diff --git a/docs/all-modules-24.04.md b/docs/all-modules-24.04.md index 5faea0eb..9bf1bf45 100644 --- a/docs/all-modules-24.04.md +++ b/docs/all-modules-24.04.md @@ -27,6 +27,10 @@ AlphaFold can predict protein structures with atomic accuracy even where no simi Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions. + - [Arriba/2.4.0-GCC-12.2.0](https://github.com/suhrig/arriba) +Arriba is a command-line tool for the detection of gene fusions from RNA-Seq data. + It was developed for the use in a clinical research setting. Therefore, short runtimes and high + sensitivity were important design criteria. - [Arrow/16.1.0-gfbf-2023b](https://arrow.apache.org) Apache Arrow (incl. PyArrow Python bindings), a cross-language development platform for in-memory data. @@ -44,27 +48,69 @@ Automake: GNU Standards-compliant Makefile generator This bundle collect the standard GNU build tools: Autoconf, Automake and libtool + - [BAli-Phy/4.0-beta8-gfbf-2022b](http://www.bali-phy.org/) +[easyconfig](https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/b/BAli-Phy/BAli-Phy-4.0-beta8-gfbf-2022b.eb) +BAli-Phy estimates multiple sequence alignments and evolutionary trees from DNA, amino acid, +or codon sequences. - [BCFtools/1.19-GCC-13.2.0](https://www.htslib.org/) [easyconfig](https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/b/BCFtools/BCFtools-1.19-GCC-13.2.0.eb) Samtools is a suite of programs for interacting with high-throughput sequencing data. BCFtools + - [BEDTools/2.31.0-GCC-12.3.0](https://bedtools.readthedocs.io/) +BEDTools: a powerful toolset for genome arithmetic. +The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and +computing coverage. +The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. + - [BLAST+/2.14.0-gompi-2022b](https://blast.ncbi.nlm.nih.gov/) +Basic Local Alignment Search Tool, or BLAST, is an algorithm + for comparing primary biological sequence information, such as the amino-acid + sequences of different proteins or the nucleotides of DNA sequences. - [BLIS/0.9.0-GCC-12.3.0](https://github.com/flame/blis/) BLIS is a portable software framework for instantiating high-performance BLAS-like dense linear algebra libraries. + - [BWA/0.7.17-GCCcore-12.2.0](http://bio-bwa.sourceforge.net/) +Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively + short nucleotide sequences against a long reference sequence such as the human + genome. + + - [BamTools/2.5.2-GCC-12.3.0](https://github.com/pezmaster31/bamtools) +BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files. - [Bazel/6.3.1-GCCcore-12.3.0](https://bazel.io/) Bazel is a build tool that builds code quickly and reliably. It is used to build the majority of Google's software. + - [Beast/10.5.0-beta3-GCC-12.3.0-beagle-lib-4.0.1-CUDA-12.1.1](https://beast.community) +BEAST is a cross-platform program for Bayesian analysis of molecular sequences + using MCMC. It is entirely orientated towards rooted, time-measured phylogenies inferred using + strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies + but is also a framework for testing evolutionary hypotheses without conditioning on a single + tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted + proportional to its posterior probability. + - [Beast2/2.7.7-GCC-12.3.0-beagle-lib-4.0.1-CUDA-12.1.1](https://beast2.org) +[easyconfig](https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/b/Beast2/Beast2-2.7.7-GCC-12.3.0-beagle-lib-4.0.1-CUDA-12.1.1.eb) +BEAST is a cross-platform program for Bayesian MCMC analysis of molecular + sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using + strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies + but is also a framework for testing evolutionary hypotheses without conditioning on a single + tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted + proportional to its posterior probability. - [BeautifulSoup/4.12.2-GCCcore-12.3.0](https://www.crummy.com/software/BeautifulSoup) Beautiful Soup is a Python library designed for quick turnaround projects like screen-scraping. - - [BioPerl/1.7.8-GCCcore-12.3.0](https://bioperl.org/) + - [Bio-DB-HTS/3.01-GCC-12.2.0](https://metacpan.org/release/Bio-DB-HTS) +[easyconfig](https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-12.2.0.eb) +Read files using HTSlib including BAM/CRAM, Tabix and BCF database files + - [BioPerl/1.7.8-GCCcore-12.2.0](http://www.bioperl.org/) Bioperl is the product of a community effort to produce Perl code which is useful in biology. Examples include Sequence objects, Alignment objects and database searching objects. - - [Biopython/1.83-foss-2023a](https://www.biopython.org) + - [Biopython/1.84-foss-2023b](https://www.biopython.org) +[easyconfig](https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/b/Biopython/Biopython-1.84-foss-2023b.eb) Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics. + - [Bismark/0.24.1-GCC-12.2.0](https://www.bioinformatics.babraham.ac.uk/projects/bismark/) +[easyconfig](https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/b/Bismark/Bismark-0.24.1-GCC-12.2.0.eb) +A tool to map bisulfite converted sequence reads and determine cytosine methylation states - [Bison/3.8.2-GCCcore-12.3.0](https://www.gnu.org/software/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. @@ -72,6 +118,13 @@ Bison is a general-purpose parser generator that converts an annotated context-f Blosc, an extremely fast, multi-threaded, meta-compressor library - [Boost/1.83.0-GCC-13.2.0](https://www.boost.org/) Boost provides free peer-reviewed portable C++ source libraries. + - [Bowtie2/2.5.4-GCC-13.2.0](https://github.com/BenLangmead/bowtie2) +[easyconfig](https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/b/Bowtie2/Bowtie2-2.5.4-GCC-13.2.0.eb) +Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads + to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s + of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. + Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, + its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes. - [Brotli/1.1.0-GCCcore-13.2.0](https://github.com/google/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 @@ -84,10 +137,17 @@ Brunsli is a lossless JPEG repacking library. - [CFITSIO/4.3.1-GCCcore-13.2.0](https://heasarc.gsfc.nasa.gov/fitsio/) CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format. + - [CITE-seq-Count/1.4.4-foss-2023b-Python-3.11.5](https://github.com/Hoohm/CITE-seq-Count) +[easyconfig](https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/c/CITE-seq-Count/CITE-seq-Count-1.4.4-foss-2023b-Python-3.11.5.eb) +A python package that allows to count antibody TAGS from a CITE-seq and/or cell hashing experiment. - [CMake/3.27.6-GCCcore-13.2.0](https://www.cmake.org) CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software. + - [CRISPResso2/2.3.1-foss-2023b](https://github.com/pinellolab/CRISPResso2/) +[easyconfig](https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/c/CRISPResso2/CRISPResso2-2.3.1-foss-2023b.eb) +CRISPResso2 is a software pipeline designed to enable rapid and +intuitive interpretation of genome editing experiments. - [CUDA/12.5.0](https://developer.nvidia.com/cuda-toolkit) CUDA (formerly Compute Unified Device Architecture) is a parallel computing platform and programming model created by NVIDIA and implemented by the @@ -95,11 +155,52 @@ CUDA (formerly Compute Unified Device Architecture) is a parallel to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs. - [CUDA-Python/12.1.0-gfbf-2023a-CUDA-12.1.1](https://nvidia.github.io/cuda-python/) Python bindings for CUDA - - [Catch2/2.13.9-GCCcore-12.3.0](https://github.com/catchorg/Catch2) + - [CUTLASS/3.4.0-foss-2023a-CUDA-12.1.1](https://github.com/NVIDIA/cutlass) +[easyconfig](https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/c/CUTLASS/CUTLASS-3.4.0-foss-2023a-CUDA-12.1.1.eb) +CUTLASS is a collection of CUDA C++ template +abstractions for implementing high-performance matrix-matrix +multiplication (GEMM) and related computations at all levels and scales +within CUDA. It incorporates strategies for hierarchical decomposition +and data movement similar to those used to implement cuBLAS and cuDNN. +CUTLASS decomposes these "moving parts" into reusable, modular software +components abstracted by C++ template classes. Primitives for different +levels of a conceptual parallelization hierarchy can be specialized and +tuned via custom tiling sizes, data types, and other algorithmic policy. +The resulting flexibility simplifies their use as building blocks within +custom kernels and applications. + - [Catch2/2.13.9-GCCcore-12.2.0](https://github.com/catchorg/Catch2) A modern, C++-native, header-only, test framework for unit-tests, TDD and BDD - - [DB/18.1.40-GCCcore-12.3.0](https://www.oracle.com/technetwork/products/berkeleydb) + - [CellRank/2.0.2-foss-2023a-CUDA-12.1.1](https://cellrank.readthedocs.io/en/stable/) +CellRank is a toolkit to uncover cellular dynamics based on + Markov state modeling of single-cell data. It contains two main modules: +kernels compute cell-cell transition probabilities and estimators generate +hypothesis based on these. + - [Cgl/0.60.8-foss-2023b](https://github.com/coin-or/Cgl) +The COIN-OR Cut Generation Library (Cgl) is a collection of cut generators that +can be used with other COIN-OR packages that make use of cuts, such as, among +others, the linear solver Clp or the mixed integer linear programming solvers +Cbc or BCP. Cgl uses the abstract class OsiSolverInterface (see Osi) to use or +communicate with a solver. It does not directly call a solver. + - [Clang/16.0.6-GCCcore-13.2.0](https://clang.llvm.org/) +[easyconfig](https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/c/Clang/Clang-16.0.6-GCCcore-13.2.0.eb) +C, C++, Objective-C compiler, based on LLVM. Does not + include C++ standard library -- use libstdc++ from GCC. + - [Clp/1.17.9-foss-2023b](https://github.com/coin-or/Clp) +[easyconfig](https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/c/Clp/Clp-1.17.9-foss-2023b.eb) +Clp (Coin-or linear programming) is an open-source linear programming solver. +It is primarily meant to be used as a callable library, but a basic, +stand-alone executable version is also available. + - [CoinUtils/2.11.10-GCC-13.2.0](https://github.com/coin-or/CoinUtils) +[easyconfig](https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/c/CoinUtils/CoinUtils-2.11.10-GCC-13.2.0.eb) +CoinUtils (Coin-OR Utilities) is an open-source collection of classes and +functions that are generally useful to more than one COIN-OR project. + - [Cython/3.0.8-GCCcore-12.3.0](https://cython.org/) +Cython is an optimising static compiler for both the Python programming +language and the extended Cython programming language (based on Pyrex). + + - [DB/18.1.40-GCCcore-12.2.0](https://www.oracle.com/technetwork/products/berkeleydb) Berkeley DB enables the development of custom data management solutions, without the overhead traditionally associated with such custom projects. @@ -121,13 +222,17 @@ Doxygen is a documentation system for C++, C, Java, Objective-C, Python, EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way. - - [Eigen/3.4.0-GCCcore-12.3.0](https://eigen.tuxfamily.org) + - [Eigen/3.4.0-GCCcore-13.2.0](https://eigen.tuxfamily.org) Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms. - - [FFTW/3.3.10-GCC-13.2.0](https://www.fftw.org) + - [FASTA/36.3.8i-GCC-12.2.0](https://fasta.bioch.virginia.edu/fasta_www2/fasta_list2.shtml) +The FASTA programs find regions of local or global (new) similarity between +protein or DNA sequences, either by searching Protein or DNA databases, or by identifying +local duplications within a sequence. + - [FFTW/3.3.10-GCC-12.3.0](https://www.fftw.org) FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data. - - [FFTW.MPI/3.3.10-gompi-2023a](https://www.fftw.org) + - [FFTW.MPI/3.3.10-gompi-2023b](https://www.fftw.org) FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data. - [FFmpeg/6.0-GCCcore-12.3.0](https://www.ffmpeg.org/) @@ -141,12 +246,22 @@ in standard Python IO style and relies upon familiar Python types and protocols mappings, and iterators instead of classes specific to OGR. Fiona can read and write real-world data using multi-layered GIS formats and zipped virtual file systems and integrates readily with other Python GIS packages such as pyproj, Rtree, and Shapely. + - [Flax/0.8.4-gfbf-2023a-CUDA-12.1.1](https://flax.readthedocs.io) +Flax is a high-performance neural network library and ecosystem for JAX that is +designed for flexibility: Try new forms of training by forking an example and +by modifying the training loop, not by adding features to a framework. - [FlexiBLAS/3.3.1-GCC-12.3.0](https://gitlab.mpi-magdeburg.mpg.de/software/flexiblas-release) FlexiBLAS is a wrapper library that enables the exchange of the BLAS and LAPACK implementation used by a program without recompiling or relinking it. - [FriBidi/1.0.13-GCCcore-13.2.0](https://github.com/fribidi/fribidi) The Free Implementation of the Unicode Bidirectional Algorithm. + - [GATK/4.4.0.0-GCCcore-12.2.0-Java-17](https://www.broadinstitute.org/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. - [GCC/13.2.0](https://gcc.gnu.org/) 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,...). @@ -192,15 +307,22 @@ GTK+ is the primary library used to construct user interfaces in GNOME. It user interfaces without dealing with the low-level details of drawing and device interaction. - - [Gdk-Pixbuf/2.42.10-GCCcore-12.3.0](https://docs.gtk.org/gdk-pixbuf/) + - [GTS/0.7.6-GCCcore-13.2.0](http://gts.sourceforge.net/) +[easyconfig](https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/g/GTS/GTS-0.7.6-GCCcore-13.2.0.eb) +GTS stands for the GNU Triangulated Surface Library. +It is an Open Source Free Software Library intended to provide a set of useful +functions to deal with 3D surfaces meshed with interconnected triangles. + - [Gdk-Pixbuf/2.42.10-GCCcore-13.2.0](https://docs.gtk.org/gdk-pixbuf/) The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it was distributed as part of GTK+ 2 but it was split off into a separate package in preparation for the change to GTK+ 3. - - [Ghostscript/10.01.2-GCCcore-12.3.0](https://ghostscript.com) + - [Ghostscript/10.02.1-GCCcore-13.2.0](https://ghostscript.com) Ghostscript is a versatile processor for PostScript data with the ability to render PostScript to different targets. It used to be part of the cups printing stack, but is no longer used for that. + - [GitPython/3.1.40-GCCcore-12.3.0](https://gitpython.readthedocs.org) +GitPython is a python library used to interact with Git repositories - [HDF/4.2.16-2-GCCcore-12.3.0](https://support.hdfgroup.org/products/hdf4/) HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines. @@ -241,29 +363,55 @@ IPython provides a rich architecture for interactive computing with: Easy to use, high performance tools for parallel computing. - [ISA-L/2.31.0-GCCcore-13.2.0](https://github.com/intel/isa-l) Intelligent Storage Acceleration Library + - [IgBLAST/1.22.0-x64-linux](https://ncbi.github.io/igblast) +[easyconfig](https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/i/IgBLAST/IgBLAST-1.22.0-x64-linux.eb) +IgBLAST faclilitates the analysis of immunoglobulin and T cell receptor variable domain sequences. - [ImageMagick/7.1.1-15-GCCcore-12.3.0](https://www.imagemagick.org/) ImageMagick is a software suite to create, edit, compose, or convert bitmap images - [Imath/3.1.9-GCCcore-13.2.0](https://imath.readthedocs.io/en/latest/) Imath is a C++ and python library of 2D and 3D vector, matrix, and math operations for computer graphics - - [JasPer/4.0.0-GCCcore-12.3.0](https://www.ece.uvic.ca/~frodo/jasper/) + - [Infernal/1.1.4-foss-2022b](http://eddylab.org/infernal/) +Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases + for RNA structure and sequence similarities. + - [JAGS/4.3.2-foss-2023b](http://mcmc-jags.sourceforge.net/) +[easyconfig](https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/j/JAGS/JAGS-4.3.2-foss-2023b.eb) +JAGS is Just Another Gibbs Sampler. It is a program for analysis + of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation + - [JasPer/4.0.0-GCCcore-12.2.0](https://www.ece.uvic.ca/~frodo/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. - - [Java/11.0.20](http://openjdk.java.net) + - [Java/17.0.6](http://openjdk.java.net) Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers. - [JsonCpp/1.9.5-GCCcore-12.3.0](https://open-source-parsers.github.io/jsoncpp-docs/doxygen/index.html) JsonCpp is a C++ library that allows manipulating JSON values, including serialization and deserialization to and from strings. It can also preserve existing comment in unserialization/serialization steps, making it a convenient format to store user input files. + - [Judy/1.0.5-GCCcore-12.3.0](http://judy.sourceforge.net/) +A C library that implements a dynamic array. - [Kalign/3.4.0-GCCcore-12.3.0](https://github.com/TimoLassmann/kalign) Kalign is a fast multiple sequence alignment program for biological sequences. + - [Kent_tools/468-GCC-12.3.0](https://genome.cse.ucsc.edu/) +[easyconfig](https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/k/Kent_tools/Kent_tools-468-GCC-12.3.0.eb) +Kent utilities: collection of tools used by the UCSC genome browser. + - [Kraken2/2.1.3-gompi-2022b](https://github.com/DerrickWood/kraken2/wiki) +[easyconfig](https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/k/Kraken2/Kraken2-2.1.3-gompi-2022b.eb) +Kraken is a system for assigning taxonomic labels to short DNA sequences, + usually obtained through metagenomic studies. Previous attempts by other + bioinformatics software to accomplish this task have often used sequence + alignment or machine learning techniques that were quite slow, leading to + the development of less sensitive but much faster abundance estimation + programs. Kraken aims to achieve high sensitivity and high speed by + utilizing exact alignments of k-mers and a novel classification algorithm. - [LAME/3.100-GCCcore-12.3.0](http://lame.sourceforge.net/) LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL. - - [LERC/4.0.0-GCCcore-13.2.0](https://github.com/Esri/lerc) -[easyconfig](https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/l/LERC/LERC-4.0.0-GCCcore-13.2.0.eb) + - [LDC/1.39.0-GCCcore-13.2.0](https://wiki.dlang.org/LDC) +[easyconfig](https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/l/LDC/LDC-1.39.0-GCCcore-13.2.0.eb) +The LLVM-based D Compiler + - [LERC/4.0.0-GCCcore-12.3.0](https://github.com/Esri/lerc) LERC is an open-source image or raster format which supports rapid encoding and decoding for any pixel type (not just RGB or Byte). Users set the maximum compression error per pixel while encoding, so the precision of the original input image is preserved (within user defined error bounds). @@ -275,15 +423,45 @@ The LLVM Core libraries provide a modern source- and target-independent ("LLVM IR"). The LLVM Core libraries are well documented, and it is particularly easy to invent your own language (or port an existing compiler) to use LLVM as an optimizer and code generator. + - [LMDB/0.9.29-GCCcore-12.2.0](https://symas.com/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. + - [LZO/2.10-GCCcore-12.3.0](https://www.oberhumer.com/opensource/lzo/) +Portable lossless data compression library + - [Levenshtein/0.25.1-GCCcore-13.2.0](https://pypi.org/project/python-Levenshtein/) +[easyconfig](https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/l/Levenshtein/Levenshtein-0.25.1-GCCcore-13.2.0.eb) +Python extension for computing string edit distances and similarities. - [LibTIFF/4.6.0-GCCcore-13.2.0](https://libtiff.gitlab.io/libtiff/) tiff: Library and tools for reading and writing TIFF data files - - [LittleCMS/2.15-GCCcore-13.2.0](https://www.littlecms.com/) + - [LittleCMS/2.15-GCCcore-12.3.0](https://www.littlecms.com/) Little CMS intends to be an OPEN SOURCE small-footprint color management engine, with special focus on accuracy and performance. - - [M4/1.4.19-GCCcore-13.2.0](https://www.gnu.org/software/m4/m4.html) -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. + - [Lua/5.4.4-GCCcore-12.2.0](https://www.lua.org/) +Lua is a powerful, fast, lightweight, embeddable scripting language. + Lua combines simple procedural syntax with powerful data description constructs based + on associative arrays and extensible semantics. Lua is dynamically typed, + runs by interpreting bytecode for a register-based virtual machine, + and has automatic memory management with incremental garbage collection, + making it ideal for configuration, scripting, and rapid prototyping. + - [M4/1.4.19](https://www.gnu.org/software/m4/m4.html) +GNU M4 is an implementation of the traditional Unix macro processor. It is + mostly SVR4 compatible although it has some extensions (for example, handling + more than 9 positional parameters to macros). GNU M4 also has built-in + functions for including files, running shell commands, doing arithmetic, etc. + + - [MACS2/2.2.9.1-foss-2022b](https://github.com/taoliu/MACS) +[easyconfig](https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/m/MACS2/MACS2-2.2.9.1-foss-2022b.eb) +Model Based Analysis for ChIP-Seq data + - [MACS3/3.0.0-foss-2022b](https://macs3-project.github.io/MACS/) +[easyconfig](https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/m/MACS3/MACS3-3.0.0-foss-2022b.eb) +Model Based Analysis for ChIP-Seq data + - [METIS/5.1.0-GCCcore-12.2.0](http://glaros.dtc.umn.edu/gkhome/metis/metis/overview) +METIS is a set of serial programs for partitioning graphs, partitioning + finite element meshes, and producing fill reducing orderings for sparse + matrices. The algorithms implemented in METIS are based on the multilevel + recursive-bisection, multilevel k-way, and multi-constraint partitioning + schemes. + - [MPC/1.3.1-GCCcore-12.3.0](http://www.multiprecision.org/) Gnu Mpc is a C library for the arithmetic of complex numbers with arbitrarily high precision and correct @@ -296,13 +474,32 @@ Gnu Mpc is a C library for the arithmetic of The MPFR library is a C library for multiple-precision floating-point computations with correct rounding. - - [Mako/1.2.4-GCCcore-13.2.0](https://www.makotemplates.org) + - [MUMPS/5.6.1-foss-2022b-metis](https://graal.ens-lyon.fr/MUMPS/) +A parallel sparse direct solver + - [MUSCLE/5.1.0-GCCcore-12.3.0](https://drive5.com/muscle/) +[easyconfig](https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/m/MUSCLE/MUSCLE-5.1.0-GCCcore-12.3.0.eb) +MUSCLE is one of the best-performing multiple alignment programs + according to published benchmark tests, with accuracy and speed that are consistently + better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users + learn everything they need to know about MUSCLE in a few minutes-only a handful of + command-line options are needed to perform common alignment tasks. + - [Mako/1.2.4-GCCcore-12.3.0](https://www.makotemplates.org) A super-fast templating language that borrows the best ideas from the existing templating languages + - [MariaDB/11.6.0-GCC-12.3.0](https://mariadb.org/) +MariaDB is an enhanced, drop-in replacement for MySQL. +Included engines: myISAM, Aria, InnoDB, RocksDB, TokuDB, OQGraph, Mroonga. - [Mesa/23.1.9-GCCcore-13.2.0](https://www.mesa3d.org/) Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics. - [Meson/1.2.3-GCCcore-13.2.0](https://mesonbuild.com) Meson is a cross-platform build system designed to be both as fast and as user friendly as possible. + - [MultiQC/1.21-foss-2023a](https://multiqc.info) +[easyconfig](https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/m/MultiQC/MultiQC-1.21-foss-2023a.eb) +Aggregate results from bioinformatics analyses across many samples into a single + report. + + MultiQC searches a given directory for analysis logs and compiles a HTML report. It's a general + use tool, perfect for summarising the output from numerous bioinformatics tools. - [NASM/2.16.01-GCCcore-12.3.0](https://www.nasm.us/) NASM: General-purpose x86 assembler - [NCCL/2.18.3-GCCcore-12.3.0-CUDA-12.1.1](https://developer.nvidia.com/nccl) @@ -314,14 +511,20 @@ NLTK is a leading platform for building Python programs to work with human langu 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. - - [Ninja/1.11.1-GCCcore-12.3.0](https://ninja-build.org/) + - [NSPR/4.35-GCCcore-12.2.0](https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSPR) +Netscape Portable Runtime (NSPR) provides a platform-neutral API for system level + and libc-like functions. + - [NSS/3.94-GCCcore-13.2.0](https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSS) +Network Security Services (NSS) is a set of libraries designed to support cross-platform development + of security-enabled client and server applications. + - [Ninja/1.11.1-GCCcore-12.2.0](https://ninja-build.org/) Ninja is a small build system with a focus on speed. - [OpenBLAS/0.3.24-GCC-13.2.0](http://www.openblas.net/) OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version. - [OpenEXR/3.2.0-GCCcore-13.2.0](https://www.openexr.com/) OpenEXR is a high dynamic-range (HDR) image file format developed by Industrial Light & Magic for use in computer imaging applications - - [OpenJPEG/2.5.0-GCCcore-12.3.0](https://www.openjpeg.org/) + - [OpenJPEG/2.5.0-GCCcore-13.2.0](https://www.openjpeg.org/) 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 @@ -345,11 +548,23 @@ OpenPGM is an open source implementation of the Pragmatic General Multicast 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. - - [PCRE/8.45-GCCcore-12.3.0](https://www.pcre.org/) + - [Optax/0.2.2-gfbf-2023a-CUDA-12.1.1](https://github.com/deepmind/optax) +Optax is a gradient processing and optimization library for JAX. + - [Osi/0.108.9-GCC-13.2.0](https://github.com/coin-or/Osi) +[easyconfig](https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/o/Osi/Osi-0.108.9-GCC-13.2.0.eb) +Osi (Open Solver Interface) provides an abstract base class to a generic linear +programming (LP) solver, along with derived classes for specific solvers. Many +applications may be able to use the Osi to insulate themselves from a specific +LP solver. That is, programs written to the OSI standard may be linked to any +solver with an OSI interface and should produce correct results. The OSI has +been significantly extended compared to its first incarnation. Currently, the +OSI supports linear programming solvers and has rudimentary support for integer +programming. + - [PCRE/8.45-GCCcore-12.2.0](https://www.pcre.org/) The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5. - - [PCRE2/10.42-GCCcore-13.2.0](https://www.pcre.org/) + - [PCRE2/10.42-GCCcore-12.3.0](https://www.pcre.org/) The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5. @@ -363,6 +578,8 @@ definitions - [PROJ/9.3.1-GCCcore-13.2.0](https://proj.org) Program proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates + - [Pandoc/2.13](https://pandoc.org) +If you need to convert files from one markup format into another, pandoc is your swiss-army knife - [Pango/1.51.0-GCCcore-13.2.0](https://www.pango.org/) 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 @@ -380,7 +597,7 @@ Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. - [Pillow-SIMD/9.5.0-GCCcore-12.3.0](https://github.com/uploadcare/pillow-simd) Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors. - - [PostgreSQL/16.1-GCCcore-13.2.0](https://www.postgresql.org/) + - [PostgreSQL/16.1-GCCcore-12.3.0](https://www.postgresql.org/) 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). @@ -393,6 +610,11 @@ PostgreSQL is a powerful, open source object-relational database system. [easyconfig](https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb) Tensors and Dynamic neural networks in Python with strong GPU acceleration. PyTorch is a deep learning framework that puts Python first. + - [PyTorch-Lightning/2.2.1-foss-2023a](https://pytorchlightning.ai) +PyTorch Lightning is the lightweight PyTorch wrapper for ML researchers. + - [PyTorch-bundle/2.1.2-foss-2023a-CUDA-12.1.1](https://pytorch.org/) +[easyconfig](https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/p/PyTorch-bundle/PyTorch-bundle-2.1.2-foss-2023a-CUDA-12.1.1.eb) +PyTorch with compatible versions of official Torch extensions. - [PyYAML/6.0.1-GCCcore-13.2.0](https://github.com/yaml/pyyaml) PyYAML is a YAML parser and emitter for the Python programming language. - [PyZMQ/25.1.1-GCCcore-12.3.0](https://www.zeromq.org/bindings:python) @@ -413,10 +635,24 @@ Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, higher dimensions. Qhull implements the Quickhull algorithm for computing the convex hull. + - [Qt5/5.15.7-GCCcore-12.2.0](https://qt.io/) +Qt is a comprehensive cross-platform C++ application framework. + - [Qt6/6.6.3-GCCcore-13.2.0](https://qt.io/) +Qt is a comprehensive cross-platform C++ application framework. - [R/4.4.0-gfbf-2023b](https://www.r-project.org/) [easyconfig](https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/r/R/R-4.4.0-gfbf-2023b.eb) R is a free software environment for statistical computing and graphics. + - [R-Tidyverse/4.4.0-gfbf-2023b](http://www.r-project.org/) +[easyconfig](https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/r/R-Tidyverse/R-Tidyverse-4.4.0-gfbf-2023b.eb) +R is a free software environment for statistical computing and graphics. + - [R-bundle-Bioconductor/3.18-foss-2023a-R-4.3.2](https://bioconductor.org) +[easyconfig](https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb) +Bioconductor provides tools for the analysis and coprehension + of high-throughput genomic data. + - [R-bundle-CRAN/2023.12-foss-2023a](https://www.r-project.org/) +[easyconfig](https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.12-foss-2023a.eb) +Bundle of R packages from CRAN - [RAPIDS/24.4-foss-2023a-CUDA-12.1.1](https://rapids.ai/) RAPIDS provides unmatched speed with familiar APIs that match the most popular PyData libraries. Built on state-of-the-art foundations like NVIDIA CUDA and @@ -438,7 +674,7 @@ If you need a database config one can be created with: and then used with: rserver ... --database-config-file="${MYTMP}/db.conf" - - [RapidJSON/1.1.0-20230928-GCCcore-12.3.0](https://rapidjson.org) + - [RapidJSON/1.1.0-20240409-GCCcore-13.2.0](https://rapidjson.org) A fast JSON parser/generator for C++ with both SAX/DOM style API - [Ruby/3.3.0-GCCcore-12.3.0](https://www.ruby-lang.org) Ruby is a dynamic, open source programming language with @@ -451,7 +687,10 @@ Rust is a systems programming language that runs blazingly fast, prevents segfau [easyconfig](https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/s/SAMtools/SAMtools-1.19.2-GCC-13.2.0.eb) SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. - - [SDL2/2.28.2-GCCcore-12.3.0](https://www.libsdl.org/) + - [SCOTCH/7.0.3-gompi-2022b](https://www.labri.fr/perso/pelegrin/scotch/) +Software package and libraries for sequential and parallel graph partitioning, +static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning. + - [SDL2/2.28.5-GCCcore-13.2.0](https://www.libsdl.org/) SDL: Simple DirectMedia Layer, a cross-platform multimedia library - [SOCI/4.0.3-GCC-13.2.0-Boost-1.83.0](http://soci.sourceforge.net/) SOCI is a database access library for C++ that makes the illusion of embedding SQL queries in the @@ -467,10 +706,27 @@ SQLite: SQL Database Engine in a C Library - [STAR/2.7.11b-GCC-13.2.0](https://github.com/alexdobin/STAR) [easyconfig](https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/s/STAR/STAR-2.7.11b-GCC-13.2.0.eb) STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays. + - [STAR-Fusion/1.12.0-foss-2022b](https://github.com/STAR-Fusion/STAR-Fusion) +[easyconfig](https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/s/STAR-Fusion/STAR-Fusion-1.12.0-foss-2022b.eb) +STAR-Fusion uses the STAR aligner to identify candidate fusion transcripts + supported by Illumina reads. STAR-Fusion further processes the output generated by the STAR aligner + to map junction reads and spanning reads to a reference annotation set. + - [SVclone/1.1.2-foss-2022b](https://github.com/mcmero/SVclone) +[easyconfig](https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/s/SVclone/SVclone-1.1.2-foss-2022b.eb) +Cluster structural variants of similar cancer cell fraction (CCF). - [SWIG/4.1.1-GCCcore-12.3.0](http://www.swig.org/) SWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages. - - [ScaLAPACK/2.2.0-gompi-2023b-fb](https://www.netlib.org/scalapack/) + - [SYMPHONY/5.7.2-foss-2023b](https://github.com/coin-or/SYMPHONY/wiki) +[easyconfig](https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/s/SYMPHONY/SYMPHONY-5.7.2-foss-2023b.eb) +SYMPHONY is an open-source solver for mixed-integer linear programs (MILPs) written in C. + - [Sambamba/1.0.1-GCC-13.2.0](https://lomereiter.github.io/sambamba/) +[easyconfig](https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/s/Sambamba/Sambamba-1.0.1-GCC-13.2.0.eb) +Sambamba is a high performance modern robust and fast tool + (and library), written in the D programming language, for working with SAM + and BAM files. Current functionality is an important subset of samtools + functionality, including view, index, sort, markdup, and depth. + - [ScaLAPACK/2.2.0-gompi-2023a-fb](https://www.netlib.org/scalapack/) The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers. - [Scalene/1.5.26-GCCcore-12.3.0](https://github.com/plasma-umass/scalene) @@ -479,10 +735,17 @@ that other Python profilers do not and cannot do. It runs orders of magnitude fa delivering far more detailed information. - [SciPy-bundle/2023.11-gfbf-2023b](https://python.org/) Bundle of Python packages for scientific software + - [Seaborn/0.13.2-gfbf-2023a](https://seaborn.pydata.org/) +Seaborn is a Python visualization library based on matplotlib. + It provides a high-level interface for drawing attractive statistical graphics. + - [SentencePiece/0.2.0-GCC-12.3.0](https://github.com/google/sentencepiece) +Unsupervised text tokenizer for Neural Network-based text generation. - [Shapely/2.0.1-gfbf-2023a](https://github.com/Toblerity/Shapely) Shapely is a BSD-licensed Python package for manipulation and analysis of planar geometric objects. It is based on the widely deployed GEOS (the engine of PostGIS) and JTS (from which GEOS is ported) libraries. - - [Szip/2.1.1-GCCcore-12.3.0](https://support.hdfgroup.org/doc_resource/SZIP/) + - [SoX/14.4.2-GCCcore-12.3.0](http://sox.sourceforge.net/) +Sound eXchange, the Swiss Army knife of audio manipulation + - [Szip/2.1.1-GCCcore-12.2.0](https://support.hdfgroup.org/doc_resource/SZIP/) Szip compression software, providing lossless compression of scientific data - [Tcl/8.6.13-GCCcore-12.3.0](https://www.tcl.tk/) @@ -490,15 +753,17 @@ 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. - - [TensorFlow/2.15.1-foss-2023a-CUDA-12.1.1](https://www.tensorflow.org/) + - [Telescope/1.0.3-gfbf-2022b](https://github.com/mlbendall/telescope) +[easyconfig](https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/t/Telescope/Telescope-1.0.3-gfbf-2022b.eb) +Single locus resolution of Transposable ELEment expression using next-generation sequencing. + - [TensorFlow/2.15.1-foss-2023a](https://www.tensorflow.org/) An open-source software library for Machine Intelligence - [Tk/8.6.13-GCCcore-12.3.0](https://www.tcl.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. - - [Tkinter/3.11.3-GCCcore-12.3.0](https://python.org/) -[easyconfig](https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/t/Tkinter/Tkinter-3.11.3-GCCcore-12.3.0.eb) + - [Tkinter/3.11.5-GCCcore-13.2.0](https://python.org/) Tkinter module, built with the Python buildsystem - - [UCC/1.2.0-GCCcore-13.2.0](https://www.openucx.org/) + - [UCC/1.2.0-GCCcore-12.3.0](https://www.openucx.org/) 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. @@ -518,13 +783,16 @@ This module adds the UCX CUDA support. - [UDUNITS/2.2.28-GCCcore-13.2.0](https://www.unidata.ucar.edu/software/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. + - [UMI-tools/1.1.4-foss-2023b](https://umi-tools.readthedocs.io) +[easyconfig](https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/u/UMI-tools/UMI-tools-1.1.4-foss-2023b.eb) +Tools for handling Unique Molecular Identifiers in NGS data sets - [UnZip/6.0-GCCcore-12.3.0](http://www.info-zip.org/UnZip.html) UnZip is an extraction utility for archives compressed in .zip format (also called "zipfiles"). Although highly compatible both with PKWARE's PKZIP and PKUNZIP utilities for MS-DOS and with Info-ZIP's own Zip program, our primary objectives have been portability and non-MSDOS functionality. - - [Wayland/1.22.0-GCCcore-12.3.0](https://wayland.freedesktop.org/) + - [Wayland/1.22.0-GCCcore-13.2.0](https://wayland.freedesktop.org/) 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 @@ -549,7 +817,7 @@ Xvfb is an X server that can run on machines with no display hardware and no phy It emulates a dumb framebuffer using virtual memory. - [Yasm/1.3.0-GCCcore-12.3.0](https://www.tortall.net/projects/yasm/) Yasm: Complete rewrite of the NASM assembler with BSD license - - [Z3/4.12.2-GCCcore-12.3.0](https://github.com/Z3Prover/z3) + - [Z3/4.13.0-GCCcore-13.2.0](https://github.com/Z3Prover/z3) Z3 is a theorem prover from Microsoft Research with support for bitvectors, booleans, arrays, floating point numbers, strings, and other data types. This module includes z3-solver, the Python interface of Z3. @@ -561,7 +829,7 @@ ZeroMQ looks like an embeddable networking library but acts like a concurrency f pub-sub, task distribution, and request-reply. It's fast enough to be the fabric for clustered products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous message-processing tasks. It has a score of language APIs and runs on most operating systems. - - [Zip/3.0-GCCcore-13.2.0](http://www.info-zip.org/Zip.html) + - [Zip/3.0-GCCcore-12.3.0](http://www.info-zip.org/Zip.html) 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 @@ -572,22 +840,39 @@ applications. The code is collected from Google's own Python code base, and has been extensively tested and used in production. - [aiohttp/3.8.5-GCCcore-12.3.0](https://github.com/aio-libs/aiohttp) Asynchronous HTTP client/server framework for asyncio and Python. + - [anndata/0.10.7-foss-2023b](https://github.com/scverse/anndata) +[easyconfig](https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/a/anndata/anndata-0.10.7-foss-2023b.eb) +anndata is a Python package for handling annotated data matrices in memory and on disk, + positioned between pandas and xarray - [ant/1.10.11-Java-11](https://ant.apache.org/) Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications. - [arpack-ng/3.9.0-foss-2023a](https://github.com/opencollab/arpack-ng) ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems. - - [at-spi2-atk/2.38.0-GCCcore-12.3.0](https://wiki.gnome.org/Accessibility) + - [arrow-R/14.0.1-foss-2023a-R-4.3.2](https://cran.r-project.org/web/packages/arrow) +R interface to the Apache Arrow C++ library + - [assimp/5.3.1-GCCcore-13.2.0](https://github.com/assimp/assimp) +Open Asset Import Library (assimp) is a library to import and export various + 3d-model-formats including scene-post-processing to generate missing render data. + + - [at-spi2-atk/2.38.0-GCCcore-13.2.0](https://wiki.gnome.org/Accessibility) AT-SPI 2 toolkit bridge - [at-spi2-core/2.50.0-GCCcore-13.2.0](https://wiki.gnome.org/Accessibility) Assistive Technology Service Provider Interface. - - [binutils/2.40-GCCcore-12.3.0](https://directory.fsf.org/project/binutils/) + - [bam-readcount/1.0.1-GCC-12.2.0](https://github.com/genome/bam-readcount) +[easyconfig](https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/b/bam-readcount/bam-readcount-1.0.1-GCC-12.2.0.eb) +Count DNA sequence reads in BAM files + - [beagle-lib/4.0.1-GCC-12.3.0-CUDA-12.1.1](https://github.com/beagle-dev/beagle-lib) +[easyconfig](https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/b/beagle-lib/beagle-lib-4.0.1-GCC-12.3.0-CUDA-12.1.1.eb) +beagle-lib is a high-performance library that can perform the core calculations at the heart of most + Bayesian and Maximum Likelihood phylogenetics packages. + - [binutils/2.40-GCCcore-13.2.0](https://directory.fsf.org/project/binutils/) binutils: GNU binary utilities - [bokeh/3.2.2-foss-2023a](https://github.com/bokeh/bokeh) Statistical and novel interactive HTML plots for Python - - [bzip2/1.0.8-GCCcore-13.2.0](https://sourceware.org/bzip2) + - [bzip2/1.0.8-GCCcore-12.3.0](https://sourceware.org/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 @@ -611,7 +896,9 @@ C Foreign Function Interface for Python. Interact with almost any C code from Python, based on C-like declarations that you can often copy-paste from header files or documentation. - - [cppy/1.2.1-GCCcore-12.3.0](https://github.com/nucleic/cppy) + - [cpio/2.15-GCCcore-12.2.0](https://savannah.gnu.org/projects/cpio/) +The cpio package contains tools for archiving. + - [cppy/1.2.1-GCCcore-13.2.0](https://github.com/nucleic/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 @@ -621,9 +908,14 @@ cryptography is a package designed to expose cryptographic primitives and recipe - [cuDNN/8.9.2.26-CUDA-12.1.1](https://developer.nvidia.com/cudnn) The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks. + - [cutadapt/4.4-GCCcore-12.2.0](https://opensource.scilifelab.se/projects/cutadapt/) +Cutadapt finds and removes adapter sequences, primers, poly-A tails and + other types of unwanted sequence from your high-throughput sequencing reads. - [dask/2023.9.2-foss-2023a](https://dask.org/) Dask natively scales Python. Dask provides advanced parallelism for analytics, enabling performance at scale for the tools you love. + - [deepdiff/6.7.1-GCCcore-12.3.0](https://zepworks.com/deepdiff/current/) +DeepDiff: Deep Difference of dictionaries, iterables and almost any other object recursively. - [dill/0.3.7-GCCcore-12.3.0](https://pypi.org/project/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 @@ -638,7 +930,13 @@ tree generalizes the builtin map function which only supports flat sequences, an allows to apply a function to each "leaf" preserving the overall structure. - [double-conversion/3.3.0-GCCcore-12.3.0](https://github.com/google/double-conversion) Efficient binary-decimal and decimal-binary conversion routines for IEEE doubles. - - [expat/2.5.0-GCCcore-12.3.0](https://libexpat.github.io) + - [easel/0.48-GCC-12.2.0](https://bioeasel.org/) +[easyconfig](https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/e/easel/easel-0.48-GCC-12.2.0.eb) +Easel supports computational analysis of biological sequences using probabilistic models. + - [einops/0.7.0-GCCcore-12.3.0](https://einops.rocks/) +Flexible and powerful tensor operations for readable and reliable code. +Supports numpy, pytorch, tensorflow, jax, and others. + - [expat/2.5.0-GCCcore-13.2.0](https://libexpat.github.io) 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). @@ -651,21 +949,26 @@ This library implements expect tests (also known as "golden" tests). Expect test [easyconfig](https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/f/fastp/fastp-0.23.4-GCC-13.2.0.eb) A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance. - - [ffnvcodec/12.0.16.0](https://git.videolan.org/?p=ffmpeg/nv-codec-headers.git) + - [ffnvcodec/12.1.14.0](https://git.videolan.org/?p=ffmpeg/nv-codec-headers.git) FFmpeg nvidia headers. Adds support for nvenc and nvdec. Requires Nvidia GPU and drivers to be present (picked up dynamically). + - [flash-attention/2.6.3-foss-2023a-CUDA-12.1.1](https://github.com/Dao-AILab/flash-attention) +[easyconfig](https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/f/flash-attention/flash-attention-2.6.3-foss-2023a-CUDA-12.1.1.eb) +Fast and memory-efficient exact attention. - [flatbuffers/23.5.26-GCCcore-12.3.0](https://github.com/google/flatbuffers/) FlatBuffers: Memory Efficient Serialization Library - [flatbuffers-python/23.5.26-GCCcore-12.3.0](https://github.com/google/flatbuffers/) Python Flatbuffers runtime library. - - [flex/2.6.4-GCCcore-13.2.0](https://github.com/westes/flex) + - [flex/2.6.4-GCCcore-12.2.0](http://flex.sourceforge.net/) Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, sometimes called a tokenizer, is a program which recognizes lexical patterns in text. - [flit/3.9.0-GCCcore-13.2.0](https://github.com/pypa/flit) A simple packaging tool for simple packages. - - [fontconfig/2.14.2-GCCcore-12.3.0](https://www.freedesktop.org/wiki/Software/fontconfig/) + - [fmt/9.1.0-GCCcore-12.2.0](http://fmtlib.net/) +fmt (formerly cppformat) is an open-source formatting library. + - [fontconfig/2.14.2-GCCcore-13.2.0](https://www.freedesktop.org/wiki/Software/fontconfig/) Fontconfig is a library designed to provide system-wide font configuration, customization and application access. @@ -698,20 +1001,32 @@ the LZW compression algorithm was patented. - [git/2.42.0-GCCcore-13.2.0](https://git-scm.com) Git is a free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency. - - [gmpy2/2.1.5-GCC-12.3.0](https://github.com/aleaxit/gmpy) + - [gmpy2/2.1.5-GCC-13.2.0](https://github.com/aleaxit/gmpy) GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x + - [gnupg-bundle/20240306-GCCcore-13.2.0](https://www.gnupg.org/software/index.html) +GnuPG — The Universal Crypto Engine + - [gnuplot/5.4.6-GCCcore-12.2.0](http://gnuplot.sourceforge.net) +Portable interactive, function plotting utility - [gompi/2023b]((none)) GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support. - [googletest/1.14.0-GCCcore-13.2.0](https://github.com/google/googletest) Google's framework for writing C++ tests on a variety of platforms - - [gperf/3.1-GCCcore-12.3.0](https://www.gnu.org/software/gperf/) + - [gperf/3.1-GCCcore-13.2.0](https://www.gnu.org/software/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. + - [gperftools/2.12-GCCcore-12.3.0](https://github.com/gperftools/gperftools) +gperftools is a collection of a high-performance multi-threaded malloc() +implementation, plus some pretty nifty performance analysis tools. +Includes TCMalloc, heap-checker, heap-profiler and cpu-profiler. + + - [graphite2/1.3.14-GCCcore-12.2.0](https://scripts.sil.org/cms/scripts/page.php?site_id=projects&item_id=graphite_home) +Graphite is a "smart font" system developed specifically to + handle the complexities of lesser-known languages of the world. - [groff/1.23.0-GCCcore-13.2.0](https://www.gnu.org/software/groff) Groff (GNU troff) is a typesetting system that reads plain text mixed with formatting commands and produces formatted output. @@ -721,7 +1036,8 @@ framework that can run anywhere. gRPC enables client and server applications to communicate transparently, and simplifies the building of connected systems. - [gzip/1.13-GCCcore-13.2.0](https://www.gnu.org/software/gzip/) gzip (GNU zip) is a popular data compression program as a replacement for compress - - [h5py/3.9.0-foss-2023a](https://www.h5py.org/) + - [h5py/3.11.0-foss-2023b](https://www.h5py.org/) +[easyconfig](https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/h/h5py/h5py-3.11.0-foss-2023b.eb) 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. @@ -744,19 +1060,26 @@ The Portable Hardware Locality (hwloc) software package provides a portable Hypothesis is an advanced testing library for Python. It lets you write tests which are parametrized by a source of examples, and then generates simple and comprehensible examples that make your tests fail. This lets you find more bugs in your code with less work. + - [igraph/0.10.12-foss-2023b](https://igraph.org) +igraph is a collection of network analysis tools with the emphasis on +efficiency, portability and ease of use. igraph is open source and free. igraph can be +programmed in R, Python and C/C++. - [imageio/2.33.1-gfbf-2023a](https://imageio.github.io) Imageio is a Python library that provides an easy interface to read and write a wide range of image data, including animated images, video, volumetric data, and scientific formats. - - [intltool/0.51.0-GCCcore-12.3.0](https://freedesktop.org/wiki/Software/intltool/) + - [intltool/0.51.0-GCCcore-13.2.0](https://freedesktop.org/wiki/Software/intltool/) intltool is a set of tools to centralize translation of many different file formats using GNU gettext-compatible PO files. - [jax/0.4.25-gfbf-2023a-CUDA-12.1.1](https://jax.readthedocs.io/) Composable transformations of Python+NumPy programs: differentiate, vectorize, JIT to GPU/TPU, and more - - [jbigkit/2.1-GCCcore-13.2.0](https://www.cl.cam.ac.uk/~mgk25/jbigkit/) + - [jbigkit/2.1-GCCcore-12.3.0](https://www.cl.cam.ac.uk/~mgk25/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. + - [jemalloc/5.3.0-GCCcore-12.2.0](http://jemalloc.net) +jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and + scalable concurrency support. - [json-c/0.17-GCCcore-13.2.0](https://github.com/json-c/json-c) [easyconfig](https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/j/json-c/json-c-0.17-GCCcore-13.2.0.eb) JSON-C implements a reference counting object model that allows you to easily construct JSON objects @@ -774,18 +1097,33 @@ using a path like /rstudio next to others like /lab. Alongside the python package that provides the main functionality, the JupyterLab extension (@jupyterlab/server-proxy) provides buttons in the JupyterLab launcher window to get to RStudio for example. - - [libGLU/9.0.3-GCCcore-13.2.0](https://mesa.freedesktop.org/archive/glu/) + - [kallisto/0.50.1-foss-2022b](https://pachterlab.github.io/kallisto/) +[easyconfig](https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/k/kallisto/kallisto-0.50.1-foss-2022b.eb) +kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally + of target sequences using high-throughput sequencing reads. + - [leidenalg/0.10.2-foss-2023b](https://github.com/vtraag/leidenalg) +[easyconfig](https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/l/leidenalg/leidenalg-0.10.2-foss-2023b.eb) +Implementation of the Leiden algorithm for various quality +functions to be used with igraph in Python. + - [libGLU/9.0.3-GCCcore-12.3.0](https://mesa.freedesktop.org/archive/glu/) The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. + - [libaio/0.3.113-GCCcore-12.3.0](https://pagure.io/libaio) +Asynchronous input/output library that uses the kernels native interface. - [libarchive/3.7.2-GCCcore-13.2.0](https://www.libarchive.org/) Multi-format archive and compression library + - [libcerf/2.3-GCCcore-12.2.0](https://jugit.fz-juelich.de/mlz/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. + - [libdeflate/1.19-GCCcore-13.2.0](https://github.com/ebiggers/libdeflate) Heavily optimized library for DEFLATE/zlib/gzip compression and decompression. - [libdrm/2.4.117-GCCcore-13.2.0](https://dri.freedesktop.org) Direct Rendering Manager runtime library. - - [libepoxy/1.5.10-GCCcore-13.2.0](https://github.com/anholt/libepoxy) + - [libepoxy/1.5.10-GCCcore-12.3.0](https://github.com/anholt/libepoxy) Epoxy is a library for handling OpenGL function pointer management for you - - [libevent/2.1.12-GCCcore-12.3.0](https://libevent.org/) + - [libevent/2.1.12-GCCcore-12.2.0](https://libevent.org/) 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 @@ -797,12 +1135,11 @@ the user-space API of OFI, and is typically the only software that applications deal with directly. It works in conjunction with provider libraries, which are often integrated directly into libfabric. - - [libffi/3.4.4-GCCcore-12.3.0](https://sourceware.org/libffi/) + - [libffi/3.4.4-GCCcore-12.2.0](https://sourceware.org/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. - - [libgd/2.3.3-GCCcore-13.2.0](https://libgd.github.io) -[easyconfig](https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/l/libgd/libgd-2.3.3-GCCcore-13.2.0.eb) + - [libgd/2.3.3-GCCcore-12.2.0](https://libgd.github.io) GD is an open source code library for the dynamic creation of images by programmers. - [libgeotiff/1.7.3-GCCcore-13.2.0](https://directory.fsf.org/wiki/Libgeotiff) Library for reading and writing coordinate system information from/to GeoTIFF files @@ -812,13 +1149,23 @@ linkable library with a solid API, allowing you to write native speed custom Git which supports C bindings. - [libglvnd/1.7.0-GCCcore-13.2.0](https://gitlab.freedesktop.org/glvnd/libglvnd) libglvnd is a vendor-neutral dispatch layer for arbitrating OpenGL API calls between multiple vendors. + - [libharu/2.3.0-GCCcore-13.2.0](https://github.com/libharu/libharu/) +[easyconfig](https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/l/libharu/libharu-2.3.0-GCCcore-13.2.0.eb) +libHaru is a free, cross platform, open source library for generating PDF files. - [libiconv/1.17-GCCcore-13.2.0](https://www.gnu.org/software/libiconv) Libiconv converts from one character encoding to another through Unicode conversion + - [libidn2/2.3.4-GCCcore-12.2.0](http://www.gnu.org/software/libidn2) +Libidn2 implements the revised algorithm for internationalized domain names called IDNA2008/TR46. - [libjpeg-turbo/3.0.1-GCCcore-13.2.0](https://sourceforge.net/projects/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. + - [libleidenalg/0.11.1-foss-2022b](https://github.com/vtraag/libleidenalg) +[easyconfig](https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/l/libleidenalg/libleidenalg-0.11.1-foss-2022b.eb) +Implements the Leiden algorithm in C++ + - [libmad/0.15.1b-GCCcore-12.3.0](https://www.underbit.com/products/mad/) +MAD is a high-quality MPEG audio decoder. - [libogg/1.3.5-GCCcore-12.3.0](https://xiph.org/ogg/) Ogg is a multimedia container format, and the native file and stream format for the Xiph.org multimedia codecs. @@ -831,7 +1178,7 @@ Opus is a totally open, royalty-free, highly versatile audio codec. Opus is unma Generic PCI access library. - [libpng/1.6.40-GCCcore-13.2.0](http://www.libpng.org/pub/png/libpng.html) libpng is the official PNG reference library - - [libreadline/8.2-GCCcore-13.2.0](https://tiswww.case.edu/php/chet/readline/rltop.html) + - [libreadline/8.2-GCCcore-12.2.0](https://tiswww.case.edu/php/chet/readline/rltop.html) 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 @@ -839,6 +1186,8 @@ The GNU Readline library provides a set of functions for use by applications and perhaps reedit those lines, and perform csh-like history expansion on previous commands. + - [librosa/0.10.1-foss-2023a](https://librosa.org/) +Audio and music processing in Python - [libsndfile/1.2.2-GCCcore-12.3.0](http://www.mega-nerd.com/libsndfile) [easyconfig](https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/l/libsndfile/libsndfile-1.2.2-GCCcore-12.3.0.eb) Libsndfile is a C library for reading and writing files containing sampled sound @@ -849,7 +1198,7 @@ Sodium is a modern, easy-to-use software library for encryption, decryption, - [libtirpc/1.3.4-GCCcore-13.2.0](https://sourceforge.net/projects/libtirpc/) Libtirpc is a port of Suns Transport-Independent RPC library to Linux. - - [libtool/2.4.7-GCCcore-13.2.0](https://www.gnu.org/software/libtool) + - [libtool/2.4.7-GCCcore-12.2.0](https://www.gnu.org/software/libtool) GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries behind a consistent, portable interface. @@ -874,11 +1223,13 @@ Libxml2 is the XML C parser and toolchain developed for the Gnome project - [libxslt/1.1.38-GCCcore-12.3.0](http://xmlsoft.org/) Libxslt is the XSLT C library developed for the GNOME project (but usable outside of the Gnome platform). - - [libyaml/0.2.5-GCCcore-13.2.0](https://pyyaml.org/wiki/LibYAML) + - [libyaml/0.2.5-GCCcore-12.2.0](https://pyyaml.org/wiki/LibYAML) LibYAML is a YAML parser and emitter written in C. + - [loompy/3.0.7-foss-2023a](https://loompy.org/) +Python implementation of the Loom file format, an efficient file format for large omics datasets - [lxml/4.9.2-GCCcore-12.3.0](https://lxml.de/) The lxml XML toolkit is a Pythonic binding for the C libraries libxml2 and libxslt. - - [lz4/1.9.4-GCCcore-13.2.0](https://lz4.github.io/lz4/) + - [lz4/1.9.4-GCCcore-12.3.0](https://lz4.github.io/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. - [magma/2.7.2-foss-2023a-CUDA-12.1.1](https://icl.cs.utk.edu/magma/) @@ -886,17 +1237,32 @@ The MAGMA project aims to develop a dense linear algebra library similar to LAPACK but for heterogeneous/hybrid architectures, starting with current Multicore+GPU systems. - [make/4.4.1-GCCcore-13.2.0](https://www.gnu.org/software/make/make.html) GNU version of make utility - - [matplotlib/3.7.2-gfbf-2023a](https://matplotlib.org) + - [makeinfo/7.0.3-GCCcore-12.2.0](https://www.gnu.org/software/texinfo/) +makeinfo is part of the Texinfo project, the official documentation format of the GNU project. + - [matplotlib/3.8.2-gfbf-2023b](https://matplotlib.org) matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell, web application servers, and six graphical user interface toolkits. - - [maturin/1.1.0-GCCcore-12.3.0](https://github.com/pyo3/maturin) + - [maturin/1.4.0-GCCcore-12.3.0-Rust-1.75.0](https://github.com/pyo3/maturin) This project is meant as a zero configuration replacement for setuptools-rust and milksnake. It supports building wheels for python 3.5+ on windows, linux, mac and freebsd, can upload them to pypi and has basic pypy and graalpy support. - [meson-python/0.15.0-GCCcore-13.2.0](https://github.com/mesonbuild/meson-python) Python build backend (PEP 517) for Meson projects + - [minimap2/2.26-GCCcore-12.3.0](https://github.com/lh3/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. + - [ml-collections/0.1.1-foss-2023a](https://github.com/google/ml_collections) +ML Collections is a library of Python Collections designed for ML use cases. + - [ml_dtypes/0.3.2-gfbf-2023a](https://github.com/jax-ml/ml_dtypes) ml_dtypes is a stand-alone implementation of several NumPy dtype extensions used in machine learning libraries, including: @@ -909,16 +1275,20 @@ float8_e4m3fnuz float8_e5m2 float8_e5m2fnuz - - [mpi4py/3.1.4-gompi-2023a](https://github.com/mpi4py/mpi4py) + - [mpi4py/3.1.5-gompi-2023b](https://github.com/mpi4py/mpi4py) MPI for Python (mpi4py) provides bindings of the Message Passing Interface (MPI) standard for the Python programming language, allowing any Python program to exploit multiple processors. - - [ncurses/6.4-GCCcore-12.3.0](https://www.gnu.org/software/ncurses/) + - [ncbi-vdb/3.1.1-gompi-2023b](https://github.com/ncbi/ncbi-vdb) +[easyconfig](https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/n/ncbi-vdb/ncbi-vdb-3.1.1-gompi-2023b.eb) +The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for + using data in the INSDC Sequence Read Archives. + - [ncurses/6.4](https://www.gnu.org/software/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. - - [netCDF/4.9.2-gompi-2023b](https://www.unidata.ucar.edu/software/netcdf/) + - [netCDF/4.9.2-gompi-2023a](https://www.unidata.ucar.edu/software/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. @@ -927,7 +1297,7 @@ Nettle is a cryptographic library that is designed to fit easily in more or less any context: In crypto toolkits for object-oriented languages (C++, Python, Pike, ...), in applications like LSH or GNUPG, or even in kernel space. - - [networkx/3.1-gfbf-2023a](https://pypi.python.org/pypi/networkx) + - [networkx/3.2.1-gfbf-2023b](https://pypi.python.org/pypi/networkx) NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks. - [nlohmann_json/3.11.3-GCCcore-13.2.0](https://github.com/nlohmann/json) @@ -945,7 +1315,8 @@ The numactl program allows you to run your application program on specific the operating system before running your program. The libnuma library provides convenient ways for you to add NUMA memory policies into your own program. - - [numba/0.58.1-foss-2023a](https://numba.pydata.org/) + - [numba/0.59.1-foss-2023b](https://numba.pydata.org/) +[easyconfig](https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/n/numba/numba-0.59.1-foss-2023b.eb) 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. @@ -960,7 +1331,7 @@ pigz, which stands for parallel implementation of gzip, is a fully cores to the hilt when compressing data. pigz was written by Mark Adler, and uses the zlib and pthread libraries. - - [pixman/0.42.2-GCCcore-13.2.0](http://www.pixman.org/) + - [pixman/0.42.2-GCCcore-12.3.0](http://www.pixman.org/) 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. @@ -970,9 +1341,13 @@ pkgconf is a program which helps to configure compiler and linker flags for deve It is similar to pkg-config from freedesktop.org. - [pkgconfig/1.5.5-GCCcore-12.3.0-python](https://github.com/matze/pkgconfig) pkgconfig is a Python module to interface with the pkg-config command line tool - - [poetry/1.6.1-GCCcore-13.2.0](https://python-poetry.org) + - [plotly.py/5.16.0-GCCcore-12.3.0](https://plot.ly/python) +An open-source, interactive graphing library for Python + - [poetry/1.7.1-GCCcore-12.3.0](https://python-poetry.org) Python packaging and dependency management made easy. Poetry helps you declare, manage and install dependencies of Python projects, ensuring you have the right stack everywhere. + - [poppler/24.04.0-GCC-13.2.0](https://poppler.freedesktop.org) +Poppler is a PDF rendering library - [protobuf/24.0-GCCcore-12.3.0](https://github.com/protocolbuffers/protobuf) Protocol Buffers (a.k.a., protobuf) are Google's language-neutral, platform-neutral, extensible mechanism for @@ -981,11 +1356,19 @@ serializing structured data. Python Protocol Buffers runtime library. - [psycopg2/2.9.9-GCCcore-12.3.0](https://psycopg.org/) Psycopg is the most popular PostgreSQL adapter for the Python programming language. - - [pybind11/2.11.1-GCCcore-12.3.0](https://pybind11.readthedocs.io) + - [pyEGA3/5.0.2-GCCcore-12.3.0](https://github.com/EGA-archive/ega-download-client) +A basic Python-based EGA download client + - [pybedtools/0.9.1-foss-2023a](https://daler.github.io/pybedtools) +pybedtools wraps and extends BEDTools and offers feature-level manipulations from within Python. + - [pybind11/2.11.1-GCCcore-13.2.0](https://pybind11.readthedocs.io) pybind11 is a lightweight header-only library that exposes C++ types in Python and vice versa, mainly to create Python bindings of existing C++ code. + - [pydantic/2.5.3-GCCcore-12.3.0](https://github.com/samuelcolvin/pydantic) +Data validation and settings management using Python type hinting. - [pyproj/3.6.0-GCCcore-12.3.0](https://pyproj4.github.io/pyproj) Python interface to PROJ4 library for cartographic transformations + - [pyro-ppl/1.9.0-foss-2023a-CUDA-12.1.1](https://github.com/pyro-ppl/pyro) +Pyro is a flexible, scalable deep probabilistic programming library built on PyTorch. - [pytest/7.4.2-GCCcore-12.3.0](https://docs.pytest.org/en/latest/) The pytest framework makes it easy to write small, readable tests, and can scale to support complex functional testing for @@ -1026,31 +1409,84 @@ Before running tests remotely, pytest efficiently “rsyncs” your program source code to the remote place. All test results are reported back and displayed to your local terminal. You may specify different Python versions and interpreters. + - [python-igraph/0.11.4-foss-2023b](https://igraph.org/python) +[easyconfig](https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/p/python-igraph/python-igraph-0.11.4-foss-2023b.eb) +Python interface to the igraph high performance graph library, primarily aimed at complex network + research and analysis. + - [python-isal/1.1.0-GCCcore-12.2.0](https://github.com/pycompression/python-isal) +Faster zlib and gzip compatible compression and decompression + by providing python bindings for the isa-l library. + + - [re2c/3.1-GCCcore-13.2.0](https://re2c.org) +re2c is a free and open-source lexer generator for C and C++. Its main goal is generating +fast lexers: at least as fast as their reasonably optimized hand-coded counterparts. Instead of using +traditional table-driven approach, re2c encodes the generated finite state automata directly in the form +of conditional jumps and comparisons. + - [rpy2/3.5.15-foss-2023a](https://rpy2.github.io) +rpy2 is an interface to R running embedded in a Python process. + - [samblaster/0.1.26-GCC-13.2.0](https://github.com/GregoryFaust/samblaster) +[easyconfig](https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/s/samblaster/samblaster-0.1.26-GCC-13.2.0.eb) +samblaster is a fast and flexible program for marking + duplicates in read-id grouped1 paired-end SAM files. + - [scVelo/0.3.1-foss-2023a](https://scvelo.org) +scVelo is a scalable toolkit for estimating and analyzing RNA velocities in single cells using + dynamical modeling. + - [scanpy/1.10.1-foss-2023b](https://scanpy.readthedocs.io/en/stable/) +[easyconfig](https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/s/scanpy/scanpy-1.10.1-foss-2023b.eb) +Scanpy is a scalable toolkit for analyzing single-cell gene expression data built + jointly with anndata. It includes preprocessing, visualization, clustering, trajectory inference + and differential expression testing. The Python-based implementation efficiently deals with + datasets of more than one million cells. + - [scikit-build/0.17.6-GCCcore-13.2.0](https://scikit-build.readthedocs.io/en/latest) Scikit-Build, or skbuild, is an improved build system generator for CPython C/C++/Fortran/Cython extensions. - [scikit-image/0.22.0-foss-2023a](https://scikit-image.org/) scikit-image is a collection of algorithms for image processing. - - [scikit-learn/1.3.1-gfbf-2023a](https://scikit-learn.org/stable/index.html) + - [scikit-learn/1.4.0-gfbf-2023b](https://scikit-learn.org/stable/index.html) Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, building upon numpy, scipy, and matplotlib. As a machine-learning module, it provides versatile tools for data mining and analysis in any field of science and engineering. It strives to be simple and efficient, accessible to everybody, and reusable in various contexts. + - [scikit-misc/0.3.1-foss-2023a](https://github.com/has2k1/scikit-misc) +[easyconfig](https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/s/scikit-misc/scikit-misc-0.3.1-foss-2023a.eb) +Miscellaneous tools for data analysis and scientific computing + - [scvi-tools/1.1.2-foss-2023a-CUDA-12.1.1](https://github.com/scverse/scvi-tools) +scvi-tools (single-cell variational inference tools) is a package for probabilistic modeling and +analysis of single-cell omics data, built on top of PyTorch and AnnData. - [setuptools-rust/1.8.0-GCCcore-13.2.0](https://github.com/PyO3/setuptools-rust) setuptools-rust is a plugin for setuptools to build Rust Python extensions implemented with PyO3 or rust-cpython. - - [snappy/1.1.10-GCCcore-13.2.0](https://github.com/google/snappy) + - [snappy/1.1.10-GCCcore-12.3.0](https://github.com/google/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. - - [sympy/1.12-gfbf-2023a](https://sympy.org/) + - [splitpipe/1.2.1-foss-2023b](https://support.parsebiosciences.com/hc/en-us) +splitpipe tool from Parse Biosciences. The pipeline takes FASTQ files and delivers + processed data in the form of a cell-gene count matrix, which serves as the input for various open + sources tools such as scanpy and seuratProcess sequencing results with our pipeline. + + A Parse Bioscience login ID is required to download + - [starcode/1.4-GCC-13.2.0](https://github.com/gui11aume/starcode) +Starcode is a DNA sequence clustering software. Starcode clustering is based on all pairs +search within a specified Levenshtein distance (allowing insertions and deletions), followed by a clustering +algorithm: Message Passing, Spheres or Connected Components. + - [statsmodels/0.14.1-gfbf-2023b](https://www.statsmodels.org/) +Statsmodels is a Python module that allows users to explore data, estimate statistical models, +and perform statistical tests. + - [sympy/1.12-gfbf-2023b](https://sympy.org/) SymPy is a Python library for symbolic mathematics. It aims to become a full-featured computer algebra system (CAS) while keeping the code as simple as possible in order to be comprehensible and easily extensible. SymPy is written entirely in Python and does not require any external libraries. + - [tbb/2021.10.0-GCCcore-12.2.0](https://github.com/oneapi-src/oneTBB) +Intel(R) Threading Building Blocks (Intel(R) TBB) lets you easily write parallel C++ programs that + take full advantage of multicore performance, that are portable, composable and have future-proof scalability. - [tensorboard/2.15.1-gfbf-2023a](https://github.com/tensorflow/tensorboard) TensorBoard is a suite of web applications for inspecting and understanding your TensorFlow runs and graphs. + - [tensorboardX/2.6.2.2-foss-2023a](https://github.com/lanpa/tensorboardX) +Tensorboard for PyTorch. - [tensorstore/0.1.53-foss-2023a](https://github.com/google/tensorstore) TensorStore is an open-source C++ and Python software library designed for storage and manipulation of large multi-dimensional arrays. @@ -1059,14 +1495,36 @@ Tornado is a Python web framework and asynchronous networking library. - [tqdm/4.66.2-GCCcore-13.2.0](https://github.com/tqdm/tqdm) [easyconfig](https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/t/tqdm/tqdm-4.66.2-GCCcore-13.2.0.eb) A fast, extensible progress bar for Python and CLI + - [typing-extensions/4.9.0-GCCcore-12.3.0](https://github.com/python/typing/blob/master/typing_extensions/README.rst) +Typing Extensions – Backported and Experimental Type Hints for Python + - [umap-learn/0.5.6-foss-2023b](https://umap-learn.readthedocs.io/en/latest/) +[easyconfig](https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/u/umap-learn/umap-learn-0.5.6-foss-2023b.eb) +Uniform Manifold Approximation and Projection (UMAP) is a dimension reduction technique +that can be used for visualisation similarly to t-SNE, but also for general non-linear +dimension reduction. + + - [unixODBC/2.3.12-GCC-13.2.0](https://www.unixodbc.org) +[easyconfig](https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/u/unixODBC/unixODBC-2.3.12-GCC-13.2.0.eb) +unixODBC provides a uniform interface between application and database driver - [utf8proc/2.9.0-GCCcore-13.2.0](https://github.com/JuliaStrings/utf8proc) utf8proc is a small, clean C library that provides Unicode normalization, case-folding, and other operations for data in the UTF-8 encoding. - - [util-linux/2.39-GCCcore-13.2.0](https://www.kernel.org/pub/linux/utils/util-linux) + - [util-linux/2.39-GCCcore-12.3.0](https://www.kernel.org/pub/linux/utils/util-linux) Set of Linux utilities - [virtualenv/20.24.6-GCCcore-13.2.0](https://github.com/pypa/virtualenv) A tool for creating isolated virtual python environments. - - [x264/20230226-GCCcore-12.3.0](https://www.videolan.org/developers/x264.html) + - [wandb/0.16.1-GCC-12.3.0](https://wandb.ai) +CLI and Python API for Weights and Biases (wandb), a tool for visualizing and +tracking your machine learning experiments. + - [wget/1.21.4-GCCcore-12.2.0](https://www.gnu.org/software/wget) +GNU Wget is a free software package for retrieving files using HTTP, HTTPS and FTP, + the most widely-used Internet protocols. It is a non-interactive commandline tool, + so it may easily be called from scripts, cron jobs, terminals without X-Windows support, etc. + - [wrapt/1.15.0-gfbf-2023a](https://pypi.org/project/wrapt/) +The aim of the wrapt module is to provide a transparent object +proxy for Python, which can be used as the basis for the construction of +function wrappers and decorator functions. + - [x264/20231019-GCCcore-13.2.0](https://www.videolan.org/developers/x264.html) 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. @@ -1080,7 +1538,7 @@ x265 is a free software library and application for encoding video streams xarray (formerly xray) is an open source project and Python package that aims to bring the labeled data power of pandas to the physical sciences, by providing N-dimensional variants of the core pandas data structures. - - [xorg-macros/1.20.0-GCCcore-12.3.0](https://gitlab.freedesktop.org/xorg/util/macros) + - [xorg-macros/1.20.0-GCCcore-13.2.0](https://gitlab.freedesktop.org/xorg/util/macros) X.org macros utilities. - [xxd/9.1.0307-GCCcore-13.2.0](https://www.vim.org) [easyconfig](https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/x/xxd/xxd-9.1.0307-GCCcore-13.2.0.eb) diff --git a/docs/bio-modules-24.04.md b/docs/bio-modules-24.04.md index ee2b46f4..00c8383f 100644 --- a/docs/bio-modules-24.04.md +++ b/docs/bio-modules-24.04.md @@ -2,7 +2,7 @@ title: Bio Modules 24.04 layout: single permalink: /bio-modules-24.04/ -created: 2024-10-07 +created: 2024-10-08 toc: true toc_label: "On This Page" sidebar: @@ -60,7 +60,7 @@ BEAST is a cross-platform program for Bayesian MCMC analysis of molecular - [Bio-DB-HTS/3.01-GCC-12.2.0](https://metacpan.org/release/Bio-DB-HTS) [easyconfig](https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-12.2.0.eb) Read files using HTSlib including BAM/CRAM, Tabix and BCF database files - - [BioPerl/1.7.8-GCCcore-12.3.0](https://bioperl.org/) + - [BioPerl/1.7.8-GCCcore-12.2.0](http://www.bioperl.org/) Bioperl is the product of a community effort to produce Perl code which is useful in biology. Examples include Sequence objects, Alignment objects and database searching objects. - [Biopython/1.84-foss-2023b](https://www.biopython.org) @@ -108,7 +108,7 @@ stand-alone executable version is also available. [easyconfig](https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/c/CoinUtils/CoinUtils-2.11.10-GCC-13.2.0.eb) CoinUtils (Coin-OR Utilities) is an open-source collection of classes and functions that are generally useful to more than one COIN-OR project. - - [Eigen/3.4.0-GCCcore-12.3.0](https://eigen.tuxfamily.org) + - [Eigen/3.4.0-GCCcore-13.2.0](https://eigen.tuxfamily.org) Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms. - [FASTA/36.3.8i-GCC-12.2.0](https://fasta.bioch.virginia.edu/fasta_www2/fasta_list2.shtml) @@ -239,7 +239,7 @@ PyTorch with compatible versions of official Torch extensions. - [Pysam/0.22.0-GCC-12.3.0](https://github.com/pysam-developers/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. - - [Qhull/2020.2-GCCcore-12.2.0](http://www.qhull.org) + - [Qhull/2020.2-GCCcore-13.2.0](http://www.qhull.org) 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 @@ -281,7 +281,8 @@ Sambamba is a high performance modern robust and fast tool (and library), written in the D programming language, for working with SAM and BAM files. Current functionality is an important subset of samtools functionality, including view, index, sort, markdup, and depth. - - [Seaborn/0.13.2-gfbf-2023a](https://seaborn.pydata.org/) + - [Seaborn/0.13.2-gfbf-2023b](https://seaborn.pydata.org/) +[easyconfig](https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/s/Seaborn/Seaborn-0.13.2-gfbf-2023b.eb) Seaborn is a Python visualization library based on matplotlib. It provides a high-level interface for drawing attractive statistical graphics. - [Shapely/2.0.1-gfbf-2023a](https://github.com/Toblerity/Shapely) diff --git a/fh_easyconfigs/g/Graphviz/Graphviz-10.0.1-GCCcore-13.2.0.eb b/fh_easyconfigs/g/Graphviz/Graphviz-10.0.1-GCCcore-13.2.0.eb index 3e2654b6..35b528da 100644 --- a/fh_easyconfigs/g/Graphviz/Graphviz-10.0.1-GCCcore-13.2.0.eb +++ b/fh_easyconfigs/g/Graphviz/Graphviz-10.0.1-GCCcore-13.2.0.eb @@ -17,7 +17,8 @@ source_urls = ['https://gitlab.com/graphviz/graphviz/-/archive/%(version)s'] sources = [SOURCELOWER_TAR_GZ] patches = ['%(name)s-8.1.0_skip-install-data-hook.patch'] checksums = [ - # {'Graphviz-8.1.0_skip-install-data-hook.patch': '834666f1b5a8eff35f30899419e322739d71a2936408b27c8ffb4423a99a38e1'}, + {'graphviz-10.0.1.tar.gz': '28f452ef1cb12288c8758a62f8c3fcfefdb91b251f7aae61d0d703f851bde931'}, + {'Graphviz-8.1.0_skip-install-data-hook.patch': '834666f1b5a8eff35f30899419e322739d71a2936408b27c8ffb4423a99a38e1'}, ] builddependencies = [ diff --git a/fh_easyconfigs/l/Levenshtein/Levenshtein-0.24.0-GCCcore-12.2.0.eb b/fh_easyconfigs/l/Levenshtein/Levenshtein-0.24.0-GCCcore-12.2.0.eb deleted file mode 100644 index 17d5ebcf..00000000 --- a/fh_easyconfigs/l/Levenshtein/Levenshtein-0.24.0-GCCcore-12.2.0.eb +++ /dev/null @@ -1,35 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'Levenshtein' -version = '0.25.1' - -homepage = 'https://pypi.org/project/python-Levenshtein/' -description = 'Python extension for computing string edit distances and similarities.' - -toolchain = {'name': 'GCCcore', 'version': '13.2.0'} - -builddependencies = [ - ('binutils', '2.40'), - ('scikit-build', '0.17.6'), - ('CMake', '3.27.6'), -] - -dependencies = [ - ('Python', '3.11.5'), -] - -use_pip = True - -exts_list = [ - ('rapidfuzz', '3.9.4', { - 'checksums': ['366bf8947b84e37f2f4cf31aaf5f37c39f620d8c0eddb8b633e6ba0129ca4a0a'], - }), - (name, version, { - 'modulename': 'Levenshtein', - 'checksums': ['2df14471c778c75ffbd59cb64bbecfd4b0ef320ef9f80e4804764be7d5678980'], - }), -] - -sanity_pip_check = True - -moduleclass = 'data' diff --git a/fh_easyconfigs/l/leidenalg/leidenalg-0.10.2-foss-2023b.eb b/fh_easyconfigs/l/leidenalg/leidenalg-0.10.2-foss-2023b.eb index f1258014..12773452 100644 --- a/fh_easyconfigs/l/leidenalg/leidenalg-0.10.2-foss-2023b.eb +++ b/fh_easyconfigs/l/leidenalg/leidenalg-0.10.2-foss-2023b.eb @@ -21,7 +21,7 @@ builddependencies = [ dependencies = [ ('Python', '3.11.5'), - ('igraph', '0.10.10'), + ('igraph', '0.10.12'), ('python-igraph', '0.11.4'), ('libleidenalg', '0.11.1'), ] diff --git a/fh_easyconfigs/r/RStudio-Server/RStudio-Server-2024.04.1+748-foss-2023b-Java-11-R-4.4.0.eb b/fh_easyconfigs/r/RStudio-Server/RStudio-Server-2024.04.1+748-foss-2023b-Java-11-R-4.4.0.eb index 48734cf6..d3ae29b8 100644 --- a/fh_easyconfigs/r/RStudio-Server/RStudio-Server-2024.04.1+748-foss-2023b-Java-11-R-4.4.0.eb +++ b/fh_easyconfigs/r/RStudio-Server/RStudio-Server-2024.04.1+748-foss-2023b-Java-11-R-4.4.0.eb @@ -34,7 +34,7 @@ builddependencies = [ dependencies = [ ('Boost', '1.83.0'), - ('GDAL', '3.8.4'), + ('GDAL', '3.9.0'), ('Java', '11', '', SYSTEM), ('R', '4.4.0'), ('SOCI', '4.0.3', '-Boost-1.83.0'),