Closed j23414 closed 9 months ago
I had to install
ncbi-datasets-cli
Ah I see what happened. It appears we switched from NCBI Virus to NCBI Datasets on Sept 11, 2023 and the ingest README here and in Monkeypox need to be updated. I'll ensure that the ingest README for Monkeypox is updated first, followed by a rebase of this PR. Additionally, I'll submit a PR to update the ambient documentation.
Error: Internal error (invalid zip archive)
I've encountered this error during testing in the Monkeypox repository as well. It seems to be a known intermittent issue with ncbi datasets . To mitigate this, we have a retries: 5
directive in the Snakemake rule.
(For documentation: The copy-and-pasting mpx ingest approach serves several benefits, including maintaining consistency across pathogen repositories, facilitating focused review on new changes, and providing a method to highlight changes that need to be propagated to other repositories.)
Description of proposed changes
Splitting out dengue ingest changes PR#6 into smaller, more focused pull requests. Especially since there have been significant improvements to linking reusable pathogen ingest scripts.
The primary scope of this PR includes:
ingest/vendored
subdirectory.To ease development and review, tasks that are not part of this PR but will be submitted as future PRs include:
Related issue(s)
Checklist