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freebsd-ports/biology/p5-bioperl/Makefile
Marcelo Araujo 4aaab89f57 - Take advantage of CPAN macro from bsd.sites.mk, change ${MASTER_SITE_PERL_CPAN} to CPAN. 
PR:		ports/122674
Submitted by:	Philip M. Gollucci <pgollucci@p6m7g8.com>
Reworked by:	araujo (myself)
Approved by:	portmgr (pav)
2008-04-17 14:30:31 +00:00

817 lines
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Makefile
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# New ports collection makefile for: p5-bioperl
# Date created: 28 July 2000
# Whom: Johann Visagie <johann@egenetics.com>
#
# $FreeBSD$
#
PORTNAME= bioperl
PORTVERSION= 1.4
PORTREVISION= 1
CATEGORIES= biology perl5
MASTER_SITES= http://bioperl.org/DIST/ \
CPAN
PKGNAMEPREFIX= p5-
MAINTAINER= fernan@iib.unsam.edu.ar
COMMENT= A collection of Perl modules for bioinformatics
# These are all run-time dependencies, but listing them in ${BUILD_DEPENDS}
# prevents a flood of build-time warnings.
BUILD_DEPENDS= ${SITE_PERL}/${PERL_ARCH}/Ace.pm:${PORTSDIR}/biology/p5-AcePerl \
${SITE_PERL}/${PERL_ARCH}/XML/Parser.pm:${PORTSDIR}/textproc/p5-XML-Parser \
${SITE_PERL}/HTTP/Request/Common.pm:${PORTSDIR}/www/p5-libwww \
${SITE_PERL}/IO/Scalar.pm:${PORTSDIR}/devel/p5-IO-stringy \
${SITE_PERL}/IO/String.pm:${PORTSDIR}/devel/p5-IO-String \
${SITE_PERL}/LWP/UserAgent.pm:${PORTSDIR}/www/p5-libwww \
${SITE_PERL}/XML/Node.pm:${PORTSDIR}/textproc/p5-XML-Node \
${SITE_PERL}/XML/Parser/PerlSAX.pm:${PORTSDIR}/textproc/p5-libxml \
${SITE_PERL}/XML/Writer.pm:${PORTSDIR}/textproc/p5-XML-Writer \
${SITE_PERL}/HTTP/Request/Common.pm:${PORTSDIR}/www/p5-libwww \
${SITE_PERL}/XML/Twig.pm:${PORTSDIR}/textproc/p5-XML-Twig \
${SITE_PERL}/SOAP/Lite.pm:${PORTSDIR}/net/p5-SOAP-Lite \
${SITE_PERL}/${PERL_ARCH}/HTML/Parser.pm:${PORTSDIR}/www/p5-HTML-Parser \
${SITE_PERL}/${PERL_ARCH}/DBD/mysql.pm:${PORTSDIR}/databases/p5-DBD-mysql \
${SITE_PERL}/${PERL_ARCH}/GD.pm:${PORTSDIR}/graphics/p5-GD \
${SITE_PERL}/${PERL_ARCH}/Storable.pm:${PORTSDIR}/devel/p5-Storable \
${SITE_PERL}/Parse/RecDescent.pm:${PORTSDIR}/devel/p5-Parse-RecDescent \
${SITE_PERL}/XML/DOM.pm:${PORTSDIR}/textproc/p5-XML-DOM \
${SITE_PERL}/Test/Simple.pm:${PORTSDIR}/devel/p5-Test-Simple \
${SITE_PERL}/Text/Shellwords.pm:${PORTSDIR}/textproc/p5-Text-Shellwords
RUN_DEPENDS= ${BUILD_DEPENDS}
CONFLICTS= p5-bioperl-1.[13579]*
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::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::fasta.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::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::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::Biblio.3 \
Bio::Biblio::Article.3 \
Bio::Biblio::BiblioBase.3 \
Bio::Biblio::Book.3 \
Bio::Biblio::BookArticle.3 \
Bio::Biblio::IO.3 \
Bio::Biblio::IO::medline2ref.3 \
Bio::Biblio::IO::medlinexml.3 \
Bio::Biblio::IO::pubmed2ref.3 \
Bio::Biblio::IO::pubmedxml.3 \
Bio::Biblio::Journal.3 \
Bio::Biblio::JournalArticle.3 \
Bio::Biblio::MedlineArticle.3 \
Bio::Biblio::MedlineBook.3 \
Bio::Biblio::MedlineBookArticle.3 \
Bio::Biblio::MedlineJournal.3 \
Bio::Biblio::MedlineJournalArticle.3 \
Bio::Biblio::Organisation.3 \
Bio::Biblio::Patent.3 \
Bio::Biblio::Person.3 \
Bio::Biblio::Proceeding.3 \
Bio::Biblio::Provider.3 \
Bio::Biblio::PubmedArticle.3 \
Bio::Biblio::PubmedBookArticle.3 \
Bio::Biblio::PubmedJournalArticle.3 \
Bio::Biblio::Ref.3 \
Bio::Biblio::Service.3 \
Bio::Biblio::TechReport.3 \
Bio::Biblio::Thesis.3 \
Bio::Biblio::WebResource.3 \
Bio::Cluster::ClusterFactory.3 \
Bio::Cluster::FamilyI.3 \
Bio::Cluster::SequenceFamily.3 \
Bio::Cluster::UniGene.3 \
Bio::Cluster::UniGeneI.3 \
Bio::ClusterI.3 \
Bio::ClusterIO.3 \
Bio::ClusterIO::dbsnp.3 \
Bio::ClusterIO::unigene.3 \
Bio::CodonUsage::IO.3 \
Bio::CodonUsage::Table.3 \
Bio::Coordinate::Chain.3 \
Bio::Coordinate::Collection.3 \
Bio::Coordinate::ExtrapolatingPair.3 \
Bio::Coordinate::GeneMapper.3 \
Bio::Coordinate::Graph.3 \
Bio::Coordinate::MapperI.3 \
Bio::Coordinate::Pair.3 \
Bio::Coordinate::Result.3 \
Bio::Coordinate::Result::Gap.3 \
Bio::Coordinate::Result::Match.3 \
Bio::Coordinate::ResultI.3 \
Bio::Coordinate::Utils.3 \
Bio::DB::Ace.3 \
Bio::DB::Biblio::biofetch.3 \
Bio::DB::Biblio::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 \
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::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 \
Bio::DB::GFF::Adaptor::dbi::mysql.3 \
Bio::DB::GFF::Adaptor::dbi::mysqlace.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::memory.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::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::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::RefSeq.3 \
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 \
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::FeatureGroup.3 \
Bio::Expression::FeatureI.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::Graphics.3 \
Bio::Graphics::ConfiguratorI.3 \
Bio::Graphics::Feature.3 \
Bio::Graphics::FeatureFile.3 \
Bio::Graphics::FeatureFile::Iterator.3 \
Bio::Graphics::Glyph.3 \
Bio::Graphics::Glyph::Factory.3 \
Bio::Graphics::Glyph::alignment.3 \
Bio::Graphics::Glyph::anchored_arrow.3 \
Bio::Graphics::Glyph::arrow.3 \
Bio::Graphics::Glyph::box.3 \
Bio::Graphics::Glyph::cds.3 \
Bio::Graphics::Glyph::crossbox.3 \
Bio::Graphics::Glyph::diamond.3 \
Bio::Graphics::Glyph::dna.3 \
Bio::Graphics::Glyph::dot.3 \
Bio::Graphics::Glyph::ellipse.3 \
Bio::Graphics::Glyph::ex.3 \
Bio::Graphics::Glyph::extending_arrow.3 \
Bio::Graphics::Glyph::generic.3 \
Bio::Graphics::Glyph::graded_segments.3 \
Bio::Graphics::Glyph::group.3 \
Bio::Graphics::Glyph::heterogeneous_segments.3 \
Bio::Graphics::Glyph::line.3 \
Bio::Graphics::Glyph::minmax.3 \
Bio::Graphics::Glyph::oval.3 \
Bio::Graphics::Glyph::pinsertion.3 \
Bio::Graphics::Glyph::primers.3 \
Bio::Graphics::Glyph::processed_transcript.3 \
Bio::Graphics::Glyph::redgreen_box.3 \
Bio::Graphics::Glyph::redgreen_segment.3 \
Bio::Graphics::Glyph::rndrect.3 \
Bio::Graphics::Glyph::ruler_arrow.3 \
Bio::Graphics::Glyph::segmented_keyglyph.3 \
Bio::Graphics::Glyph::segments.3 \
Bio::Graphics::Glyph::span.3 \
Bio::Graphics::Glyph::splice_site.3 \
Bio::Graphics::Glyph::toomany.3 \
Bio::Graphics::Glyph::track.3 \
Bio::Graphics::Glyph::transcript.3 \
Bio::Graphics::Glyph::transcript2.3 \
Bio::Graphics::Glyph::translation.3 \
Bio::Graphics::Glyph::triangle.3 \
Bio::Graphics::Glyph::xyplot.3 \
Bio::Graphics::Panel.3 \
Bio::Graphics::Pictogram.3 \
Bio::Graphics::RendererI.3 \
Bio::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::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::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::CytoMap.3 \
Bio::Map::CytoMarker.3 \
Bio::Map::CytoPosition.3 \
Bio::Map::LinkageMap.3 \
Bio::Map::LinkagePosition.3 \
Bio::Map::MapI.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::Position.3 \
Bio::Map::PositionI.3 \
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 \
Bio::Ontology::OntologyEngineI.3 \
Bio::Ontology::OntologyI.3 \
Bio::Ontology::OntologyStore.3 \
Bio::Ontology::Path.3 \
Bio::Ontology::PathI.3 \
Bio::Ontology::Relationship.3 \
Bio::Ontology::RelationshipFactory.3 \
Bio::Ontology::RelationshipI.3 \
Bio::Ontology::RelationshipType.3 \
Bio::Ontology::SimpleGOEngine.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::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 \
Bio::Root::HTTPget.3 \
Bio::Root::IO.3 \
Bio::Root::IOManager.3 \
Bio::Root::Object.3 \
Bio::Root::Root.3 \
Bio::Root::RootI.3 \
Bio::Root::Storable.3 \
Bio::Root::Utilities.3 \
Bio::Root::Vector.3 \
Bio::Root::Version.3 \
Bio::Root::Xref.3 \
Bio::Search::BlastUtils.3 \
Bio::Search::DatabaseI.3 \
Bio::Search::GenericDatabase.3 \
Bio::Search::HSP::BlastHSP.3 \
Bio::Search::HSP::FastaHSP.3 \
Bio::Search::HSP::GenericHSP.3 \
Bio::Search::HSP::HMMERHSP.3 \
Bio::Search::HSP::HSPFactory.3 \
Bio::Search::HSP::HSPI.3 \
Bio::Search::HSP::PSLHSP.3 \
Bio::Search::HSP::PsiBlastHSP.3 \
Bio::Search::HSP::WABAHSP.3 \
Bio::Search::Hit::BlastHit.3 \
Bio::Search::Hit::Fasta.3 \
Bio::Search::Hit::GenericHit.3 \
Bio::Search::Hit::HMMERHit.3 \
Bio::Search::Hit::HitFactory.3 \
Bio::Search::Hit::HitI.3 \
Bio::Search::Hit::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 \
Bio::Search::Result::HMMERResult.3 \
Bio::Search::Result::ResultFactory.3 \
Bio::Search::Result::ResultI.3 \
Bio::Search::Result::WABAResult.3 \
Bio::Search::SearchUtils.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::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::LargePrimarySeq.3 \
Bio::Seq::LargeSeq.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::SeqAnalysisParserI.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::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::ace.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::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::kegg.3 \
Bio::SeqIO::largefasta.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::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::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::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::Blast.3 \
Bio::Tools::Blast::HSP.3 \
Bio::Tools::Blast::HTML.3 \
Bio::Tools::Blast::Sbjct.3 \
Bio::Tools::Blat.3 \
Bio::Tools::CodonTable.3 \
Bio::Tools::Coil.3 \
Bio::Tools::ECnumber.3 \
Bio::Tools::EMBOSS::Palindrome.3 \
Bio::Tools::EPCR.3 \
Bio::Tools::ESTScan.3 \
Bio::Tools::Eponine.3 \
Bio::Tools::Est2Genome.3 \
Bio::Tools::FootPrinter.3 \
Bio::Tools::GFF.3 \
Bio::Tools::Gel.3 \
Bio::Tools::Geneid.3 \
Bio::Tools::Genemark.3 \
Bio::Tools::Genewise.3 \
Bio::Tools::Genomewise.3 \
Bio::Tools::Genscan.3 \
Bio::Tools::Glimmer.3 \
Bio::Tools::Grail.3 \
Bio::Tools::GuessSeqFormat.3 \
Bio::Tools::HMMER::Domain.3 \
Bio::Tools::HMMER::Results.3 \
Bio::Tools::HMMER::Set.3 \
Bio::Tools::Hmmpfam.3 \
Bio::Tools::IUPAC.3 \
Bio::Tools::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::Run::RemoteBlast.3 \
Bio::Tools::Run::StandAloneBlast.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::Sim4::Exon.3 \
Bio::Tools::Sim4::Results.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::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::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 \
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 \
biodatabases.3 \
biodesign.3 \
bioperl.3 \
bioscripts.3 \
bptutorial.3
.include <bsd.port.pre.mk>
.if ${PERL_LEVEL} < 500800
BUILD_DEPENDS+= ${SITE_PERL}/File/Temp.pm:${PORTSDIR}/devel/p5-File-Temp
.endif
# now install all extra stuff (docs, examples, scripts, models)
post-install:
${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}
.endif
.include <bsd.port.post.mk>
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