diff --git a/includes/data/software.yml b/includes/data/software.yml index 3308abd67..f92f1e151 100644 --- a/includes/data/software.yml +++ b/includes/data/software.yml @@ -2438,7 +2438,7 @@ software_modules: - {description: Maxima is a system for the manipulation of symbolic and numerical expressions., markedDefault: false, versionName: 5.47.0} - categories: math, deep learning - defaultVersionName: 1.0.0_py39 + defaultVersionName: 3.1.0_py312 description: Triton is a language and compiler for writing highly efficient custom Deep-Learning primitives. package: py-triton @@ -2450,6 +2450,12 @@ software_modules: properties: arch: {gpu: 1} versionName: 1.0.0_py39 + - description: Triton is a language and compiler for writing highly efficient + custom Deep-Learning primitives. + markedDefault: false + properties: + arch: {gpu: 1} + versionName: 3.1.0_py312 - categories: math, machine learning defaultVersionName: 0.15.0_py39 description: A PyTorch Library for Accelerating 3D Deep Learning Research. @@ -4803,15 +4809,21 @@ software_modules: read whole-slide images (also known as virtual slides)., markedDefault: false, versionName: 3.4.1} - categories: biology, genomics - defaultVersionName: 0.38.1 - description: breseq is a computational pipeline for finding mutations relative - to a reference sequence in short-read DNA resequencing data. - package: breseq - url: http://barricklab.org/breseq + defaultVersionName: 0.44.0 + description: kallisto is a program for quantifying abundances of transcripts + from RNA-Seq data using high-throughput sequencing reads. + package: kallisto + url: https://pachterlab.github.io/kallisto/ versions: - - {description: breseq is a computational pipeline for finding mutations relative - to a reference sequence in short-read DNA resequencing data., markedDefault: false, - versionName: 0.38.1} + - {description: kallisto is a program for quantifying abundances of transcripts + from RNA-Seq data using high-throughput sequencing reads., markedDefault: false, + versionName: 0.46.1} + - {description: kallisto is a program for quantifying abundances of transcripts + from RNA-Seq data using high-throughput sequencing reads., markedDefault: false, + versionName: 0.50.1} + - {description: kallisto is a program for quantifying abundances of transcripts + from RNA-Seq data using high-throughput sequencing reads., markedDefault: true, + versionName: 0.44.0} - categories: biology, genomics defaultVersionName: '20110325' description: The METAL software is designed to facilitate meta-analysis of large @@ -4875,14 +4887,14 @@ software_modules: is a computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology., markedDefault: false, versionName: 0.5.9.4_py36} - categories: biology, genomics - defaultVersionName: 2.2.1 - description: StringTie is a fast and highly efficient assembler of RNA-Seq alignments - into potential transcripts. - package: stringtie - url: https://ccb.jhu.edu/software/stringtie/ - versions: - - {description: StringTie is a fast and highly efficient assembler of RNA-Seq - alignments into potential transcripts., markedDefault: false, versionName: 2.2.1} + defaultVersionName: '3.4' + description: HMMER is used for searching sequence databases for sequence homologs, + and for making sequence alignments. + package: hmmer + url: http://hmmer.org/ + versions: + - {description: 'HMMER is used for searching sequence databases for sequence + homologs, and for making sequence alignments.', markedDefault: false, versionName: '3.4'} - categories: biology, genomics defaultVersionName: 1.6_py27 description: MultiQC is a reporting tool that parses summary statistics from @@ -4953,6 +4965,15 @@ software_modules: versions: - {description: RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data., markedDefault: false, versionName: 1.3.3} + - categories: biology, population genetics + defaultVersionName: 0.6.1_py36 + description: Admixfrog is a HMM to infer ancestry frogments (fragments) from + low-coverage, contaminated data. + package: py-admixfrog + url: https://github.com/BenjaminPeter/admixfrog + versions: + - {description: 'Admixfrog is a HMM to infer ancestry frogments (fragments) + from low-coverage, contaminated data.', markedDefault: false, versionName: 0.6.1_py36} - categories: biology, genomics defaultVersionName: 7.1.0 description: Cell Ranger is a set of analysis pipelines that process Chromium single-cell @@ -4978,16 +4999,25 @@ software_modules: (aka phasing) for SNP array and high coverage sequencing data., markedDefault: true, versionName: 4.0.0} - categories: biology, genomics - defaultVersionName: 2.2.9.1_py39 - description: MACS (Model-based Analysis of ChIP-Seq) implements a novel ChIP-Seq - analysis method. - package: py-macs2 - url: https://github.com/taoliu/MACS + defaultVersionName: 2.16.0 + description: NCBI BLAST+ is a suite of command-line tools to run BLAST (Basic + Local Alignment Search Tool), an algorithm for comparing primary biological + sequence information. + package: ncbi-blast+ + url: https://blast.ncbi.nlm.nih.gov/Blast.cgi versions: - - {description: MACS (Model-based Analysis of ChIP-Seq) implements a novel ChIP-Seq - analysis method., markedDefault: false, versionName: 2.1.1_py27} - - {description: MACS (Model-based Analysis of ChIP-Seq) implements a novel ChIP-Seq - analysis method., markedDefault: false, versionName: 2.2.9.1_py39} + - {description: 'NCBI BLAST+ is a suite of command-line tools to run BLAST (Basic + Local Alignment Search Tool), an algorithm for comparing primary biological + sequence information.', markedDefault: false, versionName: 2.6.0} + - {description: 'NCBI BLAST+ is a suite of command-line tools to run BLAST (Basic + Local Alignment Search Tool), an algorithm for comparing primary biological + sequence information.', markedDefault: false, versionName: 2.7.1} + - {description: 'NCBI BLAST+ is a suite of command-line tools to run BLAST (Basic + Local Alignment Search Tool), an algorithm for comparing primary biological + sequence information.', markedDefault: false, versionName: 2.11.0} + - {description: 'NCBI BLAST+ is a suite of command-line tools to run BLAST (Basic + Local Alignment Search Tool), an algorithm for comparing primary biological + sequence information.', markedDefault: false, versionName: 2.16.0} - categories: biology, genomics defaultVersionName: 0.4.2_py312 description: Reliable, scalable, efficient demultiplexing for single-cell RNA @@ -5007,14 +5037,6 @@ software_modules: - {description: 'Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples.', markedDefault: false, versionName: 2.2.1} - - categories: biology, genomics - defaultVersionName: 2.10.0 - description: 'HiC-Pro: An optimized and flexible pipeline for Hi-C data processing.' - package: hic-pro - url: https://github.com/nservant/HiC-Pro - versions: - - {description: 'HiC-Pro: An optimized and flexible pipeline for Hi-C data processing.', - markedDefault: false, versionName: 2.10.0} - categories: biology, genomics defaultVersionName: 0.98.5 description: GEMMA is a software toolkit for fast application of linear mixed @@ -5026,6 +5048,28 @@ software_modules: - {description: GEMMA is a software toolkit for fast application of linear mixed models (LMMs) and related models to genome-wide association studies (GWAS) and other large-scale data sets., markedDefault: false, versionName: 0.98.5} + - categories: biology, cryo-em + defaultVersionName: 4.11.5 + description: IMOD is a set of image processing, modeling and display programs + used for tomographic reconstruction and for 3D reconstruction of EM serial + sections and optical sections. + package: imod + url: http://bio3d.colorado.edu/imod + versions: + - description: IMOD is a set of image processing, modeling and display programs + used for tomographic reconstruction and for 3D reconstruction of EM serial + sections and optical sections. + markedDefault: false + properties: + arch: {gpu: 1} + versionName: 4.9.12 + - description: IMOD is a set of image processing, modeling and display programs + used for tomographic reconstruction and for 3D reconstruction of EM serial + sections and optical sections. + markedDefault: false + properties: + arch: {gpu: 1} + versionName: 4.11.5 - categories: biology, cryo-em defaultVersionName: 4.1.13 description: ctffind is a program for finding CTFs of electron micrographs. @@ -5078,53 +5122,15 @@ software_modules: arch: {gpu: 1} parallel: {mpi: 1} versionName: 4.0.1 - - categories: biology, cryo-em - defaultVersionName: 4.11.5 - description: IMOD is a set of image processing, modeling and display programs - used for tomographic reconstruction and for 3D reconstruction of EM serial - sections and optical sections. - package: imod - url: http://bio3d.colorado.edu/imod - versions: - - description: IMOD is a set of image processing, modeling and display programs - used for tomographic reconstruction and for 3D reconstruction of EM serial - sections and optical sections. - markedDefault: false - properties: - arch: {gpu: 1} - versionName: 4.9.12 - - description: IMOD is a set of image processing, modeling and display programs - used for tomographic reconstruction and for 3D reconstruction of EM serial - sections and optical sections. - markedDefault: false - properties: - arch: {gpu: 1} - versionName: 4.11.5 - categories: biology, genomics - defaultVersionName: 0.44.0 - description: kallisto is a program for quantifying abundances of transcripts - from RNA-Seq data using high-throughput sequencing reads. - package: kallisto - url: https://pachterlab.github.io/kallisto/ - versions: - - {description: kallisto is a program for quantifying abundances of transcripts - from RNA-Seq data using high-throughput sequencing reads., markedDefault: false, - versionName: 0.46.1} - - {description: kallisto is a program for quantifying abundances of transcripts - from RNA-Seq data using high-throughput sequencing reads., markedDefault: false, - versionName: 0.50.1} - - {description: kallisto is a program for quantifying abundances of transcripts - from RNA-Seq data using high-throughput sequencing reads., markedDefault: true, - versionName: 0.44.0} - - categories: biology, population genetics - defaultVersionName: 0.6.1_py36 - description: Admixfrog is a HMM to infer ancestry frogments (fragments) from - low-coverage, contaminated data. - package: py-admixfrog - url: https://github.com/BenjaminPeter/admixfrog + defaultVersionName: 2.2.1 + description: StringTie is a fast and highly efficient assembler of RNA-Seq alignments + into potential transcripts. + package: stringtie + url: https://ccb.jhu.edu/software/stringtie/ versions: - - {description: 'Admixfrog is a HMM to infer ancestry frogments (fragments) - from low-coverage, contaminated data.', markedDefault: false, versionName: 0.6.1_py36} + - {description: StringTie is a fast and highly efficient assembler of RNA-Seq + alignments into potential transcripts., markedDefault: false, versionName: 2.2.1} - categories: biology, neurosciences defaultVersionName: 0.10.9_py36 description: The Maastricht Diffusion Toolbox, MDT, is a framework and library @@ -5151,41 +5157,26 @@ software_modules: toolkit for reading, writing, and manipulating BAM (genome alignment) files.', markedDefault: false, versionName: 2.5.1} - categories: biology, genomics - defaultVersionName: '2.20' - description: The bcl2fastq2 conversion software can be used to convert BCL files - from MiniSeq, MiSeq, NextSeq, HiSeq, iSeq and NovaSeq sequening systems. - package: bcl2fastq - url: https://support.illumina.com/downloads/bcl2fastq-conversion-software-v2-20.html - versions: - - {description: 'The bcl2fastq2 conversion software can be used to convert BCL - files from MiniSeq, MiSeq, NextSeq, HiSeq, iSeq and NovaSeq sequening systems.', - markedDefault: false, versionName: '2.20'} - - categories: biology, genomics - defaultVersionName: '1.16' - description: BCFtools is a program for variant calling and manipulating files - in the Variant Call Format (VCF) and its binary counterpart BCF. - package: bcftools - url: https://github.com/samtools/bcftools + defaultVersionName: 0.7.3 + description: Dorado is a high-performance, easy-to-use, open source basecaller + for Oxford Nanopore reads. + package: dorado + url: https://github.com/nanoporetech/dorado versions: - - {description: BCFtools is a program for variant calling and manipulating files - in the Variant Call Format (VCF) and its binary counterpart BCF., markedDefault: false, - versionName: '1.6'} - - {description: BCFtools is a program for variant calling and manipulating files - in the Variant Call Format (VCF) and its binary counterpart BCF., markedDefault: false, - versionName: '1.8'} - - {description: BCFtools is a program for variant calling and manipulating files - in the Variant Call Format (VCF) and its binary counterpart BCF., markedDefault: false, - versionName: '1.16'} + - {description: 'Dorado is a high-performance, easy-to-use, open source basecaller + for Oxford Nanopore reads.', markedDefault: false, versionName: 0.3.4} + - {description: 'Dorado is a high-performance, easy-to-use, open source basecaller + for Oxford Nanopore reads.', markedDefault: false, versionName: 0.5.3} + - {description: 'Dorado is a high-performance, easy-to-use, open source basecaller + for Oxford Nanopore reads.', markedDefault: false, versionName: 0.7.3} - categories: biology, genomics - defaultVersionName: 0.11.8 - description: FastQC aims to provide a simple way to do some quality control - checks on raw sequence data coming from high throughput sequencing pipelines. - package: fastqc - url: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ + defaultVersionName: 3.0.7 + description: NCBI VDB is the database engine used by NCBI SRA tools. + package: ncbi-vdb + url: https://github.com/ncbi/ncbi-vdb versions: - - {description: FastQC aims to provide a simple way to do some quality control - checks on raw sequence data coming from high throughput sequencing pipelines., - markedDefault: false, versionName: 0.11.8} + - {description: NCBI VDB is the database engine used by NCBI SRA tools., markedDefault: false, + versionName: 3.0.7} - categories: biology, clinical science defaultVersionName: '20180704' description: Simvascular is a blood flow simulation and analysis toolkit. This @@ -5196,6 +5187,24 @@ software_modules: - {description: Simvascular is a blood flow simulation and analysis toolkit. This module provides the svFSI (Fluid Solid Interaction) solver., markedDefault: false, versionName: '20180704'} + - categories: biology, genomics + defaultVersionName: 3.3.1_py36 + description: Tools to process and analyze deep sequencing data. + package: py-deeptools + url: https://github.com/deeptools/deepTools/ + versions: + - {description: Tools to process and analyze deep sequencing data., markedDefault: false, + versionName: 3.3.1_py36} + - categories: biology, genomics + defaultVersionName: 0.11.8 + description: FastQC aims to provide a simple way to do some quality control + checks on raw sequence data coming from high throughput sequencing pipelines. + package: fastqc + url: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ + versions: + - {description: FastQC aims to provide a simple way to do some quality control + checks on raw sequence data coming from high throughput sequencing pipelines., + markedDefault: false, versionName: 0.11.8} - categories: biology, neurosciences defaultVersionName: '20160502' description: MRIcron is a cross-platform NIfTI format image viewer. @@ -5204,6 +5213,16 @@ software_modules: versions: - {description: MRIcron is a cross-platform NIfTI format image viewer., markedDefault: false, versionName: '20160502'} + - categories: biology, genomics + defaultVersionName: 0.38.1 + description: breseq is a computational pipeline for finding mutations relative + to a reference sequence in short-read DNA resequencing data. + package: breseq + url: http://barricklab.org/breseq + versions: + - {description: breseq is a computational pipeline for finding mutations relative + to a reference sequence in short-read DNA resequencing data., markedDefault: false, + versionName: 0.38.1} - categories: biology, genomics defaultVersionName: 2.4.40 description: BEDOPS is an open-source command-line toolkit that performs highly @@ -5272,16 +5291,14 @@ software_modules: diffusion MRI analyses, from various forms of tractography through to next-generation group-level analyses.', markedDefault: false, versionName: 3.0.3} - categories: biology, genomics - defaultVersionName: 2.30.0 - description: The bedtools utilities are a swiss-army knife of tools for a wide-range - of genomics analysis tasks. - package: bedtools - url: https://bedtools.readthedocs.io + defaultVersionName: 0.4.17_py36 + description: A visualization framework for CRISPR/Cas9 knockout screens, analyzed + with MAGeCK. + package: py-vispr + url: https://bitbucket.org/liulab/vispr versions: - - {description: The bedtools utilities are a swiss-army knife of tools for a - wide-range of genomics analysis tasks., markedDefault: false, versionName: 2.27.1} - - {description: The bedtools utilities are a swiss-army knife of tools for a - wide-range of genomics analysis tasks., markedDefault: false, versionName: 2.30.0} + - {description: 'A visualization framework for CRISPR/Cas9 knockout screens, + analyzed with MAGeCK.', markedDefault: false, versionName: 0.4.17_py36} - categories: biology, neurology defaultVersionName: 7.4.1 description: An open source software suite for processing and analyzing (human) @@ -5312,15 +5329,17 @@ software_modules: properties: arch: {gpu: 1} versionName: 1.3.4_py39 - - categories: biology, genomics - defaultVersionName: 0.4.17_py36 - description: A visualization framework for CRISPR/Cas9 knockout screens, analyzed - with MAGeCK. - package: py-vispr - url: https://bitbucket.org/liulab/vispr - versions: - - {description: 'A visualization framework for CRISPR/Cas9 knockout screens, - analyzed with MAGeCK.', markedDefault: false, versionName: 0.4.17_py36} + - categories: biology, neurosciences + defaultVersionName: 1.3.1 + description: Connectome Workbench is an open source, freely available visualization + and discovery tool used to map neuroimaging data, especially data generated + by the Human Connectome Project. + package: workbench + url: https://www.humanconnectome.org/software/connectome-workbench + versions: + - {description: 'Connectome Workbench is an open source, freely available visualization + and discovery tool used to map neuroimaging data, especially data generated + by the Human Connectome Project.', markedDefault: false, versionName: 1.3.1} - categories: biology, neurosciences defaultVersionName: 5.0.10 description: FSL is a comprehensive library of analysis tools for FMRI, MRI @@ -5340,17 +5359,17 @@ software_modules: properties: arch: {gpu: 1} versionName: 5.0.10 - - categories: biology, neurosciences - defaultVersionName: 0.7.00 - description: BART is a toolbox for Computational Magnetic Resonance Imaging. - package: bart - url: https://mrirecon.github.io/bart/ + - categories: biology, genomics + defaultVersionName: 2.30.0 + description: The bedtools utilities are a swiss-army knife of tools for a wide-range + of genomics analysis tasks. + package: bedtools + url: https://bedtools.readthedocs.io versions: - - description: BART is a toolbox for Computational Magnetic Resonance Imaging. - markedDefault: false - properties: - arch: {gpu: 1} - versionName: 0.7.00 + - {description: The bedtools utilities are a swiss-army knife of tools for a + wide-range of genomics analysis tasks., markedDefault: false, versionName: 2.27.1} + - {description: The bedtools utilities are a swiss-army knife of tools for a + wide-range of genomics analysis tasks., markedDefault: false, versionName: 2.30.0} - categories: biology, genomics defaultVersionName: 0.0.14 description: The FASTX-Toolkit is a collection of command line tools for Short-Reads @@ -5425,16 +5444,16 @@ software_modules: versions: - {description: FreeBayes is a Bayesian genetic variant detector designed to find small polymorphisms., markedDefault: false, versionName: 1.2.0} - - categories: biology, genomics - defaultVersionName: 2.13.1 - description: Trinity RNA-Seq de novo transcriptome assembly. - package: trinity - url: https://github.com/trinityrnaseq/trinityrnaseq + - categories: biology, workflow management + defaultVersionName: 23.04.3 + description: Nextflow is a bioinformatics workflow manager that enables the + development of portable and reproducible workflows. + package: nextflow + url: http://nextflow.io/ versions: - - {description: Trinity RNA-Seq de novo transcriptome assembly., markedDefault: false, - versionName: 2.8.4} - - {description: Trinity RNA-Seq de novo transcriptome assembly., markedDefault: false, - versionName: 2.13.1} + - {description: Nextflow is a bioinformatics workflow manager that enables the + development of portable and reproducible workflows., markedDefault: false, + versionName: 23.04.3} - categories: biology, genomics defaultVersionName: 1.0.0_py39 description: SCENIC+ is a python package to build enhancer driven gene regulatory @@ -5448,15 +5467,21 @@ software_modules: and single-cell chromatin accessibility (scATAC-seq) data., markedDefault: false, versionName: 1.0.0_py39} - categories: biology, genomics - defaultVersionName: 2.0.1_py39 - description: HTSeq is a Python library to facilitate processing and analysis - of data from high-throughput sequencing (HTS) experiments. - package: py-htseq - url: http://htseq.readthedocs.io/ + defaultVersionName: '1.16' + description: BCFtools is a program for variant calling and manipulating files + in the Variant Call Format (VCF) and its binary counterpart BCF. + package: bcftools + url: https://github.com/samtools/bcftools versions: - - {description: HTSeq is a Python library to facilitate processing and analysis - of data from high-throughput sequencing (HTS) experiments., markedDefault: false, - versionName: 2.0.1_py39} + - {description: BCFtools is a program for variant calling and manipulating files + in the Variant Call Format (VCF) and its binary counterpart BCF., markedDefault: false, + versionName: '1.6'} + - {description: BCFtools is a program for variant calling and manipulating files + in the Variant Call Format (VCF) and its binary counterpart BCF., markedDefault: false, + versionName: '1.8'} + - {description: BCFtools is a program for variant calling and manipulating files + in the Variant Call Format (VCF) and its binary counterpart BCF., markedDefault: false, + versionName: '1.16'} - categories: biology, genomics defaultVersionName: '0.1' description: popscle is a suite of population scale analysis tools for single-cell @@ -5487,26 +5512,15 @@ software_modules: - {description: 'Tools for manipulating biological data, particularly multiple sequence alignments.', markedDefault: false, versionName: 0.8.13_py39} - categories: biology, genomics - defaultVersionName: 2.1.0 - description: HISAT2 is a fast and sensitive alignment program for mapping next-generation - sequencing reads (both DNA and RNA) to a population of human genomes (as well - as to a single reference genome). - package: hisat2 - url: http://ccb.jhu.edu/software/hisat2 - versions: - - {description: HISAT2 is a fast and sensitive alignment program for mapping - next-generation sequencing reads (both DNA and RNA) to a population of human - genomes (as well as to a single reference genome)., markedDefault: false, - versionName: 2.1.0} - - categories: biology, genomics - defaultVersionName: 2.1.0 - description: Cell Ranger ATAC is a set of analysis pipelines that process Chromium - Single Cell ATAC data. - package: cellranger-atac - url: https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac + defaultVersionName: 2.0.1_py39 + description: HTSeq is a Python library to facilitate processing and analysis + of data from high-throughput sequencing (HTS) experiments. + package: py-htseq + url: http://htseq.readthedocs.io/ versions: - - {description: Cell Ranger ATAC is a set of analysis pipelines that process - Chromium Single Cell ATAC data., markedDefault: false, versionName: 2.1.0} + - {description: HTSeq is a Python library to facilitate processing and analysis + of data from high-throughput sequencing (HTS) experiments., markedDefault: false, + versionName: 2.0.1_py39} - categories: biology, genomics defaultVersionName: 0.9.0_py39 description: Pybedtools wraps and extends BEDTools and offers feature-level @@ -5520,16 +5534,15 @@ software_modules: manipulations from within Python., markedDefault: false, versionName: 0.8.2_py36} - {description: Pybedtools wraps and extends BEDTools and offers feature-level manipulations from within Python., markedDefault: false, versionName: 0.9.0_py39} - - categories: biology, workflow management - defaultVersionName: 23.04.3 - description: Nextflow is a bioinformatics workflow manager that enables the - development of portable and reproducible workflows. - package: nextflow - url: http://nextflow.io/ + - categories: biology, genomics + defaultVersionName: 2.1.0 + description: Cell Ranger ATAC is a set of analysis pipelines that process Chromium + Single Cell ATAC data. + package: cellranger-atac + url: https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac versions: - - {description: Nextflow is a bioinformatics workflow manager that enables the - development of portable and reproducible workflows., markedDefault: false, - versionName: 23.04.3} + - {description: Cell Ranger ATAC is a set of analysis pipelines that process + Chromium Single Cell ATAC data., markedDefault: false, versionName: 2.1.0} - categories: biology, molecular biology defaultVersionName: 3.0.0 description: Library to work with mmCIF and PDB files. @@ -5539,22 +5552,15 @@ software_modules: - {description: Library to work with mmCIF and PDB files., markedDefault: false, versionName: 3.0.0} - categories: biology, genomics - defaultVersionName: 3.0.7 - description: NCBI VDB is the database engine used by NCBI SRA tools. - package: ncbi-vdb - url: https://github.com/ncbi/ncbi-vdb - versions: - - {description: NCBI VDB is the database engine used by NCBI SRA tools., markedDefault: false, - versionName: 3.0.7} - - categories: biology, genomics - defaultVersionName: 2.5.1 - description: A C code library and several stand-alone programs for the prediction - and comparison of RNA secondary structures. - package: viennarna - url: https://github.com/ViennaRNA/ViennaRNA + defaultVersionName: 2.13.1 + description: Trinity RNA-Seq de novo transcriptome assembly. + package: trinity + url: https://github.com/trinityrnaseq/trinityrnaseq versions: - - {description: A C code library and several stand-alone programs for the prediction - and comparison of RNA secondary structures., markedDefault: false, versionName: 2.5.1} + - {description: Trinity RNA-Seq de novo transcriptome assembly., markedDefault: false, + versionName: 2.8.4} + - {description: Trinity RNA-Seq de novo transcriptome assembly., markedDefault: false, + versionName: 2.13.1} - categories: biology, cryo-em defaultVersionName: 0.2.5_py39 description: A pipeline for particle detection in cryo-electron microscopy images @@ -5576,6 +5582,15 @@ software_modules: properties: arch: {gpu: 1} versionName: 0.2.5_py39 + - categories: biology, genomics + defaultVersionName: 2.5.1 + description: A C code library and several stand-alone programs for the prediction + and comparison of RNA secondary structures. + package: viennarna + url: https://github.com/ViennaRNA/ViennaRNA + versions: + - {description: A C code library and several stand-alone programs for the prediction + and comparison of RNA secondary structures., markedDefault: false, versionName: 2.5.1} - categories: biology, genomics defaultVersionName: 1.2.13_py27 description: OBITools is a set of programs designed for analyzing NGS data in @@ -5585,6 +5600,16 @@ software_modules: versions: - {description: OBITools is a set of programs designed for analyzing NGS data in a DNA metabarcoding context., markedDefault: false, versionName: 1.2.13_py27} + - categories: biology, genomics + defaultVersionName: '2.20' + description: The bcl2fastq2 conversion software can be used to convert BCL files + from MiniSeq, MiSeq, NextSeq, HiSeq, iSeq and NovaSeq sequening systems. + package: bcl2fastq + url: https://support.illumina.com/downloads/bcl2fastq-conversion-software-v2-20.html + versions: + - {description: 'The bcl2fastq2 conversion software can be used to convert BCL + files from MiniSeq, MiSeq, NextSeq, HiSeq, iSeq and NovaSeq sequening systems.', + markedDefault: false, versionName: '2.20'} - categories: biology, radiology defaultVersionName: '4.2' description: The NBIA Data Retriever is an application to download radiology @@ -5594,15 +5619,19 @@ software_modules: versions: - {description: The NBIA Data Retriever is an application to download radiology images from the TCIA Radiology Portal., markedDefault: false, versionName: '4.2'} - - categories: biology, genomics - defaultVersionName: 2.3.4.1 - description: Bowtie 2 is an ultrafast and memory-efficient tool for aligning - sequencing reads to long reference sequences. - package: bowtie2 - url: http://bowtie-bio.sourceforge.net/bowtie2 + - categories: biology, neurosciences + defaultVersionName: 2.4.0 + description: ANTs computes high-dimensional mappings to capture the statistics + of brain structure and function. + package: ants + url: https://stnava.github.io/ANTs versions: - - {description: Bowtie 2 is an ultrafast and memory-efficient tool for aligning - sequencing reads to long reference sequences., markedDefault: false, versionName: 2.3.4.1} + - {description: ANTs computes high-dimensional mappings to capture the statistics + of brain structure and function., markedDefault: false, versionName: 2.1.0} + - {description: ANTs computes high-dimensional mappings to capture the statistics + of brain structure and function., markedDefault: false, versionName: 2.3.1} + - {description: ANTs computes high-dimensional mappings to capture the statistics + of brain structure and function., markedDefault: false, versionName: 2.4.0} - categories: biology, genomics defaultVersionName: 0.5.0 description: Trim Galore! is a wrapper script to automate quality and adapter @@ -5650,19 +5679,18 @@ software_modules: properties: arch: {gpu: 1} versionName: 1.3.1 - - categories: biology, neurosciences - defaultVersionName: 2.4.0 - description: ANTs computes high-dimensional mappings to capture the statistics - of brain structure and function. - package: ants - url: https://stnava.github.io/ANTs + - categories: biology, genomics + defaultVersionName: 2.1.0 + description: HISAT2 is a fast and sensitive alignment program for mapping next-generation + sequencing reads (both DNA and RNA) to a population of human genomes (as well + as to a single reference genome). + package: hisat2 + url: http://ccb.jhu.edu/software/hisat2 versions: - - {description: ANTs computes high-dimensional mappings to capture the statistics - of brain structure and function., markedDefault: false, versionName: 2.1.0} - - {description: ANTs computes high-dimensional mappings to capture the statistics - of brain structure and function., markedDefault: false, versionName: 2.3.1} - - {description: ANTs computes high-dimensional mappings to capture the statistics - of brain structure and function., markedDefault: false, versionName: 2.4.0} + - {description: HISAT2 is a fast and sensitive alignment program for mapping + next-generation sequencing reads (both DNA and RNA) to a population of human + genomes (as well as to a single reference genome)., markedDefault: false, + versionName: 2.1.0} - categories: biology, genomics defaultVersionName: 3.0.2_py27 description: Assessing genome assembly and annotation completeness with Benchmarking @@ -5672,14 +5700,6 @@ software_modules: versions: - {description: Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs (BUSCO)., markedDefault: false, versionName: 3.0.2_py27} - - categories: biology, genomics - defaultVersionName: 3.3.1_py36 - description: Tools to process and analyze deep sequencing data. - package: py-deeptools - url: https://github.com/deeptools/deepTools/ - versions: - - {description: Tools to process and analyze deep sequencing data., markedDefault: false, - versionName: 3.3.1_py36} - categories: biology, genomics defaultVersionName: 1.16.1 description: Tools (written in C using htslib) for manipulating next-generation @@ -5693,6 +5713,26 @@ software_modules: sequencing data., markedDefault: false, versionName: '1.8'} - {description: Tools (written in C using htslib) for manipulating next-generation sequencing data., markedDefault: false, versionName: 1.16.1} + - categories: biology, genomics + defaultVersionName: 2.3.4.1 + description: Bowtie 2 is an ultrafast and memory-efficient tool for aligning + sequencing reads to long reference sequences. + package: bowtie2 + url: http://bowtie-bio.sourceforge.net/bowtie2 + versions: + - {description: Bowtie 2 is an ultrafast and memory-efficient tool for aligning + sequencing reads to long reference sequences., markedDefault: false, versionName: 2.3.4.1} + - categories: biology, neurosciences + defaultVersionName: 0.7.00 + description: BART is a toolbox for Computational Magnetic Resonance Imaging. + package: bart + url: https://mrirecon.github.io/bart/ + versions: + - description: BART is a toolbox for Computational Magnetic Resonance Imaging. + markedDefault: false + properties: + arch: {gpu: 1} + versionName: 0.7.00 - categories: biology, computational biology defaultVersionName: '3.14' description: Rosetta is the premier software suite for modeling macromolecular @@ -5752,19 +5792,6 @@ software_modules: properties: arch: {gpu: 1} versionName: 2.3.10_py39 - - categories: biology, genomics - defaultVersionName: 0.7.3 - description: Dorado is a high-performance, easy-to-use, open source basecaller - for Oxford Nanopore reads. - package: dorado - url: https://github.com/nanoporetech/dorado - versions: - - {description: 'Dorado is a high-performance, easy-to-use, open source basecaller - for Oxford Nanopore reads.', markedDefault: false, versionName: 0.3.4} - - {description: 'Dorado is a high-performance, easy-to-use, open source basecaller - for Oxford Nanopore reads.', markedDefault: false, versionName: 0.5.3} - - {description: 'Dorado is a high-performance, easy-to-use, open source basecaller - for Oxford Nanopore reads.', markedDefault: false, versionName: 0.7.3} - categories: biology, genomics defaultVersionName: '1.16' description: C library for high-throughput sequencing data formats. @@ -5821,17 +5848,6 @@ software_modules: versions: - {description: Longshot is a variant calling tool for diploid genomes using long error prone reads., markedDefault: false, versionName: 1.0.0} - - categories: biology, neurosciences - defaultVersionName: 1.3.1 - description: Connectome Workbench is an open source, freely available visualization - and discovery tool used to map neuroimaging data, especially data generated - by the Human Connectome Project. - package: workbench - url: https://www.humanconnectome.org/software/connectome-workbench - versions: - - {description: 'Connectome Workbench is an open source, freely available visualization - and discovery tool used to map neuroimaging data, especially data generated - by the Human Connectome Project.', markedDefault: false, versionName: 1.3.1} - categories: biology, genomics defaultVersionName: '1.8' description: A single molecule sequence assembler for genomes large and small. @@ -5841,25 +5857,24 @@ software_modules: - {description: A single molecule sequence assembler for genomes large and small., markedDefault: false, versionName: '1.8'} - categories: biology, genomics - defaultVersionName: 2.16.0 - description: NCBI BLAST+ is a suite of command-line tools to run BLAST (Basic - Local Alignment Search Tool), an algorithm for comparing primary biological - sequence information. - package: ncbi-blast+ - url: https://blast.ncbi.nlm.nih.gov/Blast.cgi + defaultVersionName: 2.10.0 + description: 'HiC-Pro: An optimized and flexible pipeline for Hi-C data processing.' + package: hic-pro + url: https://github.com/nservant/HiC-Pro versions: - - {description: 'NCBI BLAST+ is a suite of command-line tools to run BLAST (Basic - Local Alignment Search Tool), an algorithm for comparing primary biological - sequence information.', markedDefault: false, versionName: 2.6.0} - - {description: 'NCBI BLAST+ is a suite of command-line tools to run BLAST (Basic - Local Alignment Search Tool), an algorithm for comparing primary biological - sequence information.', markedDefault: false, versionName: 2.7.1} - - {description: 'NCBI BLAST+ is a suite of command-line tools to run BLAST (Basic - Local Alignment Search Tool), an algorithm for comparing primary biological - sequence information.', markedDefault: false, versionName: 2.11.0} - - {description: 'NCBI BLAST+ is a suite of command-line tools to run BLAST (Basic - Local Alignment Search Tool), an algorithm for comparing primary biological - sequence information.', markedDefault: false, versionName: 2.16.0} + - {description: 'HiC-Pro: An optimized and flexible pipeline for Hi-C data processing.', + markedDefault: false, versionName: 2.10.0} + - categories: biology, genomics + defaultVersionName: 2.2.9.1_py39 + description: MACS (Model-based Analysis of ChIP-Seq) implements a novel ChIP-Seq + analysis method. + package: py-macs2 + url: https://github.com/taoliu/MACS + versions: + - {description: MACS (Model-based Analysis of ChIP-Seq) implements a novel ChIP-Seq + analysis method., markedDefault: false, versionName: 2.1.1_py27} + - {description: MACS (Model-based Analysis of ChIP-Seq) implements a novel ChIP-Seq + analysis method., markedDefault: false, versionName: 2.2.9.1_py39} - categories: biology, genomics defaultVersionName: 2.2.1_py36 description: mapDamage2 is a computational framework which tracks and quantifies @@ -5921,17 +5936,27 @@ software_modules: arch: {gpu: 1} parallel: {mpi: 1} versionName: '20230802' - - categories: chemistry, docking - defaultVersionName: 1.0.2 - description: A deep learning framework for molecular docking - package: gnina - url: https://github.com/gnina/gnina + - categories: chemistry, computational chemistry + defaultVersionName: g16.B01 + description: Gaussian is a general purpose computational chemistry software + package. + package: gaussian + url: https://www.gaussian.com versions: - - description: A deep learning framework for molecular docking + - description: Gaussian is a general purpose computational chemistry software + package. markedDefault: false properties: arch: {gpu: 1} - versionName: 1.0.2 + license: {restricted: 1} + versionName: g16.A03 + - description: Gaussian is a general purpose computational chemistry software + package. + markedDefault: false + properties: + arch: {gpu: 1} + license: {restricted: 1} + versionName: g16.B01 - categories: chemistry, computational chemistry defaultVersionName: 5.2.2 description: Libxc is a library of exchange-correlation functionals for density-functional @@ -6038,21 +6063,39 @@ software_modules: versions: - {description: Crystallographic automation and complex data manipulation libraries., markedDefault: false, versionName: 2.1.20180802} - - categories: chemistry, cheminformatics - defaultVersionName: 2018.09.1_py27 - description: RDKit is a collection of cheminformatics and machine-learning software - written in C++ and Python. - package: py-rdkit - url: http://www.rdkit.org + - categories: chemistry, quantum chemistry + defaultVersionName: '7.1' + description: Quantum ESPRESSO is an integrated suite of Open-Source computer + codes for electronic-structure calculations and materials modeling at the + nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials. + package: quantum-espresso_gpu + url: https://www.quantum-espresso.org versions: - - {description: RDKit is a collection of cheminformatics and machine-learning - software written in C++ and Python., markedDefault: false, versionName: 2018.09.1_py36} - - {description: RDKit is a collection of cheminformatics and machine-learning - software written in C++ and Python., markedDefault: false, versionName: 2022.09.1_py39} - - {description: RDKit is a collection of cheminformatics and machine-learning - software written in C++ and Python., markedDefault: false, versionName: 2024.3.2_py312} - - {description: RDKit is a collection of cheminformatics and machine-learning - software written in C++ and Python., markedDefault: true, versionName: 2018.09.1_py27} + - description: GPU-accelerated Quantum ESPRESSO using CUDA FORTRAN + family: qe + markedDefault: false + properties: + arch: {gpu: 1} + parallel: {mpi: 1} + versionName: '1.1' + - description: Quantum ESPRESSO is an integrated suite of Open-Source computer + codes for electronic-structure calculations and materials modeling at the + nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials. + family: qe + markedDefault: false + properties: + arch: {gpu: 1} + parallel: {mpi: 1} + versionName: '7.0' + - description: Quantum ESPRESSO is an integrated suite of Open-Source computer + codes for electronic-structure calculations and materials modeling at the + nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials. + family: qe + markedDefault: false + properties: + arch: {gpu: 1} + parallel: {mpi: 1} + versionName: '7.1' - categories: chemistry, computational chemistry defaultVersionName: 2021-1 description: Schrödinger Suites (Small-molecule Drug Discovery Suite, Material @@ -6177,6 +6220,13 @@ software_modules: license: {restricted: 1} parallel: {mpi: 1} versionName: 5.4.1 + - categories: chemistry, modelling + defaultVersionName: 3.0.0_py312 + description: AlphaFold is an artificial intelligence (AI) system that predicts + the 3D structures of proteins from their amino acid sequences. + package: .py-alphafold + url: https://deepmind.google/technologies/alphafold/ + versions: [] - categories: chemistry, molecular dynamics defaultVersionName: 2.3.2 description: PLUMED is an open source library for free energy calculations in @@ -6305,18 +6355,14 @@ software_modules: properties: parallel: {mpi: 1} versionName: '20220426' - - categories: chemistry, x-ray spectroscopy - defaultVersionName: 0.9.80_py312 - description: Larch is a open-source library and set of applications for processing - and analyzing X-ray absorption and fluorescence spectroscopy data and X-ray - fluorescence and diffraction image data from synchrotron beamlines. - package: py-xraylarch - url: https://xraypy.github.io/xraylarch/ + - categories: chemistry, crystallography + defaultVersionName: '1.4' + description: A macromolecular superposition library. + package: ssm + url: https://www.ccp4.ac.uk/ versions: - - {description: Larch is a open-source library and set of applications for processing - and analyzing X-ray absorption and fluorescence spectroscopy data and X-ray - fluorescence and diffraction image data from synchrotron beamlines., markedDefault: false, - versionName: 0.9.80_py312} + - {description: A macromolecular superposition library., markedDefault: false, + versionName: '1.4'} - categories: chemistry, molecular dynamics defaultVersionName: 1.65.0 description: Qbox is a First-Principles Molecular Dynamics code. @@ -6340,35 +6386,29 @@ software_modules: Lipid Membranes” and its goal is to provide an efficient, yet robust, tool to extract physical parameters from MD trajectories.', markedDefault: false, versionName: 0.2.2_py39} - - categories: chemistry, crystallography - defaultVersionName: '1.4' - description: A macromolecular superposition library. - package: ssm - url: https://www.ccp4.ac.uk/ + - categories: chemistry, x-ray spectroscopy + defaultVersionName: 0.9.80_py312 + description: Larch is a open-source library and set of applications for processing + and analyzing X-ray absorption and fluorescence spectroscopy data and X-ray + fluorescence and diffraction image data from synchrotron beamlines. + package: py-xraylarch + url: https://xraypy.github.io/xraylarch/ versions: - - {description: A macromolecular superposition library., markedDefault: false, - versionName: '1.4'} - - categories: chemistry, quantum chemistry - defaultVersionName: 1.95A - description: TeraChem is general purpose quantum chemistry software designed - to run on NVIDIA GPU architectures. - package: terachem - url: http://www.petachem.com/ + - {description: Larch is a open-source library and set of applications for processing + and analyzing X-ray absorption and fluorescence spectroscopy data and X-ray + fluorescence and diffraction image data from synchrotron beamlines., markedDefault: false, + versionName: 0.9.80_py312} + - categories: chemistry, docking + defaultVersionName: 1.0.2 + description: A deep learning framework for molecular docking + package: gnina + url: https://github.com/gnina/gnina versions: - - description: TeraChem is general purpose quantum chemistry software designed - to run on NVIDIA GPU architectures. + - description: A deep learning framework for molecular docking markedDefault: false properties: arch: {gpu: 1} - license: {restricted: 1} - versionName: 1.96H-beta - - description: TeraChem is general purpose quantum chemistry software designed - to run on NVIDIA GPU architectures. - markedDefault: true - properties: - arch: {gpu: 1} - license: {restricted: 1} - versionName: 1.95A + versionName: 1.0.2 - categories: chemistry, quantum chemistry defaultVersionName: '7.1' description: Quantum ESPRESSO is an integrated suite of Open-Source computer @@ -6411,6 +6451,27 @@ software_modules: properties: parallel: {mpi: 1} versionName: '7.1' + - categories: chemistry, quantum chemistry + defaultVersionName: 1.95A + description: TeraChem is general purpose quantum chemistry software designed + to run on NVIDIA GPU architectures. + package: terachem + url: http://www.petachem.com/ + versions: + - description: TeraChem is general purpose quantum chemistry software designed + to run on NVIDIA GPU architectures. + markedDefault: false + properties: + arch: {gpu: 1} + license: {restricted: 1} + versionName: 1.96H-beta + - description: TeraChem is general purpose quantum chemistry software designed + to run on NVIDIA GPU architectures. + markedDefault: true + properties: + arch: {gpu: 1} + license: {restricted: 1} + versionName: 1.95A - categories: chemistry, molecular dynamics defaultVersionName: 1.0.0 description: A collection of tools for characterizing membrane structure and @@ -6424,27 +6485,6 @@ software_modules: properties: parallel: {mpi: 1} versionName: 1.0.0 - - categories: chemistry, computational chemistry - defaultVersionName: g16.B01 - description: Gaussian is a general purpose computational chemistry software - package. - package: gaussian - url: https://www.gaussian.com - versions: - - description: Gaussian is a general purpose computational chemistry software - package. - markedDefault: false - properties: - arch: {gpu: 1} - license: {restricted: 1} - versionName: g16.A03 - - description: Gaussian is a general purpose computational chemistry software - package. - markedDefault: false - properties: - arch: {gpu: 1} - license: {restricted: 1} - versionName: g16.B01 - categories: chemistry, electrostatics defaultVersionName: '1.5' description: APBS solves the equations of continuum electrostatics for large @@ -6464,39 +6504,21 @@ software_modules: - {description: 'VESTA is a 3D visualization program for structural models, volumetric data such as electron/nuclear densities, and crystal morphologies.', markedDefault: false, versionName: 3.4.4} - - categories: chemistry, quantum chemistry - defaultVersionName: '7.1' - description: Quantum ESPRESSO is an integrated suite of Open-Source computer - codes for electronic-structure calculations and materials modeling at the - nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials. - package: quantum-espresso_gpu - url: https://www.quantum-espresso.org + - categories: chemistry, cheminformatics + defaultVersionName: 2018.09.1_py27 + description: RDKit is a collection of cheminformatics and machine-learning software + written in C++ and Python. + package: py-rdkit + url: http://www.rdkit.org versions: - - description: GPU-accelerated Quantum ESPRESSO using CUDA FORTRAN - family: qe - markedDefault: false - properties: - arch: {gpu: 1} - parallel: {mpi: 1} - versionName: '1.1' - - description: Quantum ESPRESSO is an integrated suite of Open-Source computer - codes for electronic-structure calculations and materials modeling at the - nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials. - family: qe - markedDefault: false - properties: - arch: {gpu: 1} - parallel: {mpi: 1} - versionName: '7.0' - - description: Quantum ESPRESSO is an integrated suite of Open-Source computer - codes for electronic-structure calculations and materials modeling at the - nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials. - family: qe - markedDefault: false - properties: - arch: {gpu: 1} - parallel: {mpi: 1} - versionName: '7.1' + - {description: RDKit is a collection of cheminformatics and machine-learning + software written in C++ and Python., markedDefault: false, versionName: 2018.09.1_py36} + - {description: RDKit is a collection of cheminformatics and machine-learning + software written in C++ and Python., markedDefault: false, versionName: 2022.09.1_py39} + - {description: RDKit is a collection of cheminformatics and machine-learning + software written in C++ and Python., markedDefault: false, versionName: 2024.3.2_py312} + - {description: RDKit is a collection of cheminformatics and machine-learning + software written in C++ and Python., markedDefault: true, versionName: 2018.09.1_py27} - categories: chemistry, molecular dynamics defaultVersionName: 8.1.1_py312 description: A high performance toolkit for molecular simulation. @@ -6539,23 +6561,50 @@ software_modules: arch: {gpu: 1} parallel: {mpi: 1} versionName: 0.5.1 - - categories: devel, parser - defaultVersionName: 3.2.1 - description: Xerces-C++ is a validating XML parser written in a portable subset - of C++. - package: xerces-c - url: https://xerces.apache.org/xerces-c/index.html + - categories: devel, data + defaultVersionName: 4.5.4 + description: NetCDF is a set of software libraries and self-describing, machine-independent + data formats that support the creation, access, and sharing of array-oriented + scientific data. This module provides Fortran libraries. + package: netcdf-fortran + url: https://www.unidata.ucar.edu/software/netcdf versions: - - {description: Xerces-C++ is a validating XML parser written in a portable - subset of C++., markedDefault: false, versionName: 3.2.1} + - description: NetCDF is a set of software libraries and self-describing, machine-independent + data formats that support the creation, access, and sharing of array-oriented + scientific data. This module provides Fortran libraries. + markedDefault: false + properties: + parallel: {mpi: 1} + versionName: 4.5.4 - categories: devel, lib - defaultVersionName: 2.0.0 - description: libtree prints shared object dependencies as a tree. - package: libtree - url: https://github.com/haampie/libtree + defaultVersionName: '2019' + description: Intel® Threading Building Blocks (Intel® TBB) is a widely used + C++ library for shared-memory parallel programming and heterogeneous computing + (intra-node distributed memory programming). + package: tbb + url: https://software.intel.com/en-us/intel-tbb versions: - - {description: libtree prints shared object dependencies as a tree., markedDefault: false, - versionName: 2.0.0} + - {description: Intel® Threading Building Blocks (Intel® TBB) is a widely used + C++ library for shared-memory parallel programming and heterogeneous computing + (intra-node distributed memory programming)., markedDefault: false, versionName: 2017.u2} + - {description: Intel® Threading Building Blocks (Intel® TBB) is a widely used + C++ library for shared-memory parallel programming and heterogeneous computing + (intra-node distributed memory programming)., markedDefault: false, versionName: 2018.u1} + - {description: Intel® Threading Building Blocks (Intel® TBB) is a widely used + C++ library for shared-memory parallel programming and heterogeneous computing + (intra-node distributed memory programming)., markedDefault: false, versionName: '2018'} + - {description: Intel® Threading Building Blocks (Intel® TBB) is a widely used + C++ library for shared-memory parallel programming and heterogeneous computing + (intra-node distributed memory programming)., markedDefault: false, versionName: '2019'} + - categories: devel, engine + defaultVersionName: 8.4.371.22 + description: V8 is Google’s open source high-performance JavaScript and WebAssembly + engine, written in C++. + package: v8 + url: https://v8.dev + versions: + - {description: 'V8 is Google’s open source high-performance JavaScript and + WebAssembly engine, written in C++.', markedDefault: false, versionName: 8.4.371.22} - categories: devel, data defaultVersionName: 6.6.2 description: NCL is a free interpreted language designed specifically for scientific @@ -6672,14 +6721,15 @@ software_modules: - {description: '.NET is a free, cross-platform, open source developer platform for building many different types of applications.', markedDefault: false, versionName: 6.0.413} - - categories: devel, lib - defaultVersionName: 3.7.13 - description: RabbitMQ is an open-source message broker. - package: rabbitmq - url: http://rabbitmq.com + - categories: devel, data + defaultVersionName: 4.0.1 + description: Redis is an open source, in-memory data structure store, used as + a database, cache and message broker. + package: redis + url: https://redis.io versions: - - {description: RabbitMQ is an open-source message broker., markedDefault: false, - versionName: 3.7.13} + - {description: 'Redis is an open source, in-memory data structure store, used + as a database, cache and message broker.', markedDefault: false, versionName: 4.0.1} - categories: devel, language defaultVersionName: 2.6.14 description: GCL is the official Common Lisp for the GNU project. @@ -6699,68 +6749,38 @@ software_modules: and integer arrays that support high throughput read and write random access., markedDefault: false, versionName: 1.0.0} - categories: devel, compiler - defaultVersionName: 7.0.0 - description: The LLVM Project is a collection of modular and reusable compiler - and toolchain technologies. Clang is an LLVM native C/C++/Objective-C compiler, - package: llvm - url: http://llvm.org - versions: - - {description: 'The LLVM Project is a collection of modular and reusable compiler - and toolchain technologies. Clang is an LLVM native C/C++/Objective-C compiler,', - markedDefault: false, versionName: 3.8.1} - - {description: 'The LLVM Project is a collection of modular and reusable compiler - and toolchain technologies. Clang is an LLVM native C/C++/Objective-C compiler,', - markedDefault: false, versionName: 4.0.0} - - {description: 'The LLVM Project is a collection of modular and reusable compiler - and toolchain technologies. Clang is an LLVM native C/C++/Objective-C compiler,', - markedDefault: false, versionName: 5.0.0} - - {description: 'The LLVM Project is a collection of modular and reusable compiler - and toolchain technologies. Clang is an LLVM native C/C++/Objective-C compiler,', - markedDefault: false, versionName: 9.0.1} - - {description: 'The LLVM Project is a collection of modular and reusable compiler - and toolchain technologies. Clang is an LLVM native C/C++/Objective-C compiler,', - markedDefault: false, versionName: 15.0.3} - - {description: 'The LLVM Project is a collection of modular and reusable compiler - and toolchain technologies. Clang is an LLVM native C/C++/Objective-C compiler,', - markedDefault: false, versionName: 17.0.6} - - {description: 'The LLVM Project is a collection of modular and reusable compiler - and toolchain technologies. Clang is an LLVM native C/C++/Objective-C compiler,', - markedDefault: true, versionName: 7.0.0} - - categories: devel, data - defaultVersionName: 3.4.0 - description: Protocol Buffers (a.k.a., protobuf) are Google's language-neutral, - platform-neutral, extensible mechanism for serializing structured data. - package: protobuf - url: https://developers.google.com/protocol-buffers/ + defaultVersionName: '2019' + description: Intel C++ Compiler, also known as icc or icl, is a group of C and + C++ compilers from Intel + package: icc + url: https://software.intel.com/en-us/c-compilers versions: - - {description: 'Protocol Buffers (a.k.a., protobuf) are Google''s language-neutral, - platform-neutral, extensible mechanism for serializing structured data.', - markedDefault: false, versionName: 3.20.0} - - {description: 'Protocol Buffers (a.k.a., protobuf) are Google''s language-neutral, - platform-neutral, extensible mechanism for serializing structured data.', - markedDefault: false, versionName: '21.9'} - - {description: 'Protocol Buffers (a.k.a., protobuf) are Google''s language-neutral, - platform-neutral, extensible mechanism for serializing structured data.', - markedDefault: false, versionName: '29.1'} - - {description: 'Protocol Buffers (a.k.a., protobuf) are Google''s language-neutral, - platform-neutral, extensible mechanism for serializing structured data.', - markedDefault: true, versionName: 3.4.0} - - categories: devel, networking - defaultVersionName: 1.30.0 - description: GASNet is a language-independent, low-level networking layer that - provides network-independent, high-performance communication primitives tailored - for implementing parallel global address space SPMD languages and libraries. - package: gasnet - url: https://gasnet.lbl.gov + - {description: 'Intel C++ Compiler, also known as icc or icl, is a group of + C and C++ compilers from Intel', family: compiler_c, markedDefault: false, + versionName: 2017.u2} + - {description: 'Intel C++ Compiler, also known as icc or icl, is a group of + C and C++ compilers from Intel', family: compiler_c, markedDefault: false, + versionName: 2018.u1} + - {description: 'Intel C++ Compiler, also known as icc or icl, is a group of + C and C++ compilers from Intel', family: compiler_c, markedDefault: false, + versionName: '2018'} + - {description: 'Intel C++ Compiler, also known as icc or icl, is a group of + C and C++ compilers from Intel', family: compiler_c, markedDefault: false, + versionName: '2019'} + - categories: devel, lib + defaultVersionName: 2.2.2 + description: Copy-hiding array abstraction to automatically migrate data between + memory spaces. + package: chai + url: https://github.com/LLNL/CHAI versions: - - description: GASNet is a language-independent, low-level networking layer - that provides network-independent, high-performance communication primitives - tailored for implementing parallel global address space SPMD languages and - libraries. + - description: Copy-hiding array abstraction to automatically migrate data between + memory spaces. markedDefault: false properties: + arch: {gpu: 1} parallel: {mpi: 1} - versionName: 1.30.0 + versionName: 2.2.2 - categories: devel, build defaultVersionName: 3.24.2 description: CMake is an extensible, open-source system that manages the build @@ -6783,6 +6803,25 @@ software_modules: - {description: 'CMake is an extensible, open-source system that manages the build process in an operating system and in a compiler-independent manner.', markedDefault: false, versionName: 3.24.2} + - categories: devel, language + defaultVersionName: 0.29.28_py39 + description: Cython is an optimising static compiler for both the Python programming + language and the extended Cython programming language (based on Pyrex). + package: py-cython + url: http://cython.org/ + versions: + - {description: Cython is an optimising static compiler for both the Python + programming language and the extended Cython programming language (based + on Pyrex)., markedDefault: false, versionName: 0.27.3_py27} + - {description: Cython is an optimising static compiler for both the Python + programming language and the extended Cython programming language (based + on Pyrex)., markedDefault: false, versionName: 0.27.3_py36} + - {description: Cython is an optimising static compiler for both the Python + programming language and the extended Cython programming language (based + on Pyrex)., markedDefault: false, versionName: 0.29.21_py36} + - {description: Cython is an optimising static compiler for both the Python + programming language and the extended Cython programming language (based + on Pyrex)., markedDefault: false, versionName: 0.29.28_py39} - categories: devel, data defaultVersionName: 1.12.3 description: Parallel netCDF (PnetCDF) is a parallel I/O library for accessing @@ -6812,25 +6851,6 @@ software_modules: - {description: 'ZeroMQ (also spelled ØMQ, 0MQ or ZMQ) is a high-performance asynchronous messaging library, aimed at use in distributed or concurrent applications.', markedDefault: false, versionName: 4.2.2} - - categories: devel, language - defaultVersionName: 0.29.28_py39 - description: Cython is an optimising static compiler for both the Python programming - language and the extended Cython programming language (based on Pyrex). - package: py-cython - url: http://cython.org/ - versions: - - {description: Cython is an optimising static compiler for both the Python - programming language and the extended Cython programming language (based - on Pyrex)., markedDefault: false, versionName: 0.27.3_py27} - - {description: Cython is an optimising static compiler for both the Python - programming language and the extended Cython programming language (based - on Pyrex)., markedDefault: false, versionName: 0.27.3_py36} - - {description: Cython is an optimising static compiler for both the Python - programming language and the extended Cython programming language (based - on Pyrex)., markedDefault: false, versionName: 0.29.21_py36} - - {description: Cython is an optimising static compiler for both the Python - programming language and the extended Cython programming language (based - on Pyrex)., markedDefault: false, versionName: 0.29.28_py39} - categories: devel, mpi defaultVersionName: '2019' description: Intel® MPI Library is a multi-fabric message passing library that @@ -6866,6 +6886,25 @@ software_modules: properties: parallel: {mpi: 1} versionName: '2019' + - categories: devel, lib + defaultVersionName: 2021.1_py36 + description: PyCUDA lets you access Nvidia‘s CUDA parallel computation API from + Python. + package: py-pycuda + url: https://mathema.tician.de/software/pycuda/ + versions: + - description: PyCUDA lets you access Nvidia‘s CUDA parallel computation API + from Python. + markedDefault: false + properties: + arch: {gpu: 1} + versionName: 2017.1.1_py27 + - description: PyCUDA lets you access Nvidia‘s CUDA parallel computation API + from Python. + markedDefault: false + properties: + arch: {gpu: 1} + versionName: 2021.1_py36 - categories: devel, package management defaultVersionName: 0.3.5 description: An extremely fast Python package and project manager, written in @@ -6886,25 +6925,6 @@ software_modules: - {description: 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., markedDefault: false, versionName: 2.1.12} - - categories: devel, compiler - defaultVersionName: '2019' - description: Intel C++ Compiler, also known as icc or icl, is a group of C and - C++ compilers from Intel - package: icc - url: https://software.intel.com/en-us/c-compilers - versions: - - {description: 'Intel C++ Compiler, also known as icc or icl, is a group of - C and C++ compilers from Intel', family: compiler_c, markedDefault: false, - versionName: 2017.u2} - - {description: 'Intel C++ Compiler, also known as icc or icl, is a group of - C and C++ compilers from Intel', family: compiler_c, markedDefault: false, - versionName: 2018.u1} - - {description: 'Intel C++ Compiler, also known as icc or icl, is a group of - C and C++ compilers from Intel', family: compiler_c, markedDefault: false, - versionName: '2018'} - - {description: 'Intel C++ Compiler, also known as icc or icl, is a group of - C and C++ compilers from Intel', family: compiler_c, markedDefault: false, - versionName: '2019'} - categories: devel, analytics defaultVersionName: 18.1.0_py312 description: Python library for Apache Arrow, a development platform for in-memory @@ -6914,6 +6934,17 @@ software_modules: versions: - {description: 'Python library for Apache Arrow, a development platform for in-memory analytics.', markedDefault: false, versionName: 18.1.0_py312} + - categories: devel, lib + defaultVersionName: 0.7.5 + description: Library to manipulate tensors on the GPU. + package: libgpuarray + url: http://deeplearning.net/software/libgpuarray + versions: + - description: Library to manipulate tensors on the GPU. + markedDefault: false + properties: + arch: {gpu: 1} + versionName: 0.7.5 - categories: devel, language defaultVersionName: 2.7.13 description: Python is an interpreted, interactive, object-oriented programming @@ -6933,17 +6964,6 @@ software_modules: - {description: 'Python is an interpreted, interactive, object-oriented programming language.', family: python, help: 'https://www.sherlock.stanford.edu/docs/software/using/python', markedDefault: true, versionName: 2.7.13} - - categories: devel, lib - defaultVersionName: 0.7.5 - description: Library to manipulate tensors on the GPU. - package: libgpuarray - url: http://deeplearning.net/software/libgpuarray - versions: - - description: Library to manipulate tensors on the GPU. - markedDefault: false - properties: - arch: {gpu: 1} - versionName: 0.7.5 - categories: devel, build defaultVersionName: 1.8.0 description: Bazelisk is a wrapper for Bazel written in Go. @@ -6954,6 +6974,25 @@ software_modules: markedDefault: false, versionName: 1.3.0} - {description: Bazelisk is a wrapper for Bazel written in Go., family: bazel, markedDefault: false, versionName: 1.8.0} + - categories: devel, lib + defaultVersionName: 2.7.1_py27 + description: The h5py package is a Pythonic interface to the HDF5 binary data + format. + package: py-h5py + url: http://www.h5py.org + versions: + - {description: The h5py package is a Pythonic interface to the HDF5 binary + data format., markedDefault: false, versionName: 2.8.0_py36} + - {description: The h5py package is a Pythonic interface to the HDF5 binary + data format., markedDefault: false, versionName: 2.10.0_py36} + - {description: The h5py package is a Pythonic interface to the HDF5 binary + data format., markedDefault: false, versionName: 3.1.0_py36} + - {description: The h5py package is a Pythonic interface to the HDF5 binary + data format., markedDefault: false, versionName: 3.7.0_py39} + - {description: The h5py package is a Pythonic interface to the HDF5 binary + data format., markedDefault: false, versionName: 3.10.0_py312} + - {description: The h5py package is a Pythonic interface to the HDF5 binary + data format., markedDefault: true, versionName: 2.7.1_py27} - categories: devel, data defaultVersionName: 4.3.1 description: NetCDF is a set of software libraries and self-describing, machine-independent @@ -7023,16 +7062,17 @@ software_modules: - {description: Parsl is a flexible and scalable parallel programming library for Python., markedDefault: false, versionName: 1.2.0_py39} - categories: devel, language - defaultVersionName: 7.3.0 - description: 'PHP (recursive acronym for PHP: Hypertext Preprocessor) is an - open source general-purpose scripting language that is especially suited for - web development.' - package: php - url: http://www.php.net + defaultVersionName: 5.3.4 + description: Lua is a powerful, efficient, lightweight, embeddable scripting + language. It supports procedural programming, object-oriented programming, + functional programming, data-driven programming, and data description. + package: lua + url: https://www.lua.org versions: - - {description: 'PHP (recursive acronym for PHP: Hypertext Preprocessor) is - an open source general-purpose scripting language that is especially suited - for web development.', markedDefault: false, versionName: 7.3.0} + - {description: 'Lua is a powerful, efficient, lightweight, embeddable scripting + language. It supports procedural programming, object-oriented programming, + functional programming, data-driven programming, and data description.', + markedDefault: false, versionName: 5.3.4} - categories: devel, profiling defaultVersionName: '2024.4' description: NVIDIA Nsight™ Systems is a system-wide performance analysis tool @@ -7165,19 +7205,20 @@ software_modules: versions: - {description: Erlang is a programming language used to build massively scalable soft real-time systems with requirements on high availability., markedDefault: false, - versionName: '21.3'} - - categories: devel, language - defaultVersionName: 5.3.4 - description: Lua is a powerful, efficient, lightweight, embeddable scripting - language. It supports procedural programming, object-oriented programming, - functional programming, data-driven programming, and data description. - package: lua - url: https://www.lua.org + versionName: '21.3'} + - categories: devel, lib + defaultVersionName: 3.4.0 + description: 'Eigen is a C++ template library for linear algebra: matrices, + vectors, numerical solvers, and related algorithms.' + package: eigen + url: http://eigen.tuxfamily.org versions: - - {description: 'Lua is a powerful, efficient, lightweight, embeddable scripting - language. It supports procedural programming, object-oriented programming, - functional programming, data-driven programming, and data description.', - markedDefault: false, versionName: 5.3.4} + - {description: 'Eigen is a C++ template library for linear algebra: matrices, + vectors, numerical solvers, and related algorithms.', markedDefault: false, + versionName: 3.3.3} + - {description: 'Eigen is a C++ template library for linear algebra: matrices, + vectors, numerical solvers, and related algorithms.', markedDefault: false, + versionName: 3.4.0} - categories: devel, data defaultVersionName: 3.10.1_py312 description: A Python package to manage extremely large amounts of data. @@ -7209,15 +7250,59 @@ software_modules: markedDefault: false, versionName: 1.3.1_py36} - {description: netcdf4-python is a Python interface to the netCDF C library., markedDefault: true, versionName: 1.3.1_py27} - - categories: devel, framework - defaultVersionName: 1.5.0_py312 - description: Warp is a Python framework for writing high-performance simulation - and graphics code. - package: py-warp-lang - url: https://nvidia.github.io/warp/ + - categories: devel, lib + defaultVersionName: 1.87.0 + description: Boost is a set of libraries for the C++ programming language that + provide support for tasks and structures such as linear algebra, pseudorandom + number generation, multithreading, image processing, regular expressions, + and unit testing. + package: boost + url: http://www.boost.org versions: - - {description: Warp is a Python framework for writing high-performance simulation - and graphics code., markedDefault: false, versionName: 1.5.0_py312} + - {description: 'Boost is a set of libraries for the C++ programming language + that provide support for tasks and structures such as linear algebra, pseudorandom + number generation, multithreading, image processing, regular expressions, + and unit testing.', markedDefault: false, versionName: 1.64.0} + - description: Boost is a set of libraries for the C++ programming language + that provide support for tasks and structures such as linear algebra, pseudorandom + number generation, multithreading, image processing, regular expressions, + and unit testing. + markedDefault: false + properties: + parallel: {mpi: 1} + versionName: 1.69.0 + - description: Boost is a set of libraries for the C++ programming language + that provide support for tasks and structures such as linear algebra, pseudorandom + number generation, multithreading, image processing, regular expressions, + and unit testing. + markedDefault: false + properties: + parallel: {mpi: 1} + versionName: 1.75.0 + - description: Boost is a set of libraries for the C++ programming language + that provide support for tasks and structures such as linear algebra, pseudorandom + number generation, multithreading, image processing, regular expressions, + and unit testing. + markedDefault: false + properties: + parallel: {mpi: 1} + versionName: 1.76.0 + - description: Boost is a set of libraries for the C++ programming language + that provide support for tasks and structures such as linear algebra, pseudorandom + number generation, multithreading, image processing, regular expressions, + and unit testing. + markedDefault: false + properties: + parallel: {mpi: 1} + versionName: 1.79.0 + - description: Boost is a set of libraries for the C++ programming language + that provide support for tasks and structures such as linear algebra, pseudorandom + number generation, multithreading, image processing, regular expressions, + and unit testing. + markedDefault: false + properties: + parallel: {mpi: 1} + versionName: 1.87.0 - categories: devel, lib defaultVersionName: 0.12.1 description: Collection of C++ software abstractions that enable architecture @@ -7232,30 +7317,22 @@ software_modules: arch: {gpu: 1} parallel: {mpi: 1} versionName: 0.12.1 - - categories: devel, data - defaultVersionName: 4.5.4 - description: NetCDF is a set of software libraries and self-describing, machine-independent - data formats that support the creation, access, and sharing of array-oriented - scientific data. This module provides Fortran libraries. - package: netcdf-fortran - url: https://www.unidata.ucar.edu/software/netcdf + - categories: devel, lib + defaultVersionName: 3.7.13 + description: RabbitMQ is an open-source message broker. + package: rabbitmq + url: http://rabbitmq.com versions: - - description: NetCDF is a set of software libraries and self-describing, machine-independent - data formats that support the creation, access, and sharing of array-oriented - scientific data. This module provides Fortran libraries. - markedDefault: false - properties: - parallel: {mpi: 1} - versionName: 4.5.4 - - categories: devel, engine - defaultVersionName: 8.4.371.22 - description: V8 is Google’s open source high-performance JavaScript and WebAssembly - engine, written in C++. - package: v8 - url: https://v8.dev + - {description: RabbitMQ is an open-source message broker., markedDefault: false, + versionName: 3.7.13} + - categories: devel, lib + defaultVersionName: 2.0.0 + description: libtree prints shared object dependencies as a tree. + package: libtree + url: https://github.com/haampie/libtree versions: - - {description: 'V8 is Google’s open source high-performance JavaScript and - WebAssembly engine, written in C++.', markedDefault: false, versionName: 8.4.371.22} + - {description: libtree prints shared object dependencies as a tree., markedDefault: false, + versionName: 2.0.0} - categories: devel, networking defaultVersionName: 0.24.0_py39 description: Python bindinbgs for UCX. @@ -7264,19 +7341,16 @@ software_modules: versions: - {description: Python bindinbgs for UCX., markedDefault: false, versionName: 0.24.0_py39} - categories: devel, lib - defaultVersionName: 2.2.2 - description: Copy-hiding array abstraction to automatically migrate data between - memory spaces. - package: chai - url: https://github.com/LLNL/CHAI + defaultVersionName: 23.04.00_py39 + description: Python interface for RMM + package: py-rmm + url: https://github.com/rapidsai/rmm versions: - - description: Copy-hiding array abstraction to automatically migrate data between - memory spaces. + - description: Python interface for RMM markedDefault: false properties: arch: {gpu: 1} - parallel: {mpi: 1} - versionName: 2.2.2 + versionName: 23.04.00_py39 - categories: devel, data defaultVersionName: 3.4.0_py27 description: Python bindings for Google's Protocol Buffers data interchange @@ -7357,17 +7431,14 @@ software_modules: versions: - {description: Ninja is a small build system with a focus on speed., markedDefault: false, versionName: 1.9.0} - - categories: devel, lib - defaultVersionName: 23.04.00_py39 - description: Python interface for RMM - package: py-rmm - url: https://github.com/rapidsai/rmm + - categories: devel, profiling + defaultVersionName: 3.3.462 + description: AMD uProf is a performance analysis tool for applications. + package: amd-uprof + url: https://developer.amd.com/amd-uprof/ versions: - - description: Python interface for RMM - markedDefault: false - properties: - arch: {gpu: 1} - versionName: 23.04.00_py39 + - {description: AMD uProf is a performance analysis tool for applications., + markedDefault: false, versionName: 3.3.462} - categories: devel, language defaultVersionName: 1.10.5 description: Julia is a high-level, high-performance dynamic programming language @@ -7405,32 +7476,34 @@ software_modules: machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.', markedDefault: false, versionName: 4.8.1} - categories: devel, data - defaultVersionName: 1.12.1 - description: h5utils is a set of utilities for visualization and conversion - of scientific data in the free, portable HDF5 format. - package: h5utils - url: http://ab-initio.mit.edu/wiki/index.php/H5utils + defaultVersionName: 3.4.0 + description: Protocol Buffers (a.k.a., protobuf) are Google's language-neutral, + platform-neutral, extensible mechanism for serializing structured data. + package: protobuf + url: https://developers.google.com/protocol-buffers/ versions: - - {description: 'h5utils is a set of utilities for visualization and conversion - of scientific data in the free, portable HDF5 format.', markedDefault: false, - versionName: 1.12.1} + - {description: 'Protocol Buffers (a.k.a., protobuf) are Google''s language-neutral, + platform-neutral, extensible mechanism for serializing structured data.', + markedDefault: false, versionName: 3.20.0} + - {description: 'Protocol Buffers (a.k.a., protobuf) are Google''s language-neutral, + platform-neutral, extensible mechanism for serializing structured data.', + markedDefault: false, versionName: '21.9'} + - {description: 'Protocol Buffers (a.k.a., protobuf) are Google''s language-neutral, + platform-neutral, extensible mechanism for serializing structured data.', + markedDefault: false, versionName: '29.1'} + - {description: 'Protocol Buffers (a.k.a., protobuf) are Google''s language-neutral, + platform-neutral, extensible mechanism for serializing structured data.', + markedDefault: true, versionName: 3.4.0} - categories: devel, language - defaultVersionName: 3.1.2 - description: A dynamic, open source programming language with a focus on simplicity - and productivity. It has an elegant syntax that is natural to read and easy - to write. - package: ruby - url: https://www.ruby-lang.org + defaultVersionName: 8.6.5 + description: Haskell is a statically typed, purely functional programming language + with type inference and lazy evaluation. + package: haskell + url: https://www.haskell.org/ versions: - - {description: 'A dynamic, open source programming language with a focus on - simplicity and productivity. It has an elegant syntax that is natural to - read and easy to write.', markedDefault: false, versionName: 2.4.1} - - {description: 'A dynamic, open source programming language with a focus on - simplicity and productivity. It has an elegant syntax that is natural to - read and easy to write.', markedDefault: false, versionName: 2.7.1} - - {description: 'A dynamic, open source programming language with a focus on - simplicity and productivity. It has an elegant syntax that is natural to - read and easy to write.', markedDefault: false, versionName: 3.1.2} + - {description: 'Haskell is a statically typed, purely functional programming + language with type inference and lazy evaluation.', markedDefault: false, + versionName: 8.6.5} - categories: devel, networking defaultVersionName: 1.3.0 description: UCC is a collective communication operations API and library that @@ -7447,14 +7520,13 @@ software_modules: arch: {gpu: 1} versionName: 1.3.0 - categories: devel, data - defaultVersionName: 4.0.1 - description: Redis is an open source, in-memory data structure store, used as - a database, cache and message broker. - package: redis - url: https://redis.io + defaultVersionName: 0.13.3 + description: Hiredis is a minimalistic C client library for the Redis database. + package: hiredis + url: https://github.com/redis/hiredis versions: - - {description: 'Redis is an open source, in-memory data structure store, used - as a database, cache and message broker.', markedDefault: false, versionName: 4.0.1} + - {description: Hiredis is a minimalistic C client library for the Redis database., + markedDefault: false, versionName: 0.13.3} - categories: devel, language defaultVersionName: '20180301' description: Manticore is a high-level parallel programming language aimed at @@ -7494,19 +7566,15 @@ software_modules: url: https://github.com/nose-devs/nose versions: - {description: nose is nicer testing for python., markedDefault: false, versionName: 1.3.7_py39} - - categories: devel, lib - defaultVersionName: 3.4.0 - description: 'Eigen is a C++ template library for linear algebra: matrices, - vectors, numerical solvers, and related algorithms.' - package: eigen - url: http://eigen.tuxfamily.org + - categories: devel, framework + defaultVersionName: 1.5.0_py312 + description: Warp is a Python framework for writing high-performance simulation + and graphics code. + package: py-warp-lang + url: https://nvidia.github.io/warp/ versions: - - {description: 'Eigen is a C++ template library for linear algebra: matrices, - vectors, numerical solvers, and related algorithms.', markedDefault: false, - versionName: 3.3.3} - - {description: 'Eigen is a C++ template library for linear algebra: matrices, - vectors, numerical solvers, and related algorithms.', markedDefault: false, - versionName: 3.4.0} + - {description: Warp is a Python framework for writing high-performance simulation + and graphics code., markedDefault: false, versionName: 1.5.0_py312} - categories: devel, language defaultVersionName: 5.36.1 description: Perl 5 is a highly capable, feature-rich programming language with @@ -7588,16 +7656,6 @@ software_modules: properties: arch: {gpu: 1} versionName: 1.55.4_py312 - - categories: devel, language - defaultVersionName: 8.6.5 - description: Haskell is a statically typed, purely functional programming language - with type inference and lazy evaluation. - package: haskell - url: https://www.haskell.org/ - versions: - - {description: 'Haskell is a statically typed, purely functional programming - language with type inference and lazy evaluation.', markedDefault: false, - versionName: 8.6.5} - categories: devel, lib defaultVersionName: 0.13.0_py312 description: Python bindings for CV_CUDA. @@ -7625,23 +7683,46 @@ software_modules: markedDefault: false properties: parallel: {mpi: 1} - versionName: 0.3.1_py36 - - description: schwimmbad provides a uniform interface to parallel processing - pools and enables switching easily between local development (e.g., serial - processing or with multiprocessing) and deployment on a cluster or supercomputer - (via, e.g., MPI or JobLib). + versionName: 0.3.1_py36 + - description: schwimmbad provides a uniform interface to parallel processing + pools and enables switching easily between local development (e.g., serial + processing or with multiprocessing) and deployment on a cluster or supercomputer + (via, e.g., MPI or JobLib). + markedDefault: false + properties: + parallel: {mpi: 1} + versionName: 0.3.2_py39 + - categories: devel, networking + defaultVersionName: 1.30.0 + description: GASNet is a language-independent, low-level networking layer that + provides network-independent, high-performance communication primitives tailored + for implementing parallel global address space SPMD languages and libraries. + package: gasnet + url: https://gasnet.lbl.gov + versions: + - description: GASNet is a language-independent, low-level networking layer + that provides network-independent, high-performance communication primitives + tailored for implementing parallel global address space SPMD languages and + libraries. + markedDefault: false + properties: + parallel: {mpi: 1} + versionName: 1.30.0 + - categories: devel, lib + defaultVersionName: 0.13.0 + description: CV-CUDA is an open-source project that enables building efficient + cloud-scale Artificial Intelligence (AI) imaging and computer vision (CV) + applications. + package: cvcuda + url: https://github.com/CVCUDA/CV-CUDA + versions: + - description: CV-CUDA is an open-source project that enables building efficient + cloud-scale Artificial Intelligence (AI) imaging and computer vision (CV) + applications. markedDefault: false properties: - parallel: {mpi: 1} - versionName: 0.3.2_py39 - - categories: devel, data - defaultVersionName: 0.13.3 - description: Hiredis is a minimalistic C client library for the Redis database. - package: hiredis - url: https://github.com/redis/hiredis - versions: - - {description: Hiredis is a minimalistic C client library for the Redis database., - markedDefault: false, versionName: 0.13.3} + arch: {gpu: 1} + versionName: 0.13.0 - categories: devel, lib defaultVersionName: 0.35.0_py27 description: Numba is a compiler for Python array and numerical functions that @@ -7668,23 +7749,16 @@ software_modules: - {description: Numba is a compiler for Python array and numerical functions that gives you the power to speed up your applications with high performance functions written directly in Python.., markedDefault: true, versionName: 0.35.0_py27} - - categories: devel, language - defaultVersionName: 1.81.0 - description: A language empowering everyone to build reliable and efficient - software. - package: rust - url: https://www.rust-lang.org/ + - categories: devel, data analytics + defaultVersionName: 3.2.1_py312 + description: 'Launching and controlling spark on HPC clusters ' + package: py-pyspark + url: https://sparkhpc.readthedocs.io versions: - - {description: A language empowering everyone to build reliable and efficient - software., markedDefault: false, versionName: 1.35.0} - - {description: A language empowering everyone to build reliable and efficient - software., markedDefault: false, versionName: 1.56.1} - - {description: A language empowering everyone to build reliable and efficient - software., markedDefault: false, versionName: 1.63.0} - - {description: A language empowering everyone to build reliable and efficient - software., markedDefault: false, versionName: 1.72.0} - - {description: A language empowering everyone to build reliable and efficient - software., markedDefault: false, versionName: 1.81.0} + - {description: 'Launching and controlling spark on HPC clusters ', markedDefault: false, + versionName: 3.2.1_py39} + - {description: 'Launching and controlling spark on HPC clusters ', markedDefault: false, + versionName: 3.2.1_py312} - categories: devel, data defaultVersionName: 1.6.3_py312 description: Official API for https://www.kaggle.com, accessible using a command @@ -7721,22 +7795,16 @@ software_modules: versions: - {description: Kerl is a tool to easily build and install Erlang/OTP instances., markedDefault: false, versionName: 1.8.5} - - categories: devel, language - defaultVersionName: 1.0.0_py27 - description: Jupyter is a browser-based interactive notebook for programming, - mathematics, and data science. It supports a number of languages via plugins. - package: py-jupyter - url: https://jupyter.org + - categories: devel, build + defaultVersionName: 0.51.1_py36 + description: Meson is an open source build system meant to be both extremely + fast, and, even more importantly, as user friendly as possible. + package: py-meson + url: https://mesonbuild.com/ versions: - - {description: 'Jupyter is a browser-based interactive notebook for programming, - mathematics, and data science. It supports a number of languages via plugins.', - markedDefault: false, versionName: 1.0.0_py36} - - {description: 'Jupyter is a browser-based interactive notebook for programming, - mathematics, and data science. It supports a number of languages via plugins.', - markedDefault: false, versionName: 1.0.0_py39} - - {description: 'Jupyter is a browser-based interactive notebook for programming, - mathematics, and data science. It supports a number of languages via plugins.', - markedDefault: true, versionName: 1.0.0_py27} + - {description: 'Meson is an open source build system meant to be both extremely + fast, and, even more importantly, as user friendly as possible.', markedDefault: false, + versionName: 0.51.1_py36} - categories: devel, compiler defaultVersionName: 2.2.0 description: AMD Optimizing C/C++ Compiler - AOCC is a highly optimized C, C++ @@ -7809,47 +7877,43 @@ software_modules: properties: parallel: {mpi: 1} versionName: 1.10.6 - - categories: devel, compiler - defaultVersionName: '19.10' - description: PGI compilers and tools, including Open MPI (Community Edition). - package: pgi - url: https://developer.nvidia.com/legacy-pgi-support + - categories: devel, language + defaultVersionName: 1.0.0_py27 + description: Jupyter is a browser-based interactive notebook for programming, + mathematics, and data science. It supports a number of languages via plugins. + package: py-jupyter + url: https://jupyter.org versions: - - {description: 'PGI compilers and tools, including Open MPI (Community Edition).', - family: mpi, markedDefault: false, versionName: '19.10'} - - categories: devel, lib - defaultVersionName: 0.13.0 - description: CV-CUDA is an open-source project that enables building efficient - cloud-scale Artificial Intelligence (AI) imaging and computer vision (CV) - applications. - package: cvcuda - url: https://github.com/CVCUDA/CV-CUDA + - {description: 'Jupyter is a browser-based interactive notebook for programming, + mathematics, and data science. It supports a number of languages via plugins.', + markedDefault: false, versionName: 1.0.0_py36} + - {description: 'Jupyter is a browser-based interactive notebook for programming, + mathematics, and data science. It supports a number of languages via plugins.', + markedDefault: false, versionName: 1.0.0_py39} + - {description: 'Jupyter is a browser-based interactive notebook for programming, + mathematics, and data science. It supports a number of languages via plugins.', + markedDefault: true, versionName: 1.0.0_py27} + - categories: devel, compiler + defaultVersionName: 1.40.0 + description: The LLVM-based D Compiler. + package: ldc + url: https://github.com/ldc-developers/ldc versions: - - description: CV-CUDA is an open-source project that enables building efficient - cloud-scale Artificial Intelligence (AI) imaging and computer vision (CV) - applications. - markedDefault: false - properties: - arch: {gpu: 1} - versionName: 0.13.0 - - categories: devel, lib - defaultVersionName: 3.1.0 - description: CUTLASS is a collection of CUDA C++ template abstractions for implementing - high-performance matrix-multiplication (GEMM) at all levels and scales within - CUDA. - package: cutlass - url: https://github.com/NVIDIA/cutlass + - {description: The LLVM-based D Compiler., markedDefault: false, versionName: 1.26.0} + - {description: The LLVM-based D Compiler., markedDefault: false, versionName: 1.40.0} + - categories: devel, language + defaultVersionName: 2.2.2 + description: GNU Guile is the preferred extension system for the GNU Project, + which features an implementation of the Scheme programming language. + package: guile + url: https://www.gnu.org/software/guile/ versions: - - {description: CUTLASS is a collection of CUDA C++ template abstractions for - implementing high-performance matrix-multiplication (GEMM) at all levels - and scales within CUDA., markedDefault: false, versionName: 0.1.0} - - description: CUTLASS is a collection of CUDA C++ template abstractions for - implementing high-performance matrix-multiplication (GEMM) at all levels - and scales within CUDA. - markedDefault: false - properties: - arch: {gpu: 1} - versionName: 3.1.0 + - {description: 'GNU Guile is the preferred extension system for the GNU Project, + which features an implementation of the Scheme programming language.', markedDefault: false, + versionName: 2.0.11} + - {description: 'GNU Guile is the preferred extension system for the GNU Project, + which features an implementation of the Scheme programming language.', markedDefault: false, + versionName: 2.2.2} - categories: devel, data analytics defaultVersionName: 3.1.0 description: The Apache Hadoop software library is a framework that allows for @@ -8088,16 +8152,18 @@ software_modules: - {description: 'Jupyter is a browser-based interactive notebook for programming, mathematics, and data science. It supports a number of languages via plugins.', markedDefault: false, versionName: 4.3.2_py312} - - categories: devel, build - defaultVersionName: 0.51.1_py36 - description: Meson is an open source build system meant to be both extremely - fast, and, even more importantly, as user friendly as possible. - package: py-meson - url: https://mesonbuild.com/ + - categories: devel, lib + defaultVersionName: 20247.24_py312 + description: Alternative regular expression module for Python, to replace re. + package: py-regex + url: https://github.com/mrabarnett/mrab-regex versions: - - {description: 'Meson is an open source build system meant to be both extremely - fast, and, even more importantly, as user friendly as possible.', markedDefault: false, - versionName: 0.51.1_py36} + - {description: 'Alternative regular expression module for Python, to replace + re.', markedDefault: false, versionName: 20247.24_py36} + - {description: 'Alternative regular expression module for Python, to replace + re.', markedDefault: false, versionName: 20247.24_py39} + - {description: 'Alternative regular expression module for Python, to replace + re.', markedDefault: false, versionName: 20247.24_py312} - categories: devel, lib defaultVersionName: 8.1.0 description: C++ wrappers for SIMD intrinsics and parallelized, optimized mathematical @@ -8111,6 +8177,30 @@ software_modules: - {description: 'C++ wrappers for SIMD intrinsics and parallelized, optimized mathematical functions (SSE, AVX, NEON, AVX512)', markedDefault: false, versionName: 8.1.0} + - categories: devel, lib + defaultVersionName: 0.3.0 + description: libcircle is an API for distributing embarrassingly parallel workloads + using self-stabilization. + package: libcircle + url: https://github.com/hpc/libcircle + versions: + - description: libcircle is an API for distributing embarrassingly parallel + workloads using self-stabilization. + markedDefault: false + properties: + parallel: {mpi: 1} + versionName: 0.3.0 + - categories: devel, lib + defaultVersionName: 3.1.0_py39 + description: Python interface for CUTLASS + package: py-cutlass + url: https://github.com/NVIDIA/cutlass/ + versions: + - description: Python interface for CUTLASS + markedDefault: false + properties: + arch: {gpu: 1} + versionName: 3.1.0_py39 - categories: devel, networking defaultVersionName: 1.17.0 description: UCX is a communication library implementing high-performance messaging @@ -8156,30 +8246,6 @@ software_modules: properties: arch: {gpu: 1} versionName: 1.17.0 - - categories: devel, lib - defaultVersionName: 3.1.0_py39 - description: Python interface for CUTLASS - package: py-cutlass - url: https://github.com/NVIDIA/cutlass/ - versions: - - description: Python interface for CUTLASS - markedDefault: false - properties: - arch: {gpu: 1} - versionName: 3.1.0_py39 - - categories: devel, lib - defaultVersionName: 0.3.0 - description: libcircle is an API for distributing embarrassingly parallel workloads - using self-stabilization. - package: libcircle - url: https://github.com/hpc/libcircle - versions: - - description: libcircle is an API for distributing embarrassingly parallel - workloads using self-stabilization. - markedDefault: false - properties: - parallel: {mpi: 1} - versionName: 0.3.0 - categories: devel, lib defaultVersionName: 1.10.0 description: CUB is a flexible library of cooperative threadblock primitives @@ -8199,19 +8265,34 @@ software_modules: properties: arch: {gpu: 1} versionName: 1.10.0 - - categories: devel, language - defaultVersionName: 2.2.2 - description: GNU Guile is the preferred extension system for the GNU Project, - which features an implementation of the Scheme programming language. - package: guile - url: https://www.gnu.org/software/guile/ + - categories: devel, compiler + defaultVersionName: 7.0.0 + description: The LLVM Project is a collection of modular and reusable compiler + and toolchain technologies. Clang is an LLVM native C/C++/Objective-C compiler, + package: llvm + url: http://llvm.org versions: - - {description: 'GNU Guile is the preferred extension system for the GNU Project, - which features an implementation of the Scheme programming language.', markedDefault: false, - versionName: 2.0.11} - - {description: 'GNU Guile is the preferred extension system for the GNU Project, - which features an implementation of the Scheme programming language.', markedDefault: false, - versionName: 2.2.2} + - {description: 'The LLVM Project is a collection of modular and reusable compiler + and toolchain technologies. Clang is an LLVM native C/C++/Objective-C compiler,', + markedDefault: false, versionName: 3.8.1} + - {description: 'The LLVM Project is a collection of modular and reusable compiler + and toolchain technologies. Clang is an LLVM native C/C++/Objective-C compiler,', + markedDefault: false, versionName: 4.0.0} + - {description: 'The LLVM Project is a collection of modular and reusable compiler + and toolchain technologies. Clang is an LLVM native C/C++/Objective-C compiler,', + markedDefault: false, versionName: 5.0.0} + - {description: 'The LLVM Project is a collection of modular and reusable compiler + and toolchain technologies. Clang is an LLVM native C/C++/Objective-C compiler,', + markedDefault: false, versionName: 9.0.1} + - {description: 'The LLVM Project is a collection of modular and reusable compiler + and toolchain technologies. Clang is an LLVM native C/C++/Objective-C compiler,', + markedDefault: false, versionName: 15.0.3} + - {description: 'The LLVM Project is a collection of modular and reusable compiler + and toolchain technologies. Clang is an LLVM native C/C++/Objective-C compiler,', + markedDefault: false, versionName: 17.0.6} + - {description: 'The LLVM Project is a collection of modular and reusable compiler + and toolchain technologies. Clang is an LLVM native C/C++/Objective-C compiler,', + markedDefault: true, versionName: 7.0.0} - categories: devel, lib defaultVersionName: 1.10.1 description: Apache Ant is a Java library and command-line tool whose mission @@ -8250,15 +8331,13 @@ software_modules: easy-to-use data structures and data analysis tools for the Python programming language.', family: pandas, markedDefault: false, versionName: 2.2.1_py312} - categories: devel, data analytics - defaultVersionName: 3.2.1_py312 + defaultVersionName: 0.3_py27 description: 'Launching and controlling spark on HPC clusters ' - package: py-pyspark + package: py-sparkhpc url: https://sparkhpc.readthedocs.io versions: - {description: 'Launching and controlling spark on HPC clusters ', markedDefault: false, - versionName: 3.2.1_py39} - - {description: 'Launching and controlling spark on HPC clusters ', markedDefault: false, - versionName: 3.2.1_py312} + versionName: 0.3_py27} - categories: devel, lib defaultVersionName: 1.0.4 description: The Light-weight Group Library provides methods for MPI codes to @@ -8273,17 +8352,23 @@ software_modules: parallel: {mpi: 1} versionName: 1.0.4 - categories: devel, lib - defaultVersionName: 20247.24_py312 - description: Alternative regular expression module for Python, to replace re. - package: py-regex - url: https://github.com/mrabarnett/mrab-regex + defaultVersionName: 3.1.0 + description: CUTLASS is a collection of CUDA C++ template abstractions for implementing + high-performance matrix-multiplication (GEMM) at all levels and scales within + CUDA. + package: cutlass + url: https://github.com/NVIDIA/cutlass versions: - - {description: 'Alternative regular expression module for Python, to replace - re.', markedDefault: false, versionName: 20247.24_py36} - - {description: 'Alternative regular expression module for Python, to replace - re.', markedDefault: false, versionName: 20247.24_py39} - - {description: 'Alternative regular expression module for Python, to replace - re.', markedDefault: false, versionName: 20247.24_py312} + - {description: CUTLASS is a collection of CUDA C++ template abstractions for + implementing high-performance matrix-multiplication (GEMM) at all levels + and scales within CUDA., markedDefault: false, versionName: 0.1.0} + - description: CUTLASS is a collection of CUDA C++ template abstractions for + implementing high-performance matrix-multiplication (GEMM) at all levels + and scales within CUDA. + markedDefault: false + properties: + arch: {gpu: 1} + versionName: 3.1.0 - categories: devel, build defaultVersionName: '2.38' description: The GNU Binutils are a collection of binary tools. @@ -8292,34 +8377,31 @@ software_modules: versions: - {description: The GNU Binutils are a collection of binary tools., markedDefault: false, versionName: '2.38'} - - categories: devel, lib - defaultVersionName: '2019' - description: Intel® Threading Building Blocks (Intel® TBB) is a widely used - C++ library for shared-memory parallel programming and heterogeneous computing - (intra-node distributed memory programming). - package: tbb - url: https://software.intel.com/en-us/intel-tbb + - categories: devel, compiler + defaultVersionName: '19.10' + description: PGI compilers and tools, including Open MPI (Community Edition). + package: pgi + url: https://developer.nvidia.com/legacy-pgi-support versions: - - {description: Intel® Threading Building Blocks (Intel® TBB) is a widely used - C++ library for shared-memory parallel programming and heterogeneous computing - (intra-node distributed memory programming)., markedDefault: false, versionName: 2017.u2} - - {description: Intel® Threading Building Blocks (Intel® TBB) is a widely used - C++ library for shared-memory parallel programming and heterogeneous computing - (intra-node distributed memory programming)., markedDefault: false, versionName: 2018.u1} - - {description: Intel® Threading Building Blocks (Intel® TBB) is a widely used - C++ library for shared-memory parallel programming and heterogeneous computing - (intra-node distributed memory programming)., markedDefault: false, versionName: '2018'} - - {description: Intel® Threading Building Blocks (Intel® TBB) is a widely used - C++ library for shared-memory parallel programming and heterogeneous computing - (intra-node distributed memory programming)., markedDefault: false, versionName: '2019'} - - categories: devel, profiling - defaultVersionName: 3.3.462 - description: AMD uProf is a performance analysis tool for applications. - package: amd-uprof - url: https://developer.amd.com/amd-uprof/ + - {description: 'PGI compilers and tools, including Open MPI (Community Edition).', + family: mpi, markedDefault: false, versionName: '19.10'} + - categories: devel, language + defaultVersionName: 3.1.2 + description: A dynamic, open source programming language with a focus on simplicity + and productivity. It has an elegant syntax that is natural to read and easy + to write. + package: ruby + url: https://www.ruby-lang.org versions: - - {description: AMD uProf is a performance analysis tool for applications., - markedDefault: false, versionName: 3.3.462} + - {description: 'A dynamic, open source programming language with a focus on + simplicity and productivity. It has an elegant syntax that is natural to + read and easy to write.', markedDefault: false, versionName: 2.4.1} + - {description: 'A dynamic, open source programming language with a focus on + simplicity and productivity. It has an elegant syntax that is natural to + read and easy to write.', markedDefault: false, versionName: 2.7.1} + - {description: 'A dynamic, open source programming language with a focus on + simplicity and productivity. It has an elegant syntax that is natural to + read and easy to write.', markedDefault: false, versionName: 3.1.2} - categories: devel, lib defaultVersionName: 3.0.12 description: SWIG is an interface compiler that connects programs written in @@ -8330,6 +8412,15 @@ software_modules: - {description: 'SWIG is an interface compiler that connects programs written in C and C++ with scripting languages such as Perl, Python, Ruby, and Tcl.', markedDefault: false, versionName: 3.0.12} + - categories: devel, parser + defaultVersionName: 3.2.1 + description: Xerces-C++ is a validating XML parser written in a portable subset + of C++. + package: xerces-c + url: https://xerces.apache.org/xerces-c/index.html + versions: + - {description: Xerces-C++ is a validating XML parser written in a portable + subset of C++., markedDefault: false, versionName: 3.2.1} - categories: devel, data defaultVersionName: 4.9.0 description: NetCDF is a set of software libraries and self-describing, machine-independent @@ -8354,15 +8445,6 @@ software_modules: versions: - {description: 'Kedro is an open-source Python framework for creating reproducible, maintainable and modular data science code.', markedDefault: false, versionName: 0.18.0_py39} - - categories: devel, debug - defaultVersionName: 3.14.0 - description: Valgrind is an instrumentation framework for building dynamic analysis - tools. - package: valgrind - url: http://valgrind.org/ - versions: - - {description: Valgrind is an instrumentation framework for building dynamic - analysis tools., markedDefault: false, versionName: 3.14.0} - categories: devel, language defaultVersionName: 1.8.0_131 description: Java is a general-purpose computer programming language that is @@ -8473,25 +8555,16 @@ software_modules: arch: {gpu: 1} parallel: {mpi: 1} versionName: 4.1.2 - - categories: devel, lib - defaultVersionName: 2.7.1_py27 - description: The h5py package is a Pythonic interface to the HDF5 binary data - format. - package: py-h5py - url: http://www.h5py.org + - categories: devel, data + defaultVersionName: 1.12.1 + description: h5utils is a set of utilities for visualization and conversion + of scientific data in the free, portable HDF5 format. + package: h5utils + url: http://ab-initio.mit.edu/wiki/index.php/H5utils versions: - - {description: The h5py package is a Pythonic interface to the HDF5 binary - data format., markedDefault: false, versionName: 2.8.0_py36} - - {description: The h5py package is a Pythonic interface to the HDF5 binary - data format., markedDefault: false, versionName: 2.10.0_py36} - - {description: The h5py package is a Pythonic interface to the HDF5 binary - data format., markedDefault: false, versionName: 3.1.0_py36} - - {description: The h5py package is a Pythonic interface to the HDF5 binary - data format., markedDefault: false, versionName: 3.7.0_py39} - - {description: The h5py package is a Pythonic interface to the HDF5 binary - data format., markedDefault: false, versionName: 3.10.0_py312} - - {description: The h5py package is a Pythonic interface to the HDF5 binary - data format., markedDefault: true, versionName: 2.7.1_py27} + - {description: 'h5utils is a set of utilities for visualization and conversion + of scientific data in the free, portable HDF5 format.', markedDefault: false, + versionName: 1.12.1} - categories: devel, data defaultVersionName: 1.44.0_py312 description: The NVIDIA Data Loading Library (DALI) is a GPU-accelerated library @@ -8551,25 +8624,17 @@ software_modules: properties: parallel: {mpi: 1} versionName: 1.3.2 - - categories: devel, lib - defaultVersionName: 2021.1_py36 - description: PyCUDA lets you access Nvidia‘s CUDA parallel computation API from - Python. - package: py-pycuda - url: https://mathema.tician.de/software/pycuda/ + - categories: devel, language + defaultVersionName: 7.3.0 + description: 'PHP (recursive acronym for PHP: Hypertext Preprocessor) is an + open source general-purpose scripting language that is especially suited for + web development.' + package: php + url: http://www.php.net versions: - - description: PyCUDA lets you access Nvidia‘s CUDA parallel computation API - from Python. - markedDefault: false - properties: - arch: {gpu: 1} - versionName: 2017.1.1_py27 - - description: PyCUDA lets you access Nvidia‘s CUDA parallel computation API - from Python. - markedDefault: false - properties: - arch: {gpu: 1} - versionName: 2021.1_py36 + - {description: 'PHP (recursive acronym for PHP: Hypertext Preprocessor) is + an open source general-purpose scripting language that is especially suited + for web development.', markedDefault: false, versionName: 7.3.0} - categories: devel, package management defaultVersionName: 0.28.1 description: Pixi is a package management tool for developers. It allows the @@ -8608,14 +8673,23 @@ software_modules: - {description: 'Intel Fortran Compiler, also known as ifort, is a group of Fortran compilers from Intel', family: compiler_f, markedDefault: false, versionName: '2019'} - - categories: devel, lib - defaultVersionName: 1.12.1 - description: Light-weight, simple and fast XML parser for C++ with XPath support. - package: pugixml - url: http://pugixml.org/ + - categories: devel, language + defaultVersionName: 1.81.0 + description: A language empowering everyone to build reliable and efficient + software. + package: rust + url: https://www.rust-lang.org/ versions: - - {description: 'Light-weight, simple and fast XML parser for C++ with XPath - support.', markedDefault: false, versionName: 1.12.1} + - {description: A language empowering everyone to build reliable and efficient + software., markedDefault: false, versionName: 1.35.0} + - {description: A language empowering everyone to build reliable and efficient + software., markedDefault: false, versionName: 1.56.1} + - {description: A language empowering everyone to build reliable and efficient + software., markedDefault: false, versionName: 1.63.0} + - {description: A language empowering everyone to build reliable and efficient + software., markedDefault: false, versionName: 1.72.0} + - {description: A language empowering everyone to build reliable and efficient + software., markedDefault: false, versionName: 1.81.0} - categories: devel, IDE defaultVersionName: 4.93.1 description: Run VS Code on any machine anywhere and access it in the browser. @@ -8626,6 +8700,23 @@ software_modules: markedDefault: false, versionName: 4.16.1} - {description: Run VS Code on any machine anywhere and access it in the browser., markedDefault: false, versionName: 4.93.1} + - categories: devel, lib + defaultVersionName: 1.12.1 + description: Light-weight, simple and fast XML parser for C++ with XPath support. + package: pugixml + url: http://pugixml.org/ + versions: + - {description: 'Light-weight, simple and fast XML parser for C++ with XPath + support.', markedDefault: false, versionName: 1.12.1} + - categories: devel, debug + defaultVersionName: 3.14.0 + description: Valgrind is an instrumentation framework for building dynamic analysis + tools. + package: valgrind + url: http://valgrind.org/ + versions: + - {description: Valgrind is an instrumentation framework for building dynamic + analysis tools., markedDefault: false, versionName: 3.14.0} - categories: devel, lib defaultVersionName: 1.0.0 description: CNMeM is a simple library to help the Deep Learning frameworks @@ -8639,67 +8730,6 @@ software_modules: properties: arch: {gpu: 1} versionName: 1.0.0 - - categories: devel, lib - defaultVersionName: 1.87.0 - description: Boost is a set of libraries for the C++ programming language that - provide support for tasks and structures such as linear algebra, pseudorandom - number generation, multithreading, image processing, regular expressions, - and unit testing. - package: boost - url: http://www.boost.org - versions: - - {description: 'Boost is a set of libraries for the C++ programming language - that provide support for tasks and structures such as linear algebra, pseudorandom - number generation, multithreading, image processing, regular expressions, - and unit testing.', markedDefault: false, versionName: 1.64.0} - - description: Boost is a set of libraries for the C++ programming language - that provide support for tasks and structures such as linear algebra, pseudorandom - number generation, multithreading, image processing, regular expressions, - and unit testing. - markedDefault: false - properties: - parallel: {mpi: 1} - versionName: 1.69.0 - - description: Boost is a set of libraries for the C++ programming language - that provide support for tasks and structures such as linear algebra, pseudorandom - number generation, multithreading, image processing, regular expressions, - and unit testing. - markedDefault: false - properties: - parallel: {mpi: 1} - versionName: 1.75.0 - - description: Boost is a set of libraries for the C++ programming language - that provide support for tasks and structures such as linear algebra, pseudorandom - number generation, multithreading, image processing, regular expressions, - and unit testing. - markedDefault: false - properties: - parallel: {mpi: 1} - versionName: 1.76.0 - - description: Boost is a set of libraries for the C++ programming language - that provide support for tasks and structures such as linear algebra, pseudorandom - number generation, multithreading, image processing, regular expressions, - and unit testing. - markedDefault: false - properties: - parallel: {mpi: 1} - versionName: 1.79.0 - - description: Boost is a set of libraries for the C++ programming language - that provide support for tasks and structures such as linear algebra, pseudorandom - number generation, multithreading, image processing, regular expressions, - and unit testing. - markedDefault: false - properties: - parallel: {mpi: 1} - versionName: 1.87.0 - - categories: devel, data analytics - defaultVersionName: 0.3_py27 - description: 'Launching and controlling spark on HPC clusters ' - package: py-sparkhpc - url: https://sparkhpc.readthedocs.io - versions: - - {description: 'Launching and controlling spark on HPC clusters ', markedDefault: false, - versionName: 0.3_py27} - categories: devel, compiler defaultVersionName: '110.81' description: Standard ML of New Jersey (abbreviated SML/NJ) is a compiler for diff --git a/src/docs/software/updates.xml b/src/docs/software/updates.xml index a9fec88f9..05be2ff8e 100644 --- a/src/docs/software/updates.xml +++ b/src/docs/software/updates.xml @@ -5,6 +5,42 @@ Sherlock software update feed https://www.sherlock.stanford.edu/docs/software/list + + New version: devel/ldc version 1.40.0 + The LLVM-based D Compiler. + https://github.com/ldc-developers/ldc + https://www.sherlock.stanford.edu/docs/software/list/?add:v=1.40.0#ldc + devel, compiler + kilian@stanford.edu (Kilian Cavalotti) + Wed, 8 Jan 2025 15:43:21 -0800 + + + New module: devel/ldc version 1.26.0 + The LLVM-based D Compiler. + https://github.com/ldc-developers/ldc + https://www.sherlock.stanford.edu/docs/software/list/?add:v=1.26.0#ldc + devel, compiler + kilian@stanford.edu (Kilian Cavalotti) + Tue, 7 Jan 2025 15:50:33 -0800 + + + New version: math/py-triton version 3.1.0_py312 + Triton is a language and compiler for writing highly efficient custom Deep-Learning primitives. + https://github.com/openai/triton + https://www.sherlock.stanford.edu/docs/software/list/?add:v=3.1.0_py312#py-triton + math, deep learning + kilian@stanford.edu (Kilian Cavalotti) + Thu, 19 Dec 2024 16:26:36 -0800 + + + New module: biology/hmmer version 3.4 + HMMER is used for searching sequence databases for sequence homologs, and for making sequence alignments. + http://hmmer.org/ + https://www.sherlock.stanford.edu/docs/software/list/?add:v=3.4#hmmer + biology, genomics + kilian@stanford.edu (Kilian Cavalotti) + Thu, 19 Dec 2024 16:13:42 -0800 + New module: chemistry/py-boltz version 0.3.2_py312 Boltz-1 is the state-of-the-art open-source model that predicts the 3D structure of proteins, RNA, DNA, and small molecules. @@ -545,140 +581,5 @@ kilian@stanford.edu (Kilian Cavalotti) Tue, 15 Oct 2024 14:28:13 -0700 - - New version: chemistry/orca version 6.0.0 - ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry. - https://orcaforum.kofo.mpg.de/ - https://www.sherlock.stanford.edu/docs/software/list/?add:v=6.0.0#orca - chemistry, quantum chemistry - kilian@stanford.edu (Kilian Cavalotti) - Wed, 9 Oct 2024 14:49:07 -0700 - - - New module: math/py-flash-attention version 2.6.3_py312 - Fast and memory-efficient exact attention - https://github.com/Dao-AILab/flash-attention - https://www.sherlock.stanford.edu/docs/software/list/?add:v=2.6.3_py312#py-flash-attention - math, deep learning - kilian@stanford.edu (Kilian Cavalotti) - Fri, 4 Oct 2024 12:08:23 -0700 - - - New module: math/py-evaluate version 0.4.3_py312 - Hugging Face Evaluate is a library for easily evaluating machine learning models and datasets. - https://huggingface.co/docs/evaluate - https://www.sherlock.stanford.edu/docs/software/list/?add:v=0.4.3_py312#py-evaluate - math, machine learning - kilian@stanford.edu (Kilian Cavalotti) - Thu, 3 Oct 2024 09:11:43 -0700 - - - New version: devel/rust version 1.81.0 - A language empowering everyone to build reliable and efficient software. - https://www.rust-lang.org/ - https://www.sherlock.stanford.edu/docs/software/list/?add:v=1.81.0#rust - devel, language - kilian@stanford.edu (Kilian Cavalotti) - Wed, 2 Oct 2024 12:00:04 -0700 - - - New version: devel/ucx version 1.17.0 - UCX is a communication library implementing high-performance messaging for MPI/PGAS frameworks. - http://www.openucx.org - https://www.sherlock.stanford.edu/docs/software/list/?add:v=1.17.0#ucx - devel, networking - kilian@stanford.edu (Kilian Cavalotti) - Tue, 24 Sep 2024 15:01:12 -0700 - - - New version: math/py-pytorch version 2.4.1_py312 - PyTorch is a deep learning framework that puts Python first. - http://pytorch.org - https://www.sherlock.stanford.edu/docs/software/list/?add:v=2.4.1_py312#py-pytorch - math, deep learning - kilian@stanford.edu (Kilian Cavalotti) - Mon, 23 Sep 2024 15:13:10 -0700 - - - New version: math/py-torchvision version 0.19.1_py312 - Datasets, model architectures, and common image transformations for computer vision for PyTorch. - http://pytorch.org/vision - https://www.sherlock.stanford.edu/docs/software/list/?add:v=0.19.1_py312#py-torchvision - math, deep learning - kilian@stanford.edu (Kilian Cavalotti) - Mon, 23 Sep 2024 15:12:44 -0700 - - - New version: system/libpng version 1.6.44 - libpng is the official PNG reference library. It supports almost all PNG features, is extensible, and has been extensively tested for over 20 years. - http://libpng.sourceforge.net - https://www.sherlock.stanford.edu/docs/software/list/?add:v=1.6.44#libpng - system, libs - kilian@stanford.edu (Kilian Cavalotti) - Mon, 23 Sep 2024 14:44:58 -0700 - - - New version: system/zlib version 1.3.1 - 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. - http://zlib.net - https://www.sherlock.stanford.edu/docs/software/list/?add:v=1.3.1#zlib - system, compression - kilian@stanford.edu (Kilian Cavalotti) - Mon, 23 Sep 2024 14:42:22 -0700 - - - New version: biology/py-biopython version 1.84_py312 - Biopython is a set of freely available tools for biological computation written in Python. - http://biopython.org - https://www.sherlock.stanford.edu/docs/software/list/?add:v=1.84_py312#py-biopython - biology, computational biology - kilian@stanford.edu (Kilian Cavalotti) - Mon, 23 Sep 2024 13:50:04 -0700 - - - New version: chemistry/vasp version 6.4.3 - The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, from first principles. - https://www.vasp.at - https://www.sherlock.stanford.edu/docs/software/list/?add:v=6.4.3#vasp - chemistry, computational chemistry - kilian@stanford.edu (Kilian Cavalotti) - Fri, 20 Sep 2024 16:28:32 -0700 - - - New version: devel/nvhpc version 24.7 - NVIDIA HPC Software Development Kit (SDK) including C, C++, and Fortran compilers. - https://developer.nvidia.com/hpc-sdk - https://www.sherlock.stanford.edu/docs/software/list/?add:v=24.7#nvhpc - devel, compiler - kilian@stanford.edu (Kilian Cavalotti) - Fri, 20 Sep 2024 12:30:26 -0700 - - - New version: devel/gcc version 12.1.0 - - - https://www.sherlock.stanford.edu/docs/software/list/?add:v=12.1.0#gcc - - kilian@stanford.edu (Kilian Cavalotti) - Thu, 19 Sep 2024 14:04:21 -0700 - - - New version: devel/gcc version 12.4.0 - The GNU Compiler Collection includes front ends for C, C++, Fortran, Java, and Go, as well as libraries for these languages (libstdc++, libgcj,...). - http://gcc.gnu.org - https://www.sherlock.stanford.edu/docs/software/list/?add:v=12.4.0#gcc - devel, compiler - kilian@stanford.edu (Kilian Cavalotti) - Thu, 19 Sep 2024 14:04:21 -0700 - - - New version: devel/gcc version 14.2.0 - The GNU Compiler Collection includes front ends for C, C++, Fortran, Java, and Go, as well as libraries for these languages (libstdc++, libgcj,...). - http://gcc.gnu.org - https://www.sherlock.stanford.edu/docs/software/list/?add:v=14.2.0#gcc - devel, compiler - kilian@stanford.edu (Kilian Cavalotti) - Thu, 19 Sep 2024 14:04:21 -0700 -