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Enhance GATK tools to utilize GALAXY_SLOTS configuration when available.

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This commit is contained in:
John Chilton
2013-11-05 13:46:06 -06:00
parent 2897607f25
commit b097a37d25
6 changed files with 6 additions and 6 deletions
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tools/gatk/count_covariates.xml
+1 -1
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@@ -17,7 +17,7 @@
-p 'java
-jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/GenomeAnalysisTK.jar"
-T "CountCovariates"
--num_threads 4 ##hard coded, for now
--num_threads \${GALAXY_SLOTS:-4}
-et "NO_ET" ##ET no phone home
##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
#if $reference_source.reference_source_selector != "history":
tools/gatk/realigner_target_creator.xml
+1 -1
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@@ -19,7 +19,7 @@
-T "RealignerTargetCreator"
-o "${output_interval}"
-et "NO_ET" ##ET no phone home
--num_threads 4 ##hard coded, for now
--num_threads \${GALAXY_SLOTS:-4}
##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
#if $reference_source.reference_source_selector != "history":
-R "${reference_source.ref_file.fields.path}"
tools/gatk/unified_genotyper.xml
+1 -1
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@@ -19,7 +19,7 @@
-p 'java
-jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/GenomeAnalysisTK.jar"
-T "UnifiedGenotyper"
--num_threads 4 ##hard coded, for now
--num_threads \${GALAXY_SLOTS:-4}
--out "${output_vcf}"
--metrics_file "${output_metrics}"
-et "NO_ET" ##ET no phone home
tools/gatk/variant_eval.xml
+1 -1
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@@ -17,7 +17,7 @@
-jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/GenomeAnalysisTK.jar"
-T "VariantEval"
--out "${output_report}"
--num_threads 4 ##hard coded, for now
--num_threads \${GALAXY_SLOTS:-4}
-et "NO_ET" ##ET no phone home
##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
#if $reference_source.reference_source_selector != "history":
tools/gatk/variant_recalibrator.xml
+1 -1
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@@ -15,7 +15,7 @@
-p 'java
-jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/GenomeAnalysisTK.jar"
-T "VariantRecalibrator"
--num_threads 4 ##hard coded, for now
--num_threads \${GALAXY_SLOTS:-4}
-et "NO_ET" ##ET no phone home
##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
#if $reference_source.reference_source_selector != "history":
tools/gatk/variant_select.xml
+1 -1
View File
@@ -14,7 +14,7 @@
-p 'java
-jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/GenomeAnalysisTK.jar"
-T "SelectVariants"
--num_threads 4 ##hard coded, for now
--num_threads \${GALAXY_SLOTS:-4}
-et "NO_ET" ##ET no phone home
-o "${output_vcf}"