BioGrids installation client - Usage

Instructions for installation of the BioGrids software installation client can be found here --> Installation Instructions.

All BioGrids software is run from the the terminal. For information on how to run software from the BioGrids collection and configure your shell, check the getting started page..

General

The BioGrids software installation client is a command line-based installer for the BioGrids software collection. The application allows for selected applications to be installed in the familiar BioGrids environment.

To get started, load the BioGrids environment :

$ source /programs/biogrids.shrc
********************************************************************************
                          Software Support by BioGrids
********************************************************************************
 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.)"
********************************************************************************
This BioGrids installation last updated: 2017-10-11
 Please submit bug reports and help requests to:  help@biogrids.org.
********************************************************************************
 Capsule Status: Active
       For additional information visit https://sbgrid.org/wiki/capsules
******************************************************************

The client displays software 'Collections' as a list.

$ biogrids list
-- High-Throughput Sequencing -----------------------------------------------------------------
abyss            blat             diamond          miso             solexaqaplusplus
bamtools         bowtie           ebseq            mothur           spades          
bcftools         bowtie-2         edger            picard           sra-toolkit     
bedtools         breseq           fasta            pysam            star            
bigpre           bwa              fastqc           quartz           tophat          
bioawk           cora             hisat2           rsem             trimmomatic     
biobambam2       cufflinks        kallisto         sailfish         gorpipe         
blast            cutadapt         macs2            salmon          
blastplus        deseq2           mica             samtools        
-- Genomics -----------------------------------------------------------------------------------
bedtools         ffp              mrbayes          sam              sra-toolkit     
bioawk           infernal         plink            solexaqaplusplus
-- Proteomics ---------------------------------------------------------------------------------
amps     mafft    modeller rosetta  zdock   
-- Visualization ------------------------------------------------------------------------------
aline             cytoscape         igv               pymol-open-source weblogo          
-- Other --------------------------------------------------------------------------------------
a2ps                    cython                  miso                    python                 
anaconda                emboss                  mono                    pytz                   
biogrids-installer      fasta                   mpich                   qt                     
blast                   ghostscript             numpy                   r                      
blastplus               globus-connect-personal pandas                  rstudio                
breseq                  mafft                   perl                    tex-live  

Information about each title, including a description and links to documentation can be shown with the biogrids info command.

Example : Installing samtools

$ ./biogrids info samtools

Package: SAMtools
Name slug: samtools

Available versions:
	* 0.1.19
	* 1.3
	* 1.3.1
	* 1.4.1
	* 1.5 (default)

Grids(s): Biogrids
Collection(s): High-Throughput Sequencing

Description:
     (Sequence Alignment/Map) a generic format for storing large nucleotide
sequence alignments that provides various utilities for manipulating
alignments, including sorting, merging, indexing and generating alignments
in a per-position format.

Links:
	Website: http://www.htslib.org/
	Manual: http://www.htslib.org/doc/samtools.html
	Forum help: https://lists.sourceforge.net/lists/listinfo/samtools-help```

To install:
$ biogrids install samtools

samtools@1.5 for i386-mac installed Updating installation configuration...



### Example : Removing samtools

    $ biogrids remove samtools

results in :
Package samtools removed. Updating installation configuration...

### Version selection

Default versions are installed for each application. BioGrids makes available several versions for each software package. You can install specific versions if needed.

To do so, specify the version after the title name with an @ symbol. Use the *biogrids info <title>* command to see all available versions.

    $ biogrids info samtools
Package: SAMtools Name slug: samtools

Available versions: * 0.1.19 * 1.3 * 1.3.1 * 1.4.1 * 1.5 (default)

Grids(s): Biogrids Collection(s): High-Throughput Sequencing

Description: (Sequence Alignment/Map) a generic format for storing large nucleotide sequence alignments that provides various utilities for manipulating alignments, including sorting, merging, indexing and generating alignments in a per-position format.

Links: Website: http://www.htslib.org/ Manual: http://www.htslib.org/doc/samtools.html Forum help: https://lists.sourceforge.net/lists/listinfo/samtools-help


To install samtools version 1.4.1, add the version string like so:

    $ biogrids install samtools@1.4.1

which will produce :

samtools@1.4.1 for i386-mac installed
Updating installation configuration..
Check which versions are installed with the biogrids info command again $ biogrids info samtools
Package: SAMtools
Name slug: samtools

Available versions:
	* 0.1.19
	* 1.3
	* 1.3.1
	* 1.4.1 (installed)
	* 1.5 (default)

Grids(s): Biogrids
Collection(s): High-Throughput Sequencing

Description:
     (Sequence Alignment/Map) a generic format for storing large nucleotide
sequence alignments that provides various utilities for manipulating
alignments, including sorting, merging, indexing and generating alignments
in a per-position format.

Links:
	Website: http://www.htslib.org/
	Manual: http://www.htslib.org/doc/samtools.html
	Forum help: https://lists.sourceforge.net/lists/listinfo/samtools-help```

Reload the biogrids shell to use the new version ( or set the environment variable SAMTOOLS_M=1.4.1 ).

    $ source /programs/biogrids.shrc

Confirm with the *sbwhich* command


    $ sbwhich samtools
/programs/i386-mac/samtools/1.5/bin/samtools

Software Version Management in the BioGrids environment

If you have a single version of an application installed, explicit version selection in your environment is not needed.

In the case of multiple installed versions, the BioGrids Default version will be the version available at the terminal when it is installed, unless configured otherwise in ~/.sbgrid.conf.

In the case of multiple non-default versions installed, the latest release will be the version available in your shell. If you would like to have more than one version of a title installed, and prefer to use an older release or the non-default version when a default version is installed, you must set this explicitly in your ~/.sbgrid.conf file. This is the same as in the standard BioGrids environment.

Version priority in the shell

  1. ~/.sbgrid.conf
  2. Installed single version
  3. Installed Default version
  4. Latest installed release

There is more info on how to do that here --> BioGrids version overrides

Running BioGrids software

To use the software at the terminal in bash, open a new terminal and run

$ source /programs/biogrids.shrc

or in tcsh

$ source /programs/biogrids.cshrc

Questions, Problems and Known Issues

For questions or problems, the Help menu will direct you to the BioGrids help page. Or just email help@biogrids.org. If relevant, please include a screenshot of the GUI if possible (command + shift + 4) and please include the ~/Library/Application Support/BioGrids/biogrids.log file with your report.

Known issues

  • The application will fail if outbound port 873 and port 8080 are blocked by your institution or are otherwise not available.

  • In some cases the prompt for admin credentials fails to appear on activation. Be sure there is no prior BioGrids install on your machine at /programs or /opt/biogrids.