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updating the emmtyper blast database #1084

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updating the emmtyper blast database #1084

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erinyoung
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There is NOT a new version of emmtyper, but there ARE new emmtypes.

I use emmtyper for Group A Strep isolates (often S. pyogenes). I noticed awhile ago (MDU-PHL/emmtyper#21 (comment)) that there did not seem to be an easy way to update the fasta file used for the emm types. @Daniel-VM has created a script just for this problem at https://github.com/Daniel-VM/cdc-utilities, which I thought might be useful to add to the image.

I, therefore, took the original emmtyper Dockerfile, updated the base micromamba image to 1.5.8, simplified the lines, add a CMD line, and added in some lines to use emm_download_makedb.py to download the most-recent files.

I also updated the corresponding README.md

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

@erinyoung erinyoung closed this Oct 29, 2024
@erinyoung erinyoung deleted the erin-emmtyper branch October 29, 2024 17:54
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