On Thu, Jan 6, 2011 at 7:52 AM, Bossers, Alex <alex.boss...@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
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