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Dockerfile
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FROM nipreps/fmriprep:23.2.1
MAINTAINER Chao-Gan Yan <[email protected]>
# Update system and istall pakages
RUN apt-get -qq update
RUN apt-get -qq install -y libdbus-1-dev; exit 0
RUN dpkg --configure dbus
RUN apt-get -qq install -y x11vnc xvfb suckless-tools stterm parallel wget unzip time && \
apt-get update
# apt-get -qq install -y x11vnc xvfb suckless-tools stterm parallel wget unzip time qt5-default && \
# Setup x11vnc
RUN mkdir -p ~/.vnc && \
x11vnc -storepasswd dpabi ~/.vnc/passwd && \
chmod 0600 ~/.vnc/passwd && \
export USER=$(whoami) && \
export DISPLAY=$HOSTNAME:25
ENV XAUTHORITY /home/fmriprep/.Xauthority
# Install MATLAB MCR
ENV MATLAB_VERSION R2020a
RUN mkdir /opt/mcr_install && \
mkdir /opt/mcr && \
wget --quiet -P /opt/mcr_install http://ssd.mathworks.com/supportfiles/downloads/R2020a/Release/0/deployment_files/installer/complete/glnxa64/MATLAB_Runtime_R2020a_glnxa64.zip && \
unzip -q /opt/mcr_install/MATLAB_Runtime_R2020a_glnxa64.zip -d /opt/mcr_install && \
/opt/mcr_install/install -destinationFolder /opt/mcr -agreeToLicense yes -mode silent && \
rm -rf /opt/mcr_install /tmp/*
# Configure environment
ENV MCR_VERSION v98
ENV LD_LIBRARY_PATH $LD_LIBRARY_PATH/opt/mcr/${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 MCRPath /opt/mcr/${MCR_VERSION}
# Configure DPABI
RUN mkdir /opt/DPABI
COPY . /opt/DPABI
RUN chmod +x /opt/DPABI/DPABI_StandAlone/run_DPABI_StandAlone.sh
RUN chmod +x /opt/DPABI/DPABI_StandAlone/DPABI_StandAlone
# RUN chmod +x /opt/DPABI/DPABI_StandAlone/run_DPARSFA_run_StandAlone.sh
# RUN chmod +x /opt/DPABI/DPABI_StandAlone/DPARSFA_run_StandAlone
# RUN chmod +x /opt/DPABI/DPABI_StandAlone/run_DPABISurf_run_StandAlone.sh
# RUN chmod +x /opt/DPABI/DPABI_StandAlone/DPABISurf_run_StandAlone
COPY ./DPABIFiber/MissingCommands/mni152.register.dat /opt/freesurfer/average/
# Extract ctf for singularity support
# RUN /opt/DPABI/DPABI_StandAlone/run_DPABI_StandAlone.sh /opt/mcr/${MCR_VERSION} || true
# RUN /opt/DPABI/DPABI_StandAlone/run_DPARSFA_run_StandAlone.sh /opt/mcr/${MCR_VERSION} || true
# RUN /opt/DPABI/DPABI_StandAlone/run_DPABISurf_run_StandAlone.sh /opt/mcr/${MCR_VERSION} || true
ENV LD_LIBRARY_PATH /usr/lib/x86_64-linux-gnu:/opt/conda/lib:/opt/workbench/lib_linux64:/opt/fsl-6.0.5.1/lib:/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
RUN apt-get -qq update && apt-get -qq install -y \
libopenblas-dev && \
apt-get update
ENTRYPOINT []
# Start VNC after launching
# x11vnc -forever -shared -usepw -create -rfbport 5925 &