CMakeLists.txt has already been patched from r16 of pymoos.
Included is the patch itself for reference in case the need arises, from william's moos-to-ros bridge
First get MOOS
svn co -r 2354 svn://login2.robots.ox.ac.uk/MOOS/trunk MOOS
cd MOOS
cmake-gui
make
sudo make install
Then install pymoos
git clone https://github.com/GAVLab/pymoos.git
mkdir build && cd build
cmake .. && gksu make
cd .. && gksu python setup.py install
from pymoos.MOOSCommClient import MOOSCommClient
client = MOOSCommClient()
See examples in python code for further details.
Most current implementation is in the repo survey_gui