I completed the changes to galaxy to submit DRMAA jobs (SGE) as the actual galaxy user. You can see the code at the fork below. Below is a brief description of how to turn it which is also described in the universe_wsgi.ini.sample.
https://ichorny@bitbucket.org/ichorny/galaxy-central
# Uncomment drmaa_external_runjob_script and drmaa_external_killjob_script pameters and have them point to the # absolute path for scripts/drmaa_external_runner.py and scripts/drmaa_external_killer.py. # The scripts directory is located in the top level galaxy directory. The parameters when # uncommented allow for submission to the drmaa queue with the user name of the user submitting # the job and not the galaxy user. In order for this to work the actual user must log into galaxy # and the galaxy authentication must be consistent with the authentication on the server in which the # drmaa queue is running (i.e. the username must have an account on the server and be allowed to # submit jobs to the queue). The galaxy user must also be given sudo permission to execute # scripts/drmaa_external_runner.py and scripts/drmaa_external_killer.py in /etc/sudoers # Example: # galaxy ALL = (root) NOPASSWD: SETENV: /opt/galaxy/scripts/drmaa_external_runner.py # galaxy ALL = (root) NOPASSWD: SETENV: /opt/galaxy/scripts/drmaa_external_killer.py # Also the # Defaults requiretty # in /etc/sudoers must be commented out #drmaa_external_runjob_script = None #drmaa_external_killjob_script = None
Ilya Chorny Ph.D. Bioinformatics - Intern ichorny@illumina.commailto:ichorny@illumina.com 858-202-4582