seqio/Makefile at master · sean-dougherty/seqio · GitHub

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CXXFLAGS=-g -std=c++11 -Wall -Werror
#CXXFLAGS=-O2 -std=c++11 -Wall -Werror
shared_flags=-fPIC -shared
includes=-I src -I src/seqio

src_seqio=$(shell ls src/seqio/*.cpp src/util.cpp)
inc_seqio=$(shell ls src/seqio/*.h src/seqio/*.hpp)
target_seqio=bld/lib/libseqio.so

src_pna=$(shell ls src/tools/pna/*.cpp src/util.cpp)
target_pna=bld/bin/pna

src_fasta=$(shell ls src/tools/fasta/*.cpp)
inc_fasta=src/tools/fasta/kseq.h
target_fasta=bld/bin/fasta

src_test=$(shell ls test/src/*.cpp)
inc_test=$(shell ls test/src/*.h test/src/*.hpp)
target_test=bld/bin/test

target_doc=bld/doc/api/html/index.html

public_inc=$(shell ls src/seqio/seqio.h)


.PHONY: all clean doc lib test fasta pna

all: lib fasta pna test

lib: $(target_seqio)
fasta: $(target_fasta)
pna: $(target_pna)
doc: $(target_doc)
test: $(target_test)

$(target_seqio): $(src_seqio) $(inc_seqio) Makefile
	@mkdir -p $(@D)
	$(CXX) $(CXXFLAGS) $(src_seqio) $(includes) $(shared_flags) -o $@ -lz -lrt

$(target_pna): $(src_pna) $(inc_seqio) $(target_seqio) Makefile
	@mkdir -p $(@D)
	$(CXX) $(CXXFLAGS) $(src_pna) $(includes) -o $@ -lseqio -L bld/lib -lrt -lboost_filesystem -lboost_system

$(target_fasta): $(src_fasta) $(inc_seqio) $(target_seqio) Makefile
	@mkdir -p $(@D)
	$(CXX) $(CXXFLAGS) $(src_fasta) $(includes) -o $@ -lseqio -L bld/lib -lz -lrt -lboost_filesystem -lboost_system

$(target_test): $(src_test) $(inc_seqio) $(target_seqio) Makefile
	@mkdir -p $(@D)
	$(CXX) $(CXXFLAGS) $(src_test) $(includes) -o $@ -lseqio -L bld/lib -lrt

install:
	cp $(target_seqio) /usr/local/lib
	cp $(target_pna) /usr/local/bin
	cp $(target_fasta) /usr/local/bin
	cp $(public_inc) /usr/local/include
	ldconfig

clean:
	rm -rf bld

$(target_doc): $(target_seqio)
	mkdir -p bld/doc/api
	doxygen doc/doxygen/c-api.config