Suggested workflow for updating to GATK 2.4 code base
I'm struggling somewhat with updating my own code to the 2.4 code base, and I would be very happy for any help you might offer on how to do this. First of all, I guess I should switch my upstream repository to https://github.com/broadgsa/gatk-protected (as I'm working in an academic not-for-profit environment).
What I would like to do is to rebase my own devel branch on the master branch of the gatk-protected repository. But trying to do so gives me a lot of conflicts in files that I have not altered in my own branch. Is resolving all of these conflicts one by one the only way to do this, or have I really got some problem with my understanding of how this is done? I'm guessing the later.
Either way it would be really nice to get some pointers on how to figure this one out.