Install igv on Jupyter lab

[amirshams84]

jupyter labextension install igv Errored, use --debug for full output: ValueError: "igv" is not a valid extension: No jupyterlab key

[jrobinso]

Thanks for the report, we don't yet support jupyter lab. This has been a dormant project for sometime due to lack of staff, but we plan to pick it up again in the new year. I'll leave this open and interpret it as a request to support jupyter lab.

[amirshams84]

Thanks you are awesome by the way

Amir

[jrobinso]

Thank you very much @amirshams84. I'm actually working on this project now and will have an update in January. As I'm not a jupyter, or jupyter lab user I might ask for your help testing on Jupyter lab.

[jrobinso]

Hi @amirshams84 , after some investigation I have discovered that it is impossible, apparently, to write an extension of this type (involving javascript & python) that works in both notebook and lab. I'm currently focused on notebook. I might start another project for Jupyter Lab at some point.

[amirshams84]

That would be great Jim, Let me know when is the good time to test it on Jupyter Lab Regards Amir

On Wed, Jan 2, 2019 at 6:34 PM Jim Robinson notifications@github.com wrote:

Hi @amirshams84 https://github.com/amirshams84 , after some investigation I have discovered that it is impossible, apparently, to write an extension of this type (involving javascript & python) that works in both notebook and lab. I'm currently focused on notebook. I might start another project for Jupyter Lab at some point.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/igvteam/igv.js-jupyter/issues/13#issuecomment-451018306, or mute the thread https://github.com/notifications/unsubscribe-auth/AMtB2L83lFLIl3DU4Q_nHfhobx5PTZvYks5u_UIIgaJpZM4ZawEy .

[thondeboer]

I would also really like to be able to run IGV in JupyterLab...JupyterLab is going to be the future of Jupyter Notebooks and it would be a pity if IGV would be left behind...Is there any idea if this is going to be available? It has been a year since there was some comments about this. Which you may have interpreted as lack of interest, but for my specific use case, JupyterLab is the only option...

[jrobinso]

Hi @thondeboer yes it will be available. Until recently there was an explicit warning to extension developers on the Jupyter site that the API was unstable and guaranteed to change. I see they have removed that. I will re-open this, but don't have an ETA at this time.

[jrobinso]

@thondeboer @amirshams84 I'm just not going to have time to do this but would support someone else (support in the sense of making igv.js changes if needed). Anyone interested? Its not trivial but probably easier if you work regularly in python and Jupyter (unlike myself). In any event I'm closing this issue as the notebook extension won't work in Lab.

[cjw85]

We have a fork of igv-jupyter that now supports JupyterLab: https://github.com/epi2me-labs/igv-jupyterlab

[jrobinso]

@cjw85 Fantastic!