Using the SBGrid Environment
Support for Site Administrators
Support for Developers
Hardware Support Notes
The sbgrid-admin utility used to install the complete software collection in what we refer to as a "Site installation". This is ideal for large labs, shared and departmental installations that use a shared network file storage for their programs. The installation is updated automatically on a monthly basis. This installation is large and can take some time to install..
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.
sbgrid-admin includes built-in help:
$ sbgrid-admin -h sbgrid-admin: a tool for administering an SBGrid 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. -s Install the software branch for SGI IRIX. -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 SBGrid master installation hosted at Harvard Medical School.
The SBGrid software configuration files use both static and dynamically generated files. The main shell initialization files, /programs/sbgrid.cshrc and /programs/sbgrid.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.
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".
|SB_SITENAME||sbgrid-bene||The site name for your installation provided by SBGrid|
|SB_SITEKEY||xyxyxyxyxyxyxy||The installation key for your site provided by SBGrid|
|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||host.name:port||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|
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:
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.