Answering myself here...

I don't see the error anymore after adding "-w n":

[galaxy:tool_runners]
...
mytoolname = drmaa://-w n -l mem_free=1G -l mem_token=1G -l h_vmem=1G/
...

Is this what other Galaxy admins do when using drmaa native options for their 
SGE?

Ka Ming
________________________________________
From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu] 
On Behalf Of Ka Ming Nip [km...@bcgsc.ca]
Sent: July 26, 2011 10:39 AM
To: galaxy-dev@lists.bx.psu.edu
Subject: [galaxy-dev] DRMAA options for SGE

Hi,

I am trying to configure the proper memory resource requests for my Galaxy tool.
This is what I have under the tool_runners section of universe_wsgi.ini

[galaxy:tool_runners]
...
mytoolname = drmaa://-l mem_free=1G -l mem_token=1G -l h_vmem=1G/
...

When I execute my tool on Galaxy, I get the error below in the shell that I ran 
"sh run.sh":

galaxy.jobs.runners.drmaa ERROR 2011-07-26 09:54:01,930 Uncaught exception 
queueing job
Traceback (most recent call last):
  File "/home/kmnip/galaxy/galaxy-central/lib/galaxy/jobs/runners/drmaa.py", 
line 112, in run_next
    self.queue_job( obj )
  File "/home/kmnip/galaxy/galaxy-central/lib/galaxy/jobs/runners/drmaa.py", 
line 177, in queue_job
    job_id = self.ds.runJob(jt)
  File 
"/home/kmnip/galaxy/galaxy-central/eggs/drmaa-0.4b3-py2.4.egg/drmaa/__init__.py",
 line 331, in runJob
  File 
"/home/kmnip/galaxy/galaxy-central/eggs/drmaa-0.4b3-py2.4.egg/drmaa/helpers.py",
 line 213, in c
  File 
"/home/kmnip/galaxy/galaxy-central/eggs/drmaa-0.4b3-py2.4.egg/drmaa/errors.py", 
line 90, in error_check
DeniedByDrmException: code 17: error: no suitable queues

All the flags I used work with qsub commands on the SGE cluster I use. The tool 
runs
when I comment out the line in universe_wsgi.ini.

Thanks,
Ka Ming
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