Name: bwa
Version: 0.7.17
Release: 1%{?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
# 0.7.x versions only build on x86_64
ExclusiveArch: x86_64
BuildRequires: gcc
BuildRequires: perl-generators
BuildRequires: zlib-devel
%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
%patch0 -p1
%build
make %{?_smp_mflags} CFLAGS="%{optflags}"
%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
* Thu Apr 16 2020 Jun Aruga <jaruga@redhat.com> - 0.7.17-1
- Update to upstream release 0.7.17
- Move bwakit files to data directory to avoid conflicts.
* Thu Jan 31 2019 Fedora Release Engineering <releng@fedoraproject.org> - 0.7.15-8
- Rebuilt for https://fedoraproject.org/wiki/Fedora_30_Mass_Rebuild
* Sat Jul 21 2018 Adam Huffman <bloch@verdurin.com> - 0.7.15-7
- Add BR for gcc
* Thu Jul 12 2018 Fedora Release Engineering <releng@fedoraproject.org> - 0.7.15-6
- Rebuilt for https://fedoraproject.org/wiki/Fedora_29_Mass_Rebuild
* Wed Feb 07 2018 Fedora Release Engineering <releng@fedoraproject.org> - 0.7.15-5
- Rebuilt for https://fedoraproject.org/wiki/Fedora_28_Mass_Rebuild
* Wed Aug 02 2017 Fedora Release Engineering <releng@fedoraproject.org> - 0.7.15-4
- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Binutils_Mass_Rebuild
* Wed Jul 26 2017 Fedora Release Engineering <releng@fedoraproject.org> - 0.7.15-3
- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Mass_Rebuild
* Fri Feb 10 2017 Fedora Release Engineering <releng@fedoraproject.org> - 0.7.15-2
- Rebuilt for https://fedoraproject.org/wiki/Fedora_26_Mass_Rebuild
* Thu Jun 02 2016 Adam Huffman <bloch@verdurin.com> - 0.7.15-1
- Update to upstream release 0.7.15
* Thu Mar 24 2016 Adam Huffman <bloch@verdurin.com> - 0.7.13-1
- Update to upstream release 0.7.13
* Wed Feb 03 2016 Fedora Release Engineering <releng@fedoraproject.org> - 0.7.12-3
- Rebuilt for https://fedoraproject.org/wiki/Fedora_24_Mass_Rebuild
* Wed Jun 17 2015 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.7.12-2
- Rebuilt for https://fedoraproject.org/wiki/Fedora_23_Mass_Rebuild
* Sat Jan 03 2015 Adam Huffman <bloch@verdurin.com> - 0.7.12-1
- Update to upstream 0.7.12
* Sat Dec 27 2014 Adam Huffman <bloch@verdurin.com> - 0.7.11-1
- Update to upstream 0.7.11
- First attempt to include new bwakit packaging
* Fri Aug 15 2014 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.7.10-2
- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_22_Mass_Rebuild
* Sun Jul 20 2014 Adam Huffman <bloch@verdurin.com> - 0.7.10-1
- Update to upstream 0.7.10
* Sat Jun 07 2014 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.7.9a-2
- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_Mass_Rebuild
* Thu May 29 2014 Adam Huffman <bloch@verdurin.com> - 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 <bloch@verdurin.com> - 0.7.5a-2
- Remove nosse2 patch because 0.7+ versions only build on x86_64
* Sat Oct 26 2013 Adam Huffman <bloch@verdurin.com> - 0.7.5a-1
- Update to upstream 0.7.5a
* Sat Aug 03 2013 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.6.1-7
- Rebuilt for https://fedoraproject.org/wiki/Fedora_20_Mass_Rebuild
* Thu Jul 18 2013 Petr Pisar <ppisar@redhat.com> - 0.6.1-6
- Perl 5.18 rebuild
* Wed Feb 13 2013 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.6.1-5
- Rebuilt for https://fedoraproject.org/wiki/Fedora_19_Mass_Rebuild
* Wed Jul 18 2012 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.6.1-4
- Rebuilt for https://fedoraproject.org/wiki/Fedora_18_Mass_Rebuild
* Mon May 28 2012 Dan HorĂ¡k <dan[at]danny.cz> - 0.6.1-3
- enable SSE2 on x86_64 only, fixes build on secondary arches
* Sun May 13 2012 Adam Huffman <verdurin@fedoraproject.org> - 0.6.1-2
- add patch to avoid SSE2 on i386
* Wed Jan 11 2012 Adam Huffman <verdurin@fedoraproject.org> - 0.6.1-1
- update to 0.6.1
* Thu Feb 17 2011 Adam Huffman <bloch@verdurin.com> - 0.5.9-1
- new upstream release 0.5.9
* Tue Feb 08 2011 Fedora Release Engineering <rel-eng@lists.fedoraproject.org>
- Rebuilt for https://fedoraproject.org/wiki/Fedora_15_Mass_Rebuild
* Wed Jan 5 2011 Adam Huffman <bloch@verdurin.com> - 0.5.8c-1
- upstream bugfix release
* Tue Jul 20 2010 Adam Huffman <bloch@verdurin.com> - 0.5.8a-1
- new upstream release
* Sat May 29 2010 Adam Huffman <bloch@verdurin.com> - 0.5.7-2
- fix source URL
- install manpage
- fix cflags
* Fri May 28 2010 Adam Huffman <bloch@verdurin.com> - 0.5.7-1
- initial version