biology/p5-bioperl-run: 1.6.1 -> 1.6.901, unbreak, stagify

5 files changed, 296 insertions, 217 deletions

diff --git a/biology/p5-bioperl-run/Makefile b/biology/p5-bioperl-run/Makefile
index ca75fc23d3e9..f5f14b13fdb4 100644
--- a/biology/p5-bioperl-run/Makefile
+++ b/biology/p5-bioperl-run/Makefile
@@ -2,147 +2,57 @@
 # $FreeBSD$
 
 PORTNAME=	bioperl-run
-PORTVERSION=	1.6.1
-PORTREVISION=	4
+PORTVERSION=	1.6.901
 CATEGORIES=	biology perl5
-MASTER_SITES=	http://bioperl.org/DIST/ \
-		CPAN
 PKGNAMEPREFIX=	p5-
-DISTNAME=	BioPerl-run-${PORTVERSION}
 
 MAINTAINER=	ports@FreeBSD.org
 COMMENT=	Wrapper modules for common bioinformatics tools
 
-BROKEN=		Fails to configure
+LICENSE=	ART10 GPLv3
+LICENSE_COMB=	dual
 
 BUILD_DEPENDS=	p5-bioperl>=1.6.0:${PORTSDIR}/biology/p5-bioperl \
 		p5-IPC-Run>=0:${PORTSDIR}/devel/p5-IPC-Run \
-		p5-Algorithm-Diff>=0:${PORTSDIR}/devel/p5-Algorithm-Diff
+		p5-Algorithm-Diff>=0:${PORTSDIR}/devel/p5-Algorithm-Diff \
+		p5-XML-Twig>=0:${PORTSDIR}/textproc/p5-XML-Twig \
+		p5-File-Sort>=0:${PORTSDIR}/misc/p5-File-Sort \
+		p5-Config-Any>=0:${PORTSDIR}/devel/p5-Config-Any
+
 RUN_DEPENDS:=	${BUILD_DEPENDS}
 
 CONFLICTS=	p5-bioperl-run-1.[13579]*
 
 USES=		perl5
-USE_PERL5=	modbuild
-WRKSRC=		${WRKDIR}/BioPerl-run-1.6.0
-
-MAN1=	bp_bioperl_application_installer.pl.1 \
-	bp_multi_hmmsearch.pl.1 \
-	bp_panalysis.pl.1 \
-	bp_papplmaker.pl.1 \
-	bp_run_neighbor.pl.1 \
-	bp_run_protdist.pl.1
-
-MAN3=	Bio::Tools::Run::Phylo::Phylip::DrawGram.3 \
-	Bio::Tools::Run::Simprot.3 \
-	Bio::Tools::Run::Phylo::Phyml.3 \
-	Bio::Tools::Run::Phylo::LVB.3 \
-	Bio::Tools::Run::Alignment::Amap.3 \
-	Bio::Tools::Run::Tmhmm.3 \
-	Bio::Tools::Run::TigrAssembler.3 \
-	Bio::Tools::Run::Phylo::PAML::Baseml.3 \
-	Bio::Installer::Probcons.3 \
-	Bio::Tools::Run::Phylo::Phylip::Base.3 \
-	Bio::Tools::Run::Alignment::Exonerate.3 \
-	Bio::Tools::Run::Alignment::MAFFT.3 \
-	Bio::Tools::Run::Alignment::TCoffee.3 \
-	Bio::Tools::Run::Alignment::Sim4.3 \
-	Bio::Tools::Run::Analysis.3 \
-	Bio::Tools::Run::Phylo::PAML::Yn00.3 \
-	Bio::Tools::Run::Alignment::Clustalw.3 \
-	Bio::Tools::Run::Phylo::Molphy::ProtML.3 \
-	Bio::Tools::Run::Phylo::Hyphy::Base.3 \
-	Bio::Tools::Run::Meme.3 \
-	Bio::Tools::Run::MCS.3 \
-	Bio::Tools::Run::Eponine.3 \
-	Bio::Tools::Run::Alignment::Kalign.3 \
-	Bio::Tools::Run::TribeMCL.3 \
-	Bio::Tools::Run::Analysis::soap.3 \
-	Bio::Factory::EMBOSS.3 \
-	Bio::Installer::Clustalw.3 \
-	Bio::Tools::Run::Seg.3 \
-	Bio::Tools::Run::Alignment::Probcons.3 \
-	Bio::Tools::Run::RepeatMasker.3 \
-	Bio::Installer::TCoffee.3 \
-	Bio::Tools::Run::AnalysisFactory.3 \
-	Bio::Tools::Run::Cap3.3 \
-	Bio::Tools::Run::Alignment::Blat.3 \
-	Bio::Tools::Run::Phylo::PhyloBase.3 \
-	Bio::Tools::Run::Coil.3 \
-	Bio::Tools::Run::Promoterwise.3 \
-	Bio::Tools::Run::Alignment::Pal2Nal.3 \
-	Bio::Tools::Run::ERPIN.3 \
-	Bio::Tools::Run::Phylo::PAML::Evolver.3 \
-	Bio::Tools::Run::Phylo::Hyphy::REL.3 \
-	Bio::Tools::Run::Genscan.3 \
-	Bio::Tools::Run::EMBOSSApplication.3 \
-	Bio::Tools::Run::Phylo::Hyphy::Modeltest.3 \
-	Bio::Tools::Run::Match.3 \
-	Bio::Tools::Run::Phylo::Gumby.3 \
-	Bio::Tools::Run::Vista.3 \
-	Bio::Tools::Run::Phylo::Hyphy::SLAC.3 \
-	Bio::Tools::Run::Mdust.3 \
-	Bio::Tools::Run::Alignment::Proda.3 \
-	Bio::Installer::SLR.3 \
-	Bio::Tools::Run::Primate.3 \
-	Bio::Tools::Run::Infernal.3 \
-	Bio::Tools::Run::Genemark.3 \
-	Bio::Tools::Run::Phylo::Phylip::PhylipConf.3 \
-	Bio::Tools::Run::EMBOSSacd.3 \
-	Bio::Tools::Run::Hmmer.3 \
-	Bio::Tools::Run::AnalysisFactory::soap.3 \
-	Bio::Tools::Run::Alignment::Lagan.3 \
-	Bio::Installer::EMBOSS.3 \
-	Bio::Tools::Run::Phrap.3 \
-	Bio::Tools::Run::Alignment::Muscle.3 \
-	Bio::Tools::Run::tRNAscanSE.3 \
-	Bio::Tools::Run::Glimmer.3 \
-	Bio::Tools::Run::Phylo::Phylip::SeqBoot.3 \
-	Bio::Installer::PAML.3 \
-	Bio::Tools::Run::Phylo::Phylip::Neighbor.3 \
-	Bio::Tools::Run::Phylo::Phast::PhyloFit.3 \
-	Bio::Installer::Hyphy.3 \
-	Bio::Tools::Run::Phylo::Phast::PhastCons.3 \
-	Bio::Tools::Run::Signalp.3 \
-	Bio::Tools::Run::Phylo::Phylip::ProtDist.3 \
-	Bio::Installer::Generic.3 \
-	Bio::Tools::Run::Phylo::Phylip::DrawTree.3 \
-	Bio::Tools::Run::Phylo::SLR.3 \
-	Bio::Tools::Run::FootPrinter.3 \
-	Bio::Tools::Run::Genewise.3 \
-	Bio::Tools::Run::Phylo::Phylip::ProtPars.3 \
-	Bio::Tools::Run::RNAMotif.3 \
-	Bio::Tools::Run::Alignment::StandAloneFasta.3 \
-	Bio::Tools::Run::Alignment::Probalign.3 \
-	Bio::Tools::Run::Primer3.3 \
-	Bio::Tools::Run::Profile.3 \
-	Bio::Tools::Run::Phylo::Njtree::Best.3 \
-	Bio::Tools::Run::Phylo::QuickTree.3 \
-	Bio::Tools::Run::Pseudowise.3 \
-	Bio::Tools::Run::Alignment::DBA.3 \
-	Bio::Tools::Run::Phylo::Phylip::Consense.3 \
-	Bio::Tools::Run::Phylo::Semphy.3 \
-	Bio::Tools::Run::Ensembl.3 \
-	Bio::Tools::Run::Phylo::Gerp.3 \
-	Bio::Tools::Run::Phylo::PAML::Codeml.3 \
-	Bio::Installer::Muscle.3 \
-	Bio::Tools::Run::Prints.3 \
-	Bio::Tools::Run::Phylo::Hyphy::FEL.3
+USE_GITHUB=     yes
+GH_ACCOUNT=     bioperl
+GH_COMMIT=	96ccd93
+GH_TAGNAME=     ${GH_COMMIT}
 
-# now install all extra stuff (docs, examples, scripts)
-NO_STAGE=	yes
+USES=		perl5 shebangfix
+USE_PERL5=	modbuild
+SHEBANG_FILES=	scripts/bioperl_application_installer.PLS \
+		scripts/multi_hmmsearch.PLS \
+		scripts/panalysis.PLS \
+		scripts/papplmaker.PLS \
+		scripts/run_neighbor.PLS \
+		scripts/run_protdist.PLS \
 
 OPTIONS_DEFINE=	DOCS
 
 .include <bsd.port.options.mk>
 
+post-build:
+	cd ${WRKSRC} && ${PERL} ./Build manifest
+
 post-install:
-	${MKDIR} ${DATADIR}
-	@${CP} -Rv ${WRKSRC}/scripts ${DATADIR}
+.for i in bioperl_application_installer multi_hmmsearch panalysis papplmaker run_neighbor run_protdist
+	${CP} ${WRKSRC}/scripts/${i}.PLS ${STAGEDIR}${PREFIX}/bin/bp_${i}
+.endfor
 .if ${PORT_OPTIONS:MDOCS}
-	${MKDIR} ${DOCSDIR}
+	${MKDIR} ${STAGEDIR}${DOCSDIR}
 .for doc in AUTHORS Changes INSTALL.PROGRAMS README
-	${INSTALL_DATA} ${WRKSRC}/${doc} ${DOCSDIR}
+	${INSTALL_DATA} ${WRKSRC}/${doc} ${STAGEDIR}${DOCSDIR}
 .endfor
 .endif
 
diff --git a/biology/p5-bioperl-run/distinfo b/biology/p5-bioperl-run/distinfo
index a88dcb804f92..ea26e5422cdd 100644
--- a/biology/p5-bioperl-run/distinfo
+++ b/biology/p5-bioperl-run/distinfo
@@ -1,2 +1,2 @@
-SHA256 (BioPerl-run-1.6.1.tar.gz) = 1ecf2f3a0dd606a1522642d6dd05f8641cd5c8788f3b53e19243f4121c4d4b80
-SIZE (BioPerl-run-1.6.1.tar.gz) = 4082463
+SHA256 (bioperl-run-1.6.901.tar.gz) = 41f9b0ccadfaed31e00d187e83f4699aeeabe1bc34d9e137f87e59ec44ade697
+SIZE (bioperl-run-1.6.901.tar.gz) = 13941063
diff --git a/biology/p5-bioperl-run/files/patch-Build.PL b/biology/p5-bioperl-run/files/patch-Build.PL
new file mode 100644
index 000000000000..8af6e19b1a04
--- /dev/null
+++ b/biology/p5-bioperl-run/files/patch-Build.PL
@@ -0,0 +1,12 @@
+--- ./Build.PL.orig	2014-07-26 04:49:03.000000000 +0200
++++ ./Build.PL	2014-08-04 09:33:15.000000000 +0200
+@@ -42,7 +42,8 @@
+     #create_makefile_pl  => 'passthrough'
+ );
+ 
+-my $accept = $build->args->{accept};
++# my $accept = $build->args->{accept};
++my $accept = 1;
+ 
+ # Optionally have script files installed.
+ if ($build->args('install_scripts') or $accept ? 0 : $build->y_n("Install scripts? y/n", 'n')) {
diff --git a/biology/p5-bioperl-run/pkg-descr b/biology/p5-bioperl-run/pkg-descr
index e6b90ec6ac9f..4139c169c6d3 100644
--- a/biology/p5-bioperl-run/pkg-descr
+++ b/biology/p5-bioperl-run/pkg-descr
@@ -2,4 +2,4 @@ Bioperl-run contain modules that provides a PERL interface to various
 bioinformatics applications. This allows various applications to be used
 with common Bioperl objects.
 
-WWW: http://bioperl.org/
+WWW: https://github.com/bioperl/bioperl-run
diff --git a/biology/p5-bioperl-run/pkg-plist b/biology/p5-bioperl-run/pkg-plist
index eb1451a811cd..03c024d9bdaa 100644
--- a/biology/p5-bioperl-run/pkg-plist
+++ b/biology/p5-bioperl-run/pkg-plist
@@ -1,128 +1,285 @@
-bin/bp_papplmaker.pl
-bin/bp_panalysis.pl
-bin/bp_run_neighbor.pl
-bin/bp_multi_hmmsearch.pl
-bin/bp_bioperl_application_installer.pl
-bin/bp_run_protdist.pl
-%%DATADIR%%/scripts/bioperl_application_installer.PLS
-%%DATADIR%%/scripts/multi_hmmsearch.PLS
-%%DATADIR%%/scripts/panalysis.PLS
-%%DATADIR%%/scripts/papplmaker.PLS
-%%DATADIR%%/scripts/run_neighbor.PLS
-%%DATADIR%%/scripts/run_protdist.PLS
-@dirrm %%DATADIR%%/scripts
-@dirrm %%DATADIR%%
-%%PORTDOCS%%%%DOCSDIR%%/AUTHORS
-%%PORTDOCS%%%%DOCSDIR%%/Changes
-%%PORTDOCS%%%%DOCSDIR%%/INSTALL.PROGRAMS
-%%PORTDOCS%%%%DOCSDIR%%/README
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/
+bin/bp_bioperl_application_installer
+bin/bp_multi_hmmsearch
+bin/bp_panalysis
+bin/bp_papplmaker
+bin/bp_run_neighbor
+bin/bp_run_protdist
+%%PERL5_MAN3%%/Bio::DB::ESoap.3.gz
+%%PERL5_MAN3%%/Bio::DB::ESoap::WSDL.3.gz
+%%PERL5_MAN3%%/Bio::DB::SoapEUtilities.3.gz
+%%PERL5_MAN3%%/Bio::DB::SoapEUtilities::DocSumAdaptor.3.gz
+%%PERL5_MAN3%%/Bio::DB::SoapEUtilities::FetchAdaptor.3.gz
+%%PERL5_MAN3%%/Bio::DB::SoapEUtilities::FetchAdaptor::seq.3.gz
+%%PERL5_MAN3%%/Bio::DB::SoapEUtilities::FetchAdaptor::species.3.gz
+%%PERL5_MAN3%%/Bio::DB::SoapEUtilities::GQueryAdaptor.3.gz
+%%PERL5_MAN3%%/Bio::DB::SoapEUtilities::LinkAdaptor.3.gz
+%%PERL5_MAN3%%/Bio::DB::SoapEUtilities::Result.3.gz
+%%PERL5_MAN3%%/Bio::Factory::EMBOSS.3.gz
+%%PERL5_MAN3%%/Bio::Installer::Clustalw.3.gz
+%%PERL5_MAN3%%/Bio::Installer::EMBOSS.3.gz
+%%PERL5_MAN3%%/Bio::Installer::Generic.3.gz
+%%PERL5_MAN3%%/Bio::Installer::Hyphy.3.gz
+%%PERL5_MAN3%%/Bio::Installer::Muscle.3.gz
+%%PERL5_MAN3%%/Bio::Installer::PAML.3.gz
+%%PERL5_MAN3%%/Bio::Installer::Probcons.3.gz
+%%PERL5_MAN3%%/Bio::Installer::SLR.3.gz
+%%PERL5_MAN3%%/Bio::Installer::TCoffee.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Alignment::Amap.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Alignment::Blat.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Alignment::Clustalw.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Alignment::DBA.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Alignment::Exonerate.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Alignment::Gmap.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Alignment::Kalign.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Alignment::Lagan.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Alignment::MAFFT.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Alignment::MSAProbs.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Alignment::Muscle.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Alignment::Pal2Nal.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Alignment::Probalign.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Alignment::Probcons.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Alignment::Proda.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Alignment::Sim4.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Alignment::StandAloneFasta.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Alignment::TCoffee.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Analysis.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Analysis::soap.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::AnalysisFactory.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::AnalysisFactory::soap.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::AssemblerBase.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::BEDTools.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::BEDTools::Config.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::BWA.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::BWA::Config.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::BlastPlus.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Bowtie.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Bowtie::Config.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Cap3.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Coil.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::EMBOSSApplication.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::EMBOSSacd.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::ERPIN.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Ensembl.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Eponine.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::FootPrinter.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Genemark.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Genewise.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Genscan.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Glimmer.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Hmmer.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Infernal.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::MCS.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Maq.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Maq::Config.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Match.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Mdust.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Meme.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Minimo.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Newbler.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Phrap.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Phylo::FastTree.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Phylo::Gerp.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Phylo::Gumby.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Phylo::Hyphy::Base.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Phylo::Hyphy::BatchFile.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Phylo::Hyphy::FEL.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Phylo::Hyphy::Modeltest.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Phylo::Hyphy::REL.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Phylo::Hyphy::SLAC.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Phylo::LVB.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Phylo::Molphy::ProtML.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Phylo::Njtree::Best.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Phylo::PAML::Baseml.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Phylo::PAML::Codeml.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Phylo::PAML::Evolver.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Phylo::PAML::Yn00.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Phylo::Phast::PhastCons.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Phylo::Phast::PhyloFit.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Phylo::Phylip::Base.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Phylo::Phylip::Consense.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Phylo::Phylip::DrawGram.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Phylo::Phylip::DrawTree.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Phylo::Phylip::Neighbor.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Phylo::Phylip::PhylipConf.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Phylo::Phylip::ProtDist.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Phylo::Phylip::ProtPars.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Phylo::Phylip::SeqBoot.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Phylo::PhyloBase.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Phylo::Phyml.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Phylo::QuickTree.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Phylo::Raxml.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Phylo::SLR.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Phylo::Semphy.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Primate.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Primer3.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Prints.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Profile.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Promoterwise.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Pseudowise.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::RNAMotif.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::RepeatMasker.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Samtools.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Samtools::Config.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Seg.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Signalp.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Simprot.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::StandAloneBlastPlus.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::StandAloneBlastPlus::BlastMethods.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::TigrAssembler.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Tmhmm.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::TribeMCL.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::Vista.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::tRNAscanSE.3.gz
+%%SITE_PERL%%/Bio/DB/ESoap.pm
+%%SITE_PERL%%/Bio/DB/ESoap/WSDL.pm
+%%SITE_PERL%%/Bio/DB/SoapEUtilities.pm
+%%SITE_PERL%%/Bio/DB/SoapEUtilities/DocSumAdaptor.pm
+%%SITE_PERL%%/Bio/DB/SoapEUtilities/FetchAdaptor.pm
+%%SITE_PERL%%/Bio/DB/SoapEUtilities/FetchAdaptor/seq.pm
+%%SITE_PERL%%/Bio/DB/SoapEUtilities/FetchAdaptor/species.pm
+%%SITE_PERL%%/Bio/DB/SoapEUtilities/GQueryAdaptor.pm
+%%SITE_PERL%%/Bio/DB/SoapEUtilities/LinkAdaptor.pm
+%%SITE_PERL%%/Bio/DB/SoapEUtilities/Result.pm
 %%SITE_PERL%%/Bio/Factory/EMBOSS.pm
-%%SITE_PERL%%/Bio/Tools/Run/Alignment/DBA.pm
-%%SITE_PERL%%/Bio/Tools/Run/Alignment/Sim4.pm
-%%SITE_PERL%%/Bio/Tools/Run/Alignment/Probalign.pm
-%%SITE_PERL%%/Bio/Tools/Run/Alignment/StandAloneFasta.pm
+%%SITE_PERL%%/Bio/Installer/Clustalw.pm
+%%SITE_PERL%%/Bio/Installer/EMBOSS.pm
+%%SITE_PERL%%/Bio/Installer/Generic.pm
+%%SITE_PERL%%/Bio/Installer/Hyphy.pm
+%%SITE_PERL%%/Bio/Installer/Muscle.pm
+%%SITE_PERL%%/Bio/Installer/PAML.pm
+%%SITE_PERL%%/Bio/Installer/Probcons.pm
+%%SITE_PERL%%/Bio/Installer/SLR.pm
+%%SITE_PERL%%/Bio/Installer/TCoffee.pm
 %%SITE_PERL%%/Bio/Tools/Run/Alignment/Amap.pm
 %%SITE_PERL%%/Bio/Tools/Run/Alignment/Blat.pm
-%%SITE_PERL%%/Bio/Tools/Run/Alignment/Muscle.pm
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