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
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: