Dockerfile

# Generated by Neurodocker v0.3.2.
#
# 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: 2018-06-29 18:14:08

FROM debian:stretch

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"
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
ENTRYPOINT ["/neurodocker/startup.sh"]

#------------------------
# Install dcm2niix v1.0.20180622
#------------------------
WORKDIR /tmp
RUN deps='cmake g++ gcc git make pigz zlib1g-dev' \
    && apt-get update -qq && apt-get install -yq --no-install-recommends $deps \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
    && mkdir dcm2niix \
    && curl -sSL https://github.com/rordenlab/dcm2niix/tarball/v1.0.20180622 | tar xz -C dcm2niix --strip-components 1 \
    && mkdir dcm2niix/build && cd dcm2niix/build \
    && cmake .. && make \
    && make install \
    && rm -rf /tmp/* \
    && apt-get purge -y --auto-remove $deps

#--------------------------------------------------
# Add NeuroDebian repository
# Please note that some packages downloaded through
# NeuroDebian may have restrictive licenses.
#--------------------------------------------------
RUN apt-get update -qq && apt-get install -yq --no-install-recommends dirmngr gnupg \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
    && curl -sSL http://neuro.debian.net/lists/stretch.us-nh.full \
    > /etc/apt/sources.list.d/neurodebian.sources.list \
    && curl -sSL https://dl.dropbox.com/s/zxs209o955q6vkg/neurodebian.gpg \
    | apt-key add - \
    && (apt-key adv --refresh-keys --keyserver hkp://pool.sks-keyservers.net:80 0xA5D32F012649A5A9 || true) \
    && apt-get update

# Install NeuroDebian packages
RUN apt-get update -qq && apt-get install -yq --no-install-recommends git-annex-standalone \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

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

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

#------------------
# Install Miniconda
#------------------
ENV CONDA_DIR=/opt/conda \
    PATH=/opt/conda/bin:$PATH
RUN echo "Downloading Miniconda installer ..." \
    && miniconda_installer=/tmp/miniconda.sh \
    && curl -sSL --retry 5 -o $miniconda_installer https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh \
    && /bin/bash $miniconda_installer -b -p $CONDA_DIR \
    && rm -f $miniconda_installer \
    && conda config --system --prepend channels conda-forge \
    && conda config --system --set auto_update_conda false \
    && conda config --system --set show_channel_urls true \
    && conda clean -tipsy && sync

#-------------------------
# Create conda environment
#-------------------------
RUN conda create -y -q --name neuro python=2 \
                                    traits=4.6.0 \
    && sync && conda clean -tipsy && sync \
    && /bin/bash -c "source activate neuro \
      && pip install -q --no-cache-dir https://github.com/moloney/dcmstack/tarball/master \
                                       /src/heudiconv[all]" \
    && sync \
    && sed -i '$isource activate neuro' $ND_ENTRYPOINT

ENTRYPOINT ["/neurodocker/startup.sh", "heudiconv"]

#--------------------------------------
# Save container specifications to JSON
#--------------------------------------
RUN echo '{ \
    \n  "pkg_manager": "apt", \
    \n  "check_urls": true, \
    \n  "instructions": [ \
    \n    [ \
    \n      "base", \
    \n      "debian:stretch" \
    \n    ], \
    \n    [ \
    \n      "dcm2niix", \
    \n      { \
    \n        "version": "v1.0.20180622" \
    \n      } \
    \n    ], \
    \n    [ \
    \n      "neurodebian", \
    \n      { \
    \n        "os_codename": "stretch", \
    \n        "download_server": "usa-nh", \
    \n        "pkgs": "git-annex-standalone" \
    \n      } \
    \n    ], \
    \n    [ \
    \n      "install", \
    \n      [ \
    \n        "git", \
    \n        "gcc", \
    \n        "pigz" \
    \n      ] \
    \n    ], \
    \n    [ \
    \n      "copy", \
    \n      [ \
    \n        ".", \
    \n        "/src/heudiconv" \
    \n      ] \
    \n    ], \
    \n    [ \
    \n      "miniconda", \
    \n      { \
    \n        "env_name": "neuro", \
    \n        "conda_install": "python=2 traits=4.6.0", \
    \n        "activate": true, \
    \n        "pip_install": "https://github.com/moloney/dcmstack/tarball/master /src/heudiconv[all]" \
    \n      } \
    \n    ], \
    \n    [ \
    \n      "entrypoint", \
    \n      "/neurodocker/startup.sh heudiconv" \
    \n    ] \
    \n  ], \
    \n  "generation_timestamp": "2018-06-29 18:14:08", \
    \n  "neurodocker_version": "0.3.2" \
    \n}' > /neurodocker/neurodocker_specs.json