We have a very limited set of users...most of them are analysts who run these programs from the shell anyway. It the default setting doesn't work, I don't want them asking me what's wrong. I'd like them to be able to set it themselves as an option.
On Thu, Jan 12, 2012 at 12:13 PM, Ann Black annblack@eng.uiowa.edu wrote:
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>
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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