Dockerfile

# This Dockerfile is used to generate the docker image dsarchive/histomicstk
# This docker image includes the HistomicsTK python package along with its
# dependencies.
#
# All plugins of HistomicsTK should derive from this docker image

FROM nvidia/cuda:9.2-cudnn7-devel-ubuntu18.04
LABEL maintainer="Kitware, Inc. <kitware@kitware.com>"

RUN apt-get update && \
    # We need software-properties-common for add-apt-repository \
    apt-get install --yes --no-install-recommends software-properties-common && \
    # Add python repos \
    add-apt-repository ppa:deadsnakes/ppa && \
    apt-get update && \
    apt-get install --yes --no-install-recommends \
    # Specific version of python \
    python3.8-dev \
    python3.8-distutils \
    # For installing pip \
    curl \
    ca-certificates \
    # For versioning \
    git \
    # for convenience \
    wget \
    # libcurl4-openssl-dev \
    # libssl-dev \
    # Needed for building \
    build-essential \
    # pkg-config \
    # needed for supporting CUDA \
    libcupti-dev \
    # can speed up large_image caching \
    memcached && \
    # Clean up to reduce docker size \
    apt-get autoremove && \
    rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

# Make a specific version of python the default and install pip
RUN rm -f /usr/bin/python && \
    rm -f /usr/bin/python3 && \
    ln `which python3.8` /usr/bin/python && \
    ln `which python3.8` /usr/bin/python3 && \
    curl https://bootstrap.pypa.io/get-pip.py -o get-pip.py && \
    python get-pip.py && \
    rm get-pip.py && \
    ln `which pip3` /usr/bin/pip && \
    python --version

# copy HistomicsTK files
ENV htk_path=$PWD/HistomicsTK
RUN mkdir -p $htk_path

COPY . $htk_path/
WORKDIR $htk_path

# Install HistomicsTK and its dependencies
RUN pip install --no-cache-dir --upgrade pip setuptools && \
    # Install bokeh to help debug dask \
    pip install --no-cache-dir 'bokeh>=0.12.14' && \
    # Install a specific version of numpy.  This needs to be compatible with
    # tensorflow and our wheels \
    pip install --no-cache-dir 'numpy==1.17.5' && \
    # Install large_image memcached extras \
    pip install --no-cache-dir --pre 'large-image[memcached]' --find-links https://girder.github.io/large_image_wheels && \
    # Install girder-client \
    pip install --no-cache-dir girder-client && \
    # Install HistomicsTK \
    pip install --no-cache-dir --pre . --find-links https://girder.github.io/large_image_wheels && \
    # Create separate virtual environments with CPU and GPU versions of tensorflow \
    pip install --no-cache-dir virtualenv && \
    virtualenv --system-site-packages /venv-gpu && \
    chmod +x /venv-gpu/bin/activate && \
    /venv-gpu/bin/pip install --no-cache-dir 'tensorflow-gpu>=1.3.0' && \
    # clean up \
    rm -rf /root/.cache/pip/*

# Show what was installed
RUN pip freeze && \
    /venv-gpu/bin/pip freeze

# pregenerate font cache
RUN python -c "from matplotlib import pylab"

# define entrypoint through which all CLIs can be run
WORKDIR $htk_path/histomicstk/cli

# Test our entrypoint.  If we have incompatible versions of numpy and
# openslide, one of these will fail
RUN python -m slicer_cli_web.cli_list_entrypoint --list_cli
RUN python -m slicer_cli_web.cli_list_entrypoint ColorDeconvolution --help

ENTRYPOINT ["/bin/bash", "docker-entrypoint.sh"]