Site Administrator Overrides

Software Blacklist

Site administrators can prevent the shell initialization files from configuring software on a host by creating an empty file at


where is the output of the //hostname -s// command. This is useful for encouraging users not to run jobs on bastion hosts, file servers, etc.

Administrator Software Version Overrides

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

There are two methods for site admins to configure version overrides using files placed in a /programs/local/conf/ directory.

  • Site-wide Version Overrides A file named site.conf will be read when any BioGrids shell is initialized from the installation.

  • Per-host Version Overrides A file named , where is the output of the //hostname -s// command, will be read after the site.conf on the host matching that hostname.


There are three files that will be examined for version overrides during shell initialization. In order from lowest to highest precedence:

  • /programs/local/conf/site.conf
  • /programs/local/conf/
  • $HOME/.sbgrid.conf

The overrides are reported during shell initialization:

This BioGrids installation last updated: 2018-09-18
 Please submit bug reports and help requests to:
 Configuration options in effect for this shell:
  Variable                  Setting                   Configuration
   TRINITYRNASEQ_X           2.6.6                     personal
   R_X                       3.4.1                     personal
   FASTTREE_X                2.1.10                    personal
   ULTRASCAN3_X              4.0.2536                  personal
   PICARD_X                  2.5.0                     personal
   SAMTOOLS_X                1.7                       personal