Mercurial > repos > pitagora > gatk_1_6_pitagora
changeset 4:2f7daeeaf4aa
commit
| author | pitagora <ryota.yamanaka@riken.jp> |
|---|---|
| date | Thu, 16 Apr 2015 10:53:16 +0900 |
| parents | 1a95dea5a2f0 |
| children | 04a1efe6021e |
| files | GATKRealignerTargetCreator.py GATKRealignerTargetCreator.xml |
| diffstat | 2 files changed, 2 insertions(+), 2 deletions(-) [+] |
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--- a/GATKRealignerTargetCreator.py Wed Apr 15 19:24:28 2015 +0900 +++ b/GATKRealignerTargetCreator.py Thu Apr 16 10:53:16 2015 +0900 @@ -31,7 +31,7 @@ if rtncode1 != 0: raise Exception - cmd2 = "java -Xmx2g -jar " + arg.P + "/GenomeAnalysisTK.jar -T RealignerTargetCreator -R " + args.R + " -nt " + args.nt + " -I " + gatk_filename + " -L " + args.L + " -log " + args.log + " -o " + args.O + cmd2 = "java -Xmx2g -jar " + arg.J + "/GenomeAnalysisTK.jar -T RealignerTargetCreator -R " + args.R + " -nt " + args.nt + " -I " + gatk_filename + " -L " + args.L + " -log " + args.log + " -o " + args.O print "The cmd is %s" % cmd2 proc2 = subprocess.Popen( args=cmd2, shell=True )
--- a/GATKRealignerTargetCreator.xml Wed Apr 15 19:24:28 2015 +0900 +++ b/GATKRealignerTargetCreator.xml Thu Apr 16 10:53:16 2015 +0900 @@ -2,7 +2,7 @@ <description></description> <command interpreter="python"> GATKRealignerTargetCreator.py - --J $JAVA_JAR_PATH + --J \$JAVA_JAR_PATH --I $input --O $output --L $db_beds