Improved MakeCircosPlot for better integration in ClinSeq
add test for rule class
Fixed FilterMouseBases.pm  to take in annotation files
updated jenkins submodule to e1f2824
Fix reference name
Fixes to make validator pass
Germline maf is now called protected maf
Merge branch 'copy' into gb_master
Updated class browser cache.
Updated `genome` tab completion.
Updated `gmt` tab completion.
updated diff blessed to incorporate Ben's change to MakeCircos and my changes to GetVariantSources
Sync: add 454 to inst data ap bridge
Updated blessed build for clinseq
Merge branch 'master' of ssh://git/srv/git/genome

Conflicts:
	lib/perl/Genome/Model/Build/Command/DiffBlessed.pm.YAML
Sx Result: check input count during verify output files
Standalone GMS - further fix to command that imports file based databases from github