neuroDockerfile

# Generated by Neurodocker version 0.5.0
# Timestamp: 2019-07-24 22:09:39 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/* \
    && 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' >> "$ND_ENTRYPOINT" \
    &&   echo 'export USER="${USER:=`whoami`}"' >> "$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 \
           ants \
           gcc \
           g++ \
           graphviz \
           tree \
           git-annex-standalone \
           vim \
           emacs-nox \
           nano \
           less \
           ncdu \
           tig \
           git-annex-remote-rclone \
           octave \
           netbase \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/*

ENV FREESURFER_HOME="/opt/freesurfer-6.0.0-min" \
    PATH="/opt/freesurfer-6.0.0-min/bin:$PATH"
RUN apt-get update -qq \
    && apt-get install -y -q --no-install-recommends \
           bc \
           libgomp1 \
           libxmu6 \
           libxt6 \
           perl \
           tcsh \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/* \
    && echo "Downloading FreeSurfer ..." \
    && mkdir -p /opt/freesurfer-6.0.0-min \
    && curl -fsSL --retry 5 https://dl.dropbox.com/s/nnzcfttc41qvt31/recon-all-freesurfer6-3.min.tgz \
    | tar -xz -C /opt/freesurfer-6.0.0-min --strip-components 1 \
    && sed -i '$isource "/opt/freesurfer-6.0.0-min/SetUpFreeSurfer.sh"' "$ND_ENTRYPOINT"

RUN test "$(getent passwd jovyan)" || useradd --no-user-group --create-home --shell /bin/bash jovyan
USER jovyan

ENV CONDA_DIR="/opt/miniconda-latest" \
    PATH="/opt/miniconda-latest/bin:$PATH"
RUN export PATH="/opt/miniconda-latest/bin:$PATH" \
    && echo "Downloading Miniconda installer ..." \
    && conda_installer="/tmp/miniconda.sh" \
    && curl -fsSL --retry 5 -o "$conda_installer" https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh \
    && bash "$conda_installer" -b -p /opt/miniconda-latest \
    && rm -f "$conda_installer" \
    && conda update -yq -nbase conda \
    && conda config --system --prepend channels conda-forge \
    && conda config --system --set auto_update_conda false \
    && conda config --system --set show_channel_urls true \
    && sync && conda clean --all && sync \
    && conda create -y -q --name neuro \
    && conda install -y -q --name neuro \
           'python=3.6' \
           'pytest' \
           'jupyter' \
           'jupyterlab' \
           'jupyter_contrib_nbextensions' \
           'traits' \
           'pandas' \
           'matplotlib' \
           'scikit-learn' \
           'scikit-image' \
           'seaborn' \
           'nbformat' \
           'nb_conda' \
    && sync && conda clean --all && sync \
    && bash -c "source activate neuro \
    &&   pip install --no-cache-dir  \
             'https://github.com/nipy/nipype/tarball/master' \
             'https://github.com/INCF/pybids/tarball/master' \
             'nilearn' \
             'datalad[full]' \
             'nipy' \
             'duecredit' \
             'nbval'" \
    && rm -rf ~/.cache/pip/* \
    && sync \
    && sed -i '$isource activate neuro' $ND_ENTRYPOINT

RUN bash -c 'source activate neuro && jupyter nbextension enable exercise2/main && jupyter nbextension enable spellchecker/main'

USER root

RUN mkdir /data && chmod 777 /data && chmod a+s /data

RUN mkdir /output && chmod 777 /output && chmod a+s /output

RUN test "$(getent passwd neuro)" || useradd --no-user-group --create-home --shell /bin/bash neuro
USER neuro

RUN bash -c 'source activate neuro \
        && cd /data \
        && datalad install -r ///workshops/nih-2017/ds000114 \
        && cd ds000114 \
        && datalad update -r \
        && datalad get -r sub-01/ses-test/anat sub-01/ses-test/func/*fingerfootlips*'

RUN curl -L https://files.osf.io/v1/resources/fvuh8/providers/osfstorage/580705089ad5a101f17944a9 -o /data/ds000114/derivatives/fmriprep/mni_icbm152_nlin_asym_09c.tar.gz \
        && tar xf /data/ds000114/derivatives/fmriprep/mni_icbm152_nlin_asym_09c.tar.gz -C /data/ds000114/derivatives/fmriprep/. \
        && rm /data/ds000114/derivatives/fmriprep/mni_icbm152_nlin_asym_09c.tar.gz \
        && find /data/ds000114/derivatives/fmriprep/mni_icbm152_nlin_asym_09c -type f -not -name ?mm_T1.nii.gz -not -name ?mm_brainmask.nii.gz -not -name ?mm_tpm*.nii.gz -delete

COPY [".", "/home/neuro/nipype_tutorial"]

USER root

RUN chown -R neuro /home/neuro/nipype_tutorial

RUN rm -rf /opt/conda/pkgs/*

USER neuro

RUN mkdir -p ~/.jupyter && echo c.NotebookApp.ip = \"0.0.0.0\" > ~/.jupyter/jupyter_notebook_config.py

WORKDIR /home/neuro/nipype_tutorial

CMD ["jupyter-notebook"]

RUN echo '{ \
    \n  "pkg_manager": "apt", \
    \n  "instructions": [ \
    \n    [ \
    \n      "base", \
    \n      "neurodebian:stretch-non-free" \
    \n    ], \
    \n    [ \
    \n      "install", \
    \n      [ \
    \n        "ants", \
    \n        "gcc", \
    \n        "g++", \
    \n        "graphviz", \
    \n        "tree", \
    \n        "git-annex-standalone", \
    \n        "vim", \
    \n        "emacs-nox", \
    \n        "nano", \
    \n        "less", \
    \n        "ncdu", \
    \n        "tig", \
    \n        "git-annex-remote-rclone", \
    \n        "octave", \
    \n        "netbase" \
    \n      ] \
    \n    ], \
    \n    [ \
    \n      "freesurfer", \
    \n      { \
    \n        "version": "6.0.0-min" \
    \n      } \
    \n    ], \
    \n    [ \
    \n      "user", \
    \n      "jovyan" \
    \n    ], \
    \n    [ \
    \n      "miniconda", \
    \n      { \
    \n        "conda_install": [ \
    \n          "python=3.6", \
    \n          "pytest", \
    \n          "jupyter", \
    \n          "jupyterlab", \
    \n          "jupyter_contrib_nbextensions", \
    \n          "traits", \
    \n          "pandas", \
    \n          "matplotlib", \
    \n          "scikit-learn", \
    \n          "scikit-image", \
    \n          "seaborn", \
    \n          "nbformat", \
    \n          "nb_conda" \
    \n        ], \
    \n        "pip_install": [ \
    \n          "https://github.com/nipy/nipype/tarball/master", \
    \n          "https://github.com/INCF/pybids/tarball/master", \
    \n          "nilearn", \
    \n          "datalad[full]", \
    \n          "nipy", \
    \n          "duecredit", \
    \n          "nbval" \
    \n        ], \
    \n        "create_env": "neuro", \
    \n        "activate": true \
    \n      } \
    \n    ], \
    \n    [ \
    \n      "run_bash", \
    \n      "source activate neuro && jupyter nbextension enable exercise2/main && jupyter nbextension enable spellchecker/main" \
    \n    ], \
    \n    [ \
    \n      "user", \
    \n      "root" \
    \n    ], \
    \n    [ \
    \n      "run", \
    \n      "mkdir /data && chmod 777 /data && chmod a+s /data" \
    \n    ], \
    \n    [ \
    \n      "run", \
    \n      "mkdir /output && chmod 777 /output && chmod a+s /output" \
    \n    ], \
    \n    [ \
    \n      "user", \
    \n      "neuro" \
    \n    ], \
    \n    [ \
    \n      "run_bash", \
    \n      "source activate neuro\\n    && cd /data\\n    && datalad install -r ///workshops/nih-2017/ds000114\\n    && cd ds000114\\n    && datalad update -r\\n    && datalad get -r sub-01/ses-test/anat sub-01/ses-test/func/*fingerfootlips*" \
    \n    ], \
    \n    [ \
    \n      "run", \
    \n      "curl -L https://files.osf.io/v1/resources/fvuh8/providers/osfstorage/580705089ad5a101f17944a9 -o /data/ds000114/derivatives/fmriprep/mni_icbm152_nlin_asym_09c.tar.gz\\n    && tar xf /data/ds000114/derivatives/fmriprep/mni_icbm152_nlin_asym_09c.tar.gz -C /data/ds000114/derivatives/fmriprep/.\\n    && rm /data/ds000114/derivatives/fmriprep/mni_icbm152_nlin_asym_09c.tar.gz\\n    && find /data/ds000114/derivatives/fmriprep/mni_icbm152_nlin_asym_09c -type f -not -name ?mm_T1.nii.gz -not -name ?mm_brainmask.nii.gz -not -name ?mm_tpm*.nii.gz -delete" \
    \n    ], \
    \n    [ \
    \n      "copy", \
    \n      [ \
    \n        ".", \
    \n        "/home/neuro/nipype_tutorial" \
    \n      ] \
    \n    ], \
    \n    [ \
    \n      "user", \
    \n      "root" \
    \n    ], \
    \n    [ \
    \n      "run", \
    \n      "chown -R neuro /home/neuro/nipype_tutorial" \
    \n    ], \
    \n    [ \
    \n      "run", \
    \n      "rm -rf /opt/conda/pkgs/*" \
    \n    ], \
    \n    [ \
    \n      "user", \
    \n      "neuro" \
    \n    ], \
    \n    [ \
    \n      "run", \
    \n      "mkdir -p ~/.jupyter && echo c.NotebookApp.ip = \\\"0.0.0.0\\\" > ~/.jupyter/jupyter_notebook_config.py" \
    \n    ], \
    \n    [ \
    \n      "workdir", \
    \n      "/home/neuro/nipype_tutorial" \
    \n    ], \
    \n    [ \
    \n      "cmd", \
    \n      [ \
    \n        "jupyter-notebook" \
    \n      ] \
    \n    ] \
    \n  ] \
    \n}' > /neurodocker/neurodocker_specs.json