NeuroDockerfile

# Generated by Neurodocker version 0.5.0
# Timestamp: 2019-08-23 17:19:26 UTC
# 
# Thank you for using Neurodocker. If you discover any issues
# or ways to improve this software, please submit an issue or
# pull request on our GitHub repository:
# 
#     https://github.com/kaczmarj/neurodocker

FROM ubuntu:xenial-20190122

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 \
           libgdcm-tools \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/*

ENV FSLDIR="/opt/fsl-5.0.11" \
    PATH="/opt/fsl-5.0.11/bin:$PATH"
RUN apt-get update -qq \
    && apt-get install -y -q --no-install-recommends \
           bc \
           dc \
           file \
           libfontconfig1 \
           libfreetype6 \
           libgl1-mesa-dev \
           libglu1-mesa-dev \
           libgomp1 \
           libice6 \
           libxcursor1 \
           libxft2 \
           libxinerama1 \
           libxrandr2 \
           libxrender1 \
           libxt6 \
           wget \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/* \
    && echo "Downloading FSL ..." \
    && mkdir -p /opt/fsl-5.0.11 \
    && curl -fsSL --retry 5 https://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-5.0.11-centos6_64.tar.gz \
    | tar -xz -C /opt/fsl-5.0.11 --strip-components 1 \
    && sed -i '$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-5.0.11/etc/fslconf/fslpython_install.sh -f /opt/fsl-5.0.11

ENV FREESURFER_HOME="/opt/freesurfer" \
    PATH="/opt/freesurfer/bin:$PATH"
RUN apt-get update -qq \
    && apt-get install -y -q --no-install-recommends \
           bc \
           libgomp1 \
           libxmu6 \
           libxt6 \
           perl \
           tcsh \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/* \
    && echo "Downloading FreeSurfer ..." \
    && mkdir -p /opt/freesurfer \
    && curl -fsSL --retry 5 https://dl.dropbox.com/s/nnzcfttc41qvt31/recon-all-freesurfer6-3.min.tgz \
    | tar -xz -C /opt/freesurfer --strip-components 1 \
    && sed -i '$isource "/opt/freesurfer/SetUpFreeSurfer.sh"' "$ND_ENTRYPOINT"

ENV PATH="/opt/afni-latest:$PATH" \
    AFNI_PLUGINPATH="/opt/afni-latest"
RUN apt-get update -qq \
    && apt-get install -y -q --no-install-recommends \
           ed \
           gsl-bin \
           libglib2.0-0 \
           libglu1-mesa-dev \
           libglw1-mesa \
           libgomp1 \
           libjpeg62 \
           libxm4 \
           netpbm \
           tcsh \
           xfonts-base \
           xvfb \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/* \
    && curl -sSL --retry 5 -o /tmp/toinstall.deb http://mirrors.kernel.org/debian/pool/main/libx/libxp/libxp6_1.0.2-2_amd64.deb \
    && dpkg -i /tmp/toinstall.deb \
    && rm /tmp/toinstall.deb \
    && curl -sSL --retry 5 -o /tmp/toinstall.deb http://snapshot.debian.org/archive/debian-security/20160113T213056Z/pool/updates/main/libp/libpng/libpng12-0_1.2.49-1%2Bdeb7u2_amd64.deb \
    && dpkg -i /tmp/toinstall.deb \
    && rm /tmp/toinstall.deb \
    && apt-get install -f \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/* \
    && gsl2_path="$(find / -name 'libgsl.so.19' || printf '')" \
    && if [ -n "$gsl2_path" ]; then \
         ln -sfv "$gsl2_path" "$(dirname $gsl2_path)/libgsl.so.0"; \
    fi \
    && ldconfig \
    && echo "Downloading AFNI ..." \
    && mkdir -p /opt/afni-latest \
    && curl -fsSL --retry 5 https://afni.nimh.nih.gov/pub/dist/tgz/linux_openmp_64.tgz \
    | tar -xz -C /opt/afni-latest --strip-components 1

RUN cd /opt/freesurfer && echo 'cHJpbnRmICJrcnp5c3p0b2YuZ29yZ29sZXdza2lAZ21haWwuY29tXG41MTcyXG4gKkN2dW12RVYzelRmZ1xuRlM1Si8yYzFhZ2c0RVxuIiA+IGxpY2Vuc2UudHh0Cg==' | base64 -d | sh

COPY ["GE_dcm_to_nii.sh", "/opt/"]

RUN chmod +x /opt/GE_dcm_to_nii.sh

ENTRYPOINT ["/opt/GE_dcm_to_nii.sh"]

RUN echo '{ \
    \n  "pkg_manager": "apt", \
    \n  "instructions": [ \
    \n    [ \
    \n      "base", \
    \n      "ubuntu:xenial-20190122" \
    \n    ], \
    \n    [ \
    \n      "install", \
    \n      [ \
    \n        "libgdcm-tools" \
    \n      ] \
    \n    ], \
    \n    [ \
    \n      "fsl", \
    \n      { \
    \n        "version": "5.0.11" \
    \n      } \
    \n    ], \
    \n    [ \
    \n      "freesurfer", \
    \n      { \
    \n        "version": "6.0.0-min", \
    \n        "install_path": "/opt/freesurfer" \
    \n      } \
    \n    ], \
    \n    [ \
    \n      "afni", \
    \n      { \
    \n        "version": "latest" \
    \n      } \
    \n    ], \
    \n    [ \
    \n      "run", \
    \n      "cd /opt/freesurfer && echo '"'"'cHJpbnRmICJrcnp5c3p0b2YuZ29yZ29sZXdza2lAZ21haWwuY29tXG41MTcyXG4gKkN2dW12RVYzelRmZ1xuRlM1Si8yYzFhZ2c0RVxuIiA+IGxpY2Vuc2UudHh0Cg=='"'"' | base64 -d | sh" \
    \n    ], \
    \n    [ \
    \n      "copy", \
    \n      [ \
    \n        "GE_dcm_to_nii.sh", \
    \n        "/opt/" \
    \n      ] \
    \n    ], \
    \n    [ \
    \n      "run", \
    \n      "chmod +x /opt/GE_dcm_to_nii.sh" \
    \n    ], \
    \n    [ \
    \n      "entrypoint", \
    \n      "/opt/GE_dcm_to_nii.sh" \
    \n    ] \
    \n  ] \
    \n}' > /neurodocker/neurodocker_specs.json