Blame bcftools.spec

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Name:		bcftools
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Version:	1.9
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Release:	1%{?dist}
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Summary:	Tools for genomic variant calling and manipulating VCF/BCF files
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# The bcftools source code is MIT-licensed, but the executable becomes
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# GPL-licensed when --enable-libgsl is used.
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License:	GPLv3+
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URL:		http://www.htslib.org/
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Source0:	https://github.com/samtools/bcftools/releases/download/%{version}/bcftools-%{version}.tar.bz2
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Patch0:		bcftools-1.9-python3.patch
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Patch1:		bcftools-1.9-configure.patch
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BuildRequires:	gcc
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BuildRequires:	gsl-devel
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BuildRequires:	htslib-devel
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BuildRequires:	htslib-tools
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BuildRequires:	perl-interpreter
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BuildRequires:	perl(ExtUtils::Embed)
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BuildRequires:	perl(File::Temp)
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BuildRequires:	perl(Getopt::Long)
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BuildRequires:	zlib-devel
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%description
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BCFtools is a set of utilities that manipulate genomic variant calls in the
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Variant Call Format (VCF) and its binary counterpart (BCF). All commands work
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transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.
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(This BCFtools includes the polysomy subcommand, which is implemented using
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the GNU Scientific Library. Hence this package is licensed according to the
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GNU General Public License, rather than the MIT license used when BCFtools
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is built without the polysomy subcommand.)
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%prep
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%setup -q
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%patch0 -p1 -b .py3
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%patch1 -p1 -b .conf
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sed -i '1s,/usr/bin/env perl,/usr/bin/perl,' misc/*.pl misc/plot-vcfstats
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sed -i '1s,/usr/bin/env python,%{__python3},' misc/*.py
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%build
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%configure CFLAGS="%{optflags}" LDFLAGS="%{build_ldflags}" \
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  --prefix=%{_prefix} \
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  --with-htslib=system --enable-perl-filters --enable-libgsl \
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  --with-bcf-plugin-path='%{_usr}/local/libexec/bcftools:$(plugindir)'
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%make_build
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%install
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%make_install
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%check
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make test
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%files
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%doc AUTHORS NEWS
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%license LICENSE
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%{_bindir}/*
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%{_libexecdir}/bcftools
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%{_mandir}/man1/bcftools.1*
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%changelog
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* Wed Nov 06 2019 John Marshall <jmarshall@users.sourceforge.net> - 1.9-1
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- New spec file for bcftools, now separate from samtools (#1767792).
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- Backported Python 3 and configure patches from later upstream development.