Dockerfile

# Generated by Neurodocker version 0.5.0
# Timestamp: 2019-09-28 17:57:57 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 \
           gcc \
           g++ \
           graphviz \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/*

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

WORKDIR /home/neuro

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 "$conda_installer" \
    && conda update -yq -nbase conda \
    && conda config --system --prepend channels conda-forge \
    && conda config --system --set auto_update_conda false \
    && conda config --system --set show_channel_urls true \
    && sync && conda clean --all && sync \
    && conda create -y -q --name neuro_py36 \
    && conda install -y -q --name neuro_py36 \
           'python=3.6' \
    && sync && conda clean --all && sync \
    && bash -c "source activate neuro_py36 \
    &&   pip install --no-cache-dir  \
             'jupyter' \
             'seaborn' \
             'tox'" \
    && rm -rf ~/.cache/pip/* \
    && sync \
    && sed -i '$isource activate neuro_py36' $ND_ENTRYPOINT

COPY [".", "/src/nibetaseries"]

USER root

RUN curl -o pandoc-2.2.2.1-1-amd64.deb -sSL 'https://github.com/jgm/pandoc/releases/download/2.2.2.1/pandoc-2.2.2.1-1-amd64.deb' && dpkg -i pandoc-2.2.2.1-1-amd64.deb && rm pandoc-2.2.2.1-1-amd64.deb

RUN chown -R neuro:users /src/nibetaseries

USER neuro

WORKDIR /src/nibetaseries

RUN conda run -n neuro_py36 pip install --no-cache-dir -e .

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

WORKDIR /home/neuro

RUN echo '{ \
    \n  "pkg_manager": "apt", \
    \n  "instructions": [ \
    \n    [ \
    \n      "base", \
    \n      "neurodebian:stretch-non-free" \
    \n    ], \
    \n    [ \
    \n      "install", \
    \n      [ \
    \n        "gcc", \
    \n        "g++", \
    \n        "graphviz" \
    \n      ] \
    \n    ], \
    \n    [ \
    \n      "user", \
    \n      "neuro" \
    \n    ], \
    \n    [ \
    \n      "workdir", \
    \n      "/home/neuro" \
    \n    ], \
    \n    [ \
    \n      "miniconda", \
    \n      { \
    \n        "conda_install": [ \
    \n          "python=3.6" \
    \n        ], \
    \n        "pip_install": [ \
    \n          "jupyter", \
    \n          "seaborn", \
    \n          "tox" \
    \n        ], \
    \n        "create_env": "neuro_py36", \
    \n        "activate": true \
    \n      } \
    \n    ], \
    \n    [ \
    \n      "copy", \
    \n      [ \
    \n        ".", \
    \n        "/src/nibetaseries" \
    \n      ] \
    \n    ], \
    \n    [ \
    \n      "user", \
    \n      "root" \
    \n    ], \
    \n    [ \
    \n      "run", \
    \n      "curl -o pandoc-2.2.2.1-1-amd64.deb -sSL '"'"'https://github.com/jgm/pandoc/releases/download/2.2.2.1/pandoc-2.2.2.1-1-amd64.deb'"'"' && dpkg -i pandoc-2.2.2.1-1-amd64.deb && rm pandoc-2.2.2.1-1-amd64.deb" \
    \n    ], \
    \n    [ \
    \n      "run", \
    \n      "chown -R neuro:users /src/nibetaseries" \
    \n    ], \
    \n    [ \
    \n      "user", \
    \n      "neuro" \
    \n    ], \
    \n    [ \
    \n      "workdir", \
    \n      "/src/nibetaseries" \
    \n    ], \
    \n    [ \
    \n      "run", \
    \n      "pip install --no-cache-dir ." \
    \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" \
    \n    ] \
    \n  ] \
    \n}' > /neurodocker/neurodocker_specs.json