[BioC] multiple threads on QuasR
Michael Stadler
michael.stadler at fmi.ch
Mon Apr 15 08:43:06 CEST 2013
Dear Vincent,
I am copying the list since this may be interesting to other users as well.
I am glad you find QuasR useful.
The way to use multiple (here: eight) cores for alignment is to create a
cluster object (from package parallel) and provide it to the qAlign
function as in the example below:
library(QuasR)
cl <- makeCluster(8)
proj <- qAlign(..., clObj=cl)
In that way, you do not have to modify the alignmentParameter argument;
qAlign will analyze the cluster object provided to 'clObj' and modify
the bowtie or SpliceMap command line parameters accordingly.
Regards,
Michael
On 12.04.2013 23:45, Vincent Zimmern wrote:
> Dear Dr. Stadler,
>
> I hope this message finds you well.
>
> QuasR is a wonderful tool -- really, there's no other adjective to
> describe it. I've been waiting for something like this to emerge from
> Bioconductor -- and now my wish has been granted.
>
> The program works flawlessly. There's only one aspect I would like to
> modify and that is the number of threads I can use with SpliceMap. My
> current (and failed) approach to launch QuasR with 8 threads on my
> 12-core machine is as follows:
>
> > DP19_align <- qAlign(sampleFile, genome=genomeName,
> + alignmentsDir=home_repo, paired='fr',
> + splicedAlignment=TRUE,auxiliaryFile=auxFile,
> alignmentParameter="-num_threads 8",
> + projectName="DP19")
>
> I have attached the log file from this alignment with the associated
> error in it -- in case this helps you to debug quickly.
>
> I was unable to find the proper instruction sets for modifying this one
> parameter (the other parameters can remain the same).
>
> Many thanks again for a brilliant piece of code!
>
> Kindest Regards,
>
> Vincent Zimmern
>
> Master's Student (Bioinformatics)
> Ecole Polytechnique Federale de Lausanne
>
> ------------------------------------------------------------------------
>
> UT Southwestern Medical Center
> The future of medicine, today.
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