Dockerfile

FROM ubuntu:16.04
MAINTAINER Will Tackett <william.tackett@pennmedicine.upenn.edu>

# Make directory for flywheel spec (v0)
ENV FLYWHEEL /flywheel/v0
RUN mkdir -p ${FLYWHEEL}

# Set the entrypoint
ENTRYPOINT ["/flywheel/v0/run.sh"]

# Pre-cache neurodebian key
COPY docker/files/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 \
                    jq \
                    zip \
                    unzip \
                    nano \
                    git && \
    curl -sL https://deb.nodesource.com/setup_10.x | bash - && \
    apt-get install -y --no-install-recommends \
                    nodejs && \
    apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

# 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

ENV PATH=/usr/local/miniconda/bin:$PATH \
    LANG=C.UTF-8 \
    LC_ALL=C.UTF-8 \
    PYTHONNOUSERSITE=1

# Installing Neurodebian packages (FSL, AFNI, git)
RUN curl -sSL "http://neuro.debian.net/lists/$( lsb_release -c | cut -f2 ).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 \
                    fsl-mni152-templates=5.0.7-2 \
                    afni=16.2.07~dfsg.1-5~nd16.04+1 \
                    git-annex-standalone && \
    apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

ENV FSLDIR=/usr/share/fsl/5.0 \
    PATH=/usr/share/fsl/5.0:${PATH} \
    PATH=/usr/share/fsl/5.0/bin:${PATH} \
    FSLOUTPUTTYPE="NIFTI_GZ" \
    FSLMULTIFILEQUIT="TRUE" \
    LD_LIBRARY_PATH="/usr/lib/fsl/5.0:$LD_LIBRARY_PATH"

ENV AFNI_INSTALLDIR=/usr/lib/afni \
    PATH=/usr/lib/afni/bin:${PATH} \
    AFNI_PLUGINPATH=/usr/lib/afni/plugins \
    AFNI_MODELPATH=/usr/lib/afni/models \
    AFNI_TTATLAS_DATASET=/usr/share/afni/atlases \
    AFNI_IMSAVE_WARNINGS=NO

# Installing precomputed python packages
RUN conda install -y python=3.7.1 \
                     numpy=1.15.4 \
                     scipy=1.2.0 \
                     mkl=2019.1 \
                     mkl-service \
                     scikit-learn=0.20.2 \
                     matplotlib=2.2.3 \
                     seaborn=0.9.0 \
                     pandas=0.24.0 \
                     libxml2=2.9.9 \
                     graphviz=2.40.1 \
                     traits=4.6.0 \
                     jinja2=2.11.2 \
                     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 'flywheel-sdk==12.*'
RUN pip install pandas
RUN pip install pybids
RUN pip install --no-cache fw-heudiconv==0.3.3 \
    && pip install --no-cache nipype \
    && pip install --no-cache nilearn \
    && pip install --no-cache jinja2 \
    && pip install --no-cache nibabel \
    && pip install --no-cache nistats

COPY manifest.json ${FLYWHEEL}/manifest.json
COPY run.sh /flywheel/v0/run.sh
COPY . /flywheel/v0/
RUN chmod +x ${FLYWHEEL}/*

# RUN apt-get update -y
# RUN apt-get upgrade -y
# RUN apt-get install -y unzip

# RUN conda install matplotlib
# RUN conda install scikit-learn
# RUN apt-get install -y libcairo2-dev
# RUN apt-get install -y pango-1.0

# ENV preservation for Flywheel Engine
RUN env -u HOSTNAME -u PWD | \
  awk -F = '{ print "export " $1 "=\"" $2 "\"" }' > ${FLYWHEEL}/docker-env.sh

WORKDIR /flywheel/v0