Installing Docker, JupyterHub and creating a custom Jupyter Notebook Image

jupyterhub_docker.txt

###### DOCKER ######
# Remove old version of docker
sudo apt-get remove docker docker-engine docker.io

# Allow apt install from HTTPS
sudo apt-get update && \
sudo apt-get install \
    apt-transport-https \
    ca-certificates \
    curl \
    software-properties-common

# Add repository key
curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo apt-key add - && \
sudo add-apt-repository \
   "deb [arch=amd64] https://download.docker.com/linux/ubuntu \
   $(lsb_release -cs) \
   stable"

# Installing docker CE
sudo apt-get update && \
sudo apt-get install docker-ce

# To use docker as non sudo
sudo groupadd docker && \
sudo usermod -aG docker $USER

# Log out and Log back so that the changes take effect


## Installing docker-compose
## Check https://github.com/docker/compose/releases/latest to see the latest release version
sudo curl -o /usr/local/bin/docker-compose -L "https://github.com/docker/compose/releases/download/1.16.1/docker-compose-$(uname -s)-$(uname -m)"
sudo chmod +x /usr/local/bin/docker-compose

####### JUPYTERHUB #######

### Clonning JupyterHub Docker
sudo apt-get update && \
sudo apt-get install git

mkdir jupyterhub && \
cd jupyterhub

git clone https://github.com/jupyterhub/jupyterhub-deploy-docker.git .


## Creating a self signed certificate:
mkdir secrets && \
cd secrects
openssl req -x509 -newkey rsa:4096 -keyout jupyterhub.key -out jupyterhub.crt -days 365 -nodes -subj '/CN=localhost'


## Configuring your OAuth authentication
cat > oauth.env >> EOF
GITHUB_CLIENT_ID=<github_client_id>
GITHUB_CLIENT_SECRET=<github_client_secret>
OAUTH_CALLBACK_URL=https://<myhost.mydomain>/hub/oauth_callback
EOF

## Edit the oauth.env file and add your info
## Go to https://github.com/settings/developers to create an OAuth app, there you will receive a client ID and a client SECRET

cd..

## Next create a file userlist with GitHub usernames, the file needs at least one admin. See the example below
##
## foo admin
## bar
## foobar 

## To create the JupyterHub type

make build

## To use the default notebook image:

make notebook_image

## Now you should be able to run your docker compose
docker-compose up -d

## To access your JupyterHub go to https://localhost


####### CUSTOM JUPYTER IMAGE #######

## If you want to create a custom image, you can Create a Dockerfile using a jupyter image from https://hub.docker.com/r/jupyter/
## Building your custom image
docker build -t my-image

## Using your custom image
export DOCKER_NOTEBOOK_IMAGE=my-image

## or edit the docker-compose.yml file

# Bring down the JupyterHub container, if running
docker-compose down

# Bring it back up
docker-compose up -d

## Adding a new env to your custom image:
## Here is an example of a custom image with a Python 2.7 enviroment with some additional packages

FROM jupyter/minimal-notebook

USER $NB_USER

ENV CONDA_ENV geospatial

RUN conda create --yes --name $CONDA_ENV python=2.7 

ENV PATH /opt/conda/envs/$CONDA_ENV/bin:$PATH
ENV CONDA_DEFAULT_ENV $CONDA_ENV
ENV CONDA_PREFIX /opt/conda/envs/$CONDA_ENV

RUN conda install --yes ipykernel nb_conda matplotlib scipy && \
    conda install --yes -c conda-forge geopandas gdal && \
    fix-permissions $CONDA_DIR && \
    python -m ipykernel install --user --name geospatial --display-name "Python [geospatial]"
    
RUN cd /tmp && \
    git clone https://github.com/PAIR-code/facets.git && \
    cd facets && \
    jupyter nbextension install facets-dist/ --sys-prefix && \
    rm -rf facets && \
    fix-permissions $CONDA_DIR

# Import matplotlib the first time to build the font cache.
ENV XDG_CACHE_HOME /home/$NB_USER/.cache/
RUN MPLBACKEND=Agg python -c "import matplotlib.pyplot" && \
    fix-permissions /home/$NB_USER

USER $NB_USER

### For more information see: https://github.com/jupyterhub/jupyterhub-deploy-docker