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:

Hi Andrew,

If you're not aware, it's possible to specify that only certain tools
should be run on a specific cluster with certain parameters.  See the
bottom of the Cluster documentation for detials (under the "Galaxy
Configuration" and "Tool Configuration" headers):

  https://bitbucket.org/galaxy/galaxy-central/wiki/Config/Cluster

> 
> <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.

To avoid needing a wrapper that executes qsub for you, you may be able
to just run your command behind qrsh or qlogin instead of qsub - this
will remain in the foreground until the job completes.

> 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.

To use qsub, you'd need to make a wrapper around myscript.sh along the
lines of the following:

#!/bin/sh

jobid=`qsub -terse myscript.sh`

while [ 1 ]; do
    qstat -j $jobid >/dev/null 2>&1
    [ $? -eq 1 ] && break;
    sleep 5;
done

------

The above script is the most basic option, it would probably be best to
add more error handling and reporting.

--nate

> 
> Any advice appreciated.
> 
> Thanks,
> Andrew

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