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Merge pull request #268 from mgxd/fix/dckr
maint: docker build
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‎Dockerfile

Lines changed: 84 additions & 93 deletions
Original file line numberDiff line numberDiff line change
@@ -1,142 +1,130 @@
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# Generated by Neurodocker v0.3.2.
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#
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# Generated by Neurodocker version 0.4.1
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# Timestamp: 2018-11-01 18:20:45 UTC
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#
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# Thank you for using Neurodocker. If you discover any issues
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# or ways to improve this software, please submit an issue or
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# pull request on our GitHub repository:
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#
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# https://github.com/kaczmarj/neurodocker
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#
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# Timestamp: 2018-06-29 18:14:08
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FROM debian:stretch
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FROM neurodebian:stretch
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ARG DEBIAN_FRONTEND=noninteractive
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ARG DEBIAN_FRONTEND="noninteractive"
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#----------------------------------------------------------
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# Install common dependencies and create default entrypoint
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#----------------------------------------------------------
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ENV LANG="en_US.UTF-8" \
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LC_ALL="C.UTF-8" \
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LC_ALL="en_US.UTF-8" \
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ND_ENTRYPOINT="/neurodocker/startup.sh"
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RUN apt-get update -qq && apt-get install -yq --no-install-recommends \
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apt-utils bzip2 ca-certificates curl locales unzip \
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RUN export ND_ENTRYPOINT="/neurodocker/startup.sh" \
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&& apt-get update -qq \
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&& apt-get install -y -q --no-install-recommends \
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apt-utils \
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bzip2 \
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ca-certificates \
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curl \
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locales \
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unzip \
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&& apt-get clean \
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&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
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&& localedef --force --inputfile=en_US --charmap=UTF-8 C.UTF-8 \
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&& sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen \
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&& dpkg-reconfigure --frontend=noninteractive locales \
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&& update-locale LANG="en_US.UTF-8" \
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&& chmod 777 /opt && chmod a+s /opt \
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&& mkdir -p /neurodocker \
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&& if [ ! -f "$ND_ENTRYPOINT" ]; then \
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echo '#!/usr/bin/env bash' >> $ND_ENTRYPOINT \
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&& echo 'set +x' >> $ND_ENTRYPOINT \
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&& echo 'if [ -z "$*" ]; then /usr/bin/env bash; else $*; fi' >> $ND_ENTRYPOINT; \
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fi \
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echo '#!/usr/bin/env bash' >> "$ND_ENTRYPOINT" \
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&& echo 'set -e' >> "$ND_ENTRYPOINT" \
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&& echo 'if [ -n "$1" ]; then "$@"; else /usr/bin/env bash; fi' >> "$ND_ENTRYPOINT"; \
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fi \
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&& chmod -R 777 /neurodocker && chmod a+s /neurodocker
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ENTRYPOINT ["/neurodocker/startup.sh"]
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#------------------------
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# Install dcm2niix v1.0.20180622
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#------------------------
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WORKDIR /tmp
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RUN deps='cmake g++ gcc git make pigz zlib1g-dev' \
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&& apt-get update -qq && apt-get install -yq --no-install-recommends $deps \
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ENV PATH="/opt/dcm2niix-v1.0.20180622/bin:$PATH"
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RUN apt-get update -qq \
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&& apt-get install -y -q --no-install-recommends \
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cmake \
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g++ \
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gcc \
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git \
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make \
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pigz \
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zlib1g-dev \
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&& apt-get clean \
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&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
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&& mkdir dcm2niix \
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&& curl -sSL https://github.com/rordenlab/dcm2niix/tarball/v1.0.20180622 | tar xz -C dcm2niix --strip-components 1 \
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&& mkdir dcm2niix/build && cd dcm2niix/build \
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&& cmake .. && make \
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&& git clone https://github.com/rordenlab/dcm2niix /tmp/dcm2niix \
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&& cd /tmp/dcm2niix \
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&& git fetch --tags \
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&& git checkout v1.0.20180622 \
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&& mkdir /tmp/dcm2niix/build \
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&& cd /tmp/dcm2niix/build \
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&& cmake -DCMAKE_INSTALL_PREFIX:PATH=/opt/dcm2niix-v1.0.20180622 .. \
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&& make \
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&& make install \
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&& rm -rf /tmp/* \
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&& apt-get purge -y --auto-remove $deps
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#--------------------------------------------------
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# Add NeuroDebian repository
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# Please note that some packages downloaded through
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# NeuroDebian may have restrictive licenses.
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#--------------------------------------------------
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RUN apt-get update -qq && apt-get install -yq --no-install-recommends dirmngr gnupg \
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&& apt-get clean \
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&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
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&& curl -sSL http://neuro.debian.net/lists/stretch.us-nh.full \
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> /etc/apt/sources.list.d/neurodebian.sources.list \
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&& curl -sSL https://dl.dropbox.com/s/zxs209o955q6vkg/neurodebian.gpg \
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| apt-key add - \
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&& (apt-key adv --refresh-keys --keyserver hkp://pool.sks-keyservers.net:80 0xA5D32F012649A5A9 || true) \
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&& apt-get update
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# Install NeuroDebian packages
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RUN apt-get update -qq && apt-get install -yq --no-install-recommends git-annex-standalone \
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&& apt-get clean \
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&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
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&& rm -rf /tmp/dcm2niix
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RUN apt-get update -qq \
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&& apt-get install -y -q --no-install-recommends git \
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gcc \
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pigz \
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&& apt-get install -y -q --no-install-recommends \
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git \
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gcc \
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pigz \
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liblzma-dev \
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libc-dev \
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git-annex-standalone \
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&& apt-get clean \
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&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
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COPY [".", "/src/heudiconv"]
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#------------------
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# Install Miniconda
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#------------------
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ENV CONDA_DIR=/opt/conda \
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PATH=/opt/conda/bin:$PATH
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RUN echo "Downloading Miniconda installer ..." \
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&& miniconda_installer=/tmp/miniconda.sh \
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&& curl -sSL --retry 5 -o $miniconda_installer https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh \
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&& /bin/bash $miniconda_installer -b -p $CONDA_DIR \
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&& rm -f $miniconda_installer \
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ENV CONDA_DIR="/opt/miniconda-latest" \
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PATH="/opt/miniconda-latest/bin:$PATH"
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RUN export PATH="/opt/miniconda-latest/bin:$PATH" \
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&& echo "Downloading Miniconda installer ..." \
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&& conda_installer="/tmp/miniconda.sh" \
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&& curl -fsSL --retry 5 -o "$conda_installer" https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh \
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&& bash "$conda_installer" -b -p /opt/miniconda-latest \
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&& rm -f "$conda_installer" \
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&& conda update -yq -nbase conda \
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&& conda config --system --prepend channels conda-forge \
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&& conda config --system --set auto_update_conda false \
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&& conda config --system --set show_channel_urls true \
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&& conda clean -tipsy && sync
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#-------------------------
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# Create conda environment
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#-------------------------
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RUN conda create -y -q --name neuro python=2 \
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traits=4.6.0 \
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&& sync && conda clean -tipsy && sync \
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&& /bin/bash -c "source activate neuro \
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&& pip install -q --no-cache-dir https://github.com/moloney/dcmstack/tarball/master \
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/src/heudiconv[all]" \
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&& conda create -y -q --name neuro \
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&& conda install -y -q --name neuro \
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python=3.6 \
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traits>=4.6.0 \
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&& sync && conda clean -tipsy && sync \
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&& bash -c "source activate neuro \
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&& pip install --no-cache-dir \
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/src/heudiconv[all]" \
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&& rm -rf ~/.cache/pip/* \
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&& sync \
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&& sed -i '$isource activate neuro' $ND_ENTRYPOINT
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ENTRYPOINT ["/neurodocker/startup.sh", "heudiconv"]
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#--------------------------------------
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# Save container specifications to JSON
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#--------------------------------------
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RUN echo '{ \
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\n "pkg_manager": "apt", \
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\n "check_urls": true, \
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\n "instructions": [ \
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\n [ \
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\n "base", \
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\n "debian:stretch" \
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\n "neurodebian:stretch" \
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\n ], \
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\n [ \
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\n "dcm2niix", \
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\n { \
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\n "version": "v1.0.20180622" \
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\n } \
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\n ], \
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\n [ \
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\n "neurodebian", \
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\n { \
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\n "os_codename": "stretch", \
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\n "download_server": "usa-nh", \
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\n "pkgs": "git-annex-standalone" \
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\n "version": "v1.0.20180622", \
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\n "method": "source" \
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\n } \
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\n ], \
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\n [ \
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\n "install", \
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\n [ \
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\n "git", \
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\n "gcc", \
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\n "pigz" \
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\n "pigz", \
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\n "liblzma-dev", \
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\n "libc-dev", \
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\n "git-annex-standalone" \
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\n ] \
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\n ], \
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\n [ \
@@ -149,17 +137,20 @@ RUN echo '{ \
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\n [ \
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\n "miniconda", \
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\n { \
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\n "env_name": "neuro", \
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\n "conda_install": "python=2 traits=4.6.0", \
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\n "create_env": "neuro", \
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\n "conda_install": [ \
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\n "python=3.6", \
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\n "traits>=4.6.0" \
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\n ], \
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\n "activate": true, \
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\n "pip_install": "https://github.com/moloney/dcmstack/tarball/master /src/heudiconv[all]" \
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\n "pip_install": [ \
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\n "/src/heudiconv[all]" \
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\n ] \
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\n } \
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\n ], \
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\n [ \
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\n "entrypoint", \
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\n "/neurodocker/startup.sh heudiconv" \
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\n ] \
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\n ], \
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\n "generation_timestamp": "2018-06-29 18:14:08", \
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\n "neurodocker_version": "0.3.2" \
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\n ] \
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\n}' > /neurodocker/neurodocker_specs.json

‎utils/gen-docker-image.sh

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Original file line numberDiff line numberDiff line change
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VER=$(grep -Po '(?<=^__version__ = ).*' ../heudiconv/info.py | sed 's/"//g')
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docker run --rm kaczmarj/neurodocker:v0.3.2 generate -b debian:stretch -p apt \
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--dcm2niix version=v1.0.20180622 \
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--neurodebian os_codename=stretch download_server=usa-nh pkgs=git-annex-standalone \
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--install git gcc pigz \
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docker run --rm kaczmarj/neurodocker:0.4.1 generate docker -b neurodebian:stretch -p apt \
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--dcm2niix version=v1.0.20180622 method=source \
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--install git gcc pigz liblzma-dev libc-dev git-annex-standalone \
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--copy . /src/heudiconv \
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--miniconda env_name=neuro conda_install="python=2 traits=4.6.0" activate=True \
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pip_install="https://github.com/moloney/dcmstack/tarball/master /src/heudiconv[all]" \
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--miniconda create_env=neuro conda_install="python=3.6 traits>=4.6.0" activate=True \
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pip_install="/src/heudiconv[all]" \
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--entrypoint "/neurodocker/startup.sh heudiconv" \
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> ../Dockerfile

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