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You can do this by adding cmake configuration variables to your cmakelists, like this: http://stackoverflow.com/questions/7294269/how-do-i-add-a-configuration-variable-to-my-cmake-script

Note that these won't (and shouldn't) prompt you for input at build time; instead, you can set the value of these variables using the -D flag to catkin_make (or cmake):

catkin_make -DMY_VARIABLE=42