Name: bowtie Version: 1.0.1 Release: 10%{?dist} Summary: An ultrafast, memory-efficient short read aligner Group: Applications/Engineering # The tinythread component is zlib-like, SeqAn is LGPL License: Artistic 2.0 and zlib and LGPLV3+ URL: http://bowtie-bio.sourceforge.net/index.shtml Source0: http://downloads.sourceforge.net/%{name}-bio/%{name}-%{version}-src.zip Patch0: %{name}-arm-gcc.patch #Patch0: %{name}-script-shebang.patch #Patch1: %{name}-gcc47.patch BuildRequires: perl-generators %description Bowtie, an ultrafast, memory-efficient short read aligner for short DNA sequences (reads) from next-gen sequencers. Please cite: Langmead B, et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25. %prep %setup -q #Fix compilation on ARM by removing hard-coded Makefile GCC directives %patch0 -p1 -b .%{name}-arm-gcc.patch #%patch0 -p1 #Fix compilation with GCC 4.7 #%patch1 -p1 -b .%{name}-gcc47.patch %build make %{?_smp_mflags} -p EXTRA_FLAGS="%{optflags}" %install rm -rf %{buildroot} mkdir -p %{buildroot}/%{_bindir} mkdir -p %{buildroot}/%{_datadir}/bowtie install -m 0755 bowtie %{buildroot}/%{_bindir} install -m 0755 bowtie-build %{buildroot}/%{_bindir} install -m 0755 bowtie-inspect %{buildroot}/%{_bindir} cp -a reads %{buildroot}/%{_datadir}/bowtie/ cp -a indexes %{buildroot}/%{_datadir}/bowtie/ cp -a genomes %{buildroot}/%{_datadir}/bowtie/ cp -a scripts %{buildroot}/%{_datadir}/bowtie/ %files %defattr(-,root,root,-) %doc MANUAL NEWS VERSION AUTHORS TUTORIAL doc/{manual.html,style.css} SeqAn-1.1/*GPL.txt %dir %{_datadir}/bowtie %{_bindir}/bowtie %{_bindir}/bowtie-build %{_bindir}/bowtie-inspect %{_datadir}/bowtie/genomes %{_datadir}/bowtie/indexes %{_datadir}/bowtie/reads %{_datadir}/bowtie/scripts %changelog * Wed Feb 07 2018 Fedora Release Engineering - 1.0.1-10 - Rebuilt for https://fedoraproject.org/wiki/Fedora_28_Mass_Rebuild * Wed Aug 02 2017 Fedora Release Engineering - 1.0.1-9 - Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Binutils_Mass_Rebuild * Wed Jul 26 2017 Fedora Release Engineering - 1.0.1-8 - Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Mass_Rebuild * Fri Feb 10 2017 Fedora Release Engineering - 1.0.1-7 - Rebuilt for https://fedoraproject.org/wiki/Fedora_26_Mass_Rebuild * Wed Feb 03 2016 Fedora Release Engineering - 1.0.1-6 - Rebuilt for https://fedoraproject.org/wiki/Fedora_24_Mass_Rebuild * Wed Jun 17 2015 Fedora Release Engineering - 1.0.1-5 - Rebuilt for https://fedoraproject.org/wiki/Fedora_23_Mass_Rebuild * Sat May 02 2015 Kalev Lember - 1.0.1-4 - Rebuilt for GCC 5 C++11 ABI change * Fri Aug 15 2014 Fedora Release Engineering - 1.0.1-3 - Rebuilt for https://fedoraproject.org/wiki/Fedora_21_22_Mass_Rebuild * Sat Jun 07 2014 Fedora Release Engineering - 1.0.1-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_21_Mass_Rebuild * Mon Jun 02 2014 Adam Huffman - 1.0.1-1 - Update to upstream release 1.0.1 * Wed Dec 04 2013 Adam Huffman - 1.0.0-2 - Correct licence information (thanks to Dave Love) - Reorganise documentation (thanks to Dave Love) - Fix compilation on ARM * Wed Aug 07 2013 Adam Huffman - 1.0.0-1 - Update to stable upstream release 1.0.0 - Remove unnecessary script patch * Sat Aug 03 2013 Fedora Release Engineering - 0.12.7-8 - Rebuilt for https://fedoraproject.org/wiki/Fedora_20_Mass_Rebuild * Wed Jul 17 2013 Petr Pisar - 0.12.7-7 - Perl 5.18 rebuild * Wed Feb 13 2013 Fedora Release Engineering - 0.12.7-6 - Rebuilt for https://fedoraproject.org/wiki/Fedora_19_Mass_Rebuild * Wed Jul 18 2012 Fedora Release Engineering - 0.12.7-5 - Rebuilt for https://fedoraproject.org/wiki/Fedora_18_Mass_Rebuild * Tue Feb 28 2012 Fedora Release Engineering - 0.12.7-4 - Rebuilt for c++ ABI breakage * Mon Jan 9 2012 Adam Huffman - 0.12.7-3 - add patch to fix compilation with GCC 4.7 * Mon Jun 27 2011 Adam Huffman - 0.12.7-2 - add missing doc/ - add patch to fix Perl script without shebang * Mon Sep 13 2010 Adam Huffman - 0.12.7-1 - new upstream release 0.12.7 - changelog at http://bowtie-bio.sourceforge.net/index.shtml * Tue Aug 31 2010 Adam Huffman - 0.12.5-3 - really fix compilation flags * Wed Aug 25 2010 Adam Huffman - 0.12.5-2 - fix compilation flags * Mon Aug 2 2010 Adam Huffman - 0.12.5-1 - initial version