Using the SBGrid Environment
Support for Site Administrators
Support for Developers
Hardware Support Notes
Programs of the DIALS suite are provided by DIALS, ccp4, and phenix. Currently the default DIALS suite is provided by phenix, regardless of whether you have standalone DIALS installed. As the versions provided by standalone DIALS and DIALS bundled with other software suites can differ, you may want to switch the default DIALS executables to a different source.
There are two main ways to do this, transient and persistent.
For example, if you want to process your X-ray dataset once with the newest xia2, but want to leave the default SBGrid behavior untouched, you can call xia2 and tell SBGrid to use the DIALS version (using --sbapp:a dials) like this:
xia2 --sbapp:a dials pipeline=dials /path/to/your/data
However, if you want to process your dataset step-by-step using the newest DIALS version, it may be more comfortable to set DIALS as the default source of all dials.*** executables.
To do this, do
Now all programs provided by dials that have 'dials' in their name will be called by default from the DIALS suite. Note that to use xia2 from DIALS, you will need to repeat the same steps selecting for binaries that contain 'xia2', like:
mkdir ~/.sbgrid_capsule cd ~/.sbgrid_capsule sbgrid-list dials |grep dials > list for each in $(cat list); do echo dials > $each; done rm list
To reset your configuration, simply delete the files in the ~/.sbgrid_capsule directory
cd ~/.sbgrid_capsule sbgrid-list dials |grep xia2 > list for each in $(cat list); do echo dials > $each; done rm list
Additional information on version control in SBGrid is provided here: https://sbgrid.org/wiki/capsules