This shouldn't be a particularly difficult excercise. We do some fairly similar stuff on one of my projects since half of it runs on Java using Ant to run relevant targets, and the other half is . Net (C#) for the UI.
The projects get run on windows machines for development, but the servers (Java) run linux, but in the UAT environment (linux) we need to run the nunits (integration tests). The real trick (not really a difficult trick) behind this is having a NAnt build file that can run in both environments which seems to be the same thing you're trying to do here.
It is worth noting that a lot of tools like Nant run on mono 'out of the box', i.e.
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