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enh: generate dockerfile using neurodocker
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‎install/Dockerfile

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# Generated by Neurodocker version 0.4.1
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# Timestamp: 2018-08-22 14:03:54 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' >> "$ND_ENTRYPOINT"; \
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fi \
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&& chmod -R 777 /neurodocker && chmod a+s /neurodocker
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ENTRYPOINT ["/neurodocker/startup.sh"]
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RUN apt-get update -qq \
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&& apt-get install -y -q --no-install-recommends \
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graphviz \
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tree \
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git-annex-standalone \
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vim \
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emacs-nox \
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nano \
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less \
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ncdu \
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tig \
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sed \
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build-essential \
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libsm-dev \
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libx11-dev \
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libxt-dev \
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libxext-dev \
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libglu1-mesa \
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&& apt-get clean \
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&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
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ENV FREESURFER_HOME="/opt/freesurfer-6.0.0-min" \
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PATH="/opt/freesurfer-6.0.0-min/bin:$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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bc \
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libgomp1 \
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libxmu6 \
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libxt6 \
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perl \
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tcsh \
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&& apt-get clean \
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&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
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&& echo "Downloading FreeSurfer ..." \
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&& mkdir -p /opt/freesurfer-6.0.0-min \
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&& curl -fsSL --retry 5 https://dl.dropbox.com/s/nnzcfttc41qvt31/recon-all-freesurfer6-3.min.tgz \
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| tar -xz -C /opt/freesurfer-6.0.0-min --strip-components 1 \
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&& sed -i '$isource "/opt/freesurfer-6.0.0-min/SetUpFreeSurfer.sh"' "$ND_ENTRYPOINT"
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ENV ANTSPATH="/opt/ants-b43df4bfc8/bin" \
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PATH="/opt/ants-b43df4bfc8/bin:$PATH" \
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LD_LIBRARY_PATH="/opt/ants-b43df4bfc8/lib:$LD_LIBRARY_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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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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&& mkdir -p /tmp/ants/build \
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&& git clone https://github.com/ANTsX/ANTs.git /tmp/ants/source \
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&& cd /tmp/ants/source \
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&& git fetch --tags \
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&& git checkout b43df4bfc8 \
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&& cd /tmp/ants/build \
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&& cmake -DBUILD_SHARED_LIBS=ON /tmp/ants/source \
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&& make -j 4 \
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&& mkdir -p /opt/ants-b43df4bfc8 \
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&& mv bin lib /opt/ants-b43df4bfc8/ \
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&& mv /tmp/ants/source/Scripts/* /opt/ants-b43df4bfc8/bin \
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&& rm -rf /tmp/ants
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RUN ln -s /usr/lib/x86_64-linux-gnu /usr/lib64
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ENV CONDA_DIR="/opt/miniconda-latest" \
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PATH="/opt/miniconda-latest/bin:$PATH"
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RUN export PATH="/opt/miniconda-latest/bin:$PATH" \
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&& echo "Downloading Miniconda installer ..." \
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&& conda_installer="/tmp/miniconda.sh" \
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&& curl -fsSL --retry 5 -o "$conda_installer" https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh \
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&& bash "$conda_installer" -b -p /opt/miniconda-latest \
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&& rm -f "$conda_installer" \
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&& conda update -yq -nbase conda \
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&& conda config --system --prepend channels conda-forge \
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&& conda config --system --set auto_update_conda false \
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&& conda config --system --set show_channel_urls true \
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&& sync && conda clean -tipsy && sync \
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&& conda create -y -q --name mb \
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&& conda install -y -q --name mb \
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python=3.6 \
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pip \
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jupyter \
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cmake \
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mesalib \
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vtk \
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pandas \
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matplotlib \
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colormath \
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nipype \
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&& sync && conda clean -tipsy && sync \
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&& bash -c "source activate mb \
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&& pip install --no-cache-dir \
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datalad[full] \
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duecredit" \
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&& rm -rf ~/.cache/pip/* \
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&& sync \
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&& sed -i '$isource activate mb' $ND_ENTRYPOINT
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WORKDIR /opt
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RUN mkdir -p /opt/data && cd /opt/data && \
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curl -sSL https://osf.io/download/rh9km/?revision=2 -o templates.zip && \
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unzip templates.zip && \
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rm -f /opt/data/templates.zip && \
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curl -sSL https://osf.io/download/d2cmy/ -o OASIS-TRT-20_jointfusion_DKT31_CMA_labels_in_OASIS-30_v2.nii.gz && \
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curl -sSL https://osf.io/download/qz3kx/ -o OASIS-TRT_brains_to_OASIS_Atropos_template.tar.gz && \
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tar zxf OASIS-TRT_brains_to_OASIS_Atropos_template.tar.gz && \
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rm OASIS-TRT_brains_to_OASIS_Atropos_template.tar.gz && \
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curl -sSL https://osf.io/download/dcf94/ -o OASIS-TRT_labels_to_OASIS_Atropos_template.tar.gz && \
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tar zxf OASIS-TRT_labels_to_OASIS_Atropos_template.tar.gz && \
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rm OASIS-TRT_labels_to_OASIS_Atropos_template.tar.gz
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RUN bash -c 'source /opt/miniconda-latest/etc/profile.d/conda.sh && \
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conda activate mb && \
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git clone https://github.com/nipy/mindboggle.git && \
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cd /opt/mindboggle && \
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git checkout edf95a3 && \
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python setup.py install && \
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sed -i "s/7.0/8.1/g" vtk_cpp_tools/CMakeLists.txt && \
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mkdir /opt/vtk_cpp_tools && \
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cd /opt/vtk_cpp_tools && \
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cmake /opt/mindboggle/vtk_cpp_tools && \
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make'
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ENV vtk_cpp_tools="/opt/vtk_cpp_tools"
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RUN bash -c 'source /opt/miniconda-latest/etc/profile.d/conda.sh && \
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conda activate mb && \
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conda install -y flask && \
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git clone https://github.com/akeshavan/roygbiv && \
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cd /opt/roygbiv && \
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git checkout fbbf31c29952d0ea22ed05d98e0a5a7e7d0827f9 && \
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python setup.py install && \
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cd /opt && \
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git clone https://github.com/akeshavan/nbpapaya && \
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cd /opt/nbpapaya && \
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git checkout 60119b6e1de651f250af26a3541d9cb18e971526 && \
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git submodule update --init --recursive && \
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python setup.py install && \
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rm -rf /opt/roygbiv /opt/nbpapaya'
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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 "graphviz", \
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\n "tree", \
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\n "git-annex-standalone", \
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\n "vim", \
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\n "emacs-nox", \
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\n "nano", \
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\n "less", \
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\n "ncdu", \
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\n "tig", \
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\n "sed", \
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\n "build-essential", \
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\n "libsm-dev", \
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\n "libx11-dev", \
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\n "libxt-dev", \
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\n "libxext-dev", \
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\n "libglu1-mesa" \
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\n ] \
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\n ], \
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\n [ \
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\n "freesurfer", \
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\n { \
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\n "version": "6.0.0-min" \
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\n } \
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\n ], \
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\n [ \
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\n "ants", \
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\n { \
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\n "version": "b43df4bfc8", \
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\n "method": "source", \
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\n "cmake_opts": "-DBUILD_SHARED_LIBS=ON", \
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\n "make_opts": "-j 4" \
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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 "ln -s /usr/lib/x86_64-linux-gnu /usr/lib64" \
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\n ], \
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\n [ \
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\n "miniconda", \
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\n { \
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\n "conda_install": [ \
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\n "python=3.6", \
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\n "pip", \
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\n "jupyter", \
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\n "cmake", \
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\n "mesalib", \
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\n "vtk", \
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\n "pandas", \
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\n "matplotlib", \
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\n "colormath", \
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\n "nipype" \
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\n ], \
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\n "pip_install": [ \
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\n "datalad[full]", \
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\n "duecredit" \
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\n ], \
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\n "create_env": "mb", \
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\n "activate": true \
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\n } \
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\n ], \
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\n [ \
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\n "workdir", \
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\n "/opt" \
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\n ], \
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\n [ \
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\n "run", \
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\n "mkdir -p /opt/data && cd /opt/data && \\\\n curl -sSL https://osf.io/download/rh9km/?revision=2 -o templates.zip && \\\\n unzip templates.zip && \\\\n rm -f /opt/data/templates.zip && \\\\n curl -sSL https://osf.io/download/d2cmy/ -o OASIS-TRT-20_jointfusion_DKT31_CMA_labels_in_OASIS-30_v2.nii.gz && \\\\n curl -sSL https://osf.io/download/qz3kx/ -o OASIS-TRT_brains_to_OASIS_Atropos_template.tar.gz && \\\\n tar zxf OASIS-TRT_brains_to_OASIS_Atropos_template.tar.gz && \\\\n rm OASIS-TRT_brains_to_OASIS_Atropos_template.tar.gz && \\\\n curl -sSL https://osf.io/download/dcf94/ -o OASIS-TRT_labels_to_OASIS_Atropos_template.tar.gz && \\\\n tar zxf OASIS-TRT_labels_to_OASIS_Atropos_template.tar.gz && \\\\n rm OASIS-TRT_labels_to_OASIS_Atropos_template.tar.gz" \
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\n ], \
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\n [ \
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\n "run_bash", \
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\n "source /opt/miniconda-latest/etc/profile.d/conda.sh && \\\\n conda activate mb && \\\\n git clone https://github.com/nipy/mindboggle.git && \\\\n cd /opt/mindboggle && \\\\n git checkout edf95a3 && \\\\n python setup.py install && \\\\n sed -i \"s/7.0/8.1/g\" vtk_cpp_tools/CMakeLists.txt && \\\\n mkdir /opt/vtk_cpp_tools && \\\\n cd /opt/vtk_cpp_tools && \\\\n cmake /opt/mindboggle/vtk_cpp_tools && \\\\n make" \
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\n ], \
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\n [ \
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\n "env", \
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\n { \
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\n "vtk_cpp_tools": "/opt/vtk_cpp_tools" \
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\n } \
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\n ], \
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\n [ \
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\n "run_bash", \
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\n "source /opt/miniconda-latest/etc/profile.d/conda.sh && \\\\n conda activate mb && \\\\n conda install -y flask && \\\\n git clone https://github.com/akeshavan/roygbiv && \\\\n cd /opt/roygbiv && \\\\n git checkout fbbf31c29952d0ea22ed05d98e0a5a7e7d0827f9 && \\\\n python setup.py install && \\\\n cd /opt && \\\\n git clone https://github.com/akeshavan/nbpapaya && \\\\n cd /opt/nbpapaya && \\\\n git checkout 60119b6e1de651f250af26a3541d9cb18e971526 && \\\\n git submodule update --init --recursive && \\\\n python setup.py install && \\\\n rm -rf /opt/roygbiv /opt/nbpapaya" \
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\n ] \
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\n ] \
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\n}' > /neurodocker/neurodocker_specs.json

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