Name: BEDTools Version: 2.9.0 Release: 5%{?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://code.google.com/p/bedtools/downloads/detail?name=BEDTools.v2.9.0.tar.gz Source0: http://bedtools.googlecode.com/files/%{name}.v%{version}.tar.gz Source1: http://bedtools.googlecode.com/files/%{name}-User-Manual.v3.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 RELEASE_HISTORY LICENSE %dir %{_datadir}/%{name} %{_bindir}/bamToBed %{_bindir}/bed12ToBed6 %{_bindir}/bedToBam %{_bindir}/bedToIgv %{_bindir}/closestBed %{_bindir}/complementBed %{_bindir}/coverageBed %{_bindir}/fastaFromBed %{_bindir}/genomeCoverageBed %{_bindir}/groupBy %{_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.v3.pdf %changelog * 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