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Dockerfile
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# Generated by: Neurodocker version 0.7.0
# Latest release: Neurodocker version 0.7.0
# Timestamp: 2020/05/22 21:51:32 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/ReproNim/neurodocker
FROM debian:stretch
USER root
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' >> "$ND_ENTRYPOINT"; \
fi \
&& chmod -R 777 /neurodocker && chmod a+s /neurodocker
ENTRYPOINT ["/neurodocker/startup.sh"]
ENV PATH="/opt/mrtrix3-3.0.0/bin:$PATH"
RUN echo "Downloading MRtrix3 ..." \
&& mkdir -p /opt/mrtrix3-3.0.0 \
&& curl -fsSL --retry 5 https://github.com/kaczmarj/MRtrix3-builds/releases/download/3.0.0/mrtrix3-3.0.0-Linux-centos6-x86_64.tar.gz \
| tar -xz -C /opt/mrtrix3-3.0.0 --strip-components 1
ENV ANTSPATH="/opt/ants-2.3.1" \
PATH="/opt/ants-2.3.1:$PATH"
RUN echo "Downloading ANTs ..." \
&& mkdir -p /opt/ants-2.3.1 \
&& curl -fsSL --retry 5 https://dl.dropbox.com/s/1xfhydsf4t4qoxg/ants-Linux-centos6_x86_64-v2.3.1.tar.gz \
| tar -xz -C /opt/ants-2.3.1 --strip-components 1
ENV FSLDIR="/opt/fsl-6.0.3" \
PATH="/opt/fsl-6.0.3/bin:$PATH" \
FSLOUTPUTTYPE="NIFTI_GZ" \
FSLMULTIFILEQUIT="TRUE" \
FSLTCLSH="/opt/fsl-6.0.3/bin/fsltclsh" \
FSLWISH="/opt/fsl-6.0.3/bin/fslwish" \
FSLLOCKDIR="" \
FSLMACHINELIST="" \
FSLREMOTECALL="" \
FSLGECUDAQ="cuda.q"
RUN apt-get update -qq \
&& apt-get install -y -q --no-install-recommends \
bc \
dc \
file \
libfontconfig1 \
libfreetype6 \
libgl1-mesa-dev \
libgl1-mesa-dri \
libglu1-mesa-dev \
libgomp1 \
libice6 \
libxcursor1 \
libxft2 \
libxinerama1 \
libxrandr2 \
libxrender1 \
libxt6 \
sudo \
wget \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/* \
&& echo "Downloading FSL ..." \
&& mkdir -p /opt/fsl-6.0.3 \
&& curl -fsSL --retry 5 https://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-6.0.3-centos6_64.tar.gz \
| tar -xz -C /opt/fsl-6.0.3 --strip-components 1 \
&& sed -i '$iecho Some packages in this Docker container are non-free' $ND_ENTRYPOINT \
&& sed -i '$iecho If you are considering commercial use of this container, please consult the relevant license:' $ND_ENTRYPOINT \
&& sed -i '$iecho https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Licence' $ND_ENTRYPOINT \
&& sed -i '$isource $FSLDIR/etc/fslconf/fsl.sh' $ND_ENTRYPOINT \
&& echo "Installing FSL conda environment ..." \
&& bash /opt/fsl-6.0.3/etc/fslconf/fslpython_install.sh -f /opt/fsl-6.0.3 \
RUN apt-get update -qq \
&& apt-get install -y -q --no-install-recommends \
dirmngr \
gnupg2 \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/* \
&& curl -fsSL --retry 5 http://neuro.debian.net/lists/stretch.us-nh.full \
> /etc/apt/sources.list.d/neurodebian.sources.list \
&& curl -sSL https://dl.dropbox.com/s/zxs209o955q6vkg/neurodebian.gpg | apt-key add - \
&& (apt-key adv --refresh-keys --keyserver hkp://pool.sks-keyservers.net:80 0xA5D32F012649A5A9 || true) \
&& apt-get -qq update
ENV CONDA_DIR="/opt/miniconda-latest" \
PATH="/opt/miniconda-latest/bin:$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 -y --all && sync \
&& conda install -y -q --name base \
"python" \
"pip" \
"nipype" \
"nibabel" \
&& sync && conda clean -y --all && sync \
&& bash -c "source activate base \
&& pip install --no-cache-dir \
"pybids" \
"fastcore" \
"nilearn" \
"pipetography==0.3.11"" \
&& rm -rf ~/.cache/pip/* \
&& sync \
RUN apt-get update -qq \
&& apt-get install -y -q --no-install-recommends \
git \
ssh \
tar \
gzip \
ca-certificates \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/*
RUN ldconfig
RUN echo '{ \
\n "pkg_manager": "apt", \
\n "instructions": [ \
\n [ \
\n "base", \
\n "debian:stretch" \
\n ], \
\n [ \
\n "mrtrix3", \
\n { \
\n "version": "3.0.0" \
\n } \
\n ], \
\n [ \
\n "ants", \
\n { \
\n "version": "2.3.1" \
\n } \
\n ], \
\n [ \
\n "fsl", \
\n { \
\n "version": "6.0.3" \
\n } \
\n ], \
\n [ \
\n "miniconda", \
\n { \
\n "create_env": "base", \
\n "conda_install": [ \
\n "python", \
\n "pip", \
\n "nipype", \
\n "nibabel", \
\n ], \
\n "pip_install": [ \
\n "pybids", \
\n "fastcore", \
\n "nilearn", \
\n "pipetography==0.3.11" \
\n ], \
\n } \
\n ], \
\n [ \
\n "install", \
\n [ \
\n "git", \
\n "ssh", \
\n "tar", \
\n "gzip", \
\n "ca-certificates", \
\n "fsl-first-data" \
\n ] \
\n ], \
\n [ \
\n "run", \
\n "ldconfig" \
\n ] \
\n ] \
\n}' > /neurodocker/neurodocker_specs.json