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| author | pjotrp | 2016-03-18 21:25:57 -0500 |
|---|---|---|
| committer | pjotrp | 2016-03-18 21:25:57 -0500 |
| commit | e9a4fd0b609d4d1ff6b3a622d4f590d092e6def8 (patch) | |
| tree | c24b0a2dd7a78919b6ab3a417c3ecfbd5850b5bc /delly-use-system-libraries.patch | |
| parent | 364d11268ecea6bf31a48a7942b4c599dc386212 (diff) | |
| parent | 97f4e53b34e818c06f394e5272a51fbce6589d2f (diff) | |
| download | guix-bioinformatics-e9a4fd0b609d4d1ff6b3a622d4f590d092e6def8.tar.gz | |
Merge branch 'master' into dennis
Diffstat (limited to 'delly-use-system-libraries.patch')
| -rw-r--r-- | delly-use-system-libraries.patch | 65 |
1 files changed, 65 insertions, 0 deletions
diff --git a/delly-use-system-libraries.patch b/delly-use-system-libraries.patch new file mode 100644 index 0000000..3ce817f --- /dev/null +++ b/delly-use-system-libraries.patch @@ -0,0 +1,65 @@ +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) |