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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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/31bac315084e/
changeset: 31bac315084e
user: John Duddy
date: 2011-11-01 01:16:17
summary: Add support for generic XML files for tool integrations
affected #: 1 file
diff -r ef39a111210018fb50282a352182b298c23be8f7 -r 31bac315084e82b66bcd8cd50c1047614a6664d3 datatypes_conf.xml.sample
--- a/datatypes_conf.xml.sample
+++ b/datatypes_conf.xml.sample
@@ -152,6 +152,7 @@
<datatype extension="memexml" type="galaxy.datatypes.xml:MEMEXml" mimetype="application/xml" display_in_upload="true"/><datatype extension="cisml" type="galaxy.datatypes.xml:CisML" mimetype="application/xml" display_in_upload="true"/><datatype extension="blastxml" type="galaxy.datatypes.xml:BlastXml" mimetype="application/xml" display_in_upload="true"/>
+ <datatype extension="xml" type="galaxy.datatypes.xml:GenericXml" mimetype="application/xml" display_in_upload="true"/><datatype extension="vcf" type="galaxy.datatypes.tabular:Vcf" display_in_upload="true"><converter file="vcf_to_bgzip_converter.xml" target_datatype="bgzip"/><converter file="vcf_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/>
@@ -317,6 +318,7 @@
<sniffer type="galaxy.datatypes.binary:Bam"/><sniffer type="galaxy.datatypes.binary:Sff"/><sniffer type="galaxy.datatypes.xml:BlastXml"/>
+ <sniffer type="galaxy.datatypes.xml:GenericXml"/><sniffer type="galaxy.datatypes.sequence:Maf"/><sniffer type="galaxy.datatypes.sequence:Lav"/><sniffer type="galaxy.datatypes.sequence:csFasta"/>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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