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ENH: add fetch-eggnog-proteins action #109

Merged
merged 20 commits into from
Jan 19, 2024
Merged

ENH: add fetch-eggnog-proteins action #109

merged 20 commits into from
Jan 19, 2024

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Sann5
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@Sann5 Sann5 commented Dec 24, 2023 •
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Whats New

Blocked by another PR

Run it locally

Assuming you have a working environment, run the following.

  1. First, clone the repo and checkout the PR branch:
git clone [email protected]:bokulich-lab/q2-moshpit.git
gh pr checkout 109
  1. Now we are ready to run the action locally. You need at least 18 Gb of free disk space.
qiime moshpit fetch-eggnog-fasta --o-eggnog-fasta one_taxa_data.qza --verbose
  1. Alternatively, you can run the tests for this action (nothing will be downloaded).
cd <you_local_path_to>/q2-moshpit
pytest -W ignore -vv -k fetch_eggnog_fasta

@Sann5 Sann5 self-assigned this Dec 24, 2023
@Sann5 Sann5 requested a review from misialq December 24, 2023 12:15
misialq
misialq requested changes Jan 3, 2024
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q2_moshpit/eggnog/_dbs.py Show resolved Hide resolved
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misialq
misialq reviewed Jan 3, 2024
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@Sann5 Sann5 requested a review from misialq January 11, 2024 14:11
@Sann5 Sann5 mentioned this pull request Jan 12, 2024
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misialq
misialq reviewed Jan 15, 2024
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@Sann5 Sann5 added the enhancement New feature or request label Jan 15, 2024
@Sann5 Sann5 requested a review from misialq January 15, 2024 13:46
@misialq misialq changed the title ENH: Fetch ReferenceDB[EggnogSequenceTaxa] for build-eggnog-diamond-db action ENH: fetch ReferenceDB[EggnogProteinSequences] for build-eggnog-diamond-db action Jan 15, 2024
This was referenced Jan 18, 2024
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@misialq misialq changed the title ENH: fetch ReferenceDB[EggnogProteinSequences] for build-eggnog-diamond-db action ENH: add fetch-eggnog-proteins action Jan 19, 2024
misialq
misialq approved these changes Jan 19, 2024
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Looks good, let's merge!

q2_moshpit/plugin_setup.py Outdated Show resolved Hide resolved
@misialq misialq merged commit 46164d2 into bokulich-lab:main Jan 19, 2024
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@Sann5 Sann5 deleted the fetch_eggnog_fasta branch January 19, 2024 10:33
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@misialq misialq misialq approved these changes

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ENH: Fetch EggnogSequenceTaxa for build-eggnog-diamond-db action
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