Dockerfile

FROM jupyter/scipy-notebook

USER root

# add os packages
RUN apt-get -y update && apt-get install -y --no-install-recommends\
    apt-utils \
    bash-completion \
    curl \
    gnupg \
    nodejs \
    npm \
    python-pip \
    wget \
    xorg && \
    rm -rf /var/lib/apt/lists/* && \
    apt-get clean && \
    fix-permissions $CONDA_DIR && \
    fix-permissions /home/$NB_USER

# add neurodebian repo
RUN curl -sSL http://neuro.debian.net/lists/bionic.us-nh.full >> /etc/apt/sources.list.d/neurodebian.sources.list && \
    apt-key adv \
    --recv-keys \
    --keyserver hkp://ha.pool.sks-keyservers.net:80 0xA5D32F012649A5A9
 #   --keyserver-options http-proxy=http://proxy.tch.harvard.edu:3128 0xA5D32F012649A5A9 


# add neuroimaging software
RUN apt-get update && apt-get install -y --no-install-recommends\
    fsl-complete \
    neurodebian-archive-keyring \
    octave \
    octave-pkg-dev \
    octave-image \
    software-properties-common && \
    apt-get remove -y software-properties-common && \
    rm -rf /var/lib/apt/lists/* && \
    apt-get clean


RUN git clone https://github.com/andersonwinkler/PALM.git /opt/software/palm/ && \
    cd /opt/software/palm/fileio/@file_array/private && \
    ./compile.sh


# Install MATLAB MCR
ENV MATLAB_VERSION R2017b
RUN mkdir /opt/mcr_install && \
    mkdir /opt/mcr && \
    wget --quiet -P /opt/mcr_install http://www.mathworks.com/supportfiles/downloads/${MATLAB_VERSION}/deployment_files/${MATLAB_VERSION}/installers/glnxa64/MCR_${MATLAB_VERSION}_glnxa64_installer.zip && \
    unzip -q /opt/mcr_install/MCR_${MATLAB_VERSION}_glnxa64_installer.zip -d /opt/mcr_install && \
    /opt/mcr_install/install -destinationFolder /opt/mcr -agreeToLicense yes -mode silent && \
    rm -rf /opt/mcr_install

# Configure MCR environment
ENV MCR_VERSION v93
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
ENV MCR_INHIBIT_CTF_LOCK 1
ENV MCRPath /opt/mcr/${MCR_VERSION}


# Set FSL environment variables
ENV FSLDIR /usr/share/fsl/5.0 /
ENV PALMDIR /opt/software/palm/
ENV FSLOUTPUTTYPE NIFTI_GZ
ENV PATH $PALMDIR:/usr/lib/fsl/5.0:$PATH
ENV FSLMULTIFILEQUIT TRUE
ENV LD_LIBRARY_PATH /usr/lib/fsl/5.0:$LD_LIBRARY_PATH
ENV FSLTCLSH /usr/bin/tclsh
ENV FSLWISH /usr/bin/wish
ENV XDG_RUNTIME_DIR ""

# Switch back to jovyan to avoid accidental container runs as root
USER $NB_USER

# Add to python environment
RUN pip install --no-cache-dir \
    hdf5storage \
    natsort \
    nilearn \
    pyxnat \
    termcolor \
    tqdm \
    papermill \
    && python -m ipykernel install --user
FROM jupyter/scipy-notebook

USER root

# add os packages
RUN apt-get -y update && apt-get install -y --no-install-recommends\
    apt-utils \
    bash-completion \
    curl \
    gnupg \
    nodejs \
    npm \
    python-pip \
    wget \
    xorg && \
    rm -rf /var/lib/apt/lists/* && \
    apt-get clean && \
    fix-permissions $CONDA_DIR && \
    fix-permissions /home/$NB_USER

# add neurodebian repo
RUN curl -sSL http://neuro.debian.net/lists/bionic.us-nh.full >> /etc/apt/sources.list.d/neurodebian.sources.list && \
    apt-key adv \
    --recv-keys \
    --keyserver hkp://ha.pool.sks-keyservers.net:80 0xA5D32F012649A5A9
 #   --keyserver-options http-proxy=http://proxy.tch.harvard.edu:3128 0xA5D32F012649A5A9 


# add neuroimaging software
RUN apt-get update && apt-get install -y --no-install-recommends\
    fsl-complete \
    neurodebian-archive-keyring \
    octave \
    octave-pkg-dev \
    octave-image \
    software-properties-common && \
    apt-get remove -y software-properties-common && \
    rm -rf /var/lib/apt/lists/* && \
    apt-get clean


RUN git clone https://github.com/andersonwinkler/PALM.git /opt/software/palm/ && \
    cd /opt/software/palm/fileio/@file_array/private && \
    ./compile.sh


# Install MATLAB MCR
ENV MATLAB_VERSION R2017b
RUN mkdir /opt/mcr_install && \
    mkdir /opt/mcr && \
    wget --quiet -P /opt/mcr_install http://www.mathworks.com/supportfiles/downloads/${MATLAB_VERSION}/deployment_files/${MATLAB_VERSION}/installers/glnxa64/MCR_${MATLAB_VERSION}_glnxa64_installer.zip && \
    unzip -q /opt/mcr_install/MCR_${MATLAB_VERSION}_glnxa64_installer.zip -d /opt/mcr_install && \
    /opt/mcr_install/install -destinationFolder /opt/mcr -agreeToLicense yes -mode silent && \
    rm -rf /opt/mcr_install

# Configure MCR environment
ENV MCR_VERSION v93
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
ENV MCR_INHIBIT_CTF_LOCK 1
ENV MCRPath /opt/mcr/${MCR_VERSION}


# Set FSL environment variables
ENV FSLDIR /usr/share/fsl/5.0 /
ENV PALMDIR /opt/software/palm/
ENV FSLOUTPUTTYPE NIFTI_GZ
ENV PATH $PALMDIR:/usr/lib/fsl/5.0:$PATH
ENV FSLMULTIFILEQUIT TRUE
ENV LD_LIBRARY_PATH /usr/lib/fsl/5.0:$LD_LIBRARY_PATH
ENV FSLTCLSH /usr/bin/tclsh
ENV FSLWISH /usr/bin/wish
ENV XDG_RUNTIME_DIR ""

# Switch back to jovyan to avoid accidental container runs as root
USER $NB_USER

# Add to python environment
RUN pip install --no-cache-dir \
    hdf5storage \
    natsort \
    nilearn \
    pyxnat \
    termcolor \
    tqdm \
    papermill \
    && python -m ipykernel install --user