diff options
Diffstat (limited to 'sci-biology/STAR/files/STAR-2.5.3a-fix-build-system.patch')
| -rw-r--r-- | sci-biology/STAR/files/STAR-2.5.3a-fix-build-system.patch | 123 |
1 files changed, 0 insertions, 123 deletions
diff --git a/sci-biology/STAR/files/STAR-2.5.3a-fix-build-system.patch b/sci-biology/STAR/files/STAR-2.5.3a-fix-build-system.patch deleted file mode 100644 index 8e504fa429e0..000000000000 --- a/sci-biology/STAR/files/STAR-2.5.3a-fix-build-system.patch +++ /dev/null @@ -1,123 +0,0 @@ -* unbundle htslib -* honour all user flags -* use pkg-config for linking - ---- a/source/Makefile -+++ b/source/Makefile -@@ -8,24 +8,12 @@ - LDFLAGSextra ?= - CXXFLAGSextra ?= - --# user may define the compiler --CXX ?= g++ -- - # pre-defined flags --LDFLAGS_shared := -pthread -Lhtslib -Bstatic -lhts -Bdynamic -lz -lrt --LDFLAGS_static := -static -static-libgcc -pthread -Lhtslib -lhts -lz --LDFLAGS_Mac :=-pthread -lz htslib/libhts.a --LDFLAGS_Mac_static :=-pthread -lz -static-libgcc htslib/libhts.a --LDFLAGS_gdb := $(LDFLAGS_shared) -- - COMPTIMEPLACE := -D'COMPILATION_TIME_PLACE="$(shell echo `date` $(HOSTNAME):`pwd`)"' - --CXXFLAGS_common := -pipe -std=c++11 -Wall -Wextra -fopenmp $(COMPTIMEPLACE) --CXXFLAGS_main := -O3 $(CXXFLAGS_common) --CXXFLAGS_gdb := -O0 -g $(CXXFLAGS_common) -- --CFLAGS := -O3 -pipe -Wall -Wextra $(CFLAGS) -- -+CFLAGS_common = -Wall -Wextra -pthread `$(PKG_CONFIG) --cflags htslib` `$(PKG_CONFIG) --cflags zlib` -+CXXFLAGS_common = $(CFLAGS_common) -std=c++11 -fopenmp $(COMPTIMEPLACE) -+LIBS_common = -pthread `$(PKG_CONFIG) --libs htslib` `$(PKG_CONFIG) --libs zlib` -lrt - - ########################################################################################################## - -@@ -54,10 +42,10 @@ - - - %.o : %.cpp -- $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $< -+ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGS_common) $< - - %.o : %.c -- $(CXX) -c $(CPPFLAGS) $(CFLAGS) $< -+ $(CXX) -c $(CPPFLAGS) $(CFLAGS) $(CFLAGS_common) $< - - all: STAR - -@@ -84,7 +72,7 @@ - ifneq ($(MAKECMDGOALS),CLEAN) - ifneq ($(MAKECMDGOALS),STARforMac) - ifneq ($(MAKECMDGOALS),STARforMacGDB) --Depend.list: $(SOURCES) parametersDefault.xxd htslib -+Depend.list: $(SOURCES) parametersDefault.xxd - echo $(SOURCES) - /bin/rm -f ./Depend.list - $(CXX) $(CXXFLAGS_common) -MM $^ >> Depend.list -@@ -95,57 +83,34 @@ - endif - endif - --htslib : htslib/libhts.a -- --htslib/libhts.a : -- $(MAKE) -C htslib lib-static -- - parametersDefault.xxd: parametersDefault - xxd -i parametersDefault > parametersDefault.xxd - --STAR : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) $(CXXFLAGS) --STAR : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_shared) $(LDFLAGS) - STAR : Depend.list parametersDefault.xxd $(OBJECTS) -- $(CXX) -o STAR $(CXXFLAGS) $(OBJECTS) $(LDFLAGS) -+ $(CXX) $(CXXFLAGS) $(CXXFLAGS_common) $(LDFLAGS) -o STAR $(OBJECTS) $(LIBS) $(LIBS_common) - --POSIXSHARED : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) -DPOSIX_SHARED_MEM $(CXXFLAGS) --POSIXSHARED : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_shared) $(LDFLAGS) - POSIXSHARED : Depend.list parametersDefault.xxd $(OBJECTS) -- $(CXX) -o STAR $(CXXFLAGS) $(OBJECTS) $(LDFLAGS) -+ $(CXX) $(CXXFLAGS) $(CXXFLAGS_common) $(LDFLAGS) -o STAR $(OBJECTS) $(LIBS) $(LIBS_common) - --STARstatic : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) $(CXXFLAGS) --STARstatic : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_static) $(LDFLAGS) - STARstatic : Depend.list parametersDefault.xxd $(OBJECTS) -- $(CXX) -o STAR $(CXXFLAGS) $(OBJECTS) $(LDFLAGS) -+ $(CXX) $(CXXFLAGS) $(CXXFLAGS_common) $(LDFLAGS) -o STAR $(OBJECTS) $(LIBS) $(LIBS_common) - --STARlong : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) -D'COMPILE_FOR_LONG_READS' $(CXXFLAGS) --STARlong : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_shared) $(LDFLAGS) - STARlong : Depend.list parametersDefault.xxd $(OBJECTS) -- $(CXX) -o STARlong $(CXXFLAGS) $(OBJECTS) $(LDFLAGS) -+ $(CXX) $(CXXFLAGS) $(CXXFLAGS_common) $(LDFLAGS) -o STARlong $(OBJECTS) $(LIBS) $(LIBS_common) - --STARlongStatic : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) -D'COMPILE_FOR_LONG_READS' $(CXXFLAGS) --STARlongStatic : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_static) $(LDFLAGS) - STARlongStatic : Depend.list parametersDefault.xxd $(OBJECTS) -- $(CXX) -o STARlong $(CXXFLAGS) $(OBJECTS) $(LDFLAGS) -+ $(CXX) $(CXXFLAGS) $(CXXFLAGS_common) $(LDFLAGS) -o STARlong $(OBJECTS) $(LIBS) $(LIBS_common) - --gdb : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_gdb) $(CXXFLAGS) --gdb : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_gdb) $(LDFLAGS) - gdb : Depend.list parametersDefault.xxd $(OBJECTS) -- $(CXX) -o STAR $(CXXFLAGS) $(OBJECTS) $(LDFLAGS) -+ $(CXX) $(CXXFLAGS) $(CXXFLAGS_common) $(LDFLAGS) -o STAR $(OBJECTS) $(LIBS) $(LIBS_common) - --gdb-long : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_gdb) -D'COMPILE_FOR_LONG_READS' $(CXXFLAGS) --gdb-long : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_gdb) $(LDFLAGS) - gdb-long : Depend.list parametersDefault.xxd $(OBJECTS) -- $(CXX) -o STARlong $(CXXFLAGS) $(OBJECTS) $(LDFLAGS) -+ $(CXX) $(CXXFLAGS) $(CXXFLAGS_common) $(LDFLAGS) -o STARlong $(OBJECTS) $(LIBS) $(LIBS_common) - --STARforMacStatic : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) -D'COMPILE_FOR_MAC' $(CXXFLAGS) --STARforMacStatic : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_Mac_static) $(LDFLAGS) - STARforMacStatic : Depend.list parametersDefault.xxd $(OBJECTS) -- $(CXX) -o STAR $(CXXFLAGS) $(OBJECTS) $(LDFLAGS) -+ $(CXX) $(CXXFLAGS) $(CXXFLAGS_common) $(LDFLAGS) -o STAR $(OBJECTS) $(LIBS) $(LIBS_common) - --STARlongForMacStatic : CXXFLAGS := -D'COMPILE_FOR_LONG_READS' $(CXXFLAGSextra) $(CXXFLAGS_main) -D'COMPILE_FOR_MAC' $(CXXFLAGS) --STARlongForMacStatic : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_Mac_static) $(LDFLAGS) - STARlongForMacStatic : Depend.list parametersDefault.xxd $(OBJECTS) -- $(CXX) -o STARlong $(CXXFLAGS) $(OBJECTS) $(LDFLAGS) -+ $(CXX) $(CXXFLAGS) $(CXXFLAGS_common) $(LDFLAGS) -o STARlong $(OBJECTS) $(LIBS) $(LIBS_common) - - |