CVS commit: pkgsrc/biology/bowtie2

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

Module Name:    pkgsrc
Committed By:   bacon
Date:           Fri May 24 11:32:58 UTC 2024

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

Log Message:
biology/bowtie2: Update to 2.5.4

A few bug fixes and minor enhancements
Changes: https://github.com/BenLangmead/bowtie2/releases


To generate a diff of this commit:
cvs rdiff -u -r1.10 -r1.11 pkgsrc/biology/bowtie2/Makefile
cvs rdiff -u -r1.5 -r1.6 pkgsrc/biology/bowtie2/PLIST
cvs rdiff -u -r1.7 -r1.8 pkgsrc/biology/bowtie2/distinfo
cvs rdiff -u -r1.5 -r1.6 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:1.10 pkgsrc/biology/bowtie2/Makefile:1.11
--- pkgsrc/biology/bowtie2/Makefile:1.10        Thu Jan 18 23:30:12 2024
+++ pkgsrc/biology/bowtie2/Makefile     Fri May 24 11:32:57 2024
@@ -1,6 +1,6 @@
-# $NetBSD: Makefile,v 1.10 2024/01/18 23:30:12 bacon Exp $
+# $NetBSD: Makefile,v 1.11 2024/05/24 11:32:57 bacon Exp $
 
-DISTNAME=      bowtie2-2.5.3
+DISTNAME=      bowtie2-2.5.4
 CATEGORIES=    biology
 MASTER_SITES=  ${MASTER_SITE_GITHUB:=BenLangmead/}
 GITHUB_TAG=    v${PKGVERSION_NOREV}

Index: pkgsrc/biology/bowtie2/PLIST
diff -u pkgsrc/biology/bowtie2/PLIST:1.5 pkgsrc/biology/bowtie2/PLIST:1.6
--- pkgsrc/biology/bowtie2/PLIST:1.5    Thu Jan 18 23:30:12 2024
+++ pkgsrc/biology/bowtie2/PLIST        Fri May 24 11:32:57 2024
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.5 2024/01/18 23:30:12 bacon Exp $
+@comment $NetBSD: PLIST,v 1.6 2024/05/24 11:32:57 bacon Exp $
 bin/bowtie2
 bin/bowtie2-align-l
 bin/bowtie2-align-s

Index: pkgsrc/biology/bowtie2/distinfo
diff -u pkgsrc/biology/bowtie2/distinfo:1.7 pkgsrc/biology/bowtie2/distinfo:1.8
--- pkgsrc/biology/bowtie2/distinfo:1.7 Thu Jan 18 23:30:12 2024
+++ pkgsrc/biology/bowtie2/distinfo     Fri May 24 11:32:58 2024
@@ -1,7 +1,7 @@
-$NetBSD: distinfo,v 1.7 2024/01/18 23:30:12 bacon Exp $
+$NetBSD: distinfo,v 1.8 2024/05/24 11:32:58 bacon Exp $
 
-BLAKE2s (bowtie2-2.5.3.tar.gz) = 7d1bc829a0b5c9596bbfb45504cee42688dd779bf733958ad188e9be2ddc6ee0
-SHA512 (bowtie2-2.5.3.tar.gz) = 5ef4cbbcb379e1c993e6cc11e2b851f9f80b5ceb274c8fee5b278aecaa76fc40732a0db4ef5e1dda34a35fbb0f0ce6bd86293f4d928e39eaf633e8be664066b6
-Size (bowtie2-2.5.3.tar.gz) = 10635819 bytes
+BLAKE2s (bowtie2-2.5.4.tar.gz) = 678e3a51ead89c78a000635fc860db16ecefa5880663bd3ac305c7944db4a039
+SHA512 (bowtie2-2.5.4.tar.gz) = 3357abc5e1c5b25afbb64659054c171ddb1ae4f996e5cf0336d722b118d3e7508425b0220ece5982534edffcdb9f16148aec1cbbb1ab909bdd017b99864bc93a
+Size (bowtie2-2.5.4.tar.gz) = 10638569 bytes
 SHA1 (patch-Makefile) = 59b9823472a371fa9142a69b37df406c4ed47cd9
 SHA1 (patch-scripts_bowtie2-hbb.sh) = d360774cfef0675b4c1cdd1175b394d2cf7f761a

Index: pkgsrc/biology/bowtie2/patches/patch-Makefile
diff -u pkgsrc/biology/bowtie2/patches/patch-Makefile:1.5 pkgsrc/biology/bowtie2/patches/patch-Makefile:1.6
--- pkgsrc/biology/bowtie2/patches/patch-Makefile:1.5   Thu Jan 18 23:30:12 2024
+++ pkgsrc/biology/bowtie2/patches/patch-Makefile       Fri May 24 11:32:58 2024
@@ -1,4 +1,4 @@
-$NetBSD: patch-Makefile,v 1.5 2024/01/18 23:30:12 bacon Exp $
+$NetBSD: patch-Makefile,v 1.6 2024/05/24 11:32:58 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:1.5 pkgsrc/biology/bowtie2/patches/patch-scripts_bowtie2-hbb.sh:1.6
--- pkgsrc/biology/bowtie2/patches/patch-scripts_bowtie2-hbb.sh:1.5     Thu Jan 18 23:30:12 2024
+++ pkgsrc/biology/bowtie2/patches/patch-scripts_bowtie2-hbb.sh Fri May 24 11:32:58 2024
@@ -1,4 +1,4 @@
-$NetBSD: patch-scripts_bowtie2-hbb.sh,v 1.5 2024/01/18 23:30:12 bacon Exp $
+$NetBSD: patch-scripts_bowtie2-hbb.sh,v 1.6 2024/05/24 11:32:58 bacon Exp $
 
 # Eliminate bash dependency