Name:		tophat
Version:	1.4.0
Release:	1%{?dist}
Summary:	A spliced read mapper for RNA-Seq

Group:		Applications/Engineering
License:	Artistic 2.0
URL:		http://tophat.cbcb.umd.edu/
Source0:	http://tophat.cbcb.umd.edu/downloads/%{name}-%{version}.tar.gz
Patch0:		%{name}-sam-header.patch
BuildRoot:	%{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)

BuildRequires:	autoconf
BuildRequires:	automake
BuildRequires:	python-devel
BuildRequires:	samtools-devel
BuildREquires:	zlib-devel
BuildRequires:	dos2unix

Requires:	bowtie

%description
TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns
RNA-Seq reads to mammalian-sized genomes using the ultra
high-throughput short read aligner Bowtie, and then analyzes the
mapping results to identify splice junctions between exons.

TopHat is a collaborative effort between the University of Maryland
Center for Bioinformatics and Computational Biology and the University
of California, Berkeley Departments of Mathematics and Molecular and
Cell Biology.

%prep
%setup -q
%patch0 -p1 -b .tophat-sam-header.patch

#Fix bad permissions
chmod -x src/align_status.*
chmod -x src/deletions.*
chmod -x src/insertions.*


%build
autoreconf
%configure
# normal SMP flags break build
make 


%install
rm -rf %{buildroot}
make install DESTDIR=%{buildroot}


%clean
rm -rf %{buildroot}


%files
%defattr(-,root,root,-)
%doc AUTHORS COPYING NEWS README THANKS
%{_bindir}/*


%changelog
* Mon Jan 30 2012 Adam Huffman <verdurin@fedoraproject.org> - 1.4.0-1
- update to upstream release 1.4.0
- add map2gtf.h to samtools headers patch
- update samtools headers patch

* Tue Jan  3 2012 Adam Huffman <verdurin@fedoraproject.org> - 1.3.3-1
- update to new upstream bugfix release 1.3.3

* Thu Sep 15 2011 Adam Huffman <bloch@verdurin.com> - 1.3.2-1
- new upstream bugfix release 1.3.2
- extend samtools header patch to include bam_merge.cpp

* Tue Jun 28 2011 Adam Huffman <bloch@verdurin.com> - 1.3.1-1
- update samtools patch

* Mon Jun 27 2011 Adam Huffman <bloch@verdurin.com> - 1.3.1-1
- new upstream bugfix release 1.3.1
- upstream changelog at http://tophat.cbcb.umd.edu/

* Mon Jun  6 2011 Adam Huffman <bloch@verdurin.com> - 1.3.0-1
- new upstream release

* Wed May 18 2011 Adam Huffman <bloch@verdurin.com> - 1.2.0-2
- remove Make smp flags to fix build
- fix permissions and file format problems

* Tue May 17 2011 Adam Huffman <bloch@verdurin.com> - 1.2.0-1
- initial version