This patch let's Delly use the system versions of htslib and boost. Patch by Roel Janssen --- a/Makefile 2016-03-16 13:08:49.936706607 +0100 +++ b/Makefile 2016-03-16 13:09:12.351706212 +0100 @@ -9,8 +9,8 @@ # Flags CXX=g++ -CXXFLAGS += -isystem ${SEQTK_ROOT} -isystem ${BOOST_ROOT} -pedantic -W -Wall -Wno-unknown-pragmas -LDFLAGS += -L${SEQTK_ROOT} -L${BOOST_ROOT}/stage/lib -lboost_iostreams -lboost_filesystem -lboost_system -lboost_program_options -lboost_date_time +CXXFLAGS += -pedantic -W -Wall -Wno-unknown-pragmas +LDFLAGS += -lboost_iostreams -lboost_filesystem -lboost_system -lboost_program_options -lboost_date_time # Additional flags for release/debug ifeq (${PARALLEL}, 1) @@ -23,7 +23,7 @@ ifeq (${STATIC}, 1) LDFLAGS += -static -static-libgcc -pthread -lhts -lz else - LDFLAGS += -lhts -lz -Wl,-rpath,${SEQTK_ROOT},-rpath,${BOOST_ROOT}/stage/lib + LDFLAGS += -lhts -lz endif ifeq (${DEBUG}, 1) CXXFLAGS += -g -O0 -fno-inline -DDEBUG @@ -41,32 +41,24 @@ DELLYSOURCES = $(wildcard src/*.h) $(wildcard src/*.cpp) # Targets -TARGETS = .htslib .boost src/delly src/extract src/cov src/iover src/stats +TARGETS = src/delly src/extract src/cov src/iover src/stats all: $(TARGETS) -.htslib: $(HTSLIBSOURCES) - cd src/htslib && make && make lib-static && cd ../../ && touch .htslib - -.boost: $(BOOSTSOURCES) - cd src/modular-boost && ./bootstrap.sh --prefix=${PWD}/src/modular-boost --without-icu --with-libraries=iostreams,filesystem,system,program_options,date_time && ./b2 && ./b2 headers && cd ../../ && touch .boost - -src/delly: .htslib .boost $(DELLYSOURCES) +src/delly: $(DELLYSOURCES) $(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS) -src/extract: .htslib .boost $(DELLYSOURCES) +src/extract: $(DELLYSOURCES) $(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS) -src/cov: .htslib .boost $(DELLYSOURCES) +src/cov: $(DELLYSOURCES) $(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS) -src/iover: .htslib .boost $(DELLYSOURCES) +src/iover: $(DELLYSOURCES) $(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS) -src/stats: .htslib .boost $(DELLYSOURCES) +src/stats: $(DELLYSOURCES) $(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS) clean: - cd src/htslib && make clean - cd src/modular-boost && ./b2 --clean-all - rm -f $(TARGETS) $(TARGETS:=.o) .htslib .boost + rm -f $(TARGETS) $(TARGETS:=.o)