adding krona 2.8.1 with krakentools

[sage-wright]

Krona is a pretty cool tool for visualizing metagenomic data. However, it's got a weird quirk where if you want to look at viral metagenomic data, you'll have to run it through KrakenTools before in order to make sure that the viral sequences don't show up as "other root".

This image has both the latest version of krona and the commit of krakentools used in the already existing docker image within staphb.

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
    • wanted to provide additional examples for when viral metagenomic data is used
• 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]

This isn't an issue for @sage-wright , but it is strange that GA didn't pick up the new Dockerfile.

Base commit: c032b57d096d634950b830e60659b704738ea18a
Head commit: 6aff0[7](https://github.com/StaPH-B/docker-builds/actions/runs/12585667108/job/35077931338?pr=1164#step:3:8)5d7b0daa680b7f6cba4f1493f7d59bbcfe
All: []
Added: []
Modified: []
Removed: []
Renamed: []
Added or modified: []
Added, modified or renamed: []

I'm unsure why it didn't work, so I may have to mess with this PR to see if I can trigger the GA.

[erinyoung]

Closes #632

[kapsakcj]

The GHActions is not working because the "get-changed-files" step in the workflow has a filter to look for changed files matching:

build-files/*/*/Dockerfile

and the file that is added in this PR is:

build-files/krona/Dockerfile

So I think there needs to be an additional subdir with the version number of krona, e.g. build-files/krona/2.8.1/Dockerfile

[erinyoung]

Ah. Yes. That's kind of obvious...

[sage-wright]

Oh oops haha. I knew I was forgetting something obvious. I'll fix that and make the requested changes as well 🙂

[sage-wright]

@erinyoung, it looks like the shebang for the KrakenTools scripts is incompatible w/ how I've installed Python. It's looking for /usr/bin/env python but python is at /usr/bin/python3. I'm not sure how to fix this, so I've just removed the folder from the path to avoid any confusion there. If you know how, I'd love to hear it!