Name:		cufflinks
Version:	1.3.0
Release:	1%{?dist}
Summary:	RNA-Seq transcript assembly, differential expression/regulation

Group:		Applications/Engineering
License:	Boost
URL:		http://cufflinks.cbcb.umd.edu/
Source0:	http://cufflinks.cbcb.umd.edu/downloads/%{name}-%{version}.tar.gz
Patch0:		%{name}-bam-header.patch
Patch1:		%{name}-boost-thread.patch
BuildRoot:	%{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)

BuildRequires:	boost-devel
BuildRequires:	samtools-devel
BuildRequires:	zlib-devel
BuildRequires:	autoconf
BuildRequires:	automake
BuildRequires:	python-devel


%description 
Cufflinks assembles transcripts, estimates their abundances, and tests
for differential expression and regulation in RNA-Seq samples. It
accepts aligned RNA-Seq reads and assembles the alignments into a
parsimonious set of transcripts. Cufflinks then estimates the relative
abundances of these transcripts based on how many reads support each
one.

Cufflinks is a collaborative effort between the Laboratory for
Mathematical and Computational Biology, led by Lior Pachter at UC
Berkeley, Steven Salzberg's group at the University of Maryland Center
for Bioinformatics and Computational Biology, and Barbara Wold's lab
at Caltech.

%prep
%setup -q
#Look for BAM headers in the correct Fedora location
%patch0 -p1 -b .cufflinks-bam-header.patch
%patch1 -p1 -b .cufflinks-boost-thread.patch

%build
autoreconf
%configure
make %{?_smp_mflags}


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


%clean
rm -rf %{buildroot}


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


%changelog
* Mon Jan 30 2012 Adam Huffman <verdurin@fedoraproject.org> - 1.3.0-1
- update to upstream 1.3.0

* Thu Sep 15 2011 Adam Huffman <bloch@verdurin.com> - 1.1.0-1
- New upstream bugfix release 1.1.0

* Mon Jun  6 2011 Adam Huffman <bloch@verdurin.com> - 1.0.3-1
- new upstream release

* Sun May  8 2011 Adam Huffman <bloch@verdurin.com> - 1.0.1-1
- new upstream release
- add python BR
- fix header location patch
- separate Boost thread patch

* Mon Apr  4 2011 Adam Huffman <bloch@verdurin.com> - 0.9.3-1
- initial version
- patch to fix bam.h header search and to link boost_thread-mt