CVS commit: pkgsrc/biology/hisat2

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

Module Name:    pkgsrc
Committed By:   bacon
Date:           Wed May 17 21:55:35 UTC 2023

Modified Files:
        pkgsrc/biology/hisat2: Makefile PLIST distinfo
        pkgsrc/biology/hisat2/patches: patch-Makefile patch-hisat2
            patch-processor__support.h
Added Files:
        pkgsrc/biology/hisat2/patches: patch-aligner__sw.h patch-sse__util.h

Log Message:
biology/hisat2: Add SIMDE support

SIMDE enables SSE and other x86 intrinsics on other architectures
Tested on ARM64, may work on other 64-bit platforms


To generate a diff of this commit:
cvs rdiff -u -r1.10 -r1.11 pkgsrc/biology/hisat2/Makefile
cvs rdiff -u -r1.2 -r1.3 pkgsrc/biology/hisat2/PLIST
cvs rdiff -u -r1.4 -r1.5 pkgsrc/biology/hisat2/distinfo
cvs rdiff -u -r1.1 -r1.2 pkgsrc/biology/hisat2/patches/patch-Makefile \
    pkgsrc/biology/hisat2/patches/patch-processor__support.h
cvs rdiff -u -r0 -r1.1 pkgsrc/biology/hisat2/patches/patch-aligner__sw.h \
    pkgsrc/biology/hisat2/patches/patch-sse__util.h
cvs rdiff -u -r1.2 -r1.3 pkgsrc/biology/hisat2/patches/patch-hisat2

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

Modified files:

Index: pkgsrc/biology/hisat2/Makefile
diff -u pkgsrc/biology/hisat2/Makefile:1.10 pkgsrc/biology/hisat2/Makefile:1.11
--- pkgsrc/biology/hisat2/Makefile:1.10 Wed Dec 28 15:27:16 2022
+++ pkgsrc/biology/hisat2/Makefile      Wed May 17 21:55:34 2023
@@ -1,7 +1,7 @@
-# $NetBSD: Makefile,v 1.10 2022/12/28 15:27:16 bacon Exp $
+# $NetBSD: Makefile,v 1.11 2023/05/17 21:55:34 bacon Exp $
 
 DISTNAME=      hisat2-2.2.1
-PKGREVISION=   2
+PKGREVISION=   3
 CATEGORIES=    biology
 MASTER_SITES=  ${MASTER_SITE_GITHUB:=DaehwanKimLab/}
 GITHUB_TAG=    v${PKGVERSION_NOREV}
@@ -12,7 +12,7 @@ COMMENT=      Alignment program for mapping n
 LICENSE=       gnu-gpl-v3
 
 # 64-bit code, some assembly language
-ONLY_FOR_PLATFORM=     *-*-x86_64
+ONLY_FOR_PLATFORM=     *-*-x86_64 *-*-aarch64
 
 USE_LANGUAGES= c c++
 USE_TOOLS+=    bash gmake perl
@@ -28,6 +28,7 @@ WRKSRC=                       ${WRKDIR}/hisat2-2.2.1
 post-patch:
        ${MV} ${WRKSRC}/VERSION ${WRKSRC}/HISAT2_VERSION
 
+.include "../../devel/simde/buildlink3.mk"
 .include "../../lang/python/application.mk"
 .include "../../mk/pthread.buildlink3.mk"
 .include "../../mk/bsd.pkg.mk"

Index: pkgsrc/biology/hisat2/PLIST
diff -u pkgsrc/biology/hisat2/PLIST:1.2 pkgsrc/biology/hisat2/PLIST:1.3
--- pkgsrc/biology/hisat2/PLIST:1.2     Thu Mar 17 16:01:11 2022
+++ pkgsrc/biology/hisat2/PLIST Wed May 17 21:55:34 2023
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.2 2022/03/17 16:01:11 bacon Exp $
+@comment $NetBSD: PLIST,v 1.3 2023/05/17 21:55:34 bacon Exp $
 bin/hisat2
 bin/hisat2-align-l
 bin/hisat2-align-s

Index: pkgsrc/biology/hisat2/distinfo
diff -u pkgsrc/biology/hisat2/distinfo:1.4 pkgsrc/biology/hisat2/distinfo:1.5
--- pkgsrc/biology/hisat2/distinfo:1.4  Thu Mar 17 16:01:11 2022
+++ pkgsrc/biology/hisat2/distinfo      Wed May 17 21:55:34 2023
@@ -1,8 +1,10 @@
-$NetBSD: distinfo,v 1.4 2022/03/17 16:01:11 bacon Exp $
+$NetBSD: distinfo,v 1.5 2023/05/17 21:55:34 bacon Exp $
 
 BLAKE2s (hisat2-2.2.1.tar.gz) = 1cc424a10f1fcf25c70294bef3b21e67b07cebcb7b73e36c0176a2dfdec51bdb
 SHA512 (hisat2-2.2.1.tar.gz) = a5a688ad0ccfaf326b3ec6dc97206995306aa6f5b6e58223c2113adbca2745f1e8205b436fdf8e01f42da7a38718f9f3bf214b951fb5360d53247d99a0bdbf46
 Size (hisat2-2.2.1.tar.gz) = 6761242 bytes
 SHA1 (patch-Makefile) = 067b766ecebacd840db4a287bba25d2d2264b339
+SHA1 (patch-aligner__sw.h) = 628c14bfd6b26185eada73013175e35de2b38227
 SHA1 (patch-hisat2) = 6010f5fcc1e7dfcb383a4defc4e3d9f06322370d
 SHA1 (patch-processor__support.h) = 56d9cd4ba18e37879acba521a0f431fe2b4290af
+SHA1 (patch-sse__util.h) = f0bbe72dfe3a2567e614683e3aecc10f3d6583ef

Index: pkgsrc/biology/hisat2/patches/patch-Makefile
diff -u pkgsrc/biology/hisat2/patches/patch-Makefile:1.1 pkgsrc/biology/hisat2/patches/patch-Makefile:1.2
--- pkgsrc/biology/hisat2/patches/patch-Makefile:1.1    Thu Mar 17 16:01:12 2022
+++ pkgsrc/biology/hisat2/patches/patch-Makefile        Wed May 17 21:55:34 2023
@@ -1,4 +1,4 @@
-$NetBSD: patch-Makefile,v 1.1 2022/03/17 16:01:12 bacon Exp $
+$NetBSD: patch-Makefile,v 1.2 2023/05/17 21:55:34 bacon Exp $
 
 # Respect env
 
Index: pkgsrc/biology/hisat2/patches/patch-processor__support.h
diff -u pkgsrc/biology/hisat2/patches/patch-processor__support.h:1.1 pkgsrc/biology/hisat2/patches/patch-processor__support.h:1.2
--- pkgsrc/biology/hisat2/patches/patch-processor__support.h:1.1        Thu Mar 17 16:01:12 2022
+++ pkgsrc/biology/hisat2/patches/patch-processor__support.h    Wed May 17 21:55:34 2023
@@ -1,4 +1,4 @@
-$NetBSD: patch-processor__support.h,v 1.1 2022/03/17 16:01:12 bacon Exp $
+$NetBSD: patch-processor__support.h,v 1.2 2023/05/17 21:55:34 bacon Exp $
 
 # Support non-x86
 

Index: pkgsrc/biology/hisat2/patches/patch-hisat2
diff -u pkgsrc/biology/hisat2/patches/patch-hisat2:1.2 pkgsrc/biology/hisat2/patches/patch-hisat2:1.3
--- pkgsrc/biology/hisat2/patches/patch-hisat2:1.2      Thu Mar 17 16:01:12 2022
+++ pkgsrc/biology/hisat2/patches/patch-hisat2  Wed May 17 21:55:34 2023
@@ -1,4 +1,4 @@
-$NetBSD: patch-hisat2,v 1.2 2022/03/17 16:01:12 bacon Exp $
+$NetBSD: patch-hisat2,v 1.3 2023/05/17 21:55:34 bacon Exp $
 
 # Support BSD, etc.
 

Added files:

Index: pkgsrc/biology/hisat2/patches/patch-aligner__sw.h
diff -u /dev/null pkgsrc/biology/hisat2/patches/patch-aligner__sw.h:1.1
--- /dev/null   Wed May 17 21:55:35 2023
+++ pkgsrc/biology/hisat2/patches/patch-aligner__sw.h   Wed May 17 21:55:34 2023
@@ -0,0 +1,22 @@
+$NetBSD: patch-aligner__sw.h,v 1.1 2023/05/17 21:55:34 bacon Exp $
+
+# Support non-x86
+
+--- aligner_sw.h.orig  2020-07-24 20:07:54.000000000 +0000
++++ aligner_sw.h
+@@ -66,11 +66,14 @@
+ 
+ #define INLINE_CUPS
+ 
++#define       SIMDE_ENABLE_NATIVE_ALIASES
++
++#include <simde/x86/sse2.h>
+ #include <stdint.h>
+ #include <iostream>
+ #include <limits>
+ #include "threading.h"
+-#include <emmintrin.h>
++// #include <emmintrin.h>     // Replace this with simde when possible
+ #include "aligner_sw_common.h"
+ #include "aligner_sw_nuc.h"
+ #include "ds.h"
Index: pkgsrc/biology/hisat2/patches/patch-sse__util.h
diff -u /dev/null pkgsrc/biology/hisat2/patches/patch-sse__util.h:1.1
--- /dev/null   Wed May 17 21:55:35 2023
+++ pkgsrc/biology/hisat2/patches/patch-sse__util.h     Wed May 17 21:55:34 2023
@@ -0,0 +1,22 @@
+$NetBSD: patch-sse__util.h,v 1.1 2023/05/17 21:55:34 bacon Exp $
+
+# Support non-x86
+
+--- sse_util.h.orig    2020-07-24 20:07:54.000000000 +0000
++++ sse_util.h
+@@ -20,11 +20,14 @@
+ #ifndef SSE_UTIL_H_
+ #define SSE_UTIL_H_
+ 
++#define SIMDE_ENABLE_NATIVE_ALIASES
++#include <simde/x86/sse2.h>
++
+ #include "assert_helpers.h"
+ #include "ds.h"
+ #include "limit.h"
+ #include <iostream>
+-#include <emmintrin.h>
++// #include <emmintrin.h>             // Replace with simde when possible
+ 
+ class EList_m128i {
+ public: