Name:		bowtie

Version:	0.12.7

Release:	4%{?dist}

Summary:	An ultrafast, memory-efficient short read aligner

Group:		Applications/Engineering

License:	Artistic 2.0

URL:		http://bowtie-bio.sourceforge.net/index.shtml

Source0:	http://downloads.sourceforge.net/%{name}-bio/%{name}-%{version}-src.zip

Patch0:		%{name}-script-shebang.patch

Patch1:		%{name}-gcc47.patch

BuildRoot:	%{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)

%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

%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/

%clean

rm -rf %{buildroot}

%files

%defattr(-,root,root,-)

%doc MANUAL NEWS VERSION AUTHORS TUTORIAL doc/

%dir %{_datadir}/bowtie

%{_bindir}/bowtie

%{_bindir}/bowtie-build

%{_bindir}/bowtie-inspect

%{_datadir}/bowtie/genomes

%{_datadir}/bowtie/indexes

%{_datadir}/bowtie/reads

%{_datadir}/bowtie/scripts

%changelog

* 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