Index: Makefile =================================================================== RCS file: /home/pcvs/ports/biology/p5-bioperl/Makefile,v retrieving revision 1.12 diff -u -u -r1.12 Makefile --- Makefile 12 Aug 2004 12:47:57 -0000 1.12 +++ Makefile 3 Sep 2004 01:59:20 -0000 @@ -42,40 +42,88 @@ PERL_CONFIGURE= YES +MAN1= bp_aacomp.pl.1 \ + bp_biblio.pl.1 \ + bp_biofetch_genbank_proxy.pl.1 \ + bp_biogetseq.pl.1 \ + bp_blast2tree.pl.1 \ + bp_bulk_load_gff.pl.1 \ + bp_chaos_plot.pl.1 \ + bp_composite_LD.pl.1 \ + bp_dbsplit.pl.1 \ + bp_extract_feature_seq.pl.1 \ + bp_fast_load_gff.pl.1 \ + bp_feature_draw.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_generate_histogram.pl.1 \ + bp_heterogeneity_test.pl.1 \ + bp_index.pl.1 \ + bp_load_gff.pl.1 \ + bp_local_taxonomydb_query.pl.1 \ + bp_mask_by_search.pl.1 \ + bp_mrtrans.pl.1 \ + bp_mutate.pl.1 \ + bp_nrdb.pl.1 \ + bp_oligo_count.pl.1 \ + bp_pairwise_kaks.pl.1 \ + bp_pg_bulk_load_gff.pl.1 \ + bp_process_gadfly.pl.1 \ + bp_process_ncbi_human.pl.1 \ + bp_process_sgd.pl.1 \ + bp_process_wormbase.pl.1 \ + bp_remote_blast.pl.1 \ + bp_search2BSML.pl.1 \ + bp_search2alnblocks.pl.1 \ + bp_search2gff.pl.1 \ + bp_search2tribe.pl.1 \ + bp_search_overview.pl.1 \ + bp_seq_length.pl.1 \ + bp_seqconvert.pl.1 \ + bp_split_seq.pl.1 \ + bp_sreformat.pl.1 \ + bp_taxid4species.pl.1 \ + bp_translate_seq.pl.1 MAN3= Bio::Align::AlignI.3 \ - Bio::Align::DNAStatistics.3 \ + Bio::Align::DNAStatistics.3 \ Bio::Align::PairwiseStatistics.3 \ Bio::Align::StatisticsI.3 \ Bio::Align::Utilities.3 \ Bio::AlignIO.3 \ Bio::AlignIO::bl2seq.3 \ Bio::AlignIO::clustalw.3 \ - Bio::AlignIO::emboss.3 \ + Bio::AlignIO::emboss.3 \ Bio::AlignIO::fasta.3 \ + Bio::AlignIO::maf.3 \ Bio::AlignIO::mase.3 \ - Bio::AlignIO::mega.3 \ - Bio::AlignIO::meme.3 \ + Bio::AlignIO::mega.3 \ + Bio::AlignIO::meme.3 \ + Bio::AlignIO::metafasta.3 \ Bio::AlignIO::msf.3 \ - Bio::AlignIO::nexus.3 \ + Bio::AlignIO::nexus.3 \ Bio::AlignIO::pfam.3 \ - Bio::AlignIO::phylip.3 \ + Bio::AlignIO::phylip.3 \ Bio::AlignIO::prodom.3 \ - Bio::AlignIO::psi.3 \ + Bio::AlignIO::psi.3 \ Bio::AlignIO::selex.3 \ Bio::AlignIO::stockholm.3 \ - Bio::AnalysisI.3 \ - Bio::AnalysisParserI.3 \ - Bio::AnalysisResultI.3 \ - Bio::AnnotatableI.3 \ - Bio::Annotation::AnnotationFactory.3 \ - Bio::Annotation::Collection.3 \ + Bio::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::OntologyTerm.3 \ Bio::Annotation::Reference.3 \ - Bio::Annotation::SimpleValue.3 \ - Bio::Annotation::StructuredValue.3 \ - Bio::Annotation::TypeManager.3 \ + Bio::Annotation::SimpleValue.3 \ + Bio::Annotation::StructuredValue.3 \ + Bio::Annotation::TypeManager.3 \ Bio::AnnotationCollectionI.3 \ Bio::AnnotationI.3 \ Bio::Assembly::Contig.3 \ @@ -124,6 +172,8 @@ 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 \ @@ -141,6 +191,7 @@ 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::Failover.3 \ @@ -150,10 +201,15 @@ 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::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::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 \ @@ -162,6 +218,7 @@ 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::memory.3 \ Bio::DB::GFF::Adaptor::memory_iterator.3 \ Bio::DB::GFF::Aggregator.3 \ @@ -192,6 +249,7 @@ Bio::DB::GenBank.3 \ Bio::DB::GenPept.3 \ Bio::DB::InMemoryCache.3 \ + Bio::DB::MeSH.3 \ Bio::DB::NCBIHelper.3 \ Bio::DB::Query::GenBank.3 \ Bio::DB::Query::WebQuery.3 \ @@ -201,6 +259,9 @@ Bio::DB::Registry.3 \ Bio::DB::SeqI.3 \ Bio::DB::SwissProt.3 \ + Bio::DB::Taxonomy.3 \ + Bio::DB::Taxonomy::entrez.3 \ + Bio::DB::Taxonomy::flatfile.3 \ Bio::DB::Universal.3 \ Bio::DB::UpdateableSeqI.3 \ Bio::DB::WebDBSeqI.3 \ @@ -234,8 +295,10 @@ 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 \ @@ -255,6 +318,7 @@ 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 \ @@ -275,6 +339,8 @@ Bio::Graphics::Glyph::triangle.3 \ Bio::Graphics::Glyph::xyplot.3 \ Bio::Graphics::Panel.3 \ + Bio::Graphics::Pictogram.3 \ + Bio::Graphics::RendererI.3 \ Bio::IdCollectionI.3 \ Bio::IdentifiableI.3 \ Bio::Index::Abstract.3 \ @@ -334,7 +400,25 @@ Bio::Map::SimpleMap.3 \ Bio::MapIO.3 \ Bio::MapIO::mapmaker.3 \ + Bio::Matrix::Generic.3 \ + Bio::Matrix::IO.3 \ + Bio::Matrix::IO::phylip.3 \ + Bio::Matrix::IO::scoring.3 \ + Bio::Matrix::MatrixI.3 \ + Bio::Matrix::PSM::IO.3 \ + Bio::Matrix::PSM::IO::mast.3 \ + Bio::Matrix::PSM::IO::meme.3 \ + Bio::Matrix::PSM::IO::transfac.3 \ + Bio::Matrix::PSM::InstanceSite.3 \ + Bio::Matrix::PSM::InstanceSiteI.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::Ontology::GOterm.3 \ Bio::Ontology::InterProTerm.3 \ Bio::Ontology::Ontology.3 \ @@ -353,13 +437,18 @@ 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::simplehierarchy.3 \ Bio::OntologyIO::soflat.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 \ @@ -367,10 +456,36 @@ Bio::Phenotype::OMIM::OMIMparser.3 \ Bio::Phenotype::Phenotype.3 \ Bio::Phenotype::PhenotypeI.3 \ + Bio::PopGen::Genotype.3 \ + Bio::PopGen::GenotypeI.3 \ + Bio::PopGen::IO.3 \ + Bio::PopGen::IO::csv.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::PrimarySeq.3 \ Bio::PrimarySeqI.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::withrefm.3 \ Bio::Root::Err.3 \ Bio::Root::Exception.3 \ Bio::Root::Global.3 \ @@ -380,8 +495,10 @@ Bio::Root::Object.3 \ Bio::Root::Root.3 \ Bio::Root::RootI.3 \ + Bio::Root::Storable.3 \ Bio::Root::Utilities.3 \ Bio::Root::Vector.3 \ + Bio::Root::Version.3 \ Bio::Root::Xref.3 \ Bio::Search::BlastUtils.3 \ Bio::Search::DatabaseI.3 \ @@ -392,6 +509,8 @@ Bio::Search::HSP::HMMERHSP.3 \ Bio::Search::HSP::HSPFactory.3 \ Bio::Search::HSP::HSPI.3 \ + Bio::Search::HSP::PSLHSP.3 \ + Bio::Search::HSP::PsiBlastHSP.3 \ Bio::Search::HSP::WABAHSP.3 \ Bio::Search::Hit::BlastHit.3 \ Bio::Search::Hit::Fasta.3 \ @@ -399,6 +518,9 @@ Bio::Search::Hit::HMMERHit.3 \ Bio::Search::Hit::HitFactory.3 \ Bio::Search::Hit::HitI.3 \ + Bio::Search::Hit::PsiBlastHit.3 \ + Bio::Search::Iteration::GenericIteration.3 \ + Bio::Search::Iteration::IterationI.3 \ Bio::Search::Processor.3 \ Bio::Search::Result::BlastResult.3 \ Bio::Search::Result::GenericResult.3 \ @@ -411,92 +533,118 @@ 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::axt.3 \ Bio::SearchIO::blast.3 \ + Bio::SearchIO::blasttable.3 \ Bio::SearchIO::blastxml.3 \ Bio::SearchIO::exonerate.3 \ - Bio::SearchIO::fasta.3 \ - Bio::SearchIO::hmmer.3 \ - Bio::SearchIO::waba.3 \ + Bio::SearchIO::fasta.3 \ + Bio::SearchIO::hmmer.3 \ + Bio::SearchIO::megablast.3 \ + Bio::SearchIO::psl.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::BaseSeqProcessor.3 \ + Bio::Seq::EncodedSeq.3 \ Bio::Seq::LargePrimarySeq.3 \ Bio::Seq::LargeSeq.3 \ - Bio::Seq::PrimaryQual.3 \ - Bio::Seq::PrimedSeq.3 \ - Bio::Seq::QualI.3 \ + Bio::Seq::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::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::Seq::SeqBuilder.3 \ + Bio::Seq::SeqFactory.3 \ + Bio::Seq::SeqFastaSpeedFactory.3 \ + Bio::Seq::SeqWithQuality.3 \ + Bio::Seq::SequenceTrace.3 \ + Bio::Seq::TraceI.3 \ Bio::SeqAnalysisParserI.3 \ - Bio::SeqFeature::AnnotationAdaptor.3 \ - Bio::SeqFeature::Collection.3 \ - Bio::SeqFeature::CollectionI.3 \ - Bio::SeqFeature::Computation.3 \ + Bio::SeqFeature::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::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::Gene::UTR.3 \ Bio::SeqFeature::Generic.3 \ - Bio::SeqFeature::PositionProxy.3 \ - Bio::SeqFeature::Primer.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::TypeMapper.3 \ + Bio::SeqFeature::Tools::Unflattener.3 \ Bio::SeqFeatureI.3 \ Bio::SeqI.3 \ Bio::SeqIO.3 \ Bio::SeqIO::FTHelper.3 \ Bio::SeqIO::MultiFile.3 \ - Bio::SeqIO::abi.3 \ + Bio::SeqIO::abi.3 \ Bio::SeqIO::ace.3 \ - Bio::SeqIO::alf.3 \ - Bio::SeqIO::bsml.3 \ - Bio::SeqIO::chadoxml.3 \ - Bio::SeqIO::ctf.3 \ + Bio::SeqIO::alf.3 \ + Bio::SeqIO::asciitree.3 \ + Bio::SeqIO::bsml.3 \ + Bio::SeqIO::chadoxml.3 \ + Bio::SeqIO::ctf.3 \ Bio::SeqIO::embl.3 \ - Bio::SeqIO::exp.3 \ + Bio::SeqIO::exp.3 \ Bio::SeqIO::fasta.3 \ - Bio::SeqIO::fastq.3 \ + Bio::SeqIO::fastq.3 \ Bio::SeqIO::game.3 \ - Bio::SeqIO::game::seqHandler.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::gcg.3 \ Bio::SeqIO::genbank.3 \ + Bio::SeqIO::kegg.3 \ Bio::SeqIO::largefasta.3 \ - Bio::SeqIO::locuslink.3 \ - Bio::SeqIO::phd.3 \ - Bio::SeqIO::pir.3 \ - Bio::SeqIO::pln.3 \ - Bio::SeqIO::qual.3 \ + Bio::SeqIO::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::swiss.3 \ - Bio::SeqIO::ztr.3 \ + Bio::SeqIO::tab.3 \ + Bio::SeqIO::tigr.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::Atom.3 \ + Bio::Structure::Chain.3 \ + Bio::Structure::Entry.3 \ Bio::Structure::IO.3 \ Bio::Structure::IO::pdb.3 \ Bio::Structure::Model.3 \ @@ -510,77 +658,105 @@ Bio::Symbol::ProteinAlphabet.3 \ Bio::Symbol::Symbol.3 \ Bio::Symbol::SymbolI.3 \ - Bio::Taxonomy.3 \ - Bio::Taxonomy::Taxon.3 \ - Bio::Taxonomy::Tree.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::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::BPbl2seq.3 \ Bio::Tools::BPlite.3 \ - Bio::Tools::BPlite::HSP.3 \ + Bio::Tools::BPlite::HSP.3 \ Bio::Tools::BPlite::Iteration.3 \ - Bio::Tools::BPlite::Sbjct.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::EPCR.3 \ + Bio::Tools::Coil.3 \ + Bio::Tools::ECnumber.3 \ + Bio::Tools::EMBOSS::Palindrome.3 \ + Bio::Tools::EPCR.3 \ Bio::Tools::ESTScan.3 \ - Bio::Tools::Eponine.3 \ - Bio::Tools::Est2Genome.3 \ - Bio::Tools::FootPrinter.3 \ + Bio::Tools::Eponine.3 \ + Bio::Tools::Est2Genome.3 \ + Bio::Tools::FootPrinter.3 \ Bio::Tools::GFF.3 \ - Bio::Tools::Gel.3 \ - Bio::Tools::Genemark.3 \ - Bio::Tools::Genewise.3 \ - Bio::Tools::Genomewise.3 \ + Bio::Tools::Gel.3 \ + Bio::Tools::Geneid.3 \ + Bio::Tools::Genemark.3 \ + Bio::Tools::Genewise.3 \ + Bio::Tools::Genomewise.3 \ Bio::Tools::Genscan.3 \ - Bio::Tools::Grail.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::Hmmpfam.3 \ Bio::Tools::IUPAC.3 \ - Bio::Tools::Lucy.3 \ + Bio::Tools::Lucy.3 \ Bio::Tools::MZEF.3 \ Bio::Tools::OddCodes.3 \ - Bio::Tools::Phylo::Molphy.3 \ - Bio::Tools::Phylo::Molphy::Result.3 \ - Bio::Tools::Phylo::PAML.3 \ - Bio::Tools::Phylo::PAML::Result.3 \ - Bio::Tools::Phylo::Phylip::ProtDist.3 \ + Bio::Tools::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::Prints.3 \ - Bio::Tools::Profile.3 \ - Bio::Tools::Promoterwise.3 \ - Bio::Tools::Pseudowise.3 \ - Bio::Tools::RepeatMasker.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::Pseudowise.3 \ + Bio::Tools::QRNA.3 \ + Bio::Tools::RandomDistFunctions.3 \ + Bio::Tools::RepeatMasker.3 \ Bio::Tools::RestrictionEnzyme.3 \ - Bio::Tools::Run::RemoteBlast.3 \ + Bio::Tools::Run::RemoteBlast.3 \ Bio::Tools::Run::StandAloneBlast.3 \ - Bio::Tools::Run::WrapperBase.3 \ - Bio::Tools::Seg.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::Sigcleave.3 \ - Bio::Tools::Signalp.3 \ + Bio::Tools::Signalp.3 \ Bio::Tools::Sim4::Exon.3 \ Bio::Tools::Sim4::Results.3 \ - Bio::Tools::Tmhmm.3 \ + Bio::Tools::Tmhmm.3 \ Bio::Tools::WWW.3 \ + Bio::Tools::dpAlign.3 \ + Bio::Tools::pICalculator.3 \ Bio::Tools::pSW.3 \ - Bio::Tree::AlleleNode.3 \ - Bio::Tree::Node.3 \ + Bio::Tree::AlleleNode.3 \ + Bio::Tree::Node.3 \ Bio::Tree::NodeI.3 \ Bio::Tree::NodeNHX.3 \ Bio::Tree::RandomFactory.3 \ @@ -590,8 +766,11 @@ Bio::Tree::TreeI.3 \ Bio::TreeIO.3 \ Bio::TreeIO::TreeEventBuilder.3 \ + Bio::TreeIO::lintree.3 \ Bio::TreeIO::newick.3 \ + Bio::TreeIO::nexus.3 \ Bio::TreeIO::nhx.3 \ + Bio::TreeIO::svggraph.3 \ Bio::TreeIO::tabtree.3 \ Bio::UpdateableSeqI.3 \ Bio::Variation::AAChange.3 \ @@ -605,6 +784,11 @@ 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 .include @@ -618,20 +802,16 @@ # now install all extra stuff (docs, examples, scripts, models) post-install: - -.if !defined(NOPORTDOCS) ${MKDIR} ${DATADIR} + ${CP} -R ${WRKSRC}/scripts ${WRKSRC}/models ${DATADIR} ${MKDIR} ${EXAMPLESDIR} + ${CP} -R ${WRKSRC}/examples/* ${EXAMPLESDIR} +.if !defined(NOPORTDOCS) ${MKDIR} ${DOCSDIR} - .for doc in AUTHORS BUGS Changes DEPRECATED FAQ INSTALL LICENSE PLATFORMS README ${INSTALL_MAN} ${WRKSRC}/${doc} ${DOCSDIR} .endfor - ${CP} -R ${WRKSRC}/doc ${DOCSDIR} - ${CP} -R ${WRKSRC}/examples/* ${EXAMPLESDIR} - ${CP} -R ${WRKSRC}/scripts ${DATADIR} - ${CP} -R ${WRKSRC}/models ${DATADIR} - + ${CP} -R ${WRKSRC}/doc ${DOCSDIR} .endif .include Index: pkg-plist =================================================================== RCS file: /home/pcvs/ports/biology/p5-bioperl/pkg-plist,v retrieving revision 1.7 diff -u -u -r1.7 pkg-plist --- pkg-plist 21 Jan 2004 08:34:33 -0000 1.7 +++ pkg-plist 3 Sep 2004 01:59:21 -0000 @@ -759,211 +759,211 @@ %%SITE_PERL%%/Bio/SeqIO/game/gameHandler.pm %%SITE_PERL%%/Bio/SeqIO/game/gameSubs.pm %%SITE_PERL%%/Bio/SeqIO/game/gameWriter.pm -share/doc/bioperl/AUTHORS -share/doc/bioperl/BUGS -share/doc/bioperl/Changes -share/doc/bioperl/DEPRECATED -share/doc/bioperl/FAQ -share/doc/bioperl/INSTALL -share/doc/bioperl/LICENSE -share/doc/bioperl/PLATFORMS -share/doc/bioperl/README -share/doc/bioperl/doc/faq/faq.html -share/doc/bioperl/doc/faq/faq.dtd -share/doc/bioperl/doc/faq/faq.pl -share/doc/bioperl/doc/faq/faq.xml -share/doc/bioperl/doc/howto/examples/graphics/render_features.pl -share/doc/bioperl/doc/howto/examples/graphics/data1.txt -share/doc/bioperl/doc/howto/examples/graphics/embl2picture.pl -share/doc/bioperl/doc/howto/examples/graphics/factor7.embl -share/doc/bioperl/doc/howto/examples/graphics/render_blast1.pl -share/doc/bioperl/doc/howto/examples/graphics/render_blast2.pl -share/doc/bioperl/doc/howto/examples/graphics/render_blast3.pl -share/doc/bioperl/doc/howto/examples/graphics/render_blast4.pl -share/doc/bioperl/doc/howto/examples/graphics/blastn.out -share/doc/bioperl/doc/howto/examples/README -share/doc/bioperl/doc/howto/figs/graphics/fig1.png -share/doc/bioperl/doc/howto/figs/graphics/fig2.png -share/doc/bioperl/doc/howto/figs/graphics/fig3.png -share/doc/bioperl/doc/howto/figs/graphics/fig4.png -share/doc/bioperl/doc/howto/figs/graphics/fig5.png -share/doc/bioperl/doc/howto/figs/graphics/fig6.png -share/doc/bioperl/doc/howto/figs/README 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+%%DATADIR%%/scripts/Bio-DB-GFF/process_gadfly.PLS +%%DATADIR%%/scripts/Bio-DB-GFF/process_ncbi_human.PLS +%%DATADIR%%/scripts/Bio-DB-GFF/process_sgd.PLS +%%DATADIR%%/scripts/Bio-DB-GFF/load_gff.PLS +%%DATADIR%%/scripts/searchio/filter_search.PLS +%%DATADIR%%/scripts/seq/TAG +%%DATADIR%%/scripts/seq/extract_feature_seq.PLS +%%DATADIR%%/scripts/seq/seqconvert.PLS +%%DATADIR%%/scripts/seq/split_seq.PLS +%%DATADIR%%/scripts/seq/translate_seq.PLS +%%DATADIR%%/scripts/seqstats/TAG +%%DATADIR%%/scripts/seqstats/aacomp.PLS +%%DATADIR%%/scripts/seqstats/chaos_plot.PLS +%%DATADIR%%/scripts/seqstats/gccalc.PLS +%%DATADIR%%/scripts/seqstats/oligo_count.PLS +%%DATADIR%%/scripts/taxa/TAG +%%DATADIR%%/scripts/taxa/local_taxonomydb_query.PLS +%%DATADIR%%/scripts/taxa/taxid4species.PLS +%%DATADIR%%/scripts/popgen/composite_LD.PLS +%%DATADIR%%/scripts/popgen/heterogeneity_test.PLS +%%DATADIR%%/scripts/install_bioperl_scripts.pl +%%DATADIR%%/models/population_proposal.txt +%%DATADIR%%/models/README +%%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/biblio.dia @dirrm %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio @dirrm %%SITE_PERL%%/Bio/Das @dirrm %%SITE_PERL%%/Bio/MapIO @@ -1065,50 +1065,50 @@ @dirrm %%SITE_PERL%%/Bio/SeqIO/game @dirrm %%SITE_PERL%%/Bio/SeqIO @dirrm %%SITE_PERL%%/Bio -@dirrm share/doc/bioperl/doc/faq -@dirrm share/doc/bioperl/doc/howto/examples/graphics -@dirrm share/doc/bioperl/doc/howto/examples -@dirrm share/doc/bioperl/doc/howto/figs/graphics -@dirrm share/doc/bioperl/doc/howto/figs -@dirrm share/doc/bioperl/doc/howto/html/images -@dirrm share/doc/bioperl/doc/howto/html -@dirrm share/doc/bioperl/doc/howto/pdf -@dirrm share/doc/bioperl/doc/howto/sgml -@dirrm share/doc/bioperl/doc/howto/txt -@dirrm share/doc/bioperl/doc/howto -@dirrm share/doc/bioperl/doc -@dirrm share/doc/bioperl -@dirrm share/examples/bioperl/align -@dirrm share/examples/bioperl/tools -@dirrm share/examples/bioperl/tk -@dirrm share/examples/bioperl/tree -@dirrm share/examples/bioperl/sirna -@dirrm share/examples/bioperl/searchio -@dirrm share/examples/bioperl/root/lib/Bio -@dirrm share/examples/bioperl/root/lib -@dirrm share/examples/bioperl/root -@dirrm share/examples/bioperl/db -@dirrm share/examples/bioperl/biblio -@dirrm share/examples/bioperl/popgen -@dirrm share/examples/bioperl/biographics -@dirrm share/examples/bioperl/cluster -@dirrm share/examples/bioperl/contributed -@dirrm share/examples/bioperl/liveseq -@dirrm share/examples/bioperl/Bio-DB-GFF -@dirrm share/examples/bioperl -@dirrm share/bioperl/scripts/index -@dirrm share/bioperl/scripts/utilities -@dirrm share/bioperl/scripts/DB -@dirrm share/bioperl/scripts/biblio -@dirrm share/bioperl/scripts/das -@dirrm share/bioperl/scripts/graphics -@dirrm share/bioperl/scripts/tree -@dirrm share/bioperl/scripts/Bio-DB-GFF -@dirrm share/bioperl/scripts/searchio -@dirrm share/bioperl/scripts/seq -@dirrm share/bioperl/scripts/seqstats -@dirrm share/bioperl/scripts/taxa -@dirrm share/bioperl/scripts/popgen -@dirrm share/bioperl/scripts -@dirrm share/bioperl/models -@dirrm share/bioperl +%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/faq +%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/howto/examples/graphics +%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/howto/examples +%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/howto/figs/graphics +%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/howto/figs +%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/howto/html/images +%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/howto/html +%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/howto/pdf +%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/howto/sgml +%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/howto/txt +%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/howto +%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc +%%PORTDOCS%%@dirrm %%DOCSDIR%% +@dirrm %%EXAMPLESDIR%%/align +@dirrm %%EXAMPLESDIR%%/tools +@dirrm %%EXAMPLESDIR%%/tk +@dirrm %%EXAMPLESDIR%%/tree +@dirrm %%EXAMPLESDIR%%/sirna +@dirrm %%EXAMPLESDIR%%/searchio +@dirrm %%EXAMPLESDIR%%/root/lib/Bio +@dirrm %%EXAMPLESDIR%%/root/lib +@dirrm %%EXAMPLESDIR%%/root +@dirrm %%EXAMPLESDIR%%/db +@dirrm %%EXAMPLESDIR%%/biblio +@dirrm %%EXAMPLESDIR%%/popgen +@dirrm %%EXAMPLESDIR%%/biographics +@dirrm %%EXAMPLESDIR%%/cluster +@dirrm %%EXAMPLESDIR%%/contributed +@dirrm %%EXAMPLESDIR%%/liveseq +@dirrm %%EXAMPLESDIR%%/Bio-DB-GFF +@dirrm %%EXAMPLESDIR%% +@dirrm %%DATADIR%%/scripts/index +@dirrm %%DATADIR%%/scripts/utilities +@dirrm %%DATADIR%%/scripts/DB +@dirrm %%DATADIR%%/scripts/biblio +@dirrm %%DATADIR%%/scripts/das +@dirrm %%DATADIR%%/scripts/graphics +@dirrm %%DATADIR%%/scripts/tree +@dirrm %%DATADIR%%/scripts/Bio-DB-GFF +@dirrm %%DATADIR%%/scripts/searchio +@dirrm %%DATADIR%%/scripts/seq +@dirrm %%DATADIR%%/scripts/seqstats +@dirrm %%DATADIR%%/scripts/taxa +@dirrm %%DATADIR%%/scripts/popgen +@dirrm %%DATADIR%%/scripts +@dirrm %%DATADIR%%/models +@dirrm %%DATADIR%%