Re: [galaxy-dev] Picard MarkDups

[Nate Coraor]

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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Re: [galaxy-dev] Picard MarkDups

[Ryan Golhar]

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  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  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 
> >To: galaxy-dev@lists.bx.psu.edu
> >Subject: [galaxy-dev] Picard MarkDups
> >Message-ID:
> >   <
> cafbjochhoioiw7a8t4p0gvs8zaywux82gv4bjv1rnuzjxc0...@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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Re: [galaxy-dev] Picard MarkDups

[Ann Black]

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  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 
>To: galaxy-dev@lists.bx.psu.edu
>Subject: [galaxy-dev] Picard MarkDups
>Message-ID:
>   
>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
>-- next part --
>An HTML attachment was scrubbed...
>URL: 
>f/attachment-0001.html>
>
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>
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>End of galaxy-dev Digest, Vol 67, Issue 13
>**


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