Table of Software on ARC Systems

SOFTWARE	DESCRIPTION	CLUSTER
guppyGPU	SOFTWAREDESCRIPTION	INFER 4.5.2
julia	Julia for numerical computing	INFER 1.6.1-fosscuda-2020b 1.6.1-foss-2020b TINKERCLIFFS 1.6.1-foss-2020b 1.6.1-gomkl-2020b 1.6.2-foss-2020b
matlab	MATLAB is a programming and numeric computing platform	INFER R2021a R2022b TINKERCLIFFS R2021a R2022b
AlphaFoldData	ALPHAFOLDDATADESCRIPTION	INFER 2022.02
guppy	GUPPYDESCRIPTION	INFER 6.0.1
StarCCM+	STARCCM+DESCRIPTION	INFER 15.04.010 TINKERCLIFFS 17.02.008
tinker9	Molecular Design Software	INFER 1.4.0-nvhpc-21.11
ANSYS		OWL 24.1 TINKERCLIFFS 23.2 19.5 20.1 20.2 21.1 21.2 22.1
Nastran	NASTRANDESCRIPTION	OWL 2024 TINKERCLIFFS 2021 2024
tbb	Intel(R) Threading Building Blocks (Intel(R) TBB) lets you easily write parallel C++ programs that take full advantage of multicore performance, that are portable, composable and have future-proof scalability.	OWL 2021.11.0-GCCcore-13.2.0 TINKERCLIFFS 2020.1-GCCcore-9.3.0 2020.3-GCCcore-11.2.0 2021.10.0-GCCcore-12.2.0 2021.5.0-GCCcore-11.3.0
AccelerateCFD_CE	Community Edition of AccelerateCFD platform for creating reduced order models from high fidelity CFD	TINKERCLIFFS 20210615-foss-2020a
BEDOPS	BEDOPS is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale. Tasks can be easily split by chromosome for distributing whole-genome analyses across a computational cluster.	TINKERCLIFFS 2.4.41
DLCpar	DLCPARDESCRIPTION	TINKERCLIFFS 2.0.1
DeepTMHMM	A Deep Learning Model for Transmembrane Topology Prediction and Classification	TINKERCLIFFS 1.0.24
Delft3d	DELFT3DDESCRIPTION	TINKERCLIFFS 2023.02-intel-2022b
GlobusConnectPersonal	Globus Connect Personal enables you to share and transfer files to and from your Linux laptop or desktop computer — even if it’s behind a firewall.	TINKERCLIFFS 3.2.0
Infernal		TINKERCLIFFS 1.1.5 1.1.4-foss-2022a 1.1.4-foss-2022b
InterProScan	InterPro is a database which integrates together predictive information about proteins’ function from a number of partner resources, giving an overview of the families that a protein belongs to and the domains and sites it contains.	TINKERCLIFFS 5.65-97.0-foss-2021a 5.65-97.0-foss-2022a
ls-dyna	LS-Dyna software	TINKERCLIFFS R12.0.0 10.2.0-intel-2019b 12.0.0-intel-2019b 13.0.0-intel-2019b
Patran	PATRANDESCRIPTION	TINKERCLIFFS 2021
SOAPdenovo2	SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for the human-sized genomes. The program is specially designed to assemble Illumina GA short reads. It creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost effective way.	TINKERCLIFFS r242-intel-2019b
SU2	SU2 is an open-source collection of software tools written in C++ and Python for the analysis of partial differential equations (PDEs) and PDE-constrained optimization problems on unstructured meshes with state-of-the-art numerical methods.	TINKERCLIFFS 7.2.1-foss-2020b-Python-3.8.6 8.0.0-foss-2022a-mpi 8.0.1-foss-2023b-Python-3.11.5
Trinity	Trinity assembles transcript sequences from Illumina RNA-Seq data.	TINKERCLIFFS 2.15.1-foss2022b
UNAGI	UNAGI (UNAnnotated Gene Identifier) is a pipeline allowing for the detection and annotation of transcripts from long-read sequences (usually from Oxford Nanopore Technologies Sequencers) with the help of a genome file from the studied organism.	TINKERCLIFFS 1.0.1
amd-uprof	AMD μProf for performance analysis	TINKERCLIFFS 3.4.475
aspect-2.2.0	AspectDESCRIPTION	TINKERCLIFFS intel-2019b
aspect-2.3.0	AspectDESCRIPTION	TINKERCLIFFS gcc-9.3.0 intel-2019b
bolt_llm	The BOLT-LMM algorithm computes statistics for testing association between phenotype and genotypes using a linear mixed model (LMM)	TINKERCLIFFS 2.4.1-intel2021a
boost-1.58.0	BOOSTDESCRIPTION	TINKERCLIFFS intel-2019b
bwa-mem2	The tool bwa-mem2 is the next version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case, dataset and the running machine.	TINKERCLIFFS 2.2.1-foss2022b
cifs-utils	CIFSUTILSDESCRIPTION	TINKERCLIFFS 7.0
dealii-9.2.0	SOFTWAREDESCRIPTION	TINKERCLIFFS intel-2019b
dealii-9.3.1	DEALIIDESCRIPTION	TINKERCLIFFS gcc-9.3.0
dxa	DXA Dislocation Analysis	TINKERCLIFFS 1.3.6-foss-2020b
fasta36	The FASTA package - protein and DNA sequence similarity searching and alignment programs.	TINKERCLIFFS 36.3.8
galaxy	bioinformatics software to do RNA-seq and gene expression data analysis	TINKERCLIFFS 2014
gffcompare	1) compare and evaluate the accuracy of RNA-Seq transcript assemblers (Cufflinks, Stringtie). 2) Collapse (merge) duplicate transcripts from multiple GTF/GFF3 files (e.g. resulted from assembly of different samples) 3) classify transcripts from one or multiple GTF/GFF3 files as they relate to reference transcripts provided in a annotation file (also in GTF/GFF3 format)	TINKERCLIFFS 0.12.6
gffread	GFF/GTF utility providing format conversions, filtering, FASTA sequence extraction and more.	TINKERCLIFFS 0.12.7
glm-0.9.8.5	SOFTWAREDESCRIPTION	TINKERCLIFFS intel-2019b
guppyCPU	SOFTWAREDESCRIPTION	TINKERCLIFFS Anaconda3-2020.07
hmmer3	HMMER3DESCRIPTION	TINKERCLIFFS 3.3.2.1b2-hpc
kaldi	Kaldi is a toolkit for speech recognition	TINKERCLIFFS 20210429-foss-2020b
ls-prepost	LS-PrePost	TINKERCLIFFS 4.8
lstc-licensetools	LSTC LICENSE TOOLS for checking license status and managing user-checked out licenses.	TINKERCLIFFS 77918
metis-5.1.0	METISDESCRIPTION	TINKERCLIFFS gcc-8.3.0 gcc-9.3.0 intel-2019b
miR-PREFeR		TINKERCLIFFS 0.24
nlopt	NLopt is a free/open-source library for nonlinear optimization	TINKERCLIFFS 2.7.1
p4est	P4ESTDESCRIPTION	TINKERCLIFFS gcc-8.3.0 2.2-intel-2019b 2.8-foss-2021a 2.8-intel-2021a 2.8.6-foss-2023a
p4est-2.2	P4ESTDESCRIPTION	TINKERCLIFFS gcc-9.3.0 intel-2019b
parmetis-4.0.3	PARMETIS4.0.3DESCRIPTION	TINKERCLIFFS gcc-8.3.0 gcc-9.3.0 intel-2019b
rnammer	The RNAmmer 1.2 server predicts 5s/8s, 16s/18s, and 23s/28s ribosomal RNA in full genome sequences.	TINKERCLIFFS 1.2
signalp	The SignalP 5.0 tool predicts the presence of signal peptides and the location of their cleavage sites in proteins from Archaea, Gram-positive Bacteria, Gram-negative Bacteria and Eukarya. In Bacteria and Archaea, SignalP 5.0 can discriminate between three types of signal peptides Sec/SPI (standard signal peptide), Sec/SPII (lipoprotein signal peptide) and Tat/SPI (tat signal peptide). SignalP 5.0 is based on a deep convolutional and recurrent neural network architecture including a conditional random field.	TINKERCLIFFS 5.0b
snoscan		TINKERCLIFFS 1.0
spades	SPAdes - St. Petersburg genome assembler - is an assembly toolkit containing various assembly pipelines.	TINKERCLIFFS 3.15.5
sratoolkit	The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.	TINKERCLIFFS 3.0.7
starccm+	STARCCM+DESCRIPTION	TINKERCLIFFS 12.04.011 15.04.010 17.06.007 18.02.008 18.02.010
tecplot	TECPLOTDESCRIPTION	TINKERCLIFFS 17.1.0
tmhmm	Prediction of transmembrane helices in proteins	TINKERCLIFFS 2.0
tpl-4.4.18	TPL4.4.18DESCRIPTION	TINKERCLIFFS GCC-9.3.0 intel-2019b
trilinos-12.18.1	TRILINOS12.18.1DESCRIPTION	TINKERCLIFFS gcc-8.3.0 gcc-9.3.0 intel-2019b
trimmomatic	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.	TINKERCLIFFS 0.39
gaussian	Gaussian(09.d01) is a computer program for computational quantum chemistry that includes various methods for electronic structure calculations.	TINKERCLIFFS 09.d01 09.e01
ABAQUS	Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit dynamics FEA.	TINKERCLIFFS 2018 2022 2023
ABINIT	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.	TINKERCLIFFS 8.10.3-intel-2019b
ABySS	Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler	TINKERCLIFFS 2.1.5-gompi-2020a
ANTLR	ANTLR, ANother Tool for Language Recognition, (formerly PCCTS	TINKERCLIFFS 2.7.7-GCCcore-10.3.0-Java-11 2.7.7-GCCcore-11.2.0-Java-11
APR	Apache Portable Runtime (APR) libraries.	TINKERCLIFFS 1.7.0-GCCcore-10.2.0
APR-util	Apache Portable Runtime (APR) util libraries.	TINKERCLIFFS 1.6.1-GCCcore-10.2.0
ATK	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.	TINKERCLIFFS 2.36.0-GCCcore-10.2.0 2.36.0-GCCcore-10.3.0 2.36.0-GCCcore-9.3.0 2.38.0-GCCcore-11.3.0 2.38.0-GCCcore-12.2.0
AUGUSTUS	AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences	TINKERCLIFFS 3.4.0-foss-2020b 3.5.0-foss-2022a
Anaconda3	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.	TINKERCLIFFS 2020.07 2020.11 2022.10 2024.02-1
Armadillo	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.	TINKERCLIFFS 11.4.3-foss-2022b
Arrow	Apache Arrow (incl. PyArrow Python bindings), a cross-language development platform for in-memory data.	TINKERCLIFFS 6.0.0-foss-2021a 6.0.0-foss-2021b
AtomPAW	AtomPAW is a Projector-Augmented Wave Dataset Generator that can be used both as a standalone program and a library.	TINKERCLIFFS 4.1.0.5-intel-2019b
Autoconf	Autoconf is an extensible package of M4 macros that produce shell scripts to automatically configure software source code packages. These scripts can adapt the packages to many kinds of UNIX-like systems without manual user intervention. Autoconf creates a configuration script for a package from a template file that lists the operating system features that the package can use, in the form of M4 macro calls.	TINKERCLIFFS 2.69-GCCcore-10.2.0 2.69-GCCcore-8.2.0 2.69-GCCcore-8.3.0 2.69-GCCcore-9.3.0 2.69 2.71-GCCcore-10.3.0 2.71-GCCcore-11.2.0 2.71-GCCcore-11.3.0 2.71-GCCcore-12.2.0 2.71-GCCcore-12.3.0 2.71-GCCcore-13.2.0
Automake	Automake: GNU Standards-compliant Makefile generator	TINKERCLIFFS 1.15.1-GCCcore-8.3.0 1.16.1-GCCcore-8.2.0 1.16.1-GCCcore-8.3.0 1.16.1-GCCcore-9.3.0 1.16.2-GCCcore-10.2.0 1.16.3-GCCcore-10.3.0 1.16.4-GCCcore-11.2.0 1.16.5-GCCcore-11.3.0 1.16.5-GCCcore-12.2.0 1.16.5-GCCcore-12.3.0 1.16.5-GCCcore-13.2.0
Autotools	This bundle collect the standard GNU build tools: Autoconf, Automake and libtool	TINKERCLIFFS 20180311-GCCcore-8.2.0 20180311-GCCcore-8.3.0 20180311-GCCcore-9.3.0 20200321-GCCcore-10.2.0 20210128-GCCcore-10.3.0 20210726-GCCcore-11.2.0 20220317-GCCcore-11.3.0 20220317-GCCcore-12.2.0 20220317-GCCcore-12.3.0 20220317-GCCcore-13.2.0
BBMap	BBMap short read aligner, and other bioinformatic tools.	TINKERCLIFFS 38.96-GCC-10.3.0 38.98-GCC-11.2.0 39.01-GCC-11.3.0
BCFtools	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	TINKERCLIFFS 1.10.2-GCC-9.3.0 1.11-GCC-10.2.0 1.15.1-GCC-11.3.0
BEDTools	BEDTools: a powerful toolset for genome arithmetic. The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM.	TINKERCLIFFS 2.29.2-GCC-9.3.0 2.30.0-GCC-12.2.0
BLAST+	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.	TINKERCLIFFS 2.10.1-gompi-2020a 2.11.0-gompi-2020b 2.13.0-gompi-2022a
BLIS	BLIS is a portable software framework for instantiating high-performance BLAS-like dense linear algebra libraries.	TINKERCLIFFS 0.8.1-GCC-11.2.0 0.9.0-GCC-11.3.0 0.9.0-GCC-12.2.0 0.9.0-GCC-12.3.0 0.9.0-GCC-13.2.0
BUSCO	BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs	TINKERCLIFFS 5.0.0-foss-2020b 5.4.5-foss-2022a
BamTools	BamTools provides both a programmer’s API and an end-user’s toolkit for handling BAM files.	TINKERCLIFFS 2.5.1-GCC-10.2.0 2.5.1-GCC-9.3.0 2.5.2-GCC-11.3.0 2.5.2-GCC-12.2.0
Bazel	Bazel is a build tool that builds code quickly and reliably. It is used to build the majority of Google’s software.	TINKERCLIFFS 3.7.2-GCCcore-10.2.0
BeautifulSoup	Beautiful Soup is a Python library designed for quick turnaround projects like screen-scraping.	TINKERCLIFFS 4.10.0-GCCcore-11.3.0 4.11.1-GCCcore-12.2.0 4.12.2-GCCcore-13.2.0
BioPerl	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.	TINKERCLIFFS 1.7.8-GCCcore-11.3.0
Biopython	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.	TINKERCLIFFS 1.75-intel-2019b-Python-3.7.4 1.78-foss-2020a-Python-3.8.2 1.78-foss-2020b 1.79-foss-2021a 1.79-foss-2022a 1.81-foss-2022b
Bison	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.	TINKERCLIFFS 3.0.4 3.0.5-GCCcore-8.2.0 3.0.5 3.3.2-GCCcore-8.3.0 3.3.2 3.5.3-GCCcore-9.3.0 3.5.3-intel-2019b 3.5.3 3.7.1-GCCcore-10.2.0 3.7.1 3.7.6-GCCcore-10.3.0 3.7.6-GCCcore-11.2.0 3.7.6 3.7.91 3.8.2-GCCcore-11.3.0 3.8.2-GCCcore-12.2.0 3.8.2-GCCcore-12.3.0 3.8.2-GCCcore-13.2.0 3.8.2
Boost	Boost provides free peer-reviewed portable C++ source libraries.	TINKERCLIFFS 1.71.0-gompi-2019b 1.71.0-iimpi-2019b 1.72.0-gompi-2020a 1.74.0-GCC-10.2.0 1.76.0-GCC-10.3.0 1.76.0-intel-compilers-2021.2.0 1.77.0-GCC-11.2.0 1.79.0-GCC-11.3.0 1.81.0-GCC-12.2.0 1.82.0-GCC-12.3.0
Boost.MPI	Boost provides free peer-reviewed portable C++ source libraries.	TINKERCLIFFS 1.79.0-gompi-2022a
Boost.Python	Boost.Python is a C++ library which enables seamless interoperability between C++ and the Python programming language.	TINKERCLIFFS 1.71.0-gompi-2019b
Bowtie	Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome.	TINKERCLIFFS 1.3.1-GCC-11.3.0
Bowtie2	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.	TINKERCLIFFS 2.4.1-GCC-9.3.0 2.4.5-GCC-11.3.0
Brotli	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.	TINKERCLIFFS 1.0.9-GCCcore-11.2.0 1.0.9-GCCcore-11.3.0 1.0.9-GCCcore-12.2.0 1.0.9-GCCcore-12.3.0
Brunsli	Brunsli is a lossless JPEG repacking library.	TINKERCLIFFS 0.1-GCCcore-12.2.0
CAVIAR	CAusal Variants Identication in Associated Regions. A statistical framework that quantifies the probability of each variant to be causal while allowing an arbitrary number of causal variants.	TINKERCLIFFS 2.2-20190419-foss-2019b
CD-HIT	CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences.	TINKERCLIFFS 4.8.1-GCC-11.3.0
CFITSIO	CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format.	TINKERCLIFFS 4.2.0-GCCcore-12.2.0
CGAL	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.	TINKERCLIFFS 4.14.1-foss-2019b-Python-3.7.4 4.14.3-gompi-2020a-Python-3.8.2 4.14.3-gompi-2021a 4.14.3-gompi-2022a
CMake	CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.	TINKERCLIFFS 3.12.1 3.13.3-GCCcore-8.2.0 3.15.3-GCCcore-8.3.0 3.16.4-GCCcore-9.3.0 3.16.4-intel-2019b 3.18.4-GCCcore-10.2.0 3.18.4 3.20.1-GCCcore-10.3.0 3.21.1-GCCcore-11.2.0 3.22.1-GCCcore-11.2.0 3.23.1-GCCcore-11.3.0 3.24.3-GCCcore-11.3.0 3.24.3-GCCcore-12.2.0 3.26.3-GCCcore-12.3.0 3.27.6-GCCcore-13.2.0
COMSOL	COMSOL Multiphysics is a general-purpose software platform, based on advanced numerical methods, for modeling and simulating physics-based problems.	TINKERCLIFFS 5.4.0.388
CP2K	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.	TINKERCLIFFS 2023.1-foss-2023a 6.1-foss-2020a
CUDA	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.	TINKERCLIFFS 11.4.1
Catch2	A modern, C++-native, header-only, test framework for unit-tests, TDD and BDD - using C++11, C++14, C++17 and later	TINKERCLIFFS 2.13.9-GCCcore-12.2.0 2.13.9-GCCcore-12.3.0
Cbc	Cbc (Coin-or branch and cut) is an open-source mixed integer linear programming solver written in C++. It can be used as a callable library or using a stand-alone executable.	TINKERCLIFFS 2.10.11-foss-2023a
Cereal	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 be fast, light-weight, and easy to extend - it has no external dependencies and can be easily bundled with other code or used standalone.	TINKERCLIFFS 1.3.0 1.3.2
Cgl	The COIN-OR Cut Generation Library (Cgl) is a collection of cut generators that can be used with other COIN-OR packages that make use of cuts, such as, among others, the linear solver Clp or the mixed integer linear programming solvers Cbc or BCP. Cgl uses the abstract class OsiSolverInterface (see Osi) to use or communicate with a solver. It does not directly call a solver.	TINKERCLIFFS 0.60.8-foss-2023a
Clang	C, C++, Objective-C compiler, based on LLVM. Does not include C++ standard library – use libstdc++ from GCC.	TINKERCLIFFS 11.0.1-GCCcore-10.2.0
Clp	Clp (Coin-or linear programming) is an open-source linear programming solver. It is primarily meant to be used as a callable library, but a basic, stand-alone executable version is also available.	TINKERCLIFFS 1.17.9-foss-2023a
CoinUtils	CoinUtils (Coin-OR Utilities) is an open-source collection of classes and functions that are generally useful to more than one COIN-OR project.	TINKERCLIFFS 2.11.10-GCC-12.3.0
CppUnit	CppUnit is the C++ port of the famous JUnit framework for unit testing.	TINKERCLIFFS 1.15.1-GCCcore-10.3.0 1.15.1-GCCcore-11.3.0
DB	Berkeley DB enables the development of custom data management solutions, without the overhead traditionally associated with such custom projects.	TINKERCLIFFS 18.1.32-GCCcore-8.2.0 18.1.40-GCCcore-10.2.0 18.1.40-GCCcore-10.3.0 18.1.40-GCCcore-11.2.0 18.1.40-GCCcore-11.3.0 18.1.40-GCCcore-12.2.0
DB_File	Perl5 access to Berkeley DB version 1.x.	TINKERCLIFFS 1.858-GCCcore-11.3.0
DBus	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.	TINKERCLIFFS 1.13.12-GCCcore-8.3.0 1.13.12-GCCcore-9.3.0 1.13.18-GCCcore-10.2.0 1.13.18-GCCcore-10.3.0 1.14.0-GCCcore-11.3.0 1.15.2-GCCcore-12.2.0 1.15.4-GCCcore-12.3.0
DIAMOND	Accelerated BLAST compatible local sequence aligner	TINKERCLIFFS 2.1.0-GCC-11.3.0
DOLFIN	DOLFIN is the C++/Python interface of FEniCS, providing a consistent PSE (Problem Solving Environment) for ordinary and partial differential equations.	TINKERCLIFFS 2019.1.0.post0-foss-2019b-Python-3.7.4
Dalton	The Dalton suite consists of two separate executables, Dalton and LSDalton. The Dalton code is a powerful tool for a wide range of molecular properties at different levels of theory, whereas LSDalton is a linear-scaling HF and DFT code suitable for large molecular systems, now also with some CCSD capabilites. Any published work arising from use of one of the Dalton programs must acknowledge that by a proper reference. The following list of capabilities of the Dalton programs should give you some indication of whether or not the Dalton suite is able to meet your requirements..	TINKERCLIFFS 2020-iomkl-2019b-nompi 2020-iomkl-2019b
DendroPy	A Python library for phylogenetics and phylogenetic computing: reading, writing, simulation, processing and manipulation of phylogenetic trees (phylogenies) and characters.	TINKERCLIFFS 4.5.2-GCCcore-10.2.0 4.5.2-GCCcore-11.3.0
Doxygen	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.	TINKERCLIFFS 1.8.16-GCCcore-8.3.0 1.8.17-GCCcore-9.3.0 1.8.20-GCCcore-10.2.0 1.9.1-GCCcore-10.3.0 1.9.1-GCCcore-11.2.0 1.9.4-GCCcore-11.3.0 1.9.5-GCCcore-12.2.0 1.9.7-GCCcore-12.3.0
ELPA	Eigenvalue SoLvers for Petaflop-Applications .	TINKERCLIFFS 2019.11.001-intel-2019b
ESMF	The Earth System Modeling Framework (ESMF) is a suite of software tools for developing high-performance, multi-component Earth science modeling applications.	TINKERCLIFFS 8.2.0-intel-2021a
EasyBuild	EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.	TINKERCLIFFS 4.2.2 4.3.2 4.3.3 4.3.4 4.4.0 4.4.2 4.6.1 4.7.1 4.9.0 4.9.2 4.9.4
Eigen	Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.	TINKERCLIFFS 3.3.7-GCCcore-8.3.0 3.3.7-GCCcore-9.3.0 3.3.7 3.3.8-GCCcore-10.2.0 3.3.9-GCCcore-10.3.0 3.3.9-GCCcore-11.2.0 3.4.0-GCCcore-11.2.0 3.4.0-GCCcore-11.3.0 3.4.0-GCCcore-12.2.0 3.4.0-GCCcore-12.3.0
Emacs	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.	TINKERCLIFFS 29.3-GCCcore-12.2.0
Exonerate	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.	TINKERCLIFFS 2.4.0-GCC-11.3.0
FASTX-Toolkit	The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.	TINKERCLIFFS 0.0.14-GCC-11.2.0
FDS	Fire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-speed flows, with an emphasis on smoke and heat transport from fires.	TINKERCLIFFS 6.7.1-intel-2019b 6.7.4-intel-2019b 6.7.5-intel-2019b 6.7.6-intel-2020b 6.8.0-intel-2022b
FEniCS	FEniCS is a computing platform for solving partial differential equations (PDEs).	TINKERCLIFFS 2019.1.0-foss-2019b-Python-3.7.4
FFC	The FEniCS Form Compiler (FFC) is a compiler for finite element variational forms.	TINKERCLIFFS 2019.1.0.post0-foss-2019b-Python-3.7.4
FFTW	FFTW is a C subroutine library for computing the discrete Fourier transform (DFT	TINKERCLIFFS 3.3.10-GCC-11.3.0 3.3.10-GCC-12.2.0 3.3.10-GCC-12.3.0 3.3.10-GCC-13.2.0 3.3.10-gompi-2021b 3.3.8-gompi-2019b 3.3.8-gompi-2020a 3.3.8-gompi-2020b 3.3.8-intel-2019b 3.3.9-gompi-2021a 3.3.9-intel-2021a 3.3.9-iompi-2021a
FFTW.MPI	FFTW is a C subroutine library for computing the discrete Fourier transform (DFT	TINKERCLIFFS 3.3.10-gompi-2022a 3.3.10-gompi-2022b 3.3.10-gompi-2023a 3.3.10-gompi-2023b
FFmpeg	A complete, cross-platform solution to record, convert and stream audio and video.	TINKERCLIFFS 4.2.1-GCCcore-8.3.0 4.2.2-GCCcore-9.3.0 4.3.1-GCCcore-10.2.0 4.3.2-GCCcore-10.3.0 4.3.2-GCCcore-11.2.0 4.4.2-GCCcore-11.3.0
FIAT	The FInite element Automatic Tabulator (FIAT) supports generation of arbitrary order instances of the Lagrange elements on lines, triangles, and tetrahedra. It is also capable of generating arbitrary order instances of Jacobi-type quadrature rules on the same element shapes.	TINKERCLIFFS 2019.1.0-foss-2019b-Python-3.7.4
FLAC	FLAC stands for Free Lossless Audio Codec, an audio format similar to MP3, but lossless, meaning that audio is compressed in FLAC without any loss in quality.	TINKERCLIFFS 1.3.3-GCCcore-10.2.0 1.3.3-GCCcore-10.3.0 1.3.4-GCCcore-11.3.0 1.4.2-GCCcore-11.3.0 1.4.2-GCCcore-12.2.0
FastQC	FastQC is a quality control application for high throughput sequence data. It reads in sequence data in a variety of formats and can either provide an interactive application to review the results of several different QC checks, or create an HTML based report which can be integrated into a pipeline.	TINKERCLIFFS 0.11.9-Java-11
FastTree	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.	TINKERCLIFFS 2.1.11-GCCcore-12.3.0
Flask	Flask is a lightweight WSGI web application framework. It is designed to make getting started quick and easy, with the ability to scale up to complex applications. This module includes the Flask extensions: Flask-Cors	TINKERCLIFFS 2.2.2-GCCcore-11.3.0
FlexiBLAS	FlexiBLAS is a wrapper library that enables the exchange of the BLAS and LAPACK implementation used by a program without recompiling or relinking it.	TINKERCLIFFS 3.0.4-GCC-10.3.0 3.0.4-GCC-11.2.0 3.2.0-GCC-11.3.0 3.2.1-GCC-12.2.0 3.3.1-GCC-12.3.0 3.3.1-GCC-13.2.0
Flye	Flye is a de novo assembler for long and noisy reads, such as those produced by PacBio and Oxford Nanopore Technologies.	TINKERCLIFFS 2.9-GCC-10.3.0 2.9-intel-compilers-2021.2.0 2.9.1-GCC-11.2.0
FriBidi	The Free Implementation of the Unicode Bidirectional Algorithm.	TINKERCLIFFS 1.0.10-GCCcore-10.2.0 1.0.10-GCCcore-10.3.0 1.0.10-GCCcore-11.2.0 1.0.12-GCCcore-11.3.0 1.0.12-GCCcore-12.2.0 1.0.12-GCCcore-12.3.0 1.0.5-GCCcore-8.3.0 1.0.9-GCCcore-9.3.0
GATK	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.	TINKERCLIFFS 4.3.0.0-GCCcore-11.3.0-Java-11 4.5.0.0-GCCcore-12.3.0-Java-17
GCC	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,…).	TINKERCLIFFS 10.2.0 10.3.0 11.2.0 11.3.0 12.2.0 12.3.0 13.2.0 8.2.0-2.31.1 8.3.0 9.3.0
GCCcore	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,…).	TINKERCLIFFS 10.2.0 10.3.0 11.2.0 11.3.0 12.2.0 12.3.0 13.2.0 8.2.0 8.3.0 9.3.0
GDAL	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.	TINKERCLIFFS 3.0.2-intel-2019b-Python-3.7.4 3.0.4-foss-2020a-Python-3.8.2 3.3.0-foss-2021a 3.5.0-foss-2022a 3.6.2-foss-2022b
GDB	The GNU Project Debugger	TINKERCLIFFS 10.2-GCCcore-10.3.0
GDRCopy	A low-latency GPU memory copy library based on NVIDIA GPUDirect RDMA technology.	TINKERCLIFFS 2.3-GCCcore-11.2.0
GEOS	GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)	TINKERCLIFFS 3.10.3-GCC-11.3.0 3.11.1-GCC-11.3.0 3.11.1-GCC-12.2.0 3.8.0-iccifort-2019.5.281-Python-3.7.4 3.8.1-GCC-9.3.0-Python-3.8.2 3.9.1-GCC-10.3.0
GLM	OpenGL Mathematics (GLM) is a header only C++ mathematics library for graphics software based on the OpenGL Shading Language (GLSL) specifications.	TINKERCLIFFS 0.9.9.8-GCCcore-8.3.0
GLPK	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.	TINKERCLIFFS 4.65-GCCcore-10.2.0 4.65-GCCcore-8.3.0 4.65-GCCcore-9.3.0 5.0-GCCcore-10.3.0 5.0-GCCcore-11.3.0 5.0-GCCcore-12.2.0 5.0-GCCcore-12.3.0
GLib	GLib is one of the base libraries of the GTK+ project	TINKERCLIFFS 2.62.0-GCCcore-8.3.0 2.64.1-GCCcore-9.3.0 2.66.1-GCCcore-10.2.0 2.68.2-GCCcore-10.3.0 2.72.1-GCCcore-11.3.0 2.75.0-GCCcore-11.3.0 2.75.0-GCCcore-12.2.0 2.77.1-GCCcore-12.3.0
GMAP-GSNAP	GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences GSNAP: Genomic Short-read Nucleotide Alignment Program	TINKERCLIFFS 2023-04-20-GCC-10.3.0
GMP	GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers.	TINKERCLIFFS 6.1.2-GCCcore-8.2.0 6.1.2-GCCcore-8.3.0 6.2.0-GCCcore-10.2.0 6.2.0-GCCcore-9.3.0 6.2.0-intel-2019b 6.2.1-GCCcore-10.3.0 6.2.1-GCCcore-11.2.0 6.2.1-GCCcore-11.3.0 6.2.1-GCCcore-12.2.0 6.2.1-GCCcore-12.3.0
GMT	GMT is an open source collection of about 80 command-line tools for manipulating geographic and Cartesian data sets (including filtering, trend fitting, gridding, projecting, etc.) and producing PostScript illustrations ranging from simple x-y plots via contour maps to artificially illuminated surfaces and 3D perspective views; the GMT supplements add another 40 more specialized and discipline-specific tools.	TINKERCLIFFS 5.4.5-foss-2020a
GObject-Introspection	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.	TINKERCLIFFS 1.63.1-GCCcore-8.3.0-Python-3.7.4 1.64.0-GCCcore-9.3.0-Python-3.8.2 1.66.1-GCCcore-10.2.0 1.68.0-GCCcore-10.3.0 1.72.0-GCCcore-11.3.0 1.74.0-GCCcore-11.3.0 1.74.0-GCCcore-12.2.0 1.76.1-GCCcore-12.3.0
GROMACS	GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. This is a CPU only build, containing both MPI and threadMPI builds for both single and double precision. It also contains the gmxapi extension for the single precision MPI build.	TINKERCLIFFS 2020.1-foss-2020a-Python-3.8.2 2020.3-foss-2020a-Python-3.8.2
GSL	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.	TINKERCLIFFS 2.6-GCC-10.2.0 2.6-GCC-8.3.0 2.6-GCC-9.3.0 2.6-iccifort-2019.5.281 2.7-GCC-10.3.0 2.7-GCC-11.2.0 2.7-GCC-11.3.0 2.7-GCC-12.2.0 2.7-GCC-12.3.0 2.7-intel-compilers-2021.2.0 2.7-intel-compilers-2021.4.0
GStreamer	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.	TINKERCLIFFS 1.18.4-GCC-10.3.0
GTK+	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.	TINKERCLIFFS 3.24.17-GCCcore-9.3.0 3.24.23-GCCcore-10.2.0
GTK2	The GTK+ 2 package contains libraries used for creating graphical user interfaces for applications.	TINKERCLIFFS 2.24.33-GCCcore-11.3.0
GTK3	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.	TINKERCLIFFS 3.24.29-GCCcore-10.3.0 3.24.35-GCCcore-12.2.0
Gdk-Pixbuf	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.	TINKERCLIFFS 2.40.0-GCCcore-10.2.0 2.40.0-GCCcore-9.3.0 2.42.10-GCCcore-12.2.0 2.42.6-GCCcore-10.3.0 2.42.8-GCCcore-11.3.0
GeneMark-ET	Eukaryotic gene prediction suite with automatic training	TINKERCLIFFS 4.71-GCCcore-11.3.0
GenomeTools	A comprehensive software library for efficient processing of structured genome annotations.	TINKERCLIFFS 1.6.2-GCC-11.3.0
Ghostscript	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.	TINKERCLIFFS 10.0.0-GCCcore-12.2.0 9.52-GCCcore-9.3.0 9.52-intel-2019b 9.53.3-GCCcore-10.2.0 9.54.0-GCCcore-10.3.0 9.56.1-GCCcore-11.3.0
GitPython	GitPython is a python library used to interact with Git repositories	TINKERCLIFFS 3.1.40-GCCcore-12.3.0
GlobalArrays	Global Arrays (GA) is a Partitioned Global Address Space (PGAS) programming model	TINKERCLIFFS 5.7.2-intel-2019b 5.7.2-iomkl-2019b
Go	Go is an open source programming language that makes it easy to build simple, reliable, and efficient software.	TINKERCLIFFS 1.14 1.18.3 1.21.2 1.21.3
Guile	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.	TINKERCLIFFS 1.8.8-GCCcore-9.3.0
Gurobi	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 modern architectures and multi-core processors, using the most advanced implementations of the latest algorithms.	TINKERCLIFFS 11.0.2-GCCcore-12.3.0
HDF	HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines.	TINKERCLIFFS 4.2.14-GCCcore-8.3.0 4.2.15-GCCcore-10.3.0 4.2.15-GCCcore-11.3.0 4.2.15-GCCcore-12.2.0
HDF5	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.	TINKERCLIFFS 1.10.2-intel-2019b 1.10.2-iomkl-2019b 1.10.5-gompi-2019b 1.10.5-iimpi-2019b 1.10.6-gompi-2020a 1.10.6-intel-2019b 1.10.7-gompi-2020b 1.10.7-gompi-2021a 1.10.7-iimpi-2021a 1.10.7-iompi-2021a 1.10.8-iimpi-2021a 1.12.0-gompi-2020a 1.12.1-gompi-2021b 1.12.2-gompi-2022a 1.14.0-gompi-2022a 1.14.0-gompi-2022b 1.14.0-gompi-2023a 1.14.0-iimpi-2023a
HISAT2	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).	TINKERCLIFFS 2.2.1-foss-2020a
HMMER	HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). Compared to BLAST, FASTA, and other sequence alignment and database search tools based on older scoring methodology, HMMER aims to be significantly more accurate and more able to detect remote homologs because of the strength of its underlying mathematical models. In the past, this strength came at significant computational expense, but in the new HMMER3 project, HMMER is now essentially as fast as BLAST.	TINKERCLIFFS 3.3.2-gompi-2020b 3.3.2-gompi-2022a
HMMER2	HMMER is used for searching sequence databases for sequence homologs, and for making sequence alignments.	TINKERCLIFFS 2.3.2-GCC-8.3.0
HPL	HPL is a software package that solves a (random) dense linear system in double precision (64 bits	TINKERCLIFFS 2.3-foss-2020a 2.3-gomkl-2022a 2.3-intel-2019b
HTSeq	HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.	TINKERCLIFFS 0.11.3-foss-2021b
HTSlib	A C library for reading/writing high-throughput sequencing data. This package includes the utilities bgzip and tabix	TINKERCLIFFS 1.10.2-GCC-9.3.0 1.11-GCC-10.2.0 1.14-GCC-11.2.0 1.15.1-GCC-11.3.0
HarfBuzz	HarfBuzz is an OpenType text shaping engine.	TINKERCLIFFS 2.6.4-GCCcore-8.3.0 2.6.4-GCCcore-9.3.0 2.6.7-GCCcore-10.2.0 2.8.1-GCCcore-10.3.0 4.2.1-GCCcore-11.3.0 5.3.1-GCCcore-12.2.0 5.3.1-GCCcore-12.3.0
Highway	Highway is a C++ library for SIMD (Single Instruction, Multiple Data), i.e. applying the same operation to ‘lanes’.	TINKERCLIFFS 1.0.3-GCCcore-12.2.0
Hypre	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.	TINKERCLIFFS 2.18.2-foss-2019b 2.18.2-intel-2019b 2.21.0-foss-2021a 2.25.0-foss-2022a 2.27.0-foss-2022b 2.29.0-foss-2023a
ICU	ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization support for software applications.	TINKERCLIFFS 64.2-GCCcore-8.3.0 66.1-GCCcore-9.3.0 66.1-intel-2019b 67.1-GCCcore-10.2.0 69.1-GCCcore-10.3.0 69.1-GCCcore-11.2.0 71.1-GCCcore-11.3.0 72.1-GCCcore-11.3.0 72.1-GCCcore-12.2.0 73.2-GCCcore-12.3.0
IJulia	Julia kernel for Jupyter	TINKERCLIFFS 1.24.0-Julia-1.8.5 1.24.2-Julia-1.10.3
IPython	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.	TINKERCLIFFS 8.14.0-GCCcore-12.2.0 8.14.0-GCCcore-12.3.0 8.5.0-GCCcore-11.3.0
ISA-L	Intelligent Storage Acceleration Library	TINKERCLIFFS 2.30.0-GCCcore-10.3.0 2.30.0-GCCcore-11.2.0
ISL	isl is a library for manipulating sets and relations of integer points bounded by linear constraints.	TINKERCLIFFS 0.23-GCCcore-10.3.0
ImageMagick	ImageMagick is a software suite to create, edit, compose, or convert bitmap images	TINKERCLIFFS 7.0.10-1-GCCcore-9.3.0 7.0.10-1-intel-2019b 7.0.10-35-GCCcore-10.2.0 7.0.11-14-GCCcore-10.3.0 7.1.0-37-GCCcore-11.3.0 7.1.0-53-GCCcore-12.2.0
Imath	Imath is a C++ and python library of 2D and 3D vector, matrix, and math operations for computer graphics	TINKERCLIFFS 3.1.6-GCCcore-12.2.0
Inspector	Intel Inspector is a dynamic memory and threading error checking tool for users developing serial and parallel applications	TINKERCLIFFS 2021.4.0
JAGS	JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation	TINKERCLIFFS 4.3.0-foss-2021b 4.3.1-foss-2022a
JasPer	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.	TINKERCLIFFS 2.0.14-GCCcore-8.3.0 2.0.14-GCCcore-9.3.0 2.0.24-GCCcore-10.2.0 2.0.28-GCCcore-10.3.0 2.0.33-GCCcore-11.3.0 4.0.0-GCCcore-11.3.0 4.0.0-GCCcore-12.2.0 4.0.0-GCCcore-12.3.0
Java	Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.	TINKERCLIFFS 1.8.0_292-OpenJDK 11.0.2 17.0.6
Jellyfish	Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.	TINKERCLIFFS 2.3.0-GCC-9.3.0
JsonCpp	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.	TINKERCLIFFS 1.9.4-GCCcore-10.2.0
Judy	A C library that implements a dynamic array.	TINKERCLIFFS 1.0.5-GCCcore-11.3.0
Julia	Julia is a high-level, high-performance dynamic programming language for numerical computing	TINKERCLIFFS 1.10.3-linux-x86_64 1.4.2-linux-x86_64 1.5.1-linux-x86_64 1.7.2-linux-x86_64 1.8.5-linux-x86_64 1.9.3-linux-x86_64
JupyterLab	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.	TINKERCLIFFS 3.5.0-GCCcore-11.3.0 4.0.3-GCCcore-12.2.0
JupyterNotebook	The Jupyter Notebook is the original web application for creating and sharing computational documents. It offers a simple, streamlined, document-centric experience.	TINKERCLIFFS 7.0.3-GCCcore-12.2.0
KaHIP	The graph partitioning framework KaHIP – Karlsruhe High Quality Partitioning.	TINKERCLIFFS 3.14-gompi-2022a
Kaleido	Fast static image export for web-based visualization libraries with zero dependencies	TINKERCLIFFS 0.2.1-GCCcore-10.3.0
Kent_tools	Kent utilities: collection of tools used by the UCSC genome browser.	TINKERCLIFFS 442-GCC-11.3.0
LAME	LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL.	TINKERCLIFFS 3.100-GCCcore-10.2.0 3.100-GCCcore-10.3.0 3.100-GCCcore-11.2.0 3.100-GCCcore-11.3.0 3.100-GCCcore-12.2.0 3.100-GCCcore-8.3.0 3.100-GCCcore-9.3.0
LAMMPS	LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has potentials for solid-state materials (metals, semiconductors) and soft matter (biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale. LAMMPS runs on single processors or in parallel using message-passing techniques and a spatial-decomposition of the simulation domain. The code is designed to be easy to modify or extend with new functionality.	TINKERCLIFFS 23Jun2022-foss-2021b-kokkos 3Mar2020-foss-2020a-Python-3.8.2-kokkos
LERC	LERC is an open-source image or raster format which supports rapid encoding and decoding for 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).	TINKERCLIFFS 4.0.0-GCCcore-12.2.0
LLVM	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	TINKERCLIFFS 11.0.0-GCCcore-10.2.0 11.1.0-GCCcore-10.3.0 12.0.1-GCCcore-11.2.0 14.0.3-GCCcore-11.3.0 15.0.5-GCCcore-11.3.0 15.0.5-GCCcore-12.2.0 16.0.6-GCCcore-12.3.0 7.0.1-GCCcore-8.2.0 9.0.0-GCCcore-8.3.0 9.0.1-GCCcore-9.3.0
LMDB	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.	TINKERCLIFFS 0.9.24-GCCcore-10.2.0 0.9.24-GCCcore-9.3.0 0.9.29-GCCcore-11.3.0
LTR_retriever	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.	TINKERCLIFFS 2.9.0-foss-2022a
LZO	Portable lossless data compression library	TINKERCLIFFS 2.10-GCCcore-11.3.0
LibTIFF	tiff: Library and tools for reading and writing TIFF data files	TINKERCLIFFS 4.0.10-GCCcore-8.3.0 4.1.0-GCCcore-10.2.0 4.1.0-GCCcore-8.3.0 4.1.0-GCCcore-9.3.0 4.2.0-GCCcore-10.3.0 4.3.0-GCCcore-11.2.0 4.3.0-GCCcore-11.3.0 4.4.0-GCCcore-11.3.0 4.4.0-GCCcore-12.2.0
Libint	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.	TINKERCLIFFS 1.1.6-foss-2020a 2.6.0-GCC-10.2.0-lmax-6-cp2k 2.7.2-GCC-12.3.0-lmax-6-cp2k
LittleCMS	Little CMS intends to be an OPEN SOURCE small-footprint color management engine, with special focus on accuracy and performance.	TINKERCLIFFS 2.11-GCCcore-10.2.0 2.12-GCCcore-10.3.0 2.13.1-GCCcore-11.3.0 2.14-GCCcore-11.3.0 2.14-GCCcore-12.2.0 2.9-GCCcore-8.3.0 2.9-GCCcore-9.3.0
Lua	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.	TINKERCLIFFS 5.1.5-GCCcore-8.3.0 5.4.3-GCCcore-10.3.0 5.4.4-GCCcore-11.3.0 5.4.6-GCCcore-12.3.0
M4	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.	TINKERCLIFFS 1.4.17 1.4.18-GCCcore-10.2.0 1.4.18-GCCcore-10.3.0 1.4.18-GCCcore-8.2.0 1.4.18-GCCcore-8.3.0 1.4.18-GCCcore-9.3.0 1.4.18 1.4.19-GCCcore-11.2.0 1.4.19-GCCcore-11.3.0 1.4.19-GCCcore-12.2.0 1.4.19-GCCcore-12.3.0 1.4.19-GCCcore-13.2.0 1.4.19
MAFFT	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 alignment of <∼200 sequences), FFT-NS-2 (fast; for alignment of <∼30,000 sequences), etc.	TINKERCLIFFS 7.505-GCC-11.3.0-with-extensions
MAKER	MAKER is a portable and easily configurable genome annotation pipeline. Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases.	TINKERCLIFFS 3.01.04-foss-2022a
MATIO	matio is an C library for reading and writing Matlab MAT files.	TINKERCLIFFS 1.5.17-GCCcore-8.3.0
MATLAB	MATLAB is a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and Fortran.	TINKERCLIFFS 2019b
METIS	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.	TINKERCLIFFS 5.1.0-GCCcore-10.2.0 5.1.0-GCCcore-10.3.0 5.1.0-GCCcore-11.3.0 5.1.0-GCCcore-12.2.0 5.1.0-GCCcore-12.3.0 5.1.0-GCCcore-8.2.0 5.1.0-GCCcore-8.3.0 5.1.0-GCCcore-9.3.0
MPC	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.	TINKERCLIFFS 1.1.0-GCC-8.3.0 1.2.1-GCCcore-10.3.0
MPFR	The MPFR library is a C library for multiple-precision floating-point computations with correct rounding.	TINKERCLIFFS 4.0.2-GCCcore-8.3.0 4.0.2-GCCcore-9.3.0 4.1.0-GCCcore-10.2.0 4.1.0-GCCcore-10.3.0 4.1.0-GCCcore-11.3.0 4.2.0-GCCcore-11.3.0 4.2.0-GCCcore-12.2.0 4.2.0-GCCcore-12.3.0
MPICH	MPICH is a high-performance and widely portable implementation of the Message Passing Interface (MPI) standard (MPI-1, MPI-2 and MPI-3).	TINKERCLIFFS 3.3.2-GCC-8.3.0
MUMPS	A parallel sparse direct solver	TINKERCLIFFS 5.2.1-foss-2019b-metis 5.2.1-foss-2020a-metis 5.2.1-intel-2019b-metis 5.4.0-foss-2021a-metis 5.5.1-foss-2022a-metis 5.6.1-foss-2022b-metis 5.6.1-foss-2023a-metis
Mako	A super-fast templating language that borrows the best ideas from the existing templating languages	TINKERCLIFFS 1.0.8-GCCcore-8.2.0 1.1.0-GCCcore-8.3.0 1.1.2-GCCcore-9.3.0 1.1.3-GCCcore-10.2.0 1.1.4-GCCcore-10.3.0 1.1.4-GCCcore-11.2.0 1.2.0-GCCcore-11.3.0 1.2.4-GCCcore-11.3.0 1.2.4-GCCcore-12.2.0 1.2.4-GCCcore-12.3.0
MariaDB	MariaDB is an enhanced, drop-in replacement for MySQL. Included engines: myISAM, Aria, InnoDB, RocksDB, TokuDB, OQGraph, Mroonga.	TINKERCLIFFS 10.9.3-GCC-11.3.0
MariaDB-connector-c	MariaDB Connector/C is used to connect applications developed in C/C++ to MariaDB and MySQL databases.	TINKERCLIFFS 3.1.7-GCCcore-9.3.0 3.1.7-intel-2019b
Mathematica	Mathematica is a computational software program used in many scientific, engineering, mathematical and computing fields.	TINKERCLIFFS 12.0.0 13.2.0
Mesa	Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics.	TINKERCLIFFS 19.0.1-GCCcore-8.2.0 19.1.7-GCCcore-8.3.0 19.2.1-GCCcore-8.3.0 20.0.2-GCCcore-9.3.0 20.2.1-GCCcore-10.2.0 21.1.1-GCCcore-10.3.0 21.1.7-GCCcore-11.2.0 22.0.3-GCCcore-11.3.0 22.2.4-GCCcore-11.3.0 22.2.4-GCCcore-12.2.0 23.1.4-GCCcore-12.3.0
Meson	Meson is a cross-platform build system designed to be both as fast and as user friendly as possible.	TINKERCLIFFS 0.50.0-GCCcore-8.2.0-Python-3.7.2 0.51.2-GCCcore-8.3.0-Python-3.7.4 0.53.2-GCCcore-9.3.0-Python-3.8.2 0.53.2-intel-2019b-Python-3.7.4 0.55.1-GCCcore-9.3.0-Python-3.8.2 0.55.3-GCCcore-10.2.0 0.58.0-GCCcore-10.3.0 0.58.2-GCCcore-11.2.0 0.62.1-GCCcore-11.3.0 0.64.0-GCCcore-11.3.0 0.64.0-GCCcore-12.2.0 1.1.1-GCCcore-12.3.0
MetaEuk	MetaEuk is a modular toolkit designed for large-scale gene discovery and annotation in eukaryotic metagenomic contigs.	TINKERCLIFFS 4-GCC-10.2.0 6-GCC-11.3.0
Miniconda3	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.	TINKERCLIFFS 23.9.0-0 4.7.10
Miniforge3	Miniforge is a free minimal installer for conda and Mamba specific to conda-forge.	TINKERCLIFFS 24.1.2-0
MrBayes	MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models.	TINKERCLIFFS 3.2.7-gompi-2020b
NAMD	NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.	TINKERCLIFFS 2.13-foss-2020a-mpi
NASM	NASM: General-purpose x86 assembler	TINKERCLIFFS 2.14.02-GCCcore-8.3.0 2.14.02-GCCcore-9.3.0 2.15.05-GCCcore-10.2.0 2.15.05-GCCcore-10.3.0 2.15.05-GCCcore-11.2.0 2.15.05-GCCcore-11.3.0 2.15.05-GCCcore-12.2.0 2.16.01-GCCcore-12.3.0
NCCL	The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective communication primitives that are performance optimized for NVIDIA GPUs.	TINKERCLIFFS 2.10.3-GCCcore-11.2.0-CUDA-11.4.1
NCO	The NCO toolkit manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5.	TINKERCLIFFS 5.0.3-intel-2021a
NGS	NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing.	TINKERCLIFFS 2.10.5-GCCcore-9.3.0
NLopt	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.	TINKERCLIFFS 2.6.1-GCCcore-8.3.0 2.6.1-GCCcore-9.3.0 2.6.2-GCCcore-10.2.0 2.7.0-GCCcore-10.3.0 2.7.1-GCCcore-11.3.0 2.7.1-GCCcore-12.2.0
NSPR	Netscape Portable Runtime (NSPR) provides a platform-neutral API for system level and libc-like functions.	TINKERCLIFFS 4.21-GCCcore-8.3.0 4.25-GCCcore-9.3.0 4.30-GCCcore-10.3.0 4.34-GCCcore-11.3.0 4.35-GCCcore-12.3.0
NSS	Network Security Services (NSS) is a set of libraries designed to support cross-platform development of security-enabled client and server applications.	TINKERCLIFFS 3.45-GCCcore-8.3.0 3.51-GCCcore-9.3.0 3.65-GCCcore-10.3.0 3.79-GCCcore-11.3.0 3.89.1-GCCcore-12.3.0
NVHPC	C, C++ and Fortran compilers included with the NVIDIA HPC SDK (previously: PGI)	TINKERCLIFFS 20.7 21.2
NanoPlot	Plotting suite for long read sequencing data and alignments	TINKERCLIFFS 1.33.0-foss-2021a
Nextflow	Nextflow is a reactive workflow framework and a programming DSL that eases writing computational pipelines with complex data	TINKERCLIFFS 22.10.6 24.04.2
Ninja	Ninja is a small build system with a focus on speed.	TINKERCLIFFS 1.10.0-GCCcore-9.3.0 1.10.0-intel-2019b 1.10.1-GCCcore-10.2.0 1.10.2-GCCcore-10.3.0 1.10.2-GCCcore-11.2.0 1.10.2-GCCcore-11.3.0 1.11.1-GCCcore-11.3.0 1.11.1-GCCcore-12.2.0 1.11.1-GCCcore-12.3.0 1.11.1-GCCcore-13.2.0 1.9.0-GCCcore-8.2.0 1.9.0-GCCcore-8.3.0
OpenBLAS	OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.	TINKERCLIFFS 0.3.12-GCC-10.2.0 0.3.15-GCC-10.3.0 0.3.18-GCC-11.2.0 0.3.20-GCC-11.3.0 0.3.21-GCC-12.2.0 0.3.23-GCC-12.3.0 0.3.24-GCC-13.2.0 0.3.7-GCC-8.3.0 0.3.9-GCC-9.3.0
OpenEXR	OpenEXR is a high dynamic-range (HDR) image file format developed by Industrial Light & Magic for use in computer imaging applications	TINKERCLIFFS 3.1.5-GCCcore-12.2.0
OpenFOAM	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.	TINKERCLIFFS 9-foss-2021a v2006-foss-2020a v2206-foss-2022a
OpenJPEG	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.	TINKERCLIFFS 2.5.0-GCCcore-11.3.0 2.5.0-GCCcore-12.2.0
OpenMM	OpenMM is a toolkit for molecular simulation.	TINKERCLIFFS 7.4.1-intel-2019b-Python-3.7.4
OpenMPI	The Open MPI Project is an open source MPI-3 implementation.	TINKERCLIFFS 3.1.3-GCC-8.2.0-2.31.1 3.1.4-GCC-8.3.0 3.1.4-iccifort-2019.5.281 4.0.3-GCC-9.3.0 4.0.3-iccifort-2019.5.281 4.0.5-GCC-10.2.0 4.1.1-GCC-10.3.0 4.1.1-GCC-11.2.0 4.1.1-intel-compilers-2021.2.0 4.1.4-GCC-11.3.0 4.1.4-GCC-12.2.0 4.1.5-GCC-12.3.0 4.1.6-GCC-13.2.0
OpenMolcas	OpenMolcas is a quantum chemistry software package	TINKERCLIFFS 18.09-intel-2019b-Python-3.7.4 19.11-intel-2019b-Python-3.7.4
OpenPGM	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.	TINKERCLIFFS 5.2.122-GCCcore-11.3.0 5.2.122-GCCcore-12.2.0 5.2.122-GCCcore-12.3.0 5.2.122-GCCcore-13.2.0
OpenSSL	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.	TINKERCLIFFS 1.0 1.1.1e-GCCcore-9.3.0 1.1.1e-intel-2019b 1.1
Osi	Osi (Open Solver Interface) provides an abstract base class to a generic linear programming (LP) solver, along with derived classes for specific solvers. Many applications may be able to use the Osi to insulate themselves from a specific LP solver. That is, programs written to the OSI standard may be linked to any solver with an OSI interface and should produce correct results. The OSI has been significantly extended compared to its first incarnation. Currently, the OSI supports linear programming solvers and has rudimentary support for integer programming.	TINKERCLIFFS 0.108.9-GCC-12.3.0
PCRE	The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5.	TINKERCLIFFS 8.43-GCCcore-8.3.0 8.44-GCCcore-10.2.0 8.44-GCCcore-10.3.0 8.44-GCCcore-9.3.0 8.45-GCCcore-11.2.0 8.45-GCCcore-11.3.0 8.45-GCCcore-12.2.0
PCRE2	The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5.	TINKERCLIFFS 10.33-GCCcore-8.3.0 10.34-GCCcore-9.3.0 10.34-intel-2019b 10.35-GCCcore-10.2.0 10.36-GCCcore-10.3.0 10.40-GCCcore-11.3.0 10.40-GCCcore-12.2.0 10.42-GCCcore-12.3.0
PETSc	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.	TINKERCLIFFS 3.12.4-foss-2019b-Python-3.7.4 3.12.4-intel-2019b 3.15.1-foss-2021a 3.17.4-foss-2022a 3.19.2-foss-2022b 3.20.3-foss-2023a
PLINK	PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.	TINKERCLIFFS 2.00a3.7-foss-2022a
PLUMED	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.	TINKERCLIFFS 2.5.1-foss-2020a 2.6.0-foss-2020a-Python-3.8.2 2.7.3-foss-2021b 2.9.0-foss-2023a
PLY	PLY is yet another implementation of lex and yacc for Python.	TINKERCLIFFS 3.11-GCCcore-8.3.0-Python-3.7.4
PMIx	Process Management for Exascale Environments PMI Exascale (PMIx) represents an attempt to provide an extended version of the PMI standard specifically designed to support clusters up to and including exascale sizes. The overall objective of the project is not to branch the existing pseudo-standard definitions - in fact, PMIx fully supports both of the existing PMI-1 and PMI-2 APIs - but rather to (a) augment and extend those APIs to eliminate some current restrictions that impact scalability, and (b	TINKERCLIFFS 3.1.5-GCCcore-10.2.0 3.1.5-GCCcore-8.3.0 3.2.3-GCCcore-10.3.0 4.1.0-GCCcore-11.2.0 4.1.2-GCCcore-11.3.0 4.2.2-GCCcore-12.2.0 4.2.4-GCCcore-12.3.0 4.2.6-GCCcore-13.2.0
PROJ	Program proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates	TINKERCLIFFS 6.2.1-GCCcore-8.3.0 7.0.0-GCCcore-9.3.0 8.0.1-GCCcore-10.3.0 9.0.0-GCCcore-11.3.0 9.1.1-GCCcore-12.2.0
Pango	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 the context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.	TINKERCLIFFS 1.44.7-GCCcore-8.3.0 1.44.7-GCCcore-9.3.0 1.47.0-GCCcore-10.2.0 1.48.5-GCCcore-10.3.0 1.50.12-GCCcore-12.2.0 1.50.14-GCCcore-12.3.0 1.50.7-GCCcore-11.3.0
ParMETIS	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.	TINKERCLIFFS 4.0.3-gompi-2019b 4.0.3-gompi-2022a 4.0.3-gompi-2022b 4.0.3-gompi-2023a 4.0.3-intel-2022b
ParaView	ParaView is a scientific parallel visualizer.	TINKERCLIFFS 5.10.1-foss-2022a-mpi 5.8.0-foss-2020a-Python-3.8.2-mpi 5.9.1-foss-2021a-mpi
Perl	Larry Wall’s Practical Extraction and Report Language	TINKERCLIFFS 5.28.1-GCCcore-8.2.0 5.30.0-GCCcore-8.3.0 5.30.2-GCCcore-9.3.0 5.32.0-GCCcore-10.2.0 5.32.1-GCCcore-10.3.0 5.34.0-GCCcore-11.2.0 5.34.1-GCCcore-11.3.0-minimal 5.34.1-GCCcore-11.3.0 5.36.0-GCCcore-11.3.0 5.36.0-GCCcore-12.2.0 5.36.1-GCCcore-12.3.0 5.38.0-GCCcore-13.2.0
Perl-bundle-CPAN	A set of common packages from CPAN	TINKERCLIFFS 5.36.1-GCCcore-12.3.0
Pillow	Pillow is the ‘friendly PIL fork’ by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors.	TINKERCLIFFS 6.2.1-GCCcore-8.3.0 7.0.0-GCCcore-9.3.0-Python-3.8.2 8.0.1-GCCcore-10.2.0 8.2.0-GCCcore-10.3.0 8.3.2-GCCcore-11.2.0 9.1.1-GCCcore-11.3.0
PnetCDF	Parallel netCDF: A Parallel I/O Library for NetCDF File Access	TINKERCLIFFS 1.12.1-gompi-2019b 1.12.1-gompi-2020a 1.12.2-iimpi-2021a
PostgreSQL	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.	TINKERCLIFFS 14.4-GCCcore-11.3.0
PuLP	PuLP is an LP modeler written in Python. PuLP can generate MPS or LP files and call GLPK, COIN-OR CLP/CBC, CPLEX, GUROBI, MOSEK, XPRESS, CHOCO, MIPCL, SCIP to solve linear problems.	TINKERCLIFFS 2.8.0-foss-2023a
PyCharm	PyCharm Community Edition: Python IDE for Professional Developers	TINKERCLIFFS 2019.3.1 2021.1.1
PyTorch	Tensors and Dynamic neural networks in Python with strong GPU acceleration. PyTorch is a deep learning framework that puts Python first.	TINKERCLIFFS 1.4.0-foss-2020a-Python-3.8.2 1.6.0-foss-2020a-Python-3.8.2 1.6.0-gomkl-2020a-Python-3.8.2 1.7.1-foss-2020b
PyYAML	PyYAML is a YAML parser and emitter for the Python programming language.	TINKERCLIFFS 5.1.2-GCCcore-8.3.0 5.3-GCCcore-9.3.0 5.3.1-GCCcore-10.2.0 6.0-GCCcore-12.2.0 6.0-GCCcore-12.3.0
Pysam	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.	TINKERCLIFFS 0.16.0.1-GCC-10.3.0 0.16.0.1-GCC-9.3.0 0.17.0-GCC-11.2.0 0.21.0-GCC-12.2.0
Python	Python is a programming language that lets you work more quickly and integrate your systems more effectively.	TINKERCLIFFS 2.7.15-GCCcore-8.2.0 2.7.16-GCCcore-8.3.0 2.7.18-GCCcore-10.2.0 2.7.18-GCCcore-10.3.0-bare 2.7.18-GCCcore-11.3.0-bare 2.7.18-GCCcore-9.3.0 3.10.4-GCCcore-11.3.0-bare 3.10.4-GCCcore-11.3.0 3.10.8-GCCcore-11.3.0-bare 3.10.8-GCCcore-11.3.0 3.10.8-GCCcore-12.2.0-bare 3.10.8-GCCcore-12.2.0 3.11.3-GCCcore-12.3.0 3.11.5-GCCcore-13.2.0 3.7.2-GCCcore-8.2.0 3.7.4-GCCcore-8.3.0 3.8.2-GCCcore-9.3.0 3.8.6-GCCcore-10.2.0 3.9.5-GCCcore-10.3.0-bare 3.9.5-GCCcore-10.3.0 3.9.6-GCCcore-11.2.0-bare 3.9.6-GCCcore-11.2.0
Python-bundle-PyPI	Bundle of Python packages from PyPI	TINKERCLIFFS 2023.06-GCCcore-12.3.0
QIIME2	QIIME is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data.	TINKERCLIFFS 2020.6
QUAST	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.	TINKERCLIFFS 5.2.0-foss-2022a
Qhull	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.	TINKERCLIFFS 2020.2-GCCcore-10.3.0 2020.2-GCCcore-11.2.0 2020.2-GCCcore-11.3.0 2020.2-GCCcore-12.2.0
Qt5	Qt is a comprehensive cross-platform C++ application framework.	TINKERCLIFFS 5.13.1-GCCcore-8.3.0 5.14.1-GCCcore-9.3.0 5.15.10-GCCcore-12.3.0 5.15.2-GCCcore-10.3.0 5.15.5-GCCcore-11.3.0
Qualimap	Qualimap 2 is a platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data and its derivatives like feature counts.	TINKERCLIFFS 2.2.1-foss-2020b-R-4.0.3
QuantumESPRESSO	Quantum ESPRESSO is an integrated suite of computer codes for 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).	TINKERCLIFFS 6.5-intel-2019b
R	R is a free software environment for statistical computing and graphics.	TINKERCLIFFS 4.0.2-foss-2020a 4.0.3-foss-2020b 4.1.0-foss-2021a 4.2.1-foss-2022a 4.2.2-foss-2022b
R-bundle-Bioconductor	Bioconductor provides tools for the analysis and coprehension of high-throughput genomic data.	TINKERCLIFFS 3.12-foss-2020b-R-4.0.3
RE2	RE2 is a fast, safe, thread-friendly alternative to backtracking regular expression engines like those used in PCRE, Perl, and Python. It is a C++ library.	TINKERCLIFFS 2022-02-01-GCCcore-10.3.0 2022-02-01-GCCcore-11.2.0
RECON	Patched version of RECON to be used with RepeatModeler.	TINKERCLIFFS 1.08-GCC-11.3.0
RMBlast	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.	TINKERCLIFFS 2.13.0-gompi-2022a
RapidJSON	A fast JSON parser/generator for C++ with both SAX/DOM style API	TINKERCLIFFS 1.1.0-GCCcore-10.3.0 1.1.0-GCCcore-11.2.0
RepeatMasker	RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.	TINKERCLIFFS 4.1.4-foss-2022a
RepeatModeler	RepeatModeler is a de novo transposable element (TE) family identification and modeling package.	TINKERCLIFFS 2.0.4-foss-2022a
RepeatScout	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 )	TINKERCLIFFS 1.0.6-GCC-11.3.0
Ruby	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.	TINKERCLIFFS 2.7.2-GCCcore-9.3.0
Rust	Rust is a systems programming language that runs blazingly fast, prevents segfaults, and guarantees thread safety.	TINKERCLIFFS 1.52.1-GCCcore-10.3.0 1.54.0-GCCcore-11.2.0 1.60.0-GCCcore-11.3.0 1.65.0-GCCcore-11.3.0 1.65.0-GCCcore-12.2.0 1.70.0-GCCcore-12.3.0 1.73.0-GCCcore-13.2.0
SAMtools	SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.	TINKERCLIFFS 1.11-GCC-10.2.0 1.16.1-GCC-11.3.0
SCOTCH	Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.	TINKERCLIFFS 6.0.9-gompi-2019b 6.0.9-gompi-2020a 6.0.9-iimpi-2019b 6.1.0-gompi-2021a 7.0.1-gompi-2022a 7.0.3-foss-2022b 7.0.3-gompi-2022b 7.0.3-gompi-2023a
SCons	SCons is a software construction tool.	TINKERCLIFFS 4.0.1-GCCcore-10.2.0
SEPP	SATe-enabled Phylogenetic Placement - addresses the problem of phylogenetic placement of short reads into reference alignments and trees.	TINKERCLIFFS 4.4.0-foss-2020b 4.5.1-foss-2022a
SLEPc	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.	TINKERCLIFFS 3.12.2-foss-2019b-Python-3.7.4 3.12.2-intel-2019b
SNAP-HMM	SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. SNAP is an acroynm for Semi-HMM-based Nucleic Acid Parser.	TINKERCLIFFS 20221022-GCC-11.3.0
SQLite	SQLite: SQL Database Engine in a C Library	TINKERCLIFFS 3.27.2-GCCcore-8.2.0 3.29.0-GCCcore-8.3.0 3.31.1-GCCcore-9.3.0 3.31.1-intel-2019b 3.33.0-GCCcore-10.2.0 3.35.4-GCCcore-10.3.0 3.36-GCCcore-11.2.0 3.38.3-GCCcore-11.3.0 3.39.4-GCCcore-11.3.0 3.39.4-GCCcore-12.2.0 3.42.0-GCCcore-12.3.0 3.43.1-GCCcore-13.2.0
SUNDIALS	SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers	TINKERCLIFFS 5.1.0-foss-2019b
SWIG	SWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages.	TINKERCLIFFS 3.0.12-GCCcore-8.3.0 4.0.1-GCCcore-8.3.0 4.0.1-GCCcore-9.3.0 4.0.2-GCCcore-11.2.0
Salmon	Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimate from RNA-seq data.	TINKERCLIFFS 1.10.1-GCC-12.2.0 1.4.0-GCC-11.2.0 1.9.0-GCC-11.3.0
ScaFaCoS	ScaFaCoS is a library of scalable fast coulomb solvers.	TINKERCLIFFS 1.0.1-foss-2020a 1.0.1-foss-2021b
ScaLAPACK	The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers.	TINKERCLIFFS 2.0.2-gompi-2019b 2.1.0-gompi-2020a 2.1.0-gompi-2020b 2.1.0-gompi-2021a-fb 2.1.0-gompi-2021b-fb 2.2.0-gompi-2022a-fb 2.2.0-gompi-2022b-fb 2.2.0-gompi-2023a-fb 2.2.0-gompi-2023b-fb
Schrodinger	Schrodinger aims to provide integrated software solutions and services that truly meet its customers needs. We want to empower researchers around the world to achieve their goals of improving human health and quality of life through advanced computational techniques that transform the way chemists design compounds and materials.	TINKERCLIFFS 2020-4
SciPy-bundle	Bundle of Python packages for scientific software	TINKERCLIFFS 2019.10-foss-2019b-Python-3.7.4 2019.10-intel-2019b-Python-3.7.4 2020.03-foss-2020a-Python-3.8.2 2020.03-gomkl-2020a-Python-3.8.2 2020.11-foss-2020b 2021.05-foss-2021a 2021.10-foss-2021b 2022.05-foss-2022a 2023.02-gfbf-2022b 2023.07-gfbf-2023a
Seaborn	Seaborn is a Python visualization library based on matplotlib. It provides a high-level interface for drawing attractive statistical graphics.	TINKERCLIFFS 0.11.2-foss-2021a
Serf	The serf library is a high performance C-based HTTP client library built upon the Apache Portable Runtime (APR) library	TINKERCLIFFS 1.3.9-GCCcore-10.2.0
SoX	SoX is the Swiss Army Knife of sound processing utilities. It can convert audio files to other popular audio file types and also apply sound effects and filters during the conversion.	TINKERCLIFFS 14.4.2-GCC-10.2.0
SpaceRanger	Space Ranger is a set of analysis pipelines that process Visium spatial RNA-seq output and brightfield microscope images in order to detect tissue, align reads, generate feature-spot matrices, perform clustering and gene expression analysis, and place spots in spatial context on the slide image.	TINKERCLIFFS 1.2.2-GCC-9.3.0
Spark	Spark is Hadoop MapReduce done in memory	TINKERCLIFFS 3.2.1-foss-2021b
StringTie	StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts	TINKERCLIFFS 2.1.7-GCC-10.3.0 2.2.1-GCC-11.2.0
Subread	High performance read alignment, quantification and mutation discovery	TINKERCLIFFS 2.0.3-GCC-10.3.0 2.0.3-GCC-11.2.0
Subversion	Subversion is an open source version control system.	TINKERCLIFFS 1.14.0-GCCcore-10.2.0
SuiteSparse	SuiteSparse is a collection of libraries manipulate sparse matrices.	TINKERCLIFFS 5.10.1-foss-2021a-METIS-5.1.0 5.13.0-foss-2022a-METIS-5.1.0 5.13.0-foss-2022b-METIS-5.1.0 5.6.0-foss-2019b-METIS-5.1.0 5.6.0-intel-2019b-METIS-5.1.0 5.8.1-foss-2020b-METIS-5.1.0 7.1.0-foss-2023a
SuperLU_DIST	SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines.	TINKERCLIFFS 8.1.0-foss-2022a 8.1.2-foss-2022b 8.1.2-foss-2023a
Szip	Szip compression software, providing lossless compression of scientific data	TINKERCLIFFS 2.1.1-GCCcore-10.2.0 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 2.1.1-GCCcore-13.2.0 2.1.1-GCCcore-8.3.0 2.1.1-GCCcore-9.3.0
TINKER	The TINKER molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers.	TINKERCLIFFS 8.8.1-foss-2020a
TRF	Tandem Repeats Finder: a program to analyze DNA sequences.	TINKERCLIFFS 4.09.1-GCCcore-11.3.0
TWL-NINJA	Nearly Infinite Neighbor Joining Application.	TINKERCLIFFS 0.98-cluster_only-GCC-11.3.0
Tcl	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.	TINKERCLIFFS 8.6.10-GCCcore-10.2.0 8.6.10-GCCcore-9.3.0 8.6.10-intel-2019b 8.6.11-GCCcore-10.3.0 8.6.11-GCCcore-11.2.0 8.6.12-GCCcore-11.3.0 8.6.12-GCCcore-12.2.0 8.6.13-GCCcore-12.3.0 8.6.13-GCCcore-13.2.0 8.6.9-GCCcore-8.2.0 8.6.9-GCCcore-8.3.0
TensorFlow	An open-source software library for Machine Intelligence	TINKERCLIFFS 2.4.1-foss-2020b
Tk	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.	TINKERCLIFFS 8.6.10-GCCcore-10.2.0 8.6.10-GCCcore-9.3.0 8.6.10-intel-2019b 8.6.11-GCCcore-10.3.0 8.6.11-GCCcore-11.2.0 8.6.12-GCCcore-11.3.0 8.6.12-GCCcore-12.2.0 8.6.9-GCCcore-8.3.0
Tkinter	Tkinter module, built with the Python buildsystem	TINKERCLIFFS 3.10.4-GCCcore-11.3.0 3.7.4-GCCcore-8.3.0 3.8.2-GCCcore-9.3.0 3.8.6-GCCcore-10.2.0 3.9.5-GCCcore-10.3.0 3.9.6-GCCcore-11.2.0
TopHat	TopHat is a fast splice junction mapper for RNA-Seq reads.	TINKERCLIFFS 2.1.2-iimpi-2019b
TransDecoder	TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.	TINKERCLIFFS 5.5.0-GCC-11.3.0
Trilinos	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.	TINKERCLIFFS 12.12.1-foss-2019b-Python-3.7.4
Trimmomatic	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.	TINKERCLIFFS 0.39-Java-11
UCC	UCC (Unified Collective Communication) is a collective communication operations API and library that is flexible, complete, and feature-rich for current and emerging programming models and runtimes.	TINKERCLIFFS 1.0.0-GCCcore-11.3.0 1.1.0-GCCcore-12.2.0 1.2.0-GCCcore-12.3.0 1.2.0-GCCcore-13.2.0
UCX	Unified Communication X An open-source production grade communication framework for data centric and high-performance applications	TINKERCLIFFS 1.10.0-GCCcore-10.3.0 1.11.2-GCCcore-11.2.0 1.12.1-GCCcore-11.3.0 1.13.1-GCCcore-12.2.0 1.14.1-GCCcore-12.3.0 1.15.0-GCCcore-13.2.0 1.8.0-GCCcore-8.3.0 1.8.0-GCCcore-9.3.0 1.9.0-GCCcore-10.2.0
UCX-CUDA	Unified Communication X An open-source production grade communication framework for data centric and high-performance applications This module adds the UCX CUDA support.	TINKERCLIFFS 1.11.2-GCCcore-11.2.0-CUDA-11.4.1
UDUNITS	UDUNITS supports conversion of unit specifications between formatted and binary forms, arithmetic manipulation of units, and conversion of values between compatible scales of measurement.	TINKERCLIFFS 2.2.26-GCCcore-10.2.0 2.2.26-GCCcore-8.3.0 2.2.26-GCCcore-9.3.0 2.2.28-GCCcore-10.3.0 2.2.28-GCCcore-11.2.0 2.2.28-GCCcore-11.3.0 2.2.28-GCCcore-12.2.0
UFL	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.	TINKERCLIFFS 2019.1.0-foss-2019b-Python-3.7.4
UnZip	UnZip is an extraction utility for archives compressed in .zip format (also called “zipfiles”). Although highly compatible both with PKWARE’s PKZIP and PKUNZIP utilities for MS-DOS and with Info-ZIP’s own Zip program, our primary objectives have been portability and non-MSDOS functionality.	TINKERCLIFFS 6.0-GCCcore-10.2.0 6.0-GCCcore-10.3.0 6.0-GCCcore-11.2.0 6.0-GCCcore-11.3.0 6.0-GCCcore-12.2.0 6.0-GCCcore-12.3.0 6.0-GCCcore-13.2.0
VASP	The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, from first principles.	TINKERCLIFFS 5.4.4-intel-2019b
VTK	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.	TINKERCLIFFS 8.2.0-foss-2019b-Python-3.7.4 8.2.0-foss-2020a-Python-3.8.2 9.1.0-foss-2021b
VTune	Intel VTune Amplifier XE is the premier performance profiler for C, C++, C#, Fortran, Assembly and Java.	TINKERCLIFFS 2022.2.0 2022.3.0
Valgrind	Valgrind: Debugging and profiling tools	TINKERCLIFFS 3.16.1-gompi-2020a 3.16.1-gompi-2020b 3.16.1-iimpi-2019b
VarScan	Variant calling and somatic mutation/CNV detection for next-generation sequencing data	TINKERCLIFFS 2.4.4-Java-11
ViennaRNA	The Vienna RNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.	TINKERCLIFFS 2.5.1-foss-2021b
VirtualGL	VirtualGL is an open source toolkit that gives any Linux or Unix remote display software the ability to run OpenGL applications with full hardware acceleration.	TINKERCLIFFS 2.6.2-GCCcore-9.3.0
Voro++	Voro++ is a software library for carrying out three-dimensional computations of the Voronoi tessellation. 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 that rely on cell-based statistics, where features of Voronoi cells (eg. volume, centroid, number of faces) can be used to analyze a system of particles.	TINKERCLIFFS 0.4.6-GCCcore-11.2.0 0.4.6-GCCcore-9.3.0
WPS	WRF Preprocessing System (WPS) for WRF. The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale numerical weather prediction system designed to serve both operational forecasting and atmospheric research needs.	TINKERCLIFFS 4.2-foss-2020b-dmpar
WRF	The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale numerical weather prediction system designed to serve both operational forecasting and atmospheric research needs.	TINKERCLIFFS 4.1.3-intel-2019b-dmpar 4.2.2-foss-2020b-dm+sm 4.2.2-foss-2020b-dmpar
Wannier90	A tool for obtaining maximally-localised Wannier functions	TINKERCLIFFS 2.0.1.1-intel-2019b-abinit 3.1.0-foss-2022a
X11	The X Window System (X11) is a windowing system for bitmap displays	TINKERCLIFFS 20190311-GCCcore-8.2.0 20190717-GCCcore-8.3.0 20200222-GCCcore-9.3.0 20200222-intel-2019b 20201008-GCCcore-10.2.0 20210518-GCCcore-10.3.0 20210802-GCCcore-11.2.0 20220504-GCCcore-11.3.0 20221110-GCCcore-11.3.0 20221110-GCCcore-12.2.0 20230603-GCCcore-12.3.0
XML-LibXML	Perl binding for libxml2	TINKERCLIFFS 2.0205-GCCcore-9.3.0 2.0207-GCCcore-11.3.0
XZ	xz: XZ utilities	TINKERCLIFFS 5.2.4-GCCcore-8.2.0 5.2.4-GCCcore-8.3.0 5.2.5-GCCcore-10.2.0 5.2.5-GCCcore-10.3.0 5.2.5-GCCcore-11.2.0 5.2.5-GCCcore-11.3.0 5.2.5-GCCcore-8.3.0 5.2.5-GCCcore-9.3.0 5.2.5-intel-2019b 5.2.7-GCCcore-11.3.0 5.2.7-GCCcore-12.2.0 5.4.2-GCCcore-12.3.0 5.4.4-GCCcore-13.2.0
Xerces-C++	Xerces-C++ is a validating XML parser written in a portable subset of C++. Xerces-C++ makes it easy to give your application the ability to read and write XML data. A shared library is provided for parsing, generating, manipulating, and validating XML documents using the DOM, SAX, and SAX2 APIs.	TINKERCLIFFS 3.2.4-GCCcore-12.2.0
Xvfb	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.	TINKERCLIFFS 1.20.11-GCCcore-10.3.0 1.20.9-GCCcore-10.2.0 21.1.3-GCCcore-11.3.0 21.1.6-GCCcore-11.3.0 21.1.6-GCCcore-12.2.0
Yasm	Yasm: Complete rewrite of the NASM assembler with BSD license	TINKERCLIFFS 1.3.0-GCCcore-10.2.0 1.3.0-GCCcore-10.3.0 1.3.0-GCCcore-11.2.0 1.3.0-GCCcore-11.3.0 1.3.0-GCCcore-8.3.0 1.3.0-GCCcore-9.3.0
Z3	Z3 is a theorem prover from Microsoft Research.	TINKERCLIFFS 4.8.10-GCCcore-10.2.0
ZeroMQ	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.	TINKERCLIFFS 4.3.4-GCCcore-11.3.0 4.3.4-GCCcore-12.2.0 4.3.4-GCCcore-12.3.0 4.3.5-GCCcore-13.2.0
Zip	Zip is a compression and file packaging/archive utility. Although highly compatible both with PKWARE’s PKZIP and PKUNZIP utilities for MS-DOS and with Info-ZIP’s own UnZip, our primary objectives have been portability and other-than-MSDOS functionality	TINKERCLIFFS 3.0-GCCcore-10.2.0
ant	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.	TINKERCLIFFS 1.10.12-Java-11
archspec	A library for detecting, labeling, and reasoning about microarchitectures	TINKERCLIFFS 0.1.0-GCCcore-9.3.0-Python-3.8.2 0.1.3-GCCcore-11.2.0
aria2	aria2 is a lightweight multi-protocol & multi-source command-line download utility.	TINKERCLIFFS 1.36.0-GCCcore-11.3.0
arpack-ng	ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.	TINKERCLIFFS 3.8.0-foss-2022b
at-spi2-atk	AT-SPI 2 toolkit bridge	TINKERCLIFFS 2.34.2-GCCcore-9.3.0 2.38.0-GCCcore-10.2.0 2.38.0-GCCcore-10.3.0 2.38.0-GCCcore-12.2.0
at-spi2-core	Assistive Technology Service Provider Interface.	TINKERCLIFFS 2.36.0-GCCcore-9.3.0 2.38.0-GCCcore-10.2.0 2.40.2-GCCcore-10.3.0 2.46.0-GCCcore-12.2.0
bcl2fastq2	bcl2fastq Conversion Software both demultiplexes data and converts BCL files generated by Illumina sequencing systems to standard FASTQ file formats for downstream analysis.	TINKERCLIFFS 2.20.0-GCC-9.3.0
beagle-lib	beagle-lib is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages.	TINKERCLIFFS 3.1.2-GCC-10.2.0
binutils	binutils: GNU binary utilities	TINKERCLIFFS 2.30 2.31.1-GCCcore-8.2.0 2.31.1 2.32-GCCcore-8.3.0 2.32 2.34-GCCcore-9.3.0 2.34-intel-2019b 2.34 2.35-GCCcore-10.2.0 2.35 2.36.1-GCCcore-10.3.0 2.36.1 2.37-GCCcore-11.2.0 2.37 2.38-GCCcore-11.3.0 2.38 2.39-GCCcore-11.3.0 2.39-GCCcore-12.2.0 2.39 2.40-GCCcore-12.3.0 2.40-GCCcore-13.2.0 2.40
bokeh	Statistical and novel interactive HTML plots for Python	TINKERCLIFFS 2.0.2-foss-2020a-Python-3.8.2 2.2.3-foss-2020b-Python-3.8.6
bzip2	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.	TINKERCLIFFS 1.0.6-GCCcore-8.2.0 1.0.8-GCCcore-10.2.0 1.0.8-GCCcore-10.3.0 1.0.8-GCCcore-11.2.0 1.0.8-GCCcore-11.3.0 1.0.8-GCCcore-12.2.0 1.0.8-GCCcore-12.3.0 1.0.8-GCCcore-13.2.0 1.0.8-GCCcore-8.3.0 1.0.8-GCCcore-9.3.0
c-ares	c-ares is a C library for asynchronous DNS requests (including name resolves)	TINKERCLIFFS 1.17.2-GCCcore-10.3.0 1.18.1-GCCcore-11.3.0
cURL	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.	TINKERCLIFFS 7.63.0-GCCcore-8.2.0 7.66.0-GCCcore-8.3.0 7.69.1-GCCcore-9.3.0 7.72.0-GCCcore-10.2.0 7.76.0-GCCcore-10.3.0 7.78.0-GCCcore-11.2.0 7.83.0-GCCcore-11.3.0 7.86.0-GCCcore-11.3.0 7.86.0-GCCcore-12.2.0 8.0.1-GCCcore-12.3.0 8.3.0-GCCcore-13.2.0
cairo	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	TINKERCLIFFS 1.16.0-GCCcore-10.2.0 1.16.0-GCCcore-10.3.0 1.16.0-GCCcore-8.3.0 1.16.0-GCCcore-9.3.0 1.17.4-GCCcore-11.3.0 1.17.4-GCCcore-12.2.0 1.17.8-GCCcore-12.3.0
canu	Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing	TINKERCLIFFS 1.9-GCCcore-8.3.0-Java-11
cffi	C Foreign Function Interface for Python. Interact with almost any C code from Python, based on C-like declarations that you can often copy-paste from header files or documentation.	TINKERCLIFFS 1.15.1-GCCcore-12.3.0 1.15.1-GCCcore-13.2.0
cppy	A small C++ header library which makes it easier to write Python extension modules. The primary feature is a PyObject smart pointer which automatically handles reference counting and provides convenience methods for performing common object operations.	TINKERCLIFFS 1.1.0-GCCcore-10.3.0 1.1.0-GCCcore-11.2.0 1.2.1-GCCcore-11.3.0
cryptography	cryptography is a package designed to expose cryptographic primitives and recipes to Python developers.	TINKERCLIFFS 41.0.1-GCCcore-12.3.0 41.0.5-GCCcore-13.2.0
cytosim	Cytosim is a cytoskeleton simulation engine written in C++ working on Mac OS, GNU/Linux and Windows (with Cygwin).	TINKERCLIFFS 20190117-gomkl-2019a-mkl
dask	Dask natively scales Python. Dask provides advanced parallelism for analytics, enabling performance at scale for the tools you love.	TINKERCLIFFS 2.18.1-foss-2020a-Python-3.8.2 2021.2.0-foss-2020b-Python-3.8.6
deal.II	deal.II is a C++ program library targeted at the computational solution of partial differential equations using adaptive finite elements.	TINKERCLIFFS 9.3.3-foss-2021a 9.5.2-foss-2023a
dijitso	dijitso is a Python module for distributed just-in-time shared library building.	TINKERCLIFFS 2019.1.0-foss-2019b-Python-3.7.4
double-conversion	Efficient binary-decimal and decimal-binary conversion routines for IEEE doubles.	TINKERCLIFFS 3.1.4-GCCcore-8.3.0 3.1.5-GCCcore-10.2.0 3.1.5-GCCcore-10.3.0 3.1.5-GCCcore-9.3.0 3.2.0-GCCcore-11.3.0 3.3.0-GCCcore-12.3.0
ea-utils	Command-line tools for processing biological sequencing data. Barcode demultiplexing, adapter trimming, etc. Primarily written to support an Illumina based pipeline - but should work with any FASTQs.	TINKERCLIFFS 1.04.807-intel-2019b
expat	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	TINKERCLIFFS 2.2.6-GCCcore-8.2.0 2.2.7-GCCcore-8.3.0 2.2.9-GCCcore-10.2.0 2.2.9-GCCcore-10.3.0 2.2.9-GCCcore-9.3.0 2.2.9-intel-2019b 2.4.1-GCCcore-11.2.0 2.4.1-intel-2021a 2.4.8-GCCcore-11.3.0 2.4.9-GCCcore-11.3.0 2.4.9-GCCcore-12.2.0 2.5.0-GCCcore-12.3.0 2.5.0-GCCcore-13.2.0
fastp	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.	TINKERCLIFFS 0.23.2-GCC-10.3.0 0.23.2-GCC-11.2.0
ffnvcodec	FFmpeg nvidia headers. Adds support for nvenc and nvdec. Requires Nvidia GPU and drivers to be present (picked up dynamically).	TINKERCLIFFS 11.1.5.2
file	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.	TINKERCLIFFS 5.38-GCCcore-9.3.0
flatbuffers	FlatBuffers: Memory Efficient Serialization Library	TINKERCLIFFS 1.12.0-GCCcore-10.2.0
flatbuffers-python	Python Flatbuffers runtime library.	TINKERCLIFFS 1.12-GCCcore-10.2.0
flex	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.	TINKERCLIFFS 2.5.39-GCCcore-8.2.0 2.6.4-GCCcore-10.2.0 2.6.4-GCCcore-10.3.0 2.6.4-GCCcore-11.2.0 2.6.4-GCCcore-11.3.0 2.6.4-GCCcore-12.2.0 2.6.4-GCCcore-12.3.0 2.6.4-GCCcore-13.2.0 2.6.4-GCCcore-8.2.0 2.6.4-GCCcore-8.3.0 2.6.4-GCCcore-9.3.0 2.6.4
flit	A simple packaging tool for simple packages.	TINKERCLIFFS 3.9.0-GCCcore-12.3.0 3.9.0-GCCcore-13.2.0
fontconfig	Fontconfig is a library designed to provide system-wide font configuration, customization and application access.	TINKERCLIFFS 2.13.1-GCCcore-8.2.0 2.13.1-GCCcore-8.3.0 2.13.92-GCCcore-10.2.0 2.13.92-GCCcore-9.3.0 2.13.92-intel-2019b 2.13.93-GCCcore-10.3.0 2.13.94-GCCcore-11.2.0 2.14.0-GCCcore-11.3.0 2.14.1-GCCcore-11.3.0 2.14.1-GCCcore-12.2.0 2.14.2-GCCcore-12.3.0
foss	GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.	TINKERCLIFFS 2019b 2020a 2020b 2021a 2021b 2022a 2022b 2023a 2023b
freeglut	freeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library.	TINKERCLIFFS 3.0.0-GCCcore-8.2.0
freetype	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.	TINKERCLIFFS 2.10.1-GCCcore-8.3.0 2.10.1-GCCcore-9.3.0 2.10.3-GCCcore-10.2.0 2.10.4-GCCcore-10.3.0 2.11.0-GCCcore-11.2.0 2.12.1-GCCcore-11.3.0 2.12.1-GCCcore-12.2.0 2.13.0-GCCcore-12.3.0 2.9.1-GCCcore-8.2.0
gc	The Boehm-Demers-Weiser conservative garbage collector can be used as a garbage collecting replacement for C malloc or C++ new.	TINKERCLIFFS 7.6.12-GCCcore-9.3.0
gcloud	Libraries and tools for interacting with Google Cloud products and services.	TINKERCLIFFS 382.0.0
gettext	GNU ‘gettext’ is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation	TINKERCLIFFS 0.19.8.1-GCCcore-8.2.0 0.19.8.1 0.20.1-GCCcore-8.3.0 0.20.1-GCCcore-9.3.0 0.20.1 0.21-GCCcore-10.2.0 0.21-GCCcore-10.3.0 0.21-GCCcore-11.2.0 0.21-GCCcore-11.3.0 0.21.1-GCCcore-11.3.0 0.21.1-GCCcore-12.2.0 0.21.1-GCCcore-12.3.0 0.21.1 0.21 0.22-GCCcore-13.2.0 0.22
gfbf	GNU Compiler Collection (GCC) based compiler toolchain, including FlexiBLAS (BLAS and LAPACK support) and (serial) FFTW.	TINKERCLIFFS 2022b 2023a
gffutils	Gffutils is a Python package for working with and manipulating the GFF and GTF format files typically used for genomic annotations.	TINKERCLIFFS 0.12-foss-2022b
gflags	The gflags package contains a C++ library that implements commandline flags processing. It includes built-in support for standard types such as string and the ability to define flags in the source file in which they are used.	TINKERCLIFFS 2.2.2-GCCcore-9.3.0
giflib	giflib is a library for reading and writing gif images. It is API and ABI compatible with libungif which was in wide use while the LZW compression algorithm was patented.	TINKERCLIFFS 5.2.1-GCCcore-10.2.0 5.2.1-GCCcore-12.2.0
git	Git is a free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency.	TINKERCLIFFS 2.28.0-GCCcore-10.2.0-nodocs 2.33.1-GCCcore-11.2.0-nodocs 2.36.0-GCCcore-11.3.0-nodocs 2.38.1-GCCcore-11.3.0-nodocs 2.38.1-GCCcore-12.2.0-nodocs 2.41.0-GCCcore-12.3.0-nodocs 2.42.0-GCCcore-13.2.0
git-lfs	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	TINKERCLIFFS 3.4.0
glew	The OpenGL Extension Wrangler Library The 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.	TINKERCLIFFS 2.1.0-GCCcore-8.2.0
glibc	The GNU C Library project provides the core libraries for the GNU system and GNU/Linux systems, as well as many other systems that use Linux as the kernel.	TINKERCLIFFS 2.30-GCCcore-8.3.0
glog	A C++ implementation of the Google logging module.	TINKERCLIFFS 0.4.0-GCCcore-9.3.0
gmpy2	GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x	TINKERCLIFFS 2.1.0b4-GCC-8.3.0
gmsh	Gmsh is a 3D finite element grid generator with a build-in CAD engine and post-processor.	TINKERCLIFFS 4.5.6-intel-2019b-Python-2.7.16
gnuplot	Portable interactive, function plotting utility	TINKERCLIFFS 5.2.8-GCCcore-8.3.0 5.4.2-GCCcore-10.3.0 5.4.4-GCCcore-11.3.0 5.4.8-GCCcore-12.3.0
gomkl	GNU Compiler Collection (GCC) based compiler toolchain with OpenMPI and MKL	TINKERCLIFFS 2019a 2020a 2020b 2021a 2022a
gompi	GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support.	TINKERCLIFFS 2019a 2019b 2020a 2020b 2021a 2021b 2022a 2022b 2023a 2023b
googletest	Google’s framework for writing C++ tests on a variety of platforms	TINKERCLIFFS 1.11.0-GCCcore-11.3.0 1.12.1-GCCcore-12.2.0
gperf	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.	TINKERCLIFFS 3.1-GCCcore-10.2.0 3.1-GCCcore-10.3.0 3.1-GCCcore-11.2.0 3.1-GCCcore-11.3.0 3.1-GCCcore-12.2.0 3.1-GCCcore-12.3.0 3.1-GCCcore-8.2.0 3.1-GCCcore-8.3.0 3.1-GCCcore-9.3.0
gperftools	gperftools is a collection of a high-performance multi-threaded malloc(	TINKERCLIFFS 2.8-GCCcore-10.2.0
graphite2	Graphite is a “smart font” system developed specifically to handle the complexities of lesser-known languages of the world.	TINKERCLIFFS 1.3.14-GCCcore-11.3.0 1.3.14-GCCcore-12.3.0
groff	Groff (GNU troff) is a typesetting system that reads plain text mixed with formatting commands and produces formatted output.	TINKERCLIFFS 1.22.4-GCCcore-10.3.0 1.22.4-GCCcore-11.2.0 1.22.4-GCCcore-11.3.0 1.22.4-GCCcore-12.2.0 1.22.4-GCCcore-12.3.0
gsutil	gsutil is a Python application that lets you access Cloud Storage from the command line.	TINKERCLIFFS 5.10-GCCcore-11.2.0
gzip	gzip (GNU zip) is a popular data compression program as a replacement for compress	TINKERCLIFFS 1.10-GCCcore-10.2.0 1.10-GCCcore-10.3.0 1.10-GCCcore-11.2.0 1.10-GCCcore-9.3.0 1.12-GCCcore-11.3.0 1.12-GCCcore-12.2.0 1.12-GCCcore-12.3.0
h5py	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.	TINKERCLIFFS 2.10.0-foss-2020a-Python-3.8.2 3.7.0-foss-2022a
hatch-jupyter-builder	Hatch Jupyter Builder is a plugin for the hatchling Python build backend. It is primarily targeted for package authors who are providing JavaScript as part of their Python packages. Typical use cases are Jupyter Lab Extensions and Jupyter Widgets.	TINKERCLIFFS 0.9.1-GCCcore-13.2.0
hatchling	Extensible, standards compliant build backend used by Hatch, a modern, extensible Python project manager.	TINKERCLIFFS 1.18.0-GCCcore-12.3.0 1.18.0-GCCcore-13.2.0
help2man	help2man produces simple manual pages from the ‘–help’ and ‘–version’ output of other commands.	TINKERCLIFFS 1.47.12-GCCcore-9.3.0 1.47.16-GCCcore-10.2.0 1.47.4 1.47.7-GCCcore-8.2.0 1.47.8-GCCcore-8.3.0 1.48.3-GCCcore-10.3.0 1.48.3-GCCcore-11.2.0 1.49.2-GCCcore-11.3.0 1.49.2-GCCcore-12.2.0 1.49.3-GCCcore-12.3.0 1.49.3-GCCcore-13.2.0
hwloc	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.	TINKERCLIFFS 1.11.11-GCCcore-8.2.0 1.11.12-GCCcore-8.3.0 2.2.0-GCCcore-10.2.0 2.2.0-GCCcore-8.3.0 2.2.0-GCCcore-9.3.0 2.4.1-GCCcore-10.3.0 2.5.0-GCCcore-11.2.0 2.7.1-GCCcore-11.3.0 2.8.0-GCCcore-12.2.0 2.9.1-GCCcore-12.3.0 2.9.2-GCCcore-13.2.0
hypothesis	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.	TINKERCLIFFS 4.44.2-GCCcore-8.3.0-Python-3.7.4 5.41.2-GCCcore-10.2.0 5.41.5-GCCcore-10.2.0 5.6.0-GCCcore-9.3.0-Python-3.8.2 6.13.1-GCCcore-10.3.0 6.14.6-GCCcore-11.2.0 6.46.7-GCCcore-11.3.0 6.68.2-GCCcore-12.2.0 6.82.0-GCCcore-12.3.0
iccifort	Intel C, C++ & Fortran compilers	TINKERCLIFFS 2019.5.281 2020.4.304
iimpi	Intel C/C++ and Fortran compilers, alongside Intel MPI.	TINKERCLIFFS 2019b 2020b 2021a 2021b 2022b 2023a
imkl	Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.	TINKERCLIFFS 2019.1.144-gompi-2019a 2019.5.281-gompi-2020a 2019.5.281-iimpi-2019b 2019.5.281-iompi-2019b 2020.4.304-gompi-2020b 2020.4.304-iimpi-2020b 2021.2.0-gompi-2021a 2021.2.0-iimpi-2021a 2021.2.0-iompi-2021a 2022.1.0-gompi-2022a 2022.2.1
imkl-FFTW	FFTW interfaces using Intel oneAPI Math Kernel Library	TINKERCLIFFS 2022.2.1-iimpi-2022b
impi	Intel MPI Library, compatible with MPICH ABI	TINKERCLIFFS 2018.5.288-iccifort-2019.5.281 2019.9.304-iccifort-2020.4.304 2021.2.0-intel-compilers-2021.2.0 2021.4.0-intel-compilers-2021.4.0 2021.7.1-intel-compilers-2022.2.1 2021.9.0-intel-compilers-2023.1.0
intel	Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL).	TINKERCLIFFS 2019b 2020b 2021a 2022b
intel-compilers	Intel C, C++ & Fortran compilers (classic and oneAPI)	TINKERCLIFFS 2021.2.0 2021.4.0 2022.2.1 2023.1.0
intltool	intltool is a set of tools to centralize translation of many different file formats using GNU gettext-compatible PO files.	TINKERCLIFFS 0.51.0-GCCcore-10.2.0 0.51.0-GCCcore-10.3.0 0.51.0-GCCcore-11.2.0 0.51.0-GCCcore-11.3.0 0.51.0-GCCcore-12.2.0 0.51.0-GCCcore-12.3.0 0.51.0-GCCcore-8.2.0 0.51.0-GCCcore-8.3.0 0.51.0-GCCcore-9.3.0
ioapi	The Models-3/EDSS Input/Output Applications Programming Interface (I/O API) provides the environmental model developer with an easy-to-learn, easy-to-use programming library for data storage and access, available from both Fortran and C. The same routines can be used for both file storage (using netCDF files) and model coupling (using PVM mailboxes). It is the standard data access library for both the NCSC/CMAS’s EDSS project and EPA’s Models-3, CMAQ, and SMOKE, as well as various other atmospheric and hydrological modeling systems.	TINKERCLIFFS 3.2-20200828-iimpi-2021a-nocpl
iomkl	Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & OpenMPI.	TINKERCLIFFS 2019b
iompi	Intel C/C++ and Fortran compilers, alongside Open MPI.	TINKERCLIFFS 2019b 2021a
jbigkit	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.	TINKERCLIFFS 2.1-GCCcore-11.2.0 2.1-GCCcore-11.3.0 2.1-GCCcore-12.2.0
jedi	Jedi - an awesome autocompletion, static analysis and refactoring library for Python.	TINKERCLIFFS 0.19.1-GCCcore-13.2.0
jemalloc	jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and scalable concurrency support.	TINKERCLIFFS 5.2.1-GCCcore-11.2.0 5.2.1-GCCcore-11.3.0 5.3.0-GCCcore-11.3.0 5.3.0-GCCcore-12.2.0
jq	jq is a lightweight and flexible command-line JSON processor.	TINKERCLIFFS 1.6-GCCcore-12.3.0
json-c	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 JSON objects.	TINKERCLIFFS 0.16-GCCcore-12.2.0
jupyter-server	The Jupyter Server provides the backend (i.e. the core services, APIs, and REST endpoints) for Jupyter web applications like Jupyter notebook, JupyterLab, and Voila.	TINKERCLIFFS 1.21.0-GCCcore-11.3.0 2.7.0-GCCcore-12.2.0
kim-api	Open Knowledgebase of Interatomic Models. KIM is an API and OpenKIM is a collection of interatomic models (potentials) for atomistic simulations. This is a library that can be used by simulation programs to get access to the models in the OpenKIM database. This EasyBuild only installs the API, the models can be installed with the package openkim-models, or the user can install them manually by running kim-api-collections-management install user MODELNAME or kim-api-collections-management install user OpenKIM to install them all.	TINKERCLIFFS 2.1.3-foss-2020a 2.3.0-GCCcore-11.2.0
lftp	LFTP is a sophisticated ftp/http client, and a file transfer program supporting a number of network protocols. Like BASH, it has job control and uses the readline library for input. It has bookmarks, a built-in mirror command, and can transfer several files in parallel. It was designed with reliability in mind.	TINKERCLIFFS 4.9.2-GCCcore-11.2.0
libGLU	The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL.	TINKERCLIFFS 9.0.0-GCCcore-8.2.0 9.0.1-GCCcore-10.2.0 9.0.1-GCCcore-10.3.0 9.0.1-GCCcore-8.3.0 9.0.1-GCCcore-9.3.0 9.0.2-GCCcore-11.2.0 9.0.2-GCCcore-11.3.0 9.0.2-GCCcore-12.2.0 9.0.3-GCCcore-12.3.0
libaio	Asynchronous input/output library that uses the kernels native interface.	TINKERCLIFFS 0.3.112-GCCcore-11.3.0
libarchive	Multi-format archive and compression library	TINKERCLIFFS 3.4.3-GCCcore-10.2.0 3.5.1-GCCcore-10.3.0 3.5.1-GCCcore-11.2.0 3.6.1-GCCcore-11.3.0 3.6.1-GCCcore-12.2.0 3.6.2-GCCcore-12.3.0 3.7.2-GCCcore-13.2.0
libcerf	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.	TINKERCLIFFS 1.13-GCCcore-8.3.0 1.17-GCCcore-10.3.0 2.1-GCCcore-11.3.0 2.3-GCCcore-12.3.0
libdap	A C++ SDK which contains an implementation of DAP 2.0 and DAP4.0. This includes both Client- and Server-side support classes.	TINKERCLIFFS 3.20.8-GCCcore-11.2.0 3.20.8-intel-2021a
libdeflate	Heavily optimized library for DEFLATE/zlib/gzip compression and decompression.	TINKERCLIFFS 1.10-GCCcore-11.3.0 1.15-GCCcore-11.3.0 1.15-GCCcore-12.2.0 1.7-GCCcore-10.3.0 1.8-GCCcore-11.2.0
libdrm	Direct Rendering Manager runtime library.	TINKERCLIFFS 2.4.100-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 2.4.110-GCCcore-11.3.0 2.4.114-GCCcore-11.3.0 2.4.114-GCCcore-12.2.0 2.4.115-GCCcore-12.3.0 2.4.97-GCCcore-8.2.0 2.4.99-GCCcore-8.3.0
libepoxy	Epoxy is a library for handling OpenGL function pointer management for you	TINKERCLIFFS 1.5.10-GCCcore-12.2.0 1.5.4-GCCcore-10.2.0 1.5.4-GCCcore-9.3.0 1.5.8-GCCcore-10.3.0
libevent	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.	TINKERCLIFFS 2.1.11-GCCcore-8.3.0 2.1.11-GCCcore-9.3.0 2.1.12-GCCcore-10.2.0 2.1.12-GCCcore-10.3.0 2.1.12-GCCcore-11.2.0 2.1.12-GCCcore-11.3.0 2.1.12-GCCcore-12.2.0 2.1.12-GCCcore-12.3.0 2.1.12-GCCcore-13.2.0
libfabric	Libfabric is a core component of OFI. It is the library that defines and exports the user-space API of OFI, and is typically the only software that applications deal with directly. It works in conjunction with provider libraries, which are often integrated directly into libfabric.	TINKERCLIFFS 1.11.0-GCCcore-10.2.0 1.11.0-GCCcore-8.3.0 1.12.1-GCCcore-10.3.0 1.13.2-GCCcore-11.2.0 1.15.1-GCCcore-11.3.0 1.16.1-GCCcore-12.2.0 1.18.0-GCCcore-12.3.0 1.19.0-GCCcore-13.2.0
libffi	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.	TINKERCLIFFS 3.2.1-GCCcore-8.2.0 3.2.1-GCCcore-8.3.0 3.3-GCCcore-10.2.0 3.3-GCCcore-10.3.0 3.3-GCCcore-9.3.0 3.3-intel-2019b 3.4.2-GCCcore-11.2.0 3.4.2-GCCcore-11.3.0 3.4.4-GCCcore-11.3.0 3.4.4-GCCcore-12.2.0 3.4.4-GCCcore-12.3.0 3.4.4-GCCcore-13.2.0
libgd	GD is an open source code library for the dynamic creation of images by programmers.	TINKERCLIFFS 2.2.5-GCCcore-8.3.0 2.3.1-GCCcore-10.3.0 2.3.3-GCCcore-11.2.0 2.3.3-GCCcore-11.3.0 2.3.3-GCCcore-12.3.0
libgeotiff	Library for reading and writing coordinate system information from/to GeoTIFF files	TINKERCLIFFS 1.5.1-GCCcore-8.3.0 1.5.1-GCCcore-9.3.0 1.6.0-GCCcore-10.3.0 1.7.1-GCCcore-11.3.0 1.7.1-GCCcore-12.2.0
libgit2	libgit2 is a portable, pure C implementation of the Git core methods provided as a re-entrant linkable library with a solid API, allowing you to write native speed custom Git applications in any language which supports C bindings.	TINKERCLIFFS 1.1.0-GCCcore-10.3.0 1.4.3-GCCcore-11.3.0 1.5.0-GCCcore-11.3.0 1.5.0-GCCcore-12.2.0
libglvnd	libglvnd is a vendor-neutral dispatch layer for arbitrating OpenGL API calls between multiple vendors.	TINKERCLIFFS 1.2.0-GCCcore-8.3.0 1.2.0-GCCcore-9.3.0 1.3.2-GCCcore-10.2.0 1.3.3-GCCcore-10.3.0 1.3.3-GCCcore-11.2.0 1.4.0-GCCcore-11.3.0 1.6.0-GCCcore-11.3.0 1.6.0-GCCcore-12.2.0 1.6.0-GCCcore-12.3.0
libiconv	Libiconv converts from one character encoding to another through Unicode conversion	TINKERCLIFFS 1.16-GCCcore-10.2.0 1.16-GCCcore-10.3.0 1.16-GCCcore-11.2.0 1.17-GCCcore-11.3.0 1.17-GCCcore-12.2.0 1.17-GCCcore-12.3.0 1.17-GCCcore-13.2.0
libjpeg-turbo	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.	TINKERCLIFFS 2.0.3-GCCcore-8.3.0 2.0.4-GCCcore-9.3.0 2.0.4-intel-2019b 2.0.5-GCCcore-10.2.0 2.0.6-GCCcore-10.3.0 2.0.6-GCCcore-11.2.0 2.1.3-GCCcore-11.3.0 2.1.4-GCCcore-11.3.0 2.1.4-GCCcore-12.2.0 2.1.5.1-GCCcore-12.3.0
libmatheval	GNU libmatheval is a library (callable from C and Fortran) to parse and evaluate symbolic expressions input as text.	TINKERCLIFFS 1.1.11-GCCcore-9.3.0
libogg	Ogg is a multimedia container format, and the native file and stream format for the Xiph.org multimedia codecs.	TINKERCLIFFS 1.3.4-GCCcore-10.2.0 1.3.4-GCCcore-10.3.0 1.3.5-GCCcore-11.3.0 1.3.5-GCCcore-12.2.0
libopus	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.	TINKERCLIFFS 1.3.1-GCCcore-11.3.0 1.3.1-GCCcore-12.2.0
libpciaccess	Generic PCI access library.	TINKERCLIFFS 0.14-GCCcore-8.2.0 0.14-GCCcore-8.3.0 0.16-GCCcore-10.2.0 0.16-GCCcore-10.3.0 0.16-GCCcore-11.2.0 0.16-GCCcore-11.3.0 0.16-GCCcore-8.3.0 0.16-GCCcore-9.3.0 0.16-intel-2019b 0.17-GCCcore-11.3.0 0.17-GCCcore-12.2.0 0.17-GCCcore-12.3.0 0.17-GCCcore-13.2.0
libpng	libpng is the official PNG reference library	TINKERCLIFFS 1.6.36-GCCcore-8.2.0 1.6.37-GCCcore-10.2.0 1.6.37-GCCcore-10.3.0 1.6.37-GCCcore-11.2.0 1.6.37-GCCcore-11.3.0 1.6.37-GCCcore-8.3.0 1.6.37-GCCcore-9.3.0 1.6.38-GCCcore-11.3.0 1.6.38-GCCcore-12.2.0 1.6.39-GCCcore-12.3.0
libreadline	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.	TINKERCLIFFS 8.0-GCCcore-10.2.0 8.0-GCCcore-8.2.0 8.0-GCCcore-8.3.0 8.0-GCCcore-9.3.0 8.1-GCCcore-10.3.0 8.1-GCCcore-11.2.0 8.1.2-GCCcore-11.3.0 8.2-GCCcore-11.3.0 8.2-GCCcore-12.2.0 8.2-GCCcore-12.3.0 8.2-GCCcore-13.2.0
libsndfile	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.	TINKERCLIFFS 1.0.28-GCCcore-10.2.0 1.0.28-GCCcore-8.3.0 1.0.28-GCCcore-9.3.0 1.0.31-GCCcore-10.3.0 1.1.0-GCCcore-11.3.0 1.2.0-GCCcore-11.3.0 1.2.0-GCCcore-12.2.0
libsodium	Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, password hashing and more.	TINKERCLIFFS 1.0.18-GCCcore-11.3.0 1.0.18-GCCcore-12.2.0 1.0.18-GCCcore-12.3.0 1.0.19-GCCcore-13.2.0
libtirpc	Libtirpc is a port of Suns Transport-Independent RPC library to Linux.	TINKERCLIFFS 1.2.6-GCCcore-8.3.0 1.3.2-GCCcore-10.3.0 1.3.2-GCCcore-11.2.0 1.3.2-GCCcore-11.3.0 1.3.3-GCCcore-12.2.0
libtool	GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries behind a consistent, portable interface.	TINKERCLIFFS 2.4.6-GCCcore-10.2.0 2.4.6-GCCcore-10.3.0 2.4.6-GCCcore-11.2.0 2.4.6-GCCcore-8.2.0 2.4.6-GCCcore-8.3.0 2.4.6-GCCcore-9.3.0 2.4.7-GCCcore-11.3.0 2.4.7-GCCcore-12.2.0 2.4.7-GCCcore-12.3.0 2.4.7-GCCcore-13.2.0
libunistring	This library provides functions for manipulating Unicode strings and for manipulating C strings according to the Unicode standard.	TINKERCLIFFS 0.9.10-GCCcore-9.3.0
libunwind	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	TINKERCLIFFS 1.3.1-GCCcore-8.2.0 1.3.1-GCCcore-8.3.0 1.3.1-GCCcore-9.3.0 1.4.0-GCCcore-10.2.0 1.4.0-GCCcore-10.3.0 1.5.0-GCCcore-11.2.0 1.6.2-GCCcore-11.3.0 1.6.2-GCCcore-12.2.0 1.6.2-GCCcore-12.3.0
libvorbis	Ogg Vorbis is a fully open, non-proprietary, patent-and-royalty-free, general-purpose compressed audio format	TINKERCLIFFS 1.3.7-GCCcore-10.2.0 1.3.7-GCCcore-10.3.0 1.3.7-GCCcore-11.3.0 1.3.7-GCCcore-12.2.0
libvori	C++ library implementing the Voronoi integration as well as the compressed bqb file format. The present version of libvori is a very early development version, which is hard-coded to work with the CP2k program package.	TINKERCLIFFS 220621-GCCcore-12.3.0
libxc	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.	TINKERCLIFFS 3.0.1-intel-2019b 4.2.3-intel-2019b 4.3.4-GCC-9.3.0 4.3.4-iccifort-2019.5.281 6.2.2-GCC-12.3.0
libxml2	Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform).	TINKERCLIFFS 2.10.3-GCCcore-11.3.0 2.10.3-GCCcore-12.2.0 2.11.4-GCCcore-12.3.0 2.11.5-GCCcore-13.2.0 2.9.10-GCCcore-10.2.0 2.9.10-GCCcore-10.3.0 2.9.10-GCCcore-11.2.0 2.9.10-GCCcore-8.3.0 2.9.10-GCCcore-9.3.0 2.9.10-intel-2019b 2.9.13-GCCcore-11.3.0 2.9.8-GCCcore-8.2.0 2.9.9-GCCcore-8.3.0
libxslt	Libxslt is the XSLT C library developed for the GNOME project (but usable outside of the Gnome platform).	TINKERCLIFFS 1.1.34-GCCcore-11.3.0 1.1.37-GCCcore-11.3.0 1.1.37-GCCcore-12.2.0 1.1.38-GCCcore-12.3.0 1.1.38-GCCcore-13.2.0
libxsmm	LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications targeting Intel Architecture (x86).	TINKERCLIFFS 1.10-GCC-9.3.0 1.17-GCC-12.3.0
libyaml	LibYAML is a YAML parser and emitter written in C.	TINKERCLIFFS 0.2.2-GCCcore-8.3.0 0.2.2-GCCcore-9.3.0 0.2.5-GCCcore-10.2.0 0.2.5-GCCcore-12.2.0 0.2.5-GCCcore-12.3.0 0.2.5-GCCcore-13.2.0
lpsolve	Mixed Integer Linear Programming (MILP) solver	TINKERCLIFFS 5.5.2.11-GCC-10.2.0 5.5.2.11-GCC-11.3.0
lxml	The lxml XML toolkit is a Pythonic binding for the C libraries libxml2 and libxslt.	TINKERCLIFFS 4.9.1-GCCcore-11.3.0 4.9.2-GCCcore-12.2.0 4.9.2-GCCcore-12.3.0 4.9.3-GCCcore-13.2.0
lz4	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.	TINKERCLIFFS 1.9.2-GCCcore-10.2.0 1.9.2-GCCcore-9.3.0 1.9.3-GCCcore-10.3.0 1.9.3-GCCcore-11.2.0 1.9.3-GCCcore-11.3.0 1.9.4-GCCcore-12.2.0 1.9.4-GCCcore-12.3.0
make	GNU version of make utility	TINKERCLIFFS 4.2.1-GCCcore-8.3.0 4.4.1-GCCcore-12.2.0 4.4.1-GCCcore-12.3.0 4.4.1-GCCcore-13.2.0
makeinfo	makeinfo is part of the Texinfo project, the official documentation format of the GNU project.	TINKERCLIFFS 6.7-GCCcore-10.3.0
matplotlib	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.	TINKERCLIFFS 3.1.1-foss-2019b-Python-3.7.4 3.2.1-foss-2020a-Python-3.8.2 3.3.3-foss-2020b 3.4.2-foss-2021a 3.4.3-foss-2021b 3.5.2-foss-2022a
maturin	This project is meant as a zero configuration replacement for setuptools-rust and milksnake. It supports building wheels for python 3.5+ on windows, linux, mac and freebsd, can upload them to pypi and has basic pypy and graalpy support.	TINKERCLIFFS 1.1.0-GCCcore-12.2.0 1.3.1-GCCcore-13.2.0
minimap2	Minimap2 is a fast sequence mapping and alignment program that can find overlaps between long noisy reads, or map long reads or their assemblies to a reference genome optionally with detailed alignment (i.e. CIGAR). At present, it works efficiently with query sequences from a few kilobases to ~100 megabases in length at an error rate ~15%. Minimap2 outputs in the PAF or the SAM format. On limited test data sets, minimap2 is over 20 times faster than most other long-read aligners. It will replace BWA-MEM for long reads and contig alignment.	TINKERCLIFFS 2.17-GCCcore-9.3.0
molmod	MolMod is a Python library with many compoments that are useful to write molecular modeling programs.	TINKERCLIFFS 1.4.5-foss-2020a-Python-3.8.2
mpi4py	MPI for Python (mpi4py) provides bindings of the Message Passing Interface (MPI) standard for the Python programming language, allowing any Python program to exploit multiple processors.	TINKERCLIFFS 3.0.2-gompi-2020a-timed-pingpong 3.0.2-iimpi-2019b-timed-pingpong 3.1.1-gompi-2020b-timed-pingpong 3.1.4-gompi-2022b 3.1.4-gompi-2023a
nanoget	Functions to extract information from Oxford Nanopore sequencing data and alignments	TINKERCLIFFS 1.18.1-foss-2021a
nanomath	A few simple math function for other Oxford Nanopore processing scripts	TINKERCLIFFS 1.2.1-foss-2021a
nanopolish	Software package for signal-level analysis of Oxford Nanopore sequencing data.	TINKERCLIFFS 0.13.2-foss-2020a-Python-3.8.2
ncbi-vdb	The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.	TINKERCLIFFS 2.10.7-gompi-2020a
ncdf4	ncdf4: Interface to Unidata netCDF (version 4 or earlier) format data files	TINKERCLIFFS 1.17-foss-2020b-R-4.0.3
ncdu	Ncdu is a disk usage analyzer with an ncurses interface. It is designed to find space hogs on a remote server where you don’t have an entire graphical setup available, but it is a useful tool even on regular desktop systems. Ncdu aims to be fast, simple and easy to use, and should be able to run in any minimal POSIX-like environment with ncurses installed.	TINKERCLIFFS 1.18-GCC-12.3.0
ncurses	The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.	TINKERCLIFFS 6.0 6.1-GCCcore-8.2.0 6.1-GCCcore-8.3.0 6.1 6.2-GCCcore-10.2.0 6.2-GCCcore-10.3.0 6.2-GCCcore-11.2.0 6.2-GCCcore-9.3.0 6.2-intel-2019b 6.2 6.3-GCCcore-11.3.0 6.3-GCCcore-12.2.0 6.3 6.4-GCCcore-12.3.0 6.4-GCCcore-13.2.0 6.4
ncview	Ncview is a visual browser for netCDF format files. Typically you would use ncview to get a quick and easy, push-button look at your netCDF files. You can view simple movies of the data, view along various dimensions, take a look at the actual data values, change color maps, invert the data, etc.	TINKERCLIFFS 2.1.8-iimpi-2021a
netCDF	NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.	TINKERCLIFFS 4.6.1-intel-2019b 4.7.1-gompi-2019b 4.7.1-iimpi-2019b 4.7.4-gompi-2020a 4.7.4-gompi-2020b 4.8.0-gompi-2021a 4.8.0-iompi-2021a 4.8.1-gompi-2021b 4.8.1-iimpi-2021a 4.9.0-gompi-2022a 4.9.0-gompi-2022b 4.9.2-iimpi-2023a
netCDF-C++4	NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.	TINKERCLIFFS 4.3.1-iimpi-2021a
netCDF-Fortran	NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.	TINKERCLIFFS 4.4.4-intel-2019b 4.5.2-gompi-2019b 4.5.2-iimpi-2019b 4.5.3-gompi-2020b 4.5.3-iimpi-2021a 4.5.3-iompi-2021a 4.6.1-iimpi-2023a
nettle	Nettle is a cryptographic library that is designed to fit easily in more or less any context: In crypto toolkits for object-oriented languages (C++, Python, Pike, …), in applications like LSH or GNUPG, or even in kernel space.	TINKERCLIFFS 3.4.1-GCCcore-8.2.0 3.5.1-GCCcore-8.3.0 3.6-GCCcore-10.2.0 3.7.2-GCCcore-10.3.0 3.8-GCCcore-11.3.0 3.8.1-GCCcore-11.3.0 3.8.1-GCCcore-12.2.0
networkx	NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks.	TINKERCLIFFS 2.4-foss-2020a-Python-3.8.2
nlohmann_json	JSON for Modern C++	TINKERCLIFFS 3.10.5-GCCcore-11.3.0 3.11.2-GCCcore-12.2.0
nodejs	Node.js is a platform built on Chrome’s JavaScript runtime for easily building fast, scalable network applications. Node.js uses an event-driven, non-blocking I/O model that makes it lightweight and efficient, perfect for data-intensive real-time applications that run across distributed devices.	TINKERCLIFFS 12.16.1-GCCcore-9.3.0 12.19.0-GCCcore-10.2.0 14.17.0-GCCcore-10.3.0 16.15.1-GCCcore-11.3.0 18.12.1-GCCcore-11.3.0 18.12.1-GCCcore-12.2.0 18.17.1-GCCcore-12.3.0
nsync	nsync is a C library that exports various synchronization primitives, such as mutexes	TINKERCLIFFS 1.24.0-GCCcore-10.2.0
numactl	The numactl program allows you to run your application program on specific cpu’s and memory nodes. It does this by supplying a NUMA memory policy to the operating system before running your program. The libnuma library provides convenient ways for you to add NUMA memory policies into your own program.	TINKERCLIFFS 2.0.12-GCCcore-8.2.0 2.0.12-GCCcore-8.3.0 2.0.13-GCCcore-10.2.0 2.0.13-GCCcore-8.3.0 2.0.13-GCCcore-9.3.0 2.0.14-GCCcore-10.3.0 2.0.14-GCCcore-11.2.0 2.0.14-GCCcore-11.3.0 2.0.16-GCCcore-12.2.0 2.0.16-GCCcore-12.3.0 2.0.16-GCCcore-13.2.0
p7zip	p7zip is a quick port of 7z.exe and 7za.exe (CLI version of 7zip) for Unix. 7-Zip is a file archiver with highest compression ratio.	TINKERCLIFFS 17.04-GCCcore-11.3.0
parallel	parallel: Build and execute shell commands in parallel	TINKERCLIFFS 20190922-GCCcore-8.3.0 20200522-GCCcore-9.3.0 20240322-GCCcore-13.2.0
patchelf	PatchELF is a small utility to modify the dynamic linker and RPATH of ELF executables.	TINKERCLIFFS 0.10-GCCcore-8.3.0 0.18.0-GCCcore-12.3.0 0.18.0-GCCcore-13.2.0
pauvre	Tools for plotting Oxford Nanopore and other long-read data	TINKERCLIFFS 0.2.3-foss-2021a
petsc4py	petsc4py are Python bindings for PETSc, the Portable, Extensible Toolchain for Scientific Computation.	TINKERCLIFFS 3.12.0-foss-2019b-Python-3.7.4
picard	A set of tools (in Java) for working with next generation sequencing data in the BAM format.	TINKERCLIFFS 2.21.6-Java-11 2.25.1-Java-11
pigz	pigz, which stands for parallel implementation of gzip, is a fully functional replacement for gzip that exploits multiple processors and multiple cores to the hilt when compressing data. pigz was written by Mark Adler, and uses the zlib and pthread libraries.	TINKERCLIFFS 2.6-GCCcore-10.3.0
pixman	Pixman is a low-level software library for pixel manipulation, providing features such as image compositing and trapezoid rasterization. Important users of pixman are the cairo graphics library and the X server.	TINKERCLIFFS 0.38.4-GCCcore-8.3.0 0.38.4-GCCcore-9.3.0 0.40.0-GCCcore-10.2.0 0.40.0-GCCcore-10.3.0 0.40.0-GCCcore-11.3.0 0.42.2-GCCcore-11.3.0 0.42.2-GCCcore-12.2.0 0.42.2-GCCcore-12.3.0
pkg-config	pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the correct compiler options on the command line so an application can use gcc -o test test.c pkg-config --libs --cflags glib-2.0 for instance, rather than hard-coding values on where to find glib (or other libraries).	TINKERCLIFFS 0.29.2-GCCcore-10.2.0 0.29.2-GCCcore-10.3.0 0.29.2-GCCcore-11.2.0 0.29.2-GCCcore-8.2.0 0.29.2-GCCcore-8.3.0 0.29.2-GCCcore-9.3.0 0.29.2
pkgconf	pkgconf is a program which helps to configure compiler and linker flags for development libraries. It is similar to pkg-config from freedesktop.org.	TINKERCLIFFS 1.8.0-GCCcore-11.3.0 1.8.0 1.9.3-GCCcore-11.3.0 1.9.3-GCCcore-12.2.0 1.9.5-GCCcore-12.3.0 2.0.3-GCCcore-13.2.0
pkgconfig	pkgconfig is a Python module to interface with the pkg-config command line tool	TINKERCLIFFS 1.5.1-GCCcore-10.2.0-python 1.5.1-GCCcore-8.3.0-Python-3.7.4 1.5.1-GCCcore-9.3.0-Python-3.8.2 1.5.5-GCCcore-11.3.0-python
plotly.py	An open-source, interactive graphing library for Python	TINKERCLIFFS 5.1.0-GCCcore-10.3.0
pocl	Pocl is a portable open source (MIT-licensed) implementation of the OpenCL standard	TINKERCLIFFS 1.6-GCC-10.2.0
poetry	Python packaging and dependency management made easy. Poetry helps you declare, manage and install dependencies of Python projects, ensuring you have the right stack everywhere.	TINKERCLIFFS 1.5.1-GCCcore-12.3.0 1.6.1-GCCcore-13.2.0
prodigal	Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm	TINKERCLIFFS 2.6.3-GCCcore-10.2.0 2.6.3-GCCcore-11.3.0
protobuf	Google Protocol Buffers	TINKERCLIFFS 3.10.0-GCCcore-8.3.0 3.10.0-GCCcore-9.3.0 3.14.0-GCCcore-10.2.0
protobuf-python	Python Protocol Buffers runtime library.	TINKERCLIFFS 3.10.0-foss-2020a-Python-3.8.2 3.10.0-gomkl-2020a-Python-3.8.2 3.10.0-intel-2019b-Python-3.7.4 3.14.0-GCCcore-10.2.0
pybedtools	pybedtools wraps and extends BEDTools and offers feature-level manipulations from within Python.	TINKERCLIFFS 0.9.0-GCC-12.2.0
pybind11	pybind11 is a lightweight header-only library that exposes C++ types in Python and vice versa, mainly to create Python bindings of existing C++ code.	TINKERCLIFFS 2.10.3-GCCcore-12.2.0 2.11.1-GCCcore-12.3.0 2.4.3-GCCcore-8.3.0-Python-3.7.4 2.4.3-GCCcore-9.3.0-Python-3.8.2 2.6.0-GCCcore-10.2.0 2.6.2-GCCcore-10.3.0 2.7.1-GCCcore-11.2.0 2.9.2-GCCcore-11.3.0
pyfaidx	pyfaidx: efficient pythonic random access to fasta subsequences	TINKERCLIFFS 0.7.2.1-GCCcore-12.2.0
rclone	Rclone is a command line program to sync files and directories to and from a variety of online storage services	TINKERCLIFFS 1.42-amd64 1.42-foss-2020a-amd64 1.60.0
re2c	re2c is a free and open-source lexer generator for C and C++. Its main goal is generating fast lexers: at least as fast as their reasonably optimized hand-coded counterparts. Instead of using traditional table-driven approach, re2c encodes the generated finite state automata directly in the form of conditional jumps and comparisons.	TINKERCLIFFS 1.2.1-GCCcore-8.3.0 1.3-GCCcore-9.3.0 2.1.1-GCCcore-10.3.0 2.2-GCCcore-11.3.0 3.1-GCCcore-12.3.0
scikit-build	Scikit-Build, or skbuild, is an improved build system generator for CPython C/C++/Fortran/Cython extensions.	TINKERCLIFFS 0.10.0-foss-2020a-Python-3.8.2 0.15.0-GCCcore-11.3.0 0.17.6-GCCcore-12.3.0 0.17.6-GCCcore-13.2.0
scikit-learn	Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, building upon numpy, scipy, and matplotlib. As a machine-learning module, it provides versatile tools for data mining and analysis in any field of science and engineering. It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.	TINKERCLIFFS 0.24.2-foss-2021a
seqtk	Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. It seamlessly parses both FASTA and FASTQ files which can also be optionally compressed by gzip.	TINKERCLIFFS 1.3-GCC-11.3.0
setuptools-rust	setuptools-rust is a plugin for setuptools to build Rust Python extensions implemented with PyO3 or rust-cpython.	TINKERCLIFFS 1.6.0-GCCcore-12.3.0 1.8.0-GCCcore-13.2.0
slepc4py	Python bindings for SLEPc, the Scalable Library for Eigenvalue Problem Computations.	TINKERCLIFFS 3.12.0-foss-2019b-Python-3.7.4
snakemake	The Snakemake workflow management system is a tool to create reproducible and scalable data analyses.	TINKERCLIFFS 8.4.2-foss-2023a
snappy	Snappy is a compression/decompression library. It does not aim for maximum compression, or compatibility with any other compression library; instead, it aims for very high speeds and reasonable compression.	TINKERCLIFFS 1.1.10-GCCcore-12.3.0 1.1.7-GCCcore-8.3.0 1.1.8-GCCcore-10.2.0 1.1.8-GCCcore-10.3.0 1.1.8-GCCcore-9.3.0 1.1.9-GCCcore-11.2.0 1.1.9-GCCcore-11.3.0
sparsehash	An extremely memory-efficient hash_map implementation. 2 bits/entry overhead! The SparseHash library contains several hash-map implementations, including implementations that optimize for space or speed.	TINKERCLIFFS 2.0.3-GCCcore-9.3.0
statsmodels	Statsmodels is a Python module that allows users to explore data, estimate statistical models, and perform statistical tests.	TINKERCLIFFS 0.12.2-foss-2021a
sympy	SymPy is a Python library for symbolic mathematics. It aims to become a full-featured computer algebra system (CAS) while keeping the code as simple as possible in order to be comprehensible and easily extensible. SymPy is written entirely in Python and does not require any external libraries.	TINKERCLIFFS 1.5.1-foss-2019b-Python-3.7.4
tRNAscan-SE	tRNAscan-SE is the most widely employed tool for identifying and annotating tRNA genes in genomes.	TINKERCLIFFS 2.0.12-foss-2022b
tcsh	Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). It is a command language interpreter usable both as an interactive login shell and a shell script command processor. It includes a command-line editor, programmable word completion, spelling correction, a history mechanism, job control and a C-like syntax.	TINKERCLIFFS 6.22.02-GCCcore-8.3.0 6.22.03-GCCcore-10.2.0
texinfo	Texinfo is the official documentation format of the GNU project.	TINKERCLIFFS 6.7-GCCcore-8.3.0
time	The `time’ command runs another program, then displays information about the resources used by that program, collected by the system while the program was running.	TINKERCLIFFS 1.9-GCCcore-10.2.0 1.9-GCCcore-8.3.0
tornado	Tornado is a Python web framework and asynchronous networking library.	TINKERCLIFFS 6.4-GCCcore-13.2.0
typing-extensions	Typing Extensions – Backported and Experimental Type Hints for Python	TINKERCLIFFS 3.7.4.3-GCCcore-10.2.0
utf8proc	utf8proc is a small, clean C library that provides Unicode normalization, case-folding, and other operations for data in the UTF-8 encoding.	TINKERCLIFFS 2.5.0-GCCcore-10.2.0 2.6.1-GCCcore-10.3.0 2.6.1-GCCcore-11.2.0
util-linux	Set of Linux utilities	TINKERCLIFFS 2.33-GCCcore-8.2.0 2.34-GCCcore-8.3.0 2.35-GCCcore-9.3.0 2.35-intel-2019b 2.36-GCCcore-10.2.0 2.36-GCCcore-10.3.0 2.37-GCCcore-11.2.0 2.38-GCCcore-11.3.0 2.38.1-GCCcore-11.3.0 2.38.1-GCCcore-12.2.0 2.39-GCCcore-12.3.0 2.39-GCCcore-13.2.0
virtualenv	A tool for creating isolated virtual python environments.	TINKERCLIFFS 20.23.1-GCCcore-12.3.0 20.24.6-GCCcore-13.2.0
wrapt	The aim of the wrapt module is to provide a transparent object proxy for Python, which can be used as the basis for the construction of function wrappers and decorator functions.	TINKERCLIFFS 1.15.0-gfbf-2023a
x264	x264 is a free software library and application for encoding video streams into the H.264/MPEG-4 AVC compression format, and is released under the terms of the GNU GPL.	TINKERCLIFFS 20190925-GCCcore-8.3.0 20191217-GCCcore-9.3.0 20201026-GCCcore-10.2.0 20210414-GCCcore-10.3.0 20210613-GCCcore-11.2.0 20220620-GCCcore-11.3.0
x265	x265 is a free software library and application for encoding video streams into the H.265 AVC compression format, and is released under the terms of the GNU GPL.	TINKERCLIFFS 3.2-GCCcore-8.3.0 3.3-GCCcore-10.2.0 3.3-GCCcore-9.3.0 3.5-GCCcore-10.3.0 3.5-GCCcore-11.2.0 3.5-GCCcore-11.3.0
xorg-macros	X.org macros utilities.	TINKERCLIFFS 1.19.2-GCCcore-10.2.0 1.19.2-GCCcore-8.2.0 1.19.2-GCCcore-8.3.0 1.19.2-GCCcore-9.3.0 1.19.3-GCCcore-10.3.0 1.19.3-GCCcore-11.2.0 1.19.3-GCCcore-11.3.0 1.19.3-GCCcore-12.2.0 1.20.0-GCCcore-12.3.0 1.20.0-GCCcore-13.2.0
xxd	xxd is part of the VIM package and this will only install xxd, not vim! xxd converts to/from hexdumps of binary files.	TINKERCLIFFS 8.2.4220-GCCcore-11.2.0 9.0.1696-foss-2022b 9.0.2112-GCCcore-12.3.0
yaff	Yaff stands for ‘Yet another force field’. It is a pythonic force-field code.	TINKERCLIFFS 1.6.0-foss-2020a-Python-3.8.2
yaml-cpp	yaml-cpp is a YAML parser and emitter in C++ matching the YAML 1.2 spec	TINKERCLIFFS 0.6.3-GCCcore-8.3.0
zlib	zlib is designed to be a free, general-purpose, legally unencumbered – that is, not covered by any patents – lossless data-compression library for use on virtually any computer hardware and operating system.	TINKERCLIFFS 1.2.11-GCCcore-10.2.0 1.2.11-GCCcore-10.3.0 1.2.11-GCCcore-11.2.0 1.2.11-GCCcore-8.2.0 1.2.11-GCCcore-8.3.0 1.2.11-GCCcore-9.3.0 1.2.11 1.2.12-GCCcore-11.3.0 1.2.12-GCCcore-12.2.0 1.2.12 1.2.13-GCCcore-12.3.0 1.2.13-GCCcore-13.2.0 1.2.13 1.3.1
zstd	Zstandard is a real-time compression algorithm, providing high compression ratios. It offers a very wide range of compression/speed trade-off, while being backed by a very fast decoder. It also offers a special mode for small data, called dictionary compression, and can create dictionaries from any sample set.	TINKERCLIFFS 1.4.4-GCCcore-9.3.0 1.4.5-GCCcore-10.2.0 1.4.9-GCCcore-10.3.0 1.5.0-GCCcore-11.2.0 1.5.2-GCCcore-11.3.0 1.5.2-GCCcore-12.2.0 1.5.5-GCCcore-12.3.0