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add ncbi-amrfinderplus 3.11.20 & db 2023-09-26.1 #761

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merged 4 commits into from
Oct 3, 2023

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kapsakcj
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@kapsakcj kapsakcj commented Sep 29, 2023

added dockerfile for new amrfinder & database versions. does not build successfully yet, issue in test layer

will fix later unless someone else wants to push a commit

Test layer has been fixed, the expected test results files for db release 2023-09-26.1 did not make it into the v3.11.20 release, so I had to manually download those files for the tests. Will revert back for the next dockerfile.

Here's the commit where the 2 files were updated by the authors: ncbi/amr@185a69f

Other than that, the dockerfile is identical to the previous version

Pull Request (PR) checklist:

  • Include a description of what is in this pull request in this message.
  • The dockerfile successfully builds to a test target for the user creating the PR. (i.e. docker build --tag samtools:1.15test --target test docker-builds/samtools/1.15 )
  • Directory structure as name of the tool in lower case with special characters removed with a subdirectory of the version number (i.e. spades/3.12.0/Dockerfile)
    • (optional) All test files are located in same directory as the Dockerfile (i.e. shigatyper/2.0.1/test.sh)
  • Create a simple container-specific README.md in the same directory as the Dockerfile (i.e. spades/3.12.0/README.md)
    • If this README is longer than 30 lines, there is an explanation as to why more detail was needed
  • Dockerfile includes the recommended LABELS
  • Main README.md has been updated to include the tool and/or version of the dockerfile(s) in this PR
  • Program_Licenses.md contains the tool(s) used in this PR and has been updated for any missing

@kapsakcj kapsakcj marked this pull request as ready for review October 2, 2023 15:26
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@erinyoung erinyoung left a comment

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I have no changes to recommend.

Did you want @Kincekara to review this one?

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kapsakcj commented Oct 3, 2023

Did you want @Kincekara to review this one?

Yes, please! Do not merge just yet.

We are going to meet and I'll walk him through the steps

@Kincekara Kincekara merged commit fb1bb51 into master Oct 3, 2023
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I kicked off the deploy workflow. You can follow the progress here https://github.com/StaPH-B/docker-builds/actions/runs/6398236572

@kapsakcj kapsakcj deleted the cjk-amrfinder-update-sept2023 branch March 8, 2024 21:17
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3 participants