FreeBSD Bugzilla – Attachment 46458 Details for
Bug 71322
[PATCH] biology/p5-bioperl: update PLIST
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[patch]
p5-bioperl-1.4.patch
p5-bioperl-1.4.patch (text/plain), 41.73 KB, created by
Yen-Ming Lee
on 2004-09-03 03:10:17 UTC
(
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Description:
p5-bioperl-1.4.patch
Filename:
MIME Type:
Creator:
Yen-Ming Lee
Created:
2004-09-03 03:10:17 UTC
Size:
41.73 KB
patch
obsolete
>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 <bsd.port.pre.mk> >@@ -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 <bsd.port.post.mk> >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 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>-share/doc/bioperl/doc/howto/html/images/tip.png >-share/doc/bioperl/doc/howto/html/Flat_Databases.html >-share/doc/bioperl/doc/howto/html/Graphics-HOWTO.html >-share/doc/bioperl/doc/howto/html/OBDA_Access.html >-share/doc/bioperl/doc/howto/html/PAML.html >-share/doc/bioperl/doc/howto/html/README >-share/doc/bioperl/doc/howto/html/SearchIO.html >-share/doc/bioperl/doc/howto/html/SeqIO.html >-share/doc/bioperl/doc/howto/html/SimpleWebAnalysis.html >-share/doc/bioperl/doc/howto/html/e-novative.css >-share/doc/bioperl/doc/howto/pdf/Trees.pdf >-share/doc/bioperl/doc/howto/pdf/Graphics-HOWTO.pdf >-share/doc/bioperl/doc/howto/pdf/OBDA_Access.pdf >-share/doc/bioperl/doc/howto/pdf/PAML.pdf >-share/doc/bioperl/doc/howto/pdf/SearchIO.pdf >-share/doc/bioperl/doc/howto/pdf/SeqIO.pdf >-share/doc/bioperl/doc/howto/pdf/SimpleWebAnalysis.pdf >-share/doc/bioperl/doc/howto/pdf/Flat_Databases.pdf >-share/doc/bioperl/doc/howto/sgml/Trees.sgml >-share/doc/bioperl/doc/howto/sgml/Flat_Databases.sgml 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>-share/examples/bioperl/tools/run_genscan.pl >-share/examples/bioperl/tools/seq_pattern.pl >-share/examples/bioperl/tools/gb_to_gff.pl >-share/examples/bioperl/tk/gsequence.pl >-share/examples/bioperl/tk/hitdisplay.pl >-share/examples/bioperl/tree/paup2phylip.pl >-share/examples/bioperl/sirna/TAG >-share/examples/bioperl/sirna/rnai_finder.cgi >-share/examples/bioperl/searchio/waba2gff.pl >-share/examples/bioperl/searchio/custom_writer.pl >-share/examples/bioperl/searchio/hitwriter.pl >-share/examples/bioperl/searchio/hspwriter.pl >-share/examples/bioperl/searchio/htmlwriter.pl >-share/examples/bioperl/searchio/psiblast_features.pl >-share/examples/bioperl/searchio/psiblast_iterations.pl >-share/examples/bioperl/searchio/rawwriter.pl >-share/examples/bioperl/searchio/resultwriter.pl >-share/examples/bioperl/searchio/blast_example.pl >-share/examples/bioperl/root/lib/Bio/PrimarySeq.pm >-share/examples/bioperl/root/lib/Bio/PrimarySeqI.pm >-share/examples/bioperl/root/lib/Bio/Seq.pm >-share/examples/bioperl/root/lib/Bio/SeqI.pm >-share/examples/bioperl/root/lib/Error.pm >-share/examples/bioperl/root/lib/TestInterface.pm >-share/examples/bioperl/root/lib/TestObject.pm >-share/examples/bioperl/root/README >-share/examples/bioperl/root/exceptions1.pl >-share/examples/bioperl/root/exceptions2.pl >-share/examples/bioperl/root/exceptions3.pl >-share/examples/bioperl/root/exceptions4.pl >-share/examples/bioperl/db/gb2features.pl >-share/examples/bioperl/db/dbfetch >-share/examples/bioperl/db/est_tissue_query.pl >-share/examples/bioperl/db/get_seqs.pl >-share/examples/bioperl/db/getGenBank.pl >-share/examples/bioperl/db/rfetch.pl >-share/examples/bioperl/db/use_registry.pl >-share/examples/bioperl/biblio/biblio_examples.pl >-share/examples/bioperl/biblio/biblio_soap.pl >-share/examples/bioperl/popgen/parse_calc_stats.pl >-share/examples/bioperl/biographics/all_glyphs.pl >-share/examples/bioperl/biographics/dynamic_glyphs.pl 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>+%%EXAMPLESDIR%%/tools/restriction.pl >+%%EXAMPLESDIR%%/tools/run_genscan.pl >+%%EXAMPLESDIR%%/tools/seq_pattern.pl >+%%EXAMPLESDIR%%/tools/gb_to_gff.pl >+%%EXAMPLESDIR%%/tk/gsequence.pl >+%%EXAMPLESDIR%%/tk/hitdisplay.pl >+%%EXAMPLESDIR%%/tree/paup2phylip.pl >+%%EXAMPLESDIR%%/sirna/TAG >+%%EXAMPLESDIR%%/sirna/rnai_finder.cgi >+%%EXAMPLESDIR%%/searchio/waba2gff.pl >+%%EXAMPLESDIR%%/searchio/custom_writer.pl >+%%EXAMPLESDIR%%/searchio/hitwriter.pl >+%%EXAMPLESDIR%%/searchio/hspwriter.pl >+%%EXAMPLESDIR%%/searchio/htmlwriter.pl >+%%EXAMPLESDIR%%/searchio/psiblast_features.pl >+%%EXAMPLESDIR%%/searchio/psiblast_iterations.pl >+%%EXAMPLESDIR%%/searchio/rawwriter.pl >+%%EXAMPLESDIR%%/searchio/resultwriter.pl >+%%EXAMPLESDIR%%/searchio/blast_example.pl >+%%EXAMPLESDIR%%/root/lib/Bio/PrimarySeq.pm >+%%EXAMPLESDIR%%/root/lib/Bio/PrimarySeqI.pm >+%%EXAMPLESDIR%%/root/lib/Bio/Seq.pm >+%%EXAMPLESDIR%%/root/lib/Bio/SeqI.pm >+%%EXAMPLESDIR%%/root/lib/Error.pm >+%%EXAMPLESDIR%%/root/lib/TestInterface.pm >+%%EXAMPLESDIR%%/root/lib/TestObject.pm >+%%EXAMPLESDIR%%/root/README >+%%EXAMPLESDIR%%/root/exceptions1.pl >+%%EXAMPLESDIR%%/root/exceptions2.pl >+%%EXAMPLESDIR%%/root/exceptions3.pl >+%%EXAMPLESDIR%%/root/exceptions4.pl >+%%EXAMPLESDIR%%/db/gb2features.pl >+%%EXAMPLESDIR%%/db/dbfetch >+%%EXAMPLESDIR%%/db/est_tissue_query.pl >+%%EXAMPLESDIR%%/db/get_seqs.pl >+%%EXAMPLESDIR%%/db/getGenBank.pl >+%%EXAMPLESDIR%%/db/rfetch.pl >+%%EXAMPLESDIR%%/db/use_registry.pl >+%%EXAMPLESDIR%%/biblio/biblio_examples.pl >+%%EXAMPLESDIR%%/biblio/biblio_soap.pl >+%%EXAMPLESDIR%%/popgen/parse_calc_stats.pl >+%%EXAMPLESDIR%%/biographics/all_glyphs.pl >+%%EXAMPLESDIR%%/biographics/dynamic_glyphs.pl >+%%EXAMPLESDIR%%/biographics/feature_data.gff >+%%EXAMPLESDIR%%/biographics/feature_data.txt >+%%EXAMPLESDIR%%/biographics/lots_of_glyphs.pl >+%%EXAMPLESDIR%%/biographics/render_sequence.pl >+%%EXAMPLESDIR%%/cluster/dbsnp.pl >+%%EXAMPLESDIR%%/contributed/nmrpdb_parse.pl >+%%EXAMPLESDIR%%/contributed/prosite2perl.pl >+%%EXAMPLESDIR%%/contributed/rebase2list.pl >+%%EXAMPLESDIR%%/liveseq/change_gene.pl >+%%EXAMPLESDIR%%/Bio-DB-GFF/load_ucsc.pl >+%%EXAMPLESDIR%%/subsequence.cgi >+%%EXAMPLESDIR%%/longorf.pl >+%%EXAMPLESDIR%%/make_mrna_protein.pl >+%%EXAMPLESDIR%%/bioperl.pl >+%%EXAMPLESDIR%%/make_primers.pl >+%%EXAMPLESDIR%%/rev_and_trans.pl >+%%EXAMPLESDIR%%/revcom_dir.pl >+%%EXAMPLESDIR%%/generate_random_seq.pl >+%%DATADIR%%/scripts/index/TAG >+%%DATADIR%%/scripts/index/bp_fetch.PLS >+%%DATADIR%%/scripts/index/bp_index.PLS >+%%DATADIR%%/scripts/utilities/seq_length.PLS >+%%DATADIR%%/scripts/utilities/README >+%%DATADIR%%/scripts/utilities/TAG >+%%DATADIR%%/scripts/utilities/bp_mrtrans.PLS >+%%DATADIR%%/scripts/utilities/bp_sreformat.PLS >+%%DATADIR%%/scripts/utilities/dbsplit.PLS >+%%DATADIR%%/scripts/utilities/mask_by_search.PLS >+%%DATADIR%%/scripts/utilities/mutate.PLS >+%%DATADIR%%/scripts/utilities/pairwise_kaks.PLS >+%%DATADIR%%/scripts/utilities/remote_blast.PLS >+%%DATADIR%%/scripts/utilities/search2BSML.PLS >+%%DATADIR%%/scripts/utilities/search2alnblocks.PLS >+%%DATADIR%%/scripts/utilities/search2gff.PLS >+%%DATADIR%%/scripts/utilities/search2tribe.PLS >+%%DATADIR%%/scripts/utilities/bp_nrdb.PLS >+%%DATADIR%%/scripts/DB/TAG >+%%DATADIR%%/scripts/DB/biofetch_genbank_proxy.PLS >+%%DATADIR%%/scripts/DB/bioflat_index.PLS >+%%DATADIR%%/scripts/DB/biogetseq.PLS >+%%DATADIR%%/scripts/DB/flanks.PLS >+%%DATADIR%%/scripts/biblio/TAG >+%%DATADIR%%/scripts/biblio/biblio.PLS >+%%DATADIR%%/scripts/das/README >+%%DATADIR%%/scripts/das/TAG >+%%DATADIR%%/scripts/graphics/frend.PLS >+%%DATADIR%%/scripts/graphics/README >+%%DATADIR%%/scripts/graphics/TAG >+%%DATADIR%%/scripts/graphics/feature_draw.PLS >+%%DATADIR%%/scripts/graphics/search_overview.PLS >+%%DATADIR%%/scripts/tree/TAG >+%%DATADIR%%/scripts/tree/blast2tree.PLS >+%%DATADIR%%/scripts/Bio-DB-GFF/process_wormbase.PLS >+%%DATADIR%%/scripts/Bio-DB-GFF/README >+%%DATADIR%%/scripts/Bio-DB-GFF/TAG >+%%DATADIR%%/scripts/Bio-DB-GFF/bp_genbank2gff.PLS >+%%DATADIR%%/scripts/Bio-DB-GFF/bulk_load_gff.PLS >+%%DATADIR%%/scripts/Bio-DB-GFF/fast_load_gff.PLS >+%%DATADIR%%/scripts/Bio-DB-GFF/generate_histogram.PLS >+%%DATADIR%%/scripts/Bio-DB-GFF/load_ucsc.pl >+%%DATADIR%%/scripts/Bio-DB-GFF/pg_bulk_load_gff.PLS >+%%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%%
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: 46458