Hi Ryan -
I have done similar things with our tools as well. For now I have edited the xml file to include the following option in the <command> section that would get passed into the picard script wrapper:
--maxjheap="8g"
I considered exposing this out in the UI, but have teetered on whether to expose the complexity out to the end user.
Thanks,
Ann
Message: 8 Date: Thu, 12 Jan 2012 11:37:23 -0500 From: Ryan Golhar ngsbioinformatics@gmail.com To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] Picard MarkDups Message-ID: CAFbjochhOioiw7a8t4p0gVs8ZAYWUx82gv4Bjv1RnUZjxC0G-Q@mail.gmail.com Content-Type: text/plain; charset="iso-8859-1"
I'm trying to run Picard MarkDups through Galaxy. Picard is using the standard 4g for the java max heap size. I need to increase this. Is it possible to offer this as an option to the user? If not, where do I change this? I see the entry in picard_wrapper.py. Do I change it here or in the XML file for MarkDups?
Ryan