At the interface of science and computing

The GATK License

One of the catalysts for restarting the blog was the new GATK license. GATK is a great tool for the genomics community and has historically had an open (MIT) license. However, with GATK 2.0, the license is moving to a hybrid licensing model. Per the announcement

The complete GATK 2.0 suite will be distributed as a binary only, without source code for the newest tools. We plan to release the source code for these tools, but its unclear the timeframe for this. The GATK engine and programming libraries will remain open-sourced under the MIT license, as they currently are for GATK 1.0. The current GATK 1.0 tool chain, now called GATK-lite, will remain open-source under the MIT license and distributed as a companion binary to the full GATK binary. GATK-lite includes the original base quality score recalibrator (BQSR), indel realigner, unified genotyper v1, and VQSR v2.

GATK 2.0 is being released under a software license that permits non-commercial research use only. Until the beta ends and the full GATK 2.0 suite is officially launched, commercial activities should use the unrestricted GATK-lite version. In the fall we intend to release the full version of GATK 2.0. The full version will be free-to-use version for non-commercial entities, just like the beta. A commercial license will be required for commercial entities. This commercial version will include commercial-grade support for installation, configuration, and documentation, as well as long-term support for each commercial release.

This is the wrong direction. Mixed licensing has been the bane of chemistry codes for years, but seeing it in the genomics world, especially for something that started with a more permissive license is a step in the wrong direction. Others have commented on the potential reasons; commercialization, concern about use by dodby DTC genomics sites; but all of those reasons are quite weak.

So why is this a mistake? First, it shuts out those who may not be academics, but want to (a) do good science, and (b) contribute to good science. What if I was a smart developer, perhaps at a small company, or working for myself. Suddenly, not only is the code no longer available without a license, but their ability to contribute to improving the code is severely diminished. Second, it betrays a lack of understanding of what open source means. Yes, there are plenty of open core models, but GATK is not a company or commercial service. If it plans to be one, they should say so more clearly and spin off a company that does the work of developing products around an open source core. This is neither here nor there, and all it does is come in the way of doing good science and writing good software.

In the end, this sets a terrible precendent. The world of open source has lots of good models for monetizing software. If that is the goal, it would be best to follow those models, or focus on providing quality services, but the non-commercial entity only model is a huge backward step.