Software Repositories and their Software

Below is a list of all available Software Repositories, which each provides a set of software tools that can be accessed using module load <repos> and then module load <software>. For further instructions on how to use software modules, see the page on Software Modules.

These software modules are available from different module repositories, each providing several modules (more details below). The available repositories are:

repository description
CBC
 Module Repository by Computational Biology and Informatics (CBI - formerly CBC)
Repository of modules shared by Computational Biology and Informatics (http://cbi.ucsf.edu/) which was named Computational Biology Core (CBC) until 2017. When loading this module, you will get access to a large number of software modules. When unloading the module, any software modules from this CBC repository still loaded when you unload this repository module, will remain in your list of loaded modules but will be inactivate (i.e. behave as they never were loaded) until you reload this repository module again. Example: module load CBC and then module avail.
URL: http://cbi.ucsf.edu/
Personal
 Modules in ~/modulefiles/
Personal modules in ~/modulefiles/ (created if missing). For instance, module definition file ~/modulefiles/foo/1.0.lua provides module foo/1.0, which can be loaded using module load foo/1.0. For example of module files, see the many modules under /home/shared/cbc/apps/modulefiles/CBC/.


To get access to one or more of these module repositories and see what modules they provide (see below), load them as regular modules, e.g.

module load CBC
module avail

Technical details: Loading a module repository will append its folder to the $MODULEPATH. Unloading it will undo any changes. For instance, module load CBC appends $MODULEPATH_ROOT/CBC to your $MODULEPATH.

Module Repository ‘CBC’

Maintained by: Computational Biology and Informatics (CBI - formerly CBC)

module & versions description
ack
2.22 		ack: A Tool Like Grep, Optimized for Programmers
Designed for programmers with large heterogeneous trees of source code, 'ack' is written purely in portable Perl 5 and takes advantage of the power of Perl's regular expressions. Examples: ack --version and ack --man
URL: https://beyondgrep.com/, https://beyondgrep.com/feature-comparison/
anaconda
 [DEPRECATED] Anaconda Package Manager w/ CBC-shared installations
Open Data Science Platform powered by Python
URL: https://www.continuum.io/anaconda-overview
anaconda-python
2.7.13 		[DEPRECATED] Anaconda: The Python Programming Language
The Python programming language (by Anaconda)
URL: https://www.python.org/
asciidoc
8.6.8 		AsciiDoc: Text Based Document Generation
AsciiDoc is a text document format for writing notes, documentation, articles, books, ebooks, slideshows, web pages, man pages and blogs. AsciiDoc files can be translated to many formats including HTML, PDF, EPUB, man page. Examples: asciidoc.py --version
URL: http://asciidoc.org/
asciigenome
1.11.0, 1.12.0 		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
autoconf
2.69 		autoconf: Tool for Producing Configure Scripts for Building, Installing and Packaging Software
Autoconf is an extensible package of M4 macros that produce shell scripts to automatically configure software source code packages. These scripts can adapt the packages to many kinds of UNIX-like systems without manual user intervention. Autoconf creates a configuration script for a package from a template file that lists the operating system features that the package can use, in the form of M4 macro calls. Example: autoconf --version.
URL: https://www.gnu.org/software/autoconf/autoconf.html
automake
1.15 		automake: Tool for Automatically Generating GNU-compliant Makefile.in Files
Automake is a tool for automatically generating Makefile.in files compliant with the GNU Coding Standards. Example: automake --version.
URL: https://www.gnu.org/software/automake/
bamutil
1.0.14 		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: http://genome.sph.umich.edu/wiki/BamUtil
bat
0.8.0, 0.9.0 		bat - A cat(1) clone with syntax highlighting and Git integration
A cat(1) clone with syntax highlighting and Git integration. Examples: bat README.md, bat scripts/*.sh, and bat src/*.c
URL: https://github.com/sharkdp/bat
bcftools
1.2, 1.3.1, 1.4, 1.6, 1.7 		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://samtools.github.io/bcftools/bcftools.html
bcl2fastq
2.17.1, 2.20.0 		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
bedops
1.2.2c, 2.4.30 		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/
bedtools2
2.13.4, 2.15.0, 2.16.2, 2.26.0, 2.27.1 		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.
URL: https://github.com/arq5x/bedtools2/
binutils
2.29 		binutils: GNU Binutils
The GNU Binutils are a collection of binary tools. The main ones are: ld (the GNU linker) and as (the GNU assembler). Example: ld -v.
URL: https://www.gnu.org/software/binutils/
blast
2.2.26, 2.7.1 		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
blat
34, 36 		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: http://genome.ucsc.edu/goldenPath/help/blatSpec.html
bowtie
1.2.0, 1.2.2 		Bowtie: A Fast and Sensitive Gapped Read Aligner
Bowtie is an ultrafast, memory-efficient short read aligner. NOTE: This is Bowtie v1 - not v2. Example: bowtie --version
URL: http://bowtie-bio.sourceforge.net/index.shtml
bowtie2
2.0.0-beta6, 2.1.0, 2.2.6, 2.2.9, 2.3.3.1, 2.3.4.1 		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
bwa
0.5.10, 0.6.1, 0.7.5a, 0.7.12, 0.7.17 		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/
byobu
5.124 		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
bzip2
1.0.6 		bzip2: High-quality, Open-source Data Compressor
bzip2 is a free and open-source file compression program that uses the Burrows–Wheeler algorithm. It only compresses single files and is not a file archiver. It typically compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical compressors), whilst being around twice as fast at compression and six times faster at decompression. Example: bzip2 --help and bzcat file.txt.bz2.
URL: http://www.bzip.org/
cbc-bin
0.1.0, 0.1.1, 0.1.2, 0.2.0 		CBC-shared Scripts and Binaries
Utility scripts and binaries shared by UCSF CBI (formerly CBC).
URL: http://cbi.ucsf.edu/
cbc-devel
0.1.0, 0.1.1, 0.1.2 		CBC-shared Developer's Environment
Setup for building and installing software inline with the CBI-shared setup (formerly CBC-shared setup).
URL: http://cbi.ucsf.edu/
cbc-shared
0.1.0, 0.1.1, 0.1.2, 0.1.3, 0.1.4, 0.1.5, 0.2.0, 0.2.1, 0.2.2, 0.2.3, 0.2.4, 0.2.5, 0.3.0, 0.3.1 		CBC-shared Software: Default Set
When loaded, this module loads the default set of CBC-shared software. See module show cbc-shared for details.
URL: https://ucsf-ti.github.io/tipcc-web/software/software-repositories.html
cctools
6.2.4 		cctools: Cooperative Computing Tools contains Parrot, Chirp, Makeflow, Work Queue, SAND, and other software.
The Cooperative Computing Tools (cctools) contains Parrot, Chirp, Makeflow, Work Queue, SAND, and other software. Example: parrot_run --version, parrot_run more /http/cbi.ucsf.edu, and parrot_run emacs /chirp/server.nd.edu/file.txt.
URL: http://ccl.cse.nd.edu/software/
cellranger
1.3.1, 2.1.0, 3.0.0, 3.0.2 		Cell Ranger: 10x Genomics Pipeline for Single-Cell Data Analysis
Cell Ranger is a set of analysis pipelines that perform sample demultiplexing, barcode processing, and single cell 3' gene counting. Also includes the ability to process data from Feature Barcoding technology. Reference files are available in the folder given by environment variable CELLRANGER_REFERENCES. Example: cellranger and ls $CELLRANGER_REFERENCES/
URL: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger
cmake
3.10.2 		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/
control-freec
2.5, 7.2-3 		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/
coreutils
8.6, 8.31 		coreutils: GNU Core Utilities
The GNU Core Utilities or coreutils is a package of GNU software containing reimplementations for many of the basic tools, such as cat, ls, and rm, used on Unix-like operating systems. Example: sort --version and man sort.
URL: https://www.gnu.org/software/coreutils/
cufflinks
1.0.3, 1.3.0, 2.2.1 		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/
curl
7.58.0 		curl: Command Line Tool and Library for Transferring Data with URLs
cURL is a computer software project providing a library and command-line tool for transferring data using various protocols. The cURL project produces two products, libcurl and cURL. It was first released in 1997. The name originally stood for "see URL". Example: curl --help.
URL: https://curl.haxx.se/, https://github.com/curl/curl
egademoclient
2.2.2_0 		EgaDemoClient: The European Genome-phenome Archive (EGA) Download Client
The EgaDemoClient application can be used as an interactive shell or direct command line client. Both methods provide similar functionality, but you may only use the FUSE layer option from the command line. Example: EgaDemoClient --help alias for java -jar $EGADEMOCLIENT_HOME/EgaDemoClient.jar --help.
URL: https://www.ebi.ac.uk/ega/about/your_EGA_account/download_streaming_client
emacs
24.5, 25.3 		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/
fastqc
0.10.1, 0.11.2 		FastQC: A Quality Control Tool for High Throughput Sequence Data
A quality control tool for high throughput sequence data. Example: fastqc --version.
URL: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
fiji
2.0.0-rc-54 		Fiji: an Image Processing Package
Fiji is a "batteries-included" distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis. Example: ImageJ-linux64 --help.
URL: https://imagej.net/Fiji/Downloads
gatk
1.6.2, 3.0.0, 3.4.46, 3.6.0, 3.7.0, 3.8.0, 4.0.0.0, 4.0.2.1 		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/
gawk
4.2.1 		gawk: Effective AWK Programming (GNU awk)
AWK is a programming language designed for text processing and typically used as a data extraction and reporting tool. Example: gawk --help.
URL: https://www.gnu.org/software/gawk/
gcc
4.8.1, 4.8.4, 5.1.0, 4.9.2 		GCC, the GNU Compiler Collection
The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Ada, and Go, as well as libraries for these languages (libstdc++,...). GCC was originally written as the compiler for the GNU operating system. Example: gcc --version.
URL: https://gcc.gnu.org/
gcta
1.91.2beta, 1.26.0 		GCTA: Genome-wide Complex Trait Analysis
A tool for Genome-wide Complex Trait Analysis (GCTA). Example: gcta64.
URL: http://cnsgenomics.com/software/gcta/
gdal
3.0.0 		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
gdbm
1.18.1 		GDBM: Library of Database Function (GNU dbm)
GNU dbm (or GDBM, for short) is a library of database functions that use extensible hashing and work similar to the standard UNIX dbm. These routines are provided to a programmer needing to create and manipulate a hashed database.. Example: gdbmtool --version
URL: https://www.gnu.org.ua/software/gdbm/
gdc-client
1.0.1 		GDC Data Transfer Tool: NCI Genome Data Commons Data Transfer Tools
The GDC Data Transfer Tool Client provides a command-line interface supporting both GDC data downloads and submissions. Example: gdc-client --version.
URL: https://gdc.cancer.gov/access-data/gdc-data-transfer-tool
genetorrent
3.0.2, 3.8.5a-94 		GeneTorrent: Tools for Accessing Data in the Cancer Genomics Hub (CGHub)
GeneTorrent is a set of executables for accessing data in the Cancer Genomics Hub (CGHub), a secure repository for storing, cataloging, and accessing cancer genome sequences, alignments, and mutation information from the Cancer Genome Atlas (TCGA) consortium and related projects. Example: cgquery --help.
URL: https://hpc.nih.gov/apps/GeneTorrent.html
geos
3.7.2 		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
git
2.1.1, 2.1.3, 2.16.1 		Git: Distributed Version Control System
Git is a free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency. Example: git --version.
URL: https://git-scm.com/
git-flow
0.4.2, 1.11.0 		git-flow: Git Extension Git Flow
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
git-lfs
2.3.4 		Git LFS: An Open Source Git Extension for Versioning Large Files
Git Large File Storage (LFS) replaces large files such as audio samples, videos, datasets, and graphics with text pointers inside Git, while storing the file contents on a remote server like GitHub.com or GitHub Enterprise. Example: git lfs.
URL: https://git-lfs.github.com/
go
1.8.3, 1.9.2 		Go: The Go Programming Language
Go is a cross-platform open-source programming language that makes it easy to build simple, reliable, and efficient software. Example: go version
URL: https://golang.org/
hisat2
2.1.0 		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://ccb.jhu.edu/software/hisat2/
htop
1.0.3, 2.0.2, 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: http://hisham.hm/htop/
htseq
0.5.4p3, 0.6.1 		[DEPRECATED] HTSeq: Analysing high-throughput sequencing data with Python
HTSeq is a Python package that provides infrastructure to process data from high-throughput sequencing assays. Example: htseq-count and htseq-qa.
This module is deprecated: Instead, install this Python package using pip install HTSeq following the instruction at https://ucsf-ti.github.io/tipcc-web/howto/python.html
URL: http://www-huber.embl.de/users/anders/HTSeq/
htslib
1.3.2, 1.6, 1.7 		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: http://www.htslib.org/
igv
2.1.2, 2.3.31, 2.3.68, 2.3.92, 2.4.0 		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.
URL: https://software.broadinstitute.org/software/igv/
igvtools
2.3.68, 2.3.91, 2.3.98 		IGVTools: Tools for Pre-processing HT-Seq Data Files
The igvtools utility provides a set of tools for pre-processing data files. Example: igvtools help.
URL: https://software.broadinstitute.org/software/igv/igvtools
jags
4.3.0 		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/
jdk
1.6.0, 1.7.0, 1.8.0, 6, 7, 8 		JDK: Java Development Kit
The Java programming language. Examples: java -version and javac -version.
URL: https://www.java.com/
json-c
0.13.1 		json-c: A JSON Implementation in C
JSON-C implements a reference counting object model that allows you to easily construct JSON objects in C, output them as JSON formatted strings and parse JSON formatted strings back into the C representation of JSON objects. It aims to conform to RFC 7159.
URL: https://github.com/json-c/json-c
kallisto
0.44.0 		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
lg3
2018-08-28, 2018-09-17, 2018-09-19, 2018-09-28, 2018-10-08, 2018-10-11, 2018-10-17, 2018-10-27, 2018-11-12, 2018-12-20, 2018-12-27, 2019-03-23, 2019-07-22 		LG3 Pipeline: The UCSF Costello Lab's LG3 Pipeline
This is the LG3 Pipeline developed by the UCSF Costello Lab.
URL: https://github.com/UCSF-Costello-Lab/LG3_Pipeline
libevent
2.1.8 		libevent: An Event Notification Library
The libevent API provides a mechanism to execute a callback function when a specific event occurs on a file descriptor or after a timeout has been reached. Furthermore, libevent also support callbacks due to signals or regular timeouts. Example: event_rpcgen.py.
URL: http://libevent.org/, https://github.com/libevent/libevent
libpng
1.6.34 		libpng: The Official Portable Network Graphics Reference Library
libpng is the official PNG reference library. It supports almost all PNG features, is extensible, and has been extensively tested for over 22 years. Example: libpng-config --version.
URL: http://www.libpng.org/pub/png/libpng.html
links
2.14 		Links: A Lynx-like Alternative Character Mode WWW Browser
Links runs in text mode (mouse optional) on UN*X console, ssh/telnet virtual terminal, vt100 terminal, xterm, and virtually any other text terminal. Mouse is supported for GPM, xterm, and OS/2. Links supports colors on terminal. Example: links https://www.google.com/.
URL: http://links.twibright.com/features.php
lua
5.1.4, 5.3.3, 5.3.4 		Lua: The Lua Programming Language
The Lua programming language. Example: lua -v.
URL: https://www.lua.org/
luarocks
2.4.2, 2.4.4 		LuaRocks: The Lua Package Manager
LuaRocks is the package manager for Lua modules. Example: luarocks --help and luarocks install posix.
URL: https://luarocks.org/
matlab
7.11.0.584, 7.14.0.739 		MATLAB: The MATLAB Programming Language
MATLAB (MATrix LABoratory) is a multi-paradigm numerical computing environment. Example: matlab -nosplash -nodisplay -r 'quit'.
URL: https://www.mathworks.com/products/matlab.html
mpack
1.6 		mpack: Tools for Encoding/Decoding MIME Messages
Mpack and munpack are utilities for encoding and decoding (respectively) binary files in MIME (Multipurpose Internet Mail Extensions) format mail messages. For compatibility with older forms of transferring binary files, the munpack program can also decode messages in split-uuencoded format. Example: munpack -ft < one-msg.mbox.
URL: https://packages.debian.org/sid/mail/mpack
mysql
5.1.73 		MySQL: An Open-source Relational Database Management System (RDBMS)
MySQL is an open-source relational database management system (RDBMS). Example: mysql --version
URL: https://www.mysql.com/
netcdf
4.3.0 		NetCDF: Network Common Data Form
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. Example: nc-config --version and ncdump --version.
URL: https://www.unidata.ucar.edu/software/netcdf/, https://github.com/Unidata/netcdf-c
nextflow
0.26.0.4715 		Nextflow: Data-driven Computational Pipelines
Nextflow enables scalable and reproducible scientific workflows using software containers. It allows the adaptation of pipelines written in the most common scripting languages. Its fluent DSL simplifies the implementation and the deployment of complex parallel and reactive workflows on clouds and clusters. Example: nextflow -version.
URL: https://www.nextflow.io/
openssl
1.1.1a 		OpenSSL: Cryptography and SSL/TLS Toolkit
OpenSSL is a robust, commercial-grade, and full-featured toolkit for the Transport Layer Security (TLS) and Secure Sockets Layer (SSL) protocols. It is also a general-purpose cryptography library. Example: openssl
URL: https://www.openssl.org/
pandoc
1.19.2-0, 2.0.3, 2.1.2 		Pandoc: A Universal Document Converter
Pandoc is a Haskell library for converting from one markup format to another, and a command-line tool that uses this library. Example: pandoc --version.
URL: http://pandoc.org/
pcre
8.35, 8.36, 8.41, 8.42 		PCRE: Perl Compatible Regular Expressions
The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5. PCRE has its own native API, as well as a set of wrapper functions that correspond to the POSIX regular expression API. Example: pcregrep --help and pcre-config --version.
URL: http://pcre.org/
picard
1.39, 1.51, 1.64, 1.67, 2.17.1 		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: java -jar $PICARD -h
URL: http://broadinstitute.github.io/picard/
pindel
0.2.5b8 		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
plink
1.90b5.2, 1.07 		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: http://zzz.bwh.harvard.edu/plink/index.shtml
plink2
2.00a2LM 		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/
proj
4.9.3, 6.1.0 		PROJ - Cartographic Projections and Coordinate Transformations Library
PROJ is a generic coordinate transformation software, that transforms coordinates from one coordinate reference system (CRS) to another. This includes cartographic projections as well as geodetic transformations. Examples: geod and proj.
URL: https://proj.org/, https://github.com/OSGeo/PROJ
python
2.6.5, 2.7.3, 2.7.4, 2.7.10, 2.7.15, 2.7.9 		Python: The Python Programming Language
Python is a programming language that lets you work quickly and integrate systems more effectively. Example: python --version as well as virtualenv myproject, . myproject/bin/activate, and pip install cnvkit.
URL: https://www.python.org/
python3
3.6.5 		Python 3: The Python Programming Language (WARNING: Does NOT pass all tests!)
Python is a programming language that lets you work quickly and integrate systems more effectively. Example: python3 --version as well as virtualenv myproject, . myproject/bin/activate, and pip install cnvkit. WARNING: The python3/3.6.5 module is fragile - the build does NOT pass all tests. Use at your own risk! See https://github.com/UCSF-TI/TIPCC/issues/259 for details.
URL: https://www.python.org/
qtop
0.9.20161222 		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! Examples: qtop and qtop -FGW.
URL: https://github.com/qtop/qtop
r
2.7.0, 2.8.0, 2.10.0, 2.11.0, 2.11.1, 2.12.0, 2.12.2, 2.13.0, 2.13.1, 2.13.2, 2.14.0, 2.15.0, 2.15.1, 2.15.2, 2.15.3, 3.0.0, 3.0.1, 3.0.2, 3.0.3, 3.1.0, 3.1.1, 3.1.2, 3.1.3, 3.2.0, 3.2.1, 3.2.2, 3.2.3, 3.2.4, 3.2.5, 3.3.0, 3.3.1, 3.3.2, 3.3.3, 3.4.0, 3.4.1, 3.4.2, 3.4.3, 3.4.4, 3.5.0, 3.5.1, 3.5.2, 3.5.3, 3.6.0, 3.6.1 		R: The R Programming Language
The R programming language. Example: R --version and Rscript --version.
URL: https://www.r-project.org/
ruby
2.2.0p0, 2.5.3 		Ruby: The Ruby Programming Language
Ruby is a dynamic, reflective, object-oriented, general-purpose programming language. It was designed and developed in the mid-1990s by Yukihiro 'Matz' Matsumoto in Japan. Example: ruby --version and irb
URL: https://www.ruby-lang.org/en/
s3cmd
1.5.0-alpha3 		Amazon S3 Tools: Command Line S3 Client Software and S3 Backup
ommand Line S3 Client and Backup for Linux and Mac. Example: s3cmd --help.
URL: http://s3tools.org/s3cmd
samtools
0.1.12a, 0.1.17, 0.1.18, 0.1.19-patched, 0.1.19, 1.2, 1.3.1, 1.6, 1.7 		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: http://www.htslib.org/
shellcheck
0.4.6, 0.4.7 		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/
snpeff
2.0.2 		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: java -jar $SNPEFF -help.
URL: http://snpeff.sourceforge.net/
snvmix2
0.11.8-r3 		SNVMix2: Detecting Single Nucleotide Variants from Next Generation Sequencing Data
SNVMix is designed to detect single nucleotide variants from next generation sequencing data. SNVMix is a post-alignment tool. Example: SNVMix2 -h.
URL: http://shahlab.ca/projects/snvmix/
sqlite
3.28.0 		SQLite - A Relational Database Management System (RDBMS) Contained in a C Library
SQLite is a C-language library that implements a small, fast, self-contained, high-reliability, full-featured, SQL database engine. SQLite is the most used database engine in the world. SQLite is built into all mobile phones and most computers and comes bundled inside countless other applications that people use every day. Examples: sqlite3 --version.
URL: https://www.sqlite.org/
sratoolkit
2.3.4-2, 2.4.1, 2.5.7, 2.8.2-1 		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: http://ncbi.github.io/sra-tools/
star
2.5.3a, 2.5.4b 		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
tmux
2.6 		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
tophat
1.3.0, 1.3.1, 1.4.0, 2.0.3, 2.0.9, 2.0.10, 2.1.0, 2.1.1 		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
tree
1.7.0 		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/
udocker
1.0.0, 1.1.0 		udocker: Execute Simple Docker Containers Without Root Privileges
A basic user tool to execute simple docker containers in user space without requiring root privileges. Enables basic download and execution of docker containers by non-privileged users in Linux systems where docker is not available. It can be used to access and execute the content of docker containers in Linux batch systems and interactive clusters that are managed by other entities such as grid infrastructures or externally managed batch or interactive systems. The INDIGO udocker does not require any type of privileges nor the deployment of services by system administrators. It can be downloaded and executed entirely by the end user. udocker is a wrapper around several tools to mimic a subset of the docker capabilities including pulling images and running them with minimal functionality. Example: udocker help.
URL: https://github.com/indigo-dc/udocker
udunits
2.2.26 		UDUNITS-2: API and Utility for Arithmetic Manipulation of Units of Physical Quantities
The UDUNITS package supports units of physical quantities. Its C library (libudunits2) provides for arithmetic manipulation of units and for conversion of numeric values between compatible units. The package contains an extensive unit database, which is in XML format and user-extendable. The package also contains a command-line utility (udunits2) for investigating units and converting values. Example: udunits2 -h
URL: https://www.unidata.ucar.edu/software/udunits/
valgrind
3.10.0, 3.8.1 		Valgrind: A Programming Tool for Memory Debugging, Memory Leak Detection, and Profiling
Valgrind is a programming tool for memory debugging, memory leak detection, and profiling. Example: valgrind --help.
URL: http://www.valgrind.org/
varscan
2.2.3, 2.3.9, 2.4.2 		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: java -jar $VARSCAN.
URL: https://dkoboldt.github.io/varscan/
vcf-validator
0.6 		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.
URL: https://github.com/EBIvariation/vcf-validator
vcftools
0.1.13, 0.1.15 		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/
wordspy
1.5 		WordSpy: A Steganalysis-based, Genome Scale Motif Finding Method
A steganalysis-based approach to comprehensive identification and characterization of functional regulatory elements. Example: wordspy.
URL: http://www.cs.wustl.edu/~zhang/
xmlto
0.0.28 		xmlto: Converts an XML File into a Specified Format
'xmlto' converts an XML file (DocBook or XSL-FO) into a specified format (PS, PDF, HTML, man, ASCII, XSL-FO, etc.). It applies an appropriate XSL-T stylesheet and then performs whatever post-processing is necessary. Examples: xmlto --version
URL: https://directory.fsf.org/wiki/Xmlto
xz
5.2.3 		XZ Utils: General-purpose Data Compression Software
XZ Utils is free general-purpose data compression software with a high compression ratio. XZ Utils were written for POSIX-like systems, but also work on some not-so-POSIX systems. XZ Utils are the successor to LZMA Utils. The core of the XZ Utils compression code is based on LZMA SDK, but it has been modified quite a lot to be suitable for XZ Utils. The primary compression algorithm is currently LZMA2, which is used inside the .xz container format. With typical files, XZ Utils create 30 % smaller output than gzip and 15 % smaller output than bzip2. Example: xz --version and xzcat file.txt.xz.
URL: https://tukaani.org/xz/
zeromq
4.2.5 		ZeroMQ: A High-Performance Asynchronous Messaging Library
ZeroMQ is a high-performance asynchronous messaging library, aimed at use in distributed or concurrent applications. It provides a message queue, but unlike message-oriented middleware, a ZeroMQ system can run without a dedicated message broker. The library's API is designed to resemble that of Berkeley sockets. Example: curve_keygen
URL: https://zeromq.org/
zlib
1.2.11 		zlib: A Massively Spiffy Yet Delicately Unobtrusive Compression Library
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. The zlib data format is itself portable across platforms. Not related to the Linux zlibc compressing file-I/O library. Example: No executable; only a library.
URL: https://www.zlib.net/




The above information was automatically generated on 2020-01-15 16:49:55.