Could not connect to IPython Notebook

Cause

This error occurs when the javascript in our visualisation plugin cannot connect to IPython notebook. This usually happens when galaxy and ipython are being accessed over different ports (e.g., galaxy on :8080 and ipython on :10001). The AJAX request to IPython for login is considered a Cross Origin request due to port number differences.

Solution

The solution to this issue is to do the following:

1. switch on apache_urls = True
2. Implement the information discussed in INSTALL.md.
3. Reconfigure galaxy to run under a subdirectory (e.g. /galaxy/) and implement the appropriate reverse proxy config so you can access it on http(s)://fqdn/galaxy/