Clinical DNA variant visualizer and browser.
Analyze VCFs and collaborate on solving rare diseases quicker
What is Scout?
- Simple - Analyze variants in a simple to use web interface.
- Aggregation - Combine results from multiple analyses and VCFs into a centralized database.
- Collaboration - Write comments and share cases between users and institutes.
This README only gives a brief overview of Scout, for a more complete reference, please check out our docs: https://clinical-genomics.github.io/scout .
Runnable demo image - does not require installing of software and database
A simple demo instance of Scout requires the installation of Docker and can be launched either by using the command:
docker-compose up -d or
The repository includes a Makefile with common shortcuts to simplify setting up and working with Scout. To see a full list and description of these shortcuts run:
This demo is consisting of 3 containers:
- a lightweight mongodb instance
- scout-cli --> the Scout command line, connected to the database. Populates the database with demo data
- scout-web --> the Scout web app, that serves the app on localhost, port 5000.
Once the server has started you and open the app in the web browser at the following address: http://localhost:5000/
The command to stop the demo are either
docker-compose down or
git clone https://github.com/Clinical-Genomics/scout cd scout pip install --editable .
Scout PDF reports are created using Flask-WeasyPrint. This library requires external dependencies which need be installed separately (namely Cairo and Pango). See platform-specific instructions for Linux, macOS and Windows available on the WeasyPrint installation pages.
You also need to have an instance of MongoDB running. I've found that it's easiest to do using the official Docker image:
docker run --name mongo -p 27017:27017 mongo
Demo - requires pip-installing the app in a container and a running instance of mongodb
Once installed, you can setup Scout by running a few commands using the included command line interface. Given you have a MongoDB server listening on the default port (27017), this is how you would setup a fully working Scout demo:
scout setup demo
This will setup an instance of scout with a database called
scout-demo. Now run
scout --demo serve
And play around with the interface. A user has been created with email email@example.com so use that adress to get access
To initialize a working instance with all genes, diseases etc run
scout setup database
for more info, run
The previous command initializes 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
Integration with chanjo for coverage report visualization
Integration with loqusdb for integrating local variant frequencies
Integration with Gens for displaying copy number profiles for variants
Scout needs a server config to know which databases to connect to etc. Depending on which information you provide you activate different parts of the interface automatically, including user authentication, coverage, and local observations.
This is an example of the config file:
# scoutconfig.py # list of email addresses to send errors to in production ADMINS = ['firstname.lastname@example.org'] MONGO_HOST = 'localhost' MONGO_PORT = 27017 MONGO_DBNAME = 'scout' MONGO_USERNAME = 'testUser' MONGO_PASSWORD = 'testPass' # enable user authentication using Google OAuth 2.0 GOOGLE = dict( client_id="client_id_string.apps.googleusercontent.com", client_secret="client_secret_string", discovery_url="https://accounts.google.com/.well-known/openid-configuration" ) # enable Phenomizer gene predictions from phenotype terms PHENOMIZER_USERNAME = '???' PHENOMIZER_PASSWORD = '???' # enable Chanjo coverage integration SQLALCHEMY_DATABASE_URI = '???' REPORT_LANGUAGE = 'en' # or 'sv' # other interesting settings SQLALCHEMY_TRACK_MODIFICATIONS = False # this is essential in production TEMPLATES_AUTO_RELOAD = False # consider turning off in production SECRET_KEY = 'secret key' # override in production!
Most of the config settings are optional. A minimal config would consist of SECRET_KEY and MONGO_DBNAME.
Starting the server in now really easy, for the demo and local development we will use the CLI:
scout --flask-config config.py serve
Hosting a production server
When running the server in production you will likely want to use a proper Python server solution such as Gunicorn. This is also how we can multiprocess the server and use encrypted HTTPS connections.
SCOUT_CONFIG=./config.py gunicorn --workers 4 --bind 0.0.0.0:8080 scout.server.auto:app
For added security and flexibility, we recommend a reverse proxy solution like NGINX.
Setting up a user login system
Scout currently supports 3 mutually exclusive types of login:
- Google authentication via OpenID Connect (OAuth 2.0)
- LDAP authentication
- Simple authentication using userid and password
The first 2 solutions are both suitable for a production server. A description on how to set up an advanced login system is available in the admin guide
Integration with MatchMaker Exchange
Starting from release 4.4, Scout offers integration for patient data sharing via MatchMaker Exchange. General info about MatchMaker and patient matching could be found in this paper. For a technical guideline of our implementation of MatchMaker Exchange at Clinical Genomics and its integration with Scout check scouts matchmaker docs. A user-oriented guide describing how to share case and variant data to MatchMaker using Scout can be found here.
To keep the code base consistent, formatting with Black is always applied as part of the PR submission process via GitHub Actions. While not strictly required, to avoid confusion, it is suggested that developers apply Black locally. Black defaults to 88 characters per line, we use 100.
To format all the files in the project run:
black --line-length 100 .
We recommend using Black with pre-commit.
.pre-commit-config.yaml you can find the pre-commit configuration.
To enable this configuration run:
To run unit tests:
Contributing to Scout
If you want to contribute and make Scout better, you help is very appreciated! Bug reports or feature requests are really helpful and can be submitted via github issues. Feel free to open a pull request to add a new functionality or fixing a bug, we welcome any help, regardless of the amount of code provided or your skills as a programmer. More info on how to contribute to the project and a description of the Scout branching workflow can be found in CONTRIBUTING.
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