PHonon is a QUANTUM ESPRESSO package and it is tightly bound to QUANTUM ESPRESSO. For instruction on how to download and compile QUANTUM ESPRESSO, please refer to the general Users' Guide, available in file Doc/user_guide.pdf under the main QUANTUM ESPRESSO directory, or in web site http://www.quantum-espresso.org.
Once QUANTUM ESPRESSO is correctly configured, PHonon is compiled by just typing make ph, from the main QUANTUM ESPRESSO directory; or, if you use CMake, by just typing make.