The default args will apply to all the tools. Tool-specific args will apply
only for the tool you specify and those overwrite the default (ie,
arguments will not add up).
On Thu, Aug 14, 2014 at 2:53 PM, Jim McCusker
wrote:
> Perfect, thanks! That's in addition to the default arguments?
>
>
>
>
Perfect, thanks! That's in addition to the default arguments?
On Thu, Aug 14, 2014 at 2:52 PM, Enis Afgan 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.i
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, Ji
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 wrote:
> Hi Ji
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
wrote:
> I have a galaxy/cloudman cluster where I would like to pass a "-
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
