On Thu, Jan 6, 2011 at 7:52 AM, Bossers, Alex <Alex.Bossers@wur.nl> wrote:
Yury,
If the software has this option its no problem to use them! Have a look at Peter's last blast+ wrappers. Blast+ of ncbi has the ability to specify a number of cores to use...and so can you by configuring it in a tool config. Regarding the parallelisation.. no expert in this. Have a look in the tool shed for the signalp and TMHMM wrappers. There you find a piece of python to split large jobs in batches, process them in parallel and merge them back.
No experience with cluster or grid jobs myself...
Alex
Hi Yury (& Alex), For a little clarification, like many computationally intensive command line tools the NCBI BLAST+ tools have a switch for the number of processors. Currently (like most of the other Galaxy wrappers) this is specified in the XML wrappers, in this case hard coded at 8. Some of the other tools XML files are hard coded with 4 threads (e.g. bwa). In the case of TMHMM and SignalP, the tools themselves are single threaded but I wrote a wrapper script (in Python) which divides the input FASTA file into chunks and runs multiple instances of the tool and then collates the output. Again, my wrapper tools is told how many threads to use via the XML wrapper. You can find my Galaxy wrappers for TMHMM and SignalP here at the "Galaxy Community Tool Shed" (Alex has been testing them - thanks!): http://community.g2.bx.psu.edu/ Some of the provided Galaxy wrappers have a note in the XML saying the number of threads should be configurable, perhaps via a loc file. I have suggested to the Galaxy developers there should be a general setting for number of threads per tool accessible via the XML, so that this can be configured centrally (maybe I should file an enhancement issue for this): http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-September/003393.html http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-October/003407.html http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-October/003408.html (I've CC'd the galaxy-dev list, since this discussion is heading in that direction) Peter