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Dockerfile
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# 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: 2018-03-03 16:48:45
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' >> $ND_ENTRYPOINT; \
fi \
&& chmod -R 777 /neurodocker && chmod a+s /neurodocker
ENTRYPOINT ["/neurodocker/startup.sh"]
#-----------------------------------------------------------
# Install FSL v5.0.10
# FSL is non-free. If you are considering commerical use
# of this Docker image, please consult the relevant license:
# https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Licence
#-----------------------------------------------------------
RUN apt-get update -qq && apt-get install -yq --no-install-recommends bc dc libfontconfig1 libfreetype6 libgl1-mesa-dev libglu1-mesa-dev libgomp1 libice6 libxcursor1 libxft2 libxinerama1 libxrandr2 libxrender1 libxt6 \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
&& echo "Downloading FSL ..." \
&& curl -sSL --retry 5 https://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-5.0.10-centos6_64.tar.gz \
| tar zx -C /opt \
&& /bin/bash /opt/fsl/etc/fslconf/fslpython_install.sh -q -f /opt/fsl \
&& sed -i '$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' $ND_ENTRYPOINT
ENV FSLDIR=/opt/fsl \
PATH=/opt/fsl/bin:$PATH
USER root
RUN apt-get update -qq \
&& apt-get install -y -q --no-install-recommends git \
vim \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
# Create new user: neuro
RUN useradd --no-user-group --create-home --shell /bin/bash neuro
USER neuro
#------------------
# 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 $miniconda_installer \
&& conda config --system --prepend channels conda-forge \
&& conda config --system --set auto_update_conda false \
&& conda config --system --set show_channel_urls true \
&& conda update -n base conda \
&& conda clean -tipsy && sync
#-------------
# Copy in code
#-------------
COPY . /pydeface
USER root
RUN chown -R neuro:users /pydeface
USER neuro
#-------------------------
# Create conda environment
#-------------------------
RUN conda create -y -q --name neuro --channel conda-forge python \
nipype \
nibabel \
pytest \
&& sync && conda clean -tipsy && sync \
&& /bin/bash -c "source activate neuro \
&& pip install -e /pydeface" \
&& sync \
&& sed -i '$isource activate neuro' $ND_ENTRYPOINT
WORKDIR /home/neuro
#--------------------------------------
# Save container specifications to JSON
#--------------------------------------
RUN echo '{ \
\n "pkg_manager": "apt", \
\n "check_urls": false, \
\n "instructions": [ \
\n [ \
\n "base", \
\n "debian:stretch" \
\n ], \
\n [ \
\n "fsl", \
\n { \
\n "version": "5.0.10" \
\n } \
\n ], \
\n [ \
\n "user", \
\n "root" \
\n ], \
\n [ \
\n "install", \
\n [ \
\n "git", \
\n "vim" \
\n ] \
\n ], \
\n [ \
\n "user", \
\n "neuro" \
\n ], \
\n [ \
\n "miniconda", \
\n { \
\n "env_name": "neuro", \
\n "conda_opts": "--channel conda-forge", \
\n "conda_install": "python nipype nibabel pytest", \
\n "pip_install": "git+git://github.com/poldracklab/pydeface.git", \
\n "activate": true \
\n } \
\n ], \
\n [ \
\n "workdir", \
\n "/home/neuro" \
\n ] \
\n ], \
\n "generation_timestamp": "2018-03-03 16:48:45", \
\n "neurodocker_version": "0.3.2" \
\n}' > /neurodocker/neurodocker_specs.json