diff options
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/p5-bioperl/Makefile | 397 | ||||
| -rw-r--r-- | biology/p5-bioperl/distinfo | 6 | ||||
| -rw-r--r-- | biology/p5-bioperl/files/patch-Build.PL | 97 | ||||
| -rw-r--r-- | biology/p5-bioperl/files/patch-Build.pm | 73 | ||||
| -rw-r--r-- | biology/p5-bioperl/files/patch-manify | 29 | ||||
| -rw-r--r-- | biology/p5-bioperl/pkg-plist | 2039 |
6 files changed, 1559 insertions, 1082 deletions
diff --git a/biology/p5-bioperl/Makefile b/biology/p5-bioperl/Makefile index 10fea6cdf8d2..18f9dbdd3bc8 100644 --- a/biology/p5-bioperl/Makefile +++ b/biology/p5-bioperl/Makefile @@ -6,100 +6,140 @@ # PORTNAME= bioperl -PORTVERSION= 1.4 -PORTREVISION= 2 +PORTVERSION= 1.6.0 CATEGORIES= biology perl5 MASTER_SITES= http://bioperl.org/DIST/ \ CPAN PKGNAMEPREFIX= p5- +DISTNAME= BioPerl-${PORTVERSION} 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} -# prevents a flood of build-time warnings. -BUILD_DEPENDS= ${SITE_PERL}/${PERL_ARCH}/Ace.pm:${PORTSDIR}/biology/p5-AcePerl \ - ${SITE_PERL}/${PERL_ARCH}/XML/Parser.pm:${PORTSDIR}/textproc/p5-XML-Parser \ +BUILD_DEPENDS= ${LOCALBASE}/lib/perl5/${PERL_VER}/Text/Wrap.pm:${PORTSDIR}/lang/perl5.8 \ + ${LOCALBASE}/lib/perl5/${PERL_VER}/${PERL_ARCH}/DB_File.pm:${PORTSDIR}/lang/perl5.8 \ + ${SITE_PERL}/Bio/ASN1/EntrezGene.pm:${PORTSDIR}/biology/p5-Bio-ASN1-EntrezGene \ + ${SITE_PERL}/Class/AutoClass.pm:${PORTSDIR}/devel/p5-Class-AutoClass \ + ${SITE_PERL}/Data/Stag/ITextWriter.pm:${PORTSDIR}/devel/p5-Data-Stag \ + ${SITE_PERL}/Data/Stag/SxprWriter.pm:${PORTSDIR}/devel/p5-Data-Stag \ + ${SITE_PERL}/Data/Stag/XMLWriter.pm:${PORTSDIR}/devel/p5-Data-Stag \ + ${SITE_PERL}/GD/SVG.pm:${PORTSDIR}/graphics/p5-GD-SVG \ + ${SITE_PERL}/Graph/Directed.pm:${PORTSDIR}/math/p5-Graph \ ${SITE_PERL}/HTTP/Request/Common.pm:${PORTSDIR}/www/p5-libwww \ ${SITE_PERL}/IO/Scalar.pm:${PORTSDIR}/devel/p5-IO-stringy \ ${SITE_PERL}/IO/String.pm:${PORTSDIR}/devel/p5-IO-String \ ${SITE_PERL}/LWP/UserAgent.pm:${PORTSDIR}/www/p5-libwww \ - ${SITE_PERL}/XML/Node.pm:${PORTSDIR}/textproc/p5-XML-Node \ + ${SITE_PERL}/SOAP/Lite.pm:${PORTSDIR}/net/p5-SOAP-Lite \ + ${SITE_PERL}/SVG.pm:${PORTSDIR}/textproc/p5-SVG \ + ${SITE_PERL}/SVG/Graph.pm:${PORTSDIR}/graphics/p5-SVG-Graph \ + ${SITE_PERL}/Text/Shellwords.pm:${PORTSDIR}/textproc/p5-Text-Shellwords \ + ${SITE_PERL}/XML/DOM.pm:${PORTSDIR}/textproc/p5-XML-DOM \ + ${SITE_PERL}/XML/DOM/XPath.pm:${PORTSDIR}/textproc/p5-XML-DOM-XPath \ ${SITE_PERL}/XML/Parser/PerlSAX.pm:${PORTSDIR}/textproc/p5-libxml \ - ${SITE_PERL}/XML/Writer.pm:${PORTSDIR}/textproc/p5-XML-Writer \ - ${SITE_PERL}/HTTP/Request/Common.pm:${PORTSDIR}/www/p5-libwww \ + ${SITE_PERL}/XML/SAX.pm:${PORTSDIR}/textproc/p5-XML-SAX \ + ${SITE_PERL}/XML/SAX/Base.pm:${PORTSDIR}/textproc/p5-XML-SAX \ + ${SITE_PERL}/XML/SAX/Writer.pm:${PORTSDIR}/textproc/p5-XML-SAX-Writer \ ${SITE_PERL}/XML/Twig.pm:${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 \ + ${SITE_PERL}/XML/Writer.pm:${PORTSDIR}/textproc/p5-XML-Writer \ + ${SITE_PERL}/${PERL_ARCH}/Ace.pm:${PORTSDIR}/biology/p5-AcePerl \ + ${SITE_PERL}/${PERL_ARCH}/Clone.pm:${PORTSDIR}/devel/p5-Clone \ ${SITE_PERL}/${PERL_ARCH}/DBD/mysql.pm:${PORTSDIR}/databases/p5-DBD-mysql \ ${SITE_PERL}/${PERL_ARCH}/GD.pm:${PORTSDIR}/graphics/p5-GD \ + ${SITE_PERL}/${PERL_ARCH}/HTML/Entities.pm:${PORTSDIR}/www/p5-HTML-Parser \ + ${SITE_PERL}/${PERL_ARCH}/HTML/Parser.pm:${PORTSDIR}/www/p5-HTML-Parser \ ${SITE_PERL}/${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 + ${SITE_PERL}/${PERL_ARCH}/XML/Parser.pm:${PORTSDIR}/textproc/p5-XML-Parser \ + ${SITE_PERL}/Spreadsheet/ParseExcel.pm:${PORTSDIR}/textproc/p5-Spreadsheet-ParseExcel \ + ${SITE_PERL}/${PERL_ARCH}/Convert/Binary/C.pm:${PORTSDIR}/converters/p5-Convert-Binary-C \ + ${SITE_PERL}/Test/Harness.pm:${PORTSDIR}/devel/p5-Test-Harness \ + ${SITE_PERL}/Algorithm/Munkres.pm:${PORTSDIR}/math/p5-Algorithm-Munkres \ + ${SITE_PERL}/Array/Compare.pm:${PORTSDIR}/misc/p5-Array-Compare \ + ${SITE_PERL}/GraphViz.pm:${PORTSDIR}/graphics/p5-GraphViz \ + ${SITE_PERL}/${PERL_ARCH}/Math/Random.pm:${PORTSDIR}/math/p5-Math-Random \ + ${SITE_PERL}/PostScript/TextBlock.pm:${PORTSDIR}/print/p5-PostScript \ + ${SITE_PERL}/Set/Scalar.pm:${PORTSDIR}/devel/p5-Set-Scalar \ + ${SITE_PERL}/Text/ParseWords.pm:${PORTSDIR}/textproc/p5-Text-ParseWords \ + ${SITE_PERL}/URI/Escape.pm:${PORTSDIR}/net/p5-URI + RUN_DEPENDS= ${BUILD_DEPENDS} CONFLICTS= p5-bioperl-1.[13579]* -PERL_CONFIGURE= YES +PERL_MODBUILD= YES MAN1= bp_aacomp.pl.1 \ bp_biblio.pl.1 \ bp_biofetch_genbank_proxy.pl.1 \ + bp_bioflat_index.pl.1 \ bp_biogetseq.pl.1 \ bp_blast2tree.pl.1 \ bp_bulk_load_gff.pl.1 \ 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_extract_feature_seq.pl.1 \ bp_fast_load_gff.pl.1 \ - bp_feature_draw.pl.1 \ + bp_fastam9_to_table.pl.1 \ bp_fetch.pl.1 \ bp_filter_search.pl.1 \ bp_flanks.pl.1 \ - bp_frend.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_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_pg_bulk_load_gff.pl.1 \ + bp_parse_hmmsearch.pl.1 \ bp_process_gadfly.pl.1 \ - bp_process_ncbi_human.pl.1 \ bp_process_sgd.pl.1 \ bp_process_wormbase.pl.1 \ + bp_query_entrez_taxa.pl.1 \ bp_remote_blast.pl.1 \ bp_search2BSML.pl.1 \ bp_search2alnblocks.pl.1 \ bp_search2gff.pl.1 \ + bp_search2table.pl.1 \ bp_search2tribe.pl.1 \ - bp_search_overview.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_translate_seq.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 \ @@ -109,10 +149,13 @@ MAN3= Bio::Align::AlignI.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 \ @@ -123,8 +166,12 @@ MAN3= Bio::Align::AlignI.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 \ @@ -133,8 +180,11 @@ MAN3= Bio::Align::AlignI.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 \ @@ -176,6 +226,7 @@ MAN3= Bio::Align::AlignI.3 \ Bio::ClusterIO::unigene.3 \ Bio::CodonUsage::IO.3 \ Bio::CodonUsage::Table.3 \ + Bio::ConfigData.3 \ Bio::Coordinate::Chain.3 \ Bio::Coordinate::Collection.3 \ Bio::Coordinate::ExtrapolatingPair.3 \ @@ -190,12 +241,17 @@ MAN3= Bio::Align::AlignI.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 \ @@ -205,11 +261,11 @@ MAN3= Bio::Align::AlignI.3 \ Bio::DB::Flat::BDB::fasta.3 \ Bio::DB::Flat::BDB::genbank.3 \ Bio::DB::Flat::BDB::swiss.3 \ - Bio::DB::Flat::BDB::swissprot.3 \ Bio::DB::Flat::BinarySearch.3 \ - Bio::DB::GDB.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 \ @@ -217,19 +273,25 @@ MAN3= Bio::Align::AlignI.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_iterator.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 \ @@ -250,25 +312,53 @@ MAN3= Bio::Align::AlignI.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::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::DB::XEMBL.3 \ - Bio::DB::XEMBLService.3 \ Bio::DBLinkContainerI.3 \ Bio::Das::FeatureTypeI.3 \ Bio::Das::SegmentI.3 \ @@ -276,19 +366,24 @@ MAN3= Bio::Align::AlignI.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::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::Factory::SequenceFactoryI.3 \ @@ -296,63 +391,27 @@ MAN3= Bio::Align::AlignI.3 \ Bio::Factory::SequenceStreamI.3 \ Bio::Factory::TreeFactoryI.3 \ Bio::FeatureHolderI.3 \ - Bio::Graphics.3 \ - Bio::Graphics::ConfiguratorI.3 \ - Bio::Graphics::Feature.3 \ - Bio::Graphics::FeatureFile.3 \ - Bio::Graphics::FeatureFile::Iterator.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::minmax.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::Graphics::Pictogram.3 \ - Bio::Graphics::RendererI.3 \ - Bio::Graphics::Util.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 \ @@ -363,7 +422,6 @@ MAN3= Bio::Align::AlignI.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 \ @@ -386,34 +444,58 @@ MAN3= Bio::Align::AlignI.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 \ @@ -422,8 +504,12 @@ MAN3= Bio::Align::AlignI.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 \ @@ -434,7 +520,8 @@ MAN3= Bio::Align::AlignI.3 \ Bio::Ontology::RelationshipFactory.3 \ Bio::Ontology::RelationshipI.3 \ Bio::Ontology::RelationshipType.3 \ - Bio::Ontology::SimpleGOEngine.3 \ + Bio::Ontology::SimpleGOEngine::GraphAdaptor.3 \ + Bio::Ontology::SimpleGOEngine::GraphAdaptor02.3 \ Bio::Ontology::SimpleOntologyEngine.3 \ Bio::Ontology::Term.3 \ Bio::Ontology::TermFactory.3 \ @@ -446,8 +533,10 @@ MAN3= Bio::Align::AlignI.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 \ @@ -459,10 +548,22 @@ MAN3= Bio::Align::AlignI.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 \ @@ -474,8 +575,11 @@ MAN3= Bio::Align::AlignI.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 \ @@ -488,50 +592,63 @@ MAN3= Bio::Align::AlignI.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::Err.3 \ + Bio::Root::Build.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::Storable.3 \ + Bio::Root::Test.3 \ + Bio::Root::Test::Warn.3 \ Bio::Root::Utilities.3 \ - Bio::Root::Vector.3 \ Bio::Root::Version.3 \ - Bio::Root::Xref.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::SearchDist.3 \ Bio::SearchIO.3 \ Bio::SearchIO::EventHandlerI.3 \ @@ -546,29 +663,40 @@ MAN3= Bio::Align::AlignI.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::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 \ @@ -578,6 +706,10 @@ MAN3= Bio::Align::AlignI.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 \ @@ -595,40 +727,56 @@ MAN3= Bio::Align::AlignI.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 \ @@ -637,9 +785,15 @@ MAN3= Bio::Align::AlignI.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 \ @@ -661,6 +815,7 @@ MAN3= Bio::Align::AlignI.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 \ @@ -680,25 +835,34 @@ MAN3= Bio::Align::AlignI.3 \ Bio::Tools::Analysis::Protein::Sopma.3 \ Bio::Tools::Analysis::SimpleAnalysisBase.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::Sbjct.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::Eponine.3 \ Bio::Tools::Est2Genome.3 \ + Bio::Tools::Fgenesh.3 \ Bio::Tools::FootPrinter.3 \ Bio::Tools::GFF.3 \ Bio::Tools::Gel.3 \ @@ -710,14 +874,19 @@ MAN3= Bio::Align::AlignI.3 \ Bio::Tools::Glimmer.3 \ Bio::Tools::Grail.3 \ Bio::Tools::GuessSeqFormat.3 \ + Bio::Tools::HMM.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 \ @@ -735,30 +904,47 @@ MAN3= Bio::Align::AlignI.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::RestrictionEnzyme.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::SeqAnal.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::WWW.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 \ @@ -769,10 +955,13 @@ MAN3= Bio::Align::AlignI.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 \ @@ -787,17 +976,15 @@ MAN3= Bio::Align::AlignI.3 \ Bio::Variation::SNP.3 \ Bio::Variation::SeqDiff.3 \ Bio::Variation::VariantI.3 \ - Bio::WebAgent.3 \ - biodatabases.3 \ - biodesign.3 \ - bioperl.3 \ - bioscripts.3 \ - bptutorial.3 + Bio::WebAgent.3 .include <bsd.port.pre.mk> .if ${PERL_LEVEL} < 500800 BUILD_DEPENDS+= ${SITE_PERL}/File/Temp.pm:${PORTSDIR}/devel/p5-File-Temp +.if ${PERL_LEVEL} < 500600 +IGNORE= requires Perl 5.6 or better +.endif .endif # now install all extra stuff (docs, examples, scripts, models) @@ -808,7 +995,7 @@ post-install: ${CP} -R ${WRKSRC}/examples/* ${EXAMPLESDIR} .if !defined(NOPORTDOCS) ${MKDIR} ${DOCSDIR} -.for doc in AUTHORS BUGS Changes DEPRECATED FAQ INSTALL LICENSE PLATFORMS README +.for doc in AUTHORS BUGS Changes DEPENDENCIES DEPRECATED INSTALL LICENSE MANIFEST PLATFORMS README ${INSTALL_MAN} ${WRKSRC}/${doc} ${DOCSDIR} .endfor ${CP} -R ${WRKSRC}/doc ${DOCSDIR} diff --git a/biology/p5-bioperl/distinfo b/biology/p5-bioperl/distinfo index 76333518a015..2908ee9e9b23 100644 --- a/biology/p5-bioperl/distinfo +++ b/biology/p5-bioperl/distinfo @@ -1,3 +1,3 @@ -MD5 (bioperl-1.4.tar.gz) = 5ef3e6e824c3f444e788d7fc9bda1fcb -SHA256 (bioperl-1.4.tar.gz) = 0e59ece6834c532d31f874e44b14f1c6cf103d465368c143bfac19cf49926b1a -SIZE (bioperl-1.4.tar.gz) = 4902946 +MD5 (BioPerl-1.6.0.tar.gz) = ce38cba5f06aaf3c692c1a32218cde87 +SHA256 (BioPerl-1.6.0.tar.gz) = 46d7fce2a20128f8515a9690feb27d9fd65023a2f85c83dca781d0aa1ba1e889 +SIZE (BioPerl-1.6.0.tar.gz) = 6813396 diff --git a/biology/p5-bioperl/files/patch-Build.PL b/biology/p5-bioperl/files/patch-Build.PL new file mode 100644 index 000000000000..b6f498ff7505 --- /dev/null +++ b/biology/p5-bioperl/files/patch-Build.PL @@ -0,0 +1,97 @@ +--- Build.PL.orig 2009-01-25 02:19:13.000000000 -0300 ++++ Build.PL 2009-02-22 02:21:33.000000000 -0300 +@@ -36,7 +36,7 @@ + 'Test::More' => 0, + 'Module::Build' => 0.2805, + 'Test::Harness' => 2.62, +- 'CPAN' => 1.81 ++ #'CPAN' => 1.81 + }, + 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', +@@ -214,83 +214,8 @@ + + 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 $poss ('mysql', 'Pg', 'Oracle') { +- if (grep {/$poss/i} @drivers) { +- my $choice = $poss; +- $choice =~ s/^(.)/[$1]/; +- push(@driver_choices, $choice); +- } +- } +- +- my $driver; +- if (@driver_choices > 1) { +- my ($default) = $driver_choices[0] =~ /\[(.)/; +- $driver = $build->prompt("Which database driver should be used? ".join(" ", @driver_choices), $default); +- } +- else { +- ($driver) = $driver_choices[0] =~ /\[(.)/; +- } +- if ($driver =~ /^[mM]/) { +- $driver = 'mysql'; +- } +- elsif ($driver =~ /^[pP]/) { +- $driver = 'Pg'; +- } +- elsif ($driver =~ /^[oO]/) { +- $driver = 'Oracle'; +- } +- +- 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') { +- $test_dsn = "dbi:$driver:dbname=$test_db"; +- $mysql_ok = 0; +- } +- else { +- $test_dsn = "dbi:$driver:database=$test_db"; +- $mysql_ok = 0; +- } +- if ($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", +- " DSN $test_dsn\n", +- " User $test_user\n", +- " Password $test_pass\n"); +- $build->log_info(" - will not run the BioDBSeqFeature live ". +- "database tests (requires MySQL driver)\n") unless ($driver eq 'mysql'); +- } +- 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"); + return $proceed; + } diff --git a/biology/p5-bioperl/files/patch-Build.pm b/biology/p5-bioperl/files/patch-Build.pm new file mode 100644 index 000000000000..bdca7e89404b --- /dev/null +++ b/biology/p5-bioperl/files/patch-Build.pm @@ -0,0 +1,73 @@ +--- Bio/Root/Build.pm.orig 2009-01-25 02:19:26.000000000 -0300 ++++ Bio/Root/Build.pm 2009-02-22 02:24:05.000000000 -0300 +@@ -141,48 +141,8 @@ + } + } + closedir($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]/) { +- $self->log_info(" + will install group '$group'\n"); +- push(@chosen_scripts, @script_files); +- } +- else { +- $self->log_info(" - will not install group '$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(" - will install all scripts\n"); ++ $self->notes(chosen_scripts => 'all'); + print "\n"; + } + +@@ -1177,16 +1137,9 @@ + sub prompt_for_network { + my ($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"); +- } +- else { +- $self->notes(network => 0); +- $self->log_info(" - will not run internet-requiring tests\n"); +- } ++ my $proceed = 0; ++ $self->notes(network => 0); ++ $self->log_info(" - will not run internet-requiring tests\n"); + } + + 1; diff --git a/biology/p5-bioperl/files/patch-manify b/biology/p5-bioperl/files/patch-manify deleted file mode 100644 index 9609fc951a0c..000000000000 --- a/biology/p5-bioperl/files/patch-manify +++ /dev/null @@ -1,29 +0,0 @@ ---- 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 5b1b57eec9bd..b9fb7f56c3fb 100644 --- a/biology/p5-bioperl/pkg-plist +++ b/biology/p5-bioperl/pkg-plist @@ -1,843 +1,973 @@ -bin/bp_chaos_plot.pl -bin/bp_composite_LD.pl -bin/bp_pairwise_kaks.pl +bin/bp_sreformat.pl +bin/bp_seqconvert.pl +bin/bp_parse_hmmsearch.pl +bin/bp_seqret.pl +bin/bp_tree2pag.pl +bin/bp_meta_gff.pl +bin/bp_nexus2nh.pl +bin/bp_filter_search.pl bin/bp_flanks.pl -bin/bp_translate_seq.pl -bin/bp_feature_draw.pl +bin/bp_seqfeature_gff3.pl +bin/bp_generate_histogram.pl +bin/bp_heterogeneity_test.pl +bin/bp_split_seq.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_biogetseq.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_mutate.pl +bin/bp_process_sgd.pl bin/bp_index.pl bin/bp_dbsplit.pl +bin/bp_oligo_count.pl +bin/bp_seq_length.pl +bin/bp_seqfeature_load.pl +bin/bp_process_gadfly.pl +bin/bp_hmmer_to_table.pl +bin/bp_fastam9_to_table.pl +bin/bp_genbank2gff.pl bin/bp_biofetch_genbank_proxy.pl +bin/bp_extract_feature_seq.pl +bin/bp_search2gff.pl +bin/bp_taxid4species.pl +bin/bp_bulk_load_gff.pl +bin/bp_blast2tree.pl +bin/bp_make_mrna_protein.pl +bin/bp_unflatten_seq.pl +bin/bp_search2tribe.pl bin/bp_bioflat_index.pl +bin/bp_seqfeature_delete.pl +bin/bp_query_entrez_taxa.pl +bin/bp_pairwise_kaks.pl +bin/bp_fast_load_gff.pl +bin/bp_chaos_plot.pl +bin/bp_taxonomy2tree.pl +bin/bp_mrtrans.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_download_query_genbank.pl +bin/bp_nrdb.pl bin/bp_mask_by_search.pl -bin/bp_mrtrans.pl -bin/bp_process_gadfly.pl bin/bp_gccalc.pl -bin/bp_seqconvert.pl 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