That fixed it.
Thanks a bunch!

On Jan 22, 2014, at 9:27 AM, Thomas Bellembois 
<thomas.bellemb...@ens-lyon.fr<mailto:thomas.bellemb...@ens-lyon.fr>> wrote:

I may be wrong, but may be your :

<destination id="sge_default" runner="drmaa"/>

parameter should be :

<destination id="sge_default" runner="sge"/>

Here is my configuration file for example.

<?xml version="1.0"?>
<!-- A sample job config that explicitly configures job running the way it is 
configured by default (if there is no explicit config). -->
<job_conf>
    <plugins>
        <plugin id="local" type="runner" 
load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
        <!-- SUN GRID ENGINE -->
        <plugin id="sge" type="runner" 
load="galaxy.jobs.runners.drmaa:DRMAAJobRunner"/>
    </plugins>

    <handlers default="handlers">

        <handler id="handler0" tags="handlers"/>
        <handler id="handler1" tags="handlers"/>
    </handlers>

    <destinations default="sge_default">
        <destination id="local" runner="local"/>
        <destination id="sge_default" runner="sge">
          <param id="nativeSpecification">-b n</param>
        </destination>
    </destinations>

</job_conf>

Thomas

On 22/01/2014 16:02, Cantarel, Brandi L. wrote:
Are you asking if I can submit jobs to sge with the galaxy user on the server — 
yes, I can, at least I can on the command line...



On Jan 22, 2014, at 3:00 AM, Thomas Bellembois 
<thomas.bellemb...@ens-lyon.fr<mailto:thomas.bellemb...@ens-lyon.fr>> wrote:

Hello,

Can you run a job with qsub from your Galaxy server with your Galaxy user ?

Thomas

--
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+33 4 26 73 13 67

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On 21/01/2014 22:16, Cantarel, Brandi L. wrote:
Hi all,
I have been trying to set up my galaxy instance to use SGE -- I created a 
job_conf.xml using the sample as a model and updated the galaxy user bashrc 
with the DRMAA_LIBRARY_PATH
export DRMAA_LIBRARY_PATH=/home/sge/lib/lx26-amd64/libdrmaa.so


But when I try to add data to a library I get the error:
Unable to run job due to a misconfiguration of the Galaxy job running system. 
Please contact a site administrator.

Not too comforting since I am the administrator.  The error in the log says:
galaxy.jobs.handler DEBUG 2014-01-21 14:57:39,478 (2) Dispatching to drmaa 
runner
galaxy.jobs.handler ERROR 2014-01-21 14:57:39,479 put(): (2) Invalid job 
runner: drmaa

What does that mean, Invalid job runner?  Does this mean I have an error in my 
job_conf.xml?



Here is my job_conf.xml
<?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="sge" type="runner" 
load="galaxy.jobs.runners.drmaa:DRMAAJobRunner"/>
  </plugins>
  <handlers default="handlers">
    <!-- Additional job handlers - the id should match the name of a
         [server:<id>] in universe_wsgi.ini.
      -->
    <handler id="main" tags="handlers"/>
  </handlers>
  <destinations default="sge_default">
    <!-- Destinations define details about remote resources and how jobs
         should be executed on those remote resources.
      -->
    <destination id="sge_default" runner="drmaa"/>
    <!-- Define parameters that are native to the job runner plugin. -->
</destinations>
</job_conf>


Thanks for your help!

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Brandi Cantarel, PhD
Bioinformatics Research Scientist
Baylor Institute for Immunology Research
Baylor Health Care System
214-820-9064 (office)
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