Please support vsearch 2.13 or newer (Debian Packaging) about q2-vsearch HOT 3 CLOSED

@shayandoust, vsearch is now unpinned and Qiime2 2022.8 is shipping with up-to-date vsearch v2.21.1 directly from Bioconda!

Let us know if this fixes it!
(It does not address questions about how best to build, test, and ship Qiime2, but that's over my pay grade.)

from q2-vsearch.

Actually, it seems like these commands could exist in 2.13? So I am not sure what is going on here...

from q2-vsearch.

Hi @shayandoust!

A newer version of vsearch is on our radar, however there are a few blockers here:

• QIIME 2 is currently released as a distribution of packages: we test and verify all of the primary packages in the distribution in an environment that includes all of their dependencies: https://github.com/qiime2/environment-files/blob/master/latest/staging/qiime2-latest-py36-linux-conda.yml
• Because packages are released in a distribution, there is cross-talk between dependencies. As it stands, there is a hard pin on vsearch, imposed by deblur, which is a dependency of q2-deblur. Bumping the version of vsearch used here in q2-vsearch will require coordination with those other packages. It is on our todo list, but we just haven't gotten there, yet.

So with that in mind, I just want to point out a concern I have regarding repackaging QIIME 2 - we put in a significant amount of energy building, testing, and verifying conda packages (https://busywork.qiime2.org). We are unable to provide support for packages that are built outside of our ecosystem (we have no way to verify that they work correctly). As well, the notion of the "core distribution" of QIIME 2 is quickly disappearing, as we work on building out https://library.qiime2.org, a distribution center for QIIME 2 -related conda packages. I am unsure how your approach to repackaging will scale with that shift.

Is there any chance that the Debian Med packaging team can distribute this while maintaining the conda packages? You might've noticed we don't distribute any python packages - that is because our tools aren't explicitly python packages - conda lets us work with many other runtimes, etc. We have long-term plans of developing out QIIME 2 runtimes in R, as well - hopefully that helps illustrate our view of conda.

Keep us posted!

PS - it looks like you're running python 3.8 in the log above - again, we haven't tested or verified that QIIME 2 works with Python 3.8 - this information is all embedded in the conda recipes and conda packages used to distribute QIIME 2.

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