# Description: RAxML - Randomized Axelerated Maximum Likelihood
# URL: https://cme.h-its.org/exelixis/web/software/raxml/index.html
# Maintainer: Petar Petrov, slackalaxy at gmail dot com
# Depends on: openmpi

name=raxml
version=8.2.13
release=1
source=(https://github.com/stamatak/standard-RAxML/archive/v${version}/standard-RAxML-${version}.tar.gz)

build() {
	cd standard-RAxML-$version
	
	# Sequential version
	cp Makefile.gcc Makefile
	sed -i "/^CFLAGS/s/=/+=/" Makefile
	sed -i "s|raxmlHPC|raxml|g" Makefile
	make -f Makefile -j1
	install -D -m755 raxml $PKG/usr/bin/raxml

	# Openmpi version
	cp Makefile.MPI.gcc Makefile.MPI
	sed -i "/^CFLAGS/s/=/+=/" Makefile.MPI
	sed -i "s|raxmlHPC-MPI|raxml-MPI|g" Makefile.MPI
	make -f Makefile.MPI -j1
	install -D -m755 raxml-MPI $PKG/usr/bin/raxml-MPI

	# Copy the useful scripts
	mkdir -p $PKG/usr/share/$name
	cp -a usefulScripts $PKG/usr/share/$name

##########################################################################
### You are highly encouraged to try the other optimisations below for ###
### performance enhancements. Just uncomment the corresponding lines.  ###
##########################################################################

## Default sequential version
#make -f Makefile.gcc
#install -D -m755 raxmlHPC $PKG/usr/bin/raxmlHPC

#make -f Makefile.SSE3.gcc
#install -D -m755 raxmlHPC-SSE3 $PKG/usr/bin/raxmlHPC-SSE3

#make -f Makefile.AVX.gcc
#install -D -m755 raxmlHPC-AVX $PKG/usr/bin/raxmlHPC-AVX

## Pthreads version
#make -f Makefile.PTHREADS.gcc
#install -D -m755 raxmlHPC-PTHREADS $PKG/usr/bin/raxmlHPC-PTHREADS

#make -f Makefile.SSE3.PTHREADS.gcc
#install -D -m755 raxmlHPC-PTHREADS-SSE3 $PKG/usr/bin/raxmlHPC-PTHREADS-SSE3

#make -f Makefile.AVX.PTHREADS.gcc
#install -D -m755 raxmlHPC-PTHREADS-AVX $PKG/usr/bin/raxmlHPC-PTHREADS-AVX

## Default coarse-grain MPI version
#make -f Makefile.MPI.gcc
#install -D -m755 raxmlHPC-MPI $PKG/usr/bin/raxmlHPC-MPI

#make -f Makefile.SSE3.MPI.gcc
#install -D -m755 raxmlHPC-MPI-SSE3 $PKG/usr/bin/raxmlHPC-MPI-SSE3

#make -f Makefile.AVX.MPI.gcc
#install -D -m755 raxmlHPC-MPI-AVX $PKG/usr/bin/raxmlHPC-MPI-AVX

## Hybrid MPI/Pthreads version
#  Before using this version, please read this paper here:
#  http://sco.h-its.org/exelixis/pubs/Exelixis-RRDR-2010-3.pdf
#  and look at these slides:
#  http://sco.h-its.org/exelixis/resource/doc/Phylo100225.pdf
#make -f Makefile.HYBRID.gcc
#install -D -m755 raxmlHPC-HYBRID $PKG/usr/bin/raxmlHPC-HYBRID

#make -f Makefile.SSE3.HYBRID.gcc
#install -D -m755 raxmlHPC-HYBRID-SSE3 $PKG/usr/bin/raxmlHPC-HYBRID-SSE3

#make -f Makefile.AVX.HYBRID.gcc
#install -D -m755 raxmlHPC-HYBRID-AVX $PKG/usr/bin/raxmlHPC-HYBRID-AVX
}