From 7deae6fdf422ea7d3e4097d7fdf9acae8af32245 Mon Sep 17 00:00:00 2001 From: Kilian Cavalotti Date: Fri, 15 Sep 2023 08:09:30 -0700 Subject: [PATCH] docs: updated software list --- includes/data/software.yml | 346 ++++++++++++++++++---------------- src/docs/software/updates.xml | 63 ++----- 2 files changed, 197 insertions(+), 212 deletions(-) diff --git a/includes/data/software.yml b/includes/data/software.yml index 167c47fd0..7202901e5 100644 --- a/includes/data/software.yml +++ b/includes/data/software.yml @@ -4374,32 +4374,40 @@ software_modules: - {description: 'HiC-Pro: An optimized and flexible pipeline for Hi-C data processing.', markedDefault: false, versionName: 2.10.0} - 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/ + 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: Tools to process and analyze deep sequencing data., markedDefault: false, - versionName: 3.3.1_py36} - - categories: biology, neurology - defaultVersionName: '20160502' - description: MRIcron is a cross-platform NIfTI format image viewer. - package: mricron - url: https://www.nitrc.org/projects/mricron + - {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, 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 versions: - - {description: MRIcron is a cross-platform NIfTI format image viewer., markedDefault: false, - versionName: '20160502'} - - categories: biology, neurology - defaultVersionName: 0.7.00 - description: BART is a toolbox for Computational Magnetic Resonance Imaging. - package: bart - url: https://mrirecon.github.io/bart/ + - {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: 0.11.8 + 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: BART is a toolbox for Computational Magnetic Resonance Imaging. - markedDefault: false - properties: - arch: {gpu: 1} - versionName: 0.7.00 + - {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, cryo-em defaultVersionName: 4.11.5 description: IMOD is a set of image processing, modeling and display programs @@ -4422,6 +4430,19 @@ software_modules: 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: true, + versionName: 0.44.0} - categories: biology, genomics defaultVersionName: 2.4.40 description: BEDOPS is an open-source command-line toolkit that performs highly @@ -4488,18 +4509,15 @@ 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: 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/ + 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: 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: true, - versionName: 0.44.0} + - {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, neurology defaultVersionName: 7.4.1 description: An open source software suite for processing and analyzing (human) @@ -4518,25 +4536,27 @@ software_modules: - {description: An open source software suite for processing and analyzing (human) brain MRI images., markedDefault: false, versionName: 7.4.1} - 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: 3.0.7 + description: The SRA Toolkit and SDK from NCBI is a collection of tools and + libraries for using data in the INSDC Sequence Read Archives. + package: sra-tools + url: https://github.com/ncbi/sra-tools 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: The SRA Toolkit and SDK from NCBI is a collection of tools and + libraries for using data in the INSDC Sequence Read Archives., markedDefault: false, + versionName: 2.11.0} + - {description: The SRA Toolkit and SDK from NCBI is a collection of tools and + libraries for using data in the INSDC Sequence Read Archives., markedDefault: false, + versionName: 3.0.7} - categories: biology, genomics - defaultVersionName: 1.1.3_py27 - description: Fit-Hi-C is a tool for assigning statistical confidence estimates - to chromosomal contact maps produced by genome architecture assays. - package: py-fithic - url: https://github.com/ay-lab/fithic + defaultVersionName: 0.3.4 + 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: Fit-Hi-C is a tool for assigning statistical confidence estimates - to chromosomal contact maps produced by genome architecture assays., markedDefault: false, - versionName: 1.1.3_py27} + - {description: 'Dorado is a high-performance, easy-to-use, open source basecaller + for Oxford Nanopore reads.', markedDefault: false, versionName: 0.3.4} - categories: biology, neurology defaultVersionName: 5.0.10 description: FSL is a comprehensive library of analysis tools for FMRI, MRI @@ -4550,24 +4570,25 @@ software_modules: properties: arch: {gpu: 1} versionName: 5.0.10 - - 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, neurology + defaultVersionName: 0.7.00 + description: BART is a toolbox for Computational Magnetic Resonance Imaging. + package: bart + url: https://mrirecon.github.io/bart/ 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: BART is a toolbox for Computational Magnetic Resonance Imaging. + markedDefault: false + properties: + arch: {gpu: 1} + versionName: 0.7.00 - categories: biology, genomics - defaultVersionName: 0.3.4 - description: Dorado is a high-performance, easy-to-use, open source basecaller - for Oxford Nanopore reads. - package: dorado - url: https://github.com/nanoporetech/dorado + 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: 'Dorado is a high-performance, easy-to-use, open source basecaller - for Oxford Nanopore reads.', markedDefault: false, versionName: 0.3.4} + - {description: NCBI VDB is the database engine used by NCBI SRA tools., markedDefault: false, + versionName: 3.0.7} - categories: biology, genomics defaultVersionName: 1.2.2 description: Bowtie is an ultrafast, memory-efficient short read aligner. @@ -4633,14 +4654,6 @@ 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: 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: '1.16' description: C library for high-throughput sequencing data formats. @@ -4658,15 +4671,29 @@ software_modules: - {description: C library for high-throughput sequencing data formats., markedDefault: false, versionName: '1.16'} - 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: 3.3.1_py36 + description: Tools to process and analyze deep sequencing data. + package: py-deeptools + url: https://github.com/deeptools/deepTools/ 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: Tools to process and analyze deep sequencing data., markedDefault: false, + versionName: 3.3.1_py36} + - categories: biology, computational biology + defaultVersionName: '3.8' + description: Rosetta is the premier software suite for modeling macromolecular + structures. As a flexible, multi-purpose application, it includes tools for + structure prediction, design, and remodeling of proteins and nucleic acids. + package: rosetta + url: https://www.rosettacommons.org + versions: + - description: Rosetta is the premier software suite for modeling macromolecular + structures. As a flexible, multi-purpose application, it includes tools + for structure prediction, design, and remodeling of proteins and nucleic + acids. + markedDefault: false + properties: + parallel: {mpi: 1} + versionName: '3.8' - categories: biology, genomics defaultVersionName: '0.1' description: popscle is a suite of population scale analysis tools for single-cell @@ -4707,22 +4734,16 @@ software_modules: 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, computational biology - defaultVersionName: '3.8' - description: Rosetta is the premier software suite for modeling macromolecular - structures. As a flexible, multi-purpose application, it includes tools for - structure prediction, design, and remodeling of proteins and nucleic acids. - package: rosetta - url: https://www.rosettacommons.org + - categories: biology, genomics + defaultVersionName: 2.5.1 + description: BamTools is a project that provides both a C++ API and a command-line + toolkit for reading, writing, and manipulating BAM (genome alignment) files. + package: bamtools + url: https://github.com/pezmaster31/bamtools versions: - - description: Rosetta is the premier software suite for modeling macromolecular - structures. As a flexible, multi-purpose application, it includes tools - for structure prediction, design, and remodeling of proteins and nucleic - acids. - markedDefault: false - properties: - parallel: {mpi: 1} - versionName: '3.8' + - {description: 'BamTools is a project that provides both a C++ API and a command-line + toolkit for reading, writing, and manipulating BAM (genome alignment) files.', + markedDefault: false, versionName: 2.5.1} - categories: biology, genomics defaultVersionName: 0.9.0_py39 description: Pybedtools wraps and extends BEDTools and offers feature-level @@ -4736,22 +4757,6 @@ 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, 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 - 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'} - categories: biology, genomics defaultVersionName: 0.4.17_py36 description: A visualization framework for CRISPR/Cas9 knockout screens, analyzed @@ -4774,15 +4779,6 @@ software_modules: - {description: GATK (Genome Analysis Toolkit) offers a wide variety of tools with a primary focus on variant discovery and genotyping., markedDefault: false, versionName: 4.1.4.1} - - 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: 0.8.13_py39 description: Tools for manipulating biological data, particularly multiple sequence @@ -4794,6 +4790,25 @@ software_modules: sequence alignments.', markedDefault: false, versionName: 0.8.1_py27} - {description: 'Tools for manipulating biological data, particularly multiple sequence alignments.', markedDefault: false, versionName: 0.8.13_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, 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: Nextflow is a bioinformatics workflow manager that enables the + development of portable and reproducible workflows., markedDefault: false, + versionName: 23.04.3} - categories: biology, molecular biology defaultVersionName: 3.0.0 description: Library to work with mmCIF and PDB files. @@ -4812,18 +4827,14 @@ software_modules: - {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: 3.0.7 - description: The SRA Toolkit and SDK from NCBI is a collection of tools and - libraries for using data in the INSDC Sequence Read Archives. - package: sra-tools - url: https://github.com/ncbi/sra-tools + defaultVersionName: 0.0.14 + description: The FASTX-Toolkit is a collection of command line tools for Short-Reads + FASTA/FASTQ files preprocessing. + package: fastx_toolkit + url: http://hannonlab.cshl.edu/fastx_toolkit/ versions: - - {description: The SRA Toolkit and SDK from NCBI is a collection of tools and - libraries for using data in the INSDC Sequence Read Archives., markedDefault: false, - versionName: 2.11.0} - - {description: The SRA Toolkit and SDK from NCBI is a collection of tools and - libraries for using data in the INSDC Sequence Read Archives., markedDefault: false, - versionName: 3.0.7} + - {description: The FASTX-Toolkit is a collection of command line tools for + Short-Reads FASTA/FASTQ files preprocessing., markedDefault: false, versionName: 0.0.14} - categories: biology, genomics defaultVersionName: 0.5.0 description: Trim Galore! is a wrapper script to automate quality and adapter @@ -4939,6 +4950,14 @@ software_modules: 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, neurology + defaultVersionName: '20160502' + description: MRIcron is a cross-platform NIfTI format image viewer. + package: mricron + url: https://www.nitrc.org/projects/mricron + versions: + - {description: MRIcron is a cross-platform NIfTI format image viewer., markedDefault: false, + versionName: '20160502'} - categories: biology, genomics defaultVersionName: 2.30.0 description: The bedtools utilities are a swiss-army knife of tools for a wide-range @@ -4950,15 +4969,6 @@ software_modules: 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 - FASTA/FASTQ files preprocessing. - package: fastx_toolkit - url: http://hannonlab.cshl.edu/fastx_toolkit/ - versions: - - {description: The FASTX-Toolkit is a collection of command line tools for - Short-Reads FASTA/FASTQ files preprocessing., markedDefault: false, versionName: 0.0.14} - categories: biology, clinical science defaultVersionName: '20180704' description: Simvascular is a blood flow simulation and analysis toolkit. This @@ -4988,15 +4998,15 @@ software_modules: - {description: A Python framework for the analysis and visualization of trees., markedDefault: false, versionName: 3.0.0_py27} - categories: biology, genomics - defaultVersionName: 2.5.1 - description: BamTools is a project that provides both a C++ API and a command-line - toolkit for reading, writing, and manipulating BAM (genome alignment) files. - package: bamtools - url: https://github.com/pezmaster31/bamtools + defaultVersionName: 1.1.3_py27 + description: Fit-Hi-C is a tool for assigning statistical confidence estimates + to chromosomal contact maps produced by genome architecture assays. + package: py-fithic + url: https://github.com/ay-lab/fithic versions: - - {description: 'BamTools is a project that provides both a C++ API and a command-line - toolkit for reading, writing, and manipulating BAM (genome alignment) files.', - markedDefault: false, versionName: 2.5.1} + - {description: Fit-Hi-C is a tool for assigning statistical confidence estimates + to chromosomal contact maps produced by genome architecture assays., markedDefault: false, + versionName: 1.1.3_py27} - categories: biology, genomics defaultVersionName: 0.98.5 description: GEMMA is a software toolkit for fast application of linear mixed @@ -5008,23 +5018,6 @@ 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, 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: '1.8' - description: A single molecule sequence assembler for genomes large and small. - package: canu - url: https://github.com/marbl/canu/ - versions: - - {description: A single molecule sequence assembler for genomes large and small., - markedDefault: false, versionName: '1.8'} - categories: biology, genomics defaultVersionName: 2.11.0 description: NCBI BLAST+ is a suite of command-line tools to run BLAST (Basic @@ -5042,6 +5035,23 @@ software_modules: - {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} + - categories: biology, genomics + defaultVersionName: '1.8' + description: A single molecule sequence assembler for genomes large and small. + package: canu + url: https://github.com/marbl/canu/ + versions: + - {description: A single molecule sequence assembler for genomes large and small., + markedDefault: false, versionName: '1.8'} + - 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: 2.2.1_py36 description: mapDamage2 is a computational framework which tracks and quantifies @@ -6513,7 +6523,7 @@ software_modules: 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: 1.63.0 + defaultVersionName: 1.72.0 description: A language empowering everyone to build reliable and efficient software. package: rust @@ -6525,6 +6535,8 @@ software_modules: 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} - categories: devel, language defaultVersionName: 7.3.0 description: 'PHP (recursive acronym for PHP: Hypertext Preprocessor) is an diff --git a/src/docs/software/updates.xml b/src/docs/software/updates.xml index a8ec63c2d..ff1e85707 100644 --- a/src/docs/software/updates.xml +++ b/src/docs/software/updates.xml @@ -5,6 +5,24 @@ Sherlock software update feed https://www.sherlock.stanford.edu/docs/software/list + + New module: biology/nextflow version 23.04.3 + Nextflow is a bioinformatics workflow manager that enables the development of portable and reproducible workflows. + http://nextflow.io/ + https://www.sherlock.stanford.edu/docs/software/list/?add:v=23.04.3#nextflow + biology, workflow management + kilian@stanford.edu (Kilian Cavalotti) + Fri, 15 Sep 2023 08:08:08 -0700 + + + New version: devel/rust version 1.72.0 + 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=1.72.0#rust + devel, language + mthartma@stanford.edu (Mike Hartman) + Tue, 12 Sep 2023 12:48:07 -0700 + New module: biology/dorado version 0.3.4 Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads. @@ -113,50 +131,5 @@ kilian@stanford.edu (Kilian Cavalotti) Fri, 14 Jul 2023 17:53:31 -0700 - - New version: system/nvtop version 3.0.2 - Nvtop stands for NVidia TOP, a (h)top like task monitor for NVIDIA GPUs. - https://github.com/Syllo/nvtop - https://www.sherlock.stanford.edu/docs/software/list/?add:v=3.0.2#nvtop - system, resource monitoring - kilian@stanford.edu (Kilian Cavalotti) - Thu, 15 Jun 2023 10:06:02 -0700 - - - New module: chemistry/terachem version 1.95A - TeraChem is general purpose quantum chemistry software designed to run on NVIDIA GPU architectures. - http://www.petachem.com/ - https://www.sherlock.stanford.edu/docs/software/list/?add:v=1.95A#terachem - chemistry, quantum chemistry - kilian@stanford.edu (Kilian Cavalotti) - Tue, 13 Jun 2023 12:09:35 -0700 - - - New module: chemistry/terachem version 1.96H-beta - TeraChem is general purpose quantum chemistry software designed to run on NVIDIA GPU architectures. - http://www.petachem.com/ - https://www.sherlock.stanford.edu/docs/software/list/?add:v=1.96H-beta#terachem - chemistry, quantum chemistry - kilian@stanford.edu (Kilian Cavalotti) - Tue, 13 Jun 2023 12:09:35 -0700 - - - New module: chemistry/terachem version default - TeraChem is general purpose quantum chemistry software designed to run on NVIDIA GPU architectures. - http://www.petachem.com/ - https://www.sherlock.stanford.edu/docs/software/list/?add:v=default#terachem - chemistry, quantum chemistry - kilian@stanford.edu (Kilian Cavalotti) - Tue, 13 Jun 2023 12:09:35 -0700 - - - New version: devel/py-schwimmbad version 0.3.2_py39 - 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). - http://scikit-image.org/ - https://www.sherlock.stanford.edu/docs/software/list/?add:v=0.3.2_py39#py-schwimmbad - devel, lib - kilian@stanford.edu (Kilian Cavalotti) - Tue, 13 Jun 2023 11:58:36 -0700 -