difit/Dockerfile at main · kodiweera/difit · GitHub

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# Use Ubuntu 20.04
FROM ubuntu:focal-20210921

# Prepare environment
RUN apt-get update && \
    apt-get install -y --no-install-recommends \
                    curl \
                    bzip2 \
                    ca-certificates \
                    xvfb \
                    build-essential \
                    autoconf \
                    libtool \
                    pkg-config \
                    graphviz \
                    git && \
    curl -sL https://deb.nodesource.com/setup_14.x | bash - && \
    apt-get install -y --no-install-recommends \
                    nodejs && \
    apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

# Install latest pandoc
RUN curl -o pandoc-2.2.2.1-1-amd64.deb -sSL "https://github.com/jgm/pandoc/releases/download/2.2.2.1/pandoc-2.2.2.1-1-amd64.deb" && \
    dpkg -i pandoc-2.2.2.1-1-amd64.deb && \
    rm pandoc-2.2.2.1-1-amd64.deb

# Installing and setting up miniconda
RUN curl -sSLO https://repo.continuum.io/miniconda/Miniconda3-py38_4.10.3-Linux-x86_64.sh && \
    bash Miniconda3-py38_4.10.3-Linux-x86_64.sh -b -p /usr/local/miniconda && \
    rm Miniconda3-py38_4.10.3-Linux-x86_64.sh

# Set CPATH for packages relying on compiled libs (e.g. indexed_gzip)
ENV PATH="/usr/local/miniconda/bin:$PATH" \
    CPATH="/usr/local/miniconda/include/:$CPATH" \
    LANG="C.UTF-8" \
    LC_ALL="C.UTF-8" \
    PYTHONNOUSERSITE=1

# Installing precomputed python packages
RUN conda install -y python=3.8.5 \
                     pip=20.2.4 \
                     mkl=2018.0.3 \
                     mkl-service \
                     numpy=1.15.4 \
                     scipy=1.1.0 \
                     scikit-learn=0.19.1 \
                     pandas=0.23.4 \
                     libxml2=2.9.8 \
                     libxslt=1.1.32 \
                     graphviz=2.40.1 \
                     traits=4.6.0 \
                     sphinx>=3.2.1 \
                     multiprocess \
                     zlib; sync && \
    chmod -R a+rX /usr/local/miniconda; sync && \
    chmod +x /usr/local/miniconda/bin/*; sync && \
    conda build purge-all; sync && \
    conda clean -tipsy && sync

RUN pip install nibabel dipy nilearn fury weasyprint nipype

# Unless otherwise specified each process should only use one thread - nipype
# will handle parallelization
ENV MKL_NUM_THREADS=1 \
    OMP_NUM_THREADS=1

# Create a shared $HOME directory
RUN useradd -m -s /bin/bash -G users difit
WORKDIR /home/difit
ENV HOME="/home/difit"

# # Precaching fonts, set 'Agg' as default backend for matplotlib
# RUN python -c "from matplotlib import font_manager" && \
#     sed -i 's/\(backend *: \).*$/\1Agg/g' $( python -c "import matplotlib; print(matplotlib.matplotlib_fname())" )

# Installing difit
COPY . /src/difit
ARG VERSION

RUN pip install --no-cache-dir "/src/difit[all]"

RUN find $HOME -type d -exec chmod go=u {} + && \
    find $HOME -type f -exec chmod go=u {} + && \
    rm -rf $HOME/.npm $HOME/.conda $HOME/.empty

RUN ldconfig
WORKDIR /tmp/

ARG BUILD_DATE
ARG VCS_REF
ARG VERSION
LABEL org.label-schema.build-date=$BUILD_DATE \
      org.label-schema.name="difit" \
      org.label-schema.description="difit - An MRI diffution model fitting software" \
      org.label-schema.url="http://difit.readthedocs.org" \
      org.label-schema.vcs-ref=$VCS_REF \
      org.label-schema.vcs-url="https://github.com/kodiweera/difit" \
      org.label-schema.version=$VERSION \
      org.label-schema.schema-version="1.0.0"