Manual way

First, some environement variables must be set (for example):

export G4INSTALL=/home/user/geant4.version   
export G4SYSTEM=Linux-g++ (for example)
export CLHEP\_BASE\_DIR=/home/user/CLHEP

Then the other variables should be set executing the $G4INSTALL/Configure file.

Changes of the configuration can be done directly, editing the config.sh file which is located in the $G4INSTALL/.config/bin/Linux-g++ directory. After modification, this executed in order to prepare the compilation.