Dockerfile

# Generated by Neurodocker version 0.4.1-dev
# Timestamp: 2018-07-22 14:48:52 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 neurodebian:stretch

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/* /tmp/* /var/tmp/* \
    && 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 '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 \
           wget \
           strace \
           time \
           ncdu \
           gnupg \
           curl \
           procps \
           datalad \
           git-annex-standalone \
           python-nipype \
           virtualenv \
           python-dcmstack \
           python-configparser \
           python-funcsigs \
           python-pytest \
           dcmtk \
           python-pip \
           python-wheel \
           python-setuptools \
           python-datalad \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

RUN curl -sL https://deb.nodesource.com/setup_6.x | bash -

RUN apt-get update -qq \
    && apt-get install -y -q --no-install-recommends \
           nodejs \
           npm \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

RUN npm install -g bids-validator@0.26.11

RUN mkdir /afs /inbox

RUN pip install heudiconv

ENV PATH="/opt/dcm2niix-v1.0.20180622/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/* /tmp/* /var/tmp/* \
    && git clone https://github.com/rordenlab/dcm2niix /tmp/dcm2niix \
    && cd /tmp/dcm2niix \
    && git fetch --tags \
    && git checkout v1.0.20180622 \
    && mkdir /tmp/dcm2niix/build \
    && cd /tmp/dcm2niix/build \
    && cmake  -DCMAKE_INSTALL_PREFIX:PATH=/opt/dcm2niix-v1.0.20180622 .. \
    && make \
    && make install \
    && rm -rf /tmp/dcm2niix

RUN echo '#!/bin/bash' >> /neurodocker/heudiconv.sh && echo 'heudiconv "$@"' >> /neurodocker/heudiconv.sh && chmod +x /neurodocker/heudiconv.sh

RUN useradd --no-user-group --create-home --shell /bin/bash reproin
USER reproin

ENTRYPOINT ["/neurodocker/heudiconv.sh"]

RUN echo '{ \
    \n  "pkg_manager": "apt", \
    \n  "instructions": [ \
    \n    [ \
    \n      "base", \
    \n      "neurodebian:stretch" \
    \n    ], \
    \n    [ \
    \n      "install", \
    \n      [ \
    \n        "vim", \
    \n        "wget", \
    \n        "strace", \
    \n        "time", \
    \n        "ncdu", \
    \n        "gnupg", \
    \n        "curl", \
    \n        "procps", \
    \n        "datalad", \
    \n        "git-annex-standalone", \
    \n        "python-nipype", \
    \n        "virtualenv", \
    \n        "python-dcmstack", \
    \n        "python-configparser", \
    \n        "python-funcsigs", \
    \n        "python-pytest", \
    \n        "dcmtk", \
    \n        "python-pip", \
    \n        "python-wheel", \
    \n        "python-setuptools", \
    \n        "python-datalad" \
    \n      ] \
    \n    ], \
    \n    [ \
    \n      "run", \
    \n      "curl -sL https://deb.nodesource.com/setup_6.x | bash - " \
    \n    ], \
    \n    [ \
    \n      "install", \
    \n      [ \
    \n        "nodejs", \
    \n        "npm" \
    \n      ] \
    \n    ], \
    \n    [ \
    \n      "run", \
    \n      "npm install -g bids-validator@0.26.11" \
    \n    ], \
    \n    [ \
    \n      "run", \
    \n      "mkdir /afs /inbox" \
    \n    ], \
    \n    [ \
    \n      "run", \
    \n      "pip install heudiconv" \
    \n    ], \
    \n    [ \
    \n      "dcm2niix", \
    \n      { \
    \n        "version": "v1.0.20180622", \
    \n        "method": "source" \
    \n      } \
    \n    ], \
    \n    [ \
    \n      "run", \
    \n      "echo '"'"'#!/bin/bash'"'"' >> /neurodocker/heudiconv.sh && echo '"'"'heudiconv \"$@\"'"'"' >> /neurodocker/heudiconv.sh && chmod +x /neurodocker/heudiconv.sh" \
    \n    ], \
    \n    [ \
    \n      "user", \
    \n      "reproin" \
    \n    ], \
    \n    [ \
    \n      "entrypoint", \
    \n      "/neurodocker/heudiconv.sh" \
    \n    ] \
    \n  ] \
    \n}' > /neurodocker/neurodocker_specs.json