Running scripts instead of targets

Is there a way to run scripts instead of running targets?
My software using a superbuild system similar to slicer [1] and MITK [2]. I understand that these targets are not suppored (hopefully yet...).
But we actually run our executables with wrapper scripts.
Is it possible to run these scripts in lieu of the superbuild targets?

[1] https://github.com/Slicer/Slicer
[2] https://github.com/MITK/MITK