Singularity.pnlpipe

Bootstrap: docker
From: centos:7.5.1804

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

%help
    For running container
        - https://github.com/pnlbwh/pnlpipe-containers
    For pipeline basics
        - https://github.com/pnlbwh/pnlNipype
        - https://github.com/pnlbwh/pnlpipe
    
    Please report issues on GitHub.


%post
    #
    # set up user and working directory
    mkdir /home/pnlbwh
    cd /home/pnlbwh
    export HOME=`pwd`
    #
    # install required libraries
    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
    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
    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
    cd ..
    #
    # install miniconda3
    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 $HOME/
    #
    # create conda env
    source miniconda3/bin/activate
    conda env create -f pnlpipe/python_env/environment36.yml
    conda activate pnlpipe3
    export FREESURFER_HOME=$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
    conda deactivate
    conda clean -y --all
    rm -rf $HOME/Miniconda3-latest-Linux-x86_64.sh .cache/pip/*
    cd soft_dir
    rm -rf BRAINSTools BRAINSTools-build ANTs ANTs-build ANTs-bin-*/CMakeFiles ukftractography UKFTractography-build dcm2niix
    rm -rf /tmp/* /var/tmp/*
    #
    # remove problematic aliases
    sed -i "s/alias mv='mv -i'//g" ~/.bashrc
    sed -i "s/alias cp='cp -i'//g" ~/.bashrc
    sed -i "s/alias rm='rm -i'//g" ~/.bashrc
    #
    # facilitate creation of ~/matlab/startup.m
    export FREESURFER_HOME=$HOME/freesurfer-7.1.0
    source ${FREESURFER_HOME}/SetUpFreeSurfer.sh
    #
    # provide write permissions
    chmod a+w $HOME
    chmod -R a+w $HOME/luigi-pnlpipe
    chmod -R a+w $HOME/pnlpipe
    
    
%environment
    #
    # set up bashrc i.e shell
    export HOME=/home/pnlbwh/
    export USER=`whoami`
    export LANG=en_US.UTF-8
    #
    # miniconda3 pnlpipe3
    export CONDA_SHLVL=2
    export CONDA_PROMPT_MODIFIER=(pnlpipe3)
    export CONDA_EXE=/home/pnlbwh/miniconda3/bin/conda
    export _CE_CONDA=
    export CONDA_PREFIX_1=/home/pnlbwh/miniconda3
    export CONDA_PREFIX=/home/pnlbwh/miniconda3/envs/pnlpipe3
    export CONDA_PYTHON_EXE=/home/pnlbwh/miniconda3/bin/python
    export CONDA_DEFAULT_ENV=pnlpipe3
    export PATH=/home/pnlbwh/miniconda3/envs/pnlpipe3/bin:/home/pnlbwh/miniconda3/condabin:$PATH
    #
    # pnlpipe software
    export PNLPIPE_SOFT=$HOME/pnlpipe/soft_dir
    cd $PNLPIPE_SOFT
    for d in `find . -name env.sh`; do source ${PNLPIPE_SOFT}/$d; done
    cd $HOME
    export FSLDIR=$HOME/fsl-6.0.1
    source $FSLDIR/etc/fslconf/fsl.sh
    export PATH=$FSLDIR/bin:$PATH
    export FREESURFER_HOME=$HOME/freesurfer-7.1.0
    source ${FREESURFER_HOME}/SetUpFreeSurfer.sh
    export PATH=$HOME/pnlNipype/scripts:$HOME/pnlNipype/exec:$HOME/CNN-Diffusion-MRIBrain-Segmentation/pipeline:$PATH 
    export PYTHONPATH=$HOME/luigi-pnlpipe:$PYTHONPATH