To get started, download and extract JFlex and CUP, and set two environment variables to your locations of JFlex and CUP. For example:
export JFLEX_DIR=$HOME/jflex-1.7.0
export CUP_DIR=$HOME/cup
JFlex 1.7.0 (https://jflex.de/release/jflex-1.7.0.tar.gz) and CUP 0.11b-20160615 (http://www2.cs.tum.edu/projects/cup/releases/java-cup-bin-11b-20160615.tar.gz).
cd quandary/skeleton
make
./quandary [OPTIONS] QUANDARY_PROGRAM INTEGER_ARG_TO_MAIN
cd quandary/examples