Hi all,
We are trying to write our own GATK workflow (although I guess an "official" 
one will be released...) and I realized I have to parallelize execution as some 
steps are painfully slow.
In order to run GATK quickly I need to split the whole process on specific 
genomic intervals (-L option) and merge results at the end 
(http://www.broadinstitute.org/gsa/wiki/index.php/Parallelism_and_the_GATK), 
hence I have to inform galaxy that it has to create parallel jobs, one for each 
interval, in a MapReduce way. I see from here 
http://gmod.org/mediawiki/images/5/50/April2012GalaxyUpdate.pdf that this 
feature will be somehow implemented, I also see from bitbucket commits that a 
BAM slicer has been added... Is there a release plan for this? Should I write 
my own wrapper/adapter?
Thanks

d
/*
Davide Cittaro, PhD

Coordinator of Bioinformatics Core
Center for Translational Genomics and Bioinformatics
San Raffaele Scientific Institute
Via Olgettina 58
20132 Milano
Italy

Office: +39 02 26439140
Mail: cittaro.dav...@hsr.it
Skype: daweonline
*/











--------------------------------------------------------------------------
LA TUA CURA E' SCRITTA NEL TUO DNA. AL SAN RAFFAELE LA STIAMO REALIZZANDO.
AIUTA LA RICERCA, DAI IL TUO 5XMILLE - CF: 03 06 80 153
info:www.5xmi...@hsr.it - www.5xmille.org

Disclaimer added by CodeTwo Exchange Rules 2007
http://www.codetwo.com


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Reply via email to