Ah this is exactly what I was looking for.  Thanks!

On Wed, Apr 6, 2011 at 2:56 AM, Bram Slabbinck <br...@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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>
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