diff options
| -rw-r--r-- | biology/p5-bioperl/Makefile | 744 | ||||
| -rw-r--r-- | biology/p5-bioperl/distinfo | 6 | ||||
| -rw-r--r-- | biology/p5-bioperl/files/ext.msg | 16 | ||||
| -rw-r--r-- | biology/p5-bioperl/files/patch-aa | 9 | ||||
| -rw-r--r-- | biology/p5-bioperl/files/patch-manify | 29 | ||||
| -rw-r--r-- | biology/p5-bioperl/pkg-plist | 1290 |
6 files changed, 1689 insertions, 405 deletions
diff --git a/biology/p5-bioperl/Makefile b/biology/p5-bioperl/Makefile index af0afeccb335..7b43b7ae2e85 100644 --- a/biology/p5-bioperl/Makefile +++ b/biology/p5-bioperl/Makefile @@ -6,16 +6,14 @@ # PORTNAME= bioperl -PORTVERSION= 0.7.2 +PORTVERSION= 1.4 CATEGORIES= biology perl5 -MASTER_SITES= ftp://bioperl.org/pub/DIST/ \ - http://bioperl.org/Core/Latest/ \ +MASTER_SITES= http://bioperl.org/DIST/ \ ${MASTER_SITE_PERL_CPAN} MASTER_SITE_SUBDIR= Bio PKGNAMEPREFIX= p5- -DISTFILES= ${DISTNAME}${EXTRACT_SUFX} -MAINTAINER= wjv@FreeBSD.org +MAINTAINER= fernan@iib.unsam.edu.ar COMMENT= A collection of Perl modules for bioinformatics # These are all run-time dependencies, but listing them in ${BUILD_DEPENDS} @@ -29,181 +27,603 @@ BUILD_DEPENDS= ${SITE_PERL}/${PERL_ARCH}/Ace.pm:${PORTSDIR}/biology/p5-AcePerl \ ${SITE_PERL}/LWP/UserAgent.pm:${PORTSDIR}/www/p5-libwww \ ${SITE_PERL}/XML/Node.pm:${PORTSDIR}/textproc/p5-XML-Node \ ${SITE_PERL}/XML/Parser/PerlSAX.pm:${PORTSDIR}/textproc/p5-libxml \ - ${SITE_PERL}/XML/Writer.pm:${PORTSDIR}/textproc/p5-XML-Writer + ${SITE_PERL}/XML/Writer.pm:${PORTSDIR}/textproc/p5-XML-Writer \ + ${SITE_PERL}/HTTP/Request/Common.pm:${PORTSDIR}/www/p5-libwww \ + ${SITE_PERL}/XML/Twig.pm:${PORTSDIR}/textproc/p5-XML-Twig \ + ${SITE_PERL}/SOAP/Lite.pm:${PORTSDIR}/net/p5-SOAP-Lite \ + ${SITE_PERL}/${PERL_ARCH}/HTML/Parser.pm:${PORTSDIR}/www/p5-HTML-Parser \ + ${SITE_PERL}/${PERL_ARCH}/DBD/mysql.pm:${PORTSDIR}/databases/p5-DBD-mysql \ + ${SITE_PERL}/${PERL_ARCH}/GD.pm:${PORTSDIR}/graphics/p5-GD \ + ${SITE_PERL}/${PERL_ARCH}/Storable.pm:${PORTSDIR}/devel/p5-Storable \ + ${SITE_PERL}/Parse/RecDescent.pm:${PORTSDIR}/devel/p5-Parse-RecDescent \ + ${SITE_PERL}/XML/DOM.pm:${PORTSDIR}/textproc/p5-XML-DOM \ + ${SITE_PERL}/Test/Simple.pm:${PORTSDIR}/devel/p5-Test-Simple \ + ${SITE_PERL}/Text/Shellwords.pm:${PORTSDIR}/textproc/p5-Text-Shellwords RUN_DEPENDS= ${BUILD_DEPENDS} PERL_CONFIGURE= YES -.if defined(WITH_CORBA) -WITH_CORBA_CLIENT= YES -WITH_CORBA_SERVER= YES -.endif - -EXT_VERSION= 0.6 -CORBA_CLIENT_VERSION= 0.2 -CORBA_SERVER_VERSION= 0.2 -GUI_VERSION= 0.7 -DISTFILES+= bioperl-ext-${EXT_VERSION}${EXTRACT_SUFX} -EXT_WRKSRC= ${WRKDIR}/bioperl-ext-06/Bio/Ext/Align - -.if defined(WITH_CORBA_CLIENT) -BUILD_DEPENDS+= ${SITE_PERL}/${PERL_ARCH}/CORBA/ORBit.pm:${PORTSDIR}/devel/p5-ORBit -RUN_DEPENDS+= ${SITE_PERL}/${PERL_ARCH}/CORBA/ORBit.pm:${PORTSDIR}/devel/p5-ORBit -.endif -.if defined(WITH_CORBA_SERVER) -BUILD_DEPENDS+= ${SITE_PERL}/${PERL_ARCH}/CORBA/ORBit.pm:${PORTSDIR}/devel/p5-ORBit -RUN_DEPENDS+= ${SITE_PERL}/${PERL_ARCH}/CORBA/ORBit.pm:${PORTSDIR}/devel/p5-ORBit -.endif -.if defined(WITH_GUI) -RUN_DEPENDS+= ptksh:${PORTSDIR}/x11-toolkits/p5-Tk -.endif - -.for ext in CORBA_CLIENT CORBA_SERVER GUI -.if defined(WITH_${ext}) -EXTLIST+= ${ext} -DISTFILES+= bioperl-${ext:L:S/_/-/}-${${ext}_VERSION}${EXTRACT_SUFX} -${ext}_WRKSRC= ${WRKDIR}/bioperl-${ext:L:S/_/-/} -PLIST_${ext}= "" -.else -PLIST_${ext}= "@comment " -.endif -PLIST_SUB+= PLIST_${ext}=${PLIST_${ext}} -.endfor - -MAN3= Bio::AlignIO.3 Bio::AlignIO::bl2seq.3 \ - Bio::AlignIO::clustalw.3 Bio::AlignIO::fasta.3 \ - Bio::AlignIO::mase.3 Bio::AlignIO::msf.3 Bio::AlignIO::pfam.3 \ - Bio::AlignIO::prodom.3 Bio::AlignIO::selex.3 \ - Bio::AlignIO::stockholm.3 Bio::Annotation.3 \ - Bio::Annotation::Comment.3 Bio::Annotation::DBLink.3 \ - Bio::Annotation::Reference.3 Bio::DB::Ace.3 Bio::DB::GDB.3 \ - Bio::DB::GenBank.3 Bio::DB::GenPept.3 Bio::DB::NCBIHelper.3 \ - Bio::DB::RandomAccessI.3 Bio::DB::SeqI.3 Bio::DB::SwissProt.3 \ - Bio::DB::UpdateableSeqI.3 Bio::DB::WebDBSeqI.3 \ - Bio::DBLinkContainerI.3 Bio::Factory::DriverFactory.3 \ +MAN3= Bio::Align::AlignI.3 \ + Bio::Align::DNAStatistics.3 \ + Bio::Align::PairwiseStatistics.3 \ + Bio::Align::StatisticsI.3 \ + Bio::Align::Utilities.3 \ + Bio::AlignIO.3 \ + Bio::AlignIO::bl2seq.3 \ + Bio::AlignIO::clustalw.3 \ + Bio::AlignIO::emboss.3 \ + Bio::AlignIO::fasta.3 \ + Bio::AlignIO::mase.3 \ + Bio::AlignIO::mega.3 \ + Bio::AlignIO::meme.3 \ + Bio::AlignIO::msf.3 \ + Bio::AlignIO::nexus.3 \ + Bio::AlignIO::pfam.3 \ + Bio::AlignIO::phylip.3 \ + Bio::AlignIO::prodom.3 \ + Bio::AlignIO::psi.3 \ + Bio::AlignIO::selex.3 \ + Bio::AlignIO::stockholm.3 \ + Bio::AnalysisI.3 \ + Bio::AnalysisParserI.3 \ + Bio::AnalysisResultI.3 \ + Bio::AnnotatableI.3 \ + Bio::Annotation::AnnotationFactory.3 \ + Bio::Annotation::Collection.3 \ + Bio::Annotation::Comment.3 \ + Bio::Annotation::DBLink.3 \ + Bio::Annotation::OntologyTerm.3 \ + Bio::Annotation::Reference.3 \ + Bio::Annotation::SimpleValue.3 \ + Bio::Annotation::StructuredValue.3 \ + Bio::Annotation::TypeManager.3 \ + Bio::AnnotationCollectionI.3 \ + Bio::AnnotationI.3 \ + Bio::Assembly::Contig.3 \ + Bio::Assembly::ContigAnalysis.3 \ + Bio::Assembly::IO.3 \ + Bio::Assembly::IO::ace.3 \ + Bio::Assembly::IO::phrap.3 \ + Bio::Assembly::Scaffold.3 \ + Bio::Assembly::ScaffoldI.3 \ + Bio::Biblio.3 \ + Bio::Biblio::Article.3 \ + Bio::Biblio::BiblioBase.3 \ + Bio::Biblio::Book.3 \ + Bio::Biblio::BookArticle.3 \ + Bio::Biblio::IO.3 \ + Bio::Biblio::IO::medline2ref.3 \ + Bio::Biblio::IO::medlinexml.3 \ + Bio::Biblio::IO::pubmed2ref.3 \ + Bio::Biblio::IO::pubmedxml.3 \ + Bio::Biblio::Journal.3 \ + Bio::Biblio::JournalArticle.3 \ + Bio::Biblio::MedlineArticle.3 \ + Bio::Biblio::MedlineBook.3 \ + Bio::Biblio::MedlineBookArticle.3 \ + Bio::Biblio::MedlineJournal.3 \ + Bio::Biblio::MedlineJournalArticle.3 \ + Bio::Biblio::Organisation.3 \ + Bio::Biblio::Patent.3 \ + Bio::Biblio::Person.3 \ + Bio::Biblio::Proceeding.3 \ + Bio::Biblio::Provider.3 \ + Bio::Biblio::PubmedArticle.3 \ + Bio::Biblio::PubmedBookArticle.3 \ + Bio::Biblio::PubmedJournalArticle.3 \ + Bio::Biblio::Ref.3 \ + Bio::Biblio::Service.3 \ + Bio::Biblio::TechReport.3 \ + Bio::Biblio::Thesis.3 \ + Bio::Biblio::WebResource.3 \ + Bio::Cluster::ClusterFactory.3 \ + Bio::Cluster::FamilyI.3 \ + Bio::Cluster::SequenceFamily.3 \ + Bio::Cluster::UniGene.3 \ + Bio::Cluster::UniGeneI.3 \ + Bio::ClusterI.3 \ + Bio::ClusterIO.3 \ + Bio::ClusterIO::dbsnp.3 \ + Bio::ClusterIO::unigene.3 \ + Bio::Coordinate::Chain.3 \ + Bio::Coordinate::Collection.3 \ + Bio::Coordinate::ExtrapolatingPair.3 \ + Bio::Coordinate::GeneMapper.3 \ + Bio::Coordinate::Graph.3 \ + Bio::Coordinate::MapperI.3 \ + Bio::Coordinate::Pair.3 \ + Bio::Coordinate::Result.3 \ + Bio::Coordinate::Result::Gap.3 \ + Bio::Coordinate::Result::Match.3 \ + Bio::Coordinate::ResultI.3 \ + Bio::Coordinate::Utils.3 \ + Bio::DB::Ace.3 \ + Bio::DB::Biblio::biofetch.3 \ + Bio::DB::Biblio::soap.3 \ + Bio::DB::BiblioI.3 \ + Bio::DB::BioFetch.3 \ + Bio::DB::DBFetch.3 \ + Bio::DB::EMBL.3 \ + Bio::DB::Failover.3 \ + Bio::DB::Fasta.3 \ + Bio::DB::FileCache.3 \ + Bio::DB::Flat.3 \ + Bio::DB::Flat::BDB.3 \ + Bio::DB::Flat::BDB::embl.3 \ + Bio::DB::Flat::BDB::fasta.3 \ + Bio::DB::GDB.3 \ + Bio::DB::GFF.3 \ + Bio::DB::GFF::Adaptor::ace.3 \ + Bio::DB::GFF::Adaptor::biofetch.3 \ + Bio::DB::GFF::Adaptor::dbi.3 \ + Bio::DB::GFF::Adaptor::dbi::caching_handle.3 \ + Bio::DB::GFF::Adaptor::dbi::iterator.3 \ + Bio::DB::GFF::Adaptor::dbi::mysql.3 \ + Bio::DB::GFF::Adaptor::dbi::mysqlace.3 \ + Bio::DB::GFF::Adaptor::dbi::mysqlopt.3 \ + Bio::DB::GFF::Adaptor::dbi::oracle.3 \ + Bio::DB::GFF::Adaptor::dbi::oracleace.3 \ + Bio::DB::GFF::Adaptor::memory.3 \ + Bio::DB::GFF::Adaptor::memory_iterator.3 \ + Bio::DB::GFF::Aggregator.3 \ + Bio::DB::GFF::Aggregator::alignment.3 \ + Bio::DB::GFF::Aggregator::clone.3 \ + Bio::DB::GFF::Aggregator::coding.3 \ + Bio::DB::GFF::Aggregator::match.3 \ + Bio::DB::GFF::Aggregator::none.3 \ + Bio::DB::GFF::Aggregator::processed_transcript.3 \ + Bio::DB::GFF::Aggregator::transcript.3 \ + Bio::DB::GFF::Aggregator::ucsc_acembly.3 \ + Bio::DB::GFF::Aggregator::ucsc_ensgene.3 \ + Bio::DB::GFF::Aggregator::ucsc_genscan.3 \ + Bio::DB::GFF::Aggregator::ucsc_refgene.3 \ + Bio::DB::GFF::Aggregator::ucsc_sanger22.3 \ + Bio::DB::GFF::Aggregator::ucsc_sanger22pseudo.3 \ + Bio::DB::GFF::Aggregator::ucsc_softberry.3 \ + Bio::DB::GFF::Aggregator::ucsc_twinscan.3 \ + Bio::DB::GFF::Aggregator::ucsc_unigene.3 \ + Bio::DB::GFF::Featname.3 \ + Bio::DB::GFF::Feature.3 \ + Bio::DB::GFF::Homol.3 \ + Bio::DB::GFF::RelSegment.3 \ + Bio::DB::GFF::Segment.3 \ + Bio::DB::GFF::Typename.3 \ + Bio::DB::GFF::Util::Binning.3 \ + Bio::DB::GFF::Util::Rearrange.3 \ + Bio::DB::GenBank.3 \ + Bio::DB::GenPept.3 \ + Bio::DB::InMemoryCache.3 \ + Bio::DB::NCBIHelper.3 \ + Bio::DB::Query::GenBank.3 \ + Bio::DB::Query::WebQuery.3 \ + Bio::DB::QueryI.3 \ + Bio::DB::RandomAccessI.3 \ + Bio::DB::RefSeq.3 \ + Bio::DB::Registry.3 \ + Bio::DB::SeqI.3 \ + Bio::DB::SwissProt.3 \ + Bio::DB::Universal.3 \ + Bio::DB::UpdateableSeqI.3 \ + Bio::DB::WebDBSeqI.3 \ + Bio::DB::XEMBL.3 \ + Bio::DB::XEMBLService.3 \ + Bio::DBLinkContainerI.3 \ + Bio::Das::FeatureTypeI.3 \ + Bio::Das::SegmentI.3 \ + Bio::DasI.3 \ + Bio::DescribableI.3 \ + Bio::Event::EventGeneratorI.3 \ + Bio::Event::EventHandlerI.3 \ + Bio::Expression::FeatureGroup.3 \ + Bio::Expression::FeatureI.3 \ + Bio::Factory::AnalysisI.3 \ + Bio::Factory::ApplicationFactoryI.3 \ + Bio::Factory::DriverFactory.3 \ + Bio::Factory::FTLocationFactory.3 \ + Bio::Factory::HitFactoryI.3 \ + Bio::Factory::LocationFactoryI.3 \ + Bio::Factory::MapFactoryI.3 \ + Bio::Factory::ObjectBuilderI.3 \ + Bio::Factory::ObjectFactory.3 \ + Bio::Factory::ObjectFactoryI.3 \ + Bio::Factory::ResultFactoryI.3 \ Bio::Factory::SeqAnalysisParserFactory.3 \ Bio::Factory::SeqAnalysisParserFactoryI.3 \ - Bio::Index::Abstract.3 Bio::Index::AbstractSeq.3 \ - Bio::Index::EMBL.3 Bio::Index::Fasta.3 Bio::Index::GenBank.3 \ - Bio::Index::SwissPfam.3 Bio::Index::Swissprot.3 \ - Bio::LiveSeq::AARange.3 Bio::LiveSeq::Chain.3 \ - Bio::LiveSeq::ChainI.3 Bio::LiveSeq::DNA.3 \ - Bio::LiveSeq::Exon.3 Bio::LiveSeq::Gene.3 \ - Bio::LiveSeq::IO::BioPerl.3 Bio::LiveSeq::IO::Loader.3 \ - Bio::LiveSeq::IO::SRS.3 Bio::LiveSeq::Intron.3 \ - Bio::LiveSeq::Mutation.3 Bio::LiveSeq::Mutator.3 \ - Bio::LiveSeq::Prim_Transcript.3 Bio::LiveSeq::Range.3 \ - Bio::LiveSeq::Repeat_Region.3 Bio::LiveSeq::Repeat_Unit.3 \ - Bio::LiveSeq::SeqI.3 Bio::LiveSeq::Transcript.3 \ - Bio::LiveSeq::Translation.3 Bio::LocatableSeq.3 \ + Bio::Factory::SequenceFactoryI.3 \ + Bio::Factory::SequenceProcessorI.3 \ + Bio::Factory::SequenceStreamI.3 \ + Bio::Factory::TreeFactoryI.3 \ + Bio::FeatureHolderI.3 \ + Bio::Graphics.3 \ + Bio::Graphics::Feature.3 \ + Bio::Graphics::FeatureFile.3 \ + Bio::Graphics::Glyph.3 \ + Bio::Graphics::Glyph::Factory.3 \ + Bio::Graphics::Glyph::alignment.3 \ + Bio::Graphics::Glyph::anchored_arrow.3 \ + Bio::Graphics::Glyph::arrow.3 \ + Bio::Graphics::Glyph::box.3 \ + Bio::Graphics::Glyph::cds.3 \ + Bio::Graphics::Glyph::crossbox.3 \ + Bio::Graphics::Glyph::diamond.3 \ + Bio::Graphics::Glyph::dna.3 \ + Bio::Graphics::Glyph::dot.3 \ + Bio::Graphics::Glyph::ellipse.3 \ + Bio::Graphics::Glyph::ex.3 \ + Bio::Graphics::Glyph::extending_arrow.3 \ + Bio::Graphics::Glyph::generic.3 \ + Bio::Graphics::Glyph::graded_segments.3 \ + Bio::Graphics::Glyph::group.3 \ + Bio::Graphics::Glyph::heterogeneous_segments.3 \ + Bio::Graphics::Glyph::line.3 \ + Bio::Graphics::Glyph::oval.3 \ + Bio::Graphics::Glyph::pinsertion.3 \ + Bio::Graphics::Glyph::primers.3 \ + Bio::Graphics::Glyph::processed_transcript.3 \ + Bio::Graphics::Glyph::redgreen_box.3 \ + Bio::Graphics::Glyph::redgreen_segment.3 \ + Bio::Graphics::Glyph::rndrect.3 \ + Bio::Graphics::Glyph::ruler_arrow.3 \ + Bio::Graphics::Glyph::segmented_keyglyph.3 \ + Bio::Graphics::Glyph::segments.3 \ + Bio::Graphics::Glyph::span.3 \ + Bio::Graphics::Glyph::splice_site.3 \ + Bio::Graphics::Glyph::toomany.3 \ + Bio::Graphics::Glyph::track.3 \ + Bio::Graphics::Glyph::transcript.3 \ + Bio::Graphics::Glyph::transcript2.3 \ + Bio::Graphics::Glyph::translation.3 \ + Bio::Graphics::Glyph::triangle.3 \ + Bio::Graphics::Glyph::xyplot.3 \ + Bio::Graphics::Panel.3 \ + Bio::IdCollectionI.3 \ + Bio::IdentifiableI.3 \ + Bio::Index::Abstract.3 \ + Bio::Index::AbstractSeq.3 \ + Bio::Index::Blast.3 \ + Bio::Index::EMBL.3 \ + Bio::Index::Fasta.3 \ + Bio::Index::Fastq.3 \ + Bio::Index::GenBank.3 \ + Bio::Index::SwissPfam.3 \ + Bio::Index::Swissprot.3 \ + Bio::LiveSeq::AARange.3 \ + Bio::LiveSeq::Chain.3 \ + Bio::LiveSeq::ChainI.3 \ + Bio::LiveSeq::DNA.3 \ + Bio::LiveSeq::Exon.3 \ + Bio::LiveSeq::Gene.3 \ + Bio::LiveSeq::IO::BioPerl.3 \ + Bio::LiveSeq::IO::Loader.3 \ + Bio::LiveSeq::IO::SRS.3 \ + Bio::LiveSeq::Intron.3 \ + Bio::LiveSeq::Mutation.3 \ + Bio::LiveSeq::Mutator.3 \ + Bio::LiveSeq::Prim_Transcript.3 \ + Bio::LiveSeq::Range.3 \ + Bio::LiveSeq::Repeat_Region.3 \ + Bio::LiveSeq::Repeat_Unit.3 \ + Bio::LiveSeq::SeqI.3 \ + Bio::LiveSeq::Transcript.3 \ + Bio::LiveSeq::Translation.3 \ + Bio::LocatableSeq.3 \ + Bio::Location::Atomic.3 \ Bio::Location::AvWithinCoordPolicy.3 \ - Bio::Location::CoordinatePolicyI.3 Bio::Location::Fuzzy.3 \ + Bio::Location::CoordinatePolicyI.3 \ + Bio::Location::Fuzzy.3 \ Bio::Location::FuzzyLocationI.3 \ - Bio::Location::NarrowestCoordPolicy.3 Bio::Location::Simple.3 \ - Bio::Location::Split.3 Bio::Location::SplitLocationI.3 \ - Bio::Location::WidestCoordPolicy.3 Bio::LocationI.3 \ - Bio::PrimarySeq.3 Bio::PrimarySeqI.3 Bio::Range.3 \ - Bio::RangeI.3 Bio::Root::Err.3 Bio::Root::Global.3 \ - Bio::Root::IO.3 Bio::Root::IOManager.3 Bio::Root::Object.3 \ - Bio::Root::RootI.3 Bio::Root::Utilities.3 Bio::Root::Vector.3 \ - Bio::Root::Xref.3 Bio::SearchDist.3 Bio::Seq.3 \ - Bio::Seq::LargePrimarySeq.3 Bio::Seq::LargeSeq.3 \ - Bio::Seq::RichSeq.3 Bio::Seq::RichSeqI.3 \ - Bio::SeqAnalysisParserI.3 Bio::SeqFeature::FeaturePair.3 \ - Bio::SeqFeature::Gene::Exon.3 Bio::SeqFeature::Gene::ExonI.3 \ + Bio::Location::NarrowestCoordPolicy.3 \ + Bio::Location::Simple.3 \ + Bio::Location::Split.3 \ + Bio::Location::SplitLocationI.3 \ + Bio::Location::WidestCoordPolicy.3 \ + Bio::LocationI.3 \ + Bio::Map::CytoMap.3 \ + Bio::Map::CytoMarker.3 \ + Bio::Map::CytoPosition.3 \ + Bio::Map::LinkageMap.3 \ + Bio::Map::LinkagePosition.3 \ + Bio::Map::MapI.3 \ + Bio::Map::MappableI.3 \ + Bio::Map::Marker.3 \ + Bio::Map::MarkerI.3 \ + Bio::Map::Microsatellite.3 \ + Bio::Map::OrderedPosition.3 \ + Bio::Map::OrderedPositionWithDistance.3 \ + Bio::Map::Position.3 \ + Bio::Map::PositionI.3 \ + Bio::Map::SimpleMap.3 \ + Bio::MapIO.3 \ + Bio::MapIO::mapmaker.3 \ + Bio::Matrix::PhylipDist.3 \ + Bio::Ontology::GOterm.3 \ + Bio::Ontology::InterProTerm.3 \ + Bio::Ontology::Ontology.3 \ + Bio::Ontology::OntologyEngineI.3 \ + Bio::Ontology::OntologyI.3 \ + Bio::Ontology::OntologyStore.3 \ + Bio::Ontology::Path.3 \ + Bio::Ontology::PathI.3 \ + Bio::Ontology::Relationship.3 \ + Bio::Ontology::RelationshipFactory.3 \ + Bio::Ontology::RelationshipI.3 \ + Bio::Ontology::RelationshipType.3 \ + Bio::Ontology::SimpleGOEngine.3 \ + Bio::Ontology::SimpleOntologyEngine.3 \ + Bio::Ontology::Term.3 \ + Bio::Ontology::TermFactory.3 \ + Bio::Ontology::TermI.3 \ + Bio::OntologyIO.3 \ + Bio::OntologyIO::Handlers::InterProHandler.3 \ + Bio::OntologyIO::InterProParser.3 \ + Bio::OntologyIO::dagflat.3 \ + Bio::OntologyIO::goflat.3 \ + Bio::OntologyIO::soflat.3 \ + Bio::Perl.3 \ + Bio::Phenotype::Correlate.3 \ + Bio::Phenotype::Measure.3 \ + Bio::Phenotype::OMIM::MiniMIMentry.3 \ + Bio::Phenotype::OMIM::OMIMentry.3 \ + Bio::Phenotype::OMIM::OMIMentryAllelicVariant.3 \ + Bio::Phenotype::OMIM::OMIMparser.3 \ + Bio::Phenotype::Phenotype.3 \ + Bio::Phenotype::PhenotypeI.3 \ + Bio::PrimarySeq.3 \ + Bio::PrimarySeqI.3 \ + Bio::Range.3 \ + Bio::RangeI.3 \ + Bio::Root::Err.3 \ + Bio::Root::Exception.3 \ + Bio::Root::Global.3 \ + Bio::Root::HTTPget.3 \ + Bio::Root::IO.3 \ + Bio::Root::IOManager.3 \ + Bio::Root::Object.3 \ + Bio::Root::Root.3 \ + Bio::Root::RootI.3 \ + Bio::Root::Utilities.3 \ + Bio::Root::Vector.3 \ + Bio::Root::Xref.3 \ + Bio::Search::BlastUtils.3 \ + Bio::Search::DatabaseI.3 \ + Bio::Search::GenericDatabase.3 \ + Bio::Search::HSP::BlastHSP.3 \ + Bio::Search::HSP::FastaHSP.3 \ + Bio::Search::HSP::GenericHSP.3 \ + Bio::Search::HSP::HMMERHSP.3 \ + Bio::Search::HSP::HSPFactory.3 \ + Bio::Search::HSP::HSPI.3 \ + Bio::Search::HSP::WABAHSP.3 \ + Bio::Search::Hit::BlastHit.3 \ + Bio::Search::Hit::Fasta.3 \ + Bio::Search::Hit::GenericHit.3 \ + Bio::Search::Hit::HMMERHit.3 \ + Bio::Search::Hit::HitFactory.3 \ + Bio::Search::Hit::HitI.3 \ + Bio::Search::Processor.3 \ + Bio::Search::Result::BlastResult.3 \ + Bio::Search::Result::GenericResult.3 \ + Bio::Search::Result::HMMERResult.3 \ + Bio::Search::Result::ResultFactory.3 \ + Bio::Search::Result::ResultI.3 \ + Bio::Search::Result::WABAResult.3 \ + Bio::Search::SearchUtils.3 \ + Bio::SearchDist.3 \ + Bio::SearchIO.3 \ + Bio::SearchIO::EventHandlerI.3 \ + Bio::SearchIO::FastHitEventBuilder.3 \ + Bio::SearchIO::SearchResultEventBuilder.3 \ + Bio::SearchIO::SearchWriterI.3 \ + Bio::SearchIO::Writer::HSPTableWriter.3 \ + Bio::SearchIO::Writer::HTMLResultWriter.3 \ + Bio::SearchIO::Writer::HitTableWriter.3 \ + Bio::SearchIO::Writer::ResultTableWriter.3 \ + Bio::SearchIO::Writer::TextResultWriter.3 \ + Bio::SearchIO::blast.3 \ + Bio::SearchIO::blastxml.3 \ + Bio::SearchIO::exonerate.3 \ + Bio::SearchIO::fasta.3 \ + Bio::SearchIO::hmmer.3 \ + Bio::SearchIO::waba.3 \ + Bio::Seq.3 \ + Bio::Seq::BaseSeqProcessor.3 \ + Bio::Seq::EncodedSeq.3 \ + Bio::Seq::LargePrimarySeq.3 \ + Bio::Seq::LargeSeq.3 \ + Bio::Seq::PrimaryQual.3 \ + Bio::Seq::PrimedSeq.3 \ + Bio::Seq::QualI.3 \ + Bio::Seq::RichSeq.3 \ + Bio::Seq::RichSeqI.3 \ + Bio::Seq::SeqBuilder.3 \ + Bio::Seq::SeqFactory.3 \ + Bio::Seq::SeqFastaSpeedFactory.3 \ + Bio::Seq::SeqWithQuality.3 \ + Bio::Seq::SequenceTrace.3 \ + Bio::Seq::TraceI.3 \ + Bio::SeqAnalysisParserI.3 \ + Bio::SeqFeature::AnnotationAdaptor.3 \ + Bio::SeqFeature::Collection.3 \ + Bio::SeqFeature::CollectionI.3 \ + Bio::SeqFeature::Computation.3 \ + Bio::SeqFeature::FeaturePair.3 \ + Bio::SeqFeature::Gene::Exon.3 \ + Bio::SeqFeature::Gene::ExonI.3 \ Bio::SeqFeature::Gene::GeneStructure.3 \ Bio::SeqFeature::Gene::GeneStructureI.3 \ + Bio::SeqFeature::Gene::Intron.3 \ + Bio::SeqFeature::Gene::NC_Feature.3 \ + Bio::SeqFeature::Gene::Poly_A_site.3 \ + Bio::SeqFeature::Gene::Promoter.3 \ Bio::SeqFeature::Gene::Transcript.3 \ Bio::SeqFeature::Gene::TranscriptI.3 \ - Bio::SeqFeature::Generic.3 Bio::SeqFeature::Similarity.3 \ - Bio::SeqFeature::SimilarityPair.3 Bio::SeqFeatureI.3 \ - Bio::SeqI.3 Bio::SeqIO.3 Bio::SeqIO::FTHelper.3 \ - Bio::SeqIO::MultiFile.3 Bio::SeqIO::ace.3 Bio::SeqIO::embl.3 \ - Bio::SeqIO::fasta.3 Bio::SeqIO::game.3 Bio::SeqIO::gcg.3 \ - Bio::SeqIO::genbank.3 Bio::SeqIO::largefasta.3 \ - Bio::SeqIO::raw.3 Bio::SeqIO::scf.3 Bio::SeqIO::swiss.3 \ - Bio::SeqUtils.3 Bio::SimpleAlign.3 Bio::Species.3 \ - Bio::Tools::AlignFactory.3 Bio::Tools::AnalysisResult.3 \ - Bio::Tools::BPbl2seq.3 Bio::Tools::BPlite.3 \ - Bio::Tools::BPlite::Iteration.3 Bio::Tools::BPpsilite.3 \ - Bio::Tools::Blast.3 Bio::Tools::Blast::HSP.3 \ + Bio::SeqFeature::Gene::UTR.3 \ + Bio::SeqFeature::Generic.3 \ + Bio::SeqFeature::PositionProxy.3 \ + Bio::SeqFeature::Primer.3 \ + Bio::SeqFeature::Similarity.3 \ + Bio::SeqFeature::SimilarityPair.3 \ + Bio::SeqFeatureI.3 \ + Bio::SeqI.3 \ + Bio::SeqIO.3 \ + Bio::SeqIO::FTHelper.3 \ + Bio::SeqIO::MultiFile.3 \ + Bio::SeqIO::abi.3 \ + Bio::SeqIO::ace.3 \ + Bio::SeqIO::alf.3 \ + Bio::SeqIO::bsml.3 \ + Bio::SeqIO::chadoxml.3 \ + Bio::SeqIO::ctf.3 \ + Bio::SeqIO::embl.3 \ + Bio::SeqIO::exp.3 \ + Bio::SeqIO::fasta.3 \ + Bio::SeqIO::fastq.3 \ + Bio::SeqIO::game.3 \ + Bio::SeqIO::game::seqHandler.3 \ + Bio::SeqIO::gcg.3 \ + Bio::SeqIO::genbank.3 \ + Bio::SeqIO::largefasta.3 \ + Bio::SeqIO::locuslink.3 \ + Bio::SeqIO::phd.3 \ + Bio::SeqIO::pir.3 \ + Bio::SeqIO::pln.3 \ + Bio::SeqIO::qual.3 \ + Bio::SeqIO::raw.3 \ + Bio::SeqIO::scf.3 \ + Bio::SeqIO::swiss.3 \ + Bio::SeqIO::ztr.3 \ + Bio::SeqUtils.3 \ + Bio::SimpleAlign.3 \ + Bio::Species.3 \ + Bio::Structure::Atom.3 \ + Bio::Structure::Chain.3 \ + Bio::Structure::Entry.3 \ + Bio::Structure::IO.3 \ + Bio::Structure::IO::pdb.3 \ + Bio::Structure::Model.3 \ + Bio::Structure::Residue.3 \ + Bio::Structure::SecStr::DSSP::Res.3 \ + Bio::Structure::SecStr::STRIDE::Res.3 \ + Bio::Structure::StructureI.3 \ + Bio::Symbol::Alphabet.3 \ + Bio::Symbol::AlphabetI.3 \ + Bio::Symbol::DNAAlphabet.3 \ + Bio::Symbol::ProteinAlphabet.3 \ + Bio::Symbol::Symbol.3 \ + Bio::Symbol::SymbolI.3 \ + Bio::Taxonomy.3 \ + Bio::Taxonomy::Taxon.3 \ + Bio::Taxonomy::Tree.3 \ + Bio::Tools::AlignFactory.3 \ + Bio::Tools::Alignment::Consed.3 \ + Bio::Tools::Alignment::Trim.3 \ + Bio::Tools::AnalysisResult.3 \ + Bio::Tools::BPbl2seq.3 \ + Bio::Tools::BPlite.3 \ + Bio::Tools::BPlite::HSP.3 \ + Bio::Tools::BPlite::Iteration.3 \ + Bio::Tools::BPlite::Sbjct.3 \ + Bio::Tools::BPpsilite.3 \ + Bio::Tools::Blast.3 \ + Bio::Tools::Blast::HSP.3 \ Bio::Tools::Blast::HTML.3 \ - Bio::Tools::Blast::Run::LocalBlast.3 \ - Bio::Tools::Blast::Run::Webblast.3 Bio::Tools::Blast::Sbjct.3 \ - Bio::Tools::CodonTable.3 Bio::Tools::ESTScan.3 \ - Bio::Tools::Fasta.3 Bio::Tools::GFF.3 Bio::Tools::Genscan.3 \ - Bio::Tools::HMMER::Domain.3 Bio::Tools::HMMER::Results.3 \ - Bio::Tools::HMMER::Set.3 Bio::Tools::IUPAC.3 \ - Bio::Tools::MZEF.3 Bio::Tools::OddCodes.3 \ - Bio::Tools::Prediction::Exon.3 Bio::Tools::Prediction::Gene.3 \ + Bio::Tools::Blast::Sbjct.3 \ + Bio::Tools::CodonTable.3 \ + Bio::Tools::Coil.3 \ + Bio::Tools::ECnumber.3 \ + Bio::Tools::EPCR.3 \ + Bio::Tools::ESTScan.3 \ + Bio::Tools::Eponine.3 \ + Bio::Tools::Est2Genome.3 \ + Bio::Tools::FootPrinter.3 \ + Bio::Tools::GFF.3 \ + Bio::Tools::Gel.3 \ + Bio::Tools::Genemark.3 \ + Bio::Tools::Genewise.3 \ + Bio::Tools::Genomewise.3 \ + Bio::Tools::Genscan.3 \ + Bio::Tools::Grail.3 \ + Bio::Tools::HMMER::Domain.3 \ + Bio::Tools::HMMER::Results.3 \ + Bio::Tools::HMMER::Set.3 \ + Bio::Tools::Hmmpfam.3 \ + Bio::Tools::IUPAC.3 \ + Bio::Tools::Lucy.3 \ + Bio::Tools::MZEF.3 \ + Bio::Tools::OddCodes.3 \ + Bio::Tools::Phylo::Molphy.3 \ + Bio::Tools::Phylo::Molphy::Result.3 \ + Bio::Tools::Phylo::PAML.3 \ + Bio::Tools::Phylo::PAML::Result.3 \ + Bio::Tools::Phylo::Phylip::ProtDist.3 \ + Bio::Tools::Prediction::Exon.3 \ + Bio::Tools::Prediction::Gene.3 \ + Bio::Tools::Primer3.3 \ + Bio::Tools::Prints.3 \ + Bio::Tools::Profile.3 \ + Bio::Tools::Promoterwise.3 \ + Bio::Tools::Pseudowise.3 \ + Bio::Tools::RepeatMasker.3 \ Bio::Tools::RestrictionEnzyme.3 \ - Bio::Tools::Run::Alignment::Clustalw.3 \ - Bio::Tools::Run::Alignment::TCoffee.3 \ - Bio::Tools::Run::StandAloneBlast.3 Bio::Tools::SeqAnal.3 \ - Bio::Tools::SeqPattern.3 Bio::Tools::SeqStats.3 \ - Bio::Tools::SeqWords.3 Bio::Tools::Sigcleave.3 \ - Bio::Tools::Sim4::Exon.3 Bio::Tools::Sim4::Results.3 \ - Bio::Tools::WWW.3 Bio::Tools::pSW.3 Bio::UnivAln.3 \ - Bio::Variation::AAChange.3 Bio::Variation::AAReverseMutate.3 \ - Bio::Variation::Allele.3 Bio::Variation::DNAMutation.3 \ - Bio::Variation::IO.3 Bio::Variation::IO::flat.3 \ - Bio::Variation::IO::xml.3 Bio::Variation::RNAChange.3 \ - Bio::Variation::SeqDiff.3 Bio::Variation::VariantI.3 \ - bioback.3 biodesign.3 bioperl.3 biostart.3 bptutorial.3 -.if defined(WITH_CORBA_CLIENT) -MAN3+= Bio::CorbaClient::PrimarySeq.3 Bio::CorbaClient::Seq.3 \ - Bio::CorbaClient::SeqFeature.3 Bio::CorbaClient::Base.3 \ - Bio::SeqIO::biocorba.3 Bio::DB::Biocorba.3 \ - Bio::CorbaClient::Client.3 Bio::CorbaClient::ORB.3 -.endif -.if defined(WITH_CORBA_SERVER) -MAN3+= Bio::CorbaServer::BioEnv.3 Bio::CorbaServer::AnonymousSeq.3 \ - Bio::CorbaServer::PrimarySeq.3 Bio::CorbaServer::SeqFeature.3 \ - Bio::CorbaServer::PrimarySeqDB.3 \ - Bio::CorbaServer::PrimarySeqIterator.3 \ - Bio::CorbaServer::PrimarySeqVector.3 \ - Bio::CorbaServer::Seq.3 \ - Bio::CorbaServer::SeqDB.3 Bio::CorbaServer::Base.3 \ - Bio::CorbaServer::SeqFeatureIterator.3 \ - Bio::CorbaServer::SeqFeatureVector.3 \ - Bio::CorbaServer::Server.3 -.endif -.if defined(WITH_GUI) -MAN3+= Bio::Tk::HitDisplay.3 Bio::Tk::SeqCanvas.3 -.endif - -pre-fetch: -.if !defined(BATCH) && (!defined(WITH_CORBA_CLIENT) || \ - !defined(WITH_CORBA_SERVER) || !defined(WITH_GUI)) - @ ${CAT} ${FILESDIR}/ext.msg -.endif + Bio::Tools::Run::RemoteBlast.3 \ + Bio::Tools::Run::StandAloneBlast.3 \ + Bio::Tools::Run::WrapperBase.3 \ + Bio::Tools::Seg.3 \ + Bio::Tools::SeqAnal.3 \ + Bio::Tools::SeqPattern.3 \ + Bio::Tools::SeqStats.3 \ + Bio::Tools::SeqWords.3 \ + Bio::Tools::Sigcleave.3 \ + Bio::Tools::Signalp.3 \ + Bio::Tools::Sim4::Exon.3 \ + Bio::Tools::Sim4::Results.3 \ + Bio::Tools::Tmhmm.3 \ + Bio::Tools::WWW.3 \ + Bio::Tools::pSW.3 \ + Bio::Tree::AlleleNode.3 \ + Bio::Tree::Node.3 \ + Bio::Tree::NodeI.3 \ + Bio::Tree::NodeNHX.3 \ + Bio::Tree::RandomFactory.3 \ + Bio::Tree::Statistics.3 \ + Bio::Tree::Tree.3 \ + Bio::Tree::TreeFunctionsI.3 \ + Bio::Tree::TreeI.3 \ + Bio::TreeIO.3 \ + Bio::TreeIO::TreeEventBuilder.3 \ + Bio::TreeIO::newick.3 \ + Bio::TreeIO::nhx.3 \ + Bio::TreeIO::tabtree.3 \ + Bio::UpdateableSeqI.3 \ + Bio::Variation::AAChange.3 \ + Bio::Variation::AAReverseMutate.3 \ + Bio::Variation::Allele.3 \ + Bio::Variation::DNAMutation.3 \ + Bio::Variation::IO.3 \ + Bio::Variation::IO::flat.3 \ + Bio::Variation::IO::xml.3 \ + Bio::Variation::RNAChange.3 \ + Bio::Variation::SNP.3 \ + Bio::Variation::SeqDiff.3 \ + Bio::Variation::VariantI.3 \ + bptutorial.3 -post-configure: - @ cd ${EXT_WRKSRC} && \ - ${SETENV} ${CONFIGURE_ENV} \ - ${PERL5} ./${CONFIGURE_SCRIPT} ${CONFIGURE_ARGS} +# now install all extra stuff (docs, examples, scripts, models) +post-install: -.for ext in ${EXTLIST} - @ cd ${${ext}_WRKSRC} && \ - ${PERL5} ./${CONFIGURE_SCRIPT} ${CONFIGURE_ARGS} -.endfor +.if !defined(NOPORTDOCS) + ${MKDIR} ${DATADIR} + ${MKDIR} ${EXAMPLESDIR} + ${MKDIR} ${DOCSDIR} -post-build: - @ cd ${EXT_WRKSRC} && \ - ${MAKE} ${MAKE_FLAGS} ${MAKEFILE} ${MAKE_ARGS} ${ALL_TARGET} -.for ext in ${EXTLIST} - @ cd ${${ext}_WRKSRC} && ${SETENV} ${MAKE_ENV} \ - ${MAKE} ${MAKE_FLAGS} ${MAKEFILE} ${MAKE_ARGS} ${ALL_TARGET} +.for doc in AUTHORS BUGS Changes DEPRECATED FAQ INSTALL LICENSE PLATFORMS README + ${INSTALL_MAN} ${WRKSRC}/${doc} ${DOCSDIR} .endfor + ${CP} -R ${WRKSRC}/doc ${DOCSDIR} + ${CP} -R ${WRKSRC}/examples/* ${EXAMPLESDIR} + ${CP} -R ${WRKSRC}/scripts ${DATADIR} + ${CP} -R ${WRKSRC}/models ${DATADIR} -post-install: - @ cd ${EXT_WRKSRC} && \ - ${SETENV} ${MAKE_ENV} ${MAKE} ${MAKE_FLAGS} \ - ${MAKEFILE} ${MAKE_ARGS} ${INSTALL_TARGET} -.for ext in ${EXTLIST} - @ cd ${${ext}_WRKSRC} && \ - ${SETENV} ${MAKE_ENV} ${MAKE} ${MAKE_FLAGS} \ - ${MAKEFILE} ${MAKE_ARGS} ${INSTALL_TARGET} -.endfor +.endif .include <bsd.port.mk> diff --git a/biology/p5-bioperl/distinfo b/biology/p5-bioperl/distinfo index 1ba09100c78b..7e4444de4082 100644 --- a/biology/p5-bioperl/distinfo +++ b/biology/p5-bioperl/distinfo @@ -1,5 +1 @@ -MD5 (bioperl-0.7.2.tar.gz) = 7c8c39cbcdcdb4e208494a30ca02fbbe -MD5 (bioperl-ext-0.6.tar.gz) = 5bf87e0cf94d3d41fabbfd209971d240 -MD5 (bioperl-corba-client-0.2.tar.gz) = 9635488e779d771bc5f976bf56826590 -MD5 (bioperl-corba-server-0.2.tar.gz) = d5e3353ed6c8717de06e0db8f5bbc0f5 -MD5 (bioperl-gui-0.7.tar.gz) = 07b50934c5dc8fcbbb89d2d35c758dea +MD5 (bioperl-1.4.tar.gz) = 5ef3e6e824c3f444e788d7fc9bda1fcb diff --git a/biology/p5-bioperl/files/ext.msg b/biology/p5-bioperl/files/ext.msg deleted file mode 100644 index 1ba9af2f5f84..000000000000 --- a/biology/p5-bioperl/files/ext.msg +++ /dev/null @@ -1,16 +0,0 @@ ---------------------------------------------------------------------------- -This port includes support for a number of optional extensions to Bioperl. -To build the port with these extensions, set the corresponding variables: - -To build with client-side CORBA support: set WITH_CORBA_CLIENT -To build with server-side CORBA support: set WITH_CORBA_SERVER -To build with (experimental) GUI support: set WITH_GUI - -Additionally, the variable WITH_CORBA implies both WITH_CORBA_CLIENT and -WITH_CORBA_SERVER. - -For example, to build and install the Bioperl port with all the currently -available optional extensions: - - make WITH_CORBA=yes WITH_GUI=yes install ---------------------------------------------------------------------------- diff --git a/biology/p5-bioperl/files/patch-aa b/biology/p5-bioperl/files/patch-aa deleted file mode 100644 index 4aecbfe2a166..000000000000 --- a/biology/p5-bioperl/files/patch-aa +++ /dev/null @@ -1,9 +0,0 @@ ---- ../bioperl-ext-06/Bio/Ext/Align/libs/makefile.orig Thu Sep 16 15:33:08 1999 -+++ ../bioperl-ext-06/Bio/Ext/Align/libs/makefile Fri Jul 28 11:57:27 2000 -@@ -47,5 +47,5 @@ - # For NetBSD or Sun (solaris) installs, add -fPIC to the CFLAGS lines - # - --CFLAGS = -c -O -+CFLAGS+= -c -O -fPIC - CC = cc diff --git a/biology/p5-bioperl/files/patch-manify b/biology/p5-bioperl/files/patch-manify new file mode 100644 index 000000000000..9609fc951a0c --- /dev/null +++ b/biology/p5-bioperl/files/patch-manify @@ -0,0 +1,29 @@ +--- Makefile.PL.orig Sat Jan 10 00:11:42 2004 ++++ Makefile.PL Sat Jan 10 00:12:15 2004 +@@ -358,16 +358,16 @@ + ); + + +-sub MY::manifypods { +- my $self = shift; +- #print STDERR "In manifypods moment\n"; +- if( 1 ) { +- return "\nmanifypods : pure_all\n\t$self->{NOECHO}\$(NOOP)\n" +- } +- else { +- return $self->SUPER::manifypods(@_); +- } +-} ++#sub MY::manifypods { ++# my $self = shift; ++# #print STDERR "In manifypods moment\n"; ++# if( 1 ) { ++# return "\nmanifypods : pure_all\n\t$self->{NOECHO}\$(NOOP)\n" ++# } ++# else { ++# return $self->SUPER::manifypods(@_); ++# } ++#} + + sub MY::clean { + package MY; diff --git a/biology/p5-bioperl/pkg-plist b/biology/p5-bioperl/pkg-plist index 29c40be66b26..1baf442c6700 100644 --- a/biology/p5-bioperl/pkg-plist +++ b/biology/p5-bioperl/pkg-plist @@ -1,250 +1,1114 @@ -%%PLIST_CORBA_CLIENT%%%%SITE_PERL%%/Bio/CorbaClient/Base.pm -%%PLIST_CORBA_CLIENT%%%%SITE_PERL%%/Bio/CorbaClient/Client.pm -%%PLIST_CORBA_CLIENT%%%%SITE_PERL%%/Bio/CorbaClient/ORB.pm -%%PLIST_CORBA_CLIENT%%%%SITE_PERL%%/Bio/CorbaClient/PrimarySeq.pm -%%PLIST_CORBA_CLIENT%%%%SITE_PERL%%/Bio/CorbaClient/Seq.pm -%%PLIST_CORBA_CLIENT%%%%SITE_PERL%%/Bio/CorbaClient/SeqFeature.pm -%%PLIST_CORBA_CLIENT%%%%SITE_PERL%%/Bio/DB/Biocorba.pm -%%PLIST_CORBA_CLIENT%%%%SITE_PERL%%/Bio/SeqIO/biocorba.pm -%%PLIST_CORBA_SERVER%%%%SITE_PERL%%/Bio/CorbaServer/AnonymousSeq.pm -%%PLIST_CORBA_SERVER%%%%SITE_PERL%%/Bio/CorbaServer/Base.pm -%%PLIST_CORBA_SERVER%%%%SITE_PERL%%/Bio/CorbaServer/BioEnv.pm -%%PLIST_CORBA_SERVER%%%%SITE_PERL%%/Bio/CorbaServer/PrimarySeq.pm -%%PLIST_CORBA_SERVER%%%%SITE_PERL%%/Bio/CorbaServer/PrimarySeqDB.pm -%%PLIST_CORBA_SERVER%%%%SITE_PERL%%/Bio/CorbaServer/PrimarySeqIterator.pm -%%PLIST_CORBA_SERVER%%%%SITE_PERL%%/Bio/CorbaServer/PrimarySeqVector.pm -%%PLIST_CORBA_SERVER%%%%SITE_PERL%%/Bio/CorbaServer/Seq.pm -%%PLIST_CORBA_SERVER%%%%SITE_PERL%%/Bio/CorbaServer/SeqDB.pm -%%PLIST_CORBA_SERVER%%%%SITE_PERL%%/Bio/CorbaServer/SeqFeature.pm -%%PLIST_CORBA_SERVER%%%%SITE_PERL%%/Bio/CorbaServer/SeqFeatureIterator.pm -%%PLIST_CORBA_SERVER%%%%SITE_PERL%%/Bio/CorbaServer/SeqFeatureVector.pm -%%PLIST_CORBA_SERVER%%%%SITE_PERL%%/Bio/CorbaServer/Server.pm -%%PLIST_GUI%%%%SITE_PERL%%/Bio/Tk/AnnotMap.pm -%%PLIST_GUI%%%%SITE_PERL%%/Bio/Tk/BioTkPerl8_1.pm -%%PLIST_GUI%%%%SITE_PERL%%/Bio/Tk/GO_Browser.pm -%%PLIST_GUI%%%%SITE_PERL%%/Bio/Tk/HitDisplay.pm -%%PLIST_GUI%%%%SITE_PERL%%/Bio/Tk/README -%%PLIST_GUI%%%%SITE_PERL%%/Bio/Tk/SeqCanvas.pm -%%PLIST_GUI%%%%SITE_PERL%%/Bio/Tk/Tkpsh.pl -%%PLIST_GUI%%%%SITE_PERL%%/Bio/Tk/bioTk_Map.pm -%%PLIST_GUI%%%%SITE_PERL%%/Bio/Tk/bioTk_SeqSubs.pm -%%PLIST_GUI%%%%SITE_PERL%%/Bio/Tk/bioTk_Sequence.pm -%%PLIST_GUI%%%%SITE_PERL%%/Bio/Tk/bioTk_Utilities.pm -%%PLIST_GUI%%%%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio/Tk/.packlist -%%SITE_PERL%%/%%PERL_ARCH%%/Bio/Ext/Align.pm +bin/bp_chaos_plot.pl +bin/bp_composite_LD.pl +bin/bp_pairwise_kaks.pl +bin/bp_flanks.pl +bin/bp_translate_seq.pl +bin/bp_feature_draw.pl +bin/bp_load_gff.pl +bin/bp_biblio.pl +bin/bp_fast_load_gff.pl +bin/bp_search_overview.pl +bin/bp_search2tribe.pl +bin/bp_fetch.pl +bin/bp_seq_length.pl +bin/bp_search2gff.pl +bin/bp_extract_feature_seq.pl +bin/bp_pg_bulk_load_gff.pl +bin/bp_sreformat.pl +bin/bp_index.pl +bin/bp_dbsplit.pl +bin/bp_biofetch_genbank_proxy.pl +bin/bp_bioflat_index.pl +bin/bp_search2alnblocks.pl +bin/bp_local_taxonomydb_query.pl +bin/bp_biogetseq.pl +bin/bp_process_wormbase.pl +bin/bp_search2BSML.pl +bin/bp_taxid4species.pl +bin/bp_mask_by_search.pl +bin/bp_mrtrans.pl +bin/bp_process_gadfly.pl +bin/bp_gccalc.pl +bin/bp_seqconvert.pl +bin/bp_oligo_count.pl +bin/bp_process_ncbi_human.pl +bin/bp_split_seq.pl +bin/bp_remote_blast.pl +bin/bp_aacomp.pl +bin/bp_heterogeneity_test.pl +bin/bp_frend.pl +bin/bp_generate_histogram.pl +bin/bp_process_sgd.pl +bin/bp_mutate.pl +bin/bp_filter_search.pl +bin/bp_genbank2gff.pl +bin/bp_bulk_load_gff.pl +bin/bp_nrdb.pl +bin/bp_blast2tree.pl %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio/.packlist -%%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio/Ext/Align/.packlist -%%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio/Ext/Align/Align.bs -%%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio/Ext/Align/Align.so +%%SITE_PERL%%/biodatabases.pod +%%SITE_PERL%%/biodesign.pod +%%SITE_PERL%%/bptutorial.pl +%%SITE_PERL%%/bioperl.pod +%%SITE_PERL%%/bioscripts.pod +%%SITE_PERL%%/Bio/MapIO.pm +%%SITE_PERL%%/Bio/Seq.pm +%%SITE_PERL%%/Bio/DasI.pm +%%SITE_PERL%%/Bio/AnnotationCollectionI.pm +%%SITE_PERL%%/Bio/SeqAnalysisParserI.pm +%%SITE_PERL%%/Bio/SeqUtils.pm +%%SITE_PERL%%/Bio/AnalysisResultI.pm +%%SITE_PERL%%/Bio/SeqFeatureI.pm +%%SITE_PERL%%/Bio/AnnotationI.pm +%%SITE_PERL%%/Bio/SimpleAlign.pm +%%SITE_PERL%%/Bio/SearchDist.pm +%%SITE_PERL%%/Bio/Range.pm +%%SITE_PERL%%/Bio/SeqI.pm +%%SITE_PERL%%/Bio/IdCollectionI.pm +%%SITE_PERL%%/Bio/Perl.pm +%%SITE_PERL%%/Bio/ClusterI.pm +%%SITE_PERL%%/Bio/Taxonomy.pm +%%SITE_PERL%%/Bio/DescribableI.pm +%%SITE_PERL%%/Bio/PrimarySeqI.pm +%%SITE_PERL%%/Bio/AnnotatableI.pm +%%SITE_PERL%%/Bio/TreeIO.pm +%%SITE_PERL%%/Bio/Das/FeatureTypeI.pm +%%SITE_PERL%%/Bio/Das/SegmentI.pm +%%SITE_PERL%%/Bio/SeqIO.pm +%%SITE_PERL%%/Bio/OntologyIO.pm +%%SITE_PERL%%/Bio/DBLinkContainerI.pm +%%SITE_PERL%%/Bio/AnalysisI.pm +%%SITE_PERL%%/Bio/FeatureHolderI.pm +%%SITE_PERL%%/Bio/AnalysisParserI.pm +%%SITE_PERL%%/Bio/LocatableSeq.pm +%%SITE_PERL%%/Bio/LocationI.pm +%%SITE_PERL%%/Bio/Graphics.pm +%%SITE_PERL%%/Bio/WebAgent.pm %%SITE_PERL%%/Bio/AlignIO.pm -%%SITE_PERL%%/Bio/AlignIO/bl2seq.pm -%%SITE_PERL%%/Bio/AlignIO/clustalw.pm -%%SITE_PERL%%/Bio/AlignIO/fasta.pm +%%SITE_PERL%%/Bio/Biblio.pm +%%SITE_PERL%%/Bio/RangeI.pm +%%SITE_PERL%%/Bio/PrimarySeq.pm +%%SITE_PERL%%/Bio/SearchIO.pm +%%SITE_PERL%%/Bio/ClusterIO.pm +%%SITE_PERL%%/Bio/SimpleAnalysisI.pm +%%SITE_PERL%%/Bio/UpdateableSeqI.pm +%%SITE_PERL%%/Bio/Species.pm 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