add kaptive 2.0.7 & custom Vibrio parahaemolyticus serotyping db, take 2

[kapsakcj]

This PR will close #661

This PR adds a dockerfile for Kaptive v2.0.7 and adds a new database for Vibrio parahaemolyticus locus typing.

Differences from previous dockerfile:

• Added Vp databases (GBK files) to container filesystem
• Added tests for analyzing 2 Vp genomes with new Vp databases
• added default CMD to end of app stage
• moved test commands to write to /test in filesystem
• quieted down wget and gunzip commands

CC @stitam - please let us know if you have any feedback. Wanted to give you a heads up since you originally wrote the dockerfile

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]

I've pushed the docker image to my personal dockerhub in case anyone wants to test it out before we merge the PR.

https://hub.docker.com/r/kapsakcj/kaptive

kapsakcj/kaptive:2.0.7

The tests (Vp genomes included) run successfully, but I have not tested the new database extensively. Would be nice to run on more genomes before merging this PR. (not required but nice to do)

[erinyoung]

I think it works as expected. I was hoping an identification of O groups, but that doesn't seem to be what this database is for (or perhaps my test files were faulty).

Can we move the Vibrio database to /kaptive/reference_database to be with the rest of them, though?

[kapsakcj]

Can we move the Vibrio database to /kaptive/reference_database to be with the rest of them, though?

Sure, I don't see any issue with that.

Feel free to push commits here, or I can get to it in the near future (next week or so)

[kapsakcj]

also if we move the database the readme.md will need to be updated accordingly too