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LAPIS Documentation

A documentation website tailored to your LAPIS instance.

Features

  • Customizable: The documentation will generate content based on your LAPIS configuration.
  • Request Generator: An interactive wizard to help users getting started using your LAPIS instance.
  • User documentation: Detailed information on how to use the LAPIS API, explaining concepts and providing examples.
  • Maintainer documentation: Information on how to deploy and maintain your own LAPIS instance. If you want to get started setting up your own LAPIS instance, we recommend setting up this documentation first and iterating from there.
  • Config Generator: An interactive wizard to help you generate and modify the configuration of your LAPIS instance.
  • Architecture Overview: An overview of the LAPIS architecture and how it interacts with SILO.

Quickstart

IMAGE=ghcr.io/genspectrum/lapis-docs docker compose -f test-docker-compose.yml up

Visit http://localhost:4321/docs/ in your browser.

Commands

This documentation is a website built with Starlight and Astro.

Command Action
npm install Installs dependencies
npm run dev Starts local dev server at localhost:4321
npm run build Build your production site to ./dist/
npm run preview Preview your build locally, before deploying
npm run astro ... Run CLI commands like astro add, astro check
npm run astro -- --help Get help using the Astro CLI

For running and building the website, the environment variables LAPIS_URL and CONFIG_FILE must be set, e.g.:

CONFIG_FILE=../lapis-e2e/testData/testDatabaseConfig.yaml REFERENCE_GENOMES_FILE=../siloLapisTests/testData/reference_genomes.json LAPIS_URL=http://localhost:8080 npm run dev

Deploying

Starlight is meant to be used to generate static HTML files that can be hosted by any standard web server. This documentation however is meant to be specific for a given database configuration for LAPIS and SILO.

Thus, the documentation can only be built at deployment time (i.e. when the config is known), and not ahead of time. We provide Docker images that can be used to build the documentation, and then serve it.

See the Docker compose file for an example of how to use the Docker image:

  • The database config must be mounted to /config/database_config.yaml.
  • The environment variable LAPIS_URL must be set to the URL of the backing LAPIS instance. This is used to generate links to that instance.
  • Astro recommends to set the site config option. This can be done via the environment variable ASTRO_SITE.
IMAGE=ghcr.io/genspectrum/lapis-docs docker compose -f test-docker-compose.yml up

Deploying behind a proxy

The environment variable BASE_URL can be set to change the base URL of the documentation. This is especially necessary when deploying to a subdirectory of a domain.

Suppose you want to host LAPIS on your.domain and the documentation on your.domain/docs, and the documentation container will be running on 127.0.0.1:3000. Then you can set BASE_URL to /docs/ and configure your proxy to forward requests to your.domain/docs to localhost:3000/docs.