Clair3 Version 2.0.0

[RaheelSyedAhmed]

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

Update to Clair3 for version 2.0.0. This pull request includes the Dockerfile and README.md updated for v2.0.0. I refactored the builder stage a bit so that another micromamba install step was not needed. I included symlinks from /clair3 to /opt to make sure that we had backwards compatibility with what we produced before.

The README.md is longer than 30 lines since I wanted to include the micromamba list and models downloaded.

[erinyoung]

It looks like a lot of the compiler software made it to the app stage, such as autoconf and automake. These software aren't needed at runtime, so it will help reduce the image size if we exclude them from the app stage.