ENH: add fetch-eggnog-hmmer-db action

[Sann5]

What's new

• An action that fetches a HMMER database. This will be used downstream to find seed orthologues (to be implemented).
• Closes ENH: add fetch-hmmer-db action #167
• ❌ CI tests should fail until a version of q2-types with the PR mentioned below is up in conda

Blocked by...

Preview Give feedback

1. depends on ENH: add ProfileHMM[*] semantic types qiime2/q2-types#328

Run it locally

1. Checkout the PR branch.

Assuming 1) you already have a local copy of q2-moshpit that is installed in editable mode in your activated virtual environment and 2) that "origin" is the name of the remote of this GitHub repo; run the following.

cd my_q2-moshpit
PR=173
git fetch origin pull/${PR}/head:pr-${PR}
git checkout pr-${PR}

If the PR in q2-types mentioned above is not yet merged you will need to do the same for q2-types. E.g:

cd my_q2-types
PR=328
git fetch origin pull/${PR}/head:pr-${PR}
git checkout pr-${PR}

2. Test it out!

qiime moshpit fetch-eggnog-hmmer-db --p-taxon-id 1100069 --output-dir 1100069_db --verbose

[VinzentRisch]

Hi @Sann5
I don't know if i have time to look at it tomorrow. Maybe I'll only look at it next week. Hope that is not a problem :)

[VinzentRisch]

Looks very good!
I ran it and it works with no problems.
See some minor changes and typos below. :)

[VinzentRisch]

Everything looks good! :)

[Sann5]

I made quite a bit of changes @VinzentRisch since there were changes required in the dependent PR. could you give it a another look before i merge?

[misialq]

Hey @Sann5, I think this still needs a bit of work - see below.

[misialq]

Hey @Sann5, thanks for those changes! The error handling is much better now 🥇 See some more comments below.

[github-actions]

This PR/issue depends on:

• ENH: add ProfileHMM[*] semantic types qiime2/q2-types#328