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Name: bowtie
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Version: 1.0.1
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Release: 1%{?dist}
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Summary: An ultrafast, memory-efficient short read aligner
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Group: Applications/Engineering
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# The tinythread component is zlib-like, SeqAn is LGPL
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License: Artistic 2.0 and zlib and LGPLV3+
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URL: http://bowtie-bio.sourceforge.net/index.shtml
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Source0: http://downloads.sourceforge.net/%{name}-bio/%{name}-%{version}-src.zip
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Patch0: %{name}-arm-gcc.patch
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#Patch0: %{name}-script-shebang.patch
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#Patch1: %{name}-gcc47.patch
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BuildRoot: %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
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%description
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Bowtie, an ultrafast, memory-efficient short read aligner for short
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DNA sequences (reads) from next-gen sequencers. Please cite: Langmead
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B, et al. Ultrafast and memory-efficient alignment of short DNA
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sequences to the human genome. Genome Biol 10:R25.
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%prep
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%setup -q
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#Fix compilation on ARM by removing hard-coded Makefile GCC directives
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%patch0 -p1 -b .%{name}-arm-gcc.patch
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#%patch0 -p1
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#Fix compilation with GCC 4.7
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#%patch1 -p1 -b .%{name}-gcc47.patch
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%build
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make %{?_smp_mflags} -p EXTRA_FLAGS="%{optflags}"
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%install
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rm -rf %{buildroot}
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mkdir -p %{buildroot}/%{_bindir}
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mkdir -p %{buildroot}/%{_datadir}/bowtie
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install -m 0755 bowtie %{buildroot}/%{_bindir}
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install -m 0755 bowtie-build %{buildroot}/%{_bindir}
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install -m 0755 bowtie-inspect %{buildroot}/%{_bindir}
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cp -a reads %{buildroot}/%{_datadir}/bowtie/
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cp -a indexes %{buildroot}/%{_datadir}/bowtie/
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cp -a genomes %{buildroot}/%{_datadir}/bowtie/
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cp -a scripts %{buildroot}/%{_datadir}/bowtie/
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%clean
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rm -rf %{buildroot}
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%files
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%defattr(-,root,root,-)
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%doc MANUAL NEWS VERSION AUTHORS TUTORIAL doc/{manual.html,style.css} SeqAn-1.1/*GPL.txt
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%dir %{_datadir}/bowtie
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%{_bindir}/bowtie
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%{_bindir}/bowtie-build
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%{_bindir}/bowtie-inspect
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%{_datadir}/bowtie/genomes
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%{_datadir}/bowtie/indexes
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%{_datadir}/bowtie/reads
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%{_datadir}/bowtie/scripts
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%changelog
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* Mon Jun 02 2014 Adam Huffman <bloch@verdurin.com> - 1.0.1-1
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- Update to upstream release 1.0.1
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* Wed Dec 04 2013 Adam Huffman <bloch@verdurin.com> - 1.0.0-2
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- Correct licence information (thanks to Dave Love)
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- Reorganise documentation (thanks to Dave Love)
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- Fix compilation on ARM
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* Wed Aug 07 2013 Adam Huffman <bloch@verdurin.com> - 1.0.0-1
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- Update to stable upstream release 1.0.0
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- Remove unnecessary script patch
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* Sat Aug 03 2013 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.12.7-8
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- Rebuilt for https://fedoraproject.org/wiki/Fedora_20_Mass_Rebuild
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* Wed Jul 17 2013 Petr Pisar <ppisar@redhat.com> - 0.12.7-7
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- Perl 5.18 rebuild
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* Wed Feb 13 2013 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.12.7-6
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- Rebuilt for https://fedoraproject.org/wiki/Fedora_19_Mass_Rebuild
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* Wed Jul 18 2012 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.12.7-5
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- Rebuilt for https://fedoraproject.org/wiki/Fedora_18_Mass_Rebuild
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* Tue Feb 28 2012 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.12.7-4
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- Rebuilt for c++ ABI breakage
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* Mon Jan 9 2012 Adam Huffman <verdurin@fedoraproject.org> - 0.12.7-3
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- add patch to fix compilation with GCC 4.7
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* Mon Jun 27 2011 Adam Huffman <bloch@verdurin.com> - 0.12.7-2
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- add missing doc/
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- add patch to fix Perl script without shebang
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* Mon Sep 13 2010 Adam Huffman <bloch@verdurin.com> - 0.12.7-1
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- new upstream release 0.12.7
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- changelog at http://bowtie-bio.sourceforge.net/index.shtml
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* Tue Aug 31 2010 Adam Huffman <bloch@verdurin.com> - 0.12.5-3
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- really fix compilation flags
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* Wed Aug 25 2010 Adam Huffman <bloch@verdurin.com> - 0.12.5-2
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- fix compilation flags
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* Mon Aug 2 2010 Adam Huffman <bloch@verdurin.com> - 0.12.5-1
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- initial version
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