On Jan 12, 2012, at 11:37 AM, Ryan Golhar wrote:

> 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?

Hi Ryan,

You can set it in the XML by passing -x or --maxjheap= to picard_wrapper.py.  
You could also make this value come from a select list so the user can choose 
the desired heap size.

--nate

> 
> Ryan
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