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add tbprofiler version 6.2.1 #974

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sage-wright
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@sage-wright sage-wright commented May 10, 2024

There's a new version of TB-Profiler! A few bug fixes were included (samclip not being used, lineage prediction error, and issue with update_tbdb) and I've updated the database used in the docker as well to the most recent commit hash.

I'm setting this PR as draft for now as the new release is still working its way through the Bioconda PR process.

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)
  • Create a simple container-specific README.md in the same directory as the Dockerfile (i.e. spades/3.12.0/README.md)
  • 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 self-requested a review May 10, 2024 19:26
@erinyoung
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I don't know if 6.2.1 is going to get on conda.

Do you think it's worthwhile to install the dependencies from sourece?

https://github.com/jodyphelan/TBProfiler?tab=readme-ov-file#manually

@kapsakcj
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Jody's working on getting the latest version into bioconda bioconda/bioconda-recipes#47826

@jodyphelan
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jodyphelan commented May 20, 2024

Just to update you all, there seems to be an issue with bioconda CI which is blocking the uppdate being merged into bioconda.

@kapsakcj
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I just resolved README.md conflict, which triggered the CI to test building this docker image.

Should build successfully now that tb-profiler 6.2.1 is available on bioconda 🤞

@jodyphelan Thanks for the update and for all of your work and maintenance of tb-profiler!

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