FR: Include igv-jupyter in terra-jupyter-base.

[johntbates]

Please install igv-jupyter to render the IGV browser inside Terra notebook cells.

Currently, we require the user to do the following in a trusted notebook (igv-jupyter runs JS on the front end):

Cell 0:

! pip install igv-jupyter

Cell 1:

!jupyter serverextension enable --py igv
!jupyter nbextension install --py igv --user
!jupyter nbextension enable --py igv

Cell 2:

import igv
b = igv.Browser({"genome": "hg38"})
b.show()

For some reason, it's not possible to run the contents of cell 0 and cell 1 in a startup script; cloud environment creation throws an error saying that Jupyter did not start within 10 minutes.

Thanks very much!

[johntbates]

It turns out

!jupyter serverextension enable --py igv

was unnecessary and we can use the following environment startup script to get igv-jupyter working in a trusted notebook cell:

#!/usr/bin/env bash

# Install igv to view the Integrative Genomics Viewer in a Terra notebook cell
pip install igv-jupyter --upgrade
jupyter nbextension install --py igv --user
jupyter nbextension enable --py igv

However, if you attempt to launch a terminal, it appears to hang unless you remove the startup script from the cloud environment configuration.

[kyuksel]

Hi @johntbates - thank you for reporting the issue. It is tracked via this ticket and will be triaged within a week.