Singularity.def

BootStrap: debootstrap
OSVersion: focal
MirrorURL: http://us.archive.ubuntu.com/ubuntu/

%environment
export PATH=/bioinf-tools:$PATH
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib


%setup
    mkdir $SINGULARITY_ROOTFS/varifier
    rsync -a .ci/install_dependencies.sh MANIFEST.in varifier requirements.txt setup.py tests tox.ini $SINGULARITY_ROOTFS/varifier


%post
    #_____________________ setup $PATH _______________________#
    export PATH=/bioinf-tools/:$PATH
    export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib

    /varifier/install_dependencies.sh /bioinf-tools
    cd /varifier
    tox
    pip3 install .

%runscript
    varifier "$@"