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
Available Versions:
9.4.2-foss-2021a
9.2.1-intel-2020a
9.6.2-intel-2021b
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-10.2.0
1.1-GCCcore-8.3.0
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
Available Versions:
3.1.0-foss-2018b
ANSYS
Available Versions:
2022R2
2021R2
2022R1
2023R1
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
Available Versions:
2.7.7-GCCcore-10.2.0-Java-11
2.7.7-GCCcore-10.3.0-Java-11
APR
Description
Apache Portable Runtime (APR) libraries.
More Information
Available Versions:
1.7.0-GCCcore-10.2.0
1.7.0-GCCcore-11.2.0
APR-util
Description
Apache Portable Runtime (APR) util libraries.
More Information
Available Versions:
1.6.1-GCCcore-10.2.0
1.6.1-GCCcore-11.2.0
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
Available Versions:
3.22.0-foss-2021a
3.22.1-foss-2022a
3.20.1-foss-2020b
3.22.1-intel-2022a
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:
2.34.1-GCCcore-8.3.0
2.36.0-GCCcore-9.3.0
2.36.0-GCCcore-11.2.0
2.32.0-GCCcore-8.2.0
2.38.0-GCCcore-12.3.0
2.38.0-GCCcore-11.3.0
2.28.1-foss-2018b
2.38.0-GCCcore-12.2.0
2.36.0-GCCcore-10.2.0
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
Advisor
Description
Vectorization Optimization and Thread Prototyping - Vectorize & thread code or performance “dies” - Easy workflow + data + tips = faster code faster - Prioritize, Prototype & Predict performance gain
More Information
https://software.intel.com/intel-advisor-xe
Available Versions:
2019_update5
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:
2.2.2-foss-2021a-CUDA-11.3.1
2.3.1-foss-2022a-CUDA-11.7.0
2.0.0-fosscuda-2020b
2.3.0-foss-2021b-CUDA-11.4.1
2.3.4-foss-2022a-CUDA-11.7.0-ColabFold
2.3.4-foss-2022a-ColabFold
2.1.1-fosscuda-2020b
2.3.1-foss-2022a
Amber
Description
Amber (originally Assisted Model Building with Energy Refinement) is software for performing molecular dynamics and structure prediction.
More Information
Available Versions:
18-fosscuda-2018b-AmberTools-18-patchlevel-10-8
22.0-foss-2021b-AmberTools-22.0
18-foss-2018b-AmberTools-18-patchlevel-10-8
22.4-foss-2022a-AmberTools-22.5-CUDA-11.7.0
22.0-foss-2021b-AmberTools-22.3
18-foss-2019b-AmberTools-19-patchlevel-12-17-Python-2.7.16
18-fosscuda-2019b-AmberTools-19-patchlevel-12-17-Python-2.7.16
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
Available Versions:
22.3-foss-2021b
20-gompi-2019b-dba-Python-3.7.4
20-intel-2020a-Python-3.8.2
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
Available Versions:
4.2.0
2019.03
2019.10
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
Available Versions:
2020.11
2022.05
2021.11
2021.05
2023.09-0
2020.02
2022.10
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
Available Versions:
12.6.2-foss-2023a
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
Available Versions:
0.16.0-foss-2019b-Python-3.7.4
8.0.0-foss-2021b
8.0.0-foss-2022a
6.0.0-foss-2021b
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
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
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
Available Versions:
1.2.3-foss-2021b
AutoDock_Vina
Description
AutoDock Vina is an open-source program for doing molecular docking.
More Information
http://vina.scripps.edu/index.html
Available Versions:
1.1.2_linux_x86
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
2.71-GCCcore-11.2.0
2.69-GCCcore-8.1.0
2.69-GCCcore-9.3.0
2.71-GCCcore-10.3.0
2.69-GCCcore-8.3.0
2.69-GCCcore-10.2.0
2.71-GCCcore-12.2.0
2.69-GCCcore-7.3.0
2.71-GCCcore-12.3.0
2.71-GCCcore-11.3.0
2.69
2.69-GCCcore-8.2.0
Automake
Description
Automake: GNU Standards-compliant Makefile generator
More Information
https://www.gnu.org/software/automake/automake.html
Available Versions:
1.16.1-GCCcore-7.3.0
1.16.2-GCCcore-10.2.0
1.16.1-GCCcore-8.3.0
1.16.3-GCCcore-10.3.0
1.16.1-GCCcore-8.1.0
1.16.5-GCCcore-12.2.0
1.16.1-GCCcore-8.2.0
1.16.1-GCCcore-9.3.0
1.16.1-GCCcore-10.2.0
1.16.4-GCCcore-11.2.0
1.16.5-GCCcore-12.3.0
1.16.5
1.16.5-GCCcore-11.3.0
Autotools
Description
This bundle collect the standard GNU build tools: Autoconf, Automake and libtool
More Information
Available Versions:
20180311-GCCcore-9.3.0
20200321-GCCcore-10.2.0
20210128-GCCcore-10.3.0
20220317-GCCcore-11.3.0
20180311-GCCcore-8.2.0
20210726-GCCcore-11.2.0
20220317
20180311-GCCcore-8.1.0
20180311-GCCcore-10.2.0
20180311-GCCcore-7.3.0
20220317-GCCcore-12.2.0
20180311-GCCcore-8.3.0
20220317-GCCcore-12.3.0
BAGEL
Available Versions:
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
Available Versions:
1.14-GCC-11.2.0
1.10.2-GCC-8.3.0
1.10.2-GCC-9.3.0
1.9-foss-2018b
1.11-GCC-10.2.0
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:
2.29.2-GCC-9.3.0
2.30.0-GCC-11.3.0
2.30.0-GCC-11.2.0
2.29.2-GCC-8.3.0
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:
2.10.1-Linux_x86_64
2.11.0-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
2.7.1-foss-2018b
2.11.0-gompi-2020b
2.13.0-gompi-2022a
2.9.0-gompi-2019b
2.12.0-gompi-2021b
2.14.0-gompi-2022a
2.11.0-gompi-2021a
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:
0.9.0-GCC-11.3.0
0.8.1-GCC-11.2.0
0.9.0-GCC-12.3.0
0.9.0-GCC-12.2.0
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-GCC-9.3.0
0.7.17-foss-2018b
0.7.17-GCCcore-11.2.0
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-9.3.0
2.5.1-GCC-10.2.0
2.5.1-GCC-8.3.0
2.5.2-GCC-11.3.0
2.5.2-GCC-11.2.0
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
Available Versions:
4.2.2-GCCcore-11.2.0
3.7.2-GCCcore-10.3.0
3.7.2-GCCcore-11.2.0
3.6.0-GCCcore-9.3.0
0.29.1-GCCcore-8.3.0
5.1.1-GCCcore-11.3.0
5.3.0-GCCcore-11.3.0
6.1.0-GCCcore-12.2.0
0.26.1-GCCcore-8.3.0
3.7.2-GCCcore-10.2.0
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
Available Versions:
2.5.2-GCC-7.3.0-2.30
2.5.2-GCC-8.2.0-2.31.1
2.7.3-GCC-11.3.0
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
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-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
Available Versions:
1.7.8-GCCcore-11.3.0
1.7.7-GCCcore-9.3.0
1.7.8-GCCcore-10.3.0
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
Available Versions:
1.79-foss-2021b
1.78-fosscuda-2020b
1.72-foss-2018b-Python-2.7.15
1.79-foss-2022a
1.79-foss-2021a
1.78-intel-2020a-Python-3.8.2
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:
3.5.3-GCCcore-9.3.0
3.0.5-GCCcore-7.3.0
3.8.2
3.0.5
3.8.2-GCCcore-13.1.0
3.5.3
3.0.5-GCCcore-8.1.0
3.0.4
3.0.4-GCCcore-7.3.0
3.0.5-GCCcore-8.3.0
3.0.5-GCCcore-8.2.0
3.3.2-GCCcore-8.3.0
3.8.2-GCCcore-12.2.0
3.7.6-GCCcore-11.2.0
3.7.6-GCCcore-10.3.0
3.0.4-GCCcore-8.1.0
3.3.2
3.3.2-GCCcore-9.3.0
3.7.6
3.7.1-GCCcore-10.2.0
3.8.2-GCCcore-12.3.0
3.7.1
3.8.2-GCCcore-11.3.0
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
Available Versions:
2.81-foss-2019b-Python-3.7.4
Blosc
Description
Blosc, an extremely fast, multi-threaded, meta-compressor library
More Information
Available Versions:
1.21.3-GCCcore-11.3.0
1.21.0-GCCcore-10.3.0
Blosc2
Description
Blosc, an extremely fast, multi-threaded, meta-compressor library
More Information
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
Available Versions:
1.79.0-GCC-11.2.0
1.72.0-iimpi-2021b
1.79.0-GCC-11.3.0
1.76.0-GCC-10.3.0
1.74.0-GCC-10.2.0
1.71.0-gompi-2019b
1.71.0-gompic-2019b
1.72.0-iimpi-2020a
1.70.0-gompi-2019a
1.81.0-GCC-12.2.0
1.67.0-fosscuda-2018b
1.77.0-GCC-11.2.0
1.74.0-iccifort-2020.4.304
1.77.0-intel-compilers-2021.4.0
1.67.0-foss-2018b
1.82.0-GCC-12.3.0
1.72.0-gompi-2020a
Boost.MPI
Description
Boost provides free peer-reviewed portable C++ source libraries.
More Information
Available Versions:
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
http://boostorg.github.io/python
Available Versions:
1.67.0-fosscuda-2018b-Python-2.7.15
1.71.0-gompic-2019b
1.67.0-foss-2018b-Python-2.7.15
1.72.0-gompi-2020a
1.71.0-gompi-2019b
1.70.0-gompi-2019a
1.77.0-GCC-11.2.0
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:
1.3.1-GCC-11.2.0
1.2.3-GCC-9.3.0
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
2.4.4-GCC-10.3.0
2.4.4-GCC-11.2.0
2.4.5-GCC-11.2.0
2.3.4.2-foss-2018b
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
1.0.9-GCCcore-11.3.0
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-12.3.0
0.1-GCCcore-11.3.0
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
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
Available Versions:
16.11-intel-2020a
21.11-info
16.11-info
CD-HIT
Description
CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences.
More Information
http://weizhongli-lab.org/cd-hit/
Available Versions:
4.8.1-GCC-11.2.0
4.8.1-GCC-11.3.0
4.8.1-GCC-10.2.0
4.8.1-GCC-10.3.0
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
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:
4.2.0-GCCcore-11.3.0
3.49-GCCcore-11.2.0
4.3.0-GCCcore-12.3.0
3.49-GCCcore-10.2.0
3.48-GCCcore-9.3.0
3.47-GCCcore-8.3.0
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
Available Versions:
4.14.1-foss-2019b-Python-3.7.4
4.14.3-gompi-2021a
4.14.3-gompi-2020a-Python-3.8.2
5.2-gompi-2020b
4.14.3-iimpi-2020a-Python-3.8.2
4.14.3-gompi-2022a
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
2.4.4.0-GCC-10.2.0
2.4.5.1-GCC-11.2.0
2.4.6.4-GCC-12.2.0
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
Available Versions:
3.21.1-GCCcore-11.2.0
3.23.1-GCCcore-11.3.0
3.18.4
3.11.4-GCCcore-7.3.0
3.13.3-GCCcore-8.2.0
3.24.3-GCCcore-11.3.0
3.22.1-GCCcore-11.2.0
3.9.4-GCCcore-9.3.0
3.24.3-GCCcore-12.2.0
3.12.1
3.15.3-GCCcore-7.3.0
3.15.3-GCCcore-8.3.0
3.26.3-GCCcore-12.3.0
3.16.4-GCCcore-9.3.0
3.20.1-GCCcore-10.3.0
3.12.1-GCCcore-7.3.0
3.18.4-GCCcore-10.2.0
3.12.1-GCCcore-10.2.0
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
Available Versions:
6.1-foss-2020a
6.1-foss-2019b
6.1-intel-2020a
8.1-foss-2020a
6.1-foss-2019a
9.1-foss-2022a
8.2-foss-2021a
7.1-intel-2020a
7.1-intel-2020b
CPLEX
Description
IBM ILOG CPLEX Optimizer’s mathematical programming technology enables analytical decision support for improving efficiency, reducing costs, and increasing profitability.
More Information
https://www.ibm.com/analytics/cplex-optimizer
Available Versions:
20.1.0-GCCcore-8.3.0
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:
11.1.1-iccifort-2020.4.304
10.1.243-iccifort-2019.5.281
11.6.0
11.5.0
12.0.0
11.3.1
11.5.1
11.2.2
9.2.88-GCC-7.3.0-2.30
11.1.1-GCC-10.2.0
11.8.0
10.1.243-GCC-8.3.0
11.0.2-GCC-9.3.0
11.4.1
11.7.0
11.2.2-GCC-10.3.0
11.4.1-GCC-10.3.0
11.3.1-GCC-10.3.0
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-11.2.0
CVXOPT
Description
CVXOPT is a free software package for convex optimization based on the Python programming language. Its main purpose is to make the development of software for convex optimization applications straightforward by building on Python’s extensive standard library and on the strengths of Python as a high-level programming language.
More Information
Available Versions:
1.2.4-foss-2020a
1.2.4-foss-2020a-Python-3.8.2
1.2.6-foss-2021a
1.2.3-foss-2019a
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
Available Versions:
0.7.0-GCCcore-7.3.0
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
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:
2.13.9
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
Available Versions:
6.0.2
7.0.0
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
CellRank
Description
CellRank is a toolkit to uncover cellular dynamics based on Markov state modeling of single-cell data. It contains two main modules:kernels compute cell-cell transition probabilities and estimators generatehypothesis based on these.
More Information
https://cellrank.readthedocs.io/en/stable/
Available Versions:
1.4.0-foss-2021a
Cellpose
Description
a generalist algorithm for cellular segmentation
More Information
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:
1.8.11-intel-2021a
1.8.9-foss-2019a
1.8.11-foss-2021b
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-10.3.0
0.15.2-GCCcore-9.3.0
0.15.2-GCCcore-11.2.0
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
Available Versions:
13.0.1-GCCcore-11.3.0
11.0.1-gcccuda-2020b
11.0.1-GCCcore-10.2.0
16.0.0-GCCcore-12.2.0
12.0.1-GCCcore-11.2.0
16.0.0-GCCcore-11.3.0
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
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
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-10.3.0
CuPy
Description
CuPy is an open-source array library accelerated with NVIDIA CUDA.
More Information
Available Versions:
11.4.0-foss-2021b-CUDA-11.4.1
12.1.0-foss-2022a-CUDA-12.0.0
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:
4.4.4-GCCcore-9.3.0
4.8-GCCcore-11.3.0
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:
4.8-GCCcore-11.3.0
4.4.3-GCCcore-9.3.0
Cufflinks
Description
Transcript assembly, differential expression, and differential regulation for RNA-Seq
More Information
http://cole-trapnell-lab.github.io/cufflinks/
Available Versions:
2.2.1-foss-2020a
Cython
Description
Cython is an optimising static compiler for both the Python programminglanguage and the extended Cython programming language (based on Pyrex).
More Information
Available Versions:
0.29.22-GCCcore-10.2.0
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:
18.1.32-GCCcore-8.3.0
18.1.40-GCCcore-10.3.0
18.1.32-GCCcore-7.3.0
18.1.40-GCCcore-10.2.0
18.1.40-GCCcore-12.2.0
18.1.32-GCCcore-9.3.0
18.1.40-GCCcore-11.2.0
18.1.40-GCCcore-11.3.0
18.1.32-GCCcore-8.2.0
18.1.40-GCCcore-12.3.0
DB_File
Description
Perl5 access to Berkeley DB version 1.x.
More Information
https://perldoc.perl.org/DB_File.html
Available Versions:
1.857-GCCcore-11.2.0
1.856-GCCcore-10.3.0
1.835-GCCcore-9.3.0
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
Available Versions:
1.13.12-GCCcore-9.3.0
1.13.18-GCCcore-10.3.0
1.13.18-GCCcore-11.2.0
1.13.8-GCCcore-8.2.0
1.15.2-GCCcore-12.2.0
1.13.12-GCCcore-8.3.0
1.14.0-GCCcore-11.3.0
1.15.4-GCCcore-12.3.0
1.13.18-GCCcore-10.2.0
1.13.6-GCCcore-7.3.0
DFT-D3
Description
DFT-D3 implements a dispersion correction for density functionals, Hartree-Fock and semi-empirical quantum chemical methods.
More Information
http://www.thch.uni-bonn.de/tc/index.php?section=downloads&subsection=DFT-D3&lang=english
Available Versions:
3.2.0-intel-compilers-2021.2.0
DFT-D4
Description
Generally Applicable Atomic-Charge Dependent London Dispersion Correction.
More Information
https://www.chemie.uni-bonn.de/pctc/mulliken-center/software/dftd4
Available Versions:
3.4.0-foss-2020a-Python-3.8.2
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
Available Versions:
3.11.2
DIAMOND
Description
Accelerated BLAST compatible local sequence aligner
More Information
https://github.com/bbuchfink/diamond
Available Versions:
2.1.6-GCC-11.3.0
2.0.15-GCC-11.3.0
0.9.30-GCC-8.3.0
0.9.30-iccifort-2019.5.281
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:
5.0.0-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
Available Versions:
4.5.2-GCCcore-11.2.0
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
Available Versions:
1.8.20-GCCcore-10.2.0
1.9.4-GCCcore-11.3.0
1.9.1-GCCcore-10.3.0
1.8.14-GCCcore-7.3.0
1.8.17-GCCcore-9.3.0
1.8.15-GCCcore-8.2.0
1.9.7-GCCcore-12.3.0
1.9.1-GCCcore-11.2.0
1.8.16-GCCcore-8.3.0
1.9.5-GCCcore-12.2.0
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
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
Available Versions:
2020.11.001-foss-2020b
2021.05.001-intel-2021a
2020.11.001-intel-2020b
2019.11.001-intel-2020a
2021.11.001-foss-2022a
2019.11.001-foss-2020a
2021.11.001-intel-2022a
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
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:
8.0.1-foss-2020b
8.1.1-foss-2021a
8.2.0-foss-2021b
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:
4.5.1
4.8.0
4.3.4
4.6.1
4.3.1
4.7.2
4.3.2
4.8.1
4.7.0
4.6.2
4.5.4
4.4.0
4.5.2
4.5.3
4.4.2
4.5.5
4.6.0
4.3.3
4.4.1
4.5.0
4.7.1
4.8.2
Eigen
Description
Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.
More Information
Available Versions:
3.4.0-GCCcore-9.3.0
3.3.9-GCCcore-10.3.0
3.3.4
3.3.7
3.3.7-GCCcore-9.3.0
3.4.0-GCCcore-12.2.0
3.4.0-GCCcore-11.2.0
3.4.0-GCCcore-11.3.0
3.3.9-GCCcore-11.2.0
3.3.8-GCCcore-10.2.0
3.4.0-GCCcore-10.2.0
3.4.0-GCCcore-12.3.0
3.4.0-GCCcore-10.3.0
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
Available Versions:
7.0.12-foss-2020b
Emacs
Description
GNU Emacs is an extensible, customizable text editor–and more. At its core is an interpreter for Emacs Lisp, a dialect of the Lisp programming language with extensions to support text editing.
More Information
https://www.gnu.org/software/emacs/
Available Versions:
27.1-GCCcore-10.2.0
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:
2.3.1
2019.09.0
FEniCS
Description
FEniCS is a computing platform for solving partial differential equations (PDEs).
More Information
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
Available Versions:
3.3.10-GCC-12.3.0
3.3.8-gompi-2019b
3.3.10-gompi-2021b
3.3.8-gompic-2020a
3.3.9-intel-2021a
3.3.10-GCC-11.3.0
3.3.8-gompic-2020b
3.3.9-gompi-2021a
3.3.8-gompic-2019b
3.3.8-gompi-2018b
3.3.10-GCC-12.2.0
3.3.8-intel-2020b
3.3.8-gompic-2018b
3.3.8-gompi-2020a
3.3.8-intel-2020a
3.3.8-gompi-2019a
3.3.8-gompi-2020b
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
Available Versions:
3.3.10-gompi-2022b
3.3.10-gompi-2022a
3.3.10-gompi-2023a
FFmpeg
Description
A complete, cross-platform solution to record, convert and stream audio and video.
More Information
Available Versions:
4.1.3-GCCcore-8.2.0
5.1.2-GCCcore-12.2.0
4.2.1-GCCcore-8.3.0
4.3.2-GCCcore-11.2.0
4.2.2-GCCcore-9.3.0
4.3.1-GCCcore-10.2.0
4.4.2-GCCcore-11.3.0
6.0-GCCcore-12.3.0
4.3.2-GCCcore-10.3.0
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
Available Versions:
1.3.3-GCCcore-11.2.0
1.3.4-GCCcore-11.3.0
1.3.3-GCCcore-10.2.0
1.4.2-GCCcore-12.2.0
1.3.3-GCCcore-10.3.0
FLAIR
Description
FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads. FLAIR has primarily been used for nanopore cDNA, native RNA, and PacBio sequencing reads.
More Information
https://github.com/BrooksLabUCSC/flair
Available Versions:
1.5.1-20200630-foss-2019b-Python-3.7.4
FLASH
Description
FLASH (Fast Length Adjustment of SHort reads) is a very fastand accurate software tool to merge paired-end reads from next-generationsequencing experiments. FLASH is designed to merge pairs of reads when theoriginal DNA fragments are shorter than twice the length of reads. Theresulting longer reads can significantly improve genome assemblies. They canalso improve transcriptome assembly when FLASH is used to merge RNA-seq data.
More Information
https://ccb.jhu.edu/software/FLASH/
Available Versions:
2.2.00-foss-2018b
1.2.11-foss-2018b
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
Available Versions:
2.7.1-GCC-10.3.0
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
Available Versions:
1.3.5-GCC-8.3.0
1.3.5-GCCcore-10.2.0
1.3.7-GCCcore-11.2.0
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
6.0.5.1-foss-2021a
6.0.3-foss-2019b-Python-3.7.4
6.0.5.2-ARC
6.0.4-foss-2019b-Python-3.7.4
FastFold
Description
Optimizing Protein Structure Prediction Model Training and Inference on GPU Clusters
More Information
https://github.com/hpcaitech/FastFold
Available Versions:
20220729-foss-2021a-CUDA-11.3.1
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
http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Available Versions:
0.11.8-Java-1.8
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-9.3.0
2.1.11-GCCcore-11.3.0
Fiji
Description
Fiji is an image processing package—a ‘batteries-included’ distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis.This release is based on ImageJ-2.1.0 and Fiji-2.1.1
More Information
Available Versions:
20201104-1356
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:
1.8.21-foss-2021b
1.8.16-foss-2020a-Python-3.8.2
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:
2.3.3-GCCcore-12.3.0
1.1.2-GCCcore-10.2.0
1.1.2-GCCcore-8.3.0-Python-3.7.4
1.1.4-GCCcore-10.3.0
2.2.2-GCCcore-11.3.0
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:
3.2.0-GCC-11.3.0
3.0.4-GCC-10.3.0
3.3.1-GCC-12.3.0
3.2.1-GCC-12.2.0
3.0.4-GCC-11.2.0
FreeSurfer
Description
FreeSurfer is a set of tools for analysis and visualization of structural and functional brain imaging data. FreeSurfer contains a fully automatic structural imaging stream for processing cross sectional and longitudinal data.
More Information
https://surfer.nmr.mgh.harvard.edu/
Available Versions:
7.3.2-centos8_x86_64
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-12.3.0
1.0.5-GCCcore-8.3.0
1.0.6-GCCcore-11.2.0
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
1.0.5-GCCcore-8.2.0
1.0.5-GCCcore-7.3.0
1.0.10-GCCcore-11.2.0
1.0.10-GCCcore-10.2.0
1.0.9-GCCcore-9.3.0
1.0.12-GCCcore-12.2.0
1.0.5-GCCcore-8.3.0
1.0.10-GCCcore-10.3.0
1.0.12-GCCcore-11.3.0
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
4.1.8.1-GCCcore-9.3.0-Java-1.8
4.1.5.0-GCCcore-9.3.0-Java-1.8
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
Available Versions:
10.2.0
8.1.0-2.30
13.1.0
12.2.0
10.3.0
11.3.0
8.2.0-2.31.1
7.3.0-2.30
9.3.0
11.2.0
8.3.0
12.3.0
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
Available Versions:
11.2.0-multilib
11.2.0
8.1.0
12.3.0
12.1.0
11.3.0
9.3.0
8.2.0
10.3.0
8.3.0
12.2.0
13.1.0
7.3.0
10.2.0
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://developer.gnome.org/gconf/
Available Versions:
3.2.6-GCCcore-8.3.0
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
Available Versions:
3.0.0-foss-2019a-Python-2.7.15
3.2.1-fosscuda-2020b
3.0.4-intel-2020a-Python-3.8.2
3.3.2-foss-2021b
3.7.1-foss-2023a
3.7.1-foss-2023a-spatialite
3.0.4-foss-2020a-Python-3.8.2
3.5.0-foss-2022a
3.3.0-foss-2021a
GDRCopy
Description
A low-latency GPU memory copy library based on NVIDIA GPUDirect RDMA technology.
More Information
https://github.com/NVIDIA/gdrcopy
Available Versions:
2.3-GCCcore-11.2.0
2.1-GCCcore-10.2.0-CUDA-11.1.1
2.3-GCCcore-11.3.0
2.1-GCCcore-9.3.0-CUDA-11.0.2
2.2-GCCcore-10.3.0
2.1-GCCcore-10.3.0-CUDA-11.1.1
GEOS
Description
GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)
More Information
Available Versions:
3.9.1-GCC-11.2.0
3.8.0-GCC-8.3.0-Python-3.7.4
3.6.2-foss-2018b-Python-2.7.15
3.12.0-GCC-12.3.0
3.7.2-foss-2019a-Python-2.7.15
3.9.1-GCC-10.3.0
3.10.3-GCC-11.3.0
3.8.1-iccifort-2020.1.217-Python-3.8.2
3.9.1-GCC-10.2.0
3.8.1-GCC-9.3.0-Python-3.8.2
GL2PS
Description
GL2PS: an OpenGL to PostScript printing library
More Information
Available Versions:
1.4.2-GCCcore-11.2.0
1.4.0-GCCcore-8.3.0
1.4.2-GCCcore-10.2.0
GLM
Description
OpenGL Mathematics (GLM) is a header only C++ mathematics library for graphics software based on the OpenGL Shading Language (GLSL) specifications.
More Information
Available Versions:
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
4.65-GCCcore-8.3.0
4.65-GCCcore-9.3.0
5.0-GCCcore-11.3.0
4.65-GCCcore-10.2.0
5.0-GCCcore-11.2.0
5.0-GCCcore-12.2.0
GLib
Description
GLib is one of the base libraries of the GTK+ project
More Information
Available Versions:
2.54.3-GCCcore-7.3.0
2.77.1-GCCcore-12.3.0
2.62.0-GCCcore-8.3.0
2.75.0-GCCcore-12.2.0
2.69.1-GCCcore-11.2.0
2.64.1-GCCcore-9.3.0
2.66.1-GCCcore-10.2.0
2.72.1-GCCcore-11.3.0
2.60.1-GCCcore-8.2.0
2.68.2-GCCcore-10.3.0
GLibmm
Description
C++ bindings for Glib
More Information
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
Available Versions:
6.2.1-GCCcore-12.3.0
6.2.0-GCCcore-10.2.0
6.2.0-GCCcore-9.3.0
6.2.1-GCCcore-11.2.0
6.2.1-GCCcore-10.3.0
6.2.1-GCCcore-12.2.0
6.1.2-GCCcore-9.3.0
6.2.1-GCCcore-11.3.0
6.1.2-GCCcore-10.2.0
6.1.2-GCCcore-8.2.0
6.1.2-GCCcore-7.3.0
6.1.2-GCCcore-8.3.0
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://wiki.gnome.org/GObjectIntrospection/
Available Versions:
1.54.1-foss-2018b-Python-2.7.15
1.64.0-GCCcore-9.3.0-Python-3.8.2
1.74.0-GCCcore-12.2.0
1.72.0-GCCcore-11.3.0
1.63.1-GCCcore-8.3.0-Python-3.7.4
1.66.1-GCCcore-10.2.0
1.68.0-GCCcore-10.3.0
1.76.1-GCCcore-12.3.0
1.60.1-GCCcore-8.2.0-Python-3.7.2
1.68.0-GCCcore-11.2.0
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:
22.8.0-intel-2022a
23.9.1-intel-2022a
20.10.0-foss-2020b
21.6.0-foss-2021a
23.9.1-foss-2022a
22.8.0-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
Available Versions:
8.2.0-foss-2021b
GROMACS
Description
GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.This is a CPU only build, containing both MPI and threadMPI builds.
More Information
Available Versions:
2020.4-foss-2020a-PLUMED-2.6.2
2021-foss-2020b
2020-fosscuda-2019b
2021.3-foss-2021a
2022.2-foss-2021a
2021.3-foss-2021a-CUDA-11.3.1
2021.5-foss-2021b-CUDA-11.4.1
2021-foss-2021a-PLUMED-2.7.2
2021.5-foss-2021b-CUDA-11.4.1-PLUMED-2.8.0
2021.5-foss-2021b
2021.5-foss-2021b-PLUMED-2.8.0
2020.4-foss-2020a
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
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-7.3.0-2.30
2.6-GCC-10.2.0
2.6-iccifort-2020.1.217
2.6-iccifort-2020.4.304
2.7-GCC-11.3.0
2.5-GCC-8.2.0-2.31.1
2.6-GCC-8.3.0
2.7-GCC-12.3.0
2.7-GCC-10.3.0
2.7-GCC-11.2.0
2.7-GCC-12.2.0
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:
1.20.2-GCC-11.3.0
1.22.5-GCC-12.2.0
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
1.16.2-GCC-8.3.0
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:
1.22.1-GCC-12.2.0
1.20.2-GCC-11.3.0
1.22.5-GCC-12.3.0
1.16.2-GCC-8.3.0
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:
3.24.13-GCCcore-8.3.0
3.24.23-GCCcore-10.2.0
3.24.8-GCCcore-8.2.0
2.24.32-foss-2018b
GTK2
Description
The GTK+ 2 package contains libraries used for creating graphical user interfaces for applications.
More Information
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:
3.24.31-GCCcore-11.2.0
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
Available Versions:
4.7.0-GCC-11.3.0
4.13.1-GCC-12.3.0
4.11.3-GCC-12.2.0
GTS
Description
GTS stands for the GNU Triangulated Surface Library. It is an Open Source Free Software Library intended to provide a set of useful functions to deal with 3D surfaces meshed with interconnected triangles.
More Information
Available Versions:
0.7.6-GCCcore-10.3.0
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
Available Versions:
16.A.03-ARCUS-B
16.C.01
03.E.01-ARCUS-B
09.D.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://docs.gtk.org/gdk-pixbuf/
Available Versions:
2.42.10-GCCcore-12.2.0
2.38.1-GCCcore-8.2.0
2.40.0-GCCcore-10.2.0
2.38.2-GCCcore-8.3.0
2.42.6-GCCcore-11.2.0
2.36.12-foss-2018b
2.42.10-GCCcore-12.3.0
2.42.6-GCCcore-10.3.0
2.42.8-GCCcore-11.3.0
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
Available Versions:
11.0.0-foss-2021b-G4MPI
11.1.1-GCC-11.2.0
10.7.1-GCC-10.2.0
11.0.0-GCC-11.2.0
Geant4-data
Description
Datasets for Geant4.
More Information
Available Versions:
20230601
20210510
GeneMark-ET
Description
Eukaryotic gene prediction suite with automatic training
More Information
http://exon.gatech.edu/GeneMark
Available Versions:
4.69-GCCcore-8.3.0
GenomeThreader
Description
GenomeThreader is a software tool to compute gene structure predictions.
More Information
Available Versions:
1.7.3-Linux_x86_64-64bit
GenomeTools
Description
A comprehensive software library for efficient processing of structured genome annotations.
More Information
Available Versions:
1.6.2-GCC-10.3.0
1.6.1-GCC-10.2.0
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
Available Versions:
9.54.0-GCCcore-10.3.0
9.52-GCCcore-9.3.0
9.54.0-GCCcore-11.2.0
9.50-GCCcore-8.3.0
9.56.1-GCCcore-11.3.0
9.53.3-GCCcore-10.2.0
GitPython
Description
GitPython is a python library used to interact with Git repositories
More Information
https://gitpython.readthedocs.org
Available Versions:
3.1.14-GCCcore-10.2.0
3.1.24-GCCcore-11.2.0
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:
5.7.2-foss-2019b-peigs
5.8-intel-2020a
5.8.1-intel-2022a
5.8-intel-2021a
5.7-intel-2020b
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
Available Versions:
3.6.0-GCCcore-11.2.0
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
Available Versions:
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
Available Versions:
1.14.1
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-intel-2021b
5.1.25-foss-2019b-5build1
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
Available Versions:
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-8.2.0
3.0.8-GCCcore-11.3.0
1.8.8-GCCcore-9.3.0
3.0.7-GCCcore-11.2.0
1.8.8-GCCcore-8.3.0
Guppy
Available Versions:
3.6.0
6.4.2-CPU
6.5.7
6.5.7-CPU
6.4.2
5.0.11
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
Available Versions:
9.1.2-GCCcore-10.3.0
10.0.3-GCCcore-12.2.0
9.5.2-GCCcore-11.3.0
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://www.hdfgroup.org/products/hdf4/
Available Versions:
4.2.16-2-GCCcore-12.3.0
4.2.14-GCCcore-8.3.0
4.2.15-GCCcore-10.2.0
4.2.15-GCCcore-10.3.0
4.2.15-GCCcore-11.2.0
4.2.15-GCCcore-11.3.0
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:
1.10.7-gompi-2020b
1.10.6-gompic-2020a
1.10.7-iimpi-2020b
1.10.7-gompic-2020b
1.13.1-gompi-2022a
1.10.7-iimpi-2021a
1.12.1-gompi-2021b
1.14.0-iimpi-2022b
1.10.6-iimpi-2020a
1.14.0-gompi-2022b
1.10.6-gompi-2020a
1.12.1-iimpi-2021b
1.12.1-gompi-2021a
1.10.5-iimpi-2020a
1.14.0-gompi-2023a
1.12.2-gompi-2022a
1.10.5-gompi-2019b-dba
1.13.1-iimpi-2022a
1.10.5-gompi-2019b
1.10.5-gompi-2019a
1.10.7-gompi-2021a
1.12.0-gompi-2020a
1.10.5-gompic-2019b
1.10.2-intel-2020b
1.12.2-iimpi-2022a
1.10.2-foss-2018b
1.10.2-fosscuda-2018b
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-2021b
3.3.0-gompi-2021a
3.3.0-gompic-2020b
3.3.0-gompi-2022a
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
Available Versions:
3.3.2-gompic-2020b
3.3.2-gompi-2020b
3.3.2-gompi-2021b
3.3.1-iimpi-2020a
3.3.2-gompi-2022a
3.3.2-gompi-2021a
HMMER2
Description
HMMER is used for searching sequence databases for sequence homologs, and for making sequence alignments.
More Information
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:
4.4.0-foss-2022a
4.0.1-foss-2022a
HTSlib
Description
A C library for reading/writing high-throughput sequencing data. This package includes the utilities bgzip and tabix
More Information
Available Versions:
1.11-GCC-10.2.0
1.10.2-GCC-9.3.0
1.15.1-GCC-11.3.0
1.9-foss-2018b
1.12-GCC-10.2.0
1.12-GCC-10.3.0
1.14-GCC-11.2.0
1.10.2-GCC-8.3.0
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
4.2.1-GCCcore-11.3.0
5.3.1-GCCcore-12.3.0
2.6.7-GCCcore-10.2.0
5.3.1-GCCcore-12.2.0
2.8.2-GCCcore-11.2.0
2.6.4-GCCcore-9.3.0
2.2.0-foss-2018b
2.6.4-GCCcore-8.3.0
2.4.0-GCCcore-8.2.0
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
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:
1.0.3-GCCcore-11.3.0
1.0.4-GCCcore-12.3.0
1.0.4-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
2.24.0-intel-2021b
2.25.0-foss-2022a
2.20.0-foss-2020b
2.18.2-foss-2019b
2.21.0-foss-2021a
2.18.2-intel-2020a
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
http://site.icu-project.org/home
Available Versions:
64.2-GCCcore-8.3.0
72.1-GCCcore-12.2.0
66.1-GCCcore-9.3.0
67.1-GCCcore-10.2.0
71.1-GCCcore-11.3.0
64.2-GCCcore-8.2.0
61.1-GCCcore-7.3.0
73.2-GCCcore-12.3.0
69.1-GCCcore-10.3.0
69.1-GCCcore-11.2.0
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:
7.26.0-GCCcore-11.2.0
7.9.0-foss-2019b-Python-3.7.4
7.15.0-foss-2020a-Python-3.8.2
7.18.1-GCCcore-10.2.0
8.5.0-GCCcore-11.3.0
IQ-TREE
Description
Efficient phylogenomic software by maximum likelihood
More Information
Available Versions:
1.6.12-foss-2018b
2.2.2.6-gompi-2022b
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-12.2.0
2.30.0-GCCcore-11.2.0
ImageMagick
Description
ImageMagick is a software suite to create, edit, compose, or convert bitmap images
More Information
Available Versions:
7.1.0-37-GCCcore-11.3.0
7.0.10-35-GCCcore-10.2.0
7.1.0-4-GCCcore-11.2.0
7.0.10-1-GCCcore-9.3.0
7.0.11-14-GCCcore-10.3.0
7.0.9-5-GCCcore-8.3.0
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
3.1.6-GCCcore-12.2.0
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
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-2019b
4.3.0-foss-2020a
4.3.0-foss-2022a
4.3.0-foss-2021b
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
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:
2.0.14-GCCcore-10.2.0
1.900.1-intel-2020b
2.0.14-GCCcore-9.3.0
2.0.14-GCCcore-8.3.0
2.0.33-GCCcore-11.3.0
2.0.14-GCCcore-8.2.0
4.0.0-GCCcore-12.2.0
2.0.14-GCCcore-7.3.0
4.0.0-GCCcore-12.3.0
2.0.24-GCCcore-10.2.0
2.0.28-GCCcore-10.3.0
2.0.33-GCCcore-11.2.0
Java
Description
Java Platform, Standard Edition (Java SE) lets you develop and deployJava applications on desktops and servers.
More Information
Available Versions:
17.0.6
1.7.0_60
1.8.0_241
11.0.2
16.0.1
11.0.20
1.8.0_131
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-8.3.0
2.3.0-GCC-11.2.0
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:
1.9.4-GCCcore-10.3.0
1.9.3-GCCcore-8.3.0
1.9.4-GCCcore-9.3.0
1.9.4-GCCcore-11.2.0
1.9.5-GCCcore-11.3.0
1.9.4-GCCcore-10.2.0
Judy
Description
A C library that implements a dynamic array.
More Information
Available Versions:
1.0.5-GCCcore-10.2.0
1.0.5-GCCcore-10.3.0
1.0.5-GCCcore-8.3.0
Julia
Description
Julia is a high-level, high-performance dynamic programming language for numerical computing
More Information
Available Versions:
1.6.2-linux-x86_64
1.8.2-linux-x86_64
1.8.5-linux-x86_64
1.5.3-linux-x86_64
1.5.1-linux-x86_64
JupyterHub
Description
JupyterHub is a multiuser version of the Jupyter (IPython) notebook designed for centralized deployments in companies, university classrooms and research labs.
More Information
Available Versions:
1.1.0-GCCcore-10.2.0
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
Available Versions:
3.5.0-GCCcore-11.3.0
2.2.8-GCCcore-10.2.0
KMC
Description
KMC is a disk-based programm for counting k-mers from (possibly gzipped) FASTQ/FASTA files.
More Information
Available Versions:
3.1.0-foss-2018b
Kalign
Description
Kalign is a fast multiple sequence alignment program for biological sequences.
More Information
https://github.com/TimoLassmann/kalign
Available Versions:
3.3.2-GCCcore-11.2.0
3.3.1-GCCcore-10.2.0
3.3.1-GCCcore-10.3.0
3.3.5-GCCcore-11.3.0
Kent_tools
Description
Kent utilities: collection of tools used by the UCSC genome browser.
More Information
Available Versions:
411-GCC-10.2.0
401-gompi-2019b
418-GCC-10.3.0
Keras
Description
Keras is a deep learning API written in Python, running on top of the machine learning platform TensorFlow.
More Information
Available Versions:
2.4.3-fosscuda-2020b
2.3.1-foss-2019b-Python-3.7.4
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:
2.1.1-gompi-2020b
2.1.2-gompi-2021b
LAME
Description
LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL.
More Information
Available Versions:
3.100-GCCcore-11.3.0
3.100-GCCcore-8.3.0
3.100-GCCcore-9.3.0
3.100-GCCcore-10.2.0
3.100-GCCcore-8.2.0
3.100-GCCcore-12.3.0
3.100-GCCcore-12.2.0
3.100-GCCcore-10.3.0
3.100-GCCcore-11.2.0
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
Available Versions:
23Jun2022-foss-2022a-kokkos-CUDA-11.7.0
23Jun2022-foss-2021b-kokkos-CUDA-11.4.1
3Mar2020-foss-2020a-Python-3.8.2-kokkos-QUIP
3Mar2020-foss-2020a-Python-3.8.2-kokkos
23Jun2022-foss-2021b-kokkos
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-11.2.0
3.9.1-GCC-10.2.0
3.9.1-GCC-10.3.0
3.10.1-GCC-11.3.0
3.9.1-GCC-9.3.0
LDC
Description
The LLVM-based D Compiler
More Information
Available Versions:
1.26.0-GCCcore-10.3.0
1.28.1-GCCcore-8.3.0
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
Available Versions:
4.0.0-GCCcore-12.3.0
4.0.0-GCCcore-11.3.0
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
Available Versions:
7.0.1-GCCcore-8.2.0
6.0.0-GCCcore-7.3.0
8.0.1-GCCcore-8.3.0
9.0.1-GCCcore-9.3.0
9.0.0-GCCcore-8.3.0
12.0.1-GCCcore-11.2.0
11.1.0-GCCcore-10.3.0
15.0.5-GCCcore-12.2.0
11.0.0-GCCcore-10.2.0
16.0.6-GCCcore-12.3.0
14.0.3-GCCcore-11.3.0
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
Available Versions:
0.9.22-GCCcore-7.3.0
0.9.24-GCCcore-8.3.0
0.9.28-GCCcore-10.3.0
0.9.29-GCCcore-11.2.0
0.9.24-GCCcore-9.3.0
0.9.24-GCCcore-10.2.0
0.9.29-GCCcore-11.3.0
LSD2
Description
Least-squares methods to estimate rates and dates from phylogenies
More Information
https://github.com/tothuhien/lsd2
Available Versions:
2.3-GCCcore-11.3.0
2.4.1-GCCcore-12.2.0
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-2021a
2.9.0-foss-2020b
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
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
Available Versions:
1.83.0-GCCcore-11.3.0
1.78.0-GCCcore-8.2.0
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:
3.0.7-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:
4.4.0-GCCcore-12.2.0
4.0.10-GCCcore-8.2.0
4.0.9-GCCcore-7.3.0
4.2.0-GCCcore-10.3.0
4.1.0-GCCcore-9.3.0
4.3.0-GCCcore-11.2.0
4.1.0-GCCcore-10.2.0
4.3.0-GCCcore-11.3.0
4.5.0-GCCcore-12.3.0
4.0.10-GCCcore-8.3.0
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://github.com/evaleev/libint
Available Versions:
2.6.0-gompi-2020a-lmax-6-cp2k
2.6.0-iccifort-2020.4.304-lmax-6-cp2k
2.6.0-GCC-10.2.0-lmax-6-cp2k
2.6.0-GCC-10.3.0-lmax-6-cp2k
1.1.6-GCC-8.2.0-2.31.1
2.7.2-GCC-11.3.0-lmax-6-cp2k
1.1.6-foss-2019b
1.1.6-foss-2020a
2.6.0-iimpi-2020a-lmax-6-cp2k
1.1.6-intel-2020a
Lighter
Description
Fast and memory-efficient sequencing error corrector
More Information
https://github.com/mourisl/Lighter
Available Versions:
1.1.2-foss-2018b
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-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
Available Versions:
2.13.1-GCCcore-11.3.0
2.12-GCCcore-10.3.0
2.11-GCCcore-10.2.0
2.9-GCCcore-9.3.0
2.12-GCCcore-11.2.0
2.9-GCCcore-8.3.0
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
Available Versions:
5.4.3-GCCcore-10.3.0
5.4.3-GCCcore-11.2.0
5.4.2-GCCcore-10.2.0
5.3.5-GCCcore-9.3.0
5.1.5-GCCcore-8.3.0
5.4.4-GCCcore-11.3.0
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
https://www.gnu.org/software/m4/m4.html
Available Versions:
1.4.19-GCCcore-12.3.0
1.4.19-GCCcore-11.2.0
1.4.18-GCCcore-10.2.0
1.4.18-GCCcore-8.1.0
1.4.17
1.4.18
1.4.18-GCCcore-9.3.0
1.4.19-GCCcore-12.2.0
1.4.18-GCCcore-8.3.0
1.4.19-GCCcore-13.1.0
1.4.19-GCCcore-11.3.0
1.4.19
1.4.18-GCCcore-10.3.0
1.4.18-GCCcore-8.2.0
1.4.18-GCCcore-7.3.0
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
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
7.490-GCC-11.2.0-with-extensions
7.475-gompi-2020b-with-extensions
7.487-gompi-2021a-with-extensions
7.453-GCC-9.3.0-with-extensions
7.505-GCC-11.3.0-with-extensions
7.453-iimpi-2020a-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
MATLAB
Available Versions:
R2019b
R2023a
R2020b
R2022a
R2022b
R2021b
R2020a
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
Available Versions:
14.137-GCCcore-8.3.0
14.137-GCCcore-11.3.0
14.137-GCCcore-9.3.0
MDAnalysis
Description
MDAnalysis is an object-oriented Python library to analyze trajectories from molecular dynamics (MD)simulations in many popular formats.
More Information
Available Versions:
0.20.1-foss-2019b-Python-3.7.4
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:
1.1.4-foss-2018b-Python-2.7.15
1.2.9-GCCcore-9.3.0
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
http://glaros.dtc.umn.edu/gkhome/metis/metis/overview
Available Versions:
5.1.0-GCCcore-8.3.0
5.1.0-GCCcore-8.2.0
5.1.0-foss-2018b
5.1.0-GCCcore-10.2.0
5.1.0-GCCcore-9.3.0
5.1.0-GCCcore-10.3.0
5.1.0-GCCcore-11.3.0
5.1.0-GCCcore-11.2.0
MGLTools
Available Versions:
1.5.7
1.5.7.old
MIRA
Description
MIRA is a whole genome shotgun and EST sequence assembler for Sanger, 454, Solexa (Illumina), IonTorrent data and PacBio (the latter at the moment only CCS and error-corrected CLR reads).
More Information
https://sourceforge.net/p/mira-assembler/wiki/Home/
Available Versions:
4.0.2-gompi-2019b
MMseqs2
Description
MMseqs2: ultra fast and sensitive search and clustering suite
More Information
Available Versions:
10-6d92c-gompi-2019b
13-45111-gompi-2020b
MOOSE
Description
The Multiphysics Object-Oriented Simulation Environment (MOOSE) is a finite-element, multiphysicsframework primarily developed by Idaho National Laboratory
More Information
https://mooseframework.inl.gov
Available Versions:
2021-05-18-foss-2019b-Python-3.7.4
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:
1.2.1-GCCcore-10.3.0
1.1.0-GCC-8.3.0
1.1.0-GCC-9.3.0
MPFR
Description
The MPFR library is a C library for multiple-precision floating-point computations with correct rounding.
More Information
Available Versions:
4.1.0-GCCcore-11.2.0
4.1.0-GCCcore-11.3.0
4.0.2-GCCcore-9.3.0
4.0.2-GCCcore-8.2.0
4.0.1-GCCcore-7.3.0
4.0.2-GCCcore-8.3.0
4.1.0-GCCcore-10.3.0
4.1.0-GCCcore-10.2.0
MPICH2
Description
MPICH v3.x is an open source high-performance MPI 3.0 implementation.It does not support InfiniBand (use MVAPICH2 with InfiniBand devices).
More Information
Available Versions:
1.5rc3-GCC-7.3.0-2.30
MUMPS
Description
A parallel sparse direct solver
More Information
https://graal.ens-lyon.fr/MUMPS/
Available Versions:
5.5.1-foss-2022a-metis
5.3.5-foss-2020b-metis
5.2.1-foss-2019b-metis
5.2.1-foss-2019a-metis-seq
5.2.1-intel-2020a-metis
5.2.1-foss-2020a-metis
5.4.0-foss-2021a-metis
5.4.1-intel-2021b-metis
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-GCCcore-10.2.0
4.0.0beta2-foss-2018b
4.0.0rc1-GCCcore-11.2.0
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
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
Available Versions:
1.1.4-GCCcore-10.3.0
1.0.7-foss-2018b-Python-2.7.15
1.1.0-GCCcore-8.3.0
1.2.0-GCCcore-11.3.0
1.0.8-GCCcore-8.2.0
1.1.3-GCCcore-10.2.0
1.1.2-GCCcore-9.3.0
1.1.4-GCCcore-11.2.0
1.2.4-GCCcore-12.2.0
1.2.4-GCCcore-12.3.0
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
Available Versions:
4.14.0-0
MariaDB
Description
MariaDB is an enhanced, drop-in replacement for MySQL.Included engines: myISAM, Aria, InnoDB, RocksDB, TokuDB, OQGraph, Mroonga.
More Information
Available Versions:
10.5.8-GCC-10.2.0
10.4.13-gompi-2019b
10.6.4-GCC-10.3.0
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
Available Versions:
2.1-foss-2018b
Mathematica
Available Versions:
11.3.0
13.0.0
13.3.1
12.2.0
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
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
Available Versions:
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
Available Versions:
20.0.2-GCCcore-9.3.0
19.1.7-GCCcore-8.3.0
18.1.1-foss-2018b
21.1.7-GCCcore-11.2.0
22.2.4-GCCcore-12.2.0
23.1.4-GCCcore-12.3.0
21.1.1-GCCcore-10.3.0
20.2.1-GCCcore-10.2.0
22.0.3-GCCcore-11.3.0
19.0.1-GCCcore-8.2.0
Meson
Description
Meson is a cross-platform build system designed to be both as fast and as user friendly as possible.
More Information
Available Versions:
0.51.2-GCCcore-8.3.0-Python-3.7.4
0.55.1-GCCcore-9.3.0-Python-3.8.2
1.1.1-GCCcore-12.3.0
0.59.1-GCCcore-8.3.0-Python-3.7.4
0.58.0-GCCcore-10.3.0
0.55.3-GCCcore-10.2.0
0.58.2-GCCcore-11.2.0
0.62.1-GCCcore-11.3.0
0.50.0-GCCcore-8.2.0-Python-3.7.2
0.64.0-GCCcore-12.2.0
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
MetaPhlAn2
Description
MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data (i.e. not 16S) with species-level. With the newly added StrainPhlAn module, it is now possible to perform accurate strain-level microbial profiling.
More Information
https://bitbucket.org/biobakery/metaphlan2/
Available Versions:
2.7.8-foss-2018b-Python-3.6.6
MiniSat
Description
MiniSat is a minimalistic, open-source SAT solver, developed to helpresearchers and developers alike to get started on SAT.
More Information
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:
4.5.12
23.1.0-1
22.11.1-1
4.12.0
4.7.10
4.9.2
Molden
Description
Molden is a package for displaying Molecular Density from the Ab Initio packages GAMESS-UK, GAMESS-US and GAUSSIAN and the Semi-Empirical packages Mopac/Ampac
More Information
Available Versions:
5.7-foss-2018b
Mono
Description
An open source, cross-platform, implementation of C# and the CLR that is binary compatible with Microsoft.NET.
More Information
Available Versions:
6.8.0.105-GCCcore-8.3.0
6.4.0.198-foss-2018b
6.12.0.122-GCCcore-11.2.0
Mothur
Description
Mothur is a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community.
More Information
Available Versions:
1.43.0-foss-2019a-Python-3.7.2
MrBayes
Description
MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models.
More Information
https://nbisweden.github.io/MrBayes/
Available Versions:
3.2.7-gompi-2020b
MultiQC
Description
Aggregate results from bioinformatics analyses across many samples into a single report. MultiQC searches a given directory for analysis logs and compiles a HTML report. It’s a general use tool, perfect for summarising the output from numerous bioinformatics tools.
More Information
Available Versions:
1.9-foss-2020a-Python-3.8.2
1.14-foss-2022a
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
Available Versions:
3.8-intel-2021b
3.8-2023
MySQL
Description
MySQL is one of the world’s most widely used open-source relational database management system (RDBMS).
More Information
Available Versions:
5.7.21-GCCcore-9.3.0-clientonly
NAMD
Description
NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.
More Information
https://www.ks.uiuc.edu/Research/namd/
Available Versions:
2.14-fosscuda-2019b
2.14-intel-2020a-mpi
NASM
Description
NASM: General-purpose x86 assembler
More Information
Available Versions:
2.15.05-GCCcore-11.2.0
2.16.01-GCCcore-12.3.0
2.15.05-GCCcore-11.3.0
2.15.05-GCCcore-12.2.0
2.14.02-GCCcore-8.3.0
2.13.03-GCCcore-7.3.0
2.15.05-GCCcore-10.2.0
2.14.02-GCCcore-8.2.0
2.14.02-GCCcore-9.3.0
2.15.05-GCCcore-10.3.0
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:
2.4.8-gcccuda-2019b
2.8.3-GCCcore-10.2.0-CUDA-11.1.1
2.12.12-GCCcore-11.3.0-CUDA-11.7.0
2.12.12-GCCcore-11.3.0-CUDA-12.0.0
2.8.3-CUDA-11.1.1
2.8.3-CUDA-11.0.2
2.10.3-GCCcore-11.2.0-CUDA-11.4.1
2.10.3-GCCcore-10.3.0-CUDA-11.3.1
2.12.12-GCCcore-11.3.0-CUDA-11.8.0
NCO
Description
manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5
More Information
Available Versions:
4.9.7-foss-2020b
5.0.1-foss-2021a
NEURON
Description
Empirically-based simulations of neurons and networks of neurons.
More Information
http://www.neuron.yale.edu/neuron
Available Versions:
7.6.5-foss-2018b-Python-2.7.15
7.8.2-foss-2021b
7.7.2-foss-2020a-Python-3.7.4
7.6.5-foss-2019a-Python-2.7.15
NGS
Description
NGS is a new, domain-specific API for accessing reads, alignments and pileupsproduced from Next Generation Sequencing.
More Information
Available Versions:
2.10.9-GCCcore-10.2.0
2.9.3-foss-2018b-Java-1.8
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:
2.7.1-GCCcore-11.3.0
2.6.1-GCCcore-9.3.0
2.7.0-GCCcore-11.2.0
2.6.2-GCCcore-10.2.0
2.6.1-GCCcore-8.3.0
2.7.1-GCCcore-12.2.0
2.4.2-GCCcore-7.3.0
2.7.0-GCCcore-10.3.0
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:
4.29-GCCcore-10.2.0
4.30-GCCcore-10.3.0
4.21-GCCcore-8.3.0
4.20-GCCcore-7.3.0
4.25-GCCcore-9.3.0
4.34-GCCcore-11.3.0
4.32-GCCcore-11.2.0
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:
3.57-GCCcore-10.2.0
3.65-GCCcore-10.3.0
3.69-GCCcore-11.2.0
3.39-GCCcore-7.3.0
3.79-GCCcore-11.3.0
3.45-GCCcore-8.3.0
3.51-GCCcore-9.3.0
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:
21.7
21.9
21.11
20.11
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
Available Versions:
7.0.2-intel-2021a
7.2.0-intel-2022a
7.0.0-foss-2019b-Python-3.7.4
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
https://ccl.northwestern.edu/netlogo/
Available Versions:
6.2.0-64
6.0.4-64
Nextflow
Description
Nextflow is a reactive workflow framework and a programming DSL that eases writing computational pipelines with complex data
More Information
Available Versions:
23.04.2
NgsRelate
Available Versions:
2022
Ninja
Description
Ninja is a small build system with a focus on speed.
More Information
Available Versions:
1.10.2-GCCcore-10.3.0
1.9.0-GCCcore-8.3.0
1.10.0-GCCcore-9.3.0
1.11.1-GCCcore-12.2.0
1.9.0-GCCcore-8.2.0
1.10.2-GCCcore-11.2.0
1.11.1-GCCcore-12.3.0
1.10.2-GCCcore-11.3.0
1.10.1-GCCcore-10.2.0
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
Available Versions:
2.0.5-GCCcore-9.3.0
2.0.7-GCCcore-11.3.0
ORCA
Description
ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- and multireference correlated ab initio methods. It can also treat environmental and relativistic effects.
More Information
Available Versions:
5.0.1-gompi-2019b-dba
5.0.0-gompi-2019b
4.2.1-gompi-2019b-dba
5.0.2-gompi-2019b-dba
5.0.3-gompi-2021b
5.0.4-gompi-2021b
4.2.1-gompi-2019b
5.0.4-gompi-2021b-static
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
5.8-GCC-10.3.0-CUDA-11.1.1
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
Available Versions:
3.0.2-GCCcore-11.3.0
2.2-GCCcore-9.3.0
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
5.1.0-foss-2019b
OpenBLAS
Description
OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.
More Information
http://xianyi.github.com/OpenBLAS/
Available Versions:
0.3.1-GCC-7.3.0-2.30
0.3.5-GCC-8.2.0-2.31.1
0.3.9-GCC-9.3.0
0.3.12-GCC-10.2.0
0.3.21-GCC-12.2.0
0.3.7-GCC-8.3.0
0.3.15-GCC-10.3.0
0.3.23-GCC-12.3.0
0.3.20-GCC-11.3.0
0.3.18-GCC-11.2.0
OpenBabel
Description
Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It’s an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas.
More Information
Available Versions:
3.1.1-gompi-2019b-Python-3.7.4
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.
More Information
Available Versions:
3.4.7-foss-2019a-Python-3.7.2
4.5.1-fosscuda-2020b-contrib
4.8.1-foss-2023a-contrib
4.5.1-foss-2020b-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.
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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
Available Versions:
2.4.0-GCCcore-8.3.0
2.5.5-GCCcore-10.2.0
3.1.5-GCCcore-11.3.0
3.1.7-GCCcore-12.3.0
3.1.5-GCCcore-12.2.0
2.4.1-GCCcore-9.3.0
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
Available Versions:
v2006-intel-2020a
v2206-foss-2022a
10-foss-2022a
10-intel-2022a
8-foss-2020b
v2012-foss-2020a
v1912-foss-2019b
5.0-20180108-foss-2018b
11-foss-2022a
8-foss-2020a
6-intel-2020a
6-foss-2018b
9-foss-2021a
v2106-foss-2021a
v2006-foss-2020a
10-foss-2022a
6-foss-2019b
v2006-foss-2019b
OpenFOAM-ESI
Available Versions:
v2006-foss-2020a
OpenFold
Description
A faithful PyTorch reproduction of DeepMind’s AlphaFold 2
More Information
https://github.com/aqlaboratory/openfold
Available Versions:
1.0.0-foss-2021a-CUDA-11.3.1
1.0.1-foss-2021a-CUDA-11.3.1
OpenImageIO
Description
OpenImageIO is a library for reading and writing images, and a bunch of related classes, utilities, and applications.
More Information
Available Versions:
2.1.12.0-gompi-2020a
2.0.12-gompi-2019b
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
Available Versions:
2.5.0-GCCcore-12.3.0
2.4.0-GCCcore-11.2.0
2.5.0-GCCcore-12.2.0
2.5.0-GCCcore-11.3.0
OpenMM
Description
OpenMM is a toolkit for molecular simulation.
More Information
Available Versions:
7.5.0-fosscuda-2020a-Python-3.8.2
7.4.1-foss-2019b-Python-3.7.4
7.4.2-intel-2020a-Python-3.8.2
7.7.0-fosscuda-2020b
7.5.1-fosscuda-2020b
8.0.0-foss-2022a
7.5.1-foss-2021a-DeepMind-patch
8.0.0-foss-2022a-CUDA-11.7.0
7.5.1-foss-2021b-DeepMind-patch
OpenMPI
Description
The Open MPI Project is an open source MPI-3 implementation.
More Information
Available Versions:
3.1.4-GCC-8.3.0-dba
4.1.1-intel-compilers-2021.2.0
4.1.1-GCC-10.3.0-CUDA-11.1.1
4.0.5-iccifort-2020.4.304
3.1.1-GCC-7.3.0-2.30
4.0.5-gcccuda-2020b
4.1.4-GCC-11.3.0
3.1.4-PGI-19.10-GCC-8.3.0-2.32
4.0.3-gcccuda-2020a
3.1.4-gcccuda-2019b
4.1.1-GCC-11.2.0
3.1.4-GCC-8.3.0
4.1.1-GCC-11.2.0-CXX
4.0.3-GCC-9.3.0
4.0.5-GCC-10.2.0
3.1.1-gcccuda-2018b
3.1.3-GCC-8.2.0-2.31.1
4.1.1-GCC-10.3.0
4.1.4-GCC-12.2.0
4.1.5-GCC-12.3.0
OpenMolcas
Description
OpenMolcas is a quantum chemistry software package
More Information
https://gitlab.com/Molcas/OpenMolcas
Available Versions:
18.09-intel-2020b-Python-3.6.6
21.06-intel-2021a
20.10-intel-2020a-Python-3.8.2
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-10.2.0
5.2.122-GCCcore-10.3.0
5.2.122-GCCcore-11.3.0
5.2.122-GCCcore-8.3.0
5.2.122-GCCcore-11.2.0
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
Available Versions:
1.1.1t-GCCcore-12.2.0
1.1.1w-GCCcore-12.3.0
1.1.1t-GCCcore-12.3.0
1.1.1h-GCCcore-10.2.0
1.1
OpenSees
Description
Open System for Earthquake Engineering Simulation
More Information
https://opensees.berkeley.edu/index.php
Available Versions:
3.2.0-intel-2020a-Python-3.8.2
OptaDOS
Available Versions:
v2018-foss-2018b
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-10.2.0
6.0.0-GCCcore-9.3.0
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
PCMSolver
Description
An API for the Polarizable Continuum Model.
More Information
https://pcmsolver.readthedocs.org
Available Versions:
1.2.3-gompi-2019a-Python-3.7.2
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
Available Versions:
8.45-GCCcore-12.3.0
8.41-GCCcore-7.3.0
8.44-GCCcore-10.3.0
8.45-GCCcore-11.2.0
8.43-GCCcore-8.3.0
8.43-GCCcore-8.2.0
8.44-GCCcore-9.3.0
8.45-GCCcore-12.2.0
8.45-GCCcore-11.3.0
8.44-GCCcore-10.2.0
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
Available Versions:
10.35-GCCcore-10.2.0
10.34-GCCcore-9.3.0
10.33-GCCcore-8.3.0
10.40-GCCcore-12.2.0
10.36-GCCcore-10.3.0
10.37-GCCcore-11.2.0
10.40-GCCcore-11.3.0
10.42-GCCcore-12.3.0
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
Available Versions:
3.15.0-foss-2020b
3.12.4-intel-2020a-Python-3.8.2
3.19.3-intel-2021b
3.12.4-foss-2020a-Python-3.8.2
3.18.4-intel-2021b
3.17.4-foss-2021a
3.14.4-foss-2020b
3.12.4-foss-2019b-Python-3.7.4
3.15.1-foss-2021a
3.17.4-foss-2022a
PGI
Description
C, C++ and Fortran compilers from The Portland Group - PGI
More Information
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
Available Versions:
2.5.1-foss-2019a
2.8.1-foss-2022a
2.8.0-foss-2021b
2.5.1-foss-2019b
2.6.2-foss-2020a-Python-3.8.2
2.7.3-foss-2021b
2.6.0-intel-2020a-Python-3.8.2
2.7.0-intel-2020b
2.6.0-foss-2020a-Python-3.8.2
2.7.0-foss-2020b
2.7.0-foss-2020a
2.6.2-intel-2020b
2.5.1-foss-2020a
2.7.2-foss-2021a
PLY
Description
PLY is yet another implementation of lex and yacc for Python.
More Information
Available Versions:
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
Available Versions:
4.2.2-GCCcore-12.2.0
3.1.5-GCCcore-10.2.0
3.1.5-GCCcore-9.3.0
4.1.2-GCCcore-11.3.0
3.2.3-GCCcore-10.3.0
4.2.4-GCCcore-12.3.0
4.1.0-GCCcore-11.2.0
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
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-11.3.0
170427-GCC-11.2.0
170427-GCC-9.3.0
PROJ
Description
Program proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates
More Information
Available Versions:
6.0.0-GCCcore-8.2.0
5.0.0-foss-2018b
8.1.0-GCCcore-11.2.0
9.2.0-GCCcore-12.3.0
6.2.1-GCCcore-8.3.0
7.0.0-GCCcore-9.3.0
7.2.1-GCCcore-10.2.0
8.0.1-GCCcore-10.3.0
9.0.0-GCCcore-11.3.0
PSI4
Description
PSI4 is an open-source suite of ab initio quantum chemistry programs designed for efficient, high-accuracy simulations of a variety of molecular properties. We can routinely perform computations with more than 2500 basis functions running serially or in parallel.
More Information
Available Versions:
1.3.1-foss-2019a-Python-3.7.2
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
Available Versions:
1.44.7-GCCcore-9.3.0
1.43.0-GCCcore-8.2.0
1.50.14-GCCcore-12.3.0
1.50.12-GCCcore-12.2.0
1.42.4-foss-2018b
1.47.0-GCCcore-10.2.0
1.48.8-GCCcore-11.2.0
1.50.7-GCCcore-11.3.0
1.48.5-GCCcore-10.3.0
1.44.7-GCCcore-8.3.0
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-2019a
4.0.3-gompi-2020b
4.0.3-gompi-2020a
4.0.3-iimpi-2020a
4.0.3-gompi-2021a
4.0.3-gompi-2019b
4.0.3-gompi-2022a
ParaView
Description
ParaView is a scientific parallel visualizer.
More Information
Available Versions:
5.8.0-intel-2020a-Python-3.8.2-mpi
5.10.1-foss-2022a-mpi
5.8.0-foss-2020a-Python-3.8.2-mpi
5.8.1-foss-2020b-mpi
5.6.2-foss-2019b-Python-3.7.4-mpi
5.9.1-foss-2021a-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
Available Versions:
5.30.0-GCCcore-8.3.0
5.34.0-GCCcore-11.2.0-minimal
5.28.0-GCCcore-8.1.0
5.30.2-GCCcore-9.3.0
5.34.1-GCCcore-11.3.0
5.34.0-GCCcore-11.2.0-ARC
5.36.0-GCCcore-12.3.0
5.28.0-GCCcore-7.3.0
5.32.0-GCCcore-10.2.0-minimal
5.32.0-GCCcore-10.2.0
5.28.1-GCCcore-8.2.0
5.34.0-GCCcore-11.2.0
5.34.1-GCCcore-11.3.0-minimal
5.30.0-GCCcore-7.3.0
5.36.0-GCCcore-12.2.0
5.36.1-GCCcore-12.3.0
5.28.0-GCCcore-10.2.0
5.32.1-GCCcore-10.3.0-minimal
5.28.1-GCCcore-8.3.0
5.32.1-GCCcore-10.3.0
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
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
8.3.2-GCCcore-11.2.0
6.2.1-GCCcore-8.3.0
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:
6.0.x.post0-GCCcore-8.2.0
9.2.0-GCCcore-11.3.0
8.2.0-GCCcore-10.3.0
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
1.23-Java-1.8
Platypus
Description
Platypus is a tool designed for efficient and accurate variant-detection# in high-throughput sequencing data.
More Information
https://vcru.wisc.edu/simonlab/bioinformatics/programs/install/platypus.htm
Available Versions:
latest-GCC-11.2.0-Python-2.7.18
Pmw
Description
Pmw is a toolkit for building high-level compound widgets in Python using the Tkinter module.
More Information
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://trac.mcs.anl.gov/projects/parallel-netcdf
Available Versions:
1.12.2-gompic-2020b
1.12.1-gompi-2020a
1.12.3-gompi-2022a
1.12.3-gompi-2021b
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
Available Versions:
13.3-GCCcore-10.3.0
13.4-GCCcore-11.2.0
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:
1.21.0-GCCcore-11.3.0
1.18.0-foss-2018b-Python-2.7.15
1.25.0-GCCcore-12.3.0
1.20.1-GCCcore-11.2.0
1.24.0-GCCcore-12.2.0
PyCharm
Description
PyCharm Community Edition: Python IDE for Professional Developers
More Information
https://www.jetbrains.com/pycharm/
Available Versions:
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
Python Bindings for GLib/GObject/GIO/GTK+
More Information
Available Versions:
2.28.7-foss-2018b-Python-2.7.15
3.42.1-GCCcore-11.3.0
3.46.0-GCCcore-12.3.0
3.44.1-GCCcore-12.2.0
PyGTK
Description
PyGTK lets you to easily create programs with a graphical user interface using the Python programming language.
More Information
Available Versions:
2.24.0-foss-2018b-Python-2.7.15
PyHPC-bench-GPU
Description
This is a suite of benchmarks to test the sequential CPU and GPU performance of various computational backends with Python frontends.Specifically, we want to test which high-performance backend is best for geophysical (finite-difference based) simulations.
More Information
https://github.com/dionhaefner/pyhpc-benchmarks
Available Versions:
3.0-CUDA-11.4.1
PyMOL
Description
PyMOL is an OpenGL based molecular visualization system
More Information
http://sourceforge.net/projects/pymol
Available Versions:
2.5.0-foss-2020a-Python-3.8.2
2.3.0-foss-2019b-Python-2.7.16
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
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-10.2.0
5.15.4-GCCcore-11.2.0
5.15.1-GCCcore-9.3.0-Python-3.8.2
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
Available Versions:
0.13.3-foss-2022a
PySCF
Description
PySCF is an open-source collection of electronic structure modules powered by Python.
More Information
Available Versions:
2.1.1-foss-2021a
1.7.0-foss-2020a-Python-3.8.2
1.7.6-foss-2021a
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
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
Available Versions:
1.8.1-fosscuda-2019b-Python-3.7.4
1.7.1-fosscuda-2020b
1.12.0-foss-2022a-CUDA-11.8.0
1.11.0-foss-2021a-CUDA-11.3.1
1.10.0-foss-2021a
1.6.0-fosscuda-2019b-Python-3.7.4
1.6.0-foss-2019b-Python-3.7.4
1.12.0-foss-2022a-CUDA-11.7.0
1.12.0-foss-2022a
PyTorch-Lightning
Description
PyTorch Lightning is the lightweight PyTorch wrapper for ML researchers.
More Information
Available Versions:
1.5.9-foss-2021a-CUDA-11.3.1
1.7.7-foss-2022a
PyYAML
Description
PyYAML is a YAML parser and emitter for the Python programming language.
More Information
https://pypi.python.org/pypi/PyYAML/
Available Versions:
5.1-GCCcore-8.2.0
6.0-GCCcore-12.3.0
5.4.1-GCCcore-10.3.0
5.4.1-GCCcore-11.2.0
5.1.2-GCCcore-8.3.0
5.3-GCCcore-9.3.0
6.0-GCCcore-11.3.0
5.3.1-GCCcore-10.2.0
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:
0.19.1-GCC-11.3.0
0.18.0-GCC-11.2.0
0.15.3-GCC-8.3.0
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
Available Versions:
3.9.6-GCCcore-11.2.0-bare
2.7.18-GCCcore-10.2.0
2.7.18-GCCcore-9.3.0
2.7.18-GCCcore-11.2.0-bare
2.7.15-GCCcore-8.2.0
3.6.6-foss-2018b
2.7.15-fosscuda-2018b
3.7.4-GCCcore-9.3.0
3.8.2-GCCcore-9.3.0
2.7.15-GCCcore-7.3.0-bare
2.7.18-GCCcore-10.3.0-bare
3.10.8-GCCcore-12.2.0
3.9.6-GCCcore-11.2.0
3.10.8-GCCcore-12.2.0-bare
2.7.18-GCCcore-11.2.0
2.7.15-foss-2018b
3.11.3-GCCcore-12.3.0
3.10.4-GCCcore-11.3.0
3.7.2-GCCcore-8.2.0
3.9.5-GCCcore-10.3.0-bare
3.9.5-GCCcore-10.3.0-SKL
3.8.6-GCCcore-10.2.0
2.7.18-GCCcore-11.3.0-bare
2.7.16-GCCcore-8.3.0
3.9.5-GCCcore-10.3.0
3.6.6-intel-2020b
3.10.4-GCCcore-11.3.0-bare
3.7.4-GCCcore-8.3.0
Python-bundle-PyPI
Description
Bundle of Python packages from PyPI
More Information
Available Versions:
2023.06-GCCcore-12.3.0
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
Available Versions:
2.3.5-GCCcore-11.2.0
QGIS
Description
QGIS is a user friendly Open Source Geographic Information System (GIS)
More Information
Available Versions:
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
Available Versions:
2023.5
2022.8
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:
2.11.6-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
Available Versions:
2020.2-GCCcore-10.3.0
2020.2-GCCcore-11.2.0
2020.2-GCCcore-12.3.0
2020.2-GCCcore-11.3.0
2019.1-GCCcore-8.3.0
Qiskit
Description
Qiskit is an open-source framework for working with noisy quantum computers at the level of pulses, circuits, and algorithms.
More Information
Available Versions:
0.23.1-foss-2020a-Python-3.8.2
Qt5
Description
Qt is a comprehensive cross-platform C++ application framework.
More Information
Available Versions:
5.15.2-GCCcore-11.2.0
5.14.2-GCCcore-10.2.0
5.13.1-GCCcore-8.3.0
5.15.2-GCCcore-10.3.0
5.15.5-GCCcore-11.3.0
5.14.1-GCCcore-9.3.0
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
QtKeychain
Description
Platform-independent Qt API for storing passwords securely.
More Information
https://github.com/frankosterfeld/qtkeychain
Available Versions:
0.13.2-GCCcore-11.2.0
Quandl
Description
A Python library for Quandl’s RESTful API.
More Information
https://pypi.python.org/pypi/Quandl
Available Versions:
3.4.8-foss-2019a
3.5.3-foss-2020a-Python-3.8.2
3.6.1-foss-2021a
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:
6.7-intel-2020a
6.5-intel-2020a
6.7-foss-2020b
7.1-intel-2022a
6.6-intel-2020a
7.1-foss-2022a
6.6-foss-2020b
Qwt
Description
The Qwt library contains GUI Components and utility classes which are primarily useful for programs with a technical background.
More Information
Available Versions:
6.1.4-GCCcore-8.3.0
6.2.0-GCCcore-11.2.0
6.2.0-GCCcore-10.3.0
R
Description
R is a free software environment for statistical computing and graphics.
More Information
Available Versions:
4.1.0-foss-2021a-ARC
4.0.2-foss-2020a
4.2.1-foss-2021b
4.2.1-foss-2021b-ARC
4.2.1-foss-2022a
4.1.2-foss-2021b
4.1.2-foss-2021b-ARC
4.2.2-foss-2022a
4.0.2-foss-2020a-ARC
4.2.2-foss-2022a-ARC
4.1.0-foss-2021a
3.6.2-foss-2019b
4.2.1-foss-2022a-ARC
R-bundle-Bioconductor
Description
Bioconductor provides tools for the analysis and coprehension of high-throughput genomic data.
More Information
Available Versions:
3.15-foss-2022a-R-4.2.1
3.13-foss-2021a-R-4.1.0
3.14-foss-2021b-R-4.1.2
3.10-foss-2019b
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
RDKit
Description
RDKit is a collection of cheminformatics and machine-learning software written in C++ and Python.
More Information
Available Versions:
2020.03.3-foss-2020a-Python-3.8.2
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
Available Versions:
2020-07-01-GCCcore-8.3.0
2022-06-01-GCCcore-11.3.0
2021-06-01-GCCcore-10.2.0
2022-02-01-GCCcore-11.2.0
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
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-2020b
2.11.0-gompi-2021a
2.13.0-gompi-2022a
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
Available Versions:
6.22.08-foss-2020b
6.24.06-foss-2021b
6.20.04-foss-2019b-Python-3.7.4
RStudio
Available Versions:
2023.06-R-4.2.2-ARC
2022.02-R-4.2.1-ARC
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:
1.5.0-GCCcore-11.2.0
1.4.21-GCCcore-10.3.0
RapidJSON
Description
A fast JSON parser/generator for C++ with both SAX/DOM style API
More Information
Available Versions:
1.1.0-GCCcore-11.3.0
1.1.0-GCCcore-8.3.0
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
RepeatMasker
Description
RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
More Information
Available Versions:
4.1.5-foss-2022a
4.1.2-p1-foss-2021a
4.1.2-p1-foss-2020b
RepeatModeler
Description
RepeatModeler is a de novo transposable element (TE) family identification and modeling package.
More Information
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
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
Available Versions:
1.2.1-gompi-2022a
1.1.1-GCC-10.2.0
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
Available Versions:
3.0.1-GCCcore-11.2.0
2.6.1-GCCcore-7.3.0
3.0.1-GCCcore-10.3.0
Rust
Description
Rust is a systems programming language that runs blazingly fast, prevents segfaults, and guarantees thread safety.
More Information
Available Versions:
1.52.1-GCCcore-10.3.0
1.65.0-GCCcore-12.2.0
1.60.0-GCCcore-11.3.0
1.42.0-GCCcore-8.3.0
1.42.0-GCCcore-9.3.0
1.54.0-GCCcore-11.2.0
1.70.0-GCCcore-12.3.0
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
Available Versions:
1.15.1-GCC-11.2.0
0.1.20-GCC-8.3.0
1.13-GCC-10.3.0
1.16.1-GCC-11.3.0
1.14-GCC-11.2.0
1.9-foss-2018b
1.11-GCC-10.2.0
0.1.20-foss-2020a
1.12-GCC-10.2.0
1.10-GCC-9.3.0
1.10-GCC-8.3.0
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://gforge.inria.fr/projects/scotch/
Available Versions:
6.0.9-gompi-2019b
7.0.1-gompi-2022a
6.1.0-gompi-2020b
6.0.9-gompi-2020a
6.1.0-gompi-2021a
6.0.9-iimpi-2020a
6.0.6-foss-2018b
6.1.2-iimpi-2021b
6.0.6-gompi-2019a
SCons
Description
SCons is a software construction tool.
More Information
Available Versions:
3.0.1-foss-2018b-Python-2.7.15
3.0.5-GCCcore-8.2.0-Python-2.7.15
3.1.1-GCCcore-8.3.0
4.0.1-GCCcore-10.2.0
3.0.1-fosscuda-2018b-Python-2.7.15
4.2.0-GCCcore-11.2.0
3.0.5-GCCcore-8.2.0
SDL2
Description
SDL: Simple DirectMedia Layer, a cross-platform multimedia library
More Information
Available Versions:
2.0.20-GCCcore-11.2.0
2.28.2-GCCcore-12.3.0
2.26.3-GCCcore-12.2.0
2.0.14-GCCcore-10.2.0
SIONlib
Description
SIONlib is a scalable I/O library for the parallel access totask-local files. The library not only supports writing and readingbinary data to or from from several thousands of processors into asingle or a small number of physical files but also provides forglobal open and close functions to access SIONlib file inparallel. SIONlib provides different interfaces: parallel access usingMPI, OpenMp, or their combination and sequential access forpost-processing utilities.
More Information
http://www.fz-juelich.de/ias/jsc/EN/Expertise/Support/Software/SIONlib/_node.html
Available Versions:
1.7.6-foss-2019b
1.7.6-GCCcore-9.3.0-tools
1.7.6-foss-2020a
1.7.7-GCCcore-11.3.0-tools
SKESA
Description
SKESA is a de-novo sequence read assembler for cultured single isolate genomes based on DeBruijn graphs.
More Information
Available Versions:
2.3.0-foss-2018b
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
Available Versions:
3.12.2-intel-2020a-Python-3.8.2
3.12.2-foss-2019b-Python-3.7.4
3.15.1-foss-2021a
SNPsplit
Description
SNPsplit is an allele-specific alignment sorter which is designed to read alignment files in SAM/BAM format and determine the allelic origin of reads that cover known SNP positions. For this to work a library must have been aligned to a genome which had all SNP positions masked by the ambiguity base ’N’, and aligned using aligners that are capable of using a reference genome which contains ambiguity nucleobases.
More Information
https://felixkrueger.github.io/SNPsplit/
Available Versions:
0.6.0-GCC-11.2.0
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
Available Versions:
4.0.2-GCC-10.3.0
SPAdes
Description
Genome assembler for single-cell and isolates data sets
More Information
https://cab.spbu.ru/software/spades/
Available Versions:
3.13.0-GCC-10.3.0
3.13.0-foss-2018b
3.15.3-GCC-11.2.0
3.15.2-GCC-10.2.0
SQLite
Description
SQLite: SQL Database Engine in a C Library
More Information
Available Versions:
3.33.0-GCCcore-10.2.0
3.39.4-GCCcore-12.2.0
3.29.0-GCCcore-8.3.0
3.42.0-GCCcore-12.3.0
3.24.0-GCCcore-7.3.0
3.38.3-GCCcore-11.3.0
3.27.2-GCCcore-8.3.0
3.27.2-GCCcore-8.2.0
3.35.4-GCCcore-10.3.0
3.36-GCCcore-11.2.0
3.24.0-GCCcore-10.2.0
3.29.0-GCCcore-9.3.0
3.31.1-GCCcore-9.3.0
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:
2.10.9-gompi-2020b
3.0.3-gompi-2022a
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:
2.7.1a-GCC-8.2.0-2.31.1
2.7.10b-GCC-11.3.0
2.7.9a-GCC-11.2.0
2.7.3a-GCC-9.3.0
STARCCM+
Available Versions:
2021.2.1
2022.1
2020.2.1
STEAK
Description
Detects integrations of any sort in high-throughput sequencing (HTS) data. STEAK was built for validating and discovering transposable element (TE) and retroviral integrations in a variety of HTS data. The software performs on both single-end (SE) and paired-end (PE) libraries and on a variety of HTS sequencing strategies. It can be applied to a broad range of research interests and clinical uses such as population genetic studies and detecting polymorphic integrations.
More Information
https://omictools.com/steak-tool
Available Versions:
2019.09.12-foss-2019b-Python-2.7.16
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-2021a
6.3.0-foss-2021b
5.1.0-foss-2019b
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
Available Versions:
4.0.2-GCCcore-11.3.0
4.0.1-GCCcore-9.3.0
4.1.1-GCCcore-12.3.0
4.0.2-GCCcore-10.2.0
4.0.1-GCCcore-8.3.0
4.0.2-GCCcore-10.3.0
3.0.12-GCCcore-8.2.0-Python-2.7.15
3.0.12-GCCcore-8.3.0
4.0.2-GCCcore-11.2.0
3.0.12-foss-2018b-Python-2.7.15
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:
1.4.0-gompi-2020b
1.4.0-GCC-11.2.0
1.1.0-gompi-2019b
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
Available Versions:
1.0.1-intel-2020a
1.0.4-foss-2022a
1.0.1-foss-2021a
1.0.1-foss-2021b
1.0.1-foss-2020a
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-2018b-OpenBLAS-0.3.1
2.1.0-gompic-2020b
2.1.0-gompi-2020a
2.1.0-gompi-2021b-fb
2.0.2-gompic-2018b-OpenBLAS-0.3.1
2.2.0-gompi-2022a-fb
2.1.0-gompi-2020b
2.1.0-gompi-2021a-fb
2.2.0-gompi-2022b-fb
2.0.2-gompic-2019b
2.2.0-gompi-2023a-fb
2.1.0-gompic-2020a
2.0.2-gompi-2019b
2.0.2-gompi-2019a-OpenBLAS-0.3.5
Scalasca
Description
Scalasca is a software tool that supports the performance optimization of parallel programs by measuring and analyzing their runtime behavior. The analysis identifies potential performance bottlenecks – in particular those concerning communication and synchronization – and offers guidance in exploring their causes.
More Information
Available Versions:
2.5-gompi-2020a
SciPy-bundle
Description
Bundle of Python packages for scientific software
More Information
Available Versions:
2020.03-fosscuda-2020a-Python-3.8.2
2023.07-gfbf-2023a
2021.10-foss-2021b
2020.11-intel-2020b
2020.11-fosscuda-2020b
2021.05-foss-2021a
2019.03-foss-2019a
2019.10-foss-2019b-Python-2.7.16
2023.02-gfbf-2022b
2019.10-foss-2019b-Python-3.7.4
2022.05-foss-2022a
2021.05-foss-2021a-SKL
2022.05-intel-2022a
2019.10-fosscuda-2019b-Python-2.7.16
2019.10-fosscuda-2019b-Python-3.7.4
2021.10-intel-2021b
2020.03-intel-2020a-Python-3.8.2
2020.03-foss-2020a-Python-3.8.2
2020.11-foss-2020b
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
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
Available Versions:
0.10.0-foss-2019b-Python-3.7.4
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
0.1.85-GCC-8.3.0-Python-3.7.4
0.1.97-GCC-11.3.0
SeqKit
Description
SeqKit - a cross-platform and ultrafast toolkit for FASTA/Q file manipulation
More Information
https://bioinf.shenwei.me/seqkit/
Available Versions:
0.13.2
2.2.0
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
Available Versions:
1.3.9-GCCcore-11.2.0
1.3.9-GCCcore-10.2.0
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:
1.8.2-foss-2021b
1.7.1-GCC-9.3.0-Python-3.8.2
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-foss-2020a
4.1-b4-intel-2020a
4.1.5-intel-2022a
SoX
Description
Sound eXchange, the Swiss Army knife of audio manipulation
More Information
Available Versions:
14.4.2-GCCcore-11.3.0
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-GCC-8.3.0
2.53-foss-2019b
2.41-iccifort-2019.5.281
Stata
Available Versions:
14
Subversion
Description
Subversion is an open source version control system.
More Information
https://subversion.apache.org/
Available Versions:
1.14.1-GCCcore-11.2.0
1.14.0-GCCcore-10.2.0
SuiteSparse
Description
SuiteSparse is a collection of libraries manipulate sparse matrices.
More Information
https://faculty.cse.tamu.edu/davis/suitesparse.html
Available Versions:
5.7.1-intel-2020a-METIS-5.1.0
5.10.1-intel-2021b-METIS-5.1.0
5.10.1-foss-2021a-METIS-5.1.0
5.11.0-foss-2021a-METIS-5.1.0
5.7.1-foss-2020a-METIS-5.1.0
5.10.1-foss-2021b-METIS-5.1.0
5.8.1-foss-2020b-METIS-5.1.0
5.4.0-foss-2019a-METIS-5.1.0
5.13.0-foss-2022a-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:
8.1.0-foss-2022a
SymEngine
Description
SymEngine is a standalone fast C++ symbolic manipulation library
More Information
https://github.com/symengine/symengine
Available Versions:
0.7.0-GCC-10.3.0
SymEngine-python
Description
Python wrappers to the C++ library SymEngine, a fast C++ symbolic manipulation library.
More Information
https://github.com/symengine/symengine.py
Available Versions:
0.7.2-GCC-10.3.0
Szip
Description
Szip compression software, providing lossless compression of scientific data
More Information
https://www.hdfgroup.org/doc_resource/SZIP/
Available Versions:
2.1.1-intel-2020a
2.1.1-GCCcore-8.3.0
2.1.1-GCCcore-7.3.0
2.1.1-GCCcore-9.3.0
2.1.1-GCCcore-11.3.0
2.1.1-GCCcore-12.2.0
2.1.1-GCCcore-10.3.0
2.1.1-GCCcore-12.3.0
2.1.1-GCCcore-11.2.0
2.1.1-GCCcore-8.2.0
2.1.1-GCCcore-10.2.0
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
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
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-10.3.0
4.09.1-GCCcore-10.2.0
4.09.1-GCCcore-11.3.0
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
Available Versions:
8.6.10-GCCcore-9.3.0
8.6.9-GCCcore-8.2.0
8.6.9-GCCcore-9.3.0
8.6.9-GCCcore-8.3.0
8.6.12-GCCcore-11.3.0
8.6.8-GCCcore-7.3.0
8.6.8-GCCcore-10.2.0
8.6.12-GCCcore-12.2.0
8.6.11-GCCcore-11.2.0
8.6.10-GCCcore-10.2.0
8.6.11-GCCcore-10.3.0
8.6.13-GCCcore-12.3.0
TensorFlow
Description
An open-source software library for Machine Intelligence
More Information
Available Versions:
2.6.0-foss-2021a-CUDA-11.3.1
2.11.0-foss-2022a-CUDA-11.7.0
2.7.1-foss-2021b-CUDA-11.4.1
2.1.0-foss-2019b-Python-3.7.4
2.8.4-foss-2021b
1.15.2-fosscuda-2019b-Python-3.7.4
2.4.1-fosscuda-2020b
2.3.1-foss-2020a-Python-3.8.2
2.6.0-foss-2021a
2.11.0-foss-2022a
2.5.3-foss-2021a-CUDA-11.3.1
2.5.0-fosscuda-2020b
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:
1.0.4-fosscuda-2019b-Python-3.7.4
1.0.4-foss-2019b-Python-3.7.4
1.1.2-fosscuda-2020b-PyMC
1.1.2-foss-2020b-PyMC
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
Available Versions:
8.6.9-GCCcore-8.3.0
8.6.10-GCCcore-10.2.0
8.6.11-GCCcore-11.2.0
8.6.8-GCCcore-7.3.0
8.6.11-GCCcore-10.3.0
8.6.12-GCCcore-12.2.0
8.6.9-GCCcore-8.2.0
8.6.9-GCCcore-9.3.0
8.6.10-GCCcore-9.3.0
8.6.12-GCCcore-11.3.0
Tkinter
Description
Tkinter module, built with the Python buildsystem
More Information
Available Versions:
3.7.4-GCCcore-8.3.0
3.8.6-GCCcore-10.2.0
2.7.15-fosscuda-2018b-Python-2.7.15
3.7.2-GCCcore-8.2.0
3.10.4-GCCcore-11.3.0
3.9.5-GCCcore-10.3.0
2.7.16-GCCcore-8.3.0
3.9.6-GCCcore-11.2.0
2.7.15-foss-2018b-Python-2.7.15
3.8.2-GCCcore-9.3.0
Togl
Description
A Tcl/Tk widget for OpenGL rendering.
More Information
https://sourceforge.net/projects/togl/
Available Versions:
2.0-GCCcore-8.3.0
TopHat
Description
TopHat is a fast splice junction mapper for RNA-Seq reads.
More Information
http://ccb.jhu.edu/software/tophat/
Available Versions:
2.1.2-gompi-2019b
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
Available Versions:
12.12.1-foss-2019b-Python-3.7.4
Trim_Galore
Description
A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.
More Information
http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
Available Versions:
0.5.0-foss-2018b
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-1.8
0.38-Java-1.8
Trinity
Description
Trinity represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads.
More Information
https://trinityrnaseq.github.io
Available Versions:
2.14.0-foss-2019b-Python-3.7.4
2.10.0-foss-2019b-Python-3.7.4
2.13.2-foss-2019b-Python-3.7.4
2.12.0-foss-2019b-Python-3.7.4
TwoBit
Available Versions:
2022
UCC
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.
More Information
Available Versions:
1.1.0-GCCcore-12.2.0
1.2.0-GCCcore-12.3.0
1.0.0-GCCcore-11.3.0
UCX
Description
Unified Communication XAn open-source production grade communication framework for data centricand high-performance applications
More Information
Available Versions:
1.8.0-GCCcore-9.3.0
1.14.0-GCCcore-12.2.0
1.11.2-GCCcore-11.2.0
1.10.0-GCCcore-10.3.0
1.13.1-GCCcore-12.2.0
1.14.1-GCCcore-12.3.0
1.8.0-GCCcore-9.3.0-CUDA-11.0.2
1.9.0-GCCcore-10.2.0-CUDA-11.1.1
1.9.0-GCCcore-10.3.0-CUDA-11.1.1
1.12.1-GCCcore-11.3.0
1.9.0-GCCcore-10.2.0
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
Available Versions:
1.12.1-GCCcore-11.3.0-CUDA-12.0.0
1.11.2-GCCcore-11.2.0-CUDA-11.4.1
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
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:
2.2.26-GCCcore-10.2.0
2.2.28-GCCcore-11.3.0
2.2.28-GCCcore-12.2.0
2.2.26-foss-2020a
2.2.28-GCCcore-10.3.0
2.2.28-GCCcore-11.2.0
2.2.26-GCCcore-8.3.0
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-9.3.0
6.0-GCCcore-10.2.0
6.0-GCCcore-10.3.0
6.0-GCCcore-12.2.0
6.0-GCCcore-11.3.0
6.0-GCCcore-11.2.0
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:
0.5.0-gompi-2021b
0.4.9-gompi-2021a
V8
Description
R interface to Google’s open source JavaScript engine
More Information
https://cran.r-project.org/web/packages/V8/
Available Versions:
2.2-foss-2020a-R-4.0.2
3.6.0-foss-2021a-R-4.1.0
3.6.0-foss-2022a-R-4.2.1
3.6.0-foss-2021b-R-4.2.1
3.6.0-foss-2021b-R-4.1.2
3.6.0-foss-2022a-R-4.2.2
VASP
Available Versions:
1.0-info
VCF-kit
Description
VCF-kit is a command-line based collection of utilities for performing analysis on Variant Call Format (VCF) files.
More Information
https://github.com/AndersenLab/VCF-kit
Available Versions:
0.1.6-foss-2018b-Python-2.7.15
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
Available Versions:
0.1.16-GCC-9.3.0
0.1.16-GCC-11.2.0
VMD
Description
VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.
More Information
https://www.ks.uiuc.edu/Research/vmd
Available Versions:
1.9.4a51-foss-2020b
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
Available Versions:
8.2.0-foss-2019b-Python-3.7.4
8.2.0-intel-2020a-Python-3.8.2
9.2.2-foss-2022a
9.1.0-foss-2021b
9.0.1-foss-2021a
8.2.0-foss-2020a-Python-3.8.2
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:
2019_update5
2023.2.0
2020_update3
2021.9.0
Valgrind
Description
Valgrind: Debugging and profiling tools
More Information
Available Versions:
3.16.1-iimpi-2020a
3.19.0-gompi-2022a
3.18.1-gompi-2021b
3.14.0-foss-2018b
3.16.1-gompi-2020a
3.20.0-gompi-2022a
3.17.0-gompi-2021a
Vampire
Available Versions:
5.0
6.0
Velvet
Description
Sequence assembler for very short reads
More Information
http://www.ebi.ac.uk/~zerbino/velvet/
Available Versions:
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
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
Available Versions:
0.4.6-GCCcore-9.3.0
0.4.6-GCCcore-10.3.0
0.4.6-GCCcore-11.2.0
0.4.6-GCCcore-11.3.0
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
Description
The program package WIEN2k allows to perform electronic structure calculations of solidsusing density functional theory (DFT). It is based on the full-potential (linearized) augmented plane-wave((L)APW) + local orbitals (lo) method, one among the most accurate schemes for band structure calculations.WIEN2k is an all-electron scheme including relativistic effects and has many features.
More Information
Available Versions:
21.1-intel-2021a
21.1-JP-intel-2021a
1.0-info
Wannier90
Description
A tool for obtaining maximally-localised Wannier functions
More Information
Available Versions:
3.1.0-intel-2020a
3.1.0-intel-2021b
3.1.0-foss-2021b
3.1.0-foss-2020b
3.1.0-foss-2021a
WannierTools
Description
WannierTools is an open source software that studies the physical properties of given tight-binding model.
More Information
Available Versions:
2.5.1-intel-2020b
2.5.1-intel-2021b
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:
1.20.0-GCCcore-11.3.0
1.22.0-GCCcore-12.3.0
1.21.0-GCCcore-11.2.0
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
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
Available Versions:
2.37.1-GCC-11.2.0
X11
Description
The X Window System (X11) is a windowing system for bitmap displays
More Information
Available Versions:
20180604-GCCcore-7.3.0
20190717-GCCcore-8.3.0
20190717-GCCcore-9.3.0
20200222-GCCcore-9.3.0
20201008-GCCcore-10.2.0
20220504-GCCcore-11.3.0
20190311-GCCcore-8.2.0
20221110-GCCcore-12.2.0
20230603-GCCcore-12.3.0
20210518-GCCcore-10.3.0
20210802-GCCcore-11.2.0
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
Available Versions:
20190127-foss-2019a-Python-3.7.2
20190127-foss-2020a-Python-3.8.2
2.1.1-GCCcore-10.3.0
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
Available Versions:
20190127-foss-2019a-Python-3.7.2
XCrySDen
Description
XCrySDen is a crystalline and molecular structure visualisation program aiming at display of isosurfaces and contours, which can be superimposed on crystalline structures and interactively rotated and manipulated.
More Information
Available Versions:
1.6.2-foss-2019b
XMDS2
Description
The purpose of XMDS2 is to simplify the process of creating simulations that solve systems of initial-value first-order partial and ordinary differential equations.
More Information
Available Versions:
2.2.3-foss-2018b-Python-2.7.15
3.1.0-foss-2020a-Python-3.8.2
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
2.0205-GCCcore-9.3.0
2.0207-GCCcore-11.3.0
2.0207-GCCcore-10.3.0
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
Available Versions:
5.2.5-GCCcore-10.2.0
5.2.5-GCCcore-11.2.0
5.2.7-GCCcore-12.2.0
5.2.5-GCCcore-11.3.0
5.2.4-GCCcore-8.3.0
5.2.5-GCCcore-10.3.0
5.2.5-GCCcore-9.3.0
5.2.4-GCCcore-8.2.0
5.2.4-GCCcore-10.2.0
5.4.2-GCCcore-12.3.0
5.2.4-GCCcore-7.3.0
5.2.4-GCCcore-9.3.0
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
3.2.4-GCCcore-12.3.0
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:
21.1.3-GCCcore-11.3.0
21.1.6-GCCcore-12.2.0
1.20.9-GCCcore-10.2.0
1.20.13-GCCcore-11.2.0
1.20.11-GCCcore-10.3.0
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-12.3.0
1.3.0-GCCcore-8.3.0
1.3.0-GCCcore-9.3.0
1.3.0-GCCcore-12.2.0
1.3.0-GCCcore-10.2.0
1.3.0-GCCcore-8.2.0
1.3.0-GCCcore-11.3.0
1.3.0-GCCcore-11.2.0
1.3.0-GCCcore-10.3.0
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
4.8.10-GCCcore-10.2.0
4.12.2-GCCcore-12.2.0
4.10.2-GCCcore-11.3.0
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
Available Versions:
4.3.4-GCCcore-11.2.0
4.3.3-GCCcore-10.2.0
4.3.4-GCCcore-11.3.0
4.3.2-GCCcore-9.3.0
4.3.4-GCCcore-10.3.0
4.3.2-GCCcore-8.3.0
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-10.3.0
3.0-GCCcore-12.2.0
3.0-GCCcore-11.2.0
3.0-GCCcore-11.3.0
3.0-GCCcore-8.3.0
3.0-GCCcore-9.3.0
3.0-GCCcore-10.2.0
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
angsd
Description
Program for analysing NGS data.
More Information
Available Versions:
0.925-foss-2018b
0.935-GCC-10.2.0
0.933-GCC-8.3.0
annovar
Description
ANNOVAR is an efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, hg38, as well as mouse, worm, fly, yeast and many others).
More Information
http://annovar.openbioinformatics.org/en/latest/
Available Versions:
20191024-GCCcore-8.3.0-Perl-5.28.1
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
Available Versions:
1.10.11-Java-11
1.10.14-Java-11
1.10.9-Java-11
1.10.7-Java-11
1.10.12-Java-11
1.10.8-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:
0.1.0-GCCcore-9.3.0-Python-3.8.2
0.1.4-GCCcore-11.3.0
0.1.2-GCCcore-10.3.0
0.1.3-GCCcore-11.2.0
aria2
Description
aria2 is a lightweight multi-protocol & multi-source command-line download utility.
More Information
Available Versions:
1.35.0-GCCcore-10.3.0
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
3.9.0-foss-2023a
3.8.0-foss-2021b
3.7.0-foss-2020a
3.7.0-intel-2020a
arrow-R
Description
R interface to the Apache Arrow C++ library
More Information
https://cran.r-project.org/web/packages/arrow
Available Versions:
8.0.0-foss-2022a-R-4.2.1
6.0.0.2-foss-2021b-R-4.1.2
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
2.34.1-GCCcore-8.3.0
2.38.0-GCCcore-10.2.0
2.38.0-GCCcore-11.2.0
2.38.0-GCCcore-12.2.0
2.38.0-GCCcore-12.3.0
2.38.0-GCCcore-11.3.0
at-spi2-core
Description
Assistive Technology Service Provider Interface.
More Information
https://wiki.gnome.org/Accessibility
Available Versions:
2.49.91-GCCcore-12.3.0
2.32.0-GCCcore-8.2.0
2.44.1-GCCcore-11.3.0
2.40.3-GCCcore-11.2.0
2.38.0-GCCcore-10.2.0
2.34.0-GCCcore-8.3.0
2.46.0-GCCcore-12.2.0
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
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
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
3.1.2-GCC-7.3.0-2.30
4.0.0-GCC-11.3.0
3.1.2-GCC-10.2.0
binutils
Description
binutils: GNU binary utilities
More Information
https://directory.fsf.org/project/binutils/
Available Versions:
2.34
2.31.1-GCCcore-8.2.0
2.36.1-GCCcore-10.3.0
2.27
2.31.1
2.30-GCCcore-7.3.0
2.32-GCCcore-9.3.0
2.37
2.37-GCCcore-11.2.0
2.35-GCCcore-10.2.0
2.30-GCCcore-8.1.0
2.30
2.28
2.40-GCCcore-12.3.0
2.25
2.40
2.34-GCCcore-9.3.0
2.32
2.39
2.40-GCCcore-13.1.0
2.35
2.26
2.38-GCCcore-11.3.0
2.31.1-GCCcore-8.3.0
2.38
2.39-GCCcore-12.2.0
2.32-GCCcore-8.3.0
2.36.1
bokeh
Description
Statistical and novel interactive HTML plots for Python
More Information
https://github.com/bokeh/bokeh
Available Versions:
2.2.3-fosscuda-2020b
1.4.0-foss-2019b-Python-3.7.4
2.2.3-foss-2020b
2.4.3-foss-2022a
breseq
Description
breseq is a computational pipeline for the analysis of short-read re-sequencing data
More Information
Available Versions:
0.36.1-foss-2021b
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:
1.9.13-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
Available Versions:
1.0.8-GCCcore-12.3.0
1.0.6-GCCcore-8.2.0
1.0.8-GCCcore-9.3.0
1.0.6-GCCcore-10.2.0
1.0.8-GCCcore-10.2.0
1.0.8-GCCcore-11.2.0
1.0.8-GCCcore-11.3.0
1.0.6-GCCcore-8.3.0
1.0.8-GCCcore-7.3.0
1.0.8-GCCcore-12.2.0
1.0.8-GCCcore-10.3.0
1.0.6-GCCcore-7.3.0
1.0.8-GCCcore-8.3.0
c-ares
Description
c-ares is a C library for asynchronous DNS requests (including name resolves)
More Information
Available Versions:
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
Available Versions:
7.83.0-GCCcore-11.3.0
7.60.0-GCCcore-7.3.0
7.78.0-GCCcore-11.2.0
7.76.0-GCCcore-10.3.0
7.66.0-GCCcore-7.3.0
7.86.0-GCCcore-12.2.0
7.66.0-GCCcore-8.3.0
7.72.0-GCCcore-10.2.0
7.63.0-GCCcore-8.2.0
7.69.1-GCCcore-9.3.0
7.60.0-GCCcore-10.2.0
8.0.1-GCCcore-12.3.0
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
Available Versions:
1.16.0-GCCcore-8.3.0
1.16.0-GCCcore-8.2.0
1.14.12-GCCcore-7.3.0
1.16.0-GCCcore-9.3.0
1.16.0-GCCcore-10.2.0
1.17.8-GCCcore-12.3.0
1.17.4-GCCcore-12.2.0
1.16.0-GCCcore-11.2.0
1.17.4-GCCcore-11.3.0
1.16.0-GCCcore-10.3.0
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
Available Versions:
4.6.1-GCCcore-11.2.0
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:
1.15.1-GCCcore-12.3.0
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
colossalai
Description
Colossal-AI: A Unified Deep Learning System for Big Model Era
More Information
Available Versions:
0.1.8-foss-2021a-CUDA-11.3.1
configurable-http-proxy
Description
HTTP proxy for node.js including a REST API for updating the routing table. Developed as a part of the Jupyter Hub multi-user server.
More Information
https://github.com/jupyterhub/configurable-http-proxy
Available Versions:
4.2.1-GCCcore-10.2.0
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
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:
1.2.1-GCCcore-12.3.0
1.1.0-GCCcore-11.2.0
1.2.1-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:
41.0.1-GCCcore-12.3.0
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:
8.2.1.32-CUDA-11.3.1
8.2.2.26-CUDA-11.4.1
8.0.4.30-CUDA-11.1.1
8.1.1.33-CUDA-11.2.2
7.6.4.38-gcccuda-2019b
8.4.0.27-CUDA-11.6.0
8.6.0.163-CUDA-11.8.0
8.7.0.84-CUDA-11.8.0
8.8.0.121-CUDA-12.0.0
8.0.4.30-CUDA-11.0.2
8.4.1.50-CUDA-11.7.0
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:
1.7.0.1-CUDA-12.0.0
1.6.1.5-CUDA-11.4.1
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:
4.3-GCCcore-11.3.0
1.18-foss-2018b-Python-3.6.6
3.5-GCCcore-11.2.0
2.7-GCCcore-8.3.0-Python-3.7.4
4.2-GCCcore-11.3.0
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
Available Versions:
2021.2.0-foss-2020b
2022.10.0-foss-2022a
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:
0.110-GCCcore-8.3.0
0.112-GCCcore-11.2.0
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
3.4.0-keep
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:
0.3.6-GCCcore-11.3.0
0.3.4-GCCcore-10.3.0
0.3.4-GCCcore-11.2.0
0.3.3-foss-2020a-Python-3.8.2
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-10.3.0
0.1.6-GCCcore-11.2.0
0.1.5-GCCcore-10.2.0
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:
0.3.2-foss-2022a-CUDA-11.7.0
0.3.1-foss-2022a-CUDA-11.7.0
dot
Available Versions:
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-10.2.0
3.1.5-GCCcore-10.3.0
3.1.5-GCCcore-9.3.0
3.1.4-GCCcore-8.3.0
3.2.0-GCCcore-11.3.0
3.1.5-GCCcore-11.2.0
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:
2.27.0-gompi-2022a
2.20.0-gompi-2020b
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
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
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
Available Versions:
0.183-GCCcore-10.2.0
0.189-GCCcore-12.2.0
0.185-GCCcore-8.3.0
0.189-GCCcore-12.3.0
0.187-GCCcore-11.3.0
0.185-GCCcore-11.2.0
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
https://github.com/AbiWord/enchant
Available Versions:
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
Available Versions:
0.27.5-GCCcore-11.2.0
expat
Description
Expat is an XML parser library written in C. It is a stream-oriented parser in which an application registers handlers for things the parser might find in the XML document (like start tags)
More Information
Available Versions:
2.2.5-GCCcore-8.1.0
2.2.7-GCCcore-9.3.0
2.2.9-GCCcore-9.3.0
2.2.9-GCCcore-10.3.0
2.2.5-GCCcore-7.3.0
2.2.7-GCCcore-7.3.0
2.2.6-GCCcore-8.3.0
2.4.1-GCCcore-11.2.0
2.4.8-GCCcore-11.3.0
2.2.7-GCCcore-8.3.0
2.2.5-GCCcore-10.2.0
2.2.9-GCCcore-10.2.0
2.5.0-GCCcore-12.3.0
2.4.9-GCCcore-12.2.0
2.2.6-GCCcore-8.2.0
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:
0.1.3-GCCcore-11.2.0
0.1.3-GCCcore-11.3.0
0.1.3-GCCcore-10.3.0
fast-gbs
Available Versions:
v2
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:
11.1.5.2
12.0.16.0
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
https://www.darwinsys.com/file/
Available Versions:
5.43-GCCcore-11.3.0
5.39-GCCcore-10.2.0
5.35-GCCcore-7.3.0
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
flappie
Available Versions:
2.1.3
flatbuffers
Description
FlatBuffers: Memory Efficient Serialization Library
More Information
https://github.com/google/flatbuffers/
Available Versions:
2.0.0-GCCcore-11.2.0
1.12.0-GCCcore-10.2.0
2.0.7-GCCcore-11.3.0
1.12.0-GCCcore-8.3.0
1.12.0-GCCcore-9.3.0
2.0.0-GCCcore-10.3.0
flatbuffers-python
Description
Python Flatbuffers runtime library.
More Information
https://github.com/google/flatbuffers/
Available Versions:
1.12-GCCcore-10.2.0
2.0-GCCcore-11.2.0
2.0-GCCcore-11.3.0
2.0-GCCcore-10.3.0
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
Available Versions:
2.5.39-GCCcore-8.3.0
2.6.4-GCCcore-8.1.0
2.6.4-GCCcore-7.3.0
2.6.4
2.6.4-GCCcore-9.3.0
2.6.4-GCCcore-12.2.0
2.6.3
2.6.4-GCCcore-11.2.0
2.6.4-GCCcore-10.3.0
2.6.4-GCCcore-13.1.0
2.6.4-GCCcore-11.3.0
2.6.4-GCCcore-12.3.0
2.5.39
2.6.0
2.6.4-GCCcore-8.3.0
2.6.4-GCCcore-8.2.0
2.6.4-GCCcore-10.2.0
flit
Description
A simple packaging tool for simple packages.
More Information
Available Versions:
3.9.0-GCCcore-12.3.0
fluent
Available Versions:
2021R2
fontconfig
Description
Fontconfig is a library designed to provide system-wide font configuration, customization and application access.
More Information
http://www.freedesktop.org/software/fontconfig
Available Versions:
2.13.1-GCCcore-8.2.0
2.13.92-GCCcore-10.2.0
2.13.93-GCCcore-10.3.0
2.14.1-GCCcore-12.2.0
2.14.0-GCCcore-11.3.0
2.13.1-GCCcore-9.3.0
2.13.1-GCCcore-8.3.0
2.13.0-GCCcore-7.3.0
2.14.2-GCCcore-12.3.0
2.13.92-GCCcore-9.3.0
2.13.94-GCCcore-11.2.0
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:
2022b
2019b
2020b
2023a
2021b
2018b
2022a
2020a
2019a
2021a
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:
2019b
2020g
2020a
2018b
2020b
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-9.3.0
3.2.1-GCCcore-8.3.0
3.2.1-GCCcore-11.2.0
3.2.1-GCCcore-10.2.0
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
Available Versions:
2.12.1-GCCcore-12.2.0
2.9.1-GCCcore-8.2.0
2.10.1-GCCcore-8.3.0
2.12.1-GCCcore-11.3.0
2.13.0-GCCcore-12.3.0
2.11.0-GCCcore-11.2.0
2.10.3-GCCcore-10.2.0
2.9.1-GCCcore-7.3.0
2.10.4-GCCcore-10.3.0
2.10.1-GCCcore-9.3.0
fsm-lite
Available Versions:
1.0
fsom
Description
A tiny C library for managing SOM (Self-Organizing Maps) neural networks.
More Information
Available Versions:
20141119-GCCcore-11.2.0
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
gc
Description
The Boehm-Demers-Weiser conservative garbage collector can be used as agarbage collecting replacement for C malloc or C++ new.
More Information
Available Versions:
8.2.0-GCCcore-11.2.0
7.6.12-GCCcore-9.3.0
7.6.12-GCCcore-8.3.0
8.2.2-GCCcore-11.3.0
7.6.10-GCCcore-8.2.0
gcccuda
Description
GNU Compiler Collection (GCC) based compiler toolchain, along with CUDA toolkit.
More Information
(none)
Available Versions:
2019b
2020a
2018b
2020b
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
geopandas
Description
GeoPandas is a project to add support for geographic data to pandas objects.It currently implements GeoSeries and GeoDataFrame types which are subclasses of pandas.Seriesand pandas.DataFrame respectively. GeoPandas objects can act on shapely geometry objects andperform geometric operations.
More Information
https://github.com/geopandas/geopandas
Available Versions:
0.8.1-foss-2020a-Python-3.8.2
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:
0.21-GCCcore-10.3.0
0.21.1-GCCcore-12.3.0
0.21-GCCcore-10.2.0
0.19.8.1-GCCcore-7.3.0
0.20.1-GCCcore-8.3.0
0.21
0.21-GCCcore-11.2.0
0.21.1-GCCcore-12.2.0
0.19.8.1-GCCcore-8.2.0
0.21-GCCcore-11.3.0
0.20.1-GCCcore-9.3.0
0.19.8.1
0.21.1
0.20.1
gfbf
Description
GNU Compiler Collection (GCC) based compiler toolchain, including FlexiBLAS (BLAS and LAPACK support) and (serial) FFTW.
More Information
(none)
Available Versions:
2023a
2022b
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:
5.2.1-GCCcore-11.3.0
5.2.1-GCCcore-11.2.0
5.2.1-GCCcore-9.3.0
5.1.4-GCCcore-8.2.0
5.2.1-GCCcore-10.2.0
5.2.1-GCCcore-12.3.0
5.2.1-GCCcore-8.3.0
5.2.1-GCCcore-12.2.0
5.2.1-GCCcore-10.3.0
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
Available Versions:
2.36.0-GCCcore-11.3.0-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
2.41.0-GCCcore-12.3.0-nodocs
2.23.0-GCCcore-9.3.0-nodocs
2.23.0-GCCcore-8.3.0-nodocs
2.23.0-GCCcore-8.3.0
2.33.1-GCCcore-11.2.0-nodocs
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
Available Versions:
3.2.0
2.11.0
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
Available Versions:
2.1.0-GCCcore-9.3.0
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
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
gmpy2
Description
GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x
More Information
https://github.com/aleaxit/gmpy
Available Versions:
2.1.0b5-GCC-9.3.0
2.1.0b4-GCC-8.3.0
2.1.0b5-GCC-10.3.0
gmsh
Description
Gmsh is a 3D finite element grid generator with a build-in CAD engine and post-processor.
More Information
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:
5.4.1-GCCcore-10.2.0
5.2.8-GCCcore-9.3.0
5.4.2-GCCcore-11.2.0
5.4.2-GCCcore-10.3.0
5.4.4-GCCcore-11.3.0
5.2.8-GCCcore-8.3.0
gompi
Description
GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support.
More Information
(none)
Available Versions:
2021a
2019b-dba
2022a
2023a
2022b
2019b
2020a
2021b
2019a
2018b
2020b
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:
2020b
2020a
2019b
2018b
googletest
Description
Google’s framework for writing C++ tests on a variety of platforms
More Information
https://github.com/google/googletest
Available Versions:
1.11.0-GCCcore-11.3.0
1.13.0-GCCcore-12.3.0
1.11.0-GCCcore-11.2.0
1.10.0-GCCcore-10.2.0
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-9.3.0
3.1-GCCcore-8.2.0
3.1-GCCcore-11.3.0
3.1-GCCcore-12.3.0
3.1-GCCcore-7.3.0
3.1-GCCcore-11.2.0
3.1-GCCcore-8.3.0
3.1-GCCcore-10.3.0
3.1-GCCcore-12.2.0
3.1-GCCcore-10.2.0
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
2.9.1-GCCcore-10.2.0
2.10-GCCcore-11.3.0
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
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-11.2.0
1.3.14-GCCcore-11.3.0
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:
1.22.4-GCCcore-12.2.0
1.22.4-GCCcore-9.3.0
1.22.4-GCCcore-11.2.0
1.22.4-GCCcore-11.3.0
1.22.4-GCCcore-12.3.0
1.22.4-GCCcore-10.3.0
gromacs
Available Versions:
2018.4-fosscuda-2019b
gromacs-cp2k
Available Versions:
2021.1-foss-2020a
gromos
Available Versions:
1.5.0
gubbins
Description
Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences)is an algorithm that iteratively identifies loci containing elevated densities of basesubstitutions while concurrently constructing a phylogeny based on the putative point mutationsoutside of these regions. Simulations demonstrate the algorithm generates highly accuratereconstructions under realistic models of short-term bacterial evolution, and can be runin only a few hours on alignments of hundreds of bacterial genome sequences.
More Information
https://sanger-pathogens.github.io/gubbins
Available Versions:
2.4.0
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:
1.12-GCCcore-12.3.0
1.10-GCCcore-10.2.0
1.10-GCCcore-8.3.0
1.10-GCCcore-11.2.0
1.12-GCCcore-12.2.0
1.12-GCCcore-11.3.0
1.10-GCCcore-10.3.0
1.10-GCCcore-9.3.0
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
Available Versions:
2.10.0-intel-2020a-Python-3.8.2
3.6.0-foss-2021b
2.10.0-foss-2019b-Python-3.7.4
2.10.0-fosscuda-2019b-Python-3.7.4
3.1.0-foss-2020b
3.2.1-foss-2021a
3.1.0-fosscuda-2020b
2.10.0-foss-2020a-Python-3.8.2
2.9.0-foss-2019a
2.8.0-foss-2018b-Python-2.7.15
3.7.0-foss-2022a
2.10.0-fosscuda-2020a-Python-3.8.2
hatchling
Description
Extensible, standards compliant build backend used by Hatch,a modern, extensible Python project manager.
More Information
Available Versions:
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:
1.47.4-GCCcore-7.3.0
1.47.12-GCCcore-9.3.0
1.49.3-GCCcore-13.1.0
1.49.3-GCCcore-12.3.0
1.47.16-GCCcore-10.2.0
1.47.4
1.48.3-GCCcore-11.2.0
1.47.6-GCCcore-8.1.0
1.48.3-GCCcore-10.3.0
1.49.2-GCCcore-12.2.0
1.47.7-GCCcore-8.2.0
1.47.8-GCCcore-8.3.0
1.49.2-GCCcore-11.3.0
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 to make it much higher level than otherwise suggested by its minimal code base and the lack of explicit bindings for every Redis command.
More Information
https://github.com/redis/hiredis
Available Versions:
1.0.2-GCCcore-11.2.0
hptt
Available Versions:
1.0.5
htop
Description
An interactive process viewer for Unix
More Information
Available Versions:
2.0.1
hunspell
Description
Hunspell is a spell checker and morphological analyzer library and program designed for languageswith rich morphology and complex word compounding or character encoding.
More Information
Available Versions:
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:
2.9.1-GCCcore-12.3.0
2.2.0-GCCcore-10.2.0
2.4.1-GCCcore-10.3.0
2.5.0-GCCcore-11.2.0
2.8.0-GCCcore-12.2.0
2.7.1-GCCcore-11.3.0
1.11.10-GCCcore-7.3.0
2.2.0-GCCcore-9.3.0
1.11.12-GCCcore-9.3.0
1.11.11-GCCcore-8.2.0
1.11.12-GCCcore-8.3.0
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:
6.82.0-GCCcore-12.3.0
6.14.6-GCCcore-11.2.0
6.46.7-GCCcore-11.3.0
4.23.4-GCCcore-8.2.0
6.68.2-GCCcore-12.2.0
4.44.2-GCCcore-8.3.0-Python-3.7.4
5.41.5-GCCcore-10.2.0
6.13.1-GCCcore-10.3.0
5.41.2-GCCcore-10.2.0
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
https://software.intel.com/en-us/intel-compilers/
Available Versions:
2020.1.217
2020.4.304
2018.3.222-GCC-7.3.0-2.30
2019.5.281
2019.1.144-GCC-8.2.0-2.31.1
iccifortcuda
Description
Intel C, C++ & Fortran compilers with CUDA toolkit
More Information
(none)
Available Versions:
2020b
2019b
ifort
Description
Intel Fortran compiler
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
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
Available Versions:
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:
2022.05
2022b
2023.03
2023a
2020b
2021b
2022a
2020a
2021a
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:
2021.4.0
2022.2.1
2023.1.0
2022.1.0
2020.4.304-iimpi-2020b
2020.1.217-gompi-2020a
2020.1.217-iimpi-2020a
2020.4.304-iimpic-2020b
2021.2.0-iompi-2021a
2021.2.0-iimpi-2021a
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:
2022.1.0-iimpi-2022.05
2022.2.1-iimpi-2022b
2023.1.0-iimpi-2023.03
2023.1.0-iimpi-2023a
2021.4.0-iimpi-2021b
2022.1.0-iimpi-2022a
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
2019.7.217-iccifort-2020.1.217
2021.9.0-intel-compilers-2023.1.0
2021.2.0-intel-compilers-2021.2.0
2019.9.304-iccifort-2020.4.304
2021.6.0-intel-compilers-2022.1.0
2019.9.304-iccifortcuda-2020b
2021.4.0-intel-compilers-2021.4.0
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:
2022b
2022.05
2023.03
2021a
2023a
2020a
2021b
2022a
2020b
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:
2023.1.0
2022.2.1
2021.4.0
2022.1.0
2021.2.0
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
http://freedesktop.org/wiki/Software/intltool/
Available Versions:
0.51.0-GCCcore-8.3.0
0.51.0-GCCcore-12.3.0
0.51.0-GCCcore-8.2.0
0.51.0-GCCcore-10.2.0
0.51.0-GCCcore-7.3.0-Perl-5.28.0
0.51.0-GCCcore-9.3.0
0.51.0-GCCcore-10.3.0
0.51.0-GCCcore-11.3.0
0.51.0-GCCcore-11.2.0
0.51.0-GCCcore-12.2.0
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:
0.3.25-foss-2022a
0.3.9-foss-2021a-CUDA-11.3.1
0.3.25-foss-2022a-CUDA-11.7.0
0.2.19-fosscuda-2020b
0.3.23-foss-2021b-CUDA-11.4.1
0.4.4-foss-2022a-CUDA-12.0.0
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-11.3.0
2.1-GCCcore-12.3.0
2.1-GCCcore-11.2.0
2.1-GCCcore-12.2.0
jemalloc
Description
jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and scalable concurrency support.
More Information
Available Versions:
5.2.1-GCCcore-10.3.0
5.2.1-GCCcore-11.2.0
5.2.1-GCCcore-8.3.0
5.2.1-GCCcore-11.3.0
5.3.0-GCCcore-11.3.0
5.2.1-GCCcore-10.2.0
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:
0.16-GCCcore-12.3.0
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
Available Versions:
1.21.0-GCCcore-11.3.0
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:
0.46.1-foss-2019b
0.46.2-foss-2020b
0.48.0-gompi-2021b
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
Available Versions:
2.3.0-GCCcore-11.3.0
2.1.3-intel-2020a
2.1.3-foss-2020a
2.2.1-GCCcore-11.2.0
2.2.1-GCCcore-10.3.0
2.3.0-GCCcore-11.2.0
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-11.3.0
0.4.0-GCC-10.3.0
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
Available Versions:
1.4.1-foss-2019a-Python-3.7.2
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-8.3.0
9.0.0-foss-2018b
9.0.2-GCCcore-11.3.0
9.0.2-GCCcore-12.2.0
9.0.1-GCCcore-10.3.0
9.0.2-GCCcore-11.2.0
9.0.1-GCCcore-9.3.0
9.0.1-GCCcore-10.2.0
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-11.3.0
1.0.6-GCCcore-12.3.0
1.0.6-GCCcore-10.3.0
libaio
Description
Asynchronous input/output library that uses the kernels native interface.
More Information
Available Versions:
0.3.112-GCCcore-10.3.0
0.3.112-GCCcore-11.3.0
0.3.111-GCCcore-8.3.0
0.3.112-GCCcore-10.2.0
0.3.113-GCCcore-12.2.0
0.3.113-GCCcore-12.3.0
libarchive
Description
Multi-format archive and compression library
More Information
Available Versions:
3.4.3-GCCcore-10.2.0
3.5.1-GCCcore-8.3.0
3.5.1-GCCcore-10.3.0
3.6.1-GCCcore-12.2.0
3.5.1-GCCcore-11.2.0
3.4.0-GCCcore-8.2.0
3.6.1-GCCcore-11.3.0
3.6.2-GCCcore-12.3.0
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-foss-2022a
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:
1.13-GCCcore-8.3.0
1.13-GCCcore-9.3.0
1.14-GCCcore-10.2.0
1.17-GCCcore-11.2.0
2.1-GCCcore-11.3.0
1.7-GCCcore-7.3.0
1.17-GCCcore-10.3.0
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
libdeflate
Description
Heavily optimized library for DEFLATE/zlib/gzip compression and decompression.
More Information
https://github.com/ebiggers/libdeflate
Available Versions:
1.18-GCCcore-12.3.0
1.8-GCCcore-11.2.0
1.15-GCCcore-12.2.0
1.10-GCCcore-11.3.0
libdrm
Description
Direct Rendering Manager runtime library.
More Information
Available Versions:
2.4.92-GCCcore-7.3.0
2.4.99-GCCcore-9.3.0
2.4.100-GCCcore-9.3.0
2.4.110-GCCcore-11.3.0
2.4.106-GCCcore-10.3.0
2.4.114-GCCcore-12.2.0
2.4.102-GCCcore-10.2.0
2.4.97-GCCcore-8.2.0
2.4.99-GCCcore-8.3.0
2.4.115-GCCcore-12.3.0
2.4.107-GCCcore-11.2.0
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
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:
1.5.8-GCCcore-11.2.0
1.5.3-GCCcore-8.2.0
1.5.10-GCCcore-11.3.0
1.5.10-GCCcore-12.3.0
1.5.10-GCCcore-12.2.0
1.5.4-GCCcore-10.2.0
1.5.4-GCCcore-8.3.0
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
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
Available Versions:
2.1.12-GCCcore-11.2.0
2.1.12-GCCcore-11.3.0
2.1.12-GCCcore-10.2.0
2.1.12-GCCcore-10.3.0
2.1.8
2.1.12-GCCcore-12.3.0
2.1.12-GCCcore-12.2.0
2.1.11-GCCcore-8.3.0
2.1.11-GCCcore-9.3.0
libexif
Description
A library for parsing, editing, and saving EXIF data.
More Information
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:
1.16.1-GCCcore-12.2.0
1.11.0-GCCcore-9.3.0
1.11.0-GCCcore-10.2.0
1.13.2-GCCcore-11.2.0
1.15.1-GCCcore-11.3.0
1.18.0-GCCcore-12.3.0
1.12.1-GCCcore-10.3.0
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
Available Versions:
3.2.1-GCCcore-8.2.0
3.3-GCCcore-10.3.0
3.4.2-GCCcore-11.2.0
3.2.1-GCCcore-8.3.0
3.2.1-GCCcore-10.2.0
3.3-GCCcore-9.3.0
3.4.2-GCCcore-11.3.0
3.2.1-GCCcore-9.3.0
3.3-GCCcore-10.2.0
3.4.4-GCCcore-12.3.0
3.4.4-GCCcore-12.2.0
3.2.1-GCCcore-7.3.0
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:
1.9.3-GCCcore-11.2.0
libgd
Description
GD is an open source code library for the dynamic creation of images by programmers.
More Information
Available Versions:
2.3.3-GCCcore-11.2.0
2.3.0-GCCcore-10.2.0
2.2.5-GCCcore-7.3.0
2.3.3-GCCcore-12.2.0
2.2.5-GCCcore-8.3.0
2.3.0-GCCcore-9.3.0
2.3.1-GCCcore-10.3.0
2.3.3-GCCcore-11.3.0
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-10.2.0
1.7.1-GCCcore-12.3.0
1.7.0-GCCcore-11.2.0
1.4.2-foss-2018b
1.5.1-GCCcore-9.3.0
1.5.1-GCCcore-8.3.0
1.7.1-GCCcore-11.3.0
1.6.0-GCCcore-10.3.0
1.5.1-GCCcore-8.2.0
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
Available Versions:
1.1.1-GCCcore-11.2.0
1.1.0-GCCcore-10.3.0
1.4.3-GCCcore-11.3.0
libglade
Description
Libglade is a library for constructing user interfaces dynamically from XML descriptions.
More Information
https://developer.gnome.org/libglade/
Available Versions:
2.6.4-foss-2018b
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:
1.4.0-GCCcore-11.3.0
1.6.0-GCCcore-12.3.0
1.2.0-GCCcore-9.3.0
1.3.3-GCCcore-10.3.0
1.6.0-GCCcore-12.2.0
1.3.2-GCCcore-10.2.0
1.3.3-GCCcore-11.2.0
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:
1.42-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
libiconv
Description
Libiconv converts from one character encoding to another through Unicode conversion
More Information
https://www.gnu.org/software/libiconv
Available Versions:
1.17-GCCcore-12.3.0
1.17-GCCcore-12.2.0
1.16-GCCcore-9.3.0
1.17-GCCcore-11.3.0
1.15-GCCcore-7.3.0
1.16-GCCcore-11.2.0
1.16-GCCcore-10.2.0
1.16-GCCcore-8.3.0
1.16-GCCcore-10.3.0
1.16-GCCcore-8.2.0
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-11.2.0
2.3.2-GCCcore-11.3.0
2.3.0-GCCcore-10.2.0
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
https://sourceforge.net/projects/libjpeg-turbo/
Available Versions:
2.0.4-GCCcore-9.3.0
2.0.3-GCCcore-8.3.0
2.0.0-GCCcore-7.3.0
2.0.5-GCCcore-10.2.0
2.0.6-GCCcore-10.3.0
2.0.6-GCCcore-11.2.0
2.1.3-GCCcore-11.3.0
2.1.4-GCCcore-12.2.0
2.1.5.1-GCCcore-12.3.0
2.0.2-GCCcore-8.2.0
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
https://www.gnu.org/software/libmatheval/
Available Versions:
1.1.11-GCCcore-9.3.0
1.1.11-GCCcore-8.2.0
1.1.11-GCCcore-8.3.0
libogg
Description
Ogg is a multimedia container format, and the native file and stream format for the Xiph.orgmultimedia codecs.
More Information
Available Versions:
1.3.5-GCCcore-11.3.0
1.3.5-GCCcore-12.2.0
1.3.5-GCCcore-11.2.0
1.3.4-GCCcore-10.2.0
1.3.4-GCCcore-10.3.0
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
Available Versions:
1.3.1-GCCcore-11.3.0
1.3.1-GCCcore-12.2.0
libpciaccess
Description
Generic PCI access library.
More Information
http://cgit.freedesktop.org/xorg/lib/libpciaccess/
Available Versions:
0.14-GCCcore-8.2.0
0.14-GCCcore-7.3.0
0.14-GCCcore-8.3.0
0.16-GCCcore-10.2.0
0.16-GCCcore-9.3.0
0.16-GCCcore-11.2.0
0.16-GCCcore-10.3.0
0.17-GCCcore-12.2.0
0.17-GCCcore-12.3.0
0.16-GCCcore-11.3.0
libpng
Description
libpng is the official PNG reference library
More Information
http://www.libpng.org/pub/png/libpng.html
Available Versions:
1.6.37-GCCcore-10.3.0
1.6.34-GCCcore-7.3.0
1.6.38-GCCcore-12.2.0
1.6.37-GCCcore-8.3.0
1.6.37-GCCcore-9.3.0
1.6.39-GCCcore-12.3.0
1.6.36-GCCcore-8.2.0
1.6.37-GCCcore-10.2.0
1.6.37-GCCcore-11.3.0
1.6.37-GCCcore-11.2.0
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
libpsortb
Description
PSORT family of programs for subcellular localization prediction as well as other datasets and resources relevant to localization prediction.
More Information
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:
8.1.2-GCCcore-11.3.0
8.1-GCCcore-11.2.0
8.0-GCCcore-10.2.0
8.0-GCCcore-7.3.0
7.0-GCCcore-7.3.0
7.0-GCCcore-10.2.0
8.2-GCCcore-12.2.0
8.0-GCCcore-8.3.0
8.1-GCCcore-10.3.0
8.0-GCCcore-8.2.0
8.2-GCCcore-12.3.0
8.0-GCCcore-9.3.0
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-12.3.0
1.1.0-GCC-11.2.0
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
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:
1.0.28-GCCcore-7.3.0
1.1.0-GCCcore-11.3.0
1.0.28-GCCcore-9.3.0
1.2.0-GCCcore-12.2.0
1.0.28-GCCcore-10.2.0
1.0.31-GCCcore-10.3.0
1.0.31-GCCcore-11.2.0
1.0.28-GCCcore-8.3.0
libsodium
Description
Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, password hashing and more.
More Information
Available Versions:
1.0.18-GCCcore-11.3.0
1.0.18-GCCcore-9.3.0
1.0.18-GCCcore-11.2.0
1.0.18-GCCcore-10.3.0
1.0.18-GCCcore-8.3.0
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
Available Versions:
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:
4.3.0a-GCC-8.3.0-Python-3.7.4
5.0.1-GCC-12.3.0
5.0.1-GCC-11.2.0
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:
4.18.0-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:
1.3.2-GCCcore-10.3.0
1.3.1-GCCcore-10.2.0
1.2.6-GCCcore-8.3.0
1.3.2-GCCcore-11.3.0
1.3.3-GCCcore-12.3.0
1.3.2-GCCcore-11.2.0
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
https://www.gnu.org/software/libtool
Available Versions:
2.4.6-GCCcore-9.3.0
2.4.6-GCCcore-8.2.0
2.4.7
2.4.6-GCCcore-8.1.0
2.4.6-GCCcore-8.3.0
2.4.6-GCCcore-7.3.0
2.4.7-GCCcore-11.3.0
2.4.6-GCCcore-11.2.0
2.4.6-GCCcore-10.2.0
2.4.7-GCCcore-12.3.0
2.4.6-GCCcore-10.3.0
2.4.7-GCCcore-12.2.0
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
0.9.10-GCCcore-8.2.0
1.0-GCCcore-11.3.0
1.0-GCCcore-11.2.0
0.9.10-GCCcore-9.3.0
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:
1.4.0-GCCcore-10.3.0
1.3.1-GCCcore-8.2.0
1.6.2-GCCcore-11.3.0
1.6.2-GCCcore-12.3.0
1.5.0-GCCcore-11.2.0
1.4.0-GCCcore-10.2.0
1.6.2-GCCcore-12.2.0
1.3.1-GCCcore-8.3.0
1.2.1-GCCcore-7.3.0
1.3.1-GCCcore-9.3.0
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
Available Versions:
0.4.0-foss-2021a
0.4.0-foss-2020b
0.4.0-foss-2022a
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
Available Versions:
1.3.7-GCCcore-11.3.0
1.3.7-GCCcore-10.2.0
1.3.7-GCCcore-12.2.0
1.3.7-GCCcore-11.2.0
1.3.7-GCCcore-10.3.0
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:
1.3.1-GCCcore-12.3.0
1.1.0-GCCcore-10.2.0
1.2.0-GCCcore-11.2.0
1.3.1-GCCcore-12.2.0
1.2.4-GCCcore-11.3.0
1.0.2-GCCcore-8.2.0
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
Available Versions:
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:
5.2.3-intel-compilers-2022.1.0
6.2.2-GCC-12.3.0
4.3.4-intel-2020a
4.3.4-GCC-8.2.0-2.31.1
3.0.1-GCC-8.2.0-2.31.1
4.3.4-iccifort-2020.4.304
5.1.6-GCC-11.2.0
4.3.4-GCC-7.3.0-2.30
5.1.2-GCC-10.2.0
5.2.3-GCC-11.3.0
5.1.6-intel-compilers-2021.4.0
4.3.4-iccifort-2020.1.217
4.3.4-GCC-9.3.0
5.1.5-intel-compilers-2021.2.0
4.3.4-GCC-10.2.0
3.0.1-foss-2020a
5.2.3-GCC-10.3.0
5.1.6-GCC-11.3.0
4.3.4-iccifort-2019.5.281
4.3.4-GCC-8.3.0
5.1.5-GCC-10.3.0
libxml++
Description
libxml++ is a C++ wrapper for the libxml XML parser library.
More Information
http://libxmlplusplus.sourceforge.net
Available Versions:
2.42.1-GCC-10.3.0
2.40.1-GCCcore-8.3.0
libxml2
Description
Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform).
More Information
Available Versions:
2.9.8-GCCcore-8.2.0
2.9.9-GCCcore-9.3.0
2.9.10-GCCcore-10.2.0
2.9.10-GCCcore-10.3.0
2.10.3-GCCcore-12.2.0
2.9.10-GCCcore-9.3.0
2.9.10-GCCcore-11.2.0
2.11.4-GCCcore-12.3.0
2.9.8-GCCcore-7.3.0
2.9.13-GCCcore-11.3.0
2.9.9-GCCcore-8.3.0
libxslt
Description
Libxslt is the XSLT C library developed for the GNOME project (but usable outside of the Gnome platform).
More Information
Available Versions:
1.1.37-GCCcore-12.2.0
1.1.34-GCCcore-11.3.0
1.1.34-GCCcore-10.2.0
1.1.34-GCCcore-9.3.0
1.1.34-GCCcore-11.2.0
1.1.34-GCCcore-10.3.0
1.1.32-GCCcore-7.3.0
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:
1.16.1-GCC-9.3.0
1.17-GCC-11.3.0
1.10-foss-2019b
1.16.1-iccifort-2020.4.304
1.16.1-GCC-10.2.0
1.16.1-iccifort-2020.1.217
1.10-GCC-8.2.0-2.31.1
1.16.2-GCC-10.3.0
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-10.3.0
0.2.5-GCCcore-10.2.0
0.2.2-GCCcore-8.2.0
0.2.2-GCCcore-8.3.0
0.2.5-GCCcore-11.2.0
0.2.2-GCCcore-9.3.0
0.2.5-GCCcore-11.3.0
0.2.5-GCCcore-12.3.0
libzip
Description
libzip is a C library for reading, creating, and modifying zip archives.
More Information
Available Versions:
1.7.3-GCCcore-11.2.0
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
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
lxml
Description
The lxml XML toolkit is a Pythonic binding for the C libraries libxml2 and libxslt.
More Information
Available Versions:
4.6.3-GCCcore-10.3.0
4.6.3-GCCcore-11.2.0
4.5.2-foss-2020a-Python-3.8.2
4.2.5-foss-2018b-Python-2.7.15
4.9.1-GCCcore-11.3.0
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
Available Versions:
1.9.3-GCCcore-11.2.0
1.9.3-GCCcore-10.3.0
1.9.2-GCCcore-9.3.0
1.9.2-GCCcore-8.3.0
1.9.4-GCCcore-12.3.0
1.9.4-GCCcore-12.2.0
1.9.2-GCCcore-10.2.0
1.9.3-GCCcore-11.3.0
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
Available Versions:
2.5.4-fosscuda-2019b
2.6.2-foss-2022a-CUDA-11.7.0
2.5.4-fosscuda-2020b
2.6.2-foss-2022a-CUDA-11.8.0
2.6.2-foss-2021b-CUDA-11.4.1
2.5.1-fosscuda-2019b
2.6.1-foss-2021a-CUDA-11.3.1
make
Description
GNU version of make utility
More Information
https://www.gnu.org/software/make/make.html
Available Versions:
4.3-GCCcore-11.3.0
4.3-GCCcore-11.2.0
4.4.1-GCCcore-12.3.0
4.3-GCCcore-9.3.0
4.3-GCCcore-10.2.0
makeinfo
Description
makeinfo is part of the Texinfo project, the official documentation format of the GNU project.
More Information
https://www.gnu.org/software/texinfo/
Available Versions:
6.8-GCCcore-11.2.0
6.7-GCCcore-10.3.0
6.7-GCCcore-10.3.0-minimal
6.7-GCCcore-9.3.0
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
Available Versions:
3.2.1-intel-2020a-Python-3.8.2
2.2.4-fosscuda-2019b-Python-2.7.16
3.4.3-foss-2021b
3.5.2-foss-2022a
2.2.3-fosscuda-2018b-Python-2.7.15
3.4.2-foss-2021a
2.2.3-foss-2018b-Python-2.7.15
2.2.4-foss-2019b-Python-2.7.16
3.5.2-intel-2022a
3.0.3-foss-2019a-Python-3.7.2
3.1.1-foss-2019b-Python-3.7.4
3.3.3-fosscuda-2020b
3.3.3-foss-2020b
3.5.2-foss-2021b
3.2.1-foss-2020a-Python-3.8.2
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:
0.13.2-GCCcore-12.3.0
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:
2.17-GCC-8.3.0
2.24-GCCcore-11.3.0
2.22-GCCcore-11.2.0
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
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:
1.0.4-GCCcore-10.3.0
module-git
Available Versions:
module-info
Available Versions:
modules
Available Versions:
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-foss-2020a-Python-3.8.2
1.4.5-intel-2020a-Python-3.8.2
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
Available Versions:
2.3.8-GCCcore-11.2.0
2.3.8-foss-2019a
2.3.8-GCCcore-8.3.0
mpi
Available Versions:
openmpi-x86_64
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
Available Versions:
1.0.0-foss-2018b-Python-2.7.15
1.1.0-GCCcore-9.3.0-Python-3.8.2
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
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
2.9.3-foss-2018b
ncdf4
Description
ncdf4: Interface to Unidata netCDF (version 4 or earlier) format data files
More Information
https://cran.r-project.org/web/packages/ncdf4
Available Versions:
1.17-foss-2019b
1.17-foss-2021a-R-4.1.0
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:
6.3-GCCcore-11.3.0
6.1-GCCcore-9.3.0
6.2-GCCcore-10.3.0
6.2-GCCcore-10.2.0
6.1-GCCcore-8.3.0
6.4-GCCcore-12.3.0
6.1-GCCcore-8.2.0
6.3-GCCcore-12.2.0
6.3
6.1-GCCcore-7.3.0
6.2
6.2-GCCcore-11.2.0
6.1
6.1-GCCcore-10.2.0
6.0
6.2-GCCcore-9.3.0
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:
4.8.1-iimpi-2021b
4.7.1-gompi-2019b-dba
4.7.1-gompi-2019b
4.6.2-gompi-2019a
4.7.4-gompic-2020b
4.9.0-iimpi-2022b
4.6.1-foss-2018b
4.7.4-iimpi-2020b
4.9.0-gompi-2022a
4.9.2-gompi-2023a
4.9.0-iimpi-2022a
4.7.4-gompi-2020a
4.7.4-iimpi-2020a
4.7.4-gompi-2020b
4.8.0-gompi-2021a
4.7.1-gompic-2019b
4.8.1-gompi-2021b
4.6.1-fosscuda-2018b
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-iimpi-2020a
4.3.1-gompi-2021a
4.3.1-gompi-2020b
4.3.1-gompi-2021b
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
http://www.unidata.ucar.edu/software/netcdf/
Available Versions:
4.4.4-foss-2018b
4.5.3-gompi-2021b
4.5.3-gompi-2021a
4.6.0-iimpi-2022a
4.5.2-gompi-2019b
4.5.3-iimpi-2021b
4.4.4-fosscuda-2018b
4.6.0-gompi-2022a
4.5.2-gompic-2019b
4.5.3-gompic-2020b
4.5.2-gompi-2019b-dba
4.5.3-iimpi-2020b
4.5.2-iimpi-2020a
4.5.2-gompi-2020a
4.5.3-gompi-2020b
netcdf4-python
Description
Python/numpy interface to netCDF.
More Information
https://unidata.github.io/netcdf4-python/
Available Versions:
1.5.3-foss-2020a-Python-3.8.2
1.6.1-foss-2022a
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:
3.8.1-GCCcore-12.2.0
3.7.3-GCCcore-11.2.0
3.7.2-GCCcore-10.3.0
3.5.1-GCCcore-9.3.0
3.6-GCCcore-10.2.0
3.4.1-GCCcore-8.2.0
3.5.1-GCCcore-8.3.0
3.4-foss-2018b
3.8-GCCcore-11.3.0
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-2020a-Python-3.8.2
2.8.4-foss-2022a
2.5-foss-2020b
2.6.3-foss-2021b
2.2-foss-2018b-Python-2.7.15
2.4-foss-2019b-Python-3.7.4
2.5.1-foss-2021a
2.4-foss-2019a-Python-3.7.2
2.3-foss-2019a-Python-3.7.2
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
nghttp3
Description
nghttp3 is an implementation of RFC 9114 HTTP/3 mapping 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:
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:
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
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
Available Versions:
14.17.0-GCCcore-10.3.0
12.19.0-GCCcore-10.2.0
16.15.1-GCCcore-11.3.0
14.17.6-GCCcore-11.2.0
10.15.1-foss-2020a
nsync
Description
nsync is a C library that exports various synchronization primitives, such as mutexes
More Information
https://github.com/google/nsync
Available Versions:
1.24.0-GCCcore-9.3.0
1.24.0-GCCcore-8.3.0
1.24.0-GCCcore-10.2.0
1.24.0-GCCcore-11.2.0
1.24.0-GCCcore-10.3.0
1.25.0-GCCcore-11.3.0
null
Available Versions:
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
2.0.12-GCCcore-8.2.0
2.0.14-GCCcore-11.2.0
2.0.12-GCCcore-8.3.0
2.0.13-GCCcore-10.2.0
2.0.16-GCCcore-12.2.0
2.0.11-GCCcore-8.1.0
2.0.11-GCCcore-7.3.0
2.0.14-GCCcore-11.3.0
2.0.16-GCCcore-12.3.0
2.0.13-GCCcore-9.3.0
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
Available Versions:
0.56.4-foss-2022a
0.46.0-foss-2019a
0.53.1-foss-2021a
0.53.1-foss-2020b
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-11.3.0
0.24.1-GCCcore-11.2.0
panaroo
Description
A pangenome analysis pipeline.
More Information
https://gtonkinhill.github.io/panaroo/
Available Versions:
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:
20200522-GCCcore-9.3.0
20190622-GCCcore-8.2.0
20190222-GCCcore-7.3.0
20210622-GCCcore-10.3.0
20210322-GCCcore-10.2.0
20220722-GCCcore-11.3.0
20190922-GCCcore-8.3.0
20210722-GCCcore-11.2.0
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-12.3.0
0.12-GCCcore-10.3.0
0.10-GCCcore-8.3.0
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
Available Versions:
2.4-GCCcore-8.3.0
2.7-GCCcore-11.3.0
2.4-GCCcore-7.3.0
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
Available Versions:
0.38.4-GCCcore-8.3.0
0.42.2-GCCcore-12.2.0
0.42.2-GCCcore-12.3.0
0.40.0-GCCcore-10.3.0
0.34.0-GCCcore-7.3.0
0.38.0-GCCcore-8.2.0
0.38.4-GCCcore-9.3.0
0.40.0-GCCcore-11.3.0
0.40.0-GCCcore-11.2.0
0.40.0-GCCcore-10.2.0
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-10.3.0
0.29.2
0.29.2-GCCcore-11.3.0
0.29.2-GCCcore-8.2.0
0.29.2-GCCcore-10.2.0
0.29.2-GCCcore-9.3.0
0.29.2-GCCcore-8.3.0
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:
1.8.0-GCCcore-11.3.0
1.9.5-GCCcore-12.3.0
1.8.0
1.8.0-GCCcore-11.2.0
1.9.3-GCCcore-12.2.0
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:
1.3.1-foss-2018b-Python-2.7.15
1.5.4-GCCcore-10.3.0-python
1.5.5-GCCcore-11.2.0-python
1.5.1-GCCcore-10.2.0-python
1.5.1-GCCcore-8.2.0-python
1.5.1-GCCcore-9.3.0-Python-3.8.2
1.5.1-GCCcore-8.3.0-Python-3.7.4
1.5.5-GCCcore-11.3.0-python
plotly.py
Description
An open-source, interactive graphing library for Python
More Information
Available Versions:
4.8.1-GCCcore-9.3.0
5.4.0-GCCcore-11.2.0
pmi
Available Versions:
pmix-x86_64
pocl
Description
Pocl is a portable open source (MIT-licensed) implementation of the OpenCL standard
More Information
Available Versions:
1.8-GCC-11.3.0
1.6-GCC-10.2.0
1.6-gcccuda-2020b
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
Available Versions:
1.5.1-GCCcore-12.3.0
poppler
Description
Poppler is a PDF rendering library
More Information
https://poppler.freedesktop.org
Available Versions:
22.12.0-GCC-11.3.0
22.01.0-GCC-11.2.0
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
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
https://github.com/hyattpd/Prodigal/
Available Versions:
2.6.3-GCCcore-9.3.0
2.6.3-GCCcore-7.3.0
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-2021a
1.14.5-gompi-2021b
protobuf
Description
Google Protocol Buffers
More Information
https://github.com/google/protobuf/
Available Versions:
3.10.0-GCCcore-8.3.0
3.13.0-GCCcore-9.3.0
3.17.3-GCCcore-11.2.0
3.6.1-GCCcore-7.3.0
3.14.0-GCCcore-10.2.0
3.17.3-GCCcore-10.3.0
3.19.4-GCCcore-11.3.0
protobuf-python
Description
Python Protocol Buffers runtime library.
More Information
https://github.com/google/protobuf/
Available Versions:
3.10.0-fosscuda-2019b-Python-3.7.4
3.13.0-foss-2020a-Python-3.8.2
3.19.4-GCCcore-11.3.0
3.10.0-foss-2019b-Python-3.7.4
3.17.3-GCCcore-11.2.0
3.17.3-GCCcore-10.3.0
3.14.0-GCCcore-10.2.0
3.13.0-fosscuda-2020a-Python-3.8.2
psutil
Description
A cross-platform process and system utilities module for Python
More Information
https://github.com/giampaolo/psutil
Available Versions:
5.6.3-GCCcore-8.2.0
psycopg2
Description
Psycopg is the most popular PostgreSQL adapter for the Python programming language.
More Information
Available Versions:
2.9.5-GCCcore-11.2.0
pugixml
Description
pugixml is a light-weight C++ XML processing library
More Information
Available Versions:
1.12.1-GCCcore-11.2.0
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
pyABC
Description
Massively parallel, distributed and scalable ABC-SMC (Approximate BayesianComputation - Sequential Monte Carlo) for parameter estimation of complexstochastic models. Implemented in Python with support of the R language.
More Information
https://github.com/icb-dcm/pyabc
Available Versions:
0.10.4-foss-2019b-Python-3.7.4
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:
2.6.2-GCCcore-10.3.0
2.4.3-GCCcore-9.3.0-Python-3.8.2
2.9.2-GCCcore-11.3.0
2.6.0-GCCcore-10.2.0
2.11.1-GCCcore-12.3.0
2.4.3-GCCcore-8.3.0-Python-3.7.4
2.10.3-GCCcore-12.2.0
2.7.1-GCCcore-11.2.0
pyfaidx
Description
pyfaidx: efficient pythonic random access to fasta subsequences
More Information
https://pypi.python.org/pypi/pyfaidx
Available Versions:
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
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
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-10.2.0
2.3.0-GCCcore-10.3.0
2.5.0-GCCcore-11.2.0
2.5.0-GCCcore-11.3.0
python-igraph
Description
Python interface to the igraph high performance graph library, primarily aimed at complex network research and analysis.
More Information
Available Versions:
0.9.8-foss-2021b
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
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
Available Versions:
4.0.5-foss-2020a
3.1.1-foss-2020a
3.0.18-foss-2019a
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-8.3.0
1.1.2-GCCcore-11.2.0
rclone
Description
Rclone is a command line program to sync files and directories to and from a variety of online storage services
More Information
Available Versions:
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
Available Versions:
2.0.3-GCCcore-10.2.0
1.3-GCCcore-9.3.0
1.2.1-GCCcore-8.3.0
2.1.1-GCCcore-10.3.0
2.2-GCCcore-11.3.0
2.2-GCCcore-11.2.0
retworkx
Description
retworkx is a general purpose graph library for python3 written in Rust to take advantage of the performance 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 any python application. The project was originally started to build a faster directed graph to use as the underlying data structure for the DAG at the center of qiskit-terras transpiler, but it has since grown to cover all the graph usage in Qiskit and other applications.
More Information
https://retworkx.readthedocs.io/en/latest/index.html
Available Versions:
0.6.0-foss-2020a-Python-3.8.2
0.9.0-foss-2021a
rgdal
Description
Provides bindings to the ‘Geospatial’ Data Abstraction Library (‘GDAL’) (>= 1.11.4 and <= 2.5.0) and access to projection/transformation operations from the ‘PROJ.4’ library.
More Information
https://rgdal.r-forge.r-project.org/
Available Versions:
1.5-23-foss-2021a-R-4.1.0
1.4-8-foss-2020a-R-4.0.2
rose
Available Versions:
2019.01.4
rosetta
Available Versions:
3.10
rpy2
Description
rpy2 is an interface to R running embedded in a Python process.
More Information
Available Versions:
3.2.6-foss-2019b-Python-3.7.4
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-11.2.0
scVelo
Description
scVelo is a scalable toolkit for estimating and analyzing RNA velocities in single cells using dynamical modeling.
More Information
Available Versions:
0.2.3-foss-2021a
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:
0.17.6-GCCcore-12.3.0
0.11.1-GCCcore-10.3.0
0.15.0-GCCcore-11.3.0
0.11.1-foss-2020b
0.11.1-GCCcore-11.2.0
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:
0.5.0-GCCcore-12.3.0
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:
0.24.2-foss-2021a
0.23.1-foss-2020a-Python-3.8.2
1.0.1-foss-2021b
1.1.2-foss-2022a
0.20.3-foss-2019a
0.21.3-foss-2019b-Python-3.7.4
scipy
Description
SciPy is a collection of mathematical algorithms and convenience functions built on the Numpy extension for Python.
More Information
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
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
Available Versions:
1.3-foss-2018b
1.3-GCC-11.2.0
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
shovill
Description
Faster SPAdes assembly of Illumina reads
More Information
https://github.com/tseemann/shovill
Available Versions:
1.1.0-foss-2018b-Python-2.7.15
slepc4py
Description
Python bindings for SLEPc, the Scalable Library for Eigenvalue Problem Computations.
More Information
https://bitbucket.org/slepc/slepc4py
Available Versions:
3.15.1-foss-2021a
3.12.0-foss-2019b-Python-3.7.4
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:
1.1.8-GCCcore-10.3.0
1.1.8-GCCcore-9.3.0
1.1.7-GCCcore-8.3.0
1.1.8-GCCcore-10.2.0
1.1.9-GCCcore-11.2.0
1.1.9-GCCcore-11.3.0
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
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
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:
1.16.0-foss-2020b
2.0.0-foss-2022a
2.1.0-gfbf-2023a
2.0.0-intel-2022a
1.16.1-foss-2021a
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
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
Available Versions:
1.5.1-foss-2019b-Python-3.7.4
1.6.2-foss-2020a-Python-3.8.2
1.4-foss-2019a
1.8-foss-2021a
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:
2018_U5-GCCcore-7.3.0
2020.3-GCCcore-10.3.0
2020.1-GCCcore-9.3.0
2020.3-GCCcore-11.2.0
2020.3-GCCcore-10.2.0
2021.5.0-GCCcore-11.3.0
2019_U9-GCCcore-8.3.0
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:
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
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:
0.16.0-foss-2021b
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
4.1.0-GCCcore-8.2.0
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
Available Versions:
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
Available Versions:
2.3
torchaudio
Description
Data manipulation and transformation for audio signalprocessing, powered by PyTorch
More Information
https://github.com/pytorch/audio
Available Versions:
0.12.0-foss-2022a-PyTorch-1.12.0-CUDA-11.7.0
torchtext
Description
Data loaders and abstractions for text and NLP
More Information
https://github.com/pytorch/text
Available Versions:
0.14.1-foss-2022a-PyTorch-1.12.0
0.7.0-foss-2019b-Python-3.7.4-PyTorch-1.6.0
torchvision
Description
Datasets, Transforms and Models specific to Computer Vision
More Information
https://github.com/pytorch/vision
Available Versions:
0.13.1-foss-2022a-CUDA-11.7.0
0.11.3-foss-2021a-CUDA-11.3.1
tqdm
Description
A fast, extensible progress bar for Python and CLI
More Information
Available Versions:
4.41.1-GCCcore-8.3.0
4.61.2-GCCcore-10.3.0
4.56.2-GCCcore-10.2.0
4.64.0-GCCcore-11.3.0
4.62.3-GCCcore-11.2.0
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:
3.7.4.3-GCCcore-10.2.0
3.10.0.2-GCCcore-11.2.0
4.3.0-GCCcore-11.3.0
3.10.0.0-GCCcore-10.3.0
3.7.4.3-GCCcore-8.3.0-Python-3.7.4
use.own
Available Versions:
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:
2.7.0-GCCcore-11.3.0
2.6.1-GCCcore-11.2.0
2.5.0-GCCcore-10.2.0
util-linux
Description
Set of Linux utilities
More Information
https://www.kernel.org/pub/linux/utils/util-linux
Available Versions:
2.37-GCCcore-11.2.0
2.38.1-GCCcore-12.2.0
2.33-GCCcore-8.2.0
2.35-GCCcore-9.3.0
2.34-GCCcore-9.3.0
2.36-GCCcore-10.3.0
2.38-GCCcore-11.3.0
2.32-GCCcore-7.3.0
2.36-GCCcore-10.2.0
2.34-GCCcore-8.3.0
2.39-GCCcore-12.3.0
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
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
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
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
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
Available Versions:
1.13.1-GCCcore-11.2.0
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
Available Versions:
4.2.0-foss-2021b
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
Available Versions:
3.2.0-GCC-11.2.0
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:
20210414-GCCcore-10.3.0
20230226-GCCcore-12.2.0
20190925-GCCcore-8.3.0
20201026-GCCcore-10.2.0
20230226-GCCcore-12.3.0
20220620-GCCcore-11.3.0
20190413-GCCcore-8.2.0
20191217-GCCcore-9.3.0
20210613-GCCcore-11.2.0
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
Available Versions:
3.3-GCCcore-10.2.0
3.2-GCCcore-8.3.0
3.5-GCCcore-10.3.0
3.5-GCCcore-11.2.0
3.5-GCCcore-12.3.0
3.5-GCCcore-11.3.0
3.0-GCCcore-8.2.0
3.5-GCCcore-12.2.0
3.3-GCCcore-9.3.0
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
1.19.2-GCCcore-10.2.0
1.19.3-GCCcore-12.2.0
1.19.3-GCCcore-11.3.0
1.19.2-GCCcore-7.3.0
1.20.0-GCCcore-12.3.0
1.19.3-GCCcore-11.2.0
1.19.3-GCCcore-10.3.0
1.19.2-GCCcore-9.3.0
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
Available Versions:
1.2.4-GCCcore-8.3.0
1.2.3-GCCcore-7.3.0
1.2.5-GCCcore-11.2.0
1.2.5-GCCcore-10.2.0
xtb
Description
Semiempirical Extended Tight-Binding Program Package.
More Information
https://xtb-docs.readthedocs.io
Available Versions:
6.5.0-foss-2021b
6.3.3-GCCcore-9.3.0
6.4.1-intel-2021a
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
Available Versions:
8.2.4220-GCCcore-11.2.0
8.2.4220-GCCcore-11.3.0
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-foss-2020a-Python-3.8.2
1.6.0-intel-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:
0.7.0-GCCcore-11.3.0
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
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
Available Versions:
1.2.12-GCCcore-12.2.0
1.2.11-GCCcore-7.3.0
1.2.12
1.2.11-GCCcore-8.1.0
1.2.13-GCCcore-13.1.0
1.2.12-GCCcore-11.3.0
1.2.11-GCCcore-10.3.0
1.2.11-GCCcore-11.2.0
1.2.11-GCCcore-10.2.0
1.2.11-intel-2020a
1.2.8
1.2.13-GCCcore-12.3.0
1.2.11-GCCcore-9.3.0
1.2.11
1.2.11-GCCcore-8.3.0
1.2.11-GCCcore-8.2.0
1.2.13
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
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:
1.4.4-GCCcore-8.3.0
1.4.4-GCCcore-9.3.0
1.4.9-GCCcore-10.3.0
1.4.5-GCCcore-10.2.0
1.5.0-GCCcore-11.2.0
1.5.5-GCCcore-12.3.0
1.5.2-GCCcore-11.3.0
1.5.2-GCCcore-12.2.0