# Generated by Porcupine
# Modelled after Neurodocker v0.2.0-dev. https://github.com/kaczmarj/neurodocker

FROM timvanmourik/porcupine

#----------------------------------------------------------
# Install common dependencies and create default entrypoint
#----------------------------------------------------------
ARG DEBIAN_FRONTEND=noninteractive
ENV LANG="C.UTF-8" \
    LC_ALL="C" \
    ND_ENTRYPOINT="/porcupine/startup.sh"
RUN apt-get update -qq && apt-get install -yq --no-install-recommends  \
    	bzip2 ca-certificates curl unzip \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
    && chmod 777 /opt && chmod a+s /opt \
    && mkdir /porcupine \
    && echo '#!/usr/bin/env bash' >> $ND_ENTRYPOINT \
    && echo 'set +x' >> $ND_ENTRYPOINT \
    && echo 'if [ -z "$*" ]; then /usr/bin/env bash; else $*; fi' >> $ND_ENTRYPOINT \
    && chmod -R 777 /porcupine && chmod a+s /porcupine
ENTRYPOINT ["/porcupine/startup.sh"]

#---------------
# Install Nipype
#---------------
RUN curl -sSLO https://repo.continuum.io/miniconda/Miniconda3-4.3.11-Linux-x86_64.sh && \
    bash Miniconda3-4.3.11-Linux-x86_64.sh -b -p /usr/local/miniconda && \
    rm Miniconda3-4.3.11-Linux-x86_64.sh

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

# Installing precomputed python packages
RUN conda install -y mkl=2017.0.1 mkl-service &&  \
    conda install -y numpy=1.12.0 \
                     scipy=0.18.1 \
                     scikit-learn=0.18.1 \
                     matplotlib=2.0.0 \
                     pandas=0.19.2 \
                     libxml2=2.9.4 \
                     libxslt=1.1.29\
                     traits=4.6.0 \
                     boto

RUN chmod +x /usr/local/miniconda/bin/* && conda clean --all -y
RUN echo 'export PATH=/usr/local/miniconda/bin:$PATH' >> /etc/profile
RUN pip install nipype
RUN apt-get update && apt-get install -y graphviz
#--------------------
# Install AFNI latest
#--------------------
ENV PATH=/opt/afni:$PATH
RUN apt-get update -qq && apt-get install -yq --no-install-recommends ed gsl-bin libglu1-mesa-dev libglib2.0-0 libglw1-mesa \
    libgomp1 libjpeg62 libxm4 netpbm tcsh xfonts-base xvfb \
    && libs_path=/usr/lib/x86_64-linux-gnu \
    && if [ -f $libs_path/libgsl.so.19 ]; then \
           ln $libs_path/libgsl.so.19 $libs_path/libgsl.so.0; \
       fi \
    # Install libxp (not in all ubuntu/debian repositories) \
    && apt-get install -yq --no-install-recommends libxp6 \
    || /bin/bash -c " \
       curl --retry 5 -o /tmp/libxp6.deb -sSL http://mirrors.kernel.org/debian/pool/main/libx/libxp/libxp6_1.0.2-2_amd64.deb \
       && dpkg -i /tmp/libxp6.deb && rm -f /tmp/libxp6.deb" \
    # Install libpng12 (not in all ubuntu/debian repositories) \
    && apt-get install -yq --no-install-recommends libpng12-0 \
    || /bin/bash -c " \
       curl -o /tmp/libpng12.deb -sSL http://mirrors.kernel.org/debian/pool/main/libp/libpng/libpng12-0_1.2.49-1%2Bdeb7u2_amd64.deb \
       && dpkg -i /tmp/libpng12.deb && rm -f /tmp/libpng12.deb" \
    # Install R \
    && apt-get install -yq --no-install-recommends \
    	r-base-dev r-cran-rmpi \
     || /bin/bash -c " \
        curl -o /tmp/install_R.sh -sSL https://gist.githubusercontent.com/kaczmarj/8e3792ae1af70b03788163c44f453b43/raw/0577c62e4771236adf0191c826a25249eb69a130/R_installer_debian_ubuntu.sh \
        && /bin/bash /tmp/install_R.sh" \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
    && echo "Downloading AFNI ..." \
    && mkdir -p /opt/afni \
    && curl -sSL --retry 5 https://afni.nimh.nih.gov/pub/dist/tgz/linux_openmp_64.tgz \
    | tar zx -C /opt/afni --strip-components=1 \
    && /opt/afni/rPkgsInstall -pkgs ALL \
    && rm -rf /tmp/*

#--------------------------------
# Add custom analysis file as CMD
#--------------------------------
ADD ./porcupine_generated_pipeline.py /run.py
CMD ["python", "/run.py"]