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> </destination>

Hope that helps, Björn

...

Hi,

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 http://wiki.galaxyproject.org/Admin/Config/Jobs 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

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

</tools> ... "

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

regards, Andreas

-- Andreas Kuntzagk SystemAdministrator Berlin Institute for Medical Systems Biology at the Max-Delbrueck-Center for Molecular Medicine Robert-Roessle-Str. 10, 13125 Berlin, Germany http://www.mdc-berlin.de/en/bimsb/BIMSB_groups/Dieterich