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Software Repositories

In addition to the core software tools that are available by default, additional software is available via environment modules. For example, although MATLAB is installed on the system, it is not available by default. Instead, we need to “load” its module first, e.g.

[alice@dev2 ~]$ module load matlab
[alice@dev2 ~]$ module list

Currently Loaded Modules:
  1) matlab/2021a

Then we can launch MATLAB using:

[alice@dev2 ~]$ matlab -nosplash -nodesktop

To see what other “built-in” modules are available, use:

[alice@dev2 ~]$ module avail

In additional a set of built-in environment modules, there are also modules for software tools that are installed and maintained by other users or research groups. To access these, we first need to load the corresponding “Software Repository” module. For example, to get access to the repository and the software shared by the UCSF Computation Biology and Informatics core (CBI), make sure to load (“enable”) the repository first, e.g.

module load CBI

Then use module avail to list what modules and versions are available (or see below). Next, to actually get access to one or more of the shared software modules, use module load <name> or module load <name>/<version>. Here are a few examples:

module load bowtie2
module load bowtie2/2.2.6
module load r

It is possible to (i) enable a software repository and (ii) load a set of software tools in one call, e.g.

module load CBI r bwa bowtie2/2.2.6

Below are 3 software repositories, each providing a set of software tools.

Module Software Repository: built-in (9)

Maintained by: Wynton Systems Administrators, Wynton HPC
Enable repository: this software repository is always enabled
Amber11, for 64-bit
URL: http://ambermd.org/
Versions: 20, 11
The Computational Biology and Informatics (CBI) Software Repository
Repository of software shared by the Computational Biology and Informatics (http://cbi.ucsf.edu) at the UCSF Helen Diller Family Comprehensive Cancer Center.
URL: http://cbi.ucsf.edu/
Versions: 6.0.37, 7.5, 7.5.18, 8.0, 8.0.61, 9.0.176, 9.1, 9.2, 10.0.130, 10.1, 11.0, 11.5.0
Versions: 0.6.4, 1.6.0
Versions:, 2018b, 2019a, 2019b, 2020a, 2020b, 2021a, 2021b
Versions: 2020a, 2020b, 2021a, 2021b
Versions: openmpi-x86_64, openmpi3-x86_64
openjdk-runtime: Open Java Development Kit
OpenJDK is a free and open-source implementation of the Java Platform, Standard Edition. It is the result of an effort Sun Microsystems began in 2006.
Example: java -version and javac -version.
URL: https://openjdk.java.net/
Sali lab software repository

Module Software Repository: CBI (69)

Maintained by: Henrik Bengtsson, Computational Biology and Informatics
Enable repository: module load CBI
ASCIIGenome: Text Only Genome Viewer
ASCIIGenome is a genome browser based on command line interface and designed for running from console terminals. Since ASCIIGenome does not require a graphical interface it is particularly useful for quickly visualizing genomic data on remote servers while offering flexibility similar to popular GUI viewers like IGV.
Example: ASCIIGenome --help.
URL: https://github.com/dariober/ASCIIGenome
Versions: 1.15.0, 1.16.0
bamUtil: Programs for Working on SAM/BAM Files
bamUtil is a repository that contains several programs that perform operations on SAM/BAM files. All of these programs are built into a single executable, bam.
Example: bam help.
URL: https://genome.sph.umich.edu/wiki/BamUtil, https://github.com/statgen/bamUtil
Versions: 1.0.14
bat: A cat(1) Clone with Syntax Highlighting and Git Integration
A cat(1) clone with syntax highlighting and Git integration.
Example: bat README.md, bat scripts/*.sh, and bat src/*.c.
URL: https://github.com/sharkdp/bat
Warning: Only the most recent version of this software will be kept.
Versions: 0.17.1, 0.18.3
BCFtools: Utilities for Variant Calling and Manipulating VCFs and BCFs
BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.
Example: bcftools --version
URL: https://www.htslib.org/, https://github.com/samtools/bcftools
Versions: 1.9, 1.10, 1.10.2, 1.11, 1.13, 1.14
bcl2fastq: Illumina Conversion Software
bcl2fastq Conversion Software both demultiplexes data and converts BCL files generated by Illumina sequencing systems to standard FASTQ file formats for downstream analysis.
Example: bcl2fastq --version
URL: https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html
Versions: 2.20.0
BEDOPS: The Fast, Highly Scalable and Easily-Parallelizable Genome Analysis Toolkit
BEDOPS is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale. Tasks can be easily split by chromosome for distributing whole-genome analyses across a computational cluster.
Example: bedops --version
URL: https://bedops.readthedocs.io/, https://github.com/bedops/bedops
Versions: 2.4.36, 2.4.37, 2.4.38, 2.4.39, 2.4.40
bedtools2: The Swiss Army Knife for Genome Arithmetic
Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome. For example, bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF.
Example: bedtools --version and ls $BEDTOOLS2_HOME/genomes/.
URL: https://github.com/arq5x/bedtools2/
Versions: 2.26.0, 2.28.0, 2.29.1, 2.29.2, 2.30.0
BLAST+: Basic Local Alignment Search Tool
BLAST finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance.
Example: blastx -version
URL: https://blast.ncbi.nlm.nih.gov/Blast.cgi
Versions: 2.9.0, 2.10.1, 2.11.0, 2.12.0
BLAT: Fast Sequence Search Command Line Tool
BLAT - client and server combined into a single program, first building the index, then using the index, and then exiting.
Example: blat
URL: https://genome.ucsc.edu/goldenPath/help/blatSpec.html
Versions: 36x4
Bowtie: A Fast and Sensitive Gapped Read Aligner
Bowtie is an ultrafast, memory-efficient short read aligner.
Example: bowtie --version and ls $BOWTIE_HOME/{genomes,indexes}
Note: This is Bowtie v1 - not v2.
URL: http://bowtie-bio.sourceforge.net/index.shtml
Versions: 1.2.3, 1.3.0, 1.3.1
Bowtie 2: A Fast and Sensitive Gapped Read Aligner
Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.
Example: bowtie2 --version
URL: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
Versions: 2.3.5,, 2.4.1, 2.4.2, 2.4.4
BWA: Burrows-Wheeler Aligner
Burrows-Wheeler Aligner (BWA) is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome.
Example: bwa.
URL: http://bio-bwa.sourceforge.net/
Versions: 0.7.17
byobu: Elegant Enhancement of the Otherwise Functional, Plain, Practical GNU Screen
Byobu is an elegant enhancement of the otherwise functional, plain, practical GNU Screen. Byobu includes an enhanced profile, configuration utilities, and system status notifications for the GNU screen window manager as well as the Tmux terminal multiplexer.
Example: byobu --version.
URL: http://byobu.org, https://github.com/dustinkirkland/byobu
Warning: Only the most recent version of this software will be kept.
Versions: 5.133
The Computational Biology and Informatics (CBI) Software Repository - TESTING ONLY!
This repository provides prototypical environment modules that can change at any time. They will live in this CBI-testing repository until they have proven to work and be stable - only then they will be considered for the main CBI repository. WARNING: Use at your own risk.
URL: http://cbi.ucsf.edu/
Cell Ranger: 10x Genomics Pipeline for Single-Cell Data Analysis
Cell Ranger is a set of analysis pipelines that process Chromium Single Cell 3' RNA-seq output to align reads, generate gene-cell matrices and perform clustering and gene expression analysis.
Example: cellranger.
URL: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger
Warning: To prevent a single Cell Ranger process from hijacking all CPU and RAM by default, this module sets environment variable MROFLAGS='--localcores=1 --localmem=8 --limit-loadavg' making those the default.
Versions: 2.1.0, 3.0.2, 3.1.0, 4.0.0, 5.0.1, 6.1.1, 6.1.2
CMake: Open-source, Cross-platform Family of Tools Designed to Build, Test and Package Software
CMake is cross-platform free and open-source software for managing the build process of software using a compiler-independent method. It supports directory hierarchies and applications that depend on multiple libraries.
Example: cmake --version.
URL: https://cmake.org/
Versions: 3.18.2, 3.19.2
Control FREEC: Control-FREE Copy Number and Genotype Caller
Prediction of copy numbers and allelic content using deep-sequencing data.
Example: freec.
URL: http://boevalab.com/FREEC/, https://github.com/BoevaLab/FREEC/
Versions: 11.5, 11.6
Cufflinks: Transcriptome Assembly and Differential Expression Analysis for RNA-Seq
Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one, taking into account biases in library preparation protocols.
Example: cufflinks.
URL: http://cole-trapnell-lab.github.io/cufflinks/, https://github.com/cole-trapnell-lab/cufflinks
Versions: 2.2.1
GNU Emacs: An Extensible, Customizable, Free/Libre Text Editor
At its core is an interpreter for Emacs Lisp, a dialect of the Lisp programming language with extensions to support text editing.
Example: emacs --version and emacs -nw.
URL: https://www.gnu.org/software/emacs/
Warning: Only the most recent version of this software will be kept.
Versions: 26.3, 27.1, 27.2
FastQC: A Quality Control Analysis Tool for High Throughput Sequencing Data
FastQC is a program designed to spot potential problems in high througput sequencing datasets. It runs a set of analyses on one or more raw sequence files in fastq or bam format and produces a report which summarises the results.
Example: fastqc --version.
URL: https://www.bioinformatics.babraham.ac.uk/projects/download.html#fastqc, https://github.com/s-andrews/FastQC/
Versions: 0.11.8, 0.11.9
fzf - A Command-Line Fuzzy Finder
fzf is a general-purpose command-line fuzzy finder. It's an interactive Unix filter for command-line that can be used with any list; files, command history, processes, hostnames, bookmarks, git commits, etc.
Example: fzf --version and emacs "$(fzf)".
Note: To install tab completions and key bindinds to your shell, call $FZF_HOME/install. To uninstall, use $FZF_HOME/uninstall.
URL: https://github.com/junegunn/fzf, https://github.com/junegunn/fzf/wiki
Warning: Only the most recent version of this software will be kept.
Versions: 0.22.0, 0.25.1, 0.27.2, 0.29.0
Genome Analysis Toolkit (GATK): Variant Discovery in High-Throughput Sequencing Data
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Example: gatk --help and gatk --list.
URL: https://software.broadinstitute.org/gatk/, https://github.com/broadinstitute/gatk, https://github.com/broadgsa/gatk, https://console.cloud.google.com/storage/browser/gatk-software/package-archive, ftp://ftp.broadinstitute.org/pub/gsa/GenomeAnalysisTK/
GCTA: Genome-wide Complex Trait Analysis
A tool for Genome-wide Complex Trait Analysis (GCTA).
Example: gcta64.
URL: http://cnsgenomics.com/software/gcta/
Versions: 1.26.0, 1.92.3beta3, 1.92.4beta, 1.93.2beta
GDAL: Geospatial Data Abstraction Library
GDAL is an open source X/MIT licensed translator library for raster and vector geospatial data formats.
Example: gdalinfo --version
URL: https://gdal.org/, https://github.com/OSGeo/gdal
Versions: 2.4.3, 2.4.4
GEOS: Geometry Engine, Open Source
GEOS (Geometry Engine - Open Source) is a C++ port of the JTS Topology Suite (JTS). It aims to contain the complete functionality of JTS in C++. This includes all the OpenGIS Simple Features for SQL spatial predicate functions and spatial operators, as well as specific JTS enhanced functions. GEOS provides spatial functionality to many other projects and products.
Example: geos-config --version.
URL: https://trac.osgeo.org/geos/
Versions: 3.5.2, 3.7.3, 3.8.1, 3.9.1
GISTIC2: Genomic Identification of Significant Targets in Cancer (GISTIC), version 2
GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers.
Example: gistic2.
URL: https://software.broadinstitute.org/cancer/cga/gistic, https://github.com/broadinstitute/gistic2, https://www.genepattern.org/modules/docs/GISTIC_2.0/7
Versions: 2.0.23
git-flow: Git Extension Git Flow (AVH Edition)
A collection of Git extensions to provide high-level repository operations for Vincent Driessen's branching model.
Example: git flow.
URL: https://github.com/petervanderdoes/gitflow-avh, https://github.com/nvie/gitflow
Warning: Only the most recent version of this software will be kept.
Versions: 1.12.3
glow: Render Markdown on the CLI, with Pizzazz!
Glow is a terminal based markdown reader designed from the ground up to bring out the beauty—and power—of the CLI. Use it to discover markdown files, read documentation directly on the command line and stash markdown files to your own private collection so you can read them anywhere. Glow will find local markdown files in subdirectories or a local Git repository.
Example: glow README.md, glow --pager README.md.
URL: https://github.com/charmbracelet/glow
Warning: Only the most recent version of this software will be kept.
Versions: 1.3.0, 1.4.1
GSL: Gnu Scientific Library
The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. It is free software under the GNU General Public License. The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting. There are over 1000 functions in total with an extensive test suite.
Example: gsl-config --version
URL: https://www.gnu.org/software/gsl/
Versions: 2.6, 2.7
hdf5: A General Purpose Library and File Format for Storing Scientific Data
Hierarchical Data Format (HDF) is a set of file formats (HDF4, HDF5) designed to store and organize large amounts of data. The HDF5 format is designed to address some of the limitations of the HDF4 library, and to address current and anticipated requirements of modern systems and applications.
Example: h5stat --version
URL: https://www.hdfgroup.org/downloads/hdf5/
Versions: 1.10.6, 1.12.0, 1.12.1
HISAT2: Graph-based Alignment of Next Generation Sequencing Reads to a Population of Genomes
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). Based on an extension of BWT for graphs [Sirén et al. 2014], we designed and implemented a graph FM index (GFM), an original approach and its first implementation to the best of our knowledge. In addition to using one global GFM index that represents a population of human genomes, HISAT2 uses a large set of small GFM indexes that collectively cover the whole genome (each index representing a genomic region of 56 Kbp, with 55,000 indexes needed to cover the human population). These small indexes (called local indexes), combined with several alignment strategies, enable rapid and accurate alignment of sequencing reads. This new indexing scheme is called a Hierarchical Graph FM index (HGFM).
Example: hisat2 --version.
URL: https://daehwankimlab.github.io/hisat2/, https://github.com/DaehwanKimLab/hisat2/
Versions: 2.1.0, 2.2.0
htop: An Interactive Process Viewer for Unix
htop is an interactive process viewer for Unix systems. It is a text-mode application (for console or X terminals) and requires ncurses.
Example: htop.
URL: https://htop.dev, https://github.com/htop-dev/htop
Warning: Only the most recent version of this software will be kept.
Versions: 3.0.4, 3.0.5, 3.1.0, 3.1.2
HTSlib: C Library for High-Throughput Sequencing Data Formats
HTSlib is an implementation of a unified C library for accessing common file formats, such as SAM, CRAM and VCF, used for high-throughput sequencing data, and is the core library used by samtools and bcftools. HTSlib also provides the bgzip, htsfile, and tabix utilities.
Example: bgzip --version, htsfile --version, and tabix --version.
URL: https://www.htslib.org/, https://github.com/samtools/htslib
Versions: 1.9, 1.10.2, 1.11, 1.13, 1.14
htstools: Tools to Process BAM Files for Downstream Copy-Number Analysis
Contains three tools (dnafrags, ppflag-fixer, snp-pileup) written by Alex Studer to process bam files for downstream copy number analysis.
Example: snp-pileup --help.
URL: https://github.com/mskcc/htstools
Versions: 0.1.1
IGV: The Integrative Genomics Viewer
The Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations.
Example: igv.
Note: IGV (>= 2.5.0) requires Java 11. Coincidentally, igvtools is integrated with IGV (>= 2.5.0).
URL: https://software.broadinstitute.org/software/igv/, https://software.broadinstitute.org/software/igv/download
Versions: 2.4.19, 2.7.0, 2.7.2, 2.8.2, 2.8.6, 2.8.13, 2.9.1, 2.11.0, 2.11.9
IGVTools: Tools for Pre-processing HT-Seq Data Files
The igvtools utility provides a set of tools for pre-processing data files. Note, igvtools moved to IGV as of IGV (>= 2.5.0).
Example: igvtools help.
URL: https://software.broadinstitute.org/software/igv/igvtools
Versions: 2.4.19
JAGS: Just Another Gibbs Sampler
JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation not wholly unlike BUGS.
Example: jags and man jags.
URL: http://mcmc-jags.sourceforge.net/
Versions: 4.3.0
kallisto: Near-optimal RNA-Seq Quantification
kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment.
Example: kallisto version.
URL: https://pachterlab.github.io/kallisto/about.html, https://github.com/pachterlab/kallisto
Versions: 0.45.0, 0.45.1, 0.46.0, 0.46.1, 0.46.2
mc: Midnight Commander
GNU Midnight Commander is a visual file manager. It's a feature rich full-screen text mode application that allows you to copy, move and delete files and whole directory trees, search for files and run commands in the subshell. Internal viewer and editor are included.
Example: mc and mc --version.
URL: http://www.midnight-commander.org/, https://github.com/MidnightCommander/mc
Warning: Only the most recent version of this software will be kept.
Versions: 4.8.26, 4.8.27
muTect: Identification of Somatic Point Mutations in Next Generation Sequencing Data of Cancer Genomes
MuTect is a method developed at the Broad Institute for the reliable and accurate identification of somatic point mutations in next generation sequencing data of cancer genomes.
Example: mutect, which is short for java -Xmx2g -jar "$MUTECT_JAR".
URL: https://github.com/broadinstitute/mutect, https://software.broadinstitute.org/cancer/cga/mutect
Versions: 1.1.1, 1.1.4, 1.1.5
Pandoc: A Universal Document Converter
Pandoc is a Haskell library and software tool for converting from one markup format to another, and a command-line tool that uses this library.
Example: pandoc --version.
URL: https://pandoc.org/, https://github.com/jgm/pandoc
Warning: Only the most recent version of this software will be kept.
Versions: 2.11.4, 2.14.2, 2.16.2
Picard: Command-line tools for Manipulating High-throughput Sequencing Data and Formats
Picard is a set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
Example: picard -h, which is an alias for java -jar $PICARD_HOME/picard.jar -h
URL: http://broadinstitute.github.io/picard/, https://github.com/broadinstitute/picard
Versions: 2.21.1, 2.21.4, 2.22.2, 2.23.1, 2.24.0, 2.26.2, 2.26.10
pindel: Detection of Indels and Structural Variations
Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.
Example: pindel.
URL: https://www.sanger.ac.uk/science/tools/pindel, https://github.com/genome/pindel
Versions: 0.2.5b8
PLINK: Whole Genome Association Analysis Toolset
PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. The focus of PLINK is purely on analysis of genotype/phenotype data, so there is no support for steps prior to this (e.g. study design and planning, generating genotype or CNV calls from raw data).
Example: plink --help.
URL: https://www.cog-genomics.org/plink/
Versions: 1.07, 1.90b6.10, 1.90b6.16, 1.90b6.18, 1.90b6.21, 1.90b6.24
PLINK2: Whole Genome Association Analysis Toolset
PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. The focus of PLINK is purely on analysis of genotype/phenotype data, so there is no support for steps prior to this (e.g. study design and planning, generating genotype or CNV calls from raw data).
Example: plink2 --help.
URL: https://www.cog-genomics.org/plink/2.0/, https://github.com/chrchang/plink-ng
Versions: 2.00a2LM, 2.00a2.3, 2.00a3LM
PROJ: PROJ Coordinate Transformation Software Library
PROJ is a generic coordinate transformation software that transforms geospatial coordinates from one coordinate reference system (CRS) to another. This includes cartographic projections as well as geodetic transformations. PROJ includes command line applications for easy conversion of coordinates from text files or directly from user input. In addition to the command line utilities PROJ also exposes an application programming interface, or API in short. The API lets developers use the functionality of PROJ in their own software without having to implement similar functionality themselves.
Example: geod, proj and man proj.
URL: https://proj.org/
Versions: 4.9.3
qtop: Monitor the State of Queueing Systems, Along with Related Information Relevant on HPC & Grid Clusters
qtop (pronounced queue-top) is a tool written in order to monitor the state of Queueing Systems, along with related information relevant on HPC & grid clusters. At present it supports PBS, SGE & OAR families. Please help to increase that list in the Python version of the tool, qtop.py!
Example: qtop and qtop -FGW.
URL: https://github.com/qtop/qtop
Warning: Only the most recent version of this software will be kept.
Versions: 0.9.20161222
R: The R Programming Language
The R programming language.
Example: R --version and Rscript --version.
URL: https://www.r-project.org/
Versions: 2.12.2, 2.13.0, 2.14.0, 2.15.0, 3.0.0, 3.1.0, 3.2.0, 3.3.0, 3.4.0, 3.5.0, 3.5.3, 3.6.0, 3.6.1, 3.6.2, 3.6.3, 4.0.0, 4.0.1, 4.0.2, 4.0.3, 4.0.4, 4.0.5, 4.1.0-gcc8, 4.1.1-gcc8, 4.1.2-gcc8
R Site Configuration: Tweaks to R for the Current Compute Environment
Sets R options and environment variables customized for the current compute environment. Notably, it configures R to install packages from local CRAN and Bioconductor mirrors without the need for internet access.
Example: In R, install.packages("ggplot2").
Versions: 0.1, 0.2
rclone: Rsync for Cloud Storage and More
Rclone is a command line program to sync files and directories to and from a large number of end points on the local file system, or remote file systems, and in the cloud.
Example: rclone --version, rclone --help, rclone config, and info rclone.
URL: https://rclone.org/, https://github.com/rclone/rclone
Warning: Only the most recent version of this software will be kept.
Versions: 1.53.3, 1.54.0, 1.56.1, 1.57.0
ripgrep - Recursively Searches Directories for a Regex Pattern
ripgrep is a line-oriented search tool that recursively searches your current directory for a regex pattern. By default, ripgrep will respect your .gitignore and automatically skip hidden files/directories and binary files. ripgrep is similar to other popular search tools like The Silver Searcher, ack and grep.
Example: rg --version and rg -i 'lorem ipsum'.
URL: https://github.com/BurntSushi/ripgrep
Warning: Only the most recent version of this software will be kept.
Versions: 12.1.1, 13.0.0
rstudio: RStudio Desktop
The RStudio Desktop is an integrated development environment (IDE) for R, a programming language for statistical computing and graphics.
Example: rstudio. If you get blank window, retry with QMLSCENE_DEVICE=softwarecontext rstudio.
URL: https://rstudio.com/products/rstudio/#rstudio-desktop, https://www.rstudio.com/products/rstudio/release-notes/, https://www.rstudio.com/products/rstudio/download/
Warning: This software works only on the development nodes and requires that X11 Forwarding or NX is enabled. For best performance, use SSH compression when using X11 Forwarding, i.e. ssh -X -C ....
Versions: 1.4.1103, 1.4.1717, 2021.09.0+351, 2021.09.1-372
salmon: Salmon Provides Fast and Bias-Aware Quantification of Transcript Expression
Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment.
Example: salmon --version.
URL: https://combine-lab.github.io/salmon/, https://github.com/COMBINE-lab/salmon
Versions: 1.3.0, 1.4.0, 1.5.2, 1.6.0
SAMtools: Tools (written in C using htslib) for Manipulating Next-Generation Sequencing Data
SAMtools is a suite of programs for interacting with high-throughput sequencing data.
Example: samtools --version.
URL: https://www.htslib.org/, https://github.com/samtools/samtools
Versions: 1.9, 1.10, 1.11, 1.13, 1.14
SCL Developer Toolset: GNU Compiler Collection, GNU Debugger, etc.
Enables the CentOS Software Collection (SCL) devtoolset-10 in the current environment. This is an alternative to calling source scl_source enable devtoolset-10, which is an approach that is not officially supported by RedHat/CentOS.
Example: gcc --version.
URL: https://www.softwarecollections.org/en/scls/rhscl/devtoolset-10/
Versions: 4, 6, 7, 8, 9, 10
scl-python (part of CBI-testing)
SCL Python: Python with Additional Utilities via CentOS Software Collections [DEPRECATED]
Enables the CentOS Software Collection (SCL) rh-python36 in the current environment. This is an alternative to calling source scl_source enable rh-python36, which is not officially supported by RedHat/CentOS.
Example: python --version and pip --version.
URL: https://www.softwarecollections.org/en/scls/rhscl/rh-python36/
Warning: This module is DEPRECATED and should no longer be used because Python SCLs are deprecated, which in turn is because Python 3 is now available directly by CentOS.
Versions: 3.3, 3.4, 3.6
Note: To use this module, call module load CBI CBI-testing first.
SCL Ruby: Ruby
Enables the CentOS Software Collection (SCL) rh-ruby30 in the current environment. This is an alternative to calling source scl_source enable rh-ruby30, which is an approach that is not of ficially supported by RedHat/CentOS.
Example: irb --help, ruby --help, ruby script.rb.
URL: https://www.softwarecollections.org/en/scls/rhscl/rh-ruby30/
Versions: 25, 26, 27, 30
ShellCheck: A Shell Script Static Analysis Tool
ShellCheck finds bugs in your shell scripts.
Example: shellcheck --version and shellcheck -x ~/.bashrc.
URL: https://www.shellcheck.net/, https://github.com/koalaman/shellcheck/
Warning: Only the most recent version of this software will be kept.
Versions: 0.7.1, 0.7.2, 0.8.0
SnpEff: Genetic Variant Annotation and Effect Prediction Toolbox
SnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of variants on genes (such as amino acid changes).
Example: snpEff -help, SnpSift -help, and ClinEff -help, which are aliases for java -jar $SNPEFF_HOME/snpEff/snpEff.jar -help, java -jar $SNPEFF_HOME/snpEff/SnpSift.jar -help, and java -jar $SNPEFF_HOME/clinEff/ClinEff.jar -help.
URL: http://snpeff.sourceforge.net/
Versions: 4.3t, 5.0c, 5.0e
SRA Toolkit: Tools and Libraries for Using Data in the INSDC Sequence Read Archives
The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.
Example: fastq-dump --help.
URL: https://ncbi.github.io/sra-tools/, https://github.com/ncbi/sra-tools
Warning: To work around a bug where fasterq-dump crashes the local machine, it has been tweaked such that it uses $TMPDIR rather than $PWD as the default temporary folder and it will only use two threads instead of six by default.
Versions: 2.10.0, 2.10.4, 2.10.5, 2.10.7, 2.10.8, 2.10.9, 2.11.0, 2.11.1, 2.11.2, 2.11.3
STAR: Spliced Transcripts Alignment to a Reference
STAR (Spliced Transcripts Alignment to a Reference) is a fast NGS read aligner for RNA-seq data.
Example: STAR --help.
URL: https://github.com/alexdobin/STAR
Versions: 2.7.0e, 2.7.0f, 2.7.1a, 2.7.2b, 2.7.3a, 2.7.5a, 2.7.5c, 2.7.7a, 2.7.9a
tmux: A Terminal Multiplexer
tmux is a terminal multiplexer. It lets you switch easily between several programs in one terminal, detach them (they keep running in the background) and reattach them to a different terminal. And do a lot more.
Example: tmux and man tmux.
URL: https://github.com/tmux/tmux/wiki
Warning: Only the most recent version of this software will be kept.
Versions: 2.8
TopHat: A Spliced Read Mapper for RNA-Seq
TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.
Example: tophat --version.
URL: https://ccb.jhu.edu/software/tophat/index.shtml, https://github.com/infphilo/tophat
Versions: 2.1.1
tree: List Content of Directories in a Tree-like Format
Tree is a recursive directory listing command that produces a depth indented listing of files, which is colorized ala dircolors if the LS_COLORS environment variable is set and output is to tty.
Example: tree --help.
URL: http://mama.indstate.edu/users/ice/tree/,
Warning: Only the most recent version of this software will be kept.
Versions: 1.8.0
up: The Ultimate Plumber
A tool for writing Linux pipes in a terminal-based UI interactively, with instant live preview of command results. Interactively and incrementally explore textual data in Linux using text-processing utils such as grep, sort, cut, paste, awk, wc, perl, etc. When done, press Ctrl-C to view final pipe commands, or Ctrl-X to save it to file.
Example: up --help, ls | up (exit with Ctrl-C).
URL: https://github.com/akavel/up
Warning: Only the most recent version of this software will be kept.
Versions: 0.4
VarScan: Variant Detection in Massively Parallel Sequencing Data
VarScan is a platform-independent mutation caller for targeted, exome, and whole-genome resequencing data generated on Illumina, SOLiD, Life/PGM, Roche/454, and similar instruments.
Example: varscan, which is an alias to java -jar $VARSCAN_HOME/VarScan.jar.
URL: https://dkoboldt.github.io/varscan/
Versions: 2.4.2
vcf-validator: Validation Suite for Variant Call Format (VCF) Files
Validator for the Variant Call Format (VCF) implemented using C++11. It includes all the checks from the vcftools suite, and some more that involve lexical, syntactic and semantic analysis of the VCF input.
Example: vcf_validator --help, vcf-debugulator --help, and vcf-assembly-checker --help.
URL: https://github.com/EBIvariation/vcf-validator
Versions: 0.9.2, 0.9.3, 0.9.4
VCFtools: Tools Written in Perl and C++ for Working with VCF Files
VCFtools is a program package designed for working with VCF files, such as those generated by the 1000 Genomes Project. The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files.
Example: vcftools --version.
URL: https://vcftools.github.io/
Versions: 0.1.16
wynton-tools (part of CBI-testing)
Wynton Tools: Tools for the Wynton HPC Environment
A command-line tool for common Wynton HPC queries.
Example: wynton --help.
URL: https://github.com/UCSF-HPC/wynton-tools/
Versions: latest
Note: To use this module, call module load CBI CBI-testing first.

Module Software Repository: Sali (120)

Maintained by: Ben Webb, Sali Lab Software Repository
Enable repository: module load Sali
AllosMod utility library
URL: https://github.com/salilab/allosmod-lib/
Amber11, for 64-bit
URL: http://ambermd.org/
Versions: 11
Anaconda Python distribution
URL: https://www.anaconda.com/
Basic Local Alignment Search Tool
URL: https://blast.ncbi.nlm.nih.gov
Versions: 2.2.26
Basic Local Alignment Search Tool
URL: https://blast.ncbi.nlm.nih.gov/
Versions: 2.2.25, 2.2.28, 2.12.0
The free peer-reviewed portable C++ source libraries
URL: https://www.boost.org/
Versions: 1.68.0, 1.73.0
Computational Geometry Algorithms Library
URL: https://www.cgal.org/
Versions: 4.12.1, 5.1
Cross-platform make system
URL: https://cmake.org/
Versions: 3.12.2, 3.18.3
Ligand binding site prediction from protein sequence and structure
URL: https://compbio.cs.princeton.edu/concavity/
Versions: 0.1
CryptoSite utility library
URL: https://github.com/salilab/cryptosite/
Versions: 6.0.37, 7.5.18, 8.0.61, 9.0.176, 10.0.130, 11.5.0
A language for writing Python extension modules
URL: https://cython.org/
Versions: 0.25.2, 0.29.14, 0.29.24
A documentation system for C/C++
URL: http://www.doxygen.org/index.html
Versions: 1.8.6, 1.8.15
Secondary structure assignment
URL: https://swift.cmbi.umcn.nl/gv/dssp/
Versions: 2.0.4, 2.2.1
A lightweight C++ template library for vector and matrix math
URL: http://eigen.tuxfamily.org
Versions: 3.3.5
Single Particle Analysis and Electron Micrograph Analysis
URL: https://blake.bcm.edu/emanwiki/EMAN2
Versions: 2.12, 2.2
Ursula's featuresketch script; run feature_sketch.sh then feature_sketch.py
Versions: 3.0
Protein pocket (cavity) detection algorithm
URL: https://github.com/Discngine/fpocket
Versions: 2.0
Various compilers (C, C++, Objective-C, Java, ...)
URL: https://gcc.gnu.org/
Versions: 5.1.1, 6.4.1, 7.3.1, 10.2.1
A PostScript interpreter and renderer
URL: https://www.ghostscript.com/
Versions: 8.70
A program for plotting mathematical expressions and data
URL: http://www.gnuplot.info/
Versions: 5.0.5, 5.4.2
A general purpose library and file format for storing scientific data
URL: https://support.hdfgroup.org/HDF5/
Versions: 1.8.14, 1.8.17, 1.10.1, 1.10.5, 1.10.6
Intel Fortran compiler
URL: http://software.intel.com/content/www/us/en/develop/tools/oneapi/components/fortran-compiler.html
Versions: 10.1.022
An X application for displaying and manipulating images
URL: https://imagemagick.org/
Integrative Modeling Platform (version 2.16.0, with only usage checks turned on)
URL: https://integrativemodeling.org/
Versions: last_ok_build, nightly, 2.7.0, 2.8.0, 2.9.0, 2.10.0, 2.10.1, 2.11.0, 2.11.1, 2.12.0, 2.13.0, 2.14.0, 2.15.0, 2.16.0
Integrative Modeling Platform (version 2.16.0, fast build)
URL: https://integrativemodeling.org/
Versions: last_ok_build, nightly, 2.7.0, 2.8.0, 2.9.0, 2.10.0, 2.10.1, 2.11.0, 2.11.1, 2.12.0, 2.13.0, 2.14.0, 2.15.0, 2.16.0
Integrative T-cell epitope prediction
URL: https://github.com/salilab/itcell-lib
Code from the SAMBA group at TAU
URL: https://integrativemodeling.org/libTAU.html
Versions: 1.0.1
Dusan Turk's MAIN program
URL: https://stef.ijs.si/
Versions: 2013
Language for technical computing
URL: https://www.mathworks.com/products/matlab.html
MiST - Mass spectrometry interaction STatistics
URL: https://github.com/salilab/mist/
MODELLER comparative modeling
URL: https://salilab.org/modeller/
Versions: 9.10, 9.11, 9.12, 9.13, 9.14, 9.15, 9.16, 9.17, 9.18, 9.19, 9.20, 9.21, 9.22, 9.23, 9.24, 9.25, 10.0, 10.1, 10.2, SVN
ModPipe (sets $MODPIPE; only works on the cluster)
URL: https://salilab.org/modpipe/
Versions: 2.0.1, 2.0.2, 2.1.0, 2.1.1, 2.1.2, 2.1.3, 2.2.0, 2.3.0
Multiple alignment program for protein sequences
URL: http://www.drive5.com/muscle/
Versions: 3.8.31
A small build system with a focus on speed
URL: https://ninja-build.org/
Versions: 1.6.0, 1.8.2
Collection of algorithms for computer vision
URL: https://opencv.org/
Versions: 3.4.3, 4.3.0
OpenEye products (work on any 64-bit node)
URL: https://www.eyesopen.com/
Versions: 2012
Molecular Docking Based on Shape Complementarity Principles
URL: https://bioinfo3d.cs.tau.ac.il/PatchDock/
Versions: 1.3
Peptide Classification using Sequence and Structure
URL: https://github.com/salilab/pcss
Python-based Hierarchical ENvironment for Integrated Xtallography
URL: https://www.phenix-online.org/
ProFit, a protein least squares fitting program
URL: http://www.bioinf.org.uk/software/profit/
Versions: 3.1
Accurate protein secondary structure prediction
URL: http://bioinf.cs.ucl.ac.uk/psipred/
Versions: 4.0
Versions: 1.68, 1.69, 1.70
Versions: 1.2.0, 1.2.1
Versions: 0.10.0
Versions: 1.5, 2.6.1
Versions: 4.0.11, 4.2.1
Versions: 3.2.3
Versions: 2.6.0, 2.7.0, 2.7.1
Versions: 0.11
Versions: 1.5
Versions: 2.0.0, 2.0.2, 2.1.2
Versions: 2.6
Versions: 0.5.6, 0.6.2
Versions: 1.11
Versions: 1.3.7
Versions: 2.6.2, 2.6.4
Versions: 1.12.0, 1.13.0, 1.14.1
Versions: 0.19.2, 0.20.2, 0.22.0
Versions: 1.2.2
Versions: 2.3.0, 2.5.0
Versions: 2.3.6
Versions: 2.1.10
Versions: 4.1.git48ab119
Versions: 2016.10
Versions: 0.12, 0.18.1, 0.19.1
Versions: 0.18.1, 0.19.0, 1.0.0
Versions: 1.10.0
Versions: 3.3.0, 3.4.2, 3.5.2
Classes Without Boilerplate
URL: https://www.attrs.org/
Versions: 20.3.0, 21.2.0
Python tools for computational molecular biology
URL: https://biopython.org/
Versions: 1.75
Collection of fast NumPy array functions written in Cython
URL: https://github.com/pydata/bottleneck
Versions: 1.3.1
Composable style cycles
URL: https://github.com/matplotlib/cycler
Versions: 0.10.0
Powerful extensions to the standard datetime module
URL: https://dateutil.readthedocs.io/en/stable/
Versions: 2.8.1
Module to simplify usage of decorators
URL: https://github.com/micheles/decorator
Versions: 4.4.1
The modular source code checker: pep8 pyflakes and co
URL: https://gitlab.com/pycqa/flake8
Versions: 3.8.4
Clean single-source support for Python 3 and 2
URL: https://python-future.org/
Versions: 0.18.2
Python interface to the Hierarchical Data Format library
URL: https://www.h5py.org/
Versions: 2.10.0
Python package for handling IHM mmCIF files
URL: https://github.com/ihmwg/python-ihm
Versions: 0.15
Read metadata from Python packages
URL: https://github.com/python/importlib_metadata
Versions: 3.3.0
Brain-dead simple parsing of ini files
URL: https://github.com/RonnyPfannschmidt/iniconfig
Versions: 1.1.1
Lightweight pipelining: using Python functions as pipeline jobs
URL: https://joblib.readthedocs.io/en/latest/
Versions: 0.14.0, 0.17.0
A fast implementation of the Cassowary constraint solver
URL: https://github.com/nucleic/kiwi
Versions: 1.1.0
Python 2D plotting library
URL: https://matplotlib.org/
Versions: 3.1.2
McCabe checker, plugin for flake8
URL: https://github.com/pycqa/mccabe
Versions: 0.6.1
Modular toolkit for Data Processing
URL: http://mdp-toolkit.sourceforge.net/
Versions: 3.6
A Python MessagePack (de)serializer
URL: https://msgpack.org/
Versions: 0.6.2
Creates and Manipulates Graphs and Networks
URL: https://networkx.github.io/
Versions: 2.4
Discovery-based unittest extension for Python3
URL: https://nose.readthedocs.io/en/latest/
Versions: 1.3.7
Fast numerical array expression evaluator for Python and NumPy
URL: https://github.com/pydata/numexpr
Versions: 2.7.0
A fast multidimensional array facility for Python
URL: https://numpy.org/
Versions: 1.17.4, 1.19.5
Core utilities for Python packages
URL: https://github.com/pypa/packaging
Versions: 20.8
Python Data Analysis Library
URL: https://pandas.pydata.org/
Versions: 0.25.3
A Python interface to the pkg-config command line tool
URL: https://github.com/matze/pkgconfig
Versions: 1.5.1
A minimalist production ready plugin system
URL: https://github.com/pytest-dev/pluggy
Versions: 0.13.1
Protocol Buffers - Google's data interchange format
URL: https://developers.google.com/protocol-buffers/
Versions: 3.11.2
Cross-python path, ini-parsing, io, code, log facilities
URL: https://py.readthedocs.io/en/latest/
Versions: 1.10.0
Python style guide checker
URL: https://pycodestyle.readthedocs.io/
Versions: 2.6.0
Passive checker of Python programs
URL: https://github.com/PyCQA/pyflakes
Versions: 2.2.0
An object-oriented approach to text processing
URL: https://github.com/pyparsing/pyparsing/
Versions: 2.4.5
Way of performing RMSD calculations of large sets of structures
URL: https://github.com/salilab/pyRMSD
Versions: 4.1.gita558b8a
Simple powerful testing with Python
URL: https://docs.pytest.org/en/latest/
Versions: 6.2.1
pytest plugin to check FLAKE8 requirements
URL: https://github.com/tholo/pytest-flake8
Versions: 1.0.7
World Timezone Definitions for Python
URL: https://pythonhosted.org/pytz/
Versions: 2019.3
A set of python modules for machine learning and data mining
URL: https://scikit-learn.org/stable/index.html
Versions: 0.21.3
Scipy: Scientific Tools for Python
URL: https://www.scipy.org/
Versions: 1.3.2
Python 2 and 3 compatibility utilities
URL: https://github.com/benjaminp/six
Versions: 1.13.0
Hierarchical datasets in Python
URL: http://www.pytables.org/
Versions: 3.6.1
Python Library for Tom's Obvious, Minimal Language
URL: https://github.com/uiri/toml
Versions: 0.10.2
Backported and Experimental Type Hints for Python 3.5+
URL: https://pypi.org/project/typing-extensions/
Backport of pathlib-compatible object wrapper for zip files
URL: https://github.com/jaraco/zipp
Versions: 3.4.0
Electron cryo-microscopy refinement
URL: https://github.com/3dem/relion
Versions: 1.4, 2.0.6, 3.0.git9a02562
Computational modeling and analysis of protein structures
URL: https://www.rosettacommons.org/
Versions: 3.5, 3.10
Makes available libraries usually only present on the Sali interactive nodes
Protein side-chain conformation prediction program
URL: http://dunbrack.fccc.edu/SCWRL4.php
Versions: 4.0
Support Vector Machine
URL: http://svmlight.joachims.org/
Versions: 6.0.2
Connects C/C++/Objective C to some high-level programming languages
URL: http://www.swig.org/
Versions: 3.0.12, 4.0.2
High-throughput search and clustering tool
URL: http://www.drive5.com/usearch/
Versions: 4.0.43, 10.0.240
Command line interface (web_service.py) to most lab web services
URL: https://github.com/salilab/saliweb
Rigid body docking
URL: http://zdock.umassmed.edu/
Versions: 3.0.2

The above information was automatically generated on 2022-01-04 20:47:42 from querying module avail and module spider.