VTune |
Intel VTune Amplifier XE is the premier performance profiler for C, C++, C#, Fortran,
Assembly and Java. |
|
ansys |
ANSYS simulation software enables organizations to confidently predict
how their products will operate in the real world. We believe that every product is
a promise of something greater. |
|
elbencho |
A distributed storage benchmark for files, objects & blocks with support for GPUs |
|
matlab |
MATLAB is a programming and numeric computing platform |
|
starccm+ |
STARCCM+DESCRIPTION |
|
tinker9 |
Molecular Design Software |
|
ABAQUS |
Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit
dynamics FEA. |
|
ASE |
ASE is a python package providing an open source Atomic Simulation Environment
in the Python scripting language.
From version 3.20.1 we also include the ase-ext package, it contains optional reimplementations
in C of functions in ASE. ASE uses it automatically when installed. |
3.23.0-gfbf-2023a
3.24.0-gfbf-2024a |
|
ATK |
ATK provides the set of accessibility interfaces that are implemented by other
toolkits and applications. Using the ATK interfaces, accessibility tools have
full access to view and control running applications.
|
|
Abseil |
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. |
20230125.3-GCCcore-12.3.0
20240722.0-GCCcore-13.3.0 |
|
AlphaFold |
AlphaFold 3.0.1 run via Apptainer container with mounted data directories |
|
Armadillo |
Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards
a good balance between speed and ease of use. Integer, floating point and complex numbers are supported,
as well as a subset of trigonometric and statistics functions. |
12.6.2-foss-2023a
14.0.3-foss-2024a |
|
Arrow |
Apache Arrow (incl. PyArrow Python bindings), a cross-language development platform
for in-memory data. |
14.0.1-gfbf-2023a
17.0.0-gfbf-2024a |
|
Autoconf |
Autoconf is an extensible package of M4 macros that produce shell scripts
to automatically configure software source code packages. These scripts can
adapt the packages to many kinds of UNIX-like systems without manual user
intervention. Autoconf creates a configuration script for a package from a
template file that lists the operating system features that the package can
use, in the form of M4 macro calls.
|
2.71
2.71-GCCcore-11.2.0
2.71-GCCcore-11.3.0
2.71-GCCcore-12.3.0
2.71-GCCcore-13.2.0
2.72-GCCcore-13.3.0
2.72-GCCcore-14.2.0 |
|
Automake |
Automake: GNU Standards-compliant Makefile generator |
1.16.4-GCCcore-11.2.0
1.16.5
1.16.5-GCCcore-11.3.0
1.16.5-GCCcore-12.3.0
1.16.5-GCCcore-13.2.0
1.16.5-GCCcore-13.3.0
1.17-GCCcore-14.2.0 |
|
Autotools |
This bundle collect the standard GNU build tools: Autoconf, Automake
and libtool
|
20210726-GCCcore-11.2.0
20220317
20220317-GCCcore-11.3.0
20220317-GCCcore-12.3.0
20220317-GCCcore-13.2.0
20231222-GCCcore-13.3.0
20240712-GCCcore-14.2.0 |
|
BLIS |
BLIS is a portable software framework for instantiating high-performance
BLAS-like dense linear algebra libraries. |
0.9.0-GCC-11.3.0
0.9.0-GCC-12.3.0
0.9.0-GCC-13.2.0
1.0-GCC-13.3.0 |
|
Bazel |
Bazel is a build tool that builds code quickly and reliably.
It is used to build the majority of Google’s software. |
3.7.2-GCCcore-11.2.0
5.1.1-GCCcore-11.3.0
6.3.1-GCCcore-12.3.0
7.4.1-GCCcore-13.3.0 |
|
BeautifulSoup |
Beautiful Soup is a Python library designed for quick turnaround projects like screen-scraping. |
|
Biopython |
Biopython is a set of freely available tools for biological
computation written in Python by an international team of developers. It is
a distributed collaborative effort to develop Python libraries and
applications which address the needs of current and future work in
bioinformatics. |
1.79-foss-2022a
1.83-foss-2023a
1.84-foss-2024a |
|
Bison |
Bison is a general-purpose parser generator that converts an annotated context-free grammar
into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables. |
3.7.6-GCCcore-11.2.0
3.8.2
3.8.2-GCCcore-11.3.0
3.8.2-GCCcore-12.3.0
3.8.2-GCCcore-13.2.0
3.8.2-GCCcore-13.3.0
3.8.2-GCCcore-14.2.0 |
|
Boost |
Boost provides free peer-reviewed portable C++ source libraries. |
1.82.0-GCC-12.3.0
1.83.0-GCC-13.2.0
1.85.0-GCC-13.3.0 |
|
Brotli |
Brotli is a generic-purpose lossless compression algorithm that compresses data using a combination
of a modern variant of the LZ77 algorithm, Huffman coding and 2nd order context modeling, with a compression ratio
comparable to the best currently available general-purpose compression methods. It is similar in speed with deflate
but offers more dense compression.
The specification of the Brotli Compressed Data Format is defined in RFC 7932. |
1.0.9-GCCcore-11.3.0
1.0.9-GCCcore-12.3.0
1.1.0-GCCcore-13.2.0
1.1.0-GCCcore-13.3.0 |
|
Brunsli |
Brunsli is a lossless JPEG repacking library. |
0.1-GCCcore-12.3.0
0.1-GCCcore-13.3.0 |
|
CFITSIO |
CFITSIO is a library of C and Fortran subroutines for reading and writing data files in
FITS (Flexible Image Transport System) data format.
|
4.3.0-GCCcore-12.3.0
4.4.1-GCCcore-13.3.0 |
|
CGAL |
The goal of the CGAL Open Source Project is to provide easy access to efficient
and reliable geometric algorithms in the form of a C++ library. |
|
CMake |
CMake, the cross-platform, open-source build system. CMake is a family of
tools designed to build, test and package software.
|
3.18.4
3.21.1-GCCcore-11.2.0
3.22.1-GCCcore-11.2.0
3.23.1-GCCcore-11.3.0
3.26.3-GCCcore-12.3.0
3.27.6-GCCcore-13.2.0
3.29.3-GCCcore-13.3.0
3.30.8-GCCcore-12.3.0
3.31.3-GCCcore-14.2.0 |
|
CUDA |
CUDA (formerly Compute Unified Device Architecture) is a parallel
computing platform and programming model created by NVIDIA and implemented by the
graphics processing units (GPUs) that they produce. CUDA gives developers access
to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs. |
11.4.1
12.1.1
12.2.0
12.3.0
12.4.0
12.6.0 |
|
Catch2 |
A modern, C++-native, header-only,
test framework for unit-tests, TDD and BDD
- using C++11, C++14, C++17 and later
|
2.13.10-GCCcore-13.3.0
2.13.9-GCCcore-12.3.0
2.13.9-GCCcore-13.2.0 |
|
CppUnit |
CppUnit is the C++ port of the famous JUnit framework for unit testing.
|
|
Cython |
Cython is an optimising static compiler for both the Python programming
language and the extended Cython programming language (based on Pyrex).
|
3.0.10-GCCcore-13.2.0
3.0.10-GCCcore-13.3.0
3.0.8-GCCcore-12.3.0 |
|
DB |
Berkeley DB enables the development of custom data management
solutions, without the overhead traditionally associated with such custom
projects. |
18.1.40-GCCcore-11.2.0
18.1.40-GCCcore-11.3.0
18.1.40-GCCcore-12.3.0
18.1.40-GCCcore-13.3.0 |
|
DBus |
D-Bus is a message bus system, a simple way for applications to talk
to one another. In addition to interprocess communication, D-Bus helps
coordinate process lifecycle; it makes it simple and reliable to code
a “single instance” application or daemon, and to launch applications
and daemons on demand when their services are needed.
|
1.15.4-GCCcore-12.3.0
1.15.8-GCCcore-13.2.0
1.15.8-GCCcore-13.3.0 |
|
Doxygen |
Doxygen is a documentation system for C++, C, Java, Objective-C, Python,
IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some
extent D.
|
1.11.0-GCCcore-13.3.0
1.9.4-GCCcore-11.3.0
1.9.7-GCCcore-12.3.0
1.9.8-GCCcore-13.2.0 |
|
EasyBuild |
EasyBuild is a software build and installation framework
written in Python that allows you to install software in a structured,
repeatable and robust way. |
|
Eigen |
Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers,
and related algorithms. |
3.3.9-GCCcore-11.2.0
3.4.0-GCCcore-11.3.0
3.4.0-GCCcore-12.3.0
3.4.0-GCCcore-13.2.0
3.4.0-GCCcore-13.3.0 |
|
FFTW |
FFTW is a C subroutine library for computing the discrete Fourier transform (DFT |
3.3.10-GCC-11.3.0
3.3.10-GCC-12.3.0
3.3.10-GCC-13.2.0
3.3.10-GCC-13.3.0 |
|
FFTW.MPI |
FFTW is a C subroutine library for computing the discrete Fourier transform (DFT |
3.3.10-gompi-2022a
3.3.10-gompi-2023a
3.3.10-gompi-2023b
3.3.10-gompi-2024a |
|
FFmpeg |
A complete, cross-platform solution to record, convert and stream audio and video. |
6.0-GCCcore-12.3.0
6.0-GCCcore-13.2.0
7.0.2-GCCcore-13.3.0 |
|
FLAC |
FLAC stands for Free Lossless Audio Codec, an audio format similar to MP3, but lossless, meaning
that audio is compressed in FLAC without any loss in quality. |
1.4.2-GCCcore-12.3.0
1.4.3-GCCcore-13.3.0 |
|
Flask |
Flask is a lightweight WSGI web application framework. It is designed to make
getting started quick and easy, with the ability to scale up to complex
applications.
This module includes the Flask extensions: Flask-Cors
|
2.3.3-GCCcore-12.3.0
3.0.3-GCCcore-13.3.0 |
|
FlexiBLAS |
FlexiBLAS is a wrapper library that enables the exchange of the BLAS and LAPACK implementation
used by a program without recompiling or relinking it. |
3.2.0-GCC-11.3.0
3.3.1-GCC-12.3.0
3.3.1-GCC-13.2.0
3.4.4-GCC-13.3.0 |
|
FriBidi |
The Free Implementation of the Unicode Bidirectional Algorithm.
|
1.0.12-GCCcore-12.3.0
1.0.13-GCCcore-13.2.0
1.0.15-GCCcore-13.3.0 |
|
GCC |
The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada,
as well as libraries for these languages (libstdc++, libgcj,…). |
11.2.0
11.3.0
12.3.0
13.2.0
13.3.0
14.2.0 |
|
GCCcore |
The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada,
as well as libraries for these languages (libstdc++, libgcj,…). |
11.2.0
11.3.0
12.2.0
12.3.0
13.2.0
13.3.0
14.2.0 |
|
GDAL |
GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style
Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model
to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for
data translation and processing. |
3.10.0-foss-2024a
3.7.1-foss-2023a |
|
GDRCopy |
A low-latency GPU memory copy library based on NVIDIA GPUDirect RDMA technology. |
2.3-GCCcore-11.2.0
2.3.1-GCCcore-12.3.0
2.4-GCCcore-13.2.0 |
|
GEOS |
GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS) |
3.12.0-GCC-12.3.0
3.12.2-GCC-13.3.0 |
|
GLPK |
The GLPK (GNU Linear Programming Kit) package is intended for
solving large-scale linear programming (LP),
mixed integer programming (MIP), and other related problems.
It is a set of routines written in ANSI C
and organized in the form of a callable library. |
5.0-GCCcore-12.3.0
5.0-GCCcore-13.3.0 |
|
GLib |
GLib is one of the base libraries of the GTK+ project |
2.77.1-GCCcore-12.3.0
2.78.1-GCCcore-13.2.0
2.80.4-GCCcore-13.3.0 |
|
GMP |
GMP is a free library for arbitrary precision arithmetic, operating on signed
integers, rational numbers, and floating point numbers.
|
6.2.1-GCCcore-11.2.0
6.2.1-GCCcore-11.3.0
6.2.1-GCCcore-12.3.0
6.3.0-GCCcore-13.2.0
6.3.0-GCCcore-13.3.0
6.3.0-GCCcore-14.2.0 |
|
GObject-Introspection |
GObject introspection is a middleware layer between C libraries
(using GObject) and language bindings. The C library can be scanned at
compile time and generate a metadata file, in addition to the actual
native C library. Then at runtime, language bindings can read this
metadata and automatically provide bindings to call into the C library. |
1.76.1-GCCcore-12.3.0
1.78.1-GCCcore-13.2.0
1.80.1-GCCcore-13.3.0 |
|
GSL |
The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers.
The library provides a wide range of mathematical routines such as random number generators, special functions
and least-squares fitting. |
2.7-GCC-12.3.0
2.7-GCC-13.2.0
2.8-GCC-13.3.0 |
|
GTK3 |
GTK+ is the primary library used to construct user interfaces in GNOME. It
provides all the user interface controls, or widgets, used in a common
graphical application. Its object-oriented API allows you to construct
user interfaces without dealing with the low-level details of drawing and
device interaction.
|
|
Gdk-Pixbuf |
The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation.
It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it
was distributed as part of GTK+ 2 but it was split off into a separate package
in preparation for the change to GTK+ 3.
|
|
Ghostscript |
Ghostscript is a versatile processor for PostScript data with the ability to render PostScript to
different targets. It used to be part of the cups printing stack, but is no longer used for that. |
10.01.2-GCCcore-12.3.0
10.03.1-GCCcore-13.3.0 |
|
GlobalArrays |
Global Arrays (GA) is a Partitioned Global Address Space (PGAS) programming model |
5.8.2-intel-2023a
5.8.2-intel-2024a |
|
Go |
Go is an open source programming language that makes it easy to build
simple, reliable, and efficient software. |
|
HDF |
HDF (also known as HDF4) is a library and multi-object file format for
storing and managing data between machines.
|
4.2.16-2-GCCcore-12.3.0
4.3.0-GCCcore-13.3.0 |
|
HDF5 |
HDF5 is a data model, library, and file format for storing and managing data.
It supports an unlimited variety of datatypes, and is designed for flexible
and efficient I/O and for high volume and complex data. |
1.12.2-gompi-2022a
1.14.0-gompi-2023a
1.14.0-iimpi-2023a
1.14.3-gompi-2023b
1.14.5-gompi-2024a |
|
HH-suite |
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 |
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. |
3.3.2-gompi-2022a
3.4-gompi-2023a |
|
HPL |
HPL is a software package that solves a (random) dense linear system in double precision (64 bits |
2.3-foss-2024a
2.3-intel-2024a |
|
HTSlib |
A C library for reading/writing high-throughput sequencing data.
This package includes the utilities bgzip and tabix |
1.18-GCC-12.3.0
1.19.1-GCC-13.2.0
1.21-GCC-13.3.0 |
|
HarfBuzz |
HarfBuzz is an OpenType text shaping engine. |
5.3.1-GCCcore-12.3.0
8.2.2-GCCcore-13.2.0
9.0.0-GCCcore-13.3.0 |
|
ICU |
ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization
support for software applications. |
71.1-GCCcore-11.3.0
73.2-GCCcore-12.3.0
74.1-GCCcore-13.2.0
75.1-GCCcore-13.3.0 |
|
IJulia |
Julia kernel for Jupyter |
|
IPython |
IPython provides a rich architecture for interactive computing with:
Powerful interactive shells (terminal and Qt-based).
A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media.
Support for interactive data visualization and use of GUI toolkits.
Flexible, embeddable interpreters to load into your own projects.
Easy to use, high performance tools for parallel computing. |
8.14.0-GCCcore-12.3.0
8.17.2-GCCcore-13.2.0
8.28.0-GCCcore-13.3.0 |
|
ImageMagick |
ImageMagick is a software suite to create, edit, compose, or convert bitmap images |
7.1.1-15-GCCcore-12.3.0
7.1.1-38-GCCcore-13.3.0 |
|
Imath |
Imath is a C++ and python library of 2D and 3D vector, matrix, and math operations for computer graphics
|
3.1.11-GCCcore-13.3.0
3.1.7-GCCcore-12.3.0 |
|
JAGS |
JAGS is Just Another Gibbs Sampler. It is a program for analysis
of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation |
4.3.2-foss-2023a
4.3.2-foss-2024a |
|
JasPer |
The JasPer Project is an open-source initiative to provide a free
software-based reference implementation of the codec specified in
the JPEG-2000 Part-1 standard.
|
4.0.0-GCCcore-12.3.0
4.0.0-GCCcore-13.2.0
4.2.4-GCCcore-13.3.0 |
|
Java |
Java Platform, Standard Edition (Java SE) lets you develop and deploy
Java applications on desktops and servers. |
11.0.20
17.0.6
21.0.2
21.0.5 |
|
JsonCpp |
JsonCpp is a C++ library that allows manipulating JSON values,
including serialization and deserialization to and from strings. It can also preserve existing comment in
unserialization/serialization steps, making it a convenient format to store user input files. |
1.9.5-GCCcore-11.3.0
1.9.5-GCCcore-12.3.0 |
|
Julia |
Julia is a high-level, high-performance dynamic programming language for numerical computing |
1.10.3-linux-x86_64
1.10.4-linux-x86_64
1.11.3-linux-x86_64 |
|
JupyterLab |
JupyterLab is the next-generation user interface for Project Jupyter offering all the familiar
building blocks of the classic Jupyter Notebook (notebook, terminal, text editor, file browser, rich outputs,
etc.) in a flexible and powerful user interface. JupyterLab will eventually replace the classic Jupyter
Notebook. |
|
JupyterNotebook |
The Jupyter Notebook is the original web application for creating and
sharing computational documents. It offers a simple, streamlined, document-centric experience. |
|
KaHIP |
The graph partitioning framework KaHIP – Karlsruhe High Quality Partitioning. |
|
Kalign |
Kalign is a fast multiple sequence alignment program for biological sequences. |
3.3.2-GCCcore-11.2.0
3.3.5-GCCcore-11.3.0
3.4.0-GCCcore-12.3.0 |
|
LAME |
LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL. |
3.100-GCCcore-12.3.0
3.100-GCCcore-13.2.0
3.100-GCCcore-13.3.0 |
|
LAMMPS |
LAMMPS is a classical molecular dynamics code, and an acronym
for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has
potentials for solid-state materials (metals, semiconductors) and soft matter
(biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be
used to model atoms or, more generically, as a parallel particle simulator at
the atomic, meso, or continuum scale. LAMMPS runs on single processors or in
parallel using message-passing techniques and a spatial-decomposition of the
simulation domain. The code is designed to be easy to modify or extend with new
functionality.
|
29Aug2024-foss-2023b-kokkos
2Aug2023_update2-foss-2023a-kokkos-CUDA-12.1.1 |
|
LERC |
LERC is an open-source image or raster format which supports rapid encoding and decoding
for any pixel type (not just RGB or Byte). Users set the maximum compression error per pixel while encoding,
so the precision of the original input image is preserved (within user defined error bounds). |
4.0.0-GCCcore-12.3.0
4.0.0-GCCcore-13.3.0 |
|
LLVM |
The LLVM Core libraries provide a modern source- and target-independent
optimizer, along with code generation support for many popular CPUs
(as well as some less common ones!) These libraries are built around a well
specified code representation known as the LLVM intermediate representation
(“LLVM IR”). The LLVM Core libraries are well documented, and it is
particularly easy to invent your own language (or port an existing compiler |
14.0.6-GCCcore-12.3.0-llvmlite
14.0.6-GCCcore-13.2.0-llvmlite
16.0.6-GCCcore-12.3.0
16.0.6-GCCcore-13.2.0
18.1.8-GCCcore-13.3.0-minimal |
|
LMDB |
LMDB is a fast, memory-efficient database. With memory-mapped files, it has the read performance
of a pure in-memory database while retaining the persistence of standard disk-based databases. |
0.9.29-GCCcore-11.3.0
0.9.31-GCCcore-12.3.0 |
|
LibTIFF |
tiff: Library and tools for reading and writing TIFF data files |
4.3.0-GCCcore-11.3.0
4.5.0-GCCcore-12.3.0
4.6.0-GCCcore-13.2.0
4.6.0-GCCcore-13.3.0 |
|
LittleCMS |
Little CMS intends to be an OPEN SOURCE small-footprint color management engine,
with special focus on accuracy and performance. |
2.15-GCCcore-12.3.0
2.15-GCCcore-13.2.0
2.16-GCCcore-13.3.0 |
|
Lua |
Lua is a powerful, fast, lightweight, embeddable scripting language.
Lua combines simple procedural syntax with powerful data description constructs based
on associative arrays and extensible semantics. Lua is dynamically typed,
runs by interpreting bytecode for a register-based virtual machine,
and has automatic memory management with incremental garbage collection,
making it ideal for configuration, scripting, and rapid prototyping. |
5.4.6-GCCcore-12.3.0
5.4.7-GCCcore-13.3.0 |
|
M4 |
GNU M4 is an implementation of the traditional Unix macro processor. It is
mostly SVR4 compatible although it has some extensions (for example, handling
more than 9 positional parameters to macros). GNU M4 also has built-in
functions for including files, running shell commands, doing arithmetic, etc.
|
1.4.18
1.4.19
1.4.19-GCCcore-11.2.0
1.4.19-GCCcore-11.3.0
1.4.19-GCCcore-12.3.0
1.4.19-GCCcore-13.2.0
1.4.19-GCCcore-13.3.0
1.4.19-GCCcore-14.2.0 |
|
MDI |
The MolSSI Driver Interface (MDI) project provides a
standardized API for fast, on-the-fly communication between computational
chemistry codes. This greatly simplifies the process of implementing
methods that require the cooperation of multiple software packages and
enables developers to write a single implementation that works across
many different codes. The API is sufficiently general to support a wide
variety of techniques, including QM/MM, ab initio MD, machine learning,
advanced sampling, and path integral MD, while also being straightforwardly
extensible. Communication between codes is handled by the MDI Library, which
enables tight coupling between codes using either the MPI or TCP/IP methods.
|
1.4.26-gompi-2023a
1.4.29-gompi-2023b |
|
METIS |
METIS is a set of serial programs for partitioning graphs, partitioning
finite element meshes, and producing fill reducing orderings for sparse
matrices. The algorithms implemented in METIS are based on the multilevel
recursive-bisection, multilevel k-way, and multi-constraint partitioning
schemes.
|
5.1.0-GCCcore-12.3.0
5.1.0-GCCcore-13.3.0 |
|
MPC |
Gnu Mpc is a C library for the arithmetic of
complex numbers with arbitrarily high precision and correct
rounding of the result. It extends the principles of the IEEE-754
standard for fixed precision real floating point numbers to
complex numbers, providing well-defined semantics for every
operation. At the same time, speed of operation at high precision
is a major design goal. |
|
MPFR |
The MPFR library is a C library for multiple-precision floating-point
computations with correct rounding.
|
4.2.0-GCCcore-12.3.0
4.2.1-GCCcore-13.3.0 |
|
MPICH |
MPICH is a high-performance and widely portable implementation
of the Message Passing Interface (MPI) standard (MPI-1, MPI-2 and MPI-3). |
4.2.2-GCC-13.3.0
4.3.0-GCC-14.2.0 |
|
Mako |
A super-fast templating language that borrows the best ideas from the existing templating languages |
1.2.4-GCCcore-12.3.0
1.2.4-GCCcore-13.2.0
1.3.5-GCCcore-13.3.0 |
|
Mesa |
Mesa is an open-source implementation of the OpenGL specification -
a system for rendering interactive 3D graphics. |
23.1.4-GCCcore-12.3.0
23.1.9-GCCcore-13.2.0
24.1.3-GCCcore-13.3.0 |
|
Meson |
Meson is a cross-platform build system designed to be both as fast and as user friendly as possible. |
0.62.1-GCCcore-11.3.0
1.1.1-GCCcore-12.3.0
1.2.3-GCCcore-13.2.0
1.4.0-GCCcore-13.3.0 |
|
Miniconda3 |
Miniconda is a free minimal installer for conda. It is a small,
bootstrap version of Anaconda that includes only conda, Python, the packages they
depend on, and a small number of other useful packages. |
|
Miniforge3 |
Miniforge is a free minimal installer for conda and Mamba specific
to conda-forge. |
|
NASM |
NASM: General-purpose x86 assembler |
2.15.05-GCCcore-11.3.0
2.16.01-GCCcore-12.3.0
2.16.01-GCCcore-13.2.0
2.16.03-GCCcore-13.3.0 |
|
NCCL |
The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective
communication primitives that are performance optimized for NVIDIA GPUs. |
2.18.3-GCCcore-12.3.0-CUDA-12.1.1
2.20.5-GCCcore-13.2.0-CUDA-12.4.0 |
|
NLopt |
NLopt is a free/open-source library for nonlinear optimization,
providing a common interface for a number of different free optimization routines
available online as well as original implementations of various other algorithms. |
2.7.1-GCCcore-12.3.0
2.7.1-GCCcore-13.3.0 |
|
NSPR |
Netscape Portable Runtime (NSPR) provides a platform-neutral API for system level
and libc-like functions. |
4.35-GCCcore-12.3.0
4.35-GCCcore-13.2.0
4.35-GCCcore-13.3.0 |
|
NSS |
Network Security Services (NSS) is a set of libraries designed to support cross-platform development
of security-enabled client and server applications. |
3.104-GCCcore-13.3.0
3.89.1-GCCcore-12.3.0
3.94-GCCcore-13.2.0 |
|
NVHPC |
C, C++ and Fortran compilers included with the NVIDIA HPC SDK (previously: PGI) |
|
Ninja |
Ninja is a small build system with a focus on speed. |
1.10.2-GCCcore-11.3.0
1.11.1-GCCcore-12.3.0
1.11.1-GCCcore-13.2.0
1.12.1-GCCcore-13.3.0 |
|
OpenBLAS |
OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version. |
0.3.20-GCC-11.3.0
0.3.23-GCC-12.3.0
0.3.24-GCC-13.2.0
0.3.27-GCC-13.3.0 |
|
OpenEXR |
OpenEXR is a high dynamic-range (HDR) image file format developed by Industrial Light & Magic
for use in computer imaging applications |
3.1.7-GCCcore-12.3.0
3.2.4-GCCcore-13.3.0 |
|
OpenFOAM |
OpenFOAM is a free, open source CFD software package.
OpenFOAM has an extensive range of features to solve anything from complex fluid flows
involving chemical reactions, turbulence and heat transfer,
to solid dynamics and electromagnetics. |
10-foss-2023a
11-foss-2023a
12-foss-2023a
5.0-20180606-foss-2023a
6-20190620-foss-2023a
8-foss-2023a
9-foss-2023a
v2312-foss-2023a
v2406-foss-2023a |
|
OpenJPEG |
OpenJPEG is an open-source JPEG 2000 codec written in
C language. It has been developed in order to promote the use of JPEG 2000,
a still-image compression standard from the Joint Photographic Experts Group
(JPEG). Since may 2015, it is officially recognized by ISO/IEC and ITU-T as
a JPEG 2000 Reference Software. |
2.5.0-GCCcore-12.3.0
2.5.0-GCCcore-13.2.0
2.5.2-GCCcore-13.3.0 |
|
OpenMM |
OpenMM is a toolkit for molecular simulation. |
8.0.0-foss-2022a
8.1.2-foss-2023b |
|
OpenMPI |
The Open MPI Project is an open source MPI-3 implementation. |
4.1.4-GCC-11.3.0
4.1.5-GCC-12.3.0
4.1.6-GCC-13.2.0
5.0.3-GCC-13.3.0 |
|
OpenPGM |
OpenPGM is an open source implementation of the Pragmatic General Multicast
(PGM) specification in RFC 3208 available at www.ietf.org. PGM is a reliable
and scalable multicast protocol that enables receivers to detect loss, request
retransmission of lost data, or notify an application of unrecoverable loss.
PGM is a receiver-reliable protocol, which means the receiver is responsible
for ensuring all data is received, absolving the sender of reception
responsibility.
|
5.2.122-GCCcore-12.3.0
5.2.122-GCCcore-13.2.0
5.2.122-GCCcore-13.3.0 |
|
OpenSSL |
The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured,
and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1 |
|
PCRE |
The PCRE library is a set of functions that implement regular expression
pattern matching using the same syntax and semantics as Perl 5.
|
8.45-GCCcore-11.3.0
8.45-GCCcore-12.3.0
8.45-GCCcore-13.2.0
8.45-GCCcore-13.3.0 |
|
PCRE2 |
The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax
and semantics as Perl 5.
|
10.42-GCCcore-12.3.0
10.42-GCCcore-13.2.0
10.43-GCCcore-13.3.0 |
|
PLUMED |
PLUMED is an open source library for free energy calculations in molecular systems which
works together with some of the most popular molecular dynamics engines. Free energy calculations can be
performed as a function of many order parameters with a particular focus on biological problems, using
state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD.
The software, written in C++, can be easily interfaced with both fortran and C/C++ codes.
|
2.9.0-foss-2023a
2.9.2-foss-2023b |
|
PMIx |
Process Management for Exascale Environments
PMI Exascale (PMIx) represents an attempt to
provide an extended version of the PMI standard specifically designed
to support clusters up to and including exascale sizes. The overall
objective of the project is not to branch the existing pseudo-standard
definitions - in fact, PMIx fully supports both of the existing PMI-1
and PMI-2 APIs - but rather to (a) augment and extend those APIs to
eliminate some current restrictions that impact scalability, and (b |
4.1.2-GCCcore-11.3.0
4.2.4-GCCcore-12.3.0
4.2.6-GCCcore-13.2.0
5.0.2-GCCcore-13.3.0 |
|
PROJ |
Program proj is a standard Unix filter function which converts
geographic longitude and latitude coordinates into cartesian coordinates |
6.3.1-GCCcore-12.3.0
9.2.0-GCCcore-12.3.0
9.4.1-GCCcore-13.3.0 |
|
PRRTE |
PRRTE is the PMIx Reference RunTime Environment |
|
Pango |
Pango is a library for laying out and rendering of text, with an emphasis on internationalization.
Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the
context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x. |
1.50.14-GCCcore-12.3.0
1.54.0-GCCcore-13.3.0 |
|
ParaView |
ParaView is a scientific parallel visualizer. |
5.11.2-foss-2023a
5.13.2-foss-2023a |
|
Perl |
Larry Wall’s Practical Extraction and Report Language
Includes a small selection of extra CPAN packages for core functionality.
|
5.34.0-GCCcore-11.2.0
5.34.1-GCCcore-11.3.0
5.36.1-GCCcore-12.3.0
5.38.0
5.38.0-GCCcore-13.2.0
5.38.2-GCCcore-13.3.0
5.40.0-GCCcore-14.2.0 |
|
Perl-bundle-CPAN |
A set of common packages from CPAN |
5.36.1-GCCcore-12.3.0
5.38.0-GCCcore-13.2.0
5.38.2-GCCcore-13.3.0 |
|
Pillow |
Pillow is the ‘friendly PIL fork’ by Alex Clark and Contributors.
PIL is the Python Imaging Library by Fredrik Lundh and Contributors. |
10.0.0-GCCcore-12.3.0
10.2.0-GCCcore-13.2.0
10.4.0-GCCcore-13.3.0
9.1.1-GCCcore-11.3.0 |
|
PostgreSQL |
PostgreSQL is a powerful, open source object-relational database system.
It is fully ACID compliant, has full support for foreign keys,
joins, views, triggers, and stored procedures (in multiple languages).
It includes most SQL:2008 data types, including INTEGER,
NUMERIC, BOOLEAN, CHAR, VARCHAR, DATE, INTERVAL, and TIMESTAMP.
It also supports storage of binary large objects, including pictures,
sounds, or video. It has native programming interfaces for C/C++, Java,
.Net, Perl, Python, Ruby, Tcl, ODBC, among others, and exceptional documentation. |
16.1-GCCcore-12.3.0
16.1-GCCcore-13.2.0
16.4-GCCcore-13.3.0 |
|
PyYAML |
PyYAML is a YAML parser and emitter for the Python programming language. |
5.4.1-GCCcore-11.2.0
6.0-GCCcore-11.3.0
6.0-GCCcore-12.3.0
6.0.1-GCCcore-13.2.0
6.0.2-GCCcore-13.3.0 |
|
PyZMQ |
Python bindings for ZeroMQ |
25.1.1-GCCcore-12.3.0
25.1.2-GCCcore-13.2.0 |
|
Python |
Python is a programming language that lets you work more quickly and integrate your systems
more effectively. |
3.10.4-GCCcore-11.3.0
3.10.4-GCCcore-11.3.0-bare
3.11.3-GCCcore-12.3.0
3.11.5-GCCcore-13.2.0
3.12.3-GCCcore-13.3.0
3.13.1-GCCcore-14.2.0
3.9.6-GCCcore-11.2.0
3.9.6-GCCcore-11.2.0-bare |
|
Python-bundle-PyPI |
Bundle of Python packages from PyPI |
2023.06-GCCcore-12.3.0
2023.10-GCCcore-13.2.0
2024.06-GCCcore-13.3.0 |
|
Qhull |
Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram,
halfspace intersection about a point, furthest-site Delaunay triangulation,
and furthest-site Voronoi diagram. The source code runs in 2-d, 3-d, 4-d, and
higher dimensions. Qhull implements the Quickhull algorithm for computing the
convex hull.
|
2020.2-GCCcore-11.3.0
2020.2-GCCcore-12.3.0
2020.2-GCCcore-13.2.0
2020.2-GCCcore-13.3.0 |
|
Qt5 |
Qt is a comprehensive cross-platform C++ application framework. |
5.15.10-GCCcore-12.3.0
5.15.13-GCCcore-13.2.0 |
|
R |
R is a free software environment for statistical computing
and graphics. |
4.3.2-gfbf-2023a
4.3.3-gfbf-2023b
4.4.2-gfbf-2024a |
|
R-bundle-Bioconductor |
Bioconductor provides tools for the analysis and coprehension
of high-throughput genomic data. |
3.18-foss-2023a-R-4.3.2
3.20-foss-2024a-R-4.4.2 |
|
R-bundle-CRAN |
Bundle of R packages from CRAN |
2023.12-foss-2023a
2024.11-foss-2024a |
|
RE2 |
RE2 is a fast, safe, thread-friendly alternative to backtracking regular
expression engines like those used in PCRE, Perl, and Python. It is a C++
library.
|
2023-08-01-GCCcore-12.3.0
2024-07-02-GCCcore-13.3.0 |
|
RapidJSON |
A fast JSON parser/generator for C++ with both SAX/DOM style API |
1.1.0-20230928-GCCcore-12.3.0
1.1.0-20240815-GCCcore-13.3.0 |
|
Rust |
Rust is a systems programming language that runs blazingly fast, prevents segfaults,
and guarantees thread safety. |
1.54.0-GCCcore-11.2.0
1.60.0-GCCcore-11.3.0
1.70.0-GCCcore-12.3.0
1.73.0-GCCcore-13.2.0
1.75.0-GCCcore-12.3.0
1.76.0-GCCcore-13.2.0
1.78.0-GCCcore-13.3.0 |
|
SAMtools |
SAM Tools provide various utilities for manipulating alignments in the SAM format,
including sorting, merging, indexing and generating alignments in a per-position format. |
1.18-GCC-12.3.0
1.19.2-GCC-13.2.0
1.21-GCC-13.3.0 |
|
SCOTCH |
Software package and libraries for sequential and parallel graph partitioning,
static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning. |
7.0.3-gompi-2023a
7.0.4-gompi-2023b
7.0.6-gompi-2024a |
|
SDL2 |
SDL: Simple DirectMedia Layer, a cross-platform multimedia library |
2.28.2-GCCcore-12.3.0
2.28.5-GCCcore-13.2.0
2.30.6-GCCcore-13.3.0 |
|
SQLite |
SQLite: SQL Database Engine in a C Library |
3.36-GCCcore-11.2.0
3.38.3-GCCcore-11.3.0
3.42.0-GCCcore-12.3.0
3.43.1-GCCcore-13.2.0
3.45.3-GCCcore-13.3.0
3.47.2-GCCcore-14.2.0 |
|
SWIG |
SWIG is a software development tool that connects programs written in C and C++ with
a variety of high-level programming languages. |
4.0.2-GCCcore-11.3.0
4.1.1-GCCcore-12.3.0
4.1.1-GCCcore-13.2.0
4.2.1-GCCcore-13.3.0 |
|
ScaFaCoS |
ScaFaCoS is a library of scalable fast coulomb solvers. |
1.0.4-foss-2023a
1.0.4-foss-2023b |
|
ScaLAPACK |
The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines
redesigned for distributed memory MIMD parallel computers. |
2.2.0-gompi-2022a-fb
2.2.0-gompi-2023a-fb
2.2.0-gompi-2023b-fb
2.2.0-gompi-2024a-fb |
|
SciPy-bundle |
Bundle of Python packages for scientific software |
2022.05-foss-2022a
2023.07-gfbf-2023a
2023.11-gfbf-2023b
2024.05-gfbf-2024a |
|
Szip |
Szip compression software, providing lossless compression of scientific data
|
2.1.1-GCCcore-11.3.0
2.1.1-GCCcore-12.3.0
2.1.1-GCCcore-13.2.0
2.1.1-GCCcore-13.3.0 |
|
Tcl |
Tcl (Tool Command Language) is a very powerful but easy to learn dynamic
programming language, suitable for a very wide range of uses, including web
and desktop applications, networking, administration, testing and many more.
|
8.6.11-GCCcore-11.2.0
8.6.12-GCCcore-11.3.0
8.6.13-GCCcore-12.3.0
8.6.13-GCCcore-13.2.0
8.6.14-GCCcore-13.3.0
8.6.16-GCCcore-14.2.0 |
|
TensorFlow |
An open-source software library for Machine Intelligence |
2.11.0-foss-2022a
2.13.0-foss-2023a |
|
Tk |
Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for
building a graphical user interface (GUI) in many different programming languages. |
8.6.12-GCCcore-11.3.0
8.6.13-GCCcore-12.3.0
8.6.13-GCCcore-13.2.0
8.6.14-GCCcore-13.3.0 |
|
Tkinter |
Tkinter module, built with the Python buildsystem |
3.10.4-GCCcore-11.3.0
3.11.3-GCCcore-12.3.0
3.11.5-GCCcore-13.2.0
3.12.3-GCCcore-13.3.0 |
|
Trimmomatic |
Trimmomatic performs a variety of useful trimming tasks for illumina
paired-end and single ended data.The selection of trimming steps and their associated
parameters are supplied on the command line. |
|
UCC |
UCC (Unified Collective Communication) is a collective
communication operations API and library that is flexible, complete, and
feature-rich for current and emerging programming models and runtimes.
|
1.0.0-GCCcore-11.3.0
1.2.0-GCCcore-12.3.0
1.2.0-GCCcore-13.2.0
1.3.0-GCCcore-13.3.0 |
|
UCX |
Unified Communication X
An open-source production grade communication framework for data centric
and high-performance applications
|
1.11.2-GCCcore-11.2.0
1.12.1-GCCcore-11.3.0
1.14.1-GCCcore-12.3.0
1.15.0-GCCcore-13.2.0
1.16.0-GCCcore-13.3.0
1.18.0-GCCcore-14.2.0 |
|
UCX-CUDA |
Unified Communication X
An open-source production grade communication framework for data centric
and high-performance applications
This module adds the UCX CUDA support.
|
1.11.2-GCCcore-11.2.0-CUDA-11.4.1
1.14.1-GCCcore-12.3.0-CUDA-12.1.1
1.15.0-GCCcore-13.2.0-CUDA-12.4.0 |
|
UDUNITS |
UDUNITS supports conversion of unit specifications between formatted and binary forms,
arithmetic manipulation of units, and conversion of values between compatible scales of measurement. |
2.2.28-GCCcore-12.3.0
2.2.28-GCCcore-13.2.0
2.2.28-GCCcore-13.3.0 |
|
UnZip |
UnZip is an extraction utility for archives compressed
in .zip format (also called “zipfiles”). Although highly compatible both
with PKWARE’s PKZIP and PKUNZIP utilities for MS-DOS and with Info-ZIP’s
own Zip program, our primary objectives have been portability and
non-MSDOS functionality. |
6.0-GCCcore-11.2.0
6.0-GCCcore-11.3.0
6.0-GCCcore-12.3.0
6.0-GCCcore-13.2.0
6.0-GCCcore-13.3.0
6.0-GCCcore-14.2.0 |
|
VTK |
The Visualization Toolkit (VTK) is an open-source, freely available software system for
3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several
interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization
algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques
such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation. |
9.2.6-foss-2023a
9.3.0-foss-2023a
9.3.0-foss-2023b |
|
Voro++ |
Voro++ is a software library for carrying out three-dimensional computations of the Voronoi
tessellation. A distinguishing feature of the Voro++ library is that it carries out cell-based calculations,
computing the Voronoi cell for each particle individually. It is particularly well-suited for applications that
rely on cell-based statistics, where features of Voronoi cells (eg. volume, centroid, number of faces) can be used
to analyze a system of particles. |
0.4.6-GCCcore-12.3.0
0.4.6-GCCcore-13.2.0 |
|
Wayland |
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.
|
1.22.0-GCCcore-12.3.0
1.22.0-GCCcore-13.2.0
1.23.0-GCCcore-13.3.0 |
|
X11 |
The X Window System (X11) is a windowing system for bitmap displays |
20220504-GCCcore-11.3.0
20230603-GCCcore-12.3.0
20231019-GCCcore-13.2.0
20240607-GCCcore-13.3.0 |
|
XZ |
xz: XZ utilities |
5.2.5-GCCcore-11.2.0
5.2.5-GCCcore-11.3.0
5.4.2-GCCcore-12.3.0
5.4.4-GCCcore-13.2.0
5.4.5-GCCcore-13.3.0
5.6.3-GCCcore-14.2.0 |
|
Xerces-C++ |
Xerces-C++ is a validating XML parser written in a portable
subset of C++. Xerces-C++ makes it easy to give your application the ability to
read and write XML data. A shared library is provided for parsing, generating,
manipulating, and validating XML documents using the DOM, SAX, and SAX2
APIs. |
3.2.4-GCCcore-12.3.0
3.2.5-GCCcore-13.3.0 |
|
Xvfb |
Xvfb is an X server that can run on machines with no display hardware and no physical input devices.
It emulates a dumb framebuffer using virtual memory. |
21.1.14-GCCcore-13.3.0
21.1.8-GCCcore-12.3.0 |
|
Yasm |
Yasm: Complete rewrite of the NASM assembler with BSD license |
1.3.0-GCCcore-12.3.0
1.3.0-GCCcore-13.2.0
1.3.0-GCCcore-13.3.0 |
|
Z3 |
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.
|
4.12.2-GCCcore-12.3.0
4.13.0-GCCcore-13.3.0
4.13.4-GCCcore-14.2.0 |
|
ZeroMQ |
ZeroMQ looks like an embeddable networking library but acts like a concurrency framework.
It gives you sockets that carry atomic messages across various transports like in-process,
inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout,
pub-sub, task distribution, and request-reply. It’s fast enough to be the fabric for clustered
products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous
message-processing tasks. It has a score of language APIs and runs on most operating systems. |
4.3.4-GCCcore-12.3.0
4.3.5-GCCcore-13.2.0
4.3.5-GCCcore-13.3.0 |
|
Zip |
Zip is a compression and file packaging/archive utility.
Although highly compatible both with PKWARE’s PKZIP and PKUNZIP
utilities for MS-DOS and with Info-ZIP’s own UnZip, our primary objectives
have been portability and other-than-MSDOS functionality |
3.0-GCCcore-11.2.0
3.0-GCCcore-11.3.0
3.0-GCCcore-12.3.0
3.0-GCCcore-13.3.0 |
|
ant |
Apache Ant is a Java library and command-line tool whose mission is to drive processes described in
build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of
Java applications. |
|
archspec |
A library for detecting, labeling, and reasoning about microarchitectures |
0.2.1-GCCcore-12.3.0
0.2.2-GCCcore-13.2.0 |
|
aria2 |
aria2 is a lightweight multi-protocol & multi-source command-line download utility. |
|
arpack-ng |
ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems. |
3.9.0-foss-2023a
3.9.1-foss-2024a |
|
arrow-R |
R interface to the Apache Arrow C++ library |
14.0.1-foss-2023a-R-4.3.2
17.0.0.1-foss-2024a-R-4.4.2 |
|
at-spi2-atk |
AT-SPI 2 toolkit bridge |
|
at-spi2-core |
Assistive Technology Service Provider Interface.
|
|
binutils |
binutils: GNU binary utilities |
2.37
2.37-GCCcore-11.2.0
2.38
2.38-GCCcore-11.3.0
2.39
2.40
2.40-GCCcore-12.3.0
2.40-GCCcore-13.2.0
2.42
2.42-GCCcore-13.3.0
2.42-GCCcore-14.2.0 |
|
bzip2 |
bzip2 is a freely available, patent free, high-quality data compressor. It
typically compresses files to within 10% to 15% of the best available
techniques (the PPM family of statistical compressors), whilst being around
twice as fast at compression and six times faster at decompression.
|
1.0.8-GCCcore-11.2.0
1.0.8-GCCcore-11.3.0
1.0.8-GCCcore-12.3.0
1.0.8-GCCcore-13.2.0
1.0.8-GCCcore-13.3.0
1.0.8-GCCcore-14.2.0 |
|
c-ares |
c-ares is a C library for asynchronous DNS requests (including name resolves) |
|
cURL |
libcurl is a free and easy-to-use client-side URL transfer library,
supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP,
LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP.
libcurl supports SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP
form based upload, proxies, cookies, user+password authentication (Basic,
Digest, NTLM, Negotiate, Kerberos), file transfer resume, http proxy tunneling
and more.
|
7.78.0-GCCcore-11.2.0
7.83.0-GCCcore-11.3.0
8.0.1-GCCcore-12.3.0
8.11.1-GCCcore-14.2.0
8.3.0-GCCcore-13.2.0
8.7.1-GCCcore-13.3.0 |
|
cairo |
Cairo is a 2D graphics library with support for multiple output devices.
Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers,
PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB |
1.17.8-GCCcore-12.3.0
1.18.0-GCCcore-13.2.0
1.18.0-GCCcore-13.3.0 |
|
cffi |
C Foreign Function Interface for Python. Interact with almost any C code from
Python, based on C-like declarations that you can often copy-paste from header
files or documentation.
|
1.15.1-GCCcore-12.3.0
1.15.1-GCCcore-13.2.0
1.16.0-GCCcore-13.3.0 |
|
cppy |
A small C++ header library which makes it easier to write
Python extension modules. The primary feature is a PyObject smart pointer
which automatically handles reference counting and provides convenience
methods for performing common object operations. |
1.2.1-GCCcore-11.3.0
1.2.1-GCCcore-12.3.0
1.2.1-GCCcore-13.2.0
1.2.1-GCCcore-13.3.0 |
|
cryptography |
cryptography is a package designed to expose cryptographic primitives and recipes to Python developers. |
41.0.1-GCCcore-12.3.0
41.0.5-GCCcore-13.2.0
42.0.8-GCCcore-13.3.0 |
|
cuDNN |
The NVIDIA CUDA Deep Neural Network library (cuDNN) is
a GPU-accelerated library of primitives for deep neural networks. |
8.2.2.26-CUDA-11.4.1
8.9.2.26-CUDA-12.1.1
8.9.7.29-CUDA-12.3.0
9.5.0.50-CUDA-12.6.0 |
|
dill |
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. |
0.3.6-GCCcore-11.3.0
0.3.7-GCCcore-12.3.0 |
|
double-conversion |
Efficient binary-decimal and decimal-binary conversion routines for IEEE doubles. |
3.1.5-GCCcore-11.2.0
3.2.0-GCCcore-11.3.0
3.3.0-GCCcore-12.3.0
3.3.0-GCCcore-13.2.0
3.3.0-GCCcore-13.3.0 |
|
expat |
Expat is an XML parser library written in C. It is a stream-oriented parser
in which an application registers handlers for things the parser might find
in the XML document (like start tags). |
2.4.1-GCCcore-11.2.0
2.4.8-GCCcore-11.3.0
2.5.0-GCCcore-12.3.0
2.5.0-GCCcore-13.2.0
2.6.2-GCCcore-13.3.0 |
|
expecttest |
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. |
|
ffnvcodec |
FFmpeg nvidia headers. Adds support for nvenc and nvdec. Requires Nvidia GPU and drivers to be present
(picked up dynamically). |
12.0.16.0
12.1.14.0
12.2.72.0 |
|
flatbuffers |
FlatBuffers: Memory Efficient Serialization Library |
2.0.7-GCCcore-11.3.0
23.5.26-GCCcore-12.3.0 |
|
flatbuffers-python |
Python Flatbuffers runtime library. |
2.0-GCCcore-11.3.0
23.5.26-GCCcore-12.3.0 |
|
flex |
Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner,
sometimes called a tokenizer, is a program which recognizes lexical patterns
in text.
|
2.6.4
2.6.4-GCCcore-11.2.0
2.6.4-GCCcore-11.3.0
2.6.4-GCCcore-12.3.0
2.6.4-GCCcore-13.2.0
2.6.4-GCCcore-13.3.0
2.6.4-GCCcore-14.2.0 |
|
flit |
A simple packaging tool for simple packages. |
3.9.0-GCCcore-12.3.0
3.9.0-GCCcore-13.2.0
3.9.0-GCCcore-13.3.0 |
|
fontconfig |
Fontconfig is a library designed to provide system-wide font configuration,
customization and application access.
|
2.14.0-GCCcore-11.3.0
2.14.2-GCCcore-12.3.0
2.14.2-GCCcore-13.2.0
2.15.0-GCCcore-13.3.0 |
|
foss |
GNU Compiler Collection (GCC) based compiler toolchain, including
OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK. |
|
freetype |
FreeType 2 is a software font engine that is designed to be small, efficient,
highly customizable, and portable while capable of producing high-quality
output (glyph images). It can be used in graphics libraries, display servers,
font conversion tools, text image generation tools, and many other products
as well.
|
2.12.1-GCCcore-11.3.0
2.13.0-GCCcore-12.3.0
2.13.2-GCCcore-13.2.0
2.13.2-GCCcore-13.3.0 |
|
gcloud |
Libraries and tools for interacting with Google Cloud products and services. |
|
gettext |
GNU ‘gettext’ is an important step for the GNU Translation Project, as it is an asset on which we may
build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools
and documentation |
0.21
0.21-GCCcore-11.2.0
0.21-GCCcore-11.3.0
0.21.1
0.21.1-GCCcore-12.3.0
0.22
0.22-GCCcore-13.2.0
0.22.5
0.22.5-GCCcore-13.3.0 |
|
gfbf |
GNU Compiler Collection (GCC) based compiler toolchain, including
FlexiBLAS (BLAS and LAPACK support) and (serial) FFTW. |
|
giflib |
giflib is a library for reading and writing gif images.
It is API and ABI compatible with libungif which was in wide use while
the LZW compression algorithm was patented. |
5.2.1-GCCcore-11.3.0
5.2.1-GCCcore-12.3.0
5.2.1-GCCcore-13.2.0
5.2.1-GCCcore-13.3.0 |
|
git |
Git is a free and open source distributed version control system designed
to handle everything from small to very large projects with speed and efficiency. |
2.33.1-GCCcore-11.2.0-nodocs
2.36.0-GCCcore-11.3.0-nodocs
2.41.0-GCCcore-12.3.0-nodocs
2.42.0-GCCcore-13.2.0
2.45.1-GCCcore-13.3.0 |
|
gmpy2 |
GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x |
|
gnuplot |
Portable interactive, function plotting utility |
5.4.8-GCCcore-12.3.0
6.0.1-GCCcore-13.3.0 |
|
gompi |
GNU Compiler Collection (GCC) based compiler toolchain,
including OpenMPI for MPI support. |
|
googletest |
Google’s framework for writing C++ tests on a variety of platforms |
1.13.0-GCCcore-12.3.0
1.14.0-GCCcore-13.2.0
1.15.2-GCCcore-13.3.0 |
|
gperf |
GNU gperf is a perfect hash function generator. For a given list of strings,
it produces a hash function and hash table, in form of C or C++ code, for
looking up a value depending on the input string. The hash function is
perfect, which means that the hash table has no collisions, and the hash
table lookup needs a single string comparison only.
|
3.1-GCCcore-11.3.0
3.1-GCCcore-12.3.0
3.1-GCCcore-13.2.0
3.1-GCCcore-13.3.0 |
|
graphite2 |
Graphite is a “smart font” system developed specifically to
handle the complexities of lesser-known languages of the world. |
1.3.14-GCCcore-12.3.0
1.3.14-GCCcore-13.2.0
1.3.14-GCCcore-13.3.0 |
|
groff |
Groff (GNU troff) is a typesetting system that reads plain text mixed with formatting commands
and produces formatted output. |
1.22.4-GCCcore-11.2.0
1.22.4-GCCcore-11.3.0
1.22.4-GCCcore-12.3.0
1.23.0-GCCcore-13.2.0
1.23.0-GCCcore-13.3.0 |
|
gzip |
gzip (GNU zip) is a popular data compression program as a replacement for compress |
1.12-GCCcore-11.3.0
1.12-GCCcore-12.3.0
1.13-GCCcore-13.2.0
1.13-GCCcore-13.3.0 |
|
h5py |
HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library,
version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous
amounts of data. |
3.7.0-foss-2022a
3.9.0-foss-2023a |
|
hatch-jupyter-builder |
Hatch Jupyter Builder is a plugin for the hatchling Python build backend. It is
primarily targeted for package authors who are providing JavaScript as part of
their Python packages.
Typical use cases are Jupyter Lab Extensions and Jupyter Widgets. |
|
hatchling |
Extensible, standards compliant build backend used by Hatch,
a modern, extensible Python project manager. |
1.18.0-GCCcore-12.3.0
1.18.0-GCCcore-13.2.0
1.24.2-GCCcore-13.3.0 |
|
help2man |
help2man produces simple manual pages from the ‘–help’ and ‘–version’ output of other commands. |
1.48.3-GCCcore-11.2.0
1.49.2-GCCcore-11.3.0
1.49.3-GCCcore-12.3.0
1.49.3-GCCcore-13.2.0
1.49.3-GCCcore-13.3.0
1.49.3-GCCcore-14.2.0 |
|
hwloc |
The Portable Hardware Locality (hwloc) software package provides a portable
abstraction (across OS, versions, architectures, …) of the hierarchical
topology of modern architectures, including NUMA memory nodes, sockets, shared
caches, cores and simultaneous multithreading. It also gathers various system
attributes such as cache and memory information as well as the locality of I/O
devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily
aims at helping applications with gathering information about modern computing
hardware so as to exploit it accordingly and efficiently.
|
2.10.0-GCCcore-13.3.0
2.7.1-GCCcore-11.3.0
2.9.1-GCCcore-12.3.0
2.9.2-GCCcore-13.2.0 |
|
hypothesis |
Hypothesis is an advanced testing library for Python. It lets you write tests which are parametrized
by a source of examples, and then generates simple and comprehensible examples that make your tests fail. This lets
you find more bugs in your code with less work. |
6.103.1-GCCcore-13.3.0
6.14.6-GCCcore-11.2.0
6.46.7-GCCcore-11.3.0
6.82.0-GCCcore-12.3.0
6.90.0-GCCcore-13.2.0 |
|
iimpi |
Intel C/C++ and Fortran compilers, alongside Intel MPI. |
|
imkl |
Intel oneAPI Math Kernel Library |
2023.1.0
2023.1.0-gompi-2023a
2023.2.0-gompi-2023b
2024.2.0 |
|
imkl-FFTW |
FFTW interfaces using Intel oneAPI Math Kernel Library |
2023.1.0-iimpi-2023a
2024.2.0-iimpi-2024a |
|
impi |
Intel MPI Library, compatible with MPICH ABI |
2021.13.0-intel-compilers-2024.2.0
2021.9.0-intel-compilers-2023.1.0 |
|
intel |
Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL). |
|
intel-compilers |
Intel C, C++ & Fortran compilers (classic and oneAPI) |
|
intltool |
intltool is a set of tools to centralize translation of
many different file formats using GNU gettext-compatible PO files. |
0.51.0-GCCcore-11.3.0
0.51.0-GCCcore-12.3.0
0.51.0-GCCcore-13.2.0
0.51.0-GCCcore-13.3.0 |
|
jax |
Composable transformations of Python+NumPy programs:
differentiate, vectorize, JIT to GPU/TPU, and more |
|
jbigkit |
JBIG-KIT is a software implementation of the JBIG1 data
compression standard (ITU-T T.82), which was designed for bi-level image
data, such as scanned documents. |
2.1-GCCcore-11.3.0
2.1-GCCcore-12.3.0
2.1-GCCcore-13.2.0
2.1-GCCcore-13.3.0 |
|
jedi |
Jedi - an awesome autocompletion, static analysis and refactoring library for Python.
It is typically used in IDEs/editors plugins. Jedi has a focus on autocompletion and goto functionality.
Other features include refactoring, code search and finding references.
|
0.19.0-GCCcore-12.3.0
0.19.1-GCCcore-13.2.0
0.19.1-GCCcore-13.3.0 |
|
json-c |
JSON-C implements a reference counting object model that allows you to easily construct JSON objects
in C, output them as JSON formatted strings and parse JSON formatted strings back into the C representation of JSON
objects. |
0.16-GCCcore-12.3.0
0.17-GCCcore-13.3.0 |
|
jupyter-server |
The Jupyter Server provides the backend (i.e. the core services, APIs, and REST
endpoints) for Jupyter web applications like Jupyter notebook, JupyterLab, and
Voila. |
|
kim-api |
Open Knowledgebase of Interatomic Models.
KIM is an API and OpenKIM is a collection of interatomic models (potentials) for
atomistic simulations. This is a library that can be used by simulation programs
to get access to the models in the OpenKIM database.
This EasyBuild only installs the API, the models can be installed with the
package openkim-models, or the user can install them manually by running
kim-api-collections-management install user MODELNAME
or
kim-api-collections-management install user OpenKIM
to install them all.
|
2.3.0-GCC-12.3.0
2.3.0-GCC-13.2.0 |
|
kineto |
A CPU+GPU Profiling library that provides access to timeline traces and hardware performance counters |
|
libGLU |
The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. |
9.0.3-GCCcore-12.3.0
9.0.3-GCCcore-13.2.0
9.0.3-GCCcore-13.3.0 |
|
libaec |
Libaec provides fast lossless compression of 1 up to 32 bit wide signed or unsigned integers
(samples). The library achieves best results for low entropy data as often encountered in space imaging
instrument data or numerical model output from weather or climate simulations. While floating point representations
are not directly supported, they can also be efficiently coded by grouping exponents and mantissa. |
|
libaio |
Asynchronous input/output library that uses the kernels native interface. |
0.3.113-GCCcore-12.3.0
0.3.113-GCCcore-13.2.0
0.3.113-GCCcore-13.3.0 |
|
libarchive |
Multi-format archive and compression library
|
3.5.1-GCCcore-11.2.0
3.6.1-GCCcore-11.3.0
3.6.2-GCCcore-12.3.0
3.7.2-GCCcore-13.2.0
3.7.4-GCCcore-13.3.0
3.7.7-GCCcore-14.2.0 |
|
libcerf |
libcerf is a self-contained numeric library that provides an efficient and
accurate implementation of complex error functions, along with Dawson,
Faddeeva, and Voigt functions.
|
2.3-GCCcore-12.3.0
2.4-GCCcore-13.3.0 |
|
libdeflate |
Heavily optimized library for DEFLATE/zlib/gzip compression and decompression. |
1.10-GCCcore-11.3.0
1.18-GCCcore-12.3.0
1.19-GCCcore-13.2.0
1.20-GCCcore-13.3.0 |
|
libdrm |
Direct Rendering Manager runtime library. |
2.4.115-GCCcore-12.3.0
2.4.117-GCCcore-13.2.0
2.4.122-GCCcore-13.3.0 |
|
libepoxy |
Epoxy is a library for handling OpenGL function pointer management for you |
|
libevent |
The libevent API provides a mechanism to execute a callback function when
a specific event occurs on a file descriptor or after a timeout has been
reached. Furthermore, libevent also support callbacks due to signals or
regular timeouts.
|
2.1.12-GCCcore-11.2.0
2.1.12-GCCcore-11.3.0
2.1.12-GCCcore-12.3.0
2.1.12-GCCcore-13.2.0
2.1.12-GCCcore-13.3.0 |
|
libfabric |
Libfabric is a core component of OFI. It is the library that defines and exports
the user-space API of OFI, and is typically the only software that applications
deal with directly. It works in conjunction with provider libraries, which are
often integrated directly into libfabric.
|
1.15.1-GCCcore-11.3.0
1.18.0-GCCcore-12.3.0
1.19.0-GCCcore-13.2.0
1.21.0-GCCcore-13.3.0 |
|
libffi |
The libffi library provides a portable, high level programming interface to
various calling conventions. This allows a programmer to call any function
specified by a call interface description at run-time. |
3.4.2-GCCcore-11.2.0
3.4.2-GCCcore-11.3.0
3.4.4-GCCcore-12.3.0
3.4.4-GCCcore-13.2.0
3.4.5-GCCcore-13.3.0
3.4.5-GCCcore-14.2.0 |
|
libgd |
GD is an open source code library for the dynamic creation of images by programmers. |
2.3.3-GCCcore-12.3.0
2.3.3-GCCcore-13.3.0 |
|
libgeotiff |
Library for reading and writing coordinate system information from/to GeoTIFF files |
1.7.1-GCCcore-12.3.0
1.7.3-GCCcore-13.3.0 |
|
libgit2 |
libgit2 is a portable, pure C implementation of the Git core methods provided as a re-entrant
linkable library with a solid API, allowing you to write native speed custom Git applications in any language
which supports C bindings. |
1.7.1-GCCcore-12.3.0
1.7.2-GCCcore-13.2.0
1.8.1-GCCcore-13.3.0 |
|
libglvnd |
libglvnd is a vendor-neutral dispatch layer for arbitrating OpenGL API calls between multiple vendors. |
1.6.0-GCCcore-12.3.0
1.7.0-GCCcore-13.2.0
1.7.0-GCCcore-13.3.0 |
|
libiconv |
Libiconv converts from one character encoding to another through Unicode conversion |
1.17-GCCcore-11.3.0
1.17-GCCcore-12.3.0
1.17-GCCcore-13.2.0
1.17-GCCcore-13.3.0
1.18-GCCcore-14.2.0 |
|
libjpeg-turbo |
libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to
accelerate baseline JPEG compression and decompression. libjpeg is a library
that implements JPEG image encoding, decoding and transcoding.
|
2.1.3-GCCcore-11.3.0
2.1.5.1-GCCcore-12.3.0
3.0.1-GCCcore-13.2.0
3.0.1-GCCcore-13.3.0 |
|
libogg |
Ogg is a multimedia container format, and the native file and stream format for the Xiph.org
multimedia codecs. |
1.3.5-GCCcore-12.3.0
1.3.5-GCCcore-13.3.0 |
|
libopus |
Opus is a totally open, royalty-free, highly versatile audio codec. Opus is unmatched for interactive
speech and music transmission over the Internet, but is also intended for storage and streaming applications. It is
standardized by the Internet Engineering Task Force (IETF) as RFC 6716 which incorporated technology from Skype’s
SILK codec and Xiph.Org’s CELT codec. |
1.4-GCCcore-12.3.0
1.5.2-GCCcore-13.3.0 |
|
libpciaccess |
Generic PCI access library. |
0.16-GCCcore-11.3.0
0.17-GCCcore-12.3.0
0.17-GCCcore-13.2.0
0.18.1-GCCcore-13.3.0 |
|
libpng |
libpng is the official PNG reference library |
1.6.37-GCCcore-11.3.0
1.6.39-GCCcore-12.3.0
1.6.40-GCCcore-13.2.0
1.6.43-GCCcore-13.3.0 |
|
libreadline |
The GNU Readline library provides a set of functions for use by applications
that allow users to edit command lines as they are typed in. Both Emacs and
vi editing modes are available. The Readline library includes additional
functions to maintain a list of previously-entered command lines, to recall
and perhaps reedit those lines, and perform csh-like history expansion on
previous commands.
|
8.1-GCCcore-11.2.0
8.1.2-GCCcore-11.3.0
8.2-GCCcore-12.3.0
8.2-GCCcore-13.2.0
8.2-GCCcore-13.3.0
8.2-GCCcore-14.2.0 |
|
libsndfile |
Libsndfile is a C library for reading and writing files containing sampled sound
(such as MS Windows WAV and the Apple/SGI AIFF format) through one standard library interface. |
1.2.2-GCCcore-12.3.0
1.2.2-GCCcore-13.3.0 |
|
libsodium |
Sodium is a modern, easy-to-use software library for encryption, decryption,
signatures, password hashing and more.
|
1.0.18-GCCcore-12.3.0
1.0.19-GCCcore-13.2.0
1.0.20-GCCcore-13.3.0 |
|
libtirpc |
Libtirpc is a port of Suns Transport-Independent RPC library to Linux. |
1.3.3-GCCcore-12.3.0
1.3.5-GCCcore-13.3.0 |
|
libtool |
GNU libtool is a generic library support script. Libtool hides the complexity
of using shared libraries behind a consistent, portable interface.
|
2.4.6-GCCcore-11.2.0
2.4.7
2.4.7-GCCcore-11.3.0
2.4.7-GCCcore-12.3.0
2.4.7-GCCcore-13.2.0
2.4.7-GCCcore-13.3.0
2.5.4-GCCcore-14.2.0 |
|
libunwind |
The primary goal of libunwind is to define a portable and efficient C programming interface
(API) to determine the call-chain of a program. The API additionally provides the means to manipulate the
preserved (callee-saved) state of each call-frame and to resume execution at any point in the call-chain
(non-local goto). The API supports both local (same-process) and remote (across-process) operation.
As such, the API is useful in a number of applications |
1.6.2-GCCcore-12.3.0
1.6.2-GCCcore-13.2.0
1.8.1-GCCcore-13.3.0 |
|
libvorbis |
Ogg Vorbis is a fully open, non-proprietary, patent-and-royalty-free, general-purpose compressed
audio format |
1.3.7-GCCcore-12.3.0
1.3.7-GCCcore-13.3.0 |
|
libwebp |
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. |
1.3.1-GCCcore-12.3.0
1.3.2-GCCcore-13.2.0
1.4.0-GCCcore-13.3.0 |
|
libxml2 |
Libxml2 is the XML C parser and toolchain developed for the Gnome project
(but usable outside of the Gnome platform).
|
2.11.4-GCCcore-12.3.0
2.11.5-GCCcore-13.2.0
2.12.7-GCCcore-13.3.0
2.13.4-GCCcore-14.2.0
2.9.10-GCCcore-11.2.0
2.9.13-GCCcore-11.3.0 |
|
libxslt |
Libxslt is the XSLT C library developed for the GNOME project
(but usable outside of the Gnome platform). |
1.1.38-GCCcore-12.3.0
1.1.38-GCCcore-13.2.0
1.1.42-GCCcore-13.3.0 |
|
libyaml |
LibYAML is a YAML parser and emitter written in C. |
0.2.5-GCCcore-11.2.0
0.2.5-GCCcore-11.3.0
0.2.5-GCCcore-12.3.0
0.2.5-GCCcore-13.2.0
0.2.5-GCCcore-13.3.0 |
|
lxml |
The lxml XML toolkit is a Pythonic binding for the C libraries libxml2 and libxslt. |
4.9.2-GCCcore-12.3.0
4.9.3-GCCcore-13.2.0
5.3.0-GCCcore-13.3.0 |
|
lz4 |
LZ4 is lossless compression algorithm, providing compression speed at 400 MB/s per core.
It features an extremely fast decoder, with speed in multiple GB/s per core. |
1.9.3-GCCcore-11.3.0
1.9.4-GCCcore-12.3.0
1.9.4-GCCcore-13.2.0
1.9.4-GCCcore-13.3.0 |
|
magma |
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. |
| 2.7.2-foss-2023a-CUDA-12.1.1 |
|
make |
GNU version of make utility |
4.3-GCCcore-11.3.0
4.4.1-GCCcore-12.3.0
4.4.1-GCCcore-13.2.0
4.4.1-GCCcore-13.3.0 |
|
matplotlib |
matplotlib is a python 2D plotting library which produces publication quality figures in a variety of
hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python
and ipython shell, web application servers, and six graphical user interface toolkits. |
3.5.2-foss-2022a
3.7.2-gfbf-2023a
3.8.2-gfbf-2023b
3.9.2-gfbf-2024a |
|
maturin |
This project is meant as a zero configuration
replacement for setuptools-rust and milksnake. It supports building
wheels for python 3.5+ on windows, linux, mac and freebsd, can upload
them to pypi and has basic pypy and graalpy support. |
1.3.1-GCCcore-13.2.0
1.4.0-GCCcore-12.3.0-Rust-1.75.0
1.5.0-GCCcore-13.2.0-Rust-1.76.0
1.6.0-GCCcore-13.3.0 |
|
meson-python |
Python build backend (PEP 517) for Meson projects |
0.13.2-GCCcore-12.3.0
0.15.0-GCCcore-13.2.0
0.16.0-GCCcore-13.3.0 |
|
minimap2 |
Minimap2 is a fast sequence mapping and alignment
program that can find overlaps between long noisy reads, or map long
reads or their assemblies to a reference genome optionally with detailed
alignment (i.e. CIGAR). At present, it works efficiently with query
sequences from a few kilobases to ~100 megabases in length at an error
rate ~15%. Minimap2 outputs in the PAF or the SAM format. On limited
test data sets, minimap2 is over 20 times faster than most other
long-read aligners. It will replace BWA-MEM for long reads and contig
alignment. |
2.26-GCCcore-12.3.0
2.28-GCCcore-13.2.0 |
|
mpi4py |
MPI for Python (mpi4py) provides bindings of the Message Passing Interface (MPI) standard for
the Python programming language, allowing any Python program to exploit multiple processors. |
3.1.4-gompi-2023a
3.1.5-gompi-2023b
4.0.1-gompi-2024a |
|
ncurses |
The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0,
and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and
function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses. |
6.2
6.2-GCCcore-11.2.0
6.3
6.3-GCCcore-11.3.0
6.4
6.4-GCCcore-12.3.0
6.4-GCCcore-13.2.0
6.5
6.5-GCCcore-13.3.0
6.5-GCCcore-14.2.0 |
|
netCDF |
NetCDF (network Common Data Form) is a set of software libraries
and machine-independent data formats that support the creation, access, and sharing of array-oriented
scientific data. |
4.9.2-gompi-2023a
4.9.2-gompi-2023b
4.9.2-gompi-2024a |
|
nettle |
Nettle is a cryptographic library that is designed to fit easily
in more or less any context: In crypto toolkits for object-oriented
languages (C++, Python, Pike, …), in applications like LSH or GNUPG,
or even in kernel space. |
3.10-GCCcore-13.3.0
3.9.1-GCCcore-12.3.0 |
|
networkx |
NetworkX is a Python package for the creation, manipulation,
and study of the structure, dynamics, and functions of complex networks. |
2.8.4-foss-2022a
3.1-gfbf-2023a
3.2.1-gfbf-2023b |
|
nlohmann_json |
JSON for Modern C++ |
3.11.2-GCCcore-12.3.0
3.11.3-GCCcore-13.3.0 |
|
nodejs |
Node.js is a platform built on Chrome’s JavaScript runtime
for easily building fast, scalable network applications. Node.js uses an
event-driven, non-blocking I/O model that makes it lightweight and efficient,
perfect for data-intensive real-time applications that run across distributed devices. |
18.17.1-GCCcore-12.3.0
20.13.1-GCCcore-13.3.0
20.9.0-GCCcore-13.2.0 |
|
nsync |
nsync is a C library that exports various synchronization primitives, such as mutexes |
1.25.0-GCCcore-11.3.0
1.26.0-GCCcore-12.3.0 |
|
numactl |
The numactl program allows you to run your application program on specific
cpu’s and memory nodes. It does this by supplying a NUMA memory policy to
the operating system before running your program. The libnuma library provides
convenient ways for you to add NUMA memory policies into your own program.
|
2.0.14-GCCcore-11.2.0
2.0.14-GCCcore-11.3.0
2.0.16-GCCcore-12.3.0
2.0.16-GCCcore-13.2.0
2.0.18-GCCcore-13.3.0
2.0.19-GCCcore-14.2.0 |
|
p7zip |
p7zip is a quick port of 7z.exe and 7za.exe (CLI version of
7zip) for Unix. 7-Zip is a file archiver with highest compression ratio. |
17.04-GCCcore-12.3.0
17.05-GCCcore-13.3.0 |
|
parallel |
parallel: Build and execute shell commands in parallel |
|
patchelf |
PatchELF is a small utility to modify the dynamic linker and RPATH of ELF executables. |
0.18.0-GCCcore-12.3.0
0.18.0-GCCcore-13.2.0
0.18.0-GCCcore-13.3.0 |
|
pixman |
Pixman is a low-level software library for pixel manipulation, providing
features such as image compositing and trapezoid rasterization. Important
users of pixman are the cairo graphics library and the X server.
|
0.42.2-GCCcore-12.3.0
0.42.2-GCCcore-13.2.0
0.43.4-GCCcore-13.3.0 |
|
pkg-config |
pkg-config is a helper tool used when compiling applications and libraries.
It helps you insert the correct compiler options on the command line so an
application can use gcc -o test test.c pkg-config --libs --cflags glib-2.0
for instance, rather than hard-coding values on where to find glib (or other
libraries).
|
|
pkgconf |
pkgconf is a program which helps to configure compiler and linker flags for development libraries.
It is similar to pkg-config from freedesktop.org. |
1.8.0
1.8.0-GCCcore-11.3.0
1.9.5-GCCcore-12.3.0
2.0.3-GCCcore-13.2.0
2.2.0-GCCcore-13.3.0
2.3.0-GCCcore-14.2.0 |
|
pkgconfig |
pkgconfig is a Python module to interface with the pkg-config command line tool |
1.5.5-GCCcore-11.2.0-python
1.5.5-GCCcore-11.3.0-python
1.5.5-GCCcore-12.3.0-python |
|
poetry |
Python packaging and dependency management made easy. Poetry helps you declare, manage and install
dependencies of Python projects, ensuring you have the right stack everywhere. |
1.5.1-GCCcore-12.3.0
1.6.1-GCCcore-13.2.0
1.7.1-GCCcore-12.3.0
1.8.3-GCCcore-13.3.0 |
|
protobuf |
Protocol Buffers (a.k.a., protobuf) are Google’s
language-neutral, platform-neutral, extensible mechanism for
serializing structured data. |
24.0-GCCcore-12.3.0
3.17.3-GCCcore-11.2.0
3.19.4-GCCcore-11.3.0 |
|
protobuf-python |
Python Protocol Buffers runtime library. |
3.19.4-GCCcore-11.3.0
4.24.0-GCCcore-12.3.0 |
|
pybind11 |
pybind11 is a lightweight header-only library that exposes C++ types in Python and vice versa,
mainly to create Python bindings of existing C++ code. |
2.11.1-GCCcore-12.3.0
2.11.1-GCCcore-13.2.0
2.12.0-GCC-13.3.0
2.7.1-GCCcore-11.2.0
2.9.2-GCCcore-11.3.0 |
|
pytest-flakefinder |
Runs tests multiple times to expose flakiness. |
|
pytest-rerunfailures |
pytest plugin to re-run tests to eliminate flaky failures. |
|
pytest-shard |
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 |
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. |
|
rclone |
Rclone is a command line program to sync files and directories to and from
a variety of online storage services
|
|
re2c |
re2c is a free and open-source lexer generator for C and C++. Its main goal is generating
fast lexers: at least as fast as their reasonably optimized hand-coded counterparts. Instead of using
traditional table-driven approach, re2c encodes the generated finite state automata directly in the form
of conditional jumps and comparisons. |
3.1-GCCcore-12.3.0
3.1-GCCcore-13.2.0
3.1-GCCcore-13.3.0 |
|
rjags |
The rjags package is an interface to the JAGS library. |
|
scikit-build |
Scikit-Build, or skbuild, is an improved build system generator
for CPython C/C++/Fortran/Cython extensions. |
0.17.6-GCCcore-12.3.0
0.17.6-GCCcore-13.2.0
0.17.6-GCCcore-13.3.0 |
|
scikit-build-core |
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. |
0.10.6-GCCcore-13.3.0
0.5.0-GCCcore-12.3.0
0.9.3-GCCcore-13.2.0 |
|
setuptools-rust |
setuptools-rust is a plugin for setuptools to build Rust Python extensions
implemented with PyO3 or rust-cpython. |
1.6.0-GCCcore-12.3.0
1.8.0-GCCcore-13.2.0
1.9.0-GCCcore-13.3.0 |
|
snappy |
Snappy is a compression/decompression library. It does not aim
for maximum compression, or compatibility with any other compression library;
instead, it aims for very high speeds and reasonable compression. |
1.1.10-GCCcore-12.3.0
1.1.10-GCCcore-13.2.0
1.1.9-GCCcore-11.3.0
1.2.1-GCCcore-13.3.0 |
|
spglib-python |
Spglib for Python. Spglib is a library for finding and handling crystal symmetries written in C. |
2.1.0-gfbf-2023a
2.5.0-gfbf-2024a |
|
sympy |
SymPy is a Python library for symbolic mathematics. It aims to
become a full-featured computer algebra system (CAS) while keeping the code as
simple as possible in order to be comprehensible and easily extensible. SymPy
is written entirely in Python and does not require any external libraries. |
|
tbb |
Intel(R) Threading Building Blocks (Intel(R) TBB) lets you easily write parallel C++ programs that
take full advantage of multicore performance, that are portable, composable and have future-proof scalability. |
2021.11.0-GCCcore-12.3.0
2021.13.0-GCCcore-13.2.0 |
|
tornado |
Tornado is a Python web framework and asynchronous networking library. |
6.4-GCCcore-13.2.0
6.4.1-GCCcore-13.3.0 |
|
utf8proc |
utf8proc is a small, clean C library that provides Unicode normalization, case-folding,
and other operations for data in the UTF-8 encoding. |
2.8.0-GCCcore-12.3.0
2.9.0-GCCcore-13.3.0 |
|
util-linux |
Set of Linux utilities |
2.38-GCCcore-11.3.0
2.39-GCCcore-12.3.0
2.39-GCCcore-13.2.0
2.40-GCCcore-13.3.0 |
|
virtualenv |
A tool for creating isolated virtual python environments. |
20.23.1-GCCcore-12.3.0
20.24.6-GCCcore-13.2.0
20.26.2-GCCcore-13.3.0 |
|
x264 |
x264 is a free software library and application for encoding video streams
into the H.264/MPEG-4 AVC compression format, and is released under the
terms of the GNU GPL.
|
20230226-GCCcore-12.3.0
20231019-GCCcore-13.2.0
20240513-GCCcore-13.3.0 |
|
x265 |
x265 is a free software library and application for encoding video streams
into the H.265 AVC compression format, and is released under the terms of
the GNU GPL.
|
3.5-GCCcore-12.3.0
3.5-GCCcore-13.2.0
3.6-GCCcore-13.3.0 |
|
xorg-macros |
X.org macros utilities. |
1.19.3-GCCcore-11.3.0
1.20.0-GCCcore-12.3.0
1.20.0-GCCcore-13.2.0
1.20.1-GCCcore-13.3.0 |
|
xxd |
xxd is part of the VIM package and this will only install xxd, not vim!
xxd converts to/from hexdumps of binary files. |
9.0.2112-GCCcore-12.3.0
9.1.0307-GCCcore-13.2.0 |
|
yaml-cpp |
yaml-cpp is a YAML parser and emitter in C++ matching the YAML 1.2 spec |
|
zlib |
zlib is designed to be a free, general-purpose, legally unencumbered – that is,
not covered by any patents – lossless data-compression library for use on virtually any
computer hardware and operating system. |
1.2.11
1.2.11-GCCcore-11.2.0
1.2.12
1.2.12-GCCcore-11.3.0
1.2.13
1.2.13-GCCcore-12.3.0
1.2.13-GCCcore-13.2.0
1.3.1
1.3.1-GCCcore-13.3.0
1.3.1-GCCcore-14.2.0 |
|
zstd |
Zstandard is a real-time compression algorithm, providing high compression ratios.
It offers a very wide range of compression/speed trade-off, while being backed by a very fast decoder.
It also offers a special mode for small data, called dictionary compression, and can create dictionaries
from any sample set. |
1.5.2-GCCcore-11.3.0
1.5.5-GCCcore-12.3.0
1.5.5-GCCcore-13.2.0
1.5.6-GCCcore-13.3.0 |
|
AFNI |
AFNI 25.0.13 - A suite for analyzing and visualizing functional MRI data using an Apptainer container. |
|
AMD-uProf |
AMD uProf is a performance analysis tool for applications running on Windows, Linux & FreeBSD
operating systems. It allows developers to better understand the runtime performance of their application and
to identify ways to improve its performance. |
|
BEDOPS |
Tools for fast genomic feature operations |
|
Blender |
Blender is the free and open source 3D creation suite. It supports
the entirety of the 3D pipeline-modeling, rigging, animation, simulation, rendering,
compositing and motion tracking, even video editing and game creation. |
| 4.4.0-linux-x86_64-CUDA-12.6.0 |
|
COMSOL |
COMSOL Multiphysics is a general-purpose software platform, based on
advanced numerical methods, for modeling and simulating physics-based
problems.
|
|
CellRanger |
Cell Ranger is a set of analysis pipelines that process Chromium
single-cell RNA-seq output to align reads, generate gene-cell matrices and perform
clustering and gene expression analysis. |
|
CellRanger-ARC |
Cell Ranger ARC is a set of analysis pipelines that process
Chromium Single Cell Multiome ATAC + Gene Expression sequencing data to generate a
variety of analyses pertaining to gene expression, chromatin accessibility and
their linkage. Furthermore, since the ATAC and gene expression measurements are on
the very same cell, we are able to perform analyses that link chromatin
accessibility and gene expression. |
|
CellRanger-ATAC |
Cell Ranger ATAC is a set of analysis pipelines that process
Chromium Single Cell ATAC data. |
|
Chimera |
UCSF Chimera is a highly extensible program for interactive visualization
and analysis of molecular structures and related data, including density maps, supramolecular
assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. |
|
ChimeraX |
UCSF ChimeraX - Molecular visualization tool |
|
Coot |
Coot is for macromolecular model building, model completion
and validation, particularly suitable for protein modelling using X-ray data. |
| 0.9.8.92-binary-Linux-x86_64-scientific-linux-7.6-python-gtk2 |
|
DeepLabCut |
Markerless pose estimation toolbox. |
|
Delft3D4 |
Delft3D4 environment in Apptainer container |
|
Delft3D-FM |
Delft3D Flexible Mesh Suite 2024.03 for environmental modeling |
|
FSL |
FSL (FMRIB Software Library) is a set of analysis tools for FMRI, MRI, and DTI brain imaging data. |
|
FastQC |
FastQC is a quality control application for high throughput
sequence data. It reads in sequence data in a variety of formats and can either
provide an interactive application to review the results of several different
QC checks, or create an HTML based report which can be integrated into a
pipeline. |
|
Gaussian |
Gaussian provides state-of-the-art capabilities for electronic structure
modeling. Gaussian 09 is licensed for a wide variety of computer
systems. All versions of Gaussian 09 contain every scientific/modeling
feature, and none imposes any artificial limitations on calculations
other than your computing resources and patience.
This is the official gaussian AVX build.
|
|
I-TASSER |
I-TASSER - Iterative Threading ASSEmbly Refinement for protein structure and function prediction |
|
IGV |
Integrative Genomics Viewer - a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. |
|
ls-dyna |
LSDYNADESCRIPTION |
|
MATLAB |
MATLAB is a programming and numeric computing platform |
|
Nastran |
MSC Nastran is a multidisciplinary structural analysis solver that performs static, dynamic, and thermal analysis across the linear and nonlinear domains, complemented with automated structural optimisation and award-winning embedded fatigue analysis. Hexagonbs investments in high-performance computing enhancements improve productivity and get you fast, accurate results. |
|
Nextflow |
Nextflow is a reactive workflow framework and a programming DSL
that eases writing computational pipelines with complex data |
|
ORCA |
ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum
chemistry with specific emphasis on spectroscopic properties of open-shell
molecules. It features a wide variety of standard quantum chemical methods
ranging from semiempirical methods to DFT to single- and multireference
correlated ab initio methods. It can also treat environmental and relativistic
effects.
|
|
OpenMC |
OpenMC is a community-developed Monte Carlo neutron and photon transport simulation code. |
|
PSI4 |
PSI4 accessed via an Apptainer container. |
|
PyMOL |
PyMOL is a molecular visualization system. |
|
QGIS |
QGIS 3.42.2 - Open-source Geographic Information System using an Apptainer container. |
|
QIIME2 |
QIIME2 2024.10 - Microbiome bioinformatics using an Apptainer container. |
|
SageMath |
SageMath is a computer algebra system (CAS) with features covering many aspects of mathematics, including algebra, combinatorics, graph theory, group theory, differentiable manifolds, numerical analysis, number theory, calculus and statistics. |
|
USEARCH |
USEARCH is a unique sequence analysis tool which offers search and clustering algorithms that are
often orders of magnitude faster than BLAST. |
|
VarScan |
Variant calling and somatic mutation/CNV detection for next-generation sequencing data |
|
Wolfram Mathematica |
Wolfram Mathematica 14.1 symbolic and numeric computation |
|
Yade |
Yade - Discrete Element Method simulation software, containerized via Apptainer. |
|
fMRIPrep |
fMRIPrep 25.0.0 - A robust preprocessing pipeline for fMRI data using an Apptainer container. |
|
lstc-licensetools |
LSTC LICENSE TOOLS for checking license status and managing user-checked out licenses. |
|
picard |
A set of tools (in Java) for working with next generation sequencing data in the BAM format. |
2.25.1-Java-11
3.3.0-Java-17 |
|
ANTLR |
ANTLR, ANother Tool for Language Recognition, (formerly PCCTS |
| 2.7.7-GCCcore-13.3.0-Java-17 |
|
AOCC |
AMD Optimized C/C++ & Fortran compilers (AOCC) based on LLVM 13.0 |
|
APR |
Apache Portable Runtime (APR) libraries. |
|
APR-util |
Apache Portable Runtime (APR) util libraries. |
|
AUGUSTUS |
AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences |
|
AmberTools |
AmberTools consists of several independently developed packages that work well by themselves,
and with Amber itself. The suite can also be used to carry out complete molecular dynamics simulations,
with either explicit water or generalized Born solvent models. |
|
BBMap |
BBMap short read aligner, and other bioinformatic tools. |
|
BCFtools |
Samtools is a suite of programs for interacting with high-throughput sequencing data.
BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence
variants |
1.18-GCC-12.3.0
1.21-GCC-13.3.0 |
|
BEDTools |
BEDTools: a powerful toolset for genome arithmetic.
The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and
computing coverage.
The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. |
2.31.0-GCC-12.3.0
2.31.1-GCC-13.3.0 |
|
BLAST+ |
Basic Local Alignment Search Tool, or BLAST, is an algorithm
for comparing primary biological sequence information, such as the amino-acid
sequences of different proteins or the nucleotides of DNA sequences. |
|
BLAT |
BLAT on DNA is designed to quickly find sequences of 95% and
greater similarity of length 25 bases or more. |
|
BWA |
Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively
short nucleotide sequences against a long reference sequence such as the human
genome.
|
0.7.17-GCCcore-12.3.0
0.7.18-GCCcore-13.3.0 |
|
BamTools |
BamTools provides both a programmer’s API and an end-user’s toolkit for handling BAM files. |
2.5.2-GCC-12.3.0
2.5.2-GCC-13.3.0 |
|
BioPerl |
Bioperl is the product of a community effort to produce Perl code which is useful in biology.
Examples include Sequence objects, Alignment objects and database searching objects. |
1.7.8-GCCcore-12.3.0
1.7.8-GCCcore-13.3.0 |
|
Boost.MPI |
Boost provides free peer-reviewed portable C++ source libraries. |
|
Bowtie |
Bowtie is an ultrafast, memory-efficient short read aligner.
It aligns short DNA sequences (reads) to the human genome. |
|
Bowtie2 |
Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads
to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s
of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes.
Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome,
its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes. |
2.5.1-GCC-12.3.0
2.5.4-GCC-13.2.0 |
|
CD-HIT |
CD-HIT is a very widely used program for clustering and
comparing protein or nucleotide sequences. |
|
CP2K |
CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular
simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different
methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and
classical pair and many-body potentials. |
|
Cbc |
Cbc (Coin-or branch and cut) is an open-source mixed integer linear programming
solver written in C++. It can be used as a callable library or using a
stand-alone executable. |
2.10.11-foss-2023a
2.10.12-foss-2024a |
|
Cereal |
cereal is a header-only C++11 serialization library. cereal takes arbitrary data types and reversibly
turns them into different representations, such as compact binary encodings, XML, or JSON. cereal was designed to be
fast, light-weight, and easy to extend - it has no external dependencies and can be easily bundled with other code or
used standalone. |
|
Cgl |
The COIN-OR Cut Generation Library (Cgl) is a collection of cut generators that
can be used with other COIN-OR packages that make use of cuts, such as, among
others, the linear solver Clp or the mixed integer linear programming solvers
Cbc or BCP. Cgl uses the abstract class OsiSolverInterface (see Osi) to use or
communicate with a solver. It does not directly call a solver. |
0.60.8-foss-2023a
0.60.8-foss-2024a |
|
CheMPS2 |
CheMPS2 is a scientific library which contains a spin-adapted implementation of the
density matrix renormalization group (DMRG) for ab initio quantum chemistry. |
|
Clang |
C, C++, Objective-C compiler, based on LLVM. Does not
include C++ standard library – use libstdc++ from GCC. |
16.0.6-GCCcore-12.3.0
18.1.8-GCCcore-13.3.0 |
|
Clp |
Clp (Coin-or linear programming) is an open-source linear programming solver.
It is primarily meant to be used as a callable library, but a basic,
stand-alone executable version is also available. |
1.17.10-foss-2024a
1.17.9-foss-2023a |
|
CodingQuarry |
Highly accurate hidden Markov model gene prediction in fungal genomes using RNA-seq transcripts |
|
CoinUtils |
CoinUtils (Coin-OR Utilities) is an open-source collection of classes and
functions that are generally useful to more than one COIN-OR project. |
2.11.10-GCC-12.3.0
2.11.12-GCC-13.3.0 |
|
DBD-mysql |
Perl binding for MySQL |
|
DB_File |
Perl5 access to Berkeley DB version 1.x. |
1.859-GCCcore-12.3.0
1.859-GCCcore-13.3.0 |
|
DIAMOND |
Accelerated BLAST compatible local sequence aligner |
|
Dalton |
Dalton is a molecular electronic structure program. |
|
DendroPy |
A Python library for phylogenetics and phylogenetic computing:
reading, writing, simulation, processing and manipulation of phylogenetic trees
(phylogenies) and characters. |
|
ELPA |
Eigenvalue SoLvers for Petaflop-Applications. |
|
ESMF |
The Earth System Modeling Framework (ESMF) is a suite of software tools for developing
high-performance, multi-component Earth science modeling applications. |
|
ETE |
A Python framework for the analysis and visualization of trees |
|
EVidenceModeler |
EVM provides a flexible and intuitive framework for
combining diverse evidence types into a single automated gene structure annotation system. |
|
Exonerate |
Exonerate is a generic tool for pairwise sequence comparison.
It allows you to align sequences using a many alignment models, using either
exhaustive dynamic programming, or a variety of heuristics. |
|
FASTA |
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. |
|
FDS |
Fire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-speed flows,
with an emphasis on smoke and heat transport from fires. |
|
FastME |
FastME: a comprehensive, accurate and fast distance-based phylogeny inference program. |
|
FastTree |
FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide
or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of
time and memory. |
|
Flye |
Flye is a de novo assembler for long and noisy reads, such as those produced by PacBio
and Oxford Nanopore Technologies. |
|
GATK |
The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute
to analyse next-generation resequencing data. The toolkit offers a wide variety of tools,
with a primary focus on variant discovery and genotyping as well as strong emphasis on
data quality assurance. Its robust architecture, powerful processing engine and
high-performance computing features make it capable of taking on projects of any size. |
| 4.3.0.0-GCCcore-12.3.0-Java-11 |
|
GMAP-GSNAP |
GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences
GSNAP: Genomic Short-read Nucleotide Alignment Program |
|
GOATOOLS |
A Python library for Gene Ontology analyses |
|
GPAW |
GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW |
| 25.1.0-foss-2024a-ASE-3.24.0 |
|
GPAW-setups |
PAW setups for the GPAW Density Functional Theory package.
Users can install setups manually using ‘gpaw install-data’ or use setups from this package.
The versions of GPAW and GPAW-setups can be intermixed.
Compared to version 0.9.20000, version 24.1.0 contains an new improved Cr setup with 14 electrons,
which can be manually selected. Otherwise no changes are made, so no results will change.
Version 21.11.0 contains setups for the Lanthanides.
|
|
GROMACS |
GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the
Newtonian equations of motion for systems with hundreds to millions of
particles.
This is a CPU only build, containing both MPI and threadMPI binaries
for both single and double precision.
It also contains the gmxapi extension for the single precision MPI build.
|
2024.4-foss-2023b
2024.4-foss-2023b-PLUMED-2.9.2 |
|
GST-plugins-base |
GStreamer is a library for constructing graphs of media-handling
components. The applications it supports range from simple
Ogg/Vorbis playback, audio/video streaming to complex audio
(mixing) and video (non-linear editing) processing. |
|
GStreamer |
GStreamer is a library for constructing graphs of media-handling
components. The applications it supports range from simple
Ogg/Vorbis playback, audio/video streaming to complex audio
(mixing) and video (non-linear editing) processing. |
|
GTS |
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. |
|
GeneMark-ET |
Eukaryotic gene prediction suite with automatic training |
|
GitPython |
GitPython is a python library used to interact with Git repositories |
3.1.40-GCCcore-12.3.0
3.1.43-GCCcore-13.3.0 |
|
GlimmerHMM |
GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model.
Although the gene finder conforms to the overall mathematical framework of a GHMM, additionally
it incorporates splice site models adapted from the GeneSplicer program and a decision tree adapted
from GlimmerM. It also utilizes Interpolated Markov Models for the coding and noncoding models. |
|
GraphAligner |
Seed-and-extend program for aligning long error-prone reads to genome graphs. |
|
Graphene |
Graphene is a thin layer of types for graphic libraries |
|
Graphviz |
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. |
|
Greenlet |
The greenlet package is a spin-off of Stackless, a version of CPython that
supports micro-threads called “tasklets”. Tasklets run pseudo-concurrently (typically in a single
or a few OS-level threads) and are synchronized with data exchanges on “channels”.
A “greenlet”, on the other hand, is a still more primitive notion of micro-thread with no implicit
scheduling; coroutines, in other words. This is useful when you want to control exactly when your code runs.
|
|
Gurobi |
The Gurobi Optimizer is a state-of-the-art solver for mathematical programming.
The solvers in the Gurobi Optimizer were designed from the ground up to exploit modern
architectures and multi-core processors, using the most advanced implementations of the
latest algorithms. |
|
HISAT2 |
HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads
(both DNA and RNA) against the general human population (as well as against a single reference genome). |
|
HOMER |
HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and
next-gen sequencing analysis. It is a collection of command line programs for unix-style operating systems written
in Perl and C++. HOMER was primarily written as a de novo motif discovery algorithm and is well suited for finding
8-20 bp motifs in large scale genomics data. HOMER contains many useful tools for analyzing ChIP-Seq, GRO-Seq,
RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets. |
|
Hypre |
Hypre is a library for solving large, sparse linear systems of equations on massively
parallel computers. The problems of interest arise in the simulation codes being developed at LLNL
and elsewhere to study physical phenomena in the defense, environmental, energy, and biological sciences. |
|
IQ-TREE |
Efficient phylogenomic software by maximum likelihood |
|
ISA-L |
Intelligent Storage Acceleration Library |
2.30.0-GCCcore-12.3.0
2.31.0-GCCcore-13.2.0
2.31.0-GCCcore-13.3.0 |
|
Infernal |
Infernal (“INFERence of RNA ALignment”) is for searching DNA sequence databases
for RNA structure and sequence similarities. |
|
Jellyfish |
Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. |
|
Judy |
A C library that implements a dynamic array. |
1.0.5-GCCcore-12.3.0
1.0.5-GCCcore-13.3.0 |
|
Jupyter-bundle |
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 |
JupyterHub is a multiuser version of the Jupyter (IPython) notebook designed
for centralized deployments in companies, university classrooms and research labs. |
|
Kaleido |
Fast static image export for web-based visualization libraries with zero dependencies |
0.2.1-GCCcore-12.3.0
0.2.1-GCCcore-13.2.0 |
|
Kent_tools |
Kent utilities: collection of tools used by the UCSC genome browser. |
468-GCC-12.3.0
468-GCC-13.3.0 |
|
Kraken2 |
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. |
|
LIQA |
LIQA (Long-read Isoform Quantification and Analysis) is an Expectation-Maximization
based statistical method to quantify isoform expression and detect differential alternative splicing (DAS |
|
LSD2 |
Least-squares methods to estimate rates and dates from phylogenies |
|
LZO |
Portable lossless data compression library |
2.10-GCCcore-12.3.0
2.10-GCCcore-13.3.0 |
|
Libint |
Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body
matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory. |
| 2.7.2-GCC-12.3.0-lmax-6-cp2k |
|
Longshot |
Longshot is a variant calling tool for diploid genomes using long error prone reads such as Pacific
Biosciences (PacBio) SMRT and Oxford Nanopore Technologies (ONT). It takes as input an aligned BAM file and outputs
a phased VCF file with variants and haplotype information. It can also output haplotype-separated BAM files that can
be used for downstream analysis. Currently, it only calls single nucleotide variants (SNVs). |
|
MAFFT |
MAFFT is a multiple sequence alignment program for unix-like operating systems.
It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment
of <∼200 sequences), FFT-NS-2 (fast; for alignment of <∼30,000 sequences), etc. |
7.520-GCC-12.3.0-with-extensions
7.526-GCC-13.2.0-with-extensions |
|
MATIO |
matio is an C library for reading and writing Matlab MAT files. |
|
MCL |
The MCL algorithm is short for the Markov Cluster Algorithm, a fast
and scalable unsupervised cluster algorithm for graphs (also known as networks) based
on simulation of (stochastic) flow in graphs. |
|
MFiX |
Multiphase Flow with Interphase eXchanges (MFiX) version 25.1 |
|
MMseqs2 |
MMseqs2: ultra fast and sensitive search and clustering suite |
|
MOPAC |
MOPAC is a general-purpose semiempirical molecular orbital package
for the study of solid state and molecular structures and reactions. |
|
MUMPS |
A parallel sparse direct solver |
5.6.1-foss-2023a-metis
5.7.2-foss-2023b-parmetis
5.7.2-foss-2024a-metis |
|
MUSCLE |
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. |
|
MariaDB |
MariaDB is an enhanced, drop-in replacement for MySQL.
Included engines: myISAM, Aria, InnoDB, RocksDB, TokuDB, OQGraph, Mroonga. |
11.6.0-GCC-12.3.0
11.7.0-GCC-13.3.0 |
|
Markdown |
This is a Python implementation of John Gruber’s Markdown.
It is almost completely compliant with the reference implementation, though there are a few known issues.
Additional features are supported by the Available Extensions.
|
|
MashMap |
A fast approximate aligner for long DNA sequences. |
|
MrBayes |
MrBayes is a program for Bayesian inference and model choice across
a wide range of phylogenetic and evolutionary models. |
|
MultiQC |
Aggregate results from bioinformatics analyses across many samples into a single report.
MultiQC searches a given directory for analysis logs and compiles an HTML report. It’s a general
use tool, perfect for summarising the output from numerous bioinformatics tools. |
|
NAMD |
NAMD is a parallel molecular dynamics code designed for high-performance simulation of
large biomolecular systems. |
|
NCO |
The NCO toolkit manipulates and analyzes data stored in netCDF-accessible formats,
including DAP, HDF4, and HDF5. |
|
NWChem |
NWChem aims to provide its users with computational chemistry tools that are scalable both in
their ability to treat large scientific computational chemistry problems efficiently, and in their use of available
parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters.
NWChem software can handle: biomolecules, nanostructures, and solid-state; from quantum to classical, and all
combinations; Gaussian basis functions or plane-waves; scaling from one to thousands of processors; properties
and relativity. |
|
NanoFilt |
Filtering and trimming of long read sequencing data. |
|
NanoPlot |
Plotting suite for long read sequencing data and alignments |
|
OSU-Micro-Benchmarks |
OSU Micro-Benchmarks |
|
OpenMolcas |
OpenMolcas is a quantum chemistry software package. |
23.06-intel-2023a
24.10-intel-2023a |
|
OrthoFinder |
OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics |
|
Osi |
Osi (Open Solver Interface) provides an abstract base class to a generic linear
programming (LP) solver, along with derived classes for specific solvers. Many
applications may be able to use the Osi to insulate themselves from a specific
LP solver. That is, programs written to the OSI standard may be linked to any
solver with an OSI interface and should produce correct results. The OSI has
been significantly extended compared to its first incarnation. Currently, the
OSI supports linear programming solvers and has rudimentary support for integer
programming. |
0.108.11-GCC-13.3.0
0.108.9-GCC-12.3.0 |
|
PALM |
PALM is an advanced and state-of-the-art meteorological
modeling system for atmospheric and oceanic boundary layer flows. |
|
PASA |
PASA, acronym for Program to Assemble Spliced Alignments (and pronounced ‘pass-uh’),
is a eukaryotic genome annotation tool that exploits spliced alignments of expressed transcript
sequences to automatically model gene structures, and to maintain gene structure annotation consistent
with the most recently available experimental sequence data. PASA also identifies and classifies all
splicing variations supported by the transcript alignments. |
|
PDM |
A modern Python package and dependency manager supporting the latest PEP standards. |
|
PETSc |
PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the
scalable (parallel) solution of scientific applications modeled by partial differential equations. |
|
PLINK |
PLINK is a free, open-source whole genome association analysis toolset,
designed to perform a range of basic, large-scale analyses in a computationally
efficient manner. |
|
PLY |
PLY is yet another implementation of lex and yacc for Python. |
|
ParMETIS |
ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning
unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the
functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and
large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way
graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes. |
4.0.3-gompi-2023a
4.0.3-gompi-2023b |
|
Parsl |
Parsl extends parallelism in Python beyond a single computer.
You can use Parsl just like Python’s parallel executors but across multiple
cores and nodes. However, the real power of Parsl is in expressing multi-step
workflows of functions. Parsl lets you chain functions together and will launch
each function as inputs and computing resources are available.
|
|
Phonopy-Spectroscopy |
Phonopy-Spectroscopy is a project to add the capability to simulate vibrational spectra to
the Phonopy code.
|
|
Pillow-SIMD |
Pillow is the ‘friendly PIL fork’ by Alex Clark and Contributors.
PIL is the Python Imaging Library by Fredrik Lundh and Contributors. |
|
Pint |
Pint is a Python package to define, operate and
manipulate physical quantities: the product of a numerical value and a
unit of measurement. It allows arithmetic operations between them and
conversions from and to different units. |
|
PnetCDF |
Parallel netCDF: A Parallel I/O Library for NetCDF File Access |
1.12.3-gompi-2023a
1.14.0-gompi-2024a |
|
Proteinortho |
Proteinortho is a tool to detect orthologous genes within different species. |
|
PuLP |
PuLP is an LP modeler written in Python. PuLP can generate MPS or LP files and
call GLPK, COIN-OR CLP/CBC, CPLEX, GUROBI, MOSEK, XPRESS, CHOCO, MIPCL, SCIP to
solve linear problems.
|
2.8.0-foss-2023a
2.8.0-foss-2024a |
|
PyQt-builder |
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 |
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. |
|
PyTorch |
Tensors and Dynamic neural networks in Python with strong GPU acceleration.
PyTorch is a deep learning framework that puts Python first. |
|
PycURL |
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. |
|
Pysam |
Pysam is a python module for reading and manipulating Samfiles.
It’s a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix. |
0.22.0-GCC-12.3.0
0.22.1-GCC-13.3.0 |
|
Qt6 |
Qt is a comprehensive cross-platform C++ application framework. |
|
QuantumESPRESSO |
Quantum ESPRESSO is an integrated suite of computer codes
for electronic-structure calculations and materials modeling at the nanoscale.
It is based on density-functional theory, plane waves, and pseudopotentials
(both norm-conserving and ultrasoft).
|
|
Qwt |
The Qwt library contains GUI Components and utility classes which are primarily useful for programs
with a technical background. |
|
RAxML |
RAxML search algorithm for maximum likelihood based inference of phylogenetic trees. |
|
RAxML-NG |
RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood (ML |
|
RMBlast |
RMBlast is a RepeatMasker compatible version of the standard NCBI BLAST suite. The primary
difference between this distribution and the NCBI distribution is the addition of a new program ‘rmblastn’
for use with RepeatMasker and RepeatModeler. |
|
RSEM |
RNA-Seq by Expectation-Maximization |
|
Racon |
Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. |
|
Rtree |
Rtree is a ctypes Python wrapper of libspatialindex that provides a number of advanced spatial
indexing features for the spatially curious Python user. |
|
SCons |
SCons is a software construction tool. |
4.5.2-GCCcore-12.3.0
4.9.0-GCCcore-13.3.0 |
|
SIP |
SIP is a tool that makes it very easy to create Python bindings for C and C++ libraries. |
|
SNAP-HMM |
SNAP is a general purpose gene finding program suitable for both eukaryotic and
prokaryotic genomes. SNAP is an acroynm for Semi-HMM-based Nucleic Acid
Parser.
|
|
SOAPdenovo-Trans |
SOAPdenovo-Trans is a de novo transcriptome assembler basing on the SOAPdenovo framework,
adapt to alternative splicing and different expression level among transcripts.
|
|
SOCI |
SOCI is a database access library for C++ that makes the illusion of embedding SQL queries in the
regular C++ code, staying entirely within the Standard C++. |
|
SPAdes |
Genome assembler for single-cell and isolates data sets |
|
SQLAlchemy |
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. |
|
SRA-Toolkit |
The SRA Toolkit, and the source-code SRA System Development
Kit (SDK), will allow you to programmatically access data housed within SRA
and convert it from the SRA format |
3.0.10-gompi-2023a
3.2.0-gompi-2024a |
|
STAR |
STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays. |
2.7.11a-GCC-12.3.0
2.7.11b-GCC-13.2.0 |
|
su2 |
SU2DESCRIPTION |
|
SUNDIALS |
SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers |
|
Salmon |
Salmon is a wicked-fast program to produce a highly-accurate,
transcript-level quantification estimate from RNA-seq data. |
|
Seaborn |
Seaborn is a Python visualization library based on matplotlib.
It provides a high-level interface for drawing attractive statistical graphics. |
0.13.2-gfbf-2023a
0.13.2-gfbf-2024a |
|
Serf |
The serf library is a high performance C-based HTTP client library
built upon the Apache Portable Runtime (APR) library |
|
Shapelib |
Library for reading and writing ESRI Shapefiles |
|
SignalP |
SignalP predicts the presence and location of signal peptide cleavage sites
in amino acid sequences from different organisms |
|
Sniffles |
A fast structural variant caller for long-read sequencing,
Sniffles2 accurately detect SVs on germline, somatic and population-level for PacBio and Oxford Nanopore read data. |
|
SoX |
Sound eXchange, the Swiss Army knife of audio manipulation |
|
Stacks |
Stacks is a software pipeline for building loci from short-read sequences, such as those generated on
the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq,
for the purpose of building genetic maps and conducting population genomics and phylogeography.
|
|
StringTie |
StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts |
|
Subread |
High performance read alignment, quantification and mutation discovery |
|
Subversion |
Subversion is an open source version control system. |
|
SuiteSparse |
SuiteSparse is a collection of libraries to manipulate sparse matrices. |
|
SuperLU_DIST |
SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems
of linear equations on high performance machines. |
|
TINKER |
The Tinker molecular modeling software is a complete and general package for molecular mechanics
and dynamics, with some special features for biopolymers. |
|
TRF |
Tandem Repeats Finder: a program to analyze DNA sequences. |
|
Trim_Galore |
Trim Galore! is a wrapper script to automate quality and adapter
trimming as well as quality control, with some added functionality to remove biased
methylation positions for RRBS sequence files (for directional, non-directional
(or paired-end) sequencing). |
|
Trinity |
Trinity represents a novel method for the efficient and robust de novo reconstruction
of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm,
Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads. |
|
UniFrac |
UniFrac is the de facto repository for high-performance phylogenetic diversity
calculations. The methods in this repository are based on an implementation of
the Strided State UniFrac algorithm which is faster, and uses less memory than
Fast UniFrac. Strided State UniFrac supports Unweighted UniFrac, Weighted
UniFrac, Generalized UniFrac, Variance Adjusted UniFrac and meta UniFrac, in
both double and single precision (fp32). This repository also includes Stacked
Faith (manuscript in preparation), a method for calculating Faith’s PD that is
faster and uses less memory than the Fast UniFrac-based reference
implementation.
|
|
VASP |
The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale
materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics,
from first principles. |
5.4.4-intel2023a
6.4.2-intel2023a |
|
VBZ-Compression |
VBZ compression HDF5 plugin for nanopolish |
|
VCFtools |
The aim of VCFtools is to provide
easily accessible methods for working with complex
genetic variation data in the form of VCF files. |
|
Valgrind |
Valgrind: Debugging and profiling tools |
|
Verkko |
Telomere-to-telomere assembly of accurate long reads (PacBio HiFi, Oxford Nanopore Duplex,
HERRO corrected Oxford Nanopore Simplex) and Oxford Nanopore ultra-long reads. |
|
VirtualGL |
VirtualGL is an open source toolkit that gives any Linux or
Unix remote display software the ability to run OpenGL applications with full
hardware acceleration. |
|
Visit |
VisIt is an Open Source, interactive, scalable, visualization, animation
and analysis tool. From Unix, Windows or Mac workstations, users can
interactively visualize and analyze data ranging in scale from small
(<101 core) desktop-sized projects to large (>105 core) leadership-class
computing facility simulation campaigns. Users can quickly generate
visualizations, animate them through time, manipulate them with a
variety of operators and mathematical expressions, and save the
resulting images and animations for presentations. VisIt contains a rich
set of visualization features to enable users to view a wide variety of
data including scalar and vector fields defined on two- and
three-dimensional (2D and 3D) structured, adaptive and unstructured
meshes. Owing to its customizeable plugin design, VisIt is capabable of
visualizing data from over 120 different scientific data formats.
|
|
WPS |
WRF Preprocessing System (WPS) for WRF. The Weather Research and Forecasting (WRF) Model is
a next-generation mesoscale numerical weather prediction system designed to serve both operational
forecasting and atmospheric research needs. |
|
WRF |
The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale
numerical weather prediction system designed to serve both operational forecasting and atmospheric
research needs. |
|
Wannier90 |
A tool for obtaining maximally-localised Wannier functions |
3.1.0-foss-2023a
3.1.0-foss-2024a
3.1.0-gomkl-2023a
3.1.0-gomkl-2023b
3.1.0-intel-2023a
3.1.0-intel-2024a |
|
WhatsHap |
WhatsHap is a software for phasing genomic variants using DNA
sequencing reads, also called read-based phasing or haplotype assembly. It is
especially suitable for long reads, but works also well with short reads. |
|
Winnowmap |
Winnowmap is a long-read mapping algorithm, and a result of our exploration
into superior minimizer sampling techniques. |
|
XML-LibXML |
Perl binding for libxml2 |
2.0209-GCCcore-12.3.0
2.0210-GCCcore-13.3.0 |
|
XlsxWriter |
A Python module for creating Excel XLSX files |
|
Zoltan |
Zoltan Dynamic Load Balancing and Graph Algorithm Toolkit |
|
aiohttp |
Asynchronous HTTP client/server framework for asyncio and Python. |
|
annovar |
ANNOVAR is an efficient software tool to utilize update-to-date information
to functionally annotate genetic variants detected from diverse genomes (including human
genome hg18, hg19, hg38, as well as mouse, worm, fly, yeast and many others). |
|
assimp |
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.
|
|
awscli |
Universal Command Line Environment for AWS |
|
bcl2fastq2 |
bcl2fastq Conversion Software both demultiplexes data and converts BCL files generated by
Illumina sequencing systems to standard FASTQ file formats for downstream analysis. |
|
bcrypt |
Acceptable password hashing for your software and your servers (but you should
really use argon2id or scrypt |
4.0.1-GCCcore-12.3.0
4.1.3-GCCcore-13.2.0 |
|
beagle-lib |
beagle-lib is a high-performance library that can perform the core calculations at the heart of most
Bayesian and Maximum Likelihood phylogenetics packages. |
|
biom-format |
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 |
Statistical and novel interactive HTML plots for Python |
|
bwa-mem2 |
The tool bwa-mem2 is the next version of the bwa-mem algorithm in bwa. It
produces alignment identical to bwa and is ~1.3-3.1x faster depending on the
use-case, dataset and the running machine.
|
|
cimfomfa |
This library supports both MCL, a cluster algorithm for graphs, and zoem, a
macro/DSL language. It supplies abstractions for memory management, I/O,
associative arrays, strings, heaps, and a few other things. The string library
has had heavy testing as part of zoem. Both understandably and regrettably I
chose long ago to make it C-string-compatible, hence nul bytes may not be part
of a string. At some point I hope to rectify this, perhaps unrealistically. |
|
configurable-http-proxy |
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. |
|
cp2k-input-tools |
Fully validating pure-python CP2K input file parsers including preprocessing capabilities |
|
cpio |
The cpio package contains tools for archiving. |
|
ctffind |
Program for finding CTFs of electron micrographs. |
|
ctffind5 |
Program for finding CTFs of electron micrographs. |
|
cutadapt |
Cutadapt finds and removes adapter sequences, primers, poly-A tails and
other types of unwanted sequence from your high-throughput sequencing reads. |
|
deal.II |
deal.II is a C++ program library targeted at the computational solution of
partial differential equations using adaptive finite elements. |
|
decona |
fastq to polished sequenses: pipeline suitable for mixed samples and long (Nanopore) reads |
|
edlib |
Lightweight, super fast library for sequence alignment using edit (Levenshtein) distance. |
1.3.9-GCC-12.3.0
1.3.9.post1-GCC-13.3.0 |
|
eggnog-mapper |
EggNOG-mapper is a tool for fast functional annotation of novel
sequences. It uses precomputed orthologous groups and phylogenies from the
eggNOG database (http://eggnog5.embl.de) to transfer functional information from
fine-grained orthologs only. Common uses of eggNOG-mapper include the annotation
of novel genomes, transcriptomes or even metagenomic gene catalogs. |
|
elfutils |
The elfutils project provides libraries and tools for ELF files
and DWARF data.
|
|
fastp |
A tool designed to provide fast all-in-one preprocessing for FastQ files.
This tool is developed in C++ with multithreading supported to afford high performance. |
|
file |
The file command is ‘a file type guesser’, that is, a command-line tool
that tells you in words what kind of data a file contains. |
5.43-GCCcore-12.3.0
5.46-GCCcore-13.3.0 |
|
fonttools |
fontTools is a library for manipulating fonts, written in Python.
The project includes the TTX tool, that can convert TrueType and OpenType fonts to and from an XML text format,
which is also called TTX.
It supports TrueType, OpenType, AFM and to an extent Type 1 and some Mac-specific formats.
|
|
funannotate |
funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work
with higher eukaryotes) |
|
gffread |
GFF/GTF parsing utility providing format conversions,
region filtering, FASTA sequence extraction and more. |
|
gomkl |
GNU Compiler Collection (GCC) based compiler toolchain with OpenMPI and MKL |
|
iimkl |
Intel C/C++ and Fortran compilers, alongside Intel Math Kernel Library (MKL). |
|
intervaltree-python |
A mutable, self-balancing interval tree. Queries may be by
point, by range overlap, or by range containment.
|
|
ioapi |
I/O API library for environmental modeling |
|
jemalloc |
jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and
scalable concurrency support. |
5.3.0-GCCcore-12.3.0
5.3.0-GCCcore-13.3.0 |
|
jupyter-resource-usage |
Jupyter Notebook Extension for monitoring your own Resource Usage (memory and/or CPU) |
|
jupyter-server-proxy |
Jupyter Server Proxy lets you run arbitrary external processes
(such as RStudio, Shiny Server, Syncthing, PostgreSQL, Code Server, etc |
|
jupyterlmod |
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 |
kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally
of target sequences using high-throughput sequencing reads. |
|
libdap |
A C++ SDK which contains an implementation of DAP 2.0 and
DAP4.0. This includes both Client- and Server-side support classes. |
| 3.21.0-131-GCCcore-13.3.0 |
|
libdivsufsort |
libdivsufsort is a software library that implements a lightweight suffix
array construction algorithm. |
|
libidn2 |
Libidn2 implements the revised algorithm for internationalized domain names called IDNA2008/TR46. |
2.3.7-GCCcore-12.3.0
2.3.7-GCCcore-14.2.0 |
|
libmad |
MAD is a high-quality MPEG audio decoder. |
|
libnsl |
The libnsl package contains the public client interface for NIS(YP). |
|
libpsl |
C library for the Public Suffix List |
|
libspatialindex |
C++ implementation of R*-tree, an MVR-tree and a TPR-tree with C API |
|
libunistring |
This library provides functions for manipulating Unicode strings and for
manipulating C strings according to the Unicode standard. |
|
libvdwxc |
libvdwxc is a general library for evaluating energy and potential for
exchange-correlation (XC) functionals from the vdW-DF family that can be used with various
of density functional theory (DFT) codes. |
|
libvori |
C++ library implementing the Voronoi integration as well as the compressed bqb
file format. The present version of libvori is a very early development
version, which is hard-coded to work with the CP2k program package. |
|
libxc |
Libxc is a library of exchange-correlation functionals for density-functional theory.
The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals. |
6.2.2-GCC-12.3.0
6.2.2-GCC-13.3.0
6.2.2-intel-compilers-2023.1.0 |
|
libxsmm |
LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications
targeting Intel Architecture (x86). |
|
lifelines |
Lifelines is a complete survival analysis library, written in pure Python. |
|
lit |
lit is a portable tool for executing LLVM and Clang style test suites, summarizing their results, and
providing indication of failures. |
18.1.2-GCCcore-12.3.0
18.1.7-GCCcore-13.2.0
18.1.8-GCCcore-13.3.0 |
|
lpsolve |
Mixed Integer Linear Programming (MILP) solver |
|
makeinfo |
makeinfo is part of the Texinfo project, the official documentation format of the GNU project. |
|
mdust |
mdust from DFCI Gene Indices Software Tools (archived for a historical record only) |
|
medaka |
medaka is a tool to create a consensus sequence from nanopore sequencing data. |
|
mothur |
Mothur - software to process 16S rRNA gene sequence data |
|
motif |
Motif refers to both a graphical user interface (GUI) specification and the widget toolkit for building
applications that follow that specification under the X Window System on Unix and other POSIX-compliant systems.
It was the standard toolkit for the Common Desktop Environment and thus for Unix. |
|
nanoget |
Functions to extract information from Oxford Nanopore sequencing data and alignments |
|
nanomath |
A few simple math functions for other Oxford Nanopore processing scripts |
|
nanopolish |
Software package for signal-level analysis of Oxford Nanopore sequencing data. |
|
nbclassic |
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 |
The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for
using data in the INSDC Sequence Read Archives. |
3.0.10-gompi-2023a
3.2.0-gompi-2024a |
|
ncview |
Ncview is a visual browser for netCDF format files.
Typically you would use ncview to get a quick and easy, push-button
look at your netCDF files. You can view simple movies of the data,
view along various dimensions, take a look at the actual data values,
change color maps, invert the data, etc. |
|
NekRS |
High-performance spectral element CFD solver. |
|
netCDF-C++4 |
NetCDF (network Common Data Form) is a set of software libraries
and machine-independent data formats that support the creation, access, and sharing of array-oriented
scientific data. |
|
netCDF-Fortran |
NetCDF (network Common Data Form) is a set of software libraries
and machine-independent data formats that support the creation, access, and sharing of array-oriented
scientific data. |
4.6.1-gompi-2023a
4.6.1-gompi-2024a |
|
netcdf4-python |
Python/numpy interface to netCDF. |
|
nf-core |
Python package with helper tools for the nf-core community. |
|
numba |
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. |
0.58.1-foss-2023a
0.60.0-foss-2023b |
|
ont-fast5-api |
ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore .fast5 file format. |
|
openpyxl |
A Python library to read/write Excel 2010 xlsx/xlsm files |
|
p4est |
p4est is a C library to manage a collection (a forest) of multiple
connected adaptive quadtrees or octrees in parallel. |
|
paramiko |
Paramiko is a pure-Python (3.6+) implementation of the SSHv2 protocol,
providing both client and server functionality. It provides the foundation
for the high-level SSH library Fabric, which is what we recommend you use for
common client use-cases such as running remote shell commands or transferring
files.
|
|
parasail |
parasail is a SIMD C (C99) library containing implementations
of the Smith-Waterman (local), Needleman-Wunsch (global), and semi-global
pairwise sequence alignment algorithms. |
|
pauvre |
Tools for plotting Oxford Nanopore and other long-read data |
|
pblat |
When the query file format is fasta, you can specify many threads to process it.
It can reduce run time linearly, and use almost equal memory as the original blat program.
This is useful when you blat a big query file to a huge reference like human whole genome sequence. |
|
petsc4py |
petsc4py are Python bindings for PETSc, the Portable,
Extensible Toolchain for Scientific Computation. |
|
phonopy |
Phonopy is an open source package of phonon calculations based on the supercell approach. |
|
pigz |
pigz, which stands for parallel implementation of gzip, is a fully
functional replacement for gzip that exploits multiple processors and multiple
cores to the hilt when compressing data. pigz was written by Mark Adler, and
uses the zlib and pthread libraries.
|
|
plotly.py |
An open-source, interactive graphing library for Python |
5.16.0-GCCcore-12.3.0
5.18.0-GCCcore-13.2.0 |
|
pocl |
PoCL is a portable open source (MIT-licensed) implementation
of the OpenCL standard (1.2 with some 2.0 features supported). |
|
prodigal |
Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm |
|
prompt-toolkit |
prompt_toolkit is a Python library for building powerful interactive command lines and
terminal applications. |
|
psycopg |
Psycopg is the most popular PostgreSQL adapter for the Python programming language. |
|
py-cpuinfo |
py-cpuinfo gets CPU info with pure Python. |
|
pydantic |
Data validation and settings management using Python type hinting. |
2.5.3-GCCcore-12.3.0
2.7.4-GCCcore-13.2.0
2.9.1-GCCcore-13.3.0 |
|
pydot |
Python interface to Graphviz’s Dot language. |
|
pyfaidx |
pyfaidx: efficient pythonic random access to fasta subsequences |
0.8.1.1-GCCcore-12.3.0
0.8.1.2-GCCcore-13.3.0 |
|
pygraphviz |
PyGraphviz is a Python interface to the Graphviz graph layout and visualization package.
With PyGraphviz you can create, edit, read, write, and draw graphs using Python to access the Graphviz
graph data structure and layout algorithms. |
|
pyspoa |
Python bindings to spoa. |
|
pytest |
The pytest framework makes it easy to write small,
readable tests, and can scale to support complex functional testing for
applications and libraries. |
|
pytest-workflow |
Configure workflow/pipeline tests using yaml files.
pytest-workflow is a workflow-system agnostic testing framework that aims to make pipeline/workflow testing easy by
using YAML files for the test configuration.
Whether you write your pipelines in WDL, snakemake, nextflow, bash or any other workflow framework,
pytest-workflow makes testing easy.
pytest-workflow is build on top of the pytest test framework. |
|
python-isal |
Faster zlib and gzip compatible compression and decompression
by providing python bindings for the isa-l library.
|
1.1.0-GCCcore-12.3.0
1.7.0-GCCcore-13.3.0 |
|
python-parasail |
Python Bindings for the Parasail C Library |
|
python-zlib-ng |
Faster zlib and gzip compatible compression and decompression by providing Python bindings
for the zlib-ng library.
python-zlib-ng provides the bindings by offering three modules: zlib_ng, gzip_ng, gzip_ng_threaded.
zlib_ng and gzip_ng are almost fully compatible with zlib and gzip from the Python standard library. |
|
qcat |
qcat is a Python command-line tool for demultiplexing Oxford Nanopore reads from FASTQ files |
|
ruamel.yaml |
ruamel.yaml is a YAML 1.2 loader/dumper package for Python. |
|
safestringlib |
The Secure Development Lifecycle (SDL) recommends banning certain C Library
functions because they directly contribute to security vulnerabilities such as
buffer overflows. However routines for the manipulation of strings and memory
buffers are common in software and firmware, and are essential to accomplish
certain programming tasks. Safer replacements for these functions that avoid or
prevent serious security vulnerabilities (e.g. buffer overflows, string format
attacks, conversion overflows/underflows, etc.) are available in the SafeString
Library.
|
|
scNanoGPS |
Single cell Nanopore sequencing data for Genotype and Phenotype. |
|
scikit-bio |
scikit-bio is an open-source, BSD-licensed Python 3 package providing data structures, algorithms
and educational resources for bioinformatics. |
|
scikit-learn |
Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world,
building upon numpy, scipy, and matplotlib. As a machine-learning module,
it provides versatile tools for data mining and analysis in any field of science and engineering.
It strives to be simple and efficient, accessible to everybody, and reusable in various contexts. |
1.3.1-gfbf-2023a
1.5.2-gfbf-2024a |
|
sdsl-lite |
The Succinct Data Structure Library (SDSL) is a powerful and flexible C++11 library implementing
succinct data structures. In total, the library contains the highlights of 40 research publications. Succinct
data structures can represent an object (such as a bitvector or a tree) in space close to the information-theoretic
lower bound of the object while supporting operations of the original object efficiently. The theoretical time
complexity of an operation performed on the classical data structure and the equivalent succinct data structure
are (most of the time) identical. |
|
seqtk |
Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format.
It seamlessly parses both FASTA and FASTQ files which can also be optionally compressed by gzip. |
|
snakemake |
The Snakemake workflow management system is a tool to create reproducible and scalable data analyses. |
8.27.0-foss-2024a
8.4.2-foss-2023a |
|
sparsehash |
An extremely memory-efficient hash_map implementation. 2 bits/entry overhead!
The SparseHash library contains several hash-map implementations, including
implementations that optimize for space or speed.
|
|
spoa |
Spoa (SIMD POA) is a c++ implementation of the partial order alignment (POA) algorithm
which is used to generate consensus sequences |
|
statsmodels |
Statsmodels is a Python module that allows users to explore data, estimate statistical models,
and perform statistical tests. |
0.14.1-gfbf-2023a
0.14.4-gfbf-2024a |
|
tRNAscan-SE |
tRNAscan-SE is the most widely employed tool for identifying
and annotating tRNA genes in genomes. |
|
tabix |
Generic indexer for TAB-delimited genome position files |
|
tantan |
tantan identifies simple regions / low complexity / tandem repeats in DNA or protein sequences |
|
tbl2asn |
Tbl2asn is a command-line program that automates the creation of
sequence records for submission to GenBank |
|
tcsh |
Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh).
It is a command language interpreter usable both as an interactive login shell and a shell script command
processor. It includes a command-line editor, programmable word completion, spelling correction, a history
mechanism, job control and a C-like syntax. |
6.24.10-GCCcore-12.3.0
6.24.13-GCCcore-13.3.0 |
|
time |
The `time’ command runs another program, then displays information about the resources used by that
program, collected by the system while the program was running. |
|
tqdm |
A fast, extensible progress bar for Python and CLI |
4.66.1-GCCcore-12.3.0
4.66.2-GCCcore-13.2.0
4.66.5-GCCcore-13.3.0 |
|
trimAl |
EVB, FEP and LIE simulator. |
|
typing-extensions |
Typing Extensions - Backported and Experimental Type Hints for Python |
4.10.0-GCCcore-13.2.0
4.11.0-GCCcore-13.3.0
4.9.0-GCCcore-12.3.0 |
|
umap-learn |
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.
|
|
versioningit |
versioningit is yet another Python packaging plugin for automatically determining your
package’s version based on your version control repository’s tags.
Unlike others, it allows easy customization of the version format and even lets you easily override
the separate functions used for version extraction & calculation. |
|
wget |
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 |
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. |
1.15.0-gfbf-2023a
1.16.0-gfbf-2024a |
|
wxWidgets |
wxWidgets is a C++ library that lets developers create
applications for Windows, Mac OS X, Linux and other platforms with a
single code base. It has popular language bindings for Python, Perl,
Ruby and many other languages, and unlike other cross-platform toolkits,
wxWidgets gives applications a truly native look and feel because it
uses the platform’s native API rather than emulating the GUI. |
|
zlib-ng |
zlib data compression library for the next generation systems |
|