Cannot open jupyter notebook linked by the docker container

[gauravmoghe]

I downloaded the docker container using docker run -p 8888:8888 -e PASSWORD="jupyter" quay.io/cellgeni/scrna-seq-course:v5.14

Then I load the image using the following code $ docker run --user root -e GRANT_SUDO=yes <imageID>

and I get the following status message

Set username to: jovyan
usermod: no changes
Granting jovyan sudo access and appending /opt/conda/bin to sudo PATH
Executing the command: jupyter lab
[I 2022-09-05 17:56:31.142 ServerApp] jupyter_server_proxy | extension was successfully linked.
[I 2022-09-05 17:56:31.167 ServerApp] jupyterlab | extension was successfully linked.
[W 2022-09-05 17:56:31.173 NotebookApp] 'ip' has moved from NotebookApp to ServerApp. This config will be passed to ServerApp. Be sure to update your config before our next release.
[W 2022-09-05 17:56:31.174 NotebookApp] 'port' has moved from NotebookApp to ServerApp. This config will be passed to ServerApp. Be sure to update your config before our next release.
[W 2022-09-05 17:56:31.174 NotebookApp] 'port' has moved from NotebookApp to ServerApp. This config will be passed to ServerApp. Be sure to update your config before our next release.
[I 2022-09-05 17:56:31.202 ServerApp] Writing Jupyter server cookie secret to /home/jovyan/.local/share/jupyter/runtime/jupyter_cookie_secret
[I 2022-09-05 17:56:31.940 ServerApp] nbclassic | extension was successfully linked.
[I 2022-09-05 17:56:32.019 ServerApp] nbclassic | extension was successfully loaded.
[I 2022-09-05 17:56:32.571 ServerApp] jupyter_server_proxy | extension was successfully loaded.
[I 2022-09-05 17:56:32.573 LabApp] JupyterLab extension loaded from /opt/conda/lib/python3.9/site-packages/jupyterlab
[I 2022-09-05 17:56:32.574 LabApp] JupyterLab application directory is /opt/conda/share/jupyter/lab
[I 2022-09-05 17:56:32.580 ServerApp] jupyterlab | extension was successfully loaded.
[I 2022-09-05 17:56:32.581 ServerApp] Serving notebooks from local directory: /home/jovyan
[I 2022-09-05 17:56:32.582 ServerApp] Jupyter Server 1.9.0 is running at:
[I 2022-09-05 17:56:32.582 ServerApp] http://6842748b1bc3:8888/lab?token=f44920cc59face9412a8110dbc15c1776d3ac95ed0f81323
[I 2022-09-05 17:56:32.582 ServerApp]  or http://127.0.0.1:8888/lab?token=f44920cc59face9412a8110dbc15c1776d3ac95ed0f81323
[I 2022-09-05 17:56:32.583 ServerApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[C 2022-09-05 17:56:32.589 ServerApp] 

    To access the server, open this file in a browser:
        file:///home/jovyan/.local/share/jupyter/runtime/jpserver-15-open.html
    Or copy and paste one of these URLs:
        http://6842748b1bc3:8888/lab?token=f44920cc59face9412a8110dbc15c1776d3ac95ed0f81323
     or http://127.0.0.1:8888/lab?token=f44920cc59face9412a8110dbc15c1776d3ac95ed0f81323

However, when I put the link in Chrome, I get ERR_CONNECTION_REFUSED or ERR_FILE_NOT_FOUND

I tried changing 127.0.0.1 to my mac's IP address as suggested in a previous closed GitHub issue (https://github.com/hemberg-lab/scRNA.seq.course/issues/165) but that did not work. Running the docker run command without the sudo and --user arguments also does not work.

Thanks for any insights!

[prete]

Hi @gauravmoghe, when running the container you need to bind the ports from the container to your host machine: that's the -p 8888:8888 part of the launch command otherwise you won't be able to reach jupyter inside the container via the URL.

Also, I think the PASSWORD env var has been deprectaed in favor of JUPYTER_TOKEN. Try running it like this:

docker run -p 8888:8888 -e JUPYTER_TOKEN=jupyter quay.io/cellgeni/scrna-seq-course:latest

Let us know how that goes