Mercurial > repos > devteam > realigner_target_creator
diff realigner_target_creator.xml @ 1:f202477a521b default tip
Fix JAVA_JAR_PATH.
| author | Dave Bouvier <dave@bx.psu.edu> |
|---|---|
| date | Fri, 04 Apr 2014 10:27:08 -0400 |
| parents | 751f4d177d8e |
| children |
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--- a/realigner_target_creator.xml Tue Apr 01 09:12:09 2014 -0400 +++ b/realigner_target_creator.xml Fri Apr 04 10:27:08 2014 -0400 @@ -15,7 +15,7 @@ -d "" "${reference_source.input_bam.metadata.bam_index}" "bam_index" "gatk_input" ##hardcode galaxy ext type as bam_index #end if -p 'java - -jar "${JAVA_JAR_PATH}/GenomeAnalysisTK.jar" + -jar "\$JAVA_JAR_PATH/GenomeAnalysisTK.jar" -T "RealignerTargetCreator" -o "${output_interval}" -et "NO_ET" ##ET no phone home