I put the wrong link in there. The link below is to pull the code.
Ilya
https://bitbucket.org/ichorny/galaxy-central/overview
From: Chorny, Ilya
Sent: Wednesday, July 27, 2011 1:22 PM
To: galaxy-dev@lists.bx.psu.edu
Cc: Wohlfrom, Tobias; Duddy, John
Subject: Regarding submitting jobs as actual user
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
858-202-4582