Attachment #143175 for bug #190342

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# $FreeBSD: head/biology/p5-bioperl/Makefile 350675 2014-04-09 09:49:02Z bapt $

PORTNAME=	bioperl
PORTVERSION=	1.6.923
PORTREVISION=	4
CATEGORIES=	biology perl5
MASTER_SITES=	CPAN
MASTER_SITE_SUBDIR=	CPAN:CJFIELDS
PKGNAMEPREFIX=	p5-
DISTNAME=	BioPerl-${PORTVERSION}

MAINTAINER=	wen@FreeBSD.org
COMMENT=	A collection of Perl modules for bioinformatics

LICENSE=	ART10 GPLv1
LICENSE_COMB=	dual

BUILD_DEPENDS=	p5-Text-Tabs+Wrap>=0:${PORTSDIR}/textproc/p5-Text-Tabs+Wrap \
		p5-Bio-ASN1-EntrezGene>=0:${PORTSDIR}/biology/p5-Bio-ASN1-EntrezGene \
		p5-Class-AutoClass>=0:${PORTSDIR}/devel/p5-Class-AutoClass \

		p5-XML-SAX-Writer>=0:${PORTSDIR}/textproc/p5-XML-SAX-Writer \
		p5-XML-Twig>=0:${PORTSDIR}/textproc/p5-XML-Twig \
		p5-XML-Writer>=0:${PORTSDIR}/textproc/p5-XML-Writer \
		p5-AcePerl>=0:${PORTSDIR}/biology/p5-AcePerl \
		p5-Clone>=0:${PORTSDIR}/devel/p5-Clone \
		p5-DBD-mysql>=0:${PORTSDIR}/databases/p5-DBD-mysql \
		p5-GD>=0:${PORTSDIR}/graphics/p5-GD \

		p5-Math-Random>=0:${PORTSDIR}/math/p5-Math-Random \
		p5-PostScript>=0:${PORTSDIR}/print/p5-PostScript \
		p5-Set-Scalar>=0:${PORTSDIR}/devel/p5-Set-Scalar \
		p5-URI>=0:${PORTSDIR}/net/p5-URI \
		p5-Test-Most>=0:${PORTSDIR}/devel/p5-Test-Most \
		p5-HTML-TableExtract>=2:${PORTSDIR}/www/p5-HTML-TableExtract \
		p5-Sort-Naturally>=1:${PORTSDIR}/textproc/p5-Sort-Naturally \
		p5-XML-Simple>=2:${PORTSDIR}/textproc/p5-XML-Simple \
		p5-YAML>=0:${PORTSDIR}/textproc/p5-YAML \
		p5-Error>=0:${PORTSDIR}/lang/p5-Error

RUN_DEPENDS:=	${BUILD_DEPENDS}

#CONFLICTS=	p5-bioperl-1.[13579]*

USES=		perl5
USE_PERL5=	modbuild

OPTIONS_DEFINE=	DOCS PGTEST SQLITETEST
PGTEST_DESC=	Test PostGreSQL
SQLITETEST_DESC=	Test SQLite
PGTEST_RUN_DEPENDS=	p5-DBD-Pg>=3:${PORTSDIR}/databases/p5-DBD-Pg
PGTEST_BUILD_DEPENDS=	p5-DBD-Pg>=3:${PORTSDIR}/databases/p5-DBD-Pg
SQLITETEST_RUN_DEPENDS=	p5-DBD-SQLite>=1:${PORTSDIR}/databases/p5-DBD-SQLite
SQLITETEST_BUILD_DEPENDS=	p5-DBD-SQLite>=1:${PORTSDIR}/databases/p5-DBD-SQLite
		bp_chaos_plot.pl.1 \
		bp_classify_hits_kingdom.pl.1 \
		bp_composite_LD.pl.1 \
		bp_dbsplit.pl.1 \
		bp_download_query_genbank.pl.1 \
		bp_einfo.pl.1 \
		bp_extract_feature_seq.pl.1 \
		bp_fast_load_gff.pl.1 \
		bp_fastam9_to_table.pl.1 \
		bp_fetch.pl.1 \
		bp_filter_search.pl.1 \
		bp_flanks.pl.1 \
		bp_gccalc.pl.1 \
		bp_genbank2gff.pl.1 \
		bp_genbank2gff3.pl.1 \
		bp_generate_histogram.pl.1 \
		bp_heterogeneity_test.pl.1 \
		bp_hivq.pl.1 \
		bp_hmmer_to_table.pl.1 \
		bp_index.pl.1 \
		bp_load_gff.pl.1 \
		bp_local_taxonomydb_query.pl.1 \
		bp_make_mrna_protein.pl.1 \
		bp_mask_by_search.pl.1 \
		bp_meta_gff.pl.1 \
		bp_mrtrans.pl.1 \
		bp_mutate.pl.1 \
		bp_nexus2nh.pl.1 \
		bp_nrdb.pl.1 \
		bp_oligo_count.pl.1 \
		bp_pairwise_kaks.pl.1 \
		bp_parse_hmmsearch.pl.1 \
		bp_process_gadfly.pl.1 \
		bp_process_sgd.pl.1 \
		bp_process_wormbase.pl.1 \
		bp_query_entrez_taxa.pl.1 \
		bp_remote_blast.pl.1 \
		bp_revtrans-motif.pl.1 \
		bp_search2BSML.pl.1 \
		bp_search2alnblocks.pl.1 \
		bp_search2gff.pl.1 \
		bp_search2table.pl.1 \
		bp_search2tribe.pl.1 \
		bp_seq_length.pl.1 \
		bp_seqconvert.pl.1 \
		bp_seqret.pl.1 \
		bp_seqretsplit.pl.1 \
		bp_split_seq.pl.1 \
		bp_sreformat.pl.1 \
		bp_taxid4species.pl.1 \
		bp_taxonomy2tree.pl.1 \
		bp_translate_seq.pl.1 \
		bp_tree2pag.pl.1 \
		bp_unflatten_seq.pl.1

MAN3=		Bio::Align::AlignI.3 \
		Bio::Align::DNAStatistics.3 \
		Bio::Align::PairwiseStatistics.3 \
		Bio::Align::ProteinStatistics.3 \
		Bio::Align::StatisticsI.3 \
		Bio::Align::Utilities.3 \
		Bio::AlignIO.3 \
		Bio::AlignIO::Handler::GenericAlignHandler.3 \
		Bio::AlignIO::arp.3 \
		Bio::AlignIO::bl2seq.3 \
		Bio::AlignIO::clustalw.3 \
		Bio::AlignIO::emboss.3 \
		Bio::AlignIO::fasta.3 \
		Bio::AlignIO::largemultifasta.3 \
		Bio::AlignIO::maf.3 \
		Bio::AlignIO::mase.3 \
		Bio::AlignIO::mega.3 \
		Bio::AlignIO::meme.3 \
		Bio::AlignIO::metafasta.3 \
		Bio::AlignIO::msf.3 \
		Bio::AlignIO::nexus.3 \
		Bio::AlignIO::pfam.3 \
		Bio::AlignIO::phylip.3 \
		Bio::AlignIO::po.3 \
		Bio::AlignIO::proda.3 \
		Bio::AlignIO::prodom.3 \
		Bio::AlignIO::psi.3 \
		Bio::AlignIO::selex.3 \
		Bio::AlignIO::stockholm.3 \
		Bio::AlignIO::xmfa.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::Relation.3 \
		Bio::Annotation::SimpleValue.3 \
		Bio::Annotation::StructuredValue.3 \
		Bio::Annotation::TagTree.3 \
		Bio::Annotation::Target.3 \
		Bio::Annotation::Tree.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::IO::tigr.3 \
		Bio::Assembly::Scaffold.3 \
		Bio::Assembly::ScaffoldI.3 \
		Bio::Assembly::Singlet.3 \
		Bio::Assembly::Tools::ContigSpectrum.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::CodonUsage::IO.3 \
		Bio::CodonUsage::Table.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::eutils.3 \
		Bio::DB::Biblio::soap.3 \
		Bio::DB::BiblioI.3 \
		Bio::DB::BioFetch.3 \
		Bio::DB::CUTG.3 \
		Bio::DB::DBFetch.3 \
		Bio::DB::EMBL.3 \
		Bio::DB::EUtilities.3 \
		Bio::DB::EntrezGene.3 \
		Bio::DB::Expression.3 \
		Bio::DB::Expression::geo.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::Flat::BDB::genbank.3 \
		Bio::DB::Flat::BDB::swiss.3 \
		Bio::DB::Flat::BinarySearch.3 \
		Bio::DB::GFF.3 \
		Bio::DB::GFF::Adaptor::ace.3 \
		Bio::DB::GFF::Adaptor::berkeleydb.3 \
		Bio::DB::GFF::Adaptor::berkeleydb::iterator.3 \
		Bio::DB::GFF::Adaptor::biofetch.3 \
		Bio::DB::GFF::Adaptor::biofetch_oracle.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::mysqlcmap.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::dbi::pg.3 \
		Bio::DB::GFF::Adaptor::dbi::pg_fts.3 \
		Bio::DB::GFF::Adaptor::memory.3 \
		Bio::DB::GFF::Adaptor::memory::feature_serializer.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::gene.3 \
		Bio::DB::GFF::Aggregator::match.3 \
		Bio::DB::GFF::Aggregator::none.3 \
		Bio::DB::GFF::Aggregator::orf.3 \
		Bio::DB::GFF::Aggregator::processed_transcript.3 \
		Bio::DB::GFF::Aggregator::so_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::GenericWebAgent.3 \
		Bio::DB::HIV.3 \
		Bio::DB::HIV::HIVAnnotProcessor.3 \
		Bio::DB::HIV::HIVQueryHelper.3 \
		Bio::DB::InMemoryCache.3 \
		Bio::DB::LocationI.3 \
		Bio::DB::MeSH.3 \
		Bio::DB::NCBIHelper.3 \
		Bio::DB::Qual.3 \
		Bio::DB::Query::GenBank.3 \
		Bio::DB::Query::HIVQuery.3 \
		Bio::DB::Query::WebQuery.3 \
		Bio::DB::QueryI.3 \
		Bio::DB::RandomAccessI.3 \
		Bio::DB::RefSeq.3 \
		Bio::DB::ReferenceI.3 \
		Bio::DB::Registry.3 \
		Bio::DB::SeqFeature.3 \
		Bio::DB::SeqFeature::NormalizedFeature.3 \
		Bio::DB::SeqFeature::NormalizedFeatureI.3 \
		Bio::DB::SeqFeature::NormalizedTableFeatureI.3 \
		Bio::DB::SeqFeature::Segment.3 \
		Bio::DB::SeqFeature::Store.3 \
		Bio::DB::SeqFeature::Store::DBI::Iterator.3 \
		Bio::DB::SeqFeature::Store::DBI::mysql.3 \
		Bio::DB::SeqFeature::Store::DBI::Pg.3 \
		Bio::DB::SeqFeature::Store::DBI::SQLite.3 \
		Bio::DB::SeqFeature::Store::berkeleydb3.3 \
		Bio::DB::SeqFeature::Store::FeatureFileLoader.3 \
		Bio::DB::SeqFeature::Store::GFF2Loader.3 \
		Bio::DB::SeqFeature::Store::GFF3Loader.3 \
		Bio::DB::SeqFeature::Store::LoadHelper.3 \
		Bio::DB::SeqFeature::Store::Loader.3 \
		Bio::DB::SeqFeature::Store::bdb.3 \
		Bio::DB::SeqFeature::Store::berkeleydb.3 \
		Bio::DB::SeqFeature::Store::memory.3 \
		Bio::DB::SeqHound.3 \
		Bio::DB::SeqI.3 \
		Bio::DB::SeqVersion.3 \
		Bio::DB::SeqVersion::gi.3 \
		Bio::DB::SwissProt.3 \
		Bio::DB::TFBS.3 \
		Bio::DB::TFBS::transfac_pro.3 \
		Bio::DB::Taxonomy.3 \
		Bio::DB::Taxonomy::entrez.3 \
		Bio::DB::Taxonomy::flatfile.3 \
		Bio::DB::Taxonomy::list.3 \
		Bio::DB::Universal.3 \
		Bio::DB::UpdateableSeqI.3 \
		Bio::DB::WebDBSeqI.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::Contact.3 \
		Bio::Expression::DataSet.3 \
		Bio::Expression::FeatureGroup.3 \
		Bio::Expression::FeatureGroup::FeatureGroupMas50.3 \
		Bio::Expression::FeatureI.3 \
		Bio::Expression::FeatureSet::FeatureSetMas50.3 \
		Bio::Expression::Platform.3 \
		Bio::Expression::ProbeI.3 \
		Bio::Expression::Sample.3 \
		Bio::Factory::AnalysisI.3 \
		Bio::Factory::ApplicationFactoryI.3 \
		Bio::Factory::DriverFactory.3 \
		Bio::Factory::FTLocationFactory.3 \
		Bio::Factory::LocationFactoryI.3 \
		Bio::Factory::MapFactoryI.3 \
		Bio::Factory::ObjectBuilderI.3 \
		Bio::Factory::ObjectFactory.3 \
		Bio::Factory::ObjectFactoryI.3 \
		Bio::Factory::SeqAnalysisParserFactory.3 \
		Bio::Factory::SeqAnalysisParserFactoryI.3 \
		Bio::Factory::SequenceFactoryI.3 \
		Bio::Factory::SequenceProcessorI.3 \
		Bio::Factory::SequenceStreamI.3 \
		Bio::Factory::TreeFactoryI.3 \
		Bio::FeatureHolderI.3 \
		Bio::FeatureIO.3 \
		Bio::FeatureIO::bed.3 \
		Bio::FeatureIO::gff.3 \
		Bio::FeatureIO::gtf.3 \
		Bio::FeatureIO::interpro.3 \
		Bio::FeatureIO::ptt.3 \
		Bio::FeatureIO::vecscreen_simple.3 \
		Bio::HandlerBaseI.3 \
		Bio::IdCollectionI.3 \
		Bio::IdentifiableI.3 \
		Bio::Index::Abstract.3 \
		Bio::Index::AbstractSeq.3 \
		Bio::Index::Blast.3 \
		Bio::Index::BlastTable.3 \
		Bio::Index::EMBL.3 \
		Bio::Index::Fasta.3 \
		Bio::Index::Fastq.3 \
		Bio::Index::GenBank.3 \
		Bio::Index::Hmmer.3 \
		Bio::Index::Qual.3 \
		Bio::Index::Stockholm.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::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::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::Map::Clone.3 \
		Bio::Map::Contig.3 \
		Bio::Map::CytoMap.3 \
		Bio::Map::CytoMarker.3 \
		Bio::Map::CytoPosition.3 \
		Bio::Map::EntityI.3 \
		Bio::Map::FPCMarker.3 \
		Bio::Map::Gene.3 \
		Bio::Map::GeneMap.3 \
		Bio::Map::GenePosition.3 \
		Bio::Map::GeneRelative.3 \
		Bio::Map::LinkageMap.3 \
		Bio::Map::LinkagePosition.3 \
		Bio::Map::MapI.3 \
		Bio::Map::Mappable.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::Physical.3 \
		Bio::Map::Position.3 \
		Bio::Map::PositionHandler.3 \
		Bio::Map::PositionHandlerI.3 \
		Bio::Map::PositionI.3 \
		Bio::Map::PositionWithSequence.3 \
		Bio::Map::Prediction.3 \
		Bio::Map::Relative.3 \
		Bio::Map::RelativeI.3 \
		Bio::Map::SimpleMap.3 \
		Bio::Map::TranscriptionFactor.3 \
		Bio::MapIO.3 \
		Bio::MapIO::fpc.3 \
		Bio::MapIO::mapmaker.3 \
		Bio::Matrix::Generic.3 \
		Bio::Matrix::IO.3 \
		Bio::Matrix::IO::mlagan.3 \
		Bio::Matrix::IO::phylip.3 \
		Bio::Matrix::IO::scoring.3 \
		Bio::Matrix::MatrixI.3 \
		Bio::Matrix::Mlagan.3 \
		Bio::Matrix::PSM::IO.3 \
		Bio::Matrix::PSM::IO::mast.3 \
		Bio::Matrix::PSM::IO::masta.3 \
		Bio::Matrix::PSM::IO::meme.3 \
		Bio::Matrix::PSM::IO::psiblast.3 \
		Bio::Matrix::PSM::IO::transfac.3 \
		Bio::Matrix::PSM::InstanceSite.3 \
		Bio::Matrix::PSM::InstanceSiteI.3 \
		Bio::Matrix::PSM::ProtMatrix.3 \
		Bio::Matrix::PSM::ProtPsm.3 \
		Bio::Matrix::PSM::Psm.3 \
		Bio::Matrix::PSM::PsmHeader.3 \
		Bio::Matrix::PSM::PsmHeaderI.3 \
		Bio::Matrix::PSM::PsmI.3 \
		Bio::Matrix::PSM::SiteMatrix.3 \
		Bio::Matrix::PSM::SiteMatrixI.3 \
		Bio::Matrix::PhylipDist.3 \
		Bio::Matrix::Scoring.3 \
		Bio::MolEvol::CodonModel.3 \
		Bio::Ontology::DocumentRegistry.3 \
		Bio::Ontology::GOterm.3 \
		Bio::Ontology::InterProTerm.3 \
		Bio::Ontology::OBOEngine.3 \
		Bio::Ontology::OBOterm.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::GraphAdaptor.3 \
		Bio::Ontology::SimpleGOEngine::GraphAdaptor02.3 \
		Bio::Ontology::SimpleOntologyEngine.3 \
		Bio::Ontology::Term.3 \
		Bio::Ontology::TermFactory.3 \
		Bio::Ontology::TermI.3 \
		Bio::OntologyIO.3 \
		Bio::OntologyIO::Handlers::BaseSAXHandler.3 \
		Bio::OntologyIO::Handlers::InterProHandler.3 \
		Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler.3 \
		Bio::OntologyIO::InterProParser.3 \
		Bio::OntologyIO::dagflat.3 \
		Bio::OntologyIO::goflat.3 \
		Bio::OntologyIO::obo.3 \
		Bio::OntologyIO::simplehierarchy.3 \
		Bio::OntologyIO::soflat.3 \
		Bio::ParameterBaseI.3 \
		Bio::Perl.3 \
		Bio::Phenotype::Correlate.3 \
		Bio::Phenotype::MeSH::Term.3 \
		Bio::Phenotype::MeSH::Twig.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::PhyloNetwork.3 \
		Bio::PhyloNetwork::Factory.3 \
		Bio::PhyloNetwork::FactoryX.3 \
		Bio::PhyloNetwork::GraphViz.3 \
		Bio::PhyloNetwork::RandomFactory.3 \
		Bio::PhyloNetwork::TreeFactory.3 \
		Bio::PhyloNetwork::TreeFactoryMulti.3 \
		Bio::PhyloNetwork::TreeFactoryX.3 \
		Bio::PhyloNetwork::muVector.3 \
		Bio::PopGen::Genotype.3 \
		Bio::PopGen::GenotypeI.3 \
		Bio::PopGen::HtSNP.3 \
		Bio::PopGen::IO.3 \
		Bio::PopGen::IO::csv.3 \
		Bio::PopGen::IO::hapmap.3 \
		Bio::PopGen::IO::phase.3 \
		Bio::PopGen::IO::prettybase.3 \
		Bio::PopGen::Individual.3 \
		Bio::PopGen::IndividualI.3 \
		Bio::PopGen::Marker.3 \
		Bio::PopGen::MarkerI.3 \
		Bio::PopGen::PopStats.3 \
		Bio::PopGen::Population.3 \
		Bio::PopGen::PopulationI.3 \
		Bio::PopGen::Simulation::Coalescent.3 \
		Bio::PopGen::Simulation::GeneticDrift.3 \
		Bio::PopGen::Statistics.3 \
		Bio::PopGen::TagHaplotype.3 \
		Bio::PopGen::Utilities.3 \
		Bio::PrimarySeq.3 \
		Bio::PrimarySeqI.3 \
		Bio::PullParserI.3 \
		Bio::Range.3 \
		Bio::RangeI.3 \
		Bio::Restriction::Analysis.3 \
		Bio::Restriction::Enzyme.3 \
		Bio::Restriction::Enzyme::MultiCut.3 \
		Bio::Restriction::Enzyme::MultiSite.3 \
		Bio::Restriction::EnzymeCollection.3 \
		Bio::Restriction::EnzymeI.3 \
		Bio::Restriction::IO.3 \
		Bio::Restriction::IO::bairoch.3 \
		Bio::Restriction::IO::base.3 \
		Bio::Restriction::IO::itype2.3 \
		Bio::Restriction::IO::prototype.3 \
		Bio::Restriction::IO::withrefm.3 \
		Bio::Root::Build.3 \
		Bio::Root::Exception.3 \
		Bio::Root::HTTPget.3 \
		Bio::Root::IO.3 \
		Bio::Root::Root.3 \
		Bio::Root::RootI.3 \
		Bio::Root::Storable.3 \
		Bio::Root::Test.3 \
		Bio::Root::Test::Warn.3 \
		Bio::Root::Utilities.3 \
		Bio::Root::Version.3 \
		Bio::Search::BlastStatistics.3 \
		Bio::Search::BlastUtils.3 \
		Bio::Search::DatabaseI.3 \
		Bio::Search::GenericDatabase.3 \
		Bio::Search::GenericStatistics.3 \
		Bio::Search::HSP::BlastHSP.3 \
		Bio::Search::HSP::BlastPullHSP.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::HmmpfamHSP.3 \
		Bio::Search::HSP::ModelHSP.3 \
		Bio::Search::HSP::PSLHSP.3 \
		Bio::Search::HSP::PsiBlastHSP.3 \
		Bio::Search::HSP::PullHSPI.3 \
		Bio::Search::HSP::WABAHSP.3 \
		Bio::Search::Hit::BlastHit.3 \
		Bio::Search::Hit::BlastPullHit.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::Hit::HmmpfamHit.3 \
		Bio::Search::Hit::ModelHit.3 \
		Bio::Search::Hit::PsiBlastHit.3 \
		Bio::Search::Hit::PullHitI.3 \
		Bio::Search::Iteration::GenericIteration.3 \
		Bio::Search::Iteration::IterationI.3 \
		Bio::Search::Processor.3 \
		Bio::Search::Result::BlastPullResult.3 \
		Bio::Search::Result::BlastResult.3 \
		Bio::Search::Result::CrossMatchResult.3 \
		Bio::Search::Result::GenericResult.3 \
		Bio::Search::Result::HMMERResult.3 \
		Bio::Search::Result::HmmpfamResult.3 \
		Bio::Search::Result::PullResultI.3 \
		Bio::Search::Result::ResultFactory.3 \
		Bio::Search::Result::ResultI.3 \
		Bio::Search::Result::WABAResult.3 \
		Bio::Search::SearchUtils.3 \
		Bio::Search::StatisticsI.3 \
		Bio::Search::Tiling::MapTileUtils.3 \
		Bio::Search::Tiling::MapTiling.3 \
		Bio::Search::Tiling::TilingI.3 \
		Bio::SearchDist.3 \
		Bio::SearchIO.3 \
		Bio::SearchIO::EventHandlerI.3 \
		Bio::SearchIO::FastHitEventBuilder.3 \
		Bio::SearchIO::IteratedSearchResultEventBuilder.3 \
		Bio::SearchIO::SearchResultEventBuilder.3 \
		Bio::SearchIO::SearchWriterI.3 \
		Bio::SearchIO::Writer::BSMLResultWriter.3 \
		Bio::SearchIO::Writer::GbrowseGFF.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::XML::BlastHandler.3 \
		Bio::SearchIO::XML::PsiBlastHandler.3 \
		Bio::SearchIO::axt.3 \
		Bio::SearchIO::blast.3 \
		Bio::SearchIO::blast_pull.3 \
		Bio::SearchIO::blasttable.3 \
		Bio::SearchIO::blastxml.3 \
		Bio::SearchIO::cross_match.3 \
		Bio::SearchIO::erpin.3 \
		Bio::SearchIO::exonerate.3 \
		Bio::SearchIO::fasta.3 \
		Bio::SearchIO::hmmer.3 \
		Bio::SearchIO::hmmer_pull.3 \
		Bio::SearchIO::infernal.3 \
		Bio::SearchIO::gmap_f9.3 \
		Bio::SearchIO::megablast.3 \
		Bio::SearchIO::psl.3 \
		Bio::SearchIO::rnamotif.3 \
		Bio::SearchIO::sim4.3 \
		Bio::SearchIO::waba.3 \
		Bio::SearchIO::wise.3 \
		Bio::Seq.3 \
		Bio::Seq::BaseSeqProcessor.3 \
		Bio::Seq::EncodedSeq.3 \
		Bio::Seq::LargeLocatableSeq.3 \
		Bio::Seq::LargePrimarySeq.3 \
		Bio::Seq::LargeSeq.3 \
		Bio::Seq::LargeSeqI.3 \
		Bio::Seq::Meta.3 \
		Bio::Seq::Meta::Array.3 \
		Bio::Seq::MetaI.3 \
		Bio::Seq::PrimaryQual.3 \
		Bio::Seq::PrimedSeq.3 \
		Bio::Seq::QualI.3 \
		Bio::Seq::Quality.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::SeqEvolution::DNAPoint.3 \
		Bio::SeqEvolution::EvolutionI.3 \
		Bio::SeqEvolution::Factory.3 \
		Bio::SeqFeature::Annotated.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::Gene::UTR.3 \
		Bio::SeqFeature::Generic.3 \
		Bio::SeqFeature::Lite.3 \
		Bio::SeqFeature::PositionProxy.3 \
		Bio::SeqFeature::Primer.3 \
		Bio::SeqFeature::SiRNA::Oligo.3 \
		Bio::SeqFeature::SiRNA::Pair.3 \
		Bio::SeqFeature::Similarity.3 \
		Bio::SeqFeature::SimilarityPair.3 \
		Bio::SeqFeature::Tools::FeatureNamer.3 \
		Bio::SeqFeature::Tools::IDHandler.3 \
		Bio::SeqFeature::Tools::TypeMapper.3 \
		Bio::SeqFeature::Tools::Unflattener.3 \
		Bio::SeqFeature::TypedSeqFeatureI.3 \
		Bio::SeqFeatureI.3 \
		Bio::SeqI.3 \
		Bio::SeqIO.3 \
		Bio::SeqIO::FTHelper.3 \
		Bio::SeqIO::Handler::GenericRichSeqHandler.3 \
		Bio::SeqIO::MultiFile.3 \
		Bio::SeqIO::abi.3 \
		Bio::SeqIO::ace.3 \
		Bio::SeqIO::agave.3 \
		Bio::SeqIO::alf.3 \
		Bio::SeqIO::asciitree.3 \
		Bio::SeqIO::bsml.3 \
		Bio::SeqIO::bsml_sax.3 \
		Bio::SeqIO::chadoxml.3 \
		Bio::SeqIO::chaos.3 \
		Bio::SeqIO::chaosxml.3 \
		Bio::SeqIO::ctf.3 \
		Bio::SeqIO::embl.3 \
		Bio::SeqIO::embldriver.3 \
		Bio::SeqIO::entrezgene.3 \
		Bio::SeqIO::excel.3 \
		Bio::SeqIO::exp.3 \
		Bio::SeqIO::fasta.3 \
		Bio::SeqIO::fastq.3 \
		Bio::SeqIO::flybase_chadoxml.3 \
		Bio::SeqIO::game.3 \
		Bio::SeqIO::game::featHandler.3 \
		Bio::SeqIO::game::gameHandler.3 \
		Bio::SeqIO::game::gameSubs.3 \
		Bio::SeqIO::game::gameWriter.3 \
		Bio::SeqIO::game::seqHandler.3 \
		Bio::SeqIO::gbdriver.3 \
		Bio::SeqIO::gcg.3 \
		Bio::SeqIO::genbank.3 \
		Bio::SeqIO::interpro.3 \
		Bio::SeqIO::kegg.3 \
		Bio::SeqIO::largefasta.3 \
		Bio::SeqIO::lasergene.3 \
		Bio::SeqIO::locuslink.3 \
		Bio::SeqIO::metafasta.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::strider.3 \
		Bio::SeqIO::swiss.3 \
		Bio::SeqIO::swissdriver.3 \
		Bio::SeqIO::tab.3 \
		Bio::SeqIO::table.3 \
		Bio::SeqIO::tigr.3 \
		Bio::SeqIO::tigrxml.3 \
		Bio::SeqIO::tinyseq.3 \
		Bio::SeqIO::tinyseq::tinyseqHandler.3 \
		Bio::SeqIO::ztr.3 \
		Bio::SeqUtils.3 \
		Bio::SimpleAlign.3 \
		Bio::SimpleAnalysisI.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::Taxon.3 \
		Bio::Taxonomy.3 \
		Bio::Taxonomy::FactoryI.3 \
		Bio::Taxonomy::Node.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::Analysis::DNA::ESEfinder.3 \
		Bio::Tools::Analysis::Protein::Domcut.3 \
		Bio::Tools::Analysis::Protein::ELM.3 \
		Bio::Tools::Analysis::Protein::GOR4.3 \
		Bio::Tools::Analysis::Protein::HNN.3 \
		Bio::Tools::Analysis::Protein::Mitoprot.3 \
		Bio::Tools::Analysis::Protein::NetPhos.3 \
		Bio::Tools::Analysis::Protein::Scansite.3 \
		Bio::Tools::Analysis::Protein::Sopma.3 \
		Bio::Tools::Analysis::SimpleAnalysisBase.3 \
		Bio::Tools::AnalysisResult.3 \
		Bio::Tools::Blat.3 \
		Bio::Tools::CodonTable.3 \
		Bio::Tools::Coil.3 \
		Bio::Tools::ECnumber.3 \
		Bio::Tools::EMBOSS::Palindrome.3 \
		Bio::Tools::EPCR.3 \
		Bio::Tools::ERPIN.3 \
		Bio::Tools::ESTScan.3 \
		Bio::Tools::EUtilities.3 \
		Bio::Tools::EUtilities::Cookie.3 \
		Bio::Tools::EUtilities::EUtilDataI.3 \
		Bio::Tools::EUtilities::EUtilParameters.3 \
		Bio::Tools::EUtilities::History.3 \
		Bio::Tools::EUtilities::HistoryI.3 \
		Bio::Tools::EUtilities::Info.3 \
		Bio::Tools::EUtilities::Info::FieldInfo.3 \
		Bio::Tools::EUtilities::Info::LinkInfo.3 \
		Bio::Tools::EUtilities::Link.3 \
		Bio::Tools::EUtilities::Link::LinkSet.3 \
		Bio::Tools::EUtilities::Link::UrlLink.3 \
		Bio::Tools::EUtilities::Query.3 \
		Bio::Tools::EUtilities::Query::GlobalQuery.3 \
		Bio::Tools::EUtilities::Summary.3 \
		Bio::Tools::EUtilities::Summary::DocSum.3 \
		Bio::Tools::EUtilities::Summary::Item.3 \
		Bio::Tools::EUtilities::Summary::ItemContainerI.3 \
		Bio::Tools::Eponine.3 \
		Bio::Tools::Est2Genome.3 \
		Bio::Tools::Fgenesh.3 \
		Bio::Tools::FootPrinter.3 \
		Bio::Tools::GFF.3 \
		Bio::Tools::Gel.3 \
		Bio::Tools::Geneid.3 \
		Bio::Tools::Genemark.3 \
		Bio::Tools::Genewise.3 \
		Bio::Tools::Genomewise.3 \
		Bio::Tools::Genscan.3 \
		Bio::Tools::Glimmer.3 \
		Bio::Tools::Grail.3 \
		Bio::Tools::GuessSeqFormat.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::Infernal.3 \
		Bio::Tools::Lucy.3 \
		Bio::Tools::MZEF.3 \
		Bio::Tools::Match.3 \
		Bio::Tools::OddCodes.3 \
		Bio::Tools::Phylo::Gerp.3 \
		Bio::Tools::Phylo::Gumby.3 \
		Bio::Tools::Phylo::Molphy.3 \
		Bio::Tools::Phylo::Molphy::Result.3 \
		Bio::Tools::Phylo::PAML.3 \
		Bio::Tools::Phylo::PAML::ModelResult.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::Primer::Assessor::Base.3 \
		Bio::Tools::Primer::AssessorI.3 \
		Bio::Tools::Primer::Feature.3 \
		Bio::Tools::Primer::Pair.3 \
		Bio::Tools::Prints.3 \
		Bio::Tools::Profile.3 \
		Bio::Tools::Promoterwise.3 \
		Bio::Tools::PrositeScan.3 \
		Bio::Tools::Protparam.3 \
		Bio::Tools::Pseudowise.3 \
		Bio::Tools::QRNA.3 \
		Bio::Tools::RNAMotif.3 \
		Bio::Tools::RandomDistFunctions.3 \
		Bio::Tools::RepeatMasker.3 \
		Bio::Tools::Run::GenericParameters.3 \
		Bio::Tools::Run::ParametersI.3 \
		Bio::Tools::Run::RemoteBlast.3 \
		Bio::Tools::Run::StandAloneBlast.3 \
		Bio::Tools::Run::StandAloneNCBIBlast.3 \
		Bio::Tools::Run::StandAloneWUBlast.3 \
		Bio::Tools::Run::WrapperBase.3 \
		Bio::Tools::Seg.3 \
		Bio::Tools::SeqPattern::Backtranslate.3 \
		Bio::Tools::SeqPattern.3 \
		Bio::Tools::SeqStats.3 \
		Bio::Tools::SeqWords.3 \
		Bio::Tools::SiRNA.3 \
		Bio::Tools::SiRNA::Ruleset::saigo.3 \
		Bio::Tools::SiRNA::Ruleset::tuschl.3 \
		Bio::Tools::Sigcleave.3 \
		Bio::Tools::Signalp.3 \
		Bio::Tools::Signalp::ExtendedSignalp.3 \
		Bio::Tools::Sim4::Exon.3 \
		Bio::Tools::Sim4::Results.3 \
		Bio::Tools::Spidey::Exon.3 \
		Bio::Tools::Spidey::Results.3 \
		Bio::Tools::TandemRepeatsFinder.3 \
		Bio::Tools::TargetP.3 \
		Bio::Tools::Tmhmm.3 \
		Bio::Tools::dpAlign.3 \
		Bio::Tools::ipcress.3 \
		Bio::Tools::isPcr.3 \
		Bio::Tools::pICalculator.3 \
		Bio::Tools::pSW.3 \
		Bio::Tools::tRNAscanSE.3 \
		Bio::Tree::AlleleNode.3 \
		Bio::Tree::AnnotatableNode.3 \
		Bio::Tree::Compatible.3 \
		Bio::Tree::DistanceFactory.3 \
		Bio::Tree::Draw::Cladogram.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::cluster.3 \
		Bio::TreeIO::lintree.3 \
		Bio::TreeIO::newick.3 \
		Bio::TreeIO::nexus.3 \
		Bio::TreeIO::nhx.3 \
		Bio::TreeIO::pag.3 \
		Bio::TreeIO::phyloxml.3 \
		Bio::TreeIO::svggraph.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 \
		Bio::WebAgent.3

# now install all extra stuff (docs, examples, scripts, models)
NO_STAGE=	yes

OPTIONS_DEFINE=	DOCS

.include <bsd.port.options.mk>

post-install:
	${MKDIR} ${STAGEDIR}${DATADIR}
	${CP} -R ${WRKSRC}/scripts ${WRKSRC}/models ${STAGEDIR}${DATADIR}
	${MKDIR} ${STAGEDIR}${EXAMPLESDIR}
	${CP} -R ${WRKSRC}/examples/* ${STAGEDIR}${EXAMPLESDIR}
.if ${PORT_OPTIONS:MDOCS}
	${MKDIR} ${STAGEDIR}${DOCSDIR}
.for doc in AUTHORS BUGS Changes DEPENDENCIES DEPRECATED INSTALL LICENSE MANIFEST README
	${INSTALL_MAN} ${WRKSRC}/${doc} ${STAGEDIR}${DOCSDIR}
.endfor
	${CP} -R ${WRKSRC}/doc ${STAGEDIR}${DOCSDIR}
.endif

.include <bsd.port.mk>

Lines 1-2 Link Here

(-)./distinfo (-2 / +2 lines)
1	SHA256 (BioPerl-1.6.1.tar.gz) = ac36dace2b4dd973567b02cce29158beac05fd672872ca8769e02bbddddc95a3	1	SHA256 (BioPerl-1.6.923.tar.gz) = 6f6ada4ebd51ad223662e4b1ddcccc37a4fb8c47f3ecbbf060e6844d361730cd
2	SIZE (BioPerl-1.6.1.tar.gz) = 10462526	2	SIZE (BioPerl-1.6.923.tar.gz) = 12562520




--- Bio/Root/Build.pm.orig	2009-09-30 00:33:53.000000000 +0800
+++ Bio/Root/Build.pm	2009-12-01 10:31:39.000000000 +0800
@@ -127,49 +127,9 @@
         }
     }
     closedir($scripts_dir);
-    my $question = $int_ok ? "Install [a]ll BioPerl scripts, [n]one, ".
-        "or choose groups [i]nteractively?" : "Install [a]ll BioPerl scripts ".
-        "or [n]one?";
-
-    my $prompt = $accept ? 'a' : $self->prompt($question, 'a');
-
-    if ($prompt =~ /^[aA]/) {
-        $self->log_info("  - will install all scripts\n");
-        $self->notes(chosen_scripts => 'all');
-    }
-    elsif ($prompt =~ /^[iI]/) {
-        $self->log_info("  - will install interactively:\n");
-
-        my @chosen_scripts;
-        foreach my $group_dir (@group_dirs) {
-            my $group = File::Basename::basename($group_dir);
-            print "    * group '$group' has:\n";
-
-            my @script_files = @{$self->rscan_dir($group_dir, qr/\.PLS$|\.pl$/)};
-            foreach my $script_file (@script_files) {
-                my $script = File::Basename::basename($script_file);
-                print "      $script\n";
-            }
-
-            my $result = $self->prompt("    Install scripts for group '$group'? [y]es [n]o [q]uit", 'n');
-            die if $result =~ /^[qQ]/;
-            if ($result =~ /^[yY]/) {

-                $self->log_info("      - will not install group '$group'\n");
-            }
-        }
 
-        my $chosen_scripts = @chosen_scripts ? join("|", @chosen_scripts) : 'none';
-
-        $self->notes(chosen_scripts => $chosen_scripts);
-    }
-    else {
-        $self->log_info("  - won't install any scripts\n");
-        $self->notes(chosen_scripts => 'none');
-    }
+    $self->log_info("  - willt install all scripts\n");
+    $self->notes(chosen_scripts => 'all');
 
     print "\n";
 }
@@ -1136,21 +1096,9 @@
@@ -1205,16 +1165,9 @@
 sub prompt_for_network {
     my ($self, $accept) = @_;
 
-    my $proceed = $accept ? 0 : $self->y_n("Do you want to run tests that require connection to servers across the internet\n(likely to cause some failures)? y/n", 'n');
-
-    if ($proceed) {
-        $self->notes('network' => 1);
-        $self->log_info("  - will run internet-requiring tests\n");
-        my $use_email = $self->y_n("Do you want to run tests requiring a valid email address? y/n",'n');
-        if ($use_email) {
-            my $address = $self->prompt("Enter email address:");
-            $self->notes(email => $address);
-        }
-    }
-    else {
-        $self->notes(network => 0);

+    $self->log_info("  - will not run internet-requiring tests\n");
 }
 
 # override the build script warnings flag




--- Build.PL.orig	2009-09-30 00:33:45.000000000 +0800
+++ Build.PL	2009-12-01 10:25:51.000000000 +0800
@@ -187,7 +187,6 @@
                            },
 
     build_requires      => {
-                            'CPAN'                      => 1.81,
                             'Module::Build'             => 0.2805,
                             'Test::Harness'             => 2.62,
                             'Test::Most'                => 0,
@@ -376,86 +375,8 @@
                            },
     recommends          => { # does what you would expect of recommends, except more informative output and generates optional_features in META.yml
                             'Ace'                       => '0/access of ACeDB database/Bio::DB::Ace,Bio::DB::GFF::Adaptor::ace',
@@ -234,86 +234,9 @@
 
 sub prompt_for_biodb {
     my $accept = shift;
-    my $proceed = $accept ? 0 : $build->y_n("Do you want to run the Bio::DB::GFF or ".
-                              "Bio::DB::SeqFeature::Store live database tests? ".
-                              "y/n", 'n');
-
-    if ($proceed) {
-        my @driver_choices;
-        foreach my $poss ('SQLite', 'mysql', 'Pg', 'Oracle') {

-                push(@driver_choices, $choice);
-            }
-        }
-
-        my $driver;
-        if (@driver_choices > 1) {
-            my ($default) = $driver_choices[0] =~ /\[(.)/;

-        elsif ($driver =~ /^[sS]/) {
-            $driver = 'SQLite';
-        }
-
-        my $test_db = $build->prompt("Which database should I use for testing the $driver driver?\n".
-                                     "This database should already be present but doesn't have to ".
-                                     "be preloaded for any schema", 'test');
-        my $test_host = $build->prompt("On which host is database '$test_db' running (hostname, ip address or host:port)", 'localhost');
-        my $test_user = $build->prompt("User name for connecting to database '$test_db'?", 'undef');
-        my $test_pass = $build->prompt("Password for connecting to database '$test_db'?", 'undef');
-
-        my $use_host = 1;
-        if ($test_host eq 'undef' || $test_host eq 'localhost') {
-            $use_host = 0;
-        }
-
-        my $test_dsn;
-        if ($driver eq 'Pg' || $driver eq 'SQLite') {
-            $test_dsn = "dbi:$driver:dbname=$test_db";

-        if ($use_host) {
-            $test_dsn .= ";host=$test_host";
-        }
-
-        $build->notes(dbd_driver => $driver);
-        $build->notes(test_db => $test_db);
-        $build->notes(test_host => $test_host);
-        $build->notes(test_user => $test_user eq 'undef' ? undef : $test_user);
-        $build->notes(test_pass => $test_pass eq 'undef' ? undef : $test_pass);
-        $build->notes(test_dsn => $test_dsn);
-
-        $build->log_info("  - will run tests with database driver '$driver' and these settings:\n",
-                        "    Database $test_db\n",
-                        "    Host     $test_host\n",

-    else {
-        $build->log_info("  - will not run the BioDBGFF or BioDBSeqFeature live database tests\n");
-    }
-
+    my $proceed = 0;
+    $build->log_info("  - will not run the BioDBGFF or BioDBSeqFeature live database tests\n");
     $build->log_info("\n");




bin/bp_aacomp.pl
bin/bp_biofetch_genbank_proxy.pl
bin/bp_bioflat_index.pl
bin/bp_biogetseq.pl
bin/bp_blast2tree.pl
bin/bp_bulk_load_gff.pl
bin/bp_chaos_plot.pl
bin/bp_classify_hits_kingdom.pl
bin/bp_composite_LD.pl
bin/bp_das_server.pl
bin/bp_dbsplit.pl
bin/bp_download_query_genbank.pl
bin/bp_extract_feature_seq.pl
bin/bp_fast_load_gff.pl
bin/bp_fastam9_to_table.pl
bin/bp_fetch.pl
bin/bp_filter_search.pl
bin/bp_flanks.pl
bin/bp_gccalc.pl
bin/bp_genbank2gff.pl
bin/bp_genbank2gff3.pl
bin/bp_generate_histogram.pl
bin/bp_heterogeneity_test.pl
bin/bp_hivq.pl
bin/bp_hmmer_to_table.pl
bin/bp_index.pl
bin/bp_load_gff.pl
bin/bp_local_taxonomydb_query.pl
bin/bp_make_mrna_protein.pl
bin/bp_mask_by_search.pl
bin/bp_meta_gff.pl
bin/bp_mrtrans.pl
bin/bp_mutate.pl
bin/bp_netinstall.pl
bin/bp_nexus2nh.pl
bin/bp_nrdb.pl
bin/bp_oligo_count.pl
bin/bp_pairwise_kaks.pl
bin/bp_parse_hmmsearch.pl
bin/bp_process_gadfly.pl
bin/bp_process_sgd.pl
bin/bp_process_wormbase.pl
bin/bp_query_entrez_taxa.pl
bin/bp_remote_blast.pl
bin/bp_revtrans-motif.pl
bin/bp_search2BSML.pl
bin/bp_search2alnblocks.pl
bin/bp_search2gff.pl
bin/bp_search2table.pl
bin/bp_search2tribe.pl
bin/bp_seq_length.pl
bin/bp_seqconvert.pl
bin/bp_seqcut.pl
bin/bp_seqfeature_delete.pl
bin/bp_seqfeature_gff3.pl
bin/bp_seqfeature_load.pl
bin/bp_seqpart.pl
bin/bp_seqret.pl
bin/bp_seqretsplit.pl
bin/bp_split_seq.pl
bin/bp_sreformat.pl
bin/bp_taxid4species.pl
bin/bp_taxonomy2tree.pl
bin/bp_translate_seq.pl
bin/bp_tree2pag.pl
bin/bp_unflatten_seq.pl
%%PERL5_MAN3%%/Bio::Align::AlignI.3.gz
%%PERL5_MAN3%%/Bio::Align::DNAStatistics.3.gz
%%PERL5_MAN3%%/Bio::Align::Graphics.3.gz
%%PERL5_MAN3%%/Bio::Align::PairwiseStatistics.3.gz
%%PERL5_MAN3%%/Bio::Align::ProteinStatistics.3.gz
%%PERL5_MAN3%%/Bio::Align::StatisticsI.3.gz
%%PERL5_MAN3%%/Bio::Align::Utilities.3.gz
%%PERL5_MAN3%%/Bio::AlignIO.3.gz
%%PERL5_MAN3%%/Bio::AlignIO::Handler::GenericAlignHandler.3.gz
%%PERL5_MAN3%%/Bio::AlignIO::arp.3.gz
%%PERL5_MAN3%%/Bio::AlignIO::bl2seq.3.gz
%%PERL5_MAN3%%/Bio::AlignIO::clustalw.3.gz
%%PERL5_MAN3%%/Bio::AlignIO::emboss.3.gz
%%PERL5_MAN3%%/Bio::AlignIO::fasta.3.gz
%%PERL5_MAN3%%/Bio::AlignIO::largemultifasta.3.gz
%%PERL5_MAN3%%/Bio::AlignIO::maf.3.gz
%%PERL5_MAN3%%/Bio::AlignIO::mase.3.gz
%%PERL5_MAN3%%/Bio::AlignIO::mega.3.gz
%%PERL5_MAN3%%/Bio::AlignIO::meme.3.gz
%%PERL5_MAN3%%/Bio::AlignIO::metafasta.3.gz
%%PERL5_MAN3%%/Bio::AlignIO::msf.3.gz
%%PERL5_MAN3%%/Bio::AlignIO::nexml.3.gz
%%PERL5_MAN3%%/Bio::AlignIO::nexus.3.gz
%%PERL5_MAN3%%/Bio::AlignIO::pfam.3.gz
%%PERL5_MAN3%%/Bio::AlignIO::phylip.3.gz
%%PERL5_MAN3%%/Bio::AlignIO::po.3.gz
%%PERL5_MAN3%%/Bio::AlignIO::proda.3.gz
%%PERL5_MAN3%%/Bio::AlignIO::prodom.3.gz
%%PERL5_MAN3%%/Bio::AlignIO::psi.3.gz
%%PERL5_MAN3%%/Bio::AlignIO::selex.3.gz
%%PERL5_MAN3%%/Bio::AlignIO::stockholm.3.gz
%%PERL5_MAN3%%/Bio::AlignIO::xmfa.3.gz
%%PERL5_MAN3%%/Bio::AnalysisI.3.gz
%%PERL5_MAN3%%/Bio::AnalysisParserI.3.gz
%%PERL5_MAN3%%/Bio::AnalysisResultI.3.gz
%%PERL5_MAN3%%/Bio::AnnotatableI.3.gz
%%PERL5_MAN3%%/Bio::Annotation::AnnotationFactory.3.gz
%%PERL5_MAN3%%/Bio::Annotation::Collection.3.gz
%%PERL5_MAN3%%/Bio::Annotation::Comment.3.gz
%%PERL5_MAN3%%/Bio::Annotation::DBLink.3.gz
%%PERL5_MAN3%%/Bio::Annotation::OntologyTerm.3.gz
%%PERL5_MAN3%%/Bio::Annotation::Reference.3.gz
%%PERL5_MAN3%%/Bio::Annotation::Relation.3.gz
%%PERL5_MAN3%%/Bio::Annotation::SimpleValue.3.gz
%%PERL5_MAN3%%/Bio::Annotation::StructuredValue.3.gz
%%PERL5_MAN3%%/Bio::Annotation::TagTree.3.gz
%%PERL5_MAN3%%/Bio::Annotation::Target.3.gz
%%PERL5_MAN3%%/Bio::Annotation::Tree.3.gz
%%PERL5_MAN3%%/Bio::Annotation::TypeManager.3.gz
%%PERL5_MAN3%%/Bio::AnnotationCollectionI.3.gz
%%PERL5_MAN3%%/Bio::AnnotationI.3.gz
%%PERL5_MAN3%%/Bio::Assembly::Contig.3.gz
%%PERL5_MAN3%%/Bio::Assembly::ContigAnalysis.3.gz
%%PERL5_MAN3%%/Bio::Assembly::IO.3.gz
%%PERL5_MAN3%%/Bio::Assembly::IO::ace.3.gz
%%PERL5_MAN3%%/Bio::Assembly::IO::bowtie.3.gz
%%PERL5_MAN3%%/Bio::Assembly::IO::maq.3.gz
%%PERL5_MAN3%%/Bio::Assembly::IO::phrap.3.gz
%%PERL5_MAN3%%/Bio::Assembly::IO::sam.3.gz
%%PERL5_MAN3%%/Bio::Assembly::IO::tigr.3.gz
%%PERL5_MAN3%%/Bio::Assembly::Scaffold.3.gz
%%PERL5_MAN3%%/Bio::Assembly::ScaffoldI.3.gz
%%PERL5_MAN3%%/Bio::Assembly::Singlet.3.gz
%%PERL5_MAN3%%/Bio::Assembly::Tools::ContigSpectrum.3.gz
%%PERL5_MAN3%%/Bio::Cluster::ClusterFactory.3.gz
%%PERL5_MAN3%%/Bio::Cluster::FamilyI.3.gz
%%PERL5_MAN3%%/Bio::Cluster::SequenceFamily.3.gz
%%PERL5_MAN3%%/Bio::Cluster::UniGene.3.gz
%%PERL5_MAN3%%/Bio::Cluster::UniGeneI.3.gz
%%PERL5_MAN3%%/Bio::ClusterI.3.gz
%%PERL5_MAN3%%/Bio::ClusterIO.3.gz
%%PERL5_MAN3%%/Bio::ClusterIO::dbsnp.3.gz
%%PERL5_MAN3%%/Bio::ClusterIO::unigene.3.gz
%%PERL5_MAN3%%/Bio::CodonUsage::IO.3.gz
%%PERL5_MAN3%%/Bio::CodonUsage::Table.3.gz
%%PERL5_MAN3%%/Bio::Coordinate::Chain.3.gz
%%PERL5_MAN3%%/Bio::Coordinate::Collection.3.gz
%%PERL5_MAN3%%/Bio::Coordinate::ExtrapolatingPair.3.gz
%%PERL5_MAN3%%/Bio::Coordinate::GeneMapper.3.gz
%%PERL5_MAN3%%/Bio::Coordinate::Graph.3.gz
%%PERL5_MAN3%%/Bio::Coordinate::MapperI.3.gz
%%PERL5_MAN3%%/Bio::Coordinate::Pair.3.gz
%%PERL5_MAN3%%/Bio::Coordinate::Result.3.gz
%%PERL5_MAN3%%/Bio::Coordinate::Result::Gap.3.gz
%%PERL5_MAN3%%/Bio::Coordinate::Result::Match.3.gz
%%PERL5_MAN3%%/Bio::Coordinate::ResultI.3.gz
%%PERL5_MAN3%%/Bio::Coordinate::Utils.3.gz
%%PERL5_MAN3%%/Bio::DB::Ace.3.gz
%%PERL5_MAN3%%/Bio::DB::BioFetch.3.gz
%%PERL5_MAN3%%/Bio::DB::CUTG.3.gz
%%PERL5_MAN3%%/Bio::DB::DBFetch.3.gz
%%PERL5_MAN3%%/Bio::DB::EMBL.3.gz
%%PERL5_MAN3%%/Bio::DB::EntrezGene.3.gz
%%PERL5_MAN3%%/Bio::DB::Expression.3.gz
%%PERL5_MAN3%%/Bio::DB::Expression::geo.3.gz
%%PERL5_MAN3%%/Bio::DB::Failover.3.gz
%%PERL5_MAN3%%/Bio::DB::Fasta.3.gz
%%PERL5_MAN3%%/Bio::DB::FileCache.3.gz
%%PERL5_MAN3%%/Bio::DB::Flat.3.gz
%%PERL5_MAN3%%/Bio::DB::Flat::BDB.3.gz
%%PERL5_MAN3%%/Bio::DB::Flat::BDB::embl.3.gz
%%PERL5_MAN3%%/Bio::DB::Flat::BDB::fasta.3.gz
%%PERL5_MAN3%%/Bio::DB::Flat::BDB::genbank.3.gz
%%PERL5_MAN3%%/Bio::DB::Flat::BDB::swiss.3.gz
%%PERL5_MAN3%%/Bio::DB::Flat::BinarySearch.3.gz
%%PERL5_MAN3%%/Bio::DB::GFF.3.gz
%%PERL5_MAN3%%/Bio::DB::GFF::Adaptor::ace.3.gz
%%PERL5_MAN3%%/Bio::DB::GFF::Adaptor::berkeleydb.3.gz
%%PERL5_MAN3%%/Bio::DB::GFF::Adaptor::berkeleydb::iterator.3.gz
%%PERL5_MAN3%%/Bio::DB::GFF::Adaptor::biofetch.3.gz
%%PERL5_MAN3%%/Bio::DB::GFF::Adaptor::biofetch_oracle.3.gz
%%PERL5_MAN3%%/Bio::DB::GFF::Adaptor::dbi.3.gz
%%PERL5_MAN3%%/Bio::DB::GFF::Adaptor::dbi::caching_handle.3.gz
%%PERL5_MAN3%%/Bio::DB::GFF::Adaptor::dbi::iterator.3.gz
%%PERL5_MAN3%%/Bio::DB::GFF::Adaptor::dbi::mysql.3.gz
%%PERL5_MAN3%%/Bio::DB::GFF::Adaptor::dbi::mysqlace.3.gz
%%PERL5_MAN3%%/Bio::DB::GFF::Adaptor::dbi::mysqlcmap.3.gz
%%PERL5_MAN3%%/Bio::DB::GFF::Adaptor::dbi::mysqlopt.3.gz
%%PERL5_MAN3%%/Bio::DB::GFF::Adaptor::dbi::oracle.3.gz
%%PERL5_MAN3%%/Bio::DB::GFF::Adaptor::dbi::oracleace.3.gz
%%PERL5_MAN3%%/Bio::DB::GFF::Adaptor::dbi::pg.3.gz
%%PERL5_MAN3%%/Bio::DB::GFF::Adaptor::dbi::pg_fts.3.gz
%%PERL5_MAN3%%/Bio::DB::GFF::Adaptor::memory.3.gz
%%PERL5_MAN3%%/Bio::DB::GFF::Adaptor::memory::feature_serializer.3.gz
%%PERL5_MAN3%%/Bio::DB::GFF::Adaptor::memory::iterator.3.gz
%%PERL5_MAN3%%/Bio::DB::GFF::Aggregator.3.gz
%%PERL5_MAN3%%/Bio::DB::GFF::Aggregator::alignment.3.gz
%%PERL5_MAN3%%/Bio::DB::GFF::Aggregator::clone.3.gz
%%PERL5_MAN3%%/Bio::DB::GFF::Aggregator::coding.3.gz
%%PERL5_MAN3%%/Bio::DB::GFF::Aggregator::gene.3.gz
%%PERL5_MAN3%%/Bio::DB::GFF::Aggregator::match.3.gz
%%PERL5_MAN3%%/Bio::DB::GFF::Aggregator::none.3.gz
%%PERL5_MAN3%%/Bio::DB::GFF::Aggregator::orf.3.gz
%%PERL5_MAN3%%/Bio::DB::GFF::Aggregator::processed_transcript.3.gz
%%PERL5_MAN3%%/Bio::DB::GFF::Aggregator::so_transcript.3.gz
%%PERL5_MAN3%%/Bio::DB::GFF::Aggregator::transcript.3.gz
%%PERL5_MAN3%%/Bio::DB::GFF::Aggregator::ucsc_acembly.3.gz
%%PERL5_MAN3%%/Bio::DB::GFF::Aggregator::ucsc_ensgene.3.gz
%%PERL5_MAN3%%/Bio::DB::GFF::Aggregator::ucsc_genscan.3.gz
%%PERL5_MAN3%%/Bio::DB::GFF::Aggregator::ucsc_refgene.3.gz
%%PERL5_MAN3%%/Bio::DB::GFF::Aggregator::ucsc_sanger22.3.gz
%%PERL5_MAN3%%/Bio::DB::GFF::Aggregator::ucsc_sanger22pseudo.3.gz
%%PERL5_MAN3%%/Bio::DB::GFF::Aggregator::ucsc_softberry.3.gz
%%PERL5_MAN3%%/Bio::DB::GFF::Aggregator::ucsc_twinscan.3.gz
%%PERL5_MAN3%%/Bio::DB::GFF::Aggregator::ucsc_unigene.3.gz
%%PERL5_MAN3%%/Bio::DB::GFF::Featname.3.gz
%%PERL5_MAN3%%/Bio::DB::GFF::Feature.3.gz
%%PERL5_MAN3%%/Bio::DB::GFF::Homol.3.gz
%%PERL5_MAN3%%/Bio::DB::GFF::RelSegment.3.gz
%%PERL5_MAN3%%/Bio::DB::GFF::Segment.3.gz
%%PERL5_MAN3%%/Bio::DB::GFF::Typename.3.gz
%%PERL5_MAN3%%/Bio::DB::GFF::Util::Binning.3.gz
%%PERL5_MAN3%%/Bio::DB::GFF::Util::Rearrange.3.gz
%%PERL5_MAN3%%/Bio::DB::GenBank.3.gz
%%PERL5_MAN3%%/Bio::DB::GenPept.3.gz
%%PERL5_MAN3%%/Bio::DB::GenericWebAgent.3.gz
%%PERL5_MAN3%%/Bio::DB::HIV.3.gz
%%PERL5_MAN3%%/Bio::DB::HIV::HIVAnnotProcessor.3.gz
%%PERL5_MAN3%%/Bio::DB::HIV::HIVQueryHelper.3.gz
%%PERL5_MAN3%%/Bio::DB::InMemoryCache.3.gz
%%PERL5_MAN3%%/Bio::DB::IndexedBase.3.gz
%%PERL5_MAN3%%/Bio::DB::LocationI.3.gz
%%PERL5_MAN3%%/Bio::DB::MeSH.3.gz
%%PERL5_MAN3%%/Bio::DB::NCBIHelper.3.gz
%%PERL5_MAN3%%/Bio::DB::Qual.3.gz
%%PERL5_MAN3%%/Bio::DB::Query::GenBank.3.gz
%%PERL5_MAN3%%/Bio::DB::Query::HIVQuery.3.gz
%%PERL5_MAN3%%/Bio::DB::Query::WebQuery.3.gz
%%PERL5_MAN3%%/Bio::DB::QueryI.3.gz
%%PERL5_MAN3%%/Bio::DB::RandomAccessI.3.gz
%%PERL5_MAN3%%/Bio::DB::RefSeq.3.gz
%%PERL5_MAN3%%/Bio::DB::ReferenceI.3.gz
%%PERL5_MAN3%%/Bio::DB::Registry.3.gz
%%PERL5_MAN3%%/Bio::DB::SeqFeature.3.gz
%%PERL5_MAN3%%/Bio::DB::SeqFeature::NormalizedFeature.3.gz
%%PERL5_MAN3%%/Bio::DB::SeqFeature::NormalizedFeatureI.3.gz
%%PERL5_MAN3%%/Bio::DB::SeqFeature::NormalizedTableFeatureI.3.gz
%%PERL5_MAN3%%/Bio::DB::SeqFeature::Segment.3.gz
%%PERL5_MAN3%%/Bio::DB::SeqFeature::Store.3.gz
%%PERL5_MAN3%%/Bio::DB::SeqFeature::Store::DBI::Iterator.3.gz
%%PERL5_MAN3%%/Bio::DB::SeqFeature::Store::DBI::Pg.3.gz
%%PERL5_MAN3%%/Bio::DB::SeqFeature::Store::DBI::SQLite.3.gz
%%PERL5_MAN3%%/Bio::DB::SeqFeature::Store::DBI::mysql.3.gz
%%PERL5_MAN3%%/Bio::DB::SeqFeature::Store::FeatureFileLoader.3.gz
%%PERL5_MAN3%%/Bio::DB::SeqFeature::Store::GFF2Loader.3.gz
%%PERL5_MAN3%%/Bio::DB::SeqFeature::Store::GFF3Loader.3.gz
%%PERL5_MAN3%%/Bio::DB::SeqFeature::Store::LoadHelper.3.gz
%%PERL5_MAN3%%/Bio::DB::SeqFeature::Store::Loader.3.gz
%%PERL5_MAN3%%/Bio::DB::SeqFeature::Store::bdb.3.gz
%%PERL5_MAN3%%/Bio::DB::SeqFeature::Store::berkeleydb.3.gz
%%PERL5_MAN3%%/Bio::DB::SeqFeature::Store::berkeleydb3.3.gz
%%PERL5_MAN3%%/Bio::DB::SeqFeature::Store::memory.3.gz
%%PERL5_MAN3%%/Bio::DB::SeqHound.3.gz
%%PERL5_MAN3%%/Bio::DB::SeqI.3.gz
%%PERL5_MAN3%%/Bio::DB::SeqVersion.3.gz
%%PERL5_MAN3%%/Bio::DB::SeqVersion::gi.3.gz
%%PERL5_MAN3%%/Bio::DB::SwissProt.3.gz
%%PERL5_MAN3%%/Bio::DB::TFBS.3.gz
%%PERL5_MAN3%%/Bio::DB::TFBS::transfac_pro.3.gz
%%PERL5_MAN3%%/Bio::DB::Taxonomy.3.gz
%%PERL5_MAN3%%/Bio::DB::Taxonomy::entrez.3.gz
%%PERL5_MAN3%%/Bio::DB::Taxonomy::flatfile.3.gz
%%PERL5_MAN3%%/Bio::DB::Taxonomy::greengenes.3.gz
%%PERL5_MAN3%%/Bio::DB::Taxonomy::list.3.gz
%%PERL5_MAN3%%/Bio::DB::Taxonomy::silva.3.gz
%%PERL5_MAN3%%/Bio::DB::Universal.3.gz
%%PERL5_MAN3%%/Bio::DB::UpdateableSeqI.3.gz
%%PERL5_MAN3%%/Bio::DB::WebDBSeqI.3.gz
%%PERL5_MAN3%%/Bio::DBLinkContainerI.3.gz
%%PERL5_MAN3%%/Bio::Das::FeatureTypeI.3.gz
%%PERL5_MAN3%%/Bio::Das::SegmentI.3.gz
%%PERL5_MAN3%%/Bio::DasI.3.gz
%%PERL5_MAN3%%/Bio::DescribableI.3.gz
%%PERL5_MAN3%%/Bio::Draw::Pictogram.3.gz
%%PERL5_MAN3%%/Bio::Event::EventGeneratorI.3.gz
%%PERL5_MAN3%%/Bio::Event::EventHandlerI.3.gz
%%PERL5_MAN3%%/Bio::Factory::AnalysisI.3.gz
%%PERL5_MAN3%%/Bio::Factory::ApplicationFactoryI.3.gz
%%PERL5_MAN3%%/Bio::Factory::DriverFactory.3.gz
%%PERL5_MAN3%%/Bio::Factory::FTLocationFactory.3.gz
%%PERL5_MAN3%%/Bio::Factory::LocationFactoryI.3.gz
%%PERL5_MAN3%%/Bio::Factory::MapFactoryI.3.gz
%%PERL5_MAN3%%/Bio::Factory::ObjectBuilderI.3.gz
%%PERL5_MAN3%%/Bio::Factory::ObjectFactory.3.gz
%%PERL5_MAN3%%/Bio::Factory::ObjectFactoryI.3.gz
%%PERL5_MAN3%%/Bio::Factory::SeqAnalysisParserFactory.3.gz
%%PERL5_MAN3%%/Bio::Factory::SeqAnalysisParserFactoryI.3.gz
%%PERL5_MAN3%%/Bio::Factory::SequenceFactoryI.3.gz
%%PERL5_MAN3%%/Bio::Factory::SequenceProcessorI.3.gz
%%PERL5_MAN3%%/Bio::Factory::SequenceStreamI.3.gz
%%PERL5_MAN3%%/Bio::Factory::TreeFactoryI.3.gz
%%PERL5_MAN3%%/Bio::FeatureHolderI.3.gz
%%PERL5_MAN3%%/Bio::HandlerBaseI.3.gz
%%PERL5_MAN3%%/Bio::IdCollectionI.3.gz
%%PERL5_MAN3%%/Bio::IdentifiableI.3.gz
%%PERL5_MAN3%%/Bio::Index::Abstract.3.gz
%%PERL5_MAN3%%/Bio::Index::AbstractSeq.3.gz
%%PERL5_MAN3%%/Bio::Index::Blast.3.gz
%%PERL5_MAN3%%/Bio::Index::BlastTable.3.gz
%%PERL5_MAN3%%/Bio::Index::EMBL.3.gz
%%PERL5_MAN3%%/Bio::Index::Fasta.3.gz
%%PERL5_MAN3%%/Bio::Index::Fastq.3.gz
%%PERL5_MAN3%%/Bio::Index::GenBank.3.gz
%%PERL5_MAN3%%/Bio::Index::Hmmer.3.gz
%%PERL5_MAN3%%/Bio::Index::Qual.3.gz
%%PERL5_MAN3%%/Bio::Index::Stockholm.3.gz
%%PERL5_MAN3%%/Bio::Index::SwissPfam.3.gz
%%PERL5_MAN3%%/Bio::Index::Swissprot.3.gz
%%PERL5_MAN3%%/Bio::LiveSeq::AARange.3.gz
%%PERL5_MAN3%%/Bio::LiveSeq::Chain.3.gz
%%PERL5_MAN3%%/Bio::LiveSeq::ChainI.3.gz
%%PERL5_MAN3%%/Bio::LiveSeq::DNA.3.gz
%%PERL5_MAN3%%/Bio::LiveSeq::Exon.3.gz
%%PERL5_MAN3%%/Bio::LiveSeq::Gene.3.gz
%%PERL5_MAN3%%/Bio::LiveSeq::IO::BioPerl.3.gz
%%PERL5_MAN3%%/Bio::LiveSeq::IO::Loader.3.gz
%%PERL5_MAN3%%/Bio::LiveSeq::Intron.3.gz
%%PERL5_MAN3%%/Bio::LiveSeq::Mutation.3.gz
%%PERL5_MAN3%%/Bio::LiveSeq::Mutator.3.gz
%%PERL5_MAN3%%/Bio::LiveSeq::Prim_Transcript.3.gz
%%PERL5_MAN3%%/Bio::LiveSeq::Range.3.gz
%%PERL5_MAN3%%/Bio::LiveSeq::Repeat_Region.3.gz
%%PERL5_MAN3%%/Bio::LiveSeq::Repeat_Unit.3.gz
%%PERL5_MAN3%%/Bio::LiveSeq::SeqI.3.gz
%%PERL5_MAN3%%/Bio::LiveSeq::Transcript.3.gz
%%PERL5_MAN3%%/Bio::LiveSeq::Translation.3.gz
%%PERL5_MAN3%%/Bio::LocatableSeq.3.gz
%%PERL5_MAN3%%/Bio::Location::Atomic.3.gz
%%PERL5_MAN3%%/Bio::Location::AvWithinCoordPolicy.3.gz
%%PERL5_MAN3%%/Bio::Location::CoordinatePolicyI.3.gz
%%PERL5_MAN3%%/Bio::Location::Fuzzy.3.gz
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man/man1/bp_aacomp.pl.1.gz
man/man1/bp_biofetch_genbank_proxy.pl.1.gz
man/man1/bp_bioflat_index.pl.1.gz
man/man1/bp_biogetseq.pl.1.gz
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man/man1/bp_genbank2gff.pl.1.gz
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man/man1/bp_hivq.pl.1.gz
man/man1/bp_hmmer_to_table.pl.1.gz
man/man1/bp_index.pl.1.gz
man/man1/bp_load_gff.pl.1.gz
man/man1/bp_local_taxonomydb_query.pl.1.gz
man/man1/bp_make_mrna_protein.pl.1.gz
man/man1/bp_mask_by_search.pl.1.gz
man/man1/bp_meta_gff.pl.1.gz
man/man1/bp_mrtrans.pl.1.gz
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man/man1/bp_nexus2nh.pl.1.gz
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man/man1/bp_oligo_count.pl.1.gz
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man/man1/bp_process_gadfly.pl.1.gz
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man/man1/bp_process_wormbase.pl.1.gz
man/man1/bp_query_entrez_taxa.pl.1.gz
man/man1/bp_remote_blast.pl.1.gz
man/man1/bp_revtrans-motif.pl.1.gz
man/man1/bp_search2BSML.pl.1.gz
man/man1/bp_search2alnblocks.pl.1.gz
man/man1/bp_search2gff.pl.1.gz
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man/man1/bp_seq_length.pl.1.gz
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%%DATADIR%%/models/README
%%DATADIR%%/models/biblio.dia
%%DATADIR%%/models/bio_liveseq_variation.dia
%%DATADIR%%/models/bio_map.dia
%%DATADIR%%/models/bio_restriction.dia
%%DATADIR%%/models/bioperl.dia
%%DATADIR%%/models/coordinatemapper.dia
%%DATADIR%%/models/map_proposal.txt
%%DATADIR%%/models/maps_and_markers.dia
%%DATADIR%%/models/popgen.dia
%%DATADIR%%/models/population_proposal.txt
%%DATADIR%%/scripts/Bio-DB-GFF/README
%%DATADIR%%/scripts/Bio-DB-GFF/bp_bulk_load_gff.pl
%%DATADIR%%/scripts/Bio-DB-GFF/bp_fast_load_gff.pl
%%DATADIR%%/scripts/Bio-DB-GFF/bp_genbank2gff.pl
%%DATADIR%%/scripts/Bio-DB-GFF/bp_genbank2gff3.pl
%%DATADIR%%/scripts/Bio-DB-GFF/bp_generate_histogram.pl
%%DATADIR%%/scripts/Bio-DB-GFF/bp_load_gff.pl
%%DATADIR%%/scripts/Bio-DB-GFF/bp_meta_gff.pl
%%DATADIR%%/scripts/Bio-DB-GFF/bp_process_gadfly.pl
%%DATADIR%%/scripts/Bio-DB-GFF/bp_process_sgd.pl
%%DATADIR%%/scripts/Bio-DB-GFF/bp_process_wormbase.pl
%%DATADIR%%/scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_delete.pl
%%DATADIR%%/scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_gff3.pl
%%DATADIR%%/scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_load.pl
%%DATADIR%%/scripts/DB-HIV/bp_hivq.pl
%%DATADIR%%/scripts/DB/TAG
%%DATADIR%%/scripts/DB/bp_biofetch_genbank_proxy.pl
%%DATADIR%%/scripts/DB/bp_bioflat_index.pl
%%DATADIR%%/scripts/DB/bp_biogetseq.pl
%%DATADIR%%/scripts/DB/bp_flanks.pl
%%DATADIR%%/scripts/README
%%DATADIR%%/scripts/das/README
%%DATADIR%%/scripts/das/TAG
%%DATADIR%%/scripts/das/bp_das_server.pl
%%DATADIR%%/scripts/index/TAG
%%DATADIR%%/scripts/index/bp_fetch.pl
%%DATADIR%%/scripts/index/bp_index.pl
%%DATADIR%%/scripts/index/bp_seqret.pl
%%DATADIR%%/scripts/popgen/bp_composite_LD.pl
%%DATADIR%%/scripts/popgen/bp_heterogeneity_test.pl
%%DATADIR%%/scripts/searchio/README
%%DATADIR%%/scripts/searchio/TAG
%%DATADIR%%/scripts/searchio/bp_fastam9_to_table.pl
%%DATADIR%%/scripts/searchio/bp_filter_search.pl
%%DATADIR%%/scripts/searchio/bp_hmmer_to_table.pl
%%DATADIR%%/scripts/searchio/bp_parse_hmmsearch.pl
%%DATADIR%%/scripts/searchio/bp_search2table.pl
%%DATADIR%%/scripts/seq/TAG
%%DATADIR%%/scripts/seq/bp_extract_feature_seq.pl
%%DATADIR%%/scripts/seq/bp_make_mrna_protein.pl
%%DATADIR%%/scripts/seq/bp_seqconvert.pl
%%DATADIR%%/scripts/seq/bp_seqcut.pl
%%DATADIR%%/scripts/seq/bp_seqpart.pl
%%DATADIR%%/scripts/seq/bp_seqretsplit.pl
%%DATADIR%%/scripts/seq/bp_split_seq.pl
%%DATADIR%%/scripts/seq/bp_translate_seq.pl
%%DATADIR%%/scripts/seq/bp_unflatten_seq.pl
%%DATADIR%%/scripts/seqstats/TAG
%%DATADIR%%/scripts/seqstats/bp_aacomp.pl
%%DATADIR%%/scripts/seqstats/bp_chaos_plot.pl
%%DATADIR%%/scripts/seqstats/bp_gccalc.pl
%%DATADIR%%/scripts/seqstats/bp_oligo_count.pl
%%DATADIR%%/scripts/taxa/TAG
%%DATADIR%%/scripts/taxa/bp_classify_hits_kingdom.pl
%%DATADIR%%/scripts/taxa/bp_local_taxonomydb_query.pl
%%DATADIR%%/scripts/taxa/bp_query_entrez_taxa.pl
%%DATADIR%%/scripts/taxa/bp_taxid4species.pl
%%DATADIR%%/scripts/taxa/bp_taxonomy2tree.pl
%%DATADIR%%/scripts/tree/TAG
%%DATADIR%%/scripts/tree/bp_blast2tree.pl
%%DATADIR%%/scripts/tree/bp_nexus2nh.pl
%%DATADIR%%/scripts/tree/bp_tree2pag.pl
%%DATADIR%%/scripts/utilities/README
%%DATADIR%%/scripts/utilities/TAG
%%DATADIR%%/scripts/utilities/bp_dbsplit.pl
%%DATADIR%%/scripts/utilities/bp_download_query_genbank.pl
%%DATADIR%%/scripts/utilities/bp_mask_by_search.pl
%%DATADIR%%/scripts/utilities/bp_mrtrans.pl
%%DATADIR%%/scripts/utilities/bp_mutate.pl
%%DATADIR%%/scripts/utilities/bp_netinstall.pl
%%DATADIR%%/scripts/utilities/bp_nrdb.pl
%%DATADIR%%/scripts/utilities/bp_pairwise_kaks.pl
%%DATADIR%%/scripts/utilities/bp_remote_blast.pl
%%DATADIR%%/scripts/utilities/bp_revtrans-motif.pl
%%DATADIR%%/scripts/utilities/bp_search2BSML.pl
%%DATADIR%%/scripts/utilities/bp_search2alnblocks.pl
%%DATADIR%%/scripts/utilities/bp_search2gff.pl
%%DATADIR%%/scripts/utilities/bp_search2tribe.pl
%%DATADIR%%/scripts/utilities/bp_seq_length.pl
%%DATADIR%%/scripts/utilities/bp_sreformat.pl
%%PORTDOCS%%%%DOCSDIR%%/AUTHORS
%%PORTDOCS%%%%DOCSDIR%%/BUGS
%%PORTDOCS%%%%DOCSDIR%%/Changes
%%PORTDOCS%%%%DOCSDIR%%/DEPENDENCIES
%%PORTDOCS%%%%DOCSDIR%%/DEPRECATED
%%PORTDOCS%%%%DOCSDIR%%/INSTALL
%%PORTDOCS%%%%DOCSDIR%%/LICENSE
%%PORTDOCS%%%%DOCSDIR%%/MANIFEST
%%PORTDOCS%%%%DOCSDIR%%/README
%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/Build.PL
%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/Changes
%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/LICENSE
%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/MANIFEST
%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/META.yml
%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/Makefile.PL
%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/README
%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/bin/deob_index.pl
%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/bin/run-deobfuscator-update.pl
%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/cgi-bin/deob_detail.cgi
%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/cgi-bin/deob_flowchart.png
%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/cgi-bin/deob_help.html
%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/cgi-bin/deob_interface.cgi
%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/excluded_modules.txt
%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/lib/Deobfuscator.pm
%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/t/00.load.t
%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/t/pod.t
%%PORTDOCS%%%%DOCSDIR%%/doc/README
%%PORTDOCS%%%%DOCSDIR%%/doc/makedoc.PL
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Bio-DB-GFF/load_ucsc.pl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/align/FastAlign.pl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/align/align_on_codons.pl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/align/aligntutorial.pl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/align/clustalw.pl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/align/simplealign.pl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bioperl.pl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cluster/dbsnp.pl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/contributed/nmrpdb_parse.pl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/contributed/prosite2perl.pl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/contributed/rebase2list.pl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/db/dbfetch
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/db/est_tissue_query.pl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/db/gb2features.pl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/db/getGenBank.pl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/db/get_seqs.pl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/db/rfetch.pl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/db/use_registry.pl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/generate_random_seq.pl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/liveseq/change_gene.pl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/longorf.pl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/make_primers.pl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/popgen/parse_calc_stats.pl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/quality/svgtrace.pl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/rev_and_trans.pl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/revcom_dir.pl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/root/README
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/root/exceptions1.pl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/root/exceptions2.pl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/root/exceptions3.pl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/root/exceptions4.pl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/root/lib/TestInterface.pm
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/root/lib/TestObject.pm
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/blast_example.pl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/custom_writer.pl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/hitwriter.pl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/hspwriter.pl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/htmlwriter.pl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/psiblast_features.pl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/psiblast_iterations.pl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/rawwriter.pl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/resultwriter.pl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/waba2gff.pl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/waba2gff3.pl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sirna/TAG
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sirna/rnai_finder.cgi
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/structure/structure-io.pl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/subsequence.cgi
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tk/gsequence.pl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tk/hitdisplay.pl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tools/extract_genes.pl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tools/gb_to_gff.pl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tools/gff2ps.pl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tools/parse_codeml.pl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tools/psw.pl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tools/reverse-translate.pl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tools/run_genscan.pl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tools/run_primer3.pl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tools/seq_pattern.pl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tools/standaloneblast.pl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tree/paup2phylip.pl
@dirrm %%SITE_PERL%%/Bio/Align
@dirrm %%SITE_PERL%%/Bio/AlignIO/Handler
@dirrm %%SITE_PERL%%/Bio/AlignIO

@dirrm %%SITE_PERL%%/Bio/Assembly/IO
@dirrm %%SITE_PERL%%/Bio/Assembly/Tools
@dirrm %%SITE_PERL%%/Bio/Assembly
@dirrm %%SITE_PERL%%/Bio/Biblio/IO
@dirrm %%SITE_PERL%%/Bio/Biblio
@dirrm %%SITE_PERL%%/Bio/Cluster
@dirrm %%SITE_PERL%%/Bio/ClusterIO
@dirrm %%SITE_PERL%%/Bio/CodonUsage
@dirrm %%SITE_PERL%%/Bio/Coordinate/Result
@dirrm %%SITE_PERL%%/Bio/Coordinate
@dirrm %%SITE_PERL%%/Bio/DB/Biblio
@dirrm %%SITE_PERL%%/Bio/DB/Expression
@dirrm %%SITE_PERL%%/Bio/DB/Flat/BDB
@dirrm %%SITE_PERL%%/Bio/DB/Flat

@dirrm %%SITE_PERL%%/Bio/DB/Taxonomy
@dirrm %%SITE_PERL%%/Bio/DB
@dirrm %%SITE_PERL%%/Bio/Das
@dirrm %%SITE_PERL%%/Bio/Draw
@dirrm %%SITE_PERL%%/Bio/Event
@dirrm %%SITE_PERL%%/Bio/Expression/FeatureGroup
@dirrm %%SITE_PERL%%/Bio/Expression/FeatureSet
@dirrm %%SITE_PERL%%/Bio/Expression
@dirrm %%SITE_PERL%%/Bio/Factory
@dirrm %%SITE_PERL%%/Bio/FeatureIO
@dirrm %%SITE_PERL%%/Bio/Index
@dirrm %%SITE_PERL%%/Bio/LiveSeq/IO
@dirrm %%SITE_PERL%%/Bio/LiveSeq

@dirrm %%SITE_PERL%%/Bio/Matrix/PSM
@dirrm %%SITE_PERL%%/Bio/Matrix
@dirrm %%SITE_PERL%%/Bio/MolEvol
@dirrm %%SITE_PERL%%/Bio/Nexml
@dirrm %%SITE_PERL%%/Bio/OntologyIO
@dirrm %%SITE_PERL%%/Bio/Ontology/SimpleGOEngine
@dirrm %%SITE_PERL%%/Bio/Ontology
@dirrm %%SITE_PERL%%/Bio/OntologyIO/Handlers
@dirrm %%SITE_PERL%%/Bio/OntologyIO
@dirrm %%SITE_PERL%%/Bio/Phenotype/MeSH
@dirrm %%SITE_PERL%%/Bio/Phenotype/OMIM
@dirrm %%SITE_PERL%%/Bio/Phenotype

@dirrm %%SITE_PERL%%/Bio/Restriction/Enzyme
@dirrm %%SITE_PERL%%/Bio/Restriction/IO
@dirrm %%SITE_PERL%%/Bio/Restriction
@dirrm %%SITE_PERL%%/Bio/Root/Test
@dirrm %%SITE_PERL%%/Bio/Root
@dirrm %%SITE_PERL%%/Bio/Search/HSP
@dirrm %%SITE_PERL%%/Bio/Search/Hit
@dirrm %%SITE_PERL%%/Bio/SearchIO/Writer
@dirrm %%SITE_PERL%%/Bio/SearchIO/XML
@dirrm %%SITE_PERL%%/Bio/SearchIO
@dirrm %%SITE_PERL%%/Bio/Search/Iteration
@dirrm %%SITE_PERL%%/Bio/Search/Result
@dirrm %%SITE_PERL%%/Bio/Search/Tiling
@dirrm %%SITE_PERL%%/Bio/Search
@dirrm %%SITE_PERL%%/Bio/SearchIO/Writer
@dirrm %%SITE_PERL%%/Bio/SearchIO/XML
@dirrm %%SITE_PERL%%/Bio/SearchIO
@dirrm %%SITE_PERL%%/Bio/Seq/Meta
@dirrm %%SITE_PERL%%/Bio/Seq
@dirrm %%SITE_PERL%%/Bio/SeqEvolution
@dirrm %%SITE_PERL%%/Bio/SeqFeature/Gene
@dirrm %%SITE_PERL%%/Bio/SeqFeature/SiRNA

@dirrm %%SITE_PERL%%/Bio/SeqIO/game
@dirrm %%SITE_PERL%%/Bio/SeqIO/tinyseq
@dirrm %%SITE_PERL%%/Bio/SeqIO
@dirrm %%SITE_PERL%%/Bio/Seq/Meta
@dirrm %%SITE_PERL%%/Bio/Seq
@dirrm %%SITE_PERL%%/Bio/Structure/IO
@dirrm %%SITE_PERL%%/Bio/Structure/SecStr/DSSP
@dirrm %%SITE_PERL%%/Bio/Structure/SecStr/STRIDE

@dirrm %%SITE_PERL%%/Bio/Tools/Analysis/Protein
@dirrm %%SITE_PERL%%/Bio/Tools/Analysis
@dirrm %%SITE_PERL%%/Bio/Tools/EMBOSS
@dirrm %%SITE_PERL%%/Bio/Tools/EUtilities/Info
@dirrm %%SITE_PERL%%/Bio/Tools/EUtilities/Link
@dirrm %%SITE_PERL%%/Bio/Tools/EUtilities/Query
@dirrm %%SITE_PERL%%/Bio/Tools/EUtilities/Summary
@dirrm %%SITE_PERL%%/Bio/Tools/EUtilities
@dirrm %%SITE_PERL%%/Bio/Tools/HMMER
@dirrm %%SITE_PERL%%/Bio/Tools/Phylo/Molphy
@dirrm %%SITE_PERL%%/Bio/Tools/Phylo/PAML

@dirrm %%SITE_PERL%%/Bio/Tools/Prediction
@dirrm %%SITE_PERL%%/Bio/Tools/Primer/Assessor
@dirrm %%SITE_PERL%%/Bio/Tools/Primer
@dirrm %%SITE_PERL%%/Bio/Tools/Run/WrapperBase
@dirrm %%SITE_PERL%%/Bio/Tools/Run
@dirrm %%SITE_PERL%%/Bio/Tools/SeqPattern
@dirrm %%SITE_PERL%%/Bio/Tools/SiRNA/Ruleset

@dirrm %%SITE_PERL%%/Bio/TreeIO
@dirrm %%SITE_PERL%%/Bio/Variation/IO
@dirrm %%SITE_PERL%%/Bio/Variation
@dirrm %%DATADIR%%/models
@dirrm %%DATADIR%%/scripts/Bio-DB-GFF
@dirrm %%DATADIR%%/scripts/Bio-DB-SeqFeature-Store
@dirrm %%DATADIR%%/scripts/DB
@dirrm %%DATADIR%%/scripts/DB-HIV
@dirrm %%DATADIR%%/scripts/das
@dirrm %%DATADIR%%/scripts/index
@dirrm %%DATADIR%%/scripts/popgen
@dirrm %%DATADIR%%/scripts/searchio
@dirrm %%DATADIR%%/scripts/seq
@dirrm %%DATADIR%%/scripts/seqstats
@dirrm %%DATADIR%%/scripts/taxa
@dirrm %%DATADIR%%/scripts/tree
@dirrm %%DATADIR%%/scripts/utilities
@dirrm %%DATADIR%%/scripts
@dirrm %%DATADIR%%
%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/Deobfuscator/bin
%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/Deobfuscator/cgi-bin
%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/Deobfuscator/lib
%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/Deobfuscator/t
%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/Deobfuscator
%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc
%%PORTDOCS%%@dirrm %%DOCSDIR%%
%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/Bio-DB-GFF
%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/align
%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/cluster
%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/contributed
%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/db
%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/liveseq
%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/popgen
%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/quality
%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/root/lib
%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/root
%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/searchio
%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/sirna
%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/structure
%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/tk
%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/tools
%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/tree
%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%

Return to bug 190342

Lines 1-31 Link Here

(-)./files/patch-Bio-Root-Build.pm (-17 / +23 lines)
1	--- Bio/Root/Build.pm.orig 2009-09-30 00:33:53.000000000 +0800	1	--- Bio/Root/Build.pm.orig 2009-09-30 00:33:53.000000000 +0800
2	+++ Bio/Root/Build.pm 2009-12-01 10:31:39.000000000 +0800	2	+++ Bio/Root/Build.pm 2009-12-01 10:31:39.000000000 +0800
3	@@ -124,48 +124,8 @@	3	@@ -127,49 +127,9 @@
4	}	4	}
5	}	5	}
6	closedir($scripts_dir);	6	closedir($scripts_dir);
7	- my $question = $int_ok ? "Install [a]ll BioPerl scripts, [n]one, or choose groups [i]nteractively?" : "Install [a]ll BioPerl scripts or [n]one?";	7	- my $question = $int_ok ? "Install [a]ll BioPerl scripts, [n]one, ".
8	-	8	- "or choose groups [i]nteractively?" : "Install [a]ll BioPerl scripts ".
		9	- "or [n]one?";
		10	-
9	- my $prompt = $accept ? 'a' : $self->prompt($question, 'a');	11	- my $prompt = $accept ? 'a' : $self->prompt($question, 'a');
10	-	12	-
11	- if ($prompt =~ /^[aA]/) {	13	- if ($prompt =~ /^[aA]/) {
12	- $self->log_info(" - will install all scripts\n");	14	- $self->log_info(" - will install all scripts\n");
13	- $self->notes(chosen_scripts => 'all');	15	- $self->notes(chosen_scripts => 'all');
14	- }	16	- }
15	- elsif ($prompt =~ /^[iI]/) {	17	- elsif ($prompt =~ /^[iI]/) {
16	- $self->log_info(" - will install interactively:\n");	18	- $self->log_info(" - will install interactively:\n");
17	-	19	-
18	- my @chosen_scripts;	20	- my @chosen_scripts;
19	- foreach my $group_dir (@group_dirs) {	21	- foreach my $group_dir (@group_dirs) {
20	- my $group = File::Basename::basename($group_dir);	22	- my $group = File::Basename::basename($group_dir);
21	- print " * group '$group' has:\n";	23	- print " * group '$group' has:\n";
22	-	24	-
23	- my @script_files = @{$self->rscan_dir($group_dir, qr/\.PLS$\|\.pl$/)};	25	- my @script_files = @{$self->rscan_dir($group_dir, qr/\.PLS$\|\.pl$/)};
24	- foreach my $script_file (@script_files) {	26	- foreach my $script_file (@script_files) {
25	- my $script = File::Basename::basename($script_file);	27	- my $script = File::Basename::basename($script_file);
26	- print " $script\n";	28	- print " $script\n";
27	- }	29	- }
28	-	30	-
29	- my $result = $self->prompt(" Install scripts for group '$group'? [y]es [n]o [q]uit", 'n');	31	- my $result = $self->prompt(" Install scripts for group '$group'? [y]es [n]o [q]uit", 'n');
30	- die if $result =~ /^[qQ]/;	32	- die if $result =~ /^[qQ]/;
31	- if ($result =~ /^[yY]/) {	33	- if ($result =~ /^[yY]/) {
Lines 36-65 Link Here
36	- $self->log_info(" - will not install group '$group'\n");	38	- $self->log_info(" - will not install group '$group'\n");
37	- }	39	- }
38	- }	40	- }
39	-	41
40	- my $chosen_scripts = @chosen_scripts ? join("\|", @chosen_scripts) : 'none';	42	- my $chosen_scripts = @chosen_scripts ? join("\|", @chosen_scripts) : 'none';
41	-	43	-
42	- $self->notes(chosen_scripts => $chosen_scripts);	44	- $self->notes(chosen_scripts => $chosen_scripts);
43	- }	45	- }
44	- else {	46	- else {
45	- $self->log_info(" - won't install any scripts\n");	47	- $self->log_info(" - won't install any scripts\n");
46	- $self->notes(chosen_scripts => 'none');	48	- $self->notes(chosen_scripts => 'none');
47	- }	49	- }
48	-	50	+ $self->log_info(" - willt install all scripts\n");
49	+ $self->log_info(" - will install all scripts\n");	51	+ $self->notes(chosen_scripts => 'all');
50	+ $self->notes(chosen_scripts => 'all');	52
51	print "\n";	53	print "\n";
52	}	54	}
53		55	@@ -1136,21 +1096,9 @@
54	@@ -1205,16 +1165,9 @@
55	sub prompt_for_network {	56	sub prompt_for_network {
56	my ($self, $accept) = @_;	57	my ($self, $accept) = @_;
57		58
58	- my $proceed = $accept ? 0 : $self->y_n("Do you want to run tests that require connection to servers across the internet\n(likely to cause some failures)? y/n", 'n');	59	- my $proceed = $accept ? 0 : $self->y_n("Do you want to run tests that require connection to servers across the internet\n(likely to cause some failures)? y/n", 'n');
59	-	60	-
60	- if ($proceed) {	61	- if ($proceed) {
61	- $self->notes(network => 1);	62	- $self->notes('network' => 1);
62	- $self->log_info(" - will run internet-requiring tests\n");	63	- $self->log_info(" - will run internet-requiring tests\n");
		64	- my $use_email = $self->y_n("Do you want to run tests requiring a valid email address? y/n",'n');
		65	- if ($use_email) {
		66	- my $address = $self->prompt("Enter email address:");
		67	- $self->notes(email => $address);
		68	- }
63	- }	69	- }
64	- else {	70	- else {
65	- $self->notes(network => 0);	71	- $self->notes(network => 0);
Lines 70-73 Link Here
70	+ $self->log_info(" - will not run internet-requiring tests\n");	76	+ $self->log_info(" - will not run internet-requiring tests\n");
71	}	77	}
72		78
73	1;	79	# override the build script warnings flag

Lines 1-22 Link Here

(-)./files/patch-Build.PL (-16 / +15 lines)
1	--- Build.PL.orig 2009-09-30 00:33:45.000000000 +0800	1	--- Build.PL.orig 2009-09-30 00:33:45.000000000 +0800
2	+++ Build.PL 2009-12-01 10:25:51.000000000 +0800	2	+++ Build.PL 2009-12-01 10:25:51.000000000 +0800
3	@@ -37,7 +37,7 @@	3	@@ -187,7 +187,6 @@
4	'Test::More' => 0,	4	},
		5
		6	build_requires => {
		7	- 'CPAN' => 1.81,
5	'Module::Build' => 0.2805,	8	'Module::Build' => 0.2805,
6	'Test::Harness' => 2.62,	9	'Test::Harness' => 2.62,
7	- 'CPAN' => 1.81	10	'Test::Most' => 0,
8	+ #'CPAN' => 1.81	11	@@ -376,86 +375,8 @@
9	},
10	recommends => { # does what you would expect of recommends, except more informative output and generates optional_features in META.yml
11	'Ace' => '0/access of ACeDB database/Bio::DB::Ace,Bio::DB::GFF::Adaptor::ace',
12	@@ -234,86 +234,9 @@
13		12
14	sub prompt_for_biodb {	13	sub prompt_for_biodb {
15	my $accept = shift;	14	my $accept = shift;
16	- my $proceed = $accept ? 0 : $build->y_n("Do you want to run the Bio::DB::GFF or ".	15	- my $proceed = $accept ? 0 : $build->y_n("Do you want to run the Bio::DB::GFF or ".
17	- "Bio::DB::SeqFeature::Store live database tests? ".	16	- "Bio::DB::SeqFeature::Store live database tests? ".
18	- "y/n", 'n');	17	- "y/n", 'n');
19	-	18	-
20	- if ($proceed) {	19	- if ($proceed) {
21	- my @driver_choices;	20	- my @driver_choices;
22	- foreach my $poss ('SQLite', 'mysql', 'Pg', 'Oracle') {	21	- foreach my $poss ('SQLite', 'mysql', 'Pg', 'Oracle') {
Lines 26-32 Link Here
26	- push(@driver_choices, $choice);	25	- push(@driver_choices, $choice);
27	- }	26	- }
28	- }	27	- }
29	-	28	-
30	- my $driver;	29	- my $driver;
31	- if (@driver_choices > 1) {	30	- if (@driver_choices > 1) {
32	- my ($default) = $driver_choices[0] =~ /\[(.)/;	31	- my ($default) = $driver_choices[0] =~ /\[(.)/;
Lines 47-65 Link Here
47	- elsif ($driver =~ /^[sS]/) {	46	- elsif ($driver =~ /^[sS]/) {
48	- $driver = 'SQLite';	47	- $driver = 'SQLite';
49	- }	48	- }
50	-	49	-
51	- my $test_db = $build->prompt("Which database should I use for testing the $driver driver?\n".	50	- my $test_db = $build->prompt("Which database should I use for testing the $driver driver?\n".
52	- "This database should already be present but doesn't have to ".	51	- "This database should already be present but doesn't have to ".
53	- "be preloaded for any schema", 'test');	52	- "be preloaded for any schema", 'test');
54	- my $test_host = $build->prompt("On which host is database '$test_db' running (hostname, ip address or host:port)", 'localhost');	53	- my $test_host = $build->prompt("On which host is database '$test_db' running (hostname, ip address or host:port)", 'localhost');
55	- my $test_user = $build->prompt("User name for connecting to database '$test_db'?", 'undef');	54	- my $test_user = $build->prompt("User name for connecting to database '$test_db'?", 'undef');
56	- my $test_pass = $build->prompt("Password for connecting to database '$test_db'?", 'undef');	55	- my $test_pass = $build->prompt("Password for connecting to database '$test_db'?", 'undef');
57	-	56	-
58	- my $use_host = 1;	57	- my $use_host = 1;
59	- if ($test_host eq 'undef' \|\| $test_host eq 'localhost') {	58	- if ($test_host eq 'undef' \|\| $test_host eq 'localhost') {
60	- $use_host = 0;	59	- $use_host = 0;
61	- }	60	- }
62	-	61	-
63	- my $test_dsn;	62	- my $test_dsn;
64	- if ($driver eq 'Pg' \|\| $driver eq 'SQLite') {	63	- if ($driver eq 'Pg' \|\| $driver eq 'SQLite') {
65	- $test_dsn = "dbi:$driver:dbname=$test_db";	64	- $test_dsn = "dbi:$driver:dbname=$test_db";
Lines 72-85 Link Here
72	- if ($use_host) {	71	- if ($use_host) {
73	- $test_dsn .= ";host=$test_host";	72	- $test_dsn .= ";host=$test_host";
74	- }	73	- }
75	-	74	-
76	- $build->notes(dbd_driver => $driver);	75	- $build->notes(dbd_driver => $driver);
77	- $build->notes(test_db => $test_db);	76	- $build->notes(test_db => $test_db);
78	- $build->notes(test_host => $test_host);	77	- $build->notes(test_host => $test_host);
79	- $build->notes(test_user => $test_user eq 'undef' ? undef : $test_user);	78	- $build->notes(test_user => $test_user eq 'undef' ? undef : $test_user);
80	- $build->notes(test_pass => $test_pass eq 'undef' ? undef : $test_pass);	79	- $build->notes(test_pass => $test_pass eq 'undef' ? undef : $test_pass);
81	- $build->notes(test_dsn => $test_dsn);	80	- $build->notes(test_dsn => $test_dsn);
82	-	81	-
83	- $build->log_info(" - will run tests with database driver '$driver' and these settings:\n",	82	- $build->log_info(" - will run tests with database driver '$driver' and these settings:\n",
84	- " Database $test_db\n",	83	- " Database $test_db\n",
85	- " Host $test_host\n",	84	- " Host $test_host\n",
Lines 92-98 Link Here
92	- else {	91	- else {
93	- $build->log_info(" - will not run the BioDBGFF or BioDBSeqFeature live database tests\n");	92	- $build->log_info(" - will not run the BioDBGFF or BioDBSeqFeature live database tests\n");
94	- }	93	- }
95		94	-
96	+ my $proceed = 0;	95	+ my $proceed = 0;
97	+ $build->log_info(" - will not run the BioDBGFF or BioDBSeqFeature live database tests\n");	96	+ $build->log_info(" - will not run the BioDBGFF or BioDBSeqFeature live database tests\n");
98	$build->log_info("\n");	97	$build->log_info("\n");