CVS commit: pkgsrc/biology/bowtie2

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

Module Name:    pkgsrc
Committed By:   bacon
Date:           Wed Oct 18 13:34:23 UTC 2023

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

Log Message:
biology/bowtie2: Update to 2.5.2

Numerous bug fixes and enhancements since 2.4.4
Changes: https://github.com/BenLangmead/bowtie2/releases


To generate a diff of this commit:
cvs rdiff -u -r1.1 -r1.2 pkgsrc/biology/bowtie2/DESCR
cvs rdiff -u -r1.8 -r1.9 pkgsrc/biology/bowtie2/Makefile
cvs rdiff -u -r1.3 -r1.4 pkgsrc/biology/bowtie2/PLIST
cvs rdiff -u -r1.5 -r1.6 pkgsrc/biology/bowtie2/distinfo
cvs rdiff -u -r1.3 -r1.4 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/DESCR
diff -u pkgsrc/biology/bowtie2/DESCR:1.1 pkgsrc/biology/bowtie2/DESCR:1.2
--- pkgsrc/biology/bowtie2/DESCR:1.1    Thu Jan 21 17:30:12 2021
+++ pkgsrc/biology/bowtie2/DESCR        Wed Oct 18 13:34:23 2023
@@ -1,3 +1,3 @@
-Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short
-DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp
-reads per hour.
+Bowtie is an ultrafast, memory-efficient short read aligner. It aligns
+short DNA sequences (reads) to the human genome at a rate of over 25
+million 35-bp reads per hour.

Index: pkgsrc/biology/bowtie2/Makefile
diff -u pkgsrc/biology/bowtie2/Makefile:1.8 pkgsrc/biology/bowtie2/Makefile:1.9
--- pkgsrc/biology/bowtie2/Makefile:1.8 Mon Aug 14 05:23:51 2023
+++ pkgsrc/biology/bowtie2/Makefile     Wed Oct 18 13:34:23 2023
@@ -1,7 +1,6 @@
-# $NetBSD: Makefile,v 1.8 2023/08/14 05:23:51 wiz Exp $
+# $NetBSD: Makefile,v 1.9 2023/10/18 13:34:23 bacon Exp $
 
-DISTNAME=      bowtie2-2.4.4
-PKGREVISION=   4
+DISTNAME=      bowtie2-2.5.2
 CATEGORIES=    biology
 MASTER_SITES=  ${MASTER_SITE_GITHUB:=BenLangmead/}
 GITHUB_TAG=    v${PKGVERSION_NOREV}

Index: pkgsrc/biology/bowtie2/PLIST
diff -u pkgsrc/biology/bowtie2/PLIST:1.3 pkgsrc/biology/bowtie2/PLIST:1.4
--- pkgsrc/biology/bowtie2/PLIST:1.3    Thu May 18 14:16:27 2023
+++ pkgsrc/biology/bowtie2/PLIST        Wed Oct 18 13:34:23 2023
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.3 2023/05/18 14:16:27 bacon Exp $
+@comment $NetBSD: PLIST,v 1.4 2023/10/18 13:34:23 bacon Exp $
 bin/bowtie2
 bin/bowtie2-align-l
 bin/bowtie2-align-s

Index: pkgsrc/biology/bowtie2/distinfo
diff -u pkgsrc/biology/bowtie2/distinfo:1.5 pkgsrc/biology/bowtie2/distinfo:1.6
--- pkgsrc/biology/bowtie2/distinfo:1.5 Thu May 18 14:16:27 2023
+++ pkgsrc/biology/bowtie2/distinfo     Wed Oct 18 13:34:23 2023
@@ -1,7 +1,7 @@
-$NetBSD: distinfo,v 1.5 2023/05/18 14:16:27 bacon Exp $
+$NetBSD: distinfo,v 1.6 2023/10/18 13:34:23 bacon Exp $
 
-BLAKE2s (bowtie2-2.4.4.tar.gz) = 685468ca08b60b58de8ed51fec3c7a22411c278f7e8c8703461707b4de996d3e
-SHA512 (bowtie2-2.4.4.tar.gz) = 2db44e8219bcb916119b8097dd10adcc2185d3ce7df6147210c78070dce57fefddbc79c64dc2a55fdc49a46c4df80c37c8c6d786cce20a95a2e50ce0692befed
-Size (bowtie2-2.4.4.tar.gz) = 10582238 bytes
+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
 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:1.3 pkgsrc/biology/bowtie2/patches/patch-Makefile:1.4
--- pkgsrc/biology/bowtie2/patches/patch-Makefile:1.3   Thu May 18 14:16:27 2023
+++ pkgsrc/biology/bowtie2/patches/patch-Makefile       Wed Oct 18 13:34:23 2023
@@ -1,4 +1,4 @@
-$NetBSD: patch-Makefile,v 1.3 2023/05/18 14:16:27 bacon Exp $
+$NetBSD: patch-Makefile,v 1.4 2023/10/18 13:34:23 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:1.3 pkgsrc/biology/bowtie2/patches/patch-scripts_bowtie2-hbb.sh:1.4
--- pkgsrc/biology/bowtie2/patches/patch-scripts_bowtie2-hbb.sh:1.3     Thu May 18 14:16:27 2023
+++ pkgsrc/biology/bowtie2/patches/patch-scripts_bowtie2-hbb.sh Wed Oct 18 13:34:23 2023
@@ -1,4 +1,4 @@
-$NetBSD: patch-scripts_bowtie2-hbb.sh,v 1.3 2023/05/18 14:16:27 bacon Exp $
+$NetBSD: patch-scripts_bowtie2-hbb.sh,v 1.4 2023/10/18 13:34:23 bacon Exp $
 
 # Eliminate bash dependency