incorrect tmp dir handling in picard AddOrReplaceReadGroups
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
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.shirley@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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Matt Shirley
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Ross