Peter,
Thanks, I didn't see that, I was reading the paper and searching online.
Appreciate the help, we'll give it a go!
David
On Tue, May 3, 2016 at 2:16 PM Peter Cock <p.j.a.c...@googlemail.com> wrote:
> 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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