Add abricate v1.0.1 database for vibrio cholera

[cimendes]

This PR adds a custom vibrio database to the fabricate v1.0.1 container with sequences used for in silicon typing. It contains minimal alterations and tests for the custom database have been included. This is the same database as #618

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)
• 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]

Thank you for the PR! I made a few changes and I'm working on README.md right now. Will push that commit shortly.

In my commit I made the following changes:

• renamed custom database to include .fasta suffix
• changed ADD to COPY as per docker recommendation: https://docs.docker.com/develop/develop-images/instructions/#add-or-copy
• updated test to download test FASTA from NCBI FTP instead of keeping a copy in this repo to keep storage space down
• updated vibrio test commands to grep individually for expected genes, will error with exit code 1 if gene not found in output TSV

[kapsakcj]

OK, tests are passing and I've added the README specific to this tool as well as updated the main /README.md

I'll merge and deploy the docker image using the docker image name staphb/abricate:1.0.1-vibrio-cholera

I will not overwrite the :latest tag

[kapsakcj]

deploy workflow here if you'd like to follow along: https://github.com/StaPH-B/docker-builds/actions/runs/8899260163

docker image should be available shortly