All Modules 18.04

AGAT/0.9.2-GCC-11.2.0 easyconfig AGAT: Another GTF/GFF Analysis Toolkit. Suite of tools to handle gene annotations in any GTF/GFF format.
ARGoS/3.0.0-beta59-GCC-11.2.0 A parallel, multi-engine simulator for heterogeneous swarm robotics
ASE/3.22.0-foss-2020b ASE is a python package providing an open source Atomic Simulation Environment in the Python scripting language.

From version 3.20.1 we also include the ase-ext package, it contains optional reimplementations in C of functions in ASE. ASE uses it automatically when installed.

ATK/2.38.0-GCCcore-13.2.0 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.
AUGUSTUS/3.4.0-foss-2020b AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences
Abseil/20240116.1-GCCcore-13.2.0 Abseil is an open-source collection of C++ library code designed to augment the C++ standard library. The Abseil library code is collected from Google’s own C++ code base, has been extensively tested and used in production, and is the same code we depend on in our daily coding lives.
AdapterRemoval/2.2.2-foss-2018b AdapterRemoval searches for and removes remnant adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3’ end of reads following adapter removal.
AlphaFold/2.3.1-foss-2022a-CUDA-11.7.0 AlphaFold can predict protein structures with atomic accuracy even where no similar structure is known
AlphaPulldown/0.30.4-fosscuda-2020b AlphaPulldown is a Python package that streamlines protein-protein interaction screens and high-throughput modelling of higher-order oligomers using AlphaFold-Multimer
Anaconda3/2023.09-0 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.
Apptainer/1.1.6 Apptainer is a portable application stack packaging and runtime utility.
Archive-Zip/1.68-GCCcore-10.2.0 Provide an interface to ZIP archive files.
Armadillo/12.8.0-foss-2023b 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.
ArrayFire/3.8.1-foss-2019b-CUDA-10.2.89 easyconfig ArrayFire is a general-purpose library that simplifies the process of developing software that targets parallel and massively-parallel architectures including CPUs, GPUs, and other hardware acceleration devices.
Arriba/2.4.0-GCC-12.2.0 Arriba is a command-line tool for the detection of gene fusions from RNA-Seq data. It was developed for the use in a clinical research setting. Therefore, short runtimes and high sensitivity were important design criteria.
Arrow/11.0.0-gfbf-2022b Apache Arrow (incl. PyArrow Python bindings), a cross-language development platform for in-memory data.
Aspera-CLI/3.9.6.1467.159c5b1 IBM Aspera Command-Line Interface (the Aspera CLI) is a collection of Aspera tools for performing high-speed, secure data transfers from the command line. The Aspera CLI is for users and organizations who want to automate their transfer workflows.
Aspera-Connect/3.9.6 Connect is an install-on-demand Web browser plug-in that facilitates high-speed uploads and downloads with an Aspera transfer server.
Autoconf/2.71-GCCcore-13.2.0 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.
Automake/1.16.5-GCCcore-12.3.0 Automake: GNU Standards-compliant Makefile generator
Autotools/20220317-GCCcore-12.3.0 This bundle collect the standard GNU build tools: Autoconf, Automake and libtool
BAli-Phy/4.0-beta8-GCC-12.2.0 BAli-Phy estimates multiple sequence alignments and evolutionary trees from DNA, amino acid, or codon sequences.
BBMap/38.97-GCC-10.2.0 easyconfig BBMap short read aligner, and other bioinformatic tools.
BCFtools/1.19-GCC-13.2.0 easyconfig Samtools is a suite of programs for interacting with high-throughput sequencing data. BCFtools
BEDOPS/2.4.41-foss-2021b 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.
BEDTools/2.30.0-GCC-12.2.0 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.
BGEN/1.1.7 This repository contains a reference implementation of the BGEN format, written in C++. The library can be used as the basis for BGEN support in other software, or as a reference for developers writing their own implementations of the BGEN format. Please cite: Band, G. and Marchini, J., “BGEN: a binary file format for imputed genotype and haplotype data”, bioArxiv 308296; doi: https://doi.org/10.1101/308296
BGEN-enkre/1.1.7-GCC-10.2.0 easyconfig This repository contains a reference implementation of the BGEN format, written in C++. The library can be used as the basis for BGEN support in other software, or as a reference for developers writing their own implementations of the BGEN format. Please cite: Band, G. and Marchini, J., “BGEN: a binary file format for imputed genotype and haplotype data”, bioArxiv 308296; doi: https://doi.org/10.1101/308296
BLAST+/2.14.0-gompi-2022b 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.
BLAT/3.5-GCC-8.3.0 BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more.
BLIS/0.9.0-GCC-12.2.0 BLIS is a portable software framework for instantiating high-performance BLAS-like dense linear algebra libraries.
BUStools/0.40.0-foss-2019b easyconfig bustools is a program for manipulating BUS files for single cell RNA-Seq datasets. It can be used to error correct barcodes, collapse UMIs, produce gene count or transcript compatibility count matrices, and is useful for many other tasks. See the kallisto | bustools website for examples and instructions on how to use bustools as part of a single-cell RNA-seq workflow.
BWA/0.7.17-GCC-8.3.0 Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome.
BamTools/2.5.2-GCC-12.2.0 BamTools provides both a programmer’s API and an end-user’s toolkit for handling BAM files.
BaseSpaceCLI/1.5.1 easyconfig BaseSpace is a powerful website where biologists and informaticians can easily store, analyze, and share genetic data. BaseSpace is a commerical product from Illumina.
Bazel/6.3.1-GCCcore-12.2.0 Bazel is a build tool that builds code quickly and reliably. It is used to build the majority of Google’s software.
Beagle/5.2.1 easyconfig Beagle is a software package for phasing genotypes and for imputing ungenotyped markers.
Beast/2.6.4-GCC-10.2.0 BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability.
BeautifulSoup/4.12.2-GCCcore-12.3.0 Beautiful Soup is a Python library designed for quick turnaround projects like screen-scraping.
Bio-DB-HTS/3.01-GCC-10.2.0 easyconfig Read files using HTSlib including BAM/CRAM, Tabix and BCF database files
Bio-SearchIO-hmmer/1.7.3-GCC-10.2.0 Code to parse output from hmmsearch, hmmscan, phmmer and nhmmer, compatible with both version 2 and version 3 of the HMMER package from http://hmmer.org.
BioPerl/1.7.8-GCCcore-10.2.0 easyconfig 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.
Biopython/1.81-foss-2022b 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.
Bison/3.8.2-GCCcore-13.2.0 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.
Blosc/1.21.5-GCCcore-12.3.0 Blosc, an extremely fast, multi-threaded, meta-compressor library
Blosc2/2.11.0-GCCcore-12.3.0 easyconfig Blosc, an extremely fast, multi-threaded, meta-compressor library
Boost/1.83.0-GCC-13.2.0 Boost provides free peer-reviewed portable C++ source libraries.
Boost.MPI/1.74.0-gompi-2020b Boost provides free peer-reviewed portable C++ source libraries.
Boost.Python/1.67.0-foss-2018b-Python-2.7.15 Boost.Python is a C++ library which enables seamless interoperability between C++ and the Python programming language.
Bowtie/1.3.0-GCC-10.2.0 easyconfig Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome.
Bowtie2/2.4.4-GCC-11.2.0 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.
Brotli/1.1.0-GCCcore-13.2.0 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.
Brunsli/0.1-GCCcore-13.2.0 easyconfig Brunsli is a lossless JPEG repacking library.
CARBayes/5.1.1-foss-2018b-R-3.5.2 easyconfig Implements a class of univariate and multivariate spatial generalised linear mixed models for areal unit data, with inference in a Bayesian setting using Markov chain Monte Carlo (MCMC) simulation.
CD-HIT/4.8.1-foss-2019b easyconfig CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences.
CFITSIO/4.3.1-GCCcore-13.2.0 CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format.
CITE-seq-Count/1.4.2-foss-2018b-Python-3.6.6 easyconfig A python package that allows to count antibody TAGS from a CITE-seq and/or cell hashing experiment.
CMake/3.27.6-GCCcore-13.2.0 CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.
CNVkit/0.9.9-foss-2021b-R-4.2.0 easyconfig A command-line toolkit and Python library for detecting copy number variants and alterations genome-wide from high-throughput sequencing.
CRISPRCasTyper/1.2.1-foss-2020a-Python-3.8.2 easyconfig Detect CRISPR-Cas genes and arrays, and predict the subtype based on both Cas genes and CRISPR repeat sequence.
CRIU/3.13-foss-2019b-Python-3.7.4 easyconfig Checkpoint/Restore In Userspace (CRIU) is a Linux software which can freeze a running container (or an individual application) and checkpoint its state to disk. The data saved can be used to restore the application and run it exactly as it was during the time of the freeze. Using this functionality, application or container live migration, snapshots, remote debugging, and many other things are now possible.
CUDA/12.1.1 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.
CUDAcore/11.1.1-GCCcore-10.2.0 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.
CUnit/2.1-3-GCCcore-11.2.0 Automated testing framework for C.
Catch2/2.13.9-GCCcore-12.2.0 A modern, C++-native, header-only, test framework for unit-tests, TDD and BDD
CellBender/0.2.2-foss-2021b-CUDA-11.4.1 CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
CellProfiler/4.2.4-foss-2021b easyconfig CellProfiler is a free open-source software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically.
CellRanger/8.0.0 easyconfig Cell Ranger is a set of analysis pipelines that process Chromium single-cell RNA-seq output to align reads, generate gene-cell matrices and perform clustering and gene expression analysis.
CellRanger-ARC/2.0.0 easyconfig Cell Ranger ARC is a set of analysis pipelines that process Chromium Single Cell Multiome ATAC + Gene Expression sequencing data to generate a variety of analyses pertaining to gene expression, chromatin accessibility and their linkage. Furthermore, since the ATAC and gene expression measurements are on the very same cell, we are able to perform analyses that link chromatin accessibility and gene expression.
CellRanger-ATAC/2.0.0 Cell Ranger ATAC is a set of analysis pipelines that process Chromium Single Cell ATAC data.
CellRank/1.5.1-foss-2020b CellRank is a toolkit to uncover cellular dynamics based on Markov state modeling of single-cell data. It contains two main modules: kernels compute cell-cell transition probabilities and estimators generate hypothesis based on these.
Cellpose/0.6.5-fosscuda-2020b Cellpose is an anatomical segmentation algorithm written in Python 3 by Carsen Stringer and Marius Pachitariu.
Cereal/1.3.2-GCCcore-12.2.0 easyconfig 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
Cgl/0.60.8-foss-2023b 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.
Check/0.15.2-GCCcore-10.2.0 Check is a unit testing framework for C. It features a simple interface for defining unit tests, putting little in the way of the developer. Tests are run in a separate address space, so both assertion failures and code errors that cause segmentation faults or other signals can be caught. Test results are reportable in the following: Subunit, TAP, XML, and a generic logging format.
Circos/0.69-6-GCCcore-7.3.0-Perl-5.28.0 Circos is a software package for visualizing data and information. It visualizes data in a circular layout
Clamp/1.6.4
Clang/16.0.6-GCCcore-13.2.0 easyconfig C, C++, Objective-C compiler, based on LLVM. Does not include C++ standard library – use libstdc++ from GCC.
Clp/1.17.9-foss-2023b easyconfig 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.
Clustal-Omega/1.2.4-GCC-8.3.0 Clustal Omega is a multiple sequence alignment program for proteins. It produces biologically meaningful multiple sequence alignments of divergent sequences. Evolutionary relationships can be seen via viewing Cladograms or Phylograms
ClustalW2/2.1-foss-2019b ClustalW2 is a general purpose multiple sequence alignment program for DNA or proteins.
Cluster-Buster/0.0-GCC-12.2.0 Cluster-Buster is a program for finding interesting functional regions, such as transcriptional enhancers, in DNA sequences.
CoinUtils/2.11.10-GCC-13.2.0 easyconfig CoinUtils (Coin-OR Utilities) is an open-source collection of classes and functions that are generally useful to more than one COIN-OR project.
Control-FREEC/11.5-GCC-8.3.0 easyconfig Copy number and genotype annotation from whole genome and whole exome sequencing data.
Coreutils/8.32-GCCcore-8.3.0 easyconfig The GNU Core Utilities are the basic file, shell and text manipulation utilities of the GNU operating system. These are the core utilities which are expected to exist on every operating system.
CppUnit/1.15.1-GCCcore-10.2.0 CppUnit is the C++ port of the famous JUnit framework for unit testing.
Cufflinks/2.2.1-foss-2018b easyconfig Transcript assembly, differential expression, and differential regulation for RNA-Seq
Cython/3.0.7-GCCcore-12.3.0 Cython is an optimising static compiler for both the Python programming language and the extended Cython programming language (based on Pyrex).
DB/18.1.40-GCCcore-10.2.0 Berkeley DB enables the development of custom data management solutions, without the overhead traditionally associated with such custom projects.
DBD-mysql/4.050-GCC-10.2.0 Perl binding for MySQL
DB_File/1.857-GCCcore-11.2.0 Perl5 access to Berkeley DB version 1.x.
DBus/1.15.8-GCCcore-13.2.0 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.
DIAMOND/2.0.13-GCC-11.2.0 Accelerated BLAST compatible local sequence aligner
DeepCell/0.11.1-foss-2021b-CUDA-11.4.1 easyconfig deepcell-tf is a deep learning library for single-cell analysis of biological images.This library allows users to apply pre-existing models to imaging data as well as to develop new deep learning models for single-cell analysis.
DeepTCR/2.1.27-foss-2021b-CUDA-11.4.1 easyconfig DeepTCR is a python package that has a collection of unsupervised and supervised deep learning methods to parse TCRSeq data.
Delly/0.9.1-gompi-2020b Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends, split-reads and read-depth to sensitively and accurately delineate genomic rearrangements throughout the genome.
DiMSum/1.2.9-foss-2021b-R-4.2.0 easyconfig An error model and pipeline for analyzing deep mutational scanning (DMS) data and diagnosing common experimental pathologies.
Doxygen/1.9.8-GCCcore-13.2.0 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.
EIGENSOFT/7.2.1-foss-2019b The EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. 2006) and our EIGENSTRAT stratification correction method (Price et al. 2006). The EIGENSTRAT method uses principal components analysis to explicitly model ancestry differences between cases and controls along continuous axes of variation; the resulting correction is specific to a candidate marker’s variation in frequency across ancestral populations, minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT package has a built-in plotting script and supports multiple file formats and quantitative phenotypes.
EMAN2/2.3-foss-2019b-Python-2.7.16 easyconfig EMAN2 is the successor to EMAN1. It is a broadly based greyscale scientific image processing suite with a primary focus on processing data from transmission electron microscopes.
EMBOSS/6.6.0-foss-2018b easyconfig EMBOSS is ‘The European Molecular Biology Open Software Suite’ EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community.
EPACTS/3.3.2-foss-2020b easyconfig EPACTS is a versatile software pipeline to perform various statistical tests for identifying genome-wide association from sequence data through a user-friendly interface, both to scientific analysts and to method developers.
ESS/18.10.2 easyconfig Emacs Speaks Statistics (ESS) is an add-on package for emacs text editors such as GNU Emacs and XEmacs. It is designed to support editing of scripts and interaction with various statistical analysis programs such as R, S-Plus, SAS, Stata and OpenBUGS/JAGS.
EasyBuild/4.9.1 EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.
Eigen/3.4.0-GCCcore-13.2.0 Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.
Emacs/27.1-GCCcore-10.2.0 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.
Enrich2/1.3.1-foss-2020b-Python-2.7.18 Enrich2 is a general software tool for processing, analyzing, and visualizing data from deep mutational scanning experiments.
Enrich2/1.3.1-foss-2020b-Python-2.7.18 Enrich2 is a general software tool for processing, analyzing, and visualizing data from deep mutational scanning experiments.
FASTX-Toolkit/0.0.14-GCCcore-8.3.0 The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.
FFTW/3.3.10-gompi-2021b FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data.
FFTW.MPI/3.3.10-gompi-2022a FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data.
FFmpeg/6.0-GCCcore-12.3.0 A complete, cross-platform solution to record, convert and stream audio and video.
FIt-SNE/1.1.0-gompi-2018b easyconfig t-distributed stochastic neighbor embedding (t-SNE) is widely used for visualizing single-cell RNA-sequencing (scRNA-seq) data, but it scales poorly to large datasets. We dramatically accelerate t-SNE, obviating the need for data downsampling, and hence allowing visualization of rare cell populations. Furthermore, we implement a heatmap-style visualization for scRNA-seq based on one-dimensional t-SNE for simultaneously visualizing the expression patterns of thousands of genes.
FLAC/1.4.2-GCCcore-12.2.0 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.
FLASH/2.2.00-foss-2018b easyconfig FLASH (Fast Length Adjustment of SHort reads) is a very fast and accurate software tool to merge paired-end reads from next-generation sequencing experiments. FLASH is designed to merge pairs of reads when the original DNA fragments are shorter than twice the length of reads. The resulting longer reads can significantly improve genome assemblies. They can also improve transcriptome assembly when FLASH is used to merge RNA-seq data.
FLTK/1.3.5-GCC-8.3.0 FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL and its built-in GLUT emulation.
FSL/5.0.11-foss-2018b FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.
FTGL/2.3-GCCcore-10.2.0 easyconfig FTGL is a free open source library to enable developers to use arbitrary fonts in their OpenGL (www.opengl.org) applications.
FastANI/1.1-foss-2018b easyconfig FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies.
FastQC/0.11.9-Java-11 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.
FastTree/2.1.11-GCCcore-11.2.0 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.
Fiji/2.9.0-Java-1.8 Fiji is an image processing package—a ‘batteries-included’ distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis. This release is based on ImageJ-2.1.0 and Fiji-2.1.1
File-ReadBackwards/1.05-GCCcore-7.3.0-Perl-5.28.0 This Perl module reads a file backwards line by line.
FlashPCA2/2.0-GCC-10.2.0 FlashPCA performs fast principal component analysis (PCA) of single nucleotide polymorphism (SNP) data.
Flask/1.1.2-GCCcore-10.2.0 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
FlexiBLAS/3.3.1-GCC-12.3.0 FlexiBLAS is a wrapper library that enables the exchange of the BLAS and LAPACK implementation used by a program without recompiling or relinking it.
FreeImage/3.18.0-GCCcore-11.2.0 FreeImage is an Open Source library project for developers who would like to support popular graphics image formats like PNG, BMP, JPEG, TIFF and others as needed by today’s multimedia applications. FreeImage is easy to use, fast, multithreading safe.
FreeTDS/1.3.6-GCCcore-11.2.0 easyconfig FreeTDS is a set of libraries for Unix and Linux that allows your programs to natively talk to Microsoft SQL Server and Sybase databases.
FriBidi/1.0.13-GCCcore-13.2.0 The Free Implementation of the Unicode Bidirectional Algorithm.
GATK/4.4.0.0-GCCcore-12.2.0-Java-17 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.
GCC/13.2.0 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,…).
GCCcore/13.2.0 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,…).
GCTA/1.92.2beta GCTA (Genome-wide Complex Trait Analysis) was originally designed to estimate the proportion of phenotypic variance explained by all genome-wide SNPs for complex traits (the GREML method), and has subsequently extended for many other analyses to better understand the genetic architecture of complex traits.
GConf/3.2.6-GCCcore-10.2.0 easyconfig GConf is a system for storing application preferences. It is intended for user preferences; not configuration of something like Apache, or arbitrary data storage.
GD/2.69-GCCcore-7.3.0-Perl-5.28.0 GD.pm
GDAL/3.8.4-foss-2023b easyconfig 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.
GDB/11.1-GCCcore-11.2.0 The GNU Project Debugger
GDRCopy/2.3.1-GCCcore-12.3.0 A low-latency GPU memory copy library based on NVIDIA GPUDirect RDMA technology.
GEOS/3.12.1-GCC-13.2.0 easyconfig GEOS (Geometry Engine
GISTIC/2.0.23-GCCcore-8.3.0 easyconfig GISTIC is a tool to identify genes targeted by somatic copy-number alterations (SCNAs) that drive cancer growth. By separating SCNA profiles into underlying arm-level and focal alterations, GISTIC estimates the background rates for each category as well as defines the boundaries of SCNA regions.
GLFW/3.4-GCCcore-12.2.0 easyconfig GLFW is an Open Source, multi-platform library for OpenGL, OpenGL ES and Vulkan development on the desktop
GLIPH2/0.1 GLIPH 2 clusters TCRs that are predicted to bind the same MHC-restricted peptide antigen.
GLPK/5.0-GCCcore-10.3.0 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.
GLib/2.78.1-GCCcore-13.2.0 GLib is one of the base libraries of the GTK+ project
GLibmm/2.49.7-GCCcore-8.3.0 C++ bindings for Glib
GMAP-GSNAP/2018-07-04-foss-2018b GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences GSNAP: Genomic Short-read Nucleotide Alignment Program
GMP/6.3.0-GCCcore-13.2.0 GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers.
GMime/3.2.7-GCCcore-8.3.0 easyconfig The GMime package contains a set of utilities for parsing and creating messages using the Multipurpose Internet Mail Extension (MIME) as defined by the applicable RFCs.
GObject-Introspection/1.78.1-GCCcore-13.2.0 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.
GRIDSS/2.13.2-foss-2021b easyconfig GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements. GRIDSS includes a genome-wide break-end assembler, as well as a structural variation caller for Illumina sequencing data. GRIDSS calls variants based on alignment-guided positional de Bruijn graph genome-wide break-end assembly, split read, and read pair evidence.
GROMACS/2021-foss-2020b 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.

GSEA/4.3.2 Gene Set Enrichment Analysis (GSEA) is a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states (e.g. phenotypes).
GSL/2.7-GCC-11.2.0 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.
GST-plugins-base/1.22.1-GCCcore-12.2.0 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.
GStreamer/1.22.1-GCCcore-12.2.0 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.
GTK+/3.24.23-GCCcore-10.2.0 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.
GTK3/3.24.39-GCCcore-13.2.0 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.
GTS/0.7.6-GCCcore-10.2.0 GTS stands for the GNU Triangulated Surface Library. It is an Open Source Free Software Library intended to provide a set of useful functions to deal with 3D surfaces meshed with interconnected triangles.
Garnett/20220903-foss-2021b-R-4.2.2 easyconfig Garnett is a software package that faciliates automated cell type classification from single-cell expression data.
Gdk-Pixbuf/2.42.10-GCCcore-12.2.0 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.
Geekbench/5.4.1 Geekbench 5 is a cross-platform benchmark that measures your system’s performance with the press of a button.
GenomeSTRiP/2.00.1958-GCCcore-8.3.0-Java-11 Genome STRiP (Genome STRucture In Populations) is a suite of tools for discovery and genotyping of structural variation using whole-genome sequencing data. The methods used in Genome STRiP are designed to find shared variation using data from multiple individuals. Genome STRiP looks both across and within a set of sequenced genomes to detect variation.
Ghostscript/10.02.1-GCCcore-13.2.0 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.
Giotto/1.0.0-foss-2019b-R-4.0.2 easyconfig The Giotto package consists of two modules, Giotto Analyzer and Viewer, which provide tools to process, analyze and visualize single-cell spatial expression data.
GitPython/3.1.24-GCCcore-11.2.0 GitPython is a python library used to interact with Git repositories
Globus-CLI/3.6.0-GCCcore-11.2.0 A Command Line Wrapper over the Globus SDK for Python, which provides an interface to Globus services from the shell, and is suited to both interactive and simple scripting use cases.
GlobusConnectPersonal/3.2.0-GCCcore-11.2.0 Globus Connect Personal turns your laptop or other personal computer into a Globus endpoint with a just a few clicks. With Globus Connect Personal you can share and transfer files to/from a local machine—campus server, desktop computer or laptop—even if it’s behind a firewall and you don’t have administrator privileges.
GnuTLS/3.7.3-GCCcore-11.2.0 GnuTLS is a secure communications library implementing the SSL, TLS and DTLS protocols and technologies around them. It provides a simple C language application programming interface (API) to access the secure communications protocols as well as APIs to parse and write X.509, PKCS #12, OpenPGP and other required structures. It is aimed to be portable and efficient with focus on security and interoperability.
Go/1.18.1 Go is an open source programming language that makes it easy to build simple, reliable, and efficient software.
GoPeaks/1.0.0 easyconfig GoPeaks is a peak caller designed for CUT&TAG/CUT&RUN sequencing data.
Graphene/1.10.8-GCCcore-12.2.0 Graphene is a thin layer of types for graphic libraries
GraphicsMagick/1.3.31-foss-2018b easyconfig GraphicsMagick is the swiss army knife of image processing.
Graphviz/10.0.1-GCCcore-13.2.0 easyconfig Graphviz is open source graph visualization software. Graph visualization is a way of representing structural information as diagrams of abstract graphs and networks. It has important applications in networking, bioinformatics, software engineering, database and web design, machine learning, and in visual interfaces for other technical domains.
Guile/3.0.7-GCCcore-11.2.0 easyconfig 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.
Gurobi/10.0.2 easyconfig The Gurobi Optimizer allows users to state their toughest business problems as mathematical models, and then automatically considers billions or even trillions of possible solutions to find the best one. Our solver can be used as both a decision-making assistant, to help guide the choices of a skilled expert, or as a fully automated tool to make decisions with no human intervention.
HDF/4.2.16-2-GCCcore-13.2.0 easyconfig HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines.
HDF5/1.14.3-gompi-2023b 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.
HH-suite/3.3.0-gompi-2022a The HH-suite is an open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs).
HISAT2/2.2.1-gompi-2021b 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).
HLA-HD/1.6.1-GCC-11.2.0 easyconfig HLA-HD (HLA typing from High-quality Dictionary) can accurately determine HLA alleles with 6-digit precision from NGS data (fastq format). RNA-Seq data can also be applied.
HMMER/3.3.2-gompi-2022a 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.
HOME/1.0.0-foss-2019b-Python-3.7.4 easyconfig HOME (histogram of methylation) is a python package for differential methylation region (DMR) identification. The method uses histogram of methylation features and the linear Support Vector Machine (SVM) to identify DMRs from whole genome bisulfite sequencing (WGBS) data.
HTSeq/0.11.0-foss-2018b-Python-2.7.15 A framework to process and analyze data from high-throughput sequencing (HTS) assays
HTSlib/1.19.1-GCC-13.2.0 easyconfig A C library for reading/writing high-throughput sequencing data. This package includes the utilities bgzip and tabix
Hail/0.2.64-foss-2020b easyconfig Hail is an open-source, general-purpose, Python-based data analysis tool with additional data types and methods for working with genomic data.
HarfBuzz/8.2.2-GCCcore-13.2.0 HarfBuzz is an OpenType text shaping engine.
HiC-Pro/3.1.0-foss-2021b easyconfig HiC-Pro was designed to process Hi-C data, from raw fastq files (paired-end Illumina data) to the normalized contact maps.
Highway/1.0.7-GCCcore-13.2.0 Highway is a C++ library for SIMD (Single Instruction, Multiple Data), i.e. applying the same operation to ‘lanes’.
Homer/4.11-Perl-5.30.0 HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and ChIP-Seq analysis. It is a collection of command line programs for unix-style operating systems written in mostly perl and c++. Homer was primarily written as a de novo motif discovery algorithm that is well suited for finding 8-12 bp motifs in large scale genomics data.
Hypre/2.21.0-foss-2021a 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.
ICU/74.1-GCCcore-13.2.0 ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization support for software applications.
IDBA-UD/1.1.3-foss-2018b IDBA-UD is a iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data with Highly Uneven Sequencing Depth. It is an extension of IDBA algorithm. IDBA-UD also iterates from small k to a large k. In each iteration, short and low-depth contigs are removed iteratively with cutoff threshold from low to high to reduce the errors in low-depth and high-depth regions. Paired-end reads are aligned to contigs and assembled locally to generate some missing k-mers in low-depth regions. With these technologies, IDBA-UD can iterate k value of de Bruijn graph to a very large value with less gaps and less branches to form long contigs in both low-depth and high-depth regions.
IGV/2.15.4-Java-11 easyconfig This package contains command line utilities for preprocessing, computing feature count density (coverage), sorting, and indexing data files.
IGVTools/2.4.16-Java-1.8 easyconfig This package contains command line utilities for preprocessing, computing feature count density (coverage), sorting, and indexing data files. See also http://www.broadinstitute.org/software/igv/igvtools_commandline.
IPython/8.14.0-GCCcore-12.2.0 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.
IRIS/2.0.1 easyconfig IRIS Isoform peptides from RNA splicing for Immunotherapy target Screening
ISA-L/2.30.0-GCCcore-11.2.0 Intelligent Storage Acceleration Library
ISL/0.24-GCCcore-11.2.0 isl is a library for manipulating sets and relations of integer points bounded by linear constraints.
IgBLAST/1.22.0-x64-linux IgBLAST faclilitates the analysis of immunoglobulin and T cell receptor variable domain sequences.
ImageMagick/7.1.0-53-GCCcore-12.2.0 ImageMagick is a software suite to create, edit, compose, or convert bitmap images
Imath/3.1.9-GCCcore-13.2.0 Imath is a C++ and python library of 2D and 3D vector, matrix, and math operations for computer graphics
Infernal/1.1.4-foss-2021b Infernal (“INFERence of RNA ALignment”) is for searching DNA sequence databases for RNA structure and sequence similarities.
JAGS/4.3.2-foss-2022b easyconfig JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation
JUnit/4.12-Java-1.8 A programmer-oriented testing framework for Java.
Jansson/2.13.1-GCC-11.2.0 Jansson is a C library for encoding, decoding and manipulating JSON data. Its main features and design principles are:
Simple and intuitive API and data model
Comprehensive documentation
No dependencies on other libraries
Full Unicode support (UTF-8)
Extensive test suite
JasPer/4.0.0-GCCcore-12.2.0 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.
Java/17.0.6 Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.
Jellyfish/2.3.0-GCC-10.2.0 easyconfig Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.
JsonCpp/1.9.5-GCCcore-12.3.0 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.
Judy/1.0.5-GCCcore-12.2.0 A C library that implements a dynamic array.
Julia/1.7.3-linux-x86_64 Julia is a high-level, high-performance dynamic programming language for numerical computing
JupyterHub/4.0.1-GCCcore-12.2.0 JupyterHub is a multiuser version of the Jupyter (IPython) notebook designed for centralized deployments in companies, university classrooms and research labs.
JupyterLab/4.0.5-GCCcore-12.3.0 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.
Kalign/3.3.5-GCCcore-11.3.0 Kalign is a fast multiple sequence alignment program for biological sequences.
Kent_tools/20201201-linux.x86_64 easyconfig Jim Kent’s tools: collection of tools used by the UCSC genome browser.
Keras/2.4.3-foss-2020b Keras is a deep learning API written in Python, running on top of the machine learning platform TensorFlow.
Kraken2/2.1.3-gompi-2022b easyconfig Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. Kraken aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm.
Krona/2.7.1-GCCcore-9.3.0-Perl-5.30.2 easyconfig Krona allows hierarchical data to be explored with zooming, multi-layered pie charts. Krona charts can be created using an Excel template or KronaTools, which includes support for several bioinformatics tools and raw data formats.
LAME/3.100-GCCcore-10.3.0 LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL.
LAPACK/3.10.1-GCC-11.2.0 LAPACK is written in Fortran90 and provides routines for solving systems of simultaneous linear equations, least-squares solutions of linear systems of equations, eigenvalue problems, and singular value problems.
LAST/963-foss-2018b LAST finds similar regions between sequences.
LERC/4.0.0-GCCcore-12.2.0 easyconfig 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).
LIBSVM/3.25-GCCcore-10.2.0 LIBSVM is an integrated software for support vector classification, (C-SVC, nu-SVC), regression (epsilon-SVR, nu-SVR) and distribution estimation (one-class SVM). It supports multi-class classification.
LLVM/16.0.6-GCCcore-12.3.0 The LLVM Core libraries provide a modern source- and target-independent optimizer, along with code generation support for many popular CPUs (as well as some less common ones!) These libraries are built around a well specified code representation known as the LLVM intermediate representation (“LLVM IR”). The LLVM Core libraries are well documented, and it is particularly easy to invent your own language (or port an existing compiler) to use LLVM as an optimizer and code generator.
LMDB/0.9.29-GCCcore-12.2.0 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.
LZO/2.10-GCCcore-9.3.0 Portable lossless data compression library
Leptonica/1.83.0-GCCcore-11.2.0 easyconfig Leptonica is a collection of pedagogically-oriented open source software that is broadly useful for image processing and image analysis applications.
LibSoup/3.0.7-GCC-11.2.0 libsoup is an HTTP client/server library for GNOME. It uses GObjects and the glib main loop, to integrate well with GNOME applications, and also has a synchronous API, for use in threaded applications.
LibTIFF/4.6.0-GCCcore-13.2.0 tiff: Library and tools for reading and writing TIFF data files
LightGBM/2.2.3-foss-2018b easyconfig A fast, distributed, high performance gradient boosting (GBT, GBDT, GBRT, GBM or MART) framework based on decision tree algorithms, used for ranking, classification and many other machine learning tasks.
LittleCMS/2.15-GCCcore-13.2.0 Little CMS intends to be an OPEN SOURCE small-footprint color management engine, with special focus on accuracy and performance.
LoFreq/2.1.3.1-foss-2018b-Python-2.7.15 Fast and sensitive variant calling from next-gen sequencing data
LoomXpy/0.4.2-foss-2022b easyconfig Python package (compatible with SCope) to create .loom files and extend them with other data e.g.: SCENIC regulons
Lua/5.4.4-GCCcore-12.2.0 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.
M4/1.4.19-GCCcore-11.2.0 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.
MACS2/2.2.9.1-foss-2022b easyconfig Model Based Analysis for ChIP-Seq data
MACS3/3.0.0-foss-2022b easyconfig Model Based Analysis for ChIP-Seq data
MAESTRO/1.2.1-foss-2019b-Python-3.7.4 easyconfig MAESTRO(Model-based AnalysEs of Single-cell Transcriptome and RegulOme) is a comprehensive single-cell RNA-seq and ATAC-seq analysis suit built using snakemake. MAESTRO combines several dozen tools and packages to create an integrative pipeline, which enables scRNA-seq and scATAC-seq analysis from raw sequencing data (fastq files) all the way through alignment, quality control, cell filtering, normalization, unsupervised clustering, differential expression and peak calling, celltype annotation and transcription regulation analysis.
MAFFT/7.490-GCC-11.2.0-with-extensions 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.
MAGeCK-VISPR/0.5.5-Python-3.7.4 easyconfig MAGeCK-VISPR is a comprehensive quality control, analysis and visualization workflow for CRISPR/Cas9 screens The workflow combines the MAGeCK algorithm to identify essential genes from CRISPR/Cas9 screens considering multiple conditions with VISPR to interactively explore results and quality control in a web-based frontend.
MAGeCK-VISPR/0.5.5-Python-3.7.4 MAGeCK-VISPR is a comprehensive quality control, analysis and visualization workflow for CRISPR/Cas9 screens The workflow combines the MAGeCK algorithm to identify essential genes from CRISPR/Cas9 screens considering multiple conditions with VISPR to interactively explore results and quality control in a web-based frontend.
MAGeCK-VISPR/0.5.5-Python-3.7.4 MAGeCK-VISPR is a comprehensive quality control, analysis and visualization workflow for CRISPR/Cas9 screens The workflow combines the MAGeCK algorithm to identify essential genes from CRISPR/Cas9 screens considering multiple conditions with VISPR to interactively explore results and quality control in a web-based frontend.
MEME/5.5.1-gompi-2021b easyconfig The MEME Suite allows you to: * discover motifs using MEME, DREME (DNA only) or GLAM2 on groups of related DNA or protein sequences, * search sequence databases with motifs using MAST, FIMO, MCAST or GLAM2SCAN, * compare a motif to all motifs in a database of motifs, * associate motifs with Gene Ontology terms via their putative target genes, and * analyse motif enrichment using SpaMo or CentriMo.
METIS/5.1.0-GCCcore-13.2.0 easyconfig 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.
MMseqs2/13-45111-gompi-2021b MMseqs2: ultra fast and sensitive search and clustering suite
MPC/1.3.1-GCCcore-12.2.0 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.
MPFR/4.2.1-GCCcore-13.2.0 The MPFR library is a C library for multiple-precision floating-point computations with correct rounding.
MUMPS/5.4.1-foss-2021b-metis easyconfig A parallel sparse direct solver
MUMmer/4.0.0beta2-foss-2020a easyconfig MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. AMOS makes use of it.
MUSCLE/3.8.31-foss-2018b easyconfig MUSCLE is one of the best-performing multiple alignment programs according to published benchmark tests, with accuracy and speed that are consistently better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users learn everything they need to know about MUSCLE in a few minutes—only a handful of command-line options are needed to perform common alignment tasks.
Magic-BLAST/1.5.0-Linux_x86_64 easyconfig Magic-BLAST is a tool for mapping large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome.
Mako/1.2.4-GCCcore-12.2.0 A super-fast templating language that borrows the best ideas from the existing templating languages
MariaDB/10.11.2-GCC-12.2.0 MariaDB is an enhanced, drop-in replacement for MySQL. Included engines: myISAM, Aria, InnoDB, RocksDB, TokuDB, OQGraph, Mroonga.
MariaDB-connector-c/2.3.7-GCCcore-8.3.0 MariaDB Connector/C is used to connect applications developed in C/C++ to MariaDB and MySQL databases.
Maven/3.6.3 Binary maven install, Apache Maven is a software project management and comprehension tool. Based on the concept of a project object model (POM), Maven can manage a project’s build, reporting and documentation from a central piece of information.
MaxQuant/2.4.9.0-foss-2022b MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data. Several labeling techniques as well as label-free quantification are supported.
Mesa/23.1.9-GCCcore-13.2.0 Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics.
Meson/1.2.3-GCCcore-13.2.0 Meson is a cross-platform build system designed to be both as fast and as user friendly as possible.
Metal/2020-05-05-GCC-10.2.0 easyconfig Metal
MethGo/24c9319-foss-2018b-Python-2.7.15 easyconfig DNA methylation is a major epigenetic modification regulating several biological processes. A standard approach in the study of DNA methylation is bisulfite sequencing (BS-Seq). MethGo is a simple and effective tool designed for the analysis of data from whole genome bisulfite sequencing (WGBS) and reduced representation bisulfite sequencing (RRBS).
MiXCR/3.0.3-Java-1.8 easyconfig MiXCR processes big immunome data from raw sequences to quantitated clonotypes
MinCED/0.4.2-GCCcore-9.3.0-Java-11 easyconfig Mining CRISPRs in Environmental Datasets
Miniconda3/4.9.2 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.
Mono/6.12.0.199-GCCcore-12.2.0 An open source, cross-platform, implementation of C# and the CLR that is binary compatible with Microsoft.NET.
Monocle3/1.3.1-foss-2021b-R-4.2.2 easyconfig Single-cell transcriptome sequencing (sc-RNA-seq) experiments allow us to discover new cell types and help us understand how they arise in development. The Monocle 3 package provides a toolkit for analyzing single-cell gene expression experiments.
MoreRONN/4.9-foss-2019b easyconfig MoreRONN is the spiritual successor of RONN and is useful for surveying disorder in proteins as well as designing expressible constructs for X-ray crystallography.
Mothur/1.41.0-foss-2018b-Python-2.7.15 Mothur is a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community.
MotionCor2/1.4.2-gcccuda-2020b easyconfig MotionCor2 correct anisotropic image motion at the single pixel level across the whole frame, suitable for both single particle and tomographic images. Iterative, patch-based motion detection is combined with spatial and temporal constraints and dose weighting.

Cite publication: Shawn Q. Zheng, Eugene Palovcak, Jean-Paul Armache, Yifan Cheng and David A. Agard (2016) Anisotropic Correction of Beam-induced Motion for Improved Single-particle Electron Cryo-microscopy, Nature Methods, submitted. BioArxiv: https://biorxiv.org/content/early/2016/07/04/061960

MrBayes/3.2.7a-gompi-2021b easyconfig MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models.
MuSE/2.0.1-GCC-11.2.0 easyconfig An accurate and ultra-fast somatic mutation calling tool for whole-genome sequencing (WGS) and whole-exome sequencing (WES) data from heterogeneous tumor samples.
MultiQC/1.21-foss-2023a-Python-3.11.3 Aggregate results from bioinformatics analyses across many samples into a single report.

MultiQC searches a given directory for analysis logs and compiles a HTML report. It’s a general use tool, perfect for summarising the output from numerous bioinformatics tools.

MutSig/2 easyconfig MutSig stands for “Mutation Significance”. MutSig analyzes lists of mutations discovered in DNA sequencing, to identify genes that were mutated more often than expected by chance given background mutation processes.
MutSig2CV/3.11 MutSig2CV analyzes somatic point mutations discovered in DNA sequencing, identifying genes mutated more often than expected by chance given inferred background mutation processes.
MutSigCV/1.4.1 MutSigCV accepts whole genome or whole exome sequencing data from multiple samples, with information about point mutations, small insertions/deletions, and coverage, and identifies genes that are mutated more often than one would expect by chance.
NAMD/2.14-foss-2020a-mpi NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.
NASM/2.16.01-GCCcore-12.3.0 NASM: General-purpose x86 assembler
NCCL/2.18.3-GCCcore-12.3.0-CUDA-12.1.1 The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective communication primitives that are performance optimized for NVIDIA GPUs.
NGS/2.11.2-GCCcore-11.2.0 NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing.
NLopt/2.7.1-GCCcore-12.2.0 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.
NSPR/4.35-GCCcore-13.2.0 Netscape Portable Runtime (NSPR) provides a platform-neutral API for system level and libc-like functions.
NSS/3.94-GCCcore-13.2.0 Network Security Services (NSS) is a set of libraries designed to support cross-platform development of security-enabled client and server applications.
NextGenMap/0.5.5-GCC-11.2.0 NextGenMap is a flexible highly sensitive short read mapping tool that handles much higher mismatch rates than comparable algorithms while still outperforming them in terms of runtime.
Nextflow/23.04.2 Nextflow is a reactive workflow framework and a programming DSL that eases writing computational pipelines with complex data
Nim/0.19.2-GCCcore-7.3.0 Nim is a systems and applications programming language.
Ninja/1.11.1-GCCcore-13.2.0 Ninja is a small build system with a focus on speed.
OpenBLAS/0.3.24-GCC-13.2.0 OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.
OpenCV/4.5.5-foss-2021b-contrib OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library. OpenCV was built to provide a common infrastructure for computer vision applications and to accelerate the use of machine perception in the commercial products. Includes extra modules for OpenCV from the contrib repository.
OpenEXR/3.2.0-GCCcore-13.2.0 OpenEXR is a high dynamic-range (HDR) image file format developed by Industrial Light & Magic for use in computer imaging applications
OpenJPEG/2.5.0-GCCcore-13.2.0 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.
OpenMM/8.0.0-foss-2022a-CUDA-11.7.0 OpenMM is a toolkit for molecular simulation.
OpenMPI/4.1.6-GCC-13.2.0 The Open MPI Project is an open source MPI-3 implementation.
OpenPGM/5.2.122-GCCcore-11.2.0 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.
OpenSSL/1.1 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.
OpenSlide/3.4.1-GCCcore-11.2.0 OpenSlide is a C library that provides a simple interface to read whole-slide images (also known as virtual slides).
OptiType/1.3.5-foss-2019b-Python-3.7.4 easyconfig OptiType is a novel HLA genotyping algorithm based on integer linear programming, capable of producing accurate 4-digit HLA genotyping predictions from NGS data by simultaneously selecting all major and minor HLA Class I alleles.
Osi/0.108.9-GCC-13.2.0 easyconfig 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.
PANDAseq/2.11-foss-2018b easyconfig PANDASEQ is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence.
PATRIC-cli/1.035-GCC-10.2.0 Read files using HTSlib including BAM/CRAM, Tabix and BCF database files
PCRE/8.45-GCCcore-12.2.0 The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5.
PCRE2/10.42-GCCcore-12.3.0 The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5.
PDBFixer/1.7-foss-2020b PDBFixer is an easy to use application for fixing problems in Protein Data Bank files in preparation for simulating them.
PDFCrop/0.4b easyconfig PDFCrop is a Perl script that crops the white margins of PDF pages and rescales them to fit a standard size sheet of paper. It makes the printed pages far more attractive to read!
PEAR/0.9.11-foss-2018b easyconfig PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. It is fully parallelized and can run with as low as just a few kilobytes of memory.
PETSc/3.15.1-foss-2021a 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.
PHASE/2.1.2-GCCcore-8.3.0 easyconfig PHASE is a program implementing the method for reconstructing haplotypes from population data
PLINK/2.00-alpha1-x86_64 Whole-genome association analysis toolset
PLINK2/20210826-linux_x86_64 easyconfig 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. The focus of PLINK is purely on analysis of genotype/phenotype data.
PLUMED/2.7.2-foss-2020b easyconfig 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.
PMIx/4.2.6-GCCcore-13.2.0 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
PROJ/9.3.1-GCCcore-13.2.0 Program proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates
Pandoc/2.13 If you need to convert files from one markup format into another, pandoc is your swiss-army knife
Pango/1.51.0-GCCcore-13.2.0 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.
Pango/1.51.0-GCCcore-13.2.0 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.
Perl/5.38.0-GCCcore-13.2.0 Larry Wall’s Practical Extraction and Report Language

Includes a small selection of extra CPAN packages for core functionality.

Perl-bundle-CPAN/5.38.0-GCCcore-13.2.0 A set of common packages from CPAN
Pillow/10.2.0-GCCcore-13.2.0 Pillow is the ‘friendly PIL fork’ by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors.
Pillow-SIMD/9.2.0-GCCcore-11.3.0 Pillow is the ‘friendly PIL fork’ by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors.
Pindel/0.2.5b9-20170508-foss-2018b easyconfig Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.
Porechop/0.2.4-GCCcore-11.2.0 easyconfig Porechop is a tool for finding and removing adapters from Oxford Nanopore reads. Adapters on the ends of reads are trimmed off, and when a read has an adapter in its middle, it is treated as chimeric and chopped into separate reads. Porechop performs thorough alignments to effectively find adapters, even at low sequence identity
PostgreSQL/16.1-GCCcore-13.2.0 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.
PubWeb/0.4.0-foss-2021b A Python 3.8+ library for the PubWeb platform.
PyCairo/1.24.0-GCCcore-12.2.0 Python bindings for the cairo library
PyClone/2020.9b2-GCCcore-10.2.0 PyClone is a Python package that wraps rclone and provides a threaded interface for an installation at the host or container level.
PyOpenGL/3.1.5-GCCcore-8.3.0 easyconfig PyOpenGL is the most common cross platform Python binding to OpenGL and related APIs.
PyQt5/5.15.1-GCCcore-10.2.0 PyQt5 is a set of Python bindings for v5 of the Qt application framework from The Qt Company. This bundle includes PyQtWebEngine, a set of Python bindings for The Qt Company’s Qt WebEngine framework.
PySide6/6.5.0-GCCcore-12.2.0 PySide6 is the official Python module from the Qt for Python project, which provides access to the complete Qt 6.5+ framework.
PyStan/3.5.0-foss-2021b easyconfig Python interface to Stan, a package for Bayesian inference using the No-U-Turn sampler, a variant of Hamiltonian Monte Carlo.
PyTables/3.9.2-foss-2023a easyconfig PyTables is a package for managing hierarchical datasets and designed to efficiently and easily cope with extremely large amounts of data. PyTables is built on top of the HDF5 library, using the Python language and the NumPy package. It features an object-oriented interface that, combined with C extensions for the performance-critical parts of the code (generated using Cython), makes it a fast, yet extremely easy to use tool for interactively browsing, processing and searching very large amounts of data. One important feature of PyTables is that it optimizes memory and disk resources so that data takes much less space (specially if on-flight compression is used) than other solutions such as relational or object oriented databases.
PyTorch/2.1.2-foss-2023a-CUDA-12.1.1 Tensors and Dynamic neural networks in Python with strong GPU acceleration. PyTorch is a deep learning framework that puts Python first.
PyTorch-Geometric/2.0.3-fosscuda-2020b easyconfig PyTorch Geometric (PyG) is a geometric deep learning extension library for PyTorch.
PyTorch-Lightning/2.2.0.post0-foss-2023a-CUDA-12.1.1 PyTorch Lightning is the lightweight PyTorch wrapper for ML researchers.
PyYAML/6.0.1-GCCcore-13.2.0 PyYAML is a YAML parser and emitter for the Python programming language.
PyZMQ/25.1.1-GCCcore-12.3.0 Python bindings for ZeroMQ
PycURL/7.45.2-GCCcore-12.2.0 PycURL is a Python interface to libcurl. PycURL can be used to fetch objects identified by a URL from a Python program, similar to the urllib Python module. PycURL is mature, very fast, and supports a lot of features.
Pyomo/6.4.4-foss-2021b easyconfig Pyomo is a Python-based open-source software package that supports a diverse set of optimization capabilities for formulating and analyzing optimization models.
Pysam/0.22.0-GCC-13.2.0 easyconfig 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.
Python/3.11.5-GCCcore-13.2.0 Python is a programming language that lets you work more quickly and integrate your systems more effectively.
Python-bundle-PyPI/2023.10-GCCcore-13.2.0 Bundle of Python packages from PyPI
QIIME2/2020.11 QIIME is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data.
QUAST/5.1.0rc1-foss-2020b easyconfig 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.
Qhull/2020.2-GCCcore-11.2.0 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.
Qt/4.8.7-foss-2018b Qt is a comprehensive cross-platform C++ application framework.
Qt5/5.15.13-GCCcore-13.2.0 Qt is a comprehensive cross-platform C++ application framework.
Qt6/6.6.3-GCCcore-13.2.0 Qt is a comprehensive cross-platform C++ application framework.
R/4.3.3-gfbf-2023b easyconfig R is a free software environment for statistical computing and graphics.
R-Tidyverse/4.3.3-gfbf-2023b easyconfig R is a free software environment for statistical computing and graphics.
R-bundle-Bioconductor/3.16-foss-2022b-R-4.2.2 easyconfig Bioconductor provides tools for the analysis and coprehension of high-throughput genomic data.
R-keras/2.2.5.0-foss-2019b-Python-3.7.4-R-3.6.2 Interface to ‘Keras’ https://keras.io, a high-level neural networks ‘API’.
RAxML/8.2.12-GCC-10.2.0-pthreads-avx2 RAxML search algorithm for maximum likelihood based inference of phylogenetic trees.
RAxML-NG/1.0.3-GCC-10.2.0 RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion. Its search heuristic is based on iteratively performing a series of Subtree Pruning and Regrafting (SPR) moves, which allows to quickly navigate to the best-known ML tree.
RDFlib/5.0.0-GCCcore-10.2.0 RDFLib is a Python library for working with RDF, a simple yet powerful language for representing information.
RE2/2023-08-01-GCCcore-12.3.0 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.
RELION/3.1.2-fosscuda-2020b easyconfig RELION (for REgularised LIkelihood OptimisatioN) is a stand-alone computer program for Maximum A Posteriori refinement of (multiple) 3D reconstructions or 2D class averages in cryo-electron microscopy.
RNA-SeQC/2.4.2-foss-2021b Fast, efficient RNA-Seq metrics for quality control and process optimization
ROSE/1-GCCcore-8.3.0-Python-2.7.16 easyconfig To create stitched enhancers, and to separate super-enhancers from typical enhancers using sequencing data (.bam) given a file of previously identified constituent enhancers (.gff)
RPostgreSQL/0.7-6-foss-2023b easyconfig Database interface and ‘PostgreSQL’ driver for ‘R’. This package provides a Database Interface ‘DBI’ compliant driver for ‘R’ to access ‘PostgreSQL’ database systems.
RSEM/1.3.3-foss-2019b easyconfig RNA-Seq by Expectation-Maximization
RSeQC/5.0.1-foss-2021b RSeQC provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc.
RStudio-Server/2023.12.1+402-foss-2022b-Java-11-R-4.3.1 easyconfig This is the RStudio Server version. RStudio is a set of integrated tools designed to help you be more productive with R.

The server can be started with: rserver –server-daemonize=0 –www-port=8787

If you need a database config one can be created with: MYTMP=mktemp -d && echo -e “provider=sqlite\ndirectory=${MYTMP}/sqlite” > “${MYTMP}/db.conf” and then used with: rserver … –database-config-file=”${MYTMP}/db.conf”

Racon/1.5.0-GCCcore-11.2.0 easyconfig Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads.
RapidJSON/1.1.0-GCCcore-11.2.0 A fast JSON parser/generator for C++ with both SAX/DOM style API
Ray-project/2.6.2-foss-2022b easyconfig Ray is a fast and simple framework for building and running distributed applications.
Redis/7.0.12-GCC-12.2.0 Redis is an open source (BSD licensed), in-memory data structure store, used as a database, cache, and message broker. Redis provides data structures such as strings, hashes, lists, sets, sorted sets with range queries, bitmaps, hyperloglogs, geospatial indexes, and streams. Redis has built-in replication, Lua scripting, LRU eviction, transactions, and different levels of on-disk persistence, and provides high availability via Redis Sentinel and automatic partitioning with Redis Cluster.
Regenie/3.1.2-GCC-11.2.0 easyconfig Regenie is a C++ program for whole genome regression modelling of large genome-wide association studies. It is developed and supported by a team of scientists at the Regeneron Genetics Center.
RepeatMasker/4.0.8-foss-2018b-Perl-5.28.0-HMMER easyconfig RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
RevBayes/1.1.1-GCC-10.2.0 easyconfig RevBayes provides an interactive environment for statistical computation in phylogenetics. It is primarily intended for modeling, simulation, and Bayesian inference in evolutionary biology, particularly phylogenetics.
Ruby/3.0.1-GCCcore-11.2.0 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.
Rust/1.76.0-GCCcore-13.2.0 Rust is a systems programming language that runs blazingly fast, prevents segfaults, and guarantees thread safety.
SAMtools/1.19.2-GCC-13.2.0 easyconfig SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.
SCOTCH/7.0.1-gompi-2021b easyconfig Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.
SCons/4.0.1-GCCcore-10.2.0 SCons is a software construction tool.
SDL2/2.28.5-GCCcore-13.2.0 SDL: Simple DirectMedia Layer, a cross-platform multimedia library
SHAPEIT4/4.2.2-foss-2020b SHAPEIT4 is a fast and accurate method for estimation of haplotypes (aka phasing) for SNP array and high coverage sequencing data.
SKESA/2.3.0-foss-2018b SKESA is a de-novo sequence read assembler for cultured single isolate genomes based on DeBruijn graphs.
SLEPc/3.15.1-foss-2021a 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.
SOCI/4.0.3-GCC-11.2.0 easyconfig SOCI is a database access library for C++ that makes the illusion of embedding SQL queries in the regular C++ code, staying entirely within the Standard C++.
SPAdes/3.13.0-foss-2018b Genome assembler for single-cell and isolates data sets
SPRING/1.6-foss-2018b-Python-2.7.15 easyconfig SPRING is a collection of pre-processing scripts and a web browser-based tool for visualizing and interacting with high dimensional data. View an example dataset here. SPRING was developed for single cell RNA-Seq data but can be applied more generally. The minimal input is a matrix of high dimensional data points (cells) and a list of dimension names (genes).
SQANTI3/1.0-foss-2019b-Python-3.7.4 easyconfig SQANTI3 is the first module of the Functional IsoTranscriptomics (FIT) framework, that also includes IsoAnnot and tappAS. Used for new long read-defined transcriptome.
SQLite/3.43.1-GCCcore-13.2.0 SQLite: SQL Database Engine in a C Library
SRA-Toolkit/3.0.0-ubuntu64 easyconfig The SRA Toolkit, and the source-code SRA System Development Kit (SDK), will allow you to programmatically access data housed within SRA and convert it from the SRA format
SSW/1.1-GCCcore-11.2.0 SSW is a fast implementation of the Smith-Waterman algorithm, which uses the Single-Instruction Multiple-Data (SIMD) instructions to parallelize the algorithm at the instruction level. SSW library provides an API that can be flexibly used by programs written in C, C++ and other languages. We also provide a software that can do protein and genome alignment directly. Current version of our implementation is ~50 times faster than an ordinary Smith-Waterman. It can return the Smith-Waterman score, alignment location and traceback path (cigar) of the optimal alignment accurately; and return the sub-optimal alignment score and location heuristically.
STAR/2.7.11b-GCC-13.2.0 easyconfig STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays.
STAR-Fusion/1.12.0-foss-2022b easyconfig STAR-Fusion uses the STAR aligner to identify candidate fusion transcripts supported by Illumina reads. STAR-Fusion further processes the output generated by the STAR aligner to map junction reads and spanning reads to a reference annotation set.
SUM/2.5.2
SVG/2.84-foss-2019b-Perl-5.30.0 Perl binding for SVG
SVclone/1.1.2-foss-2022b easyconfig Cluster structural variants of similar cancer cell fraction (CCF).
SWIG/4.1.1-GCCcore-13.2.0 SWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages.
SYMPHONY/5.7.2-foss-2023b easyconfig SYMPHONY is an open-source solver for mixed-integer linear programs (MILPs) written in C.
Salmon/1.10.1-GCC-12.2.0 Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data.
ScaLAPACK/2.2.0-gompi-2023b-fb The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers.
SciPy-bundle/2023.11-gfbf-2023b Bundle of Python packages for scientific software
Seaborn/0.13.2-foss-2023a Seaborn is a Python visualization library based on matplotlib. It provides a high-level interface for drawing attractive statistical graphics.
SeqAn/2.4.0-GCCcore-8.3.0 SeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data.
SeqLib/1.2.0-GCC-11.2.0 C++ interface to HTSlib, BWA-MEM and Fermi.
SeqPrep/1.3.2-GCCcore-8.3.0 Tool for stripping adaptors and/or merging paired reads with overlap into single reads.
Seqmagick/0.6.2-foss-2018b-Python-2.7.15 easyconfig We often have to convert between sequence formats and do little tasks on them, and it’s not worth writing scripts for that. Seqmagick is a kickass little utility built in the spirit of imagemagick to expose the file format conversion in Biopython in a convenient way. Instead of having a big mess of scripts, there is one that takes arguments.
Seurat/5.0.1-foss-2022b-R-4.3.1 easyconfig Seurat is an R package designed for QC, analysis, and exploration of single cell RNA-seq data.
Singularity/3.5.3 Singularity is a portable application stack packaging and runtime utility.
SlamDunk/0.4.3-foss-2021b easyconfig SlamDunk is a novel, fully automated software tool for automated, robust, scalable and reproducible SLAMseq data analysis.
Sniffles/1.0.8-foss-2018b easyconfig Sniffles is a structural variation caller using third generation sequencing (PacBio or Oxford Nanopore). It detects all types of SVs (10bp+) using evidence from split-read alignments, high-mismatch regions, and coverage analysis.
SpaceRanger/2.0.0-GCC-11.2.0 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.
SparK/2.6.2-GCCcore-10.2.0 SparK
Spark/3.1.1-foss-2020b easyconfig Spark is Hadoop MapReduce done in memory
SpectrA/1.0.1-GCC-11.2.0 Spectra stands for Sparse Eigenvalue Computation Toolkit as a Redesigned ARPACK. It is a C++ library for large scale eigenvalue problems, built on top of Eigen, an open source linear algebra library.
Sphinx/1.8.1-foss-2018b-Python-3.6.6 Sphinx is a tool that makes it easy to create intelligent and beautiful documentation. It was originally created for the new Python documentation, and it has excellent facilities for the documentation of Python projects, but C/C++ is already supported as well, and it is planned to add special support for other languages as well.
Stack/2.3.3-x86_64 Stack is a cross-platform program for developing Haskell projects. It is intended for Haskellers both new and experienced.
Stacks/2.53-foss-2019b Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography.
StringTie/2.1.4-GCC-8.3.0 easyconfig StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts
Subread/2.0.3-GCC-11.2.0 High performance read alignment, quantification and mutation discovery
SuiteSparse/5.10.1-foss-2021b-METIS-5.1.0 SuiteSparse is a collection of libraries manipulate sparse matrices.
SuperLU/5.3.0-foss-2020b easyconfig SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines.
Szip/2.1.1-GCCcore-8.3.0 Szip compression software, providing lossless compression of scientific data
TOPAZ/0.2.4-foss-2020b easyconfig Topaz is a pipeline for particle picking in cryo-electron micrographs using neural networks and positive-unlabeled learning
TRF/4.09-linux64 Tandem repeats finder: a program to analyze DNA sequences. Legacy version.
TRUST4/1.0.7-GCC-11.2.0 easyconfig Tcr Receptor Utilities for Solid Tissue (TRUST) is a computational tool to analyze TCR and BCR sequences using unselected RNA sequencing data, profiled from solid tissues, including tumors. TRUST4 performs de novo assembly on V, J, C genes including the hypervariable complementarity-determining region 3 (CDR3) and reports consensus of BCR/TCR sequences. TRUST4 then realigns the contigs to IMGT reference gene sequences to report the corresponding information. TRUST4 supports both single-end and paired-end sequencing data with any read length.
TagDust/2.33-GCCcore-10.2.0 easyconfig Raw sequences produced by next generation sequencing (NGS) machines may contain adapter, linker, barcode and fingerprint sequences. TagDust2 is a program to extract and correctly label the sequences to be mapped in downstream pipelines.
Tcl/8.6.13-GCCcore-12.3.0 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.
Telescope/1.0.3-gfbf-2022b easyconfig Single locus resolution of Transposable ELEment expression using next-generation sequencing.
TensorFlow/2.11.0-foss-2022a-CUDA-11.7.0 An open-source software library for Machine Intelligence
Theano/1.1.2-foss-2020b-PyMC Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently.
Tk/8.6.13-GCCcore-12.3.0 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.
Tkinter/3.11.5-GCCcore-13.2.0 Tkinter module, built with the Python buildsystem
TopHat/2.1.2-foss-2018b easyconfig TopHat is a fast splice junction mapper for RNA-Seq reads.
Tracer/1.7.1 easyconfig Tracer is a program for analysing the trace files generated by Bayesian MCMC runs (that is, the continuous parameter values sampled from the chain). It can be used to analyse runs of BEAST, MrBayes, LAMARC and possibly other MCMC programs.
Trim_Galore/0.6.7-GCCcore-11.2.0 easyconfig Trim Galore! is a wrapper script to automate quality and adapter trimming as well as quality control, with some added functionality to remove biased methylation positions for RRBS sequence files (for directional, non-directional (or paired-end) sequencing).
Trimmomatic/0.39-Java-11 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.
Trinity/2.12.0-foss-2020b easyconfig Trinity represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads.
UCC/1.2.0-GCCcore-13.2.0 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.
UCX/1.15.0-GCCcore-13.2.0 Unified Communication X An open-source production grade communication framework for data centric and high-performance applications
UCX-CUDA/1.14.1-GCCcore-12.3.0-CUDA-12.1.1 Unified Communication X An open-source production grade communication framework for data centric and high-performance applications

This module adds the UCX CUDA support.

UDUNITS/2.2.28-GCCcore-13.2.0 UDUNITS supports conversion of unit specifications between formatted and binary forms, arithmetic manipulation of units, and conversion of values between compatible scales of measurement.
UMI-tools/1.0.1-foss-2019b-Python-3.7.4 Tools for handling Unique Molecular Identifiers in NGS data sets
UnZip/6.0-GCCcore-12.2.0 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.
V8/3.4.0-foss-2019b-R-4.0.2 easyconfig R interface to Google’s open source JavaScript engine
VCFtools/0.1.16-GCC-11.2.0 The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files.
VEP/110.1-GCC-12.2.0 easyconfig Variant Effect Predictor (VEP) determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions. Includes EnsEMBL-XS, which provides pre-compiled replacements for frequently used routines in VEP.
VSEARCH/2.21.1-GCC-11.2.0 VSEARCH supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, rereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering, conversion and merging of paired-end reads.
VTK/8.2.0-foss-2019b-Python-3.7.4 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.
Valgrind/3.16.1-gompi-2020b Valgrind: Debugging and profiling tools
VarScan/2.4.4-Java-11 Variant calling and somatic mutation/CNV detection for next-generation sequencing data
ViennaRNA/2.5.1-foss-2021b easyconfig The Vienna RNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.
Vim/9.0.0950-GCCcore-11.2.0 easyconfig Vim is an advanced text editor that seeks to provide the power of the de-facto Unix editor ‘Vi’, with a more complete feature set.
Wayland/1.22.0-GCCcore-12.2.0 Wayland is a project to define a protocol for a compositor to talk to its clients as well as a library implementation of the protocol. The compositor can be a standalone display server running on Linux kernel modesetting and evdev input devices, an X application, or a wayland client itself. The clients can be traditional applications, X servers (rootless or fullscreen) or other display servers.
Waylandpp/1.0.0-GCCcore-11.2.0 Wayland is an object oriented display protocol, which features request and events. Requests can be seen as method calls on certain objects, whereas events can be seen as signals of an object. This makes the Wayland protocol a perfect candidate for a C++ binding.

The goal of this library is to create such a C++ binding for Wayland using the most modern C++ technology currently available, providing an easy to use C++ API to Wayland.

WebKitGTK+/2.37.1-GCC-11.2.0 WebKitGTK+ is a full-featured port of the WebKit rendering engine, suitable for projects requiring any kind of web integration, from hybrid HTML/CSS applications to full-fledged web browsers. It offers WebKit’s full functionality and is useful in a wide range of systems from desktop computers to embedded systems like phones, tablets, and televisions.
WiggleTools/1.2.4-GCC-8.3.0 easyconfig The WiggleTools package allows genomewide data files to be manipulated as numerical functions, equipped with all the standard functional analysis operators (sum, product, product by a scalar, comparators), and derived statistics (mean, median, variance, stddev, t-test, Wilcoxon’s rank sum test, etc).
X11/20231019-GCCcore-13.2.0 The X Window System (X11) is a windowing system for bitmap displays
XGBoost/0.90-foss-2019b-Python-3.7.4 XGBoost is an optimized distributed gradient boosting library designed to be highly efficient, flexible and portable.
XML-Compile/1.63-GCCcore-11.2.0 Perl module for compilation based XML processing
XML-LibXML/2.0208-GCCcore-12.2.0 easyconfig Perl binding for libxml2
XML-Parser/2.44_01-GCCcore-7.3.0-Perl-5.28.0 This is a Perl extension interface to James Clark’s XML parser, expat.
XZ/5.4.4-GCCcore-13.2.0 xz: XZ utilities
XeniumRanger/1.7.1 The Xenium In Situ software suite is a set of software applications for analyzing and visualizing in situ gene expression data produced by the Xenium Analyzer.
Xerces-C++/3.2.5-GCCcore-13.2.0 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.
XlsxWriter/3.0.2-GCCcore-11.2.0 A Python module for creating Excel XLSX files
Xvfb/21.1.6-GCCcore-12.2.0 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.
YACS/0.1.8-GCCcore-10.2.0 YACS was created as a lightweight library to define and manage system configurations, such as those commonly found in software designed for scientific experimentation. These “configurations” typically cover concepts like hyperparameters used in training a machine learning model or configurable model hyperparameters, such as the depth of a convolutional neural network.
Yasm/1.3.0-GCCcore-10.3.0 Yasm: Complete rewrite of the NASM assembler with BSD license
Z3/4.13.0-GCCcore-13.2.0 Z3 is a theorem prover from Microsoft Research with support for bitvectors, booleans, arrays, floating point numbers, strings, and other data types. This module includes z3-solver, the Python interface of Z3.
ZeroMQ/4.3.5-GCCcore-13.2.0 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.
Zip/3.0-GCCcore-11.3.0 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
agrep/2.04-GCCcore-8.3.0 easyconfig AGREP
aiohttp/3.8.5-GCCcore-12.2.0 Asynchronous HTTP client/server framework for asyncio and Python.
alleleCount/4.2.1-GCC-11.2.0 The alleleCount package primarily exists to prevent code duplication between some other projects, specifically AscatNGS and Battenberg. As of v4 the perl code wraps the C implementation of allele counting code for BAM/CRAM processing.
almosthere/2.0.2-GCCcore-10.2.0 Progress indicator C library. ATHR is a simple yet powerful progress indicator library that works on Windows, Linux, and macOS. It is non-blocking as the progress update is done via a dedicated, lightweight thread, as to not impair the performance of the calling program.
ancestry/1.0.0-GCCcore-8.3.0-Python-2.7.16 easyconfig Fast individual ancestry inference from DNA sequence data leveraging allele frequencies from multiple populations. iAdmix Using population allele frequencies for computing individual admixture estimates
angsd/0.933-GCC-8.3.0 Program for analysing NGS data.
anndata/0.10.7-foss-2023b easyconfig anndata is a Python package for handling annotated data matrices in memory and on disk, positioned between pandas and xarray
annovar/20200607-GCCcore-11.2.0-Perl-5.34.0 ANNOVAR is an efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, hg38, as well as mouse, worm, fly, yeast and many others).
ant/1.10.11-Java-11 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.
arcasHLA/0.2.0-foss-2019b-Python-3.7.4 arcasHLA performs high resolution genotyping for HLA class I and class II genes from RNA sequencing, supporting both paired and single-end samples.
argtable/2.13-GCCcore-8.3.0 Argtable is an ANSI C library for parsing GNU style command line options with a minimum of fuss.
aria2/1.35.0-GCCcore-10.2.0 easyconfig aria2 is a lightweight multi-protocol and multi-source command-line download utility.
arpack-ng/3.9.1-foss-2023b ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.
arrow-R/11.0.0.3-foss-2022b-R-4.2.2 R interface to the Apache Arrow C++ library
assimp/5.3.1-GCCcore-13.2.0 Open Asset Import Library (assimp) is a library to import and export various 3d-model-formats including scene-post-processing to generate missing render data.
at-spi2-atk/2.38.0-GCCcore-12.3.0 AT-SPI 2 toolkit bridge
at-spi2-core/2.50.0-GCCcore-13.2.0 Assistive Technology Service Provider Interface.
awscli/2.11.21-GCCcore-11.2.0 easyconfig Universal Command Line Environment for AWS
bam-readcount/1.0.1-GCC-12.2.0 easyconfig Count DNA sequence reads in BAM files
bam2fastx/1.3.0 easyconfig Conversion of PacBio BAM files into gzipped fasta and fastq files, including splitting of barcoded data
bam2wig/1.5 easyconfig Conversion of a BAM alignment to wiggle and bigwig coverage files, with flexible reporting options.
basicfiltering/1.0.7-foss-2020a-Python-3.8.2 easyconfig Basic Filtering for; Variant Allele Frequency, Variat Reads, tumor-Normal Variant Allele Frequencey Ratio.
bcl-convert/4.0.3-2el7.x86_64 The Illumina BCL Convert v4.0 is a standalone local software app that converts the Binary Base Call (BCL) files produced by Illumina sequencing systems to FASTQ files.
bcl2fastq/1.8.4 easyconfig
bcl2fastq2/2.20.0-foss-2019b easyconfig bcl2fastq Conversion Software both demultiplexes data and converts BCL files generated by Illumina sequencing systems to standard FASTQ file formats for downstream analysis.
beagle-lib/3.1.2-GCC-10.2.0 easyconfig beagle-lib is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages.
bgen/4.1.3-GCCcore-10.2.0 A BGEN file format reader. It fully supports the BGEN format specifications 1.2 and 1.3.
binutils/2.40-GCCcore-12.3.0 binutils: GNU binary utilities
bioawk/1.0-foss-2018b Bioawk is an extension to Brian Kernighan’s awk, adding the support of several common biological data formats, including optionally gzip’ed BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names.
biobambam2/2.0.95-foss-2018b easyconfig Tools for processing BAM files; bamsormadup, bamcollate2, bammarkduplicates, bammaskflags, bamrecompress, bamsort, bamtofastq
bokeh/3.2.1-foss-2022b Statistical and novel interactive HTML plots for Python
boto3/1.20.13-GCCcore-11.2.0 Boto3 is the Amazon Web Services (AWS) Software Development Kit (SDK) for Python, which allows Python developers to write software that makes use of services like Amazon S3 and Amazon EC2.
brotli/1.0.9-GCC-8.3.0 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.

bsddb3/6.2.9-GCCcore-10.2.0 bsddb3 is a nearly complete Python binding of the Oracle/Sleepycat C API for the Database Environment, Database, Cursor, Log Cursor, Sequence and Transaction objects.
build/1.0.3-foss-2023a easyconfig A simple, correct Python build frontend.
bx-python/0.8.13-foss-2021b The bx-python project is a Python library and associated set of scripts to allow for rapid implementation of genome scale analyses.
bzip2/1.0.8-GCCcore-8.3.0 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.
c-ares/1.18.1-GCCcore-11.2.0 c-ares is a C library for asynchronous DNS requests (including name resolves)
cDNA_Cupcake/12.4.0-foss-2019b-Python-3.7.4 easyconfig cDNA_Cupcake is a miscellaneous collection of Python and R scripts used for analyzing sequencing data.
cURL/8.3.0-GCCcore-13.2.0 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.
cairo/1.18.0-GCCcore-13.2.0 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
canu/1.8-foss-2018b easyconfig Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing
cas-offinder/2.4-foss-2018b easyconfig Cas-OFFinder is OpenCL based, ultrafast and versatile program that searches for potential off-target sites of CRISPR/Cas-derived RNA-guided endonucleases (RGEN).
ccache/4.6.1-GCCcore-11.2.0 Ccache (or “ccache”) is a compiler cache. It speeds up recompilation by caching previous compilations and detecting when the same compilation is being done again
cctbx-base/2020.8-fosscuda-2020b The Computational Crystallography Toolbox (cctbx) is being developed as the open source component of the Phenix project. The goal of the Phenix project is to advance automation of macromolecular structure determination. Phenix depends on the cctbx, but not vice versa. This hierarchical approach enforces a clean design as a reusable library. The cctbx is therefore also useful for small-molecule crystallography and even general scientific applications.
cellranger/3.1.0 Chromium Single Cell Software Suite is a set of software applications for analyzing and visualizing single cell 3’ RNA-seq data produced by the 10x Genomics Chromium Platform.
cellranger-atac/1.1.0-foss-2018b The Chromium Single Cell ATAC Software Suite is a complete package for analyzing and visualizing single cell chromatin accessibility data produced by the Chromium Single Cell ATAC Solution on the 10x Chromium Platform.
cffi/1.15.1-GCCcore-12.3.0 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.
cget/0.2.0-foss-2021b Cmake package retrieval. This can be used to download and install cmake packages
cirro/1.0.1-foss-2022b A Python 3.8+ library for the Cirro platform.
cisTEM/1.0.0-beta-foss-2019b easyconfig cisTEM is user-friendly software to process cryo-EM images of macromolecular complexes and obtain high-resolution 3D reconstructions from them.
clusTCR/1.0.2-foss-2021b-CUDA-11.4.1 easyconfig Python interface for rapid clustering of large sets of CDR3 sequences with unknown antigen specificity.
cnpy/master-GCC-11.2.0 cnpy lets you read and write NumPy arrays saved as npy file formats in C++.
configurable-http-proxy/4.5.5-GCCcore-12.2.0 HTTP proxy for node.js including a REST API for updating the routing table. Developed as a part of the Jupyter Hub multi-user server.
cppy/1.2.1-GCCcore-12.2.0 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.
cromwell/84 easyconfig Scientific workflow engine designed for simplicity & scalability.
cryptography/41.0.5-GCCcore-13.2.0 cryptography is a package designed to expose cryptographic primitives and recipes to Python developers.
ctffind/4.1.14-fosscuda-2020b Program for finding CTFs of electron micrographs.
cuDNN/8.9.2.26-CUDA-12.1.1 The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks.
cupcake/0.0.4-foss-2019b-Python-3.7.4 easyconfig Cupcake is a thin layer over CMake and Conan that tries to offer a better user experience in the style of Yarn or Poetry.
cutadapt/4.1-GCCcore-11.2.0 easyconfig Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.
dask/2023.7.1-foss-2022b Dask natively scales Python. Dask provides advanced parallelism for analytics, enabling performance at scale for the tools you love.
datamash/1.8-GCCcore-11.2.0 easyconfig GNU datamash performs basic numeric, textual and statistical operations on input data files
dbus-glib/0.112-GCCcore-11.2.0 D-Bus is a message bus system, a simple way for applications to talk to one another.
deepTools/3.5.4.post1-gfbf-2022b deepTools is a suite of python tools particularly developed for the efficient analysis of high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq.
deepdiff/6.7.1-GCCcore-12.3.0 DeepDiff: Deep Difference of dictionaries, iterables and almost any other object recursively.
delly/0.8.3 easyconfig DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
dill/0.3.7-GCCcore-12.2.0 dill extends python’s pickle module for serializing and de-serializing python objects to the majority of the built-in python types. Serialization is the process of converting an object to a byte stream, and the inverse of which is converting a byte stream back to on python object hierarchy.
dm-tree/0.1.8-GCCcore-12.3.0 easyconfig dm-tree provides tree, a library for working with nested data structures. In a way, tree generalizes the builtin map function which only supports flat sequences, and allows to apply a function to each “leaf” preserving the overall structure.
dms_tools2/2.6.11-foss-2020b easyconfig dms_tools2 is a software package for analyzing deep mutational scanning data. It is tailored to analyze libraries created using comprehensive codon mutagenesis of protein-coding of genes.
dorado/0.5.3-foss-2022a-CUDA-11.7.0 Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads.
dotNET-SDK/3.1.300-linux-x64 .NET is a free, cross-platform, open source developer platform for building many different types of applications.
double-conversion/3.3.0-GCCcore-13.2.0 Efficient binary-decimal and decimal-binary conversion routines for IEEE doubles.
easel/0.48-GCC-12.2.0 easyconfig Easel supports computational analysis of biological sequences using probabilistic models.
edlib/1.3.8.post1-GCC-8.3.0-Python-3.7.4 Lightweight, super fast library for sequence alignment using edit (Levenshtein) distance.
eggnog-mapper/2.1.7-foss-2021b EggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only. Common uses of eggNOG-mapper include the annotation of novel genomes, transcriptomes or even metagenomic gene catalogs.
elfutils/0.189-GCCcore-12.2.0 The elfutils project provides libraries and tools for ELF files and DWARF data.
enchant-2/2.3.3-GCCcore-11.2.0 easyconfig Enchant aims to provide a simple but comprehensive abstraction for dealing with different spell checking libraries in a consistent way. A client, such as a text editor or word processor, need not know anything about a specific spell-checker, and since all back-ends are plugins, new spell-checkers can be added without needing any change to the program using Enchant.
expat/2.5.0-GCCcore-12.3.0 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).
expect/5.45.4-GCCcore-9.3.0 easyconfig Expect is a tool for automating interactive applications such as telnet, ftp, passwd, fsck, rlogin, tip, etc. Expect really makes this stuff trivial. Expect is also useful for testing these same applications.
expecttest/0.1.5-GCCcore-12.3.0 This library implements expect tests (also known as “golden” tests). Expect tests are a method of writing tests where instead of hard-coding the expected output of a test, you run the test to get the output, and the test framework automatically populates the expected output. If the output of the test changes, you can rerun the test with the environment variable EXPECTTEST_ACCEPT=1 to automatically update the expected output.
factera/1.4.4-foss-2018b-Perl-5.28.0 (Fusion And Chromosomal Translocation Enumeration and Recovery Algorithm) is a tool for detection of genomic fusions in paired-end targeted (or genome-wide) sequencing data.
faiss/1.7.3-foss-2021b-CUDA-11.4.1 easyconfig FAISS (Facebook AI Similarity Search) is a library that allows developers to quickly search for embeddings of multimedia documents that are similar to each other.
fast5/0.6.5 easyconfig A lightweight C++ library for accessing Oxford Nanopore Technologies sequencing data.
fastNGSadmix/dda93a4-GCC-10.2.0 easyconfig Program for infering admixture proportions and doing PCA with a single NGS sample. Inferences based on reference panel.
fastai/2.7.10-foss-2021b-CUDA-11.4.1 easyconfig fastai is a deep learning library which provides practitioners with high-level components.
fastp/0.20.0-GCC-8.3.0 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.
fastq-tools/0.8.3-GCC-11.2.0 This package provides a number of small and efficient programs to perform common tasks with high throughput sequencing data in the FASTQ format. All of the programs work with typical FASTQ files as well as gzipped FASTQ files.
fermi-lite/20190320-GCCcore-11.2.0 Standalone C library for assembling Illumina short reads in small regions.
ffnvcodec/12.1.14.0 FFmpeg nvidia headers. Adds support for nvenc and nvdec. Requires Nvidia GPU and drivers to be present (picked up dynamically).
fgbio/2.0.2 easyconfig A set of tools to analyze genomic data with a focus on Next Generation Sequencing.
fhCellRanger/7.1.0 Cell Ranger is a set of analysis pipelines that process Chromium single-cell RNA-seq output to align reads, generate gene-cell matrices and perform clustering and gene expression analysis.
fhCellpose/0.6.5-fosscuda-2020b Cellpose is an anatomical segmentation algorithm written in Python 3 by Carsen Stringer and Marius Pachitariu.
fhDev/GCCcore-8.3.0 fhDev Fred Hutch Development environment is a collection of development tools that will work with LMOD modules for a given environment.
fhPerl/5.34.0-GCCcore-11.2.0 easyconfig Larry Wall’s Practical Extraction and Report Language
fhPython/3.9.6-foss-2021b Fred Hutch Python
fhR/4.3.3-foss-2023b R is a free software environment for statistical computing and graphics.
fhSeurat/4.1.1-foss-2021b-R-4.2.0 Seurat is an R package designed for QC, analysis, and exploration of single cell RNA-seq data. fhSeurat module has additional Bioconductor packages for single-cell analysis.
fhStack/2.3.3-x86_64 easyconfig Stack is a cross-platform program for developing Haskell projects. It is intended for Haskellers both new and experienced.
fig2dev/3.2.6a-foss-2019b Xfig is an interactive drawing tool which runs under X Window System.
file/5.41-GCCcore-11.2.0 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.
filezilla/3.62.2-GCC-11.2.0 easyconfig FileZilla Client is a fast and reliable cross-platform FTP, FTPS and SFTP client with lots of useful features and an intuitive graphical user interface.
flatbuffers/23.5.26-GCCcore-12.3.0 FlatBuffers: Memory Efficient Serialization Library
flatbuffers-python/23.5.26-GCCcore-12.3.0 Python Flatbuffers runtime library.
flex/2.6.4 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.
flit/3.9.0-GCCcore-12.3.0 A simple packaging tool for simple packages.
fmt/9.1.0-GCCcore-12.2.0 fmt (formerly cppformat) is an open-source formatting library.
fontconfig/2.14.2-GCCcore-13.2.0 Fontconfig is a library designed to provide system-wide font configuration, customization and application access.
foss/2023b GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.
fosscuda/2020b GCC based compiler toolchain with CUDA support, and including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.
freebayes/1.3.2-GCCcore-8.3.0 Bayesian haplotype-based polymorphism discovery and genotyping.
freeglut/3.2.1-GCCcore-11.2.0 freeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library.
freetds/1.2-GCCcore-10.2.0 FreeTDS is a set of libraries for Unix and Linux that allows your programs to natively talk to Microsoft SQL Server and Sybase databases.
freetype/2.13.2-GCCcore-13.2.0 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.
future/0.18.3-foss-2021b easyconfig python-future is the missing compatibility layer between Python 2 and Python 3.
g2lib/3.1.0-foss-2018b Library contains GRIB2 encoder/decoder and search/indexing routines.
gc/8.2.0-GCCcore-11.2.0 The Boehm-Demers-Weiser conservative garbage collector can be used as a garbage collecting replacement for C malloc or C++ new.
gcccuda/2020b GNU Compiler Collection (GCC) based compiler toolchain, along with CUDA toolkit.
gcloud/439.0.0 easyconfig Libraries and tools for interacting with Google Cloud products and services.
gdc-client/1.6.1-GCCcore-10.2.0 The gdc-client provides several convenience functions over the GDC API which provides general download/upload via HTTPS.
gettext/0.22-GCCcore-13.2.0 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
gfbf/2023b GNU Compiler Collection (GCC) based compiler toolchain, including FlexiBLAS (BLAS and LAPACK support) and (serial) FFTW.
gffread/0.11.6-GCCcore-8.3.0 GFF/GTF parsing utility providing format conversions, region filtering, FASTA sequence extraction and more.
gflags/2.2.2-GCCcore-8.3.0 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.
ggVennDiagram/3484e8-foss-2019b-R-4.0.2 easyconfig A set of functions to generate high-resolution Venn and Euler plots. Includes handling for several special cases, including two-case scaling, and extensive customization of plot shape and structure.
gh/2.14.7 gh is GitHub on the command line.
giflib/5.2.1-GCCcore-12.2.0 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.
giggle/master-foss-2020b GIGGLE is a genomics search engine that identifies and ranks the significance of shared genomic loci between query features and thousands of genome interval files.
git/2.42.0-GCCcore-13.2.0 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.
git-lfs/2.11.0 easyconfig 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
glew/2.2.0-GCCcore-11.2.0-glx 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.
glib-networking/2.72.1-GCCcore-11.2.0 Network extensions for GLib
glog/0.4.0-GCCcore-8.3.0 A C++ implementation of the Google logging module.
gmpy2/2.1.5-GCC-12.3.0 GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x
gnuplot/5.4.6-GCCcore-12.2.0 Portable interactive, function plotting utility
gompi/2023b GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support.
gompic/2020b GNU Compiler Collection (GCC) based compiler toolchain along with CUDA toolkit, including OpenMPI for MPI support with CUDA features enabled.
googletest/1.14.0-GCCcore-13.2.0 Google’s framework for writing C++ tests on a variety of platforms
gperf/3.1-GCCcore-13.2.0 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.
gperftools/2.9.1-GCCcore-10.2.0 gperftools is a collection of a high-performance multi-threaded malloc() implementation, plus some pretty nifty performance analysis tools. Includes TCMalloc, heap-checker, heap-profiler and cpu-profiler.
graphite2/1.3.14-GCCcore-13.2.0 Graphite is a “smart font” system developed specifically to handle the complexities of lesser-known languages of the world.
groff/1.23.0-GCCcore-13.2.0 Groff (GNU troff) is a typesetting system that reads plain text mixed with formatting commands and produces formatted output.
gsutil/5.10-GCCcore-11.2.0 easyconfig gsutil is a Python application that lets you access Cloud Storage from the command line.
gtest/1.8.1-GCCcore-8.3.0 Google’s framework for writing C++ tests on a variety of platforms
guidescan/1.2-foss-2018b-Python-2.7.15 easyconfig A generalized CRISPR guideRNA design tool.
gzip/1.13-GCCcore-13.2.0 gzip (GNU zip) is a popular data compression program as a replacement for compress
h5py/3.11.0-foss-2023b easyconfig 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.
hatchling/1.18.0-GCCcore-12.3.0 Extensible, standards compliant build backend used by Hatch, a modern, extensible Python project manager.
help2man/1.49.3-GCCcore-12.3.0 help2man produces simple manual pages from the ‘–help’ and ‘–version’ output of other commands.
hiredis/1.0.2-GCCcore-11.2.0 Hiredis is a minimalistic C client library for the Redis database.

It is minimalistic because it just adds minimal support for the protocol, but at the same time it uses a high level printf-alike API in order to make it much higher level than otherwise suggested by its minimal code base and the lack of explicit bindings for every Redis command.

hivmmer/0.1.2-foss-2018b-Python-3.6.6 easyconfig An alignment and variant-calling pipeline for Illumina deep sequencing of HIV-1, based on the probabilistic aligner HMMER
hunspell/1.7.1-GCCcore-11.2.0 Hunspell is a spell checker and morphological analyzer library and program designed for languageswith rich morphology and complex word compounding or character encoding.
hwloc/2.9.2-GCCcore-13.2.0 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.
hyperfreq/1.2.0-foss-2020b Hypermutation analysis software using BetaRat distribution for Bayesian analysis of the relative probability ratio (RPR) of observing mutations in two contexts. Includes Alnclst, for clustering pre-aligned nucleotide sequences.
hypothesis/6.90.0-GCCcore-13.2.0 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.
iCount/20180820-foss-2018b-Python-3.6.6 iCount: protein-RNA interaction analysis is a Python module and associated command-line interface (CLI), which provides all the commands needed to process iCLIP data on protein-RNA interactions.
iVar/1.3.2-GCC-11.2.0 easyconfig iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.
iced/0.5.6-foss-2021b easyconfig ICE normalization
igraph/0.10.10-foss-2023b igraph is a collection of network analysis tools with the emphasis on efficiency, portability and ease of use. igraph is open source and free. igraph can be programmed in R, Python and C/C++.
imageio/2.31.1-foss-2022b Imageio is a Python library that provides an easy interface to read and write a wide range of image data, including animated images, video, volumetric data, and scientific formats.
imkl/2022.2.0 Intel oneAPI Math Kernel Library
index-hopping-filter/1.0.1 index-hopping-filter is a tool that filters index hopped reads from a set of demultiplexed samples. The tool detects and removes likely index hopped reads from demultiplexed FASTQs, and in turn emits new, filtered, FASTQs with similar file and directory layout as the inputs, suitable for use with cellranger count and cellranger vdj.
interop/1.1.10-foss-2019b-Python-3.7.4 easyconfig The Illumina InterOp libraries are a set of common routines used for reading InterOp metric files produced by Illumina sequencers including NextSeq 1k/2k. These libraries are backwards compatible and capable of supporting prior releases of the software, with one exception: GA systems have been excluded.
intervene/0.6.4-foss-2019b-Python-3.7.4 easyconfig Intervene a tool for intersection and visualization of multiple genomic region sets
intltool/0.51.0-GCCcore-11.2.0 intltool is a set of tools to centralize translation of many different file formats using GNU gettext-compatible PO files.
itpp/4.3.1-foss-2019b easyconfig IT++ is a C++ library of mathematical, signal processing and communication classes and functions. Its main use is in simulation of communication systems and for performing research in the area of communications.
jax/0.4.24-foss-2023a-CUDA-12.1.1 easyconfig Composable transformations of Python+NumPy programs: differentiate, vectorize, JIT to GPU/TPU, and more
jbigkit/2.1-GCCcore-8.3.0 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.
jemalloc/5.3.0-GCCcore-12.2.0 jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and scalable concurrency support.
json-c/0.17-GCCcore-13.2.0 easyconfig 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.
jupyter-server/2.7.2-GCCcore-12.3.0 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.
jupyter-server-proxy/3.2.2-GCCcore-12.2.0 Jupyter Server Proxy lets you run arbitrary external processes (such as RStudio, Shiny Server, Syncthing, PostgreSQL, Code Server, etc) alongside your notebook server and provide authenticated web access to them
using a path like /rstudio next to others like /lab. Alongside the python package that provides the main functionality, the JupyterLab extension (@jupyterlab/server-proxy) provides buttons in the JupyterLab launcher window to get to RStudio for example.
kallisto/0.50.1-foss-2022b easyconfig kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.
kineto/0.4.0-GCC-11.3.0 A CPU+GPU Profiling library that provides access to timeline traces and hardware performance counters
king/2.2.5 easyconfig KING is a toolset that makes use of high-throughput SNP data typically seen in a genome-wide association study (GWAS) or a sequencing project. Applications of KING include family relationship inference and pedigree error checking, quality control, population substructure identification, forensics, gene mapping, etc.
leidenalg/0.10.2-foss-2023b easyconfig Implementation of the Leiden algorithm for various quality functions to be used with igraph in Python.
lftp/4.9.1-GCCcore-8.3.0 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.
libBigWig/0.4.6-GCCcore-11.2.0 A C library for handling bigWig files
libGLU/9.0.3-GCCcore-12.3.0 The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL.
libXaw3d/1.6.3-GCCcore-8.3.0 X11 client-side library
libaec/1.0.6-GCCcore-11.3.0 Libaec provides fast lossless compression of 1 up to 32 bit wide signed or unsigned integers (samples). The library achieves best results for low entropy data as often encountered in space imaging instrument data or numerical model output from weather or climate simulations. While floating point representations are not directly supported, they can also be efficiently coded by grouping exponents and mantissa.
libaio/0.3.113-GCCcore-12.2.0 Asynchronous input/output library that uses the kernels native interface.
libarchive/3.7.2-GCCcore-13.2.0 Multi-format archive and compression library
libasound/1.2.2-GCCcore-8.3.0 easyconfig The libnl suite is a collection of libraries providing APIs to netlink protocol based Linux kernel interfaces.
libcerf/2.3-GCCcore-12.2.0 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.
libcroco/0.6.13-GCC-10.2.0 easyconfig Libcroco is a standalone css2 parsing and manipulation library.
libdeflate/1.19-GCCcore-13.2.0 Heavily optimized library for DEFLATE/zlib/gzip compression and decompression.
libdrm/2.4.117-GCCcore-13.2.0 Direct Rendering Manager runtime library.
libedit/20191231-GCC-8.3.0 This BSD-style licensed command line editor library provides generic line editing, history, and tokenization functions, similar to those found in GNU Readline.
libepoxy/1.5.10-GCCcore-12.2.0 Epoxy is a library for handling OpenGL function pointer management for you
libev/4.33-GCC-11.2.0 A full-featured and high-performance (see benchmark) event loop that is loosely modelled after libevent, but without its limitations and bugs. It is used in GNU Virtual Private Ethernet, rxvt-unicode, auditd, the Deliantra MORPG Server and Client, and many other programs.
libevent/2.1.12-GCCcore-10.2.0 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.
libfabric/1.19.0-GCCcore-13.2.0 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.
libffi/3.4.4-GCCcore-12.2.0 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.
libfilezilla/0.40.0-GCC-11.2.0 easyconfig libfilezilla is a small and modern C++ library, offering some basic functionality to build high-performing, platform-independent programs.
libgcrypt/1.9.3-GCCcore-11.2.0 Libgcrypt is a general purpose cryptographic library originally based on code from GnuPG
libgd/2.3.3-GCCcore-11.2.0 GD is an open source code library for the dynamic creation of images by programmers.
libgeotiff/1.7.1-GCCcore-13.2.0 easyconfig Library for reading and writing coordinate system information from/to GeoTIFF files
libgit2/1.7.2-GCCcore-13.2.0 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.
libglvnd/1.7.0-GCCcore-13.2.0 libglvnd is a vendor-neutral dispatch layer for arbitrating OpenGL API calls between multiple vendors.
libgpg-error/1.42-GCCcore-11.2.0 Libgpg-error is a small library that defines common error values for all GnuPG components.
libgtextutils/0.7-GCCcore-8.3.0 easyconfig ligtextutils is a dependency of fastx-toolkit and is provided via the same upstream
libharu/2.3.0-GCCcore-7.3.0 easyconfig libHaru is a free, cross platform, open source library for generating PDF files.
libiconv/1.17-GCCcore-12.2.0 Libiconv converts from one character encoding to another through Unicode conversion
libidn/1.38-GCCcore-11.2.0 GNU Libidn is a fully documented implementation of the Stringprep, Punycode and IDNA specifications. Libidn’s purpose is to encode and decode internationalized domain names.
libidn2/2.3.2-GCCcore-11.2.0 Libidn2 implements the revised algorithm for internationalized domain names called IDNA2008/TR46.
libjpeg-turbo/3.0.1-GCCcore-13.2.0 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.
libleidenalg/0.11.1-foss-2022b easyconfig Implements the Leiden algorithm in C++
libmaus2/2.0.611-foss-2018b easyconfig libmaus2 is a collection of data structures and algorithms.
libmicrohttpd/0.9.73-GCCcore-10.2.0 GNU libmicrohttpd is a small C library that is supposed to make it easy to run an HTTP server as part of another application.
libogg/1.3.5-GCCcore-12.2.0 Ogg is a multimedia container format, and the native file and stream format for the Xiph.org multimedia codecs.
libopus/1.3.1-GCCcore-12.2.0 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.
libpciaccess/0.17-GCCcore-12.2.0 Generic PCI access library.
libpll/0.3.2-GCCcore-7.3.0 easyconfig libpll is a versatile high-performance software library for phylogenetic analysis.
libpng/1.6.40-GCCcore-13.2.0 libpng is the official PNG reference library
libpsl/0.21.1-GCCcore-10.2.0 C library for the Public Suffix List
libpthread-stubs/0.4-GCCcore-7.3.0 The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility.
libreadline/8.2-GCCcore-13.2.0 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.
librsvg/2.58.0-GCCcore-13.2.0 easyconfig Librsvg is a library to render SVG files using cairo.
libsigc++/2.10.2-GCCcore-8.3.0 The libsigc++ package implements a typesafe callback system for standard C++.
libsndfile/1.2.0-GCCcore-12.2.0 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.
libsodium/1.0.19-GCCcore-13.2.0 Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, password hashing and more.
libtasn1/4.18.0-GCCcore-11.2.0 Libtasn1 is the ASN.1 library used by GnuTLS, GNU Shishi and some other packages. It was written by Fabio Fiorina, and has been shipped as part of GnuTLS for some time but is now a proper GNU package.
libtirpc/1.3.4-GCCcore-13.2.0 Libtirpc is a port of Suns Transport-Independent RPC library to Linux.
libtool/2.4.7-GCCcore-12.2.0 GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries behind a consistent, portable interface.
libunistring/1.0-GCCcore-11.2.0 This library provides functions for manipulating Unicode strings and for manipulating C strings according to the Unicode standard.
libunwind/1.6.2-GCCcore-12.3.0 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
libuv/1.41.0-GCCcore-10.2.0 libuv is a multi-platform support library with a focus on asynchronous I/O.
libvorbis/1.3.7-GCCcore-11.2.0 Ogg Vorbis is a fully open, non-proprietary, patent-and-royalty-free, general-purpose compressed audio format
libwebp/1.3.2-GCCcore-13.2.0 WebP is a modern image format that provides superior lossless and lossy compression for images on the web. Using WebP, webmasters and web developers can create smaller, richer images that make the web faster.
libwpe/1.13.3-GCCcore-11.2.0 WPE is the reference WebKit port for embedded and low-consumption computer devices. It has been designed from the ground-up with performance, small footprint, accelerated content rendering, and simplicity of deployment in mind, bringing the excellence of the WebKit engine to countless platforms and target devices.
libxml++/2.40.1-GCCcore-8.3.0 libxml++ is a C++ wrapper for the libxml XML parser library.
libxml2/2.11.5-GCCcore-13.2.0 Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform).
libxslt/1.1.38-GCCcore-12.3.0 Libxslt is the XSLT C library developed for the GNOME project (but usable outside of the Gnome platform).
libyaml/0.2.5-GCCcore-12.2.0 LibYAML is a YAML parser and emitter written in C.
lightning/2.2.0.post0-foss-2023a-CUDA-12.1.1 lighting for PyTorch.
loompy/3.0.7-foss-2022b easyconfig Python implementation of the Loom file format, an efficient file format for large omics datasets
lpsolve/5.5.2.11-GCC-10.2.0 Mixed Integer Linear Programming (MILP) solver
lumpy/0.2.13-foss-2018b easyconfig A probabilistic framework for structural variant discovery.
lxml/4.9.2-GCCcore-12.3.0 The lxml XML toolkit is a Pythonic binding for the C libraries libxml2 and libxslt.
lz4/1.9.4-GCCcore-12.3.0 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.
magma/2.7.2-foss-2023a-CUDA-12.1.1 The MAGMA project aims to develop a dense linear algebra library similar to LAPACK but for heterogeneous/hybrid architectures, starting with current Multicore+GPU systems.
make/4.4.1-GCCcore-13.2.0 GNU version of make utility
makeinfo/6.8-GCCcore-11.2.0 makeinfo is part of the Texinfo project, the official documentation format of the GNU project.
manta/1.6.0 easyconfig Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. It is optimized for analysis of germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs. Manta discovers, assembles and scores large-scale SVs, medium-sized indels and large insertions within a single efficient workflow.
matplotlib/3.8.2-gfbf-2023b 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.
maturin/1.4.0-GCCcore-12.3.0-Rust-1.75.0 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.
medaka/1.2.3-foss-2019b-Python-3.7.4 easyconfig medaka is a tool to create a consensus sequence from nanopore sequencing data.
meson-python/0.15.0-GCCcore-13.2.0 Python build backend (PEP 517) for Meson projects
minimap2/2.26-GCCcore-12.2.0 easyconfig 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.
ml_dtypes/0.3.2-foss-2023a ml_dtypes is a stand-alone implementation of several NumPy dtype extensions used in machine learning libraries, including:

bfloat16: an alternative to the standard float16 format float8_*: several experimental 8-bit floating point representations including: float8_e4m3b11fnuz float8_e4m3fn float8_e4m3fnuz float8_e5m2 float8_e5m2fnuz

monocle3/0.2.2-foss-2019b-R-4.0.2 Single-cell transcriptome sequencing (sc-RNA-seq) experiments allow us to discover new cell types and help us understand how they arise in development. The Monocle 3 package provides a toolkit for analyzing single-cell gene expression experiments.
monolix/2019R2 Monolix performs non-linear mixed effects modeling (NLME) for pharmacometrics.
motif/2.3.8-GCCcore-11.2.0 Motif refers to both a graphical user interface (GUI) specification and the widget toolkit for building applications that follow that specification under the X Window System on Unix and other POSIX-compliant systems. It was the standard toolkit for the Common Desktop Environment and thus for Unix.
mpi4py/3.1.5-gompi-2023b 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.
mrcfile/1.3.0-fosscuda-2020b mrcfile is a Python implementation of the MRC2014 file format, which is used in structural biology to store image and volume data. It allows MRC files to be created and opened easily using a very simple API,
which exposes the file’s header and data as numpy arrays. The code runs in
Python 2 and 3 and is fully unit-tested. This library aims to allow users and developers to read and write standard- compliant MRC files in Python as easily as possible, and with no dependencies on any compiled libraries except numpy. You can use it interactively to inspect files, correct headers and so on, or in scripts and larger software packages to provide basic MRC file I/O functions.
nanofilt/2.5.0-foss-2018b-Python-3.6.6 easyconfig Filtering and trimming of long read sequencing data.
nanopolish/0.11.1-foss-2018b-Python-2.7.15 easyconfig Software package for signal-level analysis of Oxford Nanopore sequencing data.
ncbi-vdb/3.0.0-gompi-2021b easyconfig The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.
ncdf4/1.17-foss-2019b ncdf4: Interface to Unidata netCDF (version 4 or earlier) format data files
ncdu/1.15.1-GCCcore-8.3.0 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.
ncurses/6.4-GCCcore-12.3.0 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.
ndindex/1.7-foss-2023a ndindex is a library that allows representing and manipulating objects that can be valid indices to numpy arrays, i.e., slices, integers, ellipses, None, integer and boolean arrays, and tuples thereof.
netCDF/4.9.2-gompi-2023b 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.
nettle/3.8.1-GCCcore-12.2.0 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.
networkx/3.2.1-gfbf-2023b NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks.
nextflow/23.04.0 easyconfig Nextflow is a bioinformatics workflow manager that enables the development of portable and reproducible workflows. It supports deploying workflows on a variety of execution platforms including local, HPC schedulers, AWS Batch, Google Genomics Pipelines, and Kubernetes.
nghttp2/1.48.0-GCC-11.2.0 This is an implementation of the Hypertext Transfer Protocol version 2 in C.

The framing layer of HTTP/2 is implemented as a reusable C library. On top of that, we have implemented an HTTP/2 client, server and proxy. We have also developed load test and benchmarking tools for HTTP/2.

An HPACK encoder and decoder are available as a public API.

nghttp3/0.6.0-GCCcore-11.2.0 nghttp3 is an implementation of RFC 9114 HTTP/3 mapping over QUIC and RFC 9204 QPACK in C. It does not depend on any particular QUIC transport implementation.
ngtcp2/0.7.0-GCC-11.2.0 ‘Call it TCP/2. One More Time.’

ngtcp2 project is an effort to implement RFC9000 QUIC protocol.

nlohmann_json/3.11.3-GCCcore-13.2.0 JSON for Modern C++
nodejs/20.9.0-GCCcore-13.2.0 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.
nsync/1.26.0-GCCcore-12.2.0 nsync is a C library that exports various synchronization primitives, such as mutexes
nullarbor/2.0.20191013 easyconfig Pipeline to generate complete public health microbiology reports from sequenced isolates
numactl/2.0.16-GCCcore-13.2.0 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.
numba/0.59.1-foss-2023b easyconfig Numba is an Open Source NumPy-aware optimizing compiler for Python sponsored by Continuum Analytics, Inc. It uses the remarkable LLVM compiler infrastructure to compile Python syntax to machine code.
numexpr/2.7.1-foss-2020a-Python-3.8.2 The numexpr package evaluates multiple-operator array expressions many times faster than NumPy can. It accepts the expression as a string, analyzes it, rewrites it more efficiently, and compiles it on the fly into code for its internal virtual machine (VM). Due to its integrated just-in-time (JIT) compiler, it does not require a compiler at runtime.
oncosnpseq/2.01 easyconfig OncoSNP-SEQ is an analytical tool for characterising copy number alterations and loss-of-heterozygosity (LOH) events in cancer samples from whole genome sequencing data.
ont-guppy-cpu/2.3.7 Guppy is a production basecaller provided by Oxford Nanopore, and uses a command-line interface.
openpyxl/3.1.2-GCCcore-12.3.0 A Python library to read/write Excel 2010 xlsx/xlsm files
openslide-python/1.1.2-GCCcore-11.2.0 OpenSlide Python is a Python interface to the OpenSlide library.
p11-kit/0.24.1-GCCcore-11.2.0 Provides a way to load and enumerate PKCS#11 modules. Provides a standard configuration setup for installing PKCS#11 modules in such a way that they’re discoverable. Also solves problems with coordinating the use of PKCS#11 by different components or libraries living in the same process.
packmol/20.2.2-GCC-10.2.0 Packing Optimization for Molecular Dynamics Simulations
parallel/20210322-GCCcore-10.2.0 parallel: Build and execute shell commands in parallel
parallel-fastq-dump/0.6.7-GCCcore-11.2.0 parallel fastq-dump wrapper
parasail/2.4-foss-2018b easyconfig parasail is a SIMD C (C99) library containing implementations of the Smith-Waterman (local), Needleman-Wunsch (global), and semi-global pairwise sequence alignment algorithms.
patchelf/0.18.0-GCCcore-13.2.0 PatchELF is a small utility to modify the dynamic linker and RPATH of ELF executables.
pbcopper/1.3.0-foss-2019b easyconfig The pbcopper library provides a suite of data structures, algorithms, and utilities for C++ applications.
pblat/2.5.1-GCC-11.2.0 easyconfig Parallel blat based on Jim Kent’s blat
petsc4py/3.15.0-foss-2021a petsc4py are Python bindings for PETSc, the Portable, Extensible Toolchain for Scientific Computation.
philosopher/3.3.11 easyconfig Philosopher provides easy access to third-party tools and custom algorithms allowing users to develop proteomics analysis, from Peptide Spectrum Matching to annotated protein reports. Philosopher is also tuned for Open Search analysis, providing a modified version of the prophets for peptide validation and protein inference. To this date, Philosopher is the only proteomics toolkit that allows you to process and analyze close and open search results.
picard/2.25.1-Java-11 A set of tools (in Java) for working with next generation sequencing data in the BAM format.
pigz/2.8-GCCcore-13.2.0 easyconfig 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.
pipdeptree/0.13.2-foss-2019b-Python-3.7.4 easyconfig pipdeptree is a command line utility for displaying the installed python packages in form of a dependency tree. It works for packages installed globally on a machine as well as in a virtualenv.
pixman/0.42.2-GCCcore-12.3.0 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.
pkg-config/0.29.2-GCCcore-7.3.0 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).
pkgconf/2.0.3-GCCcore-13.2.0 pkgconf is a program which helps to configure compiler and linker flags for development libraries. It is similar to pkg-config from freedesktop.org.
pkgconfig/1.5.5-GCCcore-12.3.0-python pkgconfig is a Python module to interface with the pkg-config command line tool
plink/1.9-20200616 easyconfig Whole-genome association analysis toolset
plinkliftover/0.3.0-foss-2022b easyconfig PLINKLiftOver is a utility enabling liftOver to work on genomics files from PLINK, allowing one to update the coordinates from one genome reference version to another.
plotly.py/5.13.1-GCCcore-12.2.0 An open-source, interactive graphing library for Python
pocl/4.0-GCC-12.2.0 easyconfig PoCL is a portable open source (MIT-licensed) implementation of the OpenCL standard (1.2 with some 2.0 features supported).
poetry/1.6.1-GCCcore-13.2.0 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.
poppler/24.03.0-GCC-13.2.0 easyconfig Poppler is a PDF rendering library
popscle/0.1-beta-foss-2019b A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and auxilary tools
pplacer/1.1.alpha19-foss-2018b easyconfig Pplacer places reads on a phylogenetic tree. guppy (Grand Unified Phylogenetic Placement Yanalyzer) yanalyzes them. rppr is a helpful tool for working with reference packages.
prodigal/2.6.3-GCCcore-11.2.0 Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program developed at Oak Ridge National Laboratory and the University of Tennessee.
prokka/1.14.5-gompi-2019b Prokka is a software tool for the rapid annotation of prokaryotic genomes.
protobuf/25.3-GCCcore-13.2.0 Protocol Buffers (a.k.a., protobuf) are Google’s language-neutral, platform-neutral, extensible mechanism for serializing structured data.
protobuf-c/1.3.3-GCCcore-8.3.0 easyconfig This is protobuf-c, a C implementation of the Google Protocol Buffers data serialization format
protobuf-python/4.24.0-GCCcore-12.3.0 Python Protocol Buffers runtime library.
psipred/4.02-foss-2018b easyconfig The PSIPRED Protein Sequence Analysis Workbench aggregates several UCL structure prediction methods into one location.
pugixml/1.12.1-GCCcore-11.2.0 pugixml is a light-weight C++ XML processing library
py-cpuinfo/9.0.0-GCCcore-12.2.0 py-cpuinfo gets CPU info with pure Python.
pyBigWig/0.3.22-foss-2022b easyconfig A python extension, written in C, for quick access to bigBed files and access to and creation of bigWig files.
pyGenomeTracks/3.5-foss-2019b-Python-3.7.4 easyconfig pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable.
pySCENIC/0.12.1-foss-2022b pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.
pyaml/21.10.1-GCC-11.2.0 easyconfig PyYAML-based python module to produce pretty and readable YAML-serialized data. This module is for serialization only, see ruamel.yaml module for literate YAML parsing (keeping track of comments, spacing, line/column numbers of values, etc).
pybedtools/0.9.0-GCC-12.2.0 pybedtools wraps and extends BEDTools and offers feature-level manipulations from within Python.
pybind11/2.11.1-GCCcore-13.2.0 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.
pycisTarget/1.0.2-foss-2022b easyconfig pycistarget is a python module to perform motif enrichment analysis in sets of regions with different tools and identify high confidence TF cistromes.
pyclone/0.13.1-foss-2019b-Python-2.7.16 PyClone is a Bayesian clustering method for grouping sets of deeply sequenced somatic mutations into putative clonal clusters while estimating their cellular prevalences and accounting for allelic imbalances introduced by segmental copy-number changes and normal-cell contamination.
pyclone-vi/0.1.0-foss-2019b-Python-3.7.4 PyClone is a Bayesian clustering method for grouping sets of deeply sequenced somatic mutations into putative clonal clusters while estimating their cellular prevalences and accounting for allelic imbalances introduced by segmental copy-number changes and normal-cell contamination.
pydantic/2.5.3-GCCcore-12.3.0 Data validation and settings management using Python type hinting.
pyfaidx/0.7.0-GCCcore-11.2.0 pyfaidx: efficient pythonic random access to fasta subsequences
pyspoa/0.0.4-GCC-8.3.0-Python-3.7.4 Python bindings to spoa.
pytest/7.4.2-GCCcore-12.3.0 The pytest framework makes it easy to write small, readable tests, and can scale to support complex functional testing for applications and libraries.
pytest-benchmark/3.4.1-GCCcore-10.2.0 A pytest fixture for benchmarking code.
pytest-flakefinder/1.1.0-GCCcore-12.3.0 Runs tests multiple times to expose flakiness.
pytest-rerunfailures/12.0-GCCcore-12.3.0 pytest plugin to re-run tests to eliminate flaky failures.
pytest-shard/0.1.2-GCCcore-12.3.0 pytest plugin to support parallelism across multiple machines.

Shards tests based on a hash of their test name enabling easy parallelism across machines, suitable for a wide variety of continuous integration services. Tests are split at the finest level of granularity, individual test cases, enabling parallelism even if all of your tests are in a single file (or even single parameterized test method).

pytest-xdist/3.3.1-GCCcore-12.3.0 xdist: pytest distributed testing plugin

The pytest-xdist plugin extends pytest with some unique test execution modes:

* test run parallelization: if you have multiple CPUs or hosts you
  can use those for a combined test run. This allows to speed up
  development or to use special resources of remote machines.

* --looponfail: run your tests repeatedly in a subprocess. After
    each run pytest waits until a file in your project changes and
    then re-runs the previously failing tests. This is repeated
    until all tests pass after which again a full run is
    performed.

* Multi-Platform coverage: you can specify different Python
  interpreters or different platforms and run tests in parallel on
  all of them.

Before running tests remotely, pytest efficiently “rsyncs” your program source code to the remote place. All test results are reported back and displayed to your local terminal. You may specify different Python versions and interpreters.

python-igraph/0.11.4-foss-2023b easyconfig Python interface to the igraph high performance graph library, primarily aimed at complex network research and analysis.
python-isal/0.11.1-GCCcore-11.2.0 Faster zlib and gzip compatible compression and decompression by providing python bindings for the isa-l library.
python-parasail/1.1.16-foss-2018b-Python-3.6.6 This package contains Python bindings for parasail.
qcat/1.0.7-foss-2018b-Python-3.6.6 easyconfig Qcat is Python command-line tool for demultiplexing Oxford Nanopore reads from FASTQ files.
rMATS-turbo/4.1.2-foss-2021b easyconfig rMATS turbo is the C/Cython version of rMATS (refer to http://rnaseq-mats.sourceforge.net).
re2c/3.1-GCCcore-13.2.0 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.
redis-py/4.6.0-foss-2022b easyconfig The Python interface to the Redis key-value store.
revbayes/1.0.11-foss-2018b RevBayes provides an interactive environment for statistical computation in phylogenetics. It is primarily intended for modeling, simulation, and Bayesian inference in evolutionary biology, particularly phylogenetics.
rgdal/1.4-8-foss-2019b-R-4.0.2 Provides bindings to the ‘Geospatial’ Data Abstraction Library (‘GDAL’) (>= 1.11.4 and <= 2.5.0) and access to projection/transformation operations from the ‘PROJ.4’ library.
rpy2/3.4.5-foss-2021b rpy2 is an interface to R running embedded in a Python process.
rstudio/1.3.1093-foss-2019b-Java-11-R-4.0.2 easyconfig This RStudio Server version. RStudio is a set of integrated tools designed to help you be more productive with R.
rstudio-server/1.2.5033-foss-2019b RStudio is an integrated development environment (IDE) for the R programming language.
ruamel.yaml/0.17.21-GCCcore-11.2.0 ruamel.yaml is a YAML 1.2 loader/dumper package for Python.
samblaster/0.1.24-foss-2018b easyconfig samblaster is a fast and flexible program for marking duplicates in read-id grouped1 paired-end SAM files.
savvy/2.0.1-GCC-10.2.0 easyconfig Interface to various variant calling formats.
sbt/1.7.2-Java-1.8 sbt is a build tool for Scala, Java, and more.
scVelo/0.2.4-foss-2021a easyconfig scVelo is a scalable toolkit for estimating and analyzing RNA velocities in single cells using dynamical modeling.
scanpy/1.10.1-foss-2023b easyconfig Scanpy is a scalable toolkit for analyzing single-cell gene expression data built jointly with anndata. It includes preprocessing, visualization, clustering, trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells.
scenicplus/1.0.0-foss-2022b easyconfig SCENIC+ is a python package to build enhancer driven gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) and single-cell chromatin accessibility (scATAC-seq) data.
scikit-bio/0.5.7-foss-2021b easyconfig scikit-bio is an open-source, BSD-licensed Python 3 package providing data structures, algorithms and educational resources for bioinformatics.
scikit-build/0.17.6-GCCcore-13.2.0 Scikit-Build, or skbuild, is an improved build system generator for CPython C/C++/Fortran/Cython extensions.
scikit-image/0.21.0-foss-2022b scikit-image is a collection of algorithms for image processing.
scikit-learn/1.4.0-gfbf-2023b 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.
scikit-misc/0.1.4-foss-2021b easyconfig Miscellaneous tools for data analysis and scientific computing
scikit-optimize/0.9.0-foss-2021b easyconfig Scikit-Optimize, or skopt, is a simple and efficient library to minimize (very) expensive and noisy black-box functions.
scipy/1.4.1-foss-2019b-Python-3.7.4 SciPy is a collection of mathematical algorithms and convenience functions built on the Numpy extension for Python.
scrublet/0.2.3-foss-2021b easyconfig Python code for identifying doublets in single-cell RNA-seq data
scvi-tools/0.16.4-foss-2021a-CUDA-11.3.1 scvi-tools (single-cell variational inference tools) is a package for probabilistic modeling and analysis of single-cell omics data, built on top of PyTorch and AnnData.
scvi_tools/1.1.1-foss-2023a-CUDA-12.1.1 scvi-tools (single-cell variational inference tools) is a package for probabilistic modeling and analysis of single-cell omics data, built on top of PyTorch and AnnData.
seq2HLA/2.3-foss-2019b-Python-2.7.16 easyconfig In-silico method written in Python and R to determine HLA genotypes of a sample. seq2HLA takes standard RNA-Seq sequence reads in fastq format as input, uses a bowtie index comprising all HLA alleles and outputs the most likely HLA class I and class II genotypes (in 4 digit resolution), a p-value for each call, and the expression of each class.
seqtk/1.3-GCC-10.2.0 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.
seqtools/4.44.1-foss-2019b easyconfig The SeqTools package contains three tools for visualising sequence alignments: Blixem, Dotter and Belvu.
sequenza-utils/3.0.0-GCCcore-8.3.0-Python-3.7.4 Sequenza is a software for the estimation and quantification of purity/ploidy and copy number alteration in sequencing experiments of tumor samples. Sequenza-utils provide command lines programs to transform common NGS file format
setuptools/64.0.3-GCCcore-12.2.0 Easily download, build, install, upgrade, and uninstall Python packages
setuptools-rust/1.8.0-GCCcore-13.2.0 setuptools-rust is a plugin for setuptools to build Rust Python extensions implemented with PyO3 or rust-cpython.
shrinkwrap/1.1.0-GCCcore-10.2.0 A std::streambuf wrapper for compression formats.
slepc4py/3.15.1-foss-2021a Python bindings for SLEPc, the Scalable Library for Eigenvalue Problem Computations.
smallgenomeutilities/0.2.1-foss-2018b-Python-3.6.6 easyconfig The smallgenomeutilities are a collection of scripts that is useful for dealing and manipulating NGS data of small viral genomes. They are written in Python 3 with a small number of dependencies.
snakemake/7.18.2-foss-2021b The Snakemake workflow management system is a tool to create reproducible and scalable data analyses.
snappy/1.1.10-GCCcore-13.2.0 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.
snippy/4.6.0-foss-2019b-Perl-5.30.0 Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. It will find both substitutions (snps) and insertions/deletions (indels). Rapid haploid variant calling and core genome alignment.
spams/2.6.5.4-foss-2021b easyconfig SPAMS (SPArse Modeling Software) is an optimization toolbox for solving various sparse estimation problems.
span-lite/0.10.3-GCC-11.2.0 span lite is a single-file header-only library to provide a bounds-safe view for sequences of objects. The library provides a C++20-like span for use with C++98 and later.
spdlog/1.10.0-GCCcore-11.2.0 easyconfig Very fast, header-only/compiled, C++ logging library.
spektral/1.1.0-foss-2021b-CUDA-11.4.1 easyconfig Spektral is a Python library for graph deep learning. The main goal of this project is to provide a simple but flexible framework for creating graph neural networks (GNNs).
spglib-python/1.16.0-foss-2020b Spglib for Python. Spglib is a library for finding and handling crystal symmetries written in C.
splitpipe/1.2.1-foss-2023b splitpipe tool from Parse Biosciences. The pipeline takes FASTQ files and delivers processed data in the form of a cell-gene count matrix, which serves as the input for various open sources tools such as scanpy and seuratProcess sequencing results with our pipeline.

A Parse Bioscience login ID is required to download

spoa/4.0.0-GCC-8.3.0 Spoa (SIMD POA) is a c++ implementation of the partial order alignment (POA) algorithm which is used to generate consensus sequences
stack/2.3.1
starcode/1.4-GCC-11.2.0 Starcode is a DNA sequence clustering software. Starcode clustering is based on all pairs search within a specified Levenshtein distance (allowing insertions and deletions), followed by a clustering algorithm: Message Passing, Spheres or Connected Components.
stardist/0.8.3-foss-2021b-CUDA-11.4.1 easyconfig Object Detection with Star-convex Shapes.
statsmodels/0.14.1-gfbf-2023b Statsmodels is a Python module that allows users to explore data, estimate statistical models, and perform statistical tests.
strelka/2.9.9-foss-2018b Strelka2 is a fast and accurate small variant caller optimized for analysis of germline variation in small cohorts and somatic variation in tumor/normal sample pairs.
svaba/1.1.0-GCC-10.2.0 SvABA
sympy/1.12-gfbf-2022b 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.
sysbench/1.0.20-GCC-12.2.0 sysbench is a scriptable multi-threaded benchmark tool based on LuaJIT. It is most frequently used for database benchmarks, but can also be used to create arbitrarily complex workloads that do not involve a database server.
tabix/0.2.6-GCCcore-7.3.0 easyconfig Generic indexer for TAB-delimited genome position files
tbb/2021.10.0-GCCcore-12.2.0 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.
tbl2asn/20220427-linux64 Tbl2asn is a command-line program that automates the creation of sequence records for submission to GenBank
tcsh/6.20.00-GCCcore-7.3.0 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.
tensorboard/2.8.0-foss-2021a TensorBoard is a suite of web applications for inspecting and understanding your TensorFlow runs and graphs.
tensorboardX/2.6.2.2-foss-2023a Tensorboard for PyTorch.
terminator/1.91-GCCcore-8.3.0-Python-2.7.16 Multiple terminals in one window. The goal of this project is to produce a useful tool for arranging terminals.
terraphast/master-foss-2018b easyconfig libpll is a versatile high-performance software library for phylogenetic analysis.
tesseract/5.3.0-GCCcore-11.2.0 easyconfig Tesseract is an optical character recognition engine
texinfo/6.7-GCCcore-8.3.0 Texinfo is the official documentation format of the GNU project.
texlive/20210324-GCC-11.2.0 TeX is a typesetting language. Instead of visually formatting your text, you enter your manuscript text intertwined with TeX commands in a plain text file. You then run TeX to produce formatted output, such as a PDF file. Thus, in contrast to standard word processors, your document is a separate file that does not pretend to be a representation of the final typeset output, and so can be easily edited and manipulated.
thrift/0.13.0-foss-2018b Thrift is a lightweight, language-independent software stack for point-to-point RPC implementation. Thrift provides clean abstractions and implementations for data transport, data serialization, and application level processing.
tmux/3.2a-GCCcore-11.2.0 tmux is a terminal multiplexer: it enables a number of terminals to be created, accessed, and controlled from a single screen. tmux may be detached from a screen and continue running in the background, then later reattached.
torchvision/0.13.1-foss-2022a-CUDA-11.7.0 easyconfig Datasets, Transforms and Models specific to Computer Vision
tornado/6.3.2-GCCcore-12.3.0 Tornado is a Python web framework and asynchronous networking library.
tqdm/4.66.2-GCCcore-13.2.0 easyconfig A fast, extensible progress bar for Python and CLI
typing-extensions/4.9.0-GCCcore-12.3.0 Typing Extensions – Backported and Experimental Type Hints for Python
umap-learn/0.5.6-foss-2023b easyconfig Uniform Manifold Approximation and Projection (UMAP) is a dimension reduction technique that can be used for visualisation similarly to t-SNE, but also for general non-linear dimension reduction.
unixODBC/2.3.12-GCC-13.2.0 easyconfig unixODBC provides a uniform interface between application and database driver
utf8proc/2.8.0-GCCcore-12.2.0 utf8proc is a small, clean C library that provides Unicode normalization, case-folding, and other operations for data in the UTF-8 encoding.
util-linux/2.39-GCCcore-13.2.0 Set of Linux utilities
vcf2maf/1.6.19 vcflib provides methods to manipulate and interpret sequence variation as it can be described by VCF. The Variant Call Format (VCF) is a flat-file, tab-delimited textual format intended to concisely describe reference-indexed genetic variations between individuals.
vcflib/1.0.1-GCCcore-8.3.0 easyconfig vcflib provides methods to manipulate and interpret sequence variation as it can be described by VCF. The Variant Call Format (VCF) is a flat-file, tab-delimited textual format intended to concisely describe reference-indexed genetic variations between individuals.
velocyto.R/0.6-foss-2019b-R-4.0.2 easyconfig velocyto (velox + κύτος, quick cell) is a package for the analysis of expression dynamics in single cell RNA seq data. In particular, it enables estimations of RNA velocities of single cells by distinguishing unspliced and spliced mRNAs in standard single-cell RNA sequencing protocols (see pre-print below for more information).
virtualenv/20.24.6-GCCcore-13.2.0 A tool for creating isolated virtual python environments.
vt/0.57721-foss-2018b A tool set for short variant discovery in genetic sequence data.
wget/1.21.4-GCCcore-12.2.0 GNU Wget is a free software package for retrieving files using HTTP, HTTPS and FTP, the most widely-used Internet protocols. It is a non-interactive commandline tool, so it may easily be called from scripts, cron jobs, terminals without X-Windows support, etc.
wheel/0.31.1-foss-2018b-Python-3.6.6 A built-package format for Python.
wot/1.0.8-foss-2018b-Python-3.6.6 easyconfig Single-cell RNA sequencing is a powerful technology that can reveal a lot about what happens in a group of cells as they develop. But because the technology destroys a cell, it can only provide snapshots of the cells in a group at one point in time. To really understand how cells develop over time, snapshots aren’t good enough: scientists want to fill in the gaps between snapshots and string everything together into a movie.
wpebackend-fdo/1.13.1-GCCcore-11.2.0 WPE WebKit allows embedders to create simple and performant systems based on Web platform technologies. It is a WebKit port designed with flexibility and hardware acceleration in mind, leveraging common 3D graphics APIs for best performance.
wxPython/4.2.0-foss-2021b easyconfig Wraps the wxWidgets C++ toolkit and provides access to the user interface portions of the wxWidgets API, enabling Python applications to have a native GUI on Windows, Macs or Unix systems, with a native look and feel and requiring very little (if any) platform specific code.
wxWidgets/3.2.2.1-GCCcore-12.2.0 wxWidgets is a C++ library that lets developers create applications for Windows, Mac OS X, Linux and other platforms with a single code base. It has popular language bindings for Python, Perl, Ruby and many other languages, and unlike other cross-platform toolkits, wxWidgets gives applications a truly native look and feel because it uses the platform’s native API rather than emulating the GUI.
x264/20231019-GCCcore-13.2.0 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.
x265/3.5-GCCcore-11.2.0 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.
xbitmaps/1.1.2 provides bitmaps for x
xfig/3.2.6a-foss-2019b Xfig is an interactive drawing tool which runs under X Window System.
xmlto/0.0.28-GCC-11.2.0 easyconfig A tool for converting XML files to various formats
xorg-macros/1.20.0-GCCcore-12.3.0 X.org macros utilities.
xprop/1.2.5-GCCcore-10.2.0 The xprop utility is for displaying window and font properties in an X server. One window or font is selected using the command line arguments or possibly in the case of a window, by clicking on the desired window. A list of properties is then given, possibly with formatting information.
xproto/7.0.31-GCCcore-7.3.0 X protocol and ancillary headers
xxd/9.1.0307-GCCcore-13.2.0 easyconfig xxd is part of the VIM package and this will only install xxd, not vim! xxd converts to/from hexdumps of binary files.
yaml-cpp/0.7.0-GCCcore-12.2.0 yaml-cpp is a YAML parser and emitter in C++ matching the YAML 1.2 spec
zlib/1.2.13-GCCcore-13.2.0 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.
zstd/1.5.5-GCCcore-13.2.0 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.