IMPORTANT

This repository is an example of an integration of igv.js with a Flask server. It is not an active development project and not maintained. Our efforts are focused on the igv.js component itself. For an example of a complete website integrating igv.js for use with any web server, including Flask, see igv-webapp.

Notes on sample data

The sample project includes test data in "static/data/public". The bedgraph and bigwig files in that directory contain data on chr1 (only). The "gsst1.bam" file contains data for the gstt1 locus, specifically chr22:24,374,133-24,386,311.

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).

Additional Flask Blueprints

Additional Flask Blueprints are defined in the project for the following:

UCSC Blueprint

The UCSC genome database may be directly accessed with this blueprint.

The mysql connection needs to be installed for this blueprint to work:

pip install mysql-connector==2.1.7

Restarting the application and going to (http://localhost:5000/ucsc) links up with the UCSC database.

A full set of parameters (db, table, chr, start, end) needs to be provided as GET parameters, e.g. (http://localhost:5000/ucsc?db=hg38&table=knownGene&chr=chrX&start=15560138&end=15602945). See theUCSC Table Browser for inspiration on what parameter values to use.

Alignment Blueprint

The pysam module needs to be installed for this Blueprint to work (this may be a non-trivial installation on some machines).

Restarting the application and going to (http://localhost:5000/alignments) links up with the UCSC database.

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)