Name: perl-bioperl Version: 1.6.1 Release: 4%{?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 #%%filter_from_requires /perl(Bio::Tools::Run::/d #%%?perl_default_filter %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. %prep %setup -q -n BioPerl-%{version} %patch0 -p1 cat << \EOF > %{name}-req #!/bin/sh %{__perl_requires} $* |\ sed -e '/perl(Bio::Tools::Run::Alignment::Clustalw)/d; /perl(Bio::Tools::Run::GenericParameters)/d; /perl(Bio::Tools::Run::Phylo::Molphy::ProtML)/d; /perl(Bio::Tools::Run::Phylo::Phylip::Neighbor)/d; /perl(Bio::Tools::Run::Phylo::Phylip::ProtDist)/d; /perl(Bio::Tools::Run::Phylo::Phylip::ProtPars)/d; /perl(Bio::Tools::Run::RemoteBlast)/d' EOF %global __perl_requires %{_builddir}/BioPerl-%{version}/%{name}-req chmod +x %{__perl_requires} # 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 * Mon Sep 6 2010 Adam Huffman - 1.6.1-4 - add EPEL5-compatible BR filtering * Mon Dec 7 2009 Stepan Kasal - 1.6.1-3 - rebuild against perl 5.10.1 * Thu Nov 12 2009 Stepan Kasal - 1.6.1-2 - use the new filtering macros (cf #537138) * Wed Nov 4 2009 Alex Lancaster - 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 - 1.6.0-3 - Rebuilt for https://fedoraproject.org/wiki/Fedora_12_Mass_Rebuild * Thu Feb 26 2009 Fedora Release Engineering - 1.6.0-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_11_Mass_Rebuild * Mon Jan 26 2009 Alex Lancaster - 1.6.0-1 - Update to 1.6.0 final release * Thu Jan 22 2009 Alex Lancaster - 1.5.9-0.5.4 - Update to 1.6.0 release candidate 4 * Sun Jan 18 2009 Alex Lancaster - 1.5.9-0.4.3 - Update to 1.6.0 release candidate 3 * Wed Jan 7 2009 Alex Lancaster - 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 - 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 - 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 - 1.5.2_102-13 - Fix patch fuzz * Wed Mar 5 2008 Tom "spot" Callaway 1.5.2_102-12 - bootstrapping done, building normally * Tue Mar 4 2008 Tom "spot" Callaway 1.5.2_102-11.2 - missed one * Tue Mar 4 2008 Tom "spot" Callaway 1.5.2_102-11.1 - actually disable bioperl-run requires for bootstrapping * Tue Mar 4 2008 Tom "spot" Callaway 1.5.2_102-11 - disable bioperl-run requires for bootstrapping * Tue Mar 4 2008 Tom "spot" Callaway 1.5.2_102-10 - rebuild for new perl * Mon Oct 15 2007 Alex Lancaster 1.5.2_102-9 - Add missing BR: perl(Test::More) - Clarified license terms: GPL+ or Artistic * Thu May 07 2007 Alex Lancaster 1.5.2_102-8 - Spec file cleanups. - Improve description. * Thu Apr 19 2007 Alex Lancaster 1.5.2_102-7 - Fix 'perl Build' command so that it does not attempt CPAN downloads. * Thu Apr 19 2007 Alex Lancaster 1.5.2_102-6 - Enable scripts, now that bioperl-run is in the repository. * Tue Apr 03 2007 Alex Lancaster 1.5.2_102-5 - Fix changelog * Tue Apr 03 2007 Alex Lancaster 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 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 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 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 1.5.0-3 - Review suggestions from José Pedro Oliveira * Mon Apr 01 2005 Hunter Matthews 1.5.0-2 - Added buildrequires and improved documention entries from FE mailing list. * Mon Mar 21 2005 Hunter Matthews 1.5.0-1 - Initial build. I started with the biolinux.org rpm, but broke out most of the deps and built them seperately.