Name: BEDTools Version: 2.15.0 Release: 4%{?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.v2.13.4.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 BuildRequires: python %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}/bedpeToBam %{_bindir}/bedToBam %{_bindir}/bedToIgv %{_bindir}/bedtools %{_bindir}/closestBed %{_bindir}/clusterBed %{_bindir}/complementBed %{_bindir}/coverageBed #%{_bindir}/cuffToTrans %{_bindir}/fastaFromBed #%{_bindir}/fjoin %{_bindir}/flankBed %{_bindir}/genomeCoverageBed %{_bindir}/getOverlap %{_bindir}/groupBy %{_bindir}/intersectBed %{_bindir}/linksBed %{_bindir}/maskFastaFromBed %{_bindir}/mergeBed %{_bindir}/multiBamCov %{_bindir}/multiIntersectBed %{_bindir}/nucBed %{_bindir}/pairToBed %{_bindir}/pairToPair %{_bindir}/shuffleBed %{_bindir}/slopBed %{_bindir}/sortBed %{_bindir}/subtractBed %{_bindir}/tagBam %{_bindir}/unionBedGraphs %{_bindir}/windowBed %{_bindir}/windowMaker %{_datadir}/%{name}/genomes %{_datadir}/%{name}/data %files docs %defattr(-,root,root,-) %doc %{name}-User-Manual.v4.pdf %changelog * Wed Jul 18 2012 Fedora Release Engineering - 2.15.0-4 - Rebuilt for https://fedoraproject.org/wiki/Fedora_18_Mass_Rebuild * Tue Feb 28 2012 Fedora Release Engineering - 2.15.0-3 - Rebuilt for c++ ABI breakage * Thu Jan 12 2012 Fedora Release Engineering - 2.15.0-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_17_Mass_Rebuild * Wed Jan 4 2012 Adam Huffman - 2.15.0-1 - update to new upstream release 2.15.0 - new unified command line interface 'bedtools' - add python BR for new Makefile target to generate legacy commands - remove 'overlap' - add 'bedpeToBam', 'clusterBed', 'getOverlap', 'groupBy' - add 'multiIntersectBed', 'windowMaker' * Fri Oct 28 2011 Adam Huffman - 2.13.4-1 - new upstream minor bugfix release, see http://code.google.com/p/bedtools/ * Thu Sep 8 2011 Adam Huffman - 2.13.1-1 - new upstream minor release including fixes for tagBam * Tue Sep 6 2011 Adam Huffman - 2.13.0-1 - new upstream release 2.13.0 - new tools tagBam and nucBed * Tue Apr 12 2011 Adam Huffman - 2.12.0-1 - new upstream release 2.12.0 - new tools cuffToTrans and flankBed * Thu Feb 17 2011 Adam Huffman - 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 - 2.10.1-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_15_Mass_Rebuild * Wed Nov 17 2010 Adam Huffman - 2.10.1-1 - new annotateBed tool - updated manual * Sun Sep 12 2010 Adam Huffman - 2.9.0-5 - add license for -docs * Wed Sep 1 2010 Adam Huffman - 2.9.0-4 - add -docs subpackage including PDF manual * Tue Aug 31 2010 Adam Huffman - 2.9.0-3 - remove 'curl' library properly * Tue Aug 31 2010 Adam Huffman - 2.9.0-2 - fix license and add LICENSE file - fix permissions of data/ - remove bundled 'curl' library * Wed Aug 25 2010 Adam Huffman - 2.9.0-1 - new upstream release - add new unionBedGraphs tool * Mon Aug 2 2010 Adam Huffman - 2.8.3-1 - initial version - override upstream CFLAGS - allow including gzstream header file