Name: perl-bioperl
Version: 1.6.1
Release: 10%{?dist}
Summary: Perl tools for computational molecular biology
Group: Development/Libraries
License: GPL+ or Artistic
URL: http://www.bioperl.org/
Source0: http://bioperl.org/DIST/BioPerl-%{version}.tar.bz2
Patch0: bioperl-1.6.1-paths.patch
BuildRoot: %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
BuildArch: noarch
BuildRequires: perl(Ace)
BuildRequires: perl(Class::AutoClass) >= 1
BuildRequires: perl(Clone)
BuildRequires: perl(Convert::Binary::C)
BuildRequires: perl(Data::Stag::XMLWriter)
BuildRequires: perl(DBD::mysql)
BuildRequires: perl(DBD::Pg)
BuildRequires: perl(DBD::SQLite)
BuildRequires: perl(GD) >= 1.3
BuildRequires: perl(GD::SVG)
BuildRequires: perl(Graph)
BuildRequires: perl(HTML::Entities)
BuildRequires: perl(HTML::Parser)
BuildRequires: perl(HTTP::Request::Common)
BuildRequires: perl(IO::Stringy)
BuildRequires: perl(IO::String)
BuildRequires: perl(LWP::UserAgent)
BuildRequires: perl(PostScript::TextBlock)
BuildRequires: perl(Set::Scalar)
BuildRequires: perl(SOAP::Lite)
BuildRequires: perl(Spreadsheet::ParseExcel)
BuildRequires: perl(Storable)
BuildRequires: perl(SVG) >= 2.26
BuildRequires: perl(SVG::Graph) >= 0.01
BuildRequires: perl(Text::Shellwords)
BuildRequires: perl(URI::Escape)
BuildRequires: perl(XML::DOM::XPath) >= 0.13
BuildRequires: perl(XML::Parser)
BuildRequires: perl(XML::Parser::PerlSAX)
BuildRequires: perl(XML::SAX) >= 0.14
BuildRequires: perl(XML::SAX::Writer)
BuildRequires: perl(XML::Simple)
BuildRequires: perl(XML::Twig)
BuildRequires: perl(XML::Writer) > 0.4
BuildRequires: perl(Module::Build)
BuildRequires: perl(Test::More)
BuildRequires: perl(Array::Compare)
BuildRequires: perl(GraphViz)
# disable the following BRs until they are packaged for Fedora
#BuildRequires: perl(Math::Random)
#BuildRequires: perl(Algorithm::Munkres)
Requires: perl(:MODULE_COMPAT_%(eval "`%{__perl} -V:version`"; echo $version))
# Packages perl-bioperl and perl-bioperl-run require each other. To break
# this circular edependency (e.g., for bootstrapping), filter out all
# Bio::Tools::Run::* module requirements; they are either self-satisfied
# (and thus redundant) or they bring dependency on perl-bioperl-run.
## be careful when commenting this out: macros are expanded even in comments
# RPM 4.8 style
#%%filter_from_requires /perl(Bio::Tools::Run::/d
#%%?perl_default_filter
# RPM 4.9 style
#%%global __requires_exclude %%{?__requires_exclude?__requires_exclude|}perl\\(Bio::Tools::Run::
%description
BioPerl is a toolkit of Perl modules useful in building bioinformatics
solutions in Perl. It is built in an object-oriented manner so that
many modules depend on each other to achieve a task.
# RPM 4.8 style
%{?filter_setup:
%filter_from_requires /perl(Bio::Expression::FeatureSet)/d
%{?perl_default_filter}
}
# RPM 4.9 style
%global __requires_exclude %{?__requires_exclude:__requires_exclude|}perl\\(Bio::Expression::FeatureSet\\)
%prep
%setup -q -n BioPerl-%{version}
%patch0 -p1
# temporarily remove PhyloNetwork before compiling until upstream says
# they are ready for primetime and deps Math::Random and
# Algorithm::Munkres are also packaged
rm -r Bio/PhyloNetwork*
rm -r t/Tree/PhyloNetwork
# remove all execute bits from the doc stuff
find examples -type f -exec chmod -x {} ';'
%build
%{__perl} Build.PL --installdirs vendor << EOF
n
a
n
EOF
./Build
# make sure the man page is UTF-8...
cd blib/libdoc
for i in Bio::Tools::GuessSeqFormat.3pm Bio::Tools::Geneid.3pm; do
iconv --from=ISO-8859-1 --to=UTF-8 $i > new
mv new $i
done
%install
rm -rf $RPM_BUILD_ROOT
#make pure_install PERL_INSTALL_ROOT=$RPM_BUILD_ROOT
perl Build pure_install --destdir=$RPM_BUILD_ROOT
find $RPM_BUILD_ROOT -type f -a \( -name .packlist \
-o \( -name '*.bs' -a -empty \) \) -exec rm -f {} ';'
find $RPM_BUILD_ROOT -type d -depth -exec rmdir {} 2>/dev/null ';'
# remove errant execute bit from the .pm's
find $RPM_BUILD_ROOT -type f -name '*.pm' -exec chmod -x {} 2>/dev/null ';'
# correct all binaries in /usr/bin to be 0755
find $RPM_BUILD_ROOT/%{_bindir} -type f -name '*.pl' -exec chmod 0755 {} 2>/dev/null ';'
%check
%{?_with_check:./Build test || :}
%clean
rm -rf $RPM_BUILD_ROOT
%files
%defattr(-,root,root,-)
## don't distribute "doc" subdirectory, doesn't contain docs
%doc examples models
%doc AUTHORS BUGS Changes DEPRECATED INSTALL LICENSE README
%{_bindir}/*
%{perl_vendorlib}/*
%{_mandir}/man1/*.1*
%{_mandir}/man3/*.3*
%changelog
* Fri Jul 22 2011 Petr Pisar <ppisar@redhat.com> - 1.6.1-10
- RPM 4.9 dependency filtering added
* Thu Jul 21 2011 Petr Sabata <contyk@redhat.com> - 1.6.1-9
- Perl mass rebuild
* Tue Jul 19 2011 Petr Sabata <contyk@redhat.com> - 1.6.1-8
- Perl mass rebuild
* Tue Feb 15 2011 Marcela MaÅ¡láÅová <mmaslano@redhat.com> - 1.6.1-7
- fix filter for RPM4.9
* Wed Feb 09 2011 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.6.1-6
- Rebuilt for https://fedoraproject.org/wiki/Fedora_15_Mass_Rebuild
* Wed Dec 15 2010 Marcela Maslanova <mmaslano@redhat.com> - 1.6.1-5
- 661697 rebuild for fixing problems with vendorach/lib
* Thu Apr 29 2010 Marcela Maslanova <mmaslano@redhat.com> - 1.6.1-4
- Mass rebuild with perl-5.12.0
* Mon Dec 7 2009 Stepan Kasal <skasal@redhat.com> - 1.6.1-3
- rebuild against perl 5.10.1
* Thu Nov 12 2009 Stepan Kasal <skasal@redhat.com> - 1.6.1-2
- use the new filtering macros (cf #537138)
* Wed Nov 4 2009 Alex Lancaster <alexlan[AT]fedoraproject org> - 1.6.1-1
- Update to latest upstream 1.6.1
- Add BR: perl(XML::Simple), perl(DBD:SQLite) for new modules
- Disable ExtUtils::Manifest build requirement, don't require a MANIFEST
- Fix doc distributed
* Sun Jul 26 2009 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.6.0-3
- Rebuilt for https://fedoraproject.org/wiki/Fedora_12_Mass_Rebuild
* Thu Feb 26 2009 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.6.0-2
- Rebuilt for https://fedoraproject.org/wiki/Fedora_11_Mass_Rebuild
* Mon Jan 26 2009 Alex Lancaster <alexlan[AT]fedoraproject org> - 1.6.0-1
- Update to 1.6.0 final release
* Thu Jan 22 2009 Alex Lancaster <alexlan[AT]fedoraproject org> - 1.5.9-0.5.4
- Update to 1.6.0 release candidate 4
* Sun Jan 18 2009 Alex Lancaster <alexlan[AT]fedoraproject org> - 1.5.9-0.4.3
- Update to 1.6.0 release candidate 3
* Wed Jan 7 2009 Alex Lancaster <alexlan[AT]fedoraproject org> - 1.5.9-0.3.2
- Update to 1.6.0 release candidate 2
- Remove filter for Bio::Graphics*, upstream removed them from the
tarball
* Sun Dec 28 2008 Alex Lancaster <alexlan[AT]fedoraproject org> - 1.5.9-0.2.1
- Filter unwanted Requires: Bio::Graphics and Bio::Graphics::Panel
fixes broken deps until the .pl demo scripts remove them to the
appropriate module
* Fri Dec 26 2008 Alex Lancaster <alexlan[AT]fedoraproject org> - 1.5.9-0.1.1
- Update to latest upstream, 1.5.9, which is release candidate 1 for 1.6.0
- Add BuildRequires for perl(Array::Compare) and perl(GraphViz).
- Fix patch to apply to new release.
- Remove Bio::PhyloNetwork from installation, currently has unfilled
deps and not ready for primetime according to upstream.
* Thu Sep 25 2008 Alex Lancaster <alexlan[AT]fedoraproject org> - 1.5.2_102-13
- Fix patch fuzz
* Wed Mar 5 2008 Tom "spot" Callaway <tcallawa@redhat.com> 1.5.2_102-12
- bootstrapping done, building normally
* Tue Mar 4 2008 Tom "spot" Callaway <tcallawa@redhat.com> 1.5.2_102-11.2
- missed one
* Tue Mar 4 2008 Tom "spot" Callaway <tcallawa@redhat.com> 1.5.2_102-11.1
- actually disable bioperl-run requires for bootstrapping
* Tue Mar 4 2008 Tom "spot" Callaway <tcallawa@redhat.com> 1.5.2_102-11
- disable bioperl-run requires for bootstrapping
* Tue Mar 4 2008 Tom "spot" Callaway <tcallawa@redhat.com> 1.5.2_102-10
- rebuild for new perl
* Mon Oct 15 2007 Alex Lancaster <alexl@users.sourceforge.net> 1.5.2_102-9
- Add missing BR: perl(Test::More)
- Clarified license terms: GPL+ or Artistic
* Thu May 07 2007 Alex Lancaster <alexl@users.sourceforge.net> 1.5.2_102-8
- Spec file cleanups.
- Improve description.
* Thu Apr 19 2007 Alex Lancaster <alexl@users.sourceforge.net> 1.5.2_102-7
- Fix 'perl Build' command so that it does not attempt CPAN downloads.
* Thu Apr 19 2007 Alex Lancaster <alexl@users.sourceforge.net> 1.5.2_102-6
- Enable scripts, now that bioperl-run is in the repository.
* Tue Apr 03 2007 Alex Lancaster <alexl@users.sourceforge.net> 1.5.2_102-5
- Fix changelog
* Tue Apr 03 2007 Alex Lancaster <alexl@users.sourceforge.net> 1.5.2_102-4
- Disable tests because many of them require network access, add
_with_check macro so they can be enabled during testing.
* Mon Apr 02 2007 Alex Lancaster <alexl@users.sourceforge.net> 1.5.2_102-3
- Remove BuildRequires: perl(Bio::ASN1::EntrezGene), creates a
circular dependency, the dependency is still found at install-time.
* Thu Mar 29 2007 Alex Lancaster <alexl@users.sourceforge.net> 1.5.2_102-2
- Add all BRs listed as 'recommends' in Build.PL so that it never
needs to get packages from CPAN.
- Remove unnecessary filtering of Requires
* Wed Mar 23 2007 Alex Lancaster <alexl@users.sourceforge.net> 1.5.2_102-1
- Update to 1.5.2_102
- Review suggestions from Steven Pritchard
- BR: perl(IO::String)
- Disable scripts for now as they require bioperl-run (not yet packaged)
- Don't mark non-documentation files as documentation.
* Wed Apr 06 2005 Hunter Matthews <thm@duke.edu> 1.5.0-3
- Review suggestions from José Pedro Oliveira
* Mon Apr 01 2005 Hunter Matthews <thm@duke.edu> 1.5.0-2
- Added buildrequires and improved documention entries from FE mailing list.
* Mon Mar 21 2005 Hunter Matthews <thm@duke.edu> 1.5.0-1
- Initial build. I started with the biolinux.org rpm, but broke out
most of the deps and built them seperately.
