LANG: python 3.9 update (metagenome)

[lizgehret]

No description provided.

[ebolyen]

This seed env sans-q2 solves locally, there must be some conflict in the q2 conda recipes, but not sure where.

What I would probably do next is install the seed-environment without q2. Then using the rebuilt channel from the last run, install plugins one by one into the seed-sans-q2 env and see which one causes the solver to choke. A pain, but should be locally reproducible.

[lizgehret]

This seed env sans-q2 solves locally, there must be some conflict in the q2 conda recipes, but not sure where.

What I would probably do next is install the seed-environment without q2. Then using the rebuilt channel from the last run, install plugins one by one into the seed-sans-q2 env and see which one causes the solver to choke. A pain, but should be locally reproducible.

yep, we're on the same page! 👍

[lizgehret]

Did a local install of an environment file containing:

• external deps (non-q2) in seed env from amplicon distro (with one change for hdf5 version)
• all versioned deps from metagenome-specific plugins (assembly, fondue, moshpit, sapienns)

Then started installing Q2 plugins one-by-one in their generational order. All plugins install successfully without version conflicts except for:

• q2-assembly
• q2-moshpit

The following dependencies are in conflict with the existing/required environment (present in both assembly and moshpit):

downgrade
r-base 4.3.3 -> 4.3.1

upgrade
eggnog-mapper 2.1.10 -> 2.1.12
entrezpy 2.1.2 -> 2.1.3
notebook 6.5.5 -> 7.0.8
r-reticulate 1.36.0 -> 1.36.1
tqdm 4.62.3 -> 4.66.2

(Note that these are all external packages with pins set from other plugins in the existing environment)

• Additionally, assembly and moshpit have different requirements for the version of busco. Moshpit pins busco at 5.5.0 and assembly requires an upgrade to 5.6.1.

• The final conflict is also within moshpit, which requires the following upgrade of sepp: 4.4.0 -> 4.5.1.

Will need to play around with moshpit and assembly locally on Monday to see what we can do to fix these conflicts, but leaving this here for posterity.

[lizgehret]

Closing in favor of Prepare PR.