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adds amrfinder 4.0.19#1195

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kapsakcj merged 4 commits intoStaPH-B:masterfrom
Kincekara:amrfinder
Feb 7, 2025
Merged

adds amrfinder 4.0.19#1195
kapsakcj merged 4 commits intoStaPH-B:masterfrom
Kincekara:amrfinder

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@Kincekara Kincekara commented Feb 7, 2025

closes #1191
No major changes.

diff build-files/ncbi-amrfinderplus/4.0.15-2024-12-18.1/ build-files/ncbi-amrfinderplus/4.0.19-2024-12-18.1/
diff build-files/ncbi-amrfinderplus/4.0.15-2024-12-18.1/Dockerfile build-files/ncbi-amrfinderplus/4.0.19-2024-12-18.1/Dockerfile
3c3
< ARG AMRFINDER_VER="4.0.15"
---
> ARG AMRFINDER_VER="4.0.19"
99,100c99,100
< stxtyper --version && \
< blastn -version
\ No newline at end of file
---
>   stxtyper --version && \
>   blastn -version
\ No newline at end of file
diff build-files/ncbi-amrfinderplus/4.0.15-2024-12-18.1/README.md build-files/ncbi-amrfinderplus/4.0.19-2024-12-18.1/README.md
7c7
< - hmmer v3.3.2
---
> - hmmer v3.4
9c9
< - [stxtyper](https://github.com/ncbi/stxtyper/) v1.0.31 (Shiga toxin subtyping tool, added in AMRFinderPlus v4.0.3)
---
> - [stxtyper](https://github.com/ncbi/stxtyper/) v1.0.40 (Shiga toxin subtyping tool, added in AMRFinderPlus v4.0.3)

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/build-files/samtools/1.15 )
  • Directory structure as name of the tool in lower case with special characters removed with a subdirectory of the version number in build-files (i.e. docker-builds/build-files/spades/3.12.0/Dockerfile)
    • (optional) All test files are located in same directory as the Dockerfile (i.e. build-files/shigatyper/2.0.1/test.sh)
  • Create a simple container-specific README.md in the same directory as the Dockerfile (i.e. docker-builds/build-files/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
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kapsakcj commented Feb 7, 2025

Thank you for the PR and for updating those comment lines & LABEL. Tests pass and everything looks good so I'll merge and deploy

@kapsakcj kapsakcj merged commit 637008d into StaPH-B:master Feb 7, 2025
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kapsakcj commented Feb 7, 2025

deploy workflow here, the docker image should be available shortly: https://github.com/StaPH-B/docker-builds/actions/runs/13206256604

@Kincekara Kincekara deleted the amrfinder branch February 7, 2025 20:16
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[Request An Update]: add ncbi amrfinderplus v4.0.19

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