Revision a8d63c916245d536c3008511b52799a122094256 authored by Fabian Balsiger on 18 August 2017, 13:52:33 UTC, committed by GitHub on 18 August 2017, 13:52:33 UTC
Dockerfile
# Build Pyradiomics inside the Jupyter Datascience Notebook
FROM jupyter/datascience-notebook
MAINTAINER Radiomics Project (http://github.com/radiomics)
# Build information
ARG BUILD_DATE
ARG GIT_REF
LABEL org.label-schema.build-data=$BUILD_DATE \
org.label-schema.vcs-url="https://github.com/radiomics/pyradiomics.git" \
org.label-schema.vcs-ref=$GIT_REF \
org.label-schema.schema-version="1.0.0-rc1"
USER root
ADD . /root/pyradiomics
# Jupyter datascience notebook does not support python 2 anymore, install it manually.
# "source activate python2 || (...)" first checks if the python 2 environment exists,
# and only installs if the environment does not exist
# See also https://github.com/jupyter/docker-stacks/issues/432
# Next, also install python 2 kernel globally, so it can be found from the root
RUN /bin/bash -c "source activate python2 \
|| (conda create -n python2 python=2 ipykernel \
&& pip install kernda --no-cache \
&& $CONDA_DIR/envs/python2/bin/python -m ipykernel install \
&& kernda -o -y /usr/local/share/jupyter/kernels/python2/kernel.json \
&& pip uninstall kernda -y)"
# Install in Python 3
RUN /bin/bash -c "source activate root \
&& cd /root/pyradiomics \
&& python -m pip install --no-cache-dir -r requirements.txt \
&& python setup.py install"
# Python 2
RUN /bin/bash -c "source activate python2 \
&& cd /root/pyradiomics \
&& python -m pip install --no-cache-dir -r requirements.txt \
&& python setup.py install"
# Install sample data and notebooks
ADD data/ /home/jovyan/work/data/
ADD notebooks/RadiomicsExample.ipynb /home/jovyan/work/notebooks/
ADD notebooks/FeatureVisualization.ipynb /home/jovyan/work/notebooks/
ADD notebooks/FeatureVisualizationWithClustering.ipynb /home/jovyan/work/notebooks/
ADD notebooks/FilteringEffects.ipynb /home/jovyan/work/notebooks/
ADD notebooks/helloRadiomics.ipynb /home/jovyan/work/notebooks/
ADD notebooks/helloFeatureClass.ipynb /home/jovyan/work/notebooks/
ADD notebooks/PyRadiomicsExample.ipynb /home/jovyan/work/notebooks/
ADD examples/exampleSettings/Params.yaml /home/jovyan/work/examples/exampleSettings/
# Make a global directory and link it to the work directory
RUN mkdir /data
RUN ln -s /data /home/jovyan/work/data
RUN chown -R jovyan:users /home/jovyan/work
# Trust the notebooks that we've installed
USER jovyan
RUN jupyter trust /home/jovyan/work/notebooks/*.ipynb
# Run the notebooks
RUN jupyter nbconvert --ExecutePreprocessor.kernel_name=python2 --ExecutePreprocessor.timeout=-1 --to notebook --execute /home/jovyan/work/notebooks/helloRadiomics.ipynb /home/jovyan/work/notebooks/helloFeatureClass.ipynb /home/jovyan/work/notebooks/PyRadiomicsExample.ipynb
RUN jupyter nbconvert --ExecutePreprocessor.kernel_name=python3 --ExecutePreprocessor.timeout=-1 --to notebook --execute /home/jovyan/work/notebooks/helloRadiomics.ipynb /home/jovyan/work/notebooks/helloFeatureClass.ipynb /home/jovyan/work/notebooks/PyRadiomicsExample.ipynb
# The user's data will show up as /data
VOLUME /data
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