Overriding Software Versions

Most of the software titles installed in the BioGrids software collection have several versions available. We try to provide at least three versions of each software package, although very old or very new applications may have fewer versions.

Display Available Versions

To list the available versions of a software title, you can use the biogrids utility. Running biogrids -l will list the versions for your current platform. From a Linux machine, a search for samtools versions looks like this:

$  ./biogrids -l samtools
0.1.19
1.3
1.3.1
1.4.1
1.5 (default)

Running biogrids -L will print the available versions for the current platforms, OS X and Linux.

$  ./biogrids -L samtools
i386-mac:
 -0.1.19
 -1.3
 -1.3.1
 -1.4.1
 -1.5 (default)
x86_64-linux:
 -0.1.19
 -1.3
 -1.3.1
 -1.4.1
 -1.5 (default)

Overriding Default Versions

To override the default version of a software title, you need to create an override file. The shell configuration scripts will read this file and override the default version.

The override file is named .sbgrid.conf and should be placed in your $HOME directory. The syntax for overrides is a simple key=value pair. E.g. it should look like this:

APPLICATION_X=1.2

APPLICATION_X is the name of the application followed by an underscore and the shorthand initial for the architecture. The last field on the line is the software version number you want to use. The initials for each software branch are:

Software Directory Shorthand Initial
i386-linux _L
x86_64-linux _X
i386-mac _M

To quickly open the overrides file in your default $EDITOR, you can run sbgrid-overrides -e.

When you open a new shell, you will see a message about the overridden version. Note that a site administrator can create sitewide or machine-specific overrides as well.

The example output below shows several packages on linux being changed from the default version:

*********************************************************************
This BioGrids installation last updated: 2018-09-18
 Please submit bug reports and help requests to:  help@biogrids.org.
*********************************************************************
 Configuration options in effect for this shell:
  Variable                  Setting                   Configuration
   TRINITYRNASEQ_X           2.6.6                     personal
   R_X                       3.4.1                     personal
   PICARD_X                  2.5.0                     personal
   SAMTOOLS_X                1.7                       personal

Disabling a Software Package

To disable a specific software package, set its version to "disable" in your ~/.sbgrid.conf file.