adding in additional vadr images

[erinyoung]

I do actually feel bad about adding so many images to one PR. I decided to add them all to this PR for one reason: the PR associated with individual images would all edit the same line in the main README.md causing merging conflicts. In theory, this would mean that I would need to make these images one at a time and get each PR approved before I started on the next. I only get sporadic spans of time to work on these, though, so I would never finish at that rate.

The images with the prospective tags of 1.7-{flu,hav,mpxv,rsv,sarscov2} are different from their 1.6.4 version in that they are now built off the 1.7 image instead of rebuilding vadr for each one.

1.7-2602 is the image with all the models and should replace the 'latest' tag (finally).

I did check to see if there were new models for flu, hav, mpxv, rsv, and sarscov2, and it didn't look like there were new ones.

I updated each tools' readme to reflect updated versions of dependencies.

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

Knowing my luck, finally creating this PR means that new version of VADR will come out soon.

[kapsakcj]

A few things that likely need attention in this PR:

• Consider updating the base image for all dockerfile to ubuntu:noble (equivalent to 24.04) as it's the most up-to-date "LTS/Long Term Support" distribution from ubuntu. There are higher versions available (plucky/25.04, questing/25.10, resolute/26.10) , but none of these have the LTS designation. More info: https://hub.docker.com/_/ubuntu and https://ubuntu.com/about/release-cycle
  • I did a quick test by switching to ubuntu:noble base image for build-files/vadr/1.7/Dockerfile and it seemed to build successfully without issue. It should be the same for the other dockerfiles in this PR
• VADR's install script now installs more model files for various organisms by default. It includes sars-cov-2, rsv, corona, and mpxv, which will all increase the final image size. We will need to add some code to delete these model files after installation or some other strategy to prevent downloading them in the first place. I'm reaching out to the author to ask about this.
  • https://github.com/NLM-DIR/vadr/blob/vadr-1.7/RELEASE-NOTES.md#vadr-17-release-september-2025-major-update
• Looks like VADR has moved in GitHub, it's now under a different organization, so links throughout will need to be updated: https://github.com/NLM-DIR/vadr

[kapsakcj]

FYI, we could add a line to remove the lines within vadr-install.sh that download the model files: NLM-DIR/vadr#96 (comment)

[erinyoung]

@kapsakcj , I have removed the 1.7-2602 files from this PR, because that seems to be where most of the comments are directed towards. The remaining images are intended to be built off of the staphb/vadr:1.7 image, which does not contain any models and was built last year.

I have also added the new url for the vadr repository to the main readme and program licenses.

I think I can work on updating the 'latest' vadr version (tag 1.7-26*) sometime later. The current staphb/vadr:latest vadr version is from 1.6.4.

[erinyoung]

Next steps for this PR includes the creation of a vadr-1.7-slim base for these to use instead