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|
# Generated by Neurodocker version 0.4.2-3-gf7055a1
# Timestamp: 2018-11-13 22:04:04 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
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/* /tmp/* /var/tmp/* \
&& 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 'if [ -n "$1" ]; then "$@"; else /usr/bin/env bash; fi' >> "$ND_ENTRYPOINT"; \
fi \
&& chmod -R 777 /neurodocker && chmod a+s /neurodocker
ENTRYPOINT ["/neurodocker/startup.sh"]
ENV PATH="/opt/dcm2niix-v1.0.20190410/bin:$PATH"
RUN apt-get update -qq \
&& apt-get install -y -q --no-install-recommends \
cmake \
g++ \
gcc \
git \
make \
pigz \
zlib1g-dev \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
&& git clone https://github.com/rordenlab/dcm2niix /tmp/dcm2niix \
&& cd /tmp/dcm2niix \
&& git fetch --tags \
&& git checkout v1.0.20190410 \
&& mkdir /tmp/dcm2niix/build \
&& cd /tmp/dcm2niix/build \
&& cmake -DCMAKE_INSTALL_PREFIX:PATH=/opt/dcm2niix-v1.0.20190410 .. \
&& make \
&& make install \
&& rm -rf /tmp/dcm2niix
RUN apt-get update -qq \
&& apt-get install -y -q --no-install-recommends \
git \
gcc \
pigz \
liblzma-dev \
libc-dev \
git-annex-standalone \
netbase \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
COPY [".", "/src/heudiconv"]
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 -tipsy && sync \
&& conda install -y -q --name base \
'python=3.6' \
'traits>=4.6.0' \
'scipy' \
'numpy' \
'pandas' \
'nomkl' \
&& sync && conda clean -tipsy && sync \
&& bash -c "source activate base \
&& pip install --no-cache-dir --editable \
'/src/heudiconv[all]'" \
&& rm -rf ~/.cache/pip/* \
&& sync
ENTRYPOINT ["heudiconv"]
RUN echo '{ \
\n "pkg_manager": "apt", \
\n "instructions": [ \
\n [ \
\n "base", \
\n "neurodebian:stretch" \
\n ], \
\n [ \
\n "dcm2niix", \
\n { \
\n "version": "v1.0.20190410", \
\n "method": "source" \
\n } \
\n ], \
\n [ \
\n "install", \
\n [ \
\n "git", \
\n "gcc", \
\n "pigz", \
\n "liblzma-dev", \
\n "libc-dev", \
\n "git-annex-standalone", \
\n "netbase" \
\n ] \
\n ], \
\n [ \
\n "copy", \
\n [ \
\n ".", \
\n "/src/heudiconv" \
\n ] \
\n ], \
\n [ \
\n "miniconda", \
\n { \
\n "use_env": "base", \
\n "conda_install": [ \
\n "python=3.6", \
\n "traits>=4.6.0", \
\n "scipy", \
\n "numpy", \
\n "pandas", \
\n "nomkl" \
\n ], \
\n "pip_install": [ \
\n "/src/heudiconv[all]" \
\n ], \
\n "pip_opts": "--editable" \
\n } \
\n ], \
\n [ \
\n "entrypoint", \
\n "heudiconv" \
\n ] \
\n ] \
\n}' > /neurodocker/neurodocker_specs.json
|
