Fixed problem with the reference varianble and some shell commands
Fixed problem with the reference varianble with pindel2vcf
Merge pull request #9 from NCI-CCR-GB/master

Added ngCGH rule and fixed some bugs
 Added annotatevcf.rules, novo.rules and made multiple changes on other rules
New rules and new files added here
Merge branch 'master' of https://github.com/zhujack/serpentine
Moved resources out of serpentine home directory

I thought that having the resources keyed to the serpentine directory
might be problematic, particularly if we are installing in a system-wide
location.  Sounds like we might need to change to use another config
param for resources home.
Merged jack's recent changes
removed stray softlinks
Merge branch 'master' into dell_branch