# Description: PAML: Phylogenetic Analysis by Maximum Likelihood
# URL: http://abacus.gene.ucl.ac.uk/software/paml.html
# Maintainer: Petar Petrov, slackalaxy at gmail dot com

name=paml
version=4.10.6
release=1
source=(https://github.com/abacus-gene/paml/archive/v${version}/$name-$version.tar.gz
	https://awarnach.mathstat.dal.ca/~joeb/PAML_lab/resources/pamlDEMO_2023.pdf
	https://awarnach.mathstat.dal.ca/~joeb/PAML_lab/resources/Bielawski_book_chapter.pdf)

build() {
	cd $name-$version/src
	
	# Use our CFLAGS
	sed -i "/^C.*.*FLAGS/s/=/+=/" Makefile
	make -f Makefile

	# These are the main components, and most likely this will be all you
	# need. Check the next sections if you need some optional components.
	# They will be installed to /usr/lib/paml in case you want them.
	install -D -m 755 baseml $PKG/usr/bin/baseml
	install -D -m 755 basemlg $PKG/usr/bin/basemlg
	install -D -m 755 chi2 $PKG/usr/bin/chi2
	install -D -m 755 codeml $PKG/usr/bin/codeml
	install -D -m 755 evolver $PKG/usr/bin/evolver
	install -D -m 755 mcmctree $PKG/usr/bin/mcmctree
	install -D -m 755 pamp $PKG/usr/bin/pamp
	install -D -m 755 yn00 $PKG/usr/bin/yn00

	# Evolver variations
	cc $CFLAGS -fcommon -DCodonNSbranches -o evolverNSbranches evolver.c tools.c -lm
	cc $CFLAGS -fcommon -DCodonNSsites -o evolverNSsites evolver.c tools.c -lm
	cc $CFLAGS -fcommon -DCodonNSbranchsites -o evolverNSbranchsites evolver.c tools.c -lm

	install -D -m 755 evolverNSbranches $PKG/usr/lib/$name/evolverNSbranches
	install -D -m 755 evolverNSbranchsites $PKG/usr/lib/$name/evolverNSbranchsites
	install -D -m 755 evolverNSsites $PKG/usr/lib/$name/evolverNSsites

	# NEB, BEB and BranchSite
	cd $SRC/$name-$version/Technical/Simulation/Codon
	cc $CFLAGS -fcommon -DNEB -o PositiveSitesNEB PositiveSites.c -lm
	cc $CFLAGS -fcommon -DBEB -o PositiveSitesBEB PositiveSites.c -lm
	cc $CFLAGS -fcommon -DBranchSite -o PositiveSitesBS  PositiveSites.c -lm

	install -D -m755 PositiveSitesBEB $PKG/usr/lib/$name/PositiveSitesBEB
	install -D -m755 PositiveSitesBS $PKG/usr/lib/$name/PositiveSitesBS
	install -D -m755 PositiveSitesNEB $PKG/usr/lib/$name/PositiveSitesNEB
	install -D -m 644 README.txt $PKG/usr/share/$name/MCcodonNS/README.txt
	cp -a codeml.ctl *.dat $PKG/usr/share/$name/MCcodonNS
	
	# Multiruns
	cd $SRC/$name-$version/Technical/Simulation/
	cc -o multiruns $CFLAGS -fcommon multiruns.c -lm
	install -D -m 755 multiruns $PKG/usr/lib/$name/multiruns
	install -D -m 644 multiruns.txt $PKG/usr/share/$name/Multiruns.txt

	# Include sample system files and example experimental data.
	cd $SRC/$name-$version
	cp -a dat examples $PKG/usr/share/$name
	cp -a doc/* $PKG/usr/share/$name
	cp -a Technical/Pt/eigenQREV.pdf $PKG/usr/share/$name
	cp $SRC/pamlDEMO_2023.pdf $PKG/usr/share/$name
	cp $SRC/Bielawski_book_chapter.pdf $PKG/usr/share/$name
}