Re: [galaxy-dev] BLAST only using single core
On Thu, Jul 21, 2016 at 10:35 AM, Shane Sturrock <shane(a)biomatters.com> wrote:
I’m just using the drmaa plugin so I’m guessing I need to either specify a
job runner for BLAST which sets GALAXY_SLOTS. The documentation isn’t
entirely clear although it seems I need to create a job_conf.xml which sets
local_slots to a value for runner drmaa unless there’s a way to set that in
the galaxy.ini file instead.
There is a legacy job setting via galaxy.ini aka universe_wsgi.ini where
we used to use this:
[galaxy:tool_runners]
ncbi_blastp_wrapper = drmaa://-V -pe smp 4/
ncbi_blastn_wrapper = drmaa://-V -pe smp 4/
ncbi_blastx_wrapper = drmaa://-V -pe smp 4/
ncbi_tblastn_wrapper = drmaa://-V -pe smp 4/
ncbi_tblastx_wrapper = drmaa://-V -pe smp 4/
blast_reciprocal_best_hits = drmaa://-V -pe smp 4/
The -V was an SGE switch to copy the environment variables,
and -pe smp 4 is for a 4 core job.
For job_conf.xml I am trying something similar with less repetition:
...
<!-- Default queue on the SGE cluster (four cores) -->
<destination id="all4.q" runner="sge"
tags="gruffalo">
<param id="nativeSpecification">-pe smp 4</param>
<env file="/mnt/shared/galaxy/apps/galaxy-paths.sh"/>
</destination>
...
<tool id="ncbi_blastp_wrapper" destination="all4.q"/>
<tool id="ncbi_blastn_wrapper" destination="all4.q"/>
<tool id="ncbi_blastx_wrapper" destination="all4.q"/>
<tool id="ncbi_tblastn_wrapper" destination="all4.q"/>
<tool id="ncbi_tblastx_wrapper" destination="all4.q"/>
<tool id="ncbi_rpsblast_wrapper" destination="all4.q"/>
<tool id="ncbi_rpstblastn_wrapper"
destination="all4.q"/>
<tool id="blast_reciprocal_best_hits"
destination="all4.q"/>
...
i.e. I've set the computationally heavy BLAST+ tools to use a
destination configured to use just four cores. Because this is
SGE, we do this via the native syntax of -pe smp 4, i.e.
just like at the command line we'd do:
$ qsub -pe smp 4 ...
This detail will be different for your LSF cluster.
Peter