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
<[email protected] <mailto:[email protected]>>
wrote:
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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