head	1.32;
access;
symbols
	RELEASE_8_3_0:1.27
	RELEASE_9_0_0:1.26
	RELEASE_7_4_0:1.26
	RELEASE_8_2_0:1.26
	RELEASE_6_EOL:1.26
	RELEASE_8_1_0:1.26
	RELEASE_7_3_0:1.25
	RELEASE_8_0_0:1.22
	RELEASE_7_2_0:1.20
	RELEASE_7_1_0:1.17
	RELEASE_6_4_0:1.17
	RELEASE_5_EOL:1.17
	RELEASE_7_0_0:1.16
	RELEASE_6_3_0:1.16
	PRE_XORG_7:1.14
	RELEASE_4_EOL:1.14
	RELEASE_6_2_0:1.14
	RELEASE_6_1_0:1.14
	RELEASE_5_5_0:1.14
	RELEASE_6_0_0:1.13
	RELEASE_5_4_0:1.13
	RELEASE_4_11_0:1.13
	RELEASE_5_3_0:1.13
	RELEASE_4_10_0:1.11
	RELEASE_5_2_1:1.8
	RELEASE_5_2_0:1.8
	RELEASE_4_9_0:1.7
	RELEASE_5_1_0:1.7
	RELEASE_4_8_0:1.7
	RELEASE_5_0_0:1.6
	RELEASE_4_7_0:1.6
	RELEASE_4_6_2:1.6
	RELEASE_4_6_1:1.6
	RELEASE_4_6_0:1.6
	RELEASE_5_0_DP1:1.6
	RELEASE_4_5_0:1.5
	RELEASE_4_4_0:1.5
	RELEASE_4_3_0:1.2
	RELEASE_4_2_0:1.2
	RELEASE_4_1_1:1.1;
locks; strict;
comment	@# @;


1.32
date	2012.11.17.05.54.52;	author svnexp;	state Exp;
branches;
next	1.31;

1.31
date	2012.10.01.14.55.55;	author wen;	state Exp;
branches;
next	1.30;

1.30
date	2012.10.01.14.45.16;	author tabthorpe;	state Exp;
branches;
next	1.29;

1.29
date	2012.06.30.05.21.37;	author az;	state Exp;
branches;
next	1.28;

1.28
date	2012.06.01.05.16.29;	author dinoex;	state Exp;
branches;
next	1.27;

1.27
date	2012.01.21.17.39.32;	author eadler;	state Exp;
branches;
next	1.26;

1.26
date	2010.03.28.06.31.38;	author dinoex;	state Exp;
branches;
next	1.25;

1.25
date	2010.02.05.11.34.37;	author dinoex;	state Exp;
branches;
next	1.24;

1.24
date	2010.01.29.14.52.21;	author kuriyama;	state Exp;
branches;
next	1.23;

1.23
date	2009.12.04.11.50.10;	author wen;	state Exp;
branches;
next	1.22;

1.22
date	2009.07.31.13.49.18;	author dinoex;	state Exp;
branches;
next	1.21;

1.21
date	2009.07.22.16.26.23;	author pgollucci;	state Exp;
branches;
next	1.20;

1.20
date	2009.03.05.17.56.23;	author skv;	state Exp;
branches;
next	1.19;

1.19
date	2009.02.23.19.31.43;	author garga;	state Exp;
branches;
next	1.18;

1.18
date	2009.01.14.14.51.38;	author tobez;	state Exp;
branches;
next	1.17;

1.17
date	2008.04.17.14.24.11;	author araujo;	state Exp;
branches;
next	1.16;

1.16
date	2007.09.08.00.53.11;	author linimon;	state Exp;
branches;
next	1.15;

1.15
date	2007.05.19.20.00.25;	author flz;	state Exp;
branches;
next	1.14;

1.14
date	2005.12.04.22.11.44;	author edwin;	state Exp;
branches;
next	1.13;

1.13
date	2004.09.03.17.04.38;	author leeym;	state Exp;
branches;
next	1.12;

1.12
date	2004.08.12.12.47.57;	author mat;	state Exp;
branches;
next	1.11;

1.11
date	2004.03.08.03.29.16;	author linimon;	state Exp;
branches;
next	1.10;

1.10
date	2004.02.22.00.06.35;	author kris;	state Exp;
branches;
next	1.9;

1.9
date	2004.01.21.08.34.33;	author linimon;	state Exp;
branches;
next	1.8;

1.8
date	2003.10.24.12.01.16;	author ijliao;	state Exp;
branches;
next	1.7;

1.7
date	2003.03.07.05.56.42;	author ade;	state Exp;
branches;
next	1.6;

1.6
date	2002.01.25.11.46.09;	author wjv;	state Exp;
branches;
next	1.5;

1.5
date	2001.08.13.10.26.44;	author wjv;	state Exp;
branches;
next	1.4;

1.4
date	2001.07.04.13.22.10;	author wjv;	state Exp;
branches;
next	1.3;

1.3
date	2001.06.26.15.09.39;	author wjv;	state Exp;
branches;
next	1.2;

1.2
date	2000.10.13.12.43.24;	author jeh;	state Exp;
branches;
next	1.1;

1.1
date	2000.07.28.14.06.02;	author nbm;	state Exp;
branches;
next	;


desc
@@


1.32
log
@Switch exporter over
@
text
@# Created by: Johann Visagie <johann@@egenetics.com>
# $FreeBSD: head/biology/p5-bioperl/Makefile 305131 2012-10-01 14:55:55Z wen $

PORTNAME=	bioperl
PORTVERSION=	1.6.1
PORTREVISION=	4
CATEGORIES=	biology perl5
MASTER_SITES=	http://bioperl.org/DIST/ \
		CPAN
PKGNAMEPREFIX=	p5-
DISTNAME=	BioPerl-${PORTVERSION}

MAINTAINER=	wen@@FreeBSD.org
COMMENT=	A collection of Perl modules for bioinformatics

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/${PERL_PORT} \
		p5-Bio-ASN1-EntrezGene>=0:${PORTSDIR}/biology/p5-Bio-ASN1-EntrezGene \
		p5-Class-AutoClass>=0:${PORTSDIR}/devel/p5-Class-AutoClass \
		p5-Data-Stag>=0:${PORTSDIR}/devel/p5-Data-Stag \
		p5-Data-Stag>=0:${PORTSDIR}/devel/p5-Data-Stag \
		p5-Data-Stag>=0:${PORTSDIR}/devel/p5-Data-Stag \
		p5-GD-SVG>=0:${PORTSDIR}/graphics/p5-GD-SVG \
		p5-Graph>=0:${PORTSDIR}/math/p5-Graph \
		p5-libwww>=0:${PORTSDIR}/www/p5-libwww \
		p5-IO-stringy>=0:${PORTSDIR}/devel/p5-IO-stringy \
		p5-IO-String>=0:${PORTSDIR}/devel/p5-IO-String \
		p5-libwww>=0:${PORTSDIR}/www/p5-libwww \
		p5-SOAP-Lite>=0:${PORTSDIR}/net/p5-SOAP-Lite \
		p5-SVG>=0:${PORTSDIR}/textproc/p5-SVG \
		p5-SVG-Graph>=0:${PORTSDIR}/graphics/p5-SVG-Graph \
		p5-Text-Shellwords>=0:${PORTSDIR}/textproc/p5-Text-Shellwords \
		p5-XML-DOM>=0:${PORTSDIR}/textproc/p5-XML-DOM \
		p5-XML-DOM-XPath>=0:${PORTSDIR}/textproc/p5-XML-DOM-XPath \
		p5-libxml>=0:${PORTSDIR}/textproc/p5-libxml \
		p5-XML-SAX>=0:${PORTSDIR}/textproc/p5-XML-SAX \
		p5-XML-SAX>=0:${PORTSDIR}/textproc/p5-XML-SAX \
		p5-XML-SAX-Writer>=0:${PORTSDIR}/textproc/p5-XML-SAX-Writer \
		p5-XML-Twig>=0:${PORTSDIR}/textproc/p5-XML-Twig \
		p5-XML-Writer>=0:${PORTSDIR}/textproc/p5-XML-Writer \
		p5-AcePerl>=0:${PORTSDIR}/biology/p5-AcePerl \
		p5-Clone>=0:${PORTSDIR}/devel/p5-Clone \
		p5-DBD-mysql>=0:${PORTSDIR}/databases/p5-DBD-mysql \
		p5-GD>=0:${PORTSDIR}/graphics/p5-GD \
		p5-HTML-Parser>=0:${PORTSDIR}/www/p5-HTML-Parser \
		p5-HTML-Parser>=0:${PORTSDIR}/www/p5-HTML-Parser \
		p5-XML-Parser>=0:${PORTSDIR}/textproc/p5-XML-Parser \
		p5-Spreadsheet-ParseExcel>=0:${PORTSDIR}/textproc/p5-Spreadsheet-ParseExcel \
		p5-Convert-Binary-C>=0:${PORTSDIR}/converters/p5-Convert-Binary-C \
		p5-Algorithm-Munkres>=0:${PORTSDIR}/math/p5-Algorithm-Munkres \
		p5-Array-Compare>=0:${PORTSDIR}/misc/p5-Array-Compare \
		p5-GraphViz>=0:${PORTSDIR}/graphics/p5-GraphViz \
		p5-Math-Random>=0:${PORTSDIR}/math/p5-Math-Random \
		p5-PostScript>=0:${PORTSDIR}/print/p5-PostScript \
		p5-Set-Scalar>=0:${PORTSDIR}/devel/p5-Set-Scalar \
		p5-URI>=0:${PORTSDIR}/net/p5-URI

RUN_DEPENDS:=	${BUILD_DEPENDS}

#CONFLICTS=	p5-bioperl-1.[13579]*

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_dbsplit.pl.1 \
		bp_download_query_genbank.pl.1 \
		bp_einfo.pl.1 \
		bp_extract_feature_seq.pl.1 \
		bp_fast_load_gff.pl.1 \
		bp_fastam9_to_table.pl.1 \
		bp_fetch.pl.1 \
		bp_filter_search.pl.1 \
		bp_flanks.pl.1 \
		bp_gccalc.pl.1 \
		bp_genbank2gff.pl.1 \
		bp_genbank2gff3.pl.1 \
		bp_generate_histogram.pl.1 \
		bp_heterogeneity_test.pl.1 \
		bp_hivq.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_revtrans-motif.pl.1 \
		bp_search2BSML.pl.1 \
		bp_search2alnblocks.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_seqretsplit.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::Handler::GenericAlignHandler.3 \
		Bio::AlignIO::arp.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::proda.3 \
		Bio::AlignIO::prodom.3 \
		Bio::AlignIO::psi.3 \
		Bio::AlignIO::selex.3 \
		Bio::AlignIO::stockholm.3 \
		Bio::AlignIO::xmfa.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::Relation.3 \
		Bio::Annotation::SimpleValue.3 \
		Bio::Annotation::StructuredValue.3 \
		Bio::Annotation::TagTree.3 \
		Bio::Annotation::Target.3 \
		Bio::Annotation::Tree.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::IO::tigr.3 \
		Bio::Assembly::Scaffold.3 \
		Bio::Assembly::ScaffoldI.3 \
		Bio::Assembly::Singlet.3 \
		Bio::Assembly::Tools::ContigSpectrum.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::eutils.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::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::BinarySearch.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::gene.3 \
		Bio::DB::GFF::Aggregator::match.3 \
		Bio::DB::GFF::Aggregator::none.3 \
		Bio::DB::GFF::Aggregator::orf.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::GenericWebAgent.3 \
		Bio::DB::HIV.3 \
		Bio::DB::HIV::HIVAnnotProcessor.3 \
		Bio::DB::HIV::HIVQueryHelper.3 \
		Bio::DB::InMemoryCache.3 \
		Bio::DB::LocationI.3 \
		Bio::DB::MeSH.3 \
		Bio::DB::NCBIHelper.3 \
		Bio::DB::Qual.3 \
		Bio::DB::Query::GenBank.3 \
		Bio::DB::Query::HIVQuery.3 \
		Bio::DB::Query::WebQuery.3 \
		Bio::DB::QueryI.3 \
		Bio::DB::RandomAccessI.3 \
		Bio::DB::RefSeq.3 \
		Bio::DB::ReferenceI.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::DBI::Pg.3 \
		Bio::DB::SeqFeature::Store::DBI::SQLite.3 \
		Bio::DB::SeqFeature::Store::berkeleydb3.3 \
		Bio::DB::SeqFeature::Store::FeatureFileLoader.3 \
		Bio::DB::SeqFeature::Store::GFF2Loader.3 \
		Bio::DB::SeqFeature::Store::GFF3Loader.3 \
		Bio::DB::SeqFeature::Store::LoadHelper.3 \
		Bio::DB::SeqFeature::Store::Loader.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::TFBS.3 \
		Bio::DB::TFBS::transfac_pro.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::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::LocationFactoryI.3 \
		Bio::Factory::MapFactoryI.3 \
		Bio::Factory::ObjectBuilderI.3 \
		Bio::Factory::ObjectFactory.3 \
		Bio::Factory::ObjectFactoryI.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::FeatureIO::vecscreen_simple.3 \
		Bio::HandlerBaseI.3 \
		Bio::IdCollectionI.3 \
		Bio::IdentifiableI.3 \
		Bio::Index::Abstract.3 \
		Bio::Index::AbstractSeq.3 \
		Bio::Index::Blast.3 \
		Bio::Index::BlastTable.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::Stockholm.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::Gene.3 \
		Bio::Map::GeneMap.3 \
		Bio::Map::GenePosition.3 \
		Bio::Map::GeneRelative.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::Physical.3 \
		Bio::Map::Position.3 \
		Bio::Map::PositionHandler.3 \
		Bio::Map::PositionHandlerI.3 \
		Bio::Map::PositionI.3 \
		Bio::Map::PositionWithSequence.3 \
		Bio::Map::Prediction.3 \
		Bio::Map::Relative.3 \
		Bio::Map::RelativeI.3 \
		Bio::Map::SimpleMap.3 \
		Bio::Map::TranscriptionFactor.3 \
		Bio::MapIO.3 \
		Bio::MapIO::fpc.3 \
		Bio::MapIO::mapmaker.3 \
		Bio::Matrix::Generic.3 \
		Bio::Matrix::IO.3 \
		Bio::Matrix::IO::mlagan.3 \
		Bio::Matrix::IO::phylip.3 \
		Bio::Matrix::IO::scoring.3 \
		Bio::Matrix::MatrixI.3 \
		Bio::Matrix::Mlagan.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::MolEvol::CodonModel.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::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::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::obo.3 \
		Bio::OntologyIO::simplehierarchy.3 \
		Bio::OntologyIO::soflat.3 \
		Bio::ParameterBaseI.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::PhyloNetwork.3 \
		Bio::PhyloNetwork::Factory.3 \
		Bio::PhyloNetwork::FactoryX.3 \
		Bio::PhyloNetwork::GraphViz.3 \
		Bio::PhyloNetwork::RandomFactory.3 \
		Bio::PhyloNetwork::TreeFactory.3 \
		Bio::PhyloNetwork::TreeFactoryMulti.3 \
		Bio::PhyloNetwork::TreeFactoryX.3 \
		Bio::PhyloNetwork::muVector.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::prototype.3 \
		Bio::Restriction::IO::withrefm.3 \
		Bio::Root::Build.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::Test.3 \
		Bio::Root::Test::Warn.3 \
		Bio::Root::Utilities.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::BlastPullHSP.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::HmmpfamHSP.3 \
		Bio::Search::HSP::ModelHSP.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::BlastPullHit.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::HmmpfamHit.3 \
		Bio::Search::Hit::ModelHit.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::BlastPullResult.3 \
		Bio::Search::Result::BlastResult.3 \
		Bio::Search::Result::CrossMatchResult.3 \
		Bio::Search::Result::GenericResult.3 \
		Bio::Search::Result::HMMERResult.3 \
		Bio::Search::Result::HmmpfamResult.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::Search::Tiling::MapTileUtils.3 \
		Bio::Search::Tiling::MapTiling.3 \
		Bio::Search::Tiling::TilingI.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::XML::BlastHandler.3 \
		Bio::SearchIO::XML::PsiBlastHandler.3 \
		Bio::SearchIO::axt.3 \
		Bio::SearchIO::blast.3 \
		Bio::SearchIO::blast_pull.3 \
		Bio::SearchIO::blasttable.3 \
		Bio::SearchIO::blastxml.3 \
		Bio::SearchIO::cross_match.3 \
		Bio::SearchIO::erpin.3 \
		Bio::SearchIO::exonerate.3 \
		Bio::SearchIO::fasta.3 \
		Bio::SearchIO::hmmer.3 \
		Bio::SearchIO::hmmer_pull.3 \
		Bio::SearchIO::infernal.3 \
		Bio::SearchIO::gmap_f9.3 \
		Bio::SearchIO::megablast.3 \
		Bio::SearchIO::psl.3 \
		Bio::SearchIO::rnamotif.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::SeqEvolution::DNAPoint.3 \
		Bio::SeqEvolution::EvolutionI.3 \
		Bio::SeqEvolution::Factory.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::Lite.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::Handler::GenericRichSeqHandler.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::embldriver.3 \
		Bio::SeqIO::entrezgene.3 \
		Bio::SeqIO::excel.3 \
		Bio::SeqIO::exp.3 \
		Bio::SeqIO::fasta.3 \
		Bio::SeqIO::fastq.3 \
		Bio::SeqIO::flybase_chadoxml.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::gbdriver.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::swissdriver.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::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::ERPIN.3 \
		Bio::Tools::ESTScan.3 \
		Bio::Tools::EUtilities.3 \
		Bio::Tools::EUtilities::Cookie.3 \
		Bio::Tools::EUtilities::EUtilDataI.3 \
		Bio::Tools::EUtilities::EUtilParameters.3 \
		Bio::Tools::EUtilities::History.3 \
		Bio::Tools::EUtilities::HistoryI.3 \
		Bio::Tools::EUtilities::Info.3 \
		Bio::Tools::EUtilities::Info::FieldInfo.3 \
		Bio::Tools::EUtilities::Info::LinkInfo.3 \
		Bio::Tools::EUtilities::Link.3 \
		Bio::Tools::EUtilities::Link::LinkSet.3 \
		Bio::Tools::EUtilities::Link::UrlLink.3 \
		Bio::Tools::EUtilities::Query.3 \
		Bio::Tools::EUtilities::Query::GlobalQuery.3 \
		Bio::Tools::EUtilities::Summary.3 \
		Bio::Tools::EUtilities::Summary::DocSum.3 \
		Bio::Tools::EUtilities::Summary::Item.3 \
		Bio::Tools::EUtilities::Summary::ItemContainerI.3 \
		Bio::Tools::Eponine.3 \
		Bio::Tools::Est2Genome.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::HMMER::Domain.3 \
		Bio::Tools::HMMER::Results.3 \
		Bio::Tools::HMMER::Set.3 \
		Bio::Tools::Hmmpfam.3 \
		Bio::Tools::IUPAC.3 \
		Bio::Tools::Infernal.3 \
		Bio::Tools::Lucy.3 \
		Bio::Tools::MZEF.3 \
		Bio::Tools::Match.3 \
		Bio::Tools::OddCodes.3 \
		Bio::Tools::Phylo::Gerp.3 \
		Bio::Tools::Phylo::Gumby.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::Protparam.3 \
		Bio::Tools::Pseudowise.3 \
		Bio::Tools::QRNA.3 \
		Bio::Tools::RNAMotif.3 \
		Bio::Tools::RandomDistFunctions.3 \
		Bio::Tools::RepeatMasker.3 \
		Bio::Tools::Run::GenericParameters.3 \
		Bio::Tools::Run::ParametersI.3 \
		Bio::Tools::Run::RemoteBlast.3 \
		Bio::Tools::Run::StandAloneBlast.3 \
		Bio::Tools::Run::StandAloneNCBIBlast.3 \
		Bio::Tools::Run::StandAloneWUBlast.3 \
		Bio::Tools::Run::WrapperBase.3 \
		Bio::Tools::Seg.3 \
		Bio::Tools::SeqPattern::Backtranslate.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::Signalp::ExtendedSignalp.3 \
		Bio::Tools::Sim4::Exon.3 \
		Bio::Tools::Sim4::Results.3 \
		Bio::Tools::Spidey::Exon.3 \
		Bio::Tools::Spidey::Results.3 \
		Bio::Tools::TandemRepeatsFinder.3 \
		Bio::Tools::TargetP.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::AnnotatableNode.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::phyloxml.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

# 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 DEPENDENCIES DEPRECATED INSTALL LICENSE MANIFEST README
	${INSTALL_MAN} ${WRKSRC}/${doc} ${DOCSDIR}
.endfor
	${CP} -R ${WRKSRC}/doc ${DOCSDIR}
.endif

.include <bsd.port.mk>
@


1.31
log
@SVN rev 305131 on 2012-10-01 14:55:55Z by wen

- Take maintainership
@
text
@d2 1
a2 1
# $FreeBSD$
@


1.30
log
@SVN rev 305130 on 2012-10-01 14:45:16Z by tabthorpe

- Reassign to the heap at maintainer's request
@
text
@d13 1
a13 1
MAINTAINER=	ports@@FreeBSD.org
@


1.29
log
@- Remove SITE_PERL from *_DEPENDS

Approved by: portmgr@@ (bapt@@)
@
text
@d1 1
a1 4
# New ports collection makefile for:	p5-bioperl
# Date created:		28 July 2000
# Whom:	      		Johann Visagie <johann@@egenetics.com>
#
a2 1
#
d13 1
a13 1
MAINTAINER=	fernan@@iib.unsam.edu.ar
@


1.28
log
@- update png to 1.5.10
@
text
@d22 39
a60 39
		${SITE_PERL}/Bio/ASN1/EntrezGene.pm:${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 \
		${SITE_PERL}/SOAP/Lite.pm:${PORTSDIR}/net/p5-SOAP-Lite \
		${SITE_PERL}/SVG.pm:${PORTSDIR}/textproc/p5-SVG \
		${SITE_PERL}/SVG/Graph.pm:${PORTSDIR}/graphics/p5-SVG-Graph \
		${SITE_PERL}/Text/Shellwords.pm:${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}/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}/XML/Parser.pm:${PORTSDIR}/textproc/p5-XML-Parser \
		${SITE_PERL}/Spreadsheet/ParseExcel.pm:${PORTSDIR}/textproc/p5-Spreadsheet-ParseExcel \
		${SITE_PERL}/${PERL_ARCH}/Convert/Binary/C.pm:${PORTSDIR}/converters/p5-Convert-Binary-C \
		${SITE_PERL}/Algorithm/Munkres.pm:${PORTSDIR}/math/p5-Algorithm-Munkres \
		${SITE_PERL}/Array/Compare.pm:${PORTSDIR}/misc/p5-Array-Compare \
		${SITE_PERL}/GraphViz.pm:${PORTSDIR}/graphics/p5-GraphViz \
		${SITE_PERL}/${PERL_ARCH}/Math/Random.pm:${PORTSDIR}/math/p5-Math-Random \
		${SITE_PERL}/PostScript/TextBlock.pm:${PORTSDIR}/print/p5-PostScript \
		${SITE_PERL}/Set/Scalar.pm:${PORTSDIR}/devel/p5-Set-Scalar \
		${SITE_PERL}/URI/Escape.pm:${PORTSDIR}/net/p5-URI
@


1.27
log
@At the moment 1385 ports use BUILD_DEPENDS= ${RUN_DEPENDS} and 450
ports use BUILD_DEPENDS:= ${RUN_DEPENDS}. This patch fixes ports that are
currently broken. This is a temporary measure until we organically stop using
:= or someone(s) spend a lot of time changing all the ports over.

Explicit duplication > := > = and this just moves ports one step to the left

Approved by:	portmgr
@
text
@d10 1
a10 1
PORTREVISION=	3
@


1.26
log
@- update to 1.4.1
Reviewed by:	exp8 run on pointyhat
Supported by:	miwi
@
text
@d62 1
a62 1
RUN_DEPENDS=	${BUILD_DEPENDS}
@


1.25
log
@- update to jpeg-8
@
text
@d10 1
a10 1
PORTREVISION=	2
@


1.24
log
@- Remove unneeded dependencies which is in perl-5.8.9 dist
  (part 19; last!).

Approved by:	portmgr (itetcu)
@
text
@d10 1
a10 1
PORTREVISION=	1
@


1.23
log
@- Update to 1.6.1

Approved by:	maintainer (via Email)
@
text
@d10 1
a50 1
		${SITE_PERL}/${PERL_ARCH}/Storable.pm:${PORTSDIR}/devel/p5-Storable \
a53 1
		${SITE_PERL}/Test/Harness.pm:${PORTSDIR}/devel/p5-Test-Harness \
a59 1
		${SITE_PERL}/Text/ParseWords.pm:${PORTSDIR}/textproc/p5-Text-ParseWords \
@


1.22
log
@- bump all port that indirectly depends on libjpeg and have not yet been bumped or updated
Requested by:	edwin
@
text
@d9 1
a9 2
PORTVERSION=	1.6.0
PORTREVISION=	1
d66 1
a66 1
CONFLICTS=	p5-bioperl-1.[13579]*
d82 1
d94 1
d114 1
a231 1
		Bio::ConfigData.3 \
d342 3
d657 3
d688 1
d872 1
a886 1
		Bio::Tools::HMM.3 \
d930 1
d999 1
a999 1
.for doc in AUTHORS BUGS Changes DEPENDENCIES DEPRECATED INSTALL LICENSE MANIFEST PLATFORMS README
@


1.21
log
@- lang/perl5.6 is dead, remove PERL_LEVEL/PERL_VERSION < 500801 checks

PR:             ports/135398
Tested by:      2 -exp runs by pav
Approved by:    portmgr (pav)
@
text
@d10 1
@


1.20
log
@Remove variable PERL_VER from the ports tree at all - because
it is obsolete since Perl 5.6.0.
@
text
@a980 9
.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

d995 1
a995 1
.include <bsd.port.post.mk>
@


1.19
log
@- Update to 1.6.0

PR:		ports/131989
Submitted by:	maintainer
@
text
@d19 2
a20 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 \
@


1.18
log
@Fix plist with perl 5.8.9.

Approved by:	portmgr (pav, implicit)
@
text
@d9 1
a9 2
PORTVERSION=	1.4
PORTREVISION=	2
d14 1
d19 9
a27 4
# 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 \
d32 6
a37 1
		${SITE_PERL}/XML/Node.pm:${PORTSDIR}/textproc/p5-XML-Node \
d39 4
d44 2
a45 4
		${SITE_PERL}/HTTP/Request/Common.pm:${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 \
d48 2
d51 13
a63 4
		${SITE_PERL}/Parse/RecDescent.pm:${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
d68 1
a68 1
PERL_CONFIGURE=	YES
d73 1
d78 1
d81 1
d84 1
a84 1
		bp_feature_draw.pl.1 \
a87 1
		bp_frend.pl.1 \
d90 1
d93 1
d97 1
d99 1
d102 1
d106 1
a106 1
		bp_pg_bulk_load_gff.pl.1 \
a107 1
		bp_process_ncbi_human.pl.1 \
d110 1
d115 1
a116 1
		bp_search_overview.pl.1 \
d119 2
d124 5
a128 1
		bp_translate_seq.pl.1
d132 1
d136 2
d142 1
d152 2
d158 1
d169 1
d172 3
d183 1
d186 2
d229 1
d244 1
d251 4
a263 1
		Bio::DB::Flat::BDB::swissprot.3 \
a264 1
		Bio::DB::GDB.3 \
d267 2
d276 1
d281 1
d283 2
a284 1
		Bio::DB::GFF::Adaptor::memory_iterator.3 \
d289 1
d292 1
d294 1
d315 4
d320 1
d323 1
d325 1
d330 1
d332 17
d350 2
d353 2
d358 1
a361 2
		Bio::DB::XEMBL.3 \
		Bio::DB::XEMBLService.3 \
d369 2
d372 1
d374 4
a381 1
		Bio::Factory::HitFactoryI.3 \
a386 1
		Bio::Factory::ResultFactoryI.3 \
d394 8
a401 48
		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::Graphics::Util.3 \
d407 1
d412 3
a424 1
		Bio::LiveSeq::IO::SRS.3 \
d447 2
d452 6
d461 1
d468 1
d470 2
d473 4
d478 1
d480 1
d484 1
d488 1
d491 1
d493 1
d497 2
d507 2
d511 2
d523 2
a524 1
		Bio::Ontology::SimpleGOEngine.3 \
d536 1
d539 1
d551 9
d562 1
d565 2
d578 2
d582 1
d595 1
d597 1
a597 1
		Bio::Root::Err.3 \
a598 1
		Bio::Root::Global.3 \
a600 2
		Bio::Root::IOManager.3 \
		Bio::Root::Object.3 \
d604 2
a606 1
		Bio::Root::Vector.3 \
d608 1
a608 1
		Bio::Root::Xref.3 \
d612 1
d614 1
d620 2
d624 1
d627 1
d633 2
d636 1
d640 1
d642 1
d645 2
d651 1
d666 2
d670 1
d673 2
d678 2
d682 1
d689 1
d692 1
d699 1
d709 4
d730 1
d737 2
d741 1
d746 1
d750 1
d754 1
d756 2
d760 3
d766 1
d773 1
d776 1
d779 1
d788 1
d790 1
d792 1
d794 3
d818 1
a837 10
		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 \
d844 1
d846 17
d865 1
d877 1
d883 1
d886 1
d888 2
d907 1
d910 1
d913 2
a914 1
		Bio::Tools::RestrictionEnzyme.3 \
d917 2
a920 1
		Bio::Tools::SeqAnal.3 \
d925 2
d929 1
d932 4
a936 1
		Bio::Tools::WWW.3 \
d938 2
d942 1
d944 4
d958 1
d963 2
d979 1
a979 6
		Bio::WebAgent.3 \
		biodatabases.3 \
		biodesign.3 \
		bioperl.3 \
		bioscripts.3 \
		bptutorial.3
d985 3
d998 1
a998 1
.for doc in AUTHORS BUGS Changes DEPRECATED FAQ INSTALL LICENSE PLATFORMS README
@


1.17
log
@- 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)
@
text
@d10 1
a10 1
PORTREVISION=	1
d346 1
@


1.16
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
@d13 1
a13 2
		${MASTER_SITE_PERL_CPAN}
MASTER_SITE_SUBDIR=	Bio
@


1.15
log
@- Welcome X.org 7.2 \o/.
- Set X11BASE to ${LOCALBASE} for recent ${OSVERSION}.
- Bump PORTREVISION for ports intalling files in ${X11BASE}.
@
text
@a800 3
.if ${PERL_LEVEL} < 500600
IGNORE=			"This port requires Perl 5.6 or better"
.endif
@


1.14
log
@Add conflicst:
CONFLICTS=     p5-bioperl-1.[13579]*

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


1.13
log
@- add missing MAN1 and MAN3
- apply DATADIR, EXAMPLESDIR, and DOCSDIR in PLIST
- update the usage of NOPORTDOCS

PR:		71322
Submitted by:	leeym
Approved by:	Fernan Aguero <fernan@@iib.unsam.edu.ar>
@
text
@d43 2
@


1.12
log
@After devel/p5-File-Temp has gained an IGNORE for PERL_LEVEL > 500800, all
these ports were broken because they always depended on it. I've rearranged all
the dependencies to fit the new scheme.
@
text
@d45 46
d92 1
a92 1
		Bio::Align::DNAStatistics.3  \
d99 1
a99 1
  		Bio::AlignIO::emboss.3 \
d101 1
d103 3
a105 2
  		Bio::AlignIO::mega.3 \
  		Bio::AlignIO::meme.3 \
d107 1
a107 1
  		Bio::AlignIO::nexus.3 \
d109 1
a109 1
  		Bio::AlignIO::phylip.3 \
d111 1
a111 1
  		Bio::AlignIO::psi.3 \
d114 6
a119 6
  		Bio::AnalysisI.3 \
  		Bio::AnalysisParserI.3 \
  		Bio::AnalysisResultI.3 \
  		Bio::AnnotatableI.3 \
  		Bio::Annotation::AnnotationFactory.3 \
  		Bio::Annotation::Collection.3 \
d122 1
a122 1
  		Bio::Annotation::OntologyTerm.3 \
d124 3
a126 3
  		Bio::Annotation::SimpleValue.3 \
  		Bio::Annotation::StructuredValue.3 \
  		Bio::Annotation::TypeManager.3 \
d175 2
d194 1
d204 4
d212 1
d221 1
d252 1
d262 3
d298 1
d301 1
d321 1
d342 2
d403 17
d421 1
d440 1
d442 1
d446 1
d450 2
d459 15
d478 11
d498 1
d501 1
d512 2
d521 3
d536 1
d539 2
d546 1
d548 1
d551 7
a557 3
  		Bio::SearchIO::fasta.3 \
  		Bio::SearchIO::hmmer.3 \
  		Bio::SearchIO::waba.3 \
d559 2
a560 2
  		Bio::Seq::BaseSeqProcessor.3 \
  		Bio::Seq::EncodedSeq.3 \
d563 6
a568 3
  		Bio::Seq::PrimaryQual.3 \
  		Bio::Seq::PrimedSeq.3 \
  		Bio::Seq::QualI.3 \
d571 6
a576 6
  		Bio::Seq::SeqBuilder.3 \
  		Bio::Seq::SeqFactory.3 \
  		Bio::Seq::SeqFastaSpeedFactory.3 \
  		Bio::Seq::SeqWithQuality.3 \
  		Bio::Seq::SequenceTrace.3 \
  		Bio::Seq::TraceI.3 \
d578 4
a581 4
  		Bio::SeqFeature::AnnotationAdaptor.3 \
  		Bio::SeqFeature::Collection.3 \
  		Bio::SeqFeature::CollectionI.3 \
  		Bio::SeqFeature::Computation.3 \
d587 4
a590 4
  		Bio::SeqFeature::Gene::Intron.3 \
  		Bio::SeqFeature::Gene::NC_Feature.3 \
  		Bio::SeqFeature::Gene::Poly_A_site.3 \
  		Bio::SeqFeature::Gene::Promoter.3 \
d593 1
a593 1
  		Bio::SeqFeature::Gene::UTR.3 \
d595 4
a598 2
  		Bio::SeqFeature::PositionProxy.3 \
  		Bio::SeqFeature::Primer.3 \
d601 2
d608 1
a608 1
  		Bio::SeqIO::abi.3 \
d610 5
a614 4
  		Bio::SeqIO::alf.3 \
  		Bio::SeqIO::bsml.3 \
  		Bio::SeqIO::chadoxml.3 \
  		Bio::SeqIO::ctf.3 \
d616 1
a616 1
  		Bio::SeqIO::exp.3 \
d618 1
a618 1
  		Bio::SeqIO::fastq.3 \
d620 5
a624 1
  		Bio::SeqIO::game::seqHandler.3 \
d627 1
d629 6
a634 5
  		Bio::SeqIO::locuslink.3 \
  		Bio::SeqIO::phd.3 \
  		Bio::SeqIO::pir.3 \
  		Bio::SeqIO::pln.3 \
  		Bio::SeqIO::qual.3 \
d638 3
a640 1
  		Bio::SeqIO::ztr.3 \
d643 1
d645 3
a647 3
  		Bio::Structure::Atom.3 \
  		Bio::Structure::Chain.3 \
  		Bio::Structure::Entry.3 \
d661 5
a665 3
  		Bio::Taxonomy.3 \
  		Bio::Taxonomy::Taxon.3 \
  		Bio::Taxonomy::Tree.3 \
d667 12
a678 2
  		Bio::Tools::Alignment::Consed.3 \
  		Bio::Tools::Alignment::Trim.3 \
d682 1
a682 1
  		Bio::Tools::BPlite::HSP.3 \
d684 1
a684 1
  		Bio::Tools::BPlite::Sbjct.3 \
d690 1
d692 4
a695 3
  		Bio::Tools::Coil.3 \
  		Bio::Tools::ECnumber.3 \
  		Bio::Tools::EPCR.3 \
d697 3
a699 3
  		Bio::Tools::Eponine.3 \
  		Bio::Tools::Est2Genome.3 \
  		Bio::Tools::FootPrinter.3 \
d701 5
a705 4
  		Bio::Tools::Gel.3 \
  		Bio::Tools::Genemark.3 \
  		Bio::Tools::Genewise.3 \
  		Bio::Tools::Genomewise.3 \
d707 3
a709 1
  		Bio::Tools::Grail.3 \
d713 1
a713 1
  		Bio::Tools::Hmmpfam.3 \
d715 1
a715 1
  		Bio::Tools::Lucy.3 \
d718 6
a723 5
  		Bio::Tools::Phylo::Molphy.3 \
  		Bio::Tools::Phylo::Molphy::Result.3 \
  		Bio::Tools::Phylo::PAML.3 \
  		Bio::Tools::Phylo::PAML::Result.3 \
  		Bio::Tools::Phylo::Phylip::ProtDist.3 \
d726 13
a738 6
  		Bio::Tools::Primer3.3 \
  		Bio::Tools::Prints.3 \
  		Bio::Tools::Profile.3 \
  		Bio::Tools::Promoterwise.3 \
  		Bio::Tools::Pseudowise.3 \
  		Bio::Tools::RepeatMasker.3 \
d740 1
a740 1
  		Bio::Tools::Run::RemoteBlast.3 \
d742 2
a743 2
  		Bio::Tools::Run::WrapperBase.3 \
  		Bio::Tools::Seg.3 \
d748 1
d750 1
a750 1
  		Bio::Tools::Signalp.3 \
d753 1
a753 1
  		Bio::Tools::Tmhmm.3 \
d755 2
d758 2
a759 2
  		Bio::Tree::AlleleNode.3 \
  		Bio::Tree::Node.3 \
d769 1
d771 1
d773 1
d787 5
a804 2

.if !defined(NOPORTDOCS)
d806 1
d808 2
a810 1

d814 1
a814 5
	${CP} -R   ${WRKSRC}/doc        ${DOCSDIR}
	${CP} -R   ${WRKSRC}/examples/* ${EXAMPLESDIR}
	${CP} -R   ${WRKSRC}/scripts  	${DATADIR}
	${CP} -R   ${WRKSRC}/models   	${DATADIR}

@


1.11
log
@Unmark as broken for 4.x; instead, mark as ignore for perl < 5.6.
@
text
@a22 1
		${SITE_PERL}/File/Temp.pm:${PORTSDIR}/devel/p5-File-Temp \
d612 2
d616 1
@


1.10
log
@BROKEN on 4.x: Configure fails
@
text
@d613 2
a614 2
.if ${OSVERSION} < 500000
BROKEN=		"Configure fails"
@


1.9
log
@Major update from 0.7.2 to 1.4 by new maintainer.  This is almost a complete
rework of the port.

See the page http://news.open-bio.org/archives/cat_bioperl.html for the
changes between 1.2 and 1.4.  The older changes are in the CVS tree.

From the new maintainer:

	Note that this new port just handles the installation of bioperl and
	not of additional extra stuff (bioperl-gui, bioperl-corba-server,
	bioperl-corba-client). This is unlike the behaviour of the current
	port.

	The extra stuff, though still functional, had very little adoption
	among users, and does not appear to be currently supported/maintained.

PR:		ports/47303 (and subsequent)
Submitted by:	Fernan Aguero <fernan@@iib.unsam.edu.ar> (new maintainer)
@
text
@d611 6
d635 1
a635 1
.include <bsd.port.mk>
@


1.8
log
@utilize SITE_PERL

PR:		58166
Submitted by:	Cheng-Lung Sung <clsung@@dragon2.net>
@
text
@d9 1
a9 1
PORTVERSION=	0.7.2
d11 1
a11 2
MASTER_SITES=	ftp://bioperl.org/pub/DIST/ \
		http://bioperl.org/Core/Latest/ \
a14 1
DISTFILES=	${DISTNAME}${EXTRACT_SUFX}
d16 1
a16 1
MAINTAINER=	wjv@@FreeBSD.org
d30 12
a41 1
		${SITE_PERL}/XML/Writer.pm:${PORTSDIR}/textproc/p5-XML-Writer
d46 184
a229 47
.if defined(WITH_CORBA)
WITH_CORBA_CLIENT=	YES
WITH_CORBA_SERVER=	YES
.endif

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+=	${SITE_PERL}/${PERL_ARCH}/CORBA/ORBit.pm:${PORTSDIR}/devel/p5-ORBit
RUN_DEPENDS+=	${SITE_PERL}/${PERL_ARCH}/CORBA/ORBit.pm:${PORTSDIR}/devel/p5-ORBit
.endif
.if defined(WITH_CORBA_SERVER)
BUILD_DEPENDS+=	${SITE_PERL}/${PERL_ARCH}/CORBA/ORBit.pm:${PORTSDIR}/devel/p5-ORBit
RUN_DEPENDS+=	${SITE_PERL}/${PERL_ARCH}/CORBA/ORBit.pm:${PORTSDIR}/devel/p5-ORBit
.endif
.if defined(WITH_GUI)
RUN_DEPENDS+=	ptksh:${PORTSDIR}/x11-toolkits/p5-Tk
.endif

.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 "
.endif
PLIST_SUB+=	PLIST_${ext}=${PLIST_${ext}}
.endfor

MAN3=		Bio::AlignIO.3 Bio::AlignIO::bl2seq.3 \
		Bio::AlignIO::clustalw.3 Bio::AlignIO::fasta.3 \
		Bio::AlignIO::mase.3 Bio::AlignIO::msf.3 Bio::AlignIO::pfam.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::GDB.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::UpdateableSeqI.3 Bio::DB::WebDBSeqI.3 \
		Bio::DBLinkContainerI.3 Bio::Factory::DriverFactory.3 \
d232 79
a310 13
		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 \
d312 2
a313 1
		Bio::Location::CoordinatePolicyI.3 Bio::Location::Fuzzy.3 \
d315 137
a451 12
		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::FeaturePair.3 \
		Bio::SeqFeature::Gene::Exon.3 Bio::SeqFeature::Gene::ExonI.3 \
d454 4
d460 69
a528 12
		Bio::SeqFeature::Generic.3 Bio::SeqFeature::Similarity.3 \
		Bio::SeqFeature::SimilarityPair.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::gcg.3 \
		Bio::SeqIO::genbank.3 Bio::SeqIO::largefasta.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 \
d530 37
a566 8
		Bio::Tools::Blast::Run::LocalBlast.3 \
		Bio::Tools::Blast::Run::Webblast.3 Bio::Tools::Blast::Sbjct.3 \
		Bio::Tools::CodonTable.3 Bio::Tools::ESTScan.3 \
		Bio::Tools::Fasta.3 Bio::Tools::GFF.3 Bio::Tools::Genscan.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 \
d568 42
a609 34
		Bio::Tools::Run::Alignment::Clustalw.3 \
		Bio::Tools::Run::Alignment::TCoffee.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
d611 2
a612 5
pre-fetch:
.if !defined(BATCH) && (!defined(WITH_CORBA_CLIENT) || \
    !defined(WITH_CORBA_SERVER) || !defined(WITH_GUI))
	@@ ${CAT} ${FILESDIR}/ext.msg
.endif
d614 4
a617 9
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
d619 2
a620 6
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}
d622 4
d627 1
a627 9
post-install:
	@@ 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}
.endfor
@


1.7
log
@Clear moonlight beckons.
Requiem mors pacem pkg-comment,
And be calm ports tree.

E Nomini Patri, E Fili, E Spiritu Sancti.
@
text
@d23 10
a32 10
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/Writer.pm:${PORTSDIR}/textproc/p5-XML-Writer
d50 2
a51 2
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
d54 2
a55 2
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
a173 1
MANPREFIX=	${PREFIX}/lib/perl5/${PERL_VERSION}
@


1.6
log
@- Update to version 0.7.2, somewhat overdue.  :-)
@
text
@d19 1
@


1.5
log
@- Properly list run-time dependencies in RUN_DEPENDS in Makefile.
- Deploy %%PERL_VER%% and %%PERL_ARCH%% pragmas consistently throughout
  pkg-plist.  (Ouch, that was embarrassing.)
- Bump PORTREVISION due to the above.
- Update my email address and the project's URL in pkg-descr.
@
text
@d5 1
a5 1
# $FreeBSD: ports/biology/p5-bioperl/Makefile,v 1.4 2001/07/04 13:22:10 wjv Exp $
d9 1
a9 2
PORTVERSION=	0.7.1
PORTREVISION=	1
d76 5
a80 2
		Bio::AlignIO::stockholm.3 Bio::DB::GDB.3 \
		Bio::DB::NCBIHelper.3 Bio::DB::SwissProt.3 \
d85 3
a87 1
		Bio::Index::GenBank.3 Bio::Index::Swissprot.3 \
d97 1
a97 1
		Bio::LiveSeq::Translation.3 \
d104 9
a112 4
		Bio::Root::IO.3 Bio::Seq::LargePrimarySeq.3 \
		Bio::Seq::LargeSeq.3 Bio::Seq::RichSeq.3 Bio::Seq::RichSeqI.3 \
		Bio::SeqAnalysisParserI.3 Bio::SeqFeature::Gene::Exon.3 \
		Bio::SeqFeature::Gene::ExonI.3 \
d117 22
a138 9
		Bio::SeqFeature::Similarity.3 \
		Bio::SeqFeature::SimilarityPair.3 Bio::SeqIO::ace.3 \
		Bio::SeqIO::game.3 Bio::SeqIO::largefasta.3 Bio::SeqUtils.3 \
		Bio::Tools::AnalysisResult.3 Bio::Tools::BPbl2seq.3 \
		Bio::Tools::BPlite.3 Bio::Tools::BPlite::Iteration.3 \
		Bio::Tools::BPpsilite.3 Bio::Tools::ESTScan.3 \
		Bio::Tools::GFF.3 Bio::Tools::Genscan.3 Bio::Tools::MZEF.3 \
		Bio::Tools::OddCodes.3 Bio::Tools::Prediction::Exon.3 \
		Bio::Tools::Prediction::Gene.3 \
d141 11
a151 7
		Bio::Tools::Run::StandAloneBlast.3 Bio::Tools::Sim4::Exon.3 \
		Bio::Tools::Sim4::Results.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 bptutorial.3
@


1.4
log
@- Update to version 0.7.1
- Add a build-time message to inform the user of available options.
@
text
@d5 1
a5 1
# $FreeBSD: ports/biology/p5-bioperl/Makefile,v 1.3 2001/06/26 15:09:39 wjv Exp $
d10 1
d21 2
d33 1
d51 1
d55 1
@


1.3
log
@Embarrassingly long overdue update to 0.7.0, including optional support for
GUI (Tk) and CORBA extensions.
@
text
@d5 1
a5 1
# $FreeBSD: ports/biology/p5-bioperl/Makefile,v 1.2 2000/10/13 12:43:24 jeh Exp $
d9 1
a9 1
PORTVERSION=	0.7.0
d142 6
@


1.2
log
@Update to version 0.6.2

PR:		21954
Submitted by:	Johann Visagie <johann@@egenetics.com> MAINTAINER
@
text
@d5 1
a5 1
# $FreeBSD: ports/biology/p5-bioperl/Makefile,v 1.1 2000/07/28 14:06:02 nbm Exp $
d9 1
a9 1
PORTVERSION=	0.6.2
d11 2
a12 2
MASTER_SITES=	ftp://bio.perl.org/pub/DIST/ \
		http://bio.perl.org/Core/Latest/ \
d14 1
a14 1
MASTER_SITE_SUBDIR=Bio
d16 1
a16 1
DISTFILES=	${DISTNAME}${EXTRACT_SUFX} bioperl-ext-0.6.tar.gz
d18 1
a18 1
MAINTAINER=	johann@@egenetics.com
d20 6
a25 1
BUILD_DEPENDS=	${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/HTTP/Request/Common.pm:${PORTSDIR}/www/p5-libwww \
d27 3
a29 2
		${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/${PERL_ARCH}/Ace.pm:${PORTSDIR}/biology/p5-AcePerl \
		${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/IO/Scalar.pm:${PORTSDIR}/devel/p5-IO-stringy
d33 108
a140 38
MAN3=		Bio::Annotation.3 Bio::Annotation::Comment.3 \
		Bio::Annotation::DBLink.3 Bio::Annotation::Reference.3 \
		Bio::DB::Ace.3 Bio::DB::GenBank.3 Bio::DB::GenPept.3 \
		Bio::DB::RandomAccessI.3 Bio::DB::SeqI.3 \
		Bio::Index::Abstract.3 Bio::Index::AbstractSeq.3 \
		Bio::Index::EMBL.3 Bio::Index::Fasta.3 \
		Bio::Index::SwissPfam.3 Bio::LocatableSeq.3 \
		Bio::PrimarySeq.3 Bio::PrimarySeqI.3 Bio::Range.3 \
		Bio::RangeI.3 Bio::Root::Err.3 Bio::Root::Global.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::Search::Hit::Fasta.3 Bio::Search::Hit::HitI.3 \
		Bio::Search::Processor.3 Bio::Search::Processor::Fasta.3 \
		Bio::Search::Processor::ProcessorI.3 \
		Bio::Search::Result::Fasta.3 \
		Bio::Search::Result::ResultI.3 Bio::SearchDist.3 \
		Bio::Seq.3 Bio::SeqFeature::FeaturePair.3 \
		Bio::SeqFeature::Generic.3 Bio::SeqFeatureI.3 Bio::SeqI.3 \
		Bio::SeqIO.3 Bio::SeqIO::FTHelper.3 \
		Bio::SeqIO::MultiFile.3 Bio::SeqIO::embl.3 \
		Bio::SeqIO::fasta.3 Bio::SeqIO::gcg.3 \
		Bio::SeqIO::genbank.3 Bio::SeqIO::pir.3 Bio::SeqIO::raw.3 \
		Bio::SeqIO::scf.3 Bio::SeqIO::swiss.3 Bio::SimpleAlign.3 \
		Bio::Species.3 Bio::Tools::AlignFactory.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::Fasta.3 Bio::Tools::HMMER::Domain.3 \
		Bio::Tools::HMMER::Results.3 Bio::Tools::HMMER::Set.3 \
		Bio::Tools::IUPAC.3 Bio::Tools::RestrictionEnzyme.3 \
		Bio::Tools::SeqAnal.3 Bio::Tools::SeqPattern.3 \
		Bio::Tools::SeqStats.3 Bio::Tools::SeqWords.3 \
		Bio::Tools::Sigcleave.3 Bio::Tools::WWW.3 \
		Bio::Tools::pSW.3 Bio::UnivAln.3 \
		bioback.3 biodesign.3 bioperl.3 biostart.3
a142 2
EXT_WRKSRC=	${WRKDIR}/bioperl-ext-06/Bio/Ext/Align

d144 1
a144 1
	@@ (cd ${EXT_WRKSRC} && \
d146 6
a151 1
	  ${PERL5} ${CONFIGURE_SCRIPT} ${CONFIGURE_ARGS})
d154 6
a159 2
	@@ (cd ${EXT_WRKSRC} && \
	  ${MAKE} ${MAKE_FLAGS} ${MAKEFILE} ${MAKE_ARGS} ${ALL_TARGET})
d162 5
a166 1
	@@ (cd ${EXT_WRKSRC} && \
d168 2
a169 1
	  ${MAKEFILE} ${MAKE_ARGS} ${INSTALL_TARGET})
@


1.1
log
@Add BioPerl, a collection of Perl5 mods for bioinformatics/genomics

PR:		ports/20252
Submitted by:	Johann Visagie <johann@@egenetics.com>
@
text
@d5 1
a5 1
# $FreeBSD$
d9 1
a9 1
PORTVERSION=	0.6.1
d20 33
a52 23
BUILD_DEPENDS=	${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/LWP/UserAgent.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}/${PERL_ARCH}/Ace.pm:${PORTSDIR}/biology/p5-AcePerl

USE_PERL5=	YES

EXT_WRKSRC=	${WRKDIR}/bioperl-ext-06

MAN3=		Bio::Tools::CodonTable.3 \
		Bio::PrimarySeq.3 \
		Bio::Tools::SeqStats.3 \
		Bio::SimpleAlign.3 \
		Bio::Search::Processor::Fasta.3 \
		Bio::Root::Xref.3 \
		Bio::Annotation::DBLink.3 \
		Bio::SeqIO::swiss.3 \
		Bio::Annotation::Comment.3 \
		Bio::Tools::Sim4::Results.3 \
		Bio::Annotation::Reference.3 \
		Bio::SeqIO::pir.3 \
		Bio::Search::Hit::Fasta.3 \
		Bio::Tools::SeqAnal.3 \
		Bio::Annotation.3 \
d54 1
a54 23
		Bio::Tools::HMMER::Results.3 \
		Bio::SeqIO::scf.3 \
		Bio::SeqIO::genbank.3 \
		Bio::Root::RootI.3 \
		Bio::Tools::SeqWords.3 \
		Bio::Root::Global.3 \
		Bio::Tools::pSW.3 \
		Bio::SeqIO::raw.3 \
		Bio::Tools::Blast::HSP.3 \
		bioperl.3 \
		Bio::RangeI.3 \
		Bio::Search::Processor.3 \
		Bio::Root::Object.3 \
		Bio::Tools::WWW.3 \
		Bio::PrimarySeqI.3 \
		Bio::Index::Abstract.3 \
		Bio::DB::Ace.3 \
		Bio::SeqFeature::Generic.3 \
		Bio::DB::SeqI.3 \
		Bio::Root::Vector.3 \
		Bio::Seq.3 \
		Bio::Range.3 \
		Bio::UnivAln.3 \
d56 10
a65 41
		Bio::SeqIO::gcg.3 \
		biodesign.3 \
		Bio::Tools::RestrictionEnzyme.3 \
		Bio::DB::RandomAccessI.3 \
		biostart.3 \
		Bio::Tools::Sim4::Exon.3 \
		Bio::Search::Hit::HitI.3 \
		bioback.3 \
		Bio::Tools::HMMER::Domain.3 \
		Bio::SeqIO::FTHelper.3 \
		Bio::Root::IOManager.3 \
		Bio::LocatableSeq.3 \
		Bio::Index::AbstractSeq.3 \
		Bio::Tools::Fasta.3 \
		Bio::Tools::Blast::Sbjct.3 \
		Bio::Tools::IUPAC.3 \
		Bio::SeqIO.3 \
		Bio::SeqIO::MultiFile.3 \
		Bio::Tools::AlignFactory.3 \
		Bio::SeqIO::fasta.3 \
		Bio::SeqFeature::FeaturePair.3 \
		Bio::DB::GenBank.3 \
		Bio::SeqI.3 \
		Bio::Tools::Blast.3 \
		Bio::Tools::HMMER::Set.3 \
		Bio::SeqFeatureI.3 \
		Bio::SearchDist.3 \
		Bio::Tools::Sigcleave.3 \
		Bio::Search::Result::ResultI.3 \
		Bio::Root::Utilities.3 \
		Bio::Root::Err.3 \
		Bio::Search::Result::Fasta.3 \
		Bio::Tools::SeqPattern.3 \
		Bio::Search::Processor::ProcessorI.3 \
		Bio::Index::EMBL.3 \
		Bio::Species.3 \
		Bio::Tools::Blast::Run::LocalBlast.3 \
		Bio::SeqIO::embl.3 \
		Bio::Index::SwissPfam.3 \
		Bio::DB::GenPept.3 \
		Bio::Index::Fasta.3
d67 1
a67 1
MANPREFIX=	${PREFIX}/lib/perl5/${PERL_VERSION}
d69 13
a81 11
do-configure:
	@@(cd ${WRKSRC}; ${SETENV} ${MAKE_ENV} ${PERL5} Makefile.PL)
	@@(cd ${EXT_WRKSRC}/Bio/Ext/Align; ${SETENV} ${MAKE_ENV} ${PERL5} Makefile.PL)

do-build:
	@@(cd ${WRKSRC}; ${SETENV} ${MAKE_ENV} ${MAKE} ${MAKE_FLAGS} ${MAKEFILE} ${MAKE_ARGS} ${ALL_TARGET})
	@@(cd ${EXT_WRKSRC}/Bio/Ext/Align; ${MAKE} ${MAKE_FLAGS} ${MAKEFILE} ${MAKE_ARGS} ${ALL_TARGET})

do-install:
	@@(cd ${WRKSRC}; ${SETENV} ${MAKE_ENV} ${MAKE} ${MAKE_FLAGS} ${MAKEFILE} ${MAKE_ARGS} ${INSTALL_TARGET})
	@@(cd ${EXT_WRKSRC}/Bio/Ext/Align; ${SETENV} ${MAKE_ENV} ${MAKE} ${MAKE_FLAGS} ${MAKEFILE} ${MAKE_ARGS} ${INSTALL_TARGET})
@

