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>
>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

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