IGV with Flask

An example project for integrating igv.js and Flask

Installation

You can install all required packages including Flask using pip.

pip install -r requirements.txt

Running the app

To run the app using the simple builtin server, you can use the provided run file:

python run.py

Now that the server is running, go to (http://localhost:5000) to use IGV. To view one of the example tracks, click on it in the box in the upper left corner.

Alternatively, you can set the environment variable FLASK_APP to igvjs.py and use 'flask run':

export FLASK_APP=igvjs.py
flask run

Note: With this method, you can use the command-line options for flask run. For example, use the -p option to set port number. Use --host=0.0.0.0 to make the server externally visible (eg. flask run -p 8659 --host=0.0.0.0).

Configuration

Configuration options can be set in _config.py in the root directory.

Currently supported options are:
USES_OAUTH - whether or not data is protected using OAuth
ALLOWED_EMAILS - the filename containing the list of allowed emails when using OAuth
PUBLIC_DIR - path to directory of public data when using OAuth (eg. /static/data/public)