QIIME2 in Galaxy platform

I have not yet tried QIIME2. I was using QIIME in galaxy platform. Is it possible to have QIIME2 also in Galaxy?

Great question!

As far as I know, you are the first person to ask about Galaxy integration. Let’s see what the devs have to say?


Hi @RosePaul!

I remember stumbling across a relevant discussion about QIIME 2 in Galaxy a while back, but I can’t seem to locate it again :frowning:

In any case, QIIME 2 is designed from the ground up to be used by other tools, granted we have very limited (read: none) docs on how to accomplish this, but in principle it should be pretty straight-forward. Every action is discoverable and has a explicitly described API. This means interfaces can auto-generate UI based on that description (this is how the Artifact API, q2cli, and q2studio work).

We’re working on a bunch of docs right now which will hopefully inspire others to develop software using and on-top of the QIIME 2 ecosystem, and Galaxy is definitely something we have our eye on.

From my very limited understanding, I think the main challenges will be generating the XML specs from our plugin-manager (should be possible to do, q2cli does a similar thing for it’s JSON cache), and constraining inputs based on their semantic type instead of just the file extension (I’m less certain how that would be accomplished).

If anyone knows some Galaxy devs who would be interested in integrating QIIME 2, send them our way; we’d love to chat!


Hi, Thank you for the reply. I am not a developer, so I guess I will wait for now. Thanks again for the reply.


This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.