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:
[hidden email]
Skype: daweonline
*/
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