Atri Bhattacharya
650b23c155
Too many changes to list, for details see included NEWS file or https://github.com/samtools/bcftools/releases/tag/1.21 - Update to version 1.20: Too many changes to list, for details see included NEWS file or https://github.com/samtools/bcftools/releases/tag/1.20 OBS-URL: https://build.opensuse.org/package/show/science/bcftools?expand=0&rev=21
75 lines
2.6 KiB
RPMSpec
75 lines
2.6 KiB
RPMSpec
#
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# spec file for package bcftools
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#
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# Copyright (c) 2025 SUSE LLC
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#
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# All modifications and additions to the file contributed by third parties
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# remain the property of their copyright owners, unless otherwise agreed
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# upon. The license for this file, and modifications and additions to the
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# file, is the same license as for the pristine package itself (unless the
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# license for the pristine package is not an Open Source License, in which
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# case the license is the MIT License). An "Open Source License" is a
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# license that conforms to the Open Source Definition (Version 1.9)
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# published by the Open Source Initiative.
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# Please submit bugfixes or comments via https://bugs.opensuse.org/
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#
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Name: bcftools
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Version: 1.21
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Release: 0
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Summary: Tools for manipulating variant calls in the Variant Call Format (VCF)
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License: MIT
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Group: Productivity/Scientific/Other
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URL: http://www.htslib.org/
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# The “Source code” downloads links generated by GitHub and are incomplete as they don't bundle HTSlib and are missing some generated files
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Source: https://github.com/samtools/bcftools/releases/download/%{version}/bcftools-%{version}.tar.bz2
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# PATCH-FIX-OPENSUSE use_python3.patch -- Use python3 executable instead of python2
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Patch0: use_python3.patch
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BuildRequires: automake
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BuildRequires: gsl-devel
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BuildRequires: libbz2-devel
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BuildRequires: libhts-devel >= %{version}
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BuildRequires: lzma-devel
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BuildRequires: zlib-devel
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Requires: bgzip
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Requires: htsfile
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Requires: perl-base
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Requires: python3-base
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Requires: python3-matplotlib
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Requires: tabix
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%description
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Package for the new BCFtools: a set of utilities that manipulate variant calls in the Variant Call Format (VCF)
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and its binary counterpart BCF. It contains all the "vcf..." commands which previously lived in the HTSlib
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repository (such as vcfcheck, vcfmerge, vcfisec, etc.) and the samtools BCF calling from bcftools subdirectory
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of samtools. BCFtools are meant as a faster replacement for most of the perl VCFtools commands.
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%prep
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%autosetup -p1
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%build
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autoreconf -fi
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%configure --with-htslib=system
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%make_build USE_GSL=1
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%install
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%make_install prefix=%{_prefix} libexecdir=%{_libdir} libdir=%{_libdir}
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# CONVERT env HASHBANGS TO USE DIRECT EXECUTABLE
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sed -i "s:/usr/bin/env perl:%{_bindir}/perl:" %{buildroot}/%{_bindir}/*.pl %{buildroot}/%{_bindir}/plot-vcfstats
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sed -i -E "s:/usr/bin/env python3?:%{_bindir}/python3:" %{buildroot}/%{_bindir}/*.py
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%files
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%license LICENSE
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%doc AUTHORS README NEWS
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%{_bindir}/bcftools
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%{_bindir}/*.py
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%{_bindir}/*.pl
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%{_bindir}/plot-vcfstats
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%{_libdir}/bcftools/
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%{_mandir}/man1/*
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%changelog
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