much more error checking, stylistic consistency on variable calls, debug mode available in both scripts.

better check for missing executables
Merge pull request #6 from janders3-nmdp/initial_script_checkin

Initial script checkin
Merge pull request #8 from janders3-nmdp/script_improvements

Script improvements
merged with head, since all my PRs were approved.
Merge github.com:nmdp-bioinformatics/pipeline into script_improvements