Fixed problem with the reference varianble and some shell commands
Fixed problem with the reference varianble with pindel2vcf
 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
Added read group to novoalign rule and moved back to old naming structure
moved back to old naming scheme for bwa rules
moved back to old naming rules
generalized collectMultipleMetrics rule
slight change to bwamem params
Changed germline variant calling rules back to "general" rules
Working up through germline variant calling