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 


# 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 
# 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 
# Example:
# galaxy  ALL = (root) NOPASSWD: SETENV: 
# galaxy  ALL = (root) NOPASSWD: SETENV: 
# 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

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