Hi, Is there documentation for the proper setup and utilisation of the \${GALAXY_SLOTS:-4} style options? I noticed that tools with this setting, including BWA and GATK run single threaded, with the following settings respectively: BWA \${GALAXY_SLOTS:-4}" === ps output: python /galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/b4427dbb6ced/bwa_wrappers/bwa_wrapper.py --threads=1 --fileSource=indexed --ref=/galaxy/galaxy_references/hg19/bwa-0.5.9/base/hg19.fasta --do_not_build_index --input1=/galaxy/galaxy-dist/database/files/093/dataset_93021.dat --input2=/galaxy/galaxy-dist/database/files/093/dataset_93023.dat --output=/galaxy/galaxy-dist/database/files/000/112/dataset_112301.dat --genAlignType=paired --params=pre_set --suppressHeader=false xml config: --threads="\${GALAXY_SLOTS:-4}" GATK Base Recalibrator \${GALAXY_SLOTS:-8} ============== python /galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/gatk2/8bcc13094767/gatk2/gatk2_wrapper.py --max_jvm_heap 6g --stdout /galaxy/galaxy-dist/database/files/000/112/dataset_112292.dat -d -I /galaxy/galaxy-dist/database/files/000/112/dataset_112289.dat bam gatk_input -d /galaxy/galaxy-dist/database/files/_metadata_files/012/metadata_12686.dat bam_index gatk_input -p java -jar "$GATK2_PATH/GenomeAnalysisTK.jar" -T "BaseRecalibrator" $GATK2_SITE_OPTIONS --num_cpu_threads_per_data_thread ${GALAXY_SLOTS:-8} --no_standard_covs -R "/galaxy/galaxy_references/hg19/srma-0.1.15/hg19.fasta" --out "/galaxy/galaxy-dist/database/files/000/112/dataset_112291.dat" -cov "ContextCovariate" -cov "CycleCovariate" -d --knownSites:dbsnp,%(file_type)s /galaxy/galaxy-dist/database/files/000/101/dataset_101086.dat vcf input_dbsnp_0 -p --pedigreeValidationType "STRICT" -d --intervals /galaxy/galaxy-dist/database/files/000/100/dataset_100129.dat bed input_intervals_0 -p --interval_set_rule "UNION" -p --downsampling_type "NONE" -p --baq "OFF" --baqGapOpenPenalty "40.0" --defaultBaseQualities "-1" --validation_strictness "STRICT" --interval_merging "ALL" java -Xmx6g -jar /galaxy/galaxy-dist/tool-data/shared/jars/gatk2//GenomeAnalysisTK.jar -T BaseRecalibrator --num_cpu_threads_per_data_thread 1 --no_standard_covs -R /galaxy/galaxy_references/hg19/srma-0.1.15/hg19.fasta --out /galaxy/galaxy-dist/database/files/000/112/dataset_112291.dat -cov ContextCovariate -cov CycleCovariate --pedigreeValidationType STRICT --interval_set_rule UNION --downsampling_type NONE --baq OFF --baqGapOpenPenalty 40.0 --defaultBaseQualities -1 --validation_strictness STRICT --interval_merging ALL -I /tmp/tmp-gatk-fIuncH/gatk_input.bam --knownSites:dbsnp,vcf /tmp/tmp-gatk-fIuncH/input_dbsnp_0.vcf --intervals /tmp/tmp-gatk-fIuncH/input_intervals_0.bed Best, Geert -- Geert Vandeweyer, Ph.D. Department of Medical Genetics University of Antwerp Prins Boudewijnlaan 43 2650 Edegem Belgium Tel: +32 (0)3 275 97 56 E-mail: geert.vandeweyer@ua.ac.be http://ua.ac.be/cognitivegenetics http://www.linkedin.com/in/geertvandeweyer