Name: mmseq
Version: 0.9.18
Release: 1%{?dist}
Summary: Haplotype and isoform specific expression estimation for RNA-seq
Group: Applications/Engineering
License: GPLv2+
URL: http://www.bgx.org.uk/software/mmseq.html
Source0: http://www.bgx.org.uk/software/%{name}_%{version}.zip
Patch0: mmseq-sam-header.patch
#Patch1: mmseq-flags.patch
Patch2: mmseq-zlib.patch
BuildRoot: %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
BuildRequires: boost-devel
BuildRequires: samtools-devel
BuildRequires: gsl-devel
BuildRequires: zlib-devel
Requires: ruby
Requires: samtools
Requires: perl
%description
Software for fast, scalable haplotype and isoform expression
estimation using multi-mapping RNA-seq reads. Example scripts are included.
%prep
%setup -q -n %{name}_%{version}
#Look for samtools headers in the correct location for Fedora
%patch0 -p1 -b .mmseq-sam-header.patch
#Use Fedora compilation headers
#%%patch1 -p1 -b .mmseq-flags.patch
#Fix zlib linking
%patch2 -p1 -b .mmseq-zlib.patch
#Remove bundled binaries
rm bam2hits*-x86_64
rm mmseq*-x86_64
%build
make %{?_smp_mflags} CXXFLAGS="%{optflags}"
%install
rm -rf %{buildroot}
mkdir -p %{buildroot}%{_bindir}
install -p -m 0755 bam2hits %{buildroot}%{_bindir}
install -p -m 0755 mmseq %{buildroot}%{_bindir}
install -p -m 0755 *.sh %{buildroot}%{_bindir}
install -p -m 0755 *.rb %{buildroot}%{_bindir}
install -p -m 0755 ensembl_gtf_to_gff.pl %{buildroot}%{_bindir}
%clean
rm -rf %{buildroot}
%files
%defattr(-,root,root,-)
%doc AUTHORS COPYING
%{_bindir}/bam2hits
%{_bindir}/mmseq
%{_bindir}/fastagrep.sh
#%%{_bindir}/pileup.sh
%{_bindir}/routeB.sh
%{_bindir}/filterGTF.rb
#%%{_bindir}/get_isize.rb
%{_bindir}/haploref.rb
%{_bindir}/testregexp.rb
%{_bindir}/ensembl_gtf_to_gff.pl
%changelog
* Wed Jan 11 2012 Adam Huffman <verdurin@fedoraproject.org> - 0.9.18-1
- update to 0.9.18
- remove pileup.sh and get_isize.rb, discarded upstream
- update patches and remove flags patch
* Sun Nov 20 2011 Adam Huffman <adam@vaioz.verdurin.salon> - 0.9.14-2
- rebuild for new Boost in Rawhide
* Fri Oct 7 2011 Adam Huffman <bloch@verdurin.com> - 0.9.14-1
- new upstream bugfix release
* Wed Aug 17 2011 Adam Huffman <bloch@verdurin.com> - 0.9.12-1
- upstream release 0.9.12 fixing a possible segfault
* Thu Jul 21 2011 Adam Huffman <bloch@verdurin.com> - 0.9.11-2
- rebuild for new Boost in Rawhide
* Sat May 28 2011 Adam Huffman <bloch@verdurin.com> - 0.9.11-1
- new upstream release
- add routeB.sh script
- sam2hits.rb removed
* Fri May 27 2011 Adam Huffman <bloch@verdurin.com> - 0.9.10b-3
- patch to deal with zlib better
* Sun May 15 2011 Adam Huffman <bloch@verdurin.com> - 0.9.10b-2
- remove bundled binaries
- remove VERSION
- explicit naming for included scripts
* Sun May 8 2011 Adam Huffman <bloch@verdurin.com> - 0.9.10b-1
- new upstream version
- patch descriptions
* Sun May 8 2011 Adam Huffman <bloch@verdurin.com> - 0.9.9-3
- fix permissions for installed files
- include missing Perl script
- improve description
* Sat Apr 9 2011 Adam Huffman <bloch@verdurin.com> - 0.9.9-2
- fix compilation flags for debuginfo
- include shell and Ruby scripts
* Mon Apr 4 2011 Adam Huffman <bloch@verdurin.com> - 0.9.9-1
- initial version
