On Wed, Apr 6, 2011 at 2:56 AM, Bram Slabbinck <brsla@psb.vib-ugent.be> wrote:

Hi andrew

What you need to do is to add the qsub parameter '-sync y'. This puts a hold on the qsub command and makes it wait until the SGE job is finished.

regards
Bram

On 05/04/2011 18:27, andrew stewart wrote:
I'm aware of how to configure Galaxy to use SGE in universe_wsgi.ini, however what I want to do is a little different. Because I only want certain processes to be submitted to the queue, I'd rather control this at the tool configuration level (the xml wrapper). For example:

<command interpreter="bash">

qsub myscript.sh

</command>

This will work, except that the status of the job (in Galaxy) shows as completed even though the job has simply been submitted to SGE. Basically Galaxy 'loses track' of the process because the submission process (myscript.sh) has completed even if the actual job hasn't.

Has anyone else tried anything like this before, or have anything helpful to suggest? One thought is to somehow cause the myscript.sh process to pause until the SGE job has completed... somehow.

Any advice appreciated.

Thanks,

Andrew
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Bram Slabbinck, PhD

Bioinformatics & Systems Biology
VIB Department of Plant Systems Biology, Ghent University
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