Install

Tested on Ubuntu 20.04 VM and Ubuntu 21.10

You need Git to download the repo

sudo apt-get install git

Development

For local development, you probably just want to use your normal account:

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

Server

For a server, create a "variantgrid" user to run the services:

# Server only
export SYSTEM_VARIANTGRID_USER=variantgrid
sudo id -u ${SYSTEM_VARIANTGRID_USER} &>/dev/null || sudo useradd ${SYSTEM_VARIANTGRID_USER} --create-home --shell /bin/bash
sudo mkdir /opt/variantgrid  # Or /mnt/variantgrid
sudo chown variantgrid /opt/variantgrid
sudo su variantgrid
cd /opt/
git clone https://github.com/SACGF/variantgrid variantgrid

Code

# Installs dependencies via apt-get and PIP
sudo variantgrid/scripts/install/ubuntu_20_install_dependencies.sh
# Create DB
sudo su postgres -c "psql < scripts/dbscripts/pgsql_database_create.sql"
# Copy secret settings file
sudo mkdir /etc/variantgrid
sudo cp variantgrid/config/settings_config.json /etc/variantgrid

As the user who will run variantgrid:

# As Variantgrid user
python3 -m nltk.downloader punkt
python3 -m nltk.downloader averaged_perceptron_tagger

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

python3 manage.py migrate
python3 manage createsuperuser

Especially for production use, you'll need to adjust the settings

Required Components

• Install VEP - variant annotation
• Install VT - need a patched version

Optional Components

• Install ped_parser and Madeline2 - Pedigree graph generation
• Install Postfix - Mail server (user password reset etc)

Final Setup

• Run VariantGrid - Start the services and connect
• Install Annotation - Download / install annotation data

See also

• Clone a VM