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
Merge branch 'galaxy_apps' of https://github.com/nhazekam/cctools

* 'galaxy_apps' of https://github.com/nhazekam/cctools:
  Modified READMEs and INSTALL, also modified configure to install apps
  Minor change for helping setting up Picard
  Corrected for java version
  Modified wrappers, INSTALL and apps for compatitbility
  Added JRE to makeflow_gatk app folder
  Finalized install commands w/GATK
  Finalized install commands
  Slight change
  Added install shell and perl scripts to modify tool_conf and registry for datatypes
  Modified for new tool paths
  Slightly clarified cctools.py
  Added Galaxy Folder for wrappers and filetype descriptor
  Addition of makeflow apps and wrapper from paper submission
change_dir initialized as NULL, and call chdir when change_dir is not NULL