On Wed, Mar 12, 2014 at 3:32 PM, Geert Vandeweyer
<geert.vandewey...@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:
> ===
> 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.

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