d6d9fff7be
OBS-URL: https://build.opensuse.org/package/show/devel:languages:perl/perl-BioPerl?expand=0&rev=2
198 lines
7.1 KiB
RPMSpec
198 lines
7.1 KiB
RPMSpec
#
|
|
# 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
|