diff options
| author | Efraim Flashner <efraim@flashner.co.il> | 2020-12-07 12:24:17 +0200 |
|---|---|---|
| committer | Efraim Flashner <efraim@flashner.co.il> | 2020-12-07 12:48:07 +0200 |
| commit | 3832704aff7444e26ba7f6915bdb4f718b1bf2f4 (patch) | |
| tree | ecc3d654ad23371c540486c5b1d3d12818dd1d21 /gnu/packages/patches | |
| parent | f48cd014f3986de119b746d9181a19ed056a3d37 (diff) | |
gnu: minimap2: Fix build on aarch64-linux.
* gnu/packages/bioinformatics.scm (minimap2)[arguments]: Adjust
configure-flags to be better per-architecture.
[source]: Add patch.
* gnu/packages/patches/minimap2-aarch64-support.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
Diffstat (limited to 'gnu/packages/patches')
| -rw-r--r-- | gnu/packages/patches/minimap2-aarch64-support.patch | 52 |
1 files changed, 52 insertions, 0 deletions
diff --git a/gnu/packages/patches/minimap2-aarch64-support.patch b/gnu/packages/patches/minimap2-aarch64-support.patch new file mode 100644 index 0000000000..95db8579d6 --- /dev/null +++ b/gnu/packages/patches/minimap2-aarch64-support.patch @@ -0,0 +1,52 @@ +This patch should be removed with the next release. There is WIP upstream +support for proper support of more architectures, including aarch64 and powerpc64le. + +diff --git a/Makefile b/Makefile +index ed341f6..94dbd85 100644 +--- a/Makefile ++++ b/Makefile +@@ -6,20 +6,18 @@ PROG= minimap2 + PROG_EXTRA= sdust minimap2-lite + LIBS= -lm -lz -lpthread + +-ifeq ($(arm_neon),) # if arm_neon is not defined +-ifeq ($(sse2only),) # if sse2only is not defined +- OBJS+=ksw2_extz2_sse41.o ksw2_extd2_sse41.o ksw2_exts2_sse41.o ksw2_extz2_sse2.o ksw2_extd2_sse2.o ksw2_exts2_sse2.o ksw2_dispatch.o +-else # if sse2only is defined +- OBJS+=ksw2_extz2_sse.o ksw2_extd2_sse.o ksw2_exts2_sse.o +-endif +-else # if arm_neon is defined ++ifneq ($(arm_neon),) # if arm_neon is defined + OBJS+=ksw2_extz2_neon.o ksw2_extd2_neon.o ksw2_exts2_neon.o +- INCLUDES+=-Isse2neon +-ifeq ($(aarch64),) #if aarch64 is not defined + CFLAGS+=-D_FILE_OFFSET_BITS=64 -mfpu=neon -fsigned-char +-else #if aarch64 is defined ++ INCLUDES+=-Isse2neon ++else ifneq ($(aarch64),) #if aarch64 is defined ++ OBJS+=ksw2_extz2_neon.o ksw2_extd2_neon.o ksw2_exts2_neon.o + CFLAGS+=-D_FILE_OFFSET_BITS=64 -fsigned-char +-endif ++ INCLUDES+=-Isse2neon ++else ifneq ($(sse2only),) # if sse2only is defined ++ OBJS+=ksw2_extz2_sse.o ksw2_extd2_sse.o ksw2_exts2_sse.o ++else # none of the above ++ OBJS+=ksw2_extz2_sse41.o ksw2_extd2_sse41.o ksw2_exts2_sse41.o ksw2_extz2_sse2.o ksw2_extd2_sse2.o ksw2_exts2_sse2.o ksw2_dispatch.o + endif + + .PHONY:all extra clean depend +@@ -46,9 +44,12 @@ sdust:sdust.c kalloc.o kalloc.h kdq.h kvec.h kseq.h ketopt.h sdust.h + + # SSE-specific targets on x86/x86_64 + +-ifeq ($(arm_neon),) # if arm_neon is defined, compile this target with the default setting (i.e. no -msse2) ++ifneq ($(arm_neon),) # if arm_neon is defined, compile this target with the default setting (i.e. no -msse2) ++ksw2_ll_sse.o:ksw2_ll_sse.c ksw2.h kalloc.h ++else ifneq ($(aarch64),) + ksw2_ll_sse.o:ksw2_ll_sse.c ksw2.h kalloc.h +- $(CC) -c $(CFLAGS) -msse2 $(CPPFLAGS) $(INCLUDES) $< -o $@ ++else ++ $(CC) -c $(CFLAGS) -msse2 $(CPPFLAGS) $(INCLUDES) $< -o $@ + endif + + ksw2_extz2_sse41.o:ksw2_extz2_sse.c ksw2.h kalloc.h |