[galaxy-dev] Picard MarkDups
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 ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Picard MarkDups
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 ngsbioinformat...@gmail.com 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 -- next part -- An HTML attachment was scrubbed... URL: http://lists.bx.psu.edu/pipermail/galaxy-dev/attachments/20120112/187d8ac f/attachment-0001.html -- ___ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev End of galaxy-dev Digest, Vol 67, Issue 13 ** ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Picard MarkDups
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: --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 ngsbioinformat...@gmail.com 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 -- next part -- An HTML attachment was scrubbed... URL: http://lists.bx.psu.edu/pipermail/galaxy-dev/attachments/20120112/187d8ac f/attachment-0001.html -- ___ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev End of galaxy-dev Digest, Vol 67, Issue 13 ** ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
