Name: bwa Version: 0.7.17 Release: 13%{?dist} Summary: Burrows-Wheeler Alignment tool License: GPLv3 URL: http://bio-bwa.sourceforge.net/ Source0: http://downloads.sourceforge.net/bio-%{name}/%{name}-%{version}.tar.bz2 # Fix building against GCC 10. # https://github.com/lh3/bwa/commit/2a1ae7b6f34a96ea25be007ac9d91e57e9d32284 Patch0: bwa-fix-build-gcc10.patch # Enable non-x86_64 CPU architectures with simde. # https://github.com/lh3/bwa/pull/283 Patch1: bwa-simde.patch BuildRequires: gcc BuildRequires: perl-generators %ifnarch x86_64 BuildRequires: simde-devel %endif BuildRequires: zlib-devel BuildRequires: make %description BWA is a program for aligning sequencing reads against a large reference genome (e.g. human genome). It has two major components, one for read shorter than 150bp and the other for longer reads. %prep %setup -q %patch -P0 -p1 %patch -P1 -p1 %build # Set -O3 for the better performance. # https://github.com/lh3/bwa/pull/278 CFLAGS="%{optflags} -O3" %ifnarch x86_64 # See Makefile in the pull request. # https://github.com/lh3/bwa/pull/283 CFLAGS="${CFLAGS} -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -DSIMDE_ENABLE_OPENMP" %endif %make_build CFLAGS="${CFLAGS}" %install rm -rf %{buildroot} mkdir -p %{buildroot}/%{_bindir} mkdir -p %{buildroot}/%{_datadir}/%{name}/bwakit mkdir -p %{buildroot}/%{_mandir}/man1 install -m 0755 bwa %{buildroot}/%{_bindir} install -m 0755 qualfa2fq.pl %{buildroot}/%{_bindir} install -m 0755 xa2multi.pl %{buildroot}/%{_bindir} install -m 0755 bwakit/* %{buildroot}/%{_datadir}/%{name}/bwakit install -m 0644 bwa.1 %{buildroot}/%{_mandir}/man1/bwa.1 %check ./bwa 2>&1 | grep '^Version: %{version}' %files %doc COPYING NEWS.md README.md README-alt.md %{_bindir}/bwa %{_bindir}/qualfa2fq.pl %{_bindir}/xa2multi.pl %{_datadir}/%{name}/* %{_mandir}/man1/%{name}.1* %changelog * Wed Jul 17 2024 Fedora Release Engineering - 0.7.17-13 - Rebuilt for https://fedoraproject.org/wiki/Fedora_41_Mass_Rebuild * Tue Jan 23 2024 Fedora Release Engineering - 0.7.17-12 - Rebuilt for https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild * Fri Jan 19 2024 Fedora Release Engineering - 0.7.17-11 - Rebuilt for https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild * Wed Jul 19 2023 Fedora Release Engineering - 0.7.17-10 - Rebuilt for https://fedoraproject.org/wiki/Fedora_39_Mass_Rebuild * Wed Jan 18 2023 Fedora Release Engineering - 0.7.17-9 - Rebuilt for https://fedoraproject.org/wiki/Fedora_38_Mass_Rebuild * Wed Jul 20 2022 Fedora Release Engineering - 0.7.17-8 - Rebuilt for https://fedoraproject.org/wiki/Fedora_37_Mass_Rebuild * Wed Jan 19 2022 Fedora Release Engineering - 0.7.17-7 - Rebuilt for https://fedoraproject.org/wiki/Fedora_36_Mass_Rebuild * Wed Jul 21 2021 Fedora Release Engineering - 0.7.17-6 - Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild * Tue Jan 26 2021 Fedora Release Engineering - 0.7.17-5 - Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild * Mon Jul 27 2020 Fedora Release Engineering - 0.7.17-4 - Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild * Mon Jul 13 2020 Tom Stellard - 0.7.17-3 - Use make macros - https://fedoraproject.org/wiki/Changes/UseMakeBuildInstallMacro * Fri May 22 2020 Jun Aruga - 0.7.17-2 - Enable non-x86_64 CPU architectures with simde. - Set -O3 for the better performance. * Thu Apr 16 2020 Jun Aruga - 0.7.17-1 - Update to upstream release 0.7.17 - Move bwakit files to data directory to avoid conflicts. * Tue Jan 28 2020 Fedora Release Engineering - 0.7.15-10 - Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild * Wed Jul 24 2019 Fedora Release Engineering - 0.7.15-9 - Rebuilt for https://fedoraproject.org/wiki/Fedora_31_Mass_Rebuild * Thu Jan 31 2019 Fedora Release Engineering - 0.7.15-8 - Rebuilt for https://fedoraproject.org/wiki/Fedora_30_Mass_Rebuild * Sat Jul 21 2018 Adam Huffman - 0.7.15-7 - Add BR for gcc * Thu Jul 12 2018 Fedora Release Engineering - 0.7.15-6 - Rebuilt for https://fedoraproject.org/wiki/Fedora_29_Mass_Rebuild * Wed Feb 07 2018 Fedora Release Engineering - 0.7.15-5 - Rebuilt for https://fedoraproject.org/wiki/Fedora_28_Mass_Rebuild * Wed Aug 02 2017 Fedora Release Engineering - 0.7.15-4 - Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Binutils_Mass_Rebuild * Wed Jul 26 2017 Fedora Release Engineering - 0.7.15-3 - Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Mass_Rebuild * Fri Feb 10 2017 Fedora Release Engineering - 0.7.15-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_26_Mass_Rebuild * Thu Jun 02 2016 Adam Huffman - 0.7.15-1 - Update to upstream release 0.7.15 * Thu Mar 24 2016 Adam Huffman - 0.7.13-1 - Update to upstream release 0.7.13 * Wed Feb 03 2016 Fedora Release Engineering - 0.7.12-3 - Rebuilt for https://fedoraproject.org/wiki/Fedora_24_Mass_Rebuild * Wed Jun 17 2015 Fedora Release Engineering - 0.7.12-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_23_Mass_Rebuild * Sat Jan 03 2015 Adam Huffman - 0.7.12-1 - Update to upstream 0.7.12 * Sat Dec 27 2014 Adam Huffman - 0.7.11-1 - Update to upstream 0.7.11 - First attempt to include new bwakit packaging * Fri Aug 15 2014 Fedora Release Engineering - 0.7.10-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_21_22_Mass_Rebuild * Sun Jul 20 2014 Adam Huffman - 0.7.10-1 - Update to upstream 0.7.10 * Sat Jun 07 2014 Fedora Release Engineering - 0.7.9a-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_21_Mass_Rebuild * Thu May 29 2014 Adam Huffman - 0.7.9a-1 - Update to upstream 0.7.9a - Docs now in Markdown format, including new README.md * Sun Oct 27 2013 Adam Huffman - 0.7.5a-2 - Remove nosse2 patch because 0.7+ versions only build on x86_64 * Sat Oct 26 2013 Adam Huffman - 0.7.5a-1 - Update to upstream 0.7.5a * Sat Aug 03 2013 Fedora Release Engineering - 0.6.1-7 - Rebuilt for https://fedoraproject.org/wiki/Fedora_20_Mass_Rebuild * Thu Jul 18 2013 Petr Pisar - 0.6.1-6 - Perl 5.18 rebuild * Wed Feb 13 2013 Fedora Release Engineering - 0.6.1-5 - Rebuilt for https://fedoraproject.org/wiki/Fedora_19_Mass_Rebuild * Wed Jul 18 2012 Fedora Release Engineering - 0.6.1-4 - Rebuilt for https://fedoraproject.org/wiki/Fedora_18_Mass_Rebuild * Mon May 28 2012 Dan Horák - 0.6.1-3 - enable SSE2 on x86_64 only, fixes build on secondary arches * Sun May 13 2012 Adam Huffman - 0.6.1-2 - add patch to avoid SSE2 on i386 * Wed Jan 11 2012 Adam Huffman - 0.6.1-1 - update to 0.6.1 * Thu Feb 17 2011 Adam Huffman - 0.5.9-1 - new upstream release 0.5.9 * Tue Feb 08 2011 Fedora Release Engineering - Rebuilt for https://fedoraproject.org/wiki/Fedora_15_Mass_Rebuild * Wed Jan 5 2011 Adam Huffman - 0.5.8c-1 - upstream bugfix release * Tue Jul 20 2010 Adam Huffman - 0.5.8a-1 - new upstream release * Sat May 29 2010 Adam Huffman - 0.5.7-2 - fix source URL - install manpage - fix cflags * Fri May 28 2010 Adam Huffman - 0.5.7-1 - initial version