Name: BEDTools
Version: 2.12.0
Release: 1%{?dist}
Summary: A flexible suite of utilities for comparing genomic features
Group: Applications/Engineering
License: GPLv2+
URL: http://code.google.com/p/bedtools/
# Download is listed in an RPM-unfriendly way on the Google Code site
# The file can be obtained at
# http://bedtools.googlecode.com/files/BEDTools.v2.12.0.tar.gz
Source0: http://bedtools.googlecode.com/files/%{name}.v%{version}.tar.gz
Source1: http://bedtools.googlecode.com/files/%{name}-User-Manual.v4.pdf
BuildRoot: %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
BuildRequires: zlib-devel
%description
The BEDTools utilities allow one to address common genomics tasks such
as finding feature overlaps and computing coverage. The utilities are
largely based on four widely-used file formats: BED, GFF/GTF, VCF, and
SAM/BAM. Using BEDTools, one can develop sophisticated pipelines that
answer complicated research questions by "streaming" several BEDTools
together.
%package docs
Summary: Manual for BEDTools
Group: Documentation
License: GPLv2
%description docs
PDF manual for the BEDTools utilities.
%prep
%setup -q -n %{name}-Version-%{version}
# remove bundled curl library
rm -rf src/utils/curl
# add manual
cp -p %{SOURCE1} .
%build
# gzstream includes a local header file
make %{?_smp_mflags} CXXFLAGS="-I. %{optflags}"
%install
rm -rf %{buildroot}
mkdir -p %{buildroot}/%{_bindir}
install -m 0755 bin/* %{buildroot}/%{_bindir}
mkdir -p %{buildroot}/%{_datadir}/%{name}
cp -a genomes/ %{buildroot}/%{_datadir}/%{name}
cp -a data/ %{buildroot}/%{_datadir}/%{name}
# fix permissions
find %{buildroot}%{_datadir}/%{name} -type f -exec chmod 0644 {} \;
%clean
rm -rf %{buildroot}
%files
%defattr(-,root,root,-)
%doc README.rst RELEASE_HISTORY LICENSE
%dir %{_datadir}/%{name}
%{_bindir}/annotateBed
%{_bindir}/bamToBed
%{_bindir}/bed12ToBed6
%{_bindir}/bedToBam
%{_bindir}/bedToIgv
%{_bindir}/closestBed
%{_bindir}/complementBed
%{_bindir}/coverageBed
%{_bindir}/cuffToTrans
%{_bindir}/fastaFromBed
%{_bindir}/fjoin
%{_bindir}/flankBed
%{_bindir}/genomeCoverageBed
%{_bindir}/intersectBed
%{_bindir}/linksBed
%{_bindir}/maskFastaFromBed
%{_bindir}/mergeBed
%{_bindir}/overlap
%{_bindir}/pairToBed
%{_bindir}/pairToPair
%{_bindir}/shuffleBed
%{_bindir}/slopBed
%{_bindir}/sortBed
%{_bindir}/subtractBed
%{_bindir}/unionBedGraphs
%{_bindir}/windowBed
%{_datadir}/%{name}/genomes
%{_datadir}/%{name}/data
%files docs
%defattr(-,root,root,-)
%doc %{name}-User-Manual.v4.pdf
%changelog
* Tue Apr 12 2011 Adam Huffman <bloch@verdurin.com> - 2.12.0-1
- new upstream release 2.12.0
- new tools cuffToTrans and flankBed
* Thu Feb 17 2011 Adam Huffman <bloch@verdurin.com> - 2.11.2-1
- new upstream release
- now README.rst
- remove groupBy command, now in filo
- new fjoin command
* Mon Feb 07 2011 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 2.10.1-2
- Rebuilt for https://fedoraproject.org/wiki/Fedora_15_Mass_Rebuild
* Wed Nov 17 2010 Adam Huffman <bloch@verdurin.com> - 2.10.1-1
- new annotateBed tool
- updated manual
* Sun Sep 12 2010 Adam Huffman <bloch@verdurin.com> - 2.9.0-5
- add license for -docs
* Wed Sep 1 2010 Adam Huffman <bloch@verdurin.com> - 2.9.0-4
- add -docs subpackage including PDF manual
* Tue Aug 31 2010 Adam Huffman <bloch@verdurin.com> - 2.9.0-3
- remove 'curl' library properly
* Tue Aug 31 2010 Adam Huffman <bloch@verdurin.com> - 2.9.0-2
- fix license and add LICENSE file
- fix permissions of data/
- remove bundled 'curl' library
* Wed Aug 25 2010 Adam Huffman <bloch@verdurin.com> - 2.9.0-1
- new upstream release
- add new unionBedGraphs tool
* Mon Aug 2 2010 Adam Huffman <bloch@verdurin.com> - 2.8.3-1
- initial version
- override upstream CFLAGS
- allow including gzstream header file
