add shigapass 1.5.0

[jvhagey]

This PR includes a Dockerfile for ShigaPass v1.5.0

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) -- they are in the container as they come with the software
• 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

[kapsakcj]

Thanks for the PR. Could you please add a step in the app stage to index the database so that users do not need to index prior to running the tool? Perhaps add in another RUN command after line 44 in the dockerfile

I see you have the -u option used in the test stage but it would be helpful to have that done independently in the app stage

[jvhagey]

Need to change permissions on the database folder for use. I will update shortly.

[jvhagey]

@kapsakcj ok, you had a good suggestion so I incorporated that and provided details in the readme. Hopefully, its clear.

[kapsakcj]

Thanks for making those changes! Will save users from doing an important step. And thank you for documenting that in the README 👍

The tool-specific README looks great, thank you for putting that together. I made few small changes to this readme as well as the main /README.md table

I tested with a handful of S flexneri, S sonnei, and S dysenteriae genomes and ShigaPass ran without issue and correctly predicted serotypes.

My only complaint is the....semi-colon....delimited output format, but that's not within the scope here

[kapsakcj]

Deploy workflow is here: https://github.com/StaPH-B/docker-builds/actions/runs/10712655108

The docker image should be available on dockerhub and quay.io shortly. Thank you!