CVS commit: pkgsrc/biology/bowtie2

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

Module Name:    pkgsrc
Committed By:   bacon
Date:           Thu May 18 14:16:27 UTC 2023

Modified Files:
        pkgsrc/biology/bowtie2: Makefile PLIST distinfo
        pkgsrc/biology/bowtie2/patches: patch-Makefile
            patch-scripts_bowtie2-hbb.sh

Log Message:
biology/bowtie2: 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 -r1.6 -r1.7 pkgsrc/biology/bowtie2/Makefile
cvs rdiff -u -r1.2 -r1.3 pkgsrc/biology/bowtie2/PLIST
cvs rdiff -u -r1.4 -r1.5 pkgsrc/biology/bowtie2/distinfo
cvs rdiff -u -r1.2 -r1.3 pkgsrc/biology/bowtie2/patches/patch-Makefile \
    pkgsrc/biology/bowtie2/patches/patch-scripts_bowtie2-hbb.sh

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

Modified files:

Index: pkgsrc/biology/bowtie2/Makefile
diff -u pkgsrc/biology/bowtie2/Makefile:1.6 pkgsrc/biology/bowtie2/Makefile:1.7
--- pkgsrc/biology/bowtie2/Makefile:1.6 Wed Dec 28 15:27:16 2022
+++ pkgsrc/biology/bowtie2/Makefile     Thu May 18 14:16:27 2023
@@ -1,7 +1,7 @@
-# $NetBSD: Makefile,v 1.6 2022/12/28 15:27:16 bacon Exp $
+# $NetBSD: Makefile,v 1.7 2023/05/18 14:16:27 bacon Exp $
 
 DISTNAME=      bowtie2-2.4.4
-PKGREVISION=   2
+PKGREVISION=   3
 CATEGORIES=    biology
 MASTER_SITES=  ${MASTER_SITE_GITHUB:=BenLangmead/}
 GITHUB_TAG=    v${PKGVERSION_NOREV}
@@ -30,4 +30,5 @@ post-install:
 
 .include "../../lang/python/application.mk"
 .include "../../devel/zlib/buildlink3.mk"
+.include "../../devel/simde/buildlink3.mk"
 .include "../../mk/bsd.pkg.mk"

Index: pkgsrc/biology/bowtie2/PLIST
diff -u pkgsrc/biology/bowtie2/PLIST:1.2 pkgsrc/biology/bowtie2/PLIST:1.3
--- pkgsrc/biology/bowtie2/PLIST:1.2    Fri Dec 17 15:25:20 2021
+++ pkgsrc/biology/bowtie2/PLIST        Thu May 18 14:16:27 2023
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.2 2021/12/17 15:25:20 bacon Exp $
+@comment $NetBSD: PLIST,v 1.3 2023/05/18 14:16:27 bacon Exp $
 bin/bowtie2
 bin/bowtie2-align-l
 bin/bowtie2-align-s

Index: pkgsrc/biology/bowtie2/distinfo
diff -u pkgsrc/biology/bowtie2/distinfo:1.4 pkgsrc/biology/bowtie2/distinfo:1.5
--- pkgsrc/biology/bowtie2/distinfo:1.4 Fri Dec 17 15:25:20 2021
+++ pkgsrc/biology/bowtie2/distinfo     Thu May 18 14:16:27 2023
@@ -1,4 +1,4 @@
-$NetBSD: distinfo,v 1.4 2021/12/17 15:25:20 bacon Exp $
+$NetBSD: distinfo,v 1.5 2023/05/18 14:16:27 bacon Exp $
 
 BLAKE2s (bowtie2-2.4.4.tar.gz) = 685468ca08b60b58de8ed51fec3c7a22411c278f7e8c8703461707b4de996d3e
 SHA512 (bowtie2-2.4.4.tar.gz) = 2db44e8219bcb916119b8097dd10adcc2185d3ce7df6147210c78070dce57fefddbc79c64dc2a55fdc49a46c4df80c37c8c6d786cce20a95a2e50ce0692befed

Index: pkgsrc/biology/bowtie2/patches/patch-Makefile
diff -u pkgsrc/biology/bowtie2/patches/patch-Makefile:1.2 pkgsrc/biology/bowtie2/patches/patch-Makefile:1.3
--- pkgsrc/biology/bowtie2/patches/patch-Makefile:1.2   Fri Dec 17 15:25:20 2021
+++ pkgsrc/biology/bowtie2/patches/patch-Makefile       Thu May 18 14:16:27 2023
@@ -1,4 +1,4 @@
-$NetBSD: patch-Makefile,v 1.2 2021/12/17 15:25:20 bacon Exp $
+$NetBSD: patch-Makefile,v 1.3 2023/05/18 14:16:27 bacon Exp $
 
 # Respect pkgsrc env
 
Index: pkgsrc/biology/bowtie2/patches/patch-scripts_bowtie2-hbb.sh
diff -u pkgsrc/biology/bowtie2/patches/patch-scripts_bowtie2-hbb.sh:1.2 pkgsrc/biology/bowtie2/patches/patch-scripts_bowtie2-hbb.sh:1.3
--- pkgsrc/biology/bowtie2/patches/patch-scripts_bowtie2-hbb.sh:1.2     Fri Dec 17 15:25:20 2021
+++ pkgsrc/biology/bowtie2/patches/patch-scripts_bowtie2-hbb.sh Thu May 18 14:16:27 2023
@@ -1,4 +1,4 @@
-$NetBSD: patch-scripts_bowtie2-hbb.sh,v 1.2 2021/12/17 15:25:20 bacon Exp $
+$NetBSD: patch-scripts_bowtie2-hbb.sh,v 1.3 2023/05/18 14:16:27 bacon Exp $
 
 # Eliminate bash dependency