Script 'mail_helper' called by obssrc Hello community, here is the log from the commit of package bowtie2 for openSUSE:Factory checked in at 2026-10-06 19:20:58 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Comparing /work/SRC/openSUSE:Factory/bowtie2 (Old) and /work/SRC/openSUSE:Factory/.bowtie2.new.3698736 (New) ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Package is "bowtie2" Tue Oct 6 19:20:58 2026 rev:15 rq:1382785 version:2.5.5 Changes: -------- --- /work/SRC/openSUSE:Factory/bowtie2/bowtie2.changes 2025-03-25 22:19:15.867645847 +0100 +++ /work/SRC/openSUSE:Factory/.bowtie2.new.3698736/bowtie2.changes 2026-10-06 19:21:12.771577687 +0200 @@ -1,0 +2,18 @@ +Fri Oct 2 13:33:19 UTC 2026 - Andrea Manzini <[email protected]> + +- Update to version 2.5.5: + * Add -d command line option making -a/-k deterministic in the + way alignments are reported, running faster with less memory. + * Add support for selecting AVX version at runtime on x86_64 + CPUs. + * Respect OMP_NUM_THREADS when setting default number of threads. + * Make BAM input compatible with --interleaved, -1/2, and -U. + * Fix issue causing bowtie2 to process only the first interleaved + input if more than one is given. + * Update minimum required CMake version to 3.5. +- Spec file cleanups: + * Drop obsolete Group tag (forbidden by spec-cleaner). + * Use %{_bindir}/perl instead of `which perl` to set perl + hashbang. + +------------------------------------------------------------------- Old: ---- bowtie2-2.5.4.tar.gz New: ---- bowtie2-2.5.5.tar.gz ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Other differences: ------------------ ++++++ bowtie2.spec ++++++ --- /var/tmp/diff_new_pack.ogeMWR/_old 2026-10-06 19:21:13.689616131 +0200 +++ /var/tmp/diff_new_pack.ogeMWR/_new 2026-10-06 19:21:13.693616298 +0200 @@ -1,7 +1,7 @@ # # spec file for package bowtie2 # -# Copyright (c) 2025 SUSE LLC +# Copyright (c) 2026 SUSE LLC and contributors # # All modifications and additions to the file contributed by third parties # remain the property of their copyright owners, unless otherwise agreed @@ -17,14 +17,11 @@ %global simde_version 0.7.6 -%ifarch aarch64 -%endif Name: bowtie2 -Version: 2.5.4 +Version: 2.5.5 Release: 0 Summary: Fast and memory-efficient short read aligner License: GPL-3.0-only -Group: Productivity/Scientific/Other URL: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml Source0: https://github.com/BenLangmead/bowtie2/archive/v%{version}.tar.gz#/%{name}-%{version}.tar.gz Source1: https://github.com/simd-everywhere/simde/archive/v%{simde_version}.tar.gz#/simde-%{simde_version}.tar.gz @@ -73,7 +70,7 @@ %cmake_install # CONVERT env HASHBANGS TO USE DIRECT EXECUTABLE -perlbin=`which perl` +perlbin="%{_bindir}/perl" sed -i "s:%{_bindir}/env perl:${perlbin}:" %{buildroot}%{_bindir}/bowtie2 sed -i "s:%{_bindir}/env python:%{_bindir}/python:" %{buildroot}%{_bindir}/bowtie2-{build,inspect} ++++++ bowtie2-2.5.4.tar.gz -> bowtie2-2.5.5.tar.gz ++++++ /work/SRC/openSUSE:Factory/bowtie2/bowtie2-2.5.4.tar.gz /work/SRC/openSUSE:Factory/.bowtie2.new.3698736/bowtie2-2.5.5.tar.gz differ: char 13, line 1
