Apptainer

Bootstrap: docker
From: ubuntu:22.04
Stage: base

%environment
    export DEBIAN_FRONTEND=noninteractive

%post
    export DEBIAN_FRONTEND=noninteractive && \
    apt-get update && \
    apt-get install -y build-essential ftp tcsh wget git jq \
    python3 python3-pip gfortran tcl wish unzip dc bc \
    libglu1-mesa libglib2.0-0
    wget https://ftp.gnu.org/gnu/gawk/gawk-4.2.1.tar.gz && \
    tar -xzf gawk-4.2.1.tar.gz && \
    cd gawk-4.2.1 && \
    ./configure && \
    make && \
    make install && \
    cd .. && \
    rm -rf gawk-4.2.1.tar.gz gawk-4.2.1

Bootstrap: docker
From: ubuntu:22.04
Stage: fsl

%files from base
    / /

%post
    export DEBIAN_FRONTEND=noninteractive && \
    apt-get install -y libgl1-mesa-dev && \
    wget https://fsl.fmrib.ox.ac.uk/fsldownloads/fslinstaller.py && \
    python3 fslinstaller.py -d /opt/fsl

Bootstrap: docker
From: ubuntu:22.04
Stage: freesurfer

%files from base
    / /

%post
    export DEBIAN_FRONTEND=noninteractive && \
    wget https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.3.2/freesurfer_ubuntu22-7.3.2_amd64.deb && \
    apt install -y ./freesurfer_ubuntu22-7.3.2_amd64.deb && \
    rm freesurfer_ubuntu22-7.3.2_amd64.deb

Bootstrap: docker
From: ubuntu:22.04
Stage: connectome_workbench

%files from base
    / /

%post
    cd /opt && \
    wget https://www.humanconnectome.org/storage/app/media/workbench/workbench-linux64-v1.5.0.zip && \
    unzip workbench-linux64-v1.5.0.zip && \
    rm workbench-linux64-v1.5.0.zip

Bootstrap: docker
From: ubuntu:22.04
Stage: matlab_compiler_runtime

%files from base
    / /

%files
    tools/install_mcr.sh /opt/tools/

%post
    export MATLAB_VERSION=R2022a
    /opt/tools/install_mcr.sh

Bootstrap: docker
From: ubuntu:22.04
Stage: fdfp

%files from base
    / /

%files
    tools/FSLTransforms /opt/tools/
    tools/me_fmri /opt/tools/
    tools/refdir_extras /opt/tools/
    tools/updated_4dfp_scripts /opt/tools/
    tools/get_4dfp.sh /opt/tools/
    tools/install_4dfp.sh /opt/tools/

%post
    /opt/tools/install_4dfp.sh

Bootstrap: docker
From: ubuntu:22.04
Stage: julia

%files from base
    / /

%post
    cd /opt && \
    wget https://julialang-s3.julialang.org/bin/linux/x64/1.9/julia-1.9.3-linux-x86_64.tar.gz && \
    tar -xzf julia-1.9.3-linux-x86_64.tar.gz && \
    rm julia-1.9.3-linux-x86_64.tar.gz

Bootstrap: docker
From: ubuntu:22.04
Stage: final

%environment
    export MATLAB_VERSION=R2022a
    export DEBIAN_FRONTEND=noninteractive
    # fsl
    export FSLDIR=/opt/fsl
    export FSL_DIR=/opt/fsl
    export FSLOUTPUTTYPE=NIFTI_GZ
    export FSLMULTIFILEQUIT=TRUE
    export FSLTCLSH=${FSLDIR}/bin/tclsh
    export FSLWISH=${FSLDIR}/bin/wish
    export FSLGECUDAQ=cuda.q
    export FSL_LOAD_NIFTI_EXTENSIONS=0
    export FSL_SKIP_GLOBAL=0
    export PATH=${FSLDIR}/share/fsl/bin:${PATH}
    # freesurfer
    export FREESURFER_HOME=/usr/local/freesurfer/7.3.2
    export MNI_DIR=${FREESURFER_HOME}/mni
    export FSFAST_HOME=${FREESURFER_HOME}/fsfast
    export SUBJECTS_DIR=${FREESURFER_HOME}/user_subjects
    export PATH=${MNI_DIR}/bin:${PATH}
    export PATH=${FREESURFER_HOME}/tktools:${PATH}
    export PATH=${FSFAST_HOME}/bin:${PATH}
    export PATH=${FREESURFER_HOME}/bin:${PATH}
    # connectome workbench
    export WORKBENCH=/opt/workbench/bin_linux64
    export PATH=${WORKBENCH}:${PATH}
    # matlab compiler runtime
    export MCRROOT=/opt/mcr_runtime/v912
    # 4dfp
    export REFDIR=/opt/4dfp/refdir
    export RELEASE=/opt/4dfp/bin
    export PATH=${RELEASE}:${PATH}
    # julia
    export PATH=/opt/julia/bin:${PATH}
    # NORDIC
    export NORDIC=/opt/nordic
    export PATH=${NORDIC}:${PATH}


%setup
    ./tools/install_nordic.sh

%files from base
    / /

%files from fsl
    /opt/fsl /opt/

%files from freesurfer
    /usr/local/freesurfer /usr/local/

%files from connectome_workbench
    /opt/workbench /opt/

%files from matlab_compiler_runtime
    /opt/tools/pkg/mcr_runtime /opt/

%files from fdfp
    /opt/tools/bin /opt/4dfp/
    /opt/tools/pkg/refdir /opt/4dfp/

%files from julia
    /opt/julia-1.9.3 /opt/julia

%files
    me_pipeline /opt/processing_pipeline/
    extern/warpkit /opt/processing_pipeline/extern/
    LICENSE /opt/processing_pipeline/
    MANIFEST.in /opt/processing_pipeline/
    pyproject.toml /opt/processing_pipeline/
    README.md /opt/processing_pipeline/
    setup.cfg /opt/processing_pipeline/
    setup.py /opt/processing_pipeline/

%post
    # add symlink for msm
    export FSLDIR=/opt/fsl
    ln -s ${FSLDIR}/bin/msm ${FSLDIR}/share/fsl/bin/msm
    # add libjulia to ldconfig
    echo "/opt/julia/lib" >> /etc/ld.so.conf.d/julia.conf && ldconfig
    # add nordic
    cd /opt/ && wget https://github.com/vanandrew/NORDIC_Raw/releases/download/1.0/nordic-R2022a.zip && \
    unzip nordic-R2022a.zip && rm nordic-R2022a.zip
    export NORDIC=/opt/nordic
    chmod 755 ${NORDIC}/run_NORDIC_main.sh
    chmod 755 ${NORDIC}/NORDIC_main
    # for 4dfp refdir make sure data is readable for all users
    export REFDIR=/opt/4dfp/refdir
    chmod -R 755 ${REFDIR}
    export PATH=/opt/julia/bin:${PATH}
    # install pipeline and warpkit
    cd /opt/processing_pipeline && \
    # upgrade pip before install
    python3 -m pip install pip --upgrade && \
    python3 -m pip install -e ./\[dev\] -v --config-settings editable_mode=strict && \
    python3 -m pip install -e ./extern/warpkit -v --config-settings editable_mode=strict

%runscript
    exec run_pipeline $@