Singularity.def

BootStrap: library
From: ubuntu:20.04

%environment
PERL5LIB=/bioinf-tools/vcftools-0.1.15/install/share/perl/5.30.0/:/bioinf-tools/cortex/scripts/analyse_variants/bioinf-perl/lib:/bioinf-tools/cortex/scripts/calling/:$PERL5LIB
export PERL5LIB
PATH=/bioinf-tools/:/bioinf-tools/cortex/bin/:/bioinf-tools/cortex/scripts/analyse_variants/seq-align/bin/:/bioinf-tools/vcftools-0.1.15/install/bin:/bioinf-tools/enaBrowserTools/python3:/clockwork/scripts/:$PATH
NXF_VER=22.10.0

%setup
    mkdir $SINGULARITY_ROOTFS/clockwork
    rsync -a python nextflow scripts $SINGULARITY_ROOTFS/clockwork/

%post
    #_____________________ setup $PATH _______________________#
    export PATH=/bioinf-tools/:/bioinf-tools/cortex/bin/:/bioinf-tools/cortex/scripts/analyse_variants/seq-align/bin/:/bioinf-tools/vcftools-0.1.15/install/bin:/bioinf-tools/enaBrowserTools/python3:/clockwork/scripts/:$PATH
    export PERL5LIB=/bioinf-tools/vcftools-0.1.15/install/share/perl/5.30.0/:/bioinf-tools/cortex/scripts/analyse_variants/bioinf-perl/lib:/bioinf-tools/cortex/scripts/calling/:$PERL5LIB
    export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
    export NXF_VER=22.10.0

    #_________________ install dependencies __________________#
    /clockwork/scripts/install_dependencies.sh /bioinf-tools


    #______________________ clockwork python ________________#
    cd /clockwork/python
    python3 setup.py test
    python3 setup.py install
    service mysql stop
    apt remove -y mysql-server
    apt autoremove -y


%labels
    Version 0.12.5


%runscript
    clockwork "$@"