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In order to use the correct environment during the build process you need to prefix your command with the ${CATKIN_ENV} variable. It uses the generated env.sh script which will source the setup.sh file before calling the command passed in as an argument.

There is a short description about that in the catkin docs: http://docs.ros.org/api/catkin/html/user_guide/environment.html

You can also take a look at some code which makes use of that to invoke external commands: https://github.com/ros/catkin/blob/eeca8c4aa722666138ab9eced7bacb95e84f7f67/cmake/catkin_python_setup.cmake#L61