Dockerfile_Neuro

# Docker for neuroimaging
# Based on: https://github.com/ReproNim/neurodocker
# Author: Tiago Silva

FROM ubuntu:16.04

USER root

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-transport-https \
    && 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"]

ENV FSLDIR="/opt/fsl-5.0.10" \
    PATH="/opt/fsl-5.0.10/bin:$PATH" \
    FSLOUTPUTTYPE="NIFTI_GZ" \
    FSLMULTIFILEQUIT="TRUE" \
    FSLTCLSH="/opt/fsl-5.0.10/bin/fsltclsh" \
    FSLWISH="/opt/fsl-5.0.10/bin/fslwish" \
    FSLLOCKDIR="" \
    FSLMACHINELIST="" \
    FSLREMOTECALL="" \
    FSLGECUDAQ="cuda.q"
RUN apt-get update -qq \
    && apt-get install -y -q --no-install-recommends \
           bc \
           dc \
           file \
           libfontconfig1 \
           libfreetype6 \
           libgl1-mesa-dev \
           libgl1-mesa-dri \
           libglu1-mesa-dev \
           libgomp1 \
           libice6 \
           libxcursor1 \
           libxft2 \
           libxinerama1 \
           libxrandr2 \
           libxrender1 \
           libxt6 \
           sudo \
           wget \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/* \
    && echo "Downloading FSL ..." \
    && mkdir -p /opt/fsl-5.0.10 \
    && curl -fsSL --retry 5 https://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-5.0.10-centos6_64.tar.gz \
    | tar -xz -C /opt/fsl-5.0.10 --strip-components 1 \
    && sed -i '$iecho Some packages in this Docker container are non-free' $ND_ENTRYPOINT \
    && sed -i '$iecho If you are considering commercial use of this container, please consult the relevant license:' $ND_ENTRYPOINT \
    && sed -i '$iecho https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Licence' $ND_ENTRYPOINT \
    && sed -i '$isource $FSLDIR/etc/fslconf/fsl.sh' $ND_ENTRYPOINT \
    && echo "Installing FSL conda environment ..." \
    && bash /opt/fsl-5.0.10/etc/fslconf/fslpython_install.sh -f /opt/fsl-5.0.10

ENV FORCE_SPMMCR="1" \
    SPM_HTML_BROWSER="0" \
    LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/lib/x86_64-linux-gnu:/opt/matlabmcr-2010a/v713/runtime/glnxa64:/opt/matlabmcr-2010a/v713/bin/glnxa64:/opt/matlabmcr-2010a/v713/sys/os/glnxa64:/opt/matlabmcr-2010a/v713/extern/bin/glnxa64" \
    MATLABCMD="/opt/matlabmcr-2010a/v713/toolbox/matlab"
RUN export TMPDIR="$(mktemp -d)" \
    && apt-get update -qq \
    && apt-get install -y -q --no-install-recommends \
           bc \
           libncurses5 \
           libxext6 \
           libxmu6 \
           libxpm-dev \
           libxt6 \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/* \
    && echo "Downloading MATLAB Compiler Runtime ..." \
    && curl -sSL --retry 5 -o /tmp/toinstall.deb http://mirrors.kernel.org/debian/pool/main/libx/libxp/libxp6_1.0.2-2_amd64.deb \
    && dpkg -i /tmp/toinstall.deb \
    && rm /tmp/toinstall.deb \
    && apt-get install -f \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/* \
    && curl -fsSL --retry 5 -o "$TMPDIR/MCRInstaller.bin" https://dl.dropbox.com/s/zz6me0c3v4yq5fd/MCR_R2010a_glnxa64_installer.bin \
    && chmod +x "$TMPDIR/MCRInstaller.bin" \
    && "$TMPDIR/MCRInstaller.bin" -silent -P installLocation="/opt/matlabmcr-2010a" \
    && rm -rf "$TMPDIR" \
    && unset TMPDIR \
    && echo "Downloading standalone SPM ..." \
    && curl -fsSL --retry 5 -o /tmp/spm12.zip https://www.fil.ion.ucl.ac.uk/spm/download/restricted/utopia/previous/spm12_r7771_R2010a.zip \
    && unzip -q /tmp/spm12.zip -d /tmp \
    && mkdir -p /opt/spm12-r7771 \
    && mv /tmp/spm12/* /opt/spm12-r7771/ \
    && chmod -R 777 /opt/spm12-r7771 \
    && rm -rf /tmp/spm* \
    && /opt/spm12-r7771/run_spm12.sh /opt/matlabmcr-2010a/v713 quit \
    && sed -i '$iexport SPMMCRCMD=\"/opt/spm12-r7771/run_spm12.sh /opt/matlabmcr-2010a/v713 script\"' $ND_ENTRYPOINT

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 FREESURFER_HOME="/opt/freesurfer-6.0.1" \
    PATH="/opt/freesurfer-6.0.1/bin:$PATH"
RUN apt-get update -qq \
    && apt-get install -y -q --no-install-recommends \
           bc \
           libgomp1 \
           libxmu6 \
           libxt6 \
           perl \
           tcsh \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/* \
    && echo "Downloading FreeSurfer ..." \
    && mkdir -p /opt/freesurfer-6.0.1 \
    && curl -fsSL --retry 5 ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.1/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1.tar.gz \
    | tar -xz -C /opt/freesurfer-6.0.1 --strip-components 1 \
         --exclude='freesurfer/average/mult-comp-cor' \
         --exclude='freesurfer/lib/cuda' \
         --exclude='freesurfer/lib/qt' \
         --exclude='freesurfer/subjects/V1_average' \
         --exclude='freesurfer/subjects/bert' \
         --exclude='freesurfer/subjects/cvs_avg35' \
         --exclude='freesurfer/subjects/cvs_avg35_inMNI152' \
         --exclude='freesurfer/subjects/fsaverage3' \
         --exclude='freesurfer/subjects/fsaverage4' \
         --exclude='freesurfer/subjects/fsaverage5' \
         --exclude='freesurfer/subjects/fsaverage6' \
         --exclude='freesurfer/subjects/fsaverage_sym' \
         --exclude='freesurfer/trctrain' \
    && sed -i '$isource "/opt/freesurfer-6.0.1/SetUpFreeSurfer.sh"' "$ND_ENTRYPOINT"

ENV ANTSPATH="/opt/ants-2.3.1" \
    PATH="/opt/ants-2.3.1:$PATH"
RUN echo "Downloading ANTs ..." \
    && mkdir -p /opt/ants-2.3.1 \
    && curl -fsSL --retry 5 https://dl.dropbox.com/s/1xfhydsf4t4qoxg/ants-Linux-centos6_x86_64-v2.3.1.tar.gz \
    | tar -xz -C /opt/ants-2.3.1 --strip-components 1

ENV PATH="/opt/mrtrix3-3.0_RC3/bin:$PATH"
RUN echo "Downloading MRtrix3 ..." \
    && mkdir -p /opt/mrtrix3-3.0_RC3 \
    && curl -fsSL --retry 5 https://dl.dropbox.com/s/2oh339ehcxcf8xf/mrtrix3-3.0_RC3-Linux-centos6.9-x86_64.tar.gz \
    | tar -xz -C /opt/mrtrix3-3.0_RC3 --strip-components 1

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 -y --all && sync \
    && conda create -y -q --name neuro \
    && conda install -y -q --name neuro \
           "python=3.8" \
           "traits" \
    && sync && conda clean -y --all && sync \
    && bash -c "source activate neuro \
    &&   pip install --no-cache-dir  \
             "nipype" \
             "dipy" \
             "numpy" \
             "canvas" \
             "pydicom" \
             "nibabel" \
             "scipy" \
             "dcm2bids" \
             "matplotlib" \
             "PyPDF2" \
             "reportlab" \
             "pillow"" \
    && rm -rf ~/.cache/pip/* \
    && sync

RUN distribution=$(. /etc/os-release;echo $ID$VERSION_ID) \
    && curl -s -L https://nvidia.github.io/nvidia-docker/gpgkey | sudo apt-key add - \
    && curl -s -L https://nvidia.github.io/nvidia-docker/$distribution/nvidia-docker.list | sudo tee /etc/apt/sources.list.d/nvidia-docker.list \
    && apt-get update -qq \
    && apt-get install -y -q --no-install-recommends \
           nvidia-docker2 \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/* \
    && mkdir -p /code \
    && mkdir -p /data

RUN echo '{ \
    \n  "pkg_manager": "apt", \
    \n  "instructions": [ \
    \n    [ \
    \n      "base", \
    \n      "ubuntu:16.04" \
    \n"     "nvidia-docker2" \
    \n    ], \
    \n    [ \
    \n      "fsl", \
    \n      { \
    \n        "version": "5.0.10", \
    \n        "method": "binaries" \
    \n      } \
    \n    ], \
    \n    [ \
    \n      "spm12", \
    \n      { \
    \n        "version": "r7771", \
    \n        "method": "binaries" \
    \n      } \
    \n    ], \
    \n    [ \
    \n      "dcm2niix", \
    \n      { \
    \n        "version": "latest", \
    \n        "method": "source" \
    \n      } \
    \n    ], \
    \n    [ \
    \n      "freesurfer", \
    \n      { \
    \n        "version": "6.0.1", \
    \n        "method": "binaries" \
    \n      } \
    \n    ], \
    \n    [ \
    \n      "ants", \
    \n      { \
    \n        "version": "2.3.1", \
    \n        "method": "binaries" \
    \n      } \
    \n    ], \
    \n    [ \
    \n      "mrtrix3", \
    \n      { \
    \n        "version": "3.0_RC3" \
    \n      } \
    \n    ], \
    \n    [ \
    \n      "miniconda", \
    \n      { \
    \n        "create_env": "neuro", \
    \n        "conda_install": [ \
    \n          "python=3.8", \
    \n          "traits" \
    \n        ], \
    \n        "pip_install": [ \
    \n          "nipype", \
    \n          "dipy", \
    \n          "numpy", \
    \n          "canvas", \
    \n          "pydicom", \
    \n          "nibabel", \
    \n          "scipy", \
    \n          "dcm2bids", \
    \n          "matplotlib", \
    \n          "PyPDF2", \
    \n          "PIL" \
    \n        ] \
    \n      } \
    \n    ] \
    \n  ] \
    \n}' > /neurodocker/neurodocker_specs.json