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comparison realigner_target_creator.xml @ 1:5b8eaae854da default tip

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Fix JAVA_JAR_PATH.
author Dave Bouvier <dave@bx.psu.edu>
date Fri, 04 Apr 2014 10:28:06 -0400
parents b83a853a3156
children
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0:b83a853a3156 1:5b8eaae854da
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