Managing Your Software Installation

sbgrid-admin Utility

The sbgrid-admin utility used to install the complete software collection. A download link is provided in the initial site set up email, and the script is included in the installation itself at /programs/share/sbgrid/bin/sbgrid-admin. It includes built-in help:

 $ sbgrid-admin -h
sbgrid-admin: a tool for administering an BioGrids Software suite installation

Usage: sbgrid-admin [-chirstu]

  -c Cron mode.  Used for automated updates of the software suite.
  -h Help message.
  -i Install the software suite on this machine.
  -p Print a launchd plist for updating the software on OS X machines.
  -r Regenerate sh/csh shell configuration files.
  -t Test the configuration file.
  -u Force manual update of an existing installation.

The most commonly used option is sbgrid-admin -u to force a manual update. This will synchronize your local installation with the BioGrids master installation hosted at Harvard Medical School.

The BioGrids software configuration files use both static and dynamically generated files. The main shell initialization files, /programs/biogrids.cshrc and /programs/biogrids.shrc are static files, but the operating-system specific configurations are dynamically generated and customized for the packages available at your site. sbgrid-admin -r will regenerate the branch-specific configuration files should you accidentally delete or alter them.

Configuration Options The sbgrid-admin script has some additional configuration options to accommodate the installation requirements at different sites.

The ~sbgrid/.sbgridrc configuration file for the sbgrid-admin script must contain a sitename and site key. All other configurations are optional.

Options take the form of OPTION_NAME="setting".

Option ** Example** Description
SB_SITENAME sbgrid-bene The site name for your installation provided by BioGrids
SB_SITEKEY xyxyxyxyxyxyxy The installation key for your site provided by BioGrids
INSTALL_TARGET /nfs/programs The installation directory for the software
RSYNC_ARGS "--port 8080" Advanced arguments to rsync. Can be used to workaround blocked rsync ports.
HTTP_PROXY Proxy hostname and port for use by rsync and curl
POST_UPDATE_SCRIPT /absolute/path/to/script Optional script to be run after a successful software update
CRON_SCHEDULE 5 1 * * * Set a custom cron schedule

Rsync Transaction Logging If you want a date-stamped log of all rsync downloads, deletions and updates, you can add a line like this to the ~sbgrid/.sbgridrc file:

RSYNC_ARGS="--log-file=$HOME/logs/sbgrid-admin-`date +%Y%m%d`.log"

This will create a date-stamped log file any time an actual change to the software tree happens. In general this should not be necessary, but for troubleshooting purposes it can be useful.