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authorEfraim Flashner <efraim@flashner.co.il>2021-01-14 20:38:10 +0200
committerEfraim Flashner <efraim@flashner.co.il>2021-01-14 20:43:31 +0200
commit93309e25c7c3da5744b0a3304b89effed949f844 (patch)
tree238002bde437897a97fb036aaef07a044ed10303 /gnu/packages/patches
parentdb30d6eada7ef0f2a6d41c71f37ed3e45899e414 (diff)
gnu: vcflib: Update to 1.0.2.
* gnu/packages/bioinformatics.scm (vcflib): Update to 1.0.2. [source]: Download using git-fetch. Remove patch. Update snippet to use packaged libraries. [build-system]: Switch to cmake-build-system. [inputs]: Add bzip2. [native-inputs]: Add package-source of fsom. [arguments]: Delete custom 'set-flags, 'install phases. Don't delete 'configure phase. Adjust 'unpack-submodule-sources phase. * gnu/packages/patches/vcflib-use-shared-libraries.patch: Remove file. * gnu/local.mk (dist_patch_DATA): Remove it.
Diffstat (limited to 'gnu/packages/patches')
-rw-r--r--gnu/packages/patches/vcflib-use-shared-libraries.patch135
1 files changed, 0 insertions, 135 deletions
diff --git a/gnu/packages/patches/vcflib-use-shared-libraries.patch b/gnu/packages/patches/vcflib-use-shared-libraries.patch
deleted file mode 100644
index e198ec663c..0000000000
--- a/gnu/packages/patches/vcflib-use-shared-libraries.patch
+++ /dev/null
@@ -1,135 +0,0 @@
-This patch is a combination of many of the patches from Debian:
-https://sources.debian.org/src/libvcflib/1.0.1+dfsg-3/debian/patches/
-
----
- Makefile | 63 +++++++++++---------------------------------------------
- 1 file changed, 12 insertions(+), 51 deletions(-)
-
-diff --git a/Makefile b/Makefile
-index 6b13350..be85f22 100644
---- a/Makefile
-+++ b/Makefile
-@@ -114,43 +114,25 @@ BIN_SOURCES = src/vcfecho.cpp \
- src/vcfnull2ref.cpp \
- src/vcfinfosummarize.cpp
-
--# when we can figure out how to build on mac
--# src/vcfsom.cpp
--
- #BINS = $(BIN_SOURCES:.cpp=)
- BINS = $(addprefix $(BIN_DIR)/,$(notdir $(BIN_SOURCES:.cpp=)))
- SHORTBINS = $(notdir $(BIN_SOURCES:.cpp=))
-
--TABIX = tabixpp/tabix.o
--FASTAHACK = fastahack/Fasta.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
-
--# Work out how to find htslib
--# Use the one we ship in tabixpp unless told otherwise by the environment
--HTS_LIB ?= $(VCF_LIB_LOCAL)/tabixpp/htslib/libhts.a
--HTS_INCLUDES ?= -I$(VCF_LIB_LOCAL)/tabixpp/htslib
--HTS_LDFLAGS ?= -L$(VCF_LIB_LOCAL)/tabixpp/htslib -lhts -lbz2 -lm -lz -llzma -pthread
--
--
--INCLUDES = $(HTS_INCLUDES) -I$(INC_DIR)
--LDFLAGS = -L$(LIB_DIR) -lvcflib $(HTS_LDFLAGS) -lpthread -lz -lm -llzma -lbz2
-+INCLUDES = -I$(INC_DIR) $(shell pkg-config --cflags htslib fastahack smithwaterman tabixpp)
-+LDFLAGS = -L$(LIB_DIR) -lvcflib -lpthread -lz -lstdc++ -lm -llzma -lbz2 $(shell pkg-config --libs htslib fastahack smithwaterman tabixpp)
-
-
-
--all: $(OBJECTS) $(BINS) scriptToBin
-+all: $(OBJECTS) $(BINS) scriptToBin libvcflib.a
-
- scriptToBin: $(BINS)
- $(CP) scripts/* $(BIN_DIR)
-
- GIT_VERSION += $(shell git describe --abbrev=4 --dirty --always)
-
--CXXFLAGS = -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x
-+CXXFLAGS = -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -fPIC
- #CXXFLAGS = -O2
- #CXXFLAGS = -pedantic -Wall -Wshadow -Wpointer-arith -Wcast-qual
-
-@@ -168,7 +150,7 @@ profiling:
- gprof:
- $(MAKE) CXXFLAGS="$(CXXFLAGS) -pg" all
-
--$(OBJECTS): $(SOURCES) $(HEADERS) $(TABIX) multichoose pre $(SMITHWATERMAN) $(FILEVERCMP) $(FASTAHACK)
-+$(OBJECTS): $(SOURCES) $(HEADERS) multichoose pre $(FILEVERCMP)
- $(CXX) -c -o $@ src/$(*F).cpp $(INCLUDES) $(LDFLAGS) $(CXXFLAGS) && $(CP) src/*.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/
-
- multichoose: pre
-@@ -177,39 +159,22 @@ multichoose: pre
- intervaltree: pre
- cd intervaltree && $(MAKE) && $(CP) *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/
-
--$(TABIX): pre
-- cd tabixpp && INCLUDES="$(HTS_INCLUDES)" LIBPATH="-L. $(HTS_LDFLAGS)" HTSLIB="$(HTS_LIB)" $(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)/
--
--$(DISORDER): $(SMITHWATERMAN)
--
--$(REPEATS): $(SMITHWATERMAN)
--
--$(LEFTALIGN): $(SMITHWATERMAN)
--
--$(INDELALLELE): $(SMITHWATERMAN)
--
--$(FASTAHACK): pre
-- cd fastahack && $(MAKE) && $(CP) *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/ && $(CP) Fasta.o $(VCF_LIB_LOCAL)/$(OBJ_DIR)/
--
--#$(FSOM):
--# cd fsom && $(CXX) $(CXXFLAGS) -c fsom.c -lm
--
- $(FILEVERCMP): pre
- cd filevercmp && make && $(CP) *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/ && $(CP) *.o $(VCF_LIB_LOCAL)/$(INC_DIR)/
-
- $(SHORTBINS): pre
- $(MAKE) $(BIN_DIR)/$@
-
--$(BINS): $(BIN_SOURCES) libvcflib.a $(OBJECTS) $(SMITHWATERMAN) $(FASTAHACK) $(DISORDER) $(LEFTALIGN) $(INDELALLELE) $(SSW) $(FILEVERCMP) pre intervaltree
-+$(BINS): $(BIN_SOURCES) libvcflib.so $(OBJECTS) $(SSW) $(FILEVERCMP) pre intervaltree
- $(CXX) src/$(notdir $@).cpp -o $@ $(INCLUDES) $(LDFLAGS) $(CXXFLAGS) -DVERSION=\"$(GIT_VERSION)\"
-
--libvcflib.a: $(OBJECTS) $(SMITHWATERMAN) $(REPEATS) $(FASTAHACK) $(DISORDER) $(LEFTALIGN) $(INDELALLELE) $(SSW) $(FILEVERCMP) $(TABIX) pre
-- ar rs libvcflib.a $(OBJECTS) smithwaterman/sw.o $(FASTAHACK) $(SSW) $(FILEVERCMP) $(TABIX)
-+libvcflib.a: $(OBJECTS) $(SSW) $(FILEVERCMP) pre
-+ ar rs libvcflib.a $(OBJECTS) $(SSW) $(FILEVERCMP)
- $(CP) libvcflib.a $(LIB_DIR)
-
-+libvcflib.so: $(OBJECTS) $(SSW) $(FILEVERCMP) pre
-+ $(CXX) -shared -o libvcflib.so $(OBJECTS) $(SSW) $(FILEVERCMP)
-+ $(CP) libvcflib.so $(LIB_DIR)
-
- test: $(BINS)
- @prove -Itests/lib -w tests/*.t
-@@ -230,16 +195,12 @@ clean:
- $(RM) $(BINS) $(OBJECTS)
- $(RM) ssw_cpp.o ssw.o
- $(RM) libvcflib.a
-+ $(RM) libvcflib.so
- $(RM) -r $(BIN_DIR)
- $(RM) -r $(LIB_DIR)
- $(RM) -r $(INC_DIR)
- $(RM) -r $(OBJ_DIR)
-- $(MAKE) clean -C tabixpp
-- $(MAKE) clean -C smithwaterman
-- $(MAKE) clean -C fastahack
- $(MAKE) clean -C multichoose
-- $(MAKE) clean -C fsom
-- $(MAKE) clean -C libVCFH
- $(MAKE) clean -C test
- $(MAKE) clean -C filevercmp
- $(MAKE) clean -C intervaltree
---
-2.28.0
-