Models:
Samuel Callahan
SCallahan/
CNN-Diffusion-MRIBrain
0
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[e918fa]: / Singularity

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Bootstrap: docker

From: centos:7.5.1804



%labels

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



%help

    https://github.com/pnlbwh/CNN-Diffusion-MRIBrain-Segmentation 



    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 wget file bzip2 which vim git make libstdc++-static mesa-libGL bc tcsh libSM && \

    yum clean all && \

    #

    # 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 && \

    #

    # 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/ && \

    source miniconda3/bin/activate && \

    #

    # create conda environment

    git clone https://github.com/pnlbwh/CNN-Diffusion-MRIBrain-Segmentation.git && \

    conda env create -f CNN-Diffusion-MRIBrain-Segmentation/environment_cpu.yml && \

    #

    # install dcm2niix

    conda install -c anaconda cmake && \

    git clone https://github.com/rordenlab/dcm2niix.git && \

    cd dcm2niix && mkdir build && cd build && \

    cmake .. && make -j4 && \

    mv bin $HOME/dcmbin/ && \

    cd && rm -rf $HOME/dcm2niix && \

    #

    # clean up

    rm -rf $HOME/.cache/pip/ $HOME/Miniconda3-latest-Linux-x86_64.sh && \

    conda clean -y --all && \

    #

    # change permission so a user is able to run tests

    # to be able to run tests, increase tmpfs size in /etc/singularity/singularity.conf

    # sessiondir max size = 8000

    chmod -R o+w /home/pnlbwh/CNN-Diffusion-MRIBrain-Segmentation/tests/

    

%environment

    #

    # set up bashrc i.e shell

    # dmri_seg conda environment

    export CONDA_SHLVL=2

    export CONDA_PROMPT_MODIFIER=(dmri_seg)

    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/dmri_seg

    export CONDA_PYTHON_EXE=/home/pnlbwh/miniconda3/bin/python

    export CONDA_DEFAULT_ENV=dmri_seg

    export PATH=/home/pnlbwh/miniconda3/envs/dmri_seg/bin:/home/pnlbwh/miniconda3/condabin:$PATH

    #

    # setup FSL

    export FSLDIR=/home/pnlbwh/fsl-6.0.1

    source $FSLDIR/etc/fslconf/fsl.sh

    export PATH=$FSLDIR/bin:$PATH

    #

    # add dcm2niix and dwi_masking.py to PATH

    export PATH=/home/pnlbwh/dcmbin:/home/pnlbwh/CNN-Diffusion-MRIBrain-Segmentation/pipeline:$PATH

    #

    # setup ANTSPATH

    export ANTSPATH=/home/pnlbwh/miniconda3/envs/dmri_seg/bin