Use qrsh instead of qsub to submit the job should help, I believe.

On Tue, Apr 5, 2011 at 10:27 AM, andrew stewart
<andrew.c.stew...@gmail.com>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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