badseby/scout

VCF visualization interface

Scout

Analyze VCFs quicker and easier.

Scout makes you life easier by letting you visualize mutiple VCFs in the browser. You can quickly triage variants in search of those sneeky disease causing mutations. Scout also connects your team by linking user comments to cases and variants. The project is completely open source.

Running server is as simple as:

$ scout run
Running on http://localhost:5000...

Installation

Scout will ship as a regular Python package through pip but until then you can install it through GitHub.

$ mkvirtualenv scout && workon scout
$ pip install git+https://github.com/Clinical-Genomics/scout.git

You also need to install MongoDB and run it as a background process.

Quickstart

Run the following commands to bootstrap your development environment.

# it's always a good idea to work in a virtual environment
$ mkvirtualenv scout && workon scout
$ git clone https://github.com/Clinical-Genomics/scout.git
$ cd scout
$ pip install -r requirements/dev.txt

This doesn't mean that everything will work just like that. You also need some Google OAuth keys and other secret stuff. The config should be stored in a config file:

/scout
  /instance
    scout-dev.cfg  <-- put config here!
  /scout

When you have the instance folder in place you can start Flask like so:

$ python manage.py -c "$(pwd)/instance/scout.cfg" runserver
Running on http://localhost:5000...

Features

Scout is implemented in Python and uses the Flask web framework. Data is stored in a MongoDB database. Login is handled through Google OAuth. The raw input to Scout is any valid VCF file with one or more samples.

About

Scout is developed at SciLifeLab Clinical Genomics in close collaboration with CMMS at Karolinska Institute.

Contributors

• Robin Andeer (robinandeer)
• Måns Magnusson (moonso)
• Henrik Stranneheim (henrikstranneheim)
• Mats Dahlberg (MatsDahlberg)

License

MIT. See the LICENSE file for more details.

Contributing

Anyone can help make this project better - read CONTRIBUTION to get started!