File bedtools.spec of Package bedtools

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File bedtools.spec of Package bedtools

#
# spec file for package bedtools
#
# Copyright (c) 2024 SUSE LLC
#
# 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 https://bugs.opensuse.org/
#

Name:           bedtools
Version:        2.31.1
Release:        0
Summary:        A powerful toolset for genome arithmetic
License:        MIT
Group:          Productivity/Scientific/Other
URL:            https://github.com/arq5x/bedtools2/
Source0:        https://github.com/arq5x/bedtools2/releases/download/v%{version}/%{name}-%{version}.tar.gz
BuildRequires:  gcc-c++
BuildRequires:  python3
BuildRequires:  python3-Sphinx
BuildRequires:  zlib-devel
BuildRequires:  pkgconfig(bzip2)
BuildRequires:  pkgconfig(liblzma)
Recommends:     %{name}-data = %{version}
Recommends:     %{name}-doc = %{version}

%description
Collectively, the bedtools utilities are a swiss-army knife of tools for
a wide-range of genomics analysis tasks. The most widely-used tools enable
genome arithmetic: that is, set theory on the genome. For example, bedtools
allows one to intersect, merge, count, complement, and shuffle genomic
intervals from multiple files in widely-used genomic file formats such as
BAM, BED, GFF/GTF, VCF.

While each individual tool is designed to do a relatively simple task (e.g.,
intersect two interval files), quite sophisticated analyses can be
conducted by combining multiple bedtools operations on the UNIX command line.

%package data
Summary:        Example data for the package %{name}
Requires:       %{name} = %{version}
BuildArch:      noarch

%description data
Example data for the package %{name} (genome and genetic data samples)

%package doc
Summary:        Documentation for %{name}
Group:          Documentation/HTML
Requires:       %{name} = %{version}
BuildArch:      noarch

%description doc
Bedtools utilities are a swiss-army knife of tools for a wide-range of
genomics analysis tasks.

This package provides documentation for %{name}.

%prep
%setup -q -n bedtools2

%build
%make_build PYTHON=python3

cd docs
%make_build clean html
cd ..

# REMOVE UNNECESSARY HIDDEN BUILDINFO FILE
rm docs/_build/html/.buildinfo docs/_build/doctrees/environment.pickle

%install
mkdir -p %{buildroot}/%{_bindir}
install -m755 bin/* %{buildroot}/%{_bindir}

mkdir -p %{buildroot}%{_datadir}/%{name}
cp -a genomes/ %{buildroot}%{_datadir}/%{name}
cp -a data/ %{buildroot}%{_datadir}/%{name}

# FIX FOR EXEC BIT SET WITHOUT HASHBANG
chmod -x %{buildroot}%{_datadir}/bedtools/data/knownGene.hg18.chr21.bed

%files
%license LICENSE
%doc README.md
%{_bindir}/*

%files doc
%doc docs/_build/

%files data
%{_datadir}/%{name}
%{_datadir}/%{name}/data
%{_datadir}/%{name}/data/*
%{_datadir}/%{name}/genomes
%{_datadir}/%{name}/genomes/*

%changelog

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File bedtools.spec of Package bedtools

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