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- This patch let's Delly use the system versions of htslib and boost.
-
- Patch by Roel Janssen <roel@gnu.org>
- --- 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)
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