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.
---
 gnu/local.mk                                       |  1 +
 gnu/packages/bioinformatics.scm                    | 19 +++++---
 .../patches/minimap2-aarch64-support.patch         | 52 ++++++++++++++++++++++
 3 files changed, 65 insertions(+), 7 deletions(-)
 create mode 100644 gnu/packages/patches/minimap2-aarch64-support.patch

diff --git a/gnu/local.mk b/gnu/local.mk
index 4496cf73fa..f59d2543cd 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1348,6 +1348,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/mingw-w64-6.0.0-gcc.patch		\
   %D%/packages/patches/mingw-w64-dlltool-temp-prefix.patch	\
   %D%/packages/patches/mingw-w64-reproducible-gendef.patch	\
+  %D%/packages/patches/minimap2-aarch64-support.patch		\
   %D%/packages/patches/minisat-friend-declaration.patch		\
   %D%/packages/patches/minisat-install.patch			\
   %D%/packages/patches/mit-krb5-hurd.patch			\
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 312eb966e7..5efcfdea11 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -13056,7 +13056,8 @@ version does count multisplits.")
                            "minimap2-" version ".tar.bz2"))
        (sha256
         (base32
-         "0hi7i9pzxhvjj44khzzzj1lrn5gb5837arr4wgln7k1k5n4ci2mn"))))
+         "0hi7i9pzxhvjj44khzzzj1lrn5gb5837arr4wgln7k1k5n4ci2mn"))
+       (patches (search-patches "minimap2-aarch64-support.patch"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f                      ; there are none
@@ -13065,12 +13066,16 @@ version does count multisplits.")
              (let ((system ,(or (%current-target-system)
                                 (%current-system))))
                (cond
-                ((string-prefix? "x86_64" system)
-                 "all")
-                ((or (string-prefix? "armhf" system)
-                     (string-prefix? "aarch64" system))
-                 "arm_neon=1")
-                (else "sse2only=1"))))
+                 ((string-prefix? "x86_64" system)
+                  "all")
+                 ((or (string-prefix? "i586" system)
+                      (string-prefix? "i686" system))
+                  "sse2only=1")
+                 ((string-prefix? "armhf" system)
+                  "arm_neon=1")
+                 ((string-prefix? "aarch64" system)
+                  "aarch64=1")
+                 (else ""))))
        #:phases
        (modify-phases %standard-phases
          (delete 'configure)
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
-- 
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