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Dockerfile_spm_mcr
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Dockerfile_spm_mcr
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FROM ubuntu:18.04
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' >> "$ND_ENTRYPOINT"; \
fi \
&& chmod -R 777 /neurodocker && chmod a+s /neurodocker
ENTRYPOINT ["/neurodocker/startup.sh"]
ENV FSLDIR="/opt/fsl-5.0.10" \
PATH="/opt/fsl-5.0.10/bin:$PATH" \
FSLOUTPUTTYPE="NIFTI_GZ" \
FSLMULTIFILEQUIT="TRUE" \
FSLTCLSH="/opt/fsl-5.0.10/bin/fsltclsh" \
FSLWISH="/opt/fsl-5.0.10/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-5.0.10 \
&& curl -fsSL --retry 5 https://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-5.0.10-centos6_64.tar.gz \
| tar -xz -C /opt/fsl-5.0.10 --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' $ND_ENTRYPOINT \
&& echo "Installing FSL conda environment ..." \
&& bash /opt/fsl-5.0.10/etc/fslconf/fslpython_install.sh -f /opt/fsl-5.0.10
ENV ANTSPATH="/opt/ants-2.3.1" \
PATH="/opt/ants-2.3.1:$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 PATH="/opt/afni-latest:$PATH" \
AFNI_PLUGINPATH="/opt/afni-latest"
RUN apt-get update -qq \
&& apt-get install -y -q --no-install-recommends \
ed \
gsl-bin \
libglib2.0-0 \
libglu1-mesa-dev \
libglw1-mesa \
libgomp1 \
libjpeg62 \
libxm4 \
netpbm \
tcsh \
xfonts-base \
xvfb \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/* \
&& curl -sSL --retry 5 -o /tmp/toinstall.deb http://mirrors.kernel.org/debian/pool/main/libx/libxp/libxp6_1.0.2-2_amd64.deb \
&& dpkg -i /tmp/toinstall.deb \
&& rm /tmp/toinstall.deb \
&& curl -sSL --retry 5 -o /tmp/toinstall.deb http://snapshot.debian.org/archive/debian-security/20160113T213056Z/pool/updates/main/libp/libpng/libpng12-0_1.2.49-1%2Bdeb7u2_amd64.deb \
&& dpkg -i /tmp/toinstall.deb \
&& rm /tmp/toinstall.deb \
&& apt-get install -f \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/* \
&& gsl2_path="$(find / -name 'libgsl.so.19' || printf '')" \
&& if [ -n "$gsl2_path" ]; then \
ln -sfv "$gsl2_path" "$(dirname $gsl2_path)/libgsl.so.0"; \
fi \
&& ldconfig \
&& echo "Downloading AFNI ..." \
&& mkdir -p /opt/afni-latest \
&& curl -fsSL --retry 5 https://afni.nimh.nih.gov/pub/dist/tgz/linux_openmp_64.tgz \
| tar -xz -C /opt/afni-latest --strip-components 1
RUN echo '{ \
\n "pkg_manager": "apt", \
\n "instructions": [ \
\n [ \
\n "base", \
\n "ubuntu:focal" \
\n ], \
\n [ \
\n "fsl", \
\n { \
\n "version": "5.0.10" \
\n } \
\n ], \
\n [ \
\n "ants", \
\n { \
\n "version": "2.3.1" \
\n } \
\n ], \
\n [ \
\n "afni", \
\n { \
\n "version": "latest" \
\n } \
\n ] \
\n ] \
\n}' > /neurodocker/neurodocker_specs.json
RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get -y install \
unzip xorg wget \
&& apt-get clean \
&& rm -rf \
/tmp/hsperfdata* \
/var/*/apt/*/partial \
/var/lib/apt/lists/* \
/var/log/apt/term*
# Install MATLAB MCR in /opt/mcr/
ENV MATLAB_VERSION R2019b
ENV MCR_VERSION v97
RUN mkdir /opt/mcr_install \
&& mkdir /opt/mcr \
&& wget --progress=bar:force -P /opt/mcr_install https://ssd.mathworks.com/supportfiles/downloads/${MATLAB_VERSION}/Release/3/deployment_files/installer/complete/glnxa64/MATLAB_Runtime_${MATLAB_VERSION}_Update_3_glnxa64.zip \
&& unzip -q /opt/mcr_install/MATLAB_Runtime_${MATLAB_VERSION}_Update_3_glnxa64.zip -d /opt/mcr_install \
&& /opt/mcr_install/install -destinationFolder /opt/mcr -agreeToLicense yes -mode silent \
&& rm -rf /opt/mcr_install /tmp/*
# Install SPM Standalone in /opt/spm12/
ENV SPM_VERSION 12
ENV SPM_REVISION r7771
ENV LD_LIBRARY_PATH /opt/mcr/${MCR_VERSION}/runtime/glnxa64:/opt/mcr/${MCR_VERSION}/bin/glnxa64:/opt/mcr/${MCR_VERSION}/sys/os/glnxa64:/opt/mcr/${MCR_VERSION}/sys/opengl/lib/glnxa64:/opt/mcr/${MCR_VERSION}/extern/bin/glnxa64
ENV MCR_INHIBIT_CTF_LOCK 1
ENV SPM_HTML_BROWSER 0
# Running SPM once with "function exit" tests the succesfull installation *and*
# extracts the ctf archive which is necessary if singularity is going to be
# used later on, because singularity containers are read-only.
# Also, set +x on the entrypoint for non-root container invocations
RUN wget --no-check-certificate --progress=bar:force -P /opt https://www.fil.ion.ucl.ac.uk/spm/download/restricted/bids/spm${SPM_VERSION}_${SPM_REVISION}_Linux_${MATLAB_VERSION}.zip \
&& unzip -q /opt/spm${SPM_VERSION}_${SPM_REVISION}_Linux_${MATLAB_VERSION}.zip -d /opt \
&& rm -f /opt/spm${SPM_VERSION}_${SPM_REVISION}_Linux_${MATLAB_VERSION}.zip \
&& /opt/spm${SPM_VERSION}/spm${SPM_VERSION} function exit \
&& chmod +x /opt/spm${SPM_VERSION}/spm${SPM_VERSION}
ENV SPM_DIR /opt/spm${SPM_VERSION}
############################################# python packages
RUN apt-get update && apt-get install -y git python3-pip libpng-dev libfreetype6-dev libxft-dev libblas-dev liblapack-dev libatlas-base-dev gfortran libxml2-dev libxslt1-dev wget graphviz
#RUN apt-get install -y python3-tk
#RUN apt-get install libx11-6 libxext6 libxt6 # matlab
RUN pip3 install xvfbwrapper \
psutil \
numpy \
scipy \
matplotlib \
statsmodels \
pandas \
networkx \
mock \
prov \
click \
funcsigs \
pydotplus \
pydot \
rdflib \
pbr \
nibabel \
packaging \
pytest \
install \
graphviz \
pybids \
nipype \
nilearn \
scikit-image \
brain-slam
############################################# install macapype
RUN mkdir -p /opt/packages/
ADD https://api.github.com/repos/macatools/macapype/git/refs/heads/master version.json
WORKDIR /opt/packages/
RUN git clone https://github.com/macatools/macapype.git
WORKDIR /opt/packages/macapype
RUN git checkout docker_octave
RUN python3 setup.py develop
RUN echo $(which python) && \
echo $(which python3) && \
ln -s /usr/bin/python3 /usr/bin/python && \
ln -s /usr/bin/pip3 /usr/bin/pip