On Thu, Jul 21, 2016 at 10:35 AM, Shane Sturrock <shane@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