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 
> <ybukh...@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&#39;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: ybukh...@glbrc.wisc.edu

_______________________________________________
galaxy-user mailing list
galaxy-user@lists.bx.psu.edu
http://lists.bx.psu.edu/listinfo/galaxy-user

Reply via email to