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# Generated by Neurodocker version 0.4.0
# Timestamp: 2018-06-22 09:08:27 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-non-free
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' >> "$ND_ENTRYPOINT"; \
fi \
&& chmod -R 777 /neurodocker && chmod a+s /neurodocker
ENTRYPOINT ["/neurodocker/startup.sh"]
RUN apt-get update -qq \
&& apt-get install -y -q --no-install-recommends \
fsl-core \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
RUN sed -i '$isource /etc/fsl/fsl.sh' $ND_ENTRYPOINT
RUN echo '{ \
\n "pkg_manager": "apt", \
\n "instructions": [ \
\n [ \
\n "base", \
\n "neurodebian:stretch-non-free" \
\n ], \
\n [ \
\n "install", \
\n [ \
\n "fsl-core" \
\n ] \
\n ], \
\n [ \
\n "add_to_entrypoint", \
\n "source /etc/fsl/fsl.sh" \
\n ] \
\n ] \
\n}' > /neurodocker/neurodocker_specs.json
RUN apt-get update \
&& apt-get -y install git g++ python python-numpy libeigen3-dev zlib1g-dev libqt4-opengl-dev libgl1-mesa-dev libfftw3-dev libtiff5-dev \
&& apt-get -y install git-core \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
RUN mkdir /code && cd /code \
&& git clone https://github.com/MRtrix3/mrtrix3.git \
&& cd mrtrix3/ \
&& ./configure \
&& ./build \
&& ./set_path \
RUN /bin/bash -c "source ~/.bashrc"
RUN apt-get update \
&& apt-get -y install python-setuptools python-dev build-essential \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
&& easy_install pip \
&& pip install wheel numpy scipy nilearn matplotlib scikit-image nibabel \
&& pip install http://download.pytorch.org/whl/cpu/torch-0.4.0-cp27-cp27mu-linux_x86_64.whl \
&& pip install https://github.com/MIC-DKFZ/batchgenerators/archive/tractseg_stable.zip \
&& pip install https://github.com/MIC-DKFZ/TractSeg/archive/v1.2.zip