diff --git a/.gitignore b/.gitignore index 6ccae35..61d265c 100644 --- a/.gitignore +++ b/.gitignore @@ -1,2 +1,6 @@ /vcftools_0.1.9.tar.gz /vcftools_0.1.11.tar.gz +/vcftools-0.1.14.tar.gz +/vcftools-0.1.15.tar.gz +/vcftools-0.1.16.tar.gz +/vcftools-0.1.17.tar.gz diff --git a/changelog b/changelog new file mode 100644 index 0000000..0f37f6f --- /dev/null +++ b/changelog @@ -0,0 +1,156 @@ +* Fri Jul 25 2025 Fedora Release Engineering - 0.1.16-22 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_43_Mass_Rebuild + +* Sun Jan 19 2025 Fedora Release Engineering - 0.1.16-21 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_42_Mass_Rebuild + +* Mon Jul 29 2024 Miroslav Suchý - 0.1.16-20 +- convert license to SPDX + +* Sat Jul 20 2024 Fedora Release Engineering - 0.1.16-19 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_41_Mass_Rebuild + +* Sat Jan 27 2024 Fedora Release Engineering - 0.1.16-18 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild + +* Sat Jul 22 2023 Fedora Release Engineering - 0.1.16-17 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_39_Mass_Rebuild + +* Sat Jan 21 2023 Fedora Release Engineering - 0.1.16-16 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_38_Mass_Rebuild + +* Thu Sep 01 2022 Filipe Rosset - 0.1.16-15 +- spec cleanup and modernization + +* Sat Jul 23 2022 Fedora Release Engineering - 0.1.16-14 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_37_Mass_Rebuild + +* Mon May 30 2022 Jitka Plesnikova - 0.1.16-13 +- Perl 5.36 rebuild + +* Sat Jan 22 2022 Fedora Release Engineering - 0.1.16-12 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_36_Mass_Rebuild + +* Fri Jul 23 2021 Fedora Release Engineering - 0.1.16-11 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild + +* Fri May 21 2021 Jitka Plesnikova - 0.1.16-10 +- Perl 5.34 rebuild + +* Wed Jan 27 2021 Fedora Release Engineering - 0.1.16-9 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild + +* Wed Jul 29 2020 Fedora Release Engineering - 0.1.16-8 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild + +* Fri Jun 26 2020 Jitka Plesnikova - 0.1.16-7 +- Perl 5.32 re-rebuild of bootstrapped packages + +* Mon Jun 22 2020 Jitka Plesnikova - 0.1.16-6 +- Perl 5.32 rebuild + +* Fri Jan 31 2020 Fedora Release Engineering - 0.1.16-5 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild + +* Sat Jul 27 2019 Fedora Release Engineering - 0.1.16-4 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_31_Mass_Rebuild + +* Mon Jun 17 2019 Petr Pisar - 0.1.16-3 +- Install Perl modules into a vendor Perl path + +* Sun Feb 03 2019 Fedora Release Engineering - 0.1.16-2 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_30_Mass_Rebuild + +* Sun Aug 05 2018 Adam Huffman - 0.1.16-1 +- Update to latest upstream release 0.1.16 + +* Sat Jul 14 2018 Fedora Release Engineering - 0.1.15-7 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_29_Mass_Rebuild + +* Mon Apr 09 2018 Filipe Rosset - 0.1.15-6 +- added gcc-c++ as BR + +* Fri Feb 09 2018 Fedora Release Engineering - 0.1.15-5 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_28_Mass_Rebuild + +* Thu Aug 03 2017 Fedora Release Engineering - 0.1.15-4 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Binutils_Mass_Rebuild + +* Thu Jul 27 2017 Fedora Release Engineering - 0.1.15-3 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Mass_Rebuild + +* Mon May 15 2017 Fedora Release Engineering - 0.1.15-2 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_26_27_Mass_Rebuild + +* Fri Apr 21 2017 Filipe Rosset - 0.1.15-1 +- Update to latest upstream release 0.1.15 + +* Sat Feb 11 2017 Fedora Release Engineering - 0.1.14-2 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_26_Mass_Rebuild + +* Tue Nov 08 2016 Filipe Rosset - 0.1.14-1 +- Update to latest upstream release 0.1.14 +- Fix FTBFS rhbz #1308219 +- Fix rhbz #1365319 thanks to Aram Minasyan +- Spec modernization/clean up, new URLs from GitHub + +* Fri Feb 05 2016 Fedora Release Engineering - 0.1.11-9 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_24_Mass_Rebuild + +* Fri Jun 19 2015 Fedora Release Engineering - 0.1.11-8 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_23_Mass_Rebuild + +* Sat May 02 2015 Kalev Lember - 0.1.11-7 +- Rebuilt for GCC 5 C++11 ABI change + +* Mon Aug 18 2014 Fedora Release Engineering - 0.1.11-6 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_22_Mass_Rebuild + +* Sun Jun 08 2014 Fedora Release Engineering - 0.1.11-5 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_Mass_Rebuild + +* Sat Aug 03 2013 Petr Pisar - 0.1.11-4 +- Perl 5.18 rebuild + +* Tue Jul 30 2013 Peter Robinson 0.1.11-3 +- Use distro CFLAGS (fix FTBFS on ARM) + +* Thu Jul 18 2013 Petr Pisar - 0.1.11-2 +- Perl 5.18 rebuild + +* Wed Jul 03 2013 - 0.1.11-1 +- Update to latest upstream release 0.1.11 + +* Fri Feb 15 2013 Fedora Release Engineering - 0.1.9-2 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_19_Mass_Rebuild + +* Sun Jul 29 2012 - 0.1.9-1 +- Update to 0.1.9 +- Remove perl patch that's no longer needed + +* Thu Jan 5 2012 Adam Huffman - 0.1.7-1 +- update to upstream release 0.1.7 +- remove fill-rsIDs +- update Perl makefile patch + +* Sun Jul 31 2011 Adam Huffman - 0.1.6-1 +- update to 0.1.6 + +* Tue May 3 2011 Adam Huffman - 0.1.5-2 +- minor fix to Jack's Perl patch +- permissions fix +- hardcoded path fix +- cleaner Makefile fix + +* Sun May 1 2011 Jack Tanner - 0.1.5-1 +- bump to 0.1.5 +- rename compare-vcf, merge-vcf, and query-vcf to vcf-compare, + vcf-merge, and vcf-query +- add VcfStats.pm to perl export +- patch perl/Makefile to export VcfStats.pm + +* Mon Mar 21 2011 Adam Huffman - 0.1.4a-1 +- initial version +- fix CPPFLAGS +- fix hardcoded installation location + diff --git a/sources b/sources index e8d3711..6131466 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -ddb49e9fa2bfedae36b4dce163adfaa8 vcftools_0.1.11.tar.gz +SHA512 (vcftools-0.1.17.tar.gz) = 8adf2490b5d0886302f8f19efc735e4b96d657d70a764b6fa397acdf6f83b54da29dc73e9b96b275a793a511996c415630255610249e6eb5441bc783e82853d9 diff --git a/vcftools.spec b/vcftools.spec index b04af2d..ab1d67f 100644 --- a/vcftools.spec +++ b/vcftools.spec @@ -1,18 +1,17 @@ Name: vcftools -Version: 0.1.11 -Release: 1%{?dist} +Version: 0.1.17 +Release: %autorelease Summary: VCF file manipulation tools - -Group: Applications/Engineering -License: GPLv3 -URL: http://vcftools.sourceforge.net/ -Source0: http://downloads.sourceforge.net/%{name}/%{name}_%{version}.tar.gz - -BuildRoot: %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n) - +# Automatically converted from old format: GPLv3 - review is highly recommended. +License: GPL-3.0-only +URL: https://vcftools.github.io/ +Source0: https://github.com/%{name}/%{name}/releases/download/v%{version}/%{name}-%{version}.tar.gz +BuildRequires: make +BuildRequires: gcc-c++ +BuildRequires: perl-generators +BuildRequires: perl-interpreter BuildRequires: zlib-devel - %description A program package designed for working with VCF files, such as those generated by the 1000 Genomes Project. The aim of VCFtools is to @@ -20,28 +19,23 @@ provide methods for working with VCF files: validating, merging, comparing and calculate some basic population genetic statistics. %prep -%setup -q -n %{name}_%{version} -#%patch0 -p1 +%autosetup %build -make %{?_smp_mflags} CPPFLAGS="%{optflags}" +%configure --with-pmdir=%(perl -e 'print $ARGV[0] =~ s{\A\Q$ARGV[1]\E/}{}r' \ + %{perl_vendorlib} %{_exec_prefix}) +%make_build +%check +make check %install -rm -rf %{buildroot} -make install PREFIX=%{buildroot}/usr MODDIR="%{buildroot}/%{perl_vendorarch}" \ -BINDIR="%{buildroot}/%{_bindir}" - -install -m 0775 %{_builddir}/%{name}_%{version}/cpp/vcftools %{buildroot}/%{_bindir} - - -%clean -rm -rf %{buildroot} +%make_install %files -%defattr(-,root,root,-) -%doc README.txt +%doc README.md +%license LICENSE %{_bindir}/vcf-compare %{_bindir}/fill-aa %{_bindir}/fill-an-ac @@ -66,45 +60,12 @@ rm -rf %{buildroot} %{_bindir}/vcf-phased-join %{_bindir}/vcf-shuffle-cols %{_bindir}/vcf-tstv -%attr(0755, root, root) %{_bindir}/vcftools -%{perl_vendorarch}/FaSlice.pm -%{perl_vendorarch}/Vcf.pm -%{perl_vendorarch}/VcfStats.pm +%{_bindir}/vcf-fix-newlines +%{_bindir}/vcftools +%{perl_vendorlib}/FaSlice.pm +%{perl_vendorlib}/Vcf.pm +%{perl_vendorlib}/VcfStats.pm +%{_mandir}/man1/vcftools.1.gz %changelog -* Wed Jul 03 2013 - 0.1.11-1 -- Update to latest upstream release 0.1.11 - -* Fri Feb 15 2013 Fedora Release Engineering - 0.1.9-2 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_19_Mass_Rebuild - -* Sun Jul 29 2012 - 0.1.9-1 -- Update to 0.1.9 -- Remove perl patch that's no longer needed - -* Thu Jan 5 2012 Adam Huffman - 0.1.7-1 -- update to upstream release 0.1.7 -- remove fill-rsIDs -- update Perl makefile patch - -* Sun Jul 31 2011 Adam Huffman - 0.1.6-1 -- update to 0.1.6 - -* Tue May 3 2011 Adam Huffman - 0.1.5-2 -- minor fix to Jack's Perl patch -- permissions fix -- hardcoded path fix -- cleaner Makefile fix - -* Sun May 1 2011 Jack Tanner - 0.1.5-1 -- bump to 0.1.5 -- rename compare-vcf, merge-vcf, and query-vcf to vcf-compare, - vcf-merge, and vcf-query -- add VcfStats.pm to perl export -- patch perl/Makefile to export VcfStats.pm - -* Mon Mar 21 2011 Adam Huffman - 0.1.4a-1 -- initial version -- fix CPPFLAGS -- fix hardcoded installation location - +%autochangelog