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 <kovalic@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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