refgenieserver

This folder contains code for an API to provide reference genomes. refgenieserver can do 2 things: archive an existing refgenie folder, and then serve it.

How to serve

Building container

In the same directory as the Dockerfile:

docker build -t refgenieserverim .

Running container for development:

You can run it directly after installing with pip install, like this:

refgenieserver serve -c refgenie.yaml -p 5000

Better, though, is to use the container. Mount a directory of files to serve at /genomes:

docker run --rm -p 80:80 --name refgenieservercon \
  -v $(pwd)/files:/genomes \
  refgenieserverim refgenieserver serve -c refgenie.yaml 

Running container for production:

Run the container from the image you just built:

docker run --rm -d -p 80:80 \
  -v /path/to/genomes_archive:/genomes \
  --name refgenieservercon \
  refgenieserverim refgenieserver serve -c /genomes/genome_config.yaml 

Make sure the genome_config.yaml filename matches what you've named your configuration file! We use -d to detach so it's in background. You shouldn't need to mount the app (-v /path/to/refgenieserver:/app) because in this case we're running it directly. Terminate container when finished:

docker stop refgenieservercon

Interacting with the API web server

Navigate to http://localhost/ to see the server in action.

You can see the automatic docs and interactive swagger openAPI interface at http://localhost/docs. That will also tell you all the endpoints, etc.

Monitoring for errors

Attach to container to see debug output:

docker attach refgenieservercon

Grab errors:

docker events | grep -oP "(?<=die )[^ ]+"

View those error codes:

docker logs <error_code>

Enter an interactive shell to explore the container contents:

docker exec -it refgenieservercon sh