This server provides both a web interface and a RESTful API. Users may explore and download archived indexes from the web interface or develop tools that programmatically query the API.
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
In the same directory as the Dockerfile:
docker build -t refgenieserverim .
Running container for development:
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
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
How to archive
Refgenieserver can also archive your assets, creating the directory for asset archives needed to serve.
First, make sure the config has a genome_archive key that points to the directory where you want to store the servable archives (genome_archive is not added automatically by `refgenie init <http://refgenie.databio.org/en/latest/usage/#refgenie-init-help>`__). Your first time you will need to manually add this to tell refgenieserver where to store the archives.
refgenieserver archive -c CONFIG
It just requires a -c argument or $REFGENIE environment variable.
This command will: - create the genome_archive directory and structure that can be used to serve the assets - create a server config file in that directory, which includes a couple of extra asset attributes, like archive_digest and archive_size.
In case you already have some of the assets archived and just want to add a new one, use:
refgenieserver archive -c CONFIG GENOME/ASSET:TAG
In case you want to remove an unwanted archive, add an -r flag:
refgenieserver archive -c CONFIG -r GENOME/ASSET:TAG
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