test.makefile

PREFIX:= /usr/local/

DamMet: dammet_dam_params.cpp myargparser.cc nlopt-2.5.0/install/lib/libnlopt.a htslib/libhts.a
	g++  -O3  dammet_dam_params.cpp myargparser.cc ./htslib/libhts.a nlopt-2.5.0/install/lib/libnlopt.a -std=c++14 -I nlopt-2.5.0/install/include  -I./htslib/ -lz -lm -lbz2 -llzma -o DamMet -lpthread -lcurl
	# g++  -O3  deammeth.cc myargparser.cc ./htslib/libhts.a -std=c++11 -I./htslib/ -lz -lm -lbz2 -llzma -lnlopt_cxx -o DamMet -lpthread

nlopt-2.5.0/install/lib/libnlopt.a: v2.5.0.tar.gz
	cd nlopt-2.5.0/ && mkdir -p build/  && cd build/ && cmake -DCMAKE_INSTALL_PREFIX=../install -DNLOPT_OCTAVE=Off -DNLOPT_MATLAB=Off -DNLOPT_GUILE=Off -DBUILD_SHARED_LIBS=OFF -DCMAKE_INSTALL_LIBDIR=../install/lib .. && make && make install && cd ../..

v2.5.0.tar.gz:
	wget https://github.com/stevengj/nlopt/archive/v2.5.0.tar.gz
	tar xf v2.5.0.tar.gz

htslib/libhts.a:
	git clone https://github.com/samtools/htslib.git
	cd htslib  && make && cd ../
## cd htslib && autoheader && autoconf && ./configure && make -j2 && cd ../
.PHONY: install clean

install: DamMet
	mkdir -p ${PREFIX}/bin
	cp DamMet ${PREFIX}/bin


clean:
	rm -f DamMet
	rm -rf nlopt-2.5.0/
	rm -rf v2.5.0.tar.gz
	rm -rf htslib