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Date:      Mon, 16 Jun 2008 18:34:07 GMT
From:      Mauricio Herrera Cuadra <mauricio@arareko.net>
To:        freebsd-gnats-submit@FreeBSD.org
Subject:   ports/124648: Update port: biology/p5-bioperl-devel to version 1.5.2
Message-ID:  <200806161834.m5GIY74B009744@www.freebsd.org>
Resent-Message-ID: <200806161840.m5GIe36P014117@freefall.freebsd.org>

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>Number:         124648
>Category:       ports
>Synopsis:       Update port: biology/p5-bioperl-devel to version 1.5.2
>Confidential:   no
>Severity:       non-critical
>Priority:       low
>Responsible:    freebsd-ports-bugs
>State:          open
>Quarter:        
>Keywords:       
>Date-Required:
>Class:          change-request
>Submitter-Id:   current-users
>Arrival-Date:   Mon Jun 16 18:40:03 UTC 2008
>Closed-Date:
>Last-Modified:
>Originator:     Mauricio Herrera Cuadra
>Release:        FreeBSD 5.5-STABLE i386
>Organization:
>Environment:
FreeBSD nordwand.arareko.net 5.5-STABLE FreeBSD 5.5-STABLE #0: Mon Oct 22 10:47:04 CDT 2007     root@nordwand.arareko.net:/usr/obj/usr/src/sys/nordwand  i386
>Description:
This patch updates the biology/p5-bioperl-devel port to its 1.5.2 version.
>How-To-Repeat:

>Fix:
diff -ruN p5-bioperl-devel.old/Makefile p5-bioperl-devel/Makefile
--- p5-bioperl-devel.old/Makefile	Fri Sep  7 19:53:11 2007
+++ p5-bioperl-devel/Makefile	Sun Jun 15 02:49:47 2008
@@ -6,11 +6,11 @@
 #
 
 PORTNAME=	bioperl
-PORTVERSION=	1.5.1
-PORTREVISION=	1
+PORTVERSION=	1.5.2
 CATEGORIES=	biology perl5
 MASTER_SITES=	http://bioperl.org/DIST/
 PKGNAMEPREFIX=	p5-
+DISTNAME=	${PORTNAME}-${PORTVERSION}_102
 
 MAINTAINER=	mauricio@arareko.net
 COMMENT=	A collection of Perl modules for bioinformatics (developer release)
@@ -28,7 +28,9 @@
 		${SITE_PERL}/IO/Scalar.pm:${PORTSDIR}/devel/p5-IO-stringy \
 		${SITE_PERL}/IO/String.pm:${PORTSDIR}/devel/p5-IO-String \
 		${SITE_PERL}/LWP/UserAgent.pm:${PORTSDIR}/www/p5-libwww \
+		${SITE_PERL}/Set/Scalar.pm:${PORTSDIR}/devel/p5-Set-Scalar \
 		${SITE_PERL}/SOAP/Lite.pm:${PORTSDIR}/net/p5-SOAP-Lite \
+		${SITE_PERL}/Spreadsheet/ParseExcel.pm:${PORTSDIR}/textproc/p5-Spreadsheet-ParseExcel \
 		${SITE_PERL}/SVG.pm:${PORTSDIR}/textproc/p5-SVG \
 		${SITE_PERL}/SVG/Graph.pm:${PORTSDIR}/graphics/p5-SVG-Graph \
 		${SITE_PERL}/Text/Shellwords.pm:${PORTSDIR}/textproc/p5-Text-Shellwords \
@@ -42,6 +44,7 @@
 		${SITE_PERL}/XML/Writer.pm:${PORTSDIR}/textproc/p5-XML-Writer \
 		${SITE_PERL}/${PERL_ARCH}/Ace.pm:${PORTSDIR}/biology/p5-AcePerl \
 		${SITE_PERL}/${PERL_ARCH}/Clone.pm:${PORTSDIR}/devel/p5-Clone \
+		${SITE_PERL}/${PERL_ARCH}/Convert/Binary/C.pm:${PORTSDIR}/converters/p5-Convert-Binary-C \
 		${SITE_PERL}/${PERL_ARCH}/DBD/mysql.pm:${PORTSDIR}/databases/p5-DBD-mysql \
 		${SITE_PERL}/${PERL_ARCH}/GD.pm:${PORTSDIR}/graphics/p5-GD \
 		${SITE_PERL}/${PERL_ARCH}/HTML/Entities.pm:${PORTSDIR}/www/p5-HTML-Parser \
@@ -54,7 +57,7 @@
 
 LATEST_LINK=	p5-bioperl-devel
 
-PERL_CONFIGURE=	YES
+PERL_MODBUILD=	YES
 
 MAN1=		bp_aacomp.pl.1 \
 		bp_biblio.pl.1 \
@@ -209,6 +212,7 @@
 		Bio::ClusterIO::unigene.3 \
 		Bio::CodonUsage::IO.3 \
 		Bio::CodonUsage::Table.3 \
+		Bio::ConfigData.3 \
 		Bio::Coordinate::Chain.3 \
 		Bio::Coordinate::Collection.3 \
 		Bio::Coordinate::ExtrapolatingPair.3 \
@@ -231,6 +235,19 @@
 		Bio::DB::CUTG.3 \
 		Bio::DB::DBFetch.3 \
 		Bio::DB::EMBL.3 \
+		Bio::DB::EUtilities.3 \
+		Bio::DB::EUtilities::Cookie.3 \
+		Bio::DB::EUtilities::ElinkData.3 \
+		Bio::DB::EUtilities::efetch.3 \
+		Bio::DB::EUtilities::egquery.3 \
+		Bio::DB::EUtilities::einfo.3 \
+		Bio::DB::EUtilities::elink.3 \
+		Bio::DB::EUtilities::epost.3 \
+		Bio::DB::EUtilities::esearch.3 \
+		Bio::DB::EUtilities::esummary.3 \
+		Bio::DB::EntrezGene.3 \
+		Bio::DB::Expression.3 \
+		Bio::DB::Expression::geo.3 \
 		Bio::DB::Failover.3 \
 		Bio::DB::Fasta.3 \
 		Bio::DB::FileCache.3 \
@@ -243,6 +260,7 @@
 		Bio::DB::Flat::BDB::swissprot.3 \
 		Bio::DB::Flat::BinarySearch.3 \
 		Bio::DB::GDB.3 \
+		Bio::DB::GenericWebDBI.3 \
 		Bio::DB::GFF.3 \
 		Bio::DB::GFF::Adaptor::ace.3 \
 		Bio::DB::GFF::Adaptor::berkeleydb.3 \
@@ -259,7 +277,9 @@
 		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 \
@@ -290,20 +310,37 @@
 		Bio::DB::GenBank.3 \
 		Bio::DB::GenPept.3 \
 		Bio::DB::InMemoryCache.3 \
+		Bio::DB::LocationI.3 \
 		Bio::DB::MeSH.3 \
 		Bio::DB::NCBIHelper.3 \
 		Bio::DB::Query::GenBank.3 \
 		Bio::DB::Query::WebQuery.3 \
 		Bio::DB::QueryI.3 \
 		Bio::DB::RandomAccessI.3 \
+		Bio::DB::ReferenceI.3 \
 		Bio::DB::RefSeq.3 \
 		Bio::DB::Registry.3 \
+		Bio::DB::SeqFeature.3 \
+		Bio::DB::SeqFeature::NormalizedFeature.3 \
+		Bio::DB::SeqFeature::NormalizedFeatureI.3 \
+		Bio::DB::SeqFeature::NormalizedTableFeatureI.3 \
+		Bio::DB::SeqFeature::Segment.3 \
+		Bio::DB::SeqFeature::Store.3 \
+		Bio::DB::SeqFeature::Store::DBI::Iterator.3 \
+		Bio::DB::SeqFeature::Store::DBI::mysql.3 \
+		Bio::DB::SeqFeature::Store::GFF3Loader.3 \
+		Bio::DB::SeqFeature::Store::bdb.3 \
+		Bio::DB::SeqFeature::Store::berkeleydb.3 \
+		Bio::DB::SeqFeature::Store::memory.3 \
 		Bio::DB::SeqHound.3 \
 		Bio::DB::SeqI.3 \
+		Bio::DB::SeqVersion.3 \
+		Bio::DB::SeqVersion::gi.3 \
 		Bio::DB::SwissProt.3 \
 		Bio::DB::Taxonomy.3 \
 		Bio::DB::Taxonomy::entrez.3 \
 		Bio::DB::Taxonomy::flatfile.3 \
+		Bio::DB::Taxonomy::list.3 \
 		Bio::DB::Universal.3 \
 		Bio::DB::UpdateableSeqI.3 \
 		Bio::DB::WebDBSeqI.3 \
@@ -316,9 +353,15 @@
 		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 \
@@ -342,6 +385,7 @@
 		Bio::FeatureIO::gff.3 \
 		Bio::FeatureIO::gtf.3 \
 		Bio::FeatureIO::interpro.3 \
+		Bio::FeatureIO::ptt.3 \
 		Bio::Graph::Edge.3 \
 		Bio::Graph::IO.3 \
 		Bio::Graph::IO::dip.3 \
@@ -352,6 +396,7 @@
 		Bio::Graphics.3 \
 		Bio::Graphics::ConfiguratorI.3 \
 		Bio::Graphics::Feature.3 \
+		Bio::Graphics::FeatureBase.3 \
 		Bio::Graphics::FeatureFile.3 \
 		Bio::Graphics::FeatureFile::Iterator.3 \
 		Bio::Graphics::Glyph.3 \
@@ -373,10 +418,12 @@
 		Bio::Graphics::Glyph::ex.3 \
 		Bio::Graphics::Glyph::extending_arrow.3 \
 		Bio::Graphics::Glyph::flag.3 \
+		Bio::Graphics::Glyph::gene.3 \
 		Bio::Graphics::Glyph::generic.3 \
 		Bio::Graphics::Glyph::graded_segments.3 \
 		Bio::Graphics::Glyph::group.3 \
 		Bio::Graphics::Glyph::heterogeneous_segments.3 \
+		Bio::Graphics::Glyph::image.3 \
 		Bio::Graphics::Glyph::lightning.3 \
 		Bio::Graphics::Glyph::line.3 \
 		Bio::Graphics::Glyph::merge_parts.3 \
@@ -387,6 +434,7 @@
 		Bio::Graphics::Glyph::pinsertion.3 \
 		Bio::Graphics::Glyph::primers.3 \
 		Bio::Graphics::Glyph::processed_transcript.3 \
+		Bio::Graphics::Glyph::protein.3 \
 		Bio::Graphics::Glyph::ragged_ends.3 \
 		Bio::Graphics::Glyph::redgreen_box.3 \
 		Bio::Graphics::Glyph::redgreen_segment.3 \
@@ -416,6 +464,7 @@
 		Bio::Graphics::Panel.3 \
 		Bio::Graphics::Pictogram.3 \
 		Bio::Graphics::RendererI.3 \
+		Bio::Graphics::Util.3 \
 		Bio::IdCollectionI.3 \
 		Bio::IdentifiableI.3 \
 		Bio::Index::Abstract.3 \
@@ -437,7 +486,6 @@
 		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 \
@@ -465,19 +513,25 @@
 		Bio::Map::CytoMap.3 \
 		Bio::Map::CytoMarker.3 \
 		Bio::Map::CytoPosition.3 \
+		Bio::Map::EntityI.3 \
 		Bio::Map::FPCMarker.3 \
 		Bio::Map::LinkageMap.3 \
 		Bio::Map::LinkagePosition.3 \
 		Bio::Map::MapI.3 \
+		Bio::Map::Mappable.3 \
 		Bio::Map::MappableI.3 \
 		Bio::Map::Marker.3 \
 		Bio::Map::MarkerI.3 \
 		Bio::Map::Microsatellite.3 \
 		Bio::Map::OrderedPosition.3 \
 		Bio::Map::OrderedPositionWithDistance.3 \
+		Bio::Map::PositionHandler.3 \
+		Bio::Map::PositionHandlerI.3 \
 		Bio::Map::Physical.3 \
 		Bio::Map::Position.3 \
 		Bio::Map::PositionI.3 \
+		Bio::Map::Relative.3 \
+		Bio::Map::RelativeI.3 \
 		Bio::Map::SimpleMap.3 \
 		Bio::MapIO.3 \
 		Bio::MapIO::fpc.3 \
@@ -508,9 +562,12 @@
 		Bio::Ontology::DocumentRegistry.3 \
 		Bio::Ontology::GOterm.3 \
 		Bio::Ontology::InterProTerm.3 \
+		Bio::Ontology::OBOEngine.3 \
+		Bio::Ontology::OBOterm.3 \
 		Bio::Ontology::Ontology.3 \
 		Bio::Ontology::OntologyEngineI.3 \
 		Bio::Ontology::OntologyI.3 \
+		Bio::OntologyIO::obo.3 \
 		Bio::Ontology::OntologyStore.3 \
 		Bio::Ontology::Path.3 \
 		Bio::Ontology::PathI.3 \
@@ -567,6 +624,7 @@
 		Bio::PopGen::Utilities.3 \
 		Bio::PrimarySeq.3 \
 		Bio::PrimarySeqI.3 \
+		Bio::PullParserI.3 \
 		Bio::Range.3 \
 		Bio::RangeI.3 \
 		Bio::Restriction::Analysis.3 \
@@ -580,20 +638,13 @@
 		Bio::Restriction::IO::base.3 \
 		Bio::Restriction::IO::itype2.3 \
 		Bio::Restriction::IO::withrefm.3 \
-		Bio::Root::Err.3 \
 		Bio::Root::Exception.3 \
-		Bio::Root::Global.3 \
 		Bio::Root::HTTPget.3 \
 		Bio::Root::IO.3 \
-		Bio::Root::IOManager.3 \
-		Bio::Root::Object.3 \
 		Bio::Root::Root.3 \
 		Bio::Root::RootI.3 \
 		Bio::Root::Storable.3 \
-		Bio::Root::Utilities.3 \
-		Bio::Root::Vector.3 \
 		Bio::Root::Version.3 \
-		Bio::Root::Xref.3 \
 		Bio::Search::BlastStatistics.3 \
 		Bio::Search::BlastUtils.3 \
 		Bio::Search::DatabaseI.3 \
@@ -603,24 +654,30 @@
 		Bio::Search::HSP::FastaHSP.3 \
 		Bio::Search::HSP::GenericHSP.3 \
 		Bio::Search::HSP::HMMERHSP.3 \
+		Bio::Search::HSP::HmmpfamHSP.3 \
 		Bio::Search::HSP::HSPFactory.3 \
 		Bio::Search::HSP::HSPI.3 \
 		Bio::Search::HSP::PSLHSP.3 \
 		Bio::Search::HSP::PsiBlastHSP.3 \
+		Bio::Search::HSP::PullHSPI.3 \
 		Bio::Search::HSP::WABAHSP.3 \
 		Bio::Search::Hit::BlastHit.3 \
 		Bio::Search::Hit::Fasta.3 \
 		Bio::Search::Hit::GenericHit.3 \
+		Bio::Search::Hit::HmmpfamHit.3 \
 		Bio::Search::Hit::HMMERHit.3 \
 		Bio::Search::Hit::HitFactory.3 \
 		Bio::Search::Hit::HitI.3 \
 		Bio::Search::Hit::PsiBlastHit.3 \
+		Bio::Search::Hit::PullHitI.3 \
 		Bio::Search::Iteration::GenericIteration.3 \
 		Bio::Search::Iteration::IterationI.3 \
 		Bio::Search::Processor.3 \
 		Bio::Search::Result::BlastResult.3 \
 		Bio::Search::Result::GenericResult.3 \
+		Bio::Search::Result::HmmpfamResult.3 \
 		Bio::Search::Result::HMMERResult.3 \
+		Bio::Search::Result::PullResultI.3 \
 		Bio::Search::Result::ResultFactory.3 \
 		Bio::Search::Result::ResultI.3 \
 		Bio::Search::Result::WABAResult.3 \
@@ -647,6 +704,7 @@
 		Bio::SearchIO::exonerate.3 \
 		Bio::SearchIO::fasta.3 \
 		Bio::SearchIO::hmmer.3 \
+		Bio::SearchIO::hmmer_pull.3 \
 		Bio::SearchIO::megablast.3 \
 		Bio::SearchIO::psl.3 \
 		Bio::SearchIO::sim4.3 \
@@ -722,6 +780,7 @@
 		Bio::SeqIO::ctf.3 \
 		Bio::SeqIO::embl.3 \
 		Bio::SeqIO::entrezgene.3 \
+		Bio::SeqIO::excel.3 \
 		Bio::SeqIO::exp.3 \
 		Bio::SeqIO::fasta.3 \
 		Bio::SeqIO::fastq.3 \
@@ -736,6 +795,7 @@
 		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 \
@@ -744,8 +804,10 @@
 		Bio::SeqIO::qual.3 \
 		Bio::SeqIO::raw.3 \
 		Bio::SeqIO::scf.3 \
+		Bio::SeqIO::strider.3 \
 		Bio::SeqIO::swiss.3 \
 		Bio::SeqIO::tab.3 \
+		Bio::SeqIO::table.3 \
 		Bio::SeqIO::tigr.3 \
 		Bio::SeqIO::tigrxml.3 \
 		Bio::SeqIO::tinyseq.3 \
@@ -771,6 +833,7 @@
 		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 \
@@ -796,10 +859,6 @@
 		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 \
@@ -809,6 +868,7 @@
 		Bio::Tools::ESTScan.3 \
 		Bio::Tools::Eponine.3 \
 		Bio::Tools::Est2Genome.3 \
+		Bio::Tools::ERPIN.3 \
 		Bio::Tools::Fgenesh.3 \
 		Bio::Tools::FootPrinter.3 \
 		Bio::Tools::GFF.3 \
@@ -852,13 +912,13 @@
 		Bio::Tools::RandomDistFunctions.3 \
 		Bio::Tools::RepeatMasker.3 \
 		Bio::Tools::RestrictionEnzyme.3 \
+		Bio::Tools::RNAMotif.3 \
 		Bio::Tools::Run::GenericParameters.3 \
 		Bio::Tools::Run::ParametersI.3 \
 		Bio::Tools::Run::RemoteBlast.3 \
 		Bio::Tools::Run::StandAloneBlast.3 \
 		Bio::Tools::Run::WrapperBase.3 \
 		Bio::Tools::Seg.3 \
-		Bio::Tools::SeqAnal.3 \
 		Bio::Tools::SeqPattern.3 \
 		Bio::Tools::SeqStats.3 \
 		Bio::Tools::SeqWords.3 \
@@ -872,8 +932,6 @@
 		Bio::Tools::Spidey::Exon.3 \
 		Bio::Tools::Spidey::Results.3 \
 		Bio::Tools::Tmhmm.3 \
-		Bio::Tools::WWW.3 \
-		Bio::Tools::WebBlat.3 \
 		Bio::Tools::dpAlign.3 \
 		Bio::Tools::ipcress.3 \
 		Bio::Tools::isPcr.3 \
@@ -914,17 +972,15 @@
 		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
+		Bio::WebAgent.3
 
 .include <bsd.port.pre.mk>
 
 .if ${PERL_LEVEL} < 500800
 BUILD_DEPENDS+=	${SITE_PERL}/File/Temp.pm:${PORTSDIR}/devel/p5-File-Temp
+.if ${PERL_LEVEL} < 500600
+IGNORE=		requires Perl 5.6 or better
+.endif
 .endif
 
 # now install all extra stuff (docs, examples, scripts, models)
@@ -935,7 +991,7 @@
 	${CP} -R ${WRKSRC}/examples/* ${EXAMPLESDIR}
 .if !defined(NOPORTDOCS)
 	${MKDIR} ${DOCSDIR}
-.for doc in AUTHORS BUGS Changes DEPRECATED FAQ INSTALL LICENSE PLATFORMS README
+.for doc in AUTHORS BUGS Changes DEPENDENCIES DEPRECATED INSTALL LICENSE PLATFORMS README
 	${INSTALL_MAN} ${WRKSRC}/${doc} ${DOCSDIR}
 .endfor
 	${CP} -R ${WRKSRC}/doc ${DOCSDIR}
diff -ruN p5-bioperl-devel.old/distinfo p5-bioperl-devel/distinfo
--- p5-bioperl-devel.old/distinfo	Fri Dec  2 15:40:11 2005
+++ p5-bioperl-devel/distinfo	Sun Jun 15 01:06:15 2008
@@ -1,3 +1,3 @@
-MD5 (bioperl-1.5.1.tar.gz) = f510c871a1d17ac4ccc8ad3e6c9bad17
-SHA256 (bioperl-1.5.1.tar.gz) = 128ecbdbb22a75e165f844e38795915a909f3134c6558cd3a4d83e5ab597ea1a
-SIZE (bioperl-1.5.1.tar.gz) = 6810301
+MD5 (bioperl-1.5.2_102.tar.gz) = 4890481c5beb33e129b65b922fb0c126
+SHA256 (bioperl-1.5.2_102.tar.gz) = 277c74c785afc05ad1d9dbe938677639c33130487d15bdc4a7a10e033137bada
+SIZE (bioperl-1.5.2_102.tar.gz) = 5919092
diff -ruN p5-bioperl-devel.old/files/patch-Build.PL p5-bioperl-devel/files/patch-Build.PL
--- p5-bioperl-devel.old/files/patch-Build.PL	Wed Dec 31 18:00:00 1969
+++ p5-bioperl-devel/files/patch-Build.PL	Sun Jun 15 02:24:12 2008
@@ -0,0 +1,19 @@
+--- Build.PL.orig	Wed Feb 14 05:37:47 2007
++++ Build.PL	Sun Jun 15 02:24:07 2008
+@@ -32,7 +32,6 @@
+                             'Test::More'                => 0,
+                             'Module::Build'             => 0.2805,
+                             'Test::Harness'             => 2.62,
+-                            'CPAN'                      => 1.81
+                            },
+     recommends          => { # does what you would expect of recommends, except more informative output and generates optional_features in META.yml
+                             'Ace'                       => '0/access of ACeDB database/Bio::DB::Ace,Bio::DB::GFF::Adaptor::ace',
+@@ -174,7 +173,7 @@
+ }
+ 
+ sub prompt_for_biodbgff {
+-    my $proceed = $build->y_n("Do you want to run the BioDBGFF live database tests? y/n", 'n');
++    my $proceed = undef; # $build->y_n("Do you want to run the BioDBGFF live database tests? y/n", 'n');
+     
+     if ($proceed) {
+         my @driver_choices;
diff -ruN p5-bioperl-devel.old/files/patch-Makefile.PL p5-bioperl-devel/files/patch-Makefile.PL
--- p5-bioperl-devel.old/files/patch-Makefile.PL	Fri Dec  2 15:40:12 2005
+++ p5-bioperl-devel/files/patch-Makefile.PL	Wed Dec 31 18:00:00 1969
@@ -1,56 +0,0 @@
---- Makefile.PL.orig	Sun Oct  9 17:16:18 2005
-+++ Makefile.PL	Wed Nov 30 13:58:20 2005
-@@ -41,7 +41,7 @@
- 	     'XML::SAX'                 => '0.0/New style SAX parser/Parsers/Bio::SeqIO::tigrxml,Bio::SeqIO::bsml_sax',
- 	     'XML::SAX::Base'                 => '0.0/New style SAX parser/Parsers/Bio::SeqIO::tigrxml,Bio::SeqIO::bsml_sax',
- 	     'XML::SAX::Writer'         => '0.0/New style SAX parser/Writers/Bio::SeqIO::tigrxml,Bio::SeqIO::bsml_sax',
-- 	     'Bio::ANS1::EntrezGene'    => '0.0/Enztrez Gene Bioperl Parser/Parsers/Bio::SeqIO::entrezgene'
-+ 	     'Bio::ASN1::EntrezGene'    => '0.0/Enztrez Gene Bioperl Parser/Parsers/Bio::SeqIO::entrezgene'
- # Bio::Microarray is not in core bioperl yet
- #	     'enum'                     => '0.0/C style enumerated types and bitmask flags 
- # in Perl/Bio::Microarray::Affymetrix::*',
-@@ -95,7 +95,7 @@
- sub prompt_for_biodbgff {
-   if(  eval { require DBI } && grep {/mysql/} DBI->available_drivers) {
-     print "\n** Bio::DB::GFF Tests section** \n";
--    my $proceed = prompt("Do you want to run the BioDBGFF tests (requires a mysql, postgres or oracle database) y/n",'n');
-+    my $proceed = 'n'; # prompt("Do you want to run the BioDBGFF tests (requires a mysql, postgres or oracle database) y/n",'n');
-     if( $proceed =~ /^[yY]/) {
-       my $cfg = {dbd_driver => 'mysql'};
-       GFFQueryDb($cfg,{'prompt'=>1,'verbose'=>1});
-@@ -129,7 +129,7 @@
- sub get_scripts_to_install {
-   print "\n*** Script Install Section ****\n";
-   print "\nBioperl comes with a number of useful scripts which you may wish to install.\n";
--  my $prompt_mode = prompt("Install [a]ll Bioperl scripts, [n]one, or choose groups [i]nteractively?",'a');
-+  my $prompt_mode = 'a'; # prompt("Install [a]ll Bioperl scripts, [n]one, or choose groups [i]nteractively?",'a');
-   return if $prompt_mode =~ /^[nN]/;
-   my @scripts;
-   my $script_dir = './scripts';
-@@ -378,16 +378,16 @@
- );
- 
- 
--sub MY::manifypods {
--  my $self = shift;
--  #print STDERR "In manifypods moment\n";
--  if( 1 ) {
--    return "\nmanifypods : pure_all\n\t$self->{NOECHO}\$(NOOP)\n"
--  }
--  else {
--    return $self->SUPER::manifypods(@_);
--  }
--}
-+#sub MY::manifypods {
-+#  my $self = shift;
-+#  #print STDERR "In manifypods moment\n";
-+#  if( 1 ) {
-+#    return "\nmanifypods : pure_all\n\t$self->{NOECHO}\$(NOOP)\n"
-+#  }
-+#  else {
-+#    return $self->SUPER::manifypods(@_);
-+#  }
-+#}
- 
- sub MY::clean {
-   package MY;
diff -ruN p5-bioperl-devel.old/files/patch-ModuleBuildBioperl.pm p5-bioperl-devel/files/patch-ModuleBuildBioperl.pm
--- p5-bioperl-devel.old/files/patch-ModuleBuildBioperl.pm	Wed Dec 31 18:00:00 1969
+++ p5-bioperl-devel/files/patch-ModuleBuildBioperl.pm	Sun Jun 15 02:00:49 2008
@@ -0,0 +1,11 @@
+--- ModuleBuildBioperl.pm.orig	Wed Feb 14 05:37:47 2007
++++ ModuleBuildBioperl.pm	Sun Jun 15 02:00:34 2008
+@@ -93,7 +93,7 @@
+     closedir($scripts_dir);
+     my $question = $int_ok ? "Install [a]ll Bioperl scripts, [n]one, or choose groups [i]nteractively?" : "Install [a]ll Bioperl scripts or [n]one?";
+     
+-    my $prompt = $self->prompt($question, 'a');
++    my $prompt = 'a'; # $self->prompt($question, 'a');
+     
+     if ($prompt =~ /^[aA]/) {
+         $self->log_info("  - will install all scripts\n");
diff -ruN p5-bioperl-devel.old/pkg-plist p5-bioperl-devel/pkg-plist
--- p5-bioperl-devel.old/pkg-plist	Sat Jan 21 19:25:23 2006
+++ p5-bioperl-devel/pkg-plist	Sun Jun 15 01:06:37 2008
@@ -1,1571 +1,1272 @@
-bin/bp_aacomp.pl
-bin/bp_biblio.pl
-bin/bp_biofetch_genbank_proxy.pl
-bin/bp_bioflat_index.pl
-bin/bp_biogetseq.pl
-bin/bp_blast2tree.pl
-bin/bp_bulk_load_gff.pl
-bin/bp_chaos_plot.pl
-bin/bp_classify_hits_kingdom.pl
-bin/bp_composite_LD.pl
+bin/bp_sreformat.pl
 bin/bp_contig_draw.pl
-bin/bp_dbsplit.pl
-bin/bp_embl2picture.pl
-bin/bp_extract_feature_seq.pl
-bin/bp_fast_load_gff.pl
-bin/bp_fastam9_to_table.pl
-bin/bp_feature_draw.pl
-bin/bp_fetch.pl
-bin/bp_filter_search.pl
+bin/bp_tree2pag.pl
+bin/bp_meta_gff.pl
 bin/bp_flanks.pl
-bin/bp_frend.pl
-bin/bp_gccalc.pl
+bin/bp_heterogeneity_test.pl
+bin/bp_feature_draw.pl
+bin/bp_biogetseq.pl
 bin/bp_genbank2gff.pl
-bin/bp_genbank2gff3.pl
-bin/bp_generate_histogram.pl
+bin/bp_seqfeature_load.pl
+bin/bp_seq_length.pl
+bin/bp_frend.pl
+bin/bp_fastam9_to_table.pl
+bin/bp_taxid4species.pl
 bin/bp_glyphs1-demo.pl
+bin/bp_blast2tree.pl
+bin/bp_gccalc.pl
+bin/bp_seqret.pl
+bin/bp_query_entrez_taxa.pl
 bin/bp_glyphs2-demo.pl
-bin/bp_heterogeneity_test.pl
-bin/bp_hmmer_to_table.pl
-bin/bp_index.pl
-bin/bp_load_gff.pl
-bin/bp_local_taxonomydb_query.pl
-bin/bp_make_mrna_protein.pl
+bin/bp_search2alnblocks.pl
+bin/bp_taxonomy2tree.pl
 bin/bp_mask_by_search.pl
-bin/bp_meta_gff.pl
-bin/bp_mrtrans.pl
-bin/bp_mutate.pl
+bin/bp_aacomp.pl
+bin/bp_composite_LD.pl
+bin/bp_biblio.pl
+bin/bp_process_wormbase.pl
+bin/bp_embl2picture.pl
+bin/bp_local_taxonomydb_query.pl
+bin/bp_genbank2gff3.pl
+bin/bp_search2BSML.pl
+bin/bp_seqconvert.pl
+bin/bp_parse_hmmsearch.pl
 bin/bp_nexus2nh.pl
 bin/bp_nrdb.pl
+bin/bp_split_seq.pl
+bin/bp_filter_search.pl
+bin/bp_generate_histogram.pl
+bin/bp_load_gff.pl
+bin/bp_fetch.pl
+bin/bp_mutate.pl
+bin/bp_process_sgd.pl
+bin/bp_index.pl
+bin/bp_dbsplit.pl
 bin/bp_oligo_count.pl
-bin/bp_pairwise_kaks.pl
-bin/bp_pg_bulk_load_gff.pl
 bin/bp_process_gadfly.pl
-bin/bp_process_sgd.pl
-bin/bp_process_wormbase.pl
-bin/bp_query_entrez_taxa.pl
-bin/bp_remote_blast.pl
-bin/bp_search2BSML.pl
-bin/bp_search2alnblocks.pl
+bin/bp_hmmer_to_table.pl
+bin/bp_bulk_load_gff.pl
+bin/bp_biofetch_genbank_proxy.pl
+bin/bp_extract_feature_seq.pl
 bin/bp_search2gff.pl
-bin/bp_search2table.pl
+bin/bp_unflatten_seq.pl
+bin/bp_make_mrna_protein.pl
+bin/bp_mrtrans.pl
 bin/bp_search2tribe.pl
-bin/bp_search_overview.pl
-bin/bp_seq_length.pl
-bin/bp_seqconvert.pl
-bin/bp_seqret.pl
-bin/bp_split_seq.pl
-bin/bp_sreformat.pl
-bin/bp_taxid4species.pl
+bin/bp_bioflat_index.pl
+bin/bp_pairwise_kaks.pl
+bin/bp_fast_load_gff.pl
+bin/bp_chaos_plot.pl
+bin/bp_classify_hits_kingdom.pl
+bin/bp_remote_blast.pl
+bin/bp_search2table.pl
 bin/bp_translate_seq.pl
-bin/bp_tree2pag.pl
-bin/bp_unflatten_seq.pl
+bin/bp_search_overview.pl
+bin/bp_pg_bulk_load_gff.pl
+%%SITE_PERL%%/Bio/Align/Utilities.pm
 %%SITE_PERL%%/Bio/Align/AlignI.pm
 %%SITE_PERL%%/Bio/Align/DNAStatistics.pm
-%%SITE_PERL%%/Bio/Align/PairwiseStatistics.pm
 %%SITE_PERL%%/Bio/Align/ProteinStatistics.pm
 %%SITE_PERL%%/Bio/Align/StatisticsI.pm
-%%SITE_PERL%%/Bio/Align/Utilities.pm
-%%SITE_PERL%%/Bio/AlignIO.pm
-%%SITE_PERL%%/Bio/AlignIO/bl2seq.pm
-%%SITE_PERL%%/Bio/AlignIO/clustalw.pm
+%%SITE_PERL%%/Bio/Align/PairwiseStatistics.pm
+%%SITE_PERL%%/Bio/AlignIO/mega.pm
+%%SITE_PERL%%/Bio/AlignIO/prodom.pm
 %%SITE_PERL%%/Bio/AlignIO/emboss.pm
-%%SITE_PERL%%/Bio/AlignIO/fasta.pm
-%%SITE_PERL%%/Bio/AlignIO/largemultifasta.pm
-%%SITE_PERL%%/Bio/AlignIO/maf.pm
 %%SITE_PERL%%/Bio/AlignIO/mase.pm
-%%SITE_PERL%%/Bio/AlignIO/mega.pm
-%%SITE_PERL%%/Bio/AlignIO/meme.pm
-%%SITE_PERL%%/Bio/AlignIO/metafasta.pm
-%%SITE_PERL%%/Bio/AlignIO/msf.pm
-%%SITE_PERL%%/Bio/AlignIO/nexus.pm
-%%SITE_PERL%%/Bio/AlignIO/pfam.pm
 %%SITE_PERL%%/Bio/AlignIO/phylip.pm
-%%SITE_PERL%%/Bio/AlignIO/po.pm
-%%SITE_PERL%%/Bio/AlignIO/prodom.pm
+%%SITE_PERL%%/Bio/AlignIO/maf.pm
+%%SITE_PERL%%/Bio/AlignIO/pfam.pm
+%%SITE_PERL%%/Bio/AlignIO/nexus.pm
+%%SITE_PERL%%/Bio/AlignIO/bl2seq.pm
+%%SITE_PERL%%/Bio/AlignIO/msf.pm
 %%SITE_PERL%%/Bio/AlignIO/psi.pm
-%%SITE_PERL%%/Bio/AlignIO/selex.pm
+%%SITE_PERL%%/Bio/AlignIO/po.pm
+%%SITE_PERL%%/Bio/AlignIO/clustalw.pm
+%%SITE_PERL%%/Bio/AlignIO/largemultifasta.pm
+%%SITE_PERL%%/Bio/AlignIO/fasta.pm
+%%SITE_PERL%%/Bio/AlignIO/metafasta.pm
 %%SITE_PERL%%/Bio/AlignIO/stockholm.pm
-%%SITE_PERL%%/Bio/AnalysisI.pm
-%%SITE_PERL%%/Bio/AnalysisParserI.pm
-%%SITE_PERL%%/Bio/AnalysisResultI.pm
-%%SITE_PERL%%/Bio/AnnotatableI.pm
+%%SITE_PERL%%/Bio/AlignIO/meme.pm
+%%SITE_PERL%%/Bio/AlignIO/selex.pm
+%%SITE_PERL%%/Bio/Annotation/OntologyTerm.pm
+%%SITE_PERL%%/Bio/Annotation/Target.pm
+%%SITE_PERL%%/Bio/Annotation/SimpleValue.pm
 %%SITE_PERL%%/Bio/Annotation/AnnotationFactory.pm
+%%SITE_PERL%%/Bio/Annotation/Reference.pm
 %%SITE_PERL%%/Bio/Annotation/Collection.pm
-%%SITE_PERL%%/Bio/Annotation/Comment.pm
 %%SITE_PERL%%/Bio/Annotation/DBLink.pm
-%%SITE_PERL%%/Bio/Annotation/OntologyTerm.pm
-%%SITE_PERL%%/Bio/Annotation/Reference.pm
-%%SITE_PERL%%/Bio/Annotation/SimpleValue.pm
 %%SITE_PERL%%/Bio/Annotation/StructuredValue.pm
-%%SITE_PERL%%/Bio/Annotation/Target.pm
+%%SITE_PERL%%/Bio/Annotation/Comment.pm
 %%SITE_PERL%%/Bio/Annotation/TypeManager.pm
-%%SITE_PERL%%/Bio/AnnotationCollectionI.pm
-%%SITE_PERL%%/Bio/AnnotationI.pm
-%%SITE_PERL%%/Bio/Assembly/Contig.pm
-%%SITE_PERL%%/Bio/Assembly/ContigAnalysis.pm
-%%SITE_PERL%%/Bio/Assembly/IO.pm
-%%SITE_PERL%%/Bio/Assembly/IO/ace.pm
 %%SITE_PERL%%/Bio/Assembly/IO/phrap.pm
-%%SITE_PERL%%/Bio/Assembly/Scaffold.pm
+%%SITE_PERL%%/Bio/Assembly/IO/ace.pm
+%%SITE_PERL%%/Bio/Assembly/ContigAnalysis.pm
 %%SITE_PERL%%/Bio/Assembly/ScaffoldI.pm
 %%SITE_PERL%%/Bio/Assembly/Singlet.pm
-%%SITE_PERL%%/Bio/Biblio.pm
-%%SITE_PERL%%/Bio/Biblio/Article.pm
-%%SITE_PERL%%/Bio/Biblio/BiblioBase.pm
-%%SITE_PERL%%/Bio/Biblio/Book.pm
-%%SITE_PERL%%/Bio/Biblio/BookArticle.pm
-%%SITE_PERL%%/Bio/Biblio/IO.pm
+%%SITE_PERL%%/Bio/Assembly/Contig.pm
+%%SITE_PERL%%/Bio/Assembly/Scaffold.pm
+%%SITE_PERL%%/Bio/Assembly/IO.pm
 %%SITE_PERL%%/Bio/Biblio/IO/medline2ref.pm
-%%SITE_PERL%%/Bio/Biblio/IO/medlinexml.pm
-%%SITE_PERL%%/Bio/Biblio/IO/pubmed2ref.pm
 %%SITE_PERL%%/Bio/Biblio/IO/pubmedxml.pm
-%%SITE_PERL%%/Bio/Biblio/Journal.pm
-%%SITE_PERL%%/Bio/Biblio/JournalArticle.pm
-%%SITE_PERL%%/Bio/Biblio/MedlineArticle.pm
-%%SITE_PERL%%/Bio/Biblio/MedlineBook.pm
-%%SITE_PERL%%/Bio/Biblio/MedlineBookArticle.pm
-%%SITE_PERL%%/Bio/Biblio/MedlineJournal.pm
-%%SITE_PERL%%/Bio/Biblio/MedlineJournalArticle.pm
-%%SITE_PERL%%/Bio/Biblio/Organisation.pm
-%%SITE_PERL%%/Bio/Biblio/Patent.pm
-%%SITE_PERL%%/Bio/Biblio/Person.pm
-%%SITE_PERL%%/Bio/Biblio/Proceeding.pm
-%%SITE_PERL%%/Bio/Biblio/Provider.pm
-%%SITE_PERL%%/Bio/Biblio/PubmedArticle.pm
+%%SITE_PERL%%/Bio/Biblio/IO/pubmed2ref.pm
+%%SITE_PERL%%/Bio/Biblio/IO/medlinexml.pm
 %%SITE_PERL%%/Bio/Biblio/PubmedBookArticle.pm
+%%SITE_PERL%%/Bio/Biblio/Provider.pm
+%%SITE_PERL%%/Bio/Biblio/IO.pm
+%%SITE_PERL%%/Bio/Biblio/BiblioBase.pm
+%%SITE_PERL%%/Bio/Biblio/Thesis.pm
+%%SITE_PERL%%/Bio/Biblio/Article.pm
+%%SITE_PERL%%/Bio/Biblio/Organisation.pm
+%%SITE_PERL%%/Bio/Biblio/MedlineJournalArticle.pm
+%%SITE_PERL%%/Bio/Biblio/BookArticle.pm
+%%SITE_PERL%%/Bio/Biblio/Journal.pm
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 %%SITE_PERL%%/Bio/Biblio/Ref.pm
-%%SITE_PERL%%/Bio/Biblio/Service.pm
 %%SITE_PERL%%/Bio/Biblio/TechReport.pm
-%%SITE_PERL%%/Bio/Biblio/Thesis.pm
+%%SITE_PERL%%/Bio/Biblio/Person.pm
 %%SITE_PERL%%/Bio/Biblio/WebResource.pm
-%%SITE_PERL%%/Bio/Cluster/ClusterFactory.pm
+%%SITE_PERL%%/Bio/Biblio/MedlineBook.pm
+%%SITE_PERL%%/Bio/Biblio/JournalArticle.pm
+%%SITE_PERL%%/Bio/Biblio/MedlineBookArticle.pm
+%%SITE_PERL%%/Bio/Biblio/Patent.pm
+%%SITE_PERL%%/Bio/Biblio/Service.pm
+%%SITE_PERL%%/Bio/Biblio/MedlineArticle.pm
+%%SITE_PERL%%/Bio/Biblio/PubmedArticle.pm
+%%SITE_PERL%%/Bio/Biblio/MedlineJournal.pm
+%%SITE_PERL%%/Bio/Biblio/Proceeding.pm
+%%SITE_PERL%%/Bio/Biblio/Book.pm
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+%%SITE_PERL%%/Bio/Cluster/UniGene.pm
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+%%SITE_PERL%%/Bio/Cluster/ClusterFactory.pm
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-%%SITE_PERL%%/Bio/Cluster/UniGene.pm
-%%SITE_PERL%%/Bio/Cluster/UniGeneI.pm
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-%%SITE_PERL%%/Bio/ClusterIO/dbsnp.pm
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-%%SITE_PERL%%/Bio/CodonUsage/IO.pm
+%%SITE_PERL%%/Bio/ClusterIO/dbsnp.pm
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-%%SITE_PERL%%/Bio/Coordinate/Chain.pm
-%%SITE_PERL%%/Bio/Coordinate/Collection.pm
-%%SITE_PERL%%/Bio/Coordinate/ExtrapolatingPair.pm
-%%SITE_PERL%%/Bio/Coordinate/GeneMapper.pm
+%%SITE_PERL%%/Bio/CodonUsage/IO.pm
+%%SITE_PERL%%/Bio/Coordinate/Result/Gap.pm
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+%%SITE_PERL%%/Bio/Coordinate/Result.pm
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+%%SITE_PERL%%/Bio/Coordinate/Chain.pm
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-%%SITE_PERL%%/Bio/Coordinate/Utils.pm
-%%SITE_PERL%%/Bio/DB/Ace.pm
+%%SITE_PERL%%/Bio/Coordinate/GeneMapper.pm
+%%SITE_PERL%%/Bio/DB/Biblio/pdf.pm
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-%%SITE_PERL%%/Bio/DB/Flat/BDB/genbank.pm
+%%SITE_PERL%%/Bio/DB/EUtilities/Cookie.pm
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-%%SITE_PERL%%/Bio/DB/GFF/Adaptor/dbi.pm
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-%%SITE_PERL%%/Bio/DB/GFF/Adaptor/dbi/iterator.pm
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-%%SITE_PERL%%/Bio/DB/GFF/Adaptor/memory.pm
-%%SITE_PERL%%/Bio/DB/GFF/Adaptor/memory/feature_serializer.pm
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+%%DATADIR%%/scripts/tree/TAG
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+%%DATADIR%%/scripts/biographics/bp_glyphs1-demo.PLS
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+%%DATADIR%%/scripts/index/TAG
+%%DATADIR%%/scripts/index/bp_index.PLS
+%%DATADIR%%/scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS
+%%DATADIR%%/scripts/biblio/TAG
+%%DATADIR%%/scripts/biblio/biblio.PLS
+%%DATADIR%%/scripts/Bio-DB-GFF/process_sgd.PLS
+%%DATADIR%%/scripts/Bio-DB-GFF/process_wormbase.PLS
+%%DATADIR%%/scripts/Bio-DB-GFF/bulk_load_gff.PLS
+%%DATADIR%%/scripts/Bio-DB-GFF/README
+%%DATADIR%%/scripts/Bio-DB-GFF/meta_gff.PLS
+%%DATADIR%%/scripts/Bio-DB-GFF/generate_histogram.PLS
+%%DATADIR%%/scripts/Bio-DB-GFF/process_gadfly.PLS
+%%DATADIR%%/scripts/Bio-DB-GFF/bp_genbank2gff.PLS
+%%DATADIR%%/scripts/Bio-DB-GFF/load_gff.PLS
+%%DATADIR%%/scripts/Bio-DB-GFF/genbank2gff3.PLS
+%%DATADIR%%/scripts/Bio-DB-GFF/TAG
+%%DATADIR%%/scripts/Bio-DB-GFF/fast_load_gff.PLS
+%%DATADIR%%/scripts/das/README
+%%DATADIR%%/scripts/das/TAG
+%%DATADIR%%/scripts/popgen/composite_LD.PLS
+%%DATADIR%%/scripts/popgen/heterogeneity_test.PLS
+%%DATADIR%%/scripts/utilities/bp_nrdb.PLS
+%%DATADIR%%/scripts/utilities/dbsplit.PLS
+%%DATADIR%%/scripts/utilities/bp_mrtrans.PLS
+%%DATADIR%%/scripts/utilities/search2BSML.PLS
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+%%DATADIR%%/scripts/utilities/seq_length.PLS
+%%DATADIR%%/scripts/utilities/mutate.PLS
+%%DATADIR%%/scripts/utilities/mask_by_search.PLS
+%%DATADIR%%/scripts/utilities/search2tribe.PLS
+%%DATADIR%%/scripts/utilities/search2alnblocks.PLS
+%%DATADIR%%/scripts/utilities/TAG
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+%%DATADIR%%/scripts/utilities/remote_blast.PLS
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+%%DATADIR%%/scripts/seqstats/chaos_plot.PLS
+%%DATADIR%%/scripts/seqstats/oligo_count.PLS
+%%DATADIR%%/scripts/README
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+@dirrm %%SITE_PERL%%/Bio/AlignIO
+@dirrm %%SITE_PERL%%/Bio/Annotation
+@dirrm %%SITE_PERL%%/Bio/Assembly/IO
+@dirrm %%SITE_PERL%%/Bio/Assembly
+@dirrm %%SITE_PERL%%/Bio/Biblio/IO
+@dirrm %%SITE_PERL%%/Bio/Biblio
+@dirrm %%SITE_PERL%%/Bio/Cluster
+@dirrm %%SITE_PERL%%/Bio/ClusterIO
+@dirrm %%SITE_PERL%%/Bio/CodonUsage
+@dirrm %%SITE_PERL%%/Bio/Coordinate/Result
+@dirrm %%SITE_PERL%%/Bio/Coordinate
+@dirrm %%SITE_PERL%%/Bio/DB/Biblio
+@dirrm %%SITE_PERL%%/Bio/DB/EUtilities
+@dirrm %%SITE_PERL%%/Bio/DB/Expression
+@dirrm %%SITE_PERL%%/Bio/DB/Flat/BDB
+@dirrm %%SITE_PERL%%/Bio/DB/Flat
+@dirrm %%SITE_PERL%%/Bio/DB/GFF/Adaptor/berkeleydb
+@dirrm %%SITE_PERL%%/Bio/DB/GFF/Adaptor/dbi
+@dirrm %%SITE_PERL%%/Bio/DB/GFF/Adaptor/memory
+@dirrm %%SITE_PERL%%/Bio/DB/GFF/Adaptor
+@dirrm %%SITE_PERL%%/Bio/DB/GFF/Aggregator
+@dirrm %%SITE_PERL%%/Bio/DB/GFF/Util
+@dirrm %%SITE_PERL%%/Bio/DB/GFF
+@dirrm %%SITE_PERL%%/Bio/DB/Query
+@dirrm %%SITE_PERL%%/Bio/DB/SeqFeature/Store/DBI
+@dirrm %%SITE_PERL%%/Bio/DB/SeqFeature/Store
+@dirrm %%SITE_PERL%%/Bio/DB/SeqFeature
+@dirrm %%SITE_PERL%%/Bio/DB/SeqVersion
+@dirrm %%SITE_PERL%%/Bio/DB/Taxonomy
+@dirrm %%SITE_PERL%%/Bio/DB
+@dirrm %%SITE_PERL%%/Bio/Das
+@dirrm %%SITE_PERL%%/Bio/Event
+@dirrm %%SITE_PERL%%/Bio/Expression/FeatureGroup
+@dirrm %%SITE_PERL%%/Bio/Expression/FeatureSet
+@dirrm %%SITE_PERL%%/Bio/Expression
+@dirrm %%SITE_PERL%%/Bio/Factory
+@dirrm %%SITE_PERL%%/Bio/FeatureIO
+@dirrm %%SITE_PERL%%/Bio/Graph/IO
+@dirrm %%SITE_PERL%%/Bio/Graph/SimpleGraph
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-@dirrmtry %%SITE_PERL%%/Bio


>Release-Note:
>Audit-Trail:
>Unformatted:



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