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.