Hi Kiran,

This is a question best directed to the galaxy-dev list, which I have CC'd.

On Apr 23, 2012, at 5:23 AM, Kiran Jaycee wrote:

> Dear Nate,
> Im deploying Galaxy in the cluster environment with 8 nodes and 96 cores. Im 
> particularly interested in running NGS tools
> like BWA, BOWTIE etc in the cluster with Torque PBS. Just wondering if galaxy 
> is capable of parallel processing of data. 1 user running BWA in 10 cores in 
> which 10 instances of BWA in each core parallely processing the mapping of 
> 250 GB of reads data on to the reference genome.
> Is this possible?

The BWA tool itself supports running multithreaded, see the threads option in 
the wrapper.  Also, Galaxy can split a tool's inputs, run a tool many times, 
and merge the outputs.  I am not sure whether this is possible or implemented 
with BWA, but I would encourage you to look in to whether this would work for 
your needs.

> I have another issue as well. Im unable to finish FASTQ grooming of the reads 
> of size 250GB even after 2 days of processing. Is there a way to circumvent 
> the grooming step? or any way to make the grooming speed up?

Assuming this is on a local server, make sure you have set the config option 
set_metadata_externally = True.  You don't need to run the groomer if your 
fastq file is valid fastqsanger.


> Your quick response will be really appreciated.
> Thank you
> Regards,
> Kiran Jaycee
> Bioinformatician, BINET
> ELOGIC Technologies Pvt. Ltd.
> #1, 2nd Floor, 100 Ft. Ring Road, 
> Kathriguppe, Banashankari III Stage, 
> Bangalore - 560085 
> Phone   : +91 (0)80 4080 3829 
> Website : www.elogic.co.in

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