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Merge pull request #50 from NeuroimagingUIowa/mnt/update_image
[MNT] update build commands
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‎.circleci/config.yml‎

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‎Dockerfile‎

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# Generated by: Neurodocker version 0.7.0+0.gdc97516.dirty
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# Latest release: Neurodocker version 0.7.0
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# Timestamp: 2020/06/16 19:58:06 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/ReproNim/neurodocker
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FROM neurodebian:stretch-non-free
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USER root
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ARG DEBIAN_FRONTEND="noninteractive"
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# Generated by Neurodocker and Reproenv.
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FROM neurodebian:bookworm-non-free
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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"
@@ -26,7 +13,6 @@ RUN export ND_ENTRYPOINT="/neurodocker/startup.sh" \
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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/* \
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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 \
@@ -40,156 +26,235 @@ RUN export ND_ENTRYPOINT="/neurodocker/startup.sh" \
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&& echo 'if [ -n "$1" ]; then "$@"; else /usr/bin/env bash; fi' >> "$ND_ENTRYPOINT"; \
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fi \
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&& chmod -R 777 /neurodocker && chmod a+s /neurodocker
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ENTRYPOINT ["/neurodocker/startup.sh"]
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ENV LANG="C.UTF-8"
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ENV LC_ALL="C.UTF-8"
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RUN apt-get update -qq \
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&& apt-get install -y -q --no-install-recommends \
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pigz \
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&& apt-get clean \
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&& rm -rf /var/lib/apt/lists/*
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RUN mkdir -p /opt/dcm2niix && cd /opt/dcm2niix && curl -sSLO https://github.com/rordenlab/dcm2niix/releases/download/v1.0.20181125/dcm2niix_25-Nov-2018_lnx.zip && unzip dcm2niix_25-Nov-2018_lnx.zip && rm dcm2niix_25-Nov-2018_lnx.zip
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&& apt-get install -y -q --no-install-recommends \
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pigz \
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&& rm -rf /var/lib/apt/lists/*
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RUN mkdir -p /opt/dcm2niix && cd /opt/dcm2niix && curl -sSLO https://github.com/rordenlab/dcm2niix/releases/download/v1.0.20250506/dcm2niix_lnx.zip && unzip dcm2niix_lnx.zip && rm dcm2niix_lnx.zip
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ENV PATH="/opt/dcm2niix:$PATH"
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RUN test "$(getent passwd coder)" || useradd --no-user-group --create-home --shell /bin/bash coder
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RUN test "$(getent passwd coder)" \
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|| useradd --no-user-group --create-home --shell /bin/bash coder
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USER coder
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COPY [".", "/home/coder/project"]
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COPY [".", \
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"/home/coder/project"]
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USER root
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RUN chown -R coder /home/coder/project
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USER coder
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WORKDIR /home/coder
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SHELL [ "/bin/bash", "--login", "-c" ]
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ENV SHELL="/bin/bash"
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ENV CONDA_PLUGINS_AUTO_ACCEPT_TOS="true"
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USER root
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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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RUN apt-get update -qq \
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&& apt-get install -y -q --no-install-recommends \
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bzip2 \
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ca-certificates \
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curl \
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&& rm -rf /var/lib/apt/lists/* \
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# Install dependencies.
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&& 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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&& curl -fsSL -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 "$conda_installer" \
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&& conda update -yq -nbase conda \
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# Prefer packages in conda-forge
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&& conda config --system --prepend channels conda-forge \
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# Packages in lower-priority channels not considered if a package with the same
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# name exists in a higher priority channel. Can dramatically speed up installations.
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# Conda recommends this as a default
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# https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-channels.html
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&& conda config --set channel_priority strict \
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&& conda config --system --set auto_update_conda false \
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&& conda config --system --set show_channel_urls true \
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&& sync && conda clean -y --all && sync \
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&& conda create -y -q --name neuro \
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&& conda install -y -q --name neuro \
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"python=2.7" \
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&& sync && conda clean -y --all && sync \
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&& sed -i '$isource activate neuro' $ND_ENTRYPOINT
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# make conda activate command available from /bin/bash --login shells
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# Enable `conda activate`
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&& conda init bash \
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&& conda create -y --name neuro \
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&& conda install -y --name neuro \
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"python=3.13" \
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# Clean up
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&& sync && conda clean --all --yes && sync \
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&& rm -rf ~/.cache/pip/*
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USER coder
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RUN echo ". $CONDA_DIR/etc/profile.d/conda.sh" >> ~/.profile
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RUN conda init bash
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RUN conda activate neuro && pip install -e /home/coder/project/[test]
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USER root
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RUN bash -c 'source "${CONDA_DIR}/etc/profile.d/conda.sh" && conda activate neuro && pip install --no-cache-dir -e /home/coder/project/[test]'
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ENV PATH="/opt/miniconda-latest/envs/neuro/bin:/home/coder/.local/bin:$PATH"
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ENTRYPOINT ["/neurodocker/startup.sh", "xnat_downloader"]
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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-non-free" \
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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 "LANG": "C.UTF-8" \
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\n } \
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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 "LC_ALL": "C.UTF-8" \
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\n } \
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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 "pigz" \
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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 "mkdir -p /opt/dcm2niix && cd /opt/dcm2niix && curl -sSLO https://github.com/rordenlab/dcm2niix/releases/download/v1.0.20181125/dcm2niix_25-Nov-2018_lnx.zip && unzip dcm2niix_25-Nov-2018_lnx.zip && rm dcm2niix_25-Nov-2018_lnx.zip" \
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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 "PATH": "/opt/dcm2niix:$PATH" \
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\n } \
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\n ], \
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\n [ \
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\n "user", \
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\n "coder" \
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\n ], \
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\n [ \
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\n "copy", \
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\n [ \
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\n ".", \
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\n "/home/coder/project" \
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\n ] \
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\n ], \
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\n [ \
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\n "user", \
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\n "root" \
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\n ], \
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\n [ \
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\n "run", \
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\n "chown -R coder /home/coder/project" \
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\n ], \
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\n [ \
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\n "user", \
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\n "coder" \
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\n ], \
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\n [ \
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\n "workdir", \
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\n "/home/coder" \
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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 "SHELL": "/bin/bash" \
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\n } \
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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 "create_env": "neuro", \
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\n "conda_install": [ \
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\n "python=2.7" \
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\n ] \
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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 "conda init && . /home/coder/.bashrc && . activate neuro && pip install -e /home/coder/project/[test]" \
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\n ], \
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\n [ \
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\n "user", \
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\n "root" \
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\n ], \
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\n [ \
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\n "entrypoint", \
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\n "xnat_downloader" \
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\n ] \
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\n ] \
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\n}' > /neurodocker/neurodocker_specs.json
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# Save specification to JSON.
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RUN printf '{ \
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"pkg_manager": "apt", \
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"existing_users": [ \
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"root" \
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], \
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"instructions": [ \
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{ \
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"name": "from_", \
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"kwds": { \
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"base_image": "neurodebian:bookworm-non-free" \
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} \
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}, \
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{ \
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"name": "env", \
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"kwds": { \
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"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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} \
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}, \
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{ \
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"name": "run", \
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"kwds": { \
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"command": "export ND_ENTRYPOINT=\\"/neurodocker/startup.sh\\"\\napt-get update -qq\\napt-get install -y -q --no-install-recommends \\\\\\n apt-utils \\\\\\n bzip2 \\\\\\n ca-certificates \\\\\\n curl \\\\\\n locales \\\\\\n unzip\\nrm -rf /var/lib/apt/lists/*\\nsed -i -e '"'"'s/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/'"'"' /etc/locale.gen\\ndpkg-reconfigure --frontend=noninteractive locales\\nupdate-locale LANG=\\"en_US.UTF-8\\"\\nchmod 777 /opt && chmod a+s /opt\\nmkdir -p /neurodocker\\nif [ ! -f \\"$ND_ENTRYPOINT\\" ]; then\\n echo '"'"'#!/usr/bin/env bash'"'"' >> \\"$ND_ENTRYPOINT\\"\\n echo '"'"'set -e'"'"' >> \\"$ND_ENTRYPOINT\\"\\n echo '"'"'export USER=\\"${USER:=`whoami`}\\"'"'"' >> \\"$ND_ENTRYPOINT\\"\\n echo '"'"'if [ -n \\"$1\\" ]; then \\"$@\\"; else /usr/bin/env bash; fi'"'"' >> \\"$ND_ENTRYPOINT\\";\\nfi\\nchmod -R 777 /neurodocker && chmod a+s /neurodocker" \
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} \
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}, \
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{ \
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"name": "env", \
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"kwds": { \
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"LANG": "C.UTF-8" \
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} \
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}, \
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{ \
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"name": "env", \
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"kwds": { \
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"LC_ALL": "C.UTF-8" \
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} \
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}, \
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{ \
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"name": "install", \
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"kwds": { \
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"pkgs": [ \
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"pigz" \
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], \
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"opts": null \
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} \
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}, \
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{ \
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"name": "run", \
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"kwds": { \
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"command": "apt-get update -qq \\\\\\n && apt-get install -y -q --no-install-recommends \\\\\\n pigz \\\\\\n && rm -rf /var/lib/apt/lists/*" \
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} \
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}, \
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{ \
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"name": "run", \
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"kwds": { \
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"command": "mkdir -p /opt/dcm2niix && cd /opt/dcm2niix && curl -sSLO https://github.com/rordenlab/dcm2niix/releases/download/v1.0.20250506/dcm2niix_lnx.zip && unzip dcm2niix_lnx.zip && rm dcm2niix_lnx.zip" \
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} \
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}, \
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{ \
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"name": "env", \
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"kwds": { \
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"PATH": "/opt/dcm2niix:$PATH" \
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} \
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}, \
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{ \
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"name": "user", \
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"kwds": { \
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"user": "coder" \
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} \
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}, \
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{ \
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"name": "copy", \
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"kwds": { \
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"source": [ \
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".", \
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"/home/coder/project" \
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], \
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"destination": "/home/coder/project" \
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} \
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}, \
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{ \
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"name": "user", \
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"kwds": { \
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"user": "root" \
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} \
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}, \
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{ \
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"name": "run", \
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"kwds": { \
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"command": "chown -R coder /home/coder/project" \
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} \
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}, \
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{ \
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"name": "workdir", \
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"kwds": { \
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"path": "/home/coder" \
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} \
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}, \
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{ \
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"name": "env", \
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"kwds": { \
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"SHELL": "/bin/bash" \
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} \
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}, \
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{ \
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"name": "env", \
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"kwds": { \
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"CONDA_PLUGINS_AUTO_ACCEPT_TOS": "true" \
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} \
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}, \
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{ \
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"name": "user", \
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"kwds": { \
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"user": "root" \
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} \
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}, \
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{ \
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"name": "env", \
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"kwds": { \
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"CONDA_DIR": "/opt/miniconda-latest", \
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"PATH": "/opt/miniconda-latest/bin:$PATH" \
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} \
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}, \
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{ \
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"name": "run", \
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"kwds": { \
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"command": "apt-get update -qq\\napt-get install -y -q --no-install-recommends \\\\\\n bzip2 \\\\\\n ca-certificates \\\\\\n curl\\nrm -rf /var/lib/apt/lists/*\\n# Install dependencies.\\nexport PATH=\\"/opt/miniconda-latest/bin:$PATH\\"\\necho \\"Downloading Miniconda installer ...\\"\\nconda_installer=\\"/tmp/miniconda.sh\\"\\ncurl -fsSL -o \\"$conda_installer\\" https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh\\nbash \\"$conda_installer\\" -b -p /opt/miniconda-latest\\nrm -f \\"$conda_installer\\"\\nconda update -yq -nbase conda\\n# Prefer packages in conda-forge\\nconda config --system --prepend channels conda-forge\\n# Packages in lower-priority channels not considered if a package with the same\\n# name exists in a higher priority channel. Can dramatically speed up installations.\\n# Conda recommends this as a default\\n# https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-channels.html\\nconda config --set channel_priority strict\\nconda config --system --set auto_update_conda false\\nconda config --system --set show_channel_urls true\\n# Enable `conda activate`\\nconda init bash\\nconda create -y --name neuro\\nconda install -y --name neuro \\\\\\n \\"python=3.13\\"\\n# Clean up\\nsync && conda clean --all --yes && sync\\nrm -rf ~/.cache/pip/*" \
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} \
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}, \
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{ \
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"name": "user", \
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"kwds": { \
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"user": "coder" \
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} \
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}, \
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{ \
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"name": "run", \
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"kwds": { \
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"command": "echo \\". $CONDA_DIR/etc/profile.d/conda.sh\\" >> ~/.profile" \
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} \
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}, \
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{ \
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"name": "user", \
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"kwds": { \
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"user": "root" \
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} \
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}, \
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{ \
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"name": "run", \
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"kwds": { \
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"command": "bash -c '"'"'source \\"${CONDA_DIR}/etc/profile.d/conda.sh\\" && conda activate neuro && pip install --no-cache-dir -e /home/coder/project/[test]'"'"'" \
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} \
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}, \
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{ \
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"name": "env", \
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"kwds": { \
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"PATH": "/opt/miniconda-latest/envs/neuro/bin:/home/coder/.local/bin:$PATH" \
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} \
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}, \
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{ \
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"name": "entrypoint", \
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"kwds": { \
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"args": [ \
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"/neurodocker/startup.sh", \
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"xnat_downloader" \
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] \
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} \
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} \
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] \
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}' > /.reproenv.json
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# End saving to specification to JSON.

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