diff options
Diffstat (limited to 'biology/star/files/patch-Makefile')
| -rw-r--r-- | biology/star/files/patch-Makefile | 73 |
1 files changed, 56 insertions, 17 deletions
diff --git a/biology/star/files/patch-Makefile b/biology/star/files/patch-Makefile index 99f3c4aa1237..55d592e70c2f 100644 --- a/biology/star/files/patch-Makefile +++ b/biology/star/files/patch-Makefile @@ -1,23 +1,62 @@ ---- Makefile.orig 2019-10-08 19:10:51 UTC +--- Makefile.orig 2023-08-15 19:21:58 UTC +++ Makefile -@@ -20,11 +20,16 @@ LDFLAGS_gdb := $(LDFLAGS_shared) +@@ -11,14 +11,19 @@ CXXFLAGSextra ?= + # user may define the compiler + CXX ?= g++ - COMPTIMEPLACE := -D'COMPILATION_TIME_PLACE="$(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) -+# Defaults, overridden by make arguments or environment -+CXXFLAGS ?= -pipe -O3 -Wall -Wextra -+CFLAGS ?= -pipe -O3 -Wall -Wextra - --CFLAGS := -O3 -pipe -Wall -Wextra $(CFLAGS) -+# Unconditionally set essential flags -+CXXFLAGS_common := -std=c++11 -fopenmp $(COMPTIMEPLACE) -+CXXFLAGS_main += $(CXXFLAGS_common) ++# user may set to '' and sed "htslib/htslib/*.h" to <htslib/*.h> ++# if they don't want the bundled htslib ++HTSLIB ?= htslib + -+# -O or -O2 should work fine with gdb as well -+CXXFLAGS_gdb := -O0 -g $(CXXFLAGS_common) + # pre-defined flags +-LDFLAGS_shared := -pthread -Lhtslib -Bstatic -lhts -Bdynamic -lz +-LDFLAGS_static := -static -static-libgcc -pthread -Lhtslib -lhts -lz ++LDFLAGS_shared := -pthread -lhts -lz ++LDFLAGS_static := -static -pthread -lhts -lz + LDFLAGS_Mac :=-pthread -lz htslib/libhts.a + LDFLAGS_Mac_static :=-pthread -lz -static-libgcc htslib/libhts.a + LDFLAGS_gdb := $(LDFLAGS_shared) + +-DATE_FMT = --iso-8601=seconds ++# --iso-8601 is not portable ++DATE_FMT = -Iseconds + ifdef SOURCE_DATE_EPOCH + BUILD_DATE ?= $(shell date -u -d "@$(SOURCE_DATE_EPOCH)" "$(DATE_FMT)" 2>/dev/null || date -u -r "$(SOURCE_DATE_EPOCH)" "$(DATE_FMT)" 2>/dev/null || date -u "$(DATE_FMT)") + else +@@ -41,12 +46,12 @@ GIT_BRANCH_COMMIT_DIFF := -D'GIT_BRANCH_COMMIT_DIFF="$ + + # Defaults, can be overridden by make arguments or environment + CXXFLAGS ?= -pipe -Wall -Wextra +-CFLAGS ?= -pipe -Wall -Wextra -O3 ++CFLAGS ?= -pipe -Wall -Wextra + CXXFLAGS_SIMD ?= -mavx2 + # Unconditionally set essential flags and optimization options + CXXFLAGS_common := -std=c++11 -fopenmp $(COMPTIMEPLACE) $(GIT_BRANCH_COMMIT_DIFF) +-CXXFLAGS_main := -O3 $(CXXFLAGS_common) ++CXXFLAGS_main := $(CXXFLAGS_common) + CXXFLAGS_gdb := -O0 -g3 $(CXXFLAGS_common) ########################################################################################################## +@@ -114,7 +119,7 @@ clean: + + .PHONY: CLEAN + CLEAN: clean +- $(MAKE) -C htslib clean ++ $(MAKE) -C $(HTSLIB) clean + + + .PHONY: clean_solo +@@ -131,10 +136,10 @@ ifneq ($(MAKECMDGOALS),CLEAN) + ifneq ($(MAKECMDGOALS),clean_solo) + ifneq ($(MAKECMDGOALS),STARforMac) + ifneq ($(MAKECMDGOALS),STARforMacGDB) +-Depend.list: $(SOURCES) parametersDefault.xxd htslib ++Depend.list: $(SOURCES) parametersDefault.xxd $(HTSLIB) + echo $(SOURCES) + 'rm' -f ./Depend.list +- $(CXX) $(CXXFLAGS_common) -MM $^ >> Depend.list ++ $(CXX) $(CXXFLAGS) $(CXXFLAGS_common) -MM $^ >> Depend.list + include Depend.list + endif + endif |