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Author: Andreas Tille <tille@debian.org>
Last-Update: Thu, 23 Jun 2016 09:10:54 +0200
Description: Use Debian packaged libsmithwaterman
--- a/Makefile
+++ b/Makefile
@@ -124,8 +124,8 @@ LEFTALIGN = smithwaterman/LeftAlign.o
FSOM = fsom/fsom.o
FILEVERCMP = filevercmp/filevercmp.o
-INCLUDES = -I$(INC_DIR)
-LDFLAGS = -L$(LIB_DIR) -lvcflib -lhts -lpthread -lz -lm -fopenmp -ltabixpp
+INCLUDES = `pkg-config --cflags libsmithwaterman` -I$(INC_DIR)
+LDFLAGS += -L$(LIB_DIR) -lvcflib -lhts -lpthread -lz -lm -fopenmp -ltabixpp `pkg-config --libs libsmithwaterman`
all: $(OBJECTS) $(BINS)
@@ -156,17 +156,20 @@ $(OBJECTS): $(SOURCES) $(HEADERS) multic
$(CXX) -c -o $@ src/$(*F).cpp $(INCLUDES) $(LDFLAGS) $(CXXFLAGS) && cp src/*.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/
multichoose: pre
- cd multichoose && $(MAKE) && cp *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/
+ echo "Source does not contain dir multichoose"
+ # cd multichoose && $(MAKE) && cp *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/
intervaltree: pre
- cd intervaltree && $(MAKE) && cp *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/
+ echo "Source does not contain dir intervaltree"
+ # cd intervaltree && $(MAKE) && cp *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/
$(TABIX): pre
echo "No need to create separately packaged tabixpp"
# cd tabixpp && $(MAKE) && cp *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/
$(SMITHWATERMAN): pre
- cd smithwaterman && $(MAKE) && cp *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/ && cp *.o $(VCF_LIB_LOCAL)/$(OBJ_DIR)/
+ echo "Source does not contain dir smithwaterman"
+ # cd smithwaterman && $(MAKE) && cp *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/ && cp *.o $(VCF_LIB_LOCAL)/$(OBJ_DIR)/
$(DISORDER): $(SMITHWATERMAN)
@@ -192,7 +195,7 @@ $(BINS): $(BIN_SOURCES) libvcflib.a $(OB
$(CXX) src/$(notdir $@).cpp -o $@ $(INCLUDES) $(LDFLAGS) $(CXXFLAGS)
libvcflib.a: $(OBJECTS) $(SMITHWATERMAN) $(REPEATS) $(FASTAHACK) $(DISORDER) $(LEFTALIGN) $(INDELALLELE) $(SSW) $(FILEVERCMP) pre
- ar rs libvcflib.a $(OBJECTS) smithwaterman/sw.o $(FASTAHACK) $(SSW) $(FILEVERCMP)
+ ar rs libvcflib.a $(OBJECTS) $(FASTAHACK) $(SSW) $(FILEVERCMP)
cp libvcflib.a $(LIB_DIR)
@@ -220,7 +223,7 @@ clean:
rm -rf $(INC_DIR)
rm -rf $(OBJ_DIR)
# cd tabixpp && make clean
- cd smithwaterman && make clean
+ # cd smithwaterman && make clean
cd fastahack && make clean
.PHONY: clean all test pre
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