CVS commit: pkgsrc/biology/bwa

["Jason Bacon" <bacon%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   bacon
Date:           Thu May 18 14:05:15 UTC 2023

Modified Files:
        pkgsrc/biology/bwa: Makefile distinfo
        pkgsrc/biology/bwa/patches: patch-Makefile patch-kopen.c
Added Files:
        pkgsrc/biology/bwa/patches: patch-ksw.c

Log Message:
biology/bwa: Add support for aarch64 via devel/simde

May also work on other 64-bit architectures, but untested


To generate a diff of this commit:
cvs rdiff -u -r1.15 -r1.16 pkgsrc/biology/bwa/Makefile
cvs rdiff -u -r1.8 -r1.9 pkgsrc/biology/bwa/distinfo
cvs rdiff -u -r1.2 -r1.3 pkgsrc/biology/bwa/patches/patch-Makefile
cvs rdiff -u -r1.3 -r1.4 pkgsrc/biology/bwa/patches/patch-kopen.c
cvs rdiff -u -r0 -r1.1 pkgsrc/biology/bwa/patches/patch-ksw.c

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

Modified files:

Index: pkgsrc/biology/bwa/Makefile
diff -u pkgsrc/biology/bwa/Makefile:1.15 pkgsrc/biology/bwa/Makefile:1.16
--- pkgsrc/biology/bwa/Makefile:1.15    Wed Dec 28 15:27:16 2022
+++ pkgsrc/biology/bwa/Makefile Thu May 18 14:05:15 2023
@@ -1,8 +1,8 @@
-# $NetBSD: Makefile,v 1.15 2022/12/28 15:27:16 bacon Exp $
+# $NetBSD: Makefile,v 1.16 2023/05/18 14:05:15 bacon Exp $
 
 DISTNAME=      bwa-0.7.17
 CATEGORIES=    biology
-PKGREVISION=   6
+PKGREVISION=   7
 GITHUB_TAG=    v${PKGVERSION_NOREV}
 MASTER_SITES=  ${MASTER_SITE_GITHUB:=lh3/}
 
@@ -17,7 +17,7 @@ REPLACE_PERL= *.pl
 INSTALLATION_DIRS=     bin ${PKGMANDIR}/man1
 
 # unconditionally uses <emmintrin.h>
-ONLY_FOR_PLATFORM=     *-*-x86_64 *-*-i386 *-*-ia64
+ONLY_FOR_PLATFORM=     *-*-x86_64 *-*-i386 *-*-ia64 *-*-aarch64
 
 CFLAGS.SunOS+= -Du_int32_t=uint32_t
 LDFLAGS.SunOS+=        -lsocket -lnsl
@@ -28,4 +28,5 @@ do-install:
        ${INSTALL_MAN} ${WRKSRC}/*.1 ${DESTDIR}${PREFIX}/${PKGMANDIR}/man1
 
 .include "../../devel/zlib/buildlink3.mk"
+.include "../../devel/simde/buildlink3.mk"
 .include "../../mk/bsd.pkg.mk"

Index: pkgsrc/biology/bwa/distinfo
diff -u pkgsrc/biology/bwa/distinfo:1.8 pkgsrc/biology/bwa/distinfo:1.9
--- pkgsrc/biology/bwa/distinfo:1.8     Tue Oct 26 10:03:37 2021
+++ pkgsrc/biology/bwa/distinfo Thu May 18 14:05:15 2023
@@ -1,7 +1,8 @@
-$NetBSD: distinfo,v 1.8 2021/10/26 10:03:37 nia Exp $
+$NetBSD: distinfo,v 1.9 2023/05/18 14:05:15 bacon Exp $
 
 BLAKE2s (bwa-0.7.17.tar.gz) = be24abe7b59b3fddc3360344657c0ea38c1475aa86b9fd1729479f2bd927016d
 SHA512 (bwa-0.7.17.tar.gz) = 114e61b7cc5edcb67172d1eca7be1fa670ea33dd48b5c02c98318e254871363775c0dab327fd7ee7023200a5fedc745fa01cbe0fd9550d783f091d4df6926f48
 Size (bwa-0.7.17.tar.gz) = 232593 bytes
-SHA1 (patch-Makefile) = 72ac08d92540a88da08bf4d988ca3f6132327a6a
-SHA1 (patch-kopen.c) = ecc92efa3ebe4da484aa6760e23de9437b000644
+SHA1 (patch-Makefile) = 5da1b5453cc4c173e1bc01e37704685357b7a6c9
+SHA1 (patch-kopen.c) = 092cc6c83904aaab737ca6049ea9ee358149a2d7
+SHA1 (patch-ksw.c) = 2e7c655a40b485db99f4f8a7f844078b0065f572

Index: pkgsrc/biology/bwa/patches/patch-Makefile
diff -u pkgsrc/biology/bwa/patches/patch-Makefile:1.2 pkgsrc/biology/bwa/patches/patch-Makefile:1.3
--- pkgsrc/biology/bwa/patches/patch-Makefile:1.2       Sun Dec 17 14:30:36 2017
+++ pkgsrc/biology/bwa/patches/patch-Makefile   Thu May 18 14:05:15 2023
@@ -1,6 +1,7 @@
-$NetBSD: patch-Makefile,v 1.2 2017/12/17 14:30:36 bacon Exp $
+$NetBSD: patch-Makefile,v 1.3 2023/05/18 14:05:15 bacon Exp $
+
+# Respect env, add librt for NetBSD
 
-Respect env, add librt for NetBSD
 --- Makefile.orig      2017-10-23 17:10:17.000000000 +0000
 +++ Makefile
 @@ -1,6 +1,6 @@

Index: pkgsrc/biology/bwa/patches/patch-kopen.c
diff -u pkgsrc/biology/bwa/patches/patch-kopen.c:1.3 pkgsrc/biology/bwa/patches/patch-kopen.c:1.4
--- pkgsrc/biology/bwa/patches/patch-kopen.c:1.3        Wed Dec 27 23:44:01 2017
+++ pkgsrc/biology/bwa/patches/patch-kopen.c    Thu May 18 14:05:15 2023
@@ -1,6 +1,6 @@
-$NetBSD: patch-kopen.c,v 1.3 2017/12/27 23:44:01 he Exp $
+$NetBSD: patch-kopen.c,v 1.4 2023/05/18 14:05:15 bacon Exp $
 
-Add includes for getting timevals and select prototype into scope.
+# Add includes for getting timevals and select prototype into scope.
 
 --- kopen.c.orig       2017-10-23 17:10:17.000000000 +0000
 +++ kopen.c

Added files:

Index: pkgsrc/biology/bwa/patches/patch-ksw.c
diff -u /dev/null pkgsrc/biology/bwa/patches/patch-ksw.c:1.1
--- /dev/null   Thu May 18 14:05:15 2023
+++ pkgsrc/biology/bwa/patches/patch-ksw.c      Thu May 18 14:05:15 2023
@@ -0,0 +1,17 @@
+$NetBSD: patch-ksw.c,v 1.1 2023/05/18 14:05:15 bacon Exp $
+
+# Use SIMDE to support non-x86 architectures
+
+--- ksw.c.orig 2017-10-23 17:10:17.000000000 +0000
++++ ksw.c
+@@ -26,7 +26,9 @@
+ #include <stdlib.h>
+ #include <stdint.h>
+ #include <assert.h>
+-#include <emmintrin.h>
++// #include <emmintrin.h>
++#define SIMDE_ENABLE_NATIVE_ALIASES
++#include <simde/x86/sse2.h>
+ #include "ksw.h"
+ 
+ #ifdef USE_MALLOC_WRAPPERS