Perfect, thanks! That's in addition to the default arguments? On Thu, Aug 14, 2014 at 2:52 PM, Enis Afgan <afgane@gmail.com> wrote:
If I'm understanding your question correctly (ie, have the ability to specify SGE requirements on a per-tool basis), then yes. You'd do something like this in universe_wsgi.ini: [galaxy:tool_runners] bwa_wrapper = drmaa://-pe smp 2/ bowtie2 = drmaa://-pe smp 2/
On Thu, Aug 14, 2014 at 2:26 PM, Jim McCusker <jmccusker@5amsolutions.com> wrote:
thanks, I ended up doing subinvocations (submitting a job from within a job) because one tool in particular needs lots of memory. Is there a way to set these things on a per-tool basis (which would let me remove the subinvocation)?
Jim
On Thu, Aug 14, 2014 at 2:09 PM, Enis Afgan <afgane@gmail.com> wrote:
Hi Jim Try setting it like this: default_cluster_job_runner = drmaa://-w n -l mem_free=16G/
I've just tried it and worked fine.
Sorry for a delay in getting back to you, Enis
On Tue, Aug 5, 2014 at 6:44 PM, Jim McCusker <jmccusker@5amsolutions.com
wrote:
I have a galaxy/cloudman cluster where I would like to pass a "-l mem_free=16G" parameter when galaxy submits the job to SGE. I've tried adding it like this:
default_cluster_job_runner = drmaa://-l mem_free=16G/
(it was: default_cluster_job_runner = drmaa:/// )
but now the jobs don't even submit. Am I wiping out other important parameters? How should I do this?
Thanks, Jim
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