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Merge pull request #20 from mvdoc/enh/neurodocker
ENH: add bash files to generate dockerfile/singularity file with neurodocker
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‎Dockerfile‎

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# Generated by Neurodocker version 0.4.0.dev2
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# Timestamp: 2018-05-12 17:03:02 UTC
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#
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# Thank you for using Neurodocker. If you discover any issues
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# or ways to improve this software, please submit an issue or
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# pull request on our GitHub repository:
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#
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# https://github.com/kaczmarj/neurodocker
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FROM neurodebian:stretch
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ARG DEBIAN_FRONTEND="noninteractive"
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ENV LANG="en_US.UTF-8" \
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LC_ALL="en_US.UTF-8" \
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ND_ENTRYPOINT="/neurodocker/startup.sh"
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RUN export ND_ENTRYPOINT="/neurodocker/startup.sh" \
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&& apt-get update -qq \
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&& apt-get install -y -q --no-install-recommends \
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apt-utils \
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bzip2 \
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ca-certificates \
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curl \
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locales \
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unzip \
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&& apt-get clean \
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&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
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&& sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen \
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&& dpkg-reconfigure --frontend=noninteractive locales \
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&& update-locale LANG="en_US.UTF-8" \
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&& chmod 777 /opt && chmod a+s /opt \
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&& mkdir -p /neurodocker \
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&& if [ ! -f "$ND_ENTRYPOINT" ]; then \
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echo '#!/usr/bin/env bash' >> "$ND_ENTRYPOINT" \
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&& echo 'set -e' >> "$ND_ENTRYPOINT" \
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&& echo 'if [ -n "$1" ]; then "$@"; else /usr/bin/env bash; fi' >> "$ND_ENTRYPOINT"; \
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fi \
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&& chmod -R 777 /neurodocker && chmod a+s /neurodocker
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ENTRYPOINT ["/neurodocker/startup.sh"]
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RUN apt-get update -qq \
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&& apt-get install -y -q --no-install-recommends \
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vim \
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wget \
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strace \
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time \
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ncdu \
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gnupg \
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curl \
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procps \
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datalad \
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git-annex-standalone \
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python-nipype \
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virtualenv \
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python-dcmstack \
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python-configparser \
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python-funcsigs \
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python-pytest \
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dcmtk \
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python-pip \
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python-wheel \
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&& apt-get clean \
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&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
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RUN curl -sL https://deb.nodesource.com/setup_6.x | bash -
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RUN apt-get update -qq \
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&& apt-get install -y -q --no-install-recommends \
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nodejs \
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npm \
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&& apt-get clean \
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&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
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RUN npm install -g [email protected]
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RUN mkdir /afs /inbox
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RUN pip install heudiconv[all]
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ENV PATH="/opt/dcm2niix-v1.0.20180328/bin:$PATH"
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RUN apt-get update -qq \
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&& apt-get install -y -q --no-install-recommends \
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cmake \
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g++ \
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gcc \
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git \
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make \
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pigz \
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zlib1g-dev \
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&& apt-get clean \
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&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
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&& git clone https://github.com/rordenlab/dcm2niix /tmp/dcm2niix \
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&& cd /tmp/dcm2niix \
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&& git fetch --tags \
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&& git checkout v1.0.20180328 \
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&& mkdir /tmp/dcm2niix/build \
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&& cd /tmp/dcm2niix/build \
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&& cmake -DCMAKE_INSTALL_PREFIX:PATH=/opt/dcm2niix-v1.0.20180328 .. \
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&& make \
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&& make install \
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&& rm -rf /tmp/dcm2niix
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RUN echo '#!/bin/bash' >> /neurodocker/heudiconv.sh && echo 'if [ -z "$@" ]; then heudiconv -h; else heudiconv "$@"; fi' >> /neurodocker/heudiconv.sh && chmod +x /neurodocker/heudiconv.sh
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RUN useradd --no-user-group --create-home --shell /bin/bash reproin
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USER reproin
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ENTRYPOINT ["/neurodocker/heudiconv.sh"]
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RUN echo '{ \
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\n "pkg_manager": "apt", \
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\n "instructions": [ \
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\n [ \
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\n "base", \
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\n "neurodebian:stretch" \
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\n ], \
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\n [ \
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\n "install", \
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\n [ \
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\n "vim", \
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\n "wget", \
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\n "strace", \
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\n "time", \
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\n "ncdu", \
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\n "gnupg", \
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\n "curl", \
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\n "procps", \
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\n "datalad", \
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\n "git-annex-standalone", \
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\n "python-nipype", \
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\n "virtualenv", \
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\n "python-dcmstack", \
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\n "python-configparser", \
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\n "python-funcsigs", \
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\n "python-pytest", \
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\n "dcmtk", \
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\n "python-pip", \
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\n "python-wheel" \
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\n ] \
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\n ], \
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\n [ \
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\n "run", \
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\n "curl -sL https://deb.nodesource.com/setup_6.x | bash - " \
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\n ], \
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\n [ \
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\n "install", \
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\n [ \
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\n "nodejs", \
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\n "npm" \
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\n ] \
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\n ], \
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\n [ \
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\n "run", \
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\n "npm install -g [email protected]" \
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\n ], \
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\n [ \
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\n "run", \
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\n "mkdir /afs /inbox" \
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\n ], \
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\n [ \
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\n "run", \
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\n "pip install heudiconv[all]" \
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\n ], \
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\n [ \
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\n "dcm2niix", \
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\n { \
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\n "version": "v1.0.20180328", \
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\n "method": "source" \
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\n } \
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\n ], \
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\n [ \
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\n "run", \
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\n "echo '"'"'#!/bin/bash'"'"' >> /neurodocker/heudiconv.sh && echo '"'"'if [ -z \"$@\" ]; then heudiconv -h; else heudiconv \"$@\"; fi'"'"' >> /neurodocker/heudiconv.sh && chmod +x /neurodocker/heudiconv.sh" \
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\n ], \
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\n [ \
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\n "user", \
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\n "reproin" \
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\n ], \
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\n [ \
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\n "entrypoint", \
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\n "/neurodocker/heudiconv.sh" \
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\n ] \
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\n ] \
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\n}' > /neurodocker/neurodocker_specs.json

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