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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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 Technologiepark 927, 9052 Gent, BELGIUM Tel:+32 (0)9 33 13 822 Fax:+32 (0)9 33 13 809 Email: Bram.Slabbinck@psb.ugent.be WWW: http://bioinformatics.psb.ugent.be ========================================================= Services and consulting in bioinformatics http://www.arctix.be =========================================================