Hi, Matt.
Thanks for reporting this - it's definitely a misfeature...
The tool wrapper tools/picard/picard_AddOrReplaceReadGroups.xml does
not explicitly set the tmpdir parameter, so I've added --tmpdir
"${__new_file_path__}" to the command line generated. That will
over-ride the default value "/tmp" for opts.tmpdir in
picard_wrapper.py to use the new_file_path.
It is now in galaxy-central - please update your local copy and test
it to confirm this solves your problem?



On Tue, Apr 3, 2012 at 2:55 PM, Matt Shirley <matt.shir...@jhmi.edu> wrote:
> Every time I run Picard's AddOrReplaceReadGroups, my system tmp directory
> fills, and the tool stops. I'm left scratching my head, because it seems
> that the JVM sets the system /tmp directory on my local galaxy-central
> branch, instead of the "new_file_path" I have defined in universe_wsgi.ini.
> This issue seems to have been fixed in commit 07560293b167, and I can
> confirm that my picard_wrapper.py includes the amended line. I am using
> OpenJDK:
>
> java version "1.6.0_20"
> OpenJDK Runtime Environment (IcedTea6 1.9.10)
> (rhel-1.40.1.9.10.el6_1-x86_64)
> OpenJDK 64-Bit Server VM (build 19.0-b09, mixed mode)
>
> Since my config is pointing to /scratch/tmp, but the JVM is using /tmp, and
> other tools in galaxy are respecting the config, what could be the
> disconnect? Thank you,
>
> Matt
>
>
>
>
>
>
> --
> Matt Shirley
> Ph.D Candidate - BCMB
> Pevsner Lab
> Johns Hopkins Medicine
>
>
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-- 
Ross Lazarus MBBS MPH;
Associate Professor, Harvard Medical School;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;

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