Dockerfile.pnlpipe

FROM centos:7.5.1804

MAINTAINER Tashrif Billah <tbillah@bwh.harvard.edu>

    # set up working directory, redefine home directory, remain root user
WORKDIR /home/pnlbwh
ENV HOME=/home/pnlbwh
ENV USER="root"
ENV LANG=en_US.UTF-8

COPY startup.sh /
COPY Slicer-29402.ini /
COPY .vimrc $HOME/

    # install required libraries
RUN ln -sf /usr/share/zoneinfo/America/New_York /etc/localtime && \
    yum -y groupinstall 'development tools' && \
    yum -y install tree wget file bzip2 which vim git make libstdc++-static mesa-libGL bc tcsh libSM libXt-devel \
    psmisc && \
    #
    # libraries for SlicerDMRI/FiberTractMeasurements
    yum -y install libGLU libXrender && \
    yum clean all && \
    rm -rf /var/cache/yum && \
    #
    # install freesurfer
    echo "Downloading FreeSurfer" && \
    wget https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.1.0/freesurfer-linux-centos7_x86_64-7.1.0.tar.gz > /dev/null 2>&1 && \
    echo "Unzipping FreeSurfer tar ball" && \
    tar -xzf freesurfer-linux-centos7_x86_64-7.1.0.tar.gz && \
    rm -f freesurfer-linux-centos7_x86_64-7.1.0.tar.gz && \
    mv freesurfer freesurfer-7.1.0 && \
    #
    # install MCR for -subfields
    cd freesurfer-7.1.0 && \
    curl "https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile&do=get&target=runtime2014bLinux.tar.gz" -o "runtime2014b.tar.gz" && \
    tar -xzf runtime2014b.tar.gz && rm -f runtime2014b.tar.gz && \
    cd .. && \
    #
    # install FSL
    echo "Downloading FSL installer" && \
    wget https://fsl.fmrib.ox.ac.uk/fsldownloads/fslinstaller.py -O fslinstaller.py > /dev/null 2>&1 && \
    echo "Installing FSL" && \
    python fslinstaller.py -V 6.0.1 -d $HOME/fsl-6.0.1 -p > /dev/null 2>&1 && \
    # setup FSL environment
    export FSLDIR=$HOME/fsl-6.0.1 && \
    source $FSLDIR/etc/fslconf/fsl.sh && \
    $FSLDIR/fslpython/bin/conda clean -y --all && \
    rm -f fslinstaller.py
    
    
    # clone pnlpipe repositories
RUN git clone --recurse-submodules https://github.com/pnlbwh/pnlpipe.git && \
    git clone https://github.com/pnlbwh/pnlNipype.git && \
    git clone https://github.com/pnlbwh/luigi-pnlpipe.git && \
    #
    # install CNN-Diffusion-MRIBrain-Segmentation
    git clone https://github.com/pnlbwh/CNN-Diffusion-MRIBrain-Segmentation.git && \
    cd CNN-Diffusion-MRIBrain-Segmentation && \
    wget https://github.com/pnlbwh/CNN-Diffusion-MRIBrain-Segmentation/releases/download/v0.3/model_folder.tar.gz && \
    tar -xzvf model_folder.tar.gz
    
    # install miniconda3
RUN wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O Miniconda3-latest-Linux-x86_64.sh && \
    /bin/bash Miniconda3-latest-Linux-x86_64.sh -b -p miniconda3/ && \
    #
    # initialize bashrc
    cp /root/.bashrc $HOME/ && \
    echo "source $HOME/miniconda3/bin/activate" >> ~/.bashrc && \
    #
    # create conda env
    source miniconda3/bin/activate && \
    conda env create -f pnlpipe/python_env/environment36.yml && \
    echo "conda activate pnlpipe3" >> ~/.bashrc && \
    #
    # clean up conda cache
    conda deactivate && \
    conda clean -y --all && \
    rm -rf $HOME/Miniconda3-latest-Linux-x86_64.sh .cache/pip/*
    
    
    # conda activate is required again because we are beginning a different RUN i.e. shell
RUN source miniconda3/bin/activate && \
    conda activate pnlpipe3 && \
    export FREESURFER_HOME=$HOME/freesurfer-7.1.0 && \
    #
    # build pnlpipe dependencies
    cd pnlpipe && mkdir soft_dir && export PNLPIPE_SOFT=$HOME/pnlpipe/soft_dir && \
    ./pnlpipe std init && \
    ./pnlpipe std setup && \
    #
    # clean up sources
    cd soft_dir && \
    rm -rf BRAINSTools BRAINSTools-build ANTs ANTs-build ANTs-bin-*/CMakeFiles ukftractography UKFTractography-build dcm2niix && \
    rm -rf /tmp/* /var/tmp/*
    
    
    # set up bashrc i.e shell
RUN echo "export PNLPIPE_SOFT=$HOME/pnlpipe/soft_dir" >> ~/.bashrc && \
    echo "alias ls=\"ls --color\"" >> ~/.bashrc && \
    cd $HOME/pnlpipe/soft_dir && \
    for d in `find . -name env.sh`; do echo "source \${PNLPIPE_SOFT}/$d" >> ~/.bashrc; done && \
    cd $HOME && \
    echo "export FSLDIR=$HOME/fsl-6.0.1" >> ~/.bashrc && \
    echo "source \$FSLDIR/etc/fslconf/fsl.sh" >> ~/.bashrc && \
    echo "export PATH=\$FSLDIR/bin:\$PATH" >> ~/.bashrc && \
    echo "export FREESURFER_HOME=$HOME/freesurfer-7.1.0" >> ~/.bashrc && \
    echo "source \${FREESURFER_HOME}/SetUpFreeSurfer.sh" >> ~/.bashrc && \
    echo "export PATH=$HOME/pnlNipype/scripts:$HOME/pnlNipype/exec:$HOME/CNN-Diffusion-MRIBrain-Segmentation/pipeline:\$PATH" >> ~/.bashrc && \
    echo "export PYTHONPATH=$HOME/luigi-pnlpipe:\$PYTHONPATH" >> ~/.bashrc && \
    #
    # remove problematic aliases
    sed -i "s/alias mv='mv -i'//g" ~/.bashrc && \
    sed -i "s/alias cp='cp -i'//g" ~/.bashrc && \
    sed -i "s/alias rm='rm -i'//g" ~/.bashrc && \
    #
    # facilitate creation of ~/matlab/startup.m
    export FREESURFER_HOME=$HOME/freesurfer-7.1.0 && \
    source ${FREESURFER_HOME}/SetUpFreeSurfer.sh && \
    #
    # change permission of startup script 
    chmod +x /startup.sh
    

ENTRYPOINT ["/startup.sh"]