CVS commit: pkgsrc/biology/samtools

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

Module Name:    pkgsrc
Committed By:   bacon
Date:           Fri Oct 11 22:38:32 UTC 2024

Modified Files:
        pkgsrc/biology/samtools: Makefile PLIST distinfo
        pkgsrc/biology/samtools/patches: patch-Makefile

Log Message:
biology/samtools: Update to 1.21

Numerous bug fixes and enhancements since 1.17
Changes:        https://github.com/samtools/samtools/releases

Reported by:    portscout


To generate a diff of this commit:
cvs rdiff -u -r1.20 -r1.21 pkgsrc/biology/samtools/Makefile
cvs rdiff -u -r1.7 -r1.8 pkgsrc/biology/samtools/PLIST
cvs rdiff -u -r1.10 -r1.11 pkgsrc/biology/samtools/distinfo
cvs rdiff -u -r1.5 -r1.6 pkgsrc/biology/samtools/patches/patch-Makefile

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

Modified files:

Index: pkgsrc/biology/samtools/Makefile
diff -u pkgsrc/biology/samtools/Makefile:1.20 pkgsrc/biology/samtools/Makefile:1.21
--- pkgsrc/biology/samtools/Makefile:1.20       Mon Aug 14 05:23:52 2023
+++ pkgsrc/biology/samtools/Makefile    Fri Oct 11 22:38:32 2024
@@ -1,7 +1,6 @@
-# $NetBSD: Makefile,v 1.20 2023/08/14 05:23:52 wiz Exp $
+# $NetBSD: Makefile,v 1.21 2024/10/11 22:38:32 bacon Exp $
 
-DISTNAME=      samtools-1.17
-PKGREVISION=   1
+DISTNAME=      samtools-1.21
 CATEGORIES=    biology
 MASTER_SITES=  ${MASTER_SITE_GITHUB:=samtools/}
 GITHUB_RELEASE=        ${PKGVERSION_NOREV}
@@ -36,8 +35,7 @@ REPLACE_LUA+=         misc/*.lua
 pre-configure:
        cd ${WRKSRC} && autoreconf -if
 
-.include "../../biology/htslib/buildlink3.mk"
 .include "../../devel/zlib/buildlink3.mk"
-.include "../../lang/python/application.mk"
 .include "../../mk/curses.buildlink3.mk"
+.include "../../biology/htslib/buildlink3.mk"
 .include "../../mk/bsd.pkg.mk"

Index: pkgsrc/biology/samtools/PLIST
diff -u pkgsrc/biology/samtools/PLIST:1.7 pkgsrc/biology/samtools/PLIST:1.8
--- pkgsrc/biology/samtools/PLIST:1.7   Sat Feb 25 13:52:39 2023
+++ pkgsrc/biology/samtools/PLIST       Fri Oct 11 22:38:32 2024
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.7 2023/02/25 13:52:39 bacon Exp $
+@comment $NetBSD: PLIST,v 1.8 2024/10/11 22:38:32 bacon Exp $
 bin/ace2sam
 bin/blast2sam.pl
 bin/bowtie2sam.pl

Index: pkgsrc/biology/samtools/distinfo
diff -u pkgsrc/biology/samtools/distinfo:1.10 pkgsrc/biology/samtools/distinfo:1.11
--- pkgsrc/biology/samtools/distinfo:1.10       Sat Feb 25 13:52:39 2023
+++ pkgsrc/biology/samtools/distinfo    Fri Oct 11 22:38:32 2024
@@ -1,6 +1,6 @@
-$NetBSD: distinfo,v 1.10 2023/02/25 13:52:39 bacon Exp $
+$NetBSD: distinfo,v 1.11 2024/10/11 22:38:32 bacon Exp $
 
-BLAKE2s (samtools-1.17.tar.bz2) = 9ab61bddae955190736abf7e9198ee869396a74e195166df38ebb652fe4bc7c7
-SHA512 (samtools-1.17.tar.bz2) = 107a6df858c6bd2556ba4e86cc1922c3184df095f347039fa94bfd24e5ee21e1a4a9fba5a7cce248a06ad47f99978d9aae570efee7e30e165f33ea848a2cd3c3
-Size (samtools-1.17.tar.bz2) = 8605080 bytes
+BLAKE2s (samtools-1.21.tar.bz2) = 1afebdea83ad360ca58c1939e8c776c96c7e65539ee9c4d8ad7db7eadfc79495
+SHA512 (samtools-1.21.tar.bz2) = 4f80a4333ebb4dc0eb5f38f29474424b1acca9b677aa206b111c7a638b8ae924ab2dcdc9de15eb1b849576d0158579a476a7b78ccd73e7d2baafc3bbb88c6103
+Size (samtools-1.21.tar.bz2) = 9149284 bytes
 SHA1 (patch-Makefile) = 3fc1f1d67167c8ca8eff1ed17f7a084ec3d4579d

Index: pkgsrc/biology/samtools/patches/patch-Makefile
diff -u pkgsrc/biology/samtools/patches/patch-Makefile:1.5 pkgsrc/biology/samtools/patches/patch-Makefile:1.6
--- pkgsrc/biology/samtools/patches/patch-Makefile:1.5  Sat Feb 25 13:52:39 2023
+++ pkgsrc/biology/samtools/patches/patch-Makefile      Fri Oct 11 22:38:32 2024
@@ -1,4 +1,4 @@
-$NetBSD: patch-Makefile,v 1.5 2023/02/25 13:52:39 bacon Exp $
+$NetBSD: patch-Makefile,v 1.6 2024/10/11 22:38:32 bacon Exp $
 
 # Respect pkgsrc env