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 <jmccus...@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 <afg...@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 <jmccus...@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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>>
>
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