Tina Müller
12aa042732
- Add build dependency Gd
- Remove deps.patch (not used anymore)
- updated to 1.7.6
see /usr/share/doc/packages/perl-BioPerl/Changes
1.7.6 2019-08-28 12:37:01+01:00 Europe/London
* The program bp_classify_hits_kingdom has been removed and is
now part of the examples documentation instead.
* GD is now listed as a suggestion instead of a requirement. The
bp_chaos_plot program will now work with the GD module.
* New method Bio::Tree::Statistics::transfer_bootstrap_expectation
to compute Transfer Bootstrap Expectation (TBE) for internal
nodes based on the methods outlined in Lemoine et al, Nature,
2018.
* New method Bio::SeqIO::fasta::next_seq_fast to retrieve next
sequence in the stream faster but not perfect.
OBS-URL: https://build.opensuse.org/request/show/731701
OBS-URL: https://build.opensuse.org/package/show/devel:languages:perl/perl-BioPerl?expand=0&rev=8
143 lines
5.0 KiB
RPMSpec
143 lines
5.0 KiB
RPMSpec
#
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# spec file for package perl-BioPerl
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#
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# Copyright (c) 2019 SUSE LINUX GmbH, Nuernberg, Germany.
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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: perl-BioPerl
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Version: 1.7.6
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Release: 0
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%define cpan_name BioPerl
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Summary: Perl modules for biology
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License: Artistic-1.0 OR GPL-1.0-or-later
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Group: Development/Libraries/Perl
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Url: https://metacpan.org/release/%{cpan_name}
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Source0: https://cpan.metacpan.org/authors/id/C/CD/CDRAUG/%{cpan_name}-%{version}.tar.gz
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Source1: cpanspec.yml
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BuildArch: noarch
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BuildRoot: %{_tmppath}/%{name}-%{version}-build
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BuildRequires: perl
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BuildRequires: perl-macros
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BuildRequires: perl(Data::Stag)
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BuildRequires: perl(Error)
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BuildRequires: perl(Graph::Directed)
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BuildRequires: perl(HTTP::Request::Common)
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BuildRequires: perl(HTTP::Response)
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BuildRequires: perl(IO::Scalar)
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BuildRequires: perl(IO::String)
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BuildRequires: perl(IPC::Run)
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BuildRequires: perl(LWP::UserAgent)
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BuildRequires: perl(List::MoreUtils)
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BuildRequires: perl(Module::Build)
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BuildRequires: perl(Set::Scalar)
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BuildRequires: perl(Test::Memory::Cycle)
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BuildRequires: perl(Test::Most)
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BuildRequires: perl(Test::RequiresInternet)
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BuildRequires: perl(Test::Weaken)
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BuildRequires: perl(URI)
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BuildRequires: perl(XML::DOM)
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BuildRequires: perl(XML::DOM::XPath)
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BuildRequires: perl(XML::LibXML)
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BuildRequires: perl(XML::LibXML::Reader)
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BuildRequires: perl(XML::Parser::PerlSAX)
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BuildRequires: perl(XML::SAX)
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BuildRequires: perl(XML::SAX::Base)
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BuildRequires: perl(XML::SAX::Writer)
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BuildRequires: perl(XML::Twig)
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BuildRequires: perl(XML::Writer)
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BuildRequires: perl(YAML)
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BuildRequires: perl(parent)
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BuildRequires: perl(version)
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Requires: perl(Data::Stag)
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Requires: perl(Error)
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Requires: perl(Graph::Directed)
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Requires: perl(HTTP::Request::Common)
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Requires: perl(HTTP::Response)
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Requires: perl(IO::Scalar)
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Requires: perl(IO::String)
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Requires: perl(IPC::Run)
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Requires: perl(LWP::UserAgent)
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Requires: perl(List::MoreUtils)
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Requires: perl(Module::Build)
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Requires: perl(Set::Scalar)
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Requires: perl(Test::Most)
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Requires: perl(Test::RequiresInternet)
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Requires: perl(URI)
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Requires: perl(XML::DOM)
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Requires: perl(XML::DOM::XPath)
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Requires: perl(XML::LibXML)
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Requires: perl(XML::LibXML::Reader)
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Requires: perl(XML::Parser::PerlSAX)
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Requires: perl(XML::SAX)
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Requires: perl(XML::SAX::Base)
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Requires: perl(XML::SAX::Writer)
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Requires: perl(XML::Twig)
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Requires: perl(XML::Writer)
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Requires: perl(YAML)
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Requires: perl(parent)
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Requires: perl(version)
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%{perl_requires}
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# MANUAL BEGIN
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BuildRequires: perl(GD)
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# MANUAL END
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%description
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BioPerl is the product of a community effort to produce Perl code which is
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useful in biology. Examples include Sequence objects, Alignment objects and
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database searching objects. These objects not only do what they are
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advertised to do in the documentation, but they also interact - Alignment
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objects are made from the Sequence objects, Sequence objects have access to
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Annotation and SeqFeature objects and databases, Blast objects can be
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converted to Alignment objects, and so on. This means that the objects
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provide a coordinated and extensible framework to do computational biology.
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BioPerl development focuses on Perl classes, or code that is used to create
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objects representing biological entities. There are scripts provided in the
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scripts/ and examples/ directories but scripts are not the main focus of
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the BioPerl developers. Of course, as the objects do most of the hard work
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for you, all you have to do is combine a number of objects together
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sensibly to make useful scripts.
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The intent of the BioPerl development effort is to make reusable tools that
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aid people in creating their own sites or job-specific applications.
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The BioPerl website at http://bioperl.org also attempts to maintain links
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and archives of standalone bio-related Perl tools that are not affiliated
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or related to the core BioPerl effort. Check the site for useful code ideas
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and contribute your own if possible.
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%prep
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%setup -q -n %{cpan_name}-%{version}
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find . -type f ! -name \*.pl -print0 | xargs -0 chmod 644
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%build
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perl Makefile.PL INSTALLDIRS=vendor
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make %{?_smp_mflags}
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%check
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make test
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%install
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%perl_make_install
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%perl_process_packlist
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%perl_gen_filelist
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%files -f %{name}.files
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%defattr(-,root,root,755)
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%doc AUTHORS Changes examples HACKING.md README.md
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%license LICENSE
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%changelog
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