Install (Developer)

Setting up VariantGrid on your own machine, to run with runserver. For a deployed server see Install (Server).

The dependency installer is tested on Ubuntu 20, 22, 24 and 26 (see the header of scripts/install/ubuntu_install_dependencies.sh). Instructions below assume a recent Ubuntu. For MacOS see Install on MacOS.

Get the code

Use your normal account — no service user is needed.

sudo apt-get install git
# Wherever you want to install repo, eg cd ~/localwork
git clone https://github.com/SACGF/variantgrid

System dependencies

# Installs system dependencies via apt-get (Python packages are installed separately, into a venv)
sudo variantgrid/scripts/install/ubuntu_install_dependencies.sh

Secret settings file

VariantGrid keeps database passwords and other sensitive values out of source control, in a file it looks for at /etc/variantgrid/settings_config.json. config/settings_config.json in the repo is a template to start from:

sudo mkdir /etc/variantgrid
sudo cp variantgrid/config/settings_config.json /etc/variantgrid

Leave it owned by you, so the account you run VariantGrid as can read it.

Now edit /etc/variantgrid/settings_config.json — see Settings for which values a fresh install needs to change and how to check it parses. The database section has to match the database you create in the common steps below.

Python venv

Create the virtual environment and install the Python requirements — see Install Python venv. Every python3 manage.py ... command assumes you have activated it, and is run from the VariantGrid install dir.

Settings for this machine

Each machine gets its own settings file named after its hostname. Copy the developer template — it sets DEBUG = True and serves over plain HTTP, and lives in env_developers/ so your config stays out of source control:

cd variantgrid
# Create settings file for this machine (lowercase hostname with dashes removed)
cp variantgrid/settings/env_developers/_settings_template.py variantgrid/settings/env_developers/$(hostname | tr '[:upper:]' '[:lower:]' | tr -d -).py

The server template in env/ sets secure cookies, which browsers never store over runserver's plain HTTP — copy that one by mistake and you would be unable to log in, so runserver refuses to start and tells you why.

Common install steps

Now do the shared part of the install — database, annotation, VEP and the upgrader: Install.

Come back here when you reach the end of that page.

Running it

python3 manage.py runserver

See Run VariantGrid for the Celery workers you need for async work (imports, annotation), and Developer Setup and Tips for debugging, SCSS and linting.