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gnu: minimap2: Fix build on aarch64-linux.

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* 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.
This commit is contained in:
Efraim Flashner 2020-12-07 12:24:17 +02:00
parent f48cd014f3
commit 3832704aff
No known key found for this signature in database
GPG key ID: 41AAE7DCCA3D8351
3 changed files with 65 additions and 7 deletions
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1
gnu/local.mk
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@ -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 \

19
gnu/packages/bioinformatics.scm
View file

@ -13056,7 +13056,8 @@ (define-public minimap2
"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 @@ (define-public minimap2
(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)

52
gnu/packages/patches/minimap2-aarch64-support.patch Normal file
View file

@ -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