[galaxy-dev] how to set GridEngine parameters for tools

2013-05-21 Thread Andreas Kuntzagk
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

Re: [galaxy-dev] how to set GridEngine parameters for tools

2013-05-21 Thread Björn Grüning
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

Re: [galaxy-dev] how to set GridEngine parameters for tools

2013-05-21 Thread Andreas Kuntzagk
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