Thank you. its was the job_conf.xml that wasn't set up properly. I have a
simply job_conf.xml that works well. sharing for the group:
<!-- "workers" is the number of threads for the runner's work queue.
The default from <plugins> is used if not defined for a
<!-- <plugin id="local" type="runner"
<plugin id="sge" type="runner"
<!-- Override the $DRMAA_LIBRARY_PATH environment variable -->
<destination id="sge_cluster" runner="sge" />
On Thu, Feb 5, 2015 at 10:03 PM, John Chilton <jmchil...@gmail.com> wrote:
> 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"?>
> <plugins workers="2">
> <plugin id="gridengine" type="runner"
> <handlers default="main">
> <handler id="main" />
> <destinations default="cluster">
> <destination id="cluster" runner="gridengine"/>
> <limit type="registered_user_concurrent_jobs">2</limit>
> <limit type="unregistered_user_concurrent_jobs">1</limit>
> <limit type="job_walltime">24:00:00</limit>
> 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
> This job_conf.xml is a stripped down version of the one from that
> 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.
> On Mon, Feb 2, 2015 at 12:53 PM, Ryan G <ngsbioinformat...@gmail.com>
> > I tried setting up Galaxy to use Sun Grid Engine, but failed miserably.
> > 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
> > 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
> > 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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