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Name: bowtie2
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Version: 2.4.1
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Release: 6%{?dist}
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# Use the word "ultra fast" rather than "ultrafast".
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# https://github.com/BenLangmead/bowtie2/issues/291
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Summary: An ultra fast and memory-efficient read aligner
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# * bowtie2: GPLv3+
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# * TinyThread++: zlib, for files: tinythread.{h,cpp} fast_mutex.h
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#   https://tinythreadpp.bitsnbites.eu/
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#   https://gitorious.org/tinythread/tinythreadpp
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License: GPLv3+ and zlib
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URL: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
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Source0: https://github.com/BenLangmead/%{name}/archive/v%{version}.tar.gz
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# Fix to build with given CXXFLAGS.
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# https://github.com/BenLangmead/bowtie2/pull/296
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Patch0: bowtie2-makefile-cxxflags.patch
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BuildRequires: gcc-c++
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BuildRequires: help2man
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BuildRequires: libasan
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BuildRequires: libubsan
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BuildRequires: make
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BuildRequires: perl-generators
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BuildRequires: perl-interpreter
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BuildRequires: perl(Clone)
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BuildRequires: perl(File::Which)
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BuildRequires: perl(FindBin)
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BuildRequires: perl(Sys::Hostname)
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BuildRequires: perl(Test::Deep)
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BuildRequires: perl(lib)
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BuildRequires: python3
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%ifarch x86_64
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BuildRequires: tbb-devel
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%else
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BuildRequires: simde-devel
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%endif
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BuildRequires: zlib-devel
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# * 32-bit CPU architectures: not supported. See Makefile.
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# * s390x: not ready to ship it. We take the conservative way.
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#   as it is used for the research.
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#   https://github.com/BenLangmead/bowtie2/issues/286
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ExcludeArch: %{ix86} %{arm} s390x
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# TinyThread++
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Provides: bundled(tiny-thread) = 1.1
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%description
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Bowtie 2 is an ultra fast and memory-efficient tool for aligning sequencing
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reads to long reference sequences. It is particularly good at aligning reads
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of about 50 up to 100s or 1,000s of characters, and particularly good at
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aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the
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genome with an FM Index to keep its memory footprint small: for the human
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genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports
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gapped, local, and paired-end alignment modes.
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%prep
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%autosetup
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# Remove the directory to avoid building bowtie with bundled libraries.
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rm -rf third_party
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# Invalid double quote characters are used in the code.
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# https://github.com/BenLangmead/bowtie2/issues/278
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sed -e 's/“/"/g' -e 's/”/"/g' -i processor_support.h
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# Fix shebang to use the system interpreters.
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sed -i '1s|/usr/bin/env perl|%{_bindir}/perl|' bowtie2
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for file in bowtie2-{build,inspect}; do
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  sed -i '1s|/usr/bin/env python3|%{__python3}|' "${file}"
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done
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%build
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# Set build flags.
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# https://src.fedoraproject.org/rpms/redhat-rpm-config/blob/master/f/buildflags.md
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%set_build_flags
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# Set flags considering the upstream testing cases for each architecture.
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# https://github.com/BenLangmead/bowtie2/blob/master/.travis.yml
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%ifnarch x86_64
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export POPCNT_CAPABILITY=0
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export NO_TBB=1
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%endif
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# Build with the target "all" rather than "allall"
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# to skip the builds of debug and sanitized binaries
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# saving the build time.
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%make_build all
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%install
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%make_install PREFIX="%{_prefix}"
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mkdir -p %{buildroot}%{_mandir}/man1
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# Set version string explicitly to avoid showing the wrong command.
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# https://github.com/BenLangmead/bowtie2/issues/294
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for cmd in bowtie2 bowtie2-{build,inspect}; do
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  help2man -N -s 1 -o "%{buildroot}%{_mandir}/man1/${cmd}.1" \
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    --version-string="%{version}" \
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    "%{buildroot}%{_bindir}/${cmd}"
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done
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%check
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for cmd in bowtie2 bowtie2-{build,inspect}; do
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  ./"${cmd}" --version | grep 'version %{version}'
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done
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# Skip tests for the debug and sanitized binaries not shipped.
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sed -i '/my $binary_type/ s/"release", "debug", "sanitized"/"release"/' \
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  scripts/test/simple_tests.pl
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# See scripts/test/simple_tests.sh for the options.
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ASAN_OPTIONS="halt_on_error=1" \
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UBSAN_OPTIONS="halt_on_error=1" \
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scripts/test/simple_tests.pl \
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  --bowtie2=./bowtie2 \
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  --bowtie2-build=./bowtie2-build \
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  --compressed
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%files
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%doc AUTHORS MANUAL MANUAL.markdown NEWS TUTORIAL
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%license LICENSE
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%{_bindir}/bowtie2
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%{_bindir}/bowtie2-align-l
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%{_bindir}/bowtie2-align-s
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%{_bindir}/bowtie2-build
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%{_bindir}/bowtie2-build-l
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%{_bindir}/bowtie2-build-s
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%{_bindir}/bowtie2-inspect
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%{_bindir}/bowtie2-inspect-l
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%{_bindir}/bowtie2-inspect-s
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%{_mandir}/man1/bowtie2.1*
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%{_mandir}/man1/bowtie2-build.1*
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%{_mandir}/man1/bowtie2-inspect.1*
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%changelog
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* Wed Jul 20 2022 Fedora Release Engineering <releng@fedoraproject.org> - 2.4.1-6
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- Rebuilt for https://fedoraproject.org/wiki/Fedora_37_Mass_Rebuild
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* Wed Jan 19 2022 Fedora Release Engineering <releng@fedoraproject.org> - 2.4.1-5
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- Rebuilt for https://fedoraproject.org/wiki/Fedora_36_Mass_Rebuild
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* Wed Jul 21 2021 Fedora Release Engineering <releng@fedoraproject.org> - 2.4.1-4
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- Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild
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* Tue Jan 26 2021 Fedora Release Engineering <releng@fedoraproject.org> - 2.4.1-3
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- Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild
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* Mon Jul 27 2020 Fedora Release Engineering <releng@fedoraproject.org> - 2.4.1-2
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- Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild
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* Sat Mar 28 2020 Jun Aruga <jaruga@redhat.com> - 2.4.1-1
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- Initial package