Name: BEDTools Version: 2.30.0 Release: 3%{?dist} Summary: A flexible suite of utilities for comparing genomic features Group: Applications/Engineering License: GPLv2+ URL: https://github.com/arq5x/bedtools Source0: https://github.com/arq5x/bedtools2/releases/download/v%{version}/bedtools2-%{version}.tar.gz #Fix debuginfo canonicalization error #Patch0: BEDTools-double-parenthesis.patch Patch1: BEDTools-python3.patch BuildRoot: %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n) BuildRequires: zlib-devel BuildRequires: bzip2-devel BuildRequires: xz-devel BuildRequires: python3 BuildRequires: python3-sphinx %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. %prep %setup -q -n bedtools2-%{version} #%patch0 -p1 -b .BEDTools.double-parenthesis %patch1 -p1 -b .BEDTools.python3 # remove bundled curl library rm -rf src/utils/curl %build # gzstream includes a local header file make %{?_smp_mflags} CXXFLAGS="-I. %{optflags}" V=1 cd docs make clean html cd .. %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.md LICENSE docs/ %dir %{_datadir}/%{name} %{_bindir}/* %{_datadir}/%{name}/genomes %{_datadir}/%{name}/data %changelog * Fri Feb 10 2017 Fedora Release Engineering - 2.26.0-3 - Rebuilt for https://fedoraproject.org/wiki/Fedora_26_Mass_Rebuild * Sat Aug 06 2016 Adam Huffman - 2.26.0-2 - Fix from Kyle Powell to re-enable debuginfo * Sat Jul 09 2016 Adam Huffman - 2.26.0-1 - Update to latest upstream release 2.26.0 * Wed Feb 03 2016 Fedora Release Engineering - 2.25.0-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_24_Mass_Rebuild * Sat Sep 05 2015 Adam Huffman - 2.25.0-1 - Update to latest upstream release 2.25.0 - Disable upstreamed patches - Disable double path separator patch for now * Sun Aug 23 2015 Adam Huffman - 2.24.0-6 - Fix binary directory path * Sat Jul 18 2015 Adam Huffman - 2.24.0-5 - Re-enable 32-bit and ARM builds * Fri Jul 17 2015 Adam Huffman - 2.24.0-4 - Add temporary patches to fix 32-bit compilation derived from upstream commits * Sun Jul 12 2015 Adam Huffman - 2.24.0-3 - Disable i686 build until upstream fixes arrive * Fri Jul 3 2015 Peter Robinson 2.24.0-2 - Disable hardened build - Exclude ARMv7 for the moment (tracked rhbz 1239119) * Wed Jul 01 2015 Adam Huffman - 2.24.0-1 - Disable debuginfo for now to re-enable build - Disable debuginfo-related patches for now * Tue Jun 16 2015 Fedora Release Engineering - 2.23.0-3 - Rebuilt for https://fedoraproject.org/wiki/Fedora_23_Mass_Rebuild * Mon Apr 06 2015 Adam Huffman - 2.23.0-2 - Simplify list of included binaries * Mon Mar 09 2015 Adam Huffman - 2.23.0-1 - Update to upstream 2.23.0 * Sat Dec 27 2014 Adam Huffman - 2.22.0-1 - Update to upstream 2.22.0 * Mon Aug 25 2014 Adam Huffman - 2.20.1-4 - Update debugedit patch - Reinstate gzstream patch * Fri Aug 15 2014 Fedora Release Engineering - 2.20.1-3 - Rebuilt for https://fedoraproject.org/wiki/Fedora_21_22_Mass_Rebuild * Sat Jun 14 2014 Adam Huffman - 2.20.1-2 - More path changes to fix debuginfo build * Sat Jun 07 2014 Adam Huffman - 2.20.1-1 - Update to upstream 2.20.1 - Build integrated docs and remove obsolete PDF manual in -docs subpackage * Fri Jun 06 2014 Fedora Release Engineering - 2.19.1-3 - Rebuilt for https://fedoraproject.org/wiki/Fedora_21_Mass_Rebuild * Wed Apr 16 2014 Adam Huffman - 2.19.1-2 - Fix for debugedit canonicalization error - Don't include jaccard, reldist and sample * Wed Apr 16 2014 Adam Huffman - 2.19.1-1 - Update to upstream 2.19.1 release * Sun Mar 02 2014 Adam Huffman - 2.19.0-1 - Update to upstream 2.19.0 release - Upstream now hosted at Github, not Google Code - Add three new tools * Tue Aug 06 2013 Adam Huffman - 2.17.0-1 - Update to upstream 2.17.0 release - Fix changed tarball directory name - Add four new tools * Fri Aug 02 2013 Fedora Release Engineering - 2.15.0-6 - Rebuilt for https://fedoraproject.org/wiki/Fedora_20_Mass_Rebuild * Wed Feb 13 2013 Fedora Release Engineering - 2.15.0-5 - Rebuilt for https://fedoraproject.org/wiki/Fedora_19_Mass_Rebuild * 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