Assuming grid engine is working outside of Galaxy and the Galaxy user can say qsub files just fine - then you need to install the sun grid engine libdrmaa package - or build from scratch. Assuming you have done that and the resulting .so file is /usr/lib/gridengine-drmaa/lib/libdrmaa.so. Then all you should have to do is create a config/job_conf.xml file in your Galaxy root that looks something like this: <?xml version="1.0"?> <job_conf> <plugins workers="2"> <plugin id="gridengine" type="runner" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner"> <param id="drmaa_library_path">/usr/lib/gridengine-drmaa/lib/libdrmaa.so</param> </plugin> </plugins> <handlers default="main"> <handler id="main" /> </handlers> <destinations default="cluster"> <destination id="cluster" runner="gridengine"/> </destinations> <tools> </tools> <limits> <!-- <limit type="registered_user_concurrent_jobs">2</limit> <limit type="unregistered_user_concurrent_jobs">1</limit> <limit type="job_walltime">24:00:00</limit> --> </limits> </job_conf> A slightly more complicated setup with supervisor, uwsgi, multiple handlers, etc... all on grid engine is covered in this tutorial that Nate put together last year (https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay/AdminWalkthrough#C...). This job_conf.xml is a stripped down version of the one from that tutorial. In terms of rolling back and just getting jobs to start running again - you need to remove $GALAXY_ROOT/config/job_conf.xml and $GALAXY_ROOT/job_conf.xml and things should start working using the local runner again. If this isn't working - there maybe a problem in your galaxy.ini file - I would need to know what properties were being set in there to know more though. -John On Mon, Feb 2, 2015 at 12:53 PM, Ryan G <ngsbioinformatics@gmail.com> wrote:
I tried setting up Galaxy to use Sun Grid Engine, but failed miserably. I removed my config/job_conf.xml hoping Galaxy would revert to its default state, but jobs are no longer being dispatched. I don't see any errors in the log.
How can I get Galaxy to 1) use SGE, or 2) revert to its default state for running jobs. The page, https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster isn't 100% clear on how to set up a simply configuration for SGE. I'd be happy to contribute mine as an example, if I can get it running.
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