apptainer.def

Bootstrap: docker
From: python:3.12-slim
Stage: builder

%post
    apt update && apt -y install git build-essential cmake wget

    # Install the latest dcm2niix release from the base repository (= typically outdated)
    # apt update && apt -y install dcm2niix

    # Install the latest dcm2niix from sources
    git clone https://github.com/rordenlab/dcm2niix.git
    cd dcm2niix; mkdir build && cd build
    cmake -DZLIB_IMPLEMENTATION=Cloudflare -DUSE_JPEGLS=ON -DUSE_OPENJPEG=ON ..
    make install

    # Install the latest miniconda (needed for FSL install)
    mkdir -p /opt/miniconda3
    wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O /opt/miniconda3/miniconda.sh
    bash /opt/miniconda3/miniconda.sh -b -u -p /opt/miniconda3
    export PATH=/opt/miniconda3/bin:$PATH
    conda init bash
    conda config --set channel_priority strict      # Needed for pngappend, see: https://github.com/NeuroDesk/neurocontainers/pull/598
    . /root/.bashrc

    # Create a conda env and install FSL tools needed for (me)deface and slicereport. NB: Keep the version the same as the Docker base image
    conda create -n fsl python=3.10
    conda install -n fsl -c https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/ -c conda-forge fsl-libvis fsl-avwutils fsl-flirt

    # Pack the fsl environment into fsl.tar.gz and unpack it in /opt/fsl
    conda install -c conda-forge conda-pack
    conda pack -n fsl
    mkdir /opt/fsl && tar -xzf fsl.tar.gz -C /opt/fsl
    /opt/fsl/bin/conda-unpack

    # Clone bidscoin
    git clone https://github.com/Donders-Institute/bidscoin.git /opt/bidscoin
    cd /opt/bidscoin
    rm -rf docs tests .git


Bootstrap: docker
From: python:3.12-slim
Stage: final

%help
    This BIDScoin Apptainer image includes:

    * Debian stable,
    * BIDScoin (see https://bidscoin.readthedocs.io)
    * The latest versions of dcm2niix, pydeface, spec2nii and some FSL tools

    The general form to run BIDScoin commands is:

        apptainer exec bidscoin.sif <bidscoin_tool> <bidscoin_tool_args>

    For more information run:

        apptainer run bidscoin.sif

    NB: 1) To run GUI applications (such as the bidseditor) you probably need to run `xhost +` first
        2) In the commands above, Singularity users should replace `apptainer` with `singularity`
        3) The current image does not include the Freesurfer/synthstrip software (needed for `skullstrip`)

%files from builder
    # /opt/bidscoin /opt/bidscoin     # Only needed for pip install from github
    /usr/local/bin/dcm2niix /usr/local/bin/dcm2niix
    /opt/fsl /opt/fsl

%environment
    export FSLDIR=/opt/fsl FSLOUTPUTTYPE=NIFTI_GZ
    export PATH=$PATH:/opt/fsl/bin
    export PIP_NO_CACHE_DIR=off

%post
    # Install curl (sometimes needed by dcm2niix) and pigz (to speed up dcm2niix)
    apt update && apt -y --no-install-recommends install pigz curl

    # Pre-install essential packages
    # NOTE: PyQt is installed as Debian package to solve dependencies issues occurring when installed with pip
    apt -y --no-install-recommends install python3-pyqt6 build-essential libgl1 libxcb-cursor0 dbus qt6-wayland && apt clean     # Add build-essential for newer python:3-slim base images (pip needs gcc and wayland support is not yet provided for)

    # Install BIDScoin
    # pip install /opt/bidscoin[spec2nii2bids,deface]
    # pip install bidscoin[spec2nii2bids,deface]==VERSION
    pip install bidscoin[spec2nii2bids,deface]

    # Uncomment the line below if you get errors like: ImportError: libQt5Core.so.5: cannot open shared object file: No such file or directory
    # strip --remove-section=.note.ABI-tag /usr/lib/x86_64-linux-gnu/libQt5Core.so.5
    # strip --remove-section=.note.ABI-tag libQt6Core.so.6

    # Finally, create the necessary links and cache to the most recent shared libraries (= best practise)
    ldconfig

%runscript
    exec bidscoin