Dockerfile

# Use Ubuntu 16.04 LTS
FROM ubuntu:xenial-20161213

# Pre-cache neurodebian key
COPY .docker/neurodebian.gpg /usr/local/etc/neurodebian.gpg

# Prepare environment
RUN apt-get update && \
    apt-get install -y --no-install-recommends \
                    curl \
                    bzip2 \
                    ca-certificates \
                    xvfb \
                    cython3 \
                    build-essential \
                    autoconf \
                    libtool \
                    pkg-config \
                    git && \
    apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

# Installing Neurodebian packages (FSL, AFNI, git)
RUN curl -sSL "http://neuro.debian.net/lists/xenial.us-ca.full" >> /etc/apt/sources.list.d/neurodebian.sources.list && \
    apt-key add /usr/local/etc/neurodebian.gpg && \
    (apt-key adv --refresh-keys --keyserver hkp://ha.pool.sks-keyservers.net 0xA5D32F012649A5A9 || true)

RUN apt-get update && \
    apt-get install -y --no-install-recommends \
                    fsl-core=5.0.9-5~nd16.04+1 && \
    apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

ENV FSLDIR="/usr/share/fsl/5.0" \
    FSLOUTPUTTYPE="NIFTI_GZ" \
    FSLMULTIFILEQUIT="TRUE" \
    POSSUMDIR="/usr/share/fsl/5.0" \
    LD_LIBRARY_PATH="/usr/lib/fsl/5.0:$LD_LIBRARY_PATH" \
    FSLTCLSH="/usr/bin/tclsh" \
    FSLWISH="/usr/bin/wish"

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

# Installing and setting up miniconda
RUN curl -sSLO https://repo.continuum.io/miniconda/Miniconda3-4.5.11-Linux-x86_64.sh && \
    bash Miniconda3-4.5.11-Linux-x86_64.sh -b -p /usr/local/miniconda && \
    rm Miniconda3-4.5.11-Linux-x86_64.sh

# Set CPATH for packages relying on compiled libs (e.g. indexed_gzip)
ENV PATH="/usr/lib/fsl/5.0:/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=3.7.1 \
                     mkl=2018.0.3 \
                     mkl-service \
                     numpy=1.15.4 \
                     scipy=1.1.0 \
                     scikit-learn=0.19.1 \
                     matplotlib=2.2.2 \
                     pandas=0.23.4 \
                     libxml2=2.9.8 \
                     libxslt=1.1.32 \
                     graphviz=2.40.1 \
                     traits=4.6.0 \
                     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

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

# 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 dev requirements (packages that are not in pypi)
WORKDIR /src/
COPY requirements.txt requirements.txt
RUN pip install --no-cache-dir -r requirements.txt

# Replace FSL's imglob (which is Python 2)
RUN rm -f /usr/share/fsl/5.0/bin/imglob && \
    chmod a+rx $( python -c 'import site; print(site.getsitepackages()[0])' )/nipype/external/fsl_imglob.py && \
    ln -s $( python -c 'import site; print(site.getsitepackages()[0])' )/nipype/external/fsl_imglob.py /usr/share/fsl/5.0/bin/imglob

RUN find $HOME -type d -exec chmod go=u {} + && \
    find $HOME -type f -exec chmod go=u {} +

# Installing this module
COPY . /src/
ENV PYTHONPATH="/src:$PYTHONPATH"

RUN ldconfig
WORKDIR /tmp/
ENTRYPOINT ["/src/run.py"]