singularity-ss-noddi.def

Bootstrap: docker
From: ubuntu:focal

%labels
    AUTHOR siya sherif GIGA-CRC ivi ULiege 
    noddi-singularity version 1.0

    matlab verison 2020b

    using NODDI_toolbox_v1.05 : Gary Zang (UCL) http://mig.cs.ucl.ac.uk/index.php?n=Tutorial.NODDImatlab
     

%setup
	mkdir -p /opt/ss_noddi

%files
    # if using local 
    # ss_noddi_App /opt/ss_noddi/

%post
    # upadate the packages 
    apt-get update -y
    DEBIAN_FRONTEND=noninteractive apt-get -y install \
        wget unzip zip git openjdk-8-jre xvfb
    apt-get clean

    # MATLAB Compiled runtime
    # create folder 
    mkdir /MCR 
    # get file 
    wget -nv -P /MCR https://ssd.mathworks.com/supportfiles/downloads/R2020b/Release/5/deployment_files/installer/complete/glnxa64/MATLAB_Runtime_R2020b_Update_5_glnxa64.zip
    # unzip 
    unzip -q /MCR/MATLAB_Runtime_R2020b_Update_5_glnxa64.zip -d /MCR/MCR_R2020b_tmp
    # run install
    /MCR/MCR_R2020b_tmp/install -mode silent -agreeToLicense yes
    # delete residuals 
    rm -r /MCR/MCR_R2020b_tmp /MCR/MATLAB_Runtime_R2020b_Update_5_glnxa64.zip
    rmdir /MCR

    mkdir /In_fold && mkdir /Out_fold

    # get the noddi standalone from the git branch
    wget -nv -P /opt/ss_noddi https://github.com/CyclotronResearchCentre/NODDI_singularity/archive/refs/heads/main.zip
    unzip -q /opt/ss_noddi/main.zip -d /opt/ss_noddi_tmp
    cp -r /opt/ss_noddi_tmp/NODDI_singularity-main/ss_noddi_App/* /opt/ss_noddi/

    rm -rf /opt/ss_noddi/main.zip
    rm -rf /opt/ss_noddi_tmp

    chmod ugo+rx /opt/ss_noddi/ss_noddi
    chmod ugo+rx /opt/ss_noddi/run_ss_noddi.sh
%environment


%runscript
    bash /opt/ss_noddi/run_ss_noddi.sh \
    /usr/local/MATLAB/MATLAB_Runtime/v99 "$@"

%help 
    to run this container 
    singularity run --cleanenv \
    --bind <your_folder>:/In_fold \
    noddi-singularity.sif \
    /In_fold/<NODDI image> \
    /In_fold/<brain_mask> \
    /In_fold/<NODDI_roi> \
    /In_fold/<bval> \
    /In_fold/<bvecs> \
    /In_fold/<FittedParams.mat> \
    /in_fold/<output_map>