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.com

858-202-4582