#
# spec file for package perl-BioPerl (Version 1.6.1)
#
# Copyright (c) 2010 SUSE LINUX Products 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/
#

# norootforbuild

%bcond_with test

Name:           perl-BioPerl
%define cpan_name BioPerl
Summary:        Perl Modules for Biology
Version:        1.6.1
Release:        1
License:        GPL+ or Artistic
Group:          Development/Libraries/Perl
Url:            http://search.cpan.org/dist/BioPerl/
#Source:         http://www.cpan.org/modules/by-module/BioPerl/BioPerl-%{version}.tar.gz
Source:         %{cpan_name}-%{version}.tar.bz2
Patch0:         %{cpan_name}-1.6.1-Build.patch
BuildArch:      noarch
BuildRoot:      %{_tmppath}/%{name}-%{version}-build
BuildRequires:  perl
BuildRequires:  perl(Module::Build)
%if 0%{?suse_version} < 1120
BuildRequires:  perl-macros
%endif
BuildRequires:  perl(Test::More)
BuildRequires:  perl(Test::Harness) >= 2.62
BuildRequires:  perl(Data::Stag) >= 0.11
BuildRequires:  perl(ExtUtils::Manifest) >= 1.52
BuildRequires:  perl(IO::String)
BuildRequires:  perl(Scalar::Util)
# FIXME: not mentioned in Build.PL
BuildRequires:  perl(URI::Escape)
# recommended packages
%if %{with test}
BuildRequires:  perl(Ace)
BuildRequires:  perl(Algorithm::Munkres)
BuildRequires:  perl(Array::Compare)
# this won't actually install due to circular dep, but we have no way of doing a post-install
# the [circular dependency!] specifies it is only installed on explicit request for this specific module,
# not when simply choosing to install 'all' modules
#BuildRequires:  perl(Bio::ASN1::EntrezGene)
# we actually need 1.01 of Class::AutoClass, but unfortunately it is versioned as 1.0
BuildRequires:  perl(Clone)
BuildRequires:  perl(Convert::Binary::C)
BuildRequires:  perl(Graph)
BuildRequires:  perl(GraphViz)
BuildRequires:  perl(HTML::Entities)
BuildRequires:  perl(HTML::HeadParser) >= 3
BuildRequires:  perl(HTTP::Request::Common)
BuildRequires:  perl(LWP::UserAgent)
BuildRequires:  perl(List::MoreUtils)
BuildRequires:  perl(Math::Random)
BuildRequires:  perl(PostScript::TextBlock)
BuildRequires:  perl(SOAP::Lite)
BuildRequires:  perl(Set::Scalar)
BuildRequires:  perl(Spreadsheet::ParseExcel)
BuildRequires:  perl(Spreadsheet::WriteExcel)
BuildRequires:  perl(Storable) >= 2.05
BuildRequires:  perl(SVG) >= 2.26
BuildRequires:  perl(SVG::Graph) >= 0.01
BuildRequires:  perl(Text::ParseWords)
BuildRequires:  perl(XML::DOM::XPath) >= 0.13
BuildRequires:  perl(XML::Parser)
BuildRequires:  perl(XML::Parser::PerlSAX)
BuildRequires:  perl(XML::SAX) >= 0.15
BuildRequires:  perl(XML::SAX::Writer)
BuildRequires:  perl(XML::Simple)
BuildRequires:  perl(XML::Twig)
BuildRequires:  perl(XML::Writer) >= 0.4
%endif
#
%{perl_requires}
Requires:       perl(Data::Stag) >= 0.11
Requires:       perl(ExtUtils::Manifest) >= 1.52
Requires:       perl(IO::String)
Requires:       perl(Scalar::Util)
# FIXME: not mentioned in Build.PL
Requires:       perl(URI::Escape)
# FIXME: add reccomends :)
Recommends:     perl(Ace)
Recommends:     perl(Algorithm::Munkres)
Recommends:     perl(Array::Compare)
# this won't actually install due to circular dep, but we have no way of doing a post-install
# the [circular dependency!] specifies it is only installed on explicit request for this specific module,
# not when simply choosing to install 'all' modules
Recommends:     perl(Bio::ASN1::EntrezGene)
# we actually need 1.01 of Class::AutoClass, but unfortunately it is versioned as 1.0
Recommends:     perl(Clone)
Recommends:     perl(Convert::Binary::C)
Recommends:     perl(Graph)
Recommends:     perl(GraphViz)
Recommends:     perl(HTML::Entities)
Recommends:     perl(HTML::HeadParser) >= 3
Recommends:     perl(HTTP::Request::Common)
Recommends:     perl(LWP::UserAgent)
Recommends:     perl(List::MoreUtils)
Recommends:     perl(Math::Random)
Recommends:     perl(PostScript::TextBlock)
Recommends:     perl(SOAP::Lite)
Recommends:     perl(Set::Scalar)
Recommends:     perl(Spreadsheet::ParseExcel)
Recommends:     perl(Spreadsheet::WriteExcel)
Recommends:     perl(Storable) >= 2.05
Recommends:     perl(SVG) >= 2.26
Recommends:     perl(SVG::Graph) >= 0.01
Recommends:     perl(Text::ParseWords)
Recommends:     perl(XML::DOM::XPath) >= 0.13
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

%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.

Authors:
--------
    Georg Fuellen
    Richard Resnick
    Steven E. Brenner
    Chris Dagdigian
    Steve Chervitz
    Ewan Birney
    James Gilbert
    Elia Stupka
     and others.

%prep
%setup -q -n %{cpan_name}-%{version}
%patch0 -p1
## some rpmlint stuff :(
# script-without-shebang
find ./Bio -name "*.pm" -exec %{__chmod} 0644 {} \;
# wrong-script-end-of-line-encoding
%{__perl} -p -i -e 's|\r\n|\n|' Bio/Search/Tiling/MapTileUtils.pm
%{__perl} -p -i -e 's|\r\n|\n|' Bio/Search/Tiling/MapTileUtils.pm
%{__perl} -p -i -e 's|\r\n|\n|' ide/bioperl-mode/etc/images/bpmode-tool.xpm
%{__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|' maintenance/module_usage.pl
# zero-length
%{__rm} ide/bioperl-mode/dist/SKIP
# executable-docs
%{__chmod} a-x examples/root/README
%{__chmod} a-x ide/bioperl-mode/README
%{__chmod} a-x scripts/README 
# spurious-executable-perm
for dir in doc ide maintenance; do
  find -type f -exec %{__chmod} 0644 {} \;
done
# wrong-script-interpreter
find ./ -type f -exec %{__sed} -i -e "s@/usr/local/bin/perl@%{__perl}@" {} \;
find ./ -type f -exec %{__sed} -i -e "s@^#\!perl@#\!%{__perl}@" {} \;

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

%check
./Build test

%install
./Build install destdir=$RPM_BUILD_ROOT create_packlist=0
%perl_gen_filelist

%clean
%{__rm} -rf $RPM_BUILD_ROOT

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

%changelog