[galaxy-commits] commit/galaxy-central: jmchilton: Specify Java temp directory for picard execution should match

[Bitbucket]

1 new commit in galaxy-central:


https://bitbucket.org/galaxy/galaxy-central/changeset/d1a3889f478f/
changeset:   d1a3889f478f
branch:      set-picard-java-tmpdir
user:        jmchilton
date:        2011-12-01 22:21:41
summary:     Specify Java temp directory for picard execution should match
parameter sent to wrapper script.
affected #:  1 file

diff -r 347cd30ff32ffcb7d3796304774bc5bfa675feb0 -r d1a3889f478f96ef3bb81aacff837975cfe2c25d tools/picard/picard_wrapper.py
--- a/tools/picard/picard_wrapper.py
+++ b/tools/picard/picard_wrapper.py
@@ -140,6 +140,7 @@
         cl should be everything after the jar file name in the command
         """
         runme = ['java -Xmx%s' % self.opts.maxjheap]
+        runme.append(" -Djava.io.tmpdir='%s' " % self.opts.tmpdir)
         runme.append('-jar %s' % jar)
         runme += cl
         s,stdouts,rval = self.runCL(cl=runme, output_dir=self.opts.outdir)

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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