Changing run_tests.py (Galaxy package inspired)

Hi,


I think that there are two changes to run_tests.py that would help a bit:

Add a flag to stop in a missing dependency. This would help in use cases 
where we know we want to be sure we are testing everything. For example:

- buildbot integration testing
- Galaxy package
- travis ?

Another flag would be to exclude non-free missing dependencies from the 
above. This is because we are not able to test all applications if we do 
not have proprietary versions.

I think that this would make integration testing and galaxy packaging 
muuch more robust. Because in those cases we want to be sure we are 
testing everything.

Tiago