Below example has been tested on Elementary OS, but since we are using Docker, the procedure should be universal. We will be using official continuumio images
coil@coil:~$ ps -ef | grep docker
root 18991 1 0 19:09 ? 00:00:01 /usr/bin/dockerd -H fd:// --containerd=/run/containerd/containerd.sock
coil 25760 17917 0 19:57 pts/1 00:00:00 grep --color=auto docker
coil@coil:~$ sudo docker search continuumio
[sudo] password for coil:
NAME DESCRIPTION STARS OFFICIAL AUTOMATED
continuumio/anaconda3 Powerful and flexible python distribution 382 [OK]
continuumio/anaconda Powerful and flexible python distribution 202 [OK]
continuumio/miniconda3 Powerful and flexible package manager 138 [OK]
continuumio/miniconda Powerful and flexible package manager 67 [OK]
continuumio/conda_builder_linux A build platform for Linux packages (64-bit … 4
continuumio/centos5_gcc5_base 3
continuumio/binstar-build-linux64 1 [OK]
atavares/miniconda-rocker-geospatial This image is based on rocker/geospatial and… 1 [OK]
continuumio/anaconda2 1
continuumio/conda-concourse-ci Build and general-purpose image for Continuu… 0
continuumio/anaconda-build-linux-64 0
continuumio/ap-auth-keycloak Keycloak:3.1.0 0
continuumio/miniconda2 0
continuumio/ap-git-storage gitea:1.3.0 0
continuumio/planet-gpu Customized base image for Telekube that enab… 0
continuumio/ci-image 0
continuumio/anaconda-build-linux-32 0
continuumio/adam-node 0
continuumio/ae-conda-packages 0
continuumio/sourceclear 0
dgenchev/continuumio 0
nextjournal/python3 Python 3 docker image for nextjournal.com. B… 0 [OK]
ashander/miniconda3gcc like continuumio/miniconda3 but with compile… 0 [OK]
continuumio/nginx-ingress-ws 0
tylercoral/bam2vcf Based on continuumio/miniconda3. Includes sa… 0
coil@coil:~$ coil@coil:~$ sudo docker pull continuumio/miniconda3
[sudo] password for coil:
Using default tag: latest
latest: Pulling from continuumio/miniconda3
1ab2bdfe9778: Already exists
dd7d28bd8be5: Pull complete
af998e3a361b: Pull complete
Digest: sha256:54eb3dd4003f11f6a651b55fc2074a0ed6d9eeaa642f1c4c9a7cf8b148a30ceb
Status: Downloaded newer image for continuumio/miniconda3:latest
coil@coil:~$coil@coil:~$ sudo docker run -i -t continuumio/miniconda3 /bin/bash
(base) root@bcb882fef67d:/# conda info
active environment : base
active env location : /opt/conda
shell level : 1
user config file : /root/.condarc
populated config files :
conda version : 4.7.10
conda-build version : not installed
python version : 3.7.3.final.0
virtual packages :
base environment : /opt/conda (writable)
channel URLs : https://repo.anaconda.com/pkgs/main/linux-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/linux-64
https://repo.anaconda.com/pkgs/r/noarch
package cache : /opt/conda/pkgs
/root/.conda/pkgs
envs directories : /opt/conda/envs
/root/.conda/envs
platform : linux-64
user-agent : conda/4.7.10 requests/2.22.0 CPython/3.7.3 Linux/4.15.0-36-generic debian/10 glibc/2.28
UID:GID : 0:0
netrc file : None
offline mode : False
(base) root@bcb882fef67d:/# exit
coil@coil:~$ Run below command on one line. This runs docker container interactively, forwards default port 8888 on host machine to port 8888 in the container and passes commands to execute in bash that will install jupyter notebook and start it with proper parameters. Dont forget to add --allow-root option.
sudo docker run -i -t -p 8888:8888 continuumio/miniconda3 /bin/bash -c "/opt/conda/bin/conda install jupyter -y --quiet && mkdir /opt/notebooks && /opt/conda/bin/jupyter notebook --notebook-dir=/opt/notebooks --ip='*' --port=8888 --no-browser --allow-root"coil@coil:~$ sudo docker run -i -t -p 8888:8888 continuumio/miniconda3 /bin/bash -c "/opt/conda/bin/conda install jupyter -y --quiet && mkdir /opt/notebooks && /opt/conda/bin/jupyter notebook --notebook-dir=/opt/notebooks --ip='*' --port=8888 --no-browser --allow-root"
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /opt/conda
added / updated specs:
- jupyter
The following packages will be downloaded:
package | build
---------------------------|-----------------
attrs-19.1.0 | py37_1 57 KB
backcall-0.1.0 | py37_0 20 KB
...
jinja2-2.10.1 | py37_0 195 KB
jpeg-9b | h024ee3a_2 214 KB
jsonschema-3.0.2 | py37_0 92 KB
jupyter-1.0.0 | py37_7 6 KB
jupyter_client-5.3.1 | py_0 69 KB
jupyter_console-6.0.0 | py37_0 37 KB
jupyter_core-4.5.0 | py_0 48 KB
...
widgetsnbextension-3.5.1 | py37_0 862 KB
zeromq-4.3.1 | he6710b0_3 496 KB
------------------------------------------------------------
Total: 133.5 MB
The following NEW packages will be INSTALLED:
attrs pkgs/main/linux-64::attrs-19.1.0-py37_1
backcall pkgs/main/linux-64::backcall-0.1.0-py37_0
...
jupyter pkgs/main/linux-64::jupyter-1.0.0-py37_7
jupyter_client pkgs/main/noarch::jupyter_client-5.3.1-py_0
jupyter_console pkgs/main/linux-64::jupyter_console-6.0.0-py37_0
jupyter_core pkgs/main/noarch::jupyter_core-4.5.0-py_0
...
widgetsnbextension pkgs/main/linux-64::widgetsnbextension-3.5.1-py37_0
zeromq pkgs/main/linux-64::zeromq-4.3.1-he6710b0_3
The following packages will be UPDATED:
ca-certificates 2019.5.15-0 --> 2019.5.15-1
certifi 2019.6.16-py37_0 --> 2019.9.11-py37_0
conda 4.7.10-py37_0 --> 4.7.12-py37_0
openssl 1.1.1c-h7b6447c_1 --> 1.1.1d-h7b6447c_1
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
[I 18:47:52.235 NotebookApp] Writing notebook server cookie secret to /root/.local/share/jupyter/runtime/notebook_cookie_secret
[W 18:47:52.586 NotebookApp] WARNING: The notebook server is listening on all IP addresses and not using encryption. This is not recommended.
[I 18:47:52.592 NotebookApp] Serving notebooks from local directory: /opt/notebooks
[I 18:47:52.592 NotebookApp] The Jupyter Notebook is running at:
[I 18:47:52.592 NotebookApp] http://0bbdb63d7122:8888/?token=cc940d8ad6b36c3db18d62a67382245b687ea27d8d02f40a
[I 18:47:52.592 NotebookApp] or http://127.0.0.1:8888/?token=cc940d8ad6b36c3db18d62a67382245b687ea27d8d02f40a
[I 18:47:52.592 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[C 18:47:52.600 NotebookApp]
To access the notebook, open this file in a browser:
file:///root/.local/share/jupyter/runtime/nbserver-1-open.html
Or copy and paste one of these URLs:
http://0bbdb63d7122:8888/?token=cc940d8ad6b36c3db18d62a67382245b687ea27d8d02f40a
or http://127.0.0.1:8888/?token=cc940d8ad6b36c3db18d62a67382245b687ea27d8d02f40a
[I 18:48:16.756 NotebookApp] 302 GET / (172.17.0.1) 1.07ms
[I 18:48:16.766 NotebookApp] 302 GET /tree? (172.17.0.1) 0.98ms
[I 18:49:29.926 NotebookApp] 302 GET /?token=cc940d8ad6b36c3db18d62a67382245b687ea27d8d02f40a (172.17.0.1) 0.73msWe did not setup any password for login so we will need to use the access token. The token is shown at the end of notebook command line output in the container:
http://127.0.0.1:8888/?token=cc940d8ad6b36c3db18d62a67382245b687ea27d8d02f40aUse the above link in the web browser to access the notebook (the token will be different every time jupyter notebook server is started).
Above mentioned procedure to run Jupyter notebook in the container is not ideal. Since it is installing the packages, it takes some time to start. Everytime we start the container we need to note the access token. Also all the scripts we write in the notebook are lost when container is stopped, because the container is ephemeral. So using notebook in this way is good only for quick script prototyping.
Next steps: build your own personalized container with miniconda with all the packages that you need (so they do not need to be installed every time when container is started) mount a persistent volume to the container that will keep all the scripts that you write in the jupyter notebook
Sources: