Dash-Bio load local files into igv-component

Dash Python
2

I just had to do this also. Since the igv component expects files to be coming from a server, I just used the flask instance running the dash app to serve the files.

YOUR_DATA_DIR should be the local path. Note that this will expose anything in that directory!

Here’s a toy example.

import dash_bio
from flask import send_from_directory

server=app.server

@server.route('/tracks_bw/<path:path>')
def send_bw(path):
    response = send_from_directory(YOUR_DATA_DIR,path)
    return response

def make_igv(sample_ids,gene_ids):
    
    igv=dash_bio.Igv(
                id='reference-igv',
                tracks=[
                    {'name':'name',
                     'url':'tracks_bw/MY_TRACK.bw'
                } ]
            )
    return igv

Flask is supposedly known for not being very performant with respect to serving static files, so I suspect you could get a lot of performance improvement by setting up another server like nginx to serve the track data. But for my purposes it was sufficient.

1 Like