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# Your version: 0.6.0 Latest version: 0.9.5
# Generated by Neurodocker version 0.6.0
# Timestamp: 2023-10-24 10:25:06 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 ubuntu:20.04
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' >> "$ND_ENTRYPOINT"; \
fi \
&& chmod -R 777 /neurodocker && chmod a+s /neurodocker
ENTRYPOINT ["/neurodocker/startup.sh"]
RUN apt-get update -qq \
&& apt-get install -y -q --no-install-recommends \
git \
num-utils \
gcc \
g++ \
curl \
yarn \
build-essential \
nano \
git-annex \
npm \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/*
RUN bash -c 'curl -sL https://deb.nodesource.com/setup_15.x | bash - && apt update && apt-get install -y nodejs'
RUN bash -c 'npm install -g [email protected]'
ENV FSLDIR="/opt/fsl-6.0.1" \
PATH="/opt/fsl-6.0.1/bin:$PATH"
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-6.0.1 \
&& curl -fsSL --retry 5 https://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-6.0.1-centos6_64.tar.gz \
| tar -xz -C /opt/fsl-6.0.1 --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' $ND_ENTRYPOINT \
&& echo "Installing FSL conda environment ..." \
&& bash /opt/fsl-6.0.1/etc/fslconf/fslpython_install.sh -f /opt/fsl-6.0.1 \
&& echo "Downgrading deprecation module per https://github.com/kaczmarj/neurodocker/issues/271#issuecomment-514523420" \
&& /opt/fsl-6.0.1/fslpython/bin/conda install -n fslpython -c conda-forge -y deprecation==1.* \
&& echo "Removing bundled with FSLeyes libz likely incompatible with the one from OS" \
&& rm -f /opt/fsl-6.0.1/bin/FSLeyes/libz.so.1
ENV CONDA_DIR="/opt/miniconda-latest" \
PATH="/opt/miniconda-latest/bin:$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 --all && sync \
&& conda create -y -q --name bidsonym \
&& conda install -y -q --name bidsonym \
"python=3.10" \
"numpy" \
"nipype" \
"nibabel" \
"pandas" \
"datalad" \
&& sync && conda clean --all && sync \
&& bash -c "source activate bidsonym \
&& pip install --no-cache-dir \
"tensorflow" \
"scikit-image" \
"pydeface==2.0.2" \
"nobrainer==0.4.0" \
"quickshear==1.2.0" \
"datalad-osf"" \
&& rm -rf ~/.cache/pip/* \
&& sync \
&& sed -i '$isource activate bidsonym' $ND_ENTRYPOINT
RUN bash -c 'git config --global user.email [email protected] && git config --global user.name BIDSonym'
RUN bash -c 'mkdir -p /opt/nobrainer/models && cd /opt/nobrainer/models && source activate bidsonym && datalad clone https://github.com/neuronets/trained-models && cd trained-models && git-annex enableremote osf-storage && datalad get -s osf-storage neuronets/brainy/0.1.0/weights/brain-extraction-unet-128iso-model.h5'
RUN bash -c 'mkdir /home/mri-deface-detector && cd /home/mri-deface-detector && npm install sharp --unsafe-perm && npm install -g mri-deface-detector --unsafe-perm && cd ~'
RUN bash -c 'git clone https://github.com/miykael/gif_your_nifti && cd gif_your_nifti && source activate bidsonym && python setup.py install'
COPY [".", "/home/bm"]
RUN bash -c 'chmod a+x /home/bm/bidsonym/fs_data/mri_deface'
RUN bash -c 'source activate bidsonym && cd /home/bm && pip install -e .'
ENV IS_DOCKER="1"
WORKDIR /tmp/
ENTRYPOINT ["/neurodocker/startup.sh", "bidsonym"]
RUN echo '{ \
\n "pkg_manager": "apt", \
\n "instructions": [ \
\n [ \
\n "base", \
\n "ubuntu:20.04" \
\n ], \
\n [ \
\n "install", \
\n [ \
\n "git", \
\n "num-utils", \
\n "gcc", \
\n "g++", \
\n "curl", \
\n "yarn", \
\n "build-essential", \
\n "nano", \
\n "git-annex", \
\n "npm" \
\n ] \
\n ], \
\n [ \
\n "run_bash", \
\n "curl -sL https://deb.nodesource.com/setup_15.x | bash - && apt update && apt-get install -y nodejs" \
\n ], \
\n [ \
\n "run_bash", \
\n "npm install -g [email protected]" \
\n ], \
\n [ \
\n "fsl", \
\n { \
\n "version": "6.0.1", \
\n "method": "binaries" \
\n } \
\n ], \
\n [ \
\n "miniconda", \
\n { \
\n "conda_install": [ \
\n "python=3.10", \
\n "numpy", \
\n "nipype", \
\n "nibabel", \
\n "pandas", \
\n "datalad" \
\n ], \
\n "pip_install": [ \
\n "tensorflow", \
\n "scikit-image", \
\n "pydeface==2.0.2", \
\n "nobrainer==0.4.0", \
\n "quickshear==1.2.0", \
\n "datalad-osf" \
\n ], \
\n "create_env": "bidsonym", \
\n "activate": true \
\n } \
\n ], \
\n [ \
\n "run_bash", \
\n "git config --global user.email [email protected] && git config --global user.name BIDSonym" \
\n ], \
\n [ \
\n "run_bash", \
\n "mkdir -p /opt/nobrainer/models && cd /opt/nobrainer/models && source activate bidsonym && datalad clone https://github.com/neuronets/trained-models && cd trained-models && git-annex enableremote osf-storage && datalad get -s osf-storage neuronets/brainy/0.1.0/weights/brain-extraction-unet-128iso-model.h5" \
\n ], \
\n [ \
\n "run_bash", \
\n "mkdir /home/mri-deface-detector && cd /home/mri-deface-detector && npm install sharp --unsafe-perm && npm install -g mri-deface-detector --unsafe-perm && cd ~" \
\n ], \
\n [ \
\n "run_bash", \
\n "git clone https://github.com/miykael/gif_your_nifti && cd gif_your_nifti && source activate bidsonym && python setup.py install" \
\n ], \
\n [ \
\n "copy", \
\n [ \
\n ".", \
\n "/home/bm" \
\n ] \
\n ], \
\n [ \
\n "run_bash", \
\n "chmod a+x /home/bm/bidsonym/fs_data/mri_deface" \
\n ], \
\n [ \
\n "run_bash", \
\n "source activate bidsonym && cd /home/bm && pip install -e ." \
\n ], \
\n [ \
\n "env", \
\n { \
\n "IS_DOCKER": "1" \
\n } \
\n ], \
\n [ \
\n "workdir", \
\n "/tmp/" \
\n ], \
\n [ \
\n "entrypoint", \
\n "/neurodocker/startup.sh bidsonym" \
\n ] \
\n ] \
\n}' > /neurodocker/neurodocker_specs.json