vdjserver-airr-schema

LinkML representation of AIRR Standard schema for VDJServer data modeling and database generation.

Schema Documentation Website

https://vdjserver.github.io/vdjserver-airr-schema

Repository Structure

• docs/ - mkdocs-managed documentation
  • elements/ - generated schema documentation
• examples/ - Examples of using the schema
• project/ - project files (these files are auto-generated, do not edit)
• src/ - source files (edit these)
  • vdjserver_airr_schema
    • schema/ -- LinkML schema (edit this)
    • datamodel/ -- generated Python datamodel
• tests/ - Python tests
  • data/ - Example data

Source Code Configuration

This repository contains submodules. When doing a git clone, those submodules are not automatically populated, and an additional command is required.

There is an environment file to hold secrets like database password and other configuration information.

git clone https://github.com/vdjserver/vdjserver-airr-schema.git
cd vdjserver-airr-schema
git submodule update --init --recursive

# setup database connection and path info
cp .env.defaults .env
nano .env

Makefile commands

Running make without a target will display the help message with list of commands. LinkML uses just for running various commands

Developer Tools

There are several pre-defined command-recipes available. They are written for the command runner just. To list all pre-defined commands, run just or just --list.

Credits

This project uses the template linkml-project-copier.