uc2-factor.def

Bootstrap: localimage
From: factor.sif

%files
    cwl /opt/lofar
    templates /opt/lofar
#    prefactor /opt/lofar

%environment
    . $INSTALLDIR/init.sh

#%post -c /bin/bash
%post
        # install cwltool
        pip install cwltool

        #SM working: yum install -y nodejs nodejs-dev npm libssl-dev
        #SM commented out:apt-get clean
        curl -sL https://rpm.nodesource.com/setup_10.x | bash -
	yum install -y nodejs

        #SM: install prefactor
        git clone https://github.com/lofar-astron/prefactor.git /opt/lofar/prefactor
	cd /opt/lofar/prefactor
	git checkout 92fc0339b31a56ea9aeb49ae84ee89c334a0c543

%runscript
	#!/bin/bash
	all_args=()
	for ARGUMENT in "$@"
	do
    		KEY=$(echo $ARGUMENT | cut -f1 -d=)
    		VALUE=$(echo $ARGUMENT | cut -f2 -d=)
    		arg="--${KEY} ${VALUE}"
    		all_args+=( ${arg} )
	done
	cwltool --preserve-entire-environment /opt/lofar/cwl/uc2.cwl "${all_args[@]}"

%help
	Factor version 2.0
	Provides:
		runfactor <parset>
		checkfactor <parset>
		archivefactor <parset> <output dir>
		unarchivefactor <archive dir> <output dir>

	Command example:
	singularity exec -B /var/scratch/${USER} factor.simg runfactor factor.parset