CGHub: mv gene torrent into cg hub dir
CGHub: add command tree
Merge remote-tracking branch 'origin' into cghub
GMT CG Hub: base class
CG Hub: add query command to download metadata xml
GMT CG Hub: gene torrent uses cg hub base class
GMT CgHub: temp commit to get to github
GMT CgHub: move metadata from instdata import to gmt
GMT CgHub: make base class abstract
GMT CgHub: update gene torrent class def
GMT CgHub: add doc to query
GMT CgHub: add output file handling to query cmd
TEMP commit to push to git hub.
Merge branch 'cghub' of github.com:ebelter/genome into cghub

Conflicts:
	lib/perl/Genome/Model/Tools/CgHub/Query.pm
GM: combine extract to vcf tests into one since they all produce the same output. Added tests for resolving sources.
GM: bump test data version to 7
GM ExtractToVcf: when resolving from model, set varition list build
GM ExtractTo/Write Csv: add b allele freq to valid fields
GM: add b allele freq and vcf config
TCGA/CG Hub: rm retrieve metadata file as it is handled in the query cmd