adds cbird-util

[Kincekara]

This is part of my C-BIRD pipeline.

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

[erinyoung]

It looks like you're adding some custom scripts. Can you add some sort of test to make sure they work?

[kapsakcj]

It's good that at least the help options are pulled up, showing the scripts can be called and the python packages are accessible to those scripts

I don't think it's truly necessary to test out each script unless Kutluhan has an easy way to add some tests in.

I'd be OK to merge as is, considering this docker image is purpose built for C-BIRD. I imagine he will do testing of those scripts via the C-BIRD workflow prior to the next release.

[Kincekara]

Thank you @kapsakcj and @erinyoung. I already prepared a test folder and a script for that. I don't mind adding it here.

[kapsakcj]

Nice, thanks for adding those 👍 Looks good to me:

#14 [test 2/2] RUN cd /test && ./test.sh
#14 0.954 test_report.docx was created!
#14 1.283 test_basic_report.html was created!
#14 1.283 test_extended_report.html was created!
#14 1.943 test_QC_summary.html was created!
#14 DONE 2.0s

[erinyoung]

Looks good to me!

#14 [test 2/2] RUN cd /test && ./test.sh
#14 0.954 test_report.docx was created!
#14 1.283 test_basic_report.html was created!
#14 1.283 test_extended_report.html was created!
#14 1.943 test_QC_summary.html was created!
#14 DONE 2.0s

I'm going to merge this and deploy to dockerhub and quay.

[erinyoung]

You can check the status of the deployment here : https://github.com/StaPH-B/docker-builds/actions/runs/13161632015