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desc
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1.17
log
@2009-05-31 biology/p5-bioperl-devel: no longer under development
2009-05-31 biology/p5-bioperl-run-devel: no longer under development
2009-06-01 net-p2p/deluge05: use net-p2p/deluge instead
2009-06-03 textproc/gmat: failed to build for a long time, no maintainer and apparently no users either
@
text
@# New ports collection makefile for:	biology/p5-bioperl-devel
# Date created:		21 November 2005
# Whom:	      		Mauricio Herrera Cuadra <mauricio@@arareko.net>
#
# $FreeBSD: ports/biology/p5-bioperl-devel/Makefile,v 1.16 2009/03/19 19:29:34 miwi Exp $
#

PORTNAME=	bioperl
PORTVERSION=	1.5.2
CATEGORIES=	biology perl5
MASTER_SITES=	http://bioperl.org/DIST/
PKGNAMEPREFIX=	p5-
DISTNAME=	${PORTNAME}-${PORTVERSION}_102

MAINTAINER=	mauricio@@arareko.net
COMMENT=	A collection of Perl modules for bioinformatics (developer release)

BUILD_DEPENDS=	${LOCALBASE}/lib/perl5/${PERL_VERSION}/Text/Wrap.pm:${PORTSDIR}/lang/${PERL_PORT} \
		${LOCALBASE}/lib/perl5/${PERL_VERSION}/${PERL_ARCH}/DB_File.pm:${PORTSDIR}/lang/${PERL_PORT} \
		${SITE_PERL}/Bio/ASN1/EntrezGene.pm:${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 \
		${SITE_PERL}/Set/Scalar.pm:${PORTSDIR}/devel/p5-Set-Scalar \
		${SITE_PERL}/SOAP/Lite.pm:${PORTSDIR}/net/p5-SOAP-Lite \
		${SITE_PERL}/Spreadsheet/ParseExcel.pm:${PORTSDIR}/textproc/p5-Spreadsheet-ParseExcel \
		${SITE_PERL}/SVG.pm:${PORTSDIR}/textproc/p5-SVG \
		${SITE_PERL}/SVG/Graph.pm:${PORTSDIR}/graphics/p5-SVG-Graph \
		${SITE_PERL}/Test/Harness.pm:${PORTSDIR}/devel/p5-Test-Harness \
		${SITE_PERL}/Text/Shellwords.pm:${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 \
		${SITE_PERL}/XML/SAX.pm:${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 \
		${SITE_PERL}/XML/Writer.pm:${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}/Convert/Binary/C.pm:${PORTSDIR}/converters/p5-Convert-Binary-C \
		${SITE_PERL}/${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 \
		${SITE_PERL}/${PERL_ARCH}/XML/Parser.pm:${PORTSDIR}/textproc/p5-XML-Parser
RUN_DEPENDS=	${BUILD_DEPENDS}

CONFLICTS=	p5-bioperl-1.[02468]*

LATEST_LINK=	p5-bioperl-devel

DEPRECATED=	no longer under development
EXPIRATION_DATE=	2009-05-31

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_contig_draw.pl.1 \
		bp_dbsplit.pl.1 \
		bp_embl2picture.pl.1 \
		bp_extract_feature_seq.pl.1 \
		bp_fast_load_gff.pl.1 \
		bp_fastam9_to_table.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_genbank2gff3.pl.1 \
		bp_generate_histogram.pl.1 \
		bp_glyphs1-demo.pl.1 \
		bp_glyphs2-demo.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_parse_hmmsearch.pl.1 \
		bp_process_gadfly.pl.1 \
		bp_process_sgd.pl.1 \
		bp_process_wormbase.pl.1 \
		bp_query_entrez_taxa.pl.1 \
		bp_remote_blast.pl.1 \
		bp_search_overview.pl.1 \
		bp_search2alnblocks.pl.1 \
		bp_search2BSML.pl.1 \
		bp_search2gff.pl.1 \
		bp_search2table.pl.1 \
		bp_search2tribe.pl.1 \
		bp_seq_length.pl.1 \
		bp_seqconvert.pl.1 \
		bp_seqret.pl.1 \
		bp_split_seq.pl.1 \
		bp_sreformat.pl.1 \
		bp_taxid4species.pl.1 \
		bp_taxonomy2tree.pl.1 \
		bp_translate_seq.pl.1 \
		bp_tree2pag.pl.1 \
		bp_unflatten_seq.pl.1

MAN3=		Bio::Align::AlignI.3 \
		Bio::Align::DNAStatistics.3 \
		Bio::Align::PairwiseStatistics.3 \
		Bio::Align::ProteinStatistics.3 \
		Bio::Align::StatisticsI.3 \
		Bio::Align::Utilities.3 \
		Bio::AlignIO.3 \
		Bio::AlignIO::bl2seq.3 \
		Bio::AlignIO::clustalw.3 \
		Bio::AlignIO::emboss.3 \
		Bio::AlignIO::fasta.3 \
		Bio::AlignIO::largemultifasta.3 \
		Bio::AlignIO::maf.3 \
		Bio::AlignIO::mase.3 \
		Bio::AlignIO::mega.3 \
		Bio::AlignIO::meme.3 \
		Bio::AlignIO::metafasta.3 \
		Bio::AlignIO::msf.3 \
		Bio::AlignIO::nexus.3 \
		Bio::AlignIO::pfam.3 \
		Bio::AlignIO::phylip.3 \
		Bio::AlignIO::po.3 \
		Bio::AlignIO::prodom.3 \
		Bio::AlignIO::psi.3 \
		Bio::AlignIO::selex.3 \
		Bio::AlignIO::stockholm.3 \
		Bio::AnalysisI.3 \
		Bio::AnalysisParserI.3 \
		Bio::AnalysisResultI.3 \
		Bio::AnnotatableI.3 \
		Bio::Annotation::AnnotationFactory.3 \
		Bio::Annotation::Collection.3 \
		Bio::Annotation::Comment.3 \
		Bio::Annotation::DBLink.3 \
		Bio::Annotation::OntologyTerm.3 \
		Bio::Annotation::Reference.3 \
		Bio::Annotation::SimpleValue.3 \
		Bio::Annotation::StructuredValue.3 \
		Bio::Annotation::Target.3 \
		Bio::Annotation::TypeManager.3 \
		Bio::AnnotationCollectionI.3 \
		Bio::AnnotationI.3 \
		Bio::Assembly::Contig.3 \
		Bio::Assembly::ContigAnalysis.3 \
		Bio::Assembly::IO.3 \
		Bio::Assembly::IO::ace.3 \
		Bio::Assembly::IO::phrap.3 \
		Bio::Assembly::Scaffold.3 \
		Bio::Assembly::ScaffoldI.3 \
		Bio::Assembly::Singlet.3 \
		Bio::Biblio.3 \
		Bio::Biblio::Article.3 \
		Bio::Biblio::BiblioBase.3 \
		Bio::Biblio::Book.3 \
		Bio::Biblio::BookArticle.3 \
		Bio::Biblio::IO.3 \
		Bio::Biblio::IO::medline2ref.3 \
		Bio::Biblio::IO::medlinexml.3 \
		Bio::Biblio::IO::pubmed2ref.3 \
		Bio::Biblio::IO::pubmedxml.3 \
		Bio::Biblio::Journal.3 \
		Bio::Biblio::JournalArticle.3 \
		Bio::Biblio::MedlineArticle.3 \
		Bio::Biblio::MedlineBook.3 \
		Bio::Biblio::MedlineBookArticle.3 \
		Bio::Biblio::MedlineJournal.3 \
		Bio::Biblio::MedlineJournalArticle.3 \
		Bio::Biblio::Organisation.3 \
		Bio::Biblio::Patent.3 \
		Bio::Biblio::Person.3 \
		Bio::Biblio::Proceeding.3 \
		Bio::Biblio::Provider.3 \
		Bio::Biblio::PubmedArticle.3 \
		Bio::Biblio::PubmedBookArticle.3 \
		Bio::Biblio::PubmedJournalArticle.3 \
		Bio::Biblio::Ref.3 \
		Bio::Biblio::Service.3 \
		Bio::Biblio::TechReport.3 \
		Bio::Biblio::Thesis.3 \
		Bio::Biblio::WebResource.3 \
		Bio::Cluster::ClusterFactory.3 \
		Bio::Cluster::FamilyI.3 \
		Bio::Cluster::SequenceFamily.3 \
		Bio::Cluster::UniGene.3 \
		Bio::Cluster::UniGeneI.3 \
		Bio::ClusterI.3 \
		Bio::ClusterIO.3 \
		Bio::ClusterIO::dbsnp.3 \
		Bio::ClusterIO::unigene.3 \
		Bio::CodonUsage::IO.3 \
		Bio::CodonUsage::Table.3 \
		Bio::ConfigData.3 \
		Bio::Coordinate::Chain.3 \
		Bio::Coordinate::Collection.3 \
		Bio::Coordinate::ExtrapolatingPair.3 \
		Bio::Coordinate::GeneMapper.3 \
		Bio::Coordinate::Graph.3 \
		Bio::Coordinate::MapperI.3 \
		Bio::Coordinate::Pair.3 \
		Bio::Coordinate::Result.3 \
		Bio::Coordinate::Result::Gap.3 \
		Bio::Coordinate::Result::Match.3 \
		Bio::Coordinate::ResultI.3 \
		Bio::Coordinate::Utils.3 \
		Bio::DB::Ace.3 \
		Bio::DB::Biblio::biofetch.3 \
		Bio::DB::Biblio::eutils.3 \
		Bio::DB::Biblio::pdf.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::EUtilities::Cookie.3 \
		Bio::DB::EUtilities::ElinkData.3 \
		Bio::DB::EUtilities::efetch.3 \
		Bio::DB::EUtilities::egquery.3 \
		Bio::DB::EUtilities::einfo.3 \
		Bio::DB::EUtilities::elink.3 \
		Bio::DB::EUtilities::epost.3 \
		Bio::DB::EUtilities::esearch.3 \
		Bio::DB::EUtilities::esummary.3 \
		Bio::DB::EntrezGene.3 \
		Bio::DB::Expression.3 \
		Bio::DB::Expression::geo.3 \
		Bio::DB::Failover.3 \
		Bio::DB::Fasta.3 \
		Bio::DB::FileCache.3 \
		Bio::DB::Flat.3 \
		Bio::DB::Flat::BDB.3 \
		Bio::DB::Flat::BDB::embl.3 \
		Bio::DB::Flat::BDB::fasta.3 \
		Bio::DB::Flat::BDB::genbank.3 \
		Bio::DB::Flat::BDB::swiss.3 \
		Bio::DB::Flat::BDB::swissprot.3 \
		Bio::DB::Flat::BinarySearch.3 \
		Bio::DB::GDB.3 \
		Bio::DB::GenericWebDBI.3 \
		Bio::DB::GFF.3 \
		Bio::DB::GFF::Adaptor::ace.3 \
		Bio::DB::GFF::Adaptor::berkeleydb.3 \
		Bio::DB::GFF::Adaptor::berkeleydb::iterator.3 \
		Bio::DB::GFF::Adaptor::biofetch.3 \
		Bio::DB::GFF::Adaptor::biofetch_oracle.3 \
		Bio::DB::GFF::Adaptor::dbi.3 \
		Bio::DB::GFF::Adaptor::dbi::caching_handle.3 \
		Bio::DB::GFF::Adaptor::dbi::iterator.3 \
		Bio::DB::GFF::Adaptor::dbi::mysql.3 \
		Bio::DB::GFF::Adaptor::dbi::mysqlace.3 \
		Bio::DB::GFF::Adaptor::dbi::mysqlcmap.3 \
		Bio::DB::GFF::Adaptor::dbi::mysqlopt.3 \
		Bio::DB::GFF::Adaptor::dbi::oracle.3 \
		Bio::DB::GFF::Adaptor::dbi::oracleace.3 \
		Bio::DB::GFF::Adaptor::dbi::pg.3 \
		Bio::DB::GFF::Adaptor::dbi::pg_fts.3 \
		Bio::DB::GFF::Adaptor::memory.3 \
		Bio::DB::GFF::Adaptor::memory::feature_serializer.3 \
		Bio::DB::GFF::Adaptor::memory::iterator.3 \
		Bio::DB::GFF::Aggregator.3 \
		Bio::DB::GFF::Aggregator::alignment.3 \
		Bio::DB::GFF::Aggregator::clone.3 \
		Bio::DB::GFF::Aggregator::coding.3 \
		Bio::DB::GFF::Aggregator::match.3 \
		Bio::DB::GFF::Aggregator::none.3 \
		Bio::DB::GFF::Aggregator::processed_transcript.3 \
		Bio::DB::GFF::Aggregator::so_transcript.3 \
		Bio::DB::GFF::Aggregator::transcript.3 \
		Bio::DB::GFF::Aggregator::ucsc_acembly.3 \
		Bio::DB::GFF::Aggregator::ucsc_ensgene.3 \
		Bio::DB::GFF::Aggregator::ucsc_genscan.3 \
		Bio::DB::GFF::Aggregator::ucsc_refgene.3 \
		Bio::DB::GFF::Aggregator::ucsc_sanger22.3 \
		Bio::DB::GFF::Aggregator::ucsc_sanger22pseudo.3 \
		Bio::DB::GFF::Aggregator::ucsc_softberry.3 \
		Bio::DB::GFF::Aggregator::ucsc_twinscan.3 \
		Bio::DB::GFF::Aggregator::ucsc_unigene.3 \
		Bio::DB::GFF::Featname.3 \
		Bio::DB::GFF::Feature.3 \
		Bio::DB::GFF::Homol.3 \
		Bio::DB::GFF::RelSegment.3 \
		Bio::DB::GFF::Segment.3 \
		Bio::DB::GFF::Typename.3 \
		Bio::DB::GFF::Util::Binning.3 \
		Bio::DB::GFF::Util::Rearrange.3 \
		Bio::DB::GenBank.3 \
		Bio::DB::GenPept.3 \
		Bio::DB::InMemoryCache.3 \
		Bio::DB::LocationI.3 \
		Bio::DB::MeSH.3 \
		Bio::DB::NCBIHelper.3 \
		Bio::DB::Query::GenBank.3 \
		Bio::DB::Query::WebQuery.3 \
		Bio::DB::QueryI.3 \
		Bio::DB::RandomAccessI.3 \
		Bio::DB::ReferenceI.3 \
		Bio::DB::RefSeq.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::GFF3Loader.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::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 \
		Bio::DasI.3 \
		Bio::DescribableI.3 \
		Bio::Event::EventGeneratorI.3 \
		Bio::Event::EventHandlerI.3 \
		Bio::Expression::Contact.3 \
		Bio::Expression::DataSet.3 \
		Bio::Expression::FeatureGroup.3 \
		Bio::Expression::FeatureGroup::FeatureGroupMas50.3 \
		Bio::Expression::FeatureI.3 \
		Bio::Expression::FeatureSet::FeatureSetMas50.3 \
		Bio::Expression::Platform.3 \
		Bio::Expression::ProbeI.3 \
		Bio::Expression::Sample.3 \
		Bio::Factory::AnalysisI.3 \
		Bio::Factory::ApplicationFactoryI.3 \
		Bio::Factory::DriverFactory.3 \
		Bio::Factory::FTLocationFactory.3 \
		Bio::Factory::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 \
		Bio::Factory::SequenceProcessorI.3 \
		Bio::Factory::SequenceStreamI.3 \
		Bio::Factory::TreeFactoryI.3 \
		Bio::FeatureHolderI.3 \
		Bio::FeatureIO.3 \
		Bio::FeatureIO::bed.3 \
		Bio::FeatureIO::gff.3 \
		Bio::FeatureIO::gtf.3 \
		Bio::FeatureIO::interpro.3 \
		Bio::FeatureIO::ptt.3 \
		Bio::Graph::Edge.3 \
		Bio::Graph::IO.3 \
		Bio::Graph::IO::dip.3 \
		Bio::Graph::IO::psi_xml.3 \
		Bio::Graph::ProteinGraph.3 \
		Bio::Graph::SimpleGraph.3 \
		Bio::Graph::SimpleGraph::Traversal.3 \
		Bio::Graphics.3 \
		Bio::Graphics::ConfiguratorI.3 \
		Bio::Graphics::Feature.3 \
		Bio::Graphics::FeatureBase.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::broken_line.3 \
		Bio::Graphics::Glyph::cds.3 \
		Bio::Graphics::Glyph::christmas_arrow.3 \
		Bio::Graphics::Glyph::crossbox.3 \
		Bio::Graphics::Glyph::dashed_line.3 \
		Bio::Graphics::Glyph::diamond.3 \
		Bio::Graphics::Glyph::dna.3 \
		Bio::Graphics::Glyph::dot.3 \
		Bio::Graphics::Glyph::dumbbell.3 \
		Bio::Graphics::Glyph::ellipse.3 \
		Bio::Graphics::Glyph::ex.3 \
		Bio::Graphics::Glyph::extending_arrow.3 \
		Bio::Graphics::Glyph::flag.3 \
		Bio::Graphics::Glyph::gene.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::image.3 \
		Bio::Graphics::Glyph::lightning.3 \
		Bio::Graphics::Glyph::line.3 \
		Bio::Graphics::Glyph::merge_parts.3 \
		Bio::Graphics::Glyph::merged_alignment.3 \
		Bio::Graphics::Glyph::minmax.3 \
		Bio::Graphics::Glyph::oval.3 \
		Bio::Graphics::Glyph::pentagram.3 \
		Bio::Graphics::Glyph::pinsertion.3 \
		Bio::Graphics::Glyph::primers.3 \
		Bio::Graphics::Glyph::processed_transcript.3 \
		Bio::Graphics::Glyph::protein.3 \
		Bio::Graphics::Glyph::ragged_ends.3 \
		Bio::Graphics::Glyph::redgreen_box.3 \
		Bio::Graphics::Glyph::redgreen_segment.3 \
		Bio::Graphics::Glyph::repeating_shape.3 \
		Bio::Graphics::Glyph::rndrect.3 \
		Bio::Graphics::Glyph::ruler_arrow.3 \
		Bio::Graphics::Glyph::saw_teeth.3 \
		Bio::Graphics::Glyph::segmented_keyglyph.3 \
		Bio::Graphics::Glyph::segments.3 \
		Bio::Graphics::Glyph::so_transcript.3 \
		Bio::Graphics::Glyph::span.3 \
		Bio::Graphics::Glyph::splice_site.3 \
		Bio::Graphics::Glyph::text_in_box.3 \
		Bio::Graphics::Glyph::three_letters.3 \
		Bio::Graphics::Glyph::tic_tac_toe.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::two_bolts.3 \
		Bio::Graphics::Glyph::wave.3 \
		Bio::Graphics::Glyph::weighted_arrow.3 \
		Bio::Graphics::Glyph::whiskerplot.3 \
		Bio::Graphics::Glyph::xyplot.3 \
		Bio::Graphics::Panel.3 \
		Bio::Graphics::Pictogram.3 \
		Bio::Graphics::RendererI.3 \
		Bio::Graphics::Util.3 \
		Bio::IdCollectionI.3 \
		Bio::IdentifiableI.3 \
		Bio::Index::Abstract.3 \
		Bio::Index::AbstractSeq.3 \
		Bio::Index::Blast.3 \
		Bio::Index::EMBL.3 \
		Bio::Index::Fasta.3 \
		Bio::Index::Fastq.3 \
		Bio::Index::GenBank.3 \
		Bio::Index::Hmmer.3 \
		Bio::Index::Qual.3 \
		Bio::Index::SwissPfam.3 \
		Bio::Index::Swissprot.3 \
		Bio::LiveSeq::AARange.3 \
		Bio::LiveSeq::Chain.3 \
		Bio::LiveSeq::ChainI.3 \
		Bio::LiveSeq::DNA.3 \
		Bio::LiveSeq::Exon.3 \
		Bio::LiveSeq::Gene.3 \
		Bio::LiveSeq::IO::BioPerl.3 \
		Bio::LiveSeq::IO::Loader.3 \
		Bio::LiveSeq::Intron.3 \
		Bio::LiveSeq::Mutation.3 \
		Bio::LiveSeq::Mutator.3 \
		Bio::LiveSeq::Prim_Transcript.3 \
		Bio::LiveSeq::Range.3 \
		Bio::LiveSeq::Repeat_Region.3 \
		Bio::LiveSeq::Repeat_Unit.3 \
		Bio::LiveSeq::SeqI.3 \
		Bio::LiveSeq::Transcript.3 \
		Bio::LiveSeq::Translation.3 \
		Bio::LocatableSeq.3 \
		Bio::Location::Atomic.3 \
		Bio::Location::AvWithinCoordPolicy.3 \
		Bio::Location::CoordinatePolicyI.3 \
		Bio::Location::Fuzzy.3 \
		Bio::Location::FuzzyLocationI.3 \
		Bio::Location::NarrowestCoordPolicy.3 \
		Bio::Location::Simple.3 \
		Bio::Location::Split.3 \
		Bio::Location::SplitLocationI.3 \
		Bio::Location::WidestCoordPolicy.3 \
		Bio::LocationI.3 \
		Bio::Map::Clone.3 \
		Bio::Map::Contig.3 \
		Bio::Map::CytoMap.3 \
		Bio::Map::CytoMarker.3 \
		Bio::Map::CytoPosition.3 \
		Bio::Map::EntityI.3 \
		Bio::Map::FPCMarker.3 \
		Bio::Map::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::PositionHandler.3 \
		Bio::Map::PositionHandlerI.3 \
		Bio::Map::Physical.3 \
		Bio::Map::Position.3 \
		Bio::Map::PositionI.3 \
		Bio::Map::Relative.3 \
		Bio::Map::RelativeI.3 \
		Bio::Map::SimpleMap.3 \
		Bio::MapIO.3 \
		Bio::MapIO::fpc.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::masta.3 \
		Bio::Matrix::PSM::IO::meme.3 \
		Bio::Matrix::PSM::IO::psiblast.3 \
		Bio::Matrix::PSM::IO::transfac.3 \
		Bio::Matrix::PSM::InstanceSite.3 \
		Bio::Matrix::PSM::InstanceSiteI.3 \
		Bio::Matrix::PSM::ProtMatrix.3 \
		Bio::Matrix::PSM::ProtPsm.3 \
		Bio::Matrix::PSM::Psm.3 \
		Bio::Matrix::PSM::PsmHeader.3 \
		Bio::Matrix::PSM::PsmHeaderI.3 \
		Bio::Matrix::PSM::PsmI.3 \
		Bio::Matrix::PSM::SiteMatrix.3 \
		Bio::Matrix::PSM::SiteMatrixI.3 \
		Bio::Matrix::PhylipDist.3 \
		Bio::Matrix::Scoring.3 \
		Bio::Ontology::DocumentRegistry.3 \
		Bio::Ontology::GOterm.3 \
		Bio::Ontology::InterProTerm.3 \
		Bio::Ontology::OBOEngine.3 \
		Bio::Ontology::OBOterm.3 \
		Bio::Ontology::Ontology.3 \
		Bio::Ontology::OntologyEngineI.3 \
		Bio::Ontology::OntologyI.3 \
		Bio::OntologyIO::obo.3 \
		Bio::Ontology::OntologyStore.3 \
		Bio::Ontology::Path.3 \
		Bio::Ontology::PathI.3 \
		Bio::Ontology::Relationship.3 \
		Bio::Ontology::RelationshipFactory.3 \
		Bio::Ontology::RelationshipI.3 \
		Bio::Ontology::RelationshipType.3 \
		Bio::Ontology::SimpleGOEngine.3 \
		Bio::Ontology::SimpleGOEngine::GraphAdaptor.3 \
		Bio::Ontology::SimpleGOEngine::GraphAdaptor02.3 \
		Bio::Ontology::SimpleOntologyEngine.3 \
		Bio::Ontology::Term.3 \
		Bio::Ontology::TermFactory.3 \
		Bio::Ontology::TermI.3 \
		Bio::OntologyIO.3 \
		Bio::OntologyIO::Handlers::BaseSAXHandler.3 \
		Bio::OntologyIO::Handlers::InterProHandler.3 \
		Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler.3 \
		Bio::OntologyIO::InterProParser.3 \
		Bio::OntologyIO::dagflat.3 \
		Bio::OntologyIO::goflat.3 \
		Bio::OntologyIO::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 \
		Bio::Phenotype::OMIM::OMIMentryAllelicVariant.3 \
		Bio::Phenotype::OMIM::OMIMparser.3 \
		Bio::Phenotype::Phenotype.3 \
		Bio::Phenotype::PhenotypeI.3 \
		Bio::PopGen::Genotype.3 \
		Bio::PopGen::GenotypeI.3 \
		Bio::PopGen::HtSNP.3 \
		Bio::PopGen::IO.3 \
		Bio::PopGen::IO::csv.3 \
		Bio::PopGen::IO::hapmap.3 \
		Bio::PopGen::IO::phase.3 \
		Bio::PopGen::IO::prettybase.3 \
		Bio::PopGen::Individual.3 \
		Bio::PopGen::IndividualI.3 \
		Bio::PopGen::Marker.3 \
		Bio::PopGen::MarkerI.3 \
		Bio::PopGen::PopStats.3 \
		Bio::PopGen::Population.3 \
		Bio::PopGen::PopulationI.3 \
		Bio::PopGen::Simulation::Coalescent.3 \
		Bio::PopGen::Simulation::GeneticDrift.3 \
		Bio::PopGen::Statistics.3 \
		Bio::PopGen::TagHaplotype.3 \
		Bio::PopGen::Utilities.3 \
		Bio::PrimarySeq.3 \
		Bio::PrimarySeqI.3 \
		Bio::PullParserI.3 \
		Bio::Range.3 \
		Bio::RangeI.3 \
		Bio::Restriction::Analysis.3 \
		Bio::Restriction::Enzyme.3 \
		Bio::Restriction::Enzyme::MultiCut.3 \
		Bio::Restriction::Enzyme::MultiSite.3 \
		Bio::Restriction::EnzymeCollection.3 \
		Bio::Restriction::EnzymeI.3 \
		Bio::Restriction::IO.3 \
		Bio::Restriction::IO::bairoch.3 \
		Bio::Restriction::IO::base.3 \
		Bio::Restriction::IO::itype2.3 \
		Bio::Restriction::IO::withrefm.3 \
		Bio::Root::Exception.3 \
		Bio::Root::HTTPget.3 \
		Bio::Root::IO.3 \
		Bio::Root::Root.3 \
		Bio::Root::RootI.3 \
		Bio::Root::Storable.3 \
		Bio::Root::Version.3 \
		Bio::Search::BlastStatistics.3 \
		Bio::Search::BlastUtils.3 \
		Bio::Search::DatabaseI.3 \
		Bio::Search::GenericDatabase.3 \
		Bio::Search::GenericStatistics.3 \
		Bio::Search::HSP::BlastHSP.3 \
		Bio::Search::HSP::FastaHSP.3 \
		Bio::Search::HSP::GenericHSP.3 \
		Bio::Search::HSP::HMMERHSP.3 \
		Bio::Search::HSP::HmmpfamHSP.3 \
		Bio::Search::HSP::HSPFactory.3 \
		Bio::Search::HSP::HSPI.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::Fasta.3 \
		Bio::Search::Hit::GenericHit.3 \
		Bio::Search::Hit::HmmpfamHit.3 \
		Bio::Search::Hit::HMMERHit.3 \
		Bio::Search::Hit::HitFactory.3 \
		Bio::Search::Hit::HitI.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::BlastResult.3 \
		Bio::Search::Result::GenericResult.3 \
		Bio::Search::Result::HmmpfamResult.3 \
		Bio::Search::Result::HMMERResult.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 \
		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::hmmer_pull.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::LargeLocatableSeq.3 \
		Bio::Seq::LargePrimarySeq.3 \
		Bio::Seq::LargeSeq.3 \
		Bio::Seq::LargeSeqI.3 \
		Bio::Seq::Meta.3 \
		Bio::Seq::Meta::Array.3 \
		Bio::Seq::MetaI.3 \
		Bio::Seq::PrimaryQual.3 \
		Bio::Seq::PrimedSeq.3 \
		Bio::Seq::QualI.3 \
		Bio::Seq::Quality.3 \
		Bio::Seq::RichSeq.3 \
		Bio::Seq::RichSeqI.3 \
		Bio::Seq::SeqBuilder.3 \
		Bio::Seq::SeqFactory.3 \
		Bio::Seq::SeqFastaSpeedFactory.3 \
		Bio::Seq::SeqWithQuality.3 \
		Bio::Seq::SequenceTrace.3 \
		Bio::Seq::TraceI.3 \
		Bio::SeqAnalysisParserI.3 \
		Bio::SeqFeature::Annotated.3 \
		Bio::SeqFeature::AnnotationAdaptor.3 \
		Bio::SeqFeature::Collection.3 \
		Bio::SeqFeature::CollectionI.3 \
		Bio::SeqFeature::Computation.3 \
		Bio::SeqFeature::FeaturePair.3 \
		Bio::SeqFeature::Gene::Exon.3 \
		Bio::SeqFeature::Gene::ExonI.3 \
		Bio::SeqFeature::Gene::GeneStructure.3 \
		Bio::SeqFeature::Gene::GeneStructureI.3 \
		Bio::SeqFeature::Gene::Intron.3 \
		Bio::SeqFeature::Gene::NC_Feature.3 \
		Bio::SeqFeature::Gene::Poly_A_site.3 \
		Bio::SeqFeature::Gene::Promoter.3 \
		Bio::SeqFeature::Gene::Transcript.3 \
		Bio::SeqFeature::Gene::TranscriptI.3 \
		Bio::SeqFeature::Gene::UTR.3 \
		Bio::SeqFeature::Generic.3 \
		Bio::SeqFeature::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::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::entrezgene.3 \
		Bio::SeqIO::excel.3 \
		Bio::SeqIO::exp.3 \
		Bio::SeqIO::fasta.3 \
		Bio::SeqIO::fastq.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::gcg.3 \
		Bio::SeqIO::genbank.3 \
		Bio::SeqIO::interpro.3 \
		Bio::SeqIO::kegg.3 \
		Bio::SeqIO::largefasta.3 \
		Bio::SeqIO::lasergene.3 \
		Bio::SeqIO::locuslink.3 \
		Bio::SeqIO::metafasta.3 \
		Bio::SeqIO::phd.3 \
		Bio::SeqIO::pir.3 \
		Bio::SeqIO::pln.3 \
		Bio::SeqIO::qual.3 \
		Bio::SeqIO::raw.3 \
		Bio::SeqIO::scf.3 \
		Bio::SeqIO::strider.3 \
		Bio::SeqIO::swiss.3 \
		Bio::SeqIO::tab.3 \
		Bio::SeqIO::table.3 \
		Bio::SeqIO::tigr.3 \
		Bio::SeqIO::tigrxml.3 \
		Bio::SeqIO::tinyseq.3 \
		Bio::SeqIO::tinyseq::tinyseqHandler.3 \
		Bio::SeqIO::ztr.3 \
		Bio::SeqUtils.3 \
		Bio::SimpleAlign.3 \
		Bio::SimpleAnalysisI.3 \
		Bio::Species.3 \
		Bio::Structure::Atom.3 \
		Bio::Structure::Chain.3 \
		Bio::Structure::Entry.3 \
		Bio::Structure::IO.3 \
		Bio::Structure::IO::pdb.3 \
		Bio::Structure::Model.3 \
		Bio::Structure::Residue.3 \
		Bio::Structure::SecStr::DSSP::Res.3 \
		Bio::Structure::SecStr::STRIDE::Res.3 \
		Bio::Structure::StructureI.3 \
		Bio::Symbol::Alphabet.3 \
		Bio::Symbol::AlphabetI.3 \
		Bio::Symbol::DNAAlphabet.3 \
		Bio::Symbol::ProteinAlphabet.3 \
		Bio::Symbol::Symbol.3 \
		Bio::Symbol::SymbolI.3 \
		Bio::Taxon.3 \
		Bio::Taxonomy.3 \
		Bio::Taxonomy::FactoryI.3 \
		Bio::Taxonomy::Node.3 \
		Bio::Taxonomy::Taxon.3 \
		Bio::Taxonomy::Tree.3 \
		Bio::Tools::AlignFactory.3 \
		Bio::Tools::Alignment::Consed.3 \
		Bio::Tools::Alignment::Trim.3 \
		Bio::Tools::Analysis::DNA::ESEfinder.3 \
		Bio::Tools::Analysis::Protein::Domcut.3 \
		Bio::Tools::Analysis::Protein::ELM.3 \
		Bio::Tools::Analysis::Protein::GOR4.3 \
		Bio::Tools::Analysis::Protein::HNN.3 \
		Bio::Tools::Analysis::Protein::Mitoprot.3 \
		Bio::Tools::Analysis::Protein::NetPhos.3 \
		Bio::Tools::Analysis::Protein::Scansite.3 \
		Bio::Tools::Analysis::Protein::Sopma.3 \
		Bio::Tools::Analysis::SimpleAnalysisBase.3 \
		Bio::Tools::AnalysisResult.3 \
		Bio::Tools::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::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::ESTScan.3 \
		Bio::Tools::Eponine.3 \
		Bio::Tools::Est2Genome.3 \
		Bio::Tools::ERPIN.3 \
		Bio::Tools::Fgenesh.3 \
		Bio::Tools::FootPrinter.3 \
		Bio::Tools::GFF.3 \
		Bio::Tools::Gel.3 \
		Bio::Tools::Geneid.3 \
		Bio::Tools::Genemark.3 \
		Bio::Tools::Genewise.3 \
		Bio::Tools::Genomewise.3 \
		Bio::Tools::Genscan.3 \
		Bio::Tools::Glimmer.3 \
		Bio::Tools::Grail.3 \
		Bio::Tools::GuessSeqFormat.3 \
		Bio::Tools::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::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::ModelResult.3 \
		Bio::Tools::Phylo::PAML::Result.3 \
		Bio::Tools::Phylo::Phylip::ProtDist.3 \
		Bio::Tools::Prediction::Exon.3 \
		Bio::Tools::Prediction::Gene.3 \
		Bio::Tools::Primer3.3 \
		Bio::Tools::Primer::Assessor::Base.3 \
		Bio::Tools::Primer::AssessorI.3 \
		Bio::Tools::Primer::Feature.3 \
		Bio::Tools::Primer::Pair.3 \
		Bio::Tools::Prints.3 \
		Bio::Tools::Profile.3 \
		Bio::Tools::Promoterwise.3 \
		Bio::Tools::PrositeScan.3 \
		Bio::Tools::Pseudowise.3 \
		Bio::Tools::QRNA.3 \
		Bio::Tools::RandomDistFunctions.3 \
		Bio::Tools::RepeatMasker.3 \
		Bio::Tools::RestrictionEnzyme.3 \
		Bio::Tools::RNAMotif.3 \
		Bio::Tools::Run::GenericParameters.3 \
		Bio::Tools::Run::ParametersI.3 \
		Bio::Tools::Run::RemoteBlast.3 \
		Bio::Tools::Run::StandAloneBlast.3 \
		Bio::Tools::Run::WrapperBase.3 \
		Bio::Tools::Seg.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::Sim4::Exon.3 \
		Bio::Tools::Sim4::Results.3 \
		Bio::Tools::Spidey::Exon.3 \
		Bio::Tools::Spidey::Results.3 \
		Bio::Tools::Tmhmm.3 \
		Bio::Tools::dpAlign.3 \
		Bio::Tools::ipcress.3 \
		Bio::Tools::isPcr.3 \
		Bio::Tools::pICalculator.3 \
		Bio::Tools::pSW.3 \
		Bio::Tools::tRNAscanSE.3 \
		Bio::Tree::AlleleNode.3 \
		Bio::Tree::Compatible.3 \
		Bio::Tree::DistanceFactory.3 \
		Bio::Tree::Draw::Cladogram.3 \
		Bio::Tree::Node.3 \
		Bio::Tree::NodeI.3 \
		Bio::Tree::NodeNHX.3 \
		Bio::Tree::RandomFactory.3 \
		Bio::Tree::Statistics.3 \
		Bio::Tree::Tree.3 \
		Bio::Tree::TreeFunctionsI.3 \
		Bio::Tree::TreeI.3 \
		Bio::TreeIO.3 \
		Bio::TreeIO::TreeEventBuilder.3 \
		Bio::TreeIO::cluster.3 \
		Bio::TreeIO::lintree.3 \
		Bio::TreeIO::newick.3 \
		Bio::TreeIO::nexus.3 \
		Bio::TreeIO::nhx.3 \
		Bio::TreeIO::pag.3 \
		Bio::TreeIO::svggraph.3 \
		Bio::TreeIO::tabtree.3 \
		Bio::UpdateableSeqI.3 \
		Bio::Variation::AAChange.3 \
		Bio::Variation::AAReverseMutate.3 \
		Bio::Variation::Allele.3 \
		Bio::Variation::DNAMutation.3 \
		Bio::Variation::IO.3 \
		Bio::Variation::IO::flat.3 \
		Bio::Variation::IO::xml.3 \
		Bio::Variation::RNAChange.3 \
		Bio::Variation::SNP.3 \
		Bio::Variation::SeqDiff.3 \
		Bio::Variation::VariantI.3 \
		Bio::WebAgent.3

.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)
post-install:
	${MKDIR} ${DATADIR}
	${CP} -R ${WRKSRC}/scripts ${WRKSRC}/models ${DATADIR}
.if !defined(NOPORTEXAMPLES)
	${MKDIR} ${EXAMPLESDIR}
	${CP} -R ${WRKSRC}/examples/* ${EXAMPLESDIR}
.endif
.if !defined(NOPORTDOCS)
	${MKDIR} ${DOCSDIR}
.for doc in AUTHORS BUGS Changes DEPENDENCIES DEPRECATED INSTALL LICENSE PLATFORMS README
	${INSTALL_MAN} ${WRKSRC}/${doc} ${DOCSDIR}
.endfor
	${CP} -R ${WRKSRC}/doc ${DOCSDIR}
.endif

.include <bsd.port.post.mk>
@


1.16
log
@- Mark DEPRECATED (no longer under development)

PR:		132122
Submitted by:	Mauricio Herrera Cuadra <mauricio@@arareko.net> (maintainer)
@
text
@d5 1
a5 1
# $FreeBSD$
@


1.15
log
@Rename PERL_VER to PERL_VERSION.

Pointed by:	pav
@
text
@d61 3
@


1.14
log
@- Unbreak

PR:		ports/128193
Submitted by:	Mauricio Herrera Cuadra <mauricio at arareko.net> (maintainer)
@
text
@d18 2
a19 2
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 \
@


1.13
log
@- Mark BROKEN: missing cpan dependency (interactive loop)
@
text
@d36 1
a56 2
BROKEN=		missing dependencies

a62 4
NOPORTDOCS=	yes
NOPORTEXAMPLES=	yes
NOPORTDATA=	yes

d104 1
d122 1
a1005 1

@


1.12
log
@- Update to 1.5.2.

PR:		ports/124648
Submitted by:	Mauricio Herrera Cuadra <mauricio@@arareko.net> (maintainer)
Reviewed by:	lippe
Approved by:	gabor (mentor, implicit)
@
text
@d56 2
@


1.11
log
@Welcome bsd.perl.mk.  Add support for constructs such as USE_PERL5=5.8.0+.
Drop support for antique perl.

Work done by:	gabor
Sponsored by:	Google Summer of Code 2007
Hat:		portmgr
@
text
@d9 1
a9 2
PORTVERSION=	1.5.1
PORTREVISION=	1
d13 1
d31 1
d33 1
d47 1
d60 5
a64 1
PERL_CONFIGURE=	YES
d219 1
d242 13
d267 1
d284 1
d286 1
d317 1
d324 1
d327 12
d341 2
d347 1
d360 2
d363 1
d365 2
d368 1
d392 1
d403 1
d425 1
d430 1
d441 1
d471 1
a492 1
		Bio::LiveSeq::IO::SRS.3 \
d520 1
d525 1
d532 2
d537 2
d569 2
d574 1
d631 1
a644 1
		Bio::Root::Err.3 \
a645 1
		Bio::Root::Global.3 \
a647 2
		Bio::Root::IOManager.3 \
		Bio::Root::Object.3 \
a650 2
		Bio::Root::Utilities.3 \
		Bio::Root::Vector.3 \
a651 1
		Bio::Root::Xref.3 \
d661 1
d666 1
d671 1
d676 1
d682 1
d684 1
d711 1
d787 1
d802 1
d811 1
d814 1
d840 1
a865 4
		Bio::Tools::Blast.3 \
		Bio::Tools::Blast::HSP.3 \
		Bio::Tools::Blast::HTML.3 \
		Bio::Tools::Blast::Sbjct.3 \
d875 1
d919 1
a925 1
		Bio::Tools::SeqAnal.3 \
a938 2
		Bio::Tools::WWW.3 \
		Bio::Tools::WebBlat.3 \
d979 1
a979 6
		Bio::WebAgent.3 \
		biodatabases.3 \
		biodesign.3 \
		bioperl.3 \
		bioscripts.3 \
		bptutorial.3
d985 3
d994 1
d997 1
d1000 1
a1000 1
.for doc in AUTHORS BUGS Changes DEPRECATED FAQ INSTALL LICENSE PLATFORMS README
d1007 1
@


1.10
log
@- Welcome X.org 7.2 \o/.
- Set X11BASE to ${LOCALBASE} for recent ${OSVERSION}.
- Bump PORTREVISION for ports intalling files in ${X11BASE}.
@
text
@a927 3
.if ${PERL_LEVEL} < 500600
IGNORE=		requires Perl 5.6 or better
.endif
@


1.9
log
@Add conflicts:

    CONFLICTS= p5-bioperl-1.[02468]*

Submitted by:	Fernan Aguero <fernan@@iib.unsam.edu.ar>, Mauricio Herrera Cuadra <arareko@@yahoo.com>
@
text
@d10 1
@


1.8
log
@Fix port: biology/p5-bioperl-devel

      This patch adds a LATEST_LINK line in the Makefile to avoid
      duplication with the 'p5-bioperl' port in the packages/Latest
      directory.

PR:		ports/89916
Submitted by:	Mauricio Herrera Cuadra <mauricio@@arareko.net>
@
text
@d52 1
a52 1
CONFLICTS=	p5-bioperl-1.[0-46-9]*
@


1.7
log
@- Re-add p5-bioperl-devel, development version of biology/p5-bioperl
  (A collection of Perl modules for bioinformatics)

PR:		ports/89497
Submitted by:	Mauricio Herrera Cuadra <arareko@@yahoo.com>
@
text
@d54 2
@


1.6
log
@As announced on May 6, remove the broken p5-bioperl-devel port.
@
text
@d1 3
a3 3
# New ports collection makefile for:	p5-bioperl-devel
# Date created:		13 August 2001
# Whom:	      		Johann Visagie <wjv@@FreeBSD.org>
d5 1
a5 1
# $FreeBSD: ports/biology/p5-bioperl-devel/Makefile,v 1.5 2003/05/06 23:36:56 kris Exp $
d9 1
a9 1
PORTVERSION=	0.9.0
d11 1
a11 2
MASTER_SITES=	ftp://bioperl.org/pub/DIST/ \
		http://bioperl.org/Core/Latest/
a12 2
PKGNAMESUFFIX=	-devel
DISTFILES=	${DISTNAME}${EXTRACT_SUFX}
d14 2
a15 2
MAINTAINER=	wjv@@FreeBSD.org
COMMENT=	A collection of Perl modules for bioinformatics (developer's release)
d17 34
a50 1
BROKEN=		"Broken pkg-plist"
d52 1
a52 14
# These are all run-time dependencies, but listing them in ${BUILD_DEPENDS}
# prevents a flood of build-time warnings.
BUILD_DEPENDS=	${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/${PERL_ARCH}/Ace.pm:${PORTSDIR}/biology/p5-AcePerl \
		${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/${PERL_ARCH}/XML/Parser.pm:${PORTSDIR}/textproc/p5-XML-Parser \
		${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/File/Temp.pm:${PORTSDIR}/devel/p5-File-Temp \
		${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/HTTP/Request/Common.pm:${PORTSDIR}/www/p5-libwww \
		${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/IO/Scalar.pm:${PORTSDIR}/devel/p5-IO-stringy \
		${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/IO/String.pm:${PORTSDIR}/devel/p5-IO-String \
		${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/LWP/UserAgent.pm:${PORTSDIR}/www/p5-libwww \
		${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/XML/Node.pm:${PORTSDIR}/textproc/p5-XML-Node \
		${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/XML/Parser/PerlSAX.pm:${PORTSDIR}/textproc/p5-libxml \
		${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/XML/Twig.pm:${PORTSDIR}/textproc/p5-XML-Twig \
		${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/XML/Writer.pm:${PORTSDIR}/textproc/p5-XML-Writer
RUN_DEPENDS=	${BUILD_DEPENDS}
a54 1
NO_LATEST_LINK=	"Unstable development version."
d56 864
a919 4
.if defined(WITH_CORBA)
WITH_CORBA_CLIENT=	YES
WITH_CORBA_SERVER=	YES
.endif
d921 1
a921 18
EXT_VERSION=	0.6
CORBA_CLIENT_VERSION=	0.2
CORBA_SERVER_VERSION=	0.2
GUI_VERSION=	0.7
DISTFILES+=	bioperl-ext-${EXT_VERSION}${EXTRACT_SUFX}
EXT_WRKSRC=	${WRKDIR}/bioperl-ext-06/Bio/Ext/Align

.if defined(WITH_CORBA_CLIENT)
BUILD_DEPENDS+=	${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/${PERL_ARCH}/CORBA/ORBit.pm:${PORTSDIR}/devel/p5-ORBit
RUN_DEPENDS+=	${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/${PERL_ARCH}/CORBA/ORBit.pm:${PORTSDIR}/devel/p5-ORBit
.endif
.if defined(WITH_CORBA_SERVER)
BUILD_DEPENDS+=	${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/${PERL_ARCH}/CORBA/ORBit.pm:${PORTSDIR}/devel/p5-ORBit
RUN_DEPENDS+=	${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/${PERL_ARCH}/CORBA/ORBit.pm:${PORTSDIR}/devel/p5-ORBit
.endif
.if defined(WITH_GUI)
RUN_DEPENDS+=	ptksh:${PORTSDIR}/x11-toolkits/p5-Tk
.endif
d923 4
a926 8
.for ext in CORBA_CLIENT CORBA_SERVER GUI
.if defined(WITH_${ext})
EXTLIST+=	${ext}
DISTFILES+=	bioperl-${ext:L:S/_/-/}-${${ext}_VERSION}${EXTRACT_SUFX}
${ext}_WRKSRC=	${WRKDIR}/bioperl-${ext:L:S/_/-/}
PLIST_${ext}=	""
.else
PLIST_${ext}=	"@@comment "
a927 13
PLIST_SUB+=	PLIST_${ext}=${PLIST_${ext}}
.endfor

.include <bsd.port.pre.mk>

# Include the (extremely) long list of manpages from a separate file:
.include "${FILESDIR}/Makefile.man"
MANPREFIX=	${PREFIX}/lib/perl5/${PERL_VERSION}

pre-fetch:
.if !defined(BATCH) && (!defined(WITH_CORBA_CLIENT) || \
    !defined(WITH_CORBA_SERVER) || !defined(WITH_GUI))
	@@ ${CAT} ${FILESDIR}/ext.msg
d930 1
a930 18
post-configure:
	@@ cd ${EXT_WRKSRC} && \
	  ${SETENV} ${CONFIGURE_ENV} \
	  ${PERL5} ./${CONFIGURE_SCRIPT} ${CONFIGURE_ARGS}

.for ext in ${EXTLIST}
	@@ cd ${${ext}_WRKSRC} && \
	  ${PERL5} ./${CONFIGURE_SCRIPT} ${CONFIGURE_ARGS}
.endfor

post-build:
	@@ cd ${EXT_WRKSRC} && \
	  ${MAKE} ${MAKE_FLAGS} ${MAKEFILE} ${MAKE_ARGS} ${ALL_TARGET}
.for ext in ${EXTLIST}
	@@ cd ${${ext}_WRKSRC} && ${SETENV} ${MAKE_ENV} \
	  ${MAKE} ${MAKE_FLAGS} ${MAKEFILE} ${MAKE_ARGS} ${ALL_TARGET}
.endfor

d932 8
a939 7
	@@ cd ${EXT_WRKSRC} && \
	  ${SETENV} ${MAKE_ENV} ${MAKE} ${MAKE_FLAGS} \
	  ${MAKEFILE} ${MAKE_ARGS} ${INSTALL_TARGET}
.for ext in ${EXTLIST}
	@@ cd ${${ext}_WRKSRC} && \
	  ${SETENV} ${MAKE_ENV} ${MAKE} ${MAKE_FLAGS} \
	  ${MAKEFILE} ${MAKE_ARGS} ${INSTALL_TARGET}
d941 2
@


1.5
log
@BROKEN: Broken pkg-plist
@
text
@d5 1
a5 1
# $FreeBSD$
@


1.4
log
@Clear moonlight beckons.
Requiem mors pacem pkg-comment,
And be calm ports tree.

E Nomini Patri, E Fili, E Spiritu Sancti.
@
text
@d20 2
@


1.3
log
@- Add NO_LATEST_LINK, which should've been there in the first place.  :-(
@
text
@d5 1
a5 1
# $FreeBSD: ports/biology/p5-bioperl-devel/Makefile,v 1.2 2001/08/20 12:41:08 wjv Exp $
d18 1
@


1.2
log
@- Move the (very) long list of manpages from the port Makefile to a separate
  file.

Inspired by:	nectar's treatment of security/heimdal
@
text
@d5 1
a5 1
# $FreeBSD: ports/biology/p5-bioperl-devel/Makefile,v 1.1 2001/08/14 09:36:33 wjv Exp $
d35 1
@


1.1
log
@Add p5-bioperl-devel 0.9.0,
a collection of Perl modules for
bioinformatics (developer's release).
@
text
@d5 1
a5 1
# $FreeBSD$
d72 4
a75 122
MAN3=		Bio::AlignIO.3 Bio::AlignIO::bl2seq.3 \
		Bio::AlignIO::clustalw.3 Bio::AlignIO::fasta.3 \
		Bio::AlignIO::mase.3 Bio::AlignIO::meme.3 Bio::AlignIO::msf.3 \
		Bio::AlignIO::nexus.3 Bio::AlignIO::pfam.3 \
		Bio::AlignIO::phylip.3 Bio::AlignIO::prodom.3 \
		Bio::AlignIO::selex.3 Bio::AlignIO::stockholm.3 \
		Bio::Annotation.3 Bio::Annotation::Comment.3 \
		Bio::Annotation::DBLink.3 Bio::Annotation::Reference.3 \
		Bio::DB::Ace.3 Bio::DB::EMBL.3 Bio::DB::Fasta.3 \
		Bio::DB::GDB.3 Bio::DB::GFF.3 Bio::DB::GFF::Adaptor::dbi.3 \
		Bio::DB::GFF::Aggregator.3 \
		Bio::DB::GFF::Aggregator::alignment.3 \
		Bio::DB::GFF::Aggregator::clone.3 \
		Bio::DB::GFF::Aggregator::none.3 \
		Bio::DB::GFF::Aggregator::transcript.3 \
		Bio::DB::GFF::Featname.3 Bio::DB::GFF::Feature.3 \
		Bio::DB::GFF::Homol.3 Bio::DB::GFF::RelSegment.3 \
		Bio::DB::GFF::Segment.3 Bio::DB::GFF::Typename.3 \
		Bio::DB::GenBank.3 Bio::DB::GenPept.3 Bio::DB::NCBIHelper.3 \
		Bio::DB::RandomAccessI.3 Bio::DB::SeqI.3 Bio::DB::SwissProt.3 \
		Bio::DB::Universal.3 Bio::DB::UpdateableSeqI.3 \
		Bio::DB::WebDBSeqI.3 Bio::DBLinkContainerI.3 \
		Bio::Factory::ApplicationFactoryI.3 \
		Bio::Factory::DriverFactory.3 Bio::Factory::EMBOSS.3 \
		Bio::Factory::SeqAnalysisParserFactory.3 \
		Bio::Factory::SeqAnalysisParserFactoryI.3 \
		Bio::Index::Abstract.3 Bio::Index::AbstractSeq.3 \
		Bio::Index::EMBL.3 Bio::Index::Fasta.3 Bio::Index::GenBank.3 \
		Bio::Index::SwissPfam.3 Bio::Index::Swissprot.3 \
		Bio::LiveSeq::AARange.3 Bio::LiveSeq::Chain.3 \
		Bio::LiveSeq::ChainI.3 Bio::LiveSeq::DNA.3 \
		Bio::LiveSeq::Exon.3 Bio::LiveSeq::Gene.3 \
		Bio::LiveSeq::IO::BioPerl.3 Bio::LiveSeq::IO::Loader.3 \
		Bio::LiveSeq::IO::SRS.3 Bio::LiveSeq::Intron.3 \
		Bio::LiveSeq::Mutation.3 Bio::LiveSeq::Mutator.3 \
		Bio::LiveSeq::Prim_Transcript.3 Bio::LiveSeq::Range.3 \
		Bio::LiveSeq::Repeat_Region.3 Bio::LiveSeq::Repeat_Unit.3 \
		Bio::LiveSeq::SeqI.3 Bio::LiveSeq::Transcript.3 \
		Bio::LiveSeq::Translation.3 Bio::LocatableSeq.3 \
		Bio::Location::AvWithinCoordPolicy.3 \
		Bio::Location::CoordinatePolicyI.3 Bio::Location::Fuzzy.3 \
		Bio::Location::FuzzyLocationI.3 \
		Bio::Location::NarrowestCoordPolicy.3 Bio::Location::Simple.3 \
		Bio::Location::Split.3 Bio::Location::SplitLocationI.3 \
		Bio::Location::WidestCoordPolicy.3 Bio::LocationI.3 \
		Bio::PrimarySeq.3 Bio::PrimarySeqI.3 Bio::Range.3 \
		Bio::RangeI.3 Bio::Root::Err.3 Bio::Root::Global.3 \
		Bio::Root::IO.3 Bio::Root::IOManager.3 Bio::Root::Object.3 \
		Bio::Root::RootI.3 Bio::Root::Utilities.3 Bio::Root::Vector.3 \
		Bio::Root::Xref.3 Bio::SearchDist.3 Bio::Seq.3 \
		Bio::Seq::LargePrimarySeq.3 Bio::Seq::LargeSeq.3 \
		Bio::Seq::RichSeq.3 Bio::Seq::RichSeqI.3 \
		Bio::SeqAnalysisParserI.3 Bio::SeqFeature::Computation.3 \
		Bio::SeqFeature::Exon.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::Transcript.3 \
		Bio::SeqFeature::Gene::TranscriptI.3 \
		Bio::SeqFeature::Generic.3 Bio::SeqFeature::Intron.3 \
		Bio::SeqFeature::PolyA.3 Bio::SeqFeature::Promoter.3 \
		Bio::SeqFeature::Similarity.3 \
		Bio::SeqFeature::SimilarityPair.3 Bio::SeqFeature::UTR3.3 \
		Bio::SeqFeature::UTR5.3 Bio::SeqFeatureI.3 Bio::SeqI.3 \
		Bio::SeqIO.3 Bio::SeqIO::FTHelper.3 Bio::SeqIO::MultiFile.3 \
		Bio::SeqIO::ace.3 Bio::SeqIO::embl.3 Bio::SeqIO::fasta.3 \
		Bio::SeqIO::game.3 Bio::SeqIO::game::featureHandler.3 \
		Bio::SeqIO::game::idHandler.3 Bio::SeqIO::game::seqHandler.3 \
		Bio::SeqIO::gcg.3 Bio::SeqIO::genbank.3 \
		Bio::SeqIO::largefasta.3 Bio::SeqIO::pir.3 Bio::SeqIO::raw.3 \
		Bio::SeqIO::scf.3 Bio::SeqIO::swiss.3 Bio::SeqUtils.3 \
		Bio::SimpleAlign.3 Bio::Species.3 Bio::Tools::AlignFactory.3 \
		Bio::Tools::AnalysisResult.3 Bio::Tools::BPbl2seq.3 \
		Bio::Tools::BPlite.3 Bio::Tools::BPlite::Iteration.3 \
		Bio::Tools::BPpsilite.3 Bio::Tools::Blast.3 \
		Bio::Tools::Blast::HSP.3 Bio::Tools::Blast::HTML.3 \
		Bio::Tools::Blast::Run::LocalBlast.3 \
		Bio::Tools::Blast::Run::Webblast.3 Bio::Tools::Blast::Sbjct.3 \
		Bio::Tools::CodonTable.3 Bio::Tools::EPCR.3 \
		Bio::Tools::ESTScan.3 Bio::Tools::Fasta.3 Bio::Tools::GFF.3 \
		Bio::Tools::Genemark.3 Bio::Tools::Genscan.3 \
		Bio::Tools::Grail.3 Bio::Tools::HMMER::Domain.3 \
		Bio::Tools::HMMER::Results.3 Bio::Tools::HMMER::Set.3 \
		Bio::Tools::IUPAC.3 Bio::Tools::MZEF.3 Bio::Tools::OddCodes.3 \
		Bio::Tools::Prediction::Exon.3 Bio::Tools::Prediction::Gene.3 \
		Bio::Tools::RestrictionEnzyme.3 \
		Bio::Tools::Run::Alignment::Clustalw.3 \
		Bio::Tools::Run::Alignment::TCoffee.3 \
		Bio::Tools::Run::EMBOSSApplication.3 \
		Bio::Tools::Run::RemoteBlast.3 \
		Bio::Tools::Run::StandAloneBlast.3 Bio::Tools::SeqAnal.3 \
		Bio::Tools::SeqPattern.3 Bio::Tools::SeqStats.3 \
		Bio::Tools::SeqWords.3 Bio::Tools::Sigcleave.3 \
		Bio::Tools::Sim4::Exon.3 Bio::Tools::Sim4::Results.3 \
		Bio::Tools::WWW.3 Bio::Tools::pSW.3 Bio::UnivAln.3 \
		Bio::Variation::AAChange.3 Bio::Variation::AAReverseMutate.3 \
		Bio::Variation::Allele.3 Bio::Variation::DNAMutation.3 \
		Bio::Variation::IO.3 Bio::Variation::IO::flat.3 \
		Bio::Variation::IO::xml.3 Bio::Variation::RNAChange.3 \
		Bio::Variation::SeqDiff.3 Bio::Variation::VariantI.3 \
		bioback.3 biodesign.3 bioperl.3 biostart.3 bptutorial.3
.if defined(WITH_CORBA_CLIENT)
MAN3+=		Bio::CorbaClient::PrimarySeq.3 Bio::CorbaClient::Seq.3 \
		Bio::CorbaClient::SeqFeature.3 Bio::CorbaClient::Base.3 \
		Bio::SeqIO::biocorba.3 Bio::DB::Biocorba.3 \
		Bio::CorbaClient::Client.3 Bio::CorbaClient::ORB.3
.endif
.if defined(WITH_CORBA_SERVER)
MAN3+=		Bio::CorbaServer::BioEnv.3 Bio::CorbaServer::AnonymousSeq.3 \
		Bio::CorbaServer::PrimarySeq.3 Bio::CorbaServer::SeqFeature.3 \
		Bio::CorbaServer::PrimarySeqDB.3 \
		Bio::CorbaServer::PrimarySeqIterator.3 \
		Bio::CorbaServer::PrimarySeqVector.3 \
		Bio::CorbaServer::Seq.3 \
		Bio::CorbaServer::SeqDB.3 Bio::CorbaServer::Base.3 \
		Bio::CorbaServer::SeqFeatureIterator.3 \
		Bio::CorbaServer::SeqFeatureVector.3 \
		Bio::CorbaServer::Server.3
.endif
.if defined(WITH_GUI)
MAN3+=		Bio::Tk::HitDisplay.3 Bio::Tk::SeqCanvas.3
.endif
d112 1
a112 1
.include <bsd.port.mk>
@

