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Author: Andreas Tille <tille@debian.org>
Last-Update: Thu, 15 Sep 2016 22:26:26 +0200
Description: Create shared lib instead of static
--- a/Makefile
+++ b/Makefile
@@ -115,11 +115,11 @@ BINS = $(addprefix bin/,$(notdir $(BIN_S
SHORTBINS = $(notdir $(BIN_SOURCES:.cpp=))
# TABIX = tabixpp/tabix.o
-SMITHWATERMAN = smithwaterman/SmithWatermanGotoh.o
-REPEATS = smithwaterman/Repeats.o
-INDELALLELE = smithwaterman/IndelAllele.o
-DISORDER = smithwaterman/disorder.o
-LEFTALIGN = smithwaterman/LeftAlign.o
+# SMITHWATERMAN = smithwaterman/SmithWatermanGotoh.o
+# REPEATS = smithwaterman/Repeats.o
+# INDELALLELE = smithwaterman/IndelAllele.o
+# DISORDER = smithwaterman/disorder.o
+# LEFTALIGN = smithwaterman/LeftAlign.o
FSOM = fsom/fsom.o
FILEVERCMP = filevercmp/filevercmp.o
@@ -138,8 +138,11 @@ CXXFLAGS = -O3 -D_FILE_OFFSET_BITS=64 -s
SSW = src/ssw.o src/ssw_cpp.o
-ssw.o: src/ssw.h
-ssw_cpp.o:src/ssw_cpp.h
+src/ssw.o: src/ssw.h src/ssw.c
+ $(CXX) -c $(CFLAGS) -fPIC -o $@ src/$(*F).c
+
+src/ssw_cpp.o: src/ssw_cpp.cpp src/ssw_cpp.h
+ $(CXX) -c $(CFLAGS) -fPIC -o $@ src/$(*F).cpp
openmp:
$(MAKE) CXXFLAGS="$(CXXFLAGS) -fopenmp -D HAS_OPENMP"
@@ -151,7 +154,7 @@ gprof:
$(MAKE) CXXFLAGS="$(CXXFLAGS) -pg" all
$(OBJECTS): $(SOURCES) $(HEADERS) multichoose pre $(SMITHWATERMAN) $(FILEVERCMP)
- $(CXX) -c -o $@ src/$(*F).cpp $(INCLUDES) $(LDFLAGS) $(CXXFLAGS) && cp src/*.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/
+ $(CXX) -c $(CFLAGS) -fPIC -o $@ src/$(*F).cpp $(INCLUDES) $(LDFLAGS) $(CXXFLAGS) && cp src/*.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/
multichoose: pre
echo "Source does not contain dir multichoose"
@@ -162,22 +165,6 @@ intervaltree: pre
# cd intervaltree && $(MAKE) && cp *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/
mkdir -p $(VCF_LIB_LOCAL)/$(INC_DIR)/ && cp -a debian/include/* $(VCF_LIB_LOCAL)/$(INC_DIR)/
-$(TABIX): pre
- echo "No need to create separately packaged tabixpp"
- # cd tabixpp && $(MAKE) && cp *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/
-
-$(SMITHWATERMAN): pre
- 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): $(SMITHWATERMAN)
-
-$(REPEATS): $(SMITHWATERMAN)
-
-$(LEFTALIGN): $(SMITHWATERMAN)
-
-$(INDELALLELE): $(SMITHWATERMAN)
-
#$(FSOM):
# cd fsom && $(CXX) $(CXXFLAGS) -c fsom.c -lm
@@ -186,19 +173,20 @@ $(FILEVERCMP): pre
#cp /usr/share/gnulib/lib/filevercmp.* filevercmp
#echo 'Proper use of filevercmp would be: `gnulib-tool --import filevercmp` - but it needs ./configure.ac'
#We here go with quilt patches from upstream files
- cd filevercmp && $(CXX) $(CXXFLAGS) -c filevercmp.c
+ cd filevercmp && $(CXX) $(CXXFLAGS) -fPIC -c filevercmp.c
ln -sf ../filevercmp/filevercmp.h $(VCF_LIB_LOCAL)/$(INC_DIR)/filevercmp.h
$(SHORTBINS): pre
$(MAKE) bin/$@
-$(BINS): $(BIN_SOURCES) libvcflib.a $(OBJECTS) $(SMITHWATERMAN) $(DISORDER) $(LEFTALIGN) $(INDELALLELE) $(SSW) $(FILEVERCMP) pre intervaltree
+$(BINS): $(BIN_SOURCES) libvcflib.so $(OBJECTS) $(SMITHWATERMAN) $(DISORDER) $(LEFTALIGN) $(INDELALLELE) $(SSW) $(FILEVERCMP) pre intervaltree
$(CXX) src/$(notdir $@).cpp -o $@ $(INCLUDES) $(LDFLAGS) $(CXXFLAGS)
-libvcflib.a: $(OBJECTS) $(SMITHWATERMAN) $(REPEATS) $(DISORDER) $(LEFTALIGN) $(INDELALLELE) $(SSW) $(FILEVERCMP) pre
- ar rs libvcflib.a $(OBJECTS) $(SSW) $(FILEVERCMP)
- cp libvcflib.a $(LIB_DIR)
-
+libvcflib.so: $(OBJECTS) $(SMITHWATERMAN) $(REPEATS) $(DISORDER) $(LEFTALIGN) $(INDELALLELE) $(SSW) $(FILEVERCMP) pre
+ # ar rs libvcflib.a $(OBJECTS) $(SSW) $(FILEVERCMP)
+ gcc -shared -Wl,-soname -Wl,libvcflib.so.1 -o libvcflib.so.1 $(OBJECTS) $(SSW) $(FILEVERCMP)
+ ln -s libvcflib.so.1 libvcflib.so
+ cp -a libvcflib.so* $(LIB_DIR)
test: $(BINS)
@prove -Itests/lib -w tests/*.t
@@ -218,7 +206,7 @@ update: pull all
clean:
rm -f $(BINS) $(OBJECTS)
rm -f ssw_cpp.o ssw.o
- rm -f libvcflib.a
+ rm -f libvcflib.so
rm -rf $(BIN_DIR)
rm -rf $(LIB_DIR)
rm -rf $(INC_DIR)
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