Singularity.def

BootStrap: library
From: ubuntu:20.04

%environment
export PATH=/bioinf-tools/:/bioinf-tools/enaBrowserTools/python3/:$PATH
export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
export LANG=C.UTF-8


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


%post
    #_____________________ setup $PATH _______________________#
    export PATH=/bioinf-tools/:/bioinf-tools/enaBrowserTools/python3/:$PATH
    export LANG=C.UTF-8

    /viridian/install_dependencies.sh /bioinf-tools
    cd /viridian
    tox
    python3 -m pip install .


%runscript
    viridian "$@"