Dockerfile

# Copyright (c) Jupyter Development Team.
# Distributed under the terms of the Modified BSD License.
ARG BASE_CONTAINER=jupyter/base-notebook
FROM $BASE_CONTAINER

LABEL maintainer="Jupyter Project <jupyter@googlegroups.com>"

USER root
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 \
           git \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/*



ENV FSLDIR="/opt/fsl-5.0.10" \
    PATH="/opt/fsl-5.0.10/bin:$PATH"
RUN apt-get update -qq \
    && apt-get install -y -q --no-install-recommends \
           bc \
           dc \
           file \
           libfontconfig1 \
           libfreetype6 \
           libgl1-mesa-dev \
           libgl1-mesa-dri \
           libglu1-mesa-dev \
           libgomp1 \
           libice6 \
           libxcursor1 \
           libxft2 \
           libxinerama1 \
           libxrandr2 \
           libxrender1 \
           libxt6 \
           sudo \
           wget \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/* \
    && echo "Downloading FSL ..." \
    && mkdir -p /opt/fsl-5.0.10 \
    && curl -fsSL --retry 5 https://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-5.0.10-centos6_64.tar.gz \
    | tar -xz -C /opt/fsl-5.0.10 --strip-components 1 \
    && sed -i '$iecho Some packages in this Docker container are non-free' $ND_ENTRYPOINT \
    && sed -i '$iecho If you are considering commercial use of this container, please consult the relevant license:' $ND_ENTRYPOINT \
    && sed -i '$iecho https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Licence' $ND_ENTRYPOINT \
    && sed -i '$isource $FSLDIR/etc/fslconf/fsl.sh' $ND_ENTRYPOINT \
    && echo "Installing FSL conda environment ..." \
    && bash /opt/fsl-5.0.10/etc/fslconf/fslpython_install.sh -f /opt/fsl-5.0.10

# Install all OS dependencies for fully functional notebook server
RUN apt-get update && apt-get install -yq --no-install-recommends \
    build-essential \
    emacs \
    git \
    inkscape \
    jed \
    libsm6 \
    libxext-dev \
    libxrender1 \
    lmodern \
    netcat \
    pandoc \
    python-dev \
    texlive-fonts-extra \
    texlive-fonts-recommended \
    texlive-generic-recommended \
    texlive-latex-base \
    texlive-latex-extra \
    texlive-xetex \
    tzdata \
    unzip \
    nano \
    && rm -rf /var/lib/apt/lists/*

RUN apt-get update -qq \
    && apt-get install -y -q --no-install-recommends \
           openbox \
           tightvncserver \
           xfonts-base \
           xterm \
           xvfb \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/* \
    && echo 'Configuring VNC password ...' \
    && mkdir -p ~/.vnc \
    && echo graceiscool | vncpasswd -f > ~/.vnc/passwd \
    && chmod 0600 ~/.vnc/passwd \
    && sed -i '$iexport USER=$(whoami)' $ND_ENTRYPOINT \
    && sed -i '$iexport DISPLAY=$HOSTNAME:1' $ND_ENTRYPOINT \
    && sed -i '$ivncserver -geometry 1920x1080' $ND_ENTRYPOINT

RUN apt-get update -qq \
    && apt-get install -y -q --no-install-recommends \
           xterm \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/*