QIIME visualization on a Jupyter Server

[jwdebelius (Justine Debelius)]

Hi All,

I'm trying to use QIIME within a Jupyter Hub server instance from docker. I cannot get the jupyter serverextension enable --py qiime2 --sys-prefix to work. I've tried adding it various places in the docker build but non seem to give me the right answer. @SoilRotifer mentioned a similar issue a few weeks ago.

Best,
Justine

[ebolyen (Evan Bolyen)]

Hi @jwdebelius,

It might be docker which is the issue, but there's another user with a suspiciously similar problem

Visualization error on Jupyter notebook

Hi all, I've used qiime2 for more than 5 years on Intel Mac. Recently, while using qiime2 on Jupyter notebook, I am facing the following error when performing a visualization. As a result, interactive figures are not shown. Install QIIME 2 Jupyter extension with: jupyter serverextension enable --py qiime2 --sys-prefix then restart your server. (Interactive output not available on static notebook viewer services like nbviewer.) Of cource, I've tried to run jupyter serverextension enable -…

Could you reply with some of the same info?

Also, docker is super annoying with PATH sometimes, so you may need to run /opt/miniconda3/<yourenv or something>/bin/jupyter.

Do you get any errors, or does it just blast past your RUN command and not work anyhow.