Attachment #46458 for bug #71322

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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::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::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::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::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::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::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::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::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::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::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::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::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::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::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::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::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::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::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::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>


# 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}

.endif

.include <bsd.port.post.mk>




%%SITE_PERL%%/Bio/SeqIO/game/gameHandler.pm
%%SITE_PERL%%/Bio/SeqIO/game/gameSubs.pm
%%SITE_PERL%%/Bio/SeqIO/game/gameWriter.pm
%%PORTDOCS%%%%DOCSDIR%%/AUTHORS
%%PORTDOCS%%%%DOCSDIR%%/BUGS
%%PORTDOCS%%%%DOCSDIR%%/Changes
%%PORTDOCS%%%%DOCSDIR%%/DEPRECATED
%%PORTDOCS%%%%DOCSDIR%%/FAQ
%%PORTDOCS%%%%DOCSDIR%%/INSTALL
%%PORTDOCS%%%%DOCSDIR%%/LICENSE
%%PORTDOCS%%%%DOCSDIR%%/PLATFORMS
%%PORTDOCS%%%%DOCSDIR%%/README
%%PORTDOCS%%%%DOCSDIR%%/doc/faq/faq.html
%%PORTDOCS%%%%DOCSDIR%%/doc/faq/faq.dtd
%%PORTDOCS%%%%DOCSDIR%%/doc/faq/faq.pl
%%PORTDOCS%%%%DOCSDIR%%/doc/faq/faq.xml
%%PORTDOCS%%%%DOCSDIR%%/doc/howto/examples/graphics/render_features.pl
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%%PORTDOCS%%%%DOCSDIR%%/doc/howto/html/README
%%PORTDOCS%%%%DOCSDIR%%/doc/howto/html/SearchIO.html
%%PORTDOCS%%%%DOCSDIR%%/doc/howto/html/SeqIO.html
%%PORTDOCS%%%%DOCSDIR%%/doc/howto/html/SimpleWebAnalysis.html
%%PORTDOCS%%%%DOCSDIR%%/doc/howto/html/e-novative.css
%%PORTDOCS%%%%DOCSDIR%%/doc/howto/pdf/Trees.pdf
%%PORTDOCS%%%%DOCSDIR%%/doc/howto/pdf/Graphics-HOWTO.pdf
%%PORTDOCS%%%%DOCSDIR%%/doc/howto/pdf/OBDA_Access.pdf
%%PORTDOCS%%%%DOCSDIR%%/doc/howto/pdf/PAML.pdf
%%PORTDOCS%%%%DOCSDIR%%/doc/howto/pdf/SearchIO.pdf
%%PORTDOCS%%%%DOCSDIR%%/doc/howto/pdf/SeqIO.pdf
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%%PORTDOCS%%%%DOCSDIR%%/doc/howto/pdf/Flat_Databases.pdf
%%PORTDOCS%%%%DOCSDIR%%/doc/howto/sgml/Trees.sgml
%%PORTDOCS%%%%DOCSDIR%%/doc/howto/sgml/Flat_Databases.sgml
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%%PORTDOCS%%%%DOCSDIR%%/doc/howto/sgml/OBDA_Access.sgml
%%PORTDOCS%%%%DOCSDIR%%/doc/howto/sgml/PAML.sgml
%%PORTDOCS%%%%DOCSDIR%%/doc/howto/sgml/README
%%PORTDOCS%%%%DOCSDIR%%/doc/howto/sgml/SearchIO.sgml
%%PORTDOCS%%%%DOCSDIR%%/doc/howto/sgml/SeqIO.sgml
%%PORTDOCS%%%%DOCSDIR%%/doc/howto/sgml/SimpleWebAnalysis.sgml
%%PORTDOCS%%%%DOCSDIR%%/doc/howto/sgml/Feature-Annotation.sgml
%%PORTDOCS%%%%DOCSDIR%%/doc/howto/txt/Flat_Databases.txt
%%PORTDOCS%%%%DOCSDIR%%/doc/howto/txt/SimpleWebAnalysis.txt
%%PORTDOCS%%%%DOCSDIR%%/doc/makedoc.PL
%%EXAMPLESDIR%%/align/align_on_codons.pl
%%EXAMPLESDIR%%/align/aligntutorial.pl
%%EXAMPLESDIR%%/align/clustalw.pl
%%EXAMPLESDIR%%/align/simplealign.pl
%%EXAMPLESDIR%%/tools/standaloneblast.pl
%%EXAMPLESDIR%%/tools/gff2ps.pl
%%EXAMPLESDIR%%/tools/parse_codeml.pl
%%EXAMPLESDIR%%/tools/psw.pl
%%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
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%%EXAMPLESDIR%%/searchio/hspwriter.pl
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%%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
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%%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

@dirrm %%SITE_PERL%%/Bio/SeqIO/game
@dirrm %%SITE_PERL%%/Bio/SeqIO
@dirrm %%SITE_PERL%%/Bio
%%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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Lines 759-969 Link Here

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759	%%SITE_PERL%%/Bio/SeqIO/game/gameHandler.pm	759	%%SITE_PERL%%/Bio/SeqIO/game/gameHandler.pm
760	%%SITE_PERL%%/Bio/SeqIO/game/gameSubs.pm	760	%%SITE_PERL%%/Bio/SeqIO/game/gameSubs.pm
761	%%SITE_PERL%%/Bio/SeqIO/game/gameWriter.pm	761	%%SITE_PERL%%/Bio/SeqIO/game/gameWriter.pm
762	share/doc/bioperl/AUTHORS	762	%%PORTDOCS%%%%DOCSDIR%%/AUTHORS
763	share/doc/bioperl/BUGS	763	%%PORTDOCS%%%%DOCSDIR%%/BUGS
764	share/doc/bioperl/Changes	764	%%PORTDOCS%%%%DOCSDIR%%/Changes
765	share/doc/bioperl/DEPRECATED	765	%%PORTDOCS%%%%DOCSDIR%%/DEPRECATED
766	share/doc/bioperl/FAQ	766	%%PORTDOCS%%%%DOCSDIR%%/FAQ
767	share/doc/bioperl/INSTALL	767	%%PORTDOCS%%%%DOCSDIR%%/INSTALL
768	share/doc/bioperl/LICENSE	768	%%PORTDOCS%%%%DOCSDIR%%/LICENSE
769	share/doc/bioperl/PLATFORMS	769	%%PORTDOCS%%%%DOCSDIR%%/PLATFORMS
770	share/doc/bioperl/README	770	%%PORTDOCS%%%%DOCSDIR%%/README
771	share/doc/bioperl/doc/faq/faq.html	771	%%PORTDOCS%%%%DOCSDIR%%/doc/faq/faq.html
772	share/doc/bioperl/doc/faq/faq.dtd	772	%%PORTDOCS%%%%DOCSDIR%%/doc/faq/faq.dtd
773	share/doc/bioperl/doc/faq/faq.pl	773	%%PORTDOCS%%%%DOCSDIR%%/doc/faq/faq.pl
774	share/doc/bioperl/doc/faq/faq.xml	774	%%PORTDOCS%%%%DOCSDIR%%/doc/faq/faq.xml
775	share/doc/bioperl/doc/howto/examples/graphics/render_features.pl	775	%%PORTDOCS%%%%DOCSDIR%%/doc/howto/examples/graphics/render_features.pl
776	share/doc/bioperl/doc/howto/examples/graphics/data1.txt	776	%%PORTDOCS%%%%DOCSDIR%%/doc/howto/examples/graphics/data1.txt
777	share/doc/bioperl/doc/howto/examples/graphics/embl2picture.pl	777	%%PORTDOCS%%%%DOCSDIR%%/doc/howto/examples/graphics/embl2picture.pl
778	share/doc/bioperl/doc/howto/examples/graphics/factor7.embl	778	%%PORTDOCS%%%%DOCSDIR%%/doc/howto/examples/graphics/factor7.embl
779	share/doc/bioperl/doc/howto/examples/graphics/render_blast1.pl	779	%%PORTDOCS%%%%DOCSDIR%%/doc/howto/examples/graphics/render_blast1.pl
780	share/doc/bioperl/doc/howto/examples/graphics/render_blast2.pl	780	%%PORTDOCS%%%%DOCSDIR%%/doc/howto/examples/graphics/render_blast2.pl
781	share/doc/bioperl/doc/howto/examples/graphics/render_blast3.pl	781	%%PORTDOCS%%%%DOCSDIR%%/doc/howto/examples/graphics/render_blast3.pl
782	share/doc/bioperl/doc/howto/examples/graphics/render_blast4.pl	782	%%PORTDOCS%%%%DOCSDIR%%/doc/howto/examples/graphics/render_blast4.pl
783	share/doc/bioperl/doc/howto/examples/graphics/blastn.out	783	%%PORTDOCS%%%%DOCSDIR%%/doc/howto/examples/graphics/blastn.out
784	share/doc/bioperl/doc/howto/examples/README	784	%%PORTDOCS%%%%DOCSDIR%%/doc/howto/examples/README
785	share/doc/bioperl/doc/howto/figs/graphics/fig1.png	785	%%PORTDOCS%%%%DOCSDIR%%/doc/howto/figs/graphics/fig1.png
786	share/doc/bioperl/doc/howto/figs/graphics/fig2.png	786	%%PORTDOCS%%%%DOCSDIR%%/doc/howto/figs/graphics/fig2.png
787	share/doc/bioperl/doc/howto/figs/graphics/fig3.png	787	%%PORTDOCS%%%%DOCSDIR%%/doc/howto/figs/graphics/fig3.png
788	share/doc/bioperl/doc/howto/figs/graphics/fig4.png	788	%%PORTDOCS%%%%DOCSDIR%%/doc/howto/figs/graphics/fig4.png
789	share/doc/bioperl/doc/howto/figs/graphics/fig5.png	789	%%PORTDOCS%%%%DOCSDIR%%/doc/howto/figs/graphics/fig5.png
790	share/doc/bioperl/doc/howto/figs/graphics/fig6.png	790	%%PORTDOCS%%%%DOCSDIR%%/doc/howto/figs/graphics/fig6.png
791	share/doc/bioperl/doc/howto/figs/README	791	%%PORTDOCS%%%%DOCSDIR%%/doc/howto/figs/README
792	share/doc/bioperl/doc/howto/html/images/tip.png	792	%%PORTDOCS%%%%DOCSDIR%%/doc/howto/html/images/tip.png
793	share/doc/bioperl/doc/howto/html/Flat_Databases.html	793	%%PORTDOCS%%%%DOCSDIR%%/doc/howto/html/Flat_Databases.html
794	share/doc/bioperl/doc/howto/html/Graphics-HOWTO.html	794	%%PORTDOCS%%%%DOCSDIR%%/doc/howto/html/Graphics-HOWTO.html
795	share/doc/bioperl/doc/howto/html/OBDA_Access.html	795	%%PORTDOCS%%%%DOCSDIR%%/doc/howto/html/OBDA_Access.html
796	share/doc/bioperl/doc/howto/html/PAML.html	796	%%PORTDOCS%%%%DOCSDIR%%/doc/howto/html/PAML.html