Add GH Action workflows for ingest #52
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Automated runs of the ingest workflow for the public NCBI data. This is scheduled to run daily similar to other pathogen ingests. We are not running the phylogenetic builds automatically for now since there are frequent outgroups that need to be manually excluded.
The ingest-fauna workflow is not scheduled to run automatically since updates to fauna are done manually. This at least makes it easy to run the workflow via GH Actions instead of having to do it locally.
genehack
approved these changes
Jun 10, 2024
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Description of proposed changes
The
ingest-ncbiGH Action workflow is scheduled to run daily at 10AM PDT so that we get automated updates of the NCBI data.The
ingest-faunaGH Action workflow is available to be run manually as needed whenever new data has been uploaded to fauna.Outside of this PR, I had to add avian-flu to our supported pathogens to use the short-lived AWS credentials in
pathogen-repo-buildand added organization secretsRETHINK_AUTH_KEYandRETHINK_HOSTto this repo.Related issue(s)
Resolves #43
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