I have a pipeline for analysing sequencing data, and one of the steps is a variant calling step using GATK. I'm thinking about somehow making my pipeline easy to run and then make it publicly available (perhaps through GitHub). I'm in academia, and that's the envisioned audience for making the pipeline public (i.e. non-commersial only). I'm very new at this whole licensing thing, so I'm wondering in what way (if any) I'm allowed to use the GATK parts of my pipeline.
1) The GATK parts of my pipeline is basically a number of scripts calling the various GATK/Picard functions. Can I share these scripts? Under what license/cavets/etc?
2) Can I distribute the GATK files with the rest of my scripts, to lessen the user's need to download and install it themselves? (my guess is "no" to this, but I'm asking just to be sure.)
3) If the answer to (2) is "no", can I still provide a readme/walkthrough to the users on how to download and install GATK?
4) Granting that at least (1) is okay, what open source software license (if any) can I put on my pipeline?
