Atri Bhattacharya
7815b6ea55
- Update to 2.31.1
* Added new summary tool for basic sanity checks and quality
control of interval files.
* Added support for gzipp'ed FASTA files to getfasta and nuc.
* Various typo and minor bug fixes
OBS-URL: https://build.opensuse.org/request/show/1137140
OBS-URL: https://build.opensuse.org/package/show/science/bedtools?expand=0&rev=7
108 lines
3.2 KiB
RPMSpec
108 lines
3.2 KiB
RPMSpec
#
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# spec file for package bedtools
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#
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# Copyright (c) 2024 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: bedtools
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Version: 2.31.1
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Release: 0
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Summary: A powerful toolset for genome arithmetic
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License: MIT
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Group: Productivity/Scientific/Other
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URL: https://github.com/arq5x/bedtools2/
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Source0: https://github.com/arq5x/bedtools2/releases/download/v%{version}/%{name}-%{version}.tar.gz
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BuildRequires: gcc-c++
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BuildRequires: python3
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BuildRequires: python3-Sphinx
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BuildRequires: zlib-devel
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BuildRequires: pkgconfig(bzip2)
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BuildRequires: pkgconfig(liblzma)
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Recommends: %{name}-data = %{version}
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Recommends: %{name}-doc = %{version}
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%description
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Collectively, the bedtools utilities are a swiss-army knife of tools for
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a wide-range of genomics analysis tasks. The most widely-used tools enable
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genome arithmetic: that is, set theory on the genome. For example, bedtools
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allows one to intersect, merge, count, complement, and shuffle genomic
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intervals from multiple files in widely-used genomic file formats such as
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BAM, BED, GFF/GTF, VCF.
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While each individual tool is designed to do a relatively simple task (e.g.,
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intersect two interval files), quite sophisticated analyses can be
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conducted by combining multiple bedtools operations on the UNIX command line.
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%package data
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Summary: Example data for the package %{name}
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Requires: %{name} = %{version}
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BuildArch: noarch
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%description data
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Example data for the package %{name} (genome and genetic data samples)
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%package doc
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Summary: Documentation for %{name}
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Group: Documentation/HTML
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Requires: %{name} = %{version}
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BuildArch: noarch
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%description doc
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Bedtools utilities are a swiss-army knife of tools for a wide-range of
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genomics analysis tasks.
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This package provides documentation for %{name}.
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%prep
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%setup -q -n bedtools2
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%build
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%make_build PYTHON=python3
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cd docs
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%make_build clean html
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cd ..
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# REMOVE UNNECESSARY HIDDEN BUILDINFO FILE
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rm docs/_build/html/.buildinfo docs/_build/doctrees/environment.pickle
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%install
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mkdir -p %{buildroot}/%{_bindir}
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install -m755 bin/* %{buildroot}/%{_bindir}
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mkdir -p %{buildroot}%{_datadir}/%{name}
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cp -a genomes/ %{buildroot}%{_datadir}/%{name}
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cp -a data/ %{buildroot}%{_datadir}/%{name}
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# FIX FOR EXEC BIT SET WITHOUT HASHBANG
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chmod -x %{buildroot}%{_datadir}/bedtools/data/knownGene.hg18.chr21.bed
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%files
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%license LICENSE
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%doc README.md
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%{_bindir}/*
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%files doc
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%doc docs/_build/
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%files data
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%{_datadir}/%{name}
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%{_datadir}/%{name}/data
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%{_datadir}/%{name}/data/*
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%{_datadir}/%{name}/genomes
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%{_datadir}/%{name}/genomes/*
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%changelog
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