All Modules 24.04

AGAT/1.4.0-GCC-12.3.0 AGAT: Another GTF/GFF Analysis Toolkit. Suite of tools to handle gene annotations in any GTF/GFF format.
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.
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.
AlphaFold/2.3.2-foss-2023a-CUDA-12.1.1 AlphaFold can predict protein structures with atomic accuracy even where no similar structure is known
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.
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/16.1.0-gfbf-2023b Apache Arrow (incl. PyArrow Python bindings), a cross-language development platform for in-memory data.
Autoconf/2.72-GCCcore-13.3.0 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/20231222-GCCcore-13.3.0 This bundle collect the standard GNU build tools: Autoconf, Automake and libtool
BAli-Phy/4.0-beta8-gfbf-2022b easyconfig BAli-Phy estimates multiple sequence alignments and evolutionary trees from DNA, amino acid, or codon sequences.
BCFtools/1.19-GCC-13.2.0 easyconfig Samtools is a suite of programs for interacting with high-throughput sequencing data. BCFtools
BEDTools/2.31.0-GCC-12.3.0 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.
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.
BLIS/1.0-GCC-13.3.0 BLIS is a portable software framework for instantiating high-performance BLAS-like dense linear algebra libraries.
BWA/0.7.17-GCCcore-12.2.0 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-12.3.0 BamTools provides both a programmer’s API and an end-user’s toolkit for handling BAM files.
Bazel/6.3.1-GCCcore-12.3.0 Bazel is a build tool that builds code quickly and reliably. It is used to build the majority of Google’s software.
Beast/10.5.0-beta3-GCC-12.3.0-beagle-lib-4.0.1-CUDA-12.1.1 BEAST is a cross-platform program for Bayesian analysis of molecular sequences using MCMC. 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.
Beast2/2.7.7-GCC-12.3.0-beagle-lib-4.0.1-CUDA-12.1.1 easyconfig 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-12.2.0 easyconfig Read files using HTSlib including BAM/CRAM, Tabix and BCF database files
BioPerl/1.7.8-GCCcore-12.2.0 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/1.84-foss-2023b easyconfig 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.
Bismark/0.24.1-GCC-12.2.0 easyconfig A tool to map bisulfite converted sequence reads and determine cytosine methylation states
Bison/3.8.2 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
Blosc2/2.8.0-GCCcore-12.3.0 Blosc, an extremely fast, multi-threaded, meta-compressor library
Boost/1.85.0-GCC-13.3.0 Boost provides free peer-reviewed portable C++ source libraries.
Boost.Python/1.85.0-GCC-13.3.0 Boost.Python is a C++ library which enables seamless interoperability between C++ and the Python programming language.
Boost.Python-NumPy/1.85.0-gfbf-2024a Boost.Python is a C++ library which enables seamless interoperability between C++ and the Python programming language.
Bowtie2/2.5.4-GCC-13.2.0 easyconfig 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.
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/1.4.4-foss-2023b-Python-3.11.5 easyconfig A python package that allows to count antibody TAGS from a CITE-seq and/or cell hashing experiment.
CMake/3.29.3-GCCcore-13.3.0 CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.
CRISPResso2/2.3.1-foss-2023b easyconfig CRISPResso2 is a software pipeline designed to enable rapid and intuitive interpretation of genome editing experiments.
CUDA/12.6.2 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.
CUDA-Python/12.1.0-gfbf-2023a-CUDA-12.1.1 Python bindings for CUDA
CUTLASS/3.4.0-foss-2023a-CUDA-12.1.1 easyconfig CUTLASS is a collection of CUDA C++ template abstractions for implementing high-performance matrix-matrix multiplication (GEMM) and related computations at all levels and scales within CUDA. It incorporates strategies for hierarchical decomposition and data movement similar to those used to implement cuBLAS and cuDNN. CUTLASS decomposes these “moving parts” into reusable, modular software components abstracted by C++ template classes. Primitives for different levels of a conceptual parallelization hierarchy can be specialized and tuned via custom tiling sizes, data types, and other algorithmic policy. The resulting flexibility simplifies their use as building blocks within custom kernels and applications.
Cassiopeia/2.0.0-foss-2023a A Package for Cas9-Enabled Single Cell Lineage Tracing Tree Reconstruction.
Catch2/3.7.1-GCCcore-13.3.0 A modern, C++-native, header-only, test framework for unit-tests, TDD and BDD
Cbc/2.10.11-foss-2023a Cbc (Coin-or branch and cut) is an open-source mixed integer linear programming solver written in C++. It can be used as a callable library or using a stand-alone executable.
CellBender/0.3.0-foss-2023a CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
CellRank/2.0.2-foss-2023a easyconfig 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.
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.
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.
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.
Cython/3.0.10-GCCcore-13.3.0 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-12.2.0 Berkeley DB enables the development of custom data management solutions, without the overhead traditionally associated with such custom projects.
DB_File/1.859-GCCcore-12.3.0 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.
DeltaLake/0.15.1-gfbf-2023a Native Delta Lake Python binding based on delta-rs with Pandas integration. The Delta Lake project aims to unlock the power of the Deltalake for as many users and projects as possible by providing native low-level APIs aimed at developers and integrators, as well as a high-level operations API that lets you query, inspect, and operate your Delta Lake with ease.
Deprecated/1.2.14-foss-2023a If you need to mark a function or a method as deprecated, you can use the @deprecated decorator.
Doxygen/1.11.0-GCCcore-13.3.0 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.
ETE/3.1.3-foss-2023a A Python framework for the analysis and visualization of trees
EasyBuild/4.9.4 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-13.3.0 Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.
FASTA/36.3.8i-GCC-12.2.0 The FASTA programs find regions of local or global (new) similarity between protein or DNA sequences, either by searching Protein or DNA databases, or by identifying local duplications within a sequence.
FFTW/3.3.10-GCC-13.3.0 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-2024a 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-13.2.0 A complete, cross-platform solution to record, convert and stream audio and video.
FLAC/1.4.2-GCCcore-12.3.0 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.
FastQC/0.12.1-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.
Fiona/1.9.5-foss-2023a Fiona is designed to be simple and dependable. It focuses on reading and writing data in standard Python IO style and relies upon familiar Python types and protocols such as files, dictionaries, mappings, and iterators instead of classes specific to OGR. Fiona can read and write real-world data using multi-layered GIS formats and zipped virtual file systems and integrates readily with other Python GIS packages such as pyproj, Rtree, and Shapely.
Flax/0.8.4-gfbf-2023a-CUDA-12.1.1 Flax is a high-performance neural network library and ecosystem for JAX that is designed for flexibility: Try new forms of training by forking an example and by modifying the training loop, not by adding features to a framework.
FlexiBLAS/3.4.4-GCC-13.3.0 FlexiBLAS is a wrapper library that enables the exchange of the BLAS and LAPACK implementation used by a program without recompiling or relinking it.
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/13.3.0 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/13.3.0 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,…).
GDAL/3.9.0-foss-2023b 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.
GDRCopy/2.4.1-GCCcore-13.3.0 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
GLPK/5.0-GCCcore-13.2.0 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/2.80.4-GCCcore-13.3.0 GLib is one of the base libraries of the GTK+ project
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.
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.
GSL/2.7-GCC-12.3.0 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.
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-13.2.0 easyconfig 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.
Gdk-Pixbuf/2.42.10-GCCcore-12.3.0 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.
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.
GitPython/3.1.40-GCCcore-12.3.0 GitPython is a python library used to interact with Git repositories
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.
HDF/4.2.16-2-GCCcore-12.3.0 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-2023a The HH-suite is an open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs).
HMMER/3.4-gompi-2023a 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.
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
HarfBuzz/8.2.2-GCCcore-13.2.0 HarfBuzz is an OpenType text shaping engine.
ICU/75.1-GCCcore-13.3.0 ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization support for software applications.
IPython/8.14.0-GCCcore-12.3.0 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.
ISA-L/2.31.0-GCCcore-13.2.0 Intelligent Storage Acceleration Library
IgBLAST/1.22.0-x64-linux easyconfig IgBLAST faclilitates the analysis of immunoglobulin and T cell receptor variable domain sequences.
ImageMagick/7.1.1-32-GCCcore-13.2.0 easyconfig 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
InChI/1.07.1-GCC-13.3.0 The IUPAC International Chemical Identifier (InChI TM) is a non-proprietary identifier for chemical substances that can be used in printed and electronic data sources thus enabling easier linking of diverse data compilations.
Infernal/1.1.4-foss-2022b Infernal (“INFERence of RNA ALignment”) is for searching DNA sequence databases for RNA structure and sequence similarities.
JAGS/4.3.2-foss-2023b easyconfig JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation
JasPer/4.0.0-GCCcore-12.3.0 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.
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-12.3.0 A C library that implements a dynamic array.
Jupyter-bundle/20230823-GCCcore-12.3.0 This bundle collects a range of Jupyter interfaces (Lab, Notebook and nbclassic), extensions (Jupyter Server Proxy, Jupyter Resource Monitor, Jupyter Lmod) and the JupyterHub.
JupyterHub/4.0.2-GCCcore-12.3.0 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.
JupyterNotebook/7.0.2-GCCcore-12.3.0 The Jupyter Notebook is the original web application for creating and sharing computational documents. It offers a simple, streamlined, document-centric experience.
Kalign/3.4.0-GCCcore-12.3.0 Kalign is a fast multiple sequence alignment program for biological sequences.
Kent_tools/468-GCC-12.3.0 easyconfig Kent utilities: collection of tools used by the UCSC genome browser.
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.
LAME/3.100-GCCcore-12.3.0 LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL.
LDC/1.39.0-GCCcore-13.2.0 easyconfig The LLVM-based D Compiler
LERC/4.0.0-GCCcore-12.3.0 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).
LLVM/16.0.6-GCCcore-13.2.0 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-12.3.0 Portable lossless data compression library
Levenshtein/0.25.1-GCCcore-13.2.0 easyconfig Python extension for computing string edit distances and similarities.
LibTIFF/4.6.0-GCCcore-13.2.0 tiff: Library and tools for reading and writing TIFF data files
LittleCMS/2.16-GCCcore-13.3.0 Little CMS intends to be an OPEN SOURCE small-footprint color management engine, with special focus on accuracy and performance.
Lua/5.4.6-GCCcore-12.3.0 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 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
[MBROLA/3.3-GCCcore-12.3.0-voices-20200330]([‘https://github.com/numediart/MBROLA’, ‘https://github.com/numediart/MBROLA-voices’]) MBROLA is a speech synthesizer based on the concatenation of diphones. It takes a list of phonemes as input, together with prosodic information (duration of phonemes and a piecewise linear description of pitch), and produces speech samples on 16 bits (linear), at the sampling frequency of the diphone database.

MBROLA voices project provides list of MBROLA speech synthesizer voices. It is intended to provide easier collaboration and automatic updates for individual users and packagers.

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.
MPC/1.3.1-GCCcore-12.3.0 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/5.6.1-foss-2022b-metis A parallel sparse direct solver
MUMmer/4.0.0rc1-GCCcore-12.3.0 MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. AMOS makes use of it.
MUSCLE/5.1.0-GCCcore-12.3.0 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.
Mako/1.2.4-GCCcore-12.2.0 A super-fast templating language that borrows the best ideas from the existing templating languages
MariaDB/11.6.0-GCC-12.3.0 MariaDB is an enhanced, drop-in replacement for MySQL. Included engines: myISAM, Aria, InnoDB, RocksDB, TokuDB, OQGraph, Mroonga.
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/1.4.0-GCCcore-13.3.0 Meson is a cross-platform build system designed to be both as fast and as user friendly as possible.
MultiQC/1.21-foss-2023a easyconfig 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.

NASM/2.16.03-GCCcore-13.3.0 NASM: General-purpose x86 assembler
NCCL/2.23.4-GCCcore-13.3.0-CUDA-12.6.2 The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective communication primitives that are performance optimized for NVIDIA GPUs.
NLTK/3.8.1-foss-2023a NLTK is a leading platform for building Python programs to work with human language data.
NLopt/2.7.1-GCCcore-12.3.0 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.
Ninja/1.12.1-GCCcore-13.3.0 Ninja is a small build system with a focus on speed.
OpenBLAS/0.3.27-GCC-13.3.0 OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.
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/2.5.2-GCCcore-13.3.0 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-2023a-CUDA-12.1.1 easyconfig OpenMM is a toolkit for molecular simulation.
OpenMPI/5.0.3-GCC-13.3.0 The Open MPI Project is an open source MPI-3 implementation.
OpenPGM/5.2.122-GCCcore-13.2.0 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/3 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.
Optax/0.2.2-gfbf-2023a-CUDA-12.1.1 Optax is a gradient processing and optimization library for JAX.
Osi/0.108.9-GCC-12.3.0 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.
PCRE/8.45-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.
PCRE2/10.43-GCCcore-13.3.0 The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5.
PLY/3.11-GCCcore-12.3.0 PLY is yet another implementation of lex and yacc for Python.
PMIx/5.0.2-GCCcore-13.3.0 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
PRRTE/3.0.5-GCCcore-13.3.0 PRRTE is the PMIx Reference RunTime Environment
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.
Perl/5.38.2-GCCcore-13.3.0 Larry Wall’s Practical Extraction and Report Language

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

Perl-bundle-CPAN/5.38.2-GCCcore-13.3.0 A set of common packages from CPAN
Pillow/11.0.0-GCCcore-13.3.0 Pillow is the ‘friendly PIL fork’ by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors.
Pillow-SIMD/10.4.0-GCCcore-13.3.0 Pillow is the ‘friendly PIL fork’ by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors.
Porechop/0.2.4-GCCcore-12.3.0 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-12.3.0 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.
PuLP/2.8.0-foss-2023a PuLP is an LP modeler written in Python. PuLP can generate MPS or LP files and call GLPK, COIN-OR CLP/CBC, CPLEX, GUROBI, MOSEK, XPRESS, CHOCO, MIPCL, SCIP to solve linear problems.
PyQt-builder/1.15.4-GCCcore-12.3.0 PyQt-builder is the PEP 517 compliant build system for PyQt and projects that
extend PyQt. It extends the SIP build system and uses Qt’s qmake to perform the actual compilation and installation of extension modules.
PyQt5/5.15.10-GCCcore-12.3.0 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.
PyTables/3.8.0-foss-2023a 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 Tensors and Dynamic neural networks in Python with strong GPU acceleration. PyTorch is a deep learning framework that puts Python first.
PyTorch-Lightning/2.2.1-foss-2023a PyTorch Lightning is the lightweight PyTorch wrapper for ML researchers.
PyTorch-bundle/2.1.2-foss-2023a-CUDA-12.1.1 easyconfig PyTorch with compatible versions of official Torch extensions.
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-12.3.0 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.
Pygments/2.18.0-GCCcore-12.3.0 Generic syntax highlighter suitable for use in code hosting, forums, wikis or other applications that need to prettify source code.
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/3.12.3-GCCcore-13.3.0 Python is a programming language that lets you work more quickly and integrate your systems more effectively.
Python-bundle-PyPI/2024.06-GCCcore-13.3.0 Bundle of Python packages from PyPI
Qhull/2020.2-GCCcore-13.2.0 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.
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.
QtPy/2.4.1-GCCcore-12.3.0 QtPy is a small abstraction layer that lets you write applications using a single API call to either PyQt or PySide. It provides support for PyQt5, PyQt4, PySide2 and PySide.
Qtconsole/5.5.1-GCCcore-12.3.0 A rich Qt-based console for working with Jupyter kernels, supporting rich media output, session export, and more. The Qtconsole is a very lightweight application that largely feels like a
terminal, but provides a number of enhancements only possible in a GUI, such as inline figures, proper multiline editing with syntax highlighting, graphical
calltips, and more.
R/4.4.1-gfbf-2023b R is a free software environment for statistical computing and graphics.
R-Tidyverse/4.4.0-gfbf-2023b easyconfig R is a free software environment for statistical computing and graphics.
R-bundle-Bioconductor/3.18-foss-2023a-R-4.3.2 easyconfig Bioconductor provides tools for the analysis and coprehension of high-throughput genomic data.
R-bundle-CRAN/2023.12-foss-2023a easyconfig Bundle of R packages from CRAN
RAPIDS/24.4-foss-2023a-CUDA-12.1.1 RAPIDS provides unmatched speed with familiar APIs that match the most popular PyData libraries. Built on state-of-the-art foundations like NVIDIA CUDA and Apache Arrow, it unlocks the speed of GPUs with code you already know.
RDFlib/7.0.0-GCCcore-12.3.0 RDFLib is a Python library for working with RDF, a simple yet powerful language for representing information.
RDKit/2024.03.5-foss-2024a RDKit is a collection of cheminformatics and machine-learning software written in C++ and Python.
RE2/2024-03-01-GCCcore-13.2.0 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.
RStudio-Server/2024.04.1+748-foss-2023b-Java-11-R-4.4.0 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”

RapidJSON/1.1.0-20230928-GCCcore-12.3.0 A fast JSON parser/generator for C++ with both SAX/DOM style API
Ruby/3.3.0-GCCcore-12.3.0 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/1.78.0-GCCcore-13.3.0 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/7.0.3-gompi-2023a Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.
SDL2/2.28.5-GCCcore-13.2.0 SDL: Simple DirectMedia Layer, a cross-platform multimedia library
SIP/6.8.1-GCCcore-12.3.0 SIP is a tool that makes it very easy to create Python bindings for C and C++ libraries.
SOCI/4.0.3-GCC-13.2.0-Boost-1.83.0 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++.
SQLAlchemy/2.0.25-GCCcore-12.3.0 SQLAlchemy is the Python SQL toolkit and Object Relational Mapper that gives application developers the full power and flexibility of SQL. SQLAlchemy provides a full suite of well known enterprise-level persistence patterns, designed for efficient and high-performing database access, adapted into a simple and Pythonic domain language.
SQLite/3.45.3-GCCcore-13.3.0 SQLite: SQL Database Engine in a C Library
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.
SVclone/1.1.2-foss-2022b easyconfig Cluster structural variants of similar cancer cell fraction (CCF).
SWIG/4.1.1-GCCcore-12.3.0 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.
Sambamba/1.0.1-GCC-13.2.0 easyconfig Sambamba is a high performance modern robust and fast tool (and library), written in the D programming language, for working with SAM and BAM files. Current functionality is an important subset of samtools functionality, including view, index, sort, markdup, and depth.
ScaLAPACK/2.2.0-gompi-2022b-fb The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers.
Scalene/1.5.26-GCCcore-12.3.0 Scalene is a high-performance CPU, GPU and memory profiler for Python that does a number of things that other Python profilers do not and cannot do. It runs orders of magnitude faster than other profilers while delivering far more detailed information.
SciPy-bundle/2024.05-gfbf-2024a Bundle of Python packages for scientific software
Seaborn/0.13.2-gfbf-2023a Seaborn is a Python visualization library based on matplotlib. It provides a high-level interface for drawing attractive statistical graphics.
SentencePiece/0.2.0-GCC-12.3.0 Unsupervised text tokenizer for Neural Network-based text generation.
Shapely/2.0.1-gfbf-2023a Shapely is a BSD-licensed Python package for manipulation and analysis of planar geometric objects. It is based on the widely deployed GEOS (the engine of PostGIS) and JTS (from which GEOS is ported) libraries.
SoX/14.4.2-GCCcore-12.3.0 Sound eXchange, the Swiss Army knife of audio manipulation
Szip/2.1.1-GCCcore-12.3.0 Szip compression software, providing lossless compression of scientific data
Tcl/8.6.14-GCCcore-13.3.0 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/2.15.1-foss-2023a-CUDA-12.1.1 An open-source software library for Machine Intelligence
Tk/8.6.14-GCCcore-13.3.0 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/3.12.3-GCCcore-13.3.0 Tkinter module, built with the Python buildsystem
UCC/1.3.0-GCCcore-13.3.0 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/1.16.0-GCCcore-13.3.0 Unified Communication X An open-source production grade communication framework for data centric and high-performance applications
UCX-CUDA/1.16.0-GCCcore-13.3.0-CUDA-12.6.2 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/1.1.4-foss-2023b easyconfig Tools for handling Unique Molecular Identifiers in NGS data sets
UnZip/6.0-GCCcore-13.3.0 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.
Wayland/1.22.0-GCCcore-12.3.0 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.
X11/20240607-GCCcore-13.3.0 The X Window System (X11) is a windowing system for bitmap displays
XML-LibXML/2.0209-GCCcore-12.3.0 Perl binding for libxml2
XZ/5.4.5-GCCcore-13.3.0 xz: XZ utilities
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.
Xvfb/21.1.8-GCCcore-12.3.0 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.
Yasm/1.3.0-GCCcore-12.3.0 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-13.2.0 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
absl-py/2.1.0-GCCcore-12.3.0 absl-py is a collection of Python library code for building Python applications. The code is collected from Google’s own Python code base, and has been extensively tested and used in production.
aiohttp/3.8.5-GCCcore-12.3.0 Asynchronous HTTP client/server framework for asyncio and Python.
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
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.
arpack-ng/3.9.0-foss-2023a ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.
arrow-R/14.0.1-foss-2023a-R-4.3.2 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/2.17.54-GCCcore-13.2.0 Universal Command Line Environment for AWS
bam-readcount/1.0.1-GCC-12.2.0 easyconfig Count DNA sequence reads in BAM files
bcrypt/4.0.1-GCCcore-12.3.0 Acceptable password hashing for your software and your servers (but you should really use argon2id or scrypt)
beagle-lib/4.0.1-GCC-12.3.0-CUDA-12.1.1 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.
binutils/2.42-GCCcore-13.3.0 binutils: GNU binary utilities
biom-format/2.1.15-foss-2023a The BIOM file format (canonically pronounced biome) is designed to be a general-use format for representing biological sample by observation contingency tables. BIOM is a recognized standard for the Earth Microbiome Project and is a Genomics Standards Consortium supported project.
bokeh/3.2.2-foss-2023a Statistical and novel interactive HTML plots for Python
bzip2/1.0.8-GCCcore-12.2.0 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.
cURL/8.7.1-GCCcore-13.3.0 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-13.3.0 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
cffi/1.16.0-GCCcore-13.3.0 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.
configurable-http-proxy/4.5.6-GCCcore-12.3.0 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.
cooler/0.10.2-foss-2023a Cooler is a support library for a storage format, also called cooler, used to store genomic interaction data of any size, such as Hi-C contact matrices.
cpio/2.15-GCCcore-12.2.0 The cpio package contains tools for archiving.
cppy/1.2.1-GCCcore-13.3.0 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.
cryptography/42.0.8-GCCcore-13.3.0 cryptography is a package designed to expose cryptographic primitives and recipes to Python developers.
cuDNN/9.5.1.17-CUDA-12.6.2 The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks.
cutadapt/4.4-GCCcore-12.2.0 Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.
dask/2023.12.1-foss-2023a Dask natively scales Python. Dask provides advanced parallelism for analytics, enabling performance at scale for the tools you love.
deepdiff/6.7.1-GCCcore-12.3.0 DeepDiff: Deep Difference of dictionaries, iterables and almost any other object recursively.
dill/0.3.7-GCCcore-12.3.0 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-haiku/0.0.11-foss-2023a-CUDA-12.1.1 Haiku is a simple neural network library for JAX developed by some of the authors of Sonnet, a neural network library for TensorFlow.
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.
double-conversion/3.3.0-GCCcore-13.2.0 Efficient binary-decimal and decimal-binary conversion routines for IEEE doubles.
eSpeak-NG/1.51-gfbf-2023a The eSpeak NG is a compact open source software text-to-speech synthesizer for Linux, Windows, Android and other operating systems. It supports more than 100 languages and accents. It is based on the eSpeak engine created by Jonathan Duddington.
easel/0.48-GCC-12.2.0 easyconfig Easel supports computational analysis of biological sequences using probabilistic models.
einops/0.7.0-GCCcore-12.3.0 Flexible and powerful tensor operations for readable and reliable code. Supports numpy, pytorch, tensorflow, jax, and others.
expat/2.6.2-GCCcore-13.3.0 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).
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.
fastp/0.23.4-GCC-13.2.0 easyconfig 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.
festival/2.5.0-GCCcore-12.3.0 University of Edinburgh’s Festival Speech Synthesis Systems is a free software multi-lingual speech synthesis workbench that runs on multiple-platforms offering black box text to speech, as well as an open architecture for research in speech synthesis. It designed as a component of large speech technology systems.
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).
fhPython/3.11.3-foss-2023a easyconfig Fred Hutch Python
fhR/4.4.0-foss-2023b easyconfig R is a free software environment for statistical computing and graphics.
flash-attention/2.6.3-foss-2023a-CUDA-12.1.1 easyconfig Fast and memory-efficient exact attention.
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-GCCcore-13.3.0 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-13.2.0 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/2.15.0-GCCcore-13.3.0 Fontconfig is a library designed to provide system-wide font configuration, customization and application access.
foss/2024a GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.
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.
geopandas/0.14.2-foss-2023a GeoPandas is a project to add support for geographic data to pandas objects. It currently implements GeoSeries and GeoDataFrame types which are subclasses of pandas.Series and pandas.DataFrame respectively. GeoPandas objects can act on shapely geometry objects and perform geometric operations.
gettext/0.22.5 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/2024a GNU Compiler Collection (GCC) based compiler toolchain, including FlexiBLAS (BLAS and LAPACK support) and (serial) FFTW.
gffread/0.12.7-GCCcore-12.3.0 GFF/GTF parsing utility providing format conversions, region filtering, FASTA sequence extraction and more.
giflib/5.2.1-GCCcore-13.2.0 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.
git/2.45.1-GCCcore-13.3.0 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.
gmpy2/2.1.5-GCC-12.3.0 GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x
gnupg-bundle/20240306-GCCcore-13.2.0 GnuPG — The Universal Crypto Engine
gnuplot/5.4.8-GCCcore-12.3.0 Portable interactive, function plotting utility
gompi/2024a GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support.
googletest/1.14.0-GCCcore-13.2.0 Google’s framework for writing C++ tests on a variety of platforms
gperf/3.1-GCCcore-13.3.0 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/2.12-GCCcore-12.3.0 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-12.3.0 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.
grpcio/1.57.0-GCCcore-12.3.0 gRPC is a modern, open source, high-performance remote procedure call (RPC) framework that can run anywhere. gRPC enables client and server applications to communicate transparently, and simplifies the building of connected systems.
gzip/1.13-GCCcore-13.3.0 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.
hatch-jupyter-builder/0.9.1-GCCcore-12.3.0 Hatch Jupyter Builder is a plugin for the hatchling Python build backend. It is primarily targeted for package authors who are providing JavaScript as part of their Python packages. Typical use cases are Jupyter Lab Extensions and Jupyter Widgets.
hatchling/1.24.2-GCCcore-13.3.0 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.
hwloc/2.10.0-GCCcore-13.3.0 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.
hypothesis/6.118.8-GCCcore-13.3.0 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.
igraph/0.10.12-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/2.33.1-gfbf-2023a 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.
intltool/0.51.0-GCCcore-12.2.0 intltool is a set of tools to centralize translation of many different file formats using GNU gettext-compatible PO files.
jax/0.4.25-gfbf-2023a-CUDA-12.1.1 Composable transformations of Python+NumPy programs: differentiate, vectorize, JIT to GPU/TPU, and more
jbigkit/2.1-GCCcore-12.2.0 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-12.3.0 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-contrib-nbextensions/0.7.0-GCCcore-12.3.0 A collection of various notebook extensions for Jupyter
jupyter-resource-usage/1.0.0-GCCcore-12.3.0 Jupyter Notebook Extension for monitoring your own Resource Usage (memory and/or CPU)
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/4.0.0-GCCcore-12.3.0 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.
jupyterlmod/4.0.3-GCCcore-12.3.0 Jupyter interactive notebook server extension that allows users to interact with environment modules before launching kernels. The extension uses Lmod’s Python interface to accomplish module-related tasks like loading, unloading, saving collections, etc.
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.
leidenalg/0.10.2-foss-2023b easyconfig Implementation of the Leiden algorithm for various quality functions to be used with igraph in Python.
libGLU/9.0.3-GCCcore-13.2.0 The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL.
libaio/0.3.113-GCCcore-12.3.0 Asynchronous input/output library that uses the kernels native interface.
libarchive/3.7.4-GCCcore-13.3.0 Multi-format archive and compression library
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.
libdeflate/1.20-GCCcore-13.3.0 Heavily optimized library for DEFLATE/zlib/gzip compression and decompression.
libdrm/2.4.117-GCCcore-13.2.0 Direct Rendering Manager runtime library.
libepoxy/1.5.10-GCCcore-12.3.0 Epoxy is a library for handling OpenGL function pointer management for you
libevent/2.1.12-GCCcore-13.3.0 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/1.21.0-GCCcore-13.3.0 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/3.4.5-GCCcore-13.3.0 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.
libgd/2.3.3-GCCcore-13.2.0 easyconfig GD is an open source code library for the dynamic creation of images by programmers.
libgeotiff/1.7.3-GCCcore-13.2.0 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.
libharu/2.3.0-GCCcore-13.2.0 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
libidn2/2.3.4-GCCcore-12.2.0 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-2023b easyconfig Implements the Leiden algorithm in C++
libmad/0.15.1b-GCCcore-12.3.0 MAD is a high-quality MPEG audio decoder.
libogg/1.3.5-GCCcore-12.3.0 Ogg is a multimedia container format, and the native file and stream format for the Xiph.org multimedia codecs.
libopus/1.4-GCCcore-12.3.0 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/0.18.1-GCCcore-13.3.0 Generic PCI access library.
libpng/1.6.43-GCCcore-13.3.0 libpng is the official PNG reference library
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.
librosa/0.10.1-foss-2023a Audio and music processing in Python
librsvg/2.58.0-GCCcore-13.2.0 easyconfig Librsvg is a library to render SVG files using cairo.
libsndfile/1.2.2-GCCcore-12.3.0 easyconfig 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.
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-13.2.0 GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries behind a consistent, portable interface.
libunwind/1.6.2-GCCcore-12.2.0 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
libvorbis/1.3.7-GCCcore-12.3.0 Ogg Vorbis is a fully open, non-proprietary, patent-and-royalty-free, general-purpose compressed audio format
libwebp/1.4.0-GCCcore-13.3.0 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.
libxml2/2.12.7-GCCcore-13.3.0 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-13.2.0 LibYAML is a YAML parser and emitter written in C.
loompy/3.0.7-foss-2023a Python implementation of the Loom file format, an efficient file format for large omics datasets
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-13.3.0 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/7.0.3-GCCcore-12.2.0 makeinfo is part of the Texinfo project, the official documentation format of the GNU project.
matplotlib/3.9.2-gfbf-2024a 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/1.6.0-GCCcore-13.3.0 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.
meson-python/0.16.0-GCCcore-13.3.0 Python build backend (PEP 517) for Meson projects
minimap2/2.26-GCCcore-12.3.0 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-collections/0.1.1-foss-2023a ML Collections is a library of Python Collections designed for ML use cases.
ml_dtypes/0.3.2-gfbf-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

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.
nbclassic/1.0.0-GCCcore-12.3.0 NbClassic provides a backwards compatible Jupyter Notebook interface that you can install side-by-side with the latest versions: That way, you can fearlessly upgrade without worrying about your classic extensions and customizations breaking.
ncbi-vdb/3.1.1-gompi-2023b easyconfig The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.
ncurses/6.5-GCCcore-13.3.0 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.
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/3.9.1-GCCcore-12.3.0 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.
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-12.3.0 nsync is a C library that exports various synchronization primitives, such as mutexes
numactl/2.0.18-GCCcore-13.3.0 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.
openpyxl/3.1.2-GCCcore-12.3.0 A Python library to read/write Excel 2010 xlsx/xlsm files
parameterized/0.9.0-GCCcore-12.3.0 Parameterized testing with any Python test framework
patchelf/0.18.0-GCCcore-13.3.0 PatchELF is a small utility to modify the dynamic linker and RPATH of ELF executables.
phonemizer/3.2.1-gfbf-2023a The phonemizer allows simple phonemization of words and texts in many languages. Provides both the phonemize command-line tool and the Python function phonemizer.phonemize. It is using four backends: espeak, espeak-mbrola, festival and segments.
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.
pixman/0.43.4-GCCcore-13.3.0 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.
pkgconf/2.2.0-GCCcore-13.3.0 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
plotly.py/5.16.0-GCCcore-12.3.0 An open-source, interactive graphing library for Python
poetry/1.8.3-GCCcore-13.3.0 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.
polars/0.20.2-gfbf-2023a Polars is a blazingly fast DataFrame library for manipulating structured data. The core is written in Rust and this module provides its interface for Python.
poppler/24.04.0-GCC-13.2.0 Poppler is a PDF rendering library
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-python/4.24.0-GCCcore-12.3.0 Python Protocol Buffers runtime library.
psycopg2/2.9.9-GCCcore-12.3.0 Psycopg is the most popular PostgreSQL adapter for the Python programming language.
py-cpuinfo/9.0.0-GCCcore-12.3.0 py-cpuinfo gets CPU info with pure Python.
pyEGA3/5.0.2-GCCcore-12.3.0 A basic Python-based EGA download client
pybedtools/0.9.1-foss-2023a pybedtools wraps and extends BEDTools and offers feature-level manipulations from within Python.
pybind11/2.13.6-GCC-13.3.0 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.
pydantic/2.6.4-GCCcore-13.2.0 Data validation and settings management using Python type hinting.
pydot/2.0.0-GCCcore-12.3.0 Python interface to Graphviz’s Dot language.
pyfaidx/0.8.1.1-GCCcore-12.3.0 pyfaidx: efficient pythonic random access to fasta subsequences
pyproj/3.6.0-GCCcore-12.3.0 Python interface to PROJ4 library for cartographic transformations
pyro-ppl/1.9.0-foss-2023a Pyro is a flexible, scalable deep probabilistic programming library built on PyTorch.
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-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-2023a Python interface to the igraph high performance graph library, primarily aimed at complex network research and analysis.
python-isal/1.1.0-GCCcore-12.2.0 Faster zlib and gzip compatible compression and decompression by providing python bindings for the isa-l library.
re2c/3.1-GCCcore-12.3.0 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.
rpy2/3.5.15-foss-2023a rpy2 is an interface to R running embedded in a Python process.
ruamel.yaml/0.18.6-GCCcore-13.2.0 ruamel.yaml is a YAML 1.2 loader/dumper package for Python.
samblaster/0.1.26-GCC-13.2.0 easyconfig samblaster is a fast and flexible program for marking duplicates in read-id grouped1 paired-end SAM files.
scGPT/0.2.1-foss-2023a-CUDA-12.1.1 easyconfig scGPT: Towards Building a Foundation Model for Single-Cell Multi-omics Using Generative AI.
scVelo/0.3.1-foss-2023a 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.
scib/1.1.4-foss-2023a Benchmarking atlas-level data integration in single-cell genomics.
scikit-bio/0.6.0-foss-2023a 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-13.3.0 Scikit-Build, or skbuild, is an improved build system generator for CPython C/C++/Fortran/Cython extensions.
scikit-build-core/0.5.0-GCCcore-12.3.0 Scikit-build-core is a complete ground-up rewrite of scikit-build on top of modern packaging APIs. It provides a bridge between CMake and the Python build system, allowing you to make Python modules with CMake.
scikit-image/0.22.0-foss-2023a scikit-image is a collection of algorithms for image processing.
scikit-learn/1.4.2-gfbf-2023a 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/0.3.1-foss-2023a easyconfig Miscellaneous tools for data analysis and scientific computing
scvi-tools/1.1.2-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.
setuptools/75.3.0-GCCcore-12.3.0 Easily download, build, install, upgrade, and uninstall Python packages
setuptools-rust/1.9.0-GCCcore-13.3.0 setuptools-rust is a plugin for setuptools to build Rust Python extensions implemented with PyO3 or rust-cpython.
snakemake/8.4.2-foss-2023a The Snakemake workflow management system is a tool to create reproducible and scalable data analyses.
snappy/1.1.10-GCCcore-12.3.0 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.
sonic/20180202-gfbf-2023a Sonic is a simple algorithm for speeding up or slowing down speech. However, it’s optimized for speed ups of over 2X, unlike previous algorithms for changing speech rate. The Sonic library is a very simple ANSI C library that is designed to easily be integrated into streaming voice applications, like TTS back ends.
speech_tools/2.5.0-GCCcore-12.3.0 The Edinburgh Speech Tools Library is a collection of C++ class, functions and related programs for manipulating the sorts of objects used in speech processing. It includes support for reading and writing waveforms, parameter files (LPC, Ceptra, F0) in various formats and converting between them. It also includes support for linguistic type objects and support for various label files and ngrams (with smoothing).
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

starcode/1.4-GCC-13.2.0 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.
statsmodels/0.14.1-gfbf-2023b Statsmodels is a Python module that allows users to explore data, estimate statistical models, and perform statistical tests.
sympy/1.12-gfbf-2023b 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.
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.
tensorboard/2.15.1-gfbf-2023a 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.
tensorstore/0.1.53-foss-2023a TensorStore is an open-source C++ and Python software library designed for
storage and manipulation of large multi-dimensional arrays.
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/4.10.0-GCCcore-13.2.0 Typing Extensions
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/2.9.0-GCCcore-13.2.0 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/2.40-GCCcore-13.3.0 Set of Linux utilities
virtualenv/20.26.2-GCCcore-13.3.0 A tool for creating isolated virtual python environments.
wandb/0.16.1-GCC-12.3.0 CLI and Python API for Weights and Biases (wandb), a tool for visualizing and tracking your machine learning experiments.
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.
wrapt/1.15.0-gfbf-2023a The aim of the wrapt module is to provide a transparent object proxy for Python, which can be used as the basis for the construction of function wrappers and decorator functions.
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-12.3.0 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.
xarray/2023.9.0-gfbf-2023a xarray (formerly xray) is an open source project and Python package that aims to bring the labeled data power of pandas to the physical sciences, by providing N-dimensional variants of the core pandas data structures.
xorg-macros/1.20.1-GCCcore-13.3.0 X.org macros utilities.
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/0.8.0-GCCcore-13.2.0 yaml-cpp is a YAML parser and emitter in C++ matching the YAML 1.2 spec
zlib/1.3.1-GCCcore-13.3.0 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/1.5.6-GCCcore-13.3.0 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.