revamping artic with updated medaka

[erinyoung]

This is a new container with the most-current artic and medaka versions. I've also finally added artic to the licenses.

Both of these tools' bioconda packages lag significantly, and I'd like the current medaka models.

I've changed the directory structure of this image. It's now

artic/${artic_version}-${medaka_version}/

I would like the tag to also follow the pattern of ${artic_version}-${medaka_version}, so this one would be tagged 1.2.4-1.9.1.

I have not included any primers in this. It's already fairly large and my use-case is with non-artic primers at the moment anyway.

Lastly, in a future PR, I'd like to move the old artic* files into /artic for cleanliness purposes.

Pull Request (PR) checklist:

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• 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 )
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• 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! Since I'm downloading files from the ENA, I can't test my 'test' locally. I'll fix this in gitpod and then convert this from draft stage.

[erinyoung]

@kevinlibuit , I hope you have time to review this image. It's now ready for review (I had some typos in the test layer that I needed to resolve).

Once I finish this image, I'm going to apply the same ideas to the artic-ncov2019-epi2me Dockerfile (#689)

[erinyoung]

@kevinlibuit , does this look like it would work?

[kevinlibuit]

Will test our workflows using the UPHL's identical docker on quay to ensure things aren't breaking in any of our workflows:

[erinyoung]

There's a current version of this on UPHL's quay repo : quay.io/uphl/artic tag 1.2.4-1.9.4-1

[kevinlibuit]

Will also need to test availabilities of updated models, e.g. r103_hac_g507

[erinyoung]

@kevinlibuit , medaka has gone through a few updates recently, so I've updated the Dockerfile to use the most recent version of medaka.

The readme now lists all the supported models for medaka, or did you have something else in mind?

There's a current version of this image at quay.io/uphl/artic tag 1.2.4-1.11.1

[erinyoung]

@kevinlibuit , do you have time to review this?

[kevinlibuit]

Apologies for the delay! Tested this both locally and used the uphl quay image to ensure no issues with our workflows on Terra. Thanks, also, for adding info on available models.

[kevinlibuit]

Accidentally closed!