Analysis folder no longer compiles

[cameronc137]

Environment: (where does this bug occur, have you tried other environments)

• branch: Develop
• revision: HEAD
• OS or system: JLab ifarm1901, softenv.csh 2.4, module load cmake 3.5.1
• Special ROOT or Geant4 versions? Standard CUE 2.4

Steps to reproduce: (give a step by step account of how to trigger the bug)

1. Develop branch, load up CUE 2.4, module load cmake 3.5.1
2. execute the ./initialize.sh script (or do those steps by hand)

Expected Result: (what do you expect when you execute the steps above)

Analysis folder compiles

Actual Result: (what do you get when you execute the steps above)

The CMakeLists.txt fail to find the correct include folders within each sub-folder in analysis.
Lines 36 and 37 of analysis/pe/CMakeLists.txt have a relative path to the include folder there, which will work when running all of this on separate systems (not JLab ifarm)
If I hard code the absolute paths instead of relying on the relative path it works, but this is not a valid general solution.