| Package | Description | Version(s) |
|---|---|---|
| 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: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| BLAT | BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more. | 3.7-GCC-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| Automake | Automake: GNU Standards-compliant Makefile generator | 1.16.5: (headnodes, heroes, dwarves, moles, wizards, warlocks) 1.16.5-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) 1.16.5-GCCcore-13.2.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 1.20.0-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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 | 2.2.2-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| Imath | Imath is a C++ and python library of 2D and 3D vector, matrix, and math operations for computer graphics | 3.1.5-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 0.48.0-gompi-2022a: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 1.1.0-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| VBZ-Compression | VBZ compression HDF5 plugin for nanopolish | 1.0.3-gompi-2022a: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 3.8.2: (headnodes, heroes, dwarves, moles, wizards, warlocks) 3.8.2-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) 3.8.2-GCCcore-13.2.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| double-conversion | Efficient binary-decimal and decimal-binary conversion routines for IEEE doubles. | 3.2.0-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| PyCairo | Python bindings for the cairo library | 1.21.0-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| libyaml | LibYAML is a YAML parser and emitter written in C. | 0.2.5-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| beocat-scripts | beocat_scripts is a set of custom scripts for use on the Beocat cluster. | default: (custom) |
| Dassault/PowerFLOW | PowerFLOW is a Computational Fluid Dynamics Simulation Software Improving Product Design & Development | 2022-6: (custom) |
| Go | Go is an open source programming language that makes it easy to build simple, reliable, and efficient software. | 1.17.6: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| R-bundle-Bioconductor | Bioconductor provides tools for the analysis and coprehension of high-throughput genomic data. | 3.15-foss-2022a-R-4.2.1: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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 Companys Qt WebEngine framework. | 5.15.5-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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: (headnodes, heroes, dwarves, moles, wizards, warlocks) 1.4.19: (headnodes, heroes, dwarves, moles, wizards, warlocks) 1.4.19-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) 1.4.19-GCCcore-13.2.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 1.2.4-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| libxslt | Libxslt is the XSLT C library developed for the GNOME project (but usable outside of the Gnome platform). | 1.1.34-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 2.7.1-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) 2.9.2-GCCcore-13.2.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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 Skypes SILK codec and Xiph.Orgs CELT codec. | 1.3.1-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| Subread | High performance read alignment, quantification and mutation discovery | 2.0.6-GCC-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| elfutils | The elfutils project provides libraries and tools for ELF files and DWARF data. | 0.187-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| libsodium | Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, password hashing and more. | 1.0.18-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| Szip | Szip compression software, providing lossless compression of scientific data | 2.1.1-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 1.3.4-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| RepeatScout | De Novo Repeat Finder, Price A.L., Jones N.C. and Pevzner P.A. Developed and tested with our multiple sequence version of RepeatScout ( 1.0.6 ) | 1.0.6-GCC-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| CMake | CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software. | 3.12.1: (headnodes, heroes, dwarves, moles, wizards, warlocks) 3.23.1-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) 3.24.3-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) 3.27.6-GCCcore-13.2.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| COMSOL | COMSOL Multiphysics software, an interactive environment for modeling and simulating scientific and engineering problems | 5.3: (custom) 5.3a: (custom) 5.4: (custom) 5.5: (custom) 5.6: (custom) |
| 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. | 2.13.0-gompi-2022a: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| RepeatModeler | RepeatModeler is a de novo transposable element (TE) family identification and modeling package. | 2.0.4-foss-2022a: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 2.42.8-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| LZO | Portable lossless data compression library | 2.10-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| GST-plugins-bad | 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. | 1.20.2-GCC-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 8.5.0-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| qrupdate | qrupdate is a Fortran library for fast updates of QR and Cholesky decompositions. | 1.1.2-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| CLHEP | The CLHEP project is intended to be a set of HEP-specific foundation and utility classes such as random generators, physics vectors, geometry and linear algebra. CLHEP is structured in a set of packages independent of any external package. | 2.4.6.2-GCC-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| FriBidi | The Free Implementation of the Unicode Bidirectional Algorithm. | 1.0.12-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| FFTW.MPI | FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data. | 3.3.10-gompi-2022a: (headnodes, heroes, dwarves, moles, wizards, warlocks) 3.3.10-gompi-2023b: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 1.20.2-GCC-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| libgeotiff | Library for reading and writing coordinate system information from/to GeoTIFF files | 1.7.1-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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) provide a reference implementation of the PMI-server that demonstrates the desired level of scalability. | 4.1.2-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) 4.2.6-GCCcore-13.2.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 3.0.2-gompi-2022a: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| randfold | Minimum free energy of folding randomization test software | 2.0.1-foss-2022a: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 0.1.3-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 2022-06-01-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| scikit-bio | scikit-bio is an open-source, BSD-licensed Python 3 package providing data structures, algorithms and educational resources for bioinformatics. | 0.5.7-foss-2022a: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 0.4.0-foss-2022a: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 1.3.2-foss-2022a: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| LittleCMS | Little CMS intends to be an OPEN SOURCE small-footprint color management engine, with special focus on accuracy and performance. | 2.13.1-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| Anaconda3 | This package has no description | notprovided: (custom) |
| patchelf | PatchELF is a small utility to modify the dynamic linker and RPATH of ELF executables. | 0.15.0-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| lxml | The lxml XML toolkit is a Pythonic binding for the C libraries libxml2 and libxslt. | 4.9.1-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| FFmpeg | A complete, cross-platform solution to record, convert and stream audio and video. | 4.4.2-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| alsa-lib | The Advanced Linux Sound Architecture (ALSA) provides audio and MIDI functionality to the Linux operating system. | 1.2.8-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| OpenSSL | The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) protocols as well as a full-strength general purpose cryptography library. | 1.1: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 11.7.0: (headnodes, heroes, dwarves, wizards, warlocks) |
| Spark | Spark is Hadoop MapReduce done in memory | 3.3.1-foss-2022a: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| PROJ | Program proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates | 9.0.0-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| PyYAML | PyYAML is a YAML parser and emitter for the Python programming language. | 6.0-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| protobuf | Google Protocol Buffers | 3.19.4-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 6.24.01-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| BBMap | BBMap short read aligner, and other bioinformatic tools. | 39.01-GCC-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| X11 | The X Window System (X11) is a windowing system for bitmap displays | 20220504-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 2.7-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| Autotools | This bundle collect the standard GNU build tools: Autoconf, Automake and libtool | 20220317: (headnodes, heroes, dwarves, moles, wizards, warlocks) 20220317-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) 20220317-GCCcore-13.2.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| scikit-build | Scikit-Build, or skbuild, is an improved build system generator for CPython C/C++/Fortran/Cython extensions. | 0.15.0-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| Eigen | Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms. | 3.4.0-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 2.2-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| Kent_tools | Kent utilities: collection of tools used by the UCSC genome browser. | 442-GCC-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| tabixpp | C++ wrapper to tabix indexer | 1.1.2-GCC-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| MaSuRCA | MaSuRCA is whole genome assembly software. It combines the efficiency of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches. MaSuRCA can assemble data sets containing only short reads from Illumina sequencing or a mixture of short reads and long reads (Sanger, 454, Pacbio and Nanopore). | 4.1.0-GCC-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| TensorFlow | An open-source software library for Machine Intelligence | 2.11.0-foss-2022a: (headnodes, heroes, dwarves, moles, wizards, warlocks) 2.11.0-foss-2022a-CUDA-11.7.0: (headnodes, heroes, dwarves, wizards, warlocks) |
| 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-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| ViennaRNA | The Vienna RNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures. | 2.5.1-foss-2022a: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| AUGUSTUS | AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences | 3.5.0-foss-2022a: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| GDCM | Grassroots DICOM: Cross-platform DICOM implementation | 3.0.20-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 2.15.1-foss-2022a: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 4.7.2: (headnodes, heroes, dwarves, moles, wizards, warlocks) 4.9.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) 4.9.1: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| Pilon | Pilon is an automated genome assembly improvement and variant detection tool | 1.23-Java-11: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| picard | A set of tools (in Java) for working with next generation sequencing data in the BAM format. | 2.25.1-Java-11: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| HTSeq | HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments. | 2.0.2-foss-2022a: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| SEPP | SATe-enabled Phylogenetic Placement - addresses the problem of phylogenetic placement of short reads into reference alignments and trees. | 4.5.1-foss-2022a: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| ISA-L | Intelligent Storage Acceleration Library | 2.30.0-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 0.40.0-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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: (headnodes, heroes, dwarves, moles, wizards, warlocks) 2.6.4-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) 2.6.4-GCCcore-13.2.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 9.56.1-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| Arrow | Apache Arrow (incl. PyArrow Python bindings), a cross-language development platform for in-memory data. | 8.0.0-foss-2022a: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| Miniconda3 | This package has no description | notprovided: (custom) |
| Pillow | Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors. | 9.1.1-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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: (headnodes, heroes, dwarves, moles, wizards, warlocks) 1.19.0-GCCcore-13.2.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 2023.7.17-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 7.83.0-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) 8.3.0-GCCcore-13.2.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| STAR | STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays. | 2.7.10b-GCC-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| DMTCP | DMTCP is a tool to transparently checkpoint the state of multiple simultaneous applications, including multi-threaded and distributed applications. It operates directly on the user binary executable, without any Linux kernel modules or other kernel modifications. | 3.0.0-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| RECON | Patched version of RECON to be used with RepeatModeler. | 1.08-GCC-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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 | 1.17.4-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| Perl | Larry Wall's Practical Extraction and Report Language Includes a small selection of extra CPAN packages for core functionality. | 5.34.1-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) 5.34.1-GCCcore-11.3.0-minimal: (headnodes, heroes, dwarves, moles, wizards, warlocks) 5.38.0-GCCcore-13.2.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 5.4.4-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| PyTorch | Tensors and Dynamic neural networks in Python with strong GPU acceleration. PyTorch is a deep learning framework that puts Python first. | 1.12.1-foss-2022a: (headnodes, heroes, dwarves, moles, wizards, warlocks) 1.12.1-foss-2022a-CUDA-11.7.0: (headnodes, heroes, dwarves, wizards, warlocks) |
| freeglut | freeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library. | 3.2.2-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| Maven | Binary maven install, Apache Maven is a software project management and comprehension tool. Based on the concept of a project object model (POM), Maven can manage a project's build, reporting and documentation from a central piece of information. | 3.6.3: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| yaml-cpp | yaml-cpp is a YAML parser and emitter in C++ matching the YAML 1.2 spec | 0.7.0-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 1.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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-11.3.0-Java-11: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 0.39-Java-11: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| makeinfo | makeinfo is part of the Texinfo project, the official documentation format of the GNU project. | 6.8-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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,...). | 11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) 13.2.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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,...). | 11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) 13.2.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| Tkinter | Tkinter module, built with the Python buildsystem | 3.10.4-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| at-spi2-core | Assistive Technology Service Provider Interface. | 2.44.1-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| flatbuffers | FlatBuffers: Memory Efficient Serialization Library Includes the Flatbuffers compiler, C/C++ bindings and Python runtime library. | 2.0.7-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| Judy | A C library that implements a dynamic array. | 1.0.5-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| imkl | Intel oneAPI Math Kernel Library | 2022.1.0-iompi-2022a: (headnodes, heroes, dwarves, moles, wizards, warlocks) 2023.2.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| TWL-NINJA | Nearly Infinite Neighbor Joining Application. | 0.98-cluster_only-GCC-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 0.11.9-Java-11: (headnodes, heroes, dwarves, moles, wizards, warlocks) 0.12.1-Java-11: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| libarchive | Multi-format archive and compression library | 3.6.1-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) 3.7.2-GCCcore-13.2.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| CD-HIT | CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences. | 4.8.1-GCC-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| prodigal | Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program developed at Oak Ridge National Laboratory and the University of Tennessee. | 2.6.3-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| utf8proc | utf8proc is a small, clean C library that provides Unicode normalization, case-folding, and other operations for data in the UTF-8 encoding. | 2.7.0-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| NASM | NASM: General-purpose x86 assembler | 2.15.05-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| GPAW-setups | PAW setup for the GPAW Density Functional Theory package. Users can install setups manually using 'gpaw install-data' or use setups from this package. The versions of GPAW and GPAW-setups can be intermixed. | 0.9.20000: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| ImageMagick | ImageMagick is a software suite to create, edit, compose, or convert bitmap images | 7.1.0-37-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 2.38.0-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 2.00a5.10-foss-2022a: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| OpenCV | OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library. OpenCV was built to provide a common infrastructure for computer vision applications and to accelerate the use of machine perception in the commercial products. Includes extra modules for OpenCV from the contrib repository. | 4.6.0-foss-2022a-CUDA-11.7.0-contrib: (headnodes, heroes, dwarves, wizards, warlocks) 4.6.0-foss-2022a-contrib: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| ParaView | ParaView is a scientific parallel visualizer. | 5.10.1-foss-2022a-mpi: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| BamTools | BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files. | 2.5.2-GCC-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| Qt5 | Qt is a comprehensive cross-platform C++ application framework. | 5.15.5-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 8.1.2-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) 8.2-GCCcore-13.2.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| pkgconfig | pkgconfig is a Python module to interface with the pkg-config command line tool | 1.5.5-GCCcore-11.3.0-python: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| bokeh | Statistical and novel interactive HTML plots for Python | 2.4.3-foss-2022a: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 3.22.1-foss-2022a: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| Mesa | Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics. | 22.0.3-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| SeqKit | SeqKit - a cross-platform and ultrafast toolkit for FASTA/Q file manipulation | 2.3.1: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| MPFR | The MPFR library is a C library for multiple-precision floating-point computations with correct rounding. | 4.1.0-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 2.9.2-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| XZ | xz: XZ utilities | 5.2.5-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) 5.4.4-GCCcore-13.2.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| R | R is a free software environment for statistical computing and graphics. | 4.2.1-foss-2022a: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) 2.1.12-GCCcore-13.2.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 2.62-foss-2022a: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| FLTK | FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL and its built-in GLUT emulation. | 1.3.8-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| VMD | VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. | 1.9.4a57-foss-2022a: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| FFTW | FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data. | 3.3.10-GCC-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) 3.3.10-GCC-13.2.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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++. | 4.0.3-GCC-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| libepoxy | Epoxy is a library for handling OpenGL function pointer management for you | 1.5.10-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| xprop | The xprop utility is for displaying window and font properties in an X server. One window or font is selected using the command line arguments or possibly in the case of a window, by clicking on the desired window. A list of properties is then given, possibly with formatting information. | 1.2.5-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| PyZMQ | Python bindings for ZeroMQ | 24.0.1-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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: (headnodes, heroes, dwarves, moles, wizards, warlocks) 3.3.1-GCC-13.2.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| DB | Berkeley DB enables the development of custom data management solutions, without the overhead traditionally associated with such custom projects. | 18.1.40-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 1.10.11-Java-11: (headnodes, heroes, dwarves, moles, wizards, warlocks) 1.10.12-Java-11: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| arpack-ng | ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems. | 3.8.0-foss-2022a: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| NCCL | The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective communication primitives that are performance optimized for NVIDIA GPUs. | 2.12.12-GCCcore-11.3.0-CUDA-11.7.0: (headnodes, heroes, dwarves, wizards, warlocks) |
| foss | GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK. | 2022a: (headnodes, heroes, dwarves, moles, wizards, warlocks) 2023b: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| hifiasm | Hifiasm: a haplotype-resolved assembler for accurate Hifi reads. | 0.19.7-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| GEOS | GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS) | 3.10.3-GCC-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| UCX | Unified Communication X An open-source production grade communication framework for data centric and high-performance applications | 1.12.1-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) 1.15.0-GCCcore-13.2.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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: (headnodes, heroes, dwarves, moles, wizards, warlocks) 1.2.0-GCCcore-13.2.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 2.4.0-GCC-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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) to use LLVM as an optimizer and code generator. | 14.0.3-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| arrow-R | R interface to the Apache Arrow C++ library | 8.0.0-foss-2022a-R-4.2.1: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| SUNDIALS | SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers | 6.3.0-foss-2022a: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| cutadapt | Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. | 4.2-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| GL2PS | GL2PS: an OpenGL to PostScript printing library | 1.4.2-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| GTK4 | 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. | 4.7.0-GCC-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| GTK2 | The GTK+ 2 package contains libraries used for creating graphical user interfaces for applications. | 2.24.33-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 3.8-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| PyGObject | PyGObject is a Python package which provides bindings for GObject based libraries such as GTK, GStreamer, WebKitGTK, GLib, GIO and many more. | 3.42.1-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| scancel | This package has no description | 1.0: (custom) |
| SCOTCH | Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning. | 7.0.1-gompi-2022a: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 1.4.3-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 1.20.2-GCC-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 1.14-foss-2022a: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 2.13.0-gompi-2022a: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| libtirpc | Libtirpc is a port of Suns Transport-Independent RPC library to Linux. | 1.3.2-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 20220620-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| OpenBLAS | OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version. | 0.3.20-GCC-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) 0.3.24-GCC-13.2.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| GMP | GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers. | 6.2.1-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| jax | Composable transformations of Python+NumPy programs: differentiate, vectorize, JIT to GPU/TPU, and more | 0.3.25-foss-2022a: (headnodes, heroes, dwarves, moles, wizards, warlocks) 0.3.25-foss-2022a-CUDA-11.7.0: (headnodes, heroes, dwarves, wizards, warlocks) |
| flatbuffers-python | Python Flatbuffers runtime library. | 2.0-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| Bowtie | Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome. | 1.3.1-GCC-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| SAGEMath | SageMath is a free open-source mathematics software system. | 9.0: (custom) |
| fontconfig | Fontconfig is a library designed to provide system-wide font configuration, customization and application access. | 2.14.0-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| Bazel | Bazel is a build tool that builds code quickly and reliably. It is used to build the majority of Google's software. | 5.1.1-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| Octave | GNU Octave is a high-level interpreted language, primarily intended for numerical computations. | 7.1.0-foss-2022a: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| GPAW | GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) method and the atomic simulation environment (ASE). It uses real-space uniform grids and multigrid methods or atom-centered basis-functions. | 23.9.1-foss-2022a: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| libdeflate | Heavily optimized library for DEFLATE/zlib/gzip compression and decompression. | 1.10-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 2.4.5-GCC-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| Valgrind | Valgrind: Debugging and profiling tools | 3.20.0-gompi-2022a: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| iimpi | Intel C/C++ and Fortran compilers, alongside Intel MPI. | 2023b: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| AlphaFold | AlphaFold can predict protein structures with atomic accuracy even where no similar structure is known | 2.3.1-foss-2022a: (headnodes, heroes, dwarves, moles, wizards, warlocks) 2.3.1-foss-2022a-CUDA-11.7.0: (headnodes, heroes, dwarves, wizards, warlocks) |
| Yasm | Yasm: Complete rewrite of the NASM assembler with BSD license | 1.3.0-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 2021.5.0-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 0.19.1-GCC-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| RSEM | RNA-Seq by Expectation-Maximization | 1.3.3-foss-2022a: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| libvorbis | Ogg Vorbis is a fully open, non-proprietary, patent-and-royalty-free, general-purpose compressed audio format | 1.3.7-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| XML-LibXML | Perl binding for libxml2 | 2.0207-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| MariaDB | MariaDB is an enhanced, drop-in replacement for MySQL. Included engines: myISAM, Aria, InnoDB, RocksDB, TokuDB, OQGraph, Mroonga. | 10.9.3-GCC-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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: (headnodes, heroes, dwarves, moles, wizards, warlocks) 1.8.0-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) 2.0.3-GCCcore-13.2.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| SciPy-bundle | Bundle of Python packages for scientific software | 2022.05-foss-2022a: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| IGV | This package contains command line utilities for preprocessing, computing feature count density (coverage), sorting, and indexing data files. | 2.16.0-Java-11: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 2.1.11-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| libpciaccess | Generic PCI access library. | 0.16-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) 0.17-GCCcore-13.2.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 2.0.33-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| jemalloc | jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and scalable concurrency support. | 5.2.1-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) 5.3.0-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| Boost | Boost provides free peer-reviewed portable C++ source libraries. | 1.79.0-GCC-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 7.505-GCC-11.3.0-with-extensions: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| libaio | Asynchronous input/output library that uses the kernels native interface. | 0.3.112-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| Boost.MPI | Boost provides free peer-reviewed portable C++ source libraries. | 1.79.0-gompi-2022a: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| gompi | GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support. | 2022a: (headnodes, heroes, dwarves, moles, wizards, warlocks) 2023b: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 1.14.0-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| LibTIFF | tiff: Library and tools for reading and writing TIFF data files | 4.3.0-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| OpenEXR | OpenEXR is a high dynamic-range (HDR) image file format developed by Industrial Light & Magic for use in computer imaging applications | 3.1.5-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| libpng | libpng is the official PNG reference library | 1.6.37-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| libgd | GD is an open source code library for the dynamic creation of images by programmers. | 2.3.3-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| Jellyfish | Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. | 2.3.0-GCC-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| Kalign | Kalign is a fast multiple sequence alignment program for biological sequences. | 3.3.5-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| GraphicsMagick | GraphicsMagick is the swiss army knife of image processing. | 1.3.36-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 6.46.7-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| gawk | The awk utility interprets a special-purpose programming language that makes it possible to handle simple data-reformatting jobs with just a few lines of code. | 5.1.1-GCC-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| RStudio-Server | This is the RStudio Server version. RStudio is a set of integrated tools designed to help you be more productive with R. The server can be started with: rserver --server-daemonize=0 --www-port=8787 If you need a database config one can be created with: MYTMP=`mktemp -d` && echo -e "provider=sqlite\ndirectory=${MYTMP}/sqlite" > "${MYTMP}/db.conf" and then used with: rserver ... --database-config-file="${MYTMP}/db.conf" | 2022.07.2+576-foss-2022a-Java-11-R-4.2.1: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| libiconv | Libiconv converts from one character encoding to another through Unicode conversion | 1.17-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 8.6.12-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) 8.6.13-GCCcore-13.2.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| QIIME2 | QIIME 2 is a powerful, extensible, and decentralized microbiome bioinformatics platform that is free, open source, and community developed. | 2023.5.1-foss-2022a: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| DB_File | Perl5 access to Berkeley DB version 1.x. | 1.858-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| at-spi2-atk | AT-SPI 2 toolkit bridge | 2.38.0-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| libGLU | The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. | 9.0.2-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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). | 2.2.1-gompi-2022a: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| util-linux | Set of Linux utilities | 2.38-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| spglib-python | Spglib for Python. Spglib is a library for finding and handling crystal symmetries written in C. | 2.0.0-foss-2022a: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| lpsolve | Mixed Integer Linear Programming (MILP) solver | 5.5.2.11-GCC-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| MAKER | MAKER is a portable and easily configurable genome annotation pipeline. Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. | 3.01.04-foss-2022a: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| StdEnv | This package has no description | default: (custom) |
| protobuf-python | Python Protocol Buffers runtime library. | 3.19.4-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| Salmon | Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data. | 1.9.0-GCC-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| BeautifulSoup | Beautiful Soup is a Python library designed for quick turnaround projects like screen-scraping. | 4.10.0-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| HTSlib | A C library for reading/writing high-throughput sequencing data. This package includes the utilities bgzip and tabix | 1.15.1-GCC-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| MATLAB | MATLAB is a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and Fortran. | 2018a: (headnodes) |
| AGAT | AGAT: Another GTF/GFF Analysis Toolkit. Suite of tools to handle gene annotations in any GTF/GFF format. | 0.9.2-GCC-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| GMAP-GSNAP | GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences GSNAP: Genomic Short-read Nucleotide Alignment Program | 2023-02-17-GCC-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 6.1: (headnodes, heroes, dwarves, moles, wizards, warlocks) 6.2: (headnodes, heroes, dwarves, moles, wizards, warlocks) 6.3-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) 6.4: (headnodes, heroes, dwarves, moles, wizards, warlocks) 6.4-GCCcore-13.2.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| graphite2 | Graphite is a "smart font" system developed specifically to handle the complexities of lesser-known languages of the world. | 1.3.14-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 2.30.0-GCC-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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). | 3.3.0-gompi-2022a: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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: (headnodes, heroes, dwarves, moles, wizards, warlocks) 2.2.0-gompi-2023b-fb: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| NAMD | NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. | 2.14-foss-2022a-CUDA-11.7.0: (heroes, dwarves, wizards, warlocks) 2.14-foss-2022a-mpi: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| EDEM | Altair EDEM discrete element method software | 2021.1: (custom) |
| 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. | 1.2.12: (headnodes, heroes, dwarves, moles, wizards, warlocks) 1.2.12-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) 1.2.13: (headnodes, heroes, dwarves, moles, wizards, warlocks) 1.2.13-GCCcore-13.2.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| FLUENT | ANSYS FLUENT software contains the broad physical modeling capabilities needed to model flow, turbulence, heat transfer, and reactions for industrial applications ranging from air flow over an aircraft wing to combustion in a furnace, from bubble columns to oil platforms, from blood flow to semiconductor manufacturing, and from clean room design to wastewater treatment plants. | 19.1: (custom) 20.2: (custom) |
| 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: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| statsmodels | Statsmodels is a Python module that allows users to explore data, estimate statistical models, and perform statistical tests. | 0.13.1-foss-2022a: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 1.21.0-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| miRDeep2 | miRDeep2 is a completely overhauled tool which discovers microRNA genes by analyzing sequenced RNAs | 0.1.3-foss-2022a: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| imkl-FFTW | FFTW interfaces using Intel oneAPI Math Kernel Library | 2023.2.0-iimpi-2023b: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 16.15.1-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| libxml2 | Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform). | 2.11.5-GCCcore-13.2.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) 2.9.13-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| code-server | Run VS Code on any machine anywhere and access it in the browser. | 4.16.1: (headnodes, heroes, dwarves, moles, wizards, warlocks) 4.9.1: (headnodes) |
| 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) | 2.4.8-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| Rust | Rust is a systems programming language that runs blazingly fast, prevents segfaults, and guarantees thread safety. | 1.60.0-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 0.56.4-foss-2022a: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| canu | Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing | 2.2-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| VSEARCH | VSEARCH supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, rereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering, conversion and merging of paired-end reads. | 2.22.1-GCC-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| RapidJSON | A fast JSON parser/generator for C++ with both SAX/DOM style API | 1.1.0-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 3.5.0-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| NSPR | Netscape Portable Runtime (NSPR) provides a platform-neutral API for system level and libc-like functions. | 4.34-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| Python | Python is a programming language that lets you work more quickly and integrate your systems more effectively. | 2.7.18-GCCcore-11.3.0-bare: (headnodes, heroes, dwarves, moles, wizards, warlocks) 3.10.4-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) 3.10.4-GCCcore-11.3.0-bare: (headnodes, heroes, dwarves, moles, wizards, warlocks) 3.11.5-GCCcore-13.2.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| make | GNU version of make utility | 4.3-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) 4.4.1-GCCcore-13.2.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| NSS | Network Security Services (NSS) is a set of libraries designed to support cross-platform development of security-enabled client and server applications. | 3.79-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| BUSCO | BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs | 5.4.5-foss-2022a: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 1.16.1-GCC-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| SQLite | SQLite: SQL Database Engine in a C Library | 3.38.3-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) 3.43.1-GCCcore-13.2.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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 | 1.15.1-GCC-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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: (headnodes, heroes, dwarves, moles, wizards, warlocks) 2.71-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) 2.71-GCCcore-13.2.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| iomkl | Compiler toolchain including Intel compilers, Open MPI and Intel Math Kernel Library (MKL). | 2022a: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| OpenMM | OpenMM is a toolkit for molecular simulation. | 8.0.0-foss-2022a: (headnodes, heroes, dwarves, moles, wizards, warlocks) 8.0.0-foss-2022a-CUDA-11.7.0: (headnodes, heroes, dwarves, wizards, warlocks) |
| LAME | LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL. | 3.100-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| binutils | binutils: GNU binary utilities | 2.38: (headnodes, heroes, dwarves, moles, wizards, warlocks) 2.38-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) 2.40: (headnodes, heroes, dwarves, moles, wizards, warlocks) 2.40-GCCcore-13.2.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| gzip | gzip (GNU zip) is a popular data compression program as a replacement for compress | 1.12-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| ffnvcodec | FFmpeg nvidia headers. Adds support for nvenc and nvdec. Requires Nvidia GPU and drivers to be present (picked up dynamically). | 11.1.5.2: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| GenomeTools | A comprehensive software library for efficient processing of structured genome annotations. | 1.6.2-GCC-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| Dassault/PowerDELTA | PowerDELTA is a fully-featured surface mesh creation tool that prepares real life geometries for digital simulation with PowerFLOW | 2022-6: (custom) |
| 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. | 4.14.3-gompi-2022a: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| ELPA | Eigenvalue SoLvers for Petaflop-Applications. | 2021.11.001-foss-2022a: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 1.12.1-GCCcore-11.3.0-CUDA-11.7.0: (headnodes, heroes, dwarves, wizards, warlocks) |
| BLIS | BLIS is a portable software framework for instantiating high-performance BLAS-like dense linear algebra libraries. | 0.9.0-GCC-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) 0.9.0-GCC-13.2.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| libglvnd | libglvnd is a vendor-neutral dispatch layer for arbitrating OpenGL API calls between multiple vendors. | 1.4.0-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| SuiteSparse | SuiteSparse is a collection of libraries manipulate sparse matrices. | 5.10.1-foss-2022a-METIS-5.1.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) 5.13.0-foss-2022a-METIS-5.1.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| FASTX-Toolkit | The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing. | 0.0.14-GCC-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| CAFE5 | Software for Computational Analysis of gene Family Evolution The purpose of CAFE is to analyze changes in gene family size in a way that accounts for phylogenetic history and provides a statistical foundation for evolutionary inferences. The program uses a birth and death process to model gene gain and loss across a user-specified phylogenetic tree. The distribution of family sizes generated under this model can provide a basis for assessing the significance of the observed family size differences among taxa. | 5.1.0-GCC-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 11-foss-2022a: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 2.1-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 1.1.9-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| Ninja | Ninja is a small build system with a focus on speed. | 1.10.2-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) 6.0-GCCcore-13.2.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| libdrm | Direct Rendering Manager runtime library. | 2.4.110-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| googletest | Google's framework for writing C++ tests on a variety of platforms | 1.11.0-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) 1.14.0-GCCcore-13.2.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| intel-compilers | Intel C, C++ & Fortran compilers (classic and oneAPI) | 2022.1.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) 2023.2.1: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| POV-Ray | The Persistence of Vision Raytracer, or POV-Ray, is a ray tracing program which generates images from a text-based scene description, and is available for a variety of computer platforms. POV-Ray is a high-quality, Free Software tool for creating stunning three-dimensional graphics. The source code is available for those wanting to do their own ports. | 3.7.0.10-GCC-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| iompi | Intel C/C++ and Fortran compilers, alongside Open MPI. | 2022a: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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). | 0.6.10-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| intel | Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL). | 2023b: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) 2.0.16-GCCcore-13.2.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| GDRCopy | A low-latency GPU memory copy library based on NVIDIA GPUDirect RDMA technology. | 2.3-GCCcore-11.3.0: (headnodes, heroes, dwarves, wizards, warlocks) |
| 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. | 1.1.2-foss-2022a: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| Nextflow | Nextflow is a reactive workflow framework and a programming DSL that eases writing computational pipelines with complex data | 23.10.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| RepeatMasker | RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. | 4.1.4-foss-2022a: (headnodes, heroes, dwarves, moles, wizards, warlocks) 4.1.5-foss-2022a: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| nlohmann_json | JSON for Modern C++ | 3.10.5-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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). | 0.29.2-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| Java | Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers. | 1.8.0_292-OpenJDK: (headnodes, heroes, dwarves, moles, wizards, warlocks) 11.0.20: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| SDL2 | SDL: Simple DirectMedia Layer, a cross-platform multimedia library | 2.0.22-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 2.6.2-foss-2022a-CUDA-11.7.0: (headnodes, heroes, dwarves, wizards, warlocks) |
| 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. | 3.5.0-foss-2022a: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 5.2.3-GCC-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| cuDNN | The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks. | 8.4.1.50-CUDA-11.7.0: (headnodes, heroes, dwarves, wizards, warlocks) |
| TOPAS | TOPAS wraps and extends the Geant4 Simulation Toolkit to make advanced Monte Carlo simulation of all forms of radiotherapy easier to use for medical physicists. | 3.9: (custom) 3.9-foss-2022a: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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 | 3.0.3-gompi-2022a: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 1.9.4-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| help2man | help2man produces simple manual pages from the '--help' and '--version' output of other commands. | 1.49.2-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) 1.49.3-GCCcore-13.2.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| MetaEuk | MetaEuk is a modular toolkit designed for large-scale gene discovery and annotation in eukaryotic metagenomic contigs. | 6-GCC-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| TRF | Tandem Repeats Finder: a program to analyze DNA sequences. | 4.09.1-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 0.5.3-foss-2022a: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| TeXLive | TeX Live is an easy (we hope) way to get up and running with the TeX document production system. | 2019: (custom) |
| VCFtools | The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files. | 0.1.16-GCC-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| ACTC | ACTC converts independent triangles into triangle strips or fans. | 1.1-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| Dassault/PowerTHERM | PowerTHERM is coupled with PowerFLOW to provide a complete, extensively validated digital thermal management solution | 2021.2.2: (custom) |
| 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: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 2.5.0-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| libtool | GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries behind a consistent, portable interface. | 2.4.7: (headnodes, heroes, dwarves, moles, wizards, warlocks) 2.4.7-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) 2.4.7-GCCcore-13.2.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| GDGraph | GDGraph is a Perl package to generate charts | 1.56-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| Mako | A super-fast templating language that borrows the best ideas from the existing templating languages | 1.2.0-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 2.24-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 2.36.0-GCCcore-11.3.0-nodocs: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| xorg-macros | X.org macros utilities. | 1.19.3-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) 1.20.0-GCCcore-13.2.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| groff | Groff (GNU troff) is a typesetting system that reads plain text mixed with formatting commands and produces formatted output. | 1.22.4-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 2023.3-foss-2022a: (headnodes, heroes, dwarves, moles, wizards, warlocks) 2023.3-foss-2022a-CUDA-11.7.0: (headnodes, heroes, dwarves, wizards, warlocks) |
| LTR_retriever | LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this package. | 2.9.0-foss-2022a: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| PCRE2 | The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5. | 10.40-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 1.50.7-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| attr | Commands for Manipulating Filesystem Extended Attributes | 2.5.1-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| HDF | HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines. | 4.2.15-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| DendroPy | A Python library for phylogenetics and phylogenetic computing: reading, writing, simulation, processing and manipulation of phylogenetic trees (phylogenies) and characters. | 4.5.2-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| impi | Intel MPI Library, compatible with MPICH ABI | 2021.10.0-intel-compilers-2023.2.1: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| GLib | GLib is one of the base libraries of the GTK+ project | 2.72.1-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| nanopolish | Software package for signal-level analysis of Oxford Nanopore sequencing data. | 0.14.0-foss-2022a: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| Seaborn | Seaborn is a Python visualization library based on matplotlib. It provides a high-level interface for drawing attractive statistical graphics. | 0.12.1-foss-2022a: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 1.0.6-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) 1.0.8-GCCcore-13.2.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| gnuplot | Portable interactive, function plotting utility | 5.4.4-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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: (headnodes, heroes, dwarves, moles, wizards, warlocks) 0.21-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) 0.22: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 21.1.3-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| tqdm | A fast, extensible progress bar for Python and CLI | 4.64.0-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 1.72.0-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 20221022-GCC-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| HarfBuzz | HarfBuzz is an OpenType text shaping engine. | 4.2.1-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| libogg | Ogg is a multimedia container format, and the native file and stream format for the Xiph.org multimedia codecs. | 1.3.5-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) 3.4.4-GCCcore-13.2.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| Brotli-python | 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: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 14.4-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| Graphene | Graphene is a thin layer of types for graphic libraries | 1.10.8-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| nsync | nsync is a C library that exports various synchronization primitives, such as mutexes | 1.25.0-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| OpenMPI | The Open MPI Project is an open source MPI-3 implementation. | 4.1.4-GCC-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) 4.1.4-intel-compilers-2022.1.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) 4.1.6-GCC-13.2.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| 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. | 4.9.0-gompi-2022a: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| bwidget | The BWidget Toolkit is a high-level Widget Set for Tcl/Tk built using native Tcl/Tk 8.x namespaces. | 1.9.15-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |
| python-isal | Faster zlib and gzip compatible compression and decompression by providing python bindings for the isa-l library. | 1.1.0-GCCcore-11.3.0: (headnodes, heroes, dwarves, moles, wizards, warlocks) |