gnu/packages/patches/vcflib-use-shared-libraries.patch

   1 This patch is a combination of many of the patches from Debian:
   2 https://sources.debian.org/src/libvcflib/1.0.1+dfsg-3/debian/patches/
   3
   4 ---
   5  Makefile | 63 +++++++++++---------------------------------------------
   6  1 file changed, 12 insertions(+), 51 deletions(-)
   7
   8 diff --git a/Makefile b/Makefile
   9 index 6b13350..be85f22 100644
  10 --- a/Makefile
  11 +++ b/Makefile
  12 @@ -114,43 +114,25 @@ BIN_SOURCES = src/vcfecho.cpp \
  13                           src/vcfnull2ref.cpp \
  14                           src/vcfinfosummarize.cpp
  15
  16 -# when we can figure out how to build on mac
  17 -# src/vcfsom.cpp
  18 -
  19  #BINS = $(BIN_SOURCES:.cpp=)
  20  BINS = $(addprefix $(BIN_DIR)/,$(notdir $(BIN_SOURCES:.cpp=)))
  21  SHORTBINS = $(notdir $(BIN_SOURCES:.cpp=))
  22
  23 -TABIX = tabixpp/tabix.o
  24 -FASTAHACK = fastahack/Fasta.o
  25 -SMITHWATERMAN = smithwaterman/SmithWatermanGotoh.o
  26 -REPEATS = smithwaterman/Repeats.o
  27 -INDELALLELE = smithwaterman/IndelAllele.o
  28 -DISORDER = smithwaterman/disorder.o
  29 -LEFTALIGN = smithwaterman/LeftAlign.o
  30 -FSOM = fsom/fsom.o
  31  FILEVERCMP = filevercmp/filevercmp.o
  32
  33 -# Work out how to find htslib
  34 -# Use the one we ship in tabixpp unless told otherwise by the environment
  35 -HTS_LIB ?= $(VCF_LIB_LOCAL)/tabixpp/htslib/libhts.a
  36 -HTS_INCLUDES ?= -I$(VCF_LIB_LOCAL)/tabixpp/htslib
  37 -HTS_LDFLAGS ?= -L$(VCF_LIB_LOCAL)/tabixpp/htslib -lhts -lbz2 -lm -lz -llzma -pthread
  38 -
  39 -
  40 -INCLUDES = $(HTS_INCLUDES) -I$(INC_DIR)
  41 -LDFLAGS = -L$(LIB_DIR) -lvcflib $(HTS_LDFLAGS) -lpthread -lz -lm -llzma -lbz2
  42 +INCLUDES = -I$(INC_DIR) $(shell pkg-config --cflags htslib fastahack smithwaterman tabixpp)
  43 +LDFLAGS = -L$(LIB_DIR) -lvcflib -lpthread -lz -lstdc++ -lm -llzma -lbz2 $(shell pkg-config --libs htslib fastahack smithwaterman tabixpp)
  44
  45
  46
  47 -all: $(OBJECTS) $(BINS) scriptToBin
  48 +all: $(OBJECTS) $(BINS) scriptToBin libvcflib.a
  49
  50  scriptToBin: $(BINS)
  51         $(CP) scripts/* $(BIN_DIR)
  52
  53  GIT_VERSION += $(shell git describe --abbrev=4 --dirty --always)
  54
  55 -CXXFLAGS = -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x
  56 +CXXFLAGS = -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -fPIC
  57  #CXXFLAGS = -O2
  58  #CXXFLAGS = -pedantic -Wall -Wshadow -Wpointer-arith -Wcast-qual
  59
  60 @@ -168,7 +150,7 @@ profiling:
  61  gprof:
  62         $(MAKE) CXXFLAGS="$(CXXFLAGS) -pg" all
  63
  64 -$(OBJECTS): $(SOURCES) $(HEADERS) $(TABIX) multichoose pre $(SMITHWATERMAN) $(FILEVERCMP) $(FASTAHACK)
  65 +$(OBJECTS): $(SOURCES) $(HEADERS) multichoose pre $(FILEVERCMP)
  66         $(CXX) -c -o $@ src/$(*F).cpp $(INCLUDES) $(LDFLAGS) $(CXXFLAGS) && $(CP) src/*.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/
  67
  68  multichoose: pre
  69 @@ -177,39 +159,22 @@ multichoose: pre
  70  intervaltree: pre
  71         cd intervaltree && $(MAKE) && $(CP) *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/
  72
  73 -$(TABIX): pre
  74 -       cd tabixpp && INCLUDES="$(HTS_INCLUDES)" LIBPATH="-L. $(HTS_LDFLAGS)" HTSLIB="$(HTS_LIB)" $(MAKE) && $(CP) *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/
  75 -
  76 -$(SMITHWATERMAN): pre
  77 -       cd smithwaterman && $(MAKE) && $(CP) *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/ && $(CP) *.o $(VCF_LIB_LOCAL)/$(OBJ_DIR)/
  78 -
  79 -$(DISORDER): $(SMITHWATERMAN)
  80 -
  81 -$(REPEATS): $(SMITHWATERMAN)
  82 -
  83 -$(LEFTALIGN): $(SMITHWATERMAN)
  84 -
  85 -$(INDELALLELE): $(SMITHWATERMAN)
  86 -
  87 -$(FASTAHACK): pre
  88 -       cd fastahack && $(MAKE) && $(CP) *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/ && $(CP) Fasta.o $(VCF_LIB_LOCAL)/$(OBJ_DIR)/
  89 -
  90 -#$(FSOM):
  91 -#      cd fsom && $(CXX) $(CXXFLAGS) -c fsom.c -lm
  92 -
  93  $(FILEVERCMP): pre
  94         cd filevercmp && make && $(CP) *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/ && $(CP) *.o $(VCF_LIB_LOCAL)/$(INC_DIR)/
  95
  96  $(SHORTBINS): pre
  97         $(MAKE) $(BIN_DIR)/$@
  98
  99 -$(BINS): $(BIN_SOURCES) libvcflib.a $(OBJECTS) $(SMITHWATERMAN) $(FASTAHACK) $(DISORDER) $(LEFTALIGN) $(INDELALLELE) $(SSW) $(FILEVERCMP) pre intervaltree
 100 +$(BINS): $(BIN_SOURCES) libvcflib.so $(OBJECTS) $(SSW) $(FILEVERCMP) pre intervaltree
 101         $(CXX) src/$(notdir $@).cpp -o $@ $(INCLUDES) $(LDFLAGS) $(CXXFLAGS) -DVERSION=\"$(GIT_VERSION)\"
 102
 103 -libvcflib.a: $(OBJECTS) $(SMITHWATERMAN) $(REPEATS) $(FASTAHACK) $(DISORDER) $(LEFTALIGN) $(INDELALLELE) $(SSW) $(FILEVERCMP) $(TABIX) pre
 104 -       ar rs libvcflib.a $(OBJECTS) smithwaterman/sw.o $(FASTAHACK) $(SSW) $(FILEVERCMP) $(TABIX)
 105 +libvcflib.a: $(OBJECTS) $(SSW) $(FILEVERCMP) pre
 106 +       ar rs libvcflib.a $(OBJECTS) $(SSW) $(FILEVERCMP)
 107         $(CP) libvcflib.a $(LIB_DIR)
 108
 109 +libvcflib.so: $(OBJECTS) $(SSW) $(FILEVERCMP) pre
 110 +       $(CXX) -shared -o libvcflib.so $(OBJECTS) $(SSW) $(FILEVERCMP)
 111 +       $(CP) libvcflib.so $(LIB_DIR)
 112
 113  test: $(BINS)
 114         @prove -Itests/lib -w tests/*.t
 115 @@ -230,16 +195,12 @@ clean:
 116         $(RM) $(BINS) $(OBJECTS)
 117         $(RM) ssw_cpp.o ssw.o
 118         $(RM) libvcflib.a
 119 +       $(RM) libvcflib.so
 120         $(RM) -r $(BIN_DIR)
 121         $(RM) -r $(LIB_DIR)
 122         $(RM) -r $(INC_DIR)
 123         $(RM) -r $(OBJ_DIR)
 124 -       $(MAKE) clean -C tabixpp
 125 -       $(MAKE) clean -C smithwaterman
 126 -       $(MAKE) clean -C fastahack
 127         $(MAKE) clean -C multichoose
 128 -       $(MAKE) clean -C fsom
 129 -       $(MAKE) clean -C libVCFH
 130         $(MAKE) clean -C test
 131         $(MAKE) clean -C filevercmp
 132         $(MAKE) clean -C intervaltree
 133 --
 134 2.28.0
 135