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 <jmchilton@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 <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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