Dockerfile

# Generated by: Neurodocker version 0.7.0+0.gdc97516.dirty
# Latest release: Neurodocker version 0.7.0
# Timestamp: 2021/01/19 17:40:36 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/ReproNim/neurodocker

FROM ubuntu:18.04

USER root

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"]

ENV FSLDIR="/opt/fsl-6.0.3" \
    PATH="/opt/fsl-6.0.3/bin:$PATH" \
    FSLOUTPUTTYPE="NIFTI_GZ" \
    FSLMULTIFILEQUIT="TRUE" \
    FSLTCLSH="/opt/fsl-6.0.3/bin/fsltclsh" \
    FSLWISH="/opt/fsl-6.0.3/bin/fslwish" \
    FSLLOCKDIR="" \
    FSLMACHINELIST="" \
    FSLREMOTECALL="" \
    FSLGECUDAQ="cuda.q"
RUN apt-get update -qq \
    && apt-get install -y -q --no-install-recommends \
           bc \
           dc \
           file \
           libfontconfig1 \
           libfreetype6 \
           libgl1-mesa-dev \
           libgl1-mesa-dri \
           libglu1-mesa-dev \
           libgomp1 \
           libice6 \
           libxcursor1 \
           libxft2 \
           libxinerama1 \
           libxrandr2 \
           libxrender1 \
           libxt6 \
           sudo \
           wget \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/* \
    && echo "Downloading FSL ..." \
    && mkdir -p /opt/fsl-6.0.3 \
    && curl -fsSL --retry 5 https://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-6.0.3-centos6_64.tar.gz \
    | tar -xz -C /opt/fsl-6.0.3 --strip-components 1 \
    && sed -i '$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-6.0.3/etc/fslconf/fslpython_install.sh -f /opt/fsl-6.0.3

RUN echo '{ \
    \n  "pkg_manager": "apt", \
    \n  "instructions": [ \
    \n    [ \
    \n      "base", \
    \n      "ubuntu:18.04" \
    \n    ], \
    \n    [ \
    \n      "fsl", \
    \n      { \
    \n        "version": "6.0.3", \
    \n        "method": "binaries" \
    \n      } \
    \n    ] \
    \n  ] \
    \n}' > /neurodocker/neurodocker_specs.json

#binderhub specific https://mybinder.readthedocs.io/en/latest/tutorials/dockerfile.html
RUN apt-get update -qq && apt-get install -y -q python3-pip
RUN pip3 install --no-cache-dir \
	Cython==0.29.20 \
	notebook==5.7.10 \
	nilearn==0.7.0 \
	matplotlib==3.3.0

ARG NB_USER=jovyan
ARG NB_UID=1000
ENV USER ${NB_USER}
ENV NB_UID ${NB_UID}
ENV HOME /home/${NB_USER}

RUN adduser --disabled-password \
    --gecos "Default user" \
    --uid ${NB_UID} \
    ${NB_USER}

# Make sure the contents of our repo are in ${HOME}
COPY . ${HOME}
USER root
RUN chown -R ${NB_UID} ${HOME}
WORKDIR ${HOME}
USER ${NB_USER}

# disinherit previous entrypoints
ENTRYPOINT []