factor.def

#Bootstrap: shub
#From: tikk3r/lofar-grid-hpccloud:lofar_sksp
Bootstrap: localimage
From: lofar.sif

%files
    remotecommand.patch /opt/lofar


%post
	# Set-up environment
	export LC_ALL=C
	export INSTALLDIR=/opt/lofar

	# Make aware of existing libraries in image
	source ${INSTALLDIR}/init.sh

	# Install specific version of aplpy
	# version 2 depends on python3 which breaks compatibility
	pip install --upgrade 'aplpy>=1,<2'

        pip uninstall -y Jinja2
        pip install Jinja2==2.10.1

	# Link DPPP into lofar folder
	ln -s ${INSTALLDIR}/DPPP/bin/DPPP ${INSTALLDIR}/lofar/bin/DPPP

	# Download factor source
	git clone https://github.com/lofar-astron/factor.git ${INSTALLDIR}/factor
	cd ${INSTALLDIR}/factor

        # SM: patch script make_selfcal_images.py for logging issue
        #patch -i /opt/lofar/make_selfcal_images.patch factor/scripts/make_selfcal_images.py
	patch -i /opt/lofar/remotecommand.patch /opt/lofar/lofar/lib64/python2.7/site-packages/lofarpipe/support/remotecommand.py

	# Install factor
	python setup.py install

	# Missing dependencies after install
	# checkfactor
	pip install shapely

%runscript
	exec bash "$@"

%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