[BioC] multiple threads on QuasR

[Michael Stadler]

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.