Name: bowtie
Version: 1.0.1
Release: 11%{?dist}
Summary: An ultrafast, memory-efficient short read aligner
Group: Applications/Engineering
# The tinythread component is zlib-like, SeqAn is LGPL
License: Artistic 2.0 and zlib and LGPLV3+
URL: http://bowtie-bio.sourceforge.net/index.shtml
Source0: http://downloads.sourceforge.net/%{name}-bio/%{name}-%{version}-src.zip
Patch0: %{name}-arm-gcc.patch
#Patch0: %{name}-script-shebang.patch
#Patch1: %{name}-gcc47.patch
BuildRequires: gcc-c++
BuildRequires: perl-generators
%description
Bowtie, an ultrafast, memory-efficient short read aligner for short
DNA sequences (reads) from next-gen sequencers. Please cite: Langmead
B, et al. Ultrafast and memory-efficient alignment of short DNA
sequences to the human genome. Genome Biol 10:R25.
%prep
%setup -q
#Fix compilation on ARM by removing hard-coded Makefile GCC directives
%patch0 -p1 -b .%{name}-arm-gcc.patch
#%patch0 -p1
#Fix compilation with GCC 4.7
#%patch1 -p1 -b .%{name}-gcc47.patch
%build
make %{?_smp_mflags} -p EXTRA_FLAGS="%{optflags}"
%install
rm -rf %{buildroot}
mkdir -p %{buildroot}/%{_bindir}
mkdir -p %{buildroot}/%{_datadir}/bowtie
install -m 0755 bowtie %{buildroot}/%{_bindir}
install -m 0755 bowtie-build %{buildroot}/%{_bindir}
install -m 0755 bowtie-inspect %{buildroot}/%{_bindir}
cp -a reads %{buildroot}/%{_datadir}/bowtie/
cp -a indexes %{buildroot}/%{_datadir}/bowtie/
cp -a genomes %{buildroot}/%{_datadir}/bowtie/
cp -a scripts %{buildroot}/%{_datadir}/bowtie/
%files
%doc MANUAL NEWS VERSION AUTHORS TUTORIAL doc/{manual.html,style.css} SeqAn-1.1/*GPL.txt
%dir %{_datadir}/bowtie
%{_bindir}/bowtie
%{_bindir}/bowtie-build
%{_bindir}/bowtie-inspect
%{_datadir}/bowtie/genomes
%{_datadir}/bowtie/indexes
%{_datadir}/bowtie/reads
%{_datadir}/bowtie/scripts
%changelog
* Thu Jul 12 2018 Fedora Release Engineering <releng@fedoraproject.org> - 1.0.1-11
- Rebuilt for https://fedoraproject.org/wiki/Fedora_29_Mass_Rebuild
* Wed Feb 07 2018 Fedora Release Engineering <releng@fedoraproject.org> - 1.0.1-10
- Rebuilt for https://fedoraproject.org/wiki/Fedora_28_Mass_Rebuild
* Wed Aug 02 2017 Fedora Release Engineering <releng@fedoraproject.org> - 1.0.1-9
- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Binutils_Mass_Rebuild
* Wed Jul 26 2017 Fedora Release Engineering <releng@fedoraproject.org> - 1.0.1-8
- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Mass_Rebuild
* Fri Feb 10 2017 Fedora Release Engineering <releng@fedoraproject.org> - 1.0.1-7
- Rebuilt for https://fedoraproject.org/wiki/Fedora_26_Mass_Rebuild
* Wed Feb 03 2016 Fedora Release Engineering <releng@fedoraproject.org> - 1.0.1-6
- Rebuilt for https://fedoraproject.org/wiki/Fedora_24_Mass_Rebuild
* Wed Jun 17 2015 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.0.1-5
- Rebuilt for https://fedoraproject.org/wiki/Fedora_23_Mass_Rebuild
* Sat May 02 2015 Kalev Lember <kalevlember@gmail.com> - 1.0.1-4
- Rebuilt for GCC 5 C++11 ABI change
* Fri Aug 15 2014 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.0.1-3
- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_22_Mass_Rebuild
* Sat Jun 07 2014 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.0.1-2
- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_Mass_Rebuild
* Mon Jun 02 2014 Adam Huffman <bloch@verdurin.com> - 1.0.1-1
- Update to upstream release 1.0.1
* Wed Dec 04 2013 Adam Huffman <bloch@verdurin.com> - 1.0.0-2
- Correct licence information (thanks to Dave Love)
- Reorganise documentation (thanks to Dave Love)
- Fix compilation on ARM
* Wed Aug 07 2013 Adam Huffman <bloch@verdurin.com> - 1.0.0-1
- Update to stable upstream release 1.0.0
- Remove unnecessary script patch
* Sat Aug 03 2013 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.12.7-8
- Rebuilt for https://fedoraproject.org/wiki/Fedora_20_Mass_Rebuild
* Wed Jul 17 2013 Petr Pisar <ppisar@redhat.com> - 0.12.7-7
- Perl 5.18 rebuild
* Wed Feb 13 2013 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.12.7-6
- Rebuilt for https://fedoraproject.org/wiki/Fedora_19_Mass_Rebuild
* Wed Jul 18 2012 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.12.7-5
- Rebuilt for https://fedoraproject.org/wiki/Fedora_18_Mass_Rebuild
* Tue Feb 28 2012 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.12.7-4
- Rebuilt for c++ ABI breakage
* Mon Jan 9 2012 Adam Huffman <verdurin@fedoraproject.org> - 0.12.7-3
- add patch to fix compilation with GCC 4.7
* Mon Jun 27 2011 Adam Huffman <bloch@verdurin.com> - 0.12.7-2
- add missing doc/
- add patch to fix Perl script without shebang
* Mon Sep 13 2010 Adam Huffman <bloch@verdurin.com> - 0.12.7-1
- new upstream release 0.12.7
- changelog at http://bowtie-bio.sourceforge.net/index.shtml
* Tue Aug 31 2010 Adam Huffman <bloch@verdurin.com> - 0.12.5-3
- really fix compilation flags
* Wed Aug 25 2010 Adam Huffman <bloch@verdurin.com> - 0.12.5-2
- fix compilation flags
* Mon Aug 2 2010 Adam Huffman <bloch@verdurin.com> - 0.12.5-1
- initial version