apptainer build for deepdicomsort-dcm2niix-fsl on rockylinux8

deepdicomsort-dcm2-fsl.def

Bootstrap: docker
From: rockylinux:8.9

%post
        dnf -y update
        dnf -y install epel-release curl wget git file bzip2 which libmng libpng12 libSM gtk2 mesa-dri-drivers mesa-libGL-devel
        dnf config-manager --set-enabled powertools
        dnf -y install R
        # R brings in openblas and dependencies
        dnf -y install make cmake
        dnf module -y install python36
        dnf -y install openjpeg2-devel libstdc++-static

        # install dcm2niix
        cd /opt
        git clone https://github.com/rordenlab/dcm2niix.git
        cd /opt/dcm2niix/
        git checkout tags/v1.0.20190720
        #git clone --depth 1 --branch v1.0.20190720 https://github.com/rordenlab/dcm2niix.git
        mkdir /opt/dcm2niix/build && cd /opt/dcm2niix/build
        # drop zlib and use pigz instead since cloudflare zlib was not found
        #cmake -DZLIB_IMPLEMENTATION=Cloudflare -DUSE_JPEGLS=ON -DUSE_OPENJPEG=ON ..
        cmake -DUSE_JPEGLS=ON -DUSE_OPENJPEG=ON ..
        make -j$(nproc)


        # install fsl 5.0.9
        ### note this is grabbing the older installer per their site for versions < 6.x 
        ### 6.0.3 is apparently as far back as you can go with python fslinstaller.py --listversions
        cd /opt
        wget https://git.fmrib.ox.ac.uk/fsl/installer/-/raw/master/fslinstaller.py?inline=false -O fslinstaller.py \
        && python3 /opt/fslinstaller.py -d /usr/local/fsl -V 6.0.3 -p

        # setup FSL environment
        export FSLDIR="/usr/local/fsl" 
        export PATH="$FSLDIR/bin/:$PATH" 
	      export FSLMULTIFILEQUIT=TRUE 
	      export FSLGECUDAQ=cuda.q 
	      export FSLTCLSH="$FSLDIR/bin/fsltclsh" 
	      export FSLWISH="$FSLDIR/bin/fslwish" 
	      export FSLOUTPUTTYPE=NIFTI_GZ

        # apply patch
        $FSLDIR/fslpython/bin/conda install -y -n fslpython -c conda-forge deprecation==1.*

        ## dcmsorter 
        cd /opt
        git clone https://github.com/ErasmusMC-NeuroOnco/DeepDicomSort.git
        cd /opt/DeepDicomSort
        python3 -m pip install -r requirements.txt