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:

<?xml version="1.0"?>
<job_conf>
    <plugins workers="4">
        <!-- "workers" is the number of threads for the runner's work queue.
             The default from <plugins> is used if not defined for a
<plugin>.
          -->
        <!-- <plugin id="local" type="runner"
load="galaxy.jobs.runners.local:LocalJobRunner"/> -->
        <plugin id="sge" type="runner"
load="galaxy.jobs.runners.drmaa:DRMAAJobRunner">
            <!-- Override the $DRMAA_LIBRARY_PATH environment variable -->
            <param
id="drmaa_library_path">/opt/sge/ge2011.11/lib/linux-x64/libdrmaa.so</param>
        </plugin>
    </plugins>

    <handlers default="sge_handler">
        <handler id="sge_handler">
            <plugin id="sge"/>
        </handler>
    </handlers>

    <destinations default="sge_cluster">
        <destination id="sge_cluster" runner="sge" />
    </destinations>

</job_conf>



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"?>
> <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#Configure_Galaxy
> ).
> 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 <ngsbioinformat...@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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