V2 -- now working -- of a core walker that creates the standard GATK resource bundle 
V2 -- now working -- of a core walker that creates the standard GATK resource bundle 

See https://www.broadinstitute.org/gsa/wiki/index.php/GATK_resource_bundle

Which live locally in /humgen/gsa-hpprojects/GATK/bundle/current

You use this following command to create the bundle:

java -Djava.io.tmpdir=/broad/shptmp/depristo/tmp -jar dist/Queue.jar -S scala/qscript/core/GATKResourcesBundle.scala --gatkjarfile dist/GenomeAnalysisTK.jar -bsub -jobQueue gsa -svn 5660 $* 

Annoyingly, it must be run in the trunk directory, and requires an explicit svn version number to create the directory.  It also must be run in two stages manually.  First, the local bundle is created, and then with the -phase2 argument all of the files in the local bundle are compressed and pushed to the FTP server.  I'm likely going to shift most of my processes over to using this location for data file access, especially for b37 data sets.

git-svn-id: 4561c0a8f080806b19201efb9525134c00b76d40@5665 348d0f76-0448-11de-a6fe-93d51630548a

iontorrent/Torrent-Variant-Caller-stable,iontorrent/Torrent-Variant-Caller-stable,iontorrent/Torrent-Variant-Caller-stable,iontorrent/Torrent-Variant-Caller-stable,iontorrent/Torrent-Variant-Caller-stable,iontorrent/Torrent-Variant-Caller-stable,iontorrent/Torrent-Variant-Caller-stable,iontorrent/Torrent-Variant-Caller-stable