# Description: GUIDe tree based AligNment ConfidencE
# URL: https://github.com/HaimAshk/GUIDANCE
# Maintainer: Petar Petrov, slackalaxy at gmail dot com
# Depends on: p5-bioperl ruby muscle prank

name=guidance
version=2.02
release=5
source=(https://github.com/HaimAshk/GUIDANCE/archive/refs/tags/guidance.v${version}.tar.gz
	$name.sh)

build() {
	cd GUIDANCE-$name.v${version}
	
	# clen up prebuilt executables
	rm programs/msa_set_score/msa_set_score
	rm www/Guidance/exec/msa_set_score
	
	# this makefile does not obey the above flags
	sed -i "s:CFLAGS = -c -Wall -O3:CFLAGS = -c ${CFLAGS}:g" programs/msa_set_score/makefile
	sed -i "s:LFLAGS = -g -Wall -O3:LFLAGS = -g ${CFLAGS}:g" programs/msa_set_score/makefile
	
	make
	
	find . -type f -iname '*.pl' -exec chmod 0755 {} \;
	#find . -type f -iname '*.pl' -exec sed -i 's#/usr/bin/perl#/usr/bin/env perl#g' {} \;
	find . -type f -iname 'Makefile' -exec rm -rf {} \;
	find . -type f -iname 'makefile' -exec rm -rf {} \;
	
	# Copy only what needed
	mkdir -p $PKG/usr/lib/$name
	rsync -av \
		--exclude='*.o' \
		--exclude='*.a' \
		--exclude='*.cpp' \
		--exclude='*.h' \
		--exclude='*.dep' \
		--exclude='*.c' \
		--exclude='*.sln' \
		--exclude='*.vcproj' \
		--exclude='*.vcxproj' \
		--exclude='*.suo' \
		--exclude='*.R' \
		--exclude='*.sh' \
		--exclude='Makefile' \
		--exclude='Makefile.*' \
		--exclude='makefile' \
		--exclude='README' \
		--exclude='ChangeLog' \
		--exclude='tests' \
		--exclude='*.tests*' \
       		--exclude='knownBugs' \
       		--exclude='*.html' \
       		--exclude='*.txt' \
	. $PKG/usr/lib/$name
	
	# Further cleanups
	rm -r $PKG/usr/lib/$name/programs/semphy/{profile,running,SEMPHYOptMat}
	find $PKG/usr/lib/$name -type d -empty -delete
	
	# Just in case
	find $PKG/usr/lib/$name -type f -iname '*.pl' -exec chmod 0755 {} \;
	find $PKG/usr/lib/$name -type f -iname '*.rb' -exec chmod 0755 {} \;
	chmod 0755 $PKG/usr/lib/$name/programs/isEqualTree/isEqualTree
	chmod 0755 $PKG/usr/lib/$name/programs/msa_set_score/msa_set_score
	chmod 0755 $PKG/usr/lib/$name/programs/removeTaxa/removeTaxa
	chmod 0755 $PKG/usr/lib/$name/programs/semphy/semphy
	
	install -D -m755 $SRC/$name.sh $PKG/usr/bin/$name
}