Hi David,

The NCBI BLAST+ wrappers have a <parallelism> tag setup,
which becomes active if you have use_tasked_jobs = True in
your config/galaxy.ini file (aka universe_wsgi.ini).

Specifically, the wrappers use this:

<!-- If job splitting is enabled, break up the query file into parts -->
<parallelism method="multi" split_inputs="query" split_mode="to_size"
split_size="1000" merge_outputs="output1" />

This is hard coded to break up the query FASTA file into batches
of 1000 sequences (e.g. a transcriptome of 20k genes becomes
20 jobs), which has worked nicely on our cluster.

Separately, each job uses -num_threads "\${GALAXY_SLOTS:-8}"
in the command line string, i.e. uses the $GALAXY_SLOTS
environment variable (set via the Galaxy job configuration), or
if not set, defaults to using 8 threads.

I've essentially rephrased the README file here - did you see
that, or does it need more information added?

Thanks,

Peter


On Tue, May 3, 2016 at 6:58 PM, David Kovalic <kova...@analome.com> wrote:
> Hello,
>
> We would like to split fasta query files and run multiple concurrent jobs to
> minimize our processing wall clock time for large jobs.
>
> After chatting with folks at GCC 2015 I understand this is possible, my
> problem is I cant find instructions on hos to configure
> CloudMan/ncbi_blast_plus to do this. For those of you who know me it
> probably goes without saying that I can't figure it out myself ;)
>
> Peter/Enis/others, can you help us out with this question?
>
> Thanks,
>
> David
>
>
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