Can I run a script in an Eclipse run configuration?

To set your custom build environment:

Project Properties->C/C++ Build->Environment

To execute your program

Project Properties->Run/Debug Settings->New

Enter variables in Environment tab in Launch Configuration. Click on 'Common' tab and check Shared File radio button and check in the launcher configuration with your project.

If you want to run other programs with your build (say some pre/post processor), add a new builder with:

Project Properties->Builders->New

Hmmm, are you looking for the "environment" tab under "External Tools Configuration" (the "Play" button with the red toolbox)?

If that's not what you are looking for, please disregard my commment.