File vcftools.spec of Package vcftools

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File vcftools.spec of Package vcftools (Revision 2c3ea5a720a49a971be363d4435c5e2b)

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#
# spec file for package vcftools
#
# Copyright (c) 2018 SUSE LINUX GmbH, Nuernberg, Germany.
#
# All modifications and additions to the file contributed by third parties
# remain the property of their copyright owners, unless otherwise agreed
# upon. The license for this file, and modifications and additions to the
# file, is the same license as for the pristine package itself (unless the
# license for the pristine package is not an Open Source License, in which
# case the license is the MIT License). An "Open Source License" is a
# license that conforms to the Open Source Definition (Version 1.9)
# published by the Open Source Initiative.

# Please submit bugfixes or comments via http://bugs.opensuse.org/
#

Name:           vcftools
Version:        0.1.15
Release:        0
Summary:        Tools for manipulating VCF files (Variant Call Format)
License:        GPL-3.0-only
Group:          Productivity/Scientific/Other
URL:            https://vcftools.github.io/
Source:         https://github.com/%{name}/%{name}/releases/download/v%{version}/%{name}-%{version}.tar.gz
BuildRequires:  gcc-c++
BuildRequires:  perl
BuildRequires:  pkgconfig
BuildRequires:  zlib-devel
Requires:       perl

%description
VCFtools is a set of tools written in Perl and C++ for working with VCF files (Variant Call Format), such as those generated by the 1000 Genomes Project.

%prep
%setup -q
chmod -x LICENSE
chmod -x README.md

%build
# Remove prefix from perl_vendorarch to set up the pmdir
perl_vendorarch_short=`echo "%{perl_vendorarch}" | sed 's:%{_prefix}/:/:'`
%configure --with-pmdir=${perl_vendorarch_short}
make %{?_smp_mflags}

%install
%make_install

# CONVERT env HASHBANGS TO USE DIRECT EXECUTABLE
perlbin=`which perl`
sed -i "s:/usr/bin/env perl:${perlbin}:" %{buildroot}/%{_bindir}/fill-aa
sed -i "s:/usr/bin/env perl:${perlbin}:" %{buildroot}/%{_bindir}/fill-an-ac
sed -i "s:/usr/bin/env perl:${perlbin}:" %{buildroot}/%{_bindir}/fill-fs
sed -i "s:/usr/bin/env perl:${perlbin}:" %{buildroot}/%{_bindir}/fill-ref-md5
sed -i "s:/usr/bin/env perl:${perlbin}:" %{buildroot}/%{_bindir}/vcf-annotate
sed -i "s:/usr/bin/env perl:${perlbin}:" %{buildroot}/%{_bindir}/vcf-compare
sed -i "s:/usr/bin/env perl:${perlbin}:" %{buildroot}/%{_bindir}/vcf-concat
sed -i "s:/usr/bin/env perl:${perlbin}:" %{buildroot}/%{_bindir}/vcf-consensus
sed -i "s:/usr/bin/env perl:${perlbin}:" %{buildroot}/%{_bindir}/vcf-contrast
sed -i "s:/usr/bin/env perl:${perlbin}:" %{buildroot}/%{_bindir}/vcf-convert
sed -i "s:/usr/bin/env perl:${perlbin}:" %{buildroot}/%{_bindir}/vcf-fix-newlines
sed -i "s:/usr/bin/env perl:${perlbin}:" %{buildroot}/%{_bindir}/vcf-fix-ploidy
sed -i "s:/usr/bin/env perl:${perlbin}:" %{buildroot}/%{_bindir}/vcf-indel-stats
sed -i "s:/usr/bin/env perl:${perlbin}:" %{buildroot}/%{_bindir}/vcf-isec
sed -i "s:/usr/bin/env perl:${perlbin}:" %{buildroot}/%{_bindir}/vcf-merge
sed -i "s:/usr/bin/env perl:${perlbin}:" %{buildroot}/%{_bindir}/vcf-phased-join
sed -i "s:/usr/bin/env perl:${perlbin}:" %{buildroot}/%{_bindir}/vcf-query
sed -i "s:/usr/bin/env perl:${perlbin}:" %{buildroot}/%{_bindir}/vcf-shuffle-cols
sed -i "s:/usr/bin/env perl:${perlbin}:" %{buildroot}/%{_bindir}/vcf-sort
sed -i "s:/usr/bin/env perl:${perlbin}:" %{buildroot}/%{_bindir}/vcf-stats
sed -i "s:/usr/bin/env perl:${perlbin}:" %{buildroot}/%{_bindir}/vcf-subset
sed -i "s:/usr/bin/env perl:${perlbin}:" %{buildroot}/%{_bindir}/vcf-to-tab
sed -i "s:/usr/bin/env perl:${perlbin}:" %{buildroot}/%{_bindir}/vcf-tstv
sed -i "s:/usr/bin/env perl:${perlbin}:" %{buildroot}/%{_bindir}/vcf-validator

%files
%license LICENSE
%doc README.md
%{_bindir}/*
%{_mandir}/man1/vcftools.1%{?ext_man}
%{perl_vendorarch}/FaSlice.pm
%{perl_vendorarch}/Vcf.pm
%{perl_vendorarch}/VcfStats.pm

%changelog

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File vcftools.spec of Package vcftools (Revision 2c3ea5a720a49a971be363d4435c5e2b)

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