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# 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