| Previous changeset 0:b83a853a3156 (2014-04-01) |
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Commit message:
Fix JAVA_JAR_PATH. |
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modified:
realigner_target_creator.xml |
| b |
| diff -r b83a853a3156 -r 5b8eaae854da realigner_target_creator.xml --- a/realigner_target_creator.xml Tue Apr 01 10:49:33 2014 -0400 +++ b/realigner_target_creator.xml Fri Apr 04 10:28:06 2014 -0400 |
| b |
| @@ -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 |