Downgrading dependencies is needed when installing bakta from conda about bakta

[mmcguffi]

I also ran into this with Bakta 1.6.1 via conda

Building on what @LeonCharlesTranchevent said (thanks for documenting!), I also had to pin biopython -- here is a pinned yaml that worked for me:

name: annotation
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - bakta=1.6.1
  - diamond=2.1.8
  - ncbi-amrfinderplus=3.11.26
  - biopython=1.81

I also had to update the AMRFinderPluss internal database, here is that cmd for convenience:

amrfinder_update \
  --force_update \
  --database ${database_loc}/db/amrfinderplus-db

And of course, thank you @oschwengers for creating such a great tool

[oschwengers]

Hi and thanks for reporting both issues and potential solutions!

There is an issue with Diamond in v2.1.9 and downgrading to v2.1.8should do the trick until there is an upstream patch for Diamond.

Regarding AMRFinderplus: They recently updated its database scheme. Best you can do is to update both AMRFinderplus and its database as @mmcguffi suggested.

@mmcguffi Is there a specific issue with BioPython? If so, could you please open a dedicated issue for that? I wasn't aware of that.

Again, thanks for reporting and documenting!