Minimal Ubuntu 18.04 Dockerfile to run Jupyter examples for HistomicsTK

Dockerfile-histomicstk-jupyter

FROM ubuntu:18.04

# Prerequisites and runtimes
RUN apt-get update && apt-get upgrade -y && apt-get install -y --no-install-recommends \
    build-essential \
    git \
    python-dev \
    python-pip \
    python-setuptools \
    python-wheel \
    sudo \
    # These are optional, but large_image doesn't do as much without them
    libtiff5 \
    openslide-tools \
    # Some of our Jupyter examples use curl
    curl

RUN adduser --disabled-password --gecos '' ubuntu && \
    adduser ubuntu sudo && \
    echo '%sudo ALL=(ALL) NOPASSWD:ALL' >> /etc/sudoers

USER ubuntu
WORKDIR /home/ubuntu

# Make a bin directory so that cmake will install without sudo
RUN mkdir -p /home/ubuntu/.local/bin
ENV PATH "/home/ubuntu/.local/bin:$PATH"

RUN pip install numpy

RUN git clone https://github.com/girder/large_image.git && \
    cd large_image && \
    # We could also add memcached and mapnik, but they have other dependencies
    pip install .[openslide]

RUN git clone https://github.com/DigitalSlideArchive/HistomicsTK.git && \
    cd HistomicsTK && \ 
    # We need scikit-build to pip install HistomicsTK.  This works:
    #   pip install --no-cache-dir -r requirements.txt && \
    # but this is sufficient:
    pip install scikit-build && \
    pip install -e .

# Install Jupyter and configure it to run with any IP
RUN pip install jupyter && \
    mkdir ~/.jupyter && \
    echo 'c.NotebookApp.allow_origin = "*"\n\
c.NotebookApp.ip = "0.0.0.0"\n\
c.NotebookApp.open_browser = False\n'\
    > ~/.jupyter/jupyter_notebook_config.py

# Expose the Jupyter port
EXPOSE 8888

# Switch to the notebook examples directory
WORKDIR /home/ubuntu/HistomicsTK/docs/examples

# Run the notebook examples
CMD jupyter notebook