Update to version 0.6.2

PR:		21954
Submitted by:	Johann Visagie <johann@egenetics.com> MAINTAINER

3 files changed, 132 insertions, 174 deletions

diff --git a/biology/p5-bioperl/Makefile b/biology/p5-bioperl/Makefile
index ed8e5d58f44e..302592a9a251 100644
--- a/biology/p5-bioperl/Makefile
+++ b/biology/p5-bioperl/Makefile
@@ -6,7 +6,7 @@
 #
 
 PORTNAME=	bioperl
-PORTVERSION=	0.6.1
+PORTVERSION=	0.6.2
 CATEGORIES=	biology perl5
 MASTER_SITES=	ftp://bio.perl.org/pub/DIST/ \
 		http://bio.perl.org/Core/Latest/ \
@@ -17,108 +17,67 @@ DISTFILES=	${DISTNAME}${EXTRACT_SUFX} bioperl-ext-0.6.tar.gz
 
 MAINTAINER=	johann@egenetics.com
 
-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
+BUILD_DEPENDS=	${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/HTTP/Request/Common.pm:${PORTSDIR}/www/p5-libwww \
+		${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/LWP/UserAgent.pm:${PORTSDIR}/www/p5-libwww \
+		${LOCALBASE}/lib/perl5/site_perl/${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
 
-USE_PERL5=	YES
+PERL_CONFIGURE=	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 \
-		Bio::Tools::Blast::HTML.3 \
-		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 \
-		Bio::Tools::Blast::Run::Webblast.3 \
-		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 \
+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::Index::EMBL.3 \
-		Bio::Species.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::SeqIO::embl.3 \
-		Bio::Index::SwissPfam.3 \
-		Bio::DB::GenPept.3 \
-		Bio::Index::Fasta.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
 MANPREFIX=	${PREFIX}/lib/perl5/${PERL_VERSION}
 
-do-configure:
-	@(cd ${WRKSRC}; ${SETENV} ${MAKE_ENV} ${PERL5} Makefile.PL)
-	@(cd ${EXT_WRKSRC}/Bio/Ext/Align; ${SETENV} ${MAKE_ENV} ${PERL5} Makefile.PL)
+EXT_WRKSRC=	${WRKDIR}/bioperl-ext-06/Bio/Ext/Align
+
+post-configure:
+	@ (cd ${EXT_WRKSRC} && \
+	  ${SETENV} ${CONFIGURE_ENV} \
+	  ${PERL5} ${CONFIGURE_SCRIPT} ${CONFIGURE_ARGS})
 
-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})
+post-build:
+	@ (cd ${EXT_WRKSRC} && \
+	  ${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})
+post-install:
+	@ (cd ${EXT_WRKSRC} && \
+	  ${SETENV} ${MAKE_ENV} ${MAKE} ${MAKE_FLAGS} \
+	  ${MAKEFILE} ${MAKE_ARGS} ${INSTALL_TARGET})
 
 .include <bsd.port.mk>
diff --git a/biology/p5-bioperl/distinfo b/biology/p5-bioperl/distinfo
index dea595e5a767..2d04f782e757 100644
--- a/biology/p5-bioperl/distinfo
+++ b/biology/p5-bioperl/distinfo
@@ -1,2 +1,2 @@
-MD5 (bioperl-0.6.1.tar.gz) = e3506188027a94ea87443389a78c2fdc
+MD5 (bioperl-0.6.2.tar.gz) = 26330f4f0c1e08a4f5cbcbe8b05b72f1
 MD5 (bioperl-ext-0.6.tar.gz) = 5bf87e0cf94d3d41fabbfd209971d240
diff --git a/biology/p5-bioperl/pkg-plist b/biology/p5-bioperl/pkg-plist
index 1edf34960626..1ac85ff54cd3 100644
--- a/biology/p5-bioperl/pkg-plist
+++ b/biology/p5-bioperl/pkg-plist
@@ -1,109 +1,108 @@
-lib/perl5/site_perl/%%PERL_VER%%/Bio/DB/GenBank.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/DB/SeqI.pm
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Bio/Ext/Align.pm
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio/.packlist
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio/Ext/Align/.packlist
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio/Ext/Align/Align.bs
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio/Ext/Align/Align.so
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Annotation.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Annotation/Comment.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Annotation/DBLink.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Annotation/Reference.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/DB/Ace.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/DB/RandomAccessI.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/DB/GenBank.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/DB/GenPept.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/DB/RandomAccessI.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/DB/SeqI.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Index/Abstract.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Index/AbstractSeq.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Index/EMBL.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Index/Fasta.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Index/SwissPfam.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/LocatableSeq.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/PrimarySeq.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/PrimarySeqI.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Range.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/RangeI.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/Root/Err.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Root/RootI.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/Root/Global.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Root/Xref.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Root/IOManager.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/Root/Object.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Root/Vector.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Root/RootI.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/Root/Utilities.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Root/IOManager.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/RangeI.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Annotation.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqI.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/UnivAln.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Root/Vector.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Root/Xref.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Hit/Fasta.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Hit/HitI.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Processor.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Processor/Fasta.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Processor/ProcessorI.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Result/Fasta.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Result/ResultI.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/SearchDist.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Seq.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeature/FeaturePair.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeature/Generic.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeatureI.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/genbank.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqI.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/FTHelper.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/raw.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/MultiFile.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/embl.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/scf.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/gcg.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/swiss.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/fasta.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/gcg.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/genbank.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/pir.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/MultiFile.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Sim4/Results.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Sim4/Exon.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/IUPAC.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/CodonTable.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/raw.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/scf.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/swiss.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/SimpleAlign.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Species.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/AlignFactory.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/Run/Makefile.PL
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/Run/postclient.pl
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/Run/LocalBlast.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/Run/Webblast.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/CHANGES
 lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/HSP.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/Sbjct.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/README
 lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/HTML.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/pSW.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/SeqPattern.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/README
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/Run/LocalBlast.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/Run/Makefile.PL
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/Run/Webblast.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/Run/postclient.pl
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/Sbjct.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/CodonTable.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Fasta.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/WWW.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/HMMER/Domain.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/HMMER/Results.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/HMMER/Set.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/HMMER/Domain.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Sigcleave.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/SeqWords.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/SeqStats.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/SeqAnal.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/IUPAC.pm
 lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/RestrictionEnzyme.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/SearchDist.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Hit/HitI.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Hit/Fasta.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Processor/Fasta.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Processor/ProcessorI.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Processor.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Result/ResultI.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Result/Fasta.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Seq.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/PrimarySeqI.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Range.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/SimpleAlign.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Index/EMBL.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Index/AbstractSeq.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Index/Fasta.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Index/Abstract.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Index/SwissPfam.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Species.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/PrimarySeq.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/LocatableSeq.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Annotation/Comment.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Annotation/Reference.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Annotation/DBLink.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeature/FeaturePair.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeature/Generic.pm
-lib/perl5/site_perl/%%PERL_VER%%/bioperl.pod
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/SeqAnal.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/SeqPattern.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/SeqStats.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/SeqWords.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Sigcleave.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/WWW.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/pSW.pm
+lib/perl5/site_perl/%%PERL_VER%%/Bio/UnivAln.pm
 lib/perl5/site_perl/%%PERL_VER%%/bioback.pod
 lib/perl5/site_perl/%%PERL_VER%%/biodesign.pod
+lib/perl5/site_perl/%%PERL_VER%%/bioperl.pod
 lib/perl5/site_perl/%%PERL_VER%%/biostart.pod
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio/.packlist
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio/Ext/Align/Align.bs
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio/Ext/Align/Align.so
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Bio/Ext/Align.pm
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio/Ext/Align/.packlist
-@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/DB
-@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Root
-@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO
-@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Sim4
+@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/HMMER
 @dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/Run
 @dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast
-@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/HMMER
 @dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools
-@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Hit
-@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Processor
+@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO
+@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeature
 @dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Result
+@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Processor
+@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Hit
 @dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Search
+@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Root
 @dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Index
+@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/DB
 @dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Annotation
-@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeature
 @dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio
-@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio/Ext/Align/
+@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio/Ext/Align
 @dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio/Ext
 @dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio
+@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Bio/Ext
+@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Bio