Heads up:
We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra

Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

GATK License and galaxy

lindenblindenb FranceMember ✭✭

Our lab provides a protected instance of galaxy to our registered users ( N=~24 and growing )

Those users come from anywhere in France.

Can I legally wrap GATK into a galaxy tool for our users ?



  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi @lindenb,

    Under the terms of the academic license, you can't make GATK available as a service to users outside of your institution. If it's a closed network, eg for a collaboration between several academic institutions, it might be possible to make an accommodation, but if anyone can register for the service then you'd have to seek a custom licensing agreement. We have done this before for other projects like Trinity CTAT on Indiana U's Galaxy server (https://galaxy.ncgas-trinity.indiana.edu/), though that was for supporting specific pipelines, not for generic use of GATK. A simpler option would be to set up your instance so that your users have to upload their own GATK jar to the toolshed; I believe that's what the main public Galaxy server does. Technically you should still seek a plugin developer license to be completely covered (which would be free for academic purposes), and just a matter of some paperwork. If you'd like to pursue this further, please email me at vdauwera at broadinstitute dot org.

Sign In or Register to comment.