Mercurial > repos > devteam > realigner_target_creator
comparison 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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| 0:751f4d177d8e | 1:f202477a521b |
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| 13 -d "-I" "${reference_source.input_bam}" "${reference_source.input_bam.ext}" "gatk_input" | 13 -d "-I" "${reference_source.input_bam}" "${reference_source.input_bam.ext}" "gatk_input" |
| 14 #if str( $reference_source.input_bam.metadata.bam_index ) != "None": | 14 #if str( $reference_source.input_bam.metadata.bam_index ) != "None": |
| 15 -d "" "${reference_source.input_bam.metadata.bam_index}" "bam_index" "gatk_input" ##hardcode galaxy ext type as bam_index | 15 -d "" "${reference_source.input_bam.metadata.bam_index}" "bam_index" "gatk_input" ##hardcode galaxy ext type as bam_index |
| 16 #end if | 16 #end if |
| 17 -p 'java | 17 -p 'java |
| 18 -jar "${JAVA_JAR_PATH}/GenomeAnalysisTK.jar" | 18 -jar "\$JAVA_JAR_PATH/GenomeAnalysisTK.jar" |
| 19 -T "RealignerTargetCreator" | 19 -T "RealignerTargetCreator" |
| 20 -o "${output_interval}" | 20 -o "${output_interval}" |
| 21 -et "NO_ET" ##ET no phone home | 21 -et "NO_ET" ##ET no phone home |
| 22 --num_threads \${GALAXY_SLOTS:-4} | 22 --num_threads \${GALAXY_SLOTS:-4} |
| 23 ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout | 23 ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout |