Install Scout

This guide will walk you through how to setup a working instance of scout by cloning the repository from GitHub and installing it with the pip install command. For instructions on how to deploy Scout command line and server using containers check the Deploy Scout in containers page The instructions are divided into multiple sections. One section describes how to set up a demo version with some cases just to see how it could look like.

0. Intro

Make sure you have a mongod process running. First install mongodb and follow the instructions.

1. Install

Installation of Scout is possible via pip or GitHub. Let's start by pulling down the GitHub repository with the source code.

GitHub

git clone https://github.com/Clinical-Genomics/scout
cd scout
pip install --requirement requirements.txt --editable .

Pip

To get the latest version, use the above. When using pip the latest stable release will be installed.

pip install scout-browser

2. Setup

Full setup

To initialize a working instance with all genes, diseases etc run

scout setup database

for more info, run scout --help

If you intent to use authentication, make sure you are using a Google email!

The previous command setup the database with a curated collection of gene definitions with links to OMIM along with HPO phenotype terms. Now we will load some example data. Scout expects the analysis to be accomplished using various gene panels so let's load one and then our first analysis case:

scout load panel scout/demo/panel_1.txt
scout load case scout/demo/643594.config.yaml

For more information about populating the database, please see admin-guide.

Demo

This option is used to quickly get a operating instance with some example data

scout setup demo
scout --demo serve