Change the method of spliting `chirp` cmd into args from string_split to string_split_quotes.
Merge pull request #633 from hmeng-19/chirp_script_space

Change the method of spliting `chirp` cmd into args
Use prefer static fuse rather than dynamic.

cvmfs is being compiled with the static version.
Merge pull request #635 from btovar/static_fuse

Use prefer static fuse rather than dynamic.
Fix wrong int cast in expire_procs_running
Use uname -m instead of sys when looking for packages.
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
modify the initialization of variable change_dir;
change_dir is initialized as NULL
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