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authorEfraim Flashner <efraim@flashner.co.il>2020-12-07 12:24:17 +0200
committerEfraim Flashner <efraim@flashner.co.il>2020-12-07 12:48:07 +0200
commit3832704aff7444e26ba7f6915bdb4f718b1bf2f4 (patch)
treeecc3d654ad23371c540486c5b1d3d12818dd1d21 /gnu/packages/patches
parentf48cd014f3986de119b746d9181a19ed056a3d37 (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.patch52
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