ABINIT

Description

ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave or wavelet basis.

More Information

https://www.abinit.org/

Available Versions:

9.4.2-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

http://amos.sourceforge.net

Available Versions:

3.1.0-foss-2018b

ANSYS

Available Versions:

2022R2
2024R1
2022R1
2021R2
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

https://www.antlr2.org/

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

https://apr.apache.org/

Available Versions:

1.7.0-GCCcore-10.2.0
1.7.0-GCCcore-11.3.0
1.7.0-GCCcore-11.2.0

APR-util

Description

Apache Portable Runtime (APR) util libraries.

More Information

https://apr.apache.org/

Available Versions:

1.6.1-GCCcore-11.2.0
1.6.1-GCCcore-10.2.0
1.6.1-GCCcore-11.3.0

ASE

Description

ASE is a python package providing an open source Atomic Simulation Environment in the Python scripting language.From version 3.20.1 we also include the ase-ext package, it contains optional reimplementationsin C of functions in ASE. ASE uses it automatically when installed.

More Information

https://wiki.fysik.dtu.dk/ase

Available Versions:

3.22.1-foss-2022a
3.22.1-intel-2022a
3.22.0-foss-2021a
3.20.1-foss-2020b

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/stable/

Available Versions:

2.28.1-foss-2018b
2.34.1-GCCcore-8.3.0
2.38.0-GCCcore-12.3.0
2.38.0-GCCcore-12.2.0
2.36.0-GCCcore-9.3.0
2.36.0-GCCcore-10.2.0
2.32.0-GCCcore-8.2.0
2.38.0-GCCcore-11.3.0
2.36.0-GCCcore-11.2.0

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

Abseil

Description

Abseil is an open-source collection of C++ library code designed to augment theC++ standard library. The Abseil library code is collected from Google’s ownC++ code base, has been extensively tested and used in production, and is thesame code we depend on in our daily coding lives.

More Information

https://abseil.io/

Available Versions:

20230125.3-GCCcore-12.3.0

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 nosimilar structure is known.This package of AlphaFold contains patches for ColabFold.

More Information

https://github.com/sokrypton/alphafold

Available Versions:

2.3.4-foss-2022a-ColabFold
2.2.2-foss-2021a-CUDA-11.3.1
2.0.0-fosscuda-2020b
2.3.4-foss-2022a-CUDA-11.7.0-ColabFold
2.3.1-foss-2022a
2.1.1-fosscuda-2020b
2.3.1-foss-2022a-CUDA-11.7.0
2.3.0-foss-2021b-CUDA-11.4.1

Amber

Description

Amber (originally Assisted Model Building with Energy Refinement) is software for performing molecular dynamics and structure prediction.

More Information

https://ambermd.org

Available Versions:

18-fosscuda-2019b-AmberTools-19-patchlevel-12-17-Python-2.7.16
18-foss-2018b-AmberTools-18-patchlevel-10-8
22.0-foss-2021b-AmberTools-22.3
22.0-foss-2021b-AmberTools-22.0
18-fosscuda-2018b-AmberTools-18-patchlevel-10-8
18-foss-2019b-AmberTools-19-patchlevel-12-17-Python-2.7.16
22.4-foss-2022a-AmberTools-22.5-CUDA-11.7.0

AmberTools

Description

AmberTools consists of several independently developed packages that work well by themselves, and with Amber itself. The suite can also be used to carry out complete molecular dynamics simulations, with either explicit water or generalized Born solvent models.

More Information

https://ambermd.org/

Available Versions:

20-intel-2020a-Python-3.8.2
20-gompi-2019b-dba-Python-3.7.4
22.3-foss-2021b

Anaconda2

Description

Built to complement the rich, open source Python community,the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture.

More Information

https://www.anaconda.com

Available Versions:

2019.10
2019.03
4.2.0

Anaconda3

Description

Built to complement the rich, open source Python community,the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture.

More Information

https://www.anaconda.com

Available Versions:

2021.11
2021.05
2020.11
2022.05
2020.02
2022.10
2023.09-0

Armadillo

Description

Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions.

More Information

https://arma.sourceforge.net/

Available Versions:

9.900.1-foss-2020a
12.6.2-foss-2023a

Arriba

Description

Arriba is a command-line tool for the detection of gene fusions from RNA-Seq data. It was developed for the use in a clinical research setting. Therefore, short runtimes and high sensitivity were important design criteria.

More Information

https://github.com/suhrig/arriba

Available Versions:

2.3.0-GCC-11.2.0

Arrow

Description

Apache Arrow (incl. PyArrow Python bindings), a cross-language development platform for in-memory data.

More Information

https://arrow.apache.org

Available Versions:

8.0.0-foss-2022a
14.0.1-gfbf-2023a
0.16.0-foss-2019b-Python-3.7.4
6.0.0-foss-2021b
8.0.0-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

https://asperasoft.com

Available Versions:

3.9.6.1467.159c5b1

Aspera-Connect

Description

Connect is an install-on-demand Web browser plug-in that facilitates high-speed uploads and downloads with an Aspera transfer server.

More Information

http://downloads.asperasoft.com/connect2/

Available Versions:

3.9.6

AutoDock

Description

AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.

More Information

http://autodock.scripps.edu/

Available Versions:

4.2.6-GCC-9.3.0

AutoDock-GPU

Description

OpenCL and Cuda accelerated version of AutoDock. It leverages its embarrasinglyparallelizable LGA by processing ligand-receptor poses in parallel overmultiple compute units.AutoDock is a suite of automated docking tools. It is designed to predict howsmall molecules, such as substrates or drug candidates, bind to a receptor ofknown 3D structure.

More Information

https://github.com/ccsb-scripps/AutoDock-GPU

Available Versions:

1.5.3-GCC-11.3.0-CUDA-11.7.0

AutoDock-Vina

Description

AutoDock Vina is an open-source program for doing molecular docking.

More Information

https://vina.scripps.edu/

Available Versions:

1.2.3-foss-2021b

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:

2.69-GCCcore-8.3.0
2.69
2.69-GCCcore-9.3.0
2.69-GCCcore-8.2.0
2.69-GCCcore-7.3.0
2.69-GCCcore-8.1.0
2.69-GCCcore-10.2.0
2.71-GCCcore-12.3.0
2.71-GCCcore-12.2.0
2.71
2.71-GCCcore-11.3.0
2.71-GCCcore-11.2.0
2.71-GCCcore-10.3.0

Automake

Description

Automake: GNU Standards-compliant Makefile generator

More Information

https://www.gnu.org/software/automake/automake.html

Available Versions:

1.16.1-GCCcore-8.3.0
1.16.1-GCCcore-10.2.0
1.16.5
1.16.4-GCCcore-11.2.0
1.16.1-GCCcore-7.3.0
1.16.3-GCCcore-10.3.0
1.16.1-GCCcore-8.2.0
1.16.5-GCCcore-12.3.0
1.16.2-GCCcore-10.2.0
1.16.1-GCCcore-8.1.0
1.16.1-GCCcore-9.3.0
1.16.5-GCCcore-12.2.0
1.15.1-GCCcore-8.3.0
1.16.5-GCCcore-11.3.0

Autotools

Description

This bundle collect the standard GNU build tools: Autoconf, Automake and libtool

More Information

https://autotools.io

Available Versions:

20180311-GCCcore-9.3.0
20210128-GCCcore-10.3.0
20200321-GCCcore-10.2.0
20180311-GCCcore-8.1.0
20180311-GCCcore-10.2.0
20220317-GCCcore-12.2.0
20180311-GCCcore-7.3.0
20220317-GCCcore-12.3.0
20180311-GCCcore-8.3.0
20220317
20180311-GCCcore-8.2.0
20210726-GCCcore-11.2.0
20220317-GCCcore-11.3.0

BAGEL

Description

BAGEL (Brilliantly Advanced General Electronic-structure Library)is a parallel electronic-structure program.

More Information

http://www.nubakery.org

Available Versions:

1.2.2-foss-2019a
1.2.2-intel-2020a

BCFtools

Description

Samtools is a suite of programs for interacting with high-throughput sequencing data. BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants

More Information

https://www.htslib.org/

Available Versions:

1.11-GCC-10.2.0
1.9-foss-2018b
1.10.2-GCC-9.3.0
1.10.2-GCC-8.3.0
1.14-GCC-11.2.0

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-11.2.0
2.30.0-GCC-11.3.0
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:

2.11.0-Linux_x86_64
2.10.1-Linux_x86_64

BLAST+

Description

Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences.

More Information

https://blast.ncbi.nlm.nih.gov/

Available Versions:

2.9.0-gompi-2019b
2.13.0-gompi-2022a
2.7.1-foss-2018b
2.10.1-iimpi-2020a
2.12.0-gompi-2021b
2.11.0-gompi-2020b
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
0.9.0-GCC-12.2.0
0.8.1-GCC-11.2.0
0.9.0-GCC-12.3.0

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-GCCcore-11.2.0
0.7.17-foss-2018b

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:

2.5.2-GCC-11.2.0
2.5.1-GCC-8.3.0
2.5.2-GCC-11.3.0
2.5.1-GCC-10.2.0
2.5.1-GCC-9.3.0

BayeScEnv

Description

BayeScEnv is a Fst-based, genome-scan method that uses environmental variables to detectlocal adaptation.

More Information

https://github.com/devillemereuil/bayescenv

Available Versions:

1.1-GCC-8.3.0

BayesTraits

Description

BayesTraits is a computer package for performing analyses of trait evolution among groups of species for which a phylogeny or sample of phylogenies is available. This new package incoporates our earlier and separate programes Multistate, Discrete and Continuous. BayesTraits can be applied to the analysis of traits that adopt a finite number of discrete states, or to the analysis of continuously varying traits. Hypotheses can be tested about models of evolution, about ancestral states and about correlations among pairs of traits.

More Information

http://www.evolution.reading.ac.uk/BayesTraitsV1.html

Available Versions:

2.0-Beta-Linux64

Bazel

Description

Bazel is a build tool that builds code quickly and reliably.It is used to build the majority of Google’s software.

More Information

https://bazel.io/

Available Versions:

5.1.1-GCCcore-11.3.0
5.3.0-GCCcore-11.3.0
3.6.0-GCCcore-9.3.0
3.7.2-GCCcore-10.3.0
0.26.1-GCCcore-8.3.0
3.7.2-GCCcore-11.2.0
0.29.1-GCCcore-8.3.0
6.1.0-GCCcore-12.2.0
4.2.2-GCCcore-11.2.0
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

http://beast2.org/

Available Versions:

2.5.2-GCC-8.2.0-2.31.1
2.7.3-GCC-11.3.0
2.5.2-GCC-7.3.0-2.30

BeautifulSoup

Description

Beautiful Soup is a Python library designed for quick turnaround projects like screen-scraping.

More Information

https://www.crummy.com/software/BeautifulSoup

Available Versions:

4.10.0-GCCcore-11.3.0
4.12.2-GCCcore-12.3.0

Bio-SearchIO-hmmer

Description

Code to parse output from hmmsearch, hmmscan, phmmer and nhmmer, compatiblewith both version 2 and version 3 of the HMMER package from http://hmmer.org.

More Information

https://metacpan.org/pod/Bio::SearchIO::hmmer3

Available Versions:

1.7.3-GCC-11.2.0
1.7.3-GCC-10.3.0

BioPerl

Description

Bioperl is the product of a community effort to produce Perl code which is useful in biology. Examples include Sequence objects, Alignment objects and database searching objects.

More Information

https://bioperl.org/

Available Versions:

1.7.8-GCCcore-11.2.0
1.7.8-GCCcore-10.3.0
1.7.8-GCCcore-11.3.0
1.7.7-GCCcore-9.3.0

Biopython

Description

Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics.

More Information

https://www.biopython.org

Available Versions:

1.79-foss-2022a
1.79-foss-2021b
1.78-intel-2020a-Python-3.8.2
1.79-foss-2021a
1.78-fosscuda-2020b
1.75-foss-2019b-Python-3.7.4
1.72-foss-2018b-Python-2.7.15

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
3.8.2
3.0.5-GCCcore-8.1.0
3.0.5-GCCcore-7.3.0
3.3.2-GCCcore-9.3.0
3.8.2-GCCcore-13.1.0
3.0.5-GCCcore-8.3.0
3.0.5
3.7.6-GCCcore-11.2.0
3.8.2-GCCcore-13.2.0
3.5.3-GCCcore-9.3.0
3.3.2-GCCcore-8.3.0
3.0.4-GCCcore-8.1.0
3.7.1
3.0.4-GCCcore-7.3.0
3.0.5-GCCcore-8.2.0
3.7.1-GCCcore-10.2.0
3.7.6
3.0.4
3.3.2
3.8.2-GCCcore-12.3.0
3.8.2-GCCcore-12.2.0
3.8.2-GCCcore-11.3.0
3.7.6-GCCcore-10.3.0

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

https://www.blender.org/

Available Versions:

2.81-foss-2019b-Python-3.7.4

Blosc

Description

Blosc, an extremely fast, multi-threaded, meta-compressor library

More Information

https://www.blosc.org/

Available Versions:

1.21.0-GCCcore-10.3.0
1.21.3-GCCcore-11.3.0

Blosc2

Description

Blosc, an extremely fast, multi-threaded, meta-compressor library

More Information

https://www.blosc.org/

Available Versions:

2.6.1-GCCcore-11.3.0

Bonnie++

Description

Enhanced performance Test of Filesystem I/O

More Information

https://www.coker.com.au/bonnie++

Available Versions:

2.00a-GCC-10.3.0

Boost

Description

Boost provides free peer-reviewed portable C++ source libraries.

More Information

https://www.boost.org/

Available Versions:

1.82.0-GCC-12.3.0
1.70.0-gompi-2019a
1.77.0-GCC-11.2.0
1.72.0-iimpi-2021b
1.67.0-fosscuda-2018b
1.74.0-GCC-10.2.0
1.77.0-intel-compilers-2021.4.0
1.72.0-iimpi-2020a
1.71.0-gompic-2019b
1.79.0-GCC-11.2.0
1.76.0-GCC-10.3.0
1.67.0-foss-2018b
1.81.0-GCC-12.2.0
1.74.0-iccifort-2020.4.304
1.72.0-gompi-2020a
1.79.0-GCC-11.3.0
1.71.0-gompi-2019b

Boost.MPI

Description

Boost provides free peer-reviewed portable C++ source libraries.

More Information

https://www.boost.org/

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

https://boostorg.github.io/python

Available Versions:

1.72.0-gompi-2020a
1.67.0-fosscuda-2018b-Python-2.7.15
1.71.0-gompic-2019b
1.77.0-GCC-11.2.0
1.70.0-gompi-2019a
1.67.0-foss-2018b-Python-2.7.15
1.71.0-gompi-2019b

Bowtie

Description

Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome.

More Information

http://bowtie-bio.sourceforge.net/index.shtml

Available Versions:

1.2.3-GCC-9.3.0
1.3.1-GCC-11.2.0

Bowtie2

Description

Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.

More Information

http://bowtie-bio.sourceforge.net/bowtie2/index.shtml

Available Versions:

2.3.5.1-GCC-8.3.0
2.4.1-GCC-9.3.0
2.4.4-GCC-10.3.0
2.4.5-GCC-11.2.0
2.4.4-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-12.2.0
1.0.9-GCCcore-11.2.0
1.0.9-GCCcore-11.3.0

Brunsli

Description

Brunsli is a lossless JPEG repacking library.

More Information

https://github.com/google/brunsli/

Available Versions:

0.1-GCCcore-11.3.0
0.1-GCCcore-12.3.0

CASA

Description

CASA, the Common Astronomy Software Applications package, is the primary data processing software for the Atacama LargeMillimeter/submillimeter Array (ALMA) and NSF’s Karl G. Jansky Very Large Array (VLA), and is frequently used also forother radio telescopes. The CASA software can process data from both single-dish and aperture-synthesis telescopes, andone of its core functionalities is to support the data reduction and imaging pipelines for ALMA, VLA and the VLA SkySurvey (VLASS).

More Information

https://casa.nrao.edu/

Available Versions:

6.5.5-21-py3.8

CASTEP

Description

CASTEP is a leading code for calculating the properties of materials from first principles. Using density functional theory, it can simulate a wide range of properties of materialsproprieties including energetics, structure at the atomic level, vibrational properties, electronic response properties etc. In particular it has a wide range of spectroscopic features that link directly to experiment, such as infra-red and Raman spectroscopies, NMR, and core level spectra.

More Information

http://www.castep.org

Available Versions:

21.11-info
16.11-info
16.11-intel-2020a

CCL

Description

Clozure CL (often called CCL for short) is a free Common Lisp implementation with a long history. Some distinguishing features of the implementation include fast compilation speed, native threads, a precise, generational, compacting garbage collector, and a convenient foreign-function interface.

More Information

https://ccl.clozure.com/

Available Versions:

1.12.2-GCCcore-11.3.0

CD-HIT

Description

CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences.

More Information

http://weizhongli-lab.org/cd-hit/

Available Versions:

4.8.1-GCC-10.2.0
4.8.1-GCC-11.2.0
4.8.1-GCC-11.3.0
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
2-foss-2022a

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:

3.47-GCCcore-8.3.0
4.2.0-GCCcore-11.3.0
3.49-GCCcore-11.2.0
3.48-GCCcore-9.3.0
4.3.0-GCCcore-11.3.0
4.3.0-GCCcore-12.3.0
3.49-GCCcore-10.2.0

CGAL

Description

The goal of the CGAL Open Source Project is to provide easy access to efficient and reliable geometric algorithms in the form of a C++ library.

More Information

https://www.cgal.org/

Available Versions:

4.14.3-gompi-2022a
4.14.1-foss-2019b-Python-3.7.4
5.6-GCCcore-12.3.0
5.2-gompi-2020b
4.14.3-gompi-2020a-Python-3.8.2
4.14.3-gompi-2021a
4.14.3-iimpi-2020a-Python-3.8.2

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:

2.4.5.1-GCC-11.2.0
2.4.4.0-GCC-10.2.0
2.4.6.4-GCC-12.2.0
2.4.6.2-GCC-11.2.0

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

https://www.cmake.org

Available Versions:

3.21.1-GCCcore-11.2.0
3.12.1-GCCcore-7.3.0
3.13.3-GCCcore-8.2.0
3.15.3-GCCcore-8.3.0
3.12.1
3.12.1-GCCcore-10.2.0
3.20.1-GCCcore-10.3.0
3.24.3-GCCcore-12.2.0
3.15.3-GCCcore-7.3.0
3.24.3-GCCcore-11.3.0
3.11.4-GCCcore-7.3.0
3.18.4-GCCcore-10.2.0
3.9.4-GCCcore-9.3.0
3.26.3-GCCcore-12.3.0
3.22.1-GCCcore-11.2.0
3.18.4
3.23.1-GCCcore-11.3.0
3.16.4-GCCcore-9.3.0

CP2K

Description

CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and classical pair and many-body potentials.

More Information

http://www.cp2k.org/

Available Versions:

6.1-foss-2020a
2023.1-foss-2023a
6.1-foss-2019b
6.1-foss-2019a
6.1-intel-2020a
8.1-foss-2020a
7.1-intel-2020a
8.2-foss-2021a
9.1-foss-2022a
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:

11.7.0
11.2.2
11.4.1
11.8.0
11.1.1-GCC-10.2.0
10.1.243-GCC-8.3.0
11.5.0
11.0.2-GCC-9.3.0
10.1.243-iccifort-2019.5.281
11.4.1-GCC-10.3.0
11.5.1
11.2.2-GCC-10.3.0
9.2.88-GCC-7.3.0-2.30
11.1.1-iccifort-2020.4.304
11.3.1
11.3.1-GCC-10.3.0
12.0.0
11.6.0

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-11.2.0
2.1-3-GCCcore-11.3.0

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

http://cvxopt.org

Available Versions:

1.2.4-foss-2020a-Python-3.8.2
1.2.6-foss-2021a
1.2.3-foss-2019a
1.2.4-foss-2020a

Cactus

Description

Cactus is a reference-free whole-genome alignment program, as well as a pagenome graph construction toolkit.

More Information

https://github.com/ComparativeGenomicsToolkit/cactus

Available Versions:

2.4.0

CapnProto

Description

Cap’n Proto is an insanely fast data interchange format and capability-based RPC system.

More Information

https://capnproto.org

Available Versions:

0.7.0-GCCcore-7.3.0

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

CellProfiler

Description

CellProfiler is free, open-source software for quantitative analysis of biological images. No prior experience in programming or computer vision is required

More Information

http://cellprofiler.org

Available Versions:

4.2.1
4.2.6

CellRanger

Description

Cell Ranger is a set of analysis pipelines that process Chromium single-cell RNA-seq output to align reads, generate gene-cell matrices and perform clustering and gene expression analysis.

More Information

https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger

Available Versions:

7.0.1
5.0.0
7.0.0
6.0.2

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

https://www.cellpose.org

Available Versions:

2.2.2-foss-2022a

Cereal

Description

cereal is a header-only C++11 serialization library. cereal takes arbitrary data types and reversibly turns them into different representations, such as compact binary encodings, XML, or JSON. cereal was designed to befast, light-weight, and easy to extend - it has no external dependencies and can be easily bundled with other code or used standalone.

More Information

https://uscilab.github.io/cereal/

Available Versions:

1.3.2

CharLS

Description

CharLS is a C++ implementation of the JPEG-LS standard for lossless and near-lossless imagecompression and decompression. JPEG-LS is a low-complexity image compression standard that matches JPEG 2000compression ratios.

More Information

https://github.com/team-charls/charls

Available Versions:

2.4.1-GCCcore-11.3.0

CheMPS2

Description

CheMPS2 is a scientific library which contains a spin-adapted implementation of thedensity matrix renormalization group (DMRG) for ab initio quantum chemistry.

More Information

https://github.com/SebWouters/CheMPS2

Available Versions:

1.8.11-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-11.2.0
0.15.2-GCCcore-10.3.0
0.15.2-GCCcore-9.3.0
0.15.2-GCCcore-10.2.0

Clang

Description

C, C++, Objective-C compiler, based on LLVM. Does not include C++ standard library – use libstdc++ from GCC.

More Information

https://clang.llvm.org/

Available Versions:

11.0.1-gcccuda-2020b
16.0.0-GCCcore-11.3.0
11.0.1-GCCcore-10.2.0
13.0.1-GCCcore-11.3.0
16.0.0-GCCcore-12.2.0
12.0.1-GCCcore-11.2.0

ClermonTyping

Available Versions:

2023

ClonalFrameML

Description

Efficient Inference of Recombination in Whole Bacterial Genomes

More Information

https://github.com/xavierdidelot/ClonalFrameML

Available Versions:

1.12-foss-2022a

ClustalW2

Description

ClustalW2 is a general purpose multiple sequence alignment program for DNA or proteins.

More Information

https://www.ebi.ac.uk/Tools/msa/clustalw2/

Available Versions:

2.1-intel-2020a

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

https://cupy.dev

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:

4.4.3-GCCcore-9.3.0
4.8-GCCcore-11.3.0

Cython

Description

Cython is an optimising static compiler for both the Python programminglanguage and the extended Cython programming language (based on Pyrex).

More Information

https://cython.org/

Available Versions:

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
18.1.32-GCCcore-9.3.0
18.1.40-GCCcore-10.3.0
18.1.40-GCCcore-11.3.0
18.1.40-GCCcore-12.2.0
18.1.40-GCCcore-12.3.0
18.1.40-GCCcore-10.2.0
18.1.32-GCCcore-7.3.0
18.1.40-GCCcore-11.2.0
18.1.32-GCCcore-8.2.0

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

https://dbus.freedesktop.org/

Available Versions:

1.13.12-GCCcore-9.3.0
1.13.8-GCCcore-8.2.0
1.13.18-GCCcore-10.3.0
1.13.18-GCCcore-11.2.0
1.13.18-GCCcore-10.2.0
1.15.2-GCCcore-12.2.0
1.14.0-GCCcore-11.3.0
1.13.12-GCCcore-8.3.0
1.15.4-GCCcore-12.3.0
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

https://dials.github.io

Available Versions:

3.11.2

DIAMOND

Description

DIAMOND is a sequence aligner for protein and translated DNA searches, designed for high performance analysis of big sequence data.

More Information

https://github.com/bbuchfink/diamond

Available Versions:

0.9.30-GCC-8.3.0
2.1.6-GCC-11.3.0
0.9.30-iccifort-2019.5.281
2.0.15-GCC-11.3.0

DL_POLY_4

Description

DL_POLY is a general purpose classical molecular dynamics (MD) simulation software

More Information

https://www.scd.stfc.ac.uk/Pages/DL_POLY.aspx

Available Versions:

5.0.0-intel-2020b

DL_POLY_Classic

Description

DL_POLY Classic is a general purpose (parallel and serial)molecular dynamics simulation package.

More Information

https://gitlab.com/DL_POLY_Classic/dl_poly

Available Versions:

1.10-foss-2019b

DOLFIN

Description

DOLFIN is the C++/Python interface of FEniCS, providing a consistent PSE (Problem Solving Environment) for ordinary and partial differential equations.

More Information

https://bitbucket.org/fenics-project/dolfin

Available Versions:

2019.1.0.post0-foss-2019b-Python-3.7.4

DendroPy

Description

A Python library for phylogenetics and phylogenetic computing: reading, writing, simulation, processing and manipulation of phylogenetic trees (phylogenies) and characters.

More Information

https://dendropy.org/

Available Versions:

4.5.2-GCCcore-11.2.0

Doxygen

Description

Doxygen is a documentation system for C++, C, Java, Objective-C, Python, IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D.

More Information

https://www.doxygen.org

Available Versions:

1.8.16-GCCcore-8.3.0
1.8.20-GCCcore-10.2.0
1.9.1-GCCcore-11.2.0
1.8.15-GCCcore-8.2.0
1.9.7-GCCcore-12.3.0
1.9.4-GCCcore-11.3.0
1.8.17-GCCcore-9.3.0
1.8.14-GCCcore-7.3.0
1.9.1-GCCcore-10.3.0
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

https://elpa.rzg.mpg.de

Available Versions:

2019.11.001-intel-2020a
2019.11.001-foss-2020a
2020.11.001-intel-2020b
2020.11.001-foss-2020b
2021.11.001-foss-2022a
2021.11.001-intel-2022a
2021.05.001-intel-2021a

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
8.3.0-foss-2022a

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:

4.6.0
4.6.2
4.4.1
4.3.4
4.8.1
4.5.2
4.7.2
4.3.3
4.8.2
4.3.1
4.5.3
4.3.2
4.5.1
4.5.5
4.4.2
4.7.1
4.8.0
4.7.0
4.6.1
4.9.1
4.9.0
4.5.4
4.4.0
4.5.0

Eigen

Description

Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.

More Information

https://eigen.tuxfamily.org

Available Versions:

3.3.7-GCCcore-9.3.0
3.4.0-GCCcore-10.2.0
3.3.8-GCCcore-10.2.0
3.4.0-GCCcore-12.3.0
3.3.9-GCCcore-10.3.0
3.3.7
3.3.4
3.4.0-GCCcore-11.3.0
3.4.0-GCCcore-9.3.0
3.4.0-GCCcore-12.2.0
3.4.0-GCCcore-10.3.0
3.4.0-GCCcore-11.2.0
3.3.9-GCCcore-11.2.0

Elk

Description

An all-electron full-potential linearisedaugmented-plane wave (FP-LAPW) code with many advanced features. Writtenoriginally at Karl-Franzens-Universität Graz as a milestone of theEXCITING EU Research and Training Network, the code is designed to be assimple as possible so that new developments in the field of densityfunctional theory (DFT) can be added quickly and reliably.

More Information

http://elk.sourceforge.net/

Available Versions:

7.0.12-foss-2020b

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:

2019.09.0
2.3.1

FEniCS

Description

FEniCS is a computing platform for solving partial differential equations (PDEs).

More Information

https://fenicsproject.org/

Available Versions:

2019.1.0-foss-2019b-Python-3.7.4

FFC

Description

The FEniCS Form Compiler (FFC) is a compiler for finite element variational forms.

More Information

https://bitbucket.org/fenics-project/ffc

Available Versions:

2019.1.0.post0-foss-2019b-Python-3.7.4

FFTW

Description

FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data.

More Information

http://www.fftw.org

Available Versions:

3.3.8-intel-2020b
3.3.8-gompi-2020a
3.3.8-intel-2020a
3.3.10-gompi-2021b
3.3.8-gompi-2019a
3.3.10-GCC-12.3.0
3.3.8-gompi-2018b
3.3.8-gompi-2020b
3.3.8-gompic-2020b
3.3.8-gompic-2020a
3.3.10-GCC-12.2.0
3.3.8-gompi-2019b
3.3.8-gompic-2018b
3.3.10-GCC-11.3.0
3.3.9-intel-2021a
3.3.9-gompi-2021a
3.3.8-gompic-2019b

FFTW.MPI

Description

FFTW is a C subroutine library for computing the discrete Fourier transform (DFT)in one or more dimensions, of arbitrary input size, and of both real and complex data.

More Information

https://www.fftw.org

Available Versions:

3.3.10-gompi-2023a
3.3.10-gompi-2022a
3.3.10-gompi-2022b

FFmpeg

Description

A complete, cross-platform solution to record, convert and stream audio and video.

More Information

https://www.ffmpeg.org/

Available Versions:

4.4.2-GCCcore-11.3.0
4.2.2-GCCcore-9.3.0
6.0-GCCcore-12.3.0
4.3.2-GCCcore-10.3.0
4.2.1-GCCcore-8.3.0
4.3.1-GCCcore-10.2.0
4.3.2-GCCcore-11.2.0
4.1.3-GCCcore-8.2.0
5.1.2-GCCcore-12.2.0

FIAT

Description

The FInite element Automatic Tabulator (FIAT) supportsgeneration of arbitrary order instances of the Lagrange elements onlines, triangles, and tetrahedra. It is also capable of generatingarbitrary order instances of Jacobi-type quadrature rules on the sameelement shapes.

More Information

https://bitbucket.org/fenics-project/fiat

Available Versions:

2019.1.0-foss-2019b-Python-3.7.4

FLAC

Description

FLAC stands for Free Lossless Audio Codec, an audio format similar to MP3, but lossless, meaningthat audio is compressed in FLAC without any loss in quality.

More Information

https://xiph.org/flac/

Available Versions:

1.3.3-GCCcore-10.2.0
1.4.2-GCCcore-12.3.0
1.4.2-GCCcore-12.2.0
1.3.3-GCCcore-11.2.0
1.3.4-GCCcore-11.3.0
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

https://www.flintlib.org/

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

https://www.fltk.org

Available Versions:

1.3.5-GCCcore-10.2.0
1.3.7-GCCcore-11.2.0
1.3.5-GCC-8.3.0

FSL

Description

FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.

More Information

https://www.fmrib.ox.ac.uk/fsl/

Available Versions:

6.0.4-foss-2019b-Python-3.7.4
6.0.5.2-ARC
6.0.3-foss-2019b-Python-3.7.4
6.0.5.1-foss-2021a
6.0.6.4-ARC

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-11.3.0
2.1.11-GCCcore-9.3.0

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

https://fiji.sc/

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:

3.3.1-GCC-12.3.0
3.2.1-GCC-12.2.0
3.2.0-GCC-11.3.0
3.0.4-GCC-10.3.0
3.0.4-GCC-11.2.0

Fluka

Available Versions:

4-4.0

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-11.2.0
1.0.5-GCCcore-8.3.0
1.0.6-GCCcore-12.3.0

FriBidi

Description

The Free Implementation of the Unicode Bidirectional Algorithm.

More Information

https://github.com/fribidi/fribidi

Available Versions:

1.0.5-GCCcore-8.2.0
1.0.9-GCCcore-9.3.0
1.0.5-GCCcore-7.3.0
1.0.12-GCCcore-12.3.0
1.0.12-GCCcore-12.2.0
1.0.10-GCCcore-11.2.0
1.0.5-GCCcore-8.3.0
1.0.10-GCCcore-10.2.0
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

https://www.broadinstitute.org/gatk/

Available Versions:

4.1.5.0-GCCcore-9.3.0-Java-1.8
3.8-1-Java-1.8.0_241
4.1.8.1-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

https://gcc.gnu.org/

Available Versions:

10.2.0
13.1.0
11.2.0
11.3.0
8.3.0
12.3.0
8.2.0-2.31.1
7.3.0-2.30
9.3.0
12.2.0
8.1.0-2.30
10.3.0

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

https://gcc.gnu.org/

Available Versions:

11.2.0
8.3.0
12.2.0
8.1.0
13.1.0
7.3.0
11.3.0
9.3.0
8.2.0
12.1.0
12.3.0
10.3.0
10.2.0
13.2.0
11.2.0-multilib

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

https://www.gdal.org

Available Versions:

3.0.4-intel-2020a-Python-3.8.2
3.5.0-foss-2022a
3.7.1-foss-2023a-spatialite
3.3.2-foss-2021b
3.0.4-foss-2020a-Python-3.8.2
3.2.1-fosscuda-2020b
3.3.0-foss-2021a
3.7.1-foss-2023a
3.0.0-foss-2019a-Python-2.7.15

GDRCopy

Description

A low-latency GPU memory copy library based on NVIDIA GPUDirect RDMA technology.

More Information

https://github.com/NVIDIA/gdrcopy

Available Versions:

2.2-GCCcore-10.3.0
2.1-GCCcore-9.3.0-CUDA-11.0.2
2.1-GCCcore-10.3.0-CUDA-11.1.1
2.3-GCCcore-11.3.0
2.3-GCCcore-11.2.0
2.1-GCCcore-10.2.0-CUDA-11.1.1

GEOS

Description

GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)

More Information

http://trac.osgeo.org/geos

Available Versions:

3.6.2-foss-2018b-Python-2.7.15
3.10.3-GCC-11.3.0
3.9.1-GCC-10.3.0
3.8.1-GCC-9.3.0-Python-3.8.2
3.12.0-GCC-12.3.0
3.7.2-foss-2019a-Python-2.7.15
3.9.1-GCC-10.2.0
3.8.0-GCC-8.3.0-Python-3.7.4
3.8.1-iccifort-2020.1.217-Python-3.8.2
3.9.1-GCC-11.2.0

GL2PS

Description

GL2PS: an OpenGL to PostScript printing library

More Information

https://www.geuz.org/gl2ps/

Available Versions:

1.4.0-GCCcore-8.3.0
1.4.2-GCCcore-10.2.0
1.4.2-GCCcore-11.2.0

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

https://github.com/g-truc/glm

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:

4.65-GCCcore-10.2.0
4.65-GCCcore-8.3.0
5.0-GCCcore-10.3.0
5.0-GCCcore-11.2.0
5.0-GCCcore-12.3.0
5.0-GCCcore-12.2.0
4.65-GCCcore-9.3.0
5.0-GCCcore-11.3.0

GLib

Description

GLib is one of the base libraries of the GTK+ project

More Information

https://www.gtk.org/

Available Versions:

2.69.1-GCCcore-11.2.0
2.77.1-GCCcore-12.3.0
2.64.1-GCCcore-9.3.0
2.72.1-GCCcore-11.3.0
2.62.0-GCCcore-8.3.0
2.68.2-GCCcore-10.3.0
2.66.1-GCCcore-10.2.0
2.60.1-GCCcore-8.2.0
2.75.0-GCCcore-12.2.0
2.54.3-GCCcore-7.3.0

GLibmm

Description

C++ bindings for Glib

More Information

https://www.gtk.org/

Available Versions:

2.49.7-GCCcore-8.3.0
2.66.4-GCCcore-10.3.0

GMAP-GSNAP

Description

GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences GSNAP: Genomic Short-read Nucleotide Alignment Program

More Information

http://research-pub.gene.com/gmap/

Available Versions:

2019-09-12-GCC-8.3.0

GMP

Description

GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers.

More Information

https://gmplib.org/

Available Versions:

6.1.2-GCCcore-8.2.0
6.2.1-GCCcore-10.3.0
6.1.2-GCCcore-10.2.0
6.2.0-GCCcore-9.3.0
6.1.2-GCCcore-7.3.0
6.2.1-GCCcore-12.2.0
6.2.1-GCCcore-11.2.0
6.1.2-GCCcore-9.3.0
6.2.1-GCCcore-12.3.0
6.2.0-GCCcore-10.2.0
6.1.2-GCCcore-8.3.0
6.2.1-GCCcore-11.3.0

GONE

Available Versions:

2024

GObject-Introspection

Description

GObject introspection is a middleware layer between C libraries (using GObject) and language bindings. The C library can be scanned at compile time and generate a metadata file, in addition to the actual native C library. Then at runtime, language bindings can read this metadata and automatically provide bindings to call into the C library.

More Information

https://gi.readthedocs.io/en/latest/

Available Versions:

1.72.0-GCCcore-11.3.0
1.54.1-foss-2018b-Python-2.7.15
1.74.0-GCCcore-12.2.0
1.76.1-GCCcore-12.3.0
1.68.0-GCCcore-10.3.0
1.63.1-GCCcore-8.3.0-Python-3.7.4
1.64.0-GCCcore-9.3.0-Python-3.8.2
1.68.0-GCCcore-11.2.0
1.60.1-GCCcore-8.2.0-Python-3.7.2
1.66.1-GCCcore-10.2.0

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:

20.10.0-foss-2020b
23.9.1-intel-2022a
22.8.0-intel-2022a
22.8.0-foss-2022a
23.9.1-foss-2022a
21.6.0-foss-2021a

GPAW-setups

Description

PAW setup for the GPAW Density Functional Theory package. Users can install setups manually using ‘gpaw install-data’ or use setups from this package. The versions of GPAW and GPAW-setups can be intermixed.

More Information

https://wiki.fysik.dtu.dk/gpaw/

Available Versions:

0.9.20000

GRASS

Description

The Geographic Resources Analysis Support System - used for geospatial data management and analysis, image processing, graphics and maps production, spatial modeling, and visualization

More Information

https://grass.osgeo.org

Available Versions:

8.2.0-foss-2021b

GROMACS

Description

GROMACS is a versatile package to perform molecular dynamics, i.e. simulate theNewtonian equations of motion for systems with hundreds to millions ofparticles.This is a CPU only build, containing both MPI and threadMPI binariesfor both single and double precision.It also contains the gmxapi extension for the single precision MPI build.

More Information

https://www.gromacs.org

Available Versions:

2023.1-foss-2022a
2021.5-foss-2021b-CUDA-11.4.1-PLUMED-2.8.0
2021.5-foss-2021b-CUDA-11.4.1
2021-foss-2021a-PLUMED-2.7.2
2020.4-foss-2020a
2022.2-foss-2021a
2021.5-foss-2021b-PLUMED-2.8.0
2021.3-foss-2021a
2021-foss-2020b
2020-fosscuda-2019b
2020.4-foss-2020a-PLUMED-2.6.2
2021.3-foss-2021a-CUDA-11.3.1
2021.5-foss-2021b

GSD

Description

The GSD file format is the native file format forHOOMD-blue. GSD files store trajectories of the HOOMD-blue system statein a binary file with efficient random access to frames. GSD allows allparticle and topology properties to vary from one frame to the next. Usethe GSD Python API to specify the initial condition for a HOOMD-bluesimulation or analyze trajectory output with a script. Read a GSDtrajectory with a visualization tool to explore the behavior of thesimulation.

More Information

https://gsd.readthedocs.io

Available Versions:

3.2.0-foss-2022a

GSL

Description

The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting.

More Information

https://www.gnu.org/software/gsl/

Available Versions:

2.6-iccifort-2020.4.304
2.7-GCC-11.2.0
2.7-GCC-10.3.0
2.7-GCC-12.3.0
2.7-GCC-12.2.0
2.6-GCC-9.3.0
2.6-GCC-8.3.0
2.5-GCC-8.2.0-2.31.1
2.6-GCC-10.2.0
2.5-GCC-7.3.0-2.30
2.7-GCC-11.3.0
2.6-iccifort-2020.1.217

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-12.3.0
1.22.5-GCC-12.2.0

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
1.22.5-GCC-12.3.0
1.22.1-GCC-12.2.0
1.20.2-GCC-11.3.0
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:

1.16.2-GCC-8.3.0
1.20.2-GCC-11.3.0
1.22.1-GCC-12.2.0
1.22.5-GCC-12.3.0
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
3.24.8-GCCcore-8.2.0
3.24.23-GCCcore-10.2.0
2.24.32-foss-2018b

GTK2

Description

The GTK+ 2 package contains libraries used for creating graphical user interfaces for applications.

More Information

https://www.gtk.org

Available Versions:

2.24.33-GCCcore-11.3.0

GTK3

Description

GTK+ is the primary library used to construct user interfaces in GNOME. It provides all the user interface controls, or widgets, used in a common graphical application. Its object-oriented API allows you to construct user interfaces without dealing with the low-level details of drawing and device interaction.

More Information

https://developer.gnome.org/gtk3/stable/

Available Versions:

3.24.37-GCCcore-12.3.0
3.24.31-GCCcore-11.2.0

GTK4

Description

GTK+ is the primary library used to construct user interfaces in GNOME. It provides all the user interface controls, or widgets, used in a common graphical application. Its object-oriented API allows you to construct user interfaces without dealing with the low-level details of drawing and device interaction.

More Information

https://docs.gtk.org/gtk4/

Available Versions:

4.11.3-GCC-12.2.0
4.13.1-GCC-12.3.0
4.7.0-GCC-11.3.0

GTS

Description

GTS stands for the GNU Triangulated Surface Library. It is an Open Source Free Software Library intended to provide a set of useful functions to deal with 3D surfaces meshed with interconnected triangles.

More Information

http://gts.sourceforge.net/

Available Versions:

0.7.6-GCCcore-10.3.0

Gaussian

Description

Gaussian provides state-of-the-art capabilities for electronic structuremodeling. Gaussian 09 is licensed for a wide variety of computersystems. All versions of Gaussian 09 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 12.5 compiler and Atlas.

More Information

https://www.gaussian.com/

Available Versions:

09.D.01-ARCUS-B
16.A.03-ARCUS-B
16.C.01
03.E.01-ARCUS-B

Gaussview

Available Versions:

5.0.9

Gdk-Pixbuf

Description

The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it was distributed as part of GTK+ 2 but it was split off into a separate package in preparation for the change to GTK+ 3.

More Information

https://docs.gtk.org/gdk-pixbuf/

Available Versions:

2.42.10-GCCcore-12.3.0
2.40.0-GCCcore-10.2.0
2.38.1-GCCcore-8.2.0
2.42.6-GCCcore-11.2.0
2.38.2-GCCcore-8.3.0
2.42.8-GCCcore-11.3.0
2.36.12-foss-2018b
2.42.10-GCCcore-12.2.0
2.42.6-GCCcore-10.3.0

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

https://geant4.cern.ch/

Available Versions:

11.0.0-GCC-11.2.0
10.7.1-GCC-10.2.0
11.1.1-GCC-11.2.0
11.0.0-foss-2021b-G4MPI

Geant4-data

Description

Datasets for Geant4.

More Information

https://geant4.cern.ch/

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

http://genomethreader.org

Available Versions:

1.7.3-Linux_x86_64-64bit

GenomeTools

Description

A comprehensive software library for efficient processing of structured genome annotations.

More Information

http://genometools.org

Available Versions:

1.6.1-GCC-10.2.0
1.6.2-GCC-10.3.0

GeoMxNGSPipeline

Available Versions:

2022

Ghostscript

Description

Ghostscript is a versatile processor for PostScript data with the ability to render PostScript to different targets. It used to be part of the cups printing stack, but is no longer used for that.

More Information

https://ghostscript.com

Available Versions:

9.50-GCCcore-8.3.0
9.56.1-GCCcore-11.3.0
9.52-GCCcore-9.3.0
9.53.3-GCCcore-10.2.0
9.54.0-GCCcore-11.2.0
10.01.2-GCCcore-12.3.0
9.54.0-GCCcore-10.3.0

GitPython

Description

GitPython is a python library used to interact with Git repositories

More Information

https://github.com/gitpython-developers/GitPython

Available Versions:

3.1.0-GCCcore-8.3.0-Python-3.7.4
3.1.14-GCCcore-10.2.0
3.1.24-GCCcore-11.2.0

GlobalArrays

Description

Global Arrays (GA) is a Partitioned Global Address Space (PGAS) programming model

More Information

https://hpc.pnl.gov/globalarrays

Available Versions:

5.8-iomkl-2021a
5.8-intel-2021a
5.7-intel-2020b
5.8.2-intel-2023a
5.7.2-foss-2019b-peigs
5.8.1-intel-2022a
5.8-intel-2020a

Globus-CLI

Description

A Command Line Wrapper over the Globus SDK for Python, which provides an interface to Globus services from the shell, and is suited to both interactive and simple scripting use cases.

More Information

https://docs.globus.org/cli/

Available Versions:

3.6.0-GCCcore-11.2.0

GlobusConnectPersonal

Description

Globus Connect Personal turns your laptop or other personal computer into a Globus endpoint with a just a few clicks. With Globus Connect Personal you can share and transfer files to/from a local machine—campus server, desktop computeror laptop—even if it’s behind a firewall and you don’t have administrator privileges.

More Information

https://www.globus.org/globus-connect-personal

Available Versions:

2.3.6

Glucose

Description

Glucose is based on a new scoring scheme (well, not so new now, it wasintroduced in 2009) for the clause learning mechanism of so called Modern SATsolvers (it is based on our IJCAI’09 paper). It is designed to be parallel, since v4.0.

More Information

https://www.labri.fr/perso/lsimon/glucose/

Available Versions:

4.1-GCC-9.3.0

GnuTLS

Description

GnuTLS is a secure communications library implementing the SSL, TLS and DTLS protocols and technologies around them. It provides a simple C language application programming interface (API) to access the secure communications protocols as well as APIs to parse and write X.509, PKCS #12, OpenPGP and other required structures. It is aimed to be portable and efficient with focus on security and interoperability.

More Information

https://www.gnutls.org

Available Versions:

3.7.3-GCCcore-11.2.0

Go

Description

Go is an open source programming language that makes it easy to build simple, reliable, and efficient software.

More Information

https://www.golang.org

Available Versions:

1.17.6
1.14.1

Grace

Description

Grace is a WYSIWYG tool to make two-dimensional plots of numerical data.

More Information

https://plasma-gate.weizmann.ac.il/Grace/

Available Versions:

5.1.25-foss-2019b-5build1
5.1.25-foss-2021b
5.1.25-intel-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-12.3.0
1.10.8-GCCcore-11.3.0
1.10.8-GCCcore-12.2.0

GraphicsMagick

Description

GraphicsMagick is the swiss army knife of image processing.

More Information

http://www.graphicsmagick.org/

Available Versions:

1.3.36-GCCcore-11.2.0
1.3.34-foss-2019b

Graphviz

Description

Graphviz is open source graph visualization software. Graph visualization is a way of representing structural information as diagrams of abstract graphs and networks. It has important applications in networking, bioinformatics, software engineering, database and web design, machine learning, and in visual interfaces for other technical domains.

More Information

https://www.graphviz.org/

Available Versions:

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:

3.0.7-GCCcore-11.2.0
1.8.8-GCCcore-9.3.0
1.8.8-GCCcore-8.2.0
1.8.8-GCCcore-8.3.0
3.0.8-GCCcore-11.3.0

Guppy

Available Versions:

6.4.2-CPU
5.0.11
3.6.0
6.5.7-CPU
6.5.7
6.4.2

Gurobi

Description

The Gurobi Optimizer is a state-of-the-art solver for mathematical programming.The solvers in the Gurobi Optimizer were designed from the ground up to exploit modernarchitectures and multi-core processors, using the most advanced implementations of thelatest algorithms.

More Information

https://www.gurobi.com

Available Versions:

9.1.2-GCCcore-10.3.0
11.0.2-GCCcore-12.3.0
9.5.2-GCCcore-11.3.0
10.0.3-GCCcore-12.2.0

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:

4.2.15-GCCcore-10.2.0
4.2.15-GCCcore-10.3.0
4.2.16-2-GCCcore-12.3.0
4.2.15-GCCcore-11.2.0
4.2.15-GCCcore-11.3.0
4.2.14-GCCcore-8.3.0

HDF5

Description

HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data.

More Information

https://portal.hdfgroup.org/display/support

Available Versions:

1.10.6-gompi-2020a
1.10.5-gompi-2019a
1.10.7-gompic-2020b
1.12.1-iimpi-2021b
1.10.5-iimpi-2020a
1.10.6-iimpi-2020a
1.14.0-iimpi-2023a
1.10.5-gompi-2019b
1.12.2-gompi-2022a
1.10.7-iimpi-2020b
1.10.2-foss-2018b
1.10.2-fosscuda-2018b
1.10.2-intel-2020b
1.12.1-gompi-2021a
1.10.7-gompi-2020b
1.10.7-iompi-2021a
1.12.2-iimpi-2022a
1.12.1-gompi-2021b
1.10.5-gompi-2019b-dba
1.10.6-gompic-2020a
1.13.1-iimpi-2022a
1.10.5-gompic-2019b
1.14.0-iimpi-2022b
1.10.7-gompi-2021a
1.10.7-iimpi-2021a
1.14.0-gompi-2023a
1.13.1-gompi-2022a
1.12.0-gompi-2020a
1.14.0-gompi-2022b

HH-suite

Description

The HH-suite is an open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs).

More Information

https://github.com/soedinglab/hh-suite

Available Versions:

3.3.0-gompi-2021a
3.3.0-gompi-2021b
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

http://hmmer.org/

Available Versions:

3.3.2-gompi-2020b
3.3.2-gompi-2021b
3.3.2-gompi-2021a
3.3.2-gompic-2020b
3.3.1-iimpi-2020a
3.3.2-gompi-2022a

HMMER2

Description

HMMER is used for searching sequence databases for sequence homologs, and for making sequence alignments.

More Information

http://hmmer.org

Available Versions:

2.3.2-GCC-8.3.0

HOOMD-blue

Description

HOOMD-blue is a general-purpose particle simulationtoolkit, implementing molecular dynamics and hard particle Monte Carlooptimized for fast execution on both GPUs and CPUs.

More Information

https://bitbucket.org/glotzer/hoomd-blue

Available Versions:

4.0.1-foss-2022a
4.4.0-foss-2022a

HTSlib

Description

A C library for reading/writing high-throughput sequencing data. This package includes the utilities bgzip and tabix

More Information

https://www.htslib.org/

Available Versions:

1.10.2-GCC-8.3.0
1.15.1-GCC-11.3.0
1.14-GCC-11.2.0
1.9-foss-2018b
1.12-GCC-10.2.0
1.11-GCC-10.2.0
1.12-GCC-10.3.0
1.10.2-GCC-9.3.0

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
2.4.0-GCCcore-8.2.0
4.2.1-GCCcore-11.3.0
5.3.1-GCCcore-12.2.0
2.6.4-GCCcore-9.3.0
2.2.0-foss-2018b
2.6.7-GCCcore-10.2.0
2.6.4-GCCcore-8.3.0
5.3.1-GCCcore-12.3.0
2.8.2-GCCcore-11.2.0

HemeLB

Description

HemeLB is a high performance lattice-Boltzmann solver optimized for simulating blood flow through sparse geometries, such as those found in the human vasculature. It is routinely deployed on powerful supercomputers, scaling to hundreds of thousands of cores even for complex geometries . HemeLB has traditionally been used to model cerebral bloodflow and vascular remodelling in retinas , but is now being applied to simulating the fully coupled human arterial and venous trees.

More Information

http://hemelb.org.s3-website.eu-west-2.amazonaws.com/

Available Versions:

0.8

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-11.3.0
1.0.4-GCCcore-12.3.0

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:

2.24.0-intel-2021b
2.18.2-foss-2019b
2.18.2-intel-2020a
2.20.0-foss-2020b
2.21.0-foss-2021a
2.18.2-foss-2020a
2.25.0-foss-2022a

ICU

Description

ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization support for software applications.

More Information

https://icu.unicode.org

Available Versions:

72.1-GCCcore-12.2.0
69.1-GCCcore-10.3.0
64.2-GCCcore-8.3.0
64.2-GCCcore-8.2.0
66.1-GCCcore-9.3.0
71.1-GCCcore-11.3.0
69.1-GCCcore-11.2.0
61.1-GCCcore-7.3.0
67.1-GCCcore-10.2.0
73.2-GCCcore-12.3.0

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:

7.15.0-foss-2020a-Python-3.8.2
8.5.0-GCCcore-11.3.0
8.14.0-GCCcore-12.3.0
7.9.0-foss-2019b-Python-3.7.4
7.26.0-GCCcore-11.2.0
7.18.1-GCCcore-10.2.0

IQ-TREE

Description

Efficient phylogenomic software by maximum likelihood

More Information

http://www.iqtree.org/

Available Versions:

2.2.2.6-gompi-2022b
1.6.12-foss-2018b

ISA-L

Description

Intelligent Storage Acceleration Library

More Information

https://github.com/intel/isa-l

Available Versions:

2.30.0-GCCcore-11.3.0
2.30.0-GCCcore-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

https://www.imagemagick.org/

Available Versions:

7.0.11-14-GCCcore-10.3.0
7.0.10-1-GCCcore-9.3.0
7.1.0-4-GCCcore-11.2.0
7.1.0-37-GCCcore-11.3.0
7.0.9-5-GCCcore-8.3.0
7.1.1-15-GCCcore-12.3.0
7.0.10-35-GCCcore-10.2.0

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:

3.1.5-GCCcore-11.3.0
3.1.6-GCCcore-12.2.0
3.1.7-GCCcore-12.3.0

Infernal

Description

Infernal (“INFERence of RNA ALignment”) is for searching DNA sequence databases for RNA structure and sequence similarities.

More Information

http://eddylab.org/infernal/

Available Versions:

1.1.2-foss-2018b

InterProScan

Description

InterProScan is a sequence analysis application (nucleotide and protein sequences) that combines different protein signature recognition methods into one resource [code only: libraries and external binaries but no data].

More Information

https://www.ebi.ac.uk/interpro/

Available Versions:

5.62-94.0-foss-2022b

Ipopt

Description

Ipopt (Interior Point OPTimizer, pronounced eye-pea-Opt) is a software package for large-scale nonlinear optimization.

More Information

https://coin-or.github.io/Ipopt

Available Versions:

3.12.13-intel-2020b

JAGS

Description

JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation

More Information

http://mcmc-jags.sourceforge.net/

Available Versions:

4.3.0-foss-2021a
4.3.0-foss-2020a
4.3.0-foss-2021b
4.3.0-foss-2019b
4.3.0-foss-2022a

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:

2.14-GCC-11.3.0
2.13.1-GCC-11.2.0

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-8.3.0
2.0.14-GCCcore-10.2.0
2.0.14-GCCcore-9.3.0
2.0.24-GCCcore-10.2.0
4.0.0-GCCcore-12.2.0
1.900.1-intel-2020b
2.0.14-GCCcore-8.2.0
4.0.0-GCCcore-12.3.0
2.0.14-GCCcore-7.3.0
2.0.33-GCCcore-11.3.0
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

http://openjdk.java.net

Available Versions:

17.0.6
1.8.0_241
16.0.1
11.0.20
11.0.2
1.8.0_131
1.7.0_60

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-11.2.0
1.9.5-GCCcore-11.3.0
1.9.4-GCCcore-10.2.0
1.9.4-GCCcore-9.3.0

Judy

Description

A C library that implements a dynamic array.

More Information

http://judy.sourceforge.net/

Available Versions:

1.0.5-GCCcore-8.3.0
1.0.5-GCCcore-10.3.0
1.0.5-GCCcore-10.2.0

Julia

Description

Julia is a high-level, high-performance dynamic programming language for numerical computing

More Information

https://julialang.org

Available Versions:

1.6.2-linux-x86_64
1.8.5-linux-x86_64
1.9.3-linux-x86_64
1.8.2-linux-x86_64
1.5.1-linux-x86_64
1.5.3-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

https://jupyter.org

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

https://jupyter.org/

Available Versions:

2.2.8-GCCcore-10.2.0
4.0.5-GCCcore-12.3.0
3.5.0-GCCcore-11.3.0

JupyterNotebook

Description

The Jupyter Notebook is the original web application for creating and sharing computational documents. It offers a simple, streamlined, document-centric experience.

More Information

https://jupyter.org/

Available Versions:

7.0.2-GCCcore-12.3.0

KMC

Description

KMC is a disk-based programm for counting k-mers from (possibly gzipped) FASTQ/FASTA files.

More Information

http://sun.aei.polsl.pl/kmc

Available Versions:

3.1.0-foss-2018b

KaHIP

Description

The graph partitioning framework KaHIP – Karlsruhe High Quality Partitioning.

More Information

https://kahip.github.io/

Available Versions:

3.16-gompi-2023a

Kalign

Description

Kalign is a fast multiple sequence alignment program for biological sequences.

More Information

https://github.com/TimoLassmann/kalign

Available Versions:

3.3.1-GCCcore-10.2.0
3.3.2-GCCcore-11.2.0
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

https://genome.cse.ucsc.edu/

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

https://keras.io/

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

http://lame.sourceforge.net/

Available Versions:

3.100-GCCcore-9.3.0
3.100-GCCcore-8.2.0
3.100-GCCcore-10.2.0
3.100-GCCcore-12.3.0
3.100-GCCcore-10.3.0
3.100-GCCcore-12.2.0
3.100-GCCcore-11.2.0
3.100-GCCcore-8.3.0
3.100-GCCcore-11.3.0

LAMMPS

Description

LAMMPS is a classical molecular dynamics code, and an acronymfor Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS haspotentials for solid-state materials (metals, semiconductors) and soft matter(biomolecules, polymers) and coarse-grained or mesoscopic systems. It can beused to model atoms or, more generically, as a parallel particle simulator atthe atomic, meso, or continuum scale. LAMMPS runs on single processors or inparallel using message-passing techniques and a spatial-decomposition of thesimulation domain. The code is designed to be easy to modify or extend with newfunctionality.

More Information

https://lammps.sandia.gov/

Available Versions:

3Mar2020-foss-2020a-Python-3.8.2-kokkos-QUIP
3Mar2020-foss-2020a-Python-3.8.2-kokkos
23Jun2022-foss-2021b-kokkos
23Jun2022-foss-2021b-kokkos-CUDA-11.4.1
23Jun2022-foss-2022a-kokkos-CUDA-11.7.0

LAPACK

Description

LAPACK is written in Fortran90 and provides routines for solving systems of simultaneous linear equations, least-squares solutions of linear systems of equations, eigenvalue problems, and singular value problems.

More Information

https://www.netlib.org/lapack/

Available Versions:

3.9.1-GCC-10.2.0
3.10.1-GCC-11.3.0
3.9.1-GCC-11.2.0
3.9.1-GCC-9.3.0
3.9.1-GCC-10.3.0

LDC

Description

The LLVM-based D Compiler

More Information

https://wiki.dlang.org/LDC

Available Versions:

1.28.1-GCCcore-8.3.0
1.26.0-GCCcore-10.3.0
1.25.1-GCCcore-10.2.0
0.17.6-x86_64

LERC

Description

LERC is an open-source image or raster format which supports rapid encoding and decodingfor any pixel type (not just RGB or Byte). Users set the maximum compression error per pixel while encoding,so the precision of the original input image is preserved (within user defined error bounds).

More Information

https://github.com/Esri/lerc

Available Versions:

4.0.0-GCCcore-12.3.0
4.0.0-GCCcore-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

https://llvm.org/

Available Versions:

9.0.0-GCCcore-8.3.0
15.0.5-GCCcore-12.2.0
12.0.1-GCCcore-11.2.0
7.0.1-GCCcore-8.2.0
11.1.0-GCCcore-10.3.0
14.0.3-GCCcore-11.3.0
8.0.1-GCCcore-8.3.0
16.0.6-GCCcore-12.3.0
6.0.0-GCCcore-7.3.0
9.0.1-GCCcore-9.3.0
11.0.0-GCCcore-10.2.0

LMDB

Description

LMDB is a fast, memory-efficient database. With memory-mapped files, it has the read performance of a pure in-memory database while retaining the persistence of standard disk-based databases.

More Information

https://symas.com/lmdb

Available Versions:

0.9.22-GCCcore-7.3.0
0.9.24-GCCcore-9.3.0
0.9.24-GCCcore-8.3.0
0.9.29-GCCcore-11.2.0
0.9.24-GCCcore-10.2.0
0.9.28-GCCcore-10.3.0
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:

2.4.1-GCCcore-12.2.0
2.3-GCCcore-11.3.0

LTR_retriever

Description

LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this package.

More Information

https://github.com/oushujun/LTR_retriever

Available Versions:

2.9.0-foss-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-10.3.0
2.10-GCCcore-10.2.0
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

http://www.leptonica.org

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://www.remotesensing.org/libtiff/

Available Versions:

4.0.10-GCCcore-8.2.0
4.0.10-GCCcore-8.3.0
4.5.0-GCCcore-12.3.0
4.0.9-GCCcore-7.3.0
4.3.0-GCCcore-11.2.0
4.4.0-GCCcore-12.2.0
4.1.0-GCCcore-10.2.0
4.2.0-GCCcore-10.3.0
4.1.0-GCCcore-9.3.0
4.3.0-GCCcore-11.3.0

Libint

Description

Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.

More Information

https://sourceforge.net/p/libint/

Available Versions:

1.1.6-foss-2020a
2.6.0-iimpi-2020a-lmax-6-cp2k
1.1.6-foss-2019b
2.7.2-GCC-12.2.0-lmax-6-cp2k
2.6.0-iccifort-2020.4.304-lmax-6-cp2k
1.1.6-GCC-8.2.0-2.31.1
1.1.6-intel-2020a
2.6.0-gompi-2020a-lmax-6-cp2k
2.6.0-GCC-10.2.0-lmax-6-cp2k
2.7.2-GCC-11.3.0-lmax-6-cp2k
2.6.0-GCC-10.3.0-lmax-6-cp2k
2.7.2-GCC-12.3.0-lmax-6-cp2k

Lighter

Description

Fast and memory-efficient sequencing error corrector

More Information

https://github.com/mourisl/Lighter

Available Versions:

1.1.2-foss-2018b

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

https://www.littlecms.com/

Available Versions:

2.12-GCCcore-11.2.0
2.12-GCCcore-10.3.0
2.13.1-GCCcore-11.3.0
2.9-GCCcore-8.3.0
2.9-GCCcore-9.3.0
2.15-GCCcore-12.3.0
2.11-GCCcore-10.2.0

Lua

Description

Lua is a powerful, fast, lightweight, embeddable scripting language. Lua combines simple procedural syntax with powerful data description constructs based on associative arrays and extensible semantics. Lua is dynamically typed, runs by interpreting bytecode for a register-based virtual machine, and has automatic memory management with incremental garbage collection, making it ideal for configuration, scripting, and rapid prototyping.

More Information

https://www.lua.org/

Available Versions:

5.3.5-GCCcore-9.3.0
5.4.6-GCCcore-12.3.0
5.1.5-GCCcore-8.3.0
5.4.4-GCCcore-11.3.0
5.4.3-GCCcore-11.2.0
5.4.2-GCCcore-10.2.0
5.4.3-GCCcore-10.3.0

M4

Description

GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible although it has some extensions (for example, handling more than 9 positional parameters to macros). GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.

More Information

http://www.gnu.org/software/m4/m4.html

Available Versions:

1.4.18
1.4.18-GCCcore-10.3.0
1.4.19
1.4.19-GCCcore-13.1.0
1.4.17
1.4.19-GCCcore-13.2.0
1.4.19-GCCcore-11.3.0
1.4.18-GCCcore-8.1.0
1.4.18-GCCcore-8.3.0
1.4.18-GCCcore-10.2.0
1.4.19-GCCcore-12.3.0
1.4.18-GCCcore-7.3.0
1.4.19-GCCcore-11.2.0
1.4.18-GCCcore-8.2.0
1.4.19-GCCcore-12.2.0
1.4.18-GCCcore-9.3.0

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:

7.490-GCC-11.2.0-with-extensions
7.453-iimpi-2020a-with-extensions
7.487-gompi-2021a-with-extensions
7.475-gompi-2020b-with-extensions
7.505-GCC-11.3.0-with-extensions
7.453-GCC-9.3.0-with-extensions
7.470-gompi-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:

R2022b
R2019b
R2023a
R2021b
R2020a
R2023b
R2020b
R2022a

MCL

Description

The MCL algorithm is short for the Markov Cluster Algorithm, a fastand scalable unsupervised cluster algorithm for graphs (also known as networks) basedon simulation of (stochastic) flow in graphs.

More Information

https://micans.org/mcl/

Available Versions:

14.137-GCCcore-8.3.0
14.137-GCCcore-9.3.0
14.137-GCCcore-11.3.0

MDAnalysis

Description

MDAnalysis is an object-oriented Python library to analyze trajectories from molecular dynamics (MD)simulations in many popular formats.

More Information

https://www.mdanalysis.org/

Available Versions:

0.20.1-foss-2019b-Python-3.7.4

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-11.2.0
5.1.0-GCCcore-8.2.0
5.1.0-foss-2018b
5.1.0-GCCcore-12.3.0
5.1.0-GCCcore-11.3.0
5.1.0-GCCcore-8.3.0
5.1.0-GCCcore-9.3.0
5.1.0-GCCcore-10.2.0
5.1.0-GCCcore-10.3.0

MGLTools

Available Versions:

1.5.7.old
1.5.7

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

https://mmseqs.com

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:

1.1.0-GCC-9.3.0
1.2.1-GCCcore-10.3.0
1.1.0-GCC-8.3.0

MPFR

Description

The MPFR library is a C library for multiple-precision floating-point computations with correct rounding.

More Information

https://www.mpfr.org

Available Versions:

4.1.0-GCCcore-10.3.0
4.0.1-GCCcore-7.3.0
4.2.0-GCCcore-12.3.0
4.0.2-GCCcore-8.3.0
4.0.2-GCCcore-9.3.0
4.1.0-GCCcore-10.2.0
4.0.2-GCCcore-8.2.0
4.1.0-GCCcore-11.3.0
4.1.0-GCCcore-11.2.0

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

http://www.mpich.org/

Available Versions:

1.5rc3-GCC-7.3.0-2.30

MUMPS

Description

A parallel sparse direct solver

More Information

http://graal.ens-lyon.fr/MUMPS/

Available Versions:

5.2.1-foss-2019b-metis
5.3.5-foss-2020b-metis
5.2.1-foss-2019a-metis-seq
5.2.1-intel-2020a-metis
5.5.1-foss-2022a-metis
5.4.1-intel-2021b-metis
5.2.1-foss-2020a-metis
5.4.0-foss-2021a-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-foss-2018b
4.0.0rc1-GCCcore-11.2.0
4.0.0beta2-GCCcore-10.2.0

MUSCLE

Description

MUSCLE is one of the best-performing multiple alignment programs according to published benchmark tests, with accuracy and speed that are consistently better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users learn everything they need to know about MUSCLE in a few minutes-only a handful of command-line options are needed to perform common alignment tasks.

More Information

https://drive5.com/muscle/

Available Versions:

3.8.31-foss-2018b

MaSuRCA

Description

MaSuRCA is whole genome assembly software. It combines the efficiency of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches. MaSuRCA can assemble data sets containing only short reads from Illumina sequencing or a mixture of short reads and long reads (Sanger, 454, Pacbio and Nanopore).

More Information

https://www.genome.umd.edu/masurca.html

Available Versions:

4.0.9-foss-2021a-Perl-5.32.1

Mako

Description

A super-fast templating language that borrows the best ideas from the existing templating languages

More Information

https://www.makotemplates.org

Available Versions:

1.0.7-foss-2018b-Python-2.7.15
1.2.4-GCCcore-12.3.0
1.1.4-GCCcore-10.3.0
1.1.4-GCCcore-11.2.0
1.1.0-GCCcore-8.3.0
1.2.0-GCCcore-11.3.0
1.1.2-GCCcore-9.3.0
1.2.4-GCCcore-12.2.0
1.1.3-GCCcore-10.2.0
1.0.8-GCCcore-8.2.0

Mamba

Description

Mamba is a fast, robust, and cross-platform package manager. It runs on Windows, OS X and Linux (ARM64 and PPC64LE included) and is fully compatible with conda packages and supports most of conda’s commands.

More Information

https://mamba.readthedocs.io/

Available Versions:

4.14.0-0
23.11.0-0

MariaDB

Description

MariaDB is an enhanced, drop-in replacement for MySQL.Included engines: myISAM, Aria, InnoDB, RocksDB, TokuDB, OQGraph, Mroonga.

More Information

https://mariadb.org/

Available Versions:

10.4.13-gompi-2019b
10.5.8-GCC-10.2.0
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

http://mash.readthedocs.org

Available Versions:

2.1-foss-2018b

Mathematica

Available Versions:

13.3.1
12.2.0
13.0.0
11.3.0

MaxQuant

Description

MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data. Several labeling techniques as well as label-free quantification are supported.

More Information

https://maxquant.org/maxquant

Available Versions:

2.3.0.0-GCCcore-11.2.0

Mellanox

Available Versions:

ib_mgmt-5.8.1-1.el8

Mercurial

Description

Mercurial is a free, distributed source control management tool. It efficiently handles projectsof any size and offers an easy and intuitive interface.

More Information

https://www.mercurial-scm.org

Available Versions:

6.2-GCCcore-11.3.0
5.7.1-GCCcore-10.2.0

Mesa

Description

Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics.

More Information

https://www.mesa3d.org/

Available Versions:

18.1.1-foss-2018b
19.1.7-GCCcore-8.3.0
20.0.2-GCCcore-9.3.0
23.1.4-GCCcore-12.3.0
19.0.1-GCCcore-8.2.0
21.1.1-GCCcore-10.3.0
21.1.7-GCCcore-11.2.0
22.2.4-GCCcore-12.2.0
20.2.1-GCCcore-10.2.0
22.0.3-GCCcore-11.3.0

Meson

Description

Meson is a cross-platform build system designed to be both as fast and as user friendly as possible.

More Information

https://mesonbuild.com

Available Versions:

0.58.0-GCCcore-10.3.0
0.55.1-GCCcore-9.3.0-Python-3.8.2
0.62.1-GCCcore-11.3.0
0.58.2-GCCcore-11.2.0
0.55.3-GCCcore-10.2.0
1.1.1-GCCcore-12.3.0
0.51.2-GCCcore-8.3.0-Python-3.7.4
0.59.1-GCCcore-8.3.0-Python-3.7.4
0.64.0-GCCcore-12.2.0
0.50.0-GCCcore-8.2.0-Python-3.7.2

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

http://minisat.se/

Available Versions:

2.2.0-GCC-9.3.0

Miniconda3

Description

Miniconda is a free minimal installer for conda. It is a small, bootstrap version of Anaconda that includes only conda, Python, the packages they depend on, and a small number of other useful packages.

More Information

https://docs.conda.io/en/latest/miniconda.html

Available Versions:

23.9.0-0
4.9.2
4.5.12
22.11.1-1
4.12.0
23.1.0-1
4.7.10

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

http://www.cmbi.ru.nl/molden/

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

https://www.mono-project.com/

Available Versions:

6.4.0.198-foss-2018b
6.12.0.122-GCCcore-11.2.0
6.8.0.105-GCCcore-8.3.0

Mothur

Description

Mothur is a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community.

More Information

https://www.mothur.org/

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 an HTML report. It’s a general use tool, perfect for summarising the output from numerous bioinformatics tools.

More Information

https://multiqc.info

Available Versions:

1.14-foss-2022a
1.9-foss-2020a-Python-3.8.2

Multiwfn

Description

Multiwfn is an extremely powerful program for realizingi electronic wavefunction analysis, which is a key ingredient of quantum chemistry. Multiwfn is free, open-source, high-efficient, very user-friendly and flexible, it supports almost all of the most important wavefunction analysis methods.

More Information

http://sobereva.com/multiwfn/

Available Versions:

3.8-2023
3.8-intel-2021b

MySQL

Description

MySQL is one of the world’s most widely used open-source relational database management system (RDBMS).

More Information

http://www.mysql.com/

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

http://www.nasm.us/

Available Versions:

2.13.03-GCCcore-7.3.0
2.16.01-GCCcore-12.3.0
2.15.05-GCCcore-12.2.0
2.15.05-GCCcore-10.3.0
2.15.05-GCCcore-11.2.0
2.14.02-GCCcore-8.3.0
2.14.02-GCCcore-8.2.0
2.14.02-GCCcore-9.3.0
2.15.05-GCCcore-11.3.0
2.15.05-GCCcore-10.2.0

NCCL

Description

The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collectivecommunication primitives that are performance optimized for NVIDIA GPUs.

More Information

https://developer.nvidia.com/nccl

Available Versions:

2.8.3-CUDA-11.1.1
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-11.8.0
2.12.12-GCCcore-11.3.0-CUDA-12.0.0
2.10.3-GCCcore-11.2.0-CUDA-11.4.1
2.8.3-CUDA-11.0.2
2.10.3-GCCcore-10.3.0-CUDA-11.3.1

NCO

Description

The NCO toolkit manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5.

More Information

https://github.com/nco/nco

Available Versions:

5.0.1-foss-2021a
4.9.7-foss-2020b

NEURON

Description

Empirically-based simulations of neurons and networks of neurons.

More Information

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 pileups produced from Next Generation Sequencing.

More Information

https://github.com/ncbi/ngs

Available Versions:

2.9.3-foss-2018b-Java-1.8
2.10.9-GCCcore-10.2.0

NLopt

Description

NLopt is a free/open-source library for nonlinear optimization, providing a common interface for a number of different free optimization routines available online as well as original implementations of various other algorithms.

More Information

http://ab-initio.mit.edu/wiki/index.php/NLopt

Available Versions:

2.7.0-GCCcore-10.3.0
2.7.1-GCCcore-11.3.0
2.6.1-GCCcore-8.3.0
2.7.1-GCCcore-12.3.0
2.6.2-GCCcore-10.2.0
2.7.1-GCCcore-12.2.0
2.7.0-GCCcore-11.2.0
2.4.2-GCCcore-7.3.0
2.6.1-GCCcore-9.3.0

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:

4.32-GCCcore-11.2.0
4.30-GCCcore-10.3.0
4.25-GCCcore-9.3.0
4.35-GCCcore-12.3.0
4.21-GCCcore-8.3.0
4.20-GCCcore-7.3.0
4.34-GCCcore-11.3.0
4.29-GCCcore-10.2.0

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
3.45-GCCcore-8.3.0
3.89.1-GCCcore-12.3.0
3.79-GCCcore-11.3.0
3.69-GCCcore-11.2.0
3.51-GCCcore-9.3.0
3.65-GCCcore-10.3.0
3.39-GCCcore-7.3.0

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:

21.11
20.11
21.9
21.7

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

http://www.nwchem-sw.org

Available Versions:

7.0.0-foss-2019b-Python-3.7.4
7.2.0-intel-2022a
7.0.2-intel-2021a

Nextflow

Description

Nextflow is a reactive workflow framework and a programming DSL that eases writing computational pipelines with complex data

More Information

https://www.nextflow.io/

Available Versions:

23.04.2

NgsRelate

Available Versions:

2022

Ninja

Description

Ninja is a small build system with a focus on speed.

More Information

https://ninja-build.org/

Available Versions:

1.10.2-GCCcore-10.3.0
1.9.0-GCCcore-8.3.0
1.9.0-GCCcore-8.2.0
1.10.2-GCCcore-11.2.0
1.10.2-GCCcore-11.3.0
1.10.1-GCCcore-10.2.0
1.11.1-GCCcore-12.3.0
1.11.1-GCCcore-12.2.0
1.10.0-GCCcore-9.3.0

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

https://www.score-p.org

Available Versions:

2.0.7-GCCcore-11.3.0
2.0.5-GCCcore-9.3.0

ORCA

Description

ORCA is a flexible, efficient and easy-to-use general purpose tool for 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

https://orcaforum.kofo.mpg.de

Available Versions:

5.0.0-gompi-2019b
5.0.3-gompi-2021b
4.2.1-gompi-2019b-dba
5.0.2-gompi-2019b-dba
5.0.4-gompi-2021b
5.0.1-gompi-2019b-dba
5.0.4-gompi-2021b-static
4.2.1-gompi-2019b

OSU-Micro-Benchmarks

Description

OSU Micro-Benchmarks

More Information

https://mvapich.cse.ohio-state.edu/benchmarks/

Available Versions:

5.8-fosscuda-2020b
6.2-gompi-2022b
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

https://www.score-p.org

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:

5.1.0-foss-2019b
7.1.0-foss-2021b

OpenBLAS

Description

OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.

More Information

https://xianyi.github.com/OpenBLAS/

Available Versions:

0.3.12-GCC-10.2.0
0.3.18-GCC-11.2.0
0.3.23-GCC-12.3.0
0.3.7-GCC-8.3.0
0.3.20-GCC-11.3.0
0.3.5-GCC-8.2.0-2.31.1
0.3.1-GCC-7.3.0-2.30
0.3.9-GCC-9.3.0
0.3.15-GCC-10.3.0
0.3.21-GCC-12.2.0

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

https://openbabel.org

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. Includes extra modules for OpenCV from the contrib repository.

More Information

https://opencv.org/

Available Versions:

4.8.1-foss-2023a-contrib
4.5.1-fosscuda-2020b-contrib
3.4.7-foss-2019a-Python-3.7.2
4.6.0-foss-2022a-contrib
4.5.1-foss-2020b-contrib

OpenColorIO

Description

OpenColorIO (OCIO) is a complete color management solution geared towards motion picture production with an emphasis on visual effects and computer animation.

More Information

http://opencolorio.org/

Available Versions:

1.1.0-foss-2018b

OpenEXR

Description

OpenEXR is a high dynamic-range (HDR) image file format developed by Industrial Light & Magic for use in computer imaging applications

More Information

https://www.openexr.com/

Available Versions:

2.5.5-GCCcore-10.2.0
2.4.1-GCCcore-9.3.0
3.1.5-GCCcore-12.2.0
3.1.5-GCCcore-11.3.0
2.4.0-GCCcore-8.3.0
3.1.7-GCCcore-12.3.0

OpenFOAM

Description

OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics.

More Information

https://www.openfoam.com/

Available Versions:

v1912-foss-2019b
10-foss-2022a
v2006-foss-2019b
5.0-20180108-foss-2018b
8-foss-2020b
8-foss-2020a
v2012-foss-2020a
v2006-intel-2020a
v2206-foss-2022a
6-foss-2018b
10-foss-2022a
v2106-foss-2021a
9-foss-2021a
v2006-foss-2020a
6-foss-2019b
6-intel-2020a
11-foss-2022a
10-intel-2022a

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

https://openimageio.org/

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

https://www.openjpeg.org/

Available Versions:

2.5.0-GCCcore-11.3.0
2.5.0-GCCcore-12.2.0
2.5.0-GCCcore-12.3.0
2.4.0-GCCcore-11.2.0

OpenMM

Description

OpenMM is a toolkit for molecular simulation.

More Information

https://openmm.org

Available Versions:

7.5.1-foss-2021b-DeepMind-patch
8.0.0-foss-2022a
7.5.0-fosscuda-2020a-Python-3.8.2
7.5.1-foss-2021a-DeepMind-patch
8.0.0-foss-2022a-CUDA-11.7.0
7.5.1-fosscuda-2020b
7.4.2-intel-2020a-Python-3.8.2
7.4.1-foss-2019b-Python-3.7.4
7.7.0-fosscuda-2020b

OpenMPI

Description

The Open MPI Project is an open source MPI-3 implementation.

More Information

https://www.open-mpi.org/

Available Versions:

4.0.3-gcccuda-2020a
4.1.4-GCC-12.2.0
3.1.4-GCC-8.3.0-dba
3.1.4-gcccuda-2019b
3.1.1-GCC-7.3.0-2.30
4.0.5-gcccuda-2020b
4.1.1-GCC-10.3.0-CUDA-11.1.1
4.0.3-GCC-9.3.0
4.1.1-intel-compilers-2021.2.0
3.1.4-PGI-19.10-GCC-8.3.0-2.32
3.1.3-GCC-8.2.0-2.31.1
4.0.5-iccifort-2020.4.304
4.1.1-GCC-11.2.0-CXX
4.1.4-GCC-11.3.0
4.1.5-GCC-12.3.0
3.1.4-GCC-8.3.0
4.1.1-GCC-10.3.0
4.1.1-GCC-11.2.0
4.0.5-GCC-10.2.0
3.1.1-gcccuda-2018b

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
20.10-intel-2020a-Python-3.8.2
23.06-intel-2023a
21.06-intel-2021a

OpenPGM

Description

OpenPGM is an open source implementation of the Pragmatic General Multicast (PGM) specification in RFC 3208 available at www.ietf.org. PGM is a reliable and scalable multicast protocol that enables receivers to detect loss, request retransmission of lost data, or notify an application of unrecoverable loss. PGM is a receiver-reliable protocol, which means the receiver is responsible for ensuring all data is received, absolving the sender of reception responsibility.

More Information

https://code.google.com/p/openpgm/

Available Versions:

5.2.122-GCCcore-12.3.0
5.2.122-GCCcore-10.3.0
5.2.122-GCCcore-11.3.0
5.2.122-GCCcore-11.2.0
5.2.122-GCCcore-10.2.0
5.2.122-GCCcore-8.3.0
5.2.122-GCCcore-9.3.0

OpenSSL

Description

The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) protocols as well as a full-strength general purpose cryptography library.

More Information

https://www.openssl.org/

Available Versions:

1.1
1.1.1t-GCCcore-12.3.0
1.1.1h-GCCcore-10.2.0
1.1.1t-GCCcore-12.2.0
1.1.1w-GCCcore-12.3.0

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-2.7.16
2.3.8-foss-2019b-Python-3.7.4

PAPI

Description

PAPI provides the tool designer and application engineer with a consistent interface and methodology for use of the performance counter hardware found in most major microprocessors. PAPI enables software engineers to see, in near real time, the relation between software performance and processor events. In addition Component PAPI provides access to a collection of components that expose performance measurement opportunites across the hardware and software stack.

More Information

https://icl.cs.utk.edu/projects/papi/

Available Versions:

6.0.0-GCCcore-9.3.0
6.0.0-GCCcore-10.2.0

PAUP

Description

PAUP* (Phylogenetic Analysis Using Parsimony *and other methods) is acomputational phylogenetics program for inferring evolutionary trees.

More Information

https://paup.phylosolutions.com/

Available Versions:

4.0a168-centos64

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

https://www.pcre.org/

Available Versions:

8.45-GCCcore-12.3.0
8.44-GCCcore-10.3.0
8.44-GCCcore-9.3.0
8.41-GCCcore-7.3.0
8.45-GCCcore-12.2.0
8.43-GCCcore-8.2.0
8.45-GCCcore-11.3.0
8.45-GCCcore-11.2.0
8.44-GCCcore-10.2.0
8.43-GCCcore-8.3.0

PCRE2

Description

The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5.

More Information

https://www.pcre.org/

Available Versions:

10.33-GCCcore-8.3.0
10.36-GCCcore-10.3.0
10.34-GCCcore-9.3.0
10.40-GCCcore-12.2.0
10.35-GCCcore-10.2.0
10.42-GCCcore-12.3.0
10.37-GCCcore-11.2.0
10.42-GCCcore-13.2.0
10.40-GCCcore-11.3.0

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

https://www.mcs.anl.gov/petsc

Available Versions:

3.12.4-foss-2019b-Python-3.7.4
3.12.4-foss-2020a-Python-3.8.2
3.15.0-foss-2020b
3.18.4-intel-2021b
3.17.4-foss-2022a
3.14.4-foss-2020b
3.17.4-foss-2021a
3.12.4-intel-2020a-Python-3.8.2
3.15.1-foss-2021a
3.19.3-intel-2021b

PGI

Description

C, C++ and Fortran compilers from The Portland Group - PGI

More Information

https://www.pgroup.com/

Available Versions:

19.10-GCC-8.3.0-2.32
16.5-GCC-7.3.0-2.30
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

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

https://www.plumed.org

Available Versions:

2.7.3-foss-2021b
2.7.0-foss-2020b
2.8.0-foss-2021b
2.6.0-foss-2020a-Python-3.8.2
2.7.0-foss-2020a
2.5.1-foss-2019a
2.7.2-foss-2021a
2.6.2-foss-2020a-Python-3.8.2
2.5.1-foss-2020a
2.6.2-intel-2020b
2.9.0-foss-2023a
2.8.1-foss-2022a
2.7.0-intel-2020b
2.5.1-foss-2019b
2.6.0-intel-2020a-Python-3.8.2

PLY

Description

PLY is yet another implementation of lex and yacc for Python.

More Information

https://www.dabeaz.com/ply/

Available Versions:

3.11-GCCcore-8.3.0-Python-3.7.4

PMIx

Description

Process Management for Exascale EnvironmentsPMI Exascale (PMIx) represents an attempt toprovide an extended version of the PMI standard specifically designedto support clusters up to and including exascale sizes. The overallobjective of the project is not to branch the existing pseudo-standarddefinitions - in fact, PMIx fully supports both of the existing PMI-1and PMI-2 APIs - but rather to (a) augment and extend those APIs toeliminate some current restrictions that impact scalability, and (b)provide a reference implementation of the PMI-server that demonstratesthe desired level of scalability.

More Information

https://pmix.org/

Available Versions:

3.1.5-GCCcore-10.2.0
4.1.2-GCCcore-11.3.0
4.1.0-GCCcore-11.2.0
4.2.4-GCCcore-12.3.0
3.1.5-GCCcore-9.3.0
4.2.2-GCCcore-12.2.0
3.2.3-GCCcore-10.3.0

POV-Ray

Description

The Persistence of Vision Raytracer, or POV-Ray, is a ray tracing program which generates images from a text-based scene description, and is available for a variety of computer platforms. POV-Ray is a high-quality, Free Software tool for creating stunning three-dimensional graphics. The source code is available for those wanting to do their own ports.

More Information

https://www.povray.org/

Available Versions:

3.7.0.8-GCC-10.2.0

PRANK

Description

PRANK is a probabilistic multiple alignment program for DNA, codon and amino-acid sequences. PRANK is based on a novel algorithm that treats insertions correctly and avoids over-estimation of the number of deletion events.

More Information

http://wasabiapp.org/software/prank/

Available Versions:

170427-GCC-9.3.0
170427-GCC-11.3.0
170427-GCC-11.2.0

PROJ

Description

Program proj is a standard Unix filter function which convertsgeographic longitude and latitude coordinates into cartesian coordinates

More Information

https://proj.org

Available Versions:

8.1.0-GCCcore-11.2.0
5.0.0-foss-2018b
8.0.1-GCCcore-10.3.0
9.0.0-GCCcore-11.3.0
7.2.1-GCCcore-10.2.0
6.2.1-GCCcore-8.3.0
7.0.0-GCCcore-9.3.0
6.0.0-GCCcore-8.2.0
9.2.0-GCCcore-12.3.0

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

http://www.psicode.org/

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

https://www.pango.org/

Available Versions:

1.50.14-GCCcore-12.3.0
1.48.5-GCCcore-10.3.0
1.43.0-GCCcore-8.2.0
1.47.0-GCCcore-10.2.0
1.44.7-GCCcore-8.3.0
1.48.8-GCCcore-11.2.0
1.42.4-foss-2018b
1.50.7-GCCcore-11.3.0
1.50.12-GCCcore-12.2.0
1.44.7-GCCcore-9.3.0

ParMETIS

Description

ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.

More Information

http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview

Available Versions:

4.0.3-gompi-2019b
4.0.3-gompi-2020a
4.0.3-gompi-2020b
4.0.3-gompi-2019a
4.0.3-iimpi-2020a
4.0.3-gompi-2022a
4.0.3-gompi-2021a

ParaView

Description

ParaView is a scientific parallel visualizer.

More Information

https://www.paraview.org

Available Versions:

5.8.0-intel-2020a-Python-3.8.2-mpi
5.9.1-foss-2021a-mpi
5.8.0-foss-2020a-Python-3.8.2-mpi
5.8.1-foss-2020b-mpi
5.10.1-foss-2022a-mpi
5.6.2-foss-2019b-Python-3.7.4-mpi

PennCNV

Description

A free software tool for Copy Number Variation (CNV) detection from SNP genotyping arrays. Currently it can handle signal intensity data from Illumina and Affymetrix arrays. With appropriate preparation of file format, it can also handle other types of SNP arrays and oligonucleotide arrays.

More Information

https://penncnv.openbioinformatics.org/

Available Versions:

1.0.5-GCCcore-8.3.0

Perl

Description

Larry Wall’s Practical Extraction and Report LanguageIncludes a small selection of extra CPAN packages for core functionality.

More Information

https://www.perl.org/

Available Versions:

5.36.1-GCCcore-12.3.0
5.28.1-GCCcore-8.3.0
5.32.0-GCCcore-10.2.0-minimal
5.28.0-GCCcore-7.3.0
5.28.1-GCCcore-8.2.0
5.30.0-GCCcore-8.3.0
5.36.0-GCCcore-12.3.0
5.30.0-GCCcore-7.3.0
5.34.0-GCCcore-11.2.0
5.32.0-GCCcore-10.2.0
5.34.1-GCCcore-11.3.0-minimal
5.28.0-GCCcore-8.1.0
5.34.1-GCCcore-11.3.0
5.32.1-GCCcore-10.3.0-minimal
5.34.0-GCCcore-11.2.0-minimal
5.34.0-GCCcore-11.2.0-ARC
5.28.0-GCCcore-10.2.0
5.30.2-GCCcore-9.3.0
5.32.1-GCCcore-10.3.0
5.36.0-GCCcore-12.2.0

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

https://pillow.readthedocs.org/

Available Versions:

6.2.1-GCCcore-8.3.0
8.3.2-GCCcore-11.2.0
7.0.0-GCCcore-9.3.0-Python-3.8.2
8.0.1-GCCcore-10.2.0
6.0.0-GCCcore-8.2.0
8.2.0-GCCcore-10.3.0
9.1.1-GCCcore-11.3.0

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:

8.2.0-GCCcore-10.3.0
6.0.x.post0-GCCcore-8.2.0
9.2.0-GCCcore-11.3.0

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-1.8
1.23-Java-11

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

http://pmw.sourceforge.net

Available Versions:

2.0.1-foss-2020a-Python-3.8.2
2.0.1-foss-2019b-Python-2.7.16

PnetCDF

Description

Parallel netCDF: A Parallel I/O Library for NetCDF File Access

More Information

https://trac.mcs.anl.gov/projects/parallel-netcdf

Available Versions:

1.12.1-gompi-2020a
1.12.3-gompi-2022a
1.12.2-gompi-2020b
1.12.3-gompi-2021b
1.12.2-gompic-2020b

PostGis

Available Versions:

2

PostgreSQL

Description

PostgreSQL is a powerful, open source object-relational database system. It is fully ACID compliant, has full support for foreign keys, joins, views, triggers, and stored procedures (in multiple languages). It includes most SQL:2008 data types, including INTEGER, NUMERIC, BOOLEAN, CHAR, VARCHAR, DATE, INTERVAL, and TIMESTAMP. It also supports storage of binary large objects, including pictures, sounds, or video. It has native programming interfaces for C/C++, Java, .Net, Perl, Python, Ruby, Tcl, ODBC, among others, and exceptional documentation.

More Information

https://www.postgresql.org/

Available Versions:

13.4-GCCcore-11.2.0
14.4-GCCcore-11.3.0
13.3-GCCcore-10.3.0
16.1-GCCcore-12.3.0

ProtoMS

Available Versions:

3.4

PyCairo

Description

Python bindings for the cairo library

More Information

https://pycairo.readthedocs.io/

Available Versions:

1.25.0-GCCcore-12.3.0
1.24.0-GCCcore-12.2.0
1.18.0-foss-2018b-Python-2.7.15
1.21.0-GCCcore-11.3.0
1.20.1-GCCcore-11.2.0

PyCharm

Description

PyCharm Community Edition: Python IDE for Professional Developers

More Information

https://www.jetbrains.com/pycharm/

Available Versions:

2022.2.2

PyCifRW

Description

PyCIFRW provides support for reading and writing CIF(Crystallographic Information Format) files using Python.

More Information

https://bitbucket.org/jamesrhester/pycifrw/src/development

Available Versions:

4.4.2-GCCcore-9.3.0

PyGObject

Description

PyGObject is a Python package which provides bindings for GObject basedlibraries such as GTK, GStreamer, WebKitGTK, GLib, GIO and many more.

More Information

https://pygobject.readthedocs.io/

Available Versions:

3.42.1-GCCcore-11.3.0
3.44.1-GCCcore-12.2.0
2.28.7-foss-2018b-Python-2.7.15
3.46.0-GCCcore-12.3.0

PyGTK

Description

PyGTK lets you to easily create programs with a graphical user interface using the Python programming language.

More Information

http://www.pygtk.org/

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:

5.15.4-GCCcore-11.2.0
5.15.1-GCCcore-9.3.0-Python-3.8.2
5.15.1-GCCcore-10.2.0
5.15.5-GCCcore-11.3.0

PyQtGraph

Description

PyQtGraph is a pure-python graphics and GUI library built on PyQt5/PySide2 and numpy.

More Information

http://www.pyqtgraph.org/

Available Versions:

0.13.3-foss-2022a

PySCF

Description

PySCF is an open-source collection of electronic structure modules powered by Python.

More Information

http://www.pyscf.org

Available Versions:

1.7.0-foss-2020a-Python-3.8.2
1.7.6-foss-2021a
1.6.3-foss-2019a-Python-3.7.2
2.1.1-foss-2021a

PyTables

Description

PyTables is a package for managing hierarchical datasets and designed to efficiently and easily cope with extremely large amounts of data. PyTables is built on top of the HDF5 library, using the Python language and the NumPy package. It features an object-oriented interface that, combined with C extensions for the performance-critical parts of the code (generated using Cython), makes it a fast, yet extremely easy to use tool for interactively browse, process and search very large amounts of data. One important feature of PyTables is that it optimizes memory and disk resources so that data takes much less space (specially if on-flight compression is used) than other solutions such as relational or object oriented databases.

More Information

https://www.pytables.org

Available Versions:

3.6.1-foss-2021a

PyTorch

Description

Tensors and Dynamic neural networks in Python with strong GPU acceleration.PyTorch is a deep learning framework that puts Python first.

More Information

https://pytorch.org/

Available Versions:

1.12.0-foss-2022a-CUDA-11.7.0
1.12.0-foss-2022a-CUDA-11.8.0
1.11.0-foss-2021a-CUDA-11.3.1
1.6.0-foss-2019b-Python-3.7.4
1.8.1-fosscuda-2019b-Python-3.7.4
1.12.0-foss-2022a
1.7.1-fosscuda-2020b
1.10.0-foss-2021a
1.6.0-fosscuda-2019b-Python-3.7.4

PyTorch-Lightning

Description

PyTorch Lightning is the lightweight PyTorch wrapper for ML researchers.

More Information

https://pytorchlightning.ai

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://github.com/yaml/pyyaml

Available Versions:

5.4.1-GCCcore-10.3.0
5.4.1-GCCcore-11.2.0
6.0-GCCcore-12.3.0
6.0-GCCcore-11.3.0
5.1.2-GCCcore-8.3.0
5.3-GCCcore-9.3.0
5.1-GCCcore-8.2.0
5.3.1-GCCcore-10.2.0

PyZMQ

Description

Python bindings for ZeroMQ

More Information

https://www.zeromq.org/bindings:python

Available Versions:

25.1.1-GCCcore-12.3.0

Pysam

Description

Pysam is a python module for reading and manipulating Samfiles. It’s a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.

More Information

https://github.com/pysam-developers/pysam

Available Versions:

0.16.0.1-GCC-9.3.0
0.19.1-GCC-11.3.0
0.15.3-GCC-8.3.0
0.18.0-GCC-11.2.0

Python

Description

Python is a programming language that lets you work more quickly and integrate your systems more effectively.

More Information

https://python.org/

Available Versions:

2.7.18-GCCcore-9.3.0
3.10.8-GCCcore-12.2.0-bare
2.7.18-GCCcore-10.2.0
3.9.6-GCCcore-11.2.0
3.9.5-GCCcore-10.3.0-SKL
3.10.4-GCCcore-11.3.0
3.7.4-GCCcore-8.3.0
3.9.5-GCCcore-10.3.0
2.7.15-foss-2018b
3.10.8-GCCcore-12.2.0
2.7.15-GCCcore-8.2.0
2.7.16-GCCcore-8.3.0
2.7.15-GCCcore-7.3.0-bare
3.6.6-intel-2020b
2.7.18-GCCcore-11.2.0
2.7.18-GCCcore-11.3.0-bare
3.8.6-GCCcore-10.2.0
2.7.18-GCCcore-10.3.0-bare
3.11.3-GCCcore-12.3.0
3.8.2-GCCcore-9.3.0
3.9.6-GCCcore-11.2.0-bare
3.10.4-GCCcore-11.3.0-bare
3.7.2-GCCcore-8.2.0
2.7.15-fosscuda-2018b
3.6.6-foss-2018b
2.7.18-GCCcore-11.2.0-bare
3.9.5-GCCcore-10.3.0-bare
3.7.4-GCCcore-9.3.0

Python-bundle-PyPI

Description

Bundle of Python packages from PyPI

More Information

https://python.org/

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

https://userbase.kde.org/QCA

Available Versions:

2.3.5-GCCcore-11.2.0

QGIS

Description

QGIS is a user friendly Open Source Geographic Information System (GIS)

More Information

http://www.qgis.org/

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

http://qiime2.org/

Available Versions:

2022.8
2023.5
2019.7

QScintilla

Description

QScintilla is a port to Qt of Neil Hodgson’s Scintilla C++ editor control

More Information

https://www.riverbankcomputing.com/software/qscintilla

Available Versions:

2.11.6-GCCcore-11.2.0

QUAST

Description

QUAST evaluates genome assemblies by computing various metrics. It works both with and without reference genomes. The tool accepts multiple assemblies, thus is suitable for comparison.

More Information

https://github.com/ablab/quast

Available Versions:

5.0.2-foss-2020a-Python-3.8.2

Qhull

Description

Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, furthest-site Delaunay triangulation, and furthest-site Voronoi diagram. The source code runs in 2-d, 3-d, 4-d, and higher dimensions. Qhull implements the Quickhull algorithm for computing the convex hull.

More Information

http://www.qhull.org

Available Versions:

2020.2-GCCcore-11.2.0
2019.1-GCCcore-8.3.0
2020.2-GCCcore-10.3.0
2020.2-GCCcore-11.3.0
2020.2-GCCcore-12.3.0

Qiskit

Description

Qiskit is an open-source framework for working with noisy quantum computers at the level of pulses, circuits, and algorithms.

More Information

https://qiskit.org

Available Versions:

0.23.1-foss-2020a-Python-3.8.2

Qt5

Description

Qt is a comprehensive cross-platform C++ application framework.

More Information

https://qt.io/

Available Versions:

5.15.2-GCCcore-10.3.0
5.14.2-GCCcore-10.2.0
5.15.2-GCCcore-11.2.0
5.13.1-GCCcore-8.3.0
5.14.1-GCCcore-9.3.0
5.15.5-GCCcore-11.3.0

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
3.6.1-foss-2021a
3.5.3-foss-2020a-Python-3.8.2

QuantumESPRESSO

Description

Quantum ESPRESSO is an integrated suite of computer codesfor electronic-structure calculations and materials modeling at the nanoscale.It is based on density-functional theory, plane waves, and pseudopotentials(both norm-conserving and ultrasoft).

More Information

https://www.quantum-espresso.org

Available Versions:

7.1-intel-2022a
6.7-intel-2020a
6.7-foss-2020b
6.6-foss-2020b
6.6-intel-2020a
6.5-intel-2020a
7.1-foss-2022a

Qwt

Description

The Qwt library contains GUI Components and utility classes which are primarily useful for programs with a technical background.

More Information

https://qwt.sourceforge.net/

Available Versions:

6.1.4-GCCcore-8.3.0
6.2.0-GCCcore-11.2.0
6.2.0-GCCcore-10.3.0

R

Description

R is a free software environment for statistical computing and graphics.

More Information

https://www.r-project.org/

Available Versions:

4.2.1-foss-2021b
4.1.2-foss-2021b-ARC
4.1.0-foss-2021a
4.0.2-foss-2020a
4.2.1-foss-2021b-ARC
3.6.2-foss-2019b
4.1.2-foss-2021b
4.2.2-foss-2022a-ARC
4.0.2-foss-2020a-ARC
4.2.1-foss-2022a
4.1.0-foss-2021a-ARC
4.2.1-foss-2022a-ARC
4.3.2-gfbf-2023a
4.2.2-foss-2022a

R-bundle-Bioconductor

Description

Bioconductor provides tools for the analysis and coprehension of high-throughput genomic data.

More Information

https://bioconductor.org

Available Versions:

3.15-foss-2022a-R-4.2.1
3.14-foss-2021b-R-4.1.2
3.18-foss-2023a-R-4.3.2
3.13-foss-2021a-R-4.1.0
3.10-foss-2019b

R-bundle-CRAN

Description

Bundle of R packages from CRAN

More Information

https://www.r-project.org/

Available Versions:

2023.12-foss-2023a

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-2021b-hybrid-avx2
8.2.12-gompi-2020a-hybrid-avx2

RAxML-NG

Description

RAxML-NG is a phylogenetic tree inference tool which uses 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:

1.2.0-GCC-12.3.0
1.0.2-gompi-2020b

RDKit

Description

RDKit is a collection of cheminformatics and machine-learning software written in C++ and Python.

More Information

https://www.rdkit.org

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

https://github.com/google/re2

Available Versions:

2020-07-01-GCCcore-8.3.0
2021-06-01-GCCcore-10.2.0
2022-02-01-GCCcore-11.2.0
2023-08-01-GCCcore-12.3.0
2022-06-01-GCCcore-11.3.0

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/

Available Versions:

2.13.0-gompi-2022a
2.11.0-gompi-2020b
2.11.0-gompi-2021a

ROOT

Description

The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data in a very efficient way.

More Information

https://root.cern.ch/drupal/

Available Versions:

6.24.06-foss-2021b
6.22.08-foss-2020b
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

https://rapidjson.org

Available Versions:

1.1.0-GCCcore-11.2.0
1.1.0-GCCcore-11.3.0
1.1.0-20230928-GCCcore-12.3.0
1.1.0-GCCcore-8.3.0

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

https://www.repeatmasker.org/

Available Versions:

4.1.2-p1-foss-2021a
4.1.5-foss-2022a
4.1.2-p1-foss-2020b

RepeatModeler

Description

RepeatModeler is a de novo transposable element (TE) family identification and modeling package.

More Information

https://www.repeatmasker.org/

Available Versions:

2.0.2a-foss-2020b

RepeatScout

Description

De Novo Repeat Finder, Price A.L., Jones N.C. and Pevzner P.A. Developed and tested with our multiple sequence version of RepeatScout ( 1.0.6 )

More Information

https://www.repeatmasker.org/

Available Versions:

1.0.6-GCC-10.2.0
1.0.6-GCC-10.3.0

RevBayes

Description

RevBayes provides an interactive environment for statistical computation in phylogenetics. It is primarily intended for modeling, simulation, and Bayesian inference in evolutionary biology, particularly phylogenetics.

More Information

https://revbayes.github.io

Available Versions:

1.2.1-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

https://www.ruby-lang.org

Available Versions:

2.6.1-GCCcore-7.3.0
3.0.1-GCCcore-10.3.0
3.0.1-GCCcore-11.2.0

Rust

Description

Rust is a systems programming language that runs blazingly fast, prevents segfaults, and guarantees thread safety.

More Information

https://www.rust-lang.org

Available Versions:

1.42.0-GCCcore-9.3.0
1.42.0-GCCcore-8.3.0
1.52.1-GCCcore-10.3.0
1.60.0-GCCcore-11.3.0
1.54.0-GCCcore-11.2.0
1.70.0-GCCcore-12.3.0
1.65.0-GCCcore-12.2.0

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

https://www.htslib.org/

Available Versions:

0.1.20-GCC-8.3.0
1.13-GCC-10.3.0
1.9-foss-2018b
1.16.1-GCC-11.3.0
1.11-GCC-10.2.0
0.1.20-foss-2020a
1.12-GCC-10.2.0
1.15.1-GCC-11.2.0
1.10-GCC-8.3.0
1.14-GCC-11.2.0
1.10-GCC-9.3.0

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

http://gforge.inria.fr/projects/scotch/

Available Versions:

6.0.6-gompi-2019a
6.0.9-iimpi-2020a
6.0.9-gompi-2020a
6.1.2-iimpi-2021b
6.1.0-gompi-2020b
6.0.6-foss-2018b
7.0.3-gompi-2023a
7.0.1-gompi-2022a
6.0.9-gompi-2019b
6.1.0-gompi-2021a

SCons

Description

SCons is a software construction tool.

More Information

https://www.scons.org/

Available Versions:

4.4.0-GCCcore-11.3.0
4.2.0-GCCcore-11.2.0
3.0.5-GCCcore-8.2.0
3.1.1-GCCcore-8.3.0
4.0.1-GCCcore-10.2.0
3.0.1-fosscuda-2018b-Python-2.7.15
3.0.1-foss-2018b-Python-2.7.15
3.0.5-GCCcore-8.2.0-Python-2.7.15

SDL2

Description

SDL: Simple DirectMedia Layer, a cross-platform multimedia library

More Information

https://www.libsdl.org/

Available Versions:

2.0.20-GCCcore-11.2.0
2.26.3-GCCcore-12.2.0
2.28.2-GCCcore-12.3.0
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-foss-2020a
1.7.7-GCCcore-11.3.0-tools
1.7.6-GCCcore-9.3.0-tools

SKESA

Description

SKESA is a de-novo sequence read assembler for cultured single isolate genomes based on DeBruijn graphs.

More Information

https://github.com/ncbi/SKESA

Available Versions:

2.3.0-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

https://www.grycap.upv.es/slepc/

Available Versions:

3.15.1-foss-2021a
3.12.2-foss-2019b-Python-3.7.4
3.12.2-intel-2020a-Python-3.8.2

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

http://soci.sourceforge.net/

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:

3.15.3-GCC-11.2.0
3.15.2-GCC-10.2.0
3.13.0-foss-2018b
3.13.0-GCC-10.3.0

SQLite

Description

SQLite: SQL Database Engine in a C Library

More Information

https://www.sqlite.org/

Available Versions:

3.29.0-GCCcore-9.3.0
3.27.2-GCCcore-8.2.0
3.31.1-GCCcore-9.3.0
3.33.0-GCCcore-10.2.0
3.24.0-GCCcore-7.3.0
3.42.0-GCCcore-12.3.0
3.29.0-GCCcore-8.3.0
3.24.0-GCCcore-10.2.0
3.36-GCCcore-11.2.0
3.38.3-GCCcore-11.3.0
3.35.4-GCCcore-10.3.0
3.39.4-GCCcore-12.2.0
3.27.2-GCCcore-8.3.0

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:

2.7.9a-GCC-11.2.0
2.7.3a-GCC-9.3.0
2.7.10b-GCC-11.3.0
2.7.1a-GCC-8.2.0-2.31.1

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
5.1.0-foss-2019b
6.3.0-foss-2021b

SWIG

Description

SWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages.

More Information

http://www.swig.org/

Available Versions:

4.0.2-GCCcore-11.3.0
4.0.2-GCCcore-11.2.0
3.0.12-GCCcore-8.2.0-Python-2.7.15
4.0.2-GCCcore-10.3.0
4.1.1-GCCcore-12.3.0
3.0.12-foss-2018b-Python-2.7.15
4.0.1-GCCcore-8.3.0
3.0.12-GCCcore-8.3.0
4.1.1-GCCcore-12.2.0
4.1.1-GCCcore-13.2.0
4.0.1-GCCcore-9.3.0
4.0.2-GCCcore-10.2.0

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
1.1.0-gompi-2019b
1.10.1-GCC-11.3.0
1.4.0-GCC-11.2.0

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:

0.7.1
0.8.2-GCC-10.3.0

Satsuma2

Description

Satsuma2 is an optimised version of Satsuma, a tool to reliably align large and complex DNA sequencesproviding maximum sensitivity (to find all there is to find), specificity (to only find real homology) and speed (toaccommodate the billions of base pairs in vertebrate genomes).

More Information

https://github.com/bioinfologics/satsuma2

Available Versions:

20220304-GCC-11.3.0

ScaFaCoS

Description

ScaFaCoS is a library of scalable fast coulomb solvers.

More Information

http://www.scafacos.de/

Available Versions:

1.0.1-intel-2020a
1.0.4-foss-2022a
1.0.1-foss-2021a
1.0.1-foss-2020a
1.0.1-foss-2021b

ScaLAPACK

Description

The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers.

More Information

https://www.netlib.org/scalapack/

Available Versions:

2.2.0-gompi-2022b-fb
2.1.0-gompic-2020b
2.0.2-gompi-2019b
2.1.0-gompic-2020a
2.0.2-gompi-2018b-OpenBLAS-0.3.1
2.2.0-gompi-2022a-fb
2.0.2-gompi-2019a-OpenBLAS-0.3.5
2.1.0-gompi-2021a-fb
2.2.0-gompi-2023a-fb
2.0.2-gompic-2019b
2.0.2-gompic-2018b-OpenBLAS-0.3.1
2.1.0-gompi-2020a
2.1.0-gompi-2020b
2.1.0-gompi-2021b-fb

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

https://www.scalasca.org/

Available Versions:

2.5-gompi-2020a

SciPy-bundle

Description

Bundle of Python packages for scientific software

More Information

https://python.org/

Available Versions:

2020.03-foss-2020a-Python-3.8.2
2019.10-foss-2019b-Python-2.7.16
2019.10-fosscuda-2019b-Python-2.7.16
2021.05-foss-2021a
2019.10-foss-2019b-Python-3.7.4
2020.11-fosscuda-2020b
2023.07-gfbf-2023a
2020.03-intel-2020a-Python-3.8.2
2020.03-fosscuda-2020a-Python-3.8.2
2021.05-foss-2021a-SKL
2022.05-foss-2022a
2021.10-foss-2021b
2020.11-intel-2020b
2019.03-foss-2019a
2022.05-intel-2022a
2021.10-intel-2021b
2019.10-fosscuda-2019b-Python-3.7.4
2020.11-foss-2020b
2023.02-gfbf-2022b

Score-P

Description

The Score-P measurement infrastructure is a highly scalable and easy-to-use tool suite for profiling, event tracing, and online analysis of HPC applications.

More Information

https://www.score-p.org

Available Versions:

6.0-gompi-2020a

Seaborn

Description

Seaborn is a Python visualization library based on matplotlib. It provides a high-level interface for drawing attractive statistical graphics.

More Information

https://seaborn.pydata.org/

Available Versions:

0.10.0-foss-2019b-Python-3.7.4

SegAlign

Available Versions:

master-feb23

SentencePiece

Description

Unsupervised text tokenizer for Neural Network-based text generation.

More Information

https://github.com/google/sentencepiece

Available Versions:

0.1.96-GCC-10.2.0
0.1.97-GCC-11.3.0
0.1.85-GCC-8.3.0-Python-3.7.4

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

https://serf.apache.org/

Available Versions:

1.3.9-GCCcore-11.3.0
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:

1.7.1-GCC-9.3.0-Python-3.8.2
1.8.2-foss-2021b

Siesta

Description

SIESTA is both a method and its computer program implementation, to perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids.

More Information

http://departments.icmab.es/leem/siesta

Available Versions:

4.1.5-foss-2020a
4.1.5-intel-2022a
4.1-b4-intel-2020a

SoX

Description

Sound eXchange, the Swiss Army knife of audio manipulation

More Information

http://sox.sourceforge.net/

Available Versions:

14.4.2-GCCcore-11.3.0

Spack

Description

Spack is a package manager for supercomputers, Linux, and macOS. It makes installing scientific software easy. With Spack, you can build a package with multiple versions, configurations, platforms, and compilers, and all of these builds can coexist on the same machine.

More Information

https://spack.io/

Available Versions:

0.17.2

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
2.41-iccifort-2019.5.281
2.53-foss-2019b

Stata

Available Versions:

14

Subversion

Description

Subversion is an open source version control system.

More Information

https://subversion.apache.org/

Available Versions:

1.14.2-GCCcore-11.3.0
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:

5.8.1-foss-2020b-METIS-5.1.0
5.10.1-intel-2021b-METIS-5.1.0
5.4.0-foss-2019a-METIS-5.1.0
5.6.0-foss-2019b-METIS-5.1.0
5.10.1-foss-2021a-METIS-5.1.0
5.13.0-foss-2022a-METIS-5.1.0
5.11.0-foss-2021a-METIS-5.1.0
5.7.1-foss-2020a-METIS-5.1.0
5.7.1-intel-2020a-METIS-5.1.0
5.10.1-foss-2021b-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

http://www.hdfgroup.org/doc_resource/SZIP/

Available Versions:

2.1.1-GCCcore-7.3.0
2.1.1-GCCcore-8.3.0
2.1.1-GCCcore-9.3.0
2.1.1-GCCcore-8.2.0
2.1.1-GCCcore-10.2.0
2.1.1-intel-2020a
2.1.1-GCCcore-10.3.0
2.1.1-GCCcore-11.2.0
2.1.1-GCCcore-11.3.0
2.1.1-GCCcore-12.2.0
2.1.1-GCCcore-12.3.0

TCLAP

Description

TCLAP is a small, flexible library that provides a simple interface for defining and accessingcommand line arguments. It was intially inspired by the user friendly CLAP libary.

More Information

http://tclap.sourceforge.net/

Available Versions:

1.2.5-GCCcore-11.2.0

TEtranscripts

Description

TEtranscripts and TEcount takes RNA-seq (and similar data) and annotates readsto both genes & transposable elements.TEtranscripts then performs differential analysis using DESeq2.

More Information

https://github.com/mhammell-laboratory/TEtranscripts

Available Versions:

2.2.0-foss-2021b

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-11.3.0
4.09.1-GCCcore-10.2.0

TWL-NINJA

Description

Nearly Infinite Neighbor Joining Application.

More Information

https://github.com/TravisWheelerLab/NINJA

Available Versions:

0.97-cluster_only-GCC-10.2.0
0.97-cluster_only-GCC-10.3.0

Tcl

Description

Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.

More Information

https://www.tcl.tk/

Available Versions:

8.6.11-GCCcore-10.3.0
8.6.9-GCCcore-8.3.0
8.6.10-GCCcore-9.3.0
8.6.8-GCCcore-10.2.0
8.6.8-GCCcore-7.3.0
8.6.9-GCCcore-9.3.0
8.6.12-GCCcore-12.2.0
8.6.12-GCCcore-11.3.0
8.6.11-GCCcore-11.2.0
8.6.13-GCCcore-12.3.0
8.6.10-GCCcore-10.2.0
8.6.9-GCCcore-8.2.0

TensorFlow

Description

An open-source software library for Machine Intelligence

More Information

https://www.tensorflow.org/

Available Versions:

2.11.0-foss-2022a
2.5.0-fosscuda-2020b
2.1.0-foss-2019b-Python-3.7.4
1.15.2-fosscuda-2019b-Python-3.7.4
2.5.3-foss-2021a-CUDA-11.3.1
2.11.0-foss-2022a-CUDA-11.7.0
2.6.0-foss-2021a-CUDA-11.3.1
2.3.1-foss-2020a-Python-3.8.2
2.4.1-fosscuda-2020b
2.7.1-foss-2021b-CUDA-11.4.1
2.6.0-foss-2021a
2.8.4-foss-2021b

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
1.1.2-foss-2020b-PyMC
1.1.2-fosscuda-2020b-PyMC
1.0.4-foss-2019b-Python-3.7.4

Tinker9

Description

The Tinker molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers.

More Information

https://github.com/TinkerTools/tinker9

Available Versions:

1.0.4-GIT-31839758

Tk

Description

Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building a graphical user interface (GUI) in many different programming languages.

More Information

https://www.tcl.tk/

Available Versions:

8.6.9-GCCcore-8.3.0
8.6.9-GCCcore-8.2.0
8.6.11-GCCcore-10.3.0
8.6.12-GCCcore-12.2.0
8.6.12-GCCcore-11.3.0
8.6.9-GCCcore-9.3.0
8.6.8-GCCcore-7.3.0
8.6.13-GCCcore-12.3.0
8.6.11-GCCcore-11.2.0
8.6.10-GCCcore-10.2.0
8.6.10-GCCcore-9.3.0

Tkinter

Description

Tkinter module, built with the Python buildsystem

More Information

https://python.org/

Available Versions:

3.8.2-GCCcore-9.3.0
3.8.6-GCCcore-10.2.0
3.7.4-GCCcore-8.3.0
3.7.2-GCCcore-8.2.0
3.9.5-GCCcore-10.3.0
2.7.15-fosscuda-2018b-Python-2.7.15
3.10.4-GCCcore-11.3.0
2.7.16-GCCcore-8.3.0
2.7.15-foss-2018b-Python-2.7.15
3.9.6-GCCcore-11.2.0

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-intel-2020a
1.13-GCC-10.3.0

Trilinos

Description

The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented software framework for the solution of large-scale, complex multi-physics engineering and scientific problems. A unique design feature of Trilinos is its focus on packages.

More Information

https://trilinos.org

Available Versions:

12.12.1-foss-2019b-Python-3.7.4

Trim_Galore

Description

Trim Galore is a wrapper around Cutadapt and FastQC toconsistently apply adapter and quality trimming to FastQ files, with extrafunctionality for RRBS data.

More Information

https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/

Available Versions:

0.6.5-GCCcore-8.3.0-Java-11-Python-3.7.4
0.5.0-foss-2018b

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:

2.10.0-foss-2019b-Python-3.7.4
2.13.2-foss-2019b-Python-3.7.4
2.14.0-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

https://www.openucx.org/

Available Versions:

1.1.0-GCCcore-12.2.0
1.0.0-GCCcore-11.3.0
1.2.0-GCCcore-12.3.0

UCX

Description

Unified Communication XAn open-source production grade communication framework for data centricand high-performance applications

More Information

http://www.openucx.org/

Available Versions:

1.8.0-GCCcore-9.3.0
1.11.2-GCCcore-11.2.0
1.9.0-GCCcore-10.2.0
1.9.0-GCCcore-10.2.0-CUDA-11.1.1
1.14.1-GCCcore-12.3.0
1.13.1-GCCcore-12.2.0
1.9.0-GCCcore-10.3.0-CUDA-11.1.1
1.14.0-GCCcore-12.2.0
1.12.1-GCCcore-11.3.0
1.8.0-GCCcore-9.3.0-CUDA-11.0.2
1.10.0-GCCcore-10.3.0

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

http://www.openucx.org/

Available Versions:

1.12.1-GCCcore-11.3.0-CUDA-11.8.0
1.11.2-GCCcore-11.2.0-CUDA-11.4.1
1.12.1-GCCcore-11.3.0-CUDA-12.0.0
1.12.1-GCCcore-11.3.0-CUDA-11.7.0
1.10.0-GCCcore-10.3.0-CUDA-11.3.1

UDUNITS

Description

UDUNITS supports conversion of unit specifications between formatted and binary forms, arithmetic manipulation of units, and conversion of values between compatible scales of measurement.

More Information

https://www.unidata.ucar.edu/software/udunits/

Available Versions:

2.2.28-GCCcore-11.3.0
2.2.26-GCCcore-8.3.0
2.2.28-GCCcore-12.3.0
2.2.28-GCCcore-11.2.0
2.2.26-foss-2020a
2.2.26-GCCcore-10.2.0
2.2.28-GCCcore-12.2.0
2.2.28-GCCcore-10.3.0

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-10.3.0
6.0-GCCcore-11.3.0
6.0-GCCcore-9.3.0
6.0-GCCcore-12.2.0
6.0-GCCcore-11.2.0
6.0-GCCcore-10.2.0
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:

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-2021a-R-4.1.0
2.2-foss-2020a-R-4.0.2
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

https://vcftools.github.io

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

https://www.vtk.org

Available Versions:

8.2.0-foss-2019b-Python-3.7.4
9.1.0-foss-2021b
8.2.0-foss-2020a-Python-3.8.2
9.2.2-foss-2022a
9.0.1-foss-2021a
8.2.0-intel-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:

2020_update3
2023.2.0
2021.9.0
2019_update5

Valgrind

Description

Valgrind: Debugging and profiling tools

More Information

https://valgrind.org

Available Versions:

3.18.1-gompi-2021b
3.14.0-foss-2018b
3.16.1-iimpi-2020a
3.20.0-gompi-2022a
3.19.0-gompi-2022a
3.16.1-gompi-2020a
3.17.0-gompi-2021a

Vampire

Available Versions:

6.0
5.0

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

http://www.vim.org

Available Versions:

8.1.1209-GCCcore-8.2.0-Python-3.7.2

Voro++

Description

Voro++ is a software library for carrying out three-dimensional computations of the Voronoitessellation. A distinguishing feature of the Voro++ library is that it carries out cell-based calculations,computing the Voronoi cell for each particle individually. It is particularly well-suited for applications thatrely on cell-based statistics, where features of Voronoi cells (eg. volume, centroid, number of faces) can be usedto analyze a system of particles.

More Information

http://math.lbl.gov/voro++/

Available Versions:

0.4.6-GCCcore-11.3.0
0.4.6-GCCcore-10.3.0
0.4.6-GCCcore-11.2.0
0.4.6-GCCcore-9.3.0

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

http://www.wien2k.at/

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

http://www.wannier.org

Available Versions:

3.1.0-foss-2021b
3.1.0-intel-2021b
3.1.0-intel-2020a
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

http://www.wanniertools.com

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:

1.22.0-GCCcore-12.3.0
1.20.0-GCCcore-11.3.0
1.22.0-GCCcore-12.2.0
1.21.0-GCCcore-11.2.0

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

https://webkitgtk.org/

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

https://www.x.org

Available Versions:

20230603-GCCcore-12.3.0
20180604-GCCcore-7.3.0
20200222-GCCcore-9.3.0
20190311-GCCcore-8.2.0
20190717-GCCcore-8.3.0
20190717-GCCcore-9.3.0
20210518-GCCcore-10.3.0
20221110-GCCcore-12.2.0
20220504-GCCcore-11.3.0
20201008-GCCcore-10.2.0
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

http://dftlibs.org/xcfun/

Available Versions:

20190127-foss-2020a-Python-3.8.2
2.1.1-GCCcore-10.3.0
20190127-foss-2019a-Python-3.7.2

XCfun

Description

XCFun is a library of DFT exchange-correlation (XC) functionals. It is based on automatic differentiation and can therefore generate arbitrary order derivatives of these functionals.

More Information

http://dftlibs.org/xcfun/

Available Versions:

20190127-foss-2019a-Python-3.7.2

XCrySDen

Description

XCrySDen is a crystalline and molecular structure visualisation program aiming at display of isosurfaces and contours, which can be superimposed on crystalline structures and interactively rotated and manipulated.

More Information

http://www.xcrysden.org/

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

http://www.xmds.org/

Available Versions:

3.1.0-foss-2020a-Python-3.8.2
2.2.3-foss-2018b-Python-2.7.15

XML-LibXML

Description

Perl binding for libxml2

More Information

https://metacpan.org/pod/distribution/XML-LibXML/LibXML.pod

Available Versions:

2.0207-GCCcore-11.3.0
2.0205-GCCcore-9.3.0
2.0207-GCCcore-10.3.0
2.0207-GCCcore-11.2.0

XML-Parser

Description

This is a Perl extension interface to James Clark’s XML parser, expat.

More Information

http://search.cpan.org/~toddr/XML-Parser-2.41/

Available Versions:

2.44_01-GCCcore-7.3.0-Perl-5.28.0

XSD

Description

CodeSynthesis XSD is an open-source, cross-platform W3C XML Schema to C++ data binding compiler.

More Information

https://www.codesynthesis.com/products/xsd/

Available Versions:

4.0.0-GCCcore-10.3.0

XZ

Description

xz: XZ utilities

More Information

https://tukaani.org/xz/

Available Versions:

5.2.4-GCCcore-7.3.0
5.4.2-GCCcore-12.3.0
5.2.5-GCCcore-9.3.0
5.2.7-GCCcore-12.2.0
5.2.4-GCCcore-8.3.0
5.2.4-GCCcore-9.3.0
5.2.4-GCCcore-10.2.0
5.2.4-GCCcore-8.2.0
5.2.5-GCCcore-10.3.0
5.2.5-GCCcore-11.3.0
5.2.5-GCCcore-10.2.0
5.2.5-GCCcore-11.2.0

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:

3.2.4-GCCcore-12.3.0
3.2.3-GCCcore-10.3.0

Xvfb

Description

Xvfb is an X server that can run on machines with no display hardware and no physical input devices. It emulates a dumb framebuffer using virtual memory.

More Information

https://www.x.org/releases/X11R7.6/doc/man/man1/Xvfb.1.xhtml

Available Versions:

1.20.13-GCCcore-11.2.0
21.1.3-GCCcore-11.3.0
1.20.9-GCCcore-10.2.0
21.1.6-GCCcore-12.2.0
21.1.8-GCCcore-12.3.0
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-8.3.0
1.3.0-GCCcore-9.3.0
1.3.0-GCCcore-11.2.0
1.3.0-GCCcore-10.3.0
1.3.0-GCCcore-12.3.0
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-12.2.0

Z3

Description

Z3 is a theorem prover from Microsoft Research.

More Information

https://github.com/Z3Prover/z3

Available Versions:

4.12.2-GCCcore-12.2.0
4.8.12-GCCcore-11.2.0
4.10.2-GCCcore-11.3.0
4.8.10-GCCcore-10.2.0

ZeroMQ

Description

ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. It gives you sockets that carry atomic messages across various transports like in-process, inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, pub-sub, task distribution, and request-reply. It’s fast enough to be the fabric for clustered products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous message-processing tasks. It has a score of language APIs and runs on most operating systems.

More Information

https://www.zeromq.org/

Available Versions:

4.3.3-GCCcore-10.2.0
4.3.2-GCCcore-8.3.0
4.3.2-GCCcore-9.3.0
4.3.4-GCCcore-10.3.0
4.3.4-GCCcore-12.3.0
4.3.4-GCCcore-11.3.0
4.3.4-GCCcore-11.2.0

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-11.3.0
3.0-GCCcore-8.3.0
3.0-GCCcore-10.2.0
3.0-GCCcore-11.2.0
3.0-GCCcore-12.2.0
3.0-GCCcore-9.3.0

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

http://www.popgen.dk/angsd

Available Versions:

0.935-GCC-10.2.0
0.933-GCC-8.3.0
0.925-foss-2018b

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

https://ant.apache.org/

Available Versions:

1.10.7-Java-11
1.10.11-Java-11
1.10.9-Java-11
1.10.12-Java-11
1.10.14-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
0.1.2-GCCcore-10.3.0
0.1.4-GCCcore-11.3.0
0.1.3-GCCcore-11.2.0

aria2

Description

aria2 is a lightweight multi-protocol & multi-source command-line download utility.

More Information

https://aria2.github.io

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:

3.9.0-foss-2023a
3.7.0-intel-2020a
3.7.0-foss-2020a
3.8.0-foss-2021b
3.7.0-foss-2019b

arrow-R

Description

R interface to the Apache Arrow C++ library

More Information

https://cran.r-project.org/web/packages/arrow

Available Versions:

6.0.0.2-foss-2021b-R-4.1.2
8.0.0-foss-2022a-R-4.2.1
14.0.0.2-foss-2023a-R-4.3.2

at-spi2-atk

Description

AT-SPI 2 toolkit bridge

More Information

https://wiki.gnome.org/Accessibility

Available Versions:

2.38.0-GCCcore-11.2.0
2.34.1-GCCcore-8.3.0
2.38.0-GCCcore-12.2.0
2.38.0-GCCcore-10.2.0
2.38.0-GCCcore-12.3.0
2.38.0-GCCcore-11.3.0
2.32.0-GCCcore-8.2.0

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
2.44.1-GCCcore-11.3.0
2.32.0-GCCcore-8.2.0
2.46.0-GCCcore-12.2.0
2.38.0-GCCcore-10.2.0
2.34.0-GCCcore-8.3.0
2.40.3-GCCcore-11.2.0

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-10.2.0
4.0.0-GCC-11.3.0
3.1.2-GCC-8.2.0-2.31.1
3.1.2-GCC-7.3.0-2.30

binutils

Description

binutils: GNU binary utilities

More Information

https://directory.fsf.org/project/binutils/

Available Versions:

2.40
2.39
2.32-GCCcore-9.3.0
2.34
2.32-GCCcore-8.3.0
2.34-GCCcore-9.3.0
2.35
2.30-GCCcore-8.1.0
2.28
2.31.1-GCCcore-8.2.0
2.26
2.40-GCCcore-12.3.0
2.30
2.37-GCCcore-11.2.0
2.25
2.36.1
2.32
2.38
2.38-GCCcore-11.3.0
2.31.1-GCCcore-8.3.0
2.39-GCCcore-12.2.0
2.35-GCCcore-10.2.0
2.27
2.31.1
2.40-GCCcore-13.2.0
2.37
2.40-GCCcore-13.1.0
2.36.1-GCCcore-10.3.0
2.30-GCCcore-7.3.0

bokeh

Description

Statistical and novel interactive HTML plots for Python

More Information

https://github.com/bokeh/bokeh

Available Versions:

2.2.3-foss-2020b
2.4.3-foss-2022a
2.2.3-fosscuda-2020b
1.4.0-foss-2019b-Python-3.7.4

breseq

Description

breseq is a computational pipeline for the analysis of short-read re-sequencing data

More Information

https://barricklab.org/breseq

Available Versions:

0.36.1-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:

1.9.14-GCCcore-8.3.0
1.9.13-GCCcore-8.2.0

bzip2

Description

bzip2 is a freely available, patent free, high-quality data compressor. It typically compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical compressors), whilst being around twice as fast at compression and six times faster at decompression.

More Information

https://sourceware.org/bzip2

Available Versions:

1.0.8-GCCcore-7.3.0
1.0.8-GCCcore-10.3.0
1.0.6-GCCcore-8.2.0
1.0.6-GCCcore-7.3.0
1.0.8-GCCcore-12.3.0
1.0.6-GCCcore-8.3.0
1.0.8-GCCcore-11.3.0
1.0.8-GCCcore-12.2.0
1.0.8-GCCcore-8.3.0
1.0.8-GCCcore-9.3.0
1.0.6-GCCcore-10.2.0
1.0.8-GCCcore-11.2.0
1.0.8-GCCcore-10.2.0

c-ares

Description

c-ares is a C library for asynchronous DNS requests (including name resolves)

More Information

https://c-ares.org/

Available Versions:

1.18.1-GCCcore-11.2.0
1.17.2-GCCcore-10.3.0

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

https://curl.haxx.se

Available Versions:

7.76.0-GCCcore-10.3.0
7.86.0-GCCcore-12.2.0
7.60.0-GCCcore-10.2.0
7.66.0-GCCcore-8.3.0
7.83.0-GCCcore-11.3.0
8.0.1-GCCcore-12.3.0
7.63.0-GCCcore-8.2.0
7.72.0-GCCcore-10.2.0
7.69.1-GCCcore-9.3.0
7.78.0-GCCcore-11.2.0
7.60.0-GCCcore-7.3.0
7.66.0-GCCcore-7.3.0

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

https://cairographics.org

Available Versions:

1.16.0-GCCcore-10.2.0
1.17.4-GCCcore-12.2.0
1.14.12-GCCcore-7.3.0
1.16.0-GCCcore-11.2.0
1.17.8-GCCcore-12.3.0
1.16.0-GCCcore-8.3.0
1.16.0-GCCcore-9.3.0
1.17.4-GCCcore-11.3.0
1.16.0-GCCcore-10.3.0
1.16.0-GCCcore-8.2.0

casacore

Description

A suite of C++ libraries for radio astronomy data processing.The ephemerides data needs to be in DATA_DIR and the location must be specified at runtime.Thus user’s can update them.

More Information

https://github.com/casacore/casacore

Available Versions:

3.4.0-foss-2021b

ccache

Description

Ccache (or “ccache”) is a compiler cache. It speeds up recompilation bycaching previous compilations and detecting when the same compilation is being done again

More Information

https://ccache.dev/

Available Versions:

4.6.1-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

https://colossalai.org/

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-11.3.0
1.1.0-GCCcore-11.2.0
1.2.1-GCCcore-12.3.0

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:

8.6.0.163-CUDA-11.8.0
8.0.4.30-CUDA-11.0.2
8.4.0.27-CUDA-11.6.0
8.7.0.84-CUDA-11.8.0
8.2.1.32-CUDA-11.3.1
8.0.4.30-CUDA-11.1.1
8.1.1.33-CUDA-11.2.2
8.4.1.50-CUDA-11.7.0
7.6.4.38-gcccuda-2019b
8.8.0.121-CUDA-12.0.0
8.2.2.26-CUDA-11.4.1

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:

1.18-foss-2018b-Python-3.6.6
4.3-GCCcore-11.3.0
4.2-GCCcore-11.3.0
3.5-GCCcore-11.2.0
2.7-GCCcore-8.3.0-Python-3.7.4

cylc

Available Versions:

7.8.7

dask

Description

Dask natively scales Python. Dask provides advanced parallelism for analytics, enabling performance at scale for the tools you love.

More Information

https://dask.org/

Available Versions:

2.8.0-foss-2019b-Python-3.7.4
2022.10.0-foss-2022a
2021.2.0-foss-2020b
2021.2.0-fosscuda-2020b

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-11.2.0
0.3.3-foss-2020a-Python-3.8.2
0.3.4-GCCcore-10.3.0

dm-tree

Description

dm-tree provides tree, a library for working with nested data structures. In a way,tree generalizes the builtin map function which only supports flat sequences, andallows to apply a function to each “leaf” preserving the overall structure.

More Information

https://github.com/deepmind/tree

Available Versions:

0.1.6-GCCcore-11.2.0
0.1.6-GCCcore-10.3.0
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:

0.3.1-foss-2022a-CUDA-11.7.0
0.3.2-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:

3.2.0-GCCcore-11.3.0
3.1.4-GCCcore-8.3.0
3.1.5-GCCcore-9.3.0
3.1.5-GCCcore-10.3.0
3.3.0-GCCcore-12.3.0
3.1.5-GCCcore-10.2.0
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:

2.20.0-gompi-2020b
2.27.0-gompi-2022a

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

https://einops.rocks/

Available Versions:

0.4.1-GCCcore-10.3.0

elfutils

Description

The elfutils project provides libraries and tools for ELF files and DWARF data.

More Information

https://elfutils.org/

Available Versions:

0.187-GCCcore-11.3.0
0.183-GCCcore-10.2.0
0.185-GCCcore-8.3.0
0.189-GCCcore-12.3.0
0.185-GCCcore-11.2.0
0.189-GCCcore-12.2.0

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

https://exiv2.org

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

https://libexpat.github.io

Available Versions:

2.4.8-GCCcore-11.3.0
2.2.9-GCCcore-9.3.0
2.2.5-GCCcore-7.3.0
2.2.6-GCCcore-8.2.0
2.2.6-GCCcore-8.3.0
2.2.9-GCCcore-10.2.0
2.2.9-GCCcore-10.3.0
2.2.5-GCCcore-8.1.0
2.2.7-GCCcore-7.3.0
2.5.0-GCCcore-12.3.0
2.2.5-GCCcore-10.2.0
2.2.7-GCCcore-9.3.0
2.2.7-GCCcore-8.3.0
2.4.9-GCCcore-12.2.0
2.4.1-GCCcore-11.2.0

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-10.3.0
0.1.3-GCCcore-11.3.0
0.1.3-GCCcore-11.2.0

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:

12.0.16.0
11.1.5.2

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:

5.39-GCCcore-10.2.0
5.35-GCCcore-7.3.0
5.43-GCCcore-11.3.0

filevercmp

Description

filevercmp function as in sort –version-sort.

More Information

https://github.com/ekg/filevercmp

Available Versions:

20191210-GCCcore-11.2.0

fineRADstructure

Description

A package for population structure inference from RAD-seq data

More Information

http://cichlid.gurdon.cam.ac.uk/fineRADstructure.html

Available Versions:

20180709-intel-2020a

fineSTRUCTURE

Description

fineSTRUCTURE is a fast and powerful algorithm for identifying population structure using dense sequencing data.

More Information

https://people.maths.bris.ac.uk/~madjl/finestructure/finestructure_info.html

Available Versions:

2.1.3-intel-2020a

fio

Description

Flexible I/O tester

More Information

https://github.com/axboe/fio

Available Versions:

3.36-GCCcore-12.3.0
3.34-GCCcore-12.2.0

flappie

Available Versions:

2.1.3

flatbuffers

Description

FlatBuffers: Memory Efficient Serialization Library

More Information

https://github.com/google/flatbuffers/

Available Versions:

1.12.0-GCCcore-8.3.0
2.0.0-GCCcore-11.2.0
2.0.7-GCCcore-11.3.0
1.12.0-GCCcore-9.3.0
1.12.0-GCCcore-10.2.0
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-10.3.0
2.0-GCCcore-11.3.0
2.0-GCCcore-11.2.0

flex

Description

Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, sometimes called a tokenizer, is a program which recognizes lexical patterns in text.

More Information

http://flex.sourceforge.net/

Available Versions:

2.6.4-GCCcore-8.3.0
2.5.39
2.6.0
2.6.4-GCCcore-8.1.0
2.6.4-GCCcore-11.2.0
2.6.4-GCCcore-13.1.0
2.6.4-GCCcore-8.2.0
2.6.4
2.5.39-GCCcore-8.3.0
2.6.4-GCCcore-7.3.0
2.6.4-GCCcore-10.2.0
2.6.4-GCCcore-9.3.0
2.6.4-GCCcore-10.3.0
2.6.4-GCCcore-12.2.0
2.6.4-GCCcore-11.3.0
2.6.4-GCCcore-13.2.0
2.6.4-GCCcore-12.3.0
2.6.3

flit

Description

A simple packaging tool for simple packages.

More Information

https://github.com/pypa/flit

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

https://www.freedesktop.org/wiki/Software/fontconfig/

Available Versions:

2.13.92-GCCcore-9.3.0
2.13.92-GCCcore-10.2.0
2.13.1-GCCcore-8.3.0
2.13.93-GCCcore-10.3.0
2.14.1-GCCcore-12.2.0
2.14.0-GCCcore-11.3.0
2.13.0-GCCcore-7.3.0
2.13.1-GCCcore-8.2.0
2.13.94-GCCcore-11.2.0
2.13.1-GCCcore-9.3.0
2.14.2-GCCcore-12.3.0

foss

Description

GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.

More Information

https://easybuild.readthedocs.io/en/master/Common-toolchains.html#foss-toolchain

Available Versions:

2023a
2021a
2022a
2019b
2022b
2019a
2018b
2020a
2020b
2021b

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:

2020a
2020g
2019b
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-10.2.0
3.2.1-GCCcore-9.3.0
3.2.1-GCCcore-10.3.0
3.2.1-GCCcore-11.2.0
3.2.1-GCCcore-8.3.0

freetype

Description

FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display servers, font conversion tools, text image generation tools, and many other products as well.

More Information

https://www.freetype.org

Available Versions:

2.10.4-GCCcore-10.3.0
2.13.0-GCCcore-12.3.0
2.10.3-GCCcore-10.2.0
2.10.1-GCCcore-8.3.0
2.12.1-GCCcore-11.3.0
2.9.1-GCCcore-8.2.0
2.10.1-GCCcore-9.3.0
2.11.0-GCCcore-11.2.0
2.12.1-GCCcore-12.2.0
2.9.1-GCCcore-7.3.0

fsm-lite

Available Versions:

1.0

fsom

Description

A tiny C library for managing SOM (Self-Organizing Maps) neural networks.

More Information

https://github.com/ekg/fsom

Available Versions:

20141119-GCCcore-11.2.0

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 a garbage collecting replacement for C malloc or C++ new.

More Information

https://hboehm.info/gc/

Available Versions:

7.6.10-GCCcore-8.2.0
7.6.12-GCCcore-9.3.0
8.2.2-GCCcore-11.3.0
7.6.12-GCCcore-8.3.0
8.2.0-GCCcore-11.2.0

gcccuda

Description

GNU Compiler Collection (GCC) based compiler toolchain, along with CUDA toolkit.

More Information

(none)

Available Versions:

2020b
2020a
2018b
2019b

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:

0.21.1-GCCcore-12.2.0
0.21.1-GCCcore-12.3.0
0.20.1-GCCcore-8.3.0
0.21-GCCcore-10.3.0
0.21-GCCcore-11.3.0
0.21-GCCcore-11.2.0
0.21-GCCcore-10.2.0
0.19.8.1-GCCcore-8.2.0
0.19.8.1
0.21.1
0.20.1-GCCcore-9.3.0
0.19.8.1-GCCcore-7.3.0
0.21
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://libungif.sourceforge.net/

Available Versions:

5.1.4-GCCcore-8.2.0
5.2.1-GCCcore-12.2.0
5.2.1-GCCcore-8.3.0
5.2.1-GCCcore-10.3.0
5.2.1-GCCcore-11.2.0
5.2.1-GCCcore-12.3.0
5.2.1-GCCcore-11.3.0
5.2.1-GCCcore-10.2.0
5.2.1-GCCcore-9.3.0

git

Description

Git is a free and open source distributed version control system designedto handle everything from small to very large projects with speed and efficiency.

More Information

https://git-scm.com/

Available Versions:

2.33.1-GCCcore-11.2.0-nodocs
2.41.0-GCCcore-12.3.0-nodocs
2.32.0-GCCcore-10.3.0-nodocs
2.36.0-GCCcore-11.3.0-nodocs
2.23.0-GCCcore-8.3.0
2.23.0-GCCcore-8.3.0-nodocs
2.28.0-GCCcore-10.2.0-nodocs
2.23.0-GCCcore-9.3.0-nodocs
2.38.1-GCCcore-12.2.0-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

https://git-lfs.github.com

Available Versions:

2.11.0
3.2.0

glew

Description

The OpenGL Extension Wrangler LibraryThe OpenGL Extension Wrangler Library (GLEW) is a cross-platform open-source C/C++ extension loading library. GLEW provides efficient run-time mechanisms for determining which OpenGL extensions are supported on the target platform. OpenGL core and extension functionality is exposed in a single header file. GLEW has been tested on a variety of operating systems, including Windows, Linux, Mac OS X, FreeBSD, Irix, and Solaris.

More Information

http://glew.sourceforge.net/

Available Versions:

2.1.0-GCCcore-8.3.0
2.2.0-GCCcore-11.2.0-egl
2.1.0-GCCcore-9.3.0

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:

2.1.0b4-GCC-8.3.0
2.1.0b5-GCC-9.3.0
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

https://gmsh.info/

Available Versions:

4.7.1-intel-2020a-Python-3.8.2

gnuplot

Description

Portable interactive, function plotting utility

More Information

http://gnuplot.sourceforge.net

Available Versions:

5.4.4-GCCcore-11.3.0
5.4.2-GCCcore-10.3.0
5.4.2-GCCcore-11.2.0
5.2.8-GCCcore-9.3.0
5.4.1-GCCcore-10.2.0
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:

2020b
2019a
2018b
2021a
2019b-dba
2020a
2023a
2021b
2019b
2022b
2022a

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:

2018b
2020b
2019b
2020a

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
1.10.0-GCCcore-10.2.0
1.11.0-GCCcore-11.2.0
1.13.0-GCCcore-12.3.0

gperf

Description

GNU gperf is a perfect hash function generator. For a given list of strings, it produces a hash function and hash table, in form of C or C++ code, for looking up a value depending on the input string. The hash function is perfect, which means that the hash table has no collisions, and the hash table lookup needs a single string comparison only.

More Information

https://www.gnu.org/software/gperf/

Available Versions:

3.1-GCCcore-11.2.0
3.1-GCCcore-12.2.0
3.1-GCCcore-10.2.0
3.1-GCCcore-11.3.0
3.1-GCCcore-8.2.0
3.1-GCCcore-8.3.0
3.1-GCCcore-10.3.0
3.1-GCCcore-12.3.0
3.1-GCCcore-7.3.0
3.1-GCCcore-9.3.0

gperftools

Description

gperftools is a collection of a high-performance multi-threaded malloc()implementation, plus some pretty nifty performance analysis tools.Includes TCMalloc, heap-checker, heap-profiler and cpu-profiler.

More Information

https://github.com/gperftools/gperftools

Available Versions:

2.10-GCCcore-11.3.0
2.9.1-GCCcore-10.3.0
2.7.90-GCCcore-8.3.0
2.9.1-GCCcore-10.2.0

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-12.3.0
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-11.2.0
1.22.4-GCCcore-10.3.0
1.22.4-GCCcore-9.3.0
1.22.4-GCCcore-12.2.0
1.22.4-GCCcore-11.3.0
1.22.4-GCCcore-12.3.0

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:

1.10-GCCcore-8.3.0
1.12-GCCcore-12.3.0
1.10-GCCcore-9.3.0
1.10-GCCcore-10.2.0
1.10-GCCcore-11.2.0
1.12-GCCcore-11.3.0
1.12-GCCcore-12.2.0
1.10-GCCcore-10.3.0

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

https://www.h5py.org/

Available Versions:

2.10.0-foss-2019b-Python-3.7.4
2.8.0-foss-2018b-Python-2.7.15
2.10.0-foss-2020a-Python-3.8.2
3.1.0-fosscuda-2020b
2.10.0-fosscuda-2020a-Python-3.8.2
2.10.0-intel-2020a-Python-3.8.2
3.1.0-foss-2020b
3.2.1-foss-2021a
2.10.0-fosscuda-2019b-Python-3.7.4
2.9.0-foss-2019a
3.7.0-foss-2022a
3.6.0-foss-2021b

hatchling

Description

Extensible, standards compliant build backend used by Hatch,a modern, extensible Python project manager.

More Information

https://hatch.pypa.io

Available Versions:

1.18.0-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:

1.47.16-GCCcore-10.2.0
1.47.4-GCCcore-7.3.0
1.47.4
1.47.6-GCCcore-8.1.0
1.48.3-GCCcore-11.2.0
1.47.8-GCCcore-8.3.0
1.49.3-GCCcore-12.3.0
1.49.2-GCCcore-12.2.0
1.48.3-GCCcore-10.3.0
1.49.3-GCCcore-13.2.0
1.47.7-GCCcore-8.2.0
1.49.2-GCCcore-11.3.0
1.49.3-GCCcore-13.1.0
1.47.12-GCCcore-9.3.0

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

http://hisham.hm/htop/

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

http://hunspell.github.io/

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:

2.8.0-GCCcore-12.2.0
1.11.12-GCCcore-9.3.0
2.5.0-GCCcore-11.2.0
2.7.1-GCCcore-11.3.0
1.11.10-GCCcore-7.3.0
2.9.1-GCCcore-12.3.0
1.11.11-GCCcore-8.2.0
2.2.0-GCCcore-10.2.0
1.11.12-GCCcore-8.3.0
2.2.0-GCCcore-9.3.0
2.4.1-GCCcore-10.3.0

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:

6.68.2-GCCcore-12.2.0
5.41.2-GCCcore-10.2.0
6.46.7-GCCcore-11.3.0
6.82.0-GCCcore-12.3.0
6.14.6-GCCcore-11.2.0
5.41.5-GCCcore-10.2.0
4.44.2-GCCcore-8.3.0-Python-3.7.4
6.13.1-GCCcore-10.3.0
4.23.4-GCCcore-8.2.0

icc

Description

Intel C and C++ compilers

More Information

https://software.intel.com/en-us/intel-compilers/

Available Versions:

2018.3.222-GCC-7.3.0-2.30
2019.1.144-GCC-8.2.0-2.31.1

iccifort

Description

Intel C, C++ & Fortran compilers

More Information

http://software.intel.com/en-us/intel-cluster-toolkit-compiler/

Available Versions:

2018.3.222-GCC-7.3.0-2.30
2019.5.281
2020.1.217
2020.4.304
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:

2018.3.222-GCC-7.3.0-2.30
2019.1.144-GCC-8.2.0-2.31.1

igraph

Description

igraph is a collection of network analysis tools with the emphasis onefficiency, portability and ease of use. igraph is open source and free. igraph can beprogrammed in R, Python and C/C++.

More Information

https://igraph.org

Available Versions:

0.9.5-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
2022a
2021a
2022b
2023.03
2021b
2020b
2023a
2020a

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:

2022.1.0
2022.2.1
2021.2.0-iimpi-2021a
2023.1.0
2020.1.217-gompi-2020a
2020.4.304-iimpi-2020b
2021.2.0-iompi-2021a
2020.4.304-iimpic-2020b
2020.1.217-iimpi-2020a
2021.4.0

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:

2022.2.1-iimpi-2022b
2021.4.0-iimpi-2021b
2022.1.0-iimpi-2022.05
2022.1.0-iimpi-2022a
2023.1.0-iimpi-2023.03
2023.1.0-iimpi-2023a

impi

Description

Intel MPI Library, compatible with MPICH ABI

More Information

https://software.intel.com/en-us/intel-mpi-library/

Available Versions:

2019.9.304-iccifort-2020.4.304
2019.9.304-iccifortcuda-2020b
2021.2.0-intel-compilers-2021.2.0
2021.6.0-intel-compilers-2022.1.0
2019.7.217-iccifort-2020.1.217
2021.7.1-intel-compilers-2022.2.1
2021.4.0-intel-compilers-2021.4.0
2021.9.0-intel-compilers-2023.1.0

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:

2023a
2022.05
2021a
2021b
2022a
2020b
2023.03
2022b
2020a

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
2021.4.0
2021.2.0
2022.1.0
2022.2.1

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-7.3.0-Perl-5.28.0
0.51.0-GCCcore-8.2.0
0.51.0-GCCcore-12.3.0
0.51.0-GCCcore-10.2.0
0.51.0-GCCcore-9.3.0
0.51.0-GCCcore-12.2.0
0.51.0-GCCcore-11.3.0
0.51.0-GCCcore-10.3.0
0.51.0-GCCcore-11.2.0
0.51.0-GCCcore-8.3.0

iomkl

Description

Compiler toolchain including Intel compilers, Open MPI and Intel Math Kernel Library (MKL).

More Information

https://software.intel.com/content/www/us/en/develop/tools/oneapi/hpc-toolkit.html

Available Versions:

2021a

iompi

Description

Intel C/C++ and Fortran compilers, alongside Open MPI.

More Information

https://software.intel.com/en-us/intel-cluster-toolkit-compiler/

Available Versions:

2020b
2021a

itensor

Available Versions:

3.1.5
3.1.5-omp

jax

Description

Composable transformations of Python+NumPy programs:differentiate, vectorize, JIT to GPU/TPU, and more

More Information

https://pypi.python.org/pypi/jax

Available Versions:

0.4.4-foss-2022a-CUDA-12.0.0
0.2.19-fosscuda-2020b
0.3.23-foss-2021b-CUDA-11.4.1
0.3.9-foss-2021a-CUDA-11.3.1
0.3.25-foss-2022a
0.3.25-foss-2022a-CUDA-11.7.0

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-11.2.0
2.1-GCCcore-12.3.0
2.1-GCCcore-11.3.0
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

http://jemalloc.net

Available Versions:

5.2.1-GCCcore-11.2.0
5.2.1-GCCcore-8.3.0
5.2.1-GCCcore-10.2.0
5.2.1-GCCcore-10.3.0
5.2.1-GCCcore-11.3.0
5.3.0-GCCcore-11.3.0

json-c

Description

JSON-C implements a reference counting object model that allows you to easily construct JSON objects in C, output them as JSON formatted strings and parse JSON formatted strings back into the C representation of JSONobjects.

More Information

https://github.com/json-c/json-c

Available Versions:

0.16-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

https://jupyter.org/

Available Versions:

2.7.2-GCCcore-12.3.0
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:

0.48.0-gompi-2021b
0.46.2-foss-2020b
0.46.1-foss-2019b

kim-api

Description

Open Knowledgebase of Interatomic Models.KIM is an API and OpenKIM is a collection of interatomic models (potentials) foratomistic simulations. This is a library that can be used by simulation programsto get access to the models in the OpenKIM database.This EasyBuild only installs the API, the models can be installed with thepackage openkim-models, or the user can install them manually by running kim-api-collections-management install user MODELNAMEor kim-api-collections-management install user OpenKIMto install them all.

More Information

https://openkim.org/

Available Versions:

2.1.3-intel-2020a
2.3.0-GCCcore-11.3.0
2.2.1-GCCcore-11.2.0
2.1.3-foss-2020a
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-10.3.0
0.4.0-GCC-11.3.0

kwant

Description

Kwant is a free (open source), powerful, and easy to use Python package for numerical calculations on tight-binding models with a strong focus on quantum transport.

More Information

https://kwant-project.org/

Available Versions:

1.4.1-foss-2019a-Python-3.7.2

libGLU

Description

The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL.

More Information

https://mesa.freedesktop.org/archive/glu/

Available Versions:

9.0.2-GCCcore-12.2.0
9.0.0-foss-2018b
9.0.2-GCCcore-11.3.0
9.0.1-GCCcore-10.2.0
9.0.1-GCCcore-9.3.0
9.0.1-GCCcore-10.3.0
9.0.2-GCCcore-11.2.0
9.0.3-GCCcore-12.3.0
9.0.1-GCCcore-8.3.0

libRmath

Description

The routines supporting the distribution and special functions in R and a few others are declared in C header file Rmath.h. These can be compiled into a standalone library for linking to other applications.

More Information

https://cran.r-project.org/doc/manuals/r-release/R-admin.html#The-standalone-Rmath-library

Available Versions:

4.1.2-GCCcore-11.2.0

libaec

Description

Libaec provides fast lossless compression of 1 up to 32 bit wide signed or unsigned integers(samples). The library achieves best results for low entropy data as often encountered in space imaginginstrument data or numerical model output from weather or climate simulations. While floating point representationsare not directly supported, they can also be efficiently coded by grouping exponents and mantissa.

More Information

https://gitlab.dkrz.de/k202009/libaec

Available Versions:

1.0.6-GCCcore-12.3.0
1.0.6-GCCcore-10.3.0
1.0.6-GCCcore-11.3.0

libaio

Description

Asynchronous input/output library that uses the kernels native interface.

More Information

https://pagure.io/libaio

Available Versions:

0.3.112-GCCcore-11.3.0
0.3.113-GCCcore-12.3.0
0.3.112-GCCcore-10.3.0
0.3.112-GCCcore-10.2.0
0.3.113-GCCcore-12.2.0
0.3.111-GCCcore-8.3.0

libarchive

Description

Multi-format archive and compression library

More Information

https://www.libarchive.org/

Available Versions:

3.6.1-GCCcore-12.2.0
3.5.1-GCCcore-11.2.0
3.5.1-GCCcore-10.3.0
3.5.1-GCCcore-8.3.0
3.4.3-GCCcore-10.2.0
3.6.1-GCCcore-11.3.0
3.4.0-GCCcore-8.2.0
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
1.7-GCCcore-7.3.0
2.1-GCCcore-11.3.0
1.13-GCCcore-9.3.0
1.17-GCCcore-10.3.0
1.14-GCCcore-10.2.0
2.3-GCCcore-12.3.0
1.17-GCCcore-11.2.0

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-10.3.0
3.20.7-GCCcore-10.2.0

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
1.15-GCCcore-12.2.0
1.10-GCCcore-11.3.0
1.8-GCCcore-11.2.0

libdrm

Description

Direct Rendering Manager runtime library.

More Information

https://dri.freedesktop.org

Available Versions:

2.4.99-GCCcore-8.3.0
2.4.99-GCCcore-9.3.0
2.4.102-GCCcore-10.2.0
2.4.106-GCCcore-10.3.0
2.4.107-GCCcore-11.2.0
2.4.115-GCCcore-12.3.0
2.4.92-GCCcore-7.3.0
2.4.114-GCCcore-12.2.0
2.4.110-GCCcore-11.3.0
2.4.100-GCCcore-9.3.0
2.4.97-GCCcore-8.2.0

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

https://thrysoee.dk/editline/

Available Versions:

20191231-GCCcore-9.3.0

libelf

Description

libelf is a free ELF object file access library

More Information

https://sourceware.org/elfutils

Available Versions:

0.8.13-GCCcore-10.2.0

libepoxy

Description

Epoxy is a library for handling OpenGL function pointer management for you

More Information

https://github.com/anholt/libepoxy

Available Versions:

1.5.8-GCCcore-11.2.0
1.5.4-GCCcore-10.2.0
1.5.4-GCCcore-8.3.0
1.5.10-GCCcore-11.3.0
1.5.3-GCCcore-8.2.0
1.5.10-GCCcore-12.2.0
1.5.10-GCCcore-12.3.0

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

https://libevent.org/

Available Versions:

2.1.12-GCCcore-10.3.0
2.1.12-GCCcore-12.2.0
2.1.11-GCCcore-9.3.0
2.1.8
2.1.12-GCCcore-11.3.0
2.1.11-GCCcore-8.3.0
2.1.12-GCCcore-10.2.0
2.1.12-GCCcore-11.2.0
2.1.12-GCCcore-12.3.0

libexif

Description

A library for parsing, editing, and saving EXIF data.

More Information

https://libexif.github.io/

Available Versions:

0.6.24-GCCcore-11.2.0

libfabric

Description

Libfabric is a core component of OFI. It is the library that defines and exportsthe user-space API of OFI, and is typically the only software that applicationsdeal with directly. It works in conjunction with provider libraries, which areoften integrated directly into libfabric.

More Information

https://ofiwg.github.io/libfabric/

Available Versions:

1.13.2-GCCcore-11.2.0
1.11.0-GCCcore-10.2.0
1.12.1-GCCcore-10.3.0
1.15.1-GCCcore-11.3.0
1.11.0-GCCcore-9.3.0
1.16.1-GCCcore-12.2.0
1.18.0-GCCcore-12.3.0

libffi

Description

The libffi library provides a portable, high level programming interface to various calling conventions. This allows a programmer to call any function specified by a call interface description at run-time.

More Information

https://sourceware.org/libffi/

Available Versions:

3.4.2-GCCcore-11.2.0
3.3-GCCcore-10.3.0
3.4.4-GCCcore-12.3.0
3.3-GCCcore-10.2.0
3.4.2-GCCcore-11.3.0
3.4.4-GCCcore-12.2.0
3.2.1-GCCcore-8.2.0
3.2.1-GCCcore-9.3.0
3.2.1-GCCcore-7.3.0
3.3-GCCcore-9.3.0
3.2.1-GCCcore-8.3.0
3.2.1-GCCcore-10.2.0

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

https://libgd.github.io/

Available Versions:

2.3.1-GCCcore-10.3.0
2.3.0-GCCcore-10.2.0
2.2.5-GCCcore-8.3.0
2.3.0-GCCcore-9.3.0
2.2.5-GCCcore-7.3.0
2.3.3-GCCcore-12.3.0
2.3.3-GCCcore-11.3.0
2.3.3-GCCcore-11.2.0
2.3.3-GCCcore-12.2.0

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:

1.5.1-GCCcore-9.3.0
1.7.0-GCCcore-11.2.0
1.6.0-GCCcore-10.3.0
1.7.1-GCCcore-11.3.0
1.5.1-GCCcore-8.2.0
1.4.2-foss-2018b
1.6.0-GCCcore-10.2.0
1.5.1-GCCcore-8.3.0
1.7.1-GCCcore-12.3.0

libgit2

Description

libgit2 is a portable, pure C implementation of the Git core methods provided as a re-entrantlinkable library with a solid API, allowing you to write native speed custom Git applications in any languagewhich supports C bindings.

More Information

https://libgit2.org/

Available Versions:

1.1.1-GCCcore-11.2.0
1.4.3-GCCcore-11.3.0
1.7.1-GCCcore-12.3.0
1.1.0-GCCcore-10.3.0

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:

1.6.0-GCCcore-12.3.0
1.4.0-GCCcore-11.3.0
1.3.2-GCCcore-10.2.0
1.3.3-GCCcore-10.3.0
1.6.0-GCCcore-12.2.0
1.2.0-GCCcore-9.3.0
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-2020b
0.7.6-fosscuda-2019b-Python-3.7.4

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:

1.15-GCCcore-7.3.0
1.16-GCCcore-9.3.0
1.16-GCCcore-11.2.0
1.17-GCCcore-12.2.0
1.17-GCCcore-11.3.0
1.17-GCCcore-12.3.0
1.16-GCCcore-8.3.0
1.16-GCCcore-8.2.0
1.16-GCCcore-10.3.0
1.16-GCCcore-10.2.0

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-11.3.0
2.3.2-GCCcore-11.2.0
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

http://sourceforge.net/projects/libjpeg-turbo/

Available Versions:

2.0.0-GCCcore-7.3.0
2.0.6-GCCcore-10.3.0
2.1.4-GCCcore-12.2.0
2.0.2-GCCcore-8.2.0
2.0.5-GCCcore-10.2.0
2.0.3-GCCcore-8.3.0
2.1.3-GCCcore-11.3.0
2.0.4-GCCcore-9.3.0
2.1.5.1-GCCcore-12.3.0
2.0.6-GCCcore-11.2.0

libjxl

Description

JPEG XL image format reference implementation

More Information

https://github.com/libjxl/libjxl

Available Versions:

0.8.1-foss-2022a

libmad

Description

MAD is a high-quality MPEG audio decoder.

More Information

https://www.underbit.com/products/mad/

Available Versions:

0.15.1b-GCCcore-11.3.0

libmatheval

Description

GNU libmatheval is a library (callable from C and Fortran) to parse and evaluate symbolic expressions input as text.

More Information

http://www.gnu.org/software/libmatheval/

Available Versions:

1.1.11-GCCcore-8.2.0
1.1.11-GCCcore-8.3.0
1.1.11-GCCcore-9.3.0

libogg

Description

Ogg is a multimedia container format, and the native file and stream format for the Xiph.orgmultimedia codecs.

More Information

https://xiph.org/ogg/

Available Versions:

1.3.5-GCCcore-12.3.0
1.3.5-GCCcore-11.2.0
1.3.4-GCCcore-10.2.0
1.3.5-GCCcore-12.2.0
1.3.4-GCCcore-10.3.0
1.3.5-GCCcore-11.3.0

libopus

Description

Opus is a totally open, royalty-free, highly versatile audio codec. Opus is unmatched for interactive speech and music transmission over the Internet, but is also intended for storage and streaming applications. It is standardized by the Internet Engineering Task Force (IETF) as RFC 6716 which incorporated technology from Skype’s SILK codec and Xiph.Org’s CELT codec.

More Information

https://www.opus-codec.org/

Available Versions:

1.3.1-GCCcore-12.2.0
1.3.1-GCCcore-11.3.0
1.4-GCCcore-12.3.0

libpciaccess

Description

Generic PCI access library.

More Information

http://cgit.freedesktop.org/xorg/lib/libpciaccess/

Available Versions:

0.14-GCCcore-8.3.0
0.16-GCCcore-9.3.0
0.14-GCCcore-8.2.0
0.16-GCCcore-10.3.0
0.16-GCCcore-11.2.0
0.14-GCCcore-7.3.0
0.17-GCCcore-12.3.0
0.16-GCCcore-10.2.0
0.16-GCCcore-11.3.0
0.17-GCCcore-12.2.0

libpng

Description

libpng is the official PNG reference library

More Information

http://www.libpng.org/pub/png/libpng.html

Available Versions:

1.6.38-GCCcore-12.2.0
1.6.34-GCCcore-7.3.0
1.6.37-GCCcore-11.2.0
1.6.37-GCCcore-10.2.0
1.6.37-GCCcore-11.3.0
1.6.37-GCCcore-10.3.0
1.6.39-GCCcore-12.3.0
1.6.37-GCCcore-8.3.0
1.6.36-GCCcore-8.2.0
1.6.37-GCCcore-9.3.0

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

http://psort.org/

Available Versions:

1.0-foss-2021b

libreadline

Description

The GNU Readline library provides a set of functions for use by applications that allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. The Readline library includes additional functions to maintain a list of previously-entered command lines, to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.

More Information

https://tiswww.case.edu/php/chet/readline/rltop.html

Available Versions:

8.1-GCCcore-11.2.0
8.2-GCCcore-12.2.0
8.0-GCCcore-9.3.0
8.1-GCCcore-10.3.0
8.0-GCCcore-8.2.0
8.2-GCCcore-12.3.0
8.0-GCCcore-7.3.0
7.0-GCCcore-7.3.0
8.1.2-GCCcore-11.3.0
7.0-GCCcore-10.2.0
8.0-GCCcore-8.3.0
8.0-GCCcore-10.2.0

librttopo

Description

The RT Topology Library exposes an API to create andmanage standard (ISO 13249 aka SQL/MM) topologies using user-provideddata stores.

More Information

https://git.osgeo.org/gitea/rttopo/librttopo

Available Versions:

1.1.0-GCC-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:

2.10.2-GCCcore-8.3.0
2.10.8-GCCcore-10.3.0

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:

1.2.0-GCCcore-12.2.0
1.1.0-GCCcore-11.3.0
1.0.28-GCCcore-9.3.0
1.0.31-GCCcore-11.2.0
1.2.2-GCCcore-12.3.0
1.0.28-GCCcore-8.3.0
1.0.31-GCCcore-10.3.0
1.0.28-GCCcore-10.2.0
1.0.28-GCCcore-7.3.0

libsodium

Description

Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, password hashing and more.

More Information

https://doc.libsodium.org/

Available Versions:

1.0.18-GCCcore-10.2.0
1.0.18-GCCcore-9.3.0
1.0.18-GCCcore-8.3.0
1.0.18-GCCcore-12.3.0
1.0.18-GCCcore-11.3.0
1.0.18-GCCcore-11.2.0
1.0.18-GCCcore-10.3.0

libspatialindex

Description

C++ implementation of R*-tree, an MVR-tree and a TPR-tree with C API

More Information

https://libspatialindex.org

Available Versions:

1.9.3-GCCcore-11.2.0

libspatialite

Description

SpatiaLite is an open source library intended to extend the SQLite core to support fully fledged Spatial SQL capabilities.

More Information

https://www.gaia-gis.it/fossil/libspatialite/home

Available Versions:

5.0.1-GCC-12.3.0
5.0.1-GCC-11.2.0
4.3.0a-GCC-8.3.0-Python-3.7.4

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-11.3.0
1.3.1-GCCcore-10.2.0
1.3.2-GCCcore-10.3.0
1.3.2-GCCcore-11.2.0
1.3.3-GCCcore-12.3.0
1.2.6-GCCcore-8.3.0

libtool

Description

GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries behind a consistent, portable interface.

More Information

https://www.gnu.org/software/libtool

Available Versions:

2.4.7-GCCcore-12.3.0
2.4.6-GCCcore-10.2.0
2.4.6-GCCcore-9.3.0
2.4.7
2.4.6-GCCcore-8.3.0
2.4.6-GCCcore-8.1.0
2.4.6-GCCcore-7.3.0
2.4.7-GCCcore-11.3.0
2.4.7-GCCcore-12.2.0
2.4.6-GCCcore-10.3.0
2.4.6-GCCcore-11.2.0
2.4.6-GCCcore-8.2.0

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:

1.0-GCCcore-11.3.0
1.0-GCCcore-11.2.0
0.9.10-GCCcore-9.3.0
0.9.10-GCCcore-8.3.0
0.9.10-GCCcore-8.2.0

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-10.2.0
1.3.1-GCCcore-8.3.0
1.4.0-GCCcore-10.3.0
1.3.1-GCCcore-8.2.0
1.5.0-GCCcore-11.2.0
1.6.2-GCCcore-11.3.0
1.6.2-GCCcore-12.3.0
1.6.2-GCCcore-12.2.0
1.3.1-GCCcore-9.3.0
1.2.1-GCCcore-7.3.0

libvdwxc

Description

libvdwxc is a general library for evaluating energy and potential forexchange-correlation (XC) functionals from the vdW-DF family that can be used with variousof density functional theory (DFT) codes.

More Information

https://libvdwxc.org

Available Versions:

0.4.0-foss-2020b
0.4.0-foss-2022a
0.4.0-foss-2021a

libvips

Available Versions:

8.14.2

libvorbis

Description

Ogg Vorbis is a fully open, non-proprietary, patent-and-royalty-free, general-purpose compressedaudio format

More Information

https://xiph.org/vorbis/

Available Versions:

1.3.7-GCCcore-11.3.0
1.3.7-GCCcore-11.2.0
1.3.7-GCCcore-10.2.0
1.3.7-GCCcore-12.2.0
1.3.7-GCCcore-10.3.0
1.3.7-GCCcore-12.3.0

libvori

Description

C++ library implementing the Voronoi integration as well as the compressed bqbfile format. The present version of libvori is a very early developmentversion, which is hard-coded to work with the CP2k program package.

More Information

https://brehm-research.de/libvori.php

Available Versions:

220621-GCCcore-12.3.0

libwebp

Description

WebP is a modern image format that provides superiorlossless and lossy compression for images on the web. Using WebP,webmasters and web developers can create smaller, richer images thatmake the web faster.

More Information

https://developers.google.com/speed/webp/

Available Versions:

1.1.0-GCCcore-10.2.0
1.3.1-GCCcore-12.2.0
1.2.0-GCCcore-11.2.0
1.3.1-GCCcore-12.3.0
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

https://webkit.org/wpe

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:

3.0.1-GCC-8.2.0-2.31.1
5.1.6-intel-compilers-2021.4.0
3.0.1-foss-2020a
4.3.4-GCC-8.2.0-2.31.1
4.3.4-intel-2020a
5.1.6-GCC-11.3.0
5.2.3-GCC-11.3.0
4.3.4-GCC-8.3.0
5.1.5-GCC-10.3.0
4.3.4-iccifort-2020.1.217
4.3.4-iccifort-2020.4.304
6.2.2-GCC-12.3.0
5.1.6-GCC-11.2.0
5.2.3-GCC-10.3.0
5.2.3-intel-compilers-2022.1.0
4.3.4-iccifort-2019.5.281
4.3.4-GCC-10.2.0
4.3.4-GCC-7.3.0-2.30
5.1.5-intel-compilers-2021.2.0
4.3.4-GCC-9.3.0
5.1.2-GCC-10.2.0

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

http://xmlsoft.org/

Available Versions:

2.9.9-GCCcore-8.3.0
2.9.8-GCCcore-8.2.0
2.9.10-GCCcore-10.3.0
2.9.9-GCCcore-9.3.0
2.11.4-GCCcore-12.3.0
2.9.10-GCCcore-10.2.0
2.9.10-GCCcore-11.2.0
2.10.3-GCCcore-12.2.0
2.9.8-GCCcore-7.3.0
2.9.13-GCCcore-11.3.0
2.9.10-GCCcore-9.3.0

libxslt

Description

Libxslt is the XSLT C library developed for the GNOME project (but usable outside of the Gnome platform).

More Information

http://xmlsoft.org/

Available Versions:

1.1.37-GCCcore-12.2.0
1.1.34-GCCcore-11.2.0
1.1.32-GCCcore-7.3.0
1.1.34-GCCcore-11.3.0
1.1.38-GCCcore-12.3.0
1.1.34-GCCcore-9.3.0
1.1.34-GCCcore-10.3.0
1.1.34-GCCcore-10.2.0

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
1.16.2-GCC-10.3.0
1.16.1-iccifort-2020.1.217
1.17-GCC-11.3.0
1.16.1-iccifort-2020.4.304
1.17-GCC-12.3.0
1.16.1-GCC-10.2.0
1.10-GCC-8.2.0-2.31.1
1.10-foss-2019b

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-10.2.0
0.2.2-GCCcore-8.3.0
0.2.5-GCCcore-11.3.0
0.2.5-GCCcore-11.2.0
0.2.2-GCCcore-9.3.0
0.2.5-GCCcore-12.3.0
0.2.2-GCCcore-8.2.0
0.2.5-GCCcore-10.3.0

libzip

Description

libzip is a C library for reading, creating, and modifying zip archives.

More Information

https://libzip.org/

Available Versions:

1.7.3-GCCcore-11.2.0

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:

5.5.2.5-GCC-8.3.0
5.5.2.11-GCC-10.2.0

lxml

Description

The lxml XML toolkit is a Pythonic binding for the C libraries libxml2 and libxslt.

More Information

https://lxml.de/

Available Versions:

4.6.3-GCCcore-10.3.0
4.5.2-foss-2020a-Python-3.8.2
4.9.1-GCCcore-11.3.0
4.6.3-GCCcore-11.2.0
4.2.5-foss-2018b-Python-2.7.15
4.9.2-GCCcore-12.3.0

lz4

Description

LZ4 is lossless compression algorithm, providing compression speed at 400 MB/s per core. It features an extremely fast decoder, with speed in multiple GB/s per core.

More Information

https://lz4.github.io/lz4/

Available Versions:

1.9.2-GCCcore-9.3.0
1.9.3-GCCcore-11.3.0
1.9.2-GCCcore-10.2.0
1.9.3-GCCcore-10.3.0
1.9.4-GCCcore-12.3.0
1.9.2-GCCcore-8.3.0
1.9.3-GCCcore-11.2.0
1.9.4-GCCcore-12.2.0

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

https://icl.cs.utk.edu/magma/

Available Versions:

2.5.1-fosscuda-2019b
2.6.2-foss-2021b-CUDA-11.4.1
2.6.2-foss-2022a-CUDA-11.8.0
2.6.2-foss-2022a-CUDA-11.7.0
2.5.4-fosscuda-2019b
2.6.1-foss-2021a-CUDA-11.3.1
2.5.4-fosscuda-2020b

make

Description

GNU version of make utility

More Information

https://www.gnu.org/software/make/make.html

Available Versions:

4.3-GCCcore-11.2.0
4.3-GCCcore-9.3.0
4.2.1-GCCcore-8.3.0
4.3-GCCcore-11.3.0
4.3-GCCcore-10.2.0
4.4.1-GCCcore-12.3.0

makeinfo

Description

makeinfo is part of the Texinfo project, the official documentation format of the GNU project.This is a minimal build with very basic functionality. Should only be used for build dependencies.

More Information

https://www.gnu.org/software/texinfo/

Available Versions:

6.7-GCCcore-10.3.0-minimal
6.7-GCCcore-10.3.0
6.7-GCCcore-9.3.0
6.8-GCCcore-11.2.0

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

https://matplotlib.org

Available Versions:

2.2.4-fosscuda-2019b-Python-2.7.16
3.3.3-fosscuda-2020b
3.4.2-foss-2021a
3.5.2-foss-2022a
3.3.3-foss-2020b
2.2.4-foss-