diff options
Diffstat (limited to 'biology/minimap2/files/patch-Makefile.simde')
| -rw-r--r-- | biology/minimap2/files/patch-Makefile.simde | 66 |
1 files changed, 66 insertions, 0 deletions
diff --git a/biology/minimap2/files/patch-Makefile.simde b/biology/minimap2/files/patch-Makefile.simde new file mode 100644 index 000000000000..5d5e0ccf482c --- /dev/null +++ b/biology/minimap2/files/patch-Makefile.simde @@ -0,0 +1,66 @@ +--- Makefile.simde.orig 2021-11-18 22:11:48 UTC ++++ Makefile.simde +@@ -1,13 +1,26 @@ +-CFLAGS= -g -Wall -O2 -Wc++-compat #-Wextra +-CPPFLAGS= -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES +-INCLUDES= -Ilib/simde +-OBJS= kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o options.o index.o lchain.o align.o hit.o map.o format.o pe.o seed.o esterr.o splitidx.o \ +- ksw2_extz2_simde.o ksw2_extd2_simde.o ksw2_exts2_simde.o ksw2_ll_simde.o ++ ++# Makefile patches rejected by upstream ++ ++CFLAGS?= -g -Wall -O2 ++CFLAGS+= -Wc++-compat -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D__SSE2__ ++CPPFLAGS?= -DHAVE_KALLOC ++OBJS= kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o options.o \ ++ index.o lchain.o align.o hit.o map.o format.o pe.o seed.o \ ++ esterr.o splitidx.o ksw2_extz2_simde.o ksw2_extd2_simde.o \ ++ ksw2_exts2_simde.o ksw2_ll_simde.o + PROG= minimap2 + PROG_EXTRA= sdust minimap2-lite + LIBS= -lm -lz -lpthread + ++PREFIX?= /usr/local ++MAN1DIR?= ${PREFIX}/man/man1 ++DATADIR?= ${PREFIX}/share/minimap2 + ++MKDIR?= mkdir ++CP?= cp ++INSTALL?= install ++STRIP?= strip ++ + ifneq ($(arm_neon),) # if arm_neon is defined + ifeq ($(aarch64),) #if aarch64 is not defined + CFLAGS+=-D_FILE_OFFSET_BITS=64 -mfpu=neon -fsigned-char +@@ -26,7 +39,7 @@ ifneq ($(tsan),) + LIBS+=-fsanitize=thread + endif + +-.PHONY:all extra clean depend ++.PHONY:all extra install install-strip clean depend + .SUFFIXES:.c .o + + .c.o: +@@ -61,6 +74,22 @@ ksw2_exts2_simde.o:ksw2_exts2_sse.c ksw2.h kalloc.h + $(CC) -c $(CFLAGS) -msse4.1 $(CPPFLAGS) $(INCLUDES) $< -o $@ + + # other non-file targets ++ ++ ++install: all ++ ${MKDIR} -p ${DESTDIR}${PREFIX}/bin ++ ${MKDIR} -p ${DESTDIR}${MAN1DIR} ++ ${MKDIR} -p ${DESTDIR}${DATADIR} ++ ${INSTALL} -c minimap2 ${DESTDIR}${PREFIX}/bin ++ ${INSTALL} -c minimap2-lite ${DESTDIR}${PREFIX}/bin ++ ${INSTALL} -c sdust ${DESTDIR}${PREFIX}/bin ++ ${INSTALL} -c minimap2.1 ${DESTDIR}${MAN1DIR} ++ ${CP} -R test ${DESTDIR}${DATADIR} ++ ++install-strip: install ++ ${STRIP} ${DESTDIR}${PREFIX}/bin/minimap2 ++ ${STRIP} ${DESTDIR}${PREFIX}/bin/minimap2-lite ++ ${STRIP} ${DESTDIR}${PREFIX}/bin/sdust + + clean: + rm -fr gmon.out *.o a.out $(PROG) $(PROG_EXTRA) *~ *.a *.dSYM build dist mappy*.so mappy.c python/mappy.c mappy.egg* |