Hello,
Can you run a job with qsub from your Galaxy server with your Galaxy user ?
Thomas
-- Thomas Bellembois, network and system administrator ENS-Lyon/IGFL - 46, Allée d'Italie 69364 LYON CEDEX 07 FRANCE +33 4 26 73 13 67 .The IGFL is a member of the "portail-labos" project (https://portail-labos.ens-lyon.fr/site/). .IGFL IT documentation: http://itdoc.igfl.ens-lyon.fr/itdoc
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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