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An implementation of the Wasserman Lab IBVL portal

Dev Environment Setup

  1. Create an environment for the backend and activate if you did not do it yet
install rye for dependency management:
https://rye.astral.sh/guide/installation/

git clone git@github.com:wassermanlab/variome.git
cd variome
rye sync
  1. Set up the database
brew install postgresql (if necessary)
brew services start postgresql (if necessary) 
psql

CREATE DATABASE variome;
CREATE USER variome WITH PASSWORD 'variome';
GRANT ALL PRIVILEGES on DATABASE variome to variome;
  1. Set up configuration files (.env)
cp .env-sample .env
(edit .env DB to match with your database environment, set timezone)
  1. Load the data and create a superuser account
python manage.py migrate
python manage.py import_ibvl
python manage.py createsuperuser
  1. (for frontend) make config.json file in frontend/src/ that contains the following. Replace 8000 with the port number of the Django app, if necessary
{
    "backend_url":"http://localhost:8000/api/",
    "backend_root":"http://localhost:8000/",
    "frontend_url":"/"
}

Run the Django app

rye sync
python manage.py runserver

Run the Frontend

cd frontend
npm install
npm run dev

Please note the port number that the dev frontend is being run on, you will get CORS errors if the domain is not in the list of CORS_ALLOWED_ORIGINS in ibvl/settings.py L187