igvteam / igv.js-flask Goto Github PK

Hello, I'm running igv-flask with default settings and files but nothing appears on the BigWig or bedgraph tracks. I am not able to see any errors on the Console or Network tab of the Firefox debugger.

I also tried upgrading to the latest igv (2.9.3) but get the same behaviour. I'm running via Docker (python3.8 image) on a virtual machine. This is the output from the Flask server log:

* Serving Flask app 'igvjs' (lazy loading)
* Environment: development
* Debug mode: on
* Running on all addresses.
WARNING: This is a development server. Do not use it in a production deployment.
* Running on http://172.20.0.2:5000/ (Press CTRL+C to quit)
10.7.90.27 - - [29/Jul/2021 11:04:15] "GET / HTTP/1.1" 200 -
10.7.90.27 - - [29/Jul/2021 11:04:15] "GET /static/js/init.js HTTP/1.1" 200 -
10.7.90.27 - - [29/Jul/2021 11:04:16] "GET /static/img/favicon.ico HTTP/1.1" 200 -
10.7.90.27 - - [29/Jul/2021 11:04:17] "GET /static/data/public/test.bw HTTP/1.1" 206 -
10.7.90.27 - - [29/Jul/2021 11:04:17] "GET /static/data/public/test.bedGraph HTTP/1.1" 200 -
10.7.90.27 - - [29/Jul/2021 11:04:17] "GET /static/data/public/test.bw HTTP/1.1" 206 -
10.7.90.27 - - [29/Jul/2021 11:04:17] "GET /static/data/public/test.bw HTTP/1.1" 206 -
10.7.90.27 - - [29/Jul/2021 11:04:17] "GET /static/data/public/test.bw HTTP/1.1" 206 -

Let me know if I can provide any more information.

Hi -

I am trying to set up igv.js-flask server.
I have python3 and pip installed.

After cloning igv.js-flask.git, pip install -r requirements.txt installed all packages with out an error.

When I ran, python run.py, I get following error:

Traceback (most recent call last): File "run.py", line 2, in <module> from igvjs import app File "/usr/local/bin/igv.js-flask/igvjs/__init__.py", line 15, in <module> from igvjs.main import igvjs_blueprint File "/usr/local/bin/igv.js-flask/igvjs/main.py", line 5, in <module> from _config import basedir ModuleNotFoundError: No module named '_config'

After fixing this error by editing, igvjs/main.py with from igvjs._config import basedir, I have another error with respect to mysql,

Traceback (most recent call last): File "run.py", line 2, in <module> from igvjs import app File "/usr/local/bin/igv.js-flask/igvjs/__init__.py", line 16, in <module> from igvjs.ucsc import ucsc_blueprint File "/usr/local/bin/igv.js-flask/igvjs/ucsc.py", line 45 except mysql.connector.Error, e: ^ SyntaxError: invalid syntax

Any help would be appreciated.

Thanks,
Mahesh

@jrobinso my interest in this project today was simply to facilitate exploration and tinkering with igv.js data integration on my local machine. Along the way, I have sent a few tweaks to the project. However, a significant tweak still resides on my local machine. I'd love to issue a pull request for you to review; however, the project seems slightly too restrictive to do this at the moment.

That said, let me explain what I have: I have simply created a new "custom.py" Flask Blueprint alongside the ucsc and alignments blueprints, which simply allow access to (slightly tweaked) custom-track-click, custom-popover and customReference html templates, as examples inside this Flask project. Maybe, though, this idea could be generalized somehow to connect this project to the main igv.js. Maybe embedding the primary igv.js repo as a submodule might work(?).

Hi -

I am trying to configure flask server with uwsgi and nginx.
My uwsgi.ini file looks like:

[uwsgi]
module = run
callable = app

If I try my configuration with a sample app: run.py where app variable is initialized with Flask(name), it works fine. However, I can't seem to run IGV server.

Any thoughts to help me with this?

Thank you,
Mahesh

Hi!

I am trying to setup the flask server in this repo to incorporate some of the functionalities of the JS web app your team wrote. I'm done with the front end design part of it( navbar, track options, etc.). And CORS is already enabled in the config file by your team.

My question -- how would I go about visualizing BAM/BAI files hosted on a remote server? Right now, the flask app only has the example tracks. Once I click on the load track, and select the appropriate files, they are not loaded in the IGV browser window. I've been trying to read through the files in the JS directory of igv-webapp to find the code that is responsible for this functionality, but have been unsuccessful :(

Could you help please?

The code at:
https://github.com/igvteam/igv.js-flask/blob/master/igvjs/static/css/igv.css
appears to do nothing as it is not imported at:
https://github.com/igvteam/igv.js-flask/blob/master/igvjs/templates/igv.html
Instead that html file imports the minified igv.js, which, contains all the css that the app uses.

I would either remove
https://github.com/igvteam/igv.js-flask/blob/master/igvjs/static/css/igv.css
or indicate how it may be used to override the css contained in the minified igv.js at

The ability to over-ride the minified css would be a useful feature.