psjshep, Yes, it's not on 3rdparty building script. I managed this (on raspbian) with following (as root, adapt with 'sudo' if you need): ps: I cloned git repository in my home directory.
# build libatik cd ~/indi/3rdparty/ mkdir build_libatik cd build_libatik cmake -DCMAKE_INSTALL_PREFIX=/usr . ../libatik make make install
# build driver cd ~/indi/3rdparty/indi-atik/ mkdir build cd build cmake -DCMAKE_INSTALL_PREFIX=/usr .. make make install