Makefile.nongs

# ===========================================================================
#
#                            PUBLIC DOMAIN NOTICE
#               National Center for Biotechnology Information
#
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#  terms of the United States Copyright Act.  It was written as part of
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#setenv BOOST_PATH /netopt/ncbi_tools64/boost-1.62.0-ncbi1

ifdef BOOST_PATH
BOOST_INCL := -I $(BOOST_PATH)/include
BOOST_LIB := -L $(BOOST_PATH)/lib
endif


CC = c++ -std=c++11
CFLAGS = -D NO_NGS -Wall -Wno-format-y2k  -pthread -fPIC -O3 -finline-functions -fstrict-aliasing \
         -fomit-frame-pointer -msse4.2 $(BOOST_INCL) \
         
LIBS = -Wl,-Bstatic $(BOOST_LIB) \
       -lboost_program_options \
       -lboost_iostreams \
       -lboost_regex \
       -lboost_timer \
       -lboost_chrono \
       -lboost_system \
       -Wl,-Bdynamic -lrt -ldl -lm  -lpthread -lz

%.o: %.cpp
	$(CC) -c -o $@ $< $(CFLAGS)

all: skesa 

glb_align.o: glb_align.hpp Makefile.nongs

skesa.o: common_util.hpp concurrenthash.hpp readsgetter.hpp ngs_includes.hpp counter.hpp graphdigger.hpp assembler.hpp KmerInit.hpp DBGraph.hpp Integer.hpp LargeInt.hpp LargeInt1.hpp LargeInt2.hpp Model.hpp config.hpp Makefile.nongs
skesa: skesa.o glb_align.o
	$(CC) -o $@ $^ $(LIBS)