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 <annbl...@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:
> I considered exposing this out in the UI, but have teetered on whether to
> expose the complexity out to the end user.
> >Message: 8
> >Date: Thu, 12 Jan 2012 11:37:23 -0500
> >From: Ryan Golhar <ngsbioinformat...@gmail.com>
> >To: email@example.com
> >Subject: [galaxy-dev] Picard MarkDups
> > <
> >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
> >this? I see the entry in picard_wrapper.py. Do I change it here or in
> >XML file for MarkDups?
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