adds pangolin 4.3.1 and pangolin-data 1.23

[kapsakcj]

added dockerfile for pangolin 4.3.1 and pdata 1.23.

Still need to upgrade to usher 0.6.3 when it is available on bioconda due to the edge case bug mentioned in the pangolin-assignment release: https://github.com/cov-lineages/pangolin-assignment/releases/tag/v1.23 . Set this PR as a draft for now.

Changes from previous dockerfile:

• upgraded to micromamba 1.5.1 (which looks to be a debian:bookworm base image)
• upgraded to pangolin-data 1.23
• upgraded to scorpio 0.3.19
• upgraded to constellations 0.1.12
• (when available) upgrade to usher 0.6.3 We are sticking with v0.6.2

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]

Sorry for getting to this so late!

[erinyoung]

Actually, I just realized that it was still a draft. My apologies for filling up your inbox!!!

[kapsakcj]

No worries! I may end up just going with usher 0.6.2 instead of waiting for 0.6.3 to be released.

Probably more important to get the ability to detect the latest lineages instead of worrying about a bug with calling ancient A lineages....

[kapsakcj]

OK this is ready for review & deployment. I don't want to wait for the next version of usher to be released to get this image published & available.

I added a warning to the README.md for this docker image and will communicate the edge case bug when announcing that the docker image is available to slacks/elsewhere

We can upgrade to usher v0.6.3 the next time we release a docker image for pangolin

[erinyoung]

Everything looks good!

[erinyoung]

I have merged this PR, but I am going to let you push to dockehub and quay.

I think that it would use the tag '4.3.1-pdata-1.23', but I'd rather be "safe than sorry". :D