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delly-use-system-libraries.patch 2.3 KiB

4 years ago
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  1. This patch let's Delly use the system versions of htslib and boost.
  2. Patch by Roel Janssen <roel@gnu.org>
  3. --- a/Makefile 2016-03-16 13:08:49.936706607 +0100
  4. +++ b/Makefile 2016-03-16 13:09:12.351706212 +0100
  5. @@ -9,8 +9,8 @@
  6. # Flags
  7. CXX=g++
  8. -CXXFLAGS += -isystem ${SEQTK_ROOT} -isystem ${BOOST_ROOT} -pedantic -W -Wall -Wno-unknown-pragmas
  9. -LDFLAGS += -L${SEQTK_ROOT} -L${BOOST_ROOT}/stage/lib -lboost_iostreams -lboost_filesystem -lboost_system -lboost_program_options -lboost_date_time
  10. +CXXFLAGS += -pedantic -W -Wall -Wno-unknown-pragmas
  11. +LDFLAGS += -lboost_iostreams -lboost_filesystem -lboost_system -lboost_program_options -lboost_date_time
  12. # Additional flags for release/debug
  13. ifeq (${PARALLEL}, 1)
  14. @@ -23,7 +23,7 @@
  15. ifeq (${STATIC}, 1)
  16. LDFLAGS += -static -static-libgcc -pthread -lhts -lz
  17. else
  18. - LDFLAGS += -lhts -lz -Wl,-rpath,${SEQTK_ROOT},-rpath,${BOOST_ROOT}/stage/lib
  19. + LDFLAGS += -lhts -lz
  20. endif
  21. ifeq (${DEBUG}, 1)
  22. CXXFLAGS += -g -O0 -fno-inline -DDEBUG
  23. @@ -41,32 +41,24 @@
  24. DELLYSOURCES = $(wildcard src/*.h) $(wildcard src/*.cpp)
  25. # Targets
  26. -TARGETS = .htslib .boost src/delly src/extract src/cov src/iover src/stats
  27. +TARGETS = src/delly src/extract src/cov src/iover src/stats
  28. all: $(TARGETS)
  29. -.htslib: $(HTSLIBSOURCES)
  30. - cd src/htslib && make && make lib-static && cd ../../ && touch .htslib
  31. -
  32. -.boost: $(BOOSTSOURCES)
  33. - cd src/modular-boost && ./bootstrap.sh --prefix=${PWD}/src/modular-boost --without-icu --with-libraries=iostreams,filesystem,system,program_options,date_time && ./b2 && ./b2 headers && cd ../../ && touch .boost
  34. -
  35. -src/delly: .htslib .boost $(DELLYSOURCES)
  36. +src/delly: $(DELLYSOURCES)
  37. $(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS)
  38. -src/extract: .htslib .boost $(DELLYSOURCES)
  39. +src/extract: $(DELLYSOURCES)
  40. $(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS)
  41. -src/cov: .htslib .boost $(DELLYSOURCES)
  42. +src/cov: $(DELLYSOURCES)
  43. $(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS)
  44. -src/iover: .htslib .boost $(DELLYSOURCES)
  45. +src/iover: $(DELLYSOURCES)
  46. $(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS)
  47. -src/stats: .htslib .boost $(DELLYSOURCES)
  48. +src/stats: $(DELLYSOURCES)
  49. $(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS)
  50. clean:
  51. - cd src/htslib && make clean
  52. - cd src/modular-boost && ./b2 --clean-all
  53. - rm -f $(TARGETS) $(TARGETS:=.o) .htslib .boost
  54. + rm -f $(TARGETS) $(TARGETS:=.o)