Thanks for your answer. I will try this.

But I must say I don't like this new style very much. I need to create an extra destination for every paramater set. This blows up the configuration a lot.

regards, Andreas

On 21.05.2013 17:22, Björn Grüning wrote:
Hi Andreas,

try something like the following:

<destination id="20cores_10G" runner="drmaa">
    <param id="nativeSpecification">-l h_vmem=10G -pe "*" 20</param>

Hope that helps,


I recently updated our local galaxy instance first time after a few month. 
Afterwards I noticed that
the way to setup job runners has changed from single lines to an extra XML-file.
I now started to write a job_conf.xml but I don't understand where I put the 
parameters for GridEngine.

I already read but seem to have 
missed this info.
For example in the old style I have lines like

velveth = drmaa://-l h_vmem=25G/

In the new style I would write

         <destination id="cluster" runner="drmaa"/>
          <tool id="velveth" destination="cluster"/>


But where do I put the "-l h_vmem"?

regards, Andreas

Andreas Kuntzagk


Berlin Institute for Medical Systems Biology at the
Max-Delbrueck-Center for Molecular Medicine
Robert-Roessle-Str. 10, 13125 Berlin, Germany
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