Addition of makeflow apps and wrapper from paper submission
Added Galaxy Folder for wrappers and filetype descriptor
Slightly clarified cctools.py
Modified for new tool paths
Added install shell and perl scripts to modify tool_conf and registry for datatypes
Slight change
Finalized install commands
Finalized install commands w/GATK
Added JRE to makeflow_gatk app folder
Modified wrappers, INSTALL and apps for compatitbility
Corrected for java version
Minor change for helping setting up Picard
Modified READMEs and INSTALL, also modified configure to install apps
Merge pull request #617 from nhazekam/galaxy_apps

Galaxy-Makeflow Integration