adding ivar version 1.4.3

[erinyoung]

There's a new version of ivar!

It looks like this is mainly minor changes according to the release notes https://github.com/andersen-lab/ivar/releases/tag/v1.4.3

I, however, have made some major changes from the Dockerfile in 1.4.2:

1. I added a builder stage where samtools, htslib, and ivar are installed
2. There is no longer bedtools, bwa, or minimap2. I have tried using ivar's piping method, but it too slow for my purposes. If someone else uses this option, let me know and I can add them back in
3. I added a CMD line

Pull Request (PR) checklist:

• [X] Include a description of what is in this pull request in this message.
• [X] 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 )
• [X] 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)
  • [X] (optional) All test files are located in same directory as the Dockerfile (i.e. shigatyper/2.0.1/test.sh)
• [X] Create a simple container-specific README.md in the same directory as the Dockerfile (i.e. spades/3.12.0/README.md)
  • [X] If this README is longer than 30 lines, there is an explanation as to why more detail was needed
• [X] Dockerfile includes the recommended LABELS
• [X] Main README.md has been updated to include the tool and/or version of the dockerfile(s) in this PR
• [X] Program_Licenses.md contains the tool(s) used in this PR and has been updated for any missing

[Kincekara]

Thank you for putting all these together! I have no objection to removing bedtools, bwa, or minimap2. I will merge this if nobody says against it.

[erinyoung]

@kevinlibuit or @kapsakcj , do you use the ivar image? Do you think it'd be okay to remove bedtools, bwa, and minimap2 from it?

[kapsakcj]

We do use bwa & samtools within the ivar docker image, but don't use bedtools or minimap2

I'm fine either way if you want to remove all of those or keep some/all. We could make a custom image that includes everything we need if necessary.

[Kincekara]

Thank you for putting all this together! Deploy link: https://github.com/StaPH-B/docker-builds/actions/runs/10308039008