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<https://bitbucket.org/galaxy/galaxy-central/changeset/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 <http://pevsnerlab.kennedykrieger.org/>
Johns Hopkins Medicine
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