#
# spec file for package perl-BioPerl
#
# 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 https://bugs.opensuse.org/
#


Name:           perl-BioPerl
Version:        1.007002
Release:        0
%define cpan_name BioPerl
Summary:        Perl Modules for Biology
License:        GPL-2.0-or-later OR Artistic-1.0
Group:          Development/Libraries/Perl
Url:            http://search.cpan.org/dist/BioPerl/
Source0:        https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/%{cpan_name}-%{version}.tar.gz
Source1:        cpanspec.yml
BuildArch:      noarch
BuildRoot:      %{_tmppath}/%{name}-%{version}-build
BuildRequires:  perl
BuildRequires:  perl-macros
BuildRequires:  perl(CPAN) >= 1.81
BuildRequires:  perl(Data::Stag) >= 0.11
BuildRequires:  perl(ExtUtils::Manifest) >= 1.52
BuildRequires:  perl(IO::String)
BuildRequires:  perl(Module::Build) >= 0.420000
BuildRequires:  perl(Test::Harness) >= 2.62
BuildRequires:  perl(Test::Most)
BuildRequires:  perl(URI::Escape)
Requires:       perl(Data::Stag) >= 0.11
Requires:       perl(ExtUtils::Manifest) >= 1.52
Requires:       perl(IO::String)
Recommends:     perl(Algorithm::Munkres)
Recommends:     perl(Array::Compare)
Recommends:     perl(Bio::Phylo)
Recommends:     perl(CGI)
Recommends:     perl(Clone)
Recommends:     perl(Convert::Binary::C)
Recommends:     perl(Error)
Recommends:     perl(GD)
Recommends:     perl(Graph) >= 0.5
Recommends:     perl(GraphViz)
Recommends:     perl(HTML::Entities)
Recommends:     perl(HTML::HeadParser) >= 3
Recommends:     perl(HTML::TableExtract)
Recommends:     perl(HTTP::Request::Common)
Recommends:     perl(Inline::C) >= 0.67
Recommends:     perl(IO::Scalar)
Recommends:     perl(List::MoreUtils)
Recommends:     perl(LWP::UserAgent)
Recommends:     perl(PostScript::TextBlock)
Recommends:     perl(Set::Scalar)
Recommends:     perl(Sort::Naturally)
Recommends:     perl(Spreadsheet::ParseExcel)
Recommends:     perl(SVG) >= 2.26
Recommends:     perl(SVG::Graph) >= 0.01
Recommends:     perl(XML::DOM)
Recommends:     perl(XML::DOM::XPath)
Recommends:     perl(XML::LibXML)
Recommends:     perl(XML::Parser)
Recommends:     perl(XML::Parser::PerlSAX)
Recommends:     perl(XML::SAX) >= 0.15
Recommends:     perl(XML::SAX::Writer)
Recommends:     perl(XML::Simple)
Recommends:     perl(XML::Twig)
Recommends:     perl(XML::Writer) >= 0.4
Recommends:     perl(YAML)
%{perl_requires}

%description
BioPerl is the product of a community effort to produce Perl code which is
useful in biology. Examples include Sequence objects, Alignment objects and
database searching objects. These objects not only do what they are
advertised to do in the documentation, but they also interact - Alignment
objects are made from the Sequence objects, Sequence objects have access to
Annotation and SeqFeature objects and databases, Blast objects can be
converted to Alignment objects, and so on. This means that the objects
provide a coordinated and extensible framework to do computational biology.

BioPerl development focuses on Perl classes, or code that is used to create
objects representing biological entities. There are scripts provided in the
scripts/ and examples/ directories but scripts are not the main focus of
the BioPerl developers. Of course, as the objects do most of the hard work
for you, all you have to do is combine a number of objects together
sensibly to make useful scripts.

The intent of the BioPerl development effort is to make reusable tools that
aid people in creating their own sites or job-specific applications.

The BioPerl website at http://bioperl.org also attempts to maintain links
and archives of standalone bio-related Perl tools that are not affiliated
or related to the core BioPerl effort. Check the site for useful code ideas
and contribute your own if possible.

%prep
%setup -q -n %{cpan_name}-%{version}
find . -type f ! -name \*.pl -print0 | xargs -0 chmod 644
# fix for boo#1089992
for i in $(grep -R "/usr/local/bin/perl" * | awk -F':' '{print $1}'); do
    perl -p -i -e 's|#!/usr/local/bin/perl|#!/usr/bin/perl|' "${i}"
done
# rpmlint
perl -p -i -e 's|\r\n|\n|' ./ide/bioperl-mode/etc/images/bpmode-tool-dis.xpm
perl -p -i -e 's|\r\n|\n|' ./ide/bioperl-mode/etc/images/bpmode-tool.xpm

%build
%{__perl} Build.PL installdirs=vendor
./Build build flags=%{?_smp_mflags}

%check
./Build test

%install
./Build install destdir=%{buildroot} create_packlist=0
%perl_gen_filelist

%files -f %{name}.files
%defattr(-,root,root,755)
%doc AUTHORS Bio BUGS Changes deobfuscator DEPENDENCIES DEPRECATED examples ide maintenance models README.md scripts travis_scripts
%license LICENSE

%changelog