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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