From 3832704aff7444e26ba7f6915bdb4f718b1bf2f4 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Mon, 7 Dec 2020 12:24:17 +0200
Subject: 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.
---
 .../patches/minimap2-aarch64-support.patch         | 52 ++++++++++++++++++++++
 1 file changed, 52 insertions(+)
 create mode 100644 gnu/packages/patches/minimap2-aarch64-support.patch

(limited to 'gnu/packages/patches/minimap2-aarch64-support.patch')

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
-- 
cgit v1.2.3