6d8dd5bad7
* gnu/packages/bioinformatics.scm (vcflib)[source]: Add patch. Add snippet to adjust files for new locations. [inputs]: Add fastahack, smithwaterman, tabixpp, xz. [native-inputs]: Add pkg-config. Remove the package-source of fastahack, fsom, smithwaterman, tabixpp. [arguments]: Remove make-flags. Add custom phase to add the output lib directory to the rpath. Adjust custom 'unpack-submodule-sources for the change in native-inputs. Adjust custom 'install phase to also install libraries and headers. * gnu/packages/patches/vcflib-use-shared-libraries.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it.
136 lines
4.7 KiB
Diff
136 lines
4.7 KiB
Diff
This patch is a combination of many of the patches from Debian:
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https://sources.debian.org/src/libvcflib/1.0.1+dfsg-3/debian/patches/
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---
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Makefile | 63 +++++++++++---------------------------------------------
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1 file changed, 12 insertions(+), 51 deletions(-)
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diff --git a/Makefile b/Makefile
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index 6b13350..be85f22 100644
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--- a/Makefile
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+++ b/Makefile
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@@ -114,43 +114,25 @@ BIN_SOURCES = src/vcfecho.cpp \
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src/vcfnull2ref.cpp \
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src/vcfinfosummarize.cpp
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-# when we can figure out how to build on mac
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-# src/vcfsom.cpp
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-
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#BINS = $(BIN_SOURCES:.cpp=)
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BINS = $(addprefix $(BIN_DIR)/,$(notdir $(BIN_SOURCES:.cpp=)))
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SHORTBINS = $(notdir $(BIN_SOURCES:.cpp=))
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-TABIX = tabixpp/tabix.o
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-FASTAHACK = fastahack/Fasta.o
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-SMITHWATERMAN = smithwaterman/SmithWatermanGotoh.o
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-REPEATS = smithwaterman/Repeats.o
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-INDELALLELE = smithwaterman/IndelAllele.o
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-DISORDER = smithwaterman/disorder.o
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-LEFTALIGN = smithwaterman/LeftAlign.o
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-FSOM = fsom/fsom.o
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FILEVERCMP = filevercmp/filevercmp.o
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-# Work out how to find htslib
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-# Use the one we ship in tabixpp unless told otherwise by the environment
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-HTS_LIB ?= $(VCF_LIB_LOCAL)/tabixpp/htslib/libhts.a
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-HTS_INCLUDES ?= -I$(VCF_LIB_LOCAL)/tabixpp/htslib
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-HTS_LDFLAGS ?= -L$(VCF_LIB_LOCAL)/tabixpp/htslib -lhts -lbz2 -lm -lz -llzma -pthread
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-
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-
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-INCLUDES = $(HTS_INCLUDES) -I$(INC_DIR)
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-LDFLAGS = -L$(LIB_DIR) -lvcflib $(HTS_LDFLAGS) -lpthread -lz -lm -llzma -lbz2
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+INCLUDES = -I$(INC_DIR) $(shell pkg-config --cflags htslib fastahack smithwaterman tabixpp)
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+LDFLAGS = -L$(LIB_DIR) -lvcflib -lpthread -lz -lstdc++ -lm -llzma -lbz2 $(shell pkg-config --libs htslib fastahack smithwaterman tabixpp)
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-all: $(OBJECTS) $(BINS) scriptToBin
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+all: $(OBJECTS) $(BINS) scriptToBin libvcflib.a
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scriptToBin: $(BINS)
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$(CP) scripts/* $(BIN_DIR)
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GIT_VERSION += $(shell git describe --abbrev=4 --dirty --always)
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-CXXFLAGS = -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x
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+CXXFLAGS = -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -fPIC
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#CXXFLAGS = -O2
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#CXXFLAGS = -pedantic -Wall -Wshadow -Wpointer-arith -Wcast-qual
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@@ -168,7 +150,7 @@ profiling:
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gprof:
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$(MAKE) CXXFLAGS="$(CXXFLAGS) -pg" all
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-$(OBJECTS): $(SOURCES) $(HEADERS) $(TABIX) multichoose pre $(SMITHWATERMAN) $(FILEVERCMP) $(FASTAHACK)
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+$(OBJECTS): $(SOURCES) $(HEADERS) multichoose pre $(FILEVERCMP)
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$(CXX) -c -o $@ src/$(*F).cpp $(INCLUDES) $(LDFLAGS) $(CXXFLAGS) && $(CP) src/*.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/
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multichoose: pre
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@@ -177,39 +159,22 @@ multichoose: pre
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intervaltree: pre
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cd intervaltree && $(MAKE) && $(CP) *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/
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-$(TABIX): pre
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- cd tabixpp && INCLUDES="$(HTS_INCLUDES)" LIBPATH="-L. $(HTS_LDFLAGS)" HTSLIB="$(HTS_LIB)" $(MAKE) && $(CP) *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/
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-
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-$(SMITHWATERMAN): pre
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- cd smithwaterman && $(MAKE) && $(CP) *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/ && $(CP) *.o $(VCF_LIB_LOCAL)/$(OBJ_DIR)/
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-
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-$(DISORDER): $(SMITHWATERMAN)
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-
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-$(REPEATS): $(SMITHWATERMAN)
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-
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-$(LEFTALIGN): $(SMITHWATERMAN)
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-
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-$(INDELALLELE): $(SMITHWATERMAN)
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-
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-$(FASTAHACK): pre
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- cd fastahack && $(MAKE) && $(CP) *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/ && $(CP) Fasta.o $(VCF_LIB_LOCAL)/$(OBJ_DIR)/
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-
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-#$(FSOM):
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-# cd fsom && $(CXX) $(CXXFLAGS) -c fsom.c -lm
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-
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$(FILEVERCMP): pre
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cd filevercmp && make && $(CP) *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/ && $(CP) *.o $(VCF_LIB_LOCAL)/$(INC_DIR)/
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$(SHORTBINS): pre
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$(MAKE) $(BIN_DIR)/$@
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-$(BINS): $(BIN_SOURCES) libvcflib.a $(OBJECTS) $(SMITHWATERMAN) $(FASTAHACK) $(DISORDER) $(LEFTALIGN) $(INDELALLELE) $(SSW) $(FILEVERCMP) pre intervaltree
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+$(BINS): $(BIN_SOURCES) libvcflib.so $(OBJECTS) $(SSW) $(FILEVERCMP) pre intervaltree
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$(CXX) src/$(notdir $@).cpp -o $@ $(INCLUDES) $(LDFLAGS) $(CXXFLAGS) -DVERSION=\"$(GIT_VERSION)\"
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-libvcflib.a: $(OBJECTS) $(SMITHWATERMAN) $(REPEATS) $(FASTAHACK) $(DISORDER) $(LEFTALIGN) $(INDELALLELE) $(SSW) $(FILEVERCMP) $(TABIX) pre
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- ar rs libvcflib.a $(OBJECTS) smithwaterman/sw.o $(FASTAHACK) $(SSW) $(FILEVERCMP) $(TABIX)
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+libvcflib.a: $(OBJECTS) $(SSW) $(FILEVERCMP) pre
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+ ar rs libvcflib.a $(OBJECTS) $(SSW) $(FILEVERCMP)
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$(CP) libvcflib.a $(LIB_DIR)
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+libvcflib.so: $(OBJECTS) $(SSW) $(FILEVERCMP) pre
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+ $(CXX) -shared -o libvcflib.so $(OBJECTS) $(SSW) $(FILEVERCMP)
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+ $(CP) libvcflib.so $(LIB_DIR)
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test: $(BINS)
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@prove -Itests/lib -w tests/*.t
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@@ -230,16 +195,12 @@ clean:
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$(RM) $(BINS) $(OBJECTS)
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$(RM) ssw_cpp.o ssw.o
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$(RM) libvcflib.a
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+ $(RM) libvcflib.so
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$(RM) -r $(BIN_DIR)
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$(RM) -r $(LIB_DIR)
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$(RM) -r $(INC_DIR)
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$(RM) -r $(OBJ_DIR)
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- $(MAKE) clean -C tabixpp
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- $(MAKE) clean -C smithwaterman
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- $(MAKE) clean -C fastahack
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$(MAKE) clean -C multichoose
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- $(MAKE) clean -C fsom
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- $(MAKE) clean -C libVCFH
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$(MAKE) clean -C test
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$(MAKE) clean -C filevercmp
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$(MAKE) clean -C intervaltree
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--
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2.28.0
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