polypolish 0.6.0

[erinyoung]

Polypolish has had a recent breaking update.

Notably, the removal of polypolish_insert_filter.py, which changes how this tool is used.

I copied the prior Dockerfile, but I've made some substantial changes:

• there is now a builder stage, which uses rust as its base
  • polypolish is now built from source and the copied to the app stage
• the test had to change to accommodate the removal of polypolish_insert_filter.py
• added CMD layer

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
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[Kincekara]

Just asking out of curiosity; is the prebuilt binary not working on Jammy?

[erinyoung]

I initially tried the prebuilt binary and ran into issues. Unfortunately I didn't keep any notes and I don't remember what those issues were.

[Kincekara]

Thank you for your reply and changes. This looks great. I am merging it.

[Kincekara]

Thank you for putting altogether this!
You can check the image deployment from here: https://github.com/StaPH-B/docker-builds/actions/runs/7995283808.