to detectlocal adaptation. **More Information** https://github.com/devillemereuil/bayescenv **Available Versions**:: 1.1-GCC-8.3.0 BayesTraits ----------- **Description** BayesTraits is a computer package for performing analyses of trait evolution among groups of species for which a phylogeny or sample of phylogenies is available. This new package incoporates our earlier and separate programes Multistate, Discrete and Continuous. BayesTraits can be applied to the analysis of traits that adopt a finite number of discrete states, or to the analysis of continuously varying traits. Hypotheses can be tested about models of evolution, about ancestral states and about correlations among pairs of traits. **More Information** http://www.evolution.reading.ac.uk/BayesTraitsV1.html **Available Versions**:: 2.0-Beta-Linux64 Bazel ----- **Description** Bazel is a build tool that builds code quickly and reliably.It is used to build the majority of Google's software. **More Information** https://bazel.io/ **Available Versions**:: 4.2.2-GCCcore-11.2.0 5.3.0-GCCcore-11.3.0 3.6.0-GCCcore-9.3.0 3.7.2-GCCcore-10.3.0 5.1.1-GCCcore-11.3.0 6.1.0-GCCcore-12.3.0 3.7.2-GCCcore-11.2.0 3.7.2-GCCcore-10.2.0 6.1.0-GCCcore-12.2.0 Beagle ------ **Description** Beagle is a software package for phasing genotypes and for imputing ungenotyped markers. **More Information** https://faculty.washington.edu/browning/beagle/beagle.html **Available Versions**:: 5.4.22Jul22.46e-Java-11 Beast ----- **Description** BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. **More Information** http://beast2.org/ **Available Versions**:: 2.5.2-GCC-7.3.0-2.30 2.7.3-GCC-11.3.0 2.7.7-GCC-11.3.0 2.5.2-GCC-8.2.0-2.31.1 BeautifulSoup ------------- **Description** Beautiful Soup is a Python library designed for quick turnaround projects like screen-scraping. **More Information** https://www.crummy.com/software/BeautifulSoup **Available Versions**:: 4.10.0-GCCcore-11.3.0 4.12.2-GCCcore-12.3.0 Bio-SearchIO-hmmer ------------------ **Description** Code to parse output from hmmsearch, hmmscan, phmmer and nhmmer, compatiblewith both version 2 and version 3 of the HMMER package from http://hmmer.org. **More Information** https://metacpan.org/pod/Bio::SearchIO::hmmer3 **Available Versions**:: 1.7.3-GCC-11.2.0 1.7.3-GCC-12.3.0 1.7.3-GCC-10.3.0 BioPerl ------- **Description** Bioperl is the product of a community effort to produce Perl code which is useful in biology. Examples include Sequence objects, Alignment objects and database searching objects. **More Information** https://bioperl.org/ **Available Versions**:: 1.7.8-GCCcore-12.3.0 1.7.8-GCCcore-10.3.0 1.7.7-GCCcore-9.3.0 1.7.8-GCCcore-11.3.0 1.7.8-GCCcore-11.2.0 Biopython --------- **Description** Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics. **More Information** https://www.biopython.org **Available Versions**:: 1.78-fosscuda-2020b 1.79-foss-2022a 1.79-foss-2021b 1.72-foss-2018b-Python-2.7.15 1.83-gfbf-2023a 1.79-foss-2021a 1.83-foss-2023a 1.78-intel-2020a-Python-3.8.2 1.84-gfbf-2023b 1.75-foss-2019b-Python-3.7.4 Bismark ------- **Description** A tool to map bisulfite converted sequence reads and determine cytosine methylation states **More Information** https://www.bioinformatics.babraham.ac.uk/projects/bismark/ **Available Versions**:: 0.23.1-foss-2021b Bison ----- **Description** Bison is a general-purpose parser generator that converts an annotated context-free grammar into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables. **More Information** https://www.gnu.org/software/bison **Available Versions**:: 3.8.2-GCCcore-11.3.0 3.8.2-GCCcore-14.3.0 3.7.6 3.8.2-GCCcore-12.2.0 3.8.2-GCCcore-13.1.0 3.0.5-GCCcore-7.3.0 3.8.2-GCCcore-13.3.0 3.0.5-GCCcore-8.2.0 3.5.3 3.0.4-GCCcore-8.1.0 3.5.3-GCCcore-9.3.0 3.0.5 3.7.1-GCCcore-10.2.0 3.7.1 3.0.5-GCCcore-8.1.0 3.3.2-GCCcore-8.3.0 3.7.6-GCCcore-11.2.0 3.8.2-GCCcore-12.3.0 3.3.2 3.8.2 3.3.2-GCCcore-9.3.0 3.8.2-GCCcore-14.2.0 3.8.2-GCCcore-13.2.0 3.8.2-GCCcore-15.1.0 3.7.6-GCCcore-10.3.0 3.0.4-GCCcore-7.3.0 3.0.4 Blender ------- **Description** Blender is the free and open source 3D creation suite. It supports the entirety of the 3D pipeline-modeling, rigging, animation, simulation, rendering, compositing and motion tracking, even video editing and game creation. **More Information** https://www.blender.org/ **Available Versions**:: 4.0.1-linux-x86_64-CUDA-12.0.0 Blosc ----- **Description** Blosc, an extremely fast, multi-threaded, meta-compressor library **More Information** https://www.blosc.org/ **Available Versions**:: 1.21.0-GCCcore-10.3.0 1.21.3-GCCcore-11.3.0 Blosc2 ------ **Description** Blosc, an extremely fast, multi-threaded, meta-compressor library **More Information** https://www.blosc.org/ **Available Versions**:: 2.6.1-GCCcore-11.3.0 Bonnie++ -------- **Description** Enhanced performance Test of Filesystem I/O **More Information** https://www.coker.com.au/bonnie++ **Available Versions**:: 2.00a-GCC-10.3.0 Boost ----- **Description** Boost provides free peer-reviewed portable C++ source libraries. **More Information** http://www.boost.org/ **Available Versions**:: 1.70.0-gompi-2019a 1.82.0-GCC-12.3.0 1.81.0-GCC-12.2.0 1.71.0-gompi-2019b 1.74.0-iccifort-2020.4.304 1.85.0-GCC-13.3.0 1.72.0-iimpi-2021b 1.83.0-GCC-13.2.0 1.88.0-GCC-14.3.0 1.76.0-intel-compilers-2021.2.0 1.77.0-GCC-11.2.0 1.72.0-iimpi-2020a 1.79.0-GCC-11.3.0 1.77.0-intel-compilers-2021.4.0 1.74.0-GCC-10.2.0 1.88.0-GCC-14.2.0 1.76.0-GCC-10.3.0 1.71.0-gompic-2019b 1.67.0-fosscuda-2018b 1.72.0-gompi-2020a 1.67.0-foss-2018b 1.79.0-GCC-11.2.0 Boost.MPI --------- **Description** Boost provides free peer-reviewed portable C++ source libraries. **More Information** https://www.boost.org/ **Available Versions**:: 1.82.0-gompi-2023a 1.77.0-gompi-2023a 1.79.0-gompi-2022a Boost.Python ------------ **Description** Boost.Python is a C++ library which enables seamless interoperability between C++ and the Python programming language. **More Information** https://boostorg.github.io/python **Available Versions**:: 1.71.0-gompi-2019b 1.77.0-GCC-11.2.0 1.67.0-fosscuda-2018b-Python-2.7.15 1.71.0-gompic-2019b 1.67.0-foss-2018b-Python-2.7.15 1.82.0-GCC-12.3.0 1.72.0-gompi-2020a 1.79.0-GCC-11.3.0 1.70.0-gompi-2019a Bowtie ------ **Description** Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome. **More Information** http://bowtie-bio.sourceforge.net/index.shtml **Available Versions**:: 1.2.3-GCC-9.3.0 1.3.1-GCC-11.2.0 Bowtie2 ------- **Description** Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes. **More Information** http://bowtie-bio.sourceforge.net/bowtie2/index.shtml **Available Versions**:: 2.4.1-GCC-9.3.0 2.3.5.1-GCC-8.3.0 2.3.4.2-foss-2018b 2.4.5-GCC-11.3.0 2.5.1-GCC-12.3.0 2.4.4-GCC-10.3.0 2.5.4-GCC-13.2.0 2.4.5-GCC-11.2.0 2.4.4-GCC-11.2.0 Brotli ------ **Description** Brotli is a generic-purpose lossless compression algorithm that compresses data using a combination of a modern variant of the LZ77 algorithm, Huffman coding and 2nd order context modeling, with a compression ratio comparable to the best currently available general-purpose compression methods. It is similar in speed with deflate but offers more dense compression.The specification of the Brotli Compressed Data Format is defined in RFC 7932. **More Information** https://github.com/google/brotli **Available Versions**:: 1.0.9-GCCcore-12.3.0 1.1.0-GCCcore-13.2.0 1.0.9-GCCcore-10.2.0 1.0.9-GCCcore-10.3.0 1.1.0-GCCcore-13.3.0 1.0.9-GCCcore-11.3.0 1.1.0-GCCcore-14.2.0 1.0.9-GCCcore-12.2.0 1.0.9-GCCcore-11.2.0 Brunsli ------- **Description** Brunsli is a lossless JPEG repacking library. **More Information** https://github.com/google/brunsli/ **Available Versions**:: 0.1-GCCcore-13.2.0 0.1-GCCcore-13.3.0 0.1-GCCcore-11.3.0 0.1-GCCcore-12.3.0 CASA ---- **Description** CASA, the Common Astronomy Software Applications package, is the primary data processing software for the Atacama LargeMillimeter/submillimeter Array (ALMA) and NSF's Karl G. Jansky Very Large Array (VLA), and is frequently used also forother radio telescopes. The CASA software can process data from both single-dish and aperture-synthesis telescopes, andone of its core functionalities is to support the data reduction and imaging pipelines for ALMA, VLA and the VLA SkySurvey (VLASS). **More Information** https://casa.nrao.edu/ **Available Versions**:: 6.5.5-21-py3.8 CASTEP ------ **Description** CASTEP is a leading code for calculating the properties of materials from first principles. Using density functional theory, it can simulate a wide range of properties of materialsproprieties including energetics, structure at the atomic level, vibrational properties, electronic response properties etc. In particular it has a wide range of spectroscopic features that link directly to experiment, such as infra-red and Raman spectroscopies, NMR, and core level spectra. **More Information** http://www.castep.org **Available Versions**:: 16.11-info 21.11-info CCL --- **Description** Clozure CL (often called CCL for short) is a free Common Lisp implementation with a long history. Some distinguishing features of the implementation include fast compilation speed, native threads, a precise, generational, compacting garbage collector, and a convenient foreign-function interface. **More Information** https://ccl.clozure.com/ **Available Versions**:: 1.12.2-GCCcore-11.3.0 CD-HIT ------ **Description** CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences. **More Information** https://github.com/weizhongli/cdhit/wiki **Available Versions**:: 4.8.1-GCC-11.3.0 4.8.1-GCC-11.2.0 4.8.1-GCC-10.2.0 4.8.1-GCC-10.3.0 4.8.1-GCC-12.3.0 CDO --- **Description** CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data. **More Information** https://code.zmaw.de/projects/cdo **Available Versions**:: 1.9.10-gompi-2020b 2.2.2-gompi-2023b CESM-deps --------- **Description** CESM is a fully-coupled, community, global climate model thatprovides state-of-the-art computer simulations of the Earth's past, present,and future climate states. **More Information** https://www.cesm.ucar.edu/models/cesm2/ **Available Versions**:: 2-foss-2021b CFITSIO ------- **Description** CFITSIO is a library of C and Fortran subroutines for reading and writing data files inFITS (Flexible Image Transport System) data format. **More Information** https://heasarc.gsfc.nasa.gov/fitsio/ **Available Versions**:: 4.4.1-GCCcore-13.3.0 4.3.0-GCCcore-11.3.0 3.48-GCCcore-9.3.0 3.47-GCCcore-8.3.0 4.2.0-GCCcore-11.3.0 4.3.0-GCCcore-12.3.0 4.3.1-GCCcore-13.2.0 3.49-GCCcore-11.2.0 3.49-GCCcore-10.2.0 CGAL ---- **Description** The goal of the CGAL Open Source Project is to provide easy access to efficient and reliable geometric algorithms in the form of a C++ library. **More Information** https://www.cgal.org/ **Available Versions**:: 4.14.3-gompi-2020a-Python-3.8.2 4.14.3-iimpi-2020a-Python-3.8.2 5.6-GCCcore-12.3.0 4.14.1-foss-2019b-Python-3.7.4 4.14.3-gompi-2022a 4.14.3-gompi-2021a CIF2Cell -------- **Description** CIF2Cell is a tool to generate the geometrical setupfor various electronic structure codes from a CIF (CrystallographicInformation Framework) file. The program currently supports output for anumber of popular electronic structure programs, including ABINIT, ASE,CASTEP, CP2K, CPMD, CRYSTAL09, Elk, EMTO, Exciting, Fleur, FHI-aims,Hutsepot, MOPAC, Quantum Espresso, RSPt, Siesta, SPR-KKR, VASP. Alsoexports some related formats like .coo, .cfg and .xyz-files. **More Information** https://sourceforge.net/projects/cif2cell **Available Versions**:: 2.0.0a3-GCCcore-9.3.0-Python-3.8.2 CLHEP ----- **Description** The CLHEP project is intended to be a set of HEP-specific foundation and utility classes such as random generators, physics vectors, geometry and linear algebra. CLHEP is structured in a set of packages independent of any external package. **More Information** https://proj-clhep.web.cern.ch/proj-clhep/ **Available Versions**:: 2.4.6.2-GCC-11.2.0 2.4.5.1-GCC-11.2.0 2.4.6.2-GCC-11.3.0 2.4.7.1-GCC-13.2.0 2.4.6.4-GCC-12.2.0 2.4.4.0-GCC-10.2.0 2.4.7.1-GCC-12.3.0 CLUMPP ------ **Description** CLUMPP is a program that deals with label switching and multimodality problemsin population-genetic cluster analyses. **More Information** https://rosenberglab.stanford.edu/clumpp.html **Available Versions**:: 1.1.2-Linux64 CMake ----- **Description** CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software. **More Information** https://www.cmake.org **Available Versions**:: 3.22.1-GCCcore-11.2.0 3.16.4-GCCcore-9.3.0 3.29.3-GCCcore-13.3.0 3.24.3-GCCcore-12.2.0 3.27.6-GCCcore-13.2.0 3.21.1-GCCcore-11.2.0 3.12.1-GCCcore-7.3.0 3.20.1-GCCcore-10.3.0 3.15.3-GCCcore-8.3.0 3.13.3-GCCcore-8.2.0 3.12.1-GCCcore-10.2.0 3.23.1-GCCcore-11.3.0 3.9.4-GCCcore-9.3.0 3.31.8 3.11.4-GCCcore-7.3.0 3.26.3-GCCcore-12.3.0 3.12.1 3.24.3-GCCcore-11.3.0 4.0.3-GCCcore-14.3.0 3.18.4-GCCcore-10.2.0 3.15.3-GCCcore-7.3.0 3.18.4 3.31.3-GCCcore-14.2.0 3.26.3-GCCcore-13.2.0 CP2K ---- **Description** CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and classical pair and many-body potentials. **More Information** http://www.cp2k.org/ **Available Versions**:: 6.1-foss-2019b 6.1-foss-2020a 6.1-foss-2019a 6.1-intel-2020a 7.1-intel-2020a 8.2-foss-2021a 7.1-intel-2020b 2023.1-foss-2023a 8.1-foss-2020a 9.1-foss-2022a CPLEX ----- **Available Versions**:: 12.9.0 CREST ----- **Description** CREST is an utility/driver program for the xtb program. Originally it was designed as conformer sampling program, hence the abbreviation Conformer–Rotamer Ensemble Sampling Tool, but now offers also some utility functions for calculations with the GFNn–xTB methods. Generally the program functions as an IO based OMP scheduler (i.e., calculations are performed by the xtb program) and tool for the creation and analysation of structure ensembles. **More Information** https://xtb-docs.readthedocs.io/en/latest/crest.html **Available Versions**:: 2.11-intel-2021a CUDA ---- **Description** CUDA (formerly Compute Unified Device Architecture) is a parallel computing platform and programming model created by NVIDIA and implemented by the graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs. **More Information** https://developer.nvidia.com/cuda-toolkit **Available Versions**:: 11.3.1 11.1.1-iccifort-2020.4.304 11.7.0 11.2.2-GCC-10.3.0 11.3.1-GCC-10.3.0 12.4.0 11.4.1-GCC-10.3.0 12.0.0 9.2.88-GCC-7.3.0-2.30 12.6.0 12.9.0 11.1.1-GCC-10.2.0 11.6.0 11.0.2-GCC-9.3.0 12.1.1 12.3.0 10.1.243-GCC-8.3.0 10.1.243-iccifort-2019.5.281 11.4.1 11.2.2 11.5.0 11.8.0 11.5.1 CUDAcore -------- **Description** CUDA (formerly Compute Unified Device Architecture) is a parallel computing platform and programming model created by NVIDIA and implemented by the graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs. **More Information** https://developer.nvidia.com/cuda-toolkit **Available Versions**:: 11.2.2 11.0.2 11.1.1 CUnit ----- **Description** Automated testing framework for C. **More Information** https://sourceforge.net/projects/cunit/ **Available Versions**:: 2.1-3-GCCcore-11.3.0 2.1-3-GCCcore-12.3.0 2.1-3-GCCcore-11.2.0 Cactus ------ **Description** Cactus is a reference-free whole-genome alignment program, as well as a pagenome graph construction toolkit. **More Information** https://github.com/ComparativeGenomicsToolkit/cactus **Available Versions**:: 2.4.0 CapnProto --------- **Description** Cap’n Proto is an insanely fast data interchange format and capability-based RPC system. **More Information** https://capnproto.org **Available Versions**:: 0.7.0-GCCcore-7.3.0 1.1.0-GCCcore-13.3.0 Cartopy ------- **Description** Cartopy is a Python package designed to make drawing maps for data analysis and visualisation easy. **More Information** https://scitools.org.uk/cartopy/docs/latest/ **Available Versions**:: 0.20.3-foss-2021b 0.22.0-foss-2023a Catch2 ------ **Description** A modern, C++-native, header-only, test framework for unit-tests, TDD and BDD - using C++11, C++14, C++17 and later **More Information** https://github.com/catchorg/Catch2 **Available Versions**:: 2.13.10-GCCcore-13.3.0 3.8.0-GCCcore-13.3.0 2.13.10-GCCcore-14.2.0 2.13.9-GCCcore-12.2.0 2.13.9-GCCcore-12.3.0 2.13.10-GCCcore-14.3.0 2.13.9 2.13.9-GCCcore-13.2.0 CellRanger ---------- **Description** Cell Ranger is a set of analysis pipelines that process Chromium single-cell RNA-seq output to align reads, generate gene-cell matrices and perform clustering and gene expression analysis. **More Information** https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger **Available Versions**:: 9.0.1 6.0.2 8.0.1 7.0.1 5.0.0 CellRanger-ATAC --------------- **Description** Cell Ranger ATAC is a set of analysis pipelines that process Chromium Single Cell ATAC data. **More Information** https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac **Available Versions**:: 2.1.0 Cellpose -------- **Description** a generalist algorithm for cellular segmentation **More Information** https://www.cellpose.org **Available Versions**:: 2.2.2-foss-2022a Cereal ------ **Description** cereal is a header-only C++11 serialization library. cereal takes arbitrary data types and reversibly turns them into different representations, such as compact binary encodings, XML, or JSON. cereal was designed to befast, light-weight, and easy to extend - it has no external dependencies and can be easily bundled with other code or used standalone. **More Information** https://uscilab.github.io/cereal/ **Available Versions**:: 1.3.2 CharLS ------ **Description** CharLS is a C++ implementation of the JPEG-LS standard for lossless and near-lossless imagecompression and decompression. JPEG-LS is a low-complexity image compression standard that matches JPEG 2000compression ratios. **More Information** https://github.com/team-charls/charls **Available Versions**:: 2.4.1-GCCcore-11.3.0 CheMPS2 ------- **Description** CheMPS2 is a scientific library which contains a spin-adapted implementation of thedensity matrix renormalization group (DMRG) for ab initio quantum chemistry. **More Information** https://github.com/SebWouters/CheMPS2 **Available Versions**:: 1.8.9-foss-2019a 1.8.11-foss-2021b 1.8.11-intel-2021a Check ----- **Description** Check is a unit testing framework for C. It features a simple interface fordefining unit tests, putting little in the way of the developer. Tests arerun in a separate address space, so both assertion failures and code errorsthat cause segmentation faults or other signals can be caught. Test resultsare reportable in the following: Subunit, TAP, XML, and a generic loggingformat. **More Information** https://libcheck.github.io/check/ **Available Versions**:: 0.15.2-GCCcore-9.3.0 0.15.2-GCCcore-11.2.0 0.15.2-GCCcore-10.3.0 0.15.2-GCCcore-10.2.0 Clang ----- **Description** C, C++, Objective-C compiler, based on LLVM. Does not include C++ standard library -- use libstdc++ from GCC. **More Information** https://clang.llvm.org/ **Available Versions**:: 16.0.6-GCCcore-12.3.0 16.0.0-GCCcore-11.3.0 12.0.1-GCCcore-11.2.0 13.0.1-GCCcore-11.3.0 16.0.0-GCCcore-12.2.0 ClermonTyping ------------- **Available Versions**:: 2023 ClonalFrameML ------------- **Description** Efficient Inference of Recombination in Whole Bacterial Genomes **More Information** https://github.com/xavierdidelot/ClonalFrameML **Available Versions**:: 1.12-foss-2022a ClustalW2 --------- **Description** ClustalW2 is a general purpose multiple sequence alignment program for DNA or proteins. **More Information** https://www.ebi.ac.uk/Tools/msa/clustalw2/ **Available Versions**:: 2.1-intel-2020a CoCoALib -------- **Description** CoCoALib is a free GPL3 C++ library for doing Computations in Commutative Algebra. **More Information** https://cocoa.dima.unige.it/cocoa/cocoalib/ **Available Versions**:: 0.99818-GCC-11.3.0 Con-old ------- **Available Versions**:: 3.1.12 ConnectomeWorkbench ------------------- **Description** Connectome Workbench is an open source, freely available visualization and discovery tool used to map neuroimaging data, especially data generated by the Human Connectome Project. **More Information** https://www.humanconnectome.org/software/connectome-workbench **Available Versions**:: 1.5.0-GCCcore-10.3.0 CoordgenLibs ------------ **Description** Schrodinger-developed 2D Coordinate Generation **More Information** https://github.com/schrodinger/coordgenlibs **Available Versions**:: 3.0.1-gompi-2021a 3.0.1-gompi-2019b CppUnit ------- **Description** CppUnit is the C++ port of the famous JUnit framework for unit testing. **More Information** https://freedesktop.org/wiki/Software/cppunit/ **Available Versions**:: 1.15.1-GCCcore-11.3.0 1.15.1-GCCcore-10.3.0 CubeGUI ------- **Description** Cube, which is used as performance report explorer for Scalasca and Score-P, is a generic tool for displaying a multi-dimensional performance space consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree can be collapsed or expanded to achieve the desired level of granularity. This module provides the Cube graphical report explorer. **More Information** https://www.scalasca.org/software/cube-4.x/download.html **Available Versions**:: 4.8-GCCcore-11.3.0 4.4.4-GCCcore-9.3.0 CubeLib ------- **Description** Cube, which is used as performance report explorer for Scalasca and Score-P, is a generic tool for displaying a multi-dimensional performance space consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree can be collapsed or expanded to achieve the desired level of granularity. This module provides the Cube general purpose C++ library component and command-line tools. **More Information** https://www.scalasca.org/software/cube-4.x/download.html **Available Versions**:: 4.8-GCCcore-11.3.0 4.4.4-GCCcore-9.3.0 CubeWriter ---------- **Description** Cube, which is used as performance report explorer for Scalasca and Score-P, is a generic tool for displaying a multi-dimensional performance space consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree can be collapsed or expanded to achieve the desired level of granularity. This module provides the Cube high-performance C writer library component. **More Information** https://www.scalasca.org/software/cube-4.x/download.html **Available Versions**:: 4.4.3-GCCcore-9.3.0 4.8-GCCcore-11.3.0 Cython ------ **Description** Cython is an optimising static compiler for both the Python programminglanguage and the extended Cython programming language (based on Pyrex). **More Information** https://cython.org/ **Available Versions**:: 3.1.2-GCCcore-14.3.0 3.1.1-GCCcore-14.2.0 3.0.10-GCCcore-13.2.0 0.29.22-GCCcore-10.2.0 0.27.3-GCCcore-12.3.0-Python-2.7.18 3.0.8-GCCcore-12.3.0 3.0.10-GCCcore-13.3.0 DB -- **Description** Berkeley DB enables the development of custom data management solutions, without the overhead traditionally associated with such custom projects. **More Information** https://www.oracle.com/technetwork/products/berkeleydb **Available Versions**:: 18.1.40-GCCcore-10.3.0 18.1.32-GCCcore-8.2.0 18.1.40-GCCcore-12.2.0 18.1.40-GCCcore-11.2.0 18.1.40-GCCcore-12.3.0 18.1.40-GCCcore-10.2.0 18.1.32-GCCcore-7.3.0 18.1.32-GCCcore-8.3.0 18.1.32-GCCcore-9.3.0 18.1.40-GCCcore-11.3.0 DB_File ------- **Description** Perl5 access to Berkeley DB version 1.x. **More Information** https://perldoc.perl.org/DB_File.html **Available Versions**:: 1.859-GCCcore-12.3.0 1.856-GCCcore-10.3.0 1.835-GCCcore-9.3.0 1.857-GCCcore-11.2.0 1.858-GCCcore-11.3.0 DBus ---- **Description** D-Bus is a message bus system, a simple way for applications to talk to one another. In addition to interprocess communication, D-Bus helps coordinate process lifecycle; it makes it simple and reliable to code a "single instance" application or daemon, and to launch applications and daemons on demand when their services are needed. **More Information** https://dbus.freedesktop.org/ **Available Versions**:: 1.13.12-GCCcore-8.3.0 1.13.8-GCCcore-8.2.0 1.14.0-GCCcore-11.3.0 1.15.8-GCCcore-13.3.0 1.13.18-GCCcore-10.2.0 1.13.6-GCCcore-7.3.0 1.15.2-GCCcore-12.2.0 1.15.4-GCCcore-12.3.0 1.15.8-GCCcore-13.2.0 1.13.18-GCCcore-11.2.0 1.16.2-GCCcore-14.2.0 1.13.12-GCCcore-9.3.0 1.13.18-GCCcore-10.3.0 DFT-D3 ------ **Description** DFT-D3 implements a dispersion correction for density functionals, Hartree-Fock and semi-empirical quantum chemical methods. **More Information** https://www.chemie.uni-bonn.de/grimme/de/software/dft-d3 **Available Versions**:: 3.2.0-intel-compilers-2021.2.0 3.2.0-intel-2023a DIALS ----- **Description** X-ray crystallography for structural biology has benefited greatly from a number of advances in recent years including high performance pixel array detectors, new beamlines capable of delivering micron and sub-micron focus and new light sources such as XFELs. The DIALS project is a collaborative endeavour to develop new diffraction integration software to meet the data analysis requirements presented by these recent advances. There are three end goals: to develop an extensible framework for the development of algorithms to analyse X-ray diffraction data; the implementation of algorithms within this framework and finally a set of user facing tools using these algorithms to allow integration of data from diffraction experiments on synchrotron and free electron sources. **More Information** https://dials.github.io **Available Versions**:: 3.11.2 DIAMOND ------- **Description** Accelerated BLAST compatible local sequence aligner **More Information** https://github.com/bbuchfink/diamond **Available Versions**:: 2.0.15-GCC-11.3.0 0.9.30-iccifort-2019.5.281 2.1.6-GCC-11.3.0 0.9.30-GCC-8.3.0 DL_POLY_4 --------- **Description** DL_POLY is a general purpose classical molecular dynamics (MD) simulation software **More Information** https://www.scd.stfc.ac.uk/Pages/DL_POLY.aspx **Available Versions**:: 5.1.0-foss-2023a 5.0.0-intel-2020b DL_POLY_Classic --------------- **Description** DL_POLY Classic is a general purpose (parallel and serial)molecular dynamics simulation package. **More Information** https://gitlab.com/DL_POLY_Classic/dl_poly **Available Versions**:: 1.10-foss-2019b DOLFIN ------ **Description** DOLFIN is the C++/Python interface of FEniCS, providing a consistent PSE (Problem Solving Environment) for ordinary and partial differential equations. **More Information** https://bitbucket.org/fenics-project/dolfin **Available Versions**:: 2019.1.0.post0-foss-2019b-Python-3.7.4 DendroPy -------- **Description** A Python library for phylogenetics and phylogenetic computing: reading, writing, simulation, processing and manipulation of phylogenetic trees (phylogenies) and characters. **More Information** https://dendropy.org/ **Available Versions**:: 4.5.2-GCCcore-11.2.0 4.6.1-GCCcore-12.3.0 Doxygen ------- **Description** Doxygen is a documentation system for C++, C, Java, Objective-C, Python, IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D. **More Information** https://www.doxygen.org **Available Versions**:: 1.11.0-GCCcore-13.3.0 1.8.16-GCCcore-8.3.0 1.9.4-GCCcore-11.3.0 1.9.1-GCCcore-11.2.0 1.9.5-GCCcore-12.2.0 1.8.14-GCCcore-7.3.0 1.9.1-GCCcore-10.3.0 1.8.20-GCCcore-10.2.0 1.9.8-GCCcore-13.2.0 1.8.17-GCCcore-9.3.0 1.14.0-GCCcore-14.2.0 1.8.15-GCCcore-8.2.0 1.9.7-GCCcore-12.3.0 Dsuite ------ **Description** Fast calculation of the ABBA-BABA statistics across many populations/species **More Information** https://github.com/millanek/Dsuite **Available Versions**:: 20231103-GCC-11.3.0 E-ANTIC ------- **Description** E-ANTIC is a C/C++ library to deal with real embedded number fields built ontop of ANTIC (https://github.com/wbhart/antic). Its aim is to have as fast aspossible exact arithmetic operations and comparisons. **More Information** https://github.com/flatsurf/e-antic **Available Versions**:: 1.3.0-gfbf-2022a EGSnrc ------ **Available Versions**:: 2025 EIGENSOFT --------- **Description** The EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. 2006) and our EIGENSTRAT stratification correction method (Price et al. 2006). The EIGENSTRAT method uses principal components analysis to explicitly model ancestry differences between cases and controls along continuous axes of variation; the resulting correction is specific to a candidate marker’s variation in frequency across ancestral populations, minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT package has a built-in plotting script and supports multiple file formats and quantitative phenotypes. **More Information** https://www.hsph.harvard.edu/alkes-price/software/ **Available Versions**:: 7.2.1-foss-2019b ELPA ---- **Description** Eigenvalue SoLvers for Petaflop-Applications. **More Information** https://elpa.mpcdf.mpg.de **Available Versions**:: 2021.11.001-foss-2022a 2020.11.001-foss-2020b 2021.05.001-intel-2021a 2019.11.001-intel-2020a 2023.05.001-foss-2023a 2024.05.001-foss-2024a 2020.11.001-intel-2020b 2019.11.001-foss-2020a 2021.11.001-intel-2022a 2023.05.001-intel-2023a ESM-2 ----- **Description** ESM-2 outperforms all tested single-sequence protein language models across a range of structure prediction tasks. ESMFold harnesses the ESM-2 language model to generate accurate structure predictions end to end directly from the sequence of a protein. **More Information** https://github.com/facebookresearch/esm **Available Versions**:: 2.0.0-foss-2021a-CUDA-11.3.1 2.0.0-foss-2021a 2.0.0-foss-2022a-CUDA-11.8.0 ESMF ---- **Description** The Earth System Modeling Framework (ESMF) is a suite of software tools for developing high-performance, multi-component Earth science modeling applications. **More Information** https://www.earthsystemcog.org/projects/esmf/ **Available Versions**:: 8.2.0-foss-2021b 8.3.0-foss-2022a 8.0.1-foss-2020b 8.1.1-foss-2021a EVcouplings ----------- **Description** Predict protein structure, function and mutations using evolutionary sequence covariation. **More Information** https://github.com/debbiemarkslab/EVcouplings **Available Versions**:: 0.1.1-foss-2023a EasyBuild --------- **Description** EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way. **More Information** https://easybuilders.github.io/easybuild **Available Versions**:: 4.5.4 4.5.0 4.9.0 4.7.1 4.5.2 4.5.5 4.4.1 4.5.1 5.1.2 4.4.2 4.6.1 4.8.0 5.1.1 4.9.2 5.0.0 4.3.3 5.1.0 4.9.1 4.8.2 4.6.0 4.5.3 4.3.4 4.8.1 4.9.4 4.7.0 4.6.2 4.7.2 4.4.0 4.9.3 Eigen ----- **Description** Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms. **More Information** https://eigen.tuxfamily.org **Available Versions**:: 3.4.0-GCCcore-11.2.0 3.4.0-GCCcore-9.3.0 3.3.8-GCCcore-10.2.0 3.4.0-GCCcore-10.2.0 3.4.0-GCCcore-10.3.0 3.3.7-GCCcore-9.3.0 3.3.9-GCCcore-10.3.0 3.4.0-GCCcore-13.3.0 3.4.0-GCCcore-13.2.0 3.4.0-GCCcore-12.2.0 3.4.0-GCCcore-11.3.0 3.3.9-GCCcore-11.2.0 3.4.0-GCCcore-14.3.0 3.4.0-GCCcore-12.3.0 3.3.7 3.3.4 3.4.0-GCCcore-14.2.0 Elk --- **Description** An all-electron full-potential linearisedaugmented-plane wave (FP-LAPW) code with many advanced features. Writtenoriginally at Karl-Franzens-Universität Graz as a milestone of theEXCITING EU Research and Training Network, the code is designed to be assimple as possible so that new developments in the field of densityfunctional theory (DFT) can be added quickly and reliably. **More Information** http://elk.sourceforge.net/ **Available Versions**:: 7.0.12-foss-2020b Exonerate --------- **Description** Exonerate is a generic tool for pairwise sequence comparison. It allows you to align sequences using a many alignment models, using either exhaustive dynamic programming, or a variety of heuristics. **More Information** https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate **Available Versions**:: 2.4.0-GCC-8.3.0 Extrae ------ **Description** Extrae is the core instrumentation package developed bythe Performance Tools group at BSC. Extrae is capable of instrumentingapplications based on MPI, OpenMP, pthreads, CUDA1, OpenCL1, and StarSs1using different instrumentation approaches. The information gathered byExtrae typically includes timestamped events of runtime calls,performance counters and source code references. Besides, Extraeprovides its own API to allow the user to manually instrument his or herapplication. **More Information** https://www.bsc.es/computer-sciences/performance-tools **Available Versions**:: 3.8.0-gompi-2020b FCM --- **Description** FCM is a set of tools for managing and building source code. **More Information** http://www.metoffice.gov.uk/research/collaboration/fcm **Available Versions**:: 2019.09.0 2.3.1 FEniCS ------ **Description** FEniCS is a computing platform for solving partial differential equations (PDEs). **More Information** https://fenicsproject.org/ **Available Versions**:: 2019.1.0-foss-2019b-Python-3.7.4 FFC --- **Description** The FEniCS Form Compiler (FFC) is a compiler for finite element variational forms. **More Information** https://bitbucket.org/fenics-project/ffc **Available Versions**:: 2019.1.0.post0-foss-2019b-Python-3.7.4 FFTW ---- **Description** FFTW is a C subroutine library for computing the discrete Fourier transform (DFT)in one or more dimensions, of arbitrary input size, and of both real and complex data. **More Information** https://www.fftw.org **Available Versions**:: 3.3.10-gompi-2021b 3.3.8-gompic-2019b 3.3.8-gompic-2020a 3.3.10-GCC-13.3.0 3.3.8-intel-2020b 3.3.8-gompic-2020b 3.3.10-GCC-14.3.0 3.3.10-GCC-13.2.0 3.3.8-gompi-2020a 3.3.10-GCC-11.3.0 3.3.8-gompi-2019b 3.3.8-gompi-2020b 3.3.10-GCC-12.2.0 3.3.10-intel-compilers-2023.1.0 3.3.8-gompi-2019a 3.3.10-GCC-12.3.0 3.3.9-intel-2021a 3.3.8-gompi-2018b 3.3.9-gompi-2021a 3.3.10-NVHPC-22.7-CUDA-11.7.0 3.3.8-intel-2020a 3.3.8-gompic-2018b 3.3.10-GCC-14.2.0 FFTW.MPI -------- **Description** FFTW is a C subroutine library for computing the discrete Fourier transform (DFT)in one or more dimensions, of arbitrary input size, and of both real and complex data. **More Information** https://www.fftw.org **Available Versions**:: 3.3.10-gompi-2022b 3.3.10-gompi-2024a 3.3.10-gompi-2022.10 3.3.10-nvompi-2022.07 3.3.10-gompi-2025a 3.3.10-gompi-2023a 3.3.10-gompi-2023.09 3.3.10-gompi-2025b 3.3.10-gompi-2024.05 3.3.10-gompi-2022a 3.3.10-iimpi-2023a 3.3.10-gompi-2022.05 3.3.10-gompi-2023b FFmpeg ------ **Description** A complete, cross-platform solution to record, convert and stream audio and video. **More Information** https://www.ffmpeg.org/ **Available Versions**:: 4.2.2-GCCcore-9.3.0 7.0.2-GCCcore-13.3.0 6.0-GCCcore-13.2.0 7.1.1-GCCcore-14.2.0 4.4.2-GCCcore-11.3.0 4.3.1-GCCcore-10.2.0 6.0-GCCcore-12.3.0 4.2.1-GCCcore-8.3.0 4.3.2-GCCcore-10.3.0 5.1.2-GCCcore-12.2.0 4.3.2-GCCcore-11.2.0 4.1.3-GCCcore-8.2.0 FIAT ---- **Description** The FInite element Automatic Tabulator (FIAT) supportsgeneration of arbitrary order instances of the Lagrange elements onlines, triangles, and tetrahedra. It is also capable of generatingarbitrary order instances of Jacobi-type quadrature rules on the sameelement shapes. **More Information** https://bitbucket.org/fenics-project/fiat **Available Versions**:: 2019.1.0-foss-2019b-Python-3.7.4 FLAC ---- **Description** FLAC stands for Free Lossless Audio Codec, an audio format similar to MP3, but lossless, meaningthat audio is compressed in FLAC without any loss in quality. **More Information** https://xiph.org/flac/ **Available Versions**:: 1.4.3-GCCcore-13.2.0 1.3.3-GCCcore-11.2.0 1.4.2-GCCcore-12.3.0 1.4.2-GCCcore-12.2.0 1.3.4-GCCcore-11.3.0 1.3.3-GCCcore-10.3.0 1.3.3-GCCcore-10.2.0 1.4.3-GCCcore-13.3.0 FLASH ----- **Description** FLASH (Fast Length Adjustment of SHort reads) is a very fast and accurate software tool to merge paired-end reads from next-generation sequencing experiments. FLASH is designed to merge pairs of reads when the original DNA fragments are shorter than twice the length of reads. The resulting longer reads can significantly improve genome assemblies. They can also improve transcriptome assembly when FLASH is used to merge RNA-seq data. **More Information** https://ccb.jhu.edu/software/FLASH/ **Available Versions**:: 1.2.11-foss-2018b 2.2.00-foss-2018b 2.2.00-GCCcore-13.3.0 FLINT ----- **Description** FLINT (Fast Library for Number Theory) is a C library in support of computations in number theory. Operations that can be performed include conversions, arithmetic, computing GCDs, factoring, solving linear systems, and evaluating special functions. In addition, FLINT provides various low-level routines for fast arithmetic. FLINT is extensively documented and tested. **More Information** https://www.flintlib.org/ **Available Versions**:: 2.7.1-GCC-10.3.0 2.9.0-gfbf-2022a 3.1.1-gfbf-2023b FLTK ---- **Description** FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL and its built-in GLUT emulation. **More Information** https://www.fltk.org **Available Versions**:: 1.3.7-GCCcore-11.2.0 1.3.5-GCCcore-10.2.0 1.3.5-GCC-8.3.0 FSL --- **Description** FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data. **More Information** https://www.fmrib.ox.ac.uk/fsl/ **Available Versions**:: 6.0.6.4-ARC 6.0.5.2-ARC 6.0.3-foss-2019b-Python-3.7.4 FastME ------ **Description** FastME: a comprehensive, accurate and fast distance-based phylogeny inference program. **More Information** http://www.atgc-montpellier.fr/fastme/ **Available Versions**:: 2.1.6.2-GCC-8.3.0 FastQC ------ **Description** FastQC is a quality control application for high throughputsequence data. It reads in sequence data in a variety of formats and can eitherprovide an interactive application to review the results of several differentQC checks, or create an HTML based report which can be integrated into apipeline. **More Information** https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ **Available Versions**:: 0.11.9-Java-11 FastTree -------- **Description** FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of time and memory. **More Information** http://www.microbesonline.org/fasttree/ **Available Versions**:: 2.1.11-GCCcore-11.3.0 2.1.11-GCCcore-9.3.0 FineSTRUCTURE ------------- **Available Versions**:: 4.1.1 Fiona ----- **Description** Fiona is designed to be simple and dependable. It focuses on reading and writing datain standard Python IO style and relies upon familiar Python types and protocols such as files, dictionaries,mappings, and iterators instead of classes specific to OGR. Fiona can read and write real-world data usingmulti-layered GIS formats and zipped virtual file systems and integrates readily with other Python GISpackages such as pyproj, Rtree, and Shapely. **More Information** https://github.com/Toblerity/Fiona **Available Versions**:: 1.9.5-foss-2023a 1.8.21-foss-2021b Flask ----- **Description** Flask is a lightweight WSGI web application framework. It is designed to makegetting started quick and easy, with the ability to scale up to complexapplications.This module includes the Flask extensions: Flask-Cors **More Information** https://www.palletsprojects.com/p/flask/ **Available Versions**:: 2.2.2-GCCcore-11.3.0 1.1.2-GCCcore-10.2.0 3.0.3-GCCcore-13.3.0 2.3.3-GCCcore-12.3.0 1.1.2-GCCcore-8.3.0-Python-3.7.4 1.1.4-GCCcore-10.3.0 FlexiBLAS --------- **Description** FlexiBLAS is a wrapper library that enables the exchange of the BLAS and LAPACK implementationused by a program without recompiling or relinking it. **More Information** https://gitlab.mpi-magdeburg.mpg.de/software/flexiblas-release **Available Versions**:: 3.3.1-GCC-12.3.0 3.4.5-GCC-14.3.0 3.4.5-GCC-14.2.0 3.3.1-GCC-13.2.0 3.2.0-GCC-11.3.0 3.0.4-GCC-10.3.0 3.2.0-NVHPC-22.7-CUDA-11.7.0 3.2.1-GCC-12.2.0 3.0.4-GCC-11.2.0 3.4.4-GCC-13.3.0 Fluka ----- **Available Versions**:: 4-4.0 FreeXL ------ **Description** FreeXL is an open source library to extract valid data from within anExcel (.xls) spreadsheet. **More Information** https://www.gaia-gis.it/fossil/freexl/index **Available Versions**:: 1.0.6-GCCcore-11.2.0 1.0.6-GCCcore-12.3.0 2.0.0-GCCcore-12.3.0 1.0.5-GCCcore-8.3.0 FriBidi ------- **Description** The Free Implementation of the Unicode Bidirectional Algorithm. **More Information** https://github.com/fribidi/fribidi **Available Versions**:: 1.0.12-GCCcore-12.3.0 1.0.10-GCCcore-10.2.0 1.0.5-GCCcore-8.3.0 1.0.9-GCCcore-9.3.0 1.0.12-GCCcore-11.3.0 1.0.5-GCCcore-8.2.0 1.0.5-GCCcore-7.3.0 1.0.13-GCCcore-13.2.0 1.0.12-GCCcore-12.2.0 1.0.10-GCCcore-10.3.0 1.0.10-GCCcore-11.2.0 1.0.16-GCCcore-14.2.0 1.0.15-GCCcore-13.3.0 GATK ---- **Description** The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size. **More Information** http://www.broadinstitute.org/gatk/ **Available Versions**:: 3.8-1-Java-1.8.0_241 GCC --- **Description** The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...). **More Information** https://gcc.gnu.org/ **Available Versions**:: 15.1.0 12.3.0 10.2.0 11.2.0 14.3.0 8.1.0-2.30 14.2.0 8.2.0-2.31.1 11.3.0 9.3.0 10.3.0 13.3.0 8.3.0 13.1.0 7.3.0-2.30 12.2.0 13.2.0 GCCcore ------- **Description** The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...). **More Information** https://gcc.gnu.org/ **Available Versions**:: 14.2.0 12.2.0 10.3.0 8.3.0 11.2.0 10.2.0 15.1.0 7.3.0 8.2.0 13.3.0 11.3.0 9.3.0 13.1.0 12.1.0 12.3.0 13.2.0 14.3.0 8.1.0 GCTA ---- **Description** GCTA (Genome-wide Complex Trait Analysis) is a software package, which was initially developed to estimate the proportion of phenotypic variance explained by all genome-wide SNPs for a complex trait but has been extensively extended for many other analyses of data from genome-wide association studies (GWASs). **More Information** https://yanglab.westlake.edu.cn/software/gcta/ **Available Versions**:: 1.94.1-gfbf-2023a GConf ----- **Description** GConf is a system for storing application preferences. It is intended for user preferences; not configuration of something like Apache, or arbitrary data storage. **More Information** https://gitlab.gnome.org/iainl/gconf **Available Versions**:: 3.2.6-GCCcore-11.2.0 GDAL ---- **Description** GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for data translation and processing. **More Information** https://www.gdal.org **Available Versions**:: 3.9.0-foss-2023b 3.7.1-foss-2023a-spatialite 3.5.0-foss-2022a 3.0.0-foss-2019a-Python-2.7.15 3.2.1-fosscuda-2020b 3.3.0-foss-2021a 3.0.4-foss-2020a-Python-3.8.2 3.10.0-foss-2024a 3.3.2-foss-2021b 3.7.1-foss-2023a 3.0.4-intel-2020a-Python-3.8.2 GDRCopy ------- **Description** A low-latency GPU memory copy library based on NVIDIA GPUDirect RDMA technology. **More Information** https://github.com/NVIDIA/gdrcopy **Available Versions**:: 2.4-GCCcore-13.2.0 2.3-GCCcore-11.3.0 2.2-GCCcore-10.3.0 2.1-GCCcore-10.3.0-CUDA-11.1.1 2.1-GCCcore-10.2.0-CUDA-11.1.1 2.3.1-GCCcore-12.3.0 2.3-GCCcore-11.2.0 2.1-GCCcore-9.3.0-CUDA-11.0.2 2.3-GCCcore-12.2.0 GEOS ---- **Description** GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS) **More Information** https://trac.osgeo.org/geos **Available Versions**:: 3.9.1-GCC-10.3.0 3.6.2-foss-2018b-Python-2.7.15 3.8.1-iccifort-2020.1.217-Python-3.8.2 3.10.3-GCC-11.3.0 3.9.1-GCC-11.2.0 3.12.1-GCC-13.2.0 3.12.0-GCC-12.3.0 3.12.2-GCC-13.3.0 3.8.0-GCC-8.3.0-Python-3.7.4 3.7.2-foss-2019a-Python-2.7.15 3.6.2-foss-2018b-Python-3.6.6 3.8.1-GCC-9.3.0-Python-3.8.2 3.9.1-GCC-10.2.0 GI-DocGen --------- **Description** GI-DocGen is a document generator for GObject-based libraries. GObject isthe base type system of the GNOME project. GI-Docgen reuses theintrospection data generated by GObject-based libraries to generate the APIreference of these libraries, as well as other ancillary documentation. **More Information** https://gitlab.gnome.org/GNOME/gi-docgen **Available Versions**:: 2023.3-GCCcore-12.3.0 GL2PS ----- **Description** GL2PS: an OpenGL to PostScript printing library **More Information** https://www.geuz.org/gl2ps/ **Available Versions**:: 1.4.2-GCCcore-11.2.0 GLM --- **Description** OpenGL Mathematics (GLM) is a header only C++ mathematics library for graphicssoftware based on the OpenGL Shading Language (GLSL) specifications. **More Information** https://github.com/g-truc/glm **Available Versions**:: 0.9.9.8-GCCcore-12.3.0 0.9.9.8-GCCcore-11.3.0 0.9.9.8-GCCcore-8.3.0 0.9.9.8-GCCcore-9.3.0 GLPK ---- **Description** The GLPK (GNU Linear Programming Kit) package is intended for solving large-scale linear programming (LP), mixed integer programming (MIP), and other related problems. It is a set of routines written in ANSI C and organized in the form of a callable library. **More Information** https://www.gnu.org/software/glpk/ **Available Versions**:: 5.0-GCCcore-10.3.0 5.0-GCCcore-11.3.0 4.65-GCCcore-9.3.0 4.65-GCCcore-8.3.0 5.0-GCCcore-12.3.0 5.0-GCCcore-11.2.0 5.0-GCCcore-12.2.0 5.0-GCCcore-13.2.0 4.65-GCCcore-10.2.0 5.0-GCCcore-13.3.0 GLib ---- **Description** GLib is one of the base libraries of the GTK+ project **More Information** https://www.gtk.org/ **Available Versions**:: 2.64.1-GCCcore-9.3.0 2.68.2-GCCcore-10.3.0 2.54.3-GCCcore-7.3.0 2.72.1-GCCcore-11.3.0 2.62.0-GCCcore-8.3.0 2.85.1-GCCcore-14.2.0 2.77.1-GCCcore-12.3.0 2.80.4-GCCcore-13.3.0 2.66.1-GCCcore-10.2.0 2.75.0-GCCcore-12.2.0 2.60.1-GCCcore-8.2.0 2.69.1-GCCcore-11.2.0 2.78.1-GCCcore-13.2.0 GLibmm ------ **Description** C++ bindings for Glib **More Information** https://www.gtk.org/ **Available Versions**:: 2.66.4-GCCcore-10.3.0 2.49.7-GCCcore-8.3.0 GMAP-GSNAP ---------- **Description** GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences GSNAP: Genomic Short-read Nucleotide Alignment Program **More Information** http://research-pub.gene.com/gmap/ **Available Versions**:: 2019-09-12-GCC-8.3.0 GMP --- **Description** GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers. **More Information** https://gmplib.org/ **Available Versions**:: 6.2.1-GCCcore-10.3.0 6.1.2-GCCcore-10.2.0 6.1.2-GCCcore-8.3.0 6.2.1-GCCcore-12.2.0 6.2.1-GCCcore-11.3.0 6.2.0-GCCcore-10.2.0 6.2.1-GCCcore-11.2.0 6.3.0-GCCcore-13.3.0 6.2.0-GCCcore-9.3.0 6.1.2-GCCcore-7.3.0 6.1.2-GCCcore-8.2.0 6.3.0-GCCcore-14.2.0 6.3.0-GCCcore-13.2.0 6.2.1-GCCcore-12.3.0 GONE ---- **Available Versions**:: 2024 GObject-Introspection --------------------- **Description** GObject introspection is a middleware layer between C libraries (using GObject) and language bindings. The C library can be scanned at compile time and generate a metadata file, in addition to the actual native C library. Then at runtime, language bindings can read this metadata and automatically provide bindings to call into the C library. **More Information** https://gi.readthedocs.io/en/latest/ **Available Versions**:: 1.74.0-GCCcore-12.2.0 1.76.1-GCCcore-12.3.0 1.63.1-GCCcore-8.3.0-Python-3.7.4 1.72.0-GCCcore-11.3.0 1.66.1-GCCcore-10.2.0 1.84.0-GCCcore-14.2.0 1.64.0-GCCcore-9.3.0-Python-3.8.2 1.68.0-GCCcore-10.3.0 1.80.1-GCCcore-13.3.0 1.68.0-GCCcore-11.2.0 1.78.1-GCCcore-13.2.0 1.60.1-GCCcore-8.2.0-Python-3.7.2 GPAW ---- **Description** GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) method and the atomic simulation environment (ASE). It uses real-space uniform grids and multigrid methods or atom-centered basis-functions. **More Information** https://wiki.fysik.dtu.dk/gpaw/ **Available Versions**:: 23.9.1-intel-2022a 22.8.0-intel-2022a 22.8.0-foss-2022a 23.9.1-foss-2022a GPAW-setups ----------- **Description** PAW setup for the GPAW Density Functional Theory package. Users can install setups manually using 'gpaw install-data' or use setups from this package. The versions of GPAW and GPAW-setups can be intermixed. **More Information** https://wiki.fysik.dtu.dk/gpaw/ **Available Versions**:: 0.9.20000 GRASS ----- **Description** The Geographic Resources Analysis Support System - used for geospatial data management and analysis, image processing, graphics and maps production, spatial modeling, and visualization **More Information** https://grass.osgeo.org **Available Versions**:: 8.4.0-foss-2023a 8.2.0-foss-2021b GROMACS ------- **Description** GROMACS is a versatile package to perform molecular dynamics, i.e. simulate theNewtonian equations of motion for systems with hundreds to millions ofparticles.This is a GPU enabled build, containing both MPI and threadMPI binaries.It also contains the gmxapi extension for the single precision MPI build. **More Information** https://www.gromacs.org **Available Versions**:: 2024.4-foss-2023a-CUDA-12.4.0 2023.1-foss-2022a 2021.3-foss-2021a 2023.3-foss-2022a-CUDA-11.7.0 2020.4-foss-2020a-PLUMED-2.6.2 2024.3-foss-2023b 2022.2-foss-2021a 2021-foss-2021a-PLUMED-2.7.2 2021.3-foss-2021a-CUDA-11.3.1 2020.4-foss-2020a 2023.4-foss-2023a-CUDA-12.0.0 GSD --- **Description** The GSD file format is the native file format forHOOMD-blue. GSD files store trajectories of the HOOMD-blue system statein a binary file with efficient random access to frames. GSD allows allparticle and topology properties to vary from one frame to the next. Usethe GSD Python API to specify the initial condition for a HOOMD-bluesimulation or analyze trajectory output with a script. Read a GSDtrajectory with a visualization tool to explore the behavior of thesimulation. **More Information** https://gsd.readthedocs.io **Available Versions**:: 3.2.0-foss-2022a GSL --- **Description** The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting. **More Information** http://www.gnu.org/software/gsl/ **Available Versions**:: 2.5-GCC-8.2.0-2.31.1 2.6-iccifort-2020.1.217 2.8-GCC-13.3.0 2.6-GCC-10.2.0 2.7-GCC-10.3.0 2.7-GCC-13.2.0 2.7-GCC-12.2.0 2.7-intel-compilers-2021.2.0 2.7-GCC-12.3.0 2.7-GCC-11.2.0 2.7-GCC-11.3.0 2.8-GCC-14.2.0 2.6-GCC-8.3.0 2.6-iccifort-2020.4.304 2.5-GCC-7.3.0-2.30 2.6-GCC-9.3.0 GST-plugins-bad --------------- **Description** GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio (mixing) and video (non-linear editing) processing. **More Information** https://gstreamer.freedesktop.org/ **Available Versions**:: 1.22.5-GCC-12.2.0 1.20.2-GCC-11.3.0 1.22.5-GCC-12.3.0 GST-plugins-base ---------------- **Description** GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio (mixing) and video (non-linear editing) processing. **More Information** https://gstreamer.freedesktop.org/ **Available Versions**:: 1.18.5-GCC-11.2.0 1.20.2-GCC-11.3.0 1.22.1-GCC-12.2.0 1.22.5-GCC-12.3.0 GStreamer --------- **Description** GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio (mixing) and video (non-linear editing) processing. **More Information** https://gstreamer.freedesktop.org/ **Available Versions**:: 1.22.5-GCC-12.3.0 1.22.1-GCC-12.2.0 1.20.2-GCC-11.3.0 1.18.5-GCC-11.2.0 GTK+ ---- **Description** GTK+ is the primary library used to construct user interfaces in GNOME. It provides all the user interface controls, or widgets, used in a common graphical application. Its object-oriented API allows you to construct user interfaces without dealing with the low-level details of drawing and device interaction. **More Information** https://developer.gnome.org/gtk3/stable/ **Available Versions**:: 3.24.23-GCCcore-10.2.0 GTK2 ---- **Description** The GTK+ 2 package contains libraries used for creating graphical user interfaces for applications. **More Information** https://www.gtk.org **Available Versions**:: 2.24.33-GCCcore-11.3.0 GTK3 ---- **Description** GTK+ is the primary library used to construct user interfaces in GNOME. It provides all the user interface controls, or widgets, used in a common graphical application. Its object-oriented API allows you to construct user interfaces without dealing with the low-level details of drawing and device interaction. **More Information** https://developer.gnome.org/gtk3/stable/ **Available Versions**:: 3.24.37-GCCcore-12.3.0 3.24.31-GCCcore-11.2.0 3.24.39-GCCcore-13.2.0 3.24.33-GCCcore-11.3.0 GTK4 ---- **Description** GTK+ is the primary library used to construct user interfaces in GNOME. It provides all the user interface controls, or widgets, used in a common graphical application. Its object-oriented API allows you to construct user interfaces without dealing with the low-level details of drawing and device interaction. **More Information** https://docs.gtk.org/gtk4/ **Available Versions**:: 4.11.3-GCC-12.2.0 4.7.0-GCC-11.3.0 4.13.1-GCC-12.3.0 GTS --- **Description** GTS stands for the GNU Triangulated Surface Library.It is an Open Source Free Software Library intended to provide a set of usefulfunctions to deal with 3D surfaces meshed with interconnected triangles. **More Information** http://gts.sourceforge.net/ **Available Versions**:: 0.7.6-GCCcore-11.3.0 0.7.6-GCCcore-10.3.0 0.7.6-GCCcore-12.3.0 Gaussian -------- **Description** Gaussian provides state-of-the-art capabilities for electronic structuremodeling. Gaussian 16 is licensed for a wide variety of computersystems. All versions of Gaussian 16 contain every scientific/modelingfeature, and none imposes any artificial limitations on calculationsother than your computing resources and patience.This is the build from the legacy ARCUS-B system, using PGI 16.5 compiler and Atlas. **More Information** https://www.gaussian.com/ **Available Versions**:: 16.C.01 09.D.01-ARCUS-B 16.A.03-ARCUS-B 03.E.01-ARCUS-B Gaussview --------- **Available Versions**:: 5.0.9 Gdk-Pixbuf ---------- **Description** The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it was distributed as part of GTK+ 2 but it was split off into a separate package in preparation for the change to GTK+ 3. **More Information** https://developer.gnome.org/gdk-pixbuf/stable/ **Available Versions**:: 2.42.6-GCCcore-10.3.0 2.42.11-GCCcore-13.3.0 2.42.10-GCCcore-13.2.0 2.40.0-GCCcore-10.2.0 2.42.12-GCCcore-14.2.0 2.42.10-GCCcore-12.3.0 2.42.6-GCCcore-11.2.0 2.42.8-GCCcore-11.3.0 2.42.10-GCCcore-12.2.0 Geant4 ------ **Description** Geant4 is a toolkit for the simulation of the passage of particles through matter. Its areas of application include high energy, nuclear and accelerator physics, as well as studies in medical and space science. **More Information** https://geant4.web.cern.ch/ **Available Versions**:: 11.1.2-GCC-11.3.0 11.3.0-GCC-13.2.0 11.1.1-GCC-11.2.0 11.0.0-foss-2021b-G4MPI 11.2.2-GCC-12.3.0 11.0.0-GCC-11.2.0 10.7.1-GCC-10.2.0 Geant4-data ----------- **Description** Datasets for Geant4. **More Information** https://geant4.cern.ch/ **Available Versions**:: 20240528 20230601 11.2 11.1 11.3 20210510 GenMap ------ **Description** GenMap - Fast and Exact Computation of Genome Mappability **More Information** https://github.com/cpockrandt/genmap **Available Versions**:: 1.3.0-GCCcore-11.2.0 GeneMark-ET ----------- **Description** Eukaryotic gene prediction suite with automatic training **More Information** http://exon.gatech.edu/GeneMark **Available Versions**:: 4.72-GCCcore-12.3.0 4.69-GCCcore-8.3.0 GenomeThreader -------------- **Description** GenomeThreader is a software tool to compute gene structure predictions. **More Information** https://genomethreader.org **Available Versions**:: 1.7.3-Linux_x86_64-64bit GenomeTools ----------- **Description** A comprehensive software library for efficient processing of structured genome annotations. **More Information** http://genometools.org **Available Versions**:: 1.6.1-GCC-10.2.0 1.6.2-GCC-10.3.0 GeoMxNGSPipeline ---------------- **Available Versions**:: 2022 Ghostscript ----------- **Description** Ghostscript is a versatile processor for PostScript data with the ability to render PostScript to different targets. It used to be part of the cups printing stack, but is no longer used for that. **More Information** https://ghostscript.com **Available Versions**:: 9.52-GCCcore-9.3.0 9.50-GCCcore-8.3.0 9.56.1-GCCcore-11.3.0 10.01.2-GCCcore-12.3.0 9.53.3-GCCcore-10.2.0 9.54.0-GCCcore-10.3.0 10.03.1-GCCcore-13.3.0 10.02.1-GCCcore-13.2.0 9.54.0-GCCcore-11.2.0 GitPython --------- **Description** GitPython is a python library used to interact with Git repositories **More Information** https://gitpython.readthedocs.org **Available Versions**:: 3.1.27-GCCcore-11.3.0 3.1.24-GCCcore-11.2.0 3.1.14-GCCcore-10.2.0 3.1.0-GCCcore-8.3.0-Python-3.7.4 GlobalArrays ------------ **Description** Global Arrays (GA) is a Partitioned Global Address Space (PGAS) programming model **More Information** https://hpc.pnl.gov/globalarrays **Available Versions**:: 5.8.2-intel-2023a 5.8-iomkl-2021a 5.8.1-intel-2022a 5.8.2-foss-2023a 5.8.2-gomkl-2023a 5.8-intel-2021a 5.7-intel-2020b 5.8-intel-2020a Globus-CLI ---------- **Description** A Command Line Wrapper over the Globus SDK for Python, which provides an interface to Globus services from the shell, and is suited to both interactive and simple scripting use cases. **More Information** https://docs.globus.org/cli/ **Available Versions**:: 3.6.0-GCCcore-11.2.0 3.34.0-GCCcore-13.3.0 GlobusConnectPersonal --------------------- **Description** Globus Connect Personal turns your laptop or other personal computer into a Globus endpoint with a just a few clicks. With Globus Connect Personal you can share and transfer files to/from a local machine—campus server, desktop computeror laptop—even if it's behind a firewall and you don't have administrator privileges. **More Information** https://www.globus.org/globus-connect-personal **Available Versions**:: 2.3.6 Glucose ------- **Description** Glucose is based on a new scoring scheme (well, not so new now, it wasintroduced in 2009) for the clause learning mechanism of so called Modern SATsolvers (it is based on our IJCAI'09 paper). It is designed to be parallel, since v4.0. **More Information** https://www.labri.fr/perso/lsimon/glucose/ **Available Versions**:: 4.1-GCC-9.3.0 GnuTLS ------ **Description** GnuTLS is a secure communications library implementing the SSL, TLS and DTLS protocols and technologies around them. It provides a simple C language application programming interface (API) to access the secure communications protocols as well as APIs to parse and write X.509, PKCS #12, OpenPGP and other required structures. It is aimed to be portable and efficient with focus on security and interoperability. **More Information** https://www.gnutls.org **Available Versions**:: 3.7.8-GCCcore-12.3.0 3.7.3-GCCcore-11.2.0 Go -- **Description** Go is an open source programming language that makes it easy to build simple, reliable, and efficient software. **More Information** https://www.golang.org **Available Versions**:: 1.14.1 1.22.1 1.17.6 Grace ----- **Description** Grace is a WYSIWYG tool to make two-dimensional plots of numerical data. **More Information** https://plasma-gate.weizmann.ac.il/Grace/ **Available Versions**:: 5.1.25-foss-2021b GrapeTree --------- **Available Versions**:: 2023 Graphene -------- **Description** Graphene is a thin layer of types for graphic libraries **More Information** https://ebassi.github.io/graphene/ **Available Versions**:: 1.10.8-GCCcore-11.3.0 1.10.8-GCCcore-12.2.0 1.10.8-GCCcore-12.3.0 GraphicsMagick -------------- **Description** GraphicsMagick is the swiss army knife of image processing. **More Information** http://www.graphicsmagick.org/ **Available Versions**:: 1.3.36-GCCcore-11.2.0 1.3.34-foss-2019b Graphviz -------- **Description** Graphviz is open source graph visualization software. Graph visualization is a way of representing structural information as diagrams of abstract graphs and networks. It has important applications in networking, bioinformatics, software engineering, database and web design, machine learning, and in visual interfaces for other technical domains. **More Information** https://www.graphviz.org/ **Available Versions**:: 5.0.0-GCCcore-11.3.0 2.47.2-GCCcore-10.3.0 Guile ----- **Description** Guile is a programming language, designed to help programmers create flexible applications that can be extended by users or other programmers with plug-ins, modules, or scripts. **More Information** https://www.gnu.org/software/guile/ **Available Versions**:: 1.8.8-GCCcore-9.3.0 1.8.8-GCCcore-8.2.0 1.8.8-GCCcore-8.3.0 3.0.9-GCCcore-12.3.0 3.0.8-GCCcore-11.3.0 3.0.7-GCCcore-11.2.0 Guppy ----- **Available Versions**:: 6.5.7-CPU 6.4.2-CPU 3.6.0 5.0.11 6.4.2 6.5.7 Gurobi ------ **Description** The Gurobi Optimizer is a state-of-the-art solver for mathematical programming.The solvers in the Gurobi Optimizer were designed from the ground up to exploit modernarchitectures and multi-core processors, using the most advanced implementations of thelatest algorithms. **More Information** https://www.gurobi.com **Available Versions**:: 9.5.2-GCCcore-11.3.0 10.0.3-GCCcore-12.2.0 9.1.2-GCCcore-10.3.0 HDBSCAN ------- **Description** The hdbscan library is a suite of tools to use unsupervised learning to find clusters, or dense regions, of a dataset. The primary algorithm is HDBSCAN* as proposed by Campello, Moulavi, and Sander. The library provides a high performance implementation of this algorithm, along with tools for analysing the resulting clustering. **More Information** http://hdbscan.readthedocs.io/en/latest/ **Available Versions**:: 0.8.29-foss-2022a HDF --- **Description** HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines. **More Information** https://support.hdfgroup.org/products/hdf4/ **Available Versions**:: 4.2.15-GCCcore-9.3.0 4.2.16-2-GCCcore-12.3.0 4.2.16-2-GCCcore-13.2.0 4.2.14-GCCcore-8.3.0 4.2.15-GCCcore-11.2.0 4.2.15-GCCcore-10.3.0 4.2.15-GCCcore-11.3.0 4.2.15-GCCcore-10.2.0 4.3.0-GCCcore-13.3.0 HDF5 ---- **Description** HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data. **More Information** https://portal.hdfgroup.org/display/support **Available Versions**:: 1.10.6-gompic-2020a 1.10.2-intel-2020b 1.14.0-GCC-12.3.0-serial 1.10.5-gompic-2019b 1.14.0-GCC-11.2.0-serial 1.14.0-iimpi-2023a 1.10.5-gompi-2019b-dba 1.10.5-gompi-2019b 1.10.5-iimpi-2020a 1.14.3-gompi-2023b 1.12.1-gompi-2021b 1.12.1-gompi-2021a 1.12.2-iimpi-2022a 1.12.0-gompi-2020a 1.14.0-gompi-2023a 1.10.7-gompi-2021a 1.10.7-gompic-2020b 1.10.2-fosscuda-2018b 1.13.1-iimpi-2022a 1.12.1-iimpi-2021b 1.10.6-iimpi-2020a 1.14.0-gompi-2022b 1.13.1-gompi-2022a 1.10.5-gompi-2019a 1.12.2-gompi-2022a 1.10.7-iimpi-2020b 1.10.2-foss-2018b 1.14.5-gompi-2024a 1.14.0-iimpi-2022b 1.10.7-gompi-2020b 1.14.6-gompi-2025a 1.10.7-iompi-2021a 1.10.7-iimpi-2021a 1.10.6-gompi-2020a HH-suite -------- **Description** The HH-suite is an open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs). **More Information** https://github.com/soedinglab/hh-suite **Available Versions**:: 3.3.0-gompi-2021a 3.3.0-gompi-2023a 3.3.0-gompi-2022a 3.3.0-gompic-2020b 3.3.0-gompi-2021b HISAT2 ------ **Description** HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) against the general human population (as well as against a single reference genome). **More Information** https://daehwankimlab.github.io/hisat2 **Available Versions**:: 2.2.1-gompi-2020b HMMER ----- **Description** 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. **More Information** http://hmmer.org/ **Available Versions**:: 3.3.1-iimpi-2020a 3.3.2-gompi-2021b 3.3.2-gompi-2022a 3.3.2-gompic-2020b 3.4-gompi-2023b 3.3.2-gompi-2020b 3.4-gompi-2023a 3.3.2-gompi-2021a HMMER2 ------ **Description** HMMER is used for searching sequence databases for sequence homologs, and for making sequence alignments. **More Information** http://hmmer.org **Available Versions**:: 2.3.2-GCC-8.3.0 HOOMD-blue ---------- **Description** HOOMD-blue is a general-purpose particle simulationtoolkit, implementing molecular dynamics and hard particle Monte Carlooptimized for fast execution on both GPUs and CPUs. **More Information** https://bitbucket.org/glotzer/hoomd-blue **Available Versions**:: 4.0.1-foss-2022a 4.4.0-foss-2022a HTSlib ------ **Description** A C library for reading/writing high-throughput sequencing data. This package includes the utilities bgzip and tabix **More Information** http://www.htslib.org/ **Available Versions**:: 1.9-foss-2018b 1.10.2-GCC-8.3.0 1.18-GCC-12.3.0 1.12-GCC-10.3.0 1.11-GCC-10.2.0 1.10.2-GCC-9.3.0 1.21-GCC-13.3.0 1.15.1-GCC-11.3.0 1.14-GCC-11.2.0 1.19.1-GCC-13.2.0 1.12-GCC-10.2.0 HarfBuzz -------- **Description** HarfBuzz is an OpenType text shaping engine. **More Information** https://www.freedesktop.org/wiki/Software/HarfBuzz **Available Versions**:: 2.8.1-GCCcore-10.3.0 9.0.0-GCCcore-13.3.0 2.6.4-GCCcore-9.3.0 2.6.7-GCCcore-10.2.0 8.2.2-GCCcore-13.2.0 2.6.4-GCCcore-8.3.0 5.3.1-GCCcore-12.2.0 4.2.1-GCCcore-11.3.0 5.3.1-GCCcore-12.3.0 11.2.1-GCCcore-14.2.0 2.8.2-GCCcore-11.2.0 HemeLB ------ **Description** HemeLB is a high performance lattice-Boltzmann solver optimized for simulating blood flow through sparse geometries, such as those found in the human vasculature. It is routinely deployed on powerful supercomputers, scaling to hundreds of thousands of cores even for complex geometries . HemeLB has traditionally been used to model cerebral bloodflow and vascular remodelling in retinas , but is now being applied to simulating the fully coupled human arterial and venous trees. **More Information** http://hemelb.org.s3-website.eu-west-2.amazonaws.com/ **Available Versions**:: 0.8 HighFive -------- **Description** HighFive is a modern header-only C++11 friendly interface for libhdf5. **More Information** https://github.com/BlueBrain/HighFive **Available Versions**:: 2.6.2-gompi-2022a Highway ------- **Description** Highway is a C++ library for SIMD (Single Instruction, Multiple Data), i.e. applying the sameoperation to 'lanes'. **More Information** https://github.com/google/highway **Available Versions**:: 1.0.4-GCCcore-12.3.0 1.0.4-GCCcore-11.3.0 1.0.3-GCCcore-11.3.0 HyPhy ----- **Description** HyPhy (Hypothesis Testing using Phylogenies) is an open-source software package for the analysis of genetic sequences (in particular the inference of natural selection) using techniques in phylogenetics, molecular evolution, and machine learning **More Information** https://veg.github.io/hyphy-site/ **Available Versions**:: 2.5.1-gompi-2019a Hypre ----- **Description** Hypre is a library for solving large, sparse linear systems of equations on massively parallel computers. The problems of interest arise in the simulation codes being developed at LLNL and elsewhere to study physical phenomena in the defense, environmental, energy, and biological sciences. **More Information** https://computation.llnl.gov/projects/hypre-scalable-linear-solvers-multigrid-methods **Available Versions**:: 2.18.2-foss-2020a 2.20.0-foss-2020b 2.29.0-foss-2023a 2.33.0-foss-2025a 2.18.2-intel-2020a 2.25.0-foss-2022a 2.18.2-foss-2019b 2.21.0-foss-2021a ICU --- **Description** ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization support for software applications. **More Information** https://icu.unicode.org **Available Versions**:: 71.1-GCCcore-11.3.0 67.1-GCCcore-10.2.0 69.1-GCCcore-11.2.0 64.2-GCCcore-8.2.0 69.1-GCCcore-10.3.0 75.1-GCCcore-13.3.0 64.2-GCCcore-8.3.0 66.1-GCCcore-9.3.0 77.1-GCCcore-14.3.0 76.1-GCCcore-14.2.0 61.1-GCCcore-7.3.0 74.1-GCCcore-13.2.0 73.2-GCCcore-12.3.0 72.1-GCCcore-12.2.0 IDBA-UD ------- **Description** IDBA-UD is a iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data with Highly Uneven Sequencing Depth. It is an extension of IDBA algorithm. IDBA-UD also iterates from small k to a large k. In each iteration, short and low-depth contigs are removed iteratively with cutoff threshold from low to high to reduce the errors in low-depth and high-depth regions. Paired-end reads are aligned to contigs and assembled locally to generate some missing k-mers in low-depth regions. With these technologies, IDBA-UD can iterate k value of de Bruijn graph to a very large value with less gaps and less branches to form long contigs in both low-depth and high-depth regions. **More Information** https://i.cs.hku.hk/~alse/hkubrg/projects/idba_ud/ **Available Versions**:: 1.1.3-GCC-8.3.0 IGV --- **Description** This package contains command line utilities for preprocessing, computing feature count density (coverage), sorting, and indexing data files. **More Information** https://www.broadinstitute.org/software/igv/ **Available Versions**:: 2.8.0-Java-11 IMPUTE2 ------- **Description** IMPUTE version 2 (also known as IMPUTE2) is a genotype imputation and haplotype phasing program based on ideas from Howie et al. 2009 **More Information** http://mathgen.stats.ox.ac.uk/impute/impute_v2.html **Available Versions**:: 2.3.2_x86_64_static 2.3.2_x86_64_dynamic IOR --- **Description** The IOR software is used for benchmarking parallel file systems using POSIX, MPIIO, or HDF5 interfaces. **More Information** https://github.com/IOR-LANL/ior **Available Versions**:: 3.3.0-gompi-2020b 3.2.1-gompi-2019b IPython ------- **Description** IPython provides a rich architecture for interactive computing with: Powerful interactive shells (terminal and Qt-based). A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. Support for interactive data visualization and use of GUI toolkits. Flexible, embeddable interpreters to load into your own projects. Easy to use, high performance tools for parallel computing. **More Information** https://ipython.org/index.html **Available Versions**:: 8.14.0-GCCcore-12.3.0 8.5.0-GCCcore-11.3.0 7.18.1-GCCcore-10.2.0 7.26.0-GCCcore-11.2.0 IQ-TREE ------- **Description** Efficient phylogenomic software by maximum likelihood **More Information** http://www.iqtree.org/ **Available Versions**:: 2.2.2.6-gompi-2022b 1.6.12-foss-2018b ISA-L ----- **Description** Intelligent Storage Acceleration Library **More Information** https://github.com/intel/isa-l **Available Versions**:: 2.30.0-GCCcore-11.3.0 2.30.0-GCCcore-11.2.0 2.30.0-GCCcore-12.2.0 2.31.0-GCCcore-13.2.0 ITSTool ------- **Description** ITS Tool allows you to translate your XML documents with PO files **More Information** http://itstool.org/ **Available Versions**:: 2.0.7-GCCcore-12.3.0 ImageMagick ----------- **Description** ImageMagick is a software suite to create, edit, compose, or convert bitmap images **More Information** https://www.imagemagick.org/ **Available Versions**:: 7.1.1-38-GCCcore-13.3.0 7.1.1-34-GCCcore-13.2.0 7.1.0-37-GCCcore-11.3.0 7.0.10-1-GCCcore-9.3.0 7.1.1-15-GCCcore-12.3.0 7.1.0-4-GCCcore-11.2.0 7.0.11-14-GCCcore-10.3.0 Imath ----- **Description** Imath is a C++ and python library of 2D and 3D vector, matrix, and math operations for computer graphics **More Information** https://imath.readthedocs.io/en/latest/ **Available Versions**:: 3.1.7-GCCcore-12.3.0 3.1.9-GCCcore-13.2.0 3.1.6-GCCcore-12.2.0 3.1.11-GCCcore-13.3.0 3.1.5-GCCcore-11.3.0 Infernal -------- **Description** Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities. **More Information** http://eddylab.org/infernal/ **Available Versions**:: 1.1.2-foss-2018b InterProScan ------------ **Description** InterProScan is a sequence analysis application (nucleotide and protein sequences) that combines different protein signature recognition methods into one resource [code only: libraries and external binaries but no data]. **More Information** https://www.ebi.ac.uk/interpro/ **Available Versions**:: 5.62-94.0-foss-2022b Ipopt ----- **Description** Ipopt (Interior Point OPTimizer, pronounced eye-pea-Opt) is a software package for large-scale nonlinear optimization. **More Information** https://coin-or.github.io/Ipopt **Available Versions**:: 3.12.13-intel-2020b JAGS ---- **Description** JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation **More Information** http://mcmc-jags.sourceforge.net/ **Available Versions**:: 4.3.0-foss-2021b 4.3.0-foss-2019b 4.3.0-foss-2022a 4.3.0-foss-2020a 4.3.0-foss-2021a Jansson ------- **Description** Jansson is a C library for encoding, decoding and manipulating JSON data. Its main features and design principles are: * Simple and intuitive API and data model * Comprehensive documentation * No dependencies on other libraries * Full Unicode support (UTF-8) * Extensive test suite **More Information** https://www.digip.org/jansson/ **Available Versions**:: 2.13.1-GCC-11.2.0 2.14-GCC-11.3.0 2.14-GCC-12.3.0 JasPer ------ **Description** The JasPer Project is an open-source initiative to provide a free software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard. **More Information** https://www.ece.uvic.ca/~frodo/jasper/ **Available Versions**:: 4.0.0-GCCcore-12.2.0 2.0.33-GCCcore-11.2.0 2.0.14-GCCcore-8.2.0 2.0.14-GCCcore-9.3.0 2.0.24-GCCcore-10.2.0 4.2.5-GCCcore-14.2.0 4.0.0-GCCcore-12.3.0 2.0.14-GCCcore-8.3.0 2.0.28-GCCcore-10.3.0 2.0.14-GCCcore-7.3.0 2.0.33-GCCcore-11.3.0 4.0.0-GCCcore-13.2.0 1.900.1-intel-2020b 4.2.4-GCCcore-13.3.0 Java ---- **Description** Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers. **More Information** https://java.com/ **Available Versions**:: 1.7.0_60 1.8.0_241 17.0.6 1.8.0_131 11.0.20 16.0.1 11.0.2 Jellyfish --------- **Description** Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. **More Information** http://www.genome.umd.edu/jellyfish.html **Available Versions**:: 2.3.0-GCC-11.2.0 2.3.0-GCC-8.3.0 JsonCpp ------- **Description** JsonCpp is a C++ library that allows manipulating JSON values, including serialization and deserialization to and from strings. It can also preserve existing comment in unserialization/serialization steps, making it a convenient format to store user input files. **More Information** https://open-source-parsers.github.io/jsoncpp-docs/doxygen/index.html **Available Versions**:: 1.9.5-GCCcore-11.3.0 1.9.4-GCCcore-11.2.0 1.9.5-GCCcore-12.3.0 1.9.4-GCCcore-10.3.0 1.9.4-GCCcore-10.2.0 Judy ---- **Description** A C library that implements a dynamic array. **More Information** http://judy.sourceforge.net/ **Available Versions**:: 1.0.5-GCCcore-10.3.0 1.0.5-GCCcore-8.3.0 1.0.5-GCCcore-10.2.0 1.0.5-GCCcore-12.3.0 Julia ----- **Description** Julia is a high-level, high-performance dynamic programming language for numerical computing **More Information** https://julialang.org **Available Versions**:: 1.8.2-linux-x86_64 1.6.2-linux-x86_64 1.8.5-linux-x86_64 1.5.1-linux-x86_64 1.10.8-linux-x86_64 1.12.1-linux-x86_64 1.9.3-linux-x86_64 1.11.3-linux-x86_64 1.5.3-linux-x86_64 JupyterLab ---------- **Description** JupyterLab is the next-generation user interface for Project Jupyter offering all the familiar building blocks of the classic Jupyter Notebook (notebook, terminal, text editor, file browser, rich outputs, etc.) in a flexible and powerful user interface. JupyterLab will eventually replace the classic Jupyter Notebook. **More Information** https://jupyter.org/ **Available Versions**:: 2.2.8-GCCcore-10.2.0 3.5.0-GCCcore-11.3.0 4.0.5-GCCcore-12.3.0 JupyterNotebook --------------- **Description** The Jupyter Notebook is the original web application for creating and sharing computational documents. It offers a simple, streamlined, document-centric experience. **More Information** https://jupyter.org/ **Available Versions**:: 7.0.2-GCCcore-12.3.0 KMC --- **Description** KMC is a disk-based programm for counting k-mers from (possibly gzipped) FASTQ/FASTA files. **More Information** http://sun.aei.polsl.pl/kmc **Available Versions**:: 3.1.0-foss-2018b 3.2.4-GCC-13.3.0 KaHIP ----- **Description** The graph partitioning framework KaHIP -- Karlsruhe High Quality Partitioning. **More Information** https://kahip.github.io/ **Available Versions**:: 3.14-gompi-2022a 3.16-gompi-2023a Kalign ------ **Description** Kalign is a fast multiple sequence alignment program for biological sequences. **More Information** https://github.com/TimoLassmann/kalign **Available Versions**:: 3.3.5-GCCcore-11.3.0 3.3.2-GCCcore-11.2.0 3.3.1-GCCcore-10.3.0 3.3.1-GCCcore-10.2.0 Kent_tools ---------- **Description** Kent utilities: collection of tools used by the UCSC genome browser. **More Information** https://genome.cse.ucsc.edu/ **Available Versions**:: 468-GCC-12.3.0 418-GCC-10.3.0 411-GCC-10.2.0 Keras ----- **Description** Keras is a deep learning API written in Python, running on top of the machine learning platform TensorFlow. **More Information** https://keras.io/ **Available Versions**:: 2.4.3-fosscuda-2020b Kraken ------ **Description** Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. Kraken aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm. **More Information** https://ccb.jhu.edu/software/kraken/ **Available Versions**:: 1.1.1-GCCcore-11.3.0 Kraken2 ------- **Description** Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. Kraken aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm. **More Information** https://github.com/DerrickWood/kraken2/wiki **Available Versions**:: 2.1.2-gompi-2021b 2.1.1-gompi-2020b LAME ---- **Description** LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL. **More Information** http://lame.sourceforge.net/ **Available Versions**:: 3.100-GCCcore-12.2.0 3.100-GCCcore-10.2.0 3.100-GCCcore-11.2.0 3.100-GCCcore-13.3.0 3.100-GCCcore-13.2.0 3.100-GCCcore-9.3.0 3.100-GCCcore-8.2.0 3.100-GCCcore-11.3.0 3.100-GCCcore-12.3.0 3.100-GCCcore-10.3.0 3.100-GCCcore-8.3.0 3.100-GCCcore-14.2.0 LAMMPS ------ **Description** LAMMPS is a classical molecular dynamics code, and an acronymfor Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS haspotentials for solid-state materials (metals, semiconductors) and soft matter(biomolecules, polymers) and coarse-grained or mesoscopic systems. It can beused to model atoms or, more generically, as a parallel particle simulator atthe atomic, meso, or continuum scale. LAMMPS runs on single processors or inparallel using message-passing techniques and a spatial-decomposition of thesimulation domain. The code is designed to be easy to modify or extend with newfunctionality. **More Information** https://www.lammps.org **Available Versions**:: 2Aug2023_update2-foss-2023a-kokkos-QUIP 29Aug2024_update2-foss-2023a-kokkos 23Jun2022-foss-2022a-kokkos-CUDA-11.7.0 LAPACK ------ **Description** 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. **More Information** https://www.netlib.org/lapack/ **Available Versions**:: 3.9.1-GCC-10.3.0 3.9.1-GCC-11.2.0 3.9.1-GCC-10.2.0 3.10.1-GCC-11.3.0 3.9.1-GCC-9.3.0 LDC --- **Description** The LLVM-based D Compiler **More Information** https://wiki.dlang.org/LDC **Available Versions**:: 1.26.0-GCCcore-10.3.0 1.36.0-GCCcore-12.3.0 1.24.0-x86_64 0.17.6-x86_64 1.25.1-GCCcore-10.2.0 LERC ---- **Description** LERC is an open-source image or raster format which supports rapid encoding and decodingfor any pixel type (not just RGB or Byte). Users set the maximum compression error per pixel while encoding,so the precision of the original input image is preserved (within user defined error bounds). **More Information** https://github.com/Esri/lerc **Available Versions**:: 4.0.0-GCCcore-12.3.0 4.0.0-GCCcore-13.3.0 4.0.0-GCCcore-11.3.0 4.0.0-GCCcore-13.2.0 LIBSVM ------ **Description** 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. **More Information** https://www.csie.ntu.edu.tw/~cjlin/libsvm/ **Available Versions**:: 3.25-GCCcore-11.2.0 LLVM ---- **Description** The LLVM Core libraries provide a modern source- and target-independent optimizer, along with code generation support for many popular CPUs (as well as some less common ones!) These libraries are built around a well specified code representation known as the LLVM intermediate representation ("LLVM IR"). The LLVM Core libraries are well documented, and it is particularly easy to invent your own language (or port an existing compiler) to use LLVM as an optimizer and code generator. **More Information** https://llvm.org/ **Available Versions**:: 7.0.1-GCCcore-8.2.0 16.0.6-GCCcore-8.3.0 18.1.8-GCCcore-13.3.0 9.0.0-GCCcore-8.3.0 9.0.1-GCCcore-9.3.0 15.0.5-GCCcore-12.2.0 20.1.7-GCCcore-14.2.0 8.0.1-GCCcore-8.3.0 6.0.0-GCCcore-7.3.0 14.0.6-GCCcore-12.3.0-llvmlite 16.0.6-GCCcore-13.2.0 11.1.0-GCCcore-10.3.0 14.0.3-GCCcore-11.3.0 12.0.1-GCCcore-11.2.0 11.0.0-GCCcore-10.2.0 16.0.6-GCCcore-12.3.0 LMDB ---- **Description** LMDB is a fast, memory-efficient database. With memory-mapped files, it has the read performance of a pure in-memory database while retaining the persistence of standard disk-based databases. **More Information** https://symas.com/lmdb **Available Versions**:: 0.9.29-GCCcore-11.3.0 0.9.24-GCCcore-9.3.0 0.9.24-GCCcore-8.3.0 0.9.28-GCCcore-10.3.0 0.9.29-GCCcore-11.2.0 0.9.31-GCCcore-12.3.0 0.9.22-GCCcore-7.3.0 0.9.24-GCCcore-10.2.0 LSD --- **Available Versions**:: 2024 LSD2 ---- **Description** Least-squares methods to estimate rates and dates from phylogenies **More Information** https://github.com/tothuhien/lsd2 **Available Versions**:: 2.4.1-GCCcore-12.2.0 2.3-GCCcore-11.3.0 LTR_retriever ------------- **Description** LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this package. **More Information** https://github.com/oushujun/LTR_retriever **Available Versions**:: 2.9.0-foss-2020b 2.9.0-foss-2021a LZO --- **Description** Portable lossless data compression library **More Information** https://www.oberhumer.com/opensource/lzo/ **Available Versions**:: 2.10-GCCcore-10.2.0 2.10-GCCcore-10.3.0 2.10-GCCcore-8.3.0 2.10-GCCcore-12.3.0 Leptonica --------- **Description** Leptonica is a collection of pedagogically-oriented open source software that is broadly useful for image processing and image analysis applications. **More Information** http://www.leptonica.org **Available Versions**:: 1.78.0-GCCcore-8.2.0 1.83.0-GCCcore-11.3.0 LibLZF ------ **Description** LibLZF is a very small data compression library. It consists of only two .c and two .h filesand is very easy to incorporate into your own programs. The compression algorithm is very, very fast, yet stillwritten in portable C. **More Information** http://oldhome.schmorp.de/marc/liblzf.html **Available Versions**:: 3.6-GCCcore-11.3.0 LibSoup ------- **Description** libsoup is an HTTP client/server library for GNOME. Ituses GObjects and the glib main loop, to integrate well with GNOMEapplications, and also has a synchronous API, for use in threadedapplications. **More Information** https://wiki.gnome.org/Projects/libsoup **Available Versions**:: 3.6.1-GCC-12.3.0 3.0.7-GCC-11.2.0 LibTIFF ------- **Description** tiff: Library and tools for reading and writing TIFF data files **More Information** https://libtiff.gitlab.io/libtiff/ **Available Versions**:: 4.7.0-GCCcore-14.2.0 4.0.10-GCCcore-8.2.0 4.4.0-GCCcore-12.2.0 4.6.0-GCCcore-13.2.0 4.3.0-GCCcore-11.2.0 4.3.0-GCCcore-11.3.0 4.0.9-GCCcore-7.3.0 4.5.0-GCCcore-12.3.0 4.2.0-GCCcore-10.3.0 4.0.10-GCCcore-8.3.0 4.6.0-GCCcore-13.3.0 4.1.0-GCCcore-10.2.0 4.1.0-GCCcore-9.3.0 Libint ------ **Description** Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory. **More Information** https://sourceforge.net/p/libint/ **Available Versions**:: 1.1.6-GCC-8.2.0-2.31.1 2.6.0-iimpi-2020a-lmax-6-cp2k 2.7.2-GCC-12.2.0-lmax-6-cp2k 2.6.0-GCC-10.2.0-lmax-6-cp2k 2.7.2-GCC-12.3.0-lmax-6-cp2k 2.6.0-gompi-2020a-lmax-6-cp2k 2.6.0-iccifort-2020.4.304-lmax-6-cp2k 2.7.2-GCC-11.3.0-lmax-6-cp2k 1.1.6-intel-2020a 1.1.6-foss-2020a 1.1.6-foss-2019b 2.6.0-GCC-10.3.0-lmax-6-cp2k Lighter ------- **Description** Fast and memory-efficient sequencing error corrector **More Information** https://github.com/mourisl/Lighter **Available Versions**:: 1.1.2-foss-2018b 1.1.3-GCC-13.3.0 LinkTest -------- **Description** The mpilinktest program is a parallel ping-pong test between all connections of a machine. Output of this program is a fullcommunication matrix which shows the bandwidth between each processorpair and a report including the minimum bandwidth. The linktest runsfor n processors in n steps where in each step n/2 pairs of processorswill perform the MPI pingpong test (3 iterations, 128 kBmessages). The selection of the pairs is random but after running allsteps all possible pairs are covered. **More Information** http://www.fz-juelich.de/ias/jsc/EN/Expertise/Support/Software/LinkTest/linktest-download_node.html **Available Versions**:: 1.2p1-foss-2020a 1.2p1-foss-2022a 1.2p1-foss-2019b LittleCMS --------- **Description** Little CMS intends to be an OPEN SOURCE small-footprint color management engine, with special focus on accuracy and performance. **More Information** https://www.littlecms.com/ **Available Versions**:: 2.12-GCCcore-11.2.0 2.16-GCCcore-13.3.0 2.13.1-GCCcore-11.3.0 2.9-GCCcore-8.3.0 2.12-GCCcore-10.3.0 2.17-GCCcore-14.2.0 2.9-GCCcore-9.3.0 2.15-GCCcore-12.3.0 2.15-GCCcore-13.2.0 Lua --- **Description** Lua is a powerful, fast, lightweight, embeddable scripting language. Lua combines simple procedural syntax with powerful data description constructs based on associative arrays and extensible semantics. Lua is dynamically typed, runs by interpreting bytecode for a register-based virtual machine, and has automatic memory management with incremental garbage collection, making it ideal for configuration, scripting, and rapid prototyping. **More Information** https://www.lua.org/ **Available Versions**:: 5.4.2-GCCcore-10.2.0 5.4.3-GCCcore-11.2.0 5.4.4-GCCcore-11.3.0 5.4.3-GCCcore-10.3.0 5.4.4-GCCcore-12.2.0 5.3.5-GCCcore-9.3.0 5.1.5-GCCcore-8.3.0 5.4.6-GCCcore-12.3.0 5.4.7-GCCcore-13.3.0 M4 -- **Description** GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible although it has some extensions (for example, handling more than 9 positional parameters to macros). GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc. **More Information** http://www.gnu.org/software/m4/m4.html **Available Versions**:: 1.4.18 1.4.19-GCCcore-13.3.0 1.4.19-GCCcore-13.1.0 1.4.18-GCCcore-8.1.0 1.4.19-GCCcore-15.1.0 1.4.19-GCCcore-11.2.0 1.4.18-GCCcore-8.3.0 1.4.19-GCCcore-13.2.0 1.4.18-GCCcore-9.3.0 1.4.20-GCCcore-14.3.0 1.4.18-GCCcore-7.3.0 1.4.20 1.4.17 1.4.18-GCCcore-10.3.0 1.4.18-GCCcore-8.2.0 1.4.19 1.4.19-GCCcore-14.2.0 1.4.18-GCCcore-10.2.0 1.4.19-GCCcore-12.3.0 1.4.19-GCCcore-12.2.0 1.4.19-GCCcore-11.3.0 MACS2 ----- **Description** Model Based Analysis for ChIP-Seq data **More Information** https://github.com/taoliu/MACS/ **Available Versions**:: 2.2.5-foss-2018b-Python-3.6.6 MACS3 ----- **Description** Model Based Analysis for ChIP-Seq data **More Information** https://macs3-project.github.io/MACS/ **Available Versions**:: 3.0.1-gfbf-2023a MAFFT ----- **Description** MAFFT is a multiple sequence alignment program for unix-like operating systems.It offers a range of multiple alignment methods, L-INS-i (accurate; for alignmentof <∼200 sequences), FFT-NS-2 (fast; for alignment of <∼30,000 sequences), etc. **More Information** https://mafft.cbrc.jp/alignment/software/source.html **Available Versions**:: 7.470-gompi-2020a-with-extensions 7.453-iimpi-2020a-with-extensions 7.487-gompi-2021a-with-extensions 7.490-GCC-11.2.0-with-extensions 7.520-GCC-12.3.0-with-extensions 7.475-gompi-2020b-with-extensions 7.453-GCC-9.3.0-with-extensions 7.505-GCC-11.3.0-with-extensions MALT ---- **Available Versions**:: 0.5.3 MATIO ----- **Description** matio is an C library for reading and writing Matlab MAT files. **More Information** https://sourceforge.net/projects/matio/ **Available Versions**:: 1.5.17-GCCcore-8.3.0 1.5.23-GCCcore-11.3.0 1.5.26-GCCcore-12.3.0 MATLAB ------ **Available Versions**:: R2023a R2022a R2023b R2021b R2020a R2022b R2020b R2019b MAX --- **Available Versions**:: 0.2.0 MCL --- **Description** The MCL algorithm is short for the Markov Cluster Algorithm, a fastand scalable unsupervised cluster algorithm for graphs (also known as networks) basedon simulation of (stochastic) flow in graphs. **More Information** https://micans.org/mcl/ **Available Versions**:: 14.137-GCCcore-9.3.0 14.137-GCCcore-8.3.0 14.137-GCCcore-11.3.0 MDAnalysis ---------- **Description** MDAnalysis is an object-oriented Python library to analyze trajectories from molecular dynamics (MD)simulations in many popular formats. **More Information** https://www.mdanalysis.org/ **Available Versions**:: 0.20.1-foss-2019b-Python-3.7.4 MDI --- **Description** The MolSSI Driver Interface (MDI) project provides a standardized API for fast, on-the-fly communication between computational chemistry codes. This greatly simplifies the process of implementing methods that require the cooperation of multiple software packages and enables developers to write a single implementation that works across many different codes. The API is sufficiently general to support a wide variety of techniques, including QM/MM, ab initio MD, machine learning, advanced sampling, and path integral MD, while also being straightforwardly extensible. Communication between codes is handled by the MDI Library, which enables tight coupling between codes using either the MPI or TCP/IP methods. **More Information** https://github.com/MolSSI-MDI/MDI_Library **Available Versions**:: 1.4.26-gompi-2023a 1.4.29-gompi-2023b MEGAHIT ------- **Description** An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph **More Information** https://github.com/voutcn/megahit **Available Versions**:: 1.2.9-GCCcore-9.3.0 1.2.9-GCCcore-13.3.0 1.1.4-foss-2018b-Python-2.7.15 MEME ---- **Description** The MEME Suite allows you to: * discover motifs using MEME, DREME (DNA only) or GLAM2 on groups of related DNA or protein sequences, * search sequence databases with motifs using MAST, FIMO, MCAST or GLAM2SCAN, * compare a motif to all motifs in a database of motifs, * associate motifs with Gene Ontology terms via their putative target genes, and * analyse motif enrichment using SpaMo or CentriMo. **More Information** https://meme-suite.org/meme/index.html **Available Versions**:: 5.4.1-GCC-10.3.0 METIS ----- **Description** METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes. **More Information** https://karypis.github.io/glaros/projects/gp.html **Available Versions**:: 5.1.0-GCCcore-14.2.0 5.1.0-foss-2018b 5.1.0-GCCcore-12.3.0 5.1.0-GCCcore-9.3.0 5.1.0-GCCcore-8.2.0 5.1.0-GCCcore-8.3.0 5.1.0-GCCcore-11.3.0 5.1.0-GCCcore-10.3.0 5.1.0-GCCcore-13.2.0 5.1.0-GCCcore-13.3.0 5.1.0-GCCcore-11.2.0 5.1.0-GCCcore-10.2.0 MGLTools -------- **Available Versions**:: 1.5.7 1.5.7.old MMseqs2 ------- **Description** MMseqs2: ultra fast and sensitive search and clustering suite **More Information** https://mmseqs.com **Available Versions**:: 10-6d92c-gompi-2019b 13-45111-gompi-2020b MPC --- **Description** Gnu Mpc is a C library for the arithmetic of complex numbers with arbitrarily high precision and correct rounding of the result. It extends the principles of the IEEE-754 standard for fixed precision real floating point numbers to complex numbers, providing well-defined semantics for every operation. At the same time, speed of operation at high precision is a major design goal. **More Information** http://www.multiprecision.org/ **Available Versions**:: 1.1.0-GCC-8.3.0 1.3.1-GCCcore-12.3.0 1.1.0-GCC-9.3.0 1.3.1-GCCcore-13.2.0 1.2.1-GCCcore-10.3.0 1.2.1-GCCcore-11.3.0 MPFR ---- **Description** The MPFR library is a C library for multiple-precision floating-point computations with correct rounding. **More Information** https://www.mpfr.org **Available Versions**:: 4.1.0-GCCcore-10.3.0 4.1.0-GCCcore-10.2.0 4.1.0-GCCcore-11.3.0 4.2.2-GCCcore-14.2.0 4.2.1-GCCcore-13.3.0 4.2.1-GCCcore-13.2.0 4.0.1-GCCcore-7.3.0 4.0.2-GCCcore-9.3.0 4.0.2-GCCcore-8.2.0 4.0.2-GCCcore-8.3.0 4.2.0-GCCcore-12.3.0 4.1.0-GCCcore-11.2.0 MUMPS ----- **Description** A parallel sparse direct solver **More Information** https://graal.ens-lyon.fr/MUMPS/ **Available Versions**:: 5.6.1-foss-2023a-metis 5.3.5-foss-2020b-metis 5.4.0-foss-2021a-metis 5.2.1-intel-2020a-metis 5.5.1-foss-2022a-metis 5.2.1-foss-2020a-metis 5.8.1-foss-2025a-metis 5.2.1-foss-2019b-metis 5.2.1-foss-2019a-metis-seq MUMmer ------ **Description** MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. AMOS makes use of it. **More Information** http://mummer.sourceforge.net/ **Available Versions**:: 4.0.0beta2-foss-2018b 4.0.0rc1-GCCcore-11.2.0 4.0.0beta2-GCCcore-10.2.0 MUSCLE ------ **Description** MUSCLE is one of the best-performing multiple alignment programs according to published benchmark tests, with accuracy and speed that are consistently better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users learn everything they need to know about MUSCLE in a few minutes-only a handful of command-line options are needed to perform common alignment tasks. **More Information** https://drive5.com/muscle/ **Available Versions**:: 3.8.31-foss-2018b MaSuRCA ------- **Description** MaSuRCA is whole genome assembly software. It combines the efficiency of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches. MaSuRCA can assemble data sets containing only short reads from Illumina sequencing or a mixture of short reads and long reads (Sanger, 454, Pacbio and Nanopore). **More Information** https://www.genome.umd.edu/masurca.html **Available Versions**:: 4.0.9-foss-2021a-Perl-5.32.1 Mako ---- **Description** A super-fast templating language that borrows the best ideas from the existing templating languages **More Information** https://www.makotemplates.org **Available Versions**:: 1.2.4-GCCcore-13.2.0 1.1.4-GCCcore-11.2.0 1.3.5-GCCcore-13.3.0 1.2.4-GCCcore-12.3.0 1.1.0-GCCcore-8.3.0 1.2.0-GCCcore-11.3.0 1.1.2-GCCcore-9.3.0 1.1.4-GCCcore-10.3.0 1.0.8-GCCcore-8.2.0 1.1.3-GCCcore-10.2.0 1.2.4-GCCcore-12.2.0 1.3.10-GCCcore-14.2.0 Mamba ----- **Description** Mamba is a fast, robust, and cross-platform package manager. It runs on Windows, OS X and Linux (ARM64 and PPC64LE included) and is fully compatible with conda packages and supports most of conda's commands. **More Information** https://mamba.readthedocs.io/ **Available Versions**:: 4.14.0-0 23.11.0-0 MariaDB ------- **Description** MariaDB is an enhanced, drop-in replacement for MySQL.Included engines: myISAM, Aria, InnoDB, RocksDB, TokuDB, OQGraph, Mroonga. **More Information** https://mariadb.org/ **Available Versions**:: 10.5.8-GCC-10.2.0 10.6.4-GCC-10.3.0 11.6.0-GCC-12.3.0 MariaDB-connector-c ------------------- **Description** MariaDB Connector/C is used to connect applications developed in C/C++ to MariaDB and MySQL databases. **More Information** https://downloads.mariadb.org/connector-c/ **Available Versions**:: 2.3.7-GCCcore-8.3.0 Mash ---- **Description** Fast genome and metagenome distance estimation using MinHash **More Information** http://mash.readthedocs.org **Available Versions**:: 2.3-GCC-13.3.0 2.1-foss-2018b Mathematica ----------- **Available Versions**:: 11.3.0 12.2.0 13.0.0 13.3.1 14.1.0 MaxQuant -------- **Description** MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data. Several labeling techniques as well as label-free quantification are supported. **More Information** https://maxquant.org/maxquant **Available Versions**:: 2.3.0.0-GCCcore-11.2.0 Mellanox -------- **Available Versions**:: ib_mgmt-5.8.1-1.el8 Mercurial --------- **Description** Mercurial is a free, distributed source control management tool. It efficiently handles projectsof any size and offers an easy and intuitive interface. **More Information** https://www.mercurial-scm.org **Available Versions**:: 6.4.5-GCCcore-12.3.0 6.2-GCCcore-11.3.0 5.7.1-GCCcore-10.2.0 Mesa ---- **Description** Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics. **More Information** https://www.mesa3d.org/ **Available Versions**:: 23.1.9-GCCcore-13.2.0 19.0.1-GCCcore-8.2.0 22.0.3-GCCcore-11.3.0 22.2.4-GCCcore-12.2.0 23.1.4-GCCcore-12.3.0 20.2.1-GCCcore-10.2.0 18.1.1-foss-2018b 19.1.7-GCCcore-8.3.0 21.1.1-GCCcore-10.3.0 25.1.3-GCCcore-14.2.0 20.0.2-GCCcore-9.3.0 21.1.7-GCCcore-11.2.0 24.1.3-GCCcore-13.3.0 Meson ----- **Description** Meson is a cross-platform build system designed to be both as fast and as user friendly as possible. **More Information** https://mesonbuild.com **Available Versions**:: 1.4.0-GCCcore-13.3.0 0.50.0-GCCcore-8.2.0-Python-3.7.2 0.62.1-GCCcore-11.3.0 1.1.1-GCCcore-12.3.0 1.2.3-GCCcore-13.2.0 0.55.1-GCCcore-9.3.0-Python-3.8.2 1.6.1-GCCcore-14.2.0 0.58.2-GCCcore-11.2.0 0.59.1-GCCcore-8.3.0-Python-3.7.4 0.58.0-GCCcore-10.3.0 1.8.2-GCCcore-14.3.0 0.51.2-GCCcore-8.3.0-Python-3.7.4 0.64.0-GCCcore-12.2.0 0.55.3-GCCcore-10.2.0 MetaMorpheus ------------ **Description** 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. **More Information** https://github.com/smith-chem-wisc/MetaMorpheus **Available Versions**:: 0.0.320-GCCcore-10.3.0 MethylDackel ------------ **Description** A (mostly) universal methylation extractor for BS-seq experiments. **More Information** https://github.com/dpryan79/MethylDackel **Available Versions**:: 0.6.1-GCC-11.2.0 MiniSat ------- **Description** MiniSat is a minimalistic, open-source SAT solver, developed to helpresearchers and developers alike to get started on SAT. **More Information** http://minisat.se/ **Available Versions**:: 2.2.0-GCC-9.3.0 Miniconda3 ---------- **Description** Miniconda is a free minimal installer for conda. It is a small, bootstrap version of Anaconda that includes only conda, Python, the packages they depend on, and a small number of other useful packages. **More Information** https://docs.conda.io/en/latest/miniconda.html **Available Versions**:: 23.1.0-1 25.7.0-2 4.5.12 23.9.0-0 4.12.0 22.11.1-1 4.7.10 24.7.1-0 4.9.2 23.10.0-1 Mono ---- **Description** An open source, cross-platform, implementation of C# and the CLR that is binary compatible with Microsoft.NET. **More Information** https://www.mono-project.com/ **Available Versions**:: 6.8.0.105-GCCcore-8.3.0 6.12.0.122-GCCcore-11.2.0 6.4.0.198-foss-2018b MultiQC ------- **Description** Aggregate results from bioinformatics analyses across many samples into a single report. MultiQC searches a given directory for analysis logs and compiles an HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. **More Information** https://multiqc.info **Available Versions**:: 1.14-foss-2022a 1.9-foss-2020a-Python-3.8.2 Multiwfn -------- **Description** Multiwfn is an extremely powerful program for realizingi electronic wavefunction analysis, which is a key ingredient of quantum chemistry. Multiwfn is free, open-source, high-efficient, very user-friendly and flexible, it supports almost all of the most important wavefunction analysis methods. **More Information** http://sobereva.com/multiwfn/ **Available Versions**:: 3.8-intel-2021b-dev NASM ---- **Description** NASM: General-purpose x86 assembler **More Information** https://www.nasm.us/ **Available Versions**:: 2.14.02-GCCcore-8.3.0 2.16.03-GCCcore-14.2.0 2.15.05-GCCcore-10.2.0 2.16.01-GCCcore-13.2.0 2.16.03-GCCcore-13.3.0 2.15.05-GCCcore-10.3.0 2.16.01-GCCcore-12.3.0 2.15.05-GCCcore-11.3.0 2.14.02-GCCcore-9.3.0 2.13.03-GCCcore-7.3.0 2.14.02-GCCcore-8.2.0 2.15.05-GCCcore-11.2.0 2.15.05-GCCcore-12.2.0 NCCL ---- **Description** The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collectivecommunication primitives that are performance optimized for NVIDIA GPUs. **More Information** https://developer.nvidia.com/nccl **Available Versions**:: 2.8.3-GCCcore-10.2.0-CUDA-11.1.1 2.22.3-GCCcore-12.3.0-CUDA-12.6.0 2.4.8-gcccuda-2019b 2.18.3-GCCcore-12.3.0-CUDA-12.1.1 2.12.12-GCCcore-11.3.0-CUDA-12.0.0 2.8.3-CUDA-11.0.2 2.12.12-GCCcore-12.3.0-CUDA-12.0.0 2.12.12-GCCcore-11.3.0-CUDA-11.7.0 2.8.3-CUDA-11.1.1 2.16.2-GCCcore-12.2.0-CUDA-12.0.0 2.12.12-GCCcore-11.3.0-CUDA-11.8.0 2.10.3-GCCcore-10.3.0-CUDA-11.3.1 NCL --- **Description** NCL is an interpreted language designed specifically for scientific data analysis and visualization. **More Information** https://www.ncl.ucar.edu **Available Versions**:: 6.6.2-foss-2021a NCO --- **Description** The NCO toolkit manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5. **More Information** https://github.com/nco/nco **Available Versions**:: 5.0.1-foss-2021a 4.9.7-foss-2020b NEURON ------ **Description** Empirically-based simulations of neurons and networks of neurons. **More Information** https://www.neuron.yale.edu/neuron **Available Versions**:: 7.8.2-foss-2021b NGS --- **Description** NGS is a new, domain-specific API for accessing reads, alignments and pileupsproduced from Next Generation Sequencing. **More Information** https://github.com/ncbi/ngs **Available Versions**:: 2.10.9-GCCcore-10.2.0 NLopt ----- **Description** NLopt is a free/open-source library for nonlinear optimization, providing a common interface for a number of different free optimization routines available online as well as original implementations of various other algorithms. **More Information** http://ab-initio.mit.edu/wiki/index.php/NLopt **Available Versions**:: 2.7.0-GCCcore-11.2.0 2.7.1-GCCcore-11.3.0 2.7.1-GCCcore-13.3.0 2.6.2-GCCcore-10.2.0 2.7.1-GCCcore-13.2.0 2.7.0-GCCcore-10.3.0 2.7.1-GCCcore-12.2.0 2.6.1-GCCcore-9.3.0 2.4.2-GCCcore-7.3.0 2.6.1-GCCcore-8.3.0 2.7.1-GCCcore-12.3.0 NSPR ---- **Description** Netscape Portable Runtime (NSPR) provides a platform-neutral API for system level and libc-like functions. **More Information** https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSPR **Available Versions**:: 4.35-GCCcore-13.3.0 4.20-GCCcore-7.3.0 4.34-GCCcore-11.3.0 4.35-GCCcore-12.2.0 4.25-GCCcore-9.3.0 4.29-GCCcore-10.2.0 4.35-GCCcore-12.3.0 4.21-GCCcore-8.3.0 4.32-GCCcore-11.2.0 4.35-GCCcore-13.2.0 4.36-GCCcore-14.2.0 4.30-GCCcore-10.3.0 NSS --- **Description** Network Security Services (NSS) is a set of libraries designed to support cross-platform development of security-enabled client and server applications. **More Information** https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSS **Available Versions**:: 3.104-GCCcore-13.3.0 3.57-GCCcore-10.2.0 3.94-GCCcore-13.2.0 3.69-GCCcore-11.2.0 3.65-GCCcore-10.3.0 3.79-GCCcore-11.3.0 3.51-GCCcore-9.3.0 3.89.1-GCCcore-12.3.0 3.39-GCCcore-7.3.0 3.45-GCCcore-8.3.0 3.85-GCCcore-12.2.0 3.113-GCCcore-14.2.0 NTL --- **Description** NTL is a high-performance, portable C++ library providing data structures andalgorithms for manipulating signed, arbitrary length integers, and for vectors,matrices, and polynomials over the integers and over finite fields. **More Information** https://shoup.net/ntl/ **Available Versions**:: 11.5.1-GCC-11.3.0 11.5.1-GCC-13.2.0 NVHPC ----- **Description** C, C++ and Fortran compilers included with the NVIDIA HPC SDK (previously: PGI) **More Information** https://developer.nvidia.com/hpc-sdk/ **Available Versions**:: 20.11 22.7-CUDA-11.7.0 25.1-CUDA-12.6.0 21.7 21.9 21.11 23.1-CUDA-12.0.0 NWChem ------ **Description** NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters. NWChem software can handle: biomolecules, nanostructures, and solid-state; from quantum to classical, and all combinations; Gaussian basis functions or plane-waves; scaling from one to thousands of processors; properties and relativity. **More Information** https://www.nwchem-sw.org **Available Versions**:: 7.2.0-intel-2022a 7.0.2-intel-2021a NetLogo ------- **Description** NetLogo is a multi-agent programmable modeling environment. Itis used by tens of thousands of students, teachers and researchers worldwide.It also powers HubNet participatory simulations. It is authored by Uri Wilenskyand developed at the CCL. **More Information** http://ccl.northwestern.edu/netlogo/ **Available Versions**:: 6.0.4-64 6.2.0-64 Nextflow -------- **Description** Nextflow is a reactive workflow framework and a programming DSL that eases writing computational pipelines with complex data **More Information** https://www.nextflow.io/ **Available Versions**:: 23.04.2 22.04.0 24.04.2 NgsRelate --------- **Available Versions**:: 2022 Nim --- **Description** Nim is a systems and applications programming language. **More Information** https://nim-lang.org/ **Available Versions**:: 2.2.0-GCCcore-12.3.0 Ninja ----- **Description** Ninja is a small build system with a focus on speed. **More Information** https://ninja-build.org/ **Available Versions**:: 1.12.1-GCCcore-14.2.0 1.9.0-GCCcore-8.3.0 1.10.0-GCCcore-9.3.0 1.10.1-GCCcore-10.2.0 1.11.1-GCCcore-13.2.0 1.10.2-GCCcore-11.3.0 1.13.0-GCCcore-14.3.0 1.11.1-GCCcore-12.2.0 1.10.2-GCCcore-11.2.0 1.9.0-GCCcore-8.2.0 1.10.2-GCCcore-10.3.0 1.11.1-GCCcore-12.3.0 1.12.1-GCCcore-13.3.0 Normaliz -------- **Description** Normaliz is a open source tool for computations in affine monoids, vectorconfigurations, rational polyhedra and rational cones. Normaliz now computesrational and algebraic polyhedra, i.e., polyhedra defined over real algebraicextensions of QQ. **More Information** https://www.normaliz.uni-osnabrueck.de/ **Available Versions**:: 3.10.1-gfbf-2022a OPARI2 ------ **Description** OPARI2, the successor of Forschungszentrum Juelich's OPARI, is a source-to-source instrumentation tool for OpenMP and hybrid codes. It surrounds OpenMP directives and runtime library calls with calls to the POMP2 measurement interface. **More Information** https://www.score-p.org **Available Versions**:: 2.0.7-GCCcore-11.3.0 2.0.5-GCCcore-9.3.0 ORCA ---- **Description** ORCA is a flexible, efficient and easy-to-use general purpose tool for quantumchemistry with specific emphasis on spectroscopic properties of open-shellmolecules. It features a wide variety of standard quantum chemical methodsranging from semiempirical methods to DFT to single- and multireferencecorrelated ab initio methods. It can also treat environmental and relativisticeffects. **More Information** https://orcaforum.kofo.mpg.de **Available Versions**:: 5.0.4-gompi-2021b-static 5.0.3-gompi-2021b 5.0.0-gompi-2019b 5.0.4-gompi-2022a 4.2.1-gompi-2019b-dba 6.0.0-gompi-2023a 5.0.4-gompi-2023a 6.1.0-gompi-2024a 5.0.4-gompi-2021b 6.0.1-gompi-2023b OSPRay ------ **Description** Open, Scalable, and Portable Ray Tracing Engine **More Information** https://www.ospray.org **Available Versions**:: 3.2.0 2.12.0 OSU-Micro-Benchmarks -------------------- **Description** OSU Micro-Benchmarks **More Information** https://mvapich.cse.ohio-state.edu/benchmarks/ **Available Versions**:: 6.2-gompi-2022b 5.8-fosscuda-2020b OTF2 ---- **Description** The Open Trace Format 2 is a highly scalable, memory efficient event trace data format plus support library. It is the new standard trace format for Scalasca, Vampir, and TAU and is open for other tools. **More Information** https://www.score-p.org **Available Versions**:: 2.2-GCCcore-9.3.0 3.0.2-GCCcore-11.3.0 Octave ------ **Description** GNU Octave is a high-level interpreted language, primarily intended for numerical computations. **More Information** https://www.gnu.org/software/octave/ **Available Versions**:: 7.1.0-foss-2021b OpenBLAS -------- **Description** OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version. **More Information** https://xianyi.github.com/OpenBLAS/ **Available Versions**:: 0.3.7-GCC-8.3.0 0.3.1-GCC-7.3.0-2.30 0.3.20-NVHPC-22.7-CUDA-11.7.0 0.3.20-GCC-11.3.0 0.3.9-GCC-9.3.0 0.3.18-GCC-11.2.0 0.3.30-GCC-14.3.0 0.3.21-GCC-12.2.0 0.3.27-GCC-13.3.0 0.3.5-GCC-8.2.0-2.31.1 0.3.29-GCC-14.2.0 0.3.12-GCC-10.2.0 0.3.23-GCC-12.3.0 0.3.15-GCC-10.3.0 0.3.24-GCC-13.2.0 OpenCV ------ **Description** OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library. OpenCV was built to provide a common infrastructure for computer vision applications and to accelerate the use of machine perception in the commercial products. Includes extra modules for OpenCV from the contrib repository. **More Information** https://opencv.org/ **Available Versions**:: 4.8.1-foss-2023a-contrib 4.6.0-foss-2022a-contrib OpenColorIO ----------- **Description** OpenColorIO (OCIO) is a complete color management solution geared towards motion picture production with an emphasis on visual effects and computer animation. **More Information** http://opencolorio.org/ **Available Versions**:: 1.1.0-foss-2018b OpenEXR ------- **Description** OpenEXR is a high dynamic-range (HDR) image file format developed by Industrial Light & Magic for use in computer imaging applications **More Information** https://www.openexr.com/ **Available Versions**:: 2.4.1-GCCcore-9.3.0 2.4.0-GCCcore-8.3.0 3.1.5-GCCcore-12.2.0 3.1.7-GCCcore-12.3.0 3.2.0-GCCcore-13.2.0 2.5.5-GCCcore-10.2.0 3.2.4-GCCcore-13.3.0 3.1.5-GCCcore-11.3.0 OpenFOAM -------- **Description** OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics. **More Information** https://www.openfoam.com/ **Available Versions**:: v2012-foss-2020a 11-foss-2023a 11-foss-2022a 6-foss-2018b v2006-foss-2020a 8-foss-2020a v2206-foss-2022a v2106-foss-2021a 9-foss-2021a 10-intel-2022a 10-foss-2022a 5.0-20180108-foss-2018b 10-foss-2022a OpenFOAM-ESI ------------ **Available Versions**:: v2006-foss-2020a OpenJPEG -------- **Description** OpenJPEG is an open-source JPEG 2000 codec written in C language. It has been developed in order to promote the use of JPEG 2000, a still-image compression standard from the Joint Photographic Experts Group (JPEG). Since may 2015, it is officially recognized by ISO/IEC and ITU-T as a JPEG 2000 Reference Software. **More Information** https://www.openjpeg.org/ **Available Versions**:: 2.5.0-GCCcore-11.3.0 2.5.2-GCCcore-13.3.0 2.5.0-GCCcore-12.3.0 2.5.0-GCCcore-13.2.0 2.5.0-GCCcore-12.2.0 2.4.0-GCCcore-11.2.0 2.5.3-GCCcore-14.2.0 OpenMM ------ **Description** OpenMM is a toolkit for molecular simulation. **More Information** https://openmm.org **Available Versions**:: 7.5.1-foss-2021b-DeepMind-patch 7.5.1-foss-2021a-DeepMind-patch 7.4.2-intel-2020a-Python-3.8.2 8.0.0-foss-2022a 7.4.1-foss-2019b-Python-3.7.4 OpenMPI ------- **Description** The Open MPI Project is an open source MPI-3 implementation. **More Information** https://www.open-mpi.org/ **Available Versions**:: 4.1.1-GCC-10.3.0 4.1.4-GCC-11.3.0 5.0.8-GCC-14.3.0 4.1.5-GCC-12.3.0 4.1.6-GCC-13.2.0 4.0.3-GCC-9.3.0 4.0.5-GCC-10.2.0 4.1.4-GCC-12.2.0 3.1.1-gcccuda-2018b 3.1.4-gcccuda-2019b 4.0.5-gcccuda-2020b 3.1.4-GCC-8.3.0 3.1.4-PGI-19.10-GCC-8.3.0-2.32 3.1.3-GCC-8.2.0-2.31.1 4.0.3-gcccuda-2020a 5.0.3-GCC-13.3.0 4.1.1-intel-compilers-2021.2.0 4.1.4-NVHPC-22.7-CUDA-11.7.0 4.1.1-GCC-11.2.0 3.1.1-GCC-7.3.0-2.30 4.0.5-iccifort-2020.4.304 3.1.4-GCC-8.3.0-dba 5.0.7-GCC-14.2.0 4.1.1-GCC-11.2.0-CXX OpenMolcas ---------- **Description** OpenMolcas is a quantum chemistry software package. This package is NON-MPI and includes QCMaquis. Please use multithreading on a single node. **More Information** https://gitlab.com/Molcas/OpenMolcas **Available Versions**:: 23.06-GCC-11.2.0-QCMaquis 18.09-intel-2020b-Python-3.6.6 20.10-intel-2020a-Python-3.8.2 23.06-gomkl-2023a 21.06-intel-2021a OpenPGM ------- **Description** OpenPGM is an open source implementation of the Pragmatic General Multicast (PGM) specification in RFC 3208 available at www.ietf.org. PGM is a reliable and scalable multicast protocol that enables receivers to detect loss, request retransmission of lost data, or notify an application of unrecoverable loss. PGM is a receiver-reliable protocol, which means the receiver is responsible for ensuring all data is received, absolving the sender of reception responsibility. **More Information** https://code.google.com/p/openpgm/ **Available Versions**:: 5.2.122-GCCcore-11.2.0 5.2.122-GCCcore-11.3.0 5.2.122-GCCcore-8.3.0 5.2.122-GCCcore-12.3.0 5.2.122-GCCcore-10.3.0 5.2.122-GCCcore-10.2.0 5.2.122-GCCcore-9.3.0 OpenSSL ------- **Description** The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) protocols as well as a full-strength general purpose cryptography library. **More Information** https://www.openssl.org/ **Available Versions**:: 3 1.1.1w-GCCcore-12.3.0 1.1.1t-GCCcore-12.2.0 1.1.1w-GCCcore-13.2.0 1.1 1.1.1t-GCCcore-12.3.0 OptaDOS ------- **Available Versions**:: v2018-foss-2018b 1.2.380-GCC-11.3.0 OrthoFinder ----------- **Description** OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics **More Information** https://github.com/davidemms/OrthoFinder **Available Versions**:: 2.3.8-foss-2019b-Python-3.7.4 2.3.8-foss-2019b-Python-2.7.16 PAPI ---- **Description** PAPI provides the tool designer and application engineer with a consistent interface and methodology for use of the performance counter hardware found in most major microprocessors. PAPI enables software engineers to see, in near real time, the relation between software performance and processor events. In addition Component PAPI provides access to a collection of components that expose performance measurement opportunites across the hardware and software stack. **More Information** https://icl.cs.utk.edu/projects/papi/ **Available Versions**:: 6.0.0-GCCcore-9.3.0 6.0.0-GCCcore-10.2.0 PAUP ---- **Description** PAUP* (Phylogenetic Analysis Using Parsimony *and other methods) is acomputational phylogenetics program for inferring evolutionary trees. **More Information** https://paup.phylosolutions.com/ **Available Versions**:: 4.0a168-centos64 PCRE ---- **Description** The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5. **More Information** https://www.pcre.org/ **Available Versions**:: 8.44-GCCcore-9.3.0 8.45-GCCcore-13.2.0 8.43-GCCcore-8.3.0 8.41-GCCcore-7.3.0 8.45-GCCcore-12.2.0 8.44-GCCcore-10.2.0 8.45-GCCcore-11.2.0 8.44-GCCcore-10.3.0 8.45-GCCcore-11.3.0 8.43-GCCcore-8.2.0 8.45-GCCcore-12.3.0 8.45-GCCcore-13.3.0 PCRE2 ----- **Description** The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5. **More Information** https://www.pcre.org/ **Available Versions**:: 10.36-GCCcore-10.3.0 10.45-GCCcore-14.3.0 10.33-GCCcore-8.3.0 10.43-GCCcore-13.3.0 10.45-GCCcore-14.2.0 10.37-GCCcore-11.2.0 10.34-GCCcore-9.3.0 10.40-GCCcore-11.3.0 10.42-GCCcore-12.3.0 10.42-GCCcore-13.2.0 10.40-GCCcore-12.2.0 10.35-GCCcore-10.2.0 PDAL ---- **Description** PDAL is Point Data Abstraction Library. It is a C/C++ open source library and applications fortranslating and processing point cloud data. It is not limited to LiDAR data,although the focus and impetus for many of the tools in the library have their origins in LiDAR. **More Information** https://pdal.io/ **Available Versions**:: 2.8.2-foss-2023a PDT --- **Description** Program Database Toolkit (PDT) is a framework for analyzing source code written in several programming languages and for making rich program knowledge accessible to developers of static and dynamic analysis tools. PDT implements a standard program representation, the program database (PDB), that can be accessed in a uniform way through a class library supporting common PDB operations. **More Information** https://www.cs.uoregon.edu/research/pdt/ **Available Versions**:: 3.25.1-GCCcore-9.3.0 PEPPAN ------ **Available Versions**:: 2023 PETSc ----- **Description** PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. **More Information** https://www.mcs.anl.gov/petsc **Available Versions**:: 3.23.5-foss-2025a 3.17.4-foss-2022a 3.12.4-foss-2020a-Python-3.8.2 3.20.3-foss-2023a 3.15.1-foss-2021a 3.15.0-foss-2020b 3.12.4-foss-2019b-Python-3.7.4 3.14.4-foss-2020b 3.12.4-intel-2020a-Python-3.8.2 3.17.4-foss-2021a PGI --- **Description** C, C++ and Fortran compilers from The Portland Group - PGI **More Information** http://www.pgroup.com/ **Available Versions**:: 16.5-GCC-7.3.0-2.30 19.10-GCC-8.3.0-2.32 18.10-GCC-8.1.0-2.30 18.10-GCC-7.3.0-2.30 PGPLOT ------ **Description** The PGPLOT Graphics Subroutine Library is a Fortran- or C-callable, device-independent graphics package for making simple scientific graphs. It is intended for making graphical images of publication quality with minimum effort on the part of the user. For most applications, the program can be device-independent, and the output can be directed to the appropriate device at run time. **More Information** https://sites.astro.caltech.edu/~tjp/pgplot/ **Available Versions**:: 5.2.2-GCCcore-11.2.0 PIRATE ------ **Description** PIRATE clusters genes (or other annotated features) over a wide range of amino-acid or nucleotide identity thresholds, and classifies paralogous genes families into either putative gene fission/fusion events or gene duplications. Furthermore, PIRATE provides a measure of allelic variance and cluster homology, and orders the resulting pangenome on a pangenome graph. Additional scripts are provided for comparison and visualization. PIRATE provides a robust framework for analysing the pangenomes of bacteria, from largely clonal to panmictic species. **More Information** https://github.com/SionBayliss/PIRATE **Available Versions**:: 1.0.5 PLINK ----- **Description** plink-1.9-x86_64: Whole-genome association analysis toolset **More Information** https://www.cog-genomics.org/plink/1.9/ **Available Versions**:: 1.9b_6.21-x86_64 2.00a2.3_x86_64 PLINKSEQ -------- **Description** PLINK/SEQ is an open-source C/C++ library for working with human genetic variation data. The specific focus is to provide a platform for analytic tool development for variation data from large-scale resequencing and genotyping projects, particularly whole-exome and whole-genome studies. It is independent of (but designed to be complementary to) the existing PLINK package. **More Information** https://atgu.mgh.harvard.edu/plinkseq/ **Available Versions**:: 0.10-GCCcore-7.3.0 PLUMED ------ **Description** PLUMED is an open source library for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines. Free energy calculations can be performed as a function of many order parameters with a particular focus on biological problems, using state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. **More Information** http://www.plumed-code.org **Available Versions**:: 2.5.1-foss-2019a 2.7.0-foss-2020b 2.7.2-foss-2021a 2.6.0-intel-2020a-Python-3.8.2 2.5.1-foss-2020a 2.6.0-foss-2020a-Python-3.8.2 2.7.0-foss-2020a 2.6.2-foss-2020a-Python-3.8.2 2.8.0-foss-2021b 2.5.1-foss-2019b 2.8.1-foss-2022a 2.7.3-foss-2021b 2.6.2-intel-2020b 2.9.2-foss-2023b 2.9.4-foss-2025a 2.7.0-intel-2020b 2.9.0-foss-2023a PLY --- **Description** PLY is yet another implementation of lex and yacc for Python. **More Information** https://www.dabeaz.com/ply/ **Available Versions**:: 3.11-GCCcore-12.3.0 3.11-GCCcore-8.3.0-Python-3.7.4 PMIx ---- **Description** Process Management for Exascale EnvironmentsPMI Exascale (PMIx) represents an attempt toprovide an extended version of the PMI standard specifically designedto support clusters up to and including exascale sizes. The overallobjective of the project is not to branch the existing pseudo-standarddefinitions - in fact, PMIx fully supports both of the existing PMI-1and PMI-2 APIs - but rather to (a) augment and extend those APIs toeliminate some current restrictions that impact scalability, and (b)provide a reference implementation of the PMI-server that demonstratesthe desired level of scalability. **More Information** https://pmix.org/ **Available Versions**:: 4.2.6-GCCcore-13.2.0 3.1.5-GCCcore-10.2.0 5.0.2-GCCcore-13.3.0 3.1.5-GCCcore-9.3.0 5.0.8-GCCcore-14.3.0 5.0.6-GCCcore-14.2.0 4.1.2-GCCcore-11.3.0 3.2.3-GCCcore-10.3.0 4.1.0-GCCcore-11.2.0 4.2.2-GCCcore-12.2.0 4.2.4-GCCcore-12.3.0 POV-Ray ------- **Description** The Persistence of Vision Raytracer, or POV-Ray, is a ray tracing program which generates images from a text-based scene description, and is available for a variety of computer platforms. POV-Ray is a high-quality, Free Software tool for creating stunning three-dimensional graphics. The source code is available for those wanting to do their own ports. **More Information** https://www.povray.org/ **Available Versions**:: 3.7.0.8-GCC-10.2.0 PRANK ----- **Description** PRANK is a probabilistic multiple alignment program for DNA, codon and amino-acid sequences. PRANK is based on a novel algorithm that treats insertions correctly and avoids over-estimation of the number of deletion events. **More Information** http://wasabiapp.org/software/prank/ **Available Versions**:: 170427-GCC-9.3.0 170427-GCC-11.2.0 170427-GCC-11.3.0 170427-GCC-12.3.0 PROJ ---- **Description** Program proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates **More Information** http://trac.osgeo.org/proj/ **Available Versions**:: 6.0.0-GCCcore-8.2.0 5.0.0-foss-2018b 8.0.1-GCCcore-10.3.0 7.0.0-GCCcore-9.3.0 9.3.1-GCCcore-13.2.0 7.2.1-GCCcore-10.2.0 8.1.0-GCCcore-11.2.0 6.2.1-GCCcore-8.3.0 9.2.0-GCCcore-12.3.0 9.0.0-GCCcore-11.3.0 9.4.1-GCCcore-13.3.0 PRRTE ----- **Description** PRRTE is the PMIx Reference RunTime Environment **More Information** https://docs.prrte.org/ **Available Versions**:: 3.0.11-GCCcore-14.3.0 3.0.5-GCCcore-13.3.0 3.0.8-GCCcore-14.2.0 PSIPRED ------- **Description** Accurate protein secondary structure prediction **More Information** http://bioinf.cs.ucl.ac.uk **Available Versions**:: 4.02-GCC-12.3.0 Pango ----- **Description** Pango is a library for laying out and rendering of text, with an emphasis on internationalization.Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in thecontext of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x. **More Information** https://www.pango.org/ **Available Versions**:: 1.44.7-GCCcore-9.3.0 1.50.14-GCCcore-12.3.0 1.48.8-GCCcore-11.2.0 1.50.12-GCCcore-12.2.0 1.48.5-GCCcore-10.3.0 1.54.0-GCCcore-13.3.0 1.47.0-GCCcore-10.2.0 1.51.0-GCCcore-13.2.0 1.50.7-GCCcore-11.3.0 ParMETIS -------- **Description** ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes. **More Information** http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview **Available Versions**:: 4.0.3-gompi-2019b 4.0.3-gompi-2025a 4.0.3-gompi-2020b 4.0.3-gompi-2022a 4.0.3-gompi-2021a 4.0.3-gompi-2023a 4.0.3-iimpi-2020a 4.0.3-gompi-2019a 4.0.3-gompi-2020a ParaView -------- **Description** ParaView is a scientific parallel visualizer. **More Information** https://www.paraview.org **Available Versions**:: 5.13.2-foss-2024a 5.10.1-foss-2022a-mpi 5.9.1-foss-2021a-mpi 6.0.1-foss-2025a 5.8.0-intel-2020a-Python-3.8.2-mpi 5.8.0-foss-2020a-Python-3.8.2-mpi 5.6.2-foss-2019b-Python-3.7.4-mpi PennCNV ------- **Description** A free software tool for Copy Number Variation (CNV) detection from SNP genotyping arrays. Currently it can handle signal intensity data from Illumina and Affymetrix arrays. With appropriate preparation of file format, it can also handle other types of SNP arrays and oligonucleotide arrays. **More Information** https://penncnv.openbioinformatics.org/ **Available Versions**:: 1.0.5-GCCcore-8.3.0 Perl ---- **Description** Larry Wall's Practical Extraction and Report Language **More Information** https://www.perl.org/ **Available Versions**:: 5.30.0-GCCcore-7.3.0 5.36.0-GCCcore-12.2.0-minimal 5.30.2-GCCcore-9.3.0-minimal 5.34.1-GCCcore-11.3.0-minimal 5.34.1-GCCcore-11.3.0 5.28.0-GCCcore-10.2.0 5.38.2-GCCcore-13.3.0 5.28.0-GCCcore-8.1.0 5.38.0-GCCcore-13.2.0 5.32.1-GCCcore-10.3.0 5.38.0 5.28.1-GCCcore-8.2.0 5.40.0-GCCcore-14.2.0 5.30.0-GCCcore-8.3.0 5.40.2-GCCcore-14.3.0 5.36.1-GCCcore-12.3.0 5.36.0-GCCcore-12.3.0 5.34.0-GCCcore-11.2.0-minimal 5.28.0-GCCcore-7.3.0 5.34.0-GCCcore-11.2.0-ARC 5.36.0-GCCcore-12.2.0 5.32.0-GCCcore-10.2.0-minimal 5.32.1-GCCcore-10.3.0-minimal 5.30.0-GCCcore-8.3.0-minimal 5.30.2-GCCcore-9.3.0 5.34.0-GCCcore-11.2.0 5.32.0-GCCcore-10.2.0 Perl-bundle-CPAN ---------------- **Description** A set of common packages from CPAN **More Information** https://www.perl.org/ **Available Versions**:: 5.38.2-GCCcore-13.3.0 5.36.1-GCCcore-12.3.0 5.38.0-GCCcore-13.2.0 5.40.0-GCCcore-14.2.0 PhyDyn ------ **Available Versions**:: 1.4.0 PhyloBayes-MPI -------------- **Description** A Bayesian software for phylogenetic reconstruction using mixture models **More Information** https://github.com/bayesiancook/pbmpi **Available Versions**:: 20161021-intel-2020b Pillow ------ **Description** Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors. **More Information** http://pillow.readthedocs.org/ **Available Versions**:: 6.0.0-GCCcore-8.2.0 11.3.0-GCCcore-14.2.0 6.2.1-GCCcore-8.3.0 10.0.0-GCCcore-12.3.0 8.3.2-GCCcore-11.2.0 7.0.0-GCCcore-9.3.0-Python-3.8.2 9.1.1-GCCcore-11.3.0 8.0.1-GCCcore-10.2.0 8.2.0-GCCcore-10.3.0 10.2.0-GCCcore-13.2.0 Pillow-SIMD ----------- **Description** Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors. **More Information** https://github.com/uploadcare/pillow-simd **Available Versions**:: 9.2.0-GCCcore-11.3.0 9.5.0-GCCcore-12.3.0 6.0.x.post0-GCCcore-8.2.0 8.2.0-GCCcore-10.3.0 10.4.0-GCCcore-13.3.0 Pilon ----- **Description** Pilon is an automated genome assembly improvement and variant detection tool **More Information** https://github.com/broadinstitute/pilon **Available Versions**:: 1.23-Java-11 1.24-Java-17 Pmw --- **Description** Pmw is a toolkit for building high-level compound widgets in Python using the Tkinter module. **More Information** http://pmw.sourceforge.net **Available Versions**:: 2.0.1-foss-2020a-Python-3.8.2 2.0.1-foss-2019b-Python-2.7.16 PnetCDF ------- **Description** Parallel netCDF: A Parallel I/O Library for NetCDF File Access **More Information** https://parallel-netcdf.github.io/ **Available Versions**:: 1.12.3-iimpi-2022a 1.12.3-gompi-2023a 1.12.3-gompi-2022a 1.14.0-gompi-2024a 1.12.1-gompi-2020a 1.12.3-gompi-2021b 1.12.2-gompic-2020b 1.12.2-gompi-2020b PostGis ------- **Available Versions**:: 2 PostgreSQL ---------- **Description** PostgreSQL is a powerful, open source object-relational database system. It is fully ACID compliant, has full support for foreign keys, joins, views, triggers, and stored procedures (in multiple languages). It includes most SQL:2008 data types, including INTEGER, NUMERIC, BOOLEAN, CHAR, VARCHAR, DATE, INTERVAL, and TIMESTAMP. It also supports storage of binary large objects, including pictures, sounds, or video. It has native programming interfaces for C/C++, Java, .Net, Perl, Python, Ruby, Tcl, ODBC, among others, and exceptional documentation. **More Information** https://www.postgresql.org/ **Available Versions**:: 13.3-GCCcore-10.3.0 16.1-GCCcore-13.2.0 13.4-GCCcore-11.2.0 16.1-GCCcore-12.3.0 16.4-GCCcore-13.3.0 14.4-GCCcore-11.3.0 ProtoMS ------- **Available Versions**:: 3.4 PyCairo ------- **Description** Python bindings for the cairo library **More Information** https://pycairo.readthedocs.io/ **Available Versions**:: 1.24.0-GCCcore-12.2.0 1.25.0-GCCcore-12.3.0 1.21.0-GCCcore-11.3.0 1.20.1-GCCcore-11.2.0 PyCharm ------- **Description** PyCharm Community Edition: Python IDE for Professional Developers **More Information** https://www.jetbrains.com/pycharm/ **Available Versions**:: 2024.1.6 2022.2.2 PyCifRW ------- **Description** PyCIFRW provides support for reading and writing CIF(Crystallographic Information Format) files using Python. **More Information** https://bitbucket.org/jamesrhester/pycifrw/src/development **Available Versions**:: 4.4.2-GCCcore-9.3.0 PyGObject --------- **Description** PyGObject is a Python package which provides bindings for GObject basedlibraries such as GTK, GStreamer, WebKitGTK, GLib, GIO and many more. **More Information** https://pygobject.readthedocs.io/ **Available Versions**:: 3.44.1-GCCcore-12.2.0 3.46.0-GCCcore-12.3.0 3.42.1-GCCcore-11.3.0 PyHMMER ------- **Description** HMMER is a biological sequence analysis tool that uses profile hidden Markovmodels to search for sequence homologs. HMMER3 is developed and maintained bythe Eddy/Rivas Laboratory at Harvard University.pyhmmer is a Python package, implemented using the Cython language, thatprovides bindings to HMMER3. It directly interacts with the HMMER internals,which has the following advantages over CLI wrappers (like hmmer-py) **More Information** https://github.com/althonos/pyhmmer **Available Versions**:: 0.10.15-gompi-2023b PyMOL ----- **Description** PyMOL is an OpenGL based molecular visualization system **More Information** http://sourceforge.net/projects/pymol **Available Versions**:: 2.3.0-foss-2019b-Python-2.7.16 2.5.0-foss-2020a-Python-3.8.2 PyOpenGL -------- **Description** PyOpenGL is the most common cross platform Python binding to OpenGL and related APIs. **More Information** http://pyopengl.sourceforge.net **Available Versions**:: 3.1.6-GCCcore-11.3.0 PyQt-builder ------------ **Description** PyQt-builder is the PEP 517 compliant build system for PyQt and projects thatextend PyQt. It extends the SIP build system and uses Qt’s qmake to perform theactual compilation and installation of extension modules. **More Information** http://www.example.com **Available Versions**:: 1.15.4-GCCcore-12.3.0 PyQt5 ----- **Description** PyQt5 is a set of Python bindings for v5 of the Qt application framework from The Qt Company.This bundle includes PyQtWebEngine, a set of Python bindings for The Qt Company’s Qt WebEngine framework. **More Information** https://www.riverbankcomputing.com/software/pyqt **Available Versions**:: 5.15.1-GCCcore-9.3.0-Python-3.8.2 5.15.10-GCCcore-12.3.0 5.15.4-GCCcore-11.2.0 5.15.5-GCCcore-11.3.0 PyQtGraph --------- **Description** PyQtGraph is a pure-python graphics and GUI library built on PyQt5/PySide2 and numpy. **More Information** http://www.pyqtgraph.org/ **Available Versions**:: 0.13.3-foss-2022a PySCF ----- **Description** PySCF is an open-source collection of electronic structure modules powered by Python. **More Information** http://www.pyscf.org **Available Versions**:: 1.7.6-foss-2021a 2.1.1-foss-2021a 1.7.0-foss-2020a-Python-3.8.2 1.6.3-foss-2019a-Python-3.7.2 PyTables -------- **Description** PyTables is a package for managing hierarchical datasets and designed to efficiently and easily cope with extremely large amounts of data. PyTables is built on top of the HDF5 library, using the Python language and the NumPy package. It features an object-oriented interface that, combined with C extensions for the performance-critical parts of the code (generated using Cython), makes it a fast, yet extremely easy to use tool for interactively browse, process and search very large amounts of data. One important feature of PyTables is that it optimizes memory and disk resources so that data takes much less space (specially if on-flight compression is used) than other solutions such as relational or object oriented databases. **More Information** https://www.pytables.org **Available Versions**:: 3.6.1-foss-2021a PyTorch ------- **Description** Tensors and Dynamic neural networks in Python with strong GPU acceleration.PyTorch is a deep learning framework that puts Python first. **More Information** https://pytorch.org/ **Available Versions**:: 1.11.0-foss-2021a-CUDA-11.3.1 1.6.0-foss-2019b-Python-3.7.4 1.12.1-foss-2022a-CUDA-11.7.0 1.12.0-foss-2022a-CUDA-11.8.0 2.1.2-foss-2023a-CUDA-12.0.0 1.6.0-fosscuda-2019b-Python-3.7.4 2.0.1-foss-2023a-CUDA-12.0.0 1.12.0-foss-2022a-CUDA-11.7.0 1.10.0-foss-2021a 2.1.2-foss-2023b 1.7.1-fosscuda-2020b 1.8.1-fosscuda-2019b-Python-3.7.4 1.12.0-foss-2022a 2.1.2-foss-2023a-CUDA-12.1.1 PyYAML ------ **Description** PyYAML is a YAML parser and emitter for the Python programming language. **More Information** https://github.com/yaml/pyyaml **Available Versions**:: 6.0-GCCcore-11.3.0 6.0-GCCcore-12.3.0 5.1-GCCcore-8.2.0 6.0.2-GCCcore-14.2.0 5.4.1-GCCcore-10.3.0 6.0.1-GCCcore-13.2.0 5.3-GCCcore-9.3.0 5.3.1-GCCcore-10.2.0 5.4.1-GCCcore-11.2.0 5.1.2-GCCcore-8.3.0 PyZMQ ----- **Description** Python bindings for ZeroMQ **More Information** https://www.zeromq.org/bindings:python **Available Versions**:: 25.1.1-GCCcore-12.3.0 Pysam ----- **Description** Pysam is a python module for reading and manipulating Samfiles. It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix. **More Information** https://github.com/pysam-developers/pysam **Available Versions**:: 0.15.3-GCC-8.3.0 0.18.0-GCC-11.2.0 0.19.1-GCC-11.3.0 0.16.0.1-GCC-9.3.0 Python ------ **Description** Python is a programming language that lets you work more quickly and integrate your systems more effectively. **More Information** https://python.org/ **Available Versions**:: 2.7.16-GCCcore-8.3.0 3.6.6-foss-2018b 3.12.3-GCCcore-13.3.0 3.13.5-GCCcore-14.3.0 3.6.6-intel-2020b 3.10.4-GCCcore-11.3.0 2.7.15-fosscuda-2018b 3.9.5-GCCcore-10.3.0-bare 2.7.18-GCCcore-11.2.0 3.7.4-GCCcore-8.3.0 3.9.6-GCCcore-11.2.0-bare 3.11.3-GCCcore-12.3.0 2.7.18-GCCcore-12.3.0 2.7.18-GCCcore-10.3.0-bare 3.8.6-GCCcore-10.2.0 3.9.5-GCCcore-10.3.0 2.7.18-GCCcore-10.2.0 2.7.16-GCCcore-8.3.0-bare 2.7.18-GCCcore-11.2.0-bare 3.10.8-GCCcore-12.2.0-bare 3.11.5-GCCcore-13.2.0 2.7.15-GCCcore-8.2.0 2.7.15-GCCcore-7.3.0-bare 3.10.8-GCCcore-12.2.0 3.7.2-GCCcore-8.2.0 2.7.15-foss-2018b 3.10.4-GCCcore-11.3.0-bare 3.9.6-GCCcore-11.2.0 3.13.1-GCCcore-14.2.0 2.7.18-GCCcore-12.2.0-bare 2.7.18-GCCcore-11.3.0-bare 2.7.18-GCCcore-9.3.0 3.8.2-GCCcore-9.3.0 Python-bundle-PyPI ------------------ **Description** Bundle of Python packages from PyPI **More Information** https://python.org/ **Available Versions**:: 2023.10-GCCcore-13.2.0 2025.04-GCCcore-14.2.0 2024.06-GCCcore-13.3.0 2023.06-GCCcore-12.3.0 2025.07-GCCcore-14.3.0 QCA --- **Description** Taking a hint from the similarly-named Java Cryptography Architecture, QCA aims to provide a straightforward and cross-platform crypto API, using Qt datatypes and conventions. QCA separates the API from the implementation, using plugins known as Providers. The advantage of this model is to allow applications to avoid linking to or explicitly depending on any particular cryptographic library. This allows one to easily change or upgrade crypto implementations without even needing to recompile the application! QCA should work everywhere Qt does, including Windows/Unix/MacOSX. **More Information** https://userbase.kde.org/QCA **Available Versions**:: 2.3.5-GCCcore-11.2.0 2.3.9-GCCcore-12.3.0 QGIS ---- **Description** QGIS is a user friendly Open Source Geographic Information System (GIS). **More Information** http://www.qgis.org/ **Available Versions**:: 3.40.2-foss-2023a 3.28.1-foss-2021b QIIME2 ------ **Description** QIIME is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data. **More Information** http://qiime2.org/ **Available Versions**:: 2022.8 2023.5 2019.7 QScintilla ---------- **Description** QScintilla is a port to Qt of Neil Hodgson's Scintilla C++ editor control **More Information** https://www.riverbankcomputing.com/software/qscintilla **Available Versions**:: 2.14.1-GCCcore-12.3.0 2.11.6-GCCcore-11.2.0 QUAST ----- **Description** QUAST evaluates genome assemblies by computing various metrics. It works both with and without reference genomes. The tool accepts multiple assemblies, thus is suitable for comparison. **More Information** https://github.com/ablab/quast **Available Versions**:: 5.0.2-foss-2020a-Python-3.8.2 Qhull ----- **Description** Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, furthest-site Delaunay triangulation, and furthest-site Voronoi diagram. The source code runs in 2-d, 3-d, 4-d, and higher dimensions. Qhull implements the Quickhull algorithm for computing the convex hull. **More Information** http://www.qhull.org **Available Versions**:: 2020.2-GCCcore-13.3.0 2020.2-GCCcore-11.3.0 2020.2-GCCcore-10.3.0 2020.2-GCCcore-14.2.0 2019.1-GCCcore-8.3.0 2020.2-GCCcore-12.3.0 2020.2-GCCcore-11.2.0 2020.2-GCCcore-13.2.0 Qt5 --- **Description** Qt is a comprehensive cross-platform C++ application framework. **More Information** https://qt.io/ **Available Versions**:: 5.15.10-GCCcore-12.3.0 5.15.5-GCCcore-11.3.0 5.14.1-GCCcore-9.3.0 5.15.2-GCCcore-11.2.0 5.15.2-GCCcore-10.3.0 5.13.1-GCCcore-8.3.0 Qt5Webkit --------- **Description** Qt Port of WebKit. WebKit is an open source web browser engine. **More Information** https://github.com/qt/qtwebkit **Available Versions**:: 5.212.0-alpha4-GCCcore-11.2.0 5.212.0-alpha4-GCCcore-12.3.0 Qt6 --- **Description** Qt is a comprehensive cross-platform C++ application framework. **More Information** https://qt.io/ **Available Versions**:: 6.6.3-GCCcore-13.2.0 6.7.2-GCCcore-13.3.0 6.9.3-GCCcore-14.2.0 QtKeychain ---------- **Description** Platform-independent Qt API for storing passwords securely. **More Information** https://github.com/frankosterfeld/qtkeychain **Available Versions**:: 0.14.3-GCCcore-12.3.0 0.13.2-GCCcore-11.2.0 QtPy ---- **Description** QtPy is a small abstraction layer that lets you write applications using a single API call to either PyQt or PySide. It provides support for PyQt5, PyQt4, PySide2 and PySide. **More Information** https://github.com/spyder-ide/qtpy **Available Versions**:: 2.3.0-GCCcore-11.3.0 Qualimap -------- **Available Versions**:: 2023 Quandl ------ **Description** A Python library for Quandl’s RESTful API. **More Information** https://pypi.python.org/pypi/Quandl **Available Versions**:: 3.6.1-foss-2021a 3.4.8-foss-2019a 3.5.3-foss-2020a-Python-3.8.2 QuantumESPRESSO --------------- **Description** Quantum ESPRESSO is an integrated suite of computer codesfor electronic-structure calculations and materials modeling at the nanoscale.It is based on density-functional theory, plane waves, and pseudopotentials(both norm-conserving and ultrasoft). **More Information** https://www.quantum-espresso.org **Available Versions**:: 7.3.1-foss-2023a 7.1-foss-2022a 7.4-foss-2024a 7.1-intel-2022a 7.2-foss-2023a Qwt --- **Description** The Qwt library contains GUI Components and utility classes which are primarily useful for programs with a technical background. **More Information** https://qwt.sourceforge.net/ **Available Versions**:: 6.1.4-GCCcore-8.3.0 6.2.0-GCCcore-11.2.0 6.3.0-GCCcore-12.3.0 R - **Description** R is a free software environment for statistical computing and graphics. **More Information** http://www.r-project.org/ **Available Versions**:: 4.2.1-foss-2022a-ARC 4.2.2-foss-2022a 4.3.2-gfbf-2023a 4.2.2-foss-2022a-ARC 4.4.2-gfbf-2024a 4.2.1-foss-2021b 4.1.2-foss-2021b-ARC 4.2.1-foss-2021b-ARC 4.1.2-foss-2021b 4.4.1-gfbf-2023b 4.2.1-foss-2022a R-bundle-Bioconductor --------------------- **Description** Bioconductor provides tools for the analysis and coprehension of high-throughput genomic data. **More Information** https://bioconductor.org **Available Versions**:: 3.20-foss-2024a-R-4.4.2 3.14-foss-2021b-R-4.1.2 3.18-foss-2023a-R-4.3.2 3.15-foss-2022a-R-4.2.1 R-bundle-CRAN ------------- **Description** Bundle of R packages from CRAN **More Information** https://www.r-project.org/ **Available Versions**:: 2024.11-foss-2024a 2024.06-foss-2023b 2023.12-foss-2023a RAiSD ----- **Available Versions**:: 2025 2024 RAxML ----- **Description** RAxML search algorithm for maximum likelihood based inference of phylogenetic trees. **More Information** https://github.com/stamatak/standard-RAxML **Available Versions**:: 8.2.12-gompi-2020a-hybrid-avx2 8.2.12-gompi-2021b-hybrid-avx2 RAxML-NG -------- **Description** RAxML-NG is a phylogenetic tree inference tool whichuses maximum-likelihood (ML) optimality criterion. Its search heuristic is based on iteratively performing a series of Subtree Pruning and Regrafting (SPR) moves, which allows to quickly navigate to the best-known ML tree. **More Information** https://github.com/amkozlov/raxml-ng **Available Versions**:: 1.0.2-gompi-2020b 1.2.2-gompi-2023b 1.2.0-GCC-12.3.0 RE2 --- **Description** RE2 is a fast, safe, thread-friendly alternative to backtracking regularexpression engines like those used in PCRE, Perl, and Python. It is a C++library. **More Information** https://github.com/google/re2 **Available Versions**:: 2023-08-01-GCCcore-12.3.0 2022-02-01-GCCcore-11.2.0 2024-07-02-GCCcore-13.3.0 2022-06-01-GCCcore-11.3.0 2020-07-01-GCCcore-8.3.0 2021-06-01-GCCcore-10.2.0 RECON ----- **Description** Patched version of RECON to be used with RepeatModeler. **More Information** https://www.repeatmasker.org/RepeatModeler/ **Available Versions**:: 1.08-GCC-10.2.0 1.08-GCC-10.3.0 RELION ------ **Description** RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computer program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM). **More Information** http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page **Available Versions**:: 3.0.4-foss-2019b RFdiffusion ----------- **Description** RFdiffusion is an open source method for structure generation, with or without conditional information (a motif, target etc). It can perform a whole range of protein design challenges as we have outlined in the RFdiffusion paper. **More Information** https://github.com/RosettaCommons/RFdiffusion **Available Versions**:: 1.1.0-foss-2022a 1.1.0-foss-2022a-CUDA-11.7.0 RMBlast ------- **Description** RMBlast is a RepeatMasker compatible version of the standard NCBI BLAST suite. The primary difference between this distribution and the NCBI distribution is the addition of a new program 'rmblastn' for use with RepeatMasker and RepeatModeler. **More Information** https://www.repeatmasker.org/RMBlast.html **Available Versions**:: 2.11.0-gompi-2021a 2.13.0-gompi-2022a 2.11.0-gompi-2020b ROOT ---- **Description** The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data in a very efficient way. **More Information** https://root.cern.ch/drupal/ **Available Versions**:: 6.24.06-foss-2021b RStudio ------- **Available Versions**:: 2022.02-R-4.2.1-ARC 2025.09-R-4.4.2-ARC 2023.06-R-4.2.2-ARC RStudio-Server -------------- **Description** This is the RStudio Server version.RStudio is a set of integrated tools designed to help you be more productive with R.The server can be started with: rserver --server-daemonize=0 --www-port=8787If you need a database config one can be created with: MYTMP=`mktemp -d` && echo -e "provider=sqlite\ndirectory=${MYTMP}/sqlite" > "${MYTMP}/db.conf"and then used with: rserver ... --database-config-file="${MYTMP}/db.conf" **More Information** https://www.rstudio.com/ **Available Versions**:: 2022.07.2+576-foss-2022a-Java-11-R-4.2.1 2024.12.0+467-foss-2024a-R-4.4.2 Racon ----- **Description** Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. **More Information** https://github.com/lbcb-sci/racon **Available Versions**:: 1.4.21-GCCcore-10.3.0 1.5.0-GCCcore-11.2.0 RapidJSON --------- **Description** A fast JSON parser/generator for C++ with both SAX/DOM style API **More Information** https://rapidjson.org **Available Versions**:: 1.1.0-GCCcore-10.3.0 1.1.0-GCCcore-11.3.0 1.1.0-20230928-GCCcore-12.3.0 1.1.0-GCCcore-8.3.0 1.1.0-GCCcore-9.3.0 1.1.0-20240815-GCCcore-13.3.0 1.1.0-GCCcore-11.2.0 Ray-assembler ------------- **Description** Parallel genome assemblies for parallel DNA sequencing **More Information** http://denovoassembler.sourceforge.net/ **Available Versions**:: 2.3.1-iimpi-2020a ReFrame ------- **Description** ReFrame is a framework for writing regression tests for HPC systems. **More Information** https://github.com/reframe-hpc/reframe **Available Versions**:: 4.6.2-GCCcore-13.2.0 Redis ----- **Description** Redis is an open source (BSD licensed), in-memory data structure store, used asa database, cache, and message broker. Redis provides data structures such asstrings, hashes, lists, sets, sorted sets with range queries, bitmaps,hyperloglogs, geospatial indexes, and streams. Redis has built-in replication,Lua scripting, LRU eviction, transactions, and different levels of on-diskpersistence, and provides high availability via Redis Sentinel and automaticpartitioning with Redis Cluster. **More Information** https://redis.io **Available Versions**:: 8.0.2-GCCcore-14.2.0 RepeatMasker ------------ **Description** RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. **More Information** https://www.repeatmasker.org/ **Available Versions**:: 4.1.2-p1-foss-2020b 4.1.2-p1-foss-2021a 4.1.5-foss-2022a RepeatModeler ------------- **Description** RepeatModeler is a de novo transposable element (TE) family identification and modeling package. **More Information** https://www.repeatmasker.org/ **Available Versions**:: 2.0.2a-foss-2020b RepeatScout ----------- **Description** De Novo Repeat Finder, Price A.L., Jones N.C. and Pevzner P.A. Developed and tested with our multiple sequence version of RepeatScout ( 1.0.6 ) **More Information** https://www.repeatmasker.org/ **Available Versions**:: 1.0.6-GCC-10.2.0 1.0.6-GCC-10.3.0 RevBayes -------- **Description** RevBayes provides an interactive environment for statistical computation in phylogenetics. It is primarily intended for modeling, simulation, and Bayesian inference in evolutionary biology, particularly phylogenetics. **More Information** https://revbayes.github.io/ **Available Versions**:: 1.1.1-GCC-10.2.0 1.2.1-gompi-2022a Roary ----- **Description** Rapid large-scale prokaryote pan genome analysis **More Information** https://github.com/sanger-pathogens/Roary **Available Versions**:: 3.13.0-foss-2022a Ruby ---- **Description** Ruby is a dynamic, open source programming language with a focus on simplicity and productivity. It has an elegant syntax that is natural to read and easy to write. **More Information** https://www.ruby-lang.org **Available Versions**:: 3.0.1-GCCcore-10.3.0 3.0.3-GCCcore-12.3.0 3.0.1-GCCcore-11.2.0 3.3.0-GCCcore-12.3.0 Rust ---- **Description** Rust is a systems programming language that runs blazingly fast, prevents segfaults, and guarantees thread safety. **More Information** https://www.rust-lang.org **Available Versions**:: 1.88.0-GCCcore-14.3.0 1.73.0-GCCcore-13.2.0 1.54.0-GCCcore-11.2.0 1.60.0-GCCcore-11.3.0 1.85.0-GCCcore-13.3.0 1.65.0-GCCcore-12.2.0 1.76.0-GCCcore-13.2.0 1.85.1-GCCcore-14.2.0 1.70.0-GCCcore-12.3.0 1.52.1-GCCcore-10.3.0 1.78.0-GCCcore-13.3.0 SAMtools -------- **Description** SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. **More Information** http://www.htslib.org/ **Available Versions**:: 0.1.20-foss-2020a 1.13-GCC-11.3.0 1.9-foss-2018b 1.15.1-GCC-11.2.0 1.12-GCC-10.2.0 1.14-GCC-11.2.0 0.1.20-GCC-8.3.0 1.11-GCC-10.2.0 1.10-GCC-8.3.0 1.13-GCC-10.3.0 1.21-GCC-13.3.0 1.10-GCC-9.3.0 1.16.1-GCC-11.3.0 SCOTCH ------ **Description** Software package and libraries for sequential and parallel graph partitioning,static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning. **More Information** https://www.labri.fr/perso/pelegrin/scotch/ **Available Versions**:: 7.0.8-gompi-2025a 6.1.0-gompi-2020b 6.1.0-gompi-2021a 7.0.4-gompi-2023b 6.0.9-gompi-2020a 6.0.6-foss-2018b 7.0.3-gompi-2023a 6.0.6-gompi-2019a 6.0.9-iimpi-2020a 7.0.1-gompi-2022a 6.0.9-gompi-2019b SCons ----- **Description** SCons is a software construction tool. **More Information** https://www.scons.org/ **Available Versions**:: 4.0.1-GCCcore-10.2.0 3.1.1-GCCcore-8.3.0 3.0.5-GCCcore-8.2.0 3.0.1-fosscuda-2018b-Python-2.7.15 4.2.0-GCCcore-11.2.0 3.0.1-GCCcore-7.3.0-Python-2.7.15-bare 4.4.0-GCCcore-11.3.0 3.0.5-GCCcore-8.2.0-Python-2.7.15 SDL2 ---- **Description** SDL: Simple DirectMedia Layer, a cross-platform multimedia library **More Information** https://www.libsdl.org/ **Available Versions**:: 2.30.6-GCCcore-13.3.0 2.28.2-GCCcore-12.3.0 2.26.3-GCCcore-12.2.0 2.32.8-GCCcore-14.2.0 2.0.20-GCCcore-11.2.0 2.0.14-GCCcore-10.2.0 2.28.5-GCCcore-13.2.0 SIONlib ------- **Description** SIONlib is a scalable I/O library for parallel access to task-local files. The library not only supports writing and reading binary data to or from several thousands of processors into a single or a small number of physical files, but also provides global open and close functions to access SIONlib files in parallel. This package provides a stripped-down installation of SIONlib for use with performance tools (e.g., Score-P), with renamed symbols to avoid conflicts when an application using SIONlib itself is linked against a tool requiring a different SIONlib version. **More Information** https://www.fz-juelich.de/ias/jsc/EN/Expertise/Support/Software/SIONlib/_node.html **Available Versions**:: 1.7.6-GCCcore-9.3.0-tools 1.7.7-foss-2022a 1.7.7-GCCcore-11.3.0-tools 1.7.6-foss-2019b 1.7.6-foss-2020a 1.7.7-foss-2022b SIP --- **Description** SIP is a tool that makes it very easy to create Python bindings for C and C++ libraries. **More Information** http://www.riverbankcomputing.com/software/sip/ **Available Versions**:: 6.8.1-GCCcore-12.3.0 SKESA ----- **Description** SKESA is a de-novo sequence read assembler for cultured single isolate genomes based on DeBruijn graphs. **More Information** https://github.com/ncbi/SKESA **Available Versions**:: 2.4.0-gompi-2024a_saute.1.3.0_2 SLEPc ----- **Description** SLEPc (Scalable Library for Eigenvalue Problem Computations) is a software library for the solution of large scale sparse eigenvalue problems on parallel computers. It is an extension of PETSc and can be used for either standard or generalized eigenproblems, with real or complex arithmetic. It can also be used for computing a partial SVD of a large, sparse, rectangular matrix, and to solve quadratic eigenvalue problems. **More Information** https://www.grycap.upv.es/slepc/ **Available Versions**:: 3.15.1-foss-2021a 3.12.2-foss-2019b-Python-3.7.4 3.12.2-intel-2020a-Python-3.8.2 SNeP1 ----- **Available Versions**:: 1 SOAPdenovo2 ----------- **Description** SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for human-sized genomes. The program is specially designed to assemble Illumina short reads. It creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost effective way. SOAPdenovo2 is the successor of SOAPdenovo. **More Information** http://soap.genomics.org.cn/index.html **Available Versions**:: r241-foss-2020a SOCI ---- **Description** SOCI is a database access library for C++ that makes the illusion of embedding SQL queries in the regular C++ code, staying entirely within the Standard C++. **More Information** http://soci.sourceforge.net/ **Available Versions**:: 4.0.3-GCC-11.3.0 4.0.2-GCC-10.3.0 4.0.3-GCC-13.3.0 4.0.3-GCC-12.3.0 SPAdes ------ **Description** Genome assembler for single-cell and isolates data sets **More Information** https://github.com/ablab/spades **Available Versions**:: 4.1.0-GCC-13.3.0 3.13.0-foss-2018b 3.15.2-GCC-10.2.0 3.13.0-GCC-10.3.0 3.15.3-GCC-11.2.0 SQLite ------ **Description** SQLite: SQL Database Engine in a C Library **More Information** https://www.sqlite.org/ **Available Versions**:: 3.29.0-GCCcore-8.3.0 3.27.2-GCCcore-8.2.0 3.45.3-GCCcore-13.3.0 3.31.1-GCCcore-9.3.0 3.42.0-GCCcore-12.3.0 3.24.0-GCCcore-7.3.0 3.39.4-GCCcore-12.2.0 3.50.1-GCCcore-14.3.0 3.35.4-GCCcore-10.3.0 3.36-GCCcore-11.2.0 3.24.0-GCCcore-10.2.0 3.45.3-GCCcore-14.2.0 3.43.1-GCCcore-13.2.0 3.33.0-GCCcore-10.2.0 3.38.3-GCCcore-11.3.0 3.47.2-GCCcore-14.2.0 SRA-Toolkit ----------- **Description** The SRA Toolkit, and the source-code SRA System Development Kit (SDK), will allow you to programmatically access data housed within SRA and convert it from the SRA format **More Information** https://github.com/ncbi/sra-tools **Available Versions**:: 3.2.0-gompi-2024a 3.0.3-gompi-2022a 2.10.9-gompi-2020b SSW --- **Description** SSW is a fast implementation of the Smith-Waterman algorithm, which uses the Single-Instruction Multiple-Data (SIMD) instructions to parallelize the algorithm at the instruction level. SSW library provides an API that can be flexibly used by programs written in C, C++ and other languages. We also provide a software that can do protein and genome alignment directly. Current version of our implementation is ~50 times faster than an ordinary Smith-Waterman. It can return the Smith-Waterman score, alignment location and traceback path (cigar) of the optimal alignment accurately; and return the sub-optimal alignment score and location heuristically. **More Information** https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library **Available Versions**:: 1.1-GCCcore-11.2.0 STAR ---- **Description** STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays. **More Information** https://github.com/alexdobin/STAR **Available Versions**:: 2.7.10b-GCC-11.3.0 2.7.1a-GCC-8.2.0-2.31.1 2.7.3a-GCC-9.3.0 2.7.9a-GCC-11.2.0 STARCCM+ -------- **Available Versions**:: 2022.1 2021.2.1 2020.2.1 SUNDIALS -------- **Description** SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers **More Information** https://computing.llnl.gov/projects/sundials **Available Versions**:: 6.3.0-foss-2021b 5.1.0-foss-2019b 6.3.0-foss-2021a SWIG ---- **Description** SWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages. **More Information** http://www.swig.org/ **Available Versions**:: 4.0.2-GCCcore-11.2.0 4.2.1-GCCcore-13.3.0 3.0.12-foss-2018b-Python-3.6.6 4.0.2-GCCcore-11.3.0 4.1.1-GCCcore-12.3.0 4.1.1-GCCcore-12.2.0 4.1.1-GCCcore-13.2.0 3.0.12-GCCcore-8.3.0 4.0.2-GCCcore-10.2.0 3.0.12-GCCcore-8.2.0-Python-2.7.15 4.0.1-GCCcore-9.3.0 4.0.1-GCCcore-8.3.0 3.0.12-foss-2018b-Python-2.7.15 4.0.2-GCCcore-10.3.0 SWIPL ----- **Available Versions**:: 9.2.9 Salmon ------ **Description** Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data. **More Information** https://github.com/COMBINE-lab/salmon **Available Versions**:: 1.10.1-GCC-11.3.0 Sambamba -------- **Description** Sambamba is a high performance modern robust and fast tool (and library), written in the D programming language, for working with SAM and BAM files. Current functionality is an important subset of samtools functionality, including view, index, sort, markdup, and depth. **More Information** https://lomereiter.github.io/sambamba/ **Available Versions**:: 0.8.2-GCC-10.3.0 0.7.1 Satsuma2 -------- **Description** Satsuma2 is an optimised version of Satsuma, a tool to reliably align large and complex DNA sequencesproviding maximum sensitivity (to find all there is to find), specificity (to only find real homology) and speed (toaccommodate the billions of base pairs in vertebrate genomes). **More Information** https://github.com/bioinfologics/satsuma2 **Available Versions**:: 20220304-GCC-11.3.0 ScaFaCoS -------- **Description** ScaFaCoS is a library of scalable fast coulomb solvers. **More Information** http://www.scafacos.de/ **Available Versions**:: 1.0.4-foss-2023a 1.0.4-foss-2023b 1.0.1-foss-2020a 1.0.1-foss-2021b 1.0.1-foss-2021a 1.0.1-intel-2020a 1.0.4-foss-2022a ScaLAPACK --------- **Description** The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers. **More Information** http://www.netlib.org/scalapack/ **Available Versions**:: 2.0.2-gompi-2019b 2.2.0-gompi-2023.09-fb 2.2.2-gompi-2025b-fb 2.1.0-gompic-2020b 2.2.0-gompi-2024.05-fb 2.1.0-gompic-2020a 2.2.0-nvompi-2022.07-fb 2.1.0-gompi-2021b-fb 2.2.2-gompi-2025a-fb 2.2.0-gompi-2024a-fb 2.0.2-gompi-2019a-OpenBLAS-0.3.5 2.1.0-gompi-2020a 2.0.2-gompic-2019b 2.0.2-gompi-2018b-OpenBLAS-0.3.1 2.1.0-gompi-2021a-fb 2.2.0-gompi-2023b-fb 2.2.0-gompi-2022b-fb 2.2.0-gompi-2022a-fb 2.2.0-gompi-2022.10-fb 2.2.0-gompi-2022.05-fb 2.2.0-gompi-2023a-fb 2.0.2-gompic-2018b-OpenBLAS-0.3.1 2.1.0-gompi-2020b SciPy-bundle ------------ **Description** Bundle of Python packages for scientific software **More Information** https://python.org/ **Available Versions**:: 2019.10-fosscuda-2019b-Python-2.7.16 2021.10-gomkl-2021b 2019.10-foss-2019b-Python-3.7.4 2019.10-foss-2019b-Python-2.7.16 2020.03-foss-2020a-Python-3.8.2 2020.03-fosscuda-2020a-Python-3.8.2 2020.11-intel-2020b 2023.07-gfbf-2023a 2023.11-gfbf-2023b 2019.03-foss-2019a 2022.05-foss-2022a 2024.05-gfbf-2024a 2019.10-fosscuda-2019b-Python-3.7.4 2020.03-intel-2020a-Python-3.8.2 2020.11-foss-2020b 2021.10-intel-2021b 2023.02-gfbf-2022b 2022.05-intel-2022a 2021.10-foss-2021b 2025.06-gfbf-2025a 2020.11-fosscuda-2020b 2025.07-gfbf-2025b 2021.05-foss-2021a 2024.06-foss-2023a-Python-2.7.18 2024.05-gfbf-2024a-foss-2024a Score-P ------- **Description** The Score-P measurement infrastructure is a highly scalable and easy-to-use tool suite for profiling, event tracing, and online analysis of HPC applications. **More Information** https://www.score-p.org **Available Versions**:: 6.0-gompi-2020a Seaborn ------- **Description** Seaborn is a Python visualization library based on matplotlib. It provides a high-level interface for drawing attractive statistical graphics. **More Information** https://seaborn.pydata.org/ **Available Versions**:: 0.10.0-foss-2019b-Python-3.7.4 0.13.2-gfbf-2023a 0.12.1-foss-2022a SegAlign -------- **Available Versions**:: master-feb23 SentencePiece ------------- **Description** Unsupervised text tokenizer for Neural Network-based text generation. **More Information** https://github.com/google/sentencepiece **Available Versions**:: 0.1.96-GCC-10.2.0 0.1.97-GCC-11.3.0 SeqAn ----- **Description** SeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data. **More Information** https://github.com/seqan/seqan **Available Versions**:: 2.4.0-GCCcore-11.2.0 SeqKit ------ **Description** SeqKit - a cross-platform and ultrafast toolkit for FASTA/Q file manipulation **More Information** https://bioinf.shenwei.me/seqkit/ **Available Versions**:: 2.2.0 0.13.2 SeqLib ------ **Description** C++ interface to HTSlib, BWA-MEM and Fermi. **More Information** https://github.com/walaj/SeqLib **Available Versions**:: 1.2.0-GCC-11.2.0 Serf ---- **Description** The serf library is a high performance C-based HTTP client library built upon the Apache Portable Runtime (APR) library **More Information** https://serf.apache.org/ **Available Versions**:: 1.3.9-GCCcore-11.3.0 1.3.9-GCCcore-11.2.0 1.3.9-GCCcore-7.3.0 1.3.9-GCCcore-10.2.0 Seurat ------ **Description** Seurat is an R package designed for QC, analysis, and exploration of single cell RNA-seq data. **More Information** https://satijalab.org/seurat **Available Versions**:: 5.1.0-foss-2023a-R-4.3.2 Shapely ------- **Description** Shapely is a BSD-licensed Python package for manipulation and analysis of planar geometric objects.It is based on the widely deployed GEOS (the engine of PostGIS) and JTS (from which GEOS is ported) libraries. **More Information** https://github.com/Toblerity/Shapely **Available Versions**:: 1.7.1-GCC-9.3.0-Python-3.8.2 2.0.1-gfbf-2023a 1.8.2-foss-2021b Siesta ------ **Description** SIESTA is both a method and its computer program implementation, to perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids. **More Information** http://departments.icmab.es/leem/siesta **Available Versions**:: 4.1.5-intel-2022a 5.4.0-foss-2024a 4.1.5-foss-2020a 4.1.5-foss-2022a 4.1-b4-intel-2020a Simple-DFTD3 ------------ **Description** Reimplementation of the D3 dispersion correction. The s-dftd3 project aims toprovide a user-friendly and uniform interface to the D3 dispersion model andfor the calculation of DFT-D3 dispersion corrections. **More Information** https://dftd3.readthedocs.io **Available Versions**:: 1.2.1-gfbf-2024a Singular -------- **Description** Singular is a computer algebra system for polynomial computations,with special emphasis on commutative and non-commutative algebra, algebraic geometry,and singularity theory. **More Information** https://www.singular.uni-kl.de/ **Available Versions**:: 4.4.0-gfbf-2023b 4.3.2p10-gfbf-2022a SoX --- **Description** Sound eXchange, the Swiss Army knife of audio manipulation **More Information** http://sox.sourceforge.net/ **Available Versions**:: 14.4.2-GCCcore-11.3.0 Spack ----- **Description** Spack is a package manager for supercomputers, Linux, and macOS. It makes installing scientific software easy. With Spack, you can build a package with multiple versions, configurations, platforms, and compilers, and all of these builds can coexist on the same machine. **More Information** https://spack.io/ **Available Versions**:: 0.17.2 SpectrA ------- **Description** Spectra stands for Sparse Eigenvalue Computation Toolkit as a Redesigned ARPACK. It is a C++ library for large scale eigenvalue problems, built on top of Eigen, an open source linear algebra library. **More Information** https://spectralib.org/ **Available Versions**:: 1.0.1-GCCcore-12.3.0 Stacks ------ **Description** Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography. **More Information** http://catchenlab.life.illinois.edu/stacks **Available Versions**:: 2.41-iccifort-2019.5.281 2.53-foss-2019b 2.41-GCC-8.3.0 Stata ----- **Available Versions**:: 14 Structure --------- **Description** The program structure is a free software package for using multi-locus genotype data to investigate population structure. **More Information** https://web.stanford.edu/group/pritchardlab/structure.html **Available Versions**:: 2.3.4-GCC-11.3.0 Subversion ---------- **Description** Subversion is an open source version control system. **More Information** https://subversion.apache.org/ **Available Versions**:: 1.14.0-GCCcore-10.2.0 1.9.9-GCCcore-7.3.0 1.14.1-GCCcore-11.2.0 SuiteSparse ----------- **Description** SuiteSparse is a collection of libraries to manipulate sparse matrices. **More Information** https://faculty.cse.tamu.edu/davis/suitesparse.html **Available Versions**:: 7.10.3-foss-2025a 5.7.1-intel-2020a-METIS-5.1.0 5.4.0-foss-2019a-METIS-5.1.0 5.11.0-foss-2021a-METIS-5.1.0 5.10.1-foss-2021b-METIS-5.1.0 7.1.0-foss-2023a 5.13.0-foss-2022a-METIS-5.1.0 5.7.1-foss-2020a-METIS-5.1.0 5.10.1-foss-2021a-METIS-5.1.0 5.8.1-foss-2020b-METIS-5.1.0 5.6.0-foss-2019b-METIS-5.1.0 SuperLU ------- **Description** SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines. **More Information** https://crd-legacy.lbl.gov/~xiaoye/SuperLU/ **Available Versions**:: 5.2.2-intel-2020a SuperLU_DIST ------------ **Description** SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines. **More Information** https://crd-legacy.lbl.gov/~xiaoye/SuperLU/ **Available Versions**:: 8.1.2-foss-2023a 9.1.0-foss-2025a 8.1.0-foss-2022a SweeD ----- **Available Versions**:: 2025 Szip ---- **Description** Szip compression software, providing lossless compression of scientific data **More Information** https://support.hdfgroup.org/doc_resource/SZIP/ **Available Versions**:: 2.1.1-GCCcore-12.2.0 2.1.1-GCCcore-9.3.0 2.1.1-GCCcore-11.3.0 2.1.1-GCCcore-10.3.0 2.1.1-GCCcore-10.2.0 2.1.1-GCCcore-11.2.0 2.1.1-GCCcore-13.2.0 2.1.1-intel-2020a 2.1.1-GCCcore-12.3.0 2.1.1-GCCcore-14.2.0 2.1.1-GCCcore-8.3.0 2.1.1-GCCcore-7.3.0 2.1.1-GCCcore-8.2.0 2.1.1-GCCcore-13.3.0 TCLAP ----- **Description** TCLAP is a small, flexible library that provides a simple interface for defining and accessingcommand line arguments. It was intially inspired by the user friendly CLAP libary. **More Information** http://tclap.sourceforge.net/ **Available Versions**:: 1.2.5-GCCcore-11.2.0 TEtranscripts ------------- **Description** TEtranscripts and TEcount takes RNA-seq (and similar data) and annotates readsto both genes & transposable elements.TEtranscripts then performs differential analysis using DESeq2. **More Information** https://github.com/mhammell-laboratory/TEtranscripts **Available Versions**:: 2.2.0-foss-2021b TOML-Fortran ------------ **Description** TOML parser for Fortran projects **More Information** https://github.com/toml-f/toml-f **Available Versions**:: 0.4.2-GCC-13.3.0 TRF --- **Description** Tandem Repeats Finder: a program to analyze DNA sequences. **More Information** https://tandem.bu.edu/trf/trf.html **Available Versions**:: 4.09.1-GCCcore-11.3.0 4.09.1-GCCcore-10.2.0 4.09.1-GCC-10.3.0 4.09.1-GCCcore-10.3.0 TWL-NINJA --------- **Description** Nearly Infinite Neighbor Joining Application. **More Information** https://github.com/TravisWheelerLab/NINJA **Available Versions**:: 0.97-cluster_only-GCC-10.3.0 0.97-cluster_only-GCC-10.2.0 Tcl --- **Description** Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more. **More Information** https://www.tcl.tk/ **Available Versions**:: 8.6.10-GCCcore-10.2.0 9.0.1-GCCcore-14.3.0 8.6.8-GCCcore-7.3.0 8.6.14-GCCcore-13.3.0 8.6.11-GCCcore-10.3.0 8.6.12-GCCcore-11.3.0 8.6.13-GCCcore-13.2.0 8.6.8-GCCcore-10.2.0 8.6.9-GCCcore-8.2.0 8.6.9-GCCcore-8.3.0 8.6.10-GCCcore-9.3.0 8.6.13-GCCcore-12.3.0 8.6.12-GCCcore-12.2.0 8.6.11-GCCcore-11.2.0 8.6.16-GCCcore-14.2.0 TensorFlow ---------- **Description** An open-source software library for Machine Intelligence **More Information** https://www.tensorflow.org/ **Available Versions**:: 2.5.0-fosscuda-2020b 2.11.0-foss-2022a-CUDA-11.7.0 2.5.3-foss-2021a-CUDA-11.3.1 2.4.1-fosscuda-2020b 2.11.0-foss-2022a 2.6.0-foss-2021a Theano ------ **Description** Theano is a Python library that allows you to define, optimize,and evaluate mathematical expressions involving multi-dimensional arrays efficiently. **More Information** https://deeplearning.net/software/theano **Available Versions**:: 1.1.2-foss-2020b-PyMC 1.1.2-fosscuda-2020b-PyMC 1.0.4-fosscuda-2019b-Python-3.7.4 1.0.4-foss-2019b-Python-3.7.4 Tinker9 ------- **Description** The Tinker molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers. **More Information** https://github.com/TinkerTools/tinker9 **Available Versions**:: 1.0.4-GIT-31839758 Tk -- **Description** Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building a graphical user interface (GUI) in many different programming languages. **More Information** https://www.tcl.tk/ **Available Versions**:: 8.6.10-GCCcore-9.3.0 8.6.9-GCCcore-8.2.0 8.6.14-GCCcore-13.3.0 8.6.13-GCCcore-13.2.0 8.6.10-GCCcore-10.2.0 8.6.11-GCCcore-11.2.0 8.6.9-GCCcore-8.3.0 8.6.11-GCCcore-10.3.0 8.6.12-GCCcore-11.3.0 8.6.12-GCCcore-12.2.0 8.6.13-GCCcore-12.3.0 8.6.16-GCCcore-14.2.0 Tkinter ------- **Description** Tkinter module, built with the Python buildsystem **More Information** https://python.org/ **Available Versions**:: 3.10.4-GCCcore-11.3.0 3.9.5-GCCcore-10.3.0 3.8.6-GCCcore-10.2.0 2.7.18-GCCcore-12.3.0-Python-2.7.18 3.9.6-GCCcore-11.2.0 3.13.1-GCCcore-14.2.0 3.7.2-GCCcore-8.2.0 3.11.5-GCCcore-13.2.0 3.12.3-GCCcore-13.3.0 3.11.3-GCCcore-12.3.0 3.8.2-GCCcore-9.3.0 3.7.4-GCCcore-8.3.0 Togl ---- **Description** A Tcl/Tk widget for OpenGL rendering. **More Information** https://sourceforge.net/projects/togl/ **Available Versions**:: 2.0-GCCcore-11.3.0 2.0-GCCcore-8.3.0 TreeMix ------- **Description** TreeMix is a method for inferring the patterns of population splits and mixtures in the history of a set of populations. **More Information** http://bitbucket.org/nygcresearch/treemix **Available Versions**:: 1.13-GCC-10.3.0 1.13-intel-2020a Trilinos -------- **Description** The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented software framework for the solution of large-scale, complex multi-physics engineering and scientific problems. A unique design feature of Trilinos is its focus on packages. **More Information** https://trilinos.org **Available Versions**:: 13.4.1-foss-2022a 12.12.1-foss-2019b-Python-3.7.4 TrimAl ------ **Available Versions**:: 2024 Trim_Galore ----------- **Description** Trim Galore is a wrapper around Cutadapt and FastQC toconsistently apply adapter and quality trimming to FastQ files, with extrafunctionality for RRBS data. **More Information** https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ **Available Versions**:: 0.6.5-GCCcore-8.3.0-Java-11-Python-3.7.4 Trimmomatic ----------- **Description** Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.The selection of trimming steps and their associated parameters are supplied on the command line. **More Information** http://www.usadellab.org/cms/?page=trimmomatic **Available Versions**:: 0.39-Java-17 TwoBit ------ **Available Versions**:: 2022 UCC --- **Description** UCC (Unified Collective Communication) is a collectivecommunication operations API and library that is flexible, complete, andfeature-rich for current and emerging programming models and runtimes. **More Information** https://www.openucx.org/ **Available Versions**:: 1.4.4-GCCcore-14.3.0 1.2.0-GCCcore-13.2.0 1.3.0-GCCcore-14.2.0 1.1.0-GCCcore-12.2.0 1.3.0-GCCcore-13.3.0 1.0.0-GCCcore-11.3.0 1.2.0-GCCcore-12.3.0 UCC-CUDA -------- **Description** UCC (Unified Collective Communication) is a collectivecommunication operations API and library that is flexible, complete, and feature-rich for current and emerging programming models and runtimes.This module adds the UCC CUDA support. **More Information** https://www.openucx.org/ **Available Versions**:: 1.0.0-GCCcore-11.3.0-CUDA-11.7.0 UCX --- **Description** Unified Communication XAn open-source production grade communication framework for data centricand high-performance applications **More Information** https://www.openucx.org/ **Available Versions**:: 1.18.0-GCCcore-14.2.0 1.13.1-GCCcore-12.2.0 1.9.0-GCCcore-10.2.0 1.16.0-GCCcore-13.3.0 1.12.1-GCCcore-11.3.0 1.9.0-GCCcore-10.2.0-CUDA-11.1.1 1.8.0-GCCcore-9.3.0 1.11.2-GCCcore-11.2.0 1.10.0-GCCcore-10.3.0 1.16.0-GCCcore-12.3.0 1.14.1-GCCcore-12.3.0 1.9.0-GCCcore-10.3.0-CUDA-11.1.1 1.14.0-GCCcore-12.2.0 1.15.0-GCCcore-13.2.0 1.19.0-GCCcore-14.3.0 1.8.0-GCCcore-9.3.0-CUDA-11.0.2 UCX-CUDA -------- **Description** Unified Communication XAn open-source production grade communication framework for data centricand high-performance applicationsThis module adds the UCX CUDA support. **More Information** http://www.openucx.org/ **Available Versions**:: 1.12.1-GCCcore-11.3.0-CUDA-12.0.0 1.13.1-GCCcore-12.2.0-CUDA-12.0.0 1.15.0-GCCcore-13.2.0-CUDA-12.4.0 1.14.1-GCCcore-12.3.0-CUDA-12.4.0 1.10.0-GCCcore-10.3.0-CUDA-11.3.1 1.12.1-GCCcore-11.3.0-CUDA-11.7.0 1.12.1-GCCcore-11.3.0-CUDA-11.8.0 1.14.1-GCCcore-12.3.0-CUDA-12.0.0 1.14.1-GCCcore-12.3.0-CUDA-12.1.1 1.11.2-GCCcore-11.2.0-CUDA-11.4.1 1.16.0-GCCcore-12.3.0-CUDA-12.6.0 UDUNITS ------- **Description** UDUNITS supports conversion of unit specifications between formatted and binary forms, arithmetic manipulation of units, and conversion of values between compatible scales of measurement. **More Information** https://www.unidata.ucar.edu/software/udunits/ **Available Versions**:: 2.2.28-GCCcore-11.2.0 2.2.28-GCCcore-12.2.0 2.2.26-GCCcore-10.2.0 2.2.26-foss-2020a 2.2.28-GCCcore-12.3.0 2.2.28-GCCcore-13.2.0 2.2.26-foss-2018b 2.2.28-GCCcore-10.3.0 2.2.28-GCCcore-13.3.0 2.2.26-GCCcore-8.3.0 2.2.28-GCCcore-11.3.0 UFL --- **Description** The Unified Form Language (UFL) is a domain specific language for declaration of finite element discretizations of variational forms. More precisely, it defines a flexible interface for choosing finite element spaces and defining expressions for weak forms in a notation close to mathematical notation. **More Information** https://bitbucket.org/fenics-project/ufl **Available Versions**:: 2019.1.0-foss-2019b-Python-3.7.4 UMI-tools --------- **Description** Tools for handling Unique Molecular Identifiers in NGS data sets **More Information** https://umi-tools.readthedocs.io **Available Versions**:: 1.0.1-foss-2020a-Python-3.8.2 UNICOR ------ **Available Versions**:: 3.00 UnZip ----- **Description** UnZip is an extraction utility for archives compressedin .zip format (also called "zipfiles"). Although highly compatible bothwith PKWARE's PKZIP and PKUNZIP utilities for MS-DOS and with Info-ZIP'sown Zip program, our primary objectives have been portability andnon-MSDOS functionality. **More Information** http://www.info-zip.org/UnZip.html **Available Versions**:: 6.0-GCCcore-11.3.0 6.0-GCCcore-14.3.0 6.0-GCCcore-9.3.0 6.0-GCCcore-13.2.0 6.0-GCCcore-10.3.0 6.0-GCCcore-10.2.0 6.0-GCCcore-11.2.0 6.0-GCCcore-12.2.0 6.0-GCCcore-13.3.0 6.0-GCCcore-14.2.0 6.0-GCCcore-12.3.0 Unicycler --------- **Description** Unicycler is an assembly pipeline for bacterial genomes. It can assemble Illumina-only read sets where it functions as a SPAdes-optimiser. It can also assembly long-read-only sets (PacBio or Nanopore) where it runs a miniasm+Racon pipeline. **More Information** https://github.com/rrwick/Unicycler **Available Versions**:: 0.4.9-gompi-2021a 0.5.0-gompi-2021b V8 -- **Description** R interface to Google's open source JavaScript engine **More Information** https://cran.r-project.org/web/packages/V8/ **Available Versions**:: 3.6.0-foss-2021b-R-4.1.2 3.6.0-foss-2022a-R-4.2.2 3.6.0-foss-2022a-R-4.2.1 3.6.0-foss-2021b-R-4.2.1 VASP ---- **Available Versions**:: 1.0-info VCFtools -------- **Description** The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files. **More Information** https://vcftools.github.io **Available Versions**:: 0.1.16-GCC-11.2.0 0.1.16-GCC-9.3.0 VTK --- **Description** The Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation. **More Information** https://www.vtk.org **Available Versions**:: 8.2.0-foss-2020a-Python-3.8.2 8.2.0-intel-2020a-Python-3.8.2 9.1.0-foss-2021b 8.2.0-foss-2019b-Python-3.7.4 9.2.6-foss-2022b 9.3.0-foss-2023a 9.0.1-foss-2021a 9.2.2-foss-2022a VTune ----- **Description** Intel VTune Amplifier XE is the premier performance profiler for C, C++, C#, Fortran, Assembly and Java. **More Information** https://software.intel.com/en-us/vtune **Available Versions**:: 2023.2.0 2021.9.0 Valgrind -------- **Description** Valgrind: Debugging and profiling tools **More Information** https://valgrind.org **Available Versions**:: 3.16.1-iimpi-2020a 3.18.1-gompi-2021b 3.17.0-gompi-2021a 3.19.0-gompi-2022a 3.20.0-gompi-2022a 3.16.1-gompi-2020a 3.14.0-foss-2018b Vampire ------- **Available Versions**:: 5.0 6.0 Velvet ------ **Description** Sequence assembler for very short reads **More Information** https://github.com/dzerbino/velvet/ **Available Versions**:: 1.2.10-GCC-13.3.0-mt-kmer_191 1.2.10-foss-2018b-mt-kmer_191 Vim --- **Description** Vim is an advanced text editor that seeks to provide the power of the de-facto Unix editor 'Vi', with a more complete feature set. **More Information** http://www.vim.org **Available Versions**:: 8.1.1209-GCCcore-8.2.0-Python-3.7.2 Voro++ ------ **Description** Voro++ is a software library for carrying out three-dimensional computations of the Voronoitessellation. A distinguishing feature of the Voro++ library is that it carries out cell-based calculations,computing the Voronoi cell for each particle individually. It is particularly well-suited for applications thatrely on cell-based statistics, where features of Voronoi cells (eg. volume, centroid, number of faces) can be usedto analyze a system of particles. **More Information** http://math.lbl.gov/voro++/ **Available Versions**:: 0.4.6-GCCcore-11.2.0 0.4.6-GCCcore-12.3.0 0.4.6-GCCcore-11.3.0 0.4.6-GCCcore-9.3.0 0.4.6-GCCcore-10.3.0 0.4.6-GCCcore-13.2.0 WCSLIB ------ **Description** The FITS "World Coordinate System" (WCS) standard defines keywords and usage that provide for the description of astronomical coordinate systems in a FITS image header. **More Information** https://www.atnf.csiro.au/people/mcalabre/WCS/ **Available Versions**:: 7.11-GCC-11.2.0 WIEN2k ------ **Available Versions**:: 1.0-info 21.1-intel-2021a 21.1-JP-intel-2021a 24.1-intel-2023a Wannier90 --------- **Description** A tool for obtaining maximally-localised Wannier functions **More Information** http://www.wannier.org **Available Versions**:: 3.1.0-foss-2022a 3.1.0-foss-2021b 3.1.0-foss-2021a 3.1.0-intel-2023a 3.1.0-foss-2024a 3.1.0-intel-2020a 3.1.0-foss-2020b WannierTools ------------ **Description** WannierTools is an open source software that studies the physical properties of given tight-binding model. **More Information** http://www.wanniertools.com **Available Versions**:: 2.5.1-intel-2020b Wayland ------- **Description** Wayland is a project to define a protocol for a compositor to talk to its clients as well as a library implementation of the protocol. The compositor can be a standalone display server running on Linux kernel modesetting and evdev input devices, an X application, or a wayland client itself. The clients can be traditional applications, X servers (rootless or fullscreen) or other display servers. **More Information** https://wayland.freedesktop.org/ **Available Versions**:: 1.21.0-GCCcore-11.2.0 1.22.0-GCCcore-13.2.0 1.22.0-GCCcore-12.3.0 1.23.92-GCCcore-14.2.0 1.23.0-GCCcore-13.3.0 1.20.0-GCCcore-11.3.0 1.22.0-GCCcore-12.2.0 Waylandpp --------- **Description** Wayland is an object oriented display protocol, which features request and events. Requests can be seen as method calls on certain objects, whereas events can be seen as signals of an object. This makes the Wayland protocol a perfect candidate for a C++ binding.The goal of this library is to create such a C++ binding for Wayland using the most modern C++ technology currently available, providing an easy to use C++ API to Wayland. **More Information** https://github.com/NilsBrause/waylandpp **Available Versions**:: 1.0.0-GCCcore-11.2.0 1.0.0-GCCcore-12.3.0 WebKitGTK+ ---------- **Description** WebKitGTK+ is a full-featured port of the WebKitrendering engine, suitable for projects requiring any kind of webintegration, from hybrid HTML/CSS applications to full-fledged webbrowsers. It offers WebKit's full functionality and is useful in a widerange of systems from desktop computers to embedded systems like phones,tablets, and televisions. **More Information** https://webkitgtk.org/ **Available Versions**:: 2.37.1-GCC-11.2.0 2.41.4-foss-2023a X11 --- **Description** The X Window System (X11) is a windowing system for bitmap displays **More Information** https://www.x.org **Available Versions**:: 20190717-GCCcore-9.3.0 20240607-GCCcore-13.3.0 20210802-GCCcore-11.2.0 20190311-GCCcore-8.2.0 20201008-GCCcore-10.2.0 20220504-GCCcore-11.3.0 20221110-GCCcore-12.2.0 20200222-GCCcore-9.3.0 20230603-GCCcore-12.3.0 20190717-GCCcore-8.3.0 20250521-GCCcore-14.2.0 20210518-GCCcore-10.3.0 20231019-GCCcore-13.2.0 XCFun ----- **Description** XCFun is a library of DFT exchange-correlation (XC) functionals. It is based on automatic differentiation and can therefore generate arbitrary order derivatives of these functionals. **More Information** http://dftlibs.org/xcfun/ **Available Versions**:: 20190127-foss-2020a-Python-3.8.2 2.1.1-GCCcore-10.3.0 20190127-foss-2019a-Python-3.7.2 XCfun ----- **Description** XCFun is a library of DFT exchange-correlation (XC) functionals. It is based on automatic differentiation and can therefore generate arbitrary order derivatives of these functionals. **More Information** http://dftlibs.org/xcfun/ **Available Versions**:: 20190127-foss-2019a-Python-3.7.2 XCrySDen -------- **Description** XCrySDen is a crystalline and molecular structure visualisation program aiming at display of isosurfacesand contours, which can be superimposed on crystalline structures and interactively rotated and manipulated.It also possesses some tools for analysis of properties in reciprocal space such as interactive selectionof k-paths in the Brillouin zone for the band-structure plots, and visualisation of Fermi surfaces. **More Information** http://www.xcrysden.org/ **Available Versions**:: 1.6.2-foss-2022a 1.6.2-foss-2019b XML-LibXML ---------- **Description** Perl binding for libxml2 **More Information** https://metacpan.org/pod/distribution/XML-LibXML/LibXML.pod **Available Versions**:: 2.0207-GCCcore-11.2.0 2.0207-GCCcore-10.3.0 2.0209-GCCcore-12.3.0 2.0205-GCCcore-9.3.0 2.0207-GCCcore-11.3.0 XML-Parser ---------- **Description** This is a Perl extension interface to James Clark's XML parser, expat. **More Information** http://search.cpan.org/~toddr/XML-Parser-2.41/ **Available Versions**:: 2.44_01-GCCcore-7.3.0-Perl-5.28.0 XSD --- **Description** CodeSynthesis XSD is an open-source, cross-platform W3C XML Schema to C++ data binding compiler. **More Information** https://www.codesynthesis.com/products/xsd/ **Available Versions**:: 4.0.0-GCCcore-10.3.0 XZ -- **Description** xz: XZ utilities **More Information** https://tukaani.org/xz/ **Available Versions**:: 5.4.2-GCCcore-13.2.0 5.6.3-GCCcore-14.2.0 5.2.5-GCCcore-10.3.0 5.2.5-GCCcore-11.3.0 5.2.5-GCCcore-11.2.0 5.2.7-GCCcore-12.2.0 5.2.5-GCCcore-9.3.0 5.4.5-GCCcore-13.3.0 5.2.4-GCCcore-8.2.0 5.4.5-GCCcore-14.2.0 5.2.4-GCCcore-8.3.0 5.4.4-GCCcore-13.2.0 5.2.4-GCCcore-10.2.0 5.8.1-GCCcore-14.3.0 5.2.4-GCCcore-7.3.0 5.2.5-GCCcore-10.2.0 5.4.2-GCCcore-12.3.0 Xerces-C++ ---------- **Description** Xerces-C++ is a validating XML parser written in a portablesubset of C++. Xerces-C++ makes it easy to give your application the ability toread and write XML data. A shared library is provided for parsing, generating,manipulating, and validating XML documents using the DOM, SAX, and SAX2APIs. **More Information** https://xerces.apache.org/xerces-c/ **Available Versions**:: 3.2.3-GCCcore-10.3.0 3.2.5-GCCcore-13.3.0 3.2.5-GCCcore-13.2.0 3.2.4-GCCcore-12.3.0 3.2.4-GCCcore-11.3.0 Xvfb ---- **Description** Xvfb is an X server that can run on machines with no display hardware and no physical input devices. It emulates a dumb framebuffer using virtual memory. **More Information** https://www.x.org/releases/X11R7.6/doc/man/man1/Xvfb.1.xhtml **Available Versions**:: 1.20.11-GCCcore-10.3.0 21.1.8-GCCcore-12.3.0 21.1.6-GCCcore-12.2.0 21.1.3-GCCcore-11.3.0 21.1.9-GCCcore-13.2.0 1.20.9-GCCcore-10.2.0 1.20.13-GCCcore-11.2.0 21.1.14-GCCcore-13.3.0 YAXT ---- **Description** Yet Another eXchange Tool **More Information** https://www.dkrz.de/redmine/projects/yaxt **Available Versions**:: 0.9.0-gompi-2020b Yasm ---- **Description** Yasm: Complete rewrite of the NASM assembler with BSD license **More Information** https://www.tortall.net/projects/yasm/ **Available Versions**:: 1.3.0-GCCcore-11.2.0 1.3.0-GCCcore-13.2.0 1.3.0-GCCcore-12.2.0 1.3.0-GCCcore-11.3.0 1.3.0-GCCcore-10.3.0 1.3.0-GCCcore-8.2.0 1.3.0-GCCcore-14.2.0 1.3.0-GCCcore-10.2.0 1.3.0-GCCcore-9.3.0 1.3.0-GCCcore-12.3.0 1.3.0-GCCcore-8.3.0 1.3.0-GCCcore-13.3.0 Z3 -- **Description** Z3 is a theorem prover from Microsoft Research. **More Information** https://github.com/Z3Prover/z3 **Available Versions**:: 4.8.12-GCCcore-11.2.0 4.12.2-GCCcore-12.2.0 4.10.2-GCCcore-11.3.0 4.13.0-GCCcore-13.2.0 4.13.4-GCCcore-14.2.0 4.12.2-GCCcore-12.3.0 4.8.10-GCCcore-10.2.0 ZeroMQ ------ **Description** ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. It gives you sockets that carry atomic messages across various transports like in-process, inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, pub-sub, task distribution, and request-reply. It's fast enough to be the fabric for clustered products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous message-processing tasks. It has a score of language APIs and runs on most operating systems. **More Information** https://www.zeromq.org/ **Available Versions**:: 4.3.2-GCCcore-8.3.0 4.3.3-GCCcore-10.2.0 4.3.2-GCCcore-9.3.0 4.3.4-GCCcore-11.3.0 4.3.4-GCCcore-10.3.0 4.3.4-GCCcore-11.2.0 4.3.4-GCCcore-12.3.0 Zip --- **Description** Zip is a compression and file packaging/archive utility.Although highly compatible both with PKWARE's PKZIP and PKUNZIPutilities for MS-DOS and with Info-ZIP's own UnZip, our primary objectiveshave been portability and other-than-MSDOS functionality **More Information** http://www.info-zip.org/Zip.html **Available Versions**:: 3.0-GCCcore-10.2.0 3.0-GCCcore-8.3.0 3.0-GCCcore-10.3.0 3.0-GCCcore-9.3.0 3.0-GCCcore-12.3.0 3.0-GCCcore-12.2.0 3.0-GCCcore-11.3.0 3.0-GCCcore-11.2.0 Zoltan ------ **Description** Zoltan Dynamic Load Balancing and Graph Algorithm Toolkit **More Information** https://sandialabs.github.io/Zoltan/ **Available Versions**:: 3.901-foss-2023a Zopfli ------ **Description** Zopfli Compression Algorithm is a compression library programmed in C to performvery good, but slow, deflate or zlib compression. **More Information** https://github.com/google/zopfli **Available Versions**:: 1.0.3-GCCcore-11.3.0 aiohttp ------- **Description** Asynchronous HTTP client/server framework for asyncio and Python. **More Information** https://github.com/aio-libs/aiohttp **Available Versions**:: 3.8.1-GCCcore-11.2.0 airss ----- **Available Versions**:: 0.9.4 angsd ----- **Description** Program for analysing NGS data. **More Information** http://www.popgen.dk/angsd **Available Versions**:: 0.933-GCC-8.3.0 0.925-foss-2018b 0.935-GCC-10.2.0 ant --- **Description** Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications. **More Information** https://ant.apache.org/ **Available Versions**:: 1.10.11-Java-11 1.10.8-Java-11 1.10.12-Java-11 1.10.12-Java-17 1.10.7-Java-11 1.10.9-Java-11 1.10.14-Java-11 any2fasta --------- **Description** Convert various sequence formats to FASTA **More Information** https://github.com/tseemann/any2fasta **Available Versions**:: 0.4.2-GCCcore-11.2.0 0.4.2-GCCcore-10.3.0 arc-software ------------ **Description** Build environment for ARC software, using Easybuild with local settings. **Available Versions**:: 1.0 archspec -------- **Description** A library for detecting, labeling, and reasoning about microarchitectures **More Information** https://github.com/archspec/archspec **Available Versions**:: 0.2.5-GCCcore-12.3.0 0.1.2-GCCcore-10.3.0 0.1.3-GCCcore-11.2.0 0.2.1-GCCcore-12.3.0 0.2.2-GCCcore-13.2.0 0.1.4-GCCcore-11.3.0 0.1.0-GCCcore-9.3.0-Python-3.8.2 aria2 ----- **Description** aria2 is a lightweight multi-protocol & multi-source command-line download utility. **More Information** https://aria2.github.io **Available Versions**:: 1.35.0-GCCcore-10.3.0 1.36.0-GCCcore-11.3.0 arpack-ng --------- **Description** ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems. **More Information** https://github.com/opencollab/arpack-ng **Available Versions**:: 3.7.0-foss-2019b 3.7.0-foss-2020a 3.9.0-foss-2023b 3.9.0-foss-2023a 3.9.1-foss-2024a 3.7.0-intel-2020a 3.8.0-foss-2021b arrow-R ------- **Description** R interface to the Apache Arrow C++ library **More Information** https://cran.r-project.org/web/packages/arrow **Available Versions**:: 6.0.0.2-foss-2021b-R-4.1.2 14.0.0.2-foss-2023a-R-4.3.2 8.0.0-foss-2022a-R-4.2.1 17.0.0.1-foss-2024a-R-4.4.2 assimp ------ **Description** 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. **More Information** https://github.com/assimp/assimp **Available Versions**:: 5.3.1-GCCcore-13.2.0 6.0.2-GCCcore-14.2.0 5.4.3-GCCcore-13.3.0 at-spi2-atk ----------- **Description** AT-SPI 2 toolkit bridge **More Information** https://wiki.gnome.org/Accessibility **Available Versions**:: 2.32.0-GCCcore-8.2.0 2.38.0-GCCcore-13.2.0 2.38.0-GCCcore-11.3.0 2.38.0-GCCcore-12.2.0 2.38.0-GCCcore-11.2.0 2.38.0-GCCcore-12.3.0 2.38.0-GCCcore-10.2.0 2.34.1-GCCcore-8.3.0 at-spi2-core ------------ **Description** Assistive Technology Service Provider Interface. **More Information** https://wiki.gnome.org/Accessibility **Available Versions**:: 2.40.3-GCCcore-11.2.0 2.38.0-GCCcore-10.2.0 2.46.0-GCCcore-12.2.0 2.34.0-GCCcore-8.3.0 2.49.91-GCCcore-12.3.0 2.32.0-GCCcore-8.2.0 2.44.1-GCCcore-11.3.0 2.50.0-GCCcore-13.2.0 attrdict3 --------- **Description** AttrDict is a Python library that provides mapping objects that allow their elements to be accessed both as keys and as attributes. **More Information** https://github.com/pirofti/AttrDict3 **Available Versions**:: 2.0.2-GCCcore-11.2.0 2.0.2-GCCcore-12.3.0 autode ------ **Description** autodE is a Python module initially designed for the automated calculation of reaction profiles from SMILES strings of reactant(s) and product(s). Current features include: transition state location, conformer searching, atom mapping, Python wrappers for a range of electronic structure theory codes, SMILES parsing, association complex generation, and reaction profile generation. **More Information** https://github.com/duartegroup/autodE **Available Versions**:: 1.3.3 bakta ----- **Description** Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs. It provides dbxref-rich, sORF-including and taxon-independent annotations in machine-readable JSON & bioinformatics standard file formats for automated downstream analysis. **More Information** https://github.com/oschwengers/bakta **Available Versions**:: 1.10.1-foss-2023b bcl2fastq2 ---------- **Description** bcl2fastq Conversion Software both demultiplexes data and converts BCL files generated by Illumina sequencing systems to standard FASTQ file formats for downstream analysis. **More Information** https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html **Available Versions**:: 2.20.0-foss-2018b 2.20.0-GCC-10.2.0 beagle-lib ---------- **Description** beagle-lib is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages. **More Information** https://github.com/beagle-dev/beagle-lib **Available Versions**:: 3.1.2-GCC-8.2.0-2.31.1 4.0.0-GCC-11.3.0 3.1.2-GCC-7.3.0-2.30 binutils -------- **Description** binutils: GNU binary utilities **More Information** https://directory.fsf.org/project/binutils/ **Available Versions**:: 2.35-GCCcore-10.2.0 2.31.1-GCCcore-8.2.0 2.40-GCCcore-13.1.0 2.42-GCCcore-14.2.0 2.34-GCCcore-9.3.0 2.38 2.32-GCCcore-9.3.0 2.39 2.31.1 2.34 2.40 2.27 2.37 2.44-GCCcore-15.1.0 2.40-GCCcore-13.2.0 2.32 2.30-GCCcore-7.3.0 2.44-GCCcore-14.3.0 2.42-GCCcore-13.3.0 2.32-GCCcore-8.3.0 2.39-GCCcore-12.2.0 2.36.1 2.26 2.35 2.42 2.40-GCCcore-12.3.0 2.30-GCCcore-8.1.0 2.36.1-GCCcore-10.3.0 2.45 2.25 2.28 2.37-GCCcore-11.2.0 2.44 2.38-GCCcore-11.3.0 2.30 bokeh ----- **Description** Statistical and novel interactive HTML plots for Python **More Information** https://github.com/bokeh/bokeh **Available Versions**:: 3.2.2-foss-2023a 2.4.3-foss-2022a 1.4.0-foss-2019b-Python-3.7.4 2.2.3-foss-2020b 2.2.3-fosscuda-2020b breseq ------ **Description** breseq is a computational pipeline for the analysis of short-read re-sequencing data **More Information** https://barricklab.org/breseq **Available Versions**:: 0.38.1-foss-2022a 0.36.1-foss-2021b bwa-meth -------- **Description** Fast and accurante alignment of BS-Seq reads. **More Information** https://github.com/brentp/bwa-meth **Available Versions**:: 0.2.6-GCC-11.3.0 bwidget ------- **Description** The BWidget Toolkit is a high-level Widget Set for Tcl/Tk built using native Tcl/Tk 8.x namespaces. **More Information** https://core.tcl-lang.org/bwidget/home **Available Versions**:: 1.9.15-GCCcore-11.3.0 1.9.13-GCCcore-8.2.0 1.9.14-GCCcore-8.3.0 bzip2 ----- **Description** bzip2 is a freely available, patent free, high-quality data compressor. It typically compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical compressors), whilst being around twice as fast at compression and six times faster at decompression. **More Information** https://sourceware.org/bzip2 **Available Versions**:: 1.0.8-GCCcore-11.2.0 1.0.8-GCCcore-13.2.0 1.0.6-GCCcore-7.3.0 1.0.8-GCCcore-10.2.0 1.0.8-GCCcore-9.3.0 1.0.8-GCCcore-10.3.0 1.0.8-GCCcore-12.2.0 1.0.8-GCCcore-7.3.0 1.0.8-GCCcore-13.3.0 1.0.8-GCCcore-11.3.0 1.0.6-GCCcore-8.2.0 1.0.6-GCCcore-10.2.0 1.0.8-GCCcore-14.2.0 1.0.8-GCCcore-8.3.0 1.0.8-GCCcore-14.3.0 1.0.8-GCCcore-12.3.0 c-ares ------ **Description** c-ares is a C library for asynchronous DNS requests (including name resolves) **More Information** https://c-ares.org/ **Available Versions**:: 1.18.1-GCCcore-11.3.0 1.19.1-GCCcore-12.3.0 1.17.2-GCCcore-10.3.0 1.18.1-GCCcore-11.2.0 c2x --- **Available Versions**:: 2.40 cURL ---- **Description** libcurl is a free and easy-to-use client-side URL transfer library, supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, Kerberos), file transfer resume, http proxy tunneling and more. **More Information** http://curl.haxx.se **Available Versions**:: 7.63.0-GCCcore-8.2.0 8.3.0-GCCcore-13.2.0 7.72.0-GCCcore-10.2.0 7.66.0-GCCcore-8.3.0 8.0.1-GCCcore-12.3.0 8.7.1-GCCcore-13.3.0 8.11.1-GCCcore-14.2.0 7.76.0-GCCcore-10.3.0 7.60.0-GCCcore-10.2.0 7.86.0-GCCcore-12.2.0 7.66.0-GCCcore-7.3.0 7.83.0-GCCcore-11.3.0 7.69.1-GCCcore-9.3.0 7.60.0-GCCcore-7.3.0 7.78.0-GCCcore-11.2.0 8.14.1-GCCcore-14.3.0 8.0.1-GCCcore-13.2.0 cairo ----- **Description** Cairo is a 2D graphics library with support for multiple output devices. Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB **More Information** https://cairographics.org **Available Versions**:: 1.16.0-GCCcore-11.2.0 1.18.0-GCCcore-13.3.0 1.16.0-GCCcore-10.2.0 1.17.4-GCCcore-12.2.0 1.16.0-GCCcore-9.3.0 1.18.0-GCCcore-13.2.0 1.18.4-GCCcore-14.2.0 1.16.0-GCCcore-8.2.0 1.17.4-GCCcore-11.3.0 1.14.12-GCCcore-7.3.0 1.16.0-GCCcore-10.3.0 1.16.0-GCCcore-8.3.0 1.17.8-GCCcore-12.3.0 cairomm ------- **Description** The Cairomm package provides a C++ interface to Cairo. **More Information** http://cairographics.org **Available Versions**:: 1.16.2-GCC-11.3.0 casacore -------- **Description** A suite of C++ libraries for radio astronomy data processing.The ephemerides data needs to be in DATA_DIR and the location must be specified at runtime.Thus user's can update them. **More Information** https://github.com/casacore/casacore **Available Versions**:: 3.4.0-foss-2021b ccache ------ **Description** Ccache (or “ccache”) is a compiler cache. It speeds up recompilation bycaching previous compilations and detecting when the same compilation is being done again **More Information** https://ccache.dev/ **Available Versions**:: 4.9-GCCcore-12.3.0 4.6.1-GCCcore-11.2.0 cddlib ------ **Description** An efficient implementation of the Double Description Method **More Information** https://github.com/cddlib/cddlib **Available Versions**:: 0.94m-GCCcore-11.3.0 0.94m-GCCcore-13.2.0 cffi ---- **Description** C Foreign Function Interface for Python. Interact with almost any C code fromPython, based on C-like declarations that you can often copy-paste from headerfiles or documentation. **More Information** https://cffi.readthedocs.io/en/latest/ **Available Versions**:: 1.16.0-GCCcore-13.3.0 1.15.1-GCCcore-12.3.0 1.15.1-GCCcore-13.2.0 1.17.1-GCCcore-14.2.0 1.17.1-GCCcore-14.3.0 cfx --- **Available Versions**:: 2021R2 chewBBACA --------- **Description** chewBBACA stands for "BSR-Based Allele Calling Algorithm".chewBBACA is a comprehensive pipeline including a set of functions for thecreation and validation of whole genome and core genome MultiLocus SequenceTyping (wg/cgMLST) schemas, providing an allele calling algorithm based on BlastScore Ratio that can be run in multiprocessor settings and a set of functions tovisualize and validate allele variation in the loci. **More Information** https://github.com/B-UMMI/chewBBACA **Available Versions**:: 2.5.5-intel-2020a-Python-3.8.2 cns --- **Available Versions**:: v1.3_r9 constraint ---------- **Description** The Python constraint module offers solvers for Constraint Satisfaction Problems (CSPs) over finite domains in simple and pure Python. CSP is class of problems which may be represented in terms of variables (a, b, ...), domains (a in [1, 2, 3], ...), and constraints (a < b, ...). **More Information** https://github.com/python-constraint/python-constraint **Available Versions**:: 1.4.0-foss-2020a-Python-3.8.2 cpio ---- **Description** The cpio package contains tools for archiving. **More Information** https://savannah.gnu.org/projects/cpio/ **Available Versions**:: 2.15-GCCcore-12.3.0 2.14-GCCcore-11.3.0 cppy ---- **Description** A small C++ header library which makes it easier to writePython extension modules. The primary feature is a PyObject smart pointerwhich automatically handles reference counting and provides conveniencemethods for performing common object operations. **More Information** https://github.com/nucleic/cppy **Available Versions**:: 1.1.0-GCCcore-11.2.0 1.3.1-GCCcore-14.2.0 1.2.1-GCCcore-12.3.0 1.2.1-GCCcore-11.3.0 1.2.1-GCCcore-13.3.0 1.2.1-GCCcore-13.2.0 cppyy ----- **Description** cppyy is an automatic, run-time, Python-C++ bindings generator, for calling C++ from Python and Python from C++. **More Information** https://cppyy.readthedocs.io **Available Versions**:: 3.0.0-GCCcore-11.3.0 crest ----- **Description** CREST is an utility/driver program for the xtb program. Originally it was designed asconformer sampling program, hence the abbreviation Conformer-Rotamer Ensemble Sampling Tool, but now offers also some utility functions for calculations with the GFNn-xTB methods. Generally the program functions as an IO based OMP scheduler (i.e., calculations are performed by the xtb program) and tool for the creation and analysation of structure ensembles. **More Information** https://xtb-docs.readthedocs.io/en/latest/crest.html **Available Versions**:: 2.10.2 cryptography ------------ **Description** cryptography is a package designed to expose cryptographic primitives and recipes to Python developers. **More Information** https://github.com/pyca/cryptography **Available Versions**:: 41.0.5-GCCcore-13.2.0 44.0.2-GCCcore-14.2.0 41.0.1-GCCcore-12.3.0 45.0.5-GCCcore-14.3.0 42.0.8-GCCcore-13.3.0 cuDNN ----- **Description** The NVIDIA CUDA Deep Neural Network library (cuDNN) isa GPU-accelerated library of primitives for deep neural networks. **More Information** https://developer.nvidia.com/cudnn **Available Versions**:: 8.2.2.26-CUDA-11.4.1 8.7.0.84-CUDA-11.8.0 8.0.4.30-CUDA-11.1.1 7.6.4.38-gcccuda-2019b 8.1.1.33-CUDA-11.2.2 8.9.2.26-CUDA-12.1.1 8.2.1.32-CUDA-11.3.1 8.4.0.27-CUDA-11.6.0 8.8.0.121-CUDA-12.0.0 9.5.0.50-CUDA-12.6.0 8.0.4.30-CUDA-11.0.2 8.4.1.50-CUDA-11.7.0 8.6.0.163-CUDA-11.8.0 cuTENSOR -------- **Description** The cuTENSOR Library is a GPU-accelerated tensor linear algebra library providing tensor contraction, reduction and elementwise operations. **More Information** https://developer.nvidia.com/cutensor **Available Versions**:: 1.6.1.5-CUDA-11.4.1 1.7.0.1-CUDA-12.0.0 cutadapt -------- **Description** Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. **More Information** https://opensource.scilifelab.se/projects/cutadapt/ **Available Versions**:: 1.18-foss-2018b-Python-3.6.6 4.2-GCCcore-11.3.0 2.7-GCCcore-8.3.0-Python-3.7.4 4.3-GCCcore-11.3.0 3.5-GCCcore-11.2.0 cylc ---- **Available Versions**:: 7.8.7 dask ---- **Description** Dask natively scales Python. Dask provides advanced parallelism for analytics, enabling performance at scale for the tools you love. **More Information** https://dask.org/ **Available Versions**:: 2022.10.0-foss-2022a 2021.2.0-foss-2020b 2021.2.0-fosscuda-2020b 2.8.0-foss-2019b-Python-3.7.4 datamash -------- **Description** GNU datamash performs basic numeric, textual and statistical operations on input data files **More Information** https://www.gnu.org/software/datamash/ **Available Versions**:: 1.5-GCCcore-10.2.0 dbus-glib --------- **Description** D-Bus is a message bus system, a simple way for applications to talk to one another. **More Information** https://dbus.freedesktop.org/doc/dbus-glib **Available Versions**:: 0.112-GCCcore-11.2.0 0.110-GCCcore-8.3.0 deal.II ------- **Description** deal.II is a C++ program library targeted at the computational solution of partial differential equations using adaptive finite elements. **More Information** https://www.dealii.org **Available Versions**:: 9.5.2-foss-2022a deepTools --------- **Description** deepTools is a suite of python tools particularly developed for the efficient analysis of high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq. **More Information** https://deeptools.readthedocs.io/ **Available Versions**:: 3.5.2-foss-2022a deepdiff -------- **Description** DeepDiff: Deep Difference of dictionaries, iterables and almost any other object recursively. **More Information** https://deepdiff.readthedocs.io/en/latest/ **Available Versions**:: 4.0.6-GCCcore-8.2.0-Python-3.7.2 dftd4 ----- **Available Versions**:: 3.4.0-keep 3.4.0 dijitso ------- **Description** dijitso is a Python module for distributed just-in-time shared library building. **More Information** https://bitbucket.org/fenics-project/dijitso **Available Versions**:: 2019.1.0-foss-2019b-Python-3.7.4 dill ---- **Description** dill extends python's pickle module for serializing and de-serializing python objects to the majority of the built-in python types. Serialization is the process of converting an object to a byte stream, and the inverse of which is converting a byte stream back to on python object hierarchy. **More Information** https://pypi.org/project/dill/ **Available Versions**:: 0.3.7-GCCcore-12.3.0 0.3.4-GCCcore-10.3.0 0.3.3-foss-2020a-Python-3.8.2 0.3.9-GCCcore-13.3.0 0.3.6-GCCcore-11.3.0 0.3.4-GCCcore-11.2.0 dm-tree ------- **Description** dm-tree provides tree, a library for working with nested data structures. In a way,tree generalizes the builtin map function which only supports flat sequences, andallows to apply a function to each "leaf" preserving the overall structure. **More Information** https://github.com/deepmind/tree **Available Versions**:: 0.1.6-GCCcore-11.2.0 0.1.5-GCCcore-10.2.0 0.1.6-GCCcore-10.3.0 dmd --- **Available Versions**:: 2 dorado ------ **Description** Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads. **More Information** https://github.com/nanoporetech/dorado **Available Versions**:: 0.3.1-foss-2022a-CUDA-11.7.0 0.9.6-GCCcore-12.3.0 0.5.3-foss-2022a-CUDA-11.7.0 dot --- **Available Versions**:: False dotNET-Core-Runtime ------------------- **Description** .NET is a free, cross-platform, open source developer platform for building many different types of applications. **More Information** https://www.microsoft.com/net/ **Available Versions**:: 5.0.17-GCCcore-10.3.0 double-conversion ----------------- **Description** Efficient binary-decimal and decimal-binary conversion routines for IEEE doubles. **More Information** https://github.com/google/double-conversion **Available Versions**:: 3.1.5-GCCcore-9.3.0 3.2.1-GCCcore-12.2.0 3.3.0-GCCcore-13.3.0 3.3.1-GCCcore-14.2.0 3.2.0-GCCcore-11.3.0 3.1.5-GCCcore-11.2.0 3.1.4-GCCcore-8.3.0 3.3.0-GCCcore-13.2.0 3.3.0-GCCcore-12.3.0 3.1.5-GCCcore-10.2.0 3.1.5-GCCcore-10.3.0 draco ----- **Description** "Draco is a library for compressing and decompressing 3D geometric meshes and point clouds.It is intended to improve the storage and transmission of 3D graphics. **More Information** https://github.com/google/draco/ **Available Versions**:: 1.5.7-foss-2023a dssp ---- **Description** This is a rewrite of DSSP, now offering full mmCIF support. The difference withprevious releases of DSSP is that it now writes out an annotated mmCIF file bydefault, storing the secondary structure information in the _struct_confcategory.Another new feature in this version of DSSP is that it now defines Poly-Prolinehelices as well.The DSSP program was designed by Wolfgang Kabsch and Chris Sander to standardizesecondary structure assignment. DSSP is a database of secondary structureassignments (and much more) for all protein entries in the Protein Data Bank(PDB). DSSP is also the program that calculates DSSP entries from PDB entries.DSSP does not predict secondary structure. **More Information** https://github.com/PDB-REDO/dssp **Available Versions**:: 4.4.10-GCC-13.3.0 e3nn ---- **Description** Euclidean neural networks (e3nn) is a python library based on pytorch to create equivariant neural networks for the group O(3). **More Information** https://e3nn.org/ **Available Versions**:: 0.3.3-foss-2022a 0.3.3-foss-2022a-CUDA-11.7.0 ecBuild ------- **Description** A CMake-based build system, consisting of a collection of CMake macros andfunctions that ease the managing of software build systems **More Information** https://ecbuild.readthedocs.io/ **Available Versions**:: 3.8.0 ecCodes ------- **Description** ecCodes is a package developed by ECMWF which provides an application programming interface and a set of tools for decoding and encoding messages in the following formats: WMO FM-92 GRIB edition 1 and edition 2, WMO FM-94 BUFR edition 3 and edition 4, WMO GTS abbreviated header (only decoding). **More Information** https://software.ecmwf.int/wiki/display/ECC/ecCodes+Home **Available Versions**:: 2.20.0-gompi-2020b 2.27.0-gompi-2022a 2.31.0-gompi-2023b edlib ----- **Description** Lightweight, super fast library for sequence alignment using edit (Levenshtein) distance. **More Information** https://martinsos.github.io/edlib **Available Versions**:: 1.3.9-GCC-11.2.0 1.3.9-GCC-12.3.0 eilmer ------ **Available Versions**:: 4.0-9c87a327 einops ------ **Description** Flexible and powerful tensor operations for readable and reliable code.Supports numpy, pytorch, tensorflow, jax, and others. **More Information** https://einops.rocks/ **Available Versions**:: 0.4.1-GCCcore-10.3.0 elfutils -------- **Description** The elfutils project provides libraries and tools for ELF files and DWARF data. **More Information** https://elfutils.org/ **Available Versions**:: 0.189-GCCcore-12.2.0 0.185-GCCcore-8.3.0 0.185-GCCcore-11.2.0 0.187-GCCcore-11.3.0 0.183-GCCcore-10.2.0 0.189-GCCcore-12.3.0 enaBrowserTool -------------- **Description** enaBrowserTools is a set of scripts that interface with the ENA web services to download data from ENA easily, without any knowledge of scripting required. **More Information** https://github.com/enasequence/enaBrowserTools/ **Available Versions**:: 1.6-GCCcore-10.3.0 enaBrowserTools --------------- **Description** enaBrowserTools is a set of scripts that interface with the ENA web services to download data from ENA easily, without any knowledge of scripting required. **More Information** https://github.com/enasequence/enaBrowserTools/ **Available Versions**:: 1.6-GCCcore-8.2.0-Python-3.7.2 enchant-2 --------- **Description** Enchant aims to provide a simple but comprehensive abstraction for dealingwith different spell checking libraries in a consistent way. A client, suchas a text editor or word processor, need not know anything about a specificspell-checker, and since all back-ends are plugins, new spell-checkers canbe added without needing any change to the program using Enchant. **More Information** http://rrthomas.github.io/enchant/ **Available Versions**:: 2.6.5-GCCcore-12.3.0 2.3.3-GCCcore-11.2.0 exiv2 ----- **Description** Exiv2 is a Cross-platform C++ library and a command line utility to manage image metadata. **More Information** https://exiv2.org **Available Versions**:: 0.27.5-GCCcore-11.2.0 0.28.0-GCCcore-12.3.0 expat ----- **Description** Expat is an XML parser library written in C. It is a stream-oriented parserin which an application registers handlers for things the parser might findin the XML document (like start tags). **More Information** https://libexpat.github.io **Available Versions**:: 2.5.0-GCCcore-12.3.0 2.2.5-GCCcore-7.3.0 2.6.4-GCCcore-14.2.0 2.7.1-GCCcore-14.3.0 2.4.1-GCCcore-11.2.0 2.2.7-GCCcore-8.3.0 2.2.9-GCCcore-10.2.0 2.2.5-GCCcore-10.2.0 2.2.7-GCCcore-7.3.0 2.2.9-GCCcore-10.3.0 2.4.9-GCCcore-12.2.0 2.2.6-GCCcore-8.2.0 2.4.8-GCCcore-11.3.0 2.2.9-GCCcore-9.3.0 2.2.5-GCCcore-8.1.0 2.5.0-GCCcore-13.2.0 2.6.2-GCCcore-13.3.0 expecttest ---------- **Description** This library implements expect tests (also known as "golden" tests). Expect tests are a method of writing tests where instead of hard-coding the expected output of a test, you run the test to get the output, and the test framework automatically populates the expected output. If the output of the test changes, you can rerun the test with the environment variable EXPECTTEST_ACCEPT=1 to automatically update the expected output. **More Information** https://github.com/ezyang/expecttest **Available Versions**:: 0.2.1-GCCcore-13.2.0 0.1.3-GCCcore-11.3.0 0.1.3-GCCcore-11.2.0 0.1.5-GCCcore-12.3.0 0.1.3-GCCcore-10.3.0 fast-gbs -------- **Available Versions**:: v2 fastStructure ------------- **Description** fastStructure is a fast algorithm for inferring population structurefrom large SNP genotype data. It is based on a variational Bayesianframework for posterior inference and is written in Python2.x. **More Information** https://rajanil.github.io/fastStructure/ **Available Versions**:: 1.0-foss-2023a-Python-2.7.18 fastahack --------- **Description** Utilities for indexing and sequence extraction from FASTA files. **More Information** https://github.com/ekg/fastahack **Available Versions**:: 1.0.0-GCCcore-11.2.0 fastp ----- **Description** A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance. **More Information** https://github.com/OpenGene/fastp **Available Versions**:: 0.23.4-GCC-12.2.0 fdmnes ------ **Available Versions**:: 2021-08-10 fdmnes-parallel --------------- **Available Versions**:: 2021-08-10 fdupes ------ **Available Versions**:: 2024 fermi-lite ---------- **Description** Standalone C library for assembling Illumina short reads in small regions. **More Information** https://github.com/lh3/fermi-lite **Available Versions**:: 20190320-GCCcore-11.2.0 ffnvcodec --------- **Description** FFmpeg nvidia headers. Adds support for nvenc and nvdec. Requires Nvidia GPU and drivers to be present(picked up dynamically). **More Information** https://git.videolan.org/?p=ffmpeg/nv-codec-headers.git **Available Versions**:: 12.1.14.0 11.1.5.2 12.0.16.0 12.2.72.0 13.0.19.0 file ---- **Description** The file command is 'a file type guesser', that is, a command-line tool that tells you in words what kind of data a file contains. **More Information** http://www.darwinsys.com/file/ **Available Versions**:: 5.35-GCCcore-7.3.0 5.39-GCCcore-10.2.0 5.46-GCCcore-13.3.0 5.43-GCCcore-11.3.0 filevercmp ---------- **Description** filevercmp function as in sort --version-sort. **More Information** https://github.com/ekg/filevercmp **Available Versions**:: 20191210-GCCcore-11.2.0 fineRADstructure ---------------- **Description** A package for population structure inference from RAD-seq data **More Information** http://cichlid.gurdon.cam.ac.uk/fineRADstructure.html **Available Versions**:: 20180709-intel-2020a fineSTRUCTURE ------------- **Description** fineSTRUCTURE is a fast and powerful algorithm for identifying population structure using dense sequencing data. **More Information** https://people.maths.bris.ac.uk/~madjl/finestructure/finestructure_info.html **Available Versions**:: 2.1.3-intel-2020a fio --- **Description** Flexible I/O tester **More Information** https://github.com/axboe/fio **Available Versions**:: 3.36-GCCcore-12.3.0 3.34-GCCcore-12.2.0 3.36-GCCcore-12.3.0-centos81 flappie ------- **Available Versions**:: 2.1.3 flatbuffers ----------- **Description** FlatBuffers: Memory Efficient Serialization LibraryIncludes the Flatbuffers compiler, C/C++ bindings and Python runtime library. **More Information** https://github.com/google/flatbuffers/ **Available Versions**:: 2.0.7-GCCcore-11.3.0 2.0.0-GCCcore-10.3.0 2.0.0-GCCcore-11.2.0 23.5.26-GCCcore-12.3.0 1.12.0-GCCcore-10.2.0 flatbuffers-python ------------------ **Description** Python Flatbuffers runtime library. **More Information** https://github.com/google/flatbuffers/ **Available Versions**:: 2.0-GCCcore-11.3.0 2.0-GCCcore-11.2.0 2.0-GCCcore-10.3.0 1.12-GCCcore-10.2.0 23.5.26-GCCcore-12.3.0 flex ---- **Description** Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, sometimes called a tokenizer, is a program which recognizes lexical patterns in text. **More Information** http://flex.sourceforge.net/ **Available Versions**:: 2.6.4-GCCcore-8.1.0 2.6.4-GCCcore-7.3.0 2.6.4-GCCcore-8.3.0 2.6.4-GCCcore-11.3.0 2.6.4-GCCcore-15.1.0 2.6.4-GCCcore-12.2.0 2.5.39-GCCcore-8.3.0 2.6.4-GCCcore-10.2.0 2.6.4-GCCcore-12.3.0 2.6.4-GCCcore-9.3.0 2.6.4-GCCcore-13.3.0 2.6.4-GCCcore-11.2.0 2.6.4 2.6.4-GCCcore-8.2.0 2.6.4-GCCcore-14.2.0 2.6.0 2.5.39 2.6.4-GCCcore-13.2.0 2.6.4-GCCcore-14.3.0 2.6.3 2.6.4-GCCcore-13.1.0 2.6.4-GCCcore-10.3.0 flit ---- **Description** A simple packaging tool for simple packages. **More Information** https://github.com/pypa/flit **Available Versions**:: 3.10.1-GCCcore-14.2.0 3.9.0-GCCcore-12.3.0 3.9.0-GCCcore-13.3.0 3.9.0-GCCcore-13.2.0 3.12.0-GCCcore-14.3.0 flook ----- **Description** The fortran-Lua-hook library. **More Information** https://github.com/ElectronicStructureLibrary/flook **Available Versions**:: 0.8.4-GCC-13.3.0 fluent ------ **Available Versions**:: 2021R2 fontconfig ---------- **Description** Fontconfig is a library designed to provide system-wide font configuration, customization and application access. **More Information** https://www.freedesktop.org/wiki/Software/fontconfig/ **Available Versions**:: 2.13.92-GCCcore-9.3.0 2.13.1-GCCcore-8.3.0 2.15.0-GCCcore-13.3.0 2.13.94-GCCcore-11.2.0 2.13.1-GCCcore-8.2.0 2.13.93-GCCcore-10.3.0 2.13.92-GCCcore-10.2.0 2.16.2-GCCcore-14.2.0 2.13.0-GCCcore-7.3.0 2.14.2-GCCcore-12.3.0 2.14.1-GCCcore-12.2.0 2.14.2-GCCcore-13.2.0 2.14.0-GCCcore-11.3.0 fonttools --------- **Description** fontTools is a library for manipulating fonts, written in Python.The project includes the TTX tool, that can convert TrueType and OpenType fonts to and from an XML text format,which is also called TTX.It supports TrueType, OpenType, AFM and to an extent Type 1 and some Mac-specific formats. **More Information** https://python-markdown.github.io/ **Available Versions**:: 4.58.4-GCCcore-14.2.0 4.53.1-GCCcore-13.3.0 foss ---- **Description** GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK. **More Information** https://easybuild.readthedocs.io/en/master/Common-toolchains.html#foss-toolchain **Available Versions**:: 2021a 2020a 2020b 2023a 2025a 2023.09 2025b 2022.10 2019b 2023b 2024a 2021b 2024.05 2018b 2019a 2022a 2022.05 2022b fosscuda -------- **Description** GCC based compiler toolchain __with CUDA support__, and including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK. **More Information** (none) **Available Versions**:: 2020b 2019b 2018b 2020a freebayes --------- **Description** Bayesian haplotype-based genetic polymorphism discovery and genotyping. **More Information** https://github.com/freebayes/freebayes **Available Versions**:: 1.3.6-foss-2021b-R-4.1.2 freeglut -------- **Description** freeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library. **More Information** http://freeglut.sourceforge.net/ **Available Versions**:: 3.2.1-GCCcore-10.3.0 3.2.1-GCCcore-10.2.0 3.2.1-GCCcore-11.2.0 3.2.1-GCCcore-9.3.0 3.2.1-GCCcore-8.3.0 3.4.0-GCCcore-12.3.0 freetype -------- **Description** FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display servers, font conversion tools, text image generation tools, and many other products as well. **More Information** https://www.freetype.org **Available Versions**:: 2.13.0-GCCcore-12.3.0 2.11.0-GCCcore-11.2.0 2.10.3-GCCcore-10.2.0 2.10.1-GCCcore-9.3.0 2.9.1-GCCcore-7.3.0 2.13.2-GCCcore-13.2.0 2.10.1-GCCcore-8.3.0 2.12.1-GCCcore-12.2.0 2.10.4-GCCcore-10.3.0 2.13.2-GCCcore-13.3.0 2.9.1-GCCcore-8.2.0 2.13.3-GCCcore-14.2.0 2.12.1-GCCcore-11.3.0 fsm-lite -------- **Available Versions**:: 1.0 fsom ---- **Description** A tiny C library for managing SOM (Self-Organizing Maps) neural networks. **More Information** https://github.com/ekg/fsom **Available Versions**:: 20141119-GCCcore-11.2.0 g2clib ------ **Description** Library contains GRIB2 encoder/decoder ('C' version). **More Information** https://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/ **Available Versions**:: 1.6.3-GCCcore-10.3.0 g2lib ----- **Description** Library contains GRIB2 encoder/decoder and search/indexing routines. **More Information** https://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/ **Available Versions**:: 3.2.0-GCCcore-10.3.0 gap --- **Description** GAP is a system for computational discrete algebra,with particular emphasis on Computational Group Theory. **More Information** https://www.gap-system.org **Available Versions**:: 4.15.1-foss-2022a 4.13.0-foss-2022a 4.15.0-foss-2022a 4.14.0-foss-2022a garlic ------ **Available Versions**:: 22 gawk ---- **Description** The awk utility interprets a special-purpose programming language that makes it possible to handlesimple data-reformatting jobs with just a few lines of code. **More Information** https://www.gnu.org/software/gawk **Available Versions**:: 5.1.1-GCC-11.2.0 5.1.1-GCC-11.3.0 gc -- **Description** The Boehm-Demers-Weiser conservative garbage collector can be used as agarbage collecting replacement for C malloc or C++ new. **More Information** https://hboehm.info/gc/ **Available Versions**:: 8.2.2-GCCcore-11.3.0 7.6.10-GCCcore-8.2.0 8.2.4-GCCcore-12.3.0 7.6.12-GCCcore-9.3.0 8.2.0-GCCcore-11.2.0 7.6.12-GCCcore-8.3.0 gcccuda ------- **Description** GNU Compiler Collection (GCC) based compiler toolchain, along with CUDA toolkit. **More Information** (none) **Available Versions**:: 2018b 2020b 2019b 2020a gcloud ------ **Description** Libraries and tools for interacting with Google Cloud products and services. **More Information** https://cloud.google.com/sdk **Available Versions**:: 472.0.0 gdc-client ---------- **Description** The gdc-client provides several convenience functions over the GDC API which provides general download/upload via HTTPS. **More Information** https://gdc.nci.nih.gov/access-data/gdc-data-transfer-tool **Available Versions**:: 1.6.0-GCCcore-10.2.0 gengetopt --------- **Description** Gengetopt is a tool to write command line option parsing code for C programs. **More Information** https://www.gnu.org/software/gengetopt/gengetopt.html **Available Versions**:: 2.23-GCCcore-12.3.0 geth ---- **Available Versions**:: 2022 gettext ------- **Description** GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we maybuild many other steps. This package offers to programmers, translators, and even users, a well integrated set of toolsand documentation **More Information** https://www.gnu.org/software/gettext/ **Available Versions**:: 0.25-GCCcore-14.3.0 0.21.1-GCCcore-12.2.0 0.22.5 0.21-GCCcore-11.2.0 0.25 0.22.5-GCCcore-13.3.0 0.20.1 0.21.1 0.20.1-GCCcore-8.3.0 0.22 0.21-GCCcore-10.3.0 0.21-GCCcore-10.2.0 0.21.1-GCCcore-12.3.0 0.20.1-GCCcore-9.3.0 0.22-GCCcore-13.2.0 0.19.8.1-GCCcore-7.3.0 0.19.8.1-GCCcore-8.2.0 0.19.8.1 0.21 0.24-GCCcore-14.2.0 0.21-GCCcore-11.3.0 gfbf ---- **Description** GNU Compiler Collection (GCC) based compiler toolchain, including FlexiBLAS (BLAS and LAPACK support) and (serial) FFTW. **More Information** (none) **Available Versions**:: 2022a 2024a 2022b 2023b 2025b 2025a 2023a gflags ------ **Description** The gflags package contains a C++ library that implements commandline flagsprocessing. It includes built-in support for standard types such as stringand the ability to define flags in the source file in which they are used. **More Information** https://github.com/gflags/gflags **Available Versions**:: 2.2.2-GCCcore-8.2.0 giflib ------ **Description** giflib is a library for reading and writing gif images.It is API and ABI compatible with libungif which was in wide use whilethe LZW compression algorithm was patented. **More Information** http://giflib.sourceforge.net/ **Available Versions**:: 5.2.2-GCCcore-14.2.0 5.2.1-GCCcore-13.2.0 5.2.1-GCCcore-11.3.0 5.1.4-GCCcore-8.2.0 5.2.1-GCCcore-12.3.0 5.2.1-GCCcore-9.3.0 5.2.1-GCCcore-12.2.0 5.2.1-GCCcore-11.2.0 5.2.1-GCCcore-13.3.0 5.2.1-GCCcore-10.3.0 5.2.1-GCCcore-10.2.0 5.2.1-GCCcore-8.3.0 git --- **Description** Git is a free and open source distributed version control system designedto handle everything from small to very large projects with speed and efficiency. **More Information** https://git-scm.com **Available Versions**:: 2.42.0-GCCcore-13.2.0 2.45.1-GCCcore-13.3.0 2.36.0-GCCcore-11.3.0-nodocs 2.23.0-GCCcore-8.3.0-nodocs 2.23.0-GCCcore-9.3.0-nodocs 2.41.0-GCCcore-12.3.0-nodocs 2.33.1-GCCcore-11.2.0-nodocs 2.28.0-GCCcore-10.2.0-nodocs 2.38.1-GCCcore-12.2.0-nodocs 2.32.0-GCCcore-10.3.0-nodocs 2.50.1-GCCcore-14.3.0 2.49.0-GCCcore-14.2.0 git-lfs ------- **Description** Git Large File Storage (LFS) replaces large files such as audio samples, videos, datasets, and graphics with text pointers inside Git, while storing the file contents on a remote server like GitHub.com **More Information** https://git-lfs.github.com **Available Versions**:: 2.11.0 3.2.0 glew ---- **Description** The OpenGL Extension Wrangler Library (GLEW) is a cross-platform open-sourceC/C++ extension loading library. GLEW provides efficient run-time mechanismsfor determining which OpenGL extensions are supported on the target platform. **More Information** http://glew.sourceforge.net/ **Available Versions**:: 2.1.0-GCCcore-9.3.0 2.2.0-GCCcore-12.3.0-osmesa 2.1.0-GCCcore-8.3.0 2.2.0-GCCcore-11.2.0-egl glib-networking --------------- **Description** Network extensions for GLib **More Information** https://gitlab.gnome.org/GNOME/glib-networking **Available Versions**:: 2.72.1-GCCcore-11.2.0 2.72.1-GCCcore-12.3.0 glog ---- **Description** A C++ implementation of the Google logging module. **More Information** https://github.com/google/glog **Available Versions**:: 0.4.0-GCCcore-8.2.0 glslang-SPIRV ------------- **Description** Glslang is the official reference compiler front end for the OpenGL ES and OpenGL shading languages.It implements a strict interpretation of the specifications for these languages. It is open and free for anyone to use,either from a command line or programmatically. The OpenGL and OpenGL ES working groups are committed to maintainingconsistency between the reference compiler and the corresponding shading language specifications. **More Information** https://www.khronos.org/opengles/sdk/tools/Reference-Compiler/ **Available Versions**:: 15.3.0-GCCcore-14.2.0 gmpy2 ----- **Description** GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x **More Information** https://github.com/aleaxit/gmpy **Available Versions**:: 2.1.5-GCC-13.2.0 2.1.0b5-GCC-9.3.0 2.1.0b5-GCC-10.3.0 2.1.2-GCC-11.3.0 2.1.0b4-GCC-8.3.0 2.1.5-GCC-12.3.0 gmsh ---- **Description** Gmsh is a 3D finite element grid generator with a build-in CAD engine and post-processor. **More Information** https://gmsh.info/ **Available Versions**:: 4.7.1-intel-2020a-Python-3.8.2 gnuplot ------- **Description** Portable interactive, function plotting utility **More Information** http://gnuplot.sourceforge.net/ **Available Versions**:: 5.4.2-GCCcore-10.3.0 5.4.2-GCCcore-11.2.0 5.2.8-GCCcore-9.3.0 5.4.4-GCCcore-11.3.0 gomkl ----- **Description** GNU Compiler Collection (GCC) based compiler toolchain with OpenMPI and MKL **More Information** (none) **Available Versions**:: 2023b 2021b 2023a gompi ----- **Description** GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support. **More Information** (none) **Available Versions**:: 2022.05 2019b 2023a 2019a 2021b 2021a 2025b 2019b-dba 2024.05 2023b 2018b 2025a 2024a 2020a 2020b 2023.09 2022a 2022b 2022.10 gompic ------ **Description** GNU Compiler Collection (GCC) based compiler toolchain along with CUDA toolkit, including OpenMPI for MPI support with CUDA features enabled. **More Information** (none) **Available Versions**:: 2019b 2020b 2020a 2018b googletest ---------- **Description** Google's framework for writing C++ tests on a variety of platforms **More Information** https://github.com/google/googletest **Available Versions**:: 1.13.0-GCCcore-12.3.0 1.11.0-GCCcore-11.2.0 1.11.0-GCCcore-11.3.0 1.14.0-GCCcore-13.2.0 1.10.0-GCCcore-10.2.0 1.15.2-GCCcore-13.3.0 gperf ----- **Description** GNU gperf is a perfect hash function generator. For a given list of strings, it produces a hash function and hash table, in form of C or C++ code, for looking up a value depending on the input string. The hash function is perfect, which means that the hash table has no collisions, and the hash table lookup needs a single string comparison only. **More Information** https://www.gnu.org/software/gperf/ **Available Versions**:: 3.1-GCCcore-11.3.0 3.3-GCCcore-14.2.0 3.1-GCCcore-8.2.0 3.1-GCCcore-11.2.0 3.1-GCCcore-10.2.0 3.1-GCCcore-8.3.0 3.1-GCCcore-12.3.0 3.1-GCCcore-13.3.0 3.1-GCCcore-13.2.0 3.1-GCCcore-12.2.0 3.1-GCCcore-9.3.0 3.1-GCCcore-10.3.0 3.1-GCCcore-7.3.0 gperftools ---------- **Description** gperftools is a collection of a high-performance multi-threaded malloc()implementation, plus some pretty nifty performance analysis tools.Includes TCMalloc, heap-checker, heap-profiler and cpu-profiler. **More Information** https://github.com/gperftools/gperftools **Available Versions**:: 2.9.1-GCCcore-10.3.0 2.10-GCCcore-11.3.0 2.9.1-GCCcore-10.2.0 2.7.90-GCCcore-8.3.0 gptl ---- **Description** GPTL - General Purpose Timing Library, including OpenMPI for MPI support. **More Information** https://jmrosinski.github.io/GPTL **Available Versions**:: 8.1.1 graph-tool ---------- **Description** Graph-tool is an efficient Python module for manipulation and statistical analysis of graphs (a.k.a. networks). Contrary to most other python modules with similar functionality, the core data structures and algorithms are implemented in C++, making extensive use of template metaprogramming, based heavily on the Boost Graph Library. This confers it a level of performance that is comparable (both in memory usage and computation time) to that of a pure C/C++ library. **More Information** https://graph-tool.skewed.de/ **Available Versions**:: 2.55-foss-2022a graphite2 --------- **Description** Graphite is a "smart font" system developed specifically to handle the complexities of lesser-known languages of the world. **More Information** https://scripts.sil.org/cms/scripts/page.php?site_id=projects&item_id=graphite_home **Available Versions**:: 1.3.14-GCCcore-12.3.0 1.3.14-GCCcore-13.2.0 1.3.14-GCCcore-13.3.0 1.3.14-GCCcore-12.2.0 1.3.14-GCCcore-11.2.0 1.3.14-GCCcore-11.3.0 1.3.14-GCCcore-14.2.0 grib_api -------- **Description** The ECMWF GRIB API is an application program interface accessible from C, FORTRAN and Python programs developed for encoding and decoding WMO FM-92 GRIB edition 1 and edition 2 messages. A useful set of command line tools is also provided to give quick access to GRIB messages. **More Information** https://software.ecmwf.int/wiki/display/GRIB/Home **Available Versions**:: 1.24.0-intel-2020b groff ----- **Description** Groff (GNU troff) is a typesetting system that reads plain text mixed with formatting commands and produces formatted output. **More Information** https://www.gnu.org/software/groff **Available Versions**:: 1.23.0-GCCcore-14.3.0 1.23.0-GCCcore-14.2.0 1.22.4-GCCcore-11.3.0 1.22.4-GCCcore-12.3.0 1.22.4-GCCcore-12.2.0 1.22.4-GCCcore-9.3.0 1.23.0-GCCcore-13.2.0 1.22.4-GCCcore-8.3.0 1.23.0-GCCcore-13.3.0 1.22.4-GCCcore-11.2.0 1.22.4-GCCcore-10.3.0 1.22.4-GCCcore-10.2.0 gromacs ------- **Available Versions**:: 2018.4-fosscuda-2019b gromacs-cp2k ------------ **Available Versions**:: 2021.1-foss-2020a gromos ------ **Available Versions**:: 1.5.0 grpcio ------ **Description** gRPC is a modern, open source, high-performance remote procedure call (RPC)framework that can run anywhere. gRPC enables client and server applications tocommunicate transparently, and simplifies the building of connected systems. **More Information** https://grpc.io/ **Available Versions**:: 1.57.0-GCCcore-12.3.0 gulp ---- **Available Versions**:: 5.0 6.2 gzip ---- **Description** gzip (GNU zip) is a popular data compression program as a replacement for compress **More Information** https://www.gnu.org/software/gzip/ **Available Versions**:: 1.10-GCCcore-10.3.0 1.10-GCCcore-10.2.0 1.10-GCCcore-8.3.0 1.13-GCCcore-13.3.0 1.12-GCCcore-12.3.0 1.12-GCCcore-12.2.0 1.12-GCCcore-11.3.0 1.10-GCCcore-9.3.0 1.13-GCCcore-13.2.0 1.14-GCCcore-14.3.0 1.10-GCCcore-11.2.0 1.13-GCCcore-14.2.0 h5py ---- **Description** HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data. **More Information** https://www.h5py.org/ **Available Versions**:: 3.7.0-foss-2022a 3.8.0-gomkl-2021b 2.10.0-fosscuda-2019b-Python-3.7.4 2.10.0-foss-2020a-Python-3.8.2 3.2.1-foss-2021a 2.10.0-fosscuda-2020a-Python-3.8.2 2.9.0-foss-2019a 3.9.0-foss-2023a 2.10.0-intel-2020a-Python-3.8.2 3.1.0-fosscuda-2020b 3.1.0-foss-2020b 3.6.0-foss-2021b 2.10.0-foss-2019b-Python-3.7.4 hatchling --------- **Description** Extensible, standards compliant build backend used by Hatch,a modern, extensible Python project manager. **More Information** https://hatch.pypa.io **Available Versions**:: 1.24.2-GCCcore-13.3.0 1.27.0-GCCcore-14.3.0 1.27.0-GCCcore-14.2.0 1.18.0-GCCcore-13.2.0 1.18.0-GCCcore-12.3.0 help2man -------- **Description** help2man produces simple manual pages from the '--help' and '--version' output of other commands. **More Information** https://www.gnu.org/software/help2man/ **Available Versions**:: 1.49.3-GCCcore-13.3.0 1.49.2-GCCcore-12.2.0 1.49.3-GCCcore-15.1.0 1.49.3-GCCcore-13.2.0 1.49.2-GCCcore-11.3.0 1.48.3-GCCcore-10.3.0 1.47.6-GCCcore-8.1.0 1.47.16-GCCcore-10.2.0 1.47.4 1.48.3-GCCcore-11.2.0 1.47.8-GCCcore-8.3.0 1.49.3-GCCcore-13.1.0 1.47.12-GCCcore-9.3.0 1.47.4-GCCcore-7.3.0 1.49.3-GCCcore-14.2.0 1.49.3-GCCcore-12.3.0 1.49.3-GCCcore-14.3.0 1.47.7-GCCcore-8.2.0 hiredis ------- **Description** Hiredis is a minimalistic C client library for the Redis database.It is minimalistic because it just adds minimal support for the protocol,but at the same time it uses a high level printf-alike API in order tomake it much higher level than otherwise suggested by its minimal code baseand the lack of explicit bindings for every Redis command. **More Information** https://github.com/redis/hiredis **Available Versions**:: 1.2.0-GCCcore-12.3.0 1.0.2-GCCcore-11.2.0 hmmlearn -------- **Description** hmmlearn is a set of algorithms for unsupervised learning and inference of Hidden Markov Models **More Information** https://github.com/hmmlearn/hmmlearn **Available Versions**:: 0.3.0-gfbf-2023a hptt ---- **Available Versions**:: 1.0.5 hunspell -------- **Description** Hunspell is a spell checker and morphological analyzerlibrary and program designed for languages with rich morphology andcomplex word compounding or character encoding. **More Information** https://hunspell.github.io/ **Available Versions**:: 1.7.2-GCCcore-12.3.0 1.7.1-GCCcore-11.2.0 hwloc ----- **Description** The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various system attributes such as cache and memory information as well as the locality of I/O devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering information about modern computing hardware so as to exploit it accordingly and efficiently. **More Information** https://www.open-mpi.org/projects/hwloc/ **Available Versions**:: 2.7.1-GCCcore-11.3.0 1.11.12-GCCcore-9.3.0 1.11.12-GCCcore-8.3.0 2.8.0-GCCcore-12.2.0 1.11.10-GCCcore-7.3.0 2.5.0-GCCcore-11.2.0 2.9.1-GCCcore-12.3.0 2.10.0-GCCcore-13.3.0 2.4.1-GCCcore-10.3.0 2.12.1-GCCcore-14.3.0 2.11.2-GCCcore-14.2.0 2.2.0-GCCcore-10.2.0 1.11.11-GCCcore-8.2.0 2.2.0-GCCcore-9.3.0 2.9.2-GCCcore-13.2.0 hypothesis ---------- **Description** Hypothesis is an advanced testing library for Python. It lets you write tests which are parametrized by a source of examples, and then generates simple and comprehensible examples that make your tests fail. This lets you find more bugs in your code with less work. **More Information** https://github.com/HypothesisWorks/hypothesis **Available Versions**:: 6.103.1-GCCcore-13.3.0 4.57.1-GCCcore-12.3.0-Python-2.7.18 6.68.2-GCCcore-12.2.0 6.82.0-GCCcore-12.3.0 5.41.5-GCCcore-10.2.0 6.13.1-GCCcore-10.3.0 6.46.7-GCCcore-11.3.0 6.136.6-GCCcore-14.3.0 6.133.2-GCCcore-14.2.0 6.90.0-GCCcore-13.2.0 4.44.2-GCCcore-8.3.0-Python-3.7.4 5.41.2-GCCcore-10.2.0 6.14.6-GCCcore-11.2.0 icc --- **Description** Intel C and C++ compilers **More Information** https://software.intel.com/en-us/intel-compilers/ **Available Versions**:: 2019.1.144-GCC-8.2.0-2.31.1 2018.3.222-GCC-7.3.0-2.30 iccifort -------- **Description** Intel C, C++ & Fortran compilers **More Information** http://software.intel.com/en-us/intel-cluster-toolkit-compiler/ **Available Versions**:: 2018.3.222-GCC-7.3.0-2.30 2019.1.144-GCC-8.2.0-2.31.1 2020.1.217 2019.5.281 2020.4.304 iccifortcuda ------------ **Description** Intel C, C++ & Fortran compilers with CUDA toolkit **More Information** (none) **Available Versions**:: 2019b 2020b ifort ----- **Description** Intel Fortran compiler **More Information** https://software.intel.com/en-us/intel-compilers/ **Available Versions**:: 2018.3.222-GCC-7.3.0-2.30 2019.1.144-GCC-8.2.0-2.31.1 igraph ------ **Description** igraph is a collection of network analysis tools with the emphasis onefficiency, portability and ease of use. igraph is open source and free. igraph can beprogrammed in R, Python and C/C++. **More Information** https://igraph.org **Available Versions**:: 0.10.10-foss-2023a 0.9.5-foss-2021b iimpi ----- **Description** Intel C/C++ and Fortran compilers, alongside Intel MPI. **More Information** https://software.intel.com/parallel-studio-xe **Available Versions**:: 2020b 2022b 2021a 2022.05 2024a 2022a 2020a 2023a 2023b 2021b 2023.03 iimpic ------ **Description** Intel C/C++ and Fortran compilers, alongside Intel MPI and CUDA. **More Information** (none) **Available Versions**:: 2020b imagecodecs ----------- **Description** Imagecodecs is a Python library that provides block-oriented, in-memory buffer transformation,compression, and decompression functions for use in the tifffile, czifile, zarr, and otherscientific image input/output modules. **More Information** https://github.com/cgohlke/imagecodecs **Available Versions**:: 2022.9.26-foss-2022a imkl ---- **Description** Intel oneAPI Math Kernel Library **More Information** https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html **Available Versions**:: 2023.2.0 2021.2.0-iompi-2021a 2021.4.0 2020.1.217-gompi-2020a 2023.1.0 2021.2.0-iimpi-2021a 2023.1.0-gompi-2023a 2022.2.1 2023.2.0-gompi-2023b 2022.1.0 2024.2.0 2020.4.304-iimpic-2020b 2020.4.304-iimpi-2020b 2020.1.217-iimpi-2020a imkl-FFTW --------- **Description** FFTW interfaces using Intel oneAPI Math Kernel Library **More Information** https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html **Available Versions**:: 2023.1.0-iimpi-2023a 2024.2.0-iimpi-2024a 2021.4.0-iimpi-2021b 2022.2.1-iimpi-2022b 2022.1.0-iimpi-2022.05 2023.1.0-iimpi-2023.03 2022.1.0-iimpi-2022a 2023.2.0-iimpi-2023b impi ---- **Description** Intel MPI Library, compatible with MPICH ABI **More Information** https://software.intel.com/content/www/us/en/develop/tools/mpi-library.html **Available Versions**:: 2021.7.1-intel-compilers-2022.2.1 2021.10.0-intel-compilers-2023.2.1 2021.9.0-intel-compilers-2023.1.0 2021.13.0-intel-compilers-2024.2.0 2019.7.217-iccifort-2020.1.217 2021.2.0-intel-compilers-2021.2.0 2021.6.0-intel-compilers-2022.1.0 2019.9.304-iccifort-2020.4.304 2021.4.0-intel-compilers-2021.4.0 2019.9.304-iccifortcuda-2020b inih ---- **Description** Direct Rendering Manager runtime library. **More Information** https://dri.freedesktop.org **Available Versions**:: 57-GCCcore-12.3.0 intel ----- **Description** Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL). **More Information** https://easybuild.readthedocs.io/en/master/Common-toolchains.html#intel-toolchain **Available Versions**:: 2020b 2023b 2023.03 2020a 2023a 2021a 2022b 2021b 2022a 2022.05 2024a intel-compilers --------------- **Description** Intel C, C++ & Fortran compilers (classic and oneAPI) **More Information** https://software.intel.com/content/www/us/en/develop/tools/oneapi/hpc-toolkit.html **Available Versions**:: 2024.2.0 2022.2.1 2023.2.1 2022.1.0 2021.4.0 2021.2.0 2023.1.0 intelcuda --------- **Description** Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL, with CUDA toolkit **More Information** (none) **Available Versions**:: 2020b intervaltree ------------ **Description** An interval tree can be used to efficiently find a set of numeric intervals overlapping or containing another interval. This library provides a basic implementation of an interval tree using C++ templates, allowing the insertion of arbitrary types into the tree. **More Information** https://github.com/ekg/intervaltree **Available Versions**:: 0.1-GCCcore-11.2.0 intltool -------- **Description** intltool is a set of tools to centralize translation of many different file formats using GNU gettext-compatible PO files. **More Information** https://freedesktop.org/wiki/Software/intltool/ **Available Versions**:: 0.51.0-GCCcore-12.3.0 0.51.0-GCCcore-13.2.0 0.51.0-GCCcore-11.3.0 0.51.0-GCCcore-12.2.0 0.51.0-GCCcore-7.3.0-Perl-5.28.0 0.51.0-GCCcore-13.3.0 0.51.0-GCCcore-14.2.0 0.51.0-GCCcore-10.2.0 0.51.0-GCCcore-11.2.0 0.51.0-GCCcore-8.3.0 0.51.0-GCCcore-9.3.0 0.51.0-GCCcore-8.2.0 0.51.0-GCCcore-10.3.0 iomkl ----- **Description** Compiler toolchain including Intel compilers, Open MPI and Intel Math Kernel Library (MKL). **More Information** https://software.intel.com/content/www/us/en/develop/tools/oneapi/hpc-toolkit.html **Available Versions**:: 2021a iompi ----- **Description** Intel C/C++ and Fortran compilers, alongside Open MPI. **More Information** https://software.intel.com/content/www/us/en/develop/tools/oneapi/hpc-toolkit.html **Available Versions**:: 2021a 2020b itensor ------- **Available Versions**:: 3.1.5-omp 3.1.5 jax --- **Description** Composable transformations of Python+NumPy programs:differentiate, vectorize, JIT to GPU/TPU, and more **More Information** https://pypi.python.org/pypi/jax **Available Versions**:: 0.4.4-foss-2022a-CUDA-12.0.0 0.3.25-foss-2022a-CUDA-11.7.0 0.3.9-foss-2021a-CUDA-11.3.1 0.2.19-fosscuda-2020b 0.3.25-foss-2022a jbigkit ------- **Description** JBIG-KIT is a software implementation of the JBIG1 data compression standard (ITU-T T.82), which was designed for bi-level image data, such as scanned documents. **More Information** https://www.cl.cam.ac.uk/~mgk25/jbigkit/ **Available Versions**:: 2.1-GCCcore-13.2.0 2.1-GCCcore-9.3.0 2.1-GCCcore-11.2.0 2.1-GCCcore-10.2.0 2.1-GCCcore-12.3.0 2.1-GCCcore-13.3.0 2.1-GCCcore-12.2.0 2.1-GCCcore-14.2.0 2.1-GCCcore-11.3.0 2.1-GCCcore-10.3.0 jedi ---- **Description** Jedi - an awesome autocompletion, static analysis and refactoring library for Python. **More Information** https://github.com/davidhalter/jedi **Available Versions**:: 0.19.1-GCCcore-14.2.0 jemalloc -------- **Description** jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and scalable concurrency support. **More Information** http://jemalloc.net **Available Versions**:: 5.3.0-GCCcore-11.3.0 5.2.1-GCCcore-10.2.0 5.2.1-GCCcore-8.3.0 5.2.1-GCCcore-11.3.0 5.2.1-GCCcore-10.3.0 5.2.1-GCCcore-11.2.0 5.3.0-GCCcore-12.3.0 json-c ------ **Description** JSON-C implements a reference counting object model that allows you to easily construct JSON objects in C, output them as JSON formatted strings and parse JSON formatted strings back into the C representation of JSONobjects. **More Information** https://github.com/json-c/json-c **Available Versions**:: 0.17-GCCcore-13.2.0 0.13.1-GCCcore-8.2.0 0.17-GCCcore-13.3.0 0.16-GCCcore-12.3.0 json-fortran ------------ **Description** JSON-Fortran: A Modern Fortran JSON API **More Information** https://github.com/jacobwilliams/json-fortran **Available Versions**:: 9.0.3-GCC-13.3.0 jupyter-server -------------- **Description** The Jupyter Server provides the backend (i.e. the core services, APIs, and RESTendpoints) for Jupyter web applications like Jupyter notebook, JupyterLab, andVoila. **More Information** https://jupyter.org/ **Available Versions**:: 1.21.0-GCCcore-11.3.0 2.7.2-GCCcore-12.3.0 jxrlib ------ **Description** Open source implementation of jpegxr **More Information** https://github.com/4creators/jxrlib **Available Versions**:: 1.1-GCCcore-11.3.0 kallisto -------- **Description** kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. **More Information** https://pachterlab.github.io/kallisto/ **Available Versions**:: 0.48.0-gompi-2021b 0.46.1-foss-2019b 0.46.2-foss-2020b kim-api ------- **Description** Open Knowledgebase of Interatomic Models.KIM is an API and OpenKIM is a collection of interatomic models (potentials) foratomistic simulations. This is a library that can be used by simulation programsto get access to the models in the OpenKIM database.This EasyBuild only installs the API, the models can be installed with thepackage openkim-models, or the user can install them manually by running kim-api-collections-management install user MODELNAMEor kim-api-collections-management install user OpenKIMto install them all. **More Information** https://openkim.org/ **Available Versions**:: 2.3.0-GCC-12.3.0 2.3.0-GCC-11.2.0 2.3.0-GCC-13.2.0 2.2.1-GCCcore-11.2.0 2.3.0-GCC-11.3.0 2.1.3-intel-2020a 2.1.3-foss-2020a kineto ------ **Description** A CPU+GPU Profiling library that provides access to timeline traces and hardware performance counters **More Information** https://github.com/pytorch/kineto **Available Versions**:: 0.4.0-GCC-10.3.0 0.4.0-GCC-11.3.0 0.4.0-GCC-12.3.0 kwant ----- **Description** Kwant is a free (open source), powerful, and easy to use Python package for numerical calculations on tight-binding models with a strong focus on quantum transport. **More Information** https://kwant-project.org/ **Available Versions**:: 1.4.1-foss-2019a-Python-3.7.2 libBigWig --------- **Description** A C library for handling bigWig files **More Information** https://github.com/dpryan79/libBigWig **Available Versions**:: 0.4.6-GCCcore-11.2.0 libGLU ------ **Description** The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. **More Information** https://mesa.freedesktop.org/archive/glu/ **Available Versions**:: 9.0.1-GCCcore-10.2.0 9.0.1-GCCcore-9.3.0 9.0.2-GCCcore-11.2.0 9.0.3-GCCcore-13.2.0 9.0.1-GCCcore-8.3.0 9.0.3-GCCcore-12.3.0 9.0.3-GCCcore-13.3.0 9.0.2-GCCcore-11.3.0 9.0.1-GCCcore-10.3.0 9.0.3-GCCcore-14.2.0 9.0.2-GCCcore-12.2.0 libGridXC --------- **Description** A library to compute the exchange and correlation energy and potential in spherical (i.e. atoms) or periodic systems. **More Information** https://gitlab.com/siesta-project/libraries/libgridxc **Available Versions**:: 2.0.2-gompi-2024a libPSML ------- **Description** A library to handle pseudopotentials in PSML format **More Information** https://gitlab.com/siesta-project/libraries/libpsml **Available Versions**:: 2.1.0-GCC-13.3.0 libRmath -------- **Description** The routines supporting the distribution and special functions in R and a few others are declared in C header file Rmath.h. These can be compiled into a standalone library for linking to other applications. **More Information** https://cran.r-project.org/doc/manuals/r-release/R-admin.html#The-standalone-Rmath-library **Available Versions**:: 4.1.2-GCCcore-11.2.0 libaec ------ **Description** 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 imaginginstrument data or numerical model output from weather or climate simulations. While floating point representationsare not directly supported, they can also be efficiently coded by grouping exponents and mantissa. **More Information** https://gitlab.dkrz.de/k202009/libaec **Available Versions**:: 1.0.6-GCCcore-13.2.0 1.0.6-GCCcore-12.3.0 1.0.6-GCCcore-10.3.0 1.0.6-GCCcore-11.3.0 libaio ------ **Description** Asynchronous input/output library that uses the kernels native interface. **More Information** https://pagure.io/libaio **Available Versions**:: 0.3.113-GCCcore-12.2.0 0.3.112-GCCcore-10.3.0 0.3.112-GCCcore-10.2.0 0.3.112-GCCcore-11.3.0 0.3.111-GCCcore-8.3.0 0.3.113-GCCcore-12.3.0 libarchive ---------- **Description** Multi-format archive and compression library **More Information** https://www.libarchive.org/ **Available Versions**:: 3.6.2-GCCcore-12.3.0 3.6.1-GCCcore-11.3.0 3.7.2-GCCcore-13.2.0 3.6.2-GCCcore-13.2.0 3.4.0-GCCcore-8.2.0 3.8.1-GCCcore-14.3.0 3.5.1-GCCcore-11.2.0 3.5.1-GCCcore-8.3.0 3.7.4-GCCcore-13.3.0 3.5.1-GCCcore-10.3.0 3.6.1-GCCcore-12.2.0 3.7.7-GCCcore-14.2.0 3.4.3-GCCcore-10.2.0 libavif ------- **Description** This library aims to be a friendly, portable C implementation of the AV1 Image File Format,as described here: https://aomediacodec.github.io/av1-avif/ **More Information** https://github.com/AOMediaCodec/libavif **Available Versions**:: 0.11.1-GCCcore-11.3.0 1.0.4-GCCcore-12.3.0 libcerf ------- **Description** libcerf is a self-contained numeric library that provides an efficient and accurate implementation of complex error functions, along with Dawson, Faddeeva, and Voigt functions. **More Information** https://jugit.fz-juelich.de/mlz/libcerf **Available Versions**:: 2.1-GCCcore-11.3.0 2.3-GCCcore-12.3.0 1.17-GCCcore-11.2.0 1.7-GCCcore-7.3.0 1.13-GCCcore-9.3.0 2.3-GCCcore-12.2.0 1.17-GCCcore-10.3.0 1.13-GCCcore-8.3.0 1.14-GCCcore-10.2.0 libcifpp -------- **Description** This library contains code to work with mmCIF and PDB files **More Information** https://github.com/PDB-REDO/libcifpp **Available Versions**:: 7.0.8-GCC-13.3.0 libcint ------- **Description** libcint is an open source library for analytical Gaussian integrals. **More Information** https://github.com/sunqm/libcint **Available Versions**:: 5.1.6-foss-2021a 4.4.0-foss-2021a libctl ------ **Description** libctl is a free Guile-based library implementing flexible control files for scientific simulations. **More Information** https://libctl.readthedocs.io/en/latest/ **Available Versions**:: 4.1.3-GCCcore-9.3.0 libdap ------ **Description** A C++ SDK which contains an implementation of DAP 2.0 and DAP4.0. This includes both Client- and Server-side support classes. **More Information** https://www.opendap.org/software/libdap **Available Versions**:: 3.20.7-GCCcore-10.2.0 3.20.7-GCCcore-10.3.0 libde265 -------- **Description** libde265 is an open source implementation of the h.265 video codec **More Information** https://github.com/strukturag/libde265 **Available Versions**:: 1.0.11-GCC-11.3.0 1.0.15-GCCcore-13.3.0 1.0.16-GCCcore-14.2.0 libdeflate ---------- **Description** Heavily optimized library for DEFLATE/zlib/gzip compression and decompression. **More Information** https://github.com/ebiggers/libdeflate **Available Versions**:: 1.15-GCCcore-12.2.0 1.18-GCCcore-12.3.0 1.24-GCCcore-14.2.0 1.8-GCCcore-11.2.0 1.19-GCCcore-13.2.0 1.20-GCCcore-13.3.0 1.10-GCCcore-11.3.0 libdrm ------ **Description** Direct Rendering Manager runtime library. **More Information** https://dri.freedesktop.org **Available Versions**:: 2.4.107-GCCcore-11.2.0 2.4.106-GCCcore-10.3.0 2.4.110-GCCcore-11.3.0 2.4.125-GCCcore-14.2.0 2.4.117-GCCcore-13.2.0 2.4.100-GCCcore-9.3.0 2.4.97-GCCcore-8.2.0 2.4.115-GCCcore-12.3.0 2.4.99-GCCcore-8.3.0 2.4.92-GCCcore-7.3.0 2.4.102-GCCcore-10.2.0 2.4.114-GCCcore-12.2.0 2.4.122-GCCcore-13.3.0 libdwarf -------- **Description** The DWARF Debugging Information Format is of interest to programmers working on compilersand debuggers (and anyone interested in reading or writing DWARF information)) **More Information** https://www.prevanders.net/dwarf.html **Available Versions**:: 20201201-GCCcore-10.2.0 libedit ------- **Description** This BSD-style licensed command line editor library provides generic line editing,history, and tokenization functions, similar to those found in GNU Readline. **More Information** https://thrysoee.dk/editline/ **Available Versions**:: 20191231-GCCcore-9.3.0 libelf ------ **Description** libelf is a free ELF object file access library **More Information** https://sourceware.org/elfutils **Available Versions**:: 0.8.13-GCCcore-10.2.0 libepoxy -------- **Description** Epoxy is a library for handling OpenGL function pointer management for you **More Information** https://github.com/anholt/libepoxy **Available Versions**:: 1.5.10-GCCcore-13.2.0 1.5.10-GCCcore-12.3.0 1.5.10-GCCcore-11.3.0 1.5.4-GCCcore-10.2.0 1.5.3-GCCcore-8.2.0 1.5.10-GCCcore-12.2.0 1.5.4-GCCcore-8.3.0 1.5.8-GCCcore-11.2.0 libev ----- **Description** A full-featured and high-performance (see benchmark) event loop that is loosely modelled after libevent, but without its limitations and bugs. It is used in GNU Virtual Private Ethernet, rxvt-unicode, auditd, the Deliantra MORPG Server and Client, and many other programs. **More Information** http://software.schmorp.de/pkg/libev.html **Available Versions**:: 4.33-GCC-11.2.0 4.33-GCC-12.3.0 libevent -------- **Description** The libevent API provides a mechanism to execute a callback function when a specific event occurs on a file descriptor or after a timeout has been reached. Furthermore, libevent also support callbacks due to signals or regular timeouts. **More Information** https://libevent.org/ **Available Versions**:: 2.1.12-GCCcore-11.3.0 2.1.12-GCCcore-12.2.0 2.1.12-GCCcore-14.2.0 2.1.12-GCCcore-14.3.0 2.1.12-GCCcore-11.2.0 2.1.12-GCCcore-13.3.0 2.1.11-GCCcore-9.3.0 2.1.11-GCCcore-8.3.0 2.1.12-GCCcore-12.3.0 2.1.8 2.1.12-GCCcore-10.2.0 2.1.12-GCCcore-13.2.0 2.1.12-GCCcore-10.3.0 libexif ------- **Description** A library for parsing, editing, and saving EXIF data. **More Information** https://libexif.github.io/ **Available Versions**:: 0.6.24-GCCcore-11.2.0 libfabric --------- **Description** Libfabric is a core component of OFI. It is the library that defines and exportsthe user-space API of OFI, and is typically the only software that applicationsdeal with directly. It works in conjunction with provider libraries, which areoften integrated directly into libfabric. **More Information** https://ofiwg.github.io/libfabric/ **Available Versions**:: 1.19.0-GCCcore-13.2.0 1.15.1-GCCcore-11.3.0 1.12.1-GCCcore-10.3.0 1.11.0-GCCcore-10.2.0 2.0.0-GCCcore-14.2.0 1.21.0-GCCcore-13.3.0 1.11.0-GCCcore-9.3.0 1.16.1-GCCcore-12.2.0 1.18.0-GCCcore-12.3.0 1.13.2-GCCcore-11.2.0 2.1.0-GCCcore-14.3.0 libfdf ------ **Description** LibFDF is the official implementation of the FDF specifications for use in client codes. **More Information** https://gitlab.com/siesta-project/libraries/libfdf **Available Versions**:: 0.5.1-GCC-13.3.0 libffi ------ **Description** The libffi library provides a portable, high level programming interface to various calling conventions. This allows a programmer to call any function specified by a call interface description at run-time. **More Information** https://sourceware.org/libffi/ **Available Versions**:: 3.5.1-GCCcore-14.3.0 3.2.1-GCCcore-8.3.0 3.3-GCCcore-10.3.0 3.4.5-GCCcore-13.3.0 3.3-GCCcore-10.2.0 3.2.1-GCCcore-10.2.0 3.4.4-GCCcore-12.3.0 3.4.2-GCCcore-11.3.0 3.2.1-GCCcore-7.3.0 3.4.5-GCCcore-14.2.0 3.4.4-GCCcore-13.2.0 3.4.2-GCCcore-11.2.0 3.4.4-GCCcore-12.2.0 3.2.1-GCCcore-8.2.0 3.3-GCCcore-9.3.0 libgcrypt --------- **Description** Libgcrypt is a general purpose cryptographic library originally based on code from GnuPG **More Information** https://gnupg.org/related_software/libgcrypt/index.html **Available Versions**:: 1.10.3-GCCcore-12.3.0 1.9.3-GCCcore-11.2.0 libgd ----- **Description** GD is an open source code library for the dynamic creation of images by programmers. **More Information** https://libgd.github.io **Available Versions**:: 2.3.3-GCCcore-12.3.0 2.3.3-GCCcore-11.3.0 2.2.5-GCCcore-7.3.0 2.3.0-GCCcore-9.3.0 2.3.1-GCCcore-10.3.0 2.3.0-GCCcore-10.2.0 2.3.3-GCCcore-12.2.0 2.3.3-GCCcore-11.2.0 2.2.5-GCCcore-8.3.0 libgdiplus ---------- **Description** Libgdiplus is the Mono library that provides a GDI+-compatible API on non-Windows operating systems. **More Information** https://www.mono-project.com/docs/gui/libgdiplus **Available Versions**:: 6.1-GCCcore-11.2.0 libgeotiff ---------- **Description** Library for reading and writing coordinate system information from/to GeoTIFF files **More Information** https://directory.fsf.org/wiki/Libgeotiff **Available Versions**:: 1.6.0-GCCcore-10.3.0 1.6.0-GCCcore-10.2.0 1.7.1-GCCcore-12.3.0 1.7.3-GCCcore-13.2.0 1.5.1-GCCcore-8.3.0 1.7.3-GCCcore-13.3.0 1.7.1-GCCcore-11.3.0 1.5.1-GCCcore-8.2.0 1.4.2-foss-2018b 1.5.1-GCCcore-9.3.0 1.7.0-GCCcore-11.2.0 libgit2 ------- **Description** libgit2 is a portable, pure C implementation of the Git core methods provided as a re-entrantlinkable library with a solid API, allowing you to write native speed custom Git applications in any languagewhich supports C bindings. **More Information** https://libgit2.org/ **Available Versions**:: 1.7.2-GCCcore-13.2.0 1.7.1-GCCcore-12.3.0 1.8.1-GCCcore-13.3.0 1.1.0-GCCcore-10.3.0 1.4.3-GCCcore-11.3.0 1.1.1-GCCcore-11.2.0 1.9.1-GCCcore-14.2.0 1.9.1-GCCcore-14.3.0 libglvnd -------- **Description** libglvnd is a vendor-neutral dispatch layer for arbitrating OpenGL API calls between multiple vendors. **More Information** https://gitlab.freedesktop.org/glvnd/libglvnd **Available Versions**:: 1.7.0-GCCcore-13.3.0 1.4.0-GCCcore-11.3.0 1.7.0-GCCcore-13.2.0 1.3.3-GCCcore-11.2.0 1.3.3-GCCcore-10.3.0 1.7.0-GCCcore-14.2.0 1.6.0-GCCcore-12.3.0 1.3.2-GCCcore-10.2.0 1.2.0-GCCcore-9.3.0 1.6.0-GCCcore-12.2.0 libgpg-error ------------ **Description** Libgpg-error is a small library that defines common error values for all GnuPG components. **More Information** https://gnupg.org/related_software/libgpg-error/index.html **Available Versions**:: 1.48-GCCcore-12.3.0 1.42-GCCcore-11.2.0 libgpuarray ----------- **Description** Library to manipulate tensors on the GPU. **More Information** http://deeplearning.net/software/libgpuarray/ **Available Versions**:: 0.7.6-fosscuda-2019b-Python-3.7.4 0.7.6-fosscuda-2020b libheif ------- **Description** libheif is an HEIF and AVIF file format decoder and encoder **More Information** https://github.com/strukturag/libheif **Available Versions**:: 1.16.2-GCC-11.3.0 1.19.8-GCCcore-14.2.0 1.19.5-GCCcore-13.3.0 libiconv -------- **Description** Libiconv converts from one character encoding to another through Unicode conversion **More Information** https://www.gnu.org/software/libiconv **Available Versions**:: 1.18-GCCcore-14.3.0 1.16-GCCcore-10.2.0 1.16-GCCcore-10.3.0 1.15-GCCcore-7.3.0 1.16-GCCcore-9.3.0 1.18-GCCcore-14.2.0 1.16-GCCcore-8.2.0 1.17-GCCcore-11.3.0 1.17-GCCcore-13.2.0 1.16-GCCcore-11.2.0 1.16-GCCcore-8.3.0 1.17-GCCcore-13.3.0 1.17-GCCcore-12.2.0 1.17-GCCcore-12.3.0 libidn ------ **Description** GNU Libidn is a fully documented implementation of the Stringprep, Punycode and IDNA specifications.Libidn's purpose is to encode and decode internationalized domain names. **More Information** http://www.gnu.org/software/libidn **Available Versions**:: 1.38-GCCcore-11.2.0 1.41-GCCcore-11.3.0 libidn2 ------- **Description** Libidn2 implements the revised algorithm for internationalized domain names called IDNA2008/TR46. **More Information** http://www.gnu.org/software/libidn2 **Available Versions**:: 2.3.2-GCCcore-11.3.0 2.3.7-GCCcore-14.2.0 2.3.2-GCCcore-11.2.0 2.3.0-GCCcore-10.2.0 2.3.8-GCCcore-14.3.0 2.3.7-GCCcore-12.3.0 libjpeg-turbo ------------- **Description** libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelerate baseline JPEG compression and decompression. libjpeg is a library that implements JPEG image encoding, decoding and transcoding. **More Information** http://sourceforge.net/projects/libjpeg-turbo/ **Available Versions**:: 2.0.0-GCCcore-7.3.0 2.1.4-GCCcore-12.2.0 2.0.4-GCCcore-9.3.0 2.0.6-GCCcore-10.3.0 2.0.5-GCCcore-10.2.0 2.1.5.1-GCCcore-12.3.0 3.0.1-GCCcore-13.3.0 3.0.1-GCCcore-13.2.0 2.0.2-GCCcore-8.2.0 2.0.3-GCCcore-8.3.0 2.1.3-GCCcore-11.3.0 3.1.0-GCCcore-14.2.0 2.0.6-GCCcore-11.2.0 libjxl ------ **Description** JPEG XL image format reference implementation **More Information** https://github.com/libjxl/libjxl **Available Versions**:: 0.8.1-foss-2022a libmad ------ **Description** MAD is a high-quality MPEG audio decoder. **More Information** https://www.underbit.com/products/mad/ **Available Versions**:: 0.15.1b-GCCcore-11.3.0 libmatheval ----------- **Description** GNU libmatheval is a library (callable from C and Fortran) to parse and evaluate symbolic expressions input as text. **More Information** http://www.gnu.org/software/libmatheval/ **Available Versions**:: 1.1.11-GCCcore-8.2.0 1.1.11-GCCcore-8.3.0 1.1.11-GCCcore-9.3.0 libmcfp ------- **Description** A library for parsing command line arguments and configuration files and makingthem available throughout a program. **More Information** https://github.com/mhekkel/libmcfp **Available Versions**:: 1.3.4-GCCcore-13.3.0 libogg ------ **Description** Ogg is a multimedia container format, and the native file and stream format for the Xiph.orgmultimedia codecs. **More Information** https://xiph.org/ogg/ **Available Versions**:: 1.3.5-GCCcore-13.2.0 1.3.4-GCCcore-10.2.0 1.3.5-GCCcore-11.3.0 1.3.5-GCCcore-13.3.0 1.3.5-GCCcore-12.2.0 1.3.4-GCCcore-10.3.0 1.3.5-GCCcore-11.2.0 1.3.5-GCCcore-12.3.0 libopus ------- **Description** Opus is a totally open, royalty-free, highly versatile audio codec. Opus is unmatched for interactive speech and music transmission over the Internet, but is also intended for storage and streaming applications. It is standardized by the Internet Engineering Task Force (IETF) as RFC 6716 which incorporated technology from Skype’s SILK codec and Xiph.Org’s CELT codec. **More Information** https://www.opus-codec.org/ **Available Versions**:: 1.5.2-GCCcore-13.3.0 1.3.1-GCCcore-11.3.0 1.3.1-GCCcore-12.2.0 1.4-GCCcore-12.3.0 1.5.2-GCCcore-13.2.0 libpciaccess ------------ **Description** Generic PCI access library. **More Information** https://cgit.freedesktop.org/xorg/lib/libpciaccess/ **Available Versions**:: 0.18.1-GCCcore-14.2.0 0.14-GCCcore-8.2.0 0.18.1-GCCcore-13.3.0 0.17-GCCcore-13.2.0 0.16-GCCcore-10.2.0 0.18.1-GCCcore-14.3.0 0.16-GCCcore-11.2.0 0.16-GCCcore-11.3.0 0.14-GCCcore-8.3.0 0.14-GCCcore-7.3.0 0.17-GCCcore-12.3.0 0.16-GCCcore-10.3.0 0.17-GCCcore-12.2.0 0.16-GCCcore-9.3.0 libpng ------ **Description** libpng is the official PNG reference library **More Information** http://www.libpng.org/pub/png/libpng.html **Available Versions**:: 1.6.38-GCCcore-12.2.0 1.6.43-GCCcore-13.3.0 1.6.37-GCCcore-11.3.0 1.6.37-GCCcore-9.3.0 1.6.37-GCCcore-8.3.0 1.6.37-GCCcore-10.3.0 1.6.39-GCCcore-12.3.0 1.6.36-GCCcore-8.2.0 1.6.34-GCCcore-7.3.0 1.6.48-GCCcore-14.2.0 1.6.37-GCCcore-11.2.0 1.6.40-GCCcore-13.2.0 1.6.37-GCCcore-10.2.0 libpsl ------ **Description** C library for the Public Suffix List **More Information** https://rockdaboot.github.io/libpsl **Available Versions**:: 0.21.1-GCCcore-11.2.0 0.21.1-GCCcore-11.3.0 0.21.5-GCCcore-12.3.0 0.21.5-GCCcore-14.2.0 0.21.5-GCCcore-14.3.0 libpsortb --------- **Description** PSORT family of programs for subcellular localization prediction as well as other datasets and resources relevant to localization prediction. **More Information** http://psort.org/ **Available Versions**:: 1.0-foss-2021b libreadline ----------- **Description** The GNU Readline library provides a set of functions for use by applications that allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. The Readline library includes additional functions to maintain a list of previously-entered command lines, to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands. **More Information** https://tiswww.case.edu/php/chet/readline/rltop.html **Available Versions**:: 8.0-GCCcore-10.2.0 8.2-GCCcore-13.2.0 8.2-GCCcore-12.3.0 8.0-GCCcore-8.3.0 8.0-GCCcore-7.3.0 7.0-GCCcore-7.3.0 8.0-GCCcore-8.2.0 8.2-GCCcore-14.2.0 8.2-GCCcore-12.2.0 8.0-GCCcore-9.3.0 8.2-GCCcore-13.3.0 8.1-GCCcore-11.2.0 8.2-GCCcore-14.3.0 8.1-GCCcore-10.3.0 8.1.2-GCCcore-11.3.0 7.0-GCCcore-10.2.0 librttopo --------- **Description** The RT Topology Library exposes an API to create andmanage standard (ISO 13249 aka SQL/MM) topologies using user-provideddata stores. **More Information** https://git.osgeo.org/gitea/rttopo/librttopo **Available Versions**:: 1.1.0-GCC-11.2.0 1.1.0-GCC-12.3.0 libsigc++ --------- **Description** The libsigc++ package implements a typesafe callback system for standard C++. **More Information** https://libsigcplusplus.github.io/libsigcplusplus/ **Available Versions**:: 2.10.8-GCCcore-10.3.0 2.10.2-GCCcore-8.3.0 3.4.0-GCCcore-11.3.0 libsndfile ---------- **Description** Libsndfile is a C library for reading and writing files containing sampled sound (such as MS Windows WAV and the Apple/SGI AIFF format) through one standard library interface. **More Information** http://www.mega-nerd.com/libsndfile **Available Versions**:: 1.0.31-GCCcore-10.3.0 1.2.2-GCCcore-13.2.0 1.0.28-GCCcore-7.3.0 1.2.0-GCCcore-12.2.0 1.0.31-GCCcore-11.2.0 1.0.28-GCCcore-10.2.0 1.0.28-GCCcore-8.3.0 1.2.2-GCCcore-12.3.0 1.0.28-GCCcore-9.3.0 1.2.2-GCCcore-13.3.0 1.1.0-GCCcore-11.3.0 libsodium --------- **Description** Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, password hashing and more. **More Information** https://doc.libsodium.org/ **Available Versions**:: 1.0.18-GCCcore-11.2.0 1.0.18-GCCcore-12.3.0 1.0.18-GCCcore-11.3.0 1.0.18-GCCcore-8.3.0 1.0.18-GCCcore-10.3.0 1.0.18-GCCcore-9.3.0 1.0.18-GCCcore-10.2.0 libspatialindex --------------- **Description** C++ implementation of R*-tree, an MVR-tree and a TPR-tree with C API **More Information** https://libspatialindex.org **Available Versions**:: 1.9.3-GCCcore-12.3.0 1.9.3-GCCcore-11.2.0 libspatialite ------------- **Description** SpatiaLite is an open source library intended to extend the SQLite core to support fully fledged Spatial SQL capabilities. **More Information** https://www.gaia-gis.it/fossil/libspatialite/home **Available Versions**:: 5.0.1-GCC-11.2.0 5.1.0-GCC-12.3.0 5.0.1-GCC-12.3.0 libspectre ---------- **Description** libspectre is a small library for rendering Postscript documents. It provides a convenient easy to use API for handling and rendering Postscript documents. **More Information** https://www.freedesktop.org/wiki/Software/libspectre/ **Available Versions**:: 0.2.12-GCCcore-12.3.0 libtasn1 -------- **Description** Libtasn1 is the ASN.1 library used by GnuTLS, GNU Shishi and some other packages. It was written by Fabio Fiorina, and has been shipped as part of GnuTLS for some time but is now a proper GNU package. **More Information** https://www.gnu.org/software/libtasn1/ **Available Versions**:: 4.19.0-GCCcore-12.3.0 4.18.0-GCCcore-11.2.0 4.19.0-GCCcore-11.3.0 libtirpc -------- **Description** Libtirpc is a port of Suns Transport-Independent RPC library to Linux. **More Information** https://sourceforge.net/projects/libtirpc/ **Available Versions**:: 1.2.6-GCCcore-9.3.0 1.3.2-GCCcore-11.2.0 1.3.5-GCCcore-13.3.0 1.3.1-GCCcore-10.2.0 1.2.6-GCCcore-8.3.0 1.3.3-GCCcore-12.3.0 1.3.2-GCCcore-11.3.0 1.3.2-GCCcore-10.3.0 1.3.4-GCCcore-13.2.0 libtommath ---------- **Description** LibTomMath is a free open source portable number theoreticmultiple-precision integer (MPI) library written entirely in C. **More Information** https://www.libtom.net/LibTomMath/ **Available Versions**:: 1.3.0-GCCcore-14.3.0 libtool ------- **Description** GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries behind a consistent, portable interface. **More Information** http://www.gnu.org/software/libtool **Available Versions**:: 2.4.6-GCCcore-8.1.0 2.4.6-GCCcore-11.2.0 2.4.6-GCCcore-8.2.0 2.4.6-GCCcore-7.3.0 2.4.7-GCCcore-13.2.0 2.4.7 2.4.6-GCCcore-10.2.0 2.4.7-GCCcore-12.3.0 2.4.6-GCCcore-9.3.0 2.5.4-GCCcore-14.3.0 2.4.6-GCCcore-8.3.0 2.4.7-GCCcore-11.3.0 2.4.7-GCCcore-13.3.0 2.4.6-GCCcore-10.3.0 2.4.7-GCCcore-12.2.0 2.5.4-GCCcore-14.2.0 libunistring ------------ **Description** This library provides functions for manipulating Unicode strings and for manipulating C strings according to the Unicode standard. **More Information** https://www.gnu.org/software/libunistring/ **Available Versions**:: 0.9.10-GCCcore-8.3.0 1.3-GCCcore-14.2.0 0.9.10-GCCcore-9.3.0 1.0-GCCcore-11.3.0 1.3-GCCcore-14.3.0 0.9.10-GCCcore-8.2.0 1.0-GCCcore-11.2.0 1.1-GCCcore-12.3.0 libunwind --------- **Description** The primary goal of libunwind is to define a portable and efficient C programming interface (API) to determine the call-chain of a program. The API additionally provides the means to manipulate the preserved (callee-saved) state of each call-frame and to resume execution at any point in the call-chain (non-local goto). The API supports both local (same-process) and remote (across-process) operation. As such, the API is useful in a number of applications **More Information** https://www.nongnu.org/libunwind/ **Available Versions**:: 1.3.1-GCCcore-9.3.0 1.6.2-GCCcore-13.2.0 1.8.1-GCCcore-14.2.0 1.8.1-GCCcore-13.3.0 1.5.0-GCCcore-11.2.0 1.6.2-GCCcore-11.3.0 1.6.2-GCCcore-12.3.0 1.4.0-GCCcore-10.2.0 1.4.0-GCCcore-10.3.0 1.2.1-GCCcore-7.3.0 1.6.2-GCCcore-12.2.0 1.3.1-GCCcore-8.2.0 1.3.1-GCCcore-8.3.0 libvdwxc -------- **Description** libvdwxc is a general library for evaluating energy and potential forexchange-correlation (XC) functionals from the vdW-DF family that can be used with variousof density functional theory (DFT) codes. **More Information** https://libvdwxc.org **Available Versions**:: 0.4.0-foss-2021a 0.4.0-foss-2022a 0.4.0-foss-2020b libvips ------- **Available Versions**:: 8.14.2 libvorbis --------- **Description** Ogg Vorbis is a fully open, non-proprietary, patent-and-royalty-free, general-purpose compressedaudio format **More Information** https://xiph.org/vorbis/ **Available Versions**:: 1.3.7-GCCcore-12.2.0 1.3.7-GCCcore-13.3.0 1.3.7-GCCcore-13.2.0 1.3.7-GCCcore-10.3.0 1.3.7-GCCcore-12.3.0 1.3.7-GCCcore-10.2.0 1.3.7-GCCcore-11.2.0 1.3.7-GCCcore-11.3.0 libvori ------- **Description** C++ library implementing the Voronoi integration as well as the compressed bqbfile format. The present version of libvori is a very early developmentversion, which is hard-coded to work with the CP2k program package. **More Information** https://brehm-research.de/libvori.php **Available Versions**:: 220621-GCCcore-12.3.0 libwebp ------- **Description** WebP is a modern image format that provides superiorlossless and lossy compression for images on the web. Using WebP,webmasters and web developers can create smaller, richer images thatmake the web faster. **More Information** https://developers.google.com/speed/webp/ **Available Versions**:: 1.5.0-GCCcore-14.2.0 1.2.4-GCCcore-11.3.0 1.3.2-GCCcore-13.2.0 1.2.0-GCCcore-11.2.0 1.1.0-GCCcore-10.2.0 1.4.0-GCCcore-13.3.0 1.3.1-GCCcore-12.3.0 1.0.2-GCCcore-8.2.0 1.3.1-GCCcore-12.2.0 libwpe ------ **Description** WPE is the reference WebKit port for embedded andlow-consumption computer devices. It has been designed from theground-up with performance, small footprint, accelerated contentrendering, and simplicity of deployment in mind, bringing theexcellence of the WebKit engine to countless platforms and target devices. **More Information** https://webkit.org/wpe **Available Versions**:: 1.16.0-GCCcore-12.3.0 1.13.3-GCCcore-11.2.0 libxc ----- **Description** Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals. **More Information** https://www.tddft.org/programs/libxc **Available Versions**:: 4.3.4-GCC-7.3.0-2.30 4.3.4-GCC-8.2.0-2.31.1 5.2.3-GCC-10.3.0 6.2.2-GCC-13.3.0 4.3.4-iccifort-2020.1.217 5.2.3-intel-compilers-2022.1.0 6.2.2-GCC-12.3.0 5.1.5-GCC-10.3.0 3.0.1-foss-2020a 5.1.2-GCC-10.2.0 4.3.4-iccifort-2020.4.304 4.3.4-iccifort-2019.5.281 4.3.4-GCC-8.3.0 5.2.3-GCC-11.3.0 5.1.5-intel-compilers-2021.2.0 6.2.2-intel-compilers-2023.1.0 4.3.4-GCC-10.2.0 4.3.4-GCC-9.3.0 3.0.1-GCC-8.2.0-2.31.1 4.3.4-intel-2020a libxml++ -------- **Description** libxml++ is a C++ wrapper for the libxml XML parser library. **More Information** http://libxmlplusplus.sourceforge.net **Available Versions**:: 2.40.1-GCCcore-8.3.0 2.42.1-GCC-10.3.0 libxml2 ------- **Description** Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform). **More Information** http://xmlsoft.org/ **Available Versions**:: 2.9.13-GCCcore-11.3.0 2.12.7-GCCcore-13.3.0 2.11.4-GCCcore-13.2.0 2.9.9-GCCcore-8.3.0 2.11.4-GCCcore-12.3.0 2.9.10-GCCcore-9.3.0 2.9.9-GCCcore-9.3.0 2.9.8-GCCcore-8.2.0 2.11.5-GCCcore-13.2.0 2.9.10-GCCcore-11.2.0 2.9.8-GCCcore-7.3.0 2.9.10-GCCcore-10.2.0 2.9.10-GCCcore-10.3.0 2.10.3-GCCcore-12.2.0 2.13.4-GCCcore-14.2.0 2.14.3-GCCcore-14.3.0 libxml2-python -------------- **Description** Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform). This is the Python binding. **More Information** http://xmlsoft.org/ **Available Versions**:: 2.11.4-GCCcore-12.3.0 libxslt ------- **Description** Libxslt is the XSLT C library developed for the GNOME project (but usable outside of the Gnome platform). **More Information** http://xmlsoft.org/ **Available Versions**:: 1.1.38-GCCcore-13.2.0 1.1.42-GCCcore-14.2.0 1.1.32-GCCcore-7.3.0 1.1.34-GCCcore-10.3.0 1.1.34-GCCcore-11.2.0 1.1.34-GCCcore-10.2.0 1.1.37-GCCcore-12.2.0 1.1.38-GCCcore-12.3.0 1.1.42-GCCcore-13.3.0 1.1.34-GCCcore-9.3.0 1.1.34-GCCcore-11.3.0 libxsmm ------- **Description** LIBXSMM is a library for small dense and small sparse matrix-matrix multiplicationstargeting Intel Architecture (x86). **More Information** https://github.com/hfp/libxsmm **Available Versions**:: 1.17-GCC-11.3.0 1.16.2-GCC-10.3.0 1.16.1-iccifort-2020.1.217 1.10-GCC-8.2.0-2.31.1 1.17-GCC-12.3.0 1.10-foss-2019b 1.16.1-GCC-9.3.0 1.16.1-GCC-10.2.0 1.16.1-iccifort-2020.4.304 libyaml ------- **Description** LibYAML is a YAML parser and emitter written in C. **More Information** https://pyyaml.org/wiki/LibYAML **Available Versions**:: 0.2.5-GCCcore-14.2.0 0.2.5-GCCcore-10.3.0 0.2.2-GCCcore-8.2.0 0.2.5-GCCcore-12.3.0 0.2.5-GCCcore-10.2.0 0.2.5-GCCcore-13.2.0 0.2.5-GCCcore-11.2.0 0.2.2-GCCcore-9.3.0 0.2.5-GCCcore-11.3.0 0.2.2-GCCcore-8.3.0 libzip ------ **Description** libzip is a C library for reading, creating, and modifying zip archives. **More Information** https://libzip.org/ **Available Versions**:: 1.7.3-GCCcore-11.2.0 1.10.1-GCCcore-12.3.0 likwid ------ **Description** Likwid stands for Like I knew what I am doing. This project contributes easy to use command line tools for Linux to support programmers in developing high performance multi threaded programs. **More Information** https://github.com/RRZE-HPC/likwid **Available Versions**:: 5.0.1-GCCcore-8.3.0 lit --- **Description** lit is a portable tool for executing LLVM and Clang style test suites, summarizing their results, andproviding indication of failures. **More Information** https://llvm.org/docs/CommandGuide/lit.html **Available Versions**:: 18.1.8-GCCcore-14.2.0 18.1.2-GCCcore-12.3.0 lpsolve ------- **Description** Mixed Integer Linear Programming (MILP) solver **More Information** https://sourceforge.net/projects/lpsolve/ **Available Versions**:: 5.5.2.11-GCC-10.2.0 5.5.2.5-GCC-8.3.0 lrslib ------ **Description** lrslib is a self-contained ANSI C implementation of thereverse search algorithm for vertex enumeration/convex hull problems **More Information** http://cgm.cs.mcgill.ca/~avis/C/lrs.html **Available Versions**:: 7.2-gompi-2023b 7.2-gompi-2022a lxml ---- **Description** The lxml XML toolkit is a Pythonic binding for the C libraries libxml2 and libxslt. **More Information** http://lxml.de/ **Available Versions**:: 4.5.2-foss-2020a-Python-3.8.2 4.6.3-GCCcore-11.2.0 4.9.2-GCCcore-12.3.0 4.9.1-GCCcore-11.3.0 4.2.5-foss-2018b-Python-2.7.15 4.6.3-GCCcore-10.3.0 lz4 --- **Description** LZ4 is lossless compression algorithm, providing compression speed at 400 MB/s per core. It features an extremely fast decoder, with speed in multiple GB/s per core. **More Information** https://lz4.github.io/lz4/ **Available Versions**:: 1.9.2-GCCcore-10.2.0 1.9.4-GCCcore-12.2.0 1.9.4-GCCcore-13.3.0 1.9.2-GCCcore-9.3.0 1.9.4-GCCcore-12.3.0 1.9.3-GCCcore-11.3.0 1.9.3-GCCcore-11.2.0 1.9.4-GCCcore-13.2.0 1.9.3-GCCcore-10.3.0 1.10.0-GCCcore-14.3.0 1.10.0-GCCcore-14.2.0 1.9.2-GCCcore-8.3.0 maeparser --------- **Description** maeparser is a parser for Schrodinger Maestro files. **More Information** https://github.com/schrodinger/maeparser **Available Versions**:: 1.3.0-gompi-2019b 1.3.0-gompi-2021a magma ----- **Description** The MAGMA project aims to develop a dense linear algebra library similar to LAPACK but for heterogeneous/hybrid architectures, starting with current Multicore+GPU systems. **More Information** https://icl.cs.utk.edu/magma/ **Available Versions**:: 2.7.2-foss-2023a-CUDA-12.0.0 2.7.2-foss-2023a-CUDA-12.1.1 2.6.1-foss-2021a-CUDA-11.3.1 2.5.1-fosscuda-2019b 2.6.2-foss-2022a-CUDA-11.7.0 2.5.4-fosscuda-2020b 2.5.4-fosscuda-2019b 2.6.2-foss-2022a-CUDA-11.8.0 make ---- **Description** GNU version of make utility **More Information** https://www.gnu.org/software/make/make.html **Available Versions**:: 4.4.1-GCCcore-12.3.0 4.3-GCCcore-10.2.0 4.3-GCCcore-11.3.0 4.4.1-GCCcore-13.3.0 4.3-GCCcore-11.2.0 4.3-GCCcore-9.3.0 4.4.1-GCCcore-14.3.0 4.4.1-GCCcore-14.2.0 4.4.1-GCCcore-13.2.0 4.3-GCCcore-12.2.0 4.3-GCCcore-10.3.0 makedepend ---------- **Description** The makedepend package contains a C-preprocessor like utility to determine build-time dependencies. **More Information** https://linux.die.net/man/1/makedepend **Available Versions**:: 1.0.6-GCCcore-10.3.0 makeinfo -------- **Description** makeinfo is part of the Texinfo project, the official documentation format of the GNU project.This is a minimal build with very basic functionality. Should only be used for build dependencies. **More Information** https://www.gnu.org/software/texinfo/ **Available Versions**:: 6.7-GCCcore-10.2.0-minimal 7.0.3-GCCcore-12.3.0 6.8-GCCcore-11.3.0 6.8-GCCcore-11.2.0 6.7-GCCcore-9.3.0-minimal 6.7-GCCcore-9.3.0 6.7-GCCcore-8.3.0-minimal 6.7-GCCcore-10.3.0 6.7-GCCcore-10.3.0-minimal mandrake -------- **Description** Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding. **More Information** https://mandrake.readthedocs.io **Available Versions**:: 1.2.2-foss-2022a matplotlib ---------- **Description** matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell, web application servers, and six graphical user interface toolkits. **More Information** https://matplotlib.org **Available Versions**:: 2.2.5-foss-2023a-Python-2.7.18 3.5.2-intel-2022a 3.4.3-foss-2021b 3.1.1-foss-2019b-Python-3.7.4 3.5.2-foss-2022a 3.2.1-foss-2020a-Python-3.8.2 3.2.1-intel-2020a-Python-3.8.2 3.9.2-gfbf-2024a 3.5.2-foss-2021b 3.0.3-foss-2019a-Python-3.7.2 3.7.2-gfbf-2023a 3.10.3-gfbf-2025a 3.8.2-gfbf-2023b maturin ------- **Description** This project is meant as a zero configurationreplacement for setuptools-rust and milksnake. It supports buildingwheels for python 3.5+ on windows, linux, mac and freebsd, can uploadthem to pypi and has basic pypy and graalpy support. **More Information** https://github.com/pyo3/maturin **Available Versions**:: 1.8.3-GCCcore-14.2.0 1.6.0-GCCcore-13.3.0 1.9.1-GCCcore-14.3.0 1.1.0-GCCcore-12.3.0 mctc-lib -------- **Description** Common tool chain for working with molecular structure data in variousapplications. This library provides a unified way to perform operations onmolecular structure data, like reading and writing to common geometry fileformats. **More Information** https://grimme-lab.github.io/mctc-lib **Available Versions**:: 0.3.1-GCC-13.3.0 mdtep ----- **Available Versions**:: 2022 meson-python ------------ **Description** Python build backend (PEP 517) for Meson projects **More Information** https://github.com/mesonbuild/meson-python **Available Versions**:: 0.18.0-GCCcore-14.3.0 0.13.2-GCCcore-12.3.0 0.18.0-GCCcore-14.2.0 0.16.0-GCCcore-13.3.0 0.15.0-GCCcore-13.2.0 minimap2 -------- **Description** Minimap2 is a fast sequence mapping and alignmentprogram that can find overlaps between long noisy reads, or map longreads or their assemblies to a reference genome optionally with detailedalignment (i.e. CIGAR). At present, it works efficiently with querysequences from a few kilobases to ~100 megabases in length at an errorrate ~15%. Minimap2 outputs in the PAF or the SAM format. On limitedtest data sets, minimap2 is over 20 times faster than most otherlong-read aligners. It will replace BWA-MEM for long reads and contigalignment. **More Information** https://github.com/lh3/minimap2 **Available Versions**:: 2.22-GCCcore-11.2.0 2.24-GCCcore-11.3.0 2.17-GCC-8.3.0 minizip ------- **Description** Mini zip and unzip based on zlib **More Information** https://www.winimage.com/zLibDll/minizip.html **Available Versions**:: 1.1-GCCcore-11.2.0 1.1-GCCcore-12.3.0 ml_dtypes --------- **Description** ml_dtypes is a stand-alone implementation of several NumPy dtype extensions usedin machine learning libraries, including:bfloat16: an alternative to the standard float16 formatfloat8_*: several experimental 8-bit floating point representations including:float8_e4m3b11fnuzfloat8_e4m3fnfloat8_e4m3fnuzfloat8_e5m2float8_e5m2fnuz **More Information** https://github.com/jax-ml/ml_dtypes **Available Versions**:: 0.3.2-gfbf-2023a mlst ---- **Available Versions**:: 2023 mm-common --------- **Description** The mm-common module provides the build infrastructure and utilities shared among the GNOME C++ binding libraries. **More Information** https://gitlab.gnome.org/GNOME/mm-common **Available Versions**:: 1.0.5-GCCcore-11.3.0 1.0.4-GCCcore-10.3.0 module-git ---------- **Available Versions**:: False module-info ----------- **Available Versions**:: False modules ------- **Available Versions**:: False molmod ------ **Description** MolMod is a Python library with many compoments that are useful to write molecular modeling programs. **More Information** https://molmod.github.io/molmod/ **Available Versions**:: 1.4.5-intel-2020a-Python-3.8.2 1.4.5-foss-2020a-Python-3.8.2 mosdepth -------- **Description** Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing **More Information** https://github.com/brentp/mosdepth **Available Versions**:: 0.3.9-GCC-12.3.0 motif ----- **Description** Motif refers to both a graphical user interface (GUI) specification and the widget toolkit for building applications that follow that specification under the X Window System on Unix and other POSIX-compliant systems. It was the standard toolkit for the Common Desktop Environment and thus for Unix. **More Information** https://motif.ics.com/ **Available Versions**:: 2.3.8-GCCcore-11.2.0 mpi4py ------ **Description** MPI for Python (mpi4py) provides bindings of the Message Passing Interface (MPI) standard for the Python programming language, allowing any Python program to exploit multiple processors. **More Information** https://github.com/mpi4py/mpi4py **Available Versions**:: 3.1.5-gompi-2023b 4.1.0-gompi-2025a 4.1.0-gompi-2025b 3.1.4-gompi-2023a mpitest ------- **Available Versions**:: 1.0 mpmath ------ **Description** mpmath can be used as an arbitrary-precision substitute for Python's float/complex types and math/cmath modules, but also does much more advanced mathematics. Almost any calculation can be performed just as well at 10-digit or 1000-digit precision, with either real or complex numbers, and in many cases mpmath implements efficient algorithms that scale well for extremely high precision work. **More Information** https://mpmath.org/ **Available Versions**:: 1.1.0-GCCcore-9.3.0-Python-3.8.2 1.0.0-foss-2018b-Python-2.7.15 mrc --- **Description** Maartens Resource Compiler to store resources in the static section of an ELF binary. **More Information** https://github.com/mhekkel/mrc **Available Versions**:: 1.3.13-GCCcore-13.3.0 msmc2 ----- **Available Versions**:: 2025 mstore ------ **Description** Molecular structure store for testing **More Information** https://github.com/grimme-lab/mstore **Available Versions**:: 0.3.0-GCC-13.3.0 mule ---- **Available Versions**:: 4.4.0 multichoose ----------- **Description** generate multiset combinations (n multichoose k). **More Information** https://github.com/ekg/multichoose **Available Versions**:: 1.0.3-GCCcore-11.2.0 muparserx --------- **Description** A C++ Library for Parsing Expressions with Strings, Complex Numbers, Vectors, Matrices and more. **More Information** https://beltoforion.de/en/muparserx/ **Available Versions**:: 4.0.8-GCCcore-10.3.0 nauty ----- **Description** nauty and Traces are programs for computing automorphism groups of graphs anddigraphs. They can also produce a canonical label. **More Information** https://pallini.di.uniroma1.it/ **Available Versions**:: 2.8.6-GCC-11.3.0 nbo7 ---- **Available Versions**:: 2025 ncbi-vdb -------- **Description** The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. **More Information** https://github.com/ncbi/ncbi-vdb **Available Versions**:: 2.10.9-gompi-2020b 3.0.2-gompi-2022a 3.2.0-gompi-2024a ncurses ------- **Description** The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses. **More Information** https://www.gnu.org/software/ncurses/ **Available Versions**:: 6.1 6.4 6.2-GCCcore-9.3.0 6.4-GCCcore-12.3.0 6.5 6.3 6.1-GCCcore-10.2.0 6.3-GCCcore-12.2.0 6.1-GCCcore-7.3.0 6.3-GCCcore-11.3.0 6.2 6.2-GCCcore-10.2.0 6.5-GCCcore-13.3.0 6.1-GCCcore-8.2.0 6.2-GCCcore-10.3.0 6.1-GCCcore-8.3.0 6.4-GCCcore-13.2.0 6.5-GCCcore-14.2.0 6.5-GCCcore-14.3.0 6.2-GCCcore-11.2.0 6.0 ncview ------ **Description** Ncview is a visual browser for netCDF format files.Typically you would use ncview to get a quick and easy, push-buttonlook at your netCDF files. You can view simple movies of the data,view along various dimensions, take a look at the actual data values,change color maps, invert the data, etc. **More Information** https://meteora.ucsd.edu/~pierce/ncview_home_page.html **Available Versions**:: 2.1.7-foss-2019b netCDF ------ **Description** NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. **More Information** https://www.unidata.ucar.edu/software/netcdf/ **Available Versions**:: 4.6.2-gompi-2019a 4.6.1-foss-2018b 4.6.1-fosscuda-2018b 4.7.4-iimpi-2020b 4.9.0-gompi-2022a 4.9.2-gompi-2023a 4.9.2-gompi-2023b 4.7.4-iimpi-2020a 4.9.0-iimpi-2022a 4.7.4-gompic-2020b 4.8.1-gompi-2021b 4.8.0-gompi-2021a 4.9.2-gompi-2024a 4.7.1-gompic-2019b 4.9.3-gompi-2025a 4.7.4-gompi-2020a 4.9.0-iimpi-2022b 4.9.2-iimpi-2023a 4.7.1-gompi-2019b-dba 4.7.1-gompi-2019b 4.7.4-gompi-2020b 4.8.1-iimpi-2021b netCDF-C++4 ----------- **Description** NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. **More Information** https://www.unidata.ucar.edu/software/netcdf/ **Available Versions**:: 4.3.1-gompi-2022a 4.3.1-gompi-2021b 4.3.1-gompi-2020b 4.3.1-gompi-2021a 4.3.1-iimpi-2020a netCDF-Fortran -------------- **Description** NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. **More Information** https://www.unidata.ucar.edu/software/netcdf/ **Available Versions**:: 4.5.3-gompi-2021b 4.5.2-iimpi-2020a 4.5.2-gompi-2019b 4.5.3-gompic-2020b 4.4.4-fosscuda-2018b 4.4.4-foss-2018b 4.6.1-iimpi-2023a 4.5.2-gompi-2019b-dba 4.5.2-gompi-2020a 4.6.0-gompi-2022a 4.5.2-gompic-2019b 4.5.3-gompi-2020b 4.6.1-gompi-2024a 4.5.3-iimpi-2021b 4.5.3-gompi-2021a 4.5.3-iimpi-2020b 4.6.0-iimpi-2022a netcdf4-python -------------- **Description** Python/numpy interface to netCDF. **More Information** https://unidata.github.io/netcdf4-python/ **Available Versions**:: 1.6.1-foss-2022a 1.5.3-foss-2020a-Python-3.8.2 nettle ------ **Description** Nettle is a cryptographic library that is designed to fit easily in more or less any context: In crypto toolkits for object-oriented languages (C++, Python, Pike, ...), in applications like LSH or GNUPG, or even in kernel space. **More Information** https://www.lysator.liu.se/~nisse/nettle/ **Available Versions**:: 3.10-GCCcore-13.3.0 3.8.1-GCCcore-12.2.0 3.9.1-GCCcore-12.3.0 3.8-GCCcore-11.3.0 3.7.3-GCCcore-11.2.0 3.9.1-GCCcore-13.2.0 3.7.2-GCCcore-10.3.0 3.4-foss-2018b 3.4.1-GCCcore-8.2.0 3.6-GCCcore-10.2.0 3.5.1-GCCcore-8.3.0 networkx -------- **Description** NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks. **More Information** https://pypi.python.org/pypi/networkx **Available Versions**:: 2.4-foss-2019b-Python-3.7.4 2.4-foss-2019a-Python-3.7.2 2.6.3-foss-2021b 2.5-foss-2020b 2.3-foss-2019a-Python-3.7.2 2.8.8-gfbf-2022b 2.4-foss-2020a-Python-3.8.2 2.5.1-foss-2021a 3.1-gfbf-2023a 2.8.4-foss-2022a 3.2.1-gfbf-2023b 3.5-gfbf-2025b nghttp2 ------- **Description** This is an implementation of the Hypertext Transfer Protocol version 2 in C.The framing layer of HTTP/2 is implemented as a reusable C library. On top of that, we have implemented an HTTP/2 client, server and proxy. We have also developed load test and benchmarking tools for HTTP/2.An HPACK encoder and decoder are available as a public API. **More Information** https://github.com/nghttp2/nghttp2 **Available Versions**:: 1.48.0-GCC-11.2.0 1.58.0-GCC-12.3.0 nghttp3 ------- **Description** nghttp3 is an implementation of RFC 9114 HTTP/3mapping over QUIC and RFC 9204 QPACK in C.It does not depend on any particular QUIC transport implementation. **More Information** https://github.com/ngtcp2/nghttp3 **Available Versions**:: 1.3.0-GCCcore-12.3.0 0.6.0-GCCcore-11.3.0 0.6.0-GCCcore-11.2.0 ngsF ---- **Available Versions**:: 2022 ngsLD ----- **Available Versions**:: 2020 ngspice ------- **Description** Ngspice is a mixed-level/mixed-signal circuit simulator. Its code is based on three open source software packages: Spice3f5, Cider1b1 and Xspice. **More Information** https://ngspice.sourceforge.net **Available Versions**:: 31-foss-2019b ngtcp2 ------ **Description** 'Call it TCP/2. One More Time.'ngtcp2 project is an effort to implement RFC9000 QUIC protocol. **More Information** https://github.com/ngtcp2/ngtcp2 **Available Versions**:: 1.2.0-GCC-12.3.0 0.7.0-GCC-11.2.0 nlohmann_json ------------- **Description** JSON for Modern C++ **More Information** https://github.com/nlohmann/json **Available Versions**:: 3.11.2-GCCcore-12.3.0 3.10.0-GCCcore-10.3.0 3.10.5-GCCcore-11.3.0 3.11.3-GCCcore-13.3.0 3.11.3-GCCcore-13.2.0 nodejs ------ **Description** Node.js is a platform built on Chrome's JavaScript runtime for easily building fast, scalable network applications. Node.js uses an event-driven, non-blocking I/O model that makes it lightweight and efficient, perfect for data-intensive real-time applications that run across distributed devices. **More Information** https://nodejs.org **Available Versions**:: 22.16.0-GCCcore-14.2.0 12.19.0-GCCcore-10.2.0 14.17.0-GCCcore-10.3.0 14.17.6-GCCcore-11.2.0 16.15.1-GCCcore-11.3.0 20.9.0-GCCcore-13.2.0 18.17.1-GCCcore-12.3.0 20.13.1-GCCcore-13.3.0 nsync ----- **Description** nsync is a C library that exports various synchronization primitives, such as mutexes **More Information** https://github.com/google/nsync **Available Versions**:: 1.25.0-GCCcore-11.3.0 1.26.0-GCCcore-12.3.0 1.24.0-GCCcore-11.2.0 1.24.0-GCCcore-10.3.0 1.24.0-GCCcore-10.2.0 null ---- **Available Versions**:: False numactl ------- **Description** The numactl program allows you to run your application program on specific cpu's and memory nodes. It does this by supplying a NUMA memory policy to the operating system before running your program. The libnuma library provides convenient ways for you to add NUMA memory policies into your own program. **More Information** https://github.com/numactl/numactl **Available Versions**:: 2.0.14-GCCcore-10.3.0 2.0.14-GCCcore-11.2.0 2.0.14-GCCcore-11.3.0 2.0.12-GCCcore-8.3.0 2.0.12-GCCcore-8.2.0 2.0.19-GCCcore-14.3.0 2.0.16-GCCcore-12.2.0 2.0.13-GCCcore-10.2.0 2.0.11-GCCcore-7.3.0 2.0.16-GCCcore-12.3.0 2.0.11-GCCcore-8.1.0 2.0.19-GCCcore-14.2.0 2.0.18-GCCcore-13.3.0 2.0.13-GCCcore-9.3.0 2.0.16-GCCcore-13.2.0 numba ----- **Description** Numba is an Open Source NumPy-aware optimizing compiler forPython sponsored by Continuum Analytics, Inc. It uses the remarkable LLVMcompiler infrastructure to compile Python syntax to machine code. **More Information** https://numba.pydata.org/ **Available Versions**:: 0.53.1-foss-2020b 0.58.1-foss-2023a 0.46.0-foss-2019a 0.53.1-foss-2021a 0.56.4-foss-2022a numpy ----- **Description** NumPy is the fundamental package for scientific computing with Python. It contains among other things: a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases. **More Information** http://www.numpy.org **Available Versions**:: 1.16.6-foss-2023a-Python-2.7.18 nvofbf ------ **Description** NVHPC based toolchain, including OpenMPI for MPI support,OpenBLAS (via FlexiBLAS for BLAS and LAPACK support), FFTW and ScaLAPACK. **More Information** (none) **Available Versions**:: 2022.07 nvompi ------ **Description** NVHPC based compiler toolchain, including OpenMPI for MPI support. **More Information** (none) **Available Versions**:: 2022.07 nvtop ----- **Description** htop-like GPU usage monitor **More Information** https://github.com/Syllo/nvtop **Available Versions**:: 1.2.1-GCCcore-10.3.0 orthomcl -------- **Available Versions**:: v2.0.9 p11-kit ------- **Description** Provides a way to load and enumerate PKCS#11 modules. Provides a standard configuration setup for installing PKCS#11 modules in such a way that they're discoverable. Also solves problems with coordinating the use of PKCS#11 by different components or libraries living in the same process. **More Information** https://p11-glue.freedesktop.org/p11-kit.html **Available Versions**:: 0.24.1-GCCcore-11.2.0 0.24.1-GCCcore-11.3.0 0.25.3-GCCcore-12.3.0 p4est ----- **Description** p4est is a C library to manage a collection (a forest) of multipleconnected adaptive quadtrees or octrees in parallel. **More Information** https://www.p4est.org **Available Versions**:: 2.8.6-foss-2023a 2.8-foss-2021a 2.8.6-foss-2022a 2.8.7-foss-2024a p7zip ----- **Description** p7zip is a quick port of 7z.exe and 7za.exe (CLI version of7zip) for Unix. 7-Zip is a file archiver with highest compression ratio. **More Information** https://github.com/p7zip-project/p7zip/ **Available Versions**:: 17.04-GCCcore-12.3.0 17.05-GCCcore-14.3.0 17.05-GCCcore-13.3.0 panaroo ------- **Description** A pangenome analysis pipeline. **More Information** https://gtonkinhill.github.io/panaroo/ **Available Versions**:: 1.5.1-foss-2023a 1.3.2-foss-2021b parallel -------- **Description** parallel: Build and execute shell commands in parallel **More Information** https://savannah.gnu.org/projects/parallel/ **Available Versions**:: 20190922-GCCcore-8.3.0 20190222-GCCcore-7.3.0 20220722-GCCcore-11.3.0 20210722-GCCcore-11.2.0 20210622-GCCcore-10.3.0 20200522-GCCcore-9.3.0 20230722-GCCcore-12.3.0 20190622-GCCcore-8.2.0 20210322-GCCcore-10.2.0 patchelf -------- **Description** PatchELF is a small utility to modify the dynamic linker and RPATH of ELF executables. **More Information** https://github.com/NixOS/patchelf **Available Versions**:: 0.18.0-GCCcore-13.3.0 0.10-GCCcore-8.3.0 0.18.0-GCCcore-14.2.0 0.12-GCCcore-10.3.0 0.18.0-GCCcore-14.3.0 0.18.0-GCCcore-13.2.0 0.18.0-GCCcore-12.3.0 pear ---- **Available Versions**:: 0.9.11 petsc4py -------- **Description** petsc4py are Python bindings for PETSc, the Portable, Extensible Toolchain for Scientific Computation. **More Information** https://bitbucket.org/petsc/petsc4py **Available Versions**:: 3.12.0-foss-2019b-Python-3.7.4 3.15.0-foss-2021a picard ------ **Description** A set of tools (in Java) for working with next generation sequencing data in the BAM format. **More Information** https://broadinstitute.github.io/picard/ **Available Versions**:: 3.0.0-Java-17 2.6.0-Java-1.8.0_131 pigz ---- **Description** pigz, which stands for parallel implementation of gzip, is a fully functional replacement for gzip that exploits multiple processors and multiple cores to the hilt when compressing data. pigz was written by Mark Adler, and uses the zlib and pthread libraries. **More Information** https://zlib.net/pigz/ **Available Versions**:: 2.4-GCCcore-8.3.0 2.7-GCCcore-11.3.0 2.6-GCCcore-11.2.0 2.4-GCCcore-7.3.0 2.8-GCCcore-13.3.0 pixman ------ **Description** Pixman is a low-level software library for pixel manipulation, providing features such as image compositing and trapezoid rasterization. Important users of pixman are the cairo graphics library and the X server. **More Information** http://www.pixman.org/ **Available Versions**:: 0.40.0-GCCcore-11.2.0 0.40.0-GCCcore-10.3.0 0.34.0-GCCcore-7.3.0 0.38.4-GCCcore-9.3.0 0.38.4-GCCcore-8.3.0 0.43.4-GCCcore-13.3.0 0.46.2-GCCcore-14.2.0 0.40.0-GCCcore-11.3.0 0.42.2-GCCcore-12.3.0 0.42.2-GCCcore-12.2.0 0.40.0-GCCcore-10.2.0 0.42.2-GCCcore-13.2.0 0.38.0-GCCcore-8.2.0 pkg-config ---------- **Description** pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the correct compiler options on the command line so an application can use gcc -o test test.c `pkg-config --libs --cflags glib-2.0` for instance, rather than hard-coding values on where to find glib (or other libraries). **More Information** https://www.freedesktop.org/wiki/Software/pkg-config/ **Available Versions**:: 0.29.2-GCCcore-11.2.0 0.29.2-GCCcore-7.3.0 0.29.2-GCCcore-8.3.0 0.29.2-GCCcore-11.3.0 0.29.2-GCCcore-10.3.0 0.29.2-GCCcore-9.3.0 0.29.2-GCCcore-10.2.0 0.29.2 0.29.2-GCCcore-12.3.0 0.29.2-GCCcore-8.2.0 pkgconf ------- **Description** pkgconf is a program which helps to configure compiler and linker flags for development libraries. It is similar to pkg-config from freedesktop.org. **More Information** https://github.com/pkgconf/pkgconf **Available Versions**:: 1.9.3-GCCcore-12.2.0 1.9.5-GCCcore-12.3.0 1.8.0 1.8.0-GCCcore-11.2.0 1.8.0-GCCcore-11.3.0 2.4.3-GCCcore-14.3.0 2.2.0-GCCcore-13.3.0 2.3.0-GCCcore-14.2.0 2.0.3-GCCcore-13.2.0 pkgconfig --------- **Description** pkgconfig is a Python module to interface with the pkg-config command line tool **More Information** https://github.com/matze/pkgconfig **Available Versions**:: 1.5.5-GCCcore-12.3.0-python 1.5.1-GCCcore-8.3.0-Python-3.7.4 1.3.1-foss-2018b-Python-2.7.15 1.5.5-GCCcore-11.3.0-python 1.5.5-GCCcore-11.2.0-python 1.5.1-GCCcore-10.2.0-python 1.5.1-GCCcore-9.3.0-Python-3.8.2 1.5.1-GCCcore-8.2.0-python 1.5.4-GCCcore-10.3.0-python plmc ---- **Description** Inference of couplings in proteins and RNAs from sequence variation. **More Information** https://github.com/debbiemarkslab/plmc **Available Versions**:: 20230121-GCCcore-12.3.0-32bit 2025 plotly.py --------- **Description** An open-source, interactive graphing library for Python **More Information** https://plot.ly/python **Available Versions**:: 4.8.1-GCCcore-9.3.0 5.16.0-GCCcore-12.3.0 5.4.0-GCCcore-11.2.0 5.12.0-GCCcore-11.3.0 pocl ---- **Description** Pocl is a portable open source (MIT-licensed) implementation of the OpenCL standard **More Information** http://portablecl.org **Available Versions**:: 1.8-GCC-11.3.0 poetry ------ **Description** Python packaging and dependency management made easy. Poetry helps you declare, manage and install dependencies of Python projects, ensuring you have the right stack everywhere. **More Information** https://python-poetry.org **Available Versions**:: 1.5.1-GCCcore-12.3.0 1.0.9-GCCcore-9.3.0-Python-3.8.2 2.1.2-GCCcore-14.2.0 2.1.3-GCCcore-14.3.0 1.8.3-GCCcore-13.3.0 1.6.1-GCCcore-13.2.0 polyml ------ **Available Versions**:: 5.9.1 poppler ------- **Description** Poppler is a PDF rendering library **More Information** https://poppler.freedesktop.org **Available Versions**:: 22.01.0-GCC-11.2.0 22.12.0-GCC-11.3.0 poppunk ------- **Description** PopPUNK is a tool for clustering genomes. We refer to the clusters as variable-length-k-mer clusters, or VLKCs. Biologically, these clusters typically represent distinct strains. We refer to subclusters of strains as lineages. **More Information** https://poppunk.readthedocs.io **Available Versions**:: 2.6.0-foss-2022a pp-sketchlib ------------ **Description** Library of sketching functions used by PopPUNK **More Information** https://github.com/bacpop/pp-sketchlib **Available Versions**:: 2.1.1-foss-2022a ppl --- **Description** The Parma Polyhedra Library (PPL) provides numerical abstractions especially targeted at applications in the field of analysis and verification of complex systems. **More Information** https://www.bugseng.com/parma-polyhedra-library **Available Versions**:: 1.2-GCCcore-11.3.0 preseq ------ **Description** Software for predicting library complexity and genome coverage in high-throughput sequencing. **More Information** http://smithlabresearch.org/software/preseq **Available Versions**:: 3.1.2-foss-2020b 2.0.3-foss-2018b presto ------ **Description** Presto performs a fast Wilcoxon rank sum test and auROC analysis. **More Information** https://github.com/immunogenomics/presto **Available Versions**:: 1.0.0-20230113-foss-2022a-R-4.2.1 1.0.0-20230501-foss-2023a-R-4.3.2 prism ----- **Available Versions**:: 4.4-beta prodigal -------- **Description** Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program developed at Oak Ridge National Laboratory and the University of Tennessee. **More Information** http://prodigal.ornl.gov/ **Available Versions**:: 2.6.3-GCCcore-7.3.0 2.6.3-GCCcore-9.3.0 prokka ------ **Description** Prokka is a software tool for the rapid annotation of prokaryotic genomes. **More Information** https://www.vicbioinformatics.com/software.prokka.shtml **Available Versions**:: 1.14.5-gompi-2023a 1.14.5-gompi-2021a 1.14.5-gompi-2021b protobuf -------- **Description** Google Protocol Buffers **More Information** https://github.com/google/protobuf/ **Available Versions**:: 3.14.0-GCCcore-10.2.0 24.0-GCCcore-12.3.0 3.19.4-GCCcore-11.3.0 3.17.3-GCCcore-11.2.0 3.13.0-GCCcore-9.3.0 25.3-GCCcore-13.2.0 3.10.0-GCCcore-8.3.0 3.6.1-GCCcore-7.3.0 3.17.3-GCCcore-10.3.0 protobuf-python --------------- **Description** Python Protocol Buffers runtime library. **More Information** https://github.com/google/protobuf/ **Available Versions**:: 3.14.0-GCCcore-10.2.0 3.13.0-fosscuda-2020a-Python-3.8.2 3.10.0-foss-2019b-Python-3.7.4 3.17.3-GCCcore-11.2.0 3.17.3-GCCcore-10.3.0 3.10.0-fosscuda-2019b-Python-3.7.4 4.25.3-GCCcore-13.2.0 4.24.0-GCCcore-12.3.0 3.19.4-GCCcore-11.3.0 3.13.0-foss-2020a-Python-3.8.2 psmc ---- **Available Versions**:: 2025 0.6.5_20221121-GCC-12.3.0 psutil ------ **Description** A cross-platform process and system utilities module for Python **More Information** https://github.com/giampaolo/psutil **Available Versions**:: 7.0.0-GCCcore-14.2.0 5.6.3-GCCcore-8.2.0 6.1.0-GCCcore-13.2.0 psycopg2 -------- **Description** Psycopg is the most popular PostgreSQL adapter for the Python programming language. **More Information** https://psycopg.org/ **Available Versions**:: 2.9.9-GCCcore-12.3.0 2.9.5-GCCcore-11.2.0 pugixml ------- **Description** pugixml is a light-weight C++ XML processing library **More Information** https://pugixml.org/ **Available Versions**:: 1.12.1-GCCcore-11.2.0 1.14-GCCcore-12.3.0 pullseq ------- **Description** Utility program for extracting sequences from a fasta/fastq file **More Information** https://github.com/bcthomas/pullseq **Available Versions**:: 1.0.2-GCCcore-7.3.0 pyBigWig -------- **Description** A python extension, written in C, for quick access to bigBed files and access to and creation of bigWig files. **More Information** https://github.com/deeptools/pyBigWig **Available Versions**:: 0.3.18-foss-2022a pybedtools ---------- **Description** pybedtools wraps and extends BEDTools and offers feature-level manipulations from within Python. **More Information** https://daler.github.io/pybedtools **Available Versions**:: 0.8.1-foss-2019b pybind11 -------- **Description** pybind11 is a lightweight header-only library that exposes C++ types in Python and vice versa, mainly to create Python bindings of existing C++ code. **More Information** https://pybind11.readthedocs.io **Available Versions**:: 2.10.3-GCCcore-12.2.0 2.9.2-GCCcore-11.3.0 2.11.1-GCCcore-13.2.0 2.13.6-GCC-14.2.0 2.11.1-GCCcore-12.3.0 2.7.1-GCCcore-11.2.0 2.4.3-GCCcore-9.3.0-Python-3.8.2 2.12.0-GCC-13.3.0 3.0.0-GCC-14.3.0 2.6.0-GCCcore-10.2.0 2.6.2-GCCcore-10.3.0 2.4.3-GCCcore-8.3.0-Python-3.7.4 2.9.2-GCCcore-12.3.0-Python-2.7.18 pyfaidx ------- **Description** pyfaidx: efficient pythonic random access to fasta subsequences **More Information** https://pypi.python.org/pypi/pyfaidx **Available Versions**:: 0.8.1.1-GCCcore-12.3.0 0.7.0-GCCcore-11.2.0 pyproj ------ **Description** Python interface to PROJ4 library for cartographic transformations **More Information** https://pyproj4.github.io/pyproj **Available Versions**:: 2.6.1.post1-GCCcore-9.3.0-Python-3.8.2 3.6.0-GCCcore-12.3.0 pytest ------ **Description** The pytest framework makes it easy to write small,readable tests, and can scale to support complex functional testing forapplications and libraries. **More Information** https://docs.pytest.org/en/latest/ **Available Versions**:: 7.2.2-GCCcore-11.2.0 7.2.2-GCCcore-11.3.0 4.6.11-GCCcore-12.3.0-Python-2.7.18 pytest-flakefinder ------------------ **Description** Runs tests multiple times to expose flakiness. **More Information** https://github.com/dropbox/pytest-flakefinder **Available Versions**:: 1.1.0-GCCcore-12.3.0 1.1.0-GCCcore-13.2.0 pytest-rerunfailures -------------------- **Description** pytest plugin to re-run tests to eliminate flaky failures. **More Information** https://github.com/pytest-dev/pytest-rerunfailures **Available Versions**:: 14.0-GCCcore-13.2.0 12.0-GCCcore-12.3.0 pytest-shard ------------ **Description** pytest plugin to support parallelism across multiple machines.Shards tests based on a hash of their test name enabling easy parallelism across machines,suitable for a wide variety of continuous integration services.Tests are split at the finest level of granularity, individual test cases,enabling parallelism even if all of your tests are in a single file(or even single parameterized test method). **More Information** https://github.com/AdamGleave/pytest-shard **Available Versions**:: 0.1.2-GCCcore-13.2.0 0.1.2-GCCcore-12.3.0 pytest-xdist ------------ **Description** xdist: pytest distributed testing pluginThe pytest-xdist plugin extends pytest with some unique test execution modes: * test run parallelization: if you have multiple CPUs or hosts you can use those for a combined test run. This allows to speed up development or to use special resources of remote machines. * --looponfail: run your tests repeatedly in a subprocess. After each run pytest waits until a file in your project changes and then re-runs the previously failing tests. This is repeated until all tests pass after which again a full run is performed. * Multi-Platform coverage: you can specify different Python interpreters or different platforms and run tests in parallel on all of them.Before running tests remotely, pytest efficiently “rsyncs” yourprogram source code to the remote place. All test results are reportedback and displayed to your local terminal. You may specify differentPython versions and interpreters. **More Information** https://github.com/pytest-dev/pytest-xdist **Available Versions**:: 2.3.0-GCCcore-10.3.0 2.5.0-GCCcore-11.3.0 2.5.0-GCCcore-11.2.0 2.3.0-GCCcore-10.2.0 python-igraph ------------- **Description** Python interface to the igraph high performance graph library, primarily aimed at complex network research and analysis. **More Information** https://igraph.org/python **Available Versions**:: 0.9.8-foss-2021b 0.11.4-foss-2023a python-isal ----------- **Description** Faster zlib and gzip compatible compression and decompression by providing python bindings for the isa-l library. **More Information** https://github.com/pycompression/python-isal **Available Versions**:: 1.1.0-GCCcore-11.3.0 1.6.1-GCCcore-13.2.0 0.11.1-GCCcore-11.2.0 qcint ----- **Description** libcint is an open source library for analytical Gaussian integrals.qcint is an optimized libcint branch for the x86-64 platform. **More Information** http://wiki.sunqm.net/libcint **Available Versions**:: 3.0.18-foss-2019a 4.0.5-foss-2020a 3.1.1-foss-2020a qrupdate -------- **Description** qrupdate is a Fortran library for fast updates of QR and Cholesky decompositions. **More Information** https://sourceforge.net/projects/qrupdate/ **Available Versions**:: 1.1.2-GCCcore-11.2.0 1.1.2-GCCcore-8.3.0 rapidNJ ------- **Description** RapidNJ is an algorithmic engineered implementation of canonical neighbour-joining. It uses an efficient search heuristic to speed-up the core computations of the neighbour-joining method that enables RapidNJ to outperform other state-of-the-art neighbour-joining implementations. **More Information** https://github.com/somme89/rapidNJ **Available Versions**:: 2.3.3-GCCcore-11.3.0 rclone ------ **Description** Rclone is a command line program to sync files and directories to and from a variety of online storage services **More Information** https://rclone.org **Available Versions**:: 1.66.0 1.63.1-amd64 1.54.1-amd64 re2c ---- **Description** re2c is a free and open-source lexer generator for C and C++. Its main goal is generatingfast lexers: at least as fast as their reasonably optimized hand-coded counterparts. Instead of usingtraditional table-driven approach, re2c encodes the generated finite state automata directly in the formof conditional jumps and comparisons. **More Information** https://re2c.org/ **Available Versions**:: 2.0.3-GCCcore-10.2.0 3.1-GCCcore-12.3.0 2.2-GCCcore-11.3.0 4.2-GCCcore-14.2.0 1.3-GCCcore-9.3.0 2.2-GCCcore-11.2.0 3.1-GCCcore-13.2.0 1.2.1-GCCcore-8.3.0 3.1-GCCcore-13.3.0 2.1.1-GCCcore-10.3.0 3.0-GCCcore-12.2.0 retworkx -------- **Description** retworkx is a general purpose graph library for python3 written in Rust to take advantage of theperformance and safety that Rust provides. It was built as a replacement for qiskit's previous (and current)networkx usage (hence the name) but is designed to provide a high performance general purpose graph library for anypython application. The project was originally started to build a faster directed graph to use as the underlying datastructure for the DAG at the center of qiskit-terra's transpiler, but it has since grown to cover all the graph usagein Qiskit and other applications. **More Information** https://github.com/Qiskit/retworkx **Available Versions**:: 0.9.0-foss-2021a rose ---- **Available Versions**:: 2019.01.4 rosetta ------- **Available Versions**:: 3.10 ruamel.yaml ----------- **Description** ruamel.yaml is a YAML 1.2 loader/dumper package for Python. **More Information** https://sourceforge.net/projects/ruamel-yaml **Available Versions**:: 0.18.6-GCCcore-13.3.0 0.17.32-GCCcore-12.3.0 sabre ----- **Available Versions**:: 2022 samclip ------- **Description** Filter SAM file for soft and hard clipped alignments **More Information** https://github.com/tseemann/samclip **Available Versions**:: 0.2-GCCcore-7.3.0-Perl-5.28.0 0.4.0-GCCcore-13.3.0 0.4.0-GCCcore-11.2.0 sanzu ----- **Available Versions**:: 2025 scikit-build ------------ **Description** Scikit-Build, or skbuild, is an improved build system generatorfor CPython C/C++/Fortran/Cython extensions. **More Information** https://scikit-build.readthedocs.io/en/latest **Available Versions**:: 0.18.1-GCCcore-14.3.0 0.11.1-GCCcore-10.3.0 0.17.6-GCCcore-12.3.0 0.18.1-GCCcore-14.2.0 0.17.2-GCCcore-12.2.0 0.11.1-GCCcore-11.2.0 0.11.1-foss-2020b 0.17.6-GCCcore-13.3.0 0.15.0-GCCcore-11.3.0 0.17.6-GCCcore-13.2.0 scikit-build-core ----------------- **Description** Scikit-build-core is a complete ground-up rewrite of scikit-build on top ofmodern packaging APIs. It provides a bridge between CMake and the Python buildsystem, allowing you to make Python modules with CMake. **More Information** https://scikit-build.readthedocs.io/en/latest/ **Available Versions**:: 0.11.5-GCCcore-14.3.0 0.10.6-GCCcore-13.3.0 0.5.0-GCCcore-12.3.0 0.11.1-GCCcore-14.2.0 0.9.3-GCCcore-13.2.0 scikit-learn ------------ **Description** Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world,building upon numpy, scipy, and matplotlib. As a machine-learning module,it provides versatile tools for data mining and analysis in any field of science and engineering.It strives to be simple and efficient, accessible to everybody, and reusable in various contexts. **More Information** https://scikit-learn.org/stable/index.html **Available Versions**:: 1.3.1-gfbf-2023a 1.1.2-foss-2022a 0.21.3-foss-2019b-Python-3.7.4 1.0.1-foss-2021b 0.23.1-foss-2020a-Python-3.8.2 0.20.3-foss-2019a 0.24.2-foss-2021a scipy ----- **Description** SciPy is a collection of mathematical algorithms and convenience functions built on the Numpy extension for Python. **More Information** https://www.scipy.org **Available Versions**:: 1.4.1-foss-2019b-Python-3.7.4 screen ------ **Available Versions**:: 2023 ll semver ------ **Description** A Python module for semantic versioning. Simplifies comparing versions. **More Information** http://semver.org/ **Available Versions**:: 2.13.0-GCCcore-10.2.0 seqtk ----- **Description** Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. It seamlessly parses both FASTA and FASTQ files which can also be optionally compressed by gzip. **More Information** https://github.com/lh3/seqtk/ **Available Versions**:: 1.4-GCC-13.3.0 1.3-GCC-11.2.0 1.3-foss-2018b setuptools-rust --------------- **Description** setuptools-rust is a plugin for setuptools to build Rust Python extensionsimplemented with PyO3 or rust-cpython. **More Information** https://github.com/PyO3/setuptools-rust **Available Versions**:: 1.6.0-GCCcore-12.3.0 1.8.0-GCCcore-13.2.0 1.9.0-GCCcore-13.3.0 1.11.0-GCCcore-14.2.0 1.11.0-GCCcore-14.3.0 sharc ----- **Available Versions**:: 2024 3.0.1 2.1.1 shovill ------- **Description** Faster SPAdes assembly of Illumina reads **More Information** https://github.com/tseemann/shovill **Available Versions**:: 1.1.0-gompi-2024a slepc4py -------- **Description** Python bindings for SLEPc, the Scalable Library for Eigenvalue Problem Computations. **More Information** https://bitbucket.org/slepc/slepc4py **Available Versions**:: 3.12.0-foss-2019b-Python-3.7.4 3.15.1-foss-2021a smilei ------ **Available Versions**:: 4.6 smithwaterman ------------- **Description** smith-waterman-gotoh alignment algorithm. **More Information** https://github.com/ekg/smithwaterman **Available Versions**:: 20160702-GCCcore-11.2.0 snakemake --------- **Description** The Snakemake workflow management system is a tool to create reproducible and scalable data analyses. **More Information** https://snakemake.readthedocs.io **Available Versions**:: 6.1.0-foss-2020b 6.10.0-foss-2021b snappy ------ **Description** Snappy is a compression/decompression library. It does not aimfor maximum compression, or compatibility with any other compression library;instead, it aims for very high speeds and reasonable compression. **More Information** https://github.com/google/snappy **Available Versions**:: 1.1.9-GCCcore-11.3.0 1.1.10-GCCcore-13.2.0 1.1.10-GCCcore-12.3.0 1.1.8-GCCcore-10.2.0 1.1.9-GCCcore-12.2.0 1.2.2-GCCcore-14.2.0 1.1.7-GCCcore-8.3.0 1.1.8-GCCcore-10.3.0 1.1.9-GCCcore-11.2.0 1.1.8-GCCcore-9.3.0 1.2.1-GCCcore-13.3.0 snippy ------ **Description** Rapid haploid variant calling and core genome alignment **More Information** https://github.com/tseemann/snippy **Available Versions**:: 4.6.0-foss-2021b-R-4.1.2 snp-sites --------- **Description** Finds SNP sites from a multi-FASTA alignment file. **More Information** https://sanger-pathogens.github.io/snp-sites/ **Available Versions**:: 2.5.1-GCCcore-11.2.0 snpEff ------ **Description** SnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of genetic variants (such as amino acid changes). **More Information** https://pcingola.github.io/SnpEff/ **Available Versions**:: 5.0e-GCCcore-11.2.0-Java-11 spaln ----- **Description** Spaln (space-efficient spliced alignment) is a stand-alone program that maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence in a single job. **More Information** https://github.com/ogotoh/spaln **Available Versions**:: 2.4.03-foss-2019b sparsehash ---------- **Description** An extremely memory-efficient hash_map implementation. 2 bits/entry overhead! The SparseHash library contains several hash-map implementations, including implementations that optimize for space or speed. **More Information** https://github.com/sparsehash/sparsehash **Available Versions**:: 2.0.3-GCCcore-8.3.0 2.0.4-GCCcore-11.3.0 spdlog ------ **Description** Very fast, header-only/compiled, C++ logging library. **More Information** https://github.com/gabime/spdlog **Available Versions**:: 1.9.2-GCCcore-10.3.0 spglib ------ **Description** Spglib is a library for finding and handling crystal symmetries written in C. **More Information** https://atztogo.github.io/spglib/ **Available Versions**:: 1.9.9-intel-2020a 2.0.2-GCCcore-12.2.0 spglib-python ------------- **Description** Spglib for Python. Spglib is a library for finding and handling crystal symmetries written in C. **More Information** https://pypi.python.org/pypi/spglib **Available Versions**:: 2.0.0-intel-2022a 2.5.0-gfbf-2024a 2.0.0-foss-2022a 1.16.0-foss-2020b 2.1.0-gfbf-2023a 1.16.1-foss-2021a spin ---- **Description** Developer tool for scientific Python libraries **More Information** https://github.com/scientific-python/spin **Available Versions**:: 0.14-GCCcore-14.3.0 0.14-GCCcore-14.2.0 spython ------- **Description** Singularity Python is a Python API to work with the Singularity open source software. **More Information** https://singularityhub.github.io/singularity-cli/ **Available Versions**:: 0.1.14-GCCcore-10.2.0 statsmodels ----------- **Description** Statsmodels is a Python module that allows users to explore data, estimate statistical models,and perform statistical tests. **More Information** https://www.statsmodels.org/ **Available Versions**:: 0.12.2-foss-2021a sympy ----- **Description** SymPy is a Python library for symbolic mathematics. It aims to become a full-featured computer algebra system (CAS) while keeping the code as simple as possible in order to be comprehensible and easily extensible. SymPy is written entirely in Python and does not require any external libraries. **More Information** https://sympy.org/ **Available Versions**:: 1.6.2-foss-2020a-Python-3.8.2 1.4-foss-2019a 1.12-gfbf-2023a 1.5.1-foss-2019b-Python-3.7.4 1.12-gfbf-2023b 1.8-foss-2021a 1.10.1-foss-2022a tabixpp ------- **Description** C++ wrapper to tabix indexer **More Information** https://github.com/ekg/tabixpp **Available Versions**:: 1.1.0-GCC-11.2.0 tbb --- **Description** Intel(R) Threading Building Blocks (Intel(R) TBB) lets you easily write parallel C++ programs that take full advantage of multicore performance, that are portable, composable and have future-proof scalability. **More Information** https://github.com/oneapi-src/oneTBB **Available Versions**:: 2021.11.0-GCCcore-12.3.0 2018_U5-GCCcore-7.3.0 2021.5.0-GCCcore-11.3.0 2020.3-GCCcore-10.2.0 2020.3-GCCcore-11.2.0 2019_U9-GCCcore-8.3.0 2021.13.0-GCCcore-13.2.0 2020.1-GCCcore-9.3.0 2020.3-GCCcore-10.3.0 tbl2asn ------- **Description** Tbl2asn is a command-line program that automates the creation of sequence records for submission to GenBank **More Information** https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/ **Available Versions**:: 20230713-GCCcore-12.3.0 20220427-linux64 tensorboard ----------- **Description** TensorBoard is a suite of web applications for inspecting and understanding your TensorFlow runsand graphs. **More Information** https://github.com/tensorflow/tensorboard **Available Versions**:: 2.8.0-foss-2021a 2.10.0-foss-2022a 2.15.1-gfbf-2023a tensorboardX ------------ **Description** Tensorboard for PyTorch. **More Information** https://github.com/lanpa/tensorboardX **Available Versions**:: 2.5.1-foss-2022a tensorflow-probability ---------------------- **Description** TensorFlow Probability (TFP) is a library for probabilistic reasoning and statistical analysis. **More Information** https://www.tensorflow.org/probability **Available Versions**:: 0.12.1-fosscuda-2020b tesseract --------- **Description** Tesseract is an optical character recognition engine **More Information** https://github.com/tesseract-ocr/tesseract **Available Versions**:: 5.3.0-GCCcore-11.3.0 test-drive ---------- **Description** This project offers a lightweight, procedural unit testing framework based on nothing but standard Fortran. **More Information** https://github.com/fortran-lang/test-drive **Available Versions**:: 0.5.0-GCC-13.3.0 testapp ------- **Available Versions**:: 1.0 texinfo ------- **Description** Texinfo is the official documentation format of the GNU project. **More Information** https://www.gnu.org/software/texinfo/ **Available Versions**:: 6.7-GCCcore-8.3.0 texlive ------- **Description** TeX is a typesetting language. Instead of visually formatting your text, you enter your manuscript text intertwined with TeX commands in a plain text file. You then run TeX to produce formatted output, such as a PDF file. Thus, in contrast to standard word processors, your document is a separate file that does not pretend to be a representation of the final typeset output, and so can be easily edited and manipulated. **More Information** https://tug.org **Available Versions**:: 20230313-GCC-11.3.0 20220321-GCC-11.2.0 theriak-domino -------------- **Available Versions**:: 2023 tmux ---- **Description** tmux is a terminal multiplexer. It lets you switch easily between several programs in one terminal, detach them (they keep running in the background) and reattach them to a different terminal. **More Information** http://tmux.sourceforge.net/ **Available Versions**:: 2.3 tornado ------- **Description** Tornado is a Python web framework and asynchronous networking library. **More Information** https://github.com/tornadoweb/tornado **Available Versions**:: 6.3.2-GCCcore-12.3.0 tqdm ---- **Description** A fast, extensible progress bar for Python and CLI **More Information** https://github.com/tqdm/tqdm **Available Versions**:: 4.66.1-GCCcore-12.3.0 4.64.0-GCCcore-11.3.0 4.41.1-GCCcore-8.3.0 4.56.2-GCCcore-10.2.0 4.61.2-GCCcore-10.3.0 4.62.3-GCCcore-11.2.0 trimAl ------ **Description** EVB, FEP and LIE simulator. **More Information** https://github.com/scapella/trimal **Available Versions**:: 1.4.1-GCCcore-12.3.0 1.5.0-GCCcore-13.3.0 truffle ------- **Available Versions**:: 2024 typing-extensions ----------------- **Description** Typing Extensions – Backported and Experimental Type Hints for Python **More Information** https://github.com/python/typing/blob/master/typing_extensions/README.rst **Available Versions**:: 4.3.0-GCCcore-11.3.0 3.10.0.0-GCCcore-10.3.0 3.10.0.2-GCCcore-11.2.0 3.7.4.3-GCCcore-8.3.0-Python-3.7.4 3.7.4.3-GCCcore-10.2.0 unifdef ------- **Description** unifdef - selectively remove C preprocessor conditionalsThe unifdef utility selectively processes conditional C preprocessorand the additional text that they delimit, while otherwise leaving thefile alone. **More Information** https://github.com/fanf2/unifdef **Available Versions**:: 2.12-GCCcore-12.3.0 use.own ------- **Available Versions**:: False utf8proc -------- **Description** utf8proc is a small, clean C library that provides Unicode normalization, case-folding,and other operations for data in the UTF-8 encoding. **More Information** https://github.com/JuliaStrings/utf8proc **Available Versions**:: 2.9.0-GCCcore-13.3.0 2.5.0-GCCcore-10.2.0 2.6.1-GCCcore-11.2.0 2.7.0-GCCcore-11.3.0 2.8.0-GCCcore-12.3.0 util-linux ---------- **Description** Set of Linux utilities **More Information** https://www.kernel.org/pub/linux/utils/util-linux **Available Versions**:: 2.40-GCCcore-13.3.0 2.32-GCCcore-7.3.0 2.38.1-GCCcore-12.2.0 2.36-GCCcore-10.2.0 2.36-GCCcore-10.3.0 2.39-GCCcore-12.3.0 2.35-GCCcore-9.3.0 2.39-GCCcore-13.2.0 2.41-GCCcore-14.2.0 2.37-GCCcore-11.2.0 2.34-GCCcore-8.3.0 2.33-GCCcore-8.2.0 2.38-GCCcore-11.3.0 uv -- **Description** An extremely fast Python package installer and resolver, written in Rust. **More Information** https://github.com/astral-sh/uv **Available Versions**:: 0.2.30-GCCcore-13.3.0 vcflib ------ **Description** vcflib provides methods to manipulate and interpret sequence variation as it can be described by VCF. The Variant Call Format (VCF) is a flat-file, tab-delimited textual format intended to concisely describe reference-indexed genetic variations between individuals. **More Information** https://github.com/vcflib/vcflib **Available Versions**:: 1.0.3-foss-2021b-R-4.1.2 versioningit ------------ **Description** versioningit is yet another Python packaging plugin for automatically determining yourpackage’s version based on your version control repository’s tags.Unlike others, it allows easy customization of the version format and even lets you easily overridethe separate functions used for version extraction & calculation. **More Information** https://github.com/jwodder/versioningit **Available Versions**:: 3.1.2-GCCcore-13.2.0 virtualenv ---------- **Description** A tool for creating isolated virtual python environments. **More Information** https://github.com/pypa/virtualenv **Available Versions**:: 20.23.1-GCCcore-12.3.0 20.24.6-GCCcore-13.2.0 20.29.2-GCCcore-14.2.0 20.32.0-GCCcore-14.3.0 20.26.2-GCCcore-13.3.0 vt -- **Description** A tool set for short variant discovery in genetic sequence data. **More Information** https://genome.sph.umich.edu/wiki/Vt **Available Versions**:: 0.57721-GCC-11.2.0 wandb ----- **Description** CLI and Python API for Weights and Biases: a tool for visualizing and trackingyour machine learning experiments. **More Information** https://www.wandb.com/ **Available Versions**:: 0.13.4-GCCcore-11.3.0 wget ---- **Description** GNU Wget is a free software package for retrieving files using HTTP, HTTPS and FTP, the most widely-used Internet protocols. It is a non-interactive commandline tool, so it may easily be called from scripts, cron jobs, terminals without X-Windows support, etc. **More Information** https://www.gnu.org/software/wget **Available Versions**:: 1.20.3-GCCcore-10.2.0 1.21.3-GCCcore-11.3.0 1.21.2-GCCcore-11.2.0 wgsim ----- **Description** Wgsim is a small tool for simulating sequence reads from a reference genome. **More Information** https://github.com/lh3/wgsim/ **Available Versions**:: 20111017-GCC-11.2.0 wpebackend-fdo -------------- **Description** WPE WebKit allows embedders to create simple and performant systems based on Web platform technologies. It is a WebKit port designed with flexibility and hardware acceleration in mind, leveraging common 3D graphics APIs for best performance. **More Information** https://wpewebkit.org/ **Available Versions**:: 1.13.1-GCCcore-11.2.0 1.15.90-GCCcore-12.3.0 wtdbg2 ------ **Description** Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. **More Information** https://github.com/ruanjue/wtdbg2 **Available Versions**:: 2.5-GCCcore-9.3.0 wxPython -------- **Description** Wraps the wxWidgets C++ toolkit and provides access to the user interface portions of the wxWidgets API, enabling Python applications to have a native GUI on Windows, Macs or Unix systems, with a native look and feel and requiring very little (if any) platform specific code. **More Information** https://www.wxpython.org/ **Available Versions**:: 4.2.0-foss-2021b 4.2.1-foss-2023a wxWidgets --------- **Description** wxWidgets is a C++ library that lets developers createapplications for Windows, Mac OS X, Linux and other platforms with asingle code base. It has popular language bindings for Python, Perl,Ruby and many other languages, and unlike other cross-platform toolkits,wxWidgets gives applications a truly native look and feel because ituses the platform's native API rather than emulating the GUI. **More Information** https://www.wxwidgets.org **Available Versions**:: 3.2.0-GCC-11.2.0 3.2.2.1-GCC-12.3.0 x264 ---- **Description** x264 is a free software library and application for encoding video streams into the H.264/MPEG-4 AVC compression format, and is released under the terms of the GNU GPL. **More Information** https://www.videolan.org/developers/x264.html **Available Versions**:: 20201026-GCCcore-10.2.0 20210613-GCCcore-11.2.0 20250619-GCCcore-14.2.0 20190925-GCCcore-8.3.0 20190413-GCCcore-8.2.0 20210414-GCCcore-10.3.0 20230226-GCCcore-12.3.0 20240513-GCCcore-13.3.0 20230226-GCCcore-12.2.0 20231019-GCCcore-13.2.0 20191217-GCCcore-9.3.0 20220620-GCCcore-11.3.0 x265 ---- **Description** x265 is a free software library and application for encoding video streams into the H.265 AVC compression format, and is released under the terms of the GNU GPL. **More Information** https://x265.org/ **Available Versions**:: 3.2-GCCcore-8.3.0 3.3-GCCcore-10.2.0 3.0-GCCcore-8.2.0 4.1-GCCcore-14.2.0 3.6-GCCcore-13.3.0 3.5-GCCcore-10.3.0 3.5-GCCcore-11.2.0 3.5-GCCcore-12.3.0 3.5-GCCcore-12.2.0 3.5-GCCcore-11.3.0 3.5-GCCcore-13.2.0 3.3-GCCcore-9.3.0 xeniumranger ------------ **Available Versions**:: 2024 xmlf90 ------ **Description** A fast XML parser and generator in Fortran **More Information** https://gitlab.com/siesta-project/libraries/xmlf90 **Available Versions**:: 1.6.3-GCC-13.3.0 xorg-macros ----------- **Description** X.org macros utilities. **More Information** https://cgit.freedesktop.org/xorg/util/macros **Available Versions**:: 1.19.2-GCCcore-8.2.0 1.19.3-GCCcore-11.3.0 1.20.2-GCCcore-14.2.0 1.19.3-GCCcore-11.2.0 1.20.1-GCCcore-13.3.0 1.20.2-GCCcore-14.3.0 1.19.2-GCCcore-10.2.0 1.20.0-GCCcore-13.2.0 1.19.2-GCCcore-7.3.0 1.19.3-GCCcore-10.3.0 1.19.3-GCCcore-12.2.0 1.19.2-GCCcore-9.3.0 1.20.0-GCCcore-12.3.0 1.19.2-GCCcore-8.3.0 xprop ----- **Description** The xprop utility is for displaying window and font properties in an X server. One window or font is selected using the command line arguments or possibly in the case of a window, by clicking on the desired window. A list of properties is then given, possibly with formatting information. **More Information** https://www.x.org/wiki/ **Available Versions**:: 1.2.5-GCCcore-10.2.0 1.2.5-GCCcore-11.2.0 1.2.4-GCCcore-8.3.0 xproto ------ **Description** X protocol and ancillary headers **More Information** https://www.freedesktop.org/wiki/Software/xlibs **Available Versions**:: 7.0.31-GCCcore-10.3.0 xtb --- **Description** Semiempirical Extended Tight-Binding Program Package. **More Information** https://xtb-docs.readthedocs.io **Available Versions**:: 6.5.0-foss-2021b 6.4.1-intel-2021a 6.3.3-GCCcore-9.3.0 6.6.1-gfbf-2023a xxd --- **Description** xxd is part of the VIM package and this will only install xxd, not vim!xxd converts to/from hexdumps of binary files. **More Information** https://www.vim.org **Available Versions**:: 8.2.4220-GCCcore-11.2.0 8.2.4220-GCCcore-11.3.0 9.0.2112-GCCcore-12.3.0 9.1.1457-GCCcore-14.2.0 9.1.0307-GCCcore-13.2.0 yaff ---- **Description** Yaff stands for 'Yet another force field'. It is a pythonic force-field code. **More Information** https://molmod.github.io/yaff/ **Available Versions**:: 1.6.0-intel-2020a-Python-3.8.2 1.6.0-foss-2020a-Python-3.8.2 yaml-cpp -------- **Description** yaml-cpp is a YAML parser and emitter in C++ matching the YAML 1.2 spec **More Information** https://github.com/jbeder/yaml-cpp **Available Versions**:: 0.8.0-GCCcore-13.3.0 0.7.0-GCCcore-11.3.0 0.7.0-GCCcore-12.3.0 0.7.0-GCCcore-10.3.0 zfp --- **Description** zfp is a compressed format for representing multidimensional floating-point and integer arrays.zfp provides compressed-array classes that support high throughput read and write random access to individual arrayelements. zfp also supports serial and parallel (OpenMP and CUDA) compression of whole arrays, e.g., for applicationsthat read and write large data sets to and from disk. **More Information** https://github.com/LLNL/zfp **Available Versions**:: 1.0.0-GCCcore-11.3.0 zlib ---- **Description** 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. **More Information** http://www.zlib.net/ **Available Versions**:: 1.2.11-GCCcore-7.3.0 1.3.1-GCCcore-14.2.0 1.2.8 1.2.11-GCCcore-11.2.0 1.2.11-GCCcore-8.3.0 1.2.11-GCCcore-9.3.0 1.2.11-GCCcore-10.3.0 1.2.11-intel-2020a 1.2.13-GCCcore-13.2.0 1.2.13 1.2.11 1.2.12-GCCcore-12.2.0 1.3.1-GCCcore-13.3.0 1.2.13-GCCcore-13.1.0 1.3.1-GCCcore-14.3.0 1.2.11-GCCcore-8.2.0 1.2.12 1.2.12-GCCcore-11.3.0 1.2.11-GCCcore-10.2.0 1.2.11-GCCcore-8.1.0 1.3.1-GCCcore-15.1.0 1.2.13-GCCcore-12.3.0 1.3.1 zlib-ng ------- **Description** zlib data compression library for the next generation systems **More Information** https://github.com/zlib-ng/zlib-ng **Available Versions**:: 2.0.7-GCCcore-11.3.0 2.2.2-GCCcore-13.2.0 zstd ---- **Description** Zstandard is a real-time compression algorithm, providing high compression ratios. It offers a very wide range of compression/speed trade-off, while being backed by a very fast decoder. It also offers a special mode for small data, called dictionary compression, and can create dictionaries from any sample set. **More Information** https://facebook.github.io/zstd **Available Versions**:: 1.5.2-GCCcore-12.2.0 1.5.6-GCCcore-13.3.0 1.5.7-GCCcore-14.3.0 1.5.5-GCCcore-12.3.0 1.4.4-GCCcore-9.3.0 1.4.4-GCCcore-8.3.0 1.5.6-GCCcore-14.2.0 1.5.0-GCCcore-11.2.0 1.5.5-GCCcore-13.2.0 1.4.5-GCCcore-10.2.0 1.4.9-GCCcore-10.3.0 1.5.2-GCCcore-11.3.0