# Description: Coevolution Analysis using Protein Sequences
# URL: http://bioinf.gen.tcd.ie/~faresm/software/software.html
# Maintainer: Petar Petrov, slackalaxy at gmail dot com
# Depends on: gsl bpp1-phyl

name=caps-coev
version=2.0
release=2
source=(https://raw.githubusercontent.com/slackalaxy/sources/main/caps2_src.zip
	01_caps_verbose.patch 02_caps_sort_input.patch)

build() {
	cd caps${version}_src
	
	# build fails with gcc 12
	sed -i "s:CC=g++ -g:CC=g++-5 -g -std=c++11:" Makefile
		
	# This is needed for vCAPS to find its libraries at runtime. Thanks Urchlay!
	LIBDIRPATH="-Wl,-rpath,/usr/lib/Bpp1"
	
	# Use our CFLAGS and the custom (legacy) lib path
	sed -i "s:CFLAGS=:CFLAGS=$CFLAGS $LIBDIRPATH:" Makefile

	# Find the legacy bpp libraries
	sed -i "s:-lbpp-phyl:-L/usr/lib/Bpp1 -lbpp-phyl:g" Makefile
	sed -i "s:-lbpp-numcalc:-L/usr/lib/Bpp1 -lbpp-numcalc:g" Makefile
	sed -i "s:-lbpp-utils:-L/usr/lib/Bpp1 -lbpp-utils:g" Makefile
	sed -i "s:-lbpp-seq:-L/usr/lib/Bpp1 -lbpp-seq:g" Makefile

	# Rename the produced executable 
	sed -i "s:-o caps:-o vCAPS:" Makefile

	# Use our patches
	patch -p1 -i $SRC/01_caps_verbose.patch
	patch -p1 -i $SRC/02_caps_sort_input.patch

	make all

	# Install the binary produced from our patched source, as "vCAPS"
	install -D -m755 vCAPS $PKG/usr/bin/vCAPS

	mkdir -p $PKG/usr/share/$name
	cp -a sample structures trees TLR1.fa.out $PKG/usr/share/$name
}