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