Closed jvhagey closed 1 month ago
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
Need to change permissions on the database folder for use. I will update shortly.
@kapsakcj ok, you had a good suggestion so I incorporated that and provided details in the readme. Hopefully, its clear.
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
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!
This PR includes a Dockerfile for ShigaPass v1.5.0
Pull Request (PR) checklist:
docker build --tag samtools:1.15test --target test docker-builds/samtools/1.15
)spades/3.12.0/Dockerfile
)shigatyper/2.0.1/test.sh
) -- they are in the container as they come with the softwarespades/3.12.0/README.md
)