Wasserman Lab BVL

Dev Environment Setup (Python / Django module)

git clone git@github.com:wassermanlab/variome.git
cd variome

1. Set up dependencies

Option 1 - Rye (recommended)

install rye for dependency management: https://rye.astral.sh/guide/installation/ then run:

rye sync

Option 2 - Pip

pip install -R requirements.lock

Option 3 - Conda and Pip

conda env create -f environment.yaml 
conda activate variome
pip install -r requirements.lock

2. 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;

3. Set up configuration files (.env)

cp .env-sample .env
(edit .env DB to match with your database environment, set timezone, other variables)

4. Load the test fixture data and create a superuser account

python manage.py migrate
python manage.py import_bvl
python manage.py createsuperuser

Run the Django app

python manage.py runserver

(optional) - Run on a specific port

python manage.py runserver 8888

Run the Frontend

cd frontend
npm install
npm run dev