Re: [galaxy-dev] how to set GridEngine parameters for tools
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: -l h_vmem=10G -pe "*" 20 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 " ... ... " 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 ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] how to set GridEngine parameters for tools
Hi Andreas, try something like the following: -l h_vmem=10G -pe "*" 20 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 > > " > ... > > > > > > > > ... > " > > But where do I put the "-l h_vmem"? > > regards, Andreas > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] how to set GridEngine parameters for tools
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 " ... ... " 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 ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
