Dockerfile

# Generated by Neurodocker v0.3.1-13-ga8bb71e.
#
# 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
#
# Timestamp: 2017-11-27 21:13:04

FROM ubuntu:17.10

ARG DEBIAN_FRONTEND=noninteractive

#----------------------------------------------------------
# Install common dependencies and create default entrypoint
#----------------------------------------------------------
ENV LANG="en_US.UTF-8" \
    LC_ALL="C.UTF-8" \
    ND_ENTRYPOINT="/neurodocker/startup.sh" \
    AFNI_NIFTI_VIEW="orig"

RUN apt-get update -qq && apt-get install -yq --no-install-recommends  \
    	apt-utils bzip2 ca-certificates curl locales unzip \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
    && localedef --force --inputfile=en_US --charmap=UTF-8 C.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 +x' >> $ND_ENTRYPOINT \
         && echo 'if [ -z "$*" ]; then /usr/bin/env bash; else $*; fi' >> $ND_ENTRYPOINT; \
       fi \
    && chmod -R 777 /neurodocker && chmod a+s /neurodocker


#--------------------
# Install AFNI latest
#--------------------
ENV PATH=/opt/afni:$PATH
RUN apt-get update -qq && apt-get install -yq --no-install-recommends ed gsl-bin libglu1-mesa-dev libglib2.0-0 libglw1-mesa \
    libgomp1 libjpeg62 libxm4 netpbm tcsh xfonts-base xvfb python python3 python3-pip python3-setuptools python3-tk\
    && libs_path=/usr/lib/x86_64-linux-gnu \
    && if [ -f $libs_path/libgsl.so.19 ]; then \
           ln $libs_path/libgsl.so.19 $libs_path/libgsl.so.0; \
       fi \
    && echo "Install libxp (not in all ubuntu/debian repositories)" \
    && apt-get install -yq --no-install-recommends libxp6 \
    || /bin/bash -c " \
       curl --retry 5 -o /tmp/libxp6.deb -sSL http://mirrors.kernel.org/debian/pool/main/libx/libxp/libxp6_1.0.2-2_amd64.deb \
       && dpkg -i /tmp/libxp6.deb && rm -f /tmp/libxp6.deb" \
    && echo "Install libpng12 (not in all ubuntu/debian repositories" \
    && apt-get install -yq --no-install-recommends libpng12-0 \
    || /bin/bash -c " \
       curl -o /tmp/libpng12.deb -sSL http://mirrors.kernel.org/debian/pool/main/libp/libpng/libpng12-0_1.2.49-1%2Bdeb7u2_amd64.deb \
       && dpkg -i /tmp/libpng12.deb && rm -f /tmp/libpng12.deb" \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
    && echo "Downloading AFNI ..." \
    && mkdir -p /opt/afni \
    && curl -sSL --retry 5 https://afni.nimh.nih.gov/pub/dist/tgz/linux_openmp_64.tgz \
    | tar zx -C /opt/afni --strip-components=1 \
    && pip3 install jinja2 pandas matplotlib

#-----------------------
# Install bids validator
#-----------------------

RUN apt-get update && \
    apt-get install -y curl && \
    curl -sL https://deb.nodesource.com/setup_8.x | bash - && \
    apt-get remove -y curl && \
    apt-get install -y nodejs && \
    rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

RUN npm install -g bids-validator@0.24.0

COPY run.py /run.py
COPY . /code
RUN mkdir /work
COPY version /version
ENTRYPOINT ["/run.py"]

#--------------------------------------
# Save container specifications to JSON
#--------------------------------------
RUN echo '{ \
    \n  "pkg_manager": "apt", \
    \n  "check_urls": true, \
    \n  "instructions": [ \
    \n    [ \
    \n      "base", \
    \n      "ubuntu:17.04" \
    \n    ], \
    \n    [ \
    \n      "afni", \
    \n      { \
    \n        "version": "latest", \
    \n        "install_python2": "True", \
    \n        "install_python3": "True" \
    \n      } \
    \n    ] \
    \n  ], \
    \n  "generation_timestamp": "2017-11-27 21:13:04", \
    \n  "neurodocker_version": "0.3.1-13-ga8bb71e" \
    \n}' > /neurodocker/neurodocker_specs.json