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File bowtie2.spec of Package bowtie2
# # spec file for package bowtie2 # # Copyright (c) 2024 SUSE LLC # # All modifications and additions to the file contributed by third parties # remain the property of their copyright owners, unless otherwise agreed # upon. The license for this file, and modifications and additions to the # file, is the same license as for the pristine package itself (unless the # license for the pristine package is not an Open Source License, in which # case the license is the MIT License). An "Open Source License" is a # license that conforms to the Open Source Definition (Version 1.9) # published by the Open Source Initiative. # Please submit bugfixes or comments via https://bugs.opensuse.org/ # %global simde_version 0.7.6 %ifarch aarch64 %endif Name: bowtie2 Version: 2.5.4 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 BuildRequires: cmake BuildRequires: fdupes BuildRequires: gcc-c++ BuildRequires: pkgconfig BuildRequires: pkgconfig(zlib) ExclusiveArch: x86_64 s390x ppc64le ppc64 aarch64 %description Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes. %prep %setup -q %setup -q -b 1 pushd third_party rmdir simde ln -s ../../simde-*/ simde popd # Workaround to find simde/x86/*.h on aarch64 ln -s ../simde-*/simde simde %build %ifarch aarch64 sed -i -e 's/-msse2//' CMakeLists.txt sed -i -e 's/-m64//' CMakeLists.txt %endif # Note: RelWithDebInfo isn't supported and assumes fully unoptimised DEBUG mode; use Release mode instead %cmake \ %ifarch aarch64 -DNO_POPCNT_CAPABILITY=1 \ %endif -DCMAKE_BUILD_TYPE=Release %cmake_build %install %cmake_install # CONVERT env HASHBANGS TO USE DIRECT EXECUTABLE perlbin=`which perl` sed -i "s:%{_bindir}/env perl:${perlbin}:" %{buildroot}%{_bindir}/bowtie2 sed -i "s:%{_bindir}/env python:%{_bindir}/python:" %{buildroot}%{_bindir}/bowtie2-{build,inspect} %fdupes %{buildroot}%{_bindir} %files %doc AUTHORS MANUAL NEWS TUTORIAL BOWTIE2_VERSION README.md %license LICENSE %{_bindir}/bowtie2 %{_bindir}/bowtie2-build* %{_bindir}/bowtie2-inspect* %{_bindir}/bowtie2-align* %changelog
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