#FROM --platform=linux/amd64 ubuntu:xenial-20200114
FROM ubuntu:xenial-20200114

ARG DEBIAN_FRONTEND="noninteractive"

ENV LANG="en_US.UTF-8" \
    LC_ALL="en_US.UTF-8" \
    ND_ENTRYPOINT="/neurodocker/startup.sh"
RUN export ND_ENTRYPOINT="/neurodocker/startup.sh" \
    && apt-get update -qq \
    && apt-get install -y -q --no-install-recommends \
           apt-utils \
           bzip2 \
           ca-certificates \
           curl \
           locales \
           unzip \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/* \
    && sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen \
    && dpkg-reconfigure --frontend=noninteractive locales \
    && update-locale LANG="en_US.UTF-8" \
    && chmod 777 /opt && chmod a+s /opt \
    && mkdir -p /neurodocker \
    && if [ ! -f "$ND_ENTRYPOINT" ]; then \
         echo '#!/usr/bin/env bash' >> "$ND_ENTRYPOINT" \
    &&   echo 'set -e' >> "$ND_ENTRYPOINT" \
    &&   echo 'export USER="${USER:=`whoami`}"' >> "$ND_ENTRYPOINT" \
    &&   echo 'if [ -n "$1" ]; then "$@"; else /usr/bin/env bash; fi' >> "$ND_ENTRYPOINT"; \
    fi \
    && chmod -R 777 /neurodocker && chmod a+s /neurodocker

ENTRYPOINT ["/neurodocker/startup.sh"]

RUN apt-get update -qq \
    && apt-get install -y -q --no-install-recommends \
           vim \
           tree \
           grep \
           less \
           wget \
           make \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/*

ENV PATH="/opt/dcm2niix-latest/bin:$PATH"
RUN apt-get update -qq \
    && apt-get install -y -q --no-install-recommends \
           cmake \
           g++ \
           gcc \
           git \
           make \
           pigz \
           zlib1g-dev \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/* \
    && git clone https://github.com/rordenlab/dcm2niix /tmp/dcm2niix \
    && mkdir /tmp/dcm2niix/build \
    && cd /tmp/dcm2niix/build \
    && cmake  -DCMAKE_INSTALL_PREFIX:PATH=/opt/dcm2niix-latest .. \
    && make \
    && make install \
    && rm -rf /tmp/dcm2niix

ENV ANTSPATH="/opt/ants-2.2.0" \
    PATH="/opt/ants-2.2.0:$PATH"
RUN echo "Downloading ANTs ..." \
    && mkdir -p /opt/ants-2.2.0 \
    && curl -fsSL --retry 5 https://dl.dropbox.com/s/2f4sui1z6lcgyek/ANTs-Linux-centos5_x86_64-v2.2.0-0740f91.tar.gz \
    | tar -xz -C /opt/ants-2.2.0 --strip-components 1

ENV FREESURFER_HOME="/opt/freesurfer-6.0.1" \
    PATH="/opt/freesurfer-6.0.1/bin:$PATH"
RUN apt-get update -qq \
    && apt-get install -y -q --no-install-recommends \
           bc \
           libgomp1 \
           libxmu6 \
           libxt6 \
           perl \
           tcsh \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/* \
    && echo "Downloading FreeSurfer ..." \
    && mkdir -p /opt/freesurfer-6.0.1

RUN wget --progress=bar:force:noscroll -c --no-check-certificate https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.1/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1.tar.gz -O - | tar -xz -C /opt/freesurfer-6.0.1 --strip-components 1 \
         --exclude='freesurfer/average/mult-comp-cor' \
         --exclude='freesurfer/lib/cuda' \
         --exclude='freesurfer/lib/qt' \
         --exclude='freesurfer/subjects/V1_average' \
         --exclude='freesurfer/subjects/bert' \
         --exclude='freesurfer/subjects/cvs_avg35' \
         --exclude='freesurfer/subjects/cvs_avg35_inMNI152' \
         --exclude='freesurfer/subjects/fsaverage3' \
         --exclude='freesurfer/subjects/fsaverage4' \
         --exclude='freesurfer/subjects/fsaverage5' \
         --exclude='freesurfer/subjects/fsaverage6' \
         --exclude='freesurfer/subjects/fsaverage_sym' \
         --exclude='freesurfer/trctrain' \
    && sed -i '$isource "/opt/freesurfer-6.0.1/SetUpFreeSurfer.sh"' "$ND_ENTRYPOINT"

ENV CONDA_DIR="/opt/miniconda-latest" \
    PATH="/opt/miniconda-latest/bin:$PATH"
RUN export PATH="/opt/miniconda-latest/bin:$PATH" \
    && echo "Downloading Miniconda installer ..." \
    && conda_installer="/tmp/miniconda.sh" \
    && curl -fsSL --retry 5 -o "$conda_installer" https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh \
    && bash "$conda_installer" -b -p /opt/miniconda-latest \
    && rm -f "$conda_installer" \
    && conda update -yq -nbase conda \
    && conda config --system --prepend channels conda-forge \
    && conda config --system --set auto_update_conda false \
    && conda config --system --set show_channel_urls true \
    && sync && conda clean --all && sync \
    && conda create -y -q --name neuro \
    && conda install -y -q --name neuro \
           'jupyter' \
           'jupyterlab' \
           'matplotlib' \
           'nilearn' \
           'traits' \
           'nipype' \
           'seaborn' \
	   'heudiconv' \
    && sync && conda clean --all && sync

RUN wget --no-check-certificate https://ftpmirror.gnu.org/parallel/parallel-20190222.tar.bz2 \
    && bzip2 -dc parallel-20190222.tar.bz2 | tar xvf - \
    && cd parallel-20190222 \
    && ./configure && make && make install

RUN mkdir -p /workspace/assets

COPY ./license.txt /opt/freesurfer-6.0.1/license.txt
COPY ./multiproc.sh /workspace/multiproc.sh
COPY ./assets /workspace/assets
COPY ./seminar* /workspace/
COPY ./entrypoint.sh /entrypoint.sh
COPY ./heuristic.py /workspace/heuristic.py

RUN chmod +x /workspace/multiproc.sh \
            /entrypoint.sh

RUN "/neurodocker/startup.sh"

#RUN "./${FREESURFER_HOME}/SetUpFreeSurfer.sh"

ENTRYPOINT ["bash", "-c", "/entrypoint.sh"]

RUN echo '{ \
    \n  "pkg_manager": "apt", \
    \n  "instructions": [ \
    \n    [ \
    \n      "base", \
    \n      "ubuntu:xenial-20200114" \
    \n    ], \
    \n    [ \
    \n      "install", \
    \n      [ \
    \n        "vim" \
    \n      ] \
    \n    ], \
    \n    [ \
    \n      "dcm2niix", \
    \n      { \
    \n        "version": "latest", \
    \n        "method": "source" \
    \n      } \
    \n    ], \
    \n    [ \
    \n      "ants", \
    \n      { \
    \n        "version": "2.2.0" \
    \n      } \
    \n    ], \
    \n    [ \
    \n      "freesurfer", \
    \n      { \
    \n        "version": "6.0.1" \
    \n      } \
    \n    ], \
    \n    [ \
    \n      "miniconda", \
    \n      { \
    \n        "create_env": "neuro", \
    \n        "python_version": "3.6", \
    \n        "conda_install": [ \
    \n          "jupyter", \
    \n          "jupyterlab", \
    \n          "matplotlib", \
    \n          "nilearn", \
    \n          "traits", \
    \n          "nipype" \
    \n        ] \
    \n      } \
    \n    ], \
    \n    [ \
    \n      "entrypoint", \
    \n      "/usr/local/miniconda/jupyter lab --ip=0.0.0.0 --no-browser --port=8080" \
    \n    ] \
    \n  ] \
    \n}' > /neurodocker/neurodocker_specs.json