BioGrids Quick Start

( Last updated Dec 27, 2024 )

Download the BioGrids Installation Manager, GUI or CLI.

Start the BioGrids environment:

$ source /programs/biogrids.shrc

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                          **Software Support by BioGrids**

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 Developed with support from HMS Tools-and-Technologies fund.

 If your use of BioGrids compiled software was an important element in 

 your publication, please include the following statement in your work:

 "Software used in the project was installed and configured by BioGrids 

 (cite: eLife 2013;2:e01456, Collaboration gets the most out of software.)"

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This BioGrids installation last updated: 2025-02-13

 Please submit bug reports and help requests to:  help@biogrids.org.

           **For additional information visit https://biogrids.org/wiki**

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List available titles:

Linux:

$ cat /programs/x86_64-linux/biogrids_x86_64-linux

Mac:

$ cat /programs//i386-mac/biogrids_i386-mac

Get version and override info:

$ biogrids-info -l samtools
  Version information for: /programs/x86_64-linux/samtools

Default version:                    1.21
In-use version:                     1.21

Installed versions:                 1.21 1.20 1.19.2 1.18 1.17 1.16.1 1.16 1.15.1 1.15 1.14 1.13 1.12 1.10 1.9 1.8 1.7 1.6 1.5 1.4.1 1.3.1 1.3 0.1.19 0.1.19_r8
Other available versions:           1.20 1.19.2 1.18 1.17 1.16.1 1.16 1.15.1 1.15 1.14 1.13 1.12 1.10 1.9 1.8 1.7 1.6 1.5 1.4.1 1.3.1 1.3 0.1.19 0.1.19_r8 
Overrides use this shell variable:  SAMTOOLS_X

Use a specific version of a title

On Linux machines use TITLE_X:

$ export SAMTOOLS_X=1.12
$ samtools

Program: samtools (Tools for alignments in the SAM format)
Version: 1.12 (using htslib 1.12)

On Macs use TITLE_M:

$ export SAMTOOLS_M=1.12
$ samtools

Program: samtools (Tools for alignments in the SAM format)
Version: 1.12 (using htslib 1.12)

Get list of executables for a title:

$ biogrids-list samtools

ace2sam			md5fa			samtools.pl
blast2sam.pl		md5sum-lite		seq_cache_populate.pl
bowtie2sam.pl		novo2sam.pl		soap2sam.pl
export2sam.pl		plot-ampliconstats	wgsim
fasta-sanitize.pl	plot-bamstats		wgsim_eval.pl
interpolate_sam.pl	psl2sam.pl		zoom2sam.pl
maq2sam-long		sam2vcf.pl
maq2sam-short		samtools

Call executables directly:

$ samtools

More detailed information is available in the right hand side links.

Need more help? Send mail to: help@biogrids.org