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If it is a CMake project, just put a package.xml file in the source, set the build type to CMake, and then use catkin_make_isolated or catkin build (catkin_make cannot handle a workspace with non-catkin packages in it). For example, you can build gazebo and friends this way:

http://gazebosim.org/tutorials?tut=install_from_source&cat=install#Installinacatkinworkspace

If it is not a CMake project wrap it in a CMakeLists.txt and make sure the contents are extracted into the build folder. I don't have an example of that off hand, but maybe this link will give you a hint:

https://cmake.org/cmake/help/v3.2/module/ExternalProject.html