Merging the latest FMP updates.
Merging branch 'hotfix/0.0.8'
Merge branch 'master' of https://github.com/cancerregulome/gidget
Initial commit
:Merge branch 'master' of https://github.com/cancerregulome/gidget
Merge branch 'develop' of https://github.com/cancerregulome/gidget into develop
merge refactored code into gidget.  also adds modifications to miRNA processing to put intermediary output into the final output directory
update genelist location for methylation and rppa
cleaned up code, set row and col to not sort and modified test of current vs. refactor to print out run time difference
Merging branch 'release/0.0.9'
adding gidget config file to git ignore list.
adding initial configuration file handling
merging branch 'release/0.0.10'
picking up latest changes from 'develop' and merging into feature/gidget-config.
fixed infinite loop trap -- nFpJ was sometimes 0 if the overall job wasn't very big ...
Merge branch 'develop' of https://github.com/cancerregulome/gidget into develop
minor clean-up
Merge remote-tracking branch 'origin/feature/refactor' into feature/refactor to be upto date with sheila's updates
updating branch with lastest changes from 'develop' into feature/gidget-config
adding interpolation to config file; adding some programmatically-generated defaults for config; test of using config to set env vars in subprocess.