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Old 06-20-2014, 03:50 AM   #1
namikiss
Junior Member
 
Location: japan

Join Date: Dec 2011
Posts: 1
Default Galaxy & SGE

Hi, all.

We have constructed Galaxy with SGE.

The problem is that we cannot specify execution queue in job_conf.xml.
The job_conf.xml is as following, and please ignore numbers in top of lines.

We set "cluster" the default destination in #11. and "nativeSpecification" in "cluster" '-q N.q'.

In our SGE, the queue, 'N.q' has already created and we can submit a job into 'N.q' by qsub command.

However, we start a job in our Galaxy, the job is submitted into the other queue.

When we designate '-q L.q', in "nativeSpecification", the job is submitted into this queue.
The queue L.q is another queue in our SGE, and it had been already created.

We would like to submit a job into the queue N.q.

Can we ask some advice?

----
NAMIKI Nobukazu

Code:
  1 <plugins>
  2   <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="8"/>
  3   <plugin id="drmaa" type="runner" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner">
  4     <!-- Override the $DRMAA_LIBRARY_PATH environment variable -->
  5     <param id="drmaa_library_path">/xxxxx/libdrmaa.so.1.0</param>
  6   </plugin>
  7 </plugins>
  8 <handlers>
  9   <handler id="main"/>
 10 </handlers>
 11 <destinations default="cluster">
 12    <destination id="local" runner="local"/>
 13    <destination id="cluster" runner="drmaa">
 14       <param id="nativeSpecification">-q N.q</param>
 15     </destination>
 16     <destination id="Large" runner="drmaa">
 17       <param id="nativeSpecification">-q gL.q -pe smp 4</param>
 18     </destination>
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Old 06-20-2014, 07:36 AM   #2
jpummil
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Location: Fayetteville, AR

Join Date: Apr 2014
Posts: 85
Default

Namiki,

I "borrowed" this from a friend who has Galaxy submitting properly to his cluster...not sure if it will be of any help or not...

<?xml version="1.0"?>
<job_conf>
<plugins>
<plugin id="hpccqueue" type="runner" load="galaxy.jobs.runners.drmaaRMAAJobRunner"/>
</plugins>
<handlers>
<handler id="main"/>
</handlers>
<destinations>
<destination id="hpcc_default" runner="hpccqueue">
<param id="nativeSpecification">-l walltime=3:59:00</param>
</destination>
</destinations>
</job_conf>
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Old 06-20-2014, 07:38 AM   #3
jpummil
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Location: Fayetteville, AR

Join Date: Apr 2014
Posts: 85
Default

Sorry, smiley face was supposed to be a colon ":"

Forum changed it to an emoticon...
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Old 06-20-2014, 07:44 AM   #4
GenoMax
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Location: East Coast USA

Join Date: Feb 2008
Posts: 6,978
Default

Quote:
Originally Posted by jpummil View Post
Sorry, smiley face was supposed to be a colon ":"

Forum changed it to an emoticon...
Choose "Edit" --> "Go Advanced" and then you can either manually add [CODE] actual code goes here [/ CODE] (remove the space between / and CODE) tags around the code OR high-light the code and then click on the "#" icon in the menu bar to add the CODE tags automatically.
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