On Wed, Mar 12, 2014 at 3:32 PM, Geert Vandeweyer <geert.vandeweyer2@uantwerpen.be> wrote:
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}"
This is bash syntax meaning use the value of $GALAXY_SLOTS or if undefined, default to 4 (the minus sign seems to be there just to confuse everyone - joke - it is not Galaxy's fault). The value will depend on how your job runners are configured, for example we use SGE and set the threads there on a tool by tool basis, e.g. ncbi_blastp_wrapper = drmaa://-V -pe smp 4/ That results in SGE allocating 4 threads, and Galaxy will therefore set $GALAXY_SLOTS to four. In your case, evidently $GALAXY_SLOTS was set to one. Peter