palm-alpha119-octave-440.def

Bootstrap: docker
From: gnuoctave/octave:4.4.0

%post
    # installing required dependencies
    chmod 777 /tmp
    export DEBIAN_FRONTEND=noninteractive
    apt update -y
    apt install -y curl git nano tar vim wget
    octave --eval 'pkg install -forge image'

    # setting up PALM
    wget https://s3-us-west-2.amazonaws.com/andersonwinkler/palm/palm-alpha119.tar.gz
    tar -xzf palm-alpha119.tar.gz \
        && rm palm-alpha119.tar.gz

    cat << EOF >> /usr/local/share/octave/site/m/startup/octaverc
addpath('/palm-alpha119/palm')
EOF

    # recompiling .mex files per https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=fsl;f141e60f.1903
    cd /palm-alpha119/fileio/\@file_array/private/ \
        && rm -f *.mex \
        && mkoctfile --mex mat2file.c \
        && mkoctfile --mex init.c \
        && mkoctfile --mex file2mat.c

    # This step fails for miniz.c
    cd /palm-alpha119/fileio/\@gifti/private/ \
        && rm -f *.mex \
        && mkoctfile --mex zstream.c
        # && mkoctfile --mex miniz.c

    cd /palm-alpha119/fileio/\@nifti/private/ \
        && rm -f *.mex \
        && mkoctfile --mex nifti_stats_mex.c \
        && mkoctfile --mex nifti_stats.c

    cd /palm-alpha119/fileio/\@xmltree/private/ \
        && rm -f *.mex \
        && mkoctfile --mex xml_findstr.c

    cd /palm-alpha119/fileio/extras/ \
        && rm -f *.mex \
        && mkoctfile --mex spm_existfile.c

%environment
    export PATH=/palm-alpha119:$PATH