CVS commit: pkgsrc/biology/bowtie2

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

Module Name:    pkgsrc
Committed By:   bacon
Date:           Thu Jan 18 23:30:12 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 2.5.3

A few bug fixes
Add option for faster indexing of small indexes
Changes: https://github.com/BenLangmead/bowtie2/releases
Reported by: portscout


To generate a diff of this commit:
cvs rdiff -u -r1.9 -r1.10 pkgsrc/biology/bowtie2/Makefile
cvs rdiff -u -r1.4 -r1.5 pkgsrc/biology/bowtie2/PLIST
cvs rdiff -u -r1.6 -r1.7 pkgsrc/biology/bowtie2/distinfo
cvs rdiff -u -r1.4 -r1.5 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:1.9 pkgsrc/biology/bowtie2/Makefile:1.10
--- pkgsrc/biology/bowtie2/Makefile:1.9 Wed Oct 18 13:34:23 2023
+++ pkgsrc/biology/bowtie2/Makefile     Thu Jan 18 23:30:12 2024
@@ -1,6 +1,6 @@
-# $NetBSD: Makefile,v 1.9 2023/10/18 13:34:23 bacon Exp $
+# $NetBSD: Makefile,v 1.10 2024/01/18 23:30:12 bacon Exp $
 
-DISTNAME=      bowtie2-2.5.2
+DISTNAME=      bowtie2-2.5.3
 CATEGORIES=    biology
 MASTER_SITES=  ${MASTER_SITE_GITHUB:=BenLangmead/}
 GITHUB_TAG=    v${PKGVERSION_NOREV}

Index: pkgsrc/biology/bowtie2/PLIST
diff -u pkgsrc/biology/bowtie2/PLIST:1.4 pkgsrc/biology/bowtie2/PLIST:1.5
--- pkgsrc/biology/bowtie2/PLIST:1.4    Wed Oct 18 13:34:23 2023
+++ pkgsrc/biology/bowtie2/PLIST        Thu Jan 18 23:30:12 2024
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.4 2023/10/18 13:34:23 bacon Exp $
+@comment $NetBSD: PLIST,v 1.5 2024/01/18 23:30:12 bacon Exp $
 bin/bowtie2
 bin/bowtie2-align-l
 bin/bowtie2-align-s

Index: pkgsrc/biology/bowtie2/distinfo
diff -u pkgsrc/biology/bowtie2/distinfo:1.6 pkgsrc/biology/bowtie2/distinfo:1.7
--- pkgsrc/biology/bowtie2/distinfo:1.6 Wed Oct 18 13:34:23 2023
+++ pkgsrc/biology/bowtie2/distinfo     Thu Jan 18 23:30:12 2024
@@ -1,7 +1,7 @@
-$NetBSD: distinfo,v 1.6 2023/10/18 13:34:23 bacon Exp $
+$NetBSD: distinfo,v 1.7 2024/01/18 23:30:12 bacon Exp $
 
-BLAKE2s (bowtie2-2.5.2.tar.gz) = 419a51add22afdb8020a650e627275aeaf93d68c7b08af3354dd230fbefa0b18
-SHA512 (bowtie2-2.5.2.tar.gz) = e3887439fc5b2c553977451bb519b9d60756a743311690ecd4cd997251630f465f82a82bd47df7f8a76a4d6b4d62e08aa80512a6a7f08e62169dca433c45eeef
-Size (bowtie2-2.5.2.tar.gz) = 10632647 bytes
+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
 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:1.4 pkgsrc/biology/bowtie2/patches/patch-Makefile:1.5
--- pkgsrc/biology/bowtie2/patches/patch-Makefile:1.4   Wed Oct 18 13:34:23 2023
+++ pkgsrc/biology/bowtie2/patches/patch-Makefile       Thu Jan 18 23:30:12 2024
@@ -1,4 +1,4 @@
-$NetBSD: patch-Makefile,v 1.4 2023/10/18 13:34:23 bacon Exp $
+$NetBSD: patch-Makefile,v 1.5 2024/01/18 23:30:12 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:1.4 pkgsrc/biology/bowtie2/patches/patch-scripts_bowtie2-hbb.sh:1.5
--- pkgsrc/biology/bowtie2/patches/patch-scripts_bowtie2-hbb.sh:1.4     Wed Oct 18 13:34:23 2023
+++ pkgsrc/biology/bowtie2/patches/patch-scripts_bowtie2-hbb.sh Thu Jan 18 23:30:12 2024
@@ -1,4 +1,4 @@
-$NetBSD: patch-scripts_bowtie2-hbb.sh,v 1.4 2023/10/18 13:34:23 bacon Exp $
+$NetBSD: patch-scripts_bowtie2-hbb.sh,v 1.5 2024/01/18 23:30:12 bacon Exp $
 
 # Eliminate bash dependency