If you encounter error during pysam installation:
sudo easy_install -U pysam ... pysam/csamtools.c:8:22: fatal error: pyconfig.h: No such file or directory #include "pyconfig.h" ^ compilation terminated. error: Setup script exited with error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
try installing python-dev first.
sudo apt-get install python-dev
Solution found on github.