Dockerfile

# Generated by Neurodocker version 0.5.0
# Timestamp: 2019-09-17 09:07:49 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"]

ENV FREESURFER_HOME="/opt/freesurfer-6.0.0" \
    PATH="/opt/freesurfer-6.0.0/bin:$PATH"
RUN apt-get update -qq \
    && apt-get install -y -q --no-install-recommends \
           bc \
           libgomp1 \
           libxmu6 \
           libxt6 \
           perl \
           tcsh \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/* \
    && echo "Downloading FreeSurfer ..." \
    && mkdir -p /opt/freesurfer-6.0.0 \
    && curl -fsSL --retry 5 ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz \
    | tar -xz -C /opt/freesurfer-6.0.0 --strip-components 1 \
         --exclude='freesurfer/average/mult-comp-cor' \
         --exclude='freesurfer/lib/cuda' \
         --exclude='freesurfer/lib/qt' \
         --exclude='freesurfer/subjects/V1_average' \
         --exclude='freesurfer/subjects/bert' \
         --exclude='freesurfer/subjects/cvs_avg35' \
         --exclude='freesurfer/subjects/cvs_avg35_inMNI152' \
         --exclude='freesurfer/subjects/fsaverage3' \
         --exclude='freesurfer/subjects/fsaverage4' \
         --exclude='freesurfer/subjects/fsaverage5' \
         --exclude='freesurfer/subjects/fsaverage6' \
         --exclude='freesurfer/subjects/fsaverage_sym' \
         --exclude='freesurfer/trctrain' \
    && sed -i '$isource "/opt/freesurfer-6.0.0/SetUpFreeSurfer.sh"' "$ND_ENTRYPOINT"

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 "$conda_installer" \
    && conda update -yq -nbase conda \
    && conda config --system --prepend channels conda-forge \
    && conda config --system --set auto_update_conda false \
    && conda config --system --set show_channel_urls true \
    && sync && conda clean --all && sync \
    && conda create -y -q --name mb-mm \
    && conda install -y -q --name mb-mm \
           'python=3.6' \
           'numpy' \
           'pandas' \
           'sklearn-lmer' \
           'scipy' \
           'rpy2=2.9.4' \
           'r-lme4' \
           'r-lmertest' \
           'r-emmeans' \
           'tzlocal' \
           'seaborn' \
    && sync && conda clean --all && sync \
    && sed -i '$isource activate mb-mm' $ND_ENTRYPOINT

RUN echo '{ \
    \n  "pkg_manager": "apt", \
    \n  "instructions": [ \
    \n    [ \
    \n      "base", \
    \n      "neurodebian:stretch-non-free" \
    \n    ], \
    \n    [ \
    \n      "freesurfer", \
    \n      { \
    \n        "version": "6.0.0", \
    \n        "min": "true" \
    \n      } \
    \n    ], \
    \n    [ \
    \n      "miniconda", \
    \n      { \
    \n        "conda_install": [ \
    \n          "python=3.6", \
    \n          "numpy", \
    \n          "pandas", \
    \n          "sklearn-lmer", \
    \n          "scipy", \
    \n          "rpy2=2.9.4", \
    \n          "r-lme4", \
    \n          "r-lmertest", \
    \n          "r-emmeans", \
    \n          "tzlocal", \
    \n          "seaborn" \
    \n        ], \
    \n        "create_env": "mb-mm", \
    \n        "activate": true \
    \n      } \
    \n    ] \
    \n  ] \
    \n}' > /neurodocker/neurodocker_specs.json