Hello community, here is the log from the commit of package bowtie for openSUSE:Factory checked in at 2020-09-15 16:29:10 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Comparing /work/SRC/openSUSE:Factory/bowtie (Old) and /work/SRC/openSUSE:Factory/.bowtie.new.4249 (New) ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Package is "bowtie" Tue Sep 15 16:29:10 2020 rev:3 rq:834334 version:1.3.0 Changes: -------- --- /work/SRC/openSUSE:Factory/bowtie/bowtie.changes 2020-05-20 18:44:37.581169650 +0200 +++ /work/SRC/openSUSE:Factory/.bowtie.new.4249/bowtie.changes 2020-09-15 16:29:14.494651441 +0200 @@ -1,0 +2,27 @@ +Mon Sep 14 14:01:01 UTC 2020 - Christophe Giboudeaux <christo...@krop.fr> + +- Update to 1.3.0: + * Fixed an issue causing bowtie to report incorrect results + when using a Bowtie 2 index. + * New, more efficient implementation of --reorder for + keeping SAM output lines in same order as input reads + * Added -x parameter for specifying index. bowtie still + supports specifying an index via positional parameter, + but this behavior will be deprecated. + * Migrated python scripts to python3. + * Fully removed colorspace functionality. + * Added support for compiling on ARM architectures. + * Fixed an issue preventing bowtie from outputting newlines + in --max and --un output files. + * Fixed an issue causing alignment results to vary based + on read names. + * Fixed an issue preventing --no-unal from suppressing + unmapped reads. + * Removed dependence on some third-party libraries, + simplifying the code and improving portability. + * Fix an issue preventing bowtie from running with + many threads on big-endian machines. +- Spec cleanup +- Enable aarch64 and disable ppc* and s390x. + +------------------------------------------------------------------- Old: ---- v1.2.3.tar.gz New: ---- bowtie-1.3.0.tar.gz ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Other differences: ------------------ ++++++ bowtie.spec ++++++ --- /var/tmp/diff_new_pack.LiOQkw/_old 2020-09-15 16:29:15.838652727 +0200 +++ /var/tmp/diff_new_pack.LiOQkw/_new 2020-09-15 16:29:15.838652727 +0200 @@ -1,7 +1,7 @@ # # spec file for package bowtie # -# Copyright (c) 2016 SUSE LINUX GmbH, Nuernberg, Germany. +# Copyright (c) 2020 SUSE LLC # # All modifications and additions to the file contributed by third parties # remain the property of their copyright owners, unless otherwise agreed @@ -12,39 +12,42 @@ # license that conforms to the Open Source Definition (Version 1.9) # published by the Open Source Initiative. -# Please submit bugfixes or comments via http://bugs.opensuse.org/ +# Please submit bugfixes or comments via https://bugs.opensuse.org/ # Name: bowtie -Version: 1.2.3 +Version: 1.3.0 Release: 0 Summary: Fast and memory-efficient short read aligner License: Artistic-1.0 Group: Productivity/Scientific/Other -Url: http://bio-bowtie.sourceforge.net/ -Source: https://github.com/BenLangmead/%{name}/archive/v%{version}.tar.gz +URL: http://bio-bowtie.sourceforge.net/ +Source: https://github.com/BenLangmead/%{name}/archive/v%{version}.tar.gz#/%{name}-%{version}.tar.gz BuildRequires: gcc-c++ -BuildRequires: pkgconfig(zlib) +BuildRequires: pkgconfig BuildRequires: tbb-devel -BuildRoot: %{_tmppath}/%{name}-%{version}-build -ExclusiveArch: x86_64 s390x ppc64le ppc64 +BuildRequires: pkgconfig(zlib) +ExclusiveArch: x86_64 aarch64 %description -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 indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end). +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 indexes the genome with a Burrows-Wheeler index to keep +its memory footprint small: typically about 2.2 GB for the human genome +(2.9 GB for paired-end). %prep -%setup -q +%autosetup -p1 %build -make %{?_smp_mflags} +%make_build %install %make_install prefix=%{_prefix} -sed -i '1{s|^#!.*env python|#!/usr/bin/python|}' %{buildroot}%{_bindir}/bowtie* +sed -i '1{s|^#!.*env python|#!%{_bindir}/python|}' %{buildroot}%{_bindir}/bowtie* %files -%defattr(-,root,root) %doc README MANUAL AUTHORS NEWS TUTORIAL VERSION %license LICENSE %{_bindir}/*
