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Auto deploy public builds #114

Merged
merged 4 commits into from
Aug 9, 2023
Merged

Auto deploy public builds #114

merged 4 commits into from
Aug 9, 2023

Commits on Aug 2, 2023

  1. Add all_deploy rule for nextstrain-public

    Uses the Nextstrain CLI to upload all inputs for `all_public` in
    rename.smk to the provided URL.
    joverlee521 committed Aug 2, 2023
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  2. workflows/run-public-builds: auto deploy builds

    Use the new `all_deploy` rule to automatically deploy all builds
    as the last step of the public builds pipeline.
    
    The public builds should no longer have to be manually inspected since
    outliers are now automatically removed.¹
    
    ¹ #110
    joverlee521 committed Aug 2, 2023
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Commits on Aug 9, 2023

  1. nextstrain-public/all_deploy: remove log directive

    We were running into the Snakemake issue where the log directive in
    the default rule causes it to skip tasks.¹ This issue has been fixed
    since Snakemake 7.25.1, but we are still pinned to 7.24.1 in
    nextstrain/docker-base.²
    
    Just removing the log directive here is the simplest fix for this
    particular issue. We'll still be able to see the upload logs in
    the AWS Batch logs.
    
    ¹ snakemake/snakemake#2142
    ² https://github.com/nextstrain/docker-base/blob/95cea4f44a803ce27992706c87a7237492dbb083/Dockerfile#L277
    joverlee521 committed Aug 9, 2023
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  2. Configuration menu
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