How would those statements translate to pbs/torque (pbs_python)

I request resources using the nodes=1:ppn:4 syntax. The -pe argument is not available it seems...

Best,

Geert

On 03/12/2014 04:43 PM, Björn Grüning wrote:
Hi Geert,

you can give every tool a different amount of SLOTS via the job_conf.xml file.

https://wiki.galaxyproject.org/Admin/Config/Jobs

For example:

<tool id="toolshed.g2.bx.psu.edu/repos/iuc/gatk2/gatk2_variant_recalibrator" destination="12cores_24G" />


where 12cores_24G is defined with a parallel SGE environment.

Cheers,
Bjoern

Am 12.03.2014 16:32, schrieb Geert Vandeweyer:
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.vandewe...@ua.ac.be
http://ua.ac.be/cognitivegenetics
http://www.linkedin.com/in/geertvandeweyer

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