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 ________________________________________ Van: galaxy-user-bounces@lists.bx.psu.edu [galaxy-user-bounces@lists.bx.psu.edu] namens Yury Bukhman [ybukhman@glbrc.wisc.edu] Verzonden: woensdag 5 januari 2011 23:42 Aan: Leandro Hermida CC: galaxy-user@lists.bx.psu.edu Onderwerp: Re: [galaxy-user] parallel processing of multiple files on a multi-processor box? Thanks, Leandro! Sorry for the naive questions: we're just getting started with our own Galaxy server. What about running tools that can themselves utilize multiple CPUs? Would that cause any problems? We have noticed that bowtie under Galaxy doesn't have the multithreaded option. What is the reason for that? Yury On 01/05/11, Leandro Hermida wrote:
Hi Yury,
My apologies if I missed something or misunderstood you question, but I am not sure the IT group is correct saying Galaxy won't be able to utilize multiple processors on an SMP box. When running a tool the Galaxy server will fork off an asynchronous sub process, and if you run that tool multiple times in your user session in parallel it will have that many sub processes running in parallel and on an SMP box the kernel will properly utilize the available CPUs.
So you would upload the 6 FASTQ files into your history and then you would run Groomer on each (you don't have to wait for one to finish in order to launch the next) and then the same for Bowtie.
hth, Leandro
On Mon, Jan 3, 2011 at 10:52 PM, Yury Bukhman <ybukhman@glbrc.wisc.edu(javascript:main.compose()> wrote:
Hi,
I have an RNA-seq study with 6 runs. The output is 6 Illumina fastq files. I would like to be able to run FASTQ Groomer and Bowtie on all 6 in parallel, utilizing a multi-processor box. Is this possible? It appears (to our IT group) that Galaxy won't be able to utilize multiple processors on an SMP box for the same user session, and we would need to set up a cluster to do things like this. Is this so? Is there a work-around?
Thanks.
Yury
-- Yury V. Bukhman, Ph.D. Associate Scientist, Bioinformatics Great Lakes Bioenergy Research Center University of Wisconsin - Madison 445 Henry Mall, Rm. 513 Madison, WI 53706, USA Phone: 608-890-2680 Fax: 608-890-2427 Email: ybukhman@glbrc.wisc.edu _______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user