- Move biology/p5-bioperl-run to biology/p5-BioPerl-Run

- Sort *_DEPENDS
- Add NO_ARCH
- Bump PORTREVISION for biology/p5-bioperl renaming

5 files changed, 332 insertions, 0 deletions

diff --git a/biology/p5-BioPerl-Run/Makefile b/biology/p5-BioPerl-Run/Makefile
new file mode 100644
index 000000000000..881c35fd26d5
--- /dev/null
+++ b/biology/p5-BioPerl-Run/Makefile
@@ -0,0 +1,50 @@
+# Created by: Mauricio Herrera Cuadra <mauricio@arareko.net>
+# $FreeBSD$
+
+PORTNAME=	BioPerl-Run
+PORTVERSION=	1.6.901
+PORTREVISION=	2
+CATEGORIES=	biology perl5
+PKGNAMEPREFIX=	p5-
+
+MAINTAINER=	perl@FreeBSD.org
+COMMENT=	Wrapper modules for common bioinformatics tools
+
+LICENSE=	ART10 GPLv3
+LICENSE_COMB=	dual
+
+BUILD_DEPENDS=	p5-Algorithm-Diff>=0:devel/p5-Algorithm-Diff \
+		p5-BioPerl>=1.6.0:biology/p5-BioPerl \
+		p5-Config-Any>=0:devel/p5-Config-Any \
+		p5-File-Sort>=0:misc/p5-File-Sort \
+		p5-IPC-Run>=0:devel/p5-IPC-Run \
+		p5-XML-Twig>=0:textproc/p5-XML-Twig
+RUN_DEPENDS:=	${BUILD_DEPENDS}
+
+CONFLICTS=	p5-bioperl-run-1.[13579]*
+
+USE_GITHUB=	yes
+GH_ACCOUNT=	bioperl
+GH_PROJECT=	bioperl-run
+GH_TAGNAME=	96ccd93
+
+NO_ARCH=	yes
+USES=		perl5 shebangfix
+USE_PERL5=	modbuild
+SHEBANG_FILES=	scripts/*
+
+OPTIONS_DEFINE=	DOCS
+
+post-build:
+	(cd ${WRKSRC} && ${PERL} ./Build manifest)
+
+post-install:
+.for i in bioperl_application_installer multi_hmmsearch panalysis papplmaker run_neighbor run_protdist
+	${CP} ${WRKSRC}/scripts/${i}.PLS ${STAGEDIR}${PREFIX}/bin/bp_${i}
+.endfor
+	@${MKDIR} ${STAGEDIR}${DOCSDIR}
+.for doc in AUTHORS Changes INSTALL.PROGRAMS README
+	${INSTALL_DATA} ${WRKSRC}/${doc} ${STAGEDIR}${DOCSDIR}
+.endfor
+
+.include <bsd.port.mk>
diff --git a/biology/p5-BioPerl-Run/distinfo b/biology/p5-BioPerl-Run/distinfo
new file mode 100644
index 000000000000..1005fa30a806
--- /dev/null
+++ b/biology/p5-BioPerl-Run/distinfo
@@ -0,0 +1,2 @@
+SHA256 (bioperl-bioperl-run-1.6.901-96ccd93_GH0.tar.gz) = 13f6c0b47b70a2bc5e9f633bc011378a85f78a7f0c0d334246acbc1a8f3b343c
+SIZE (bioperl-bioperl-run-1.6.901-96ccd93_GH0.tar.gz) = 13941085
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
new file mode 100644
index 000000000000..4139c169c6d3
--- /dev/null
+++ b/biology/p5-BioPerl-Run/pkg-descr
@@ -0,0 +1,5 @@
+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: https://github.com/bioperl/bioperl-run
diff --git a/biology/p5-BioPerl-Run/pkg-plist b/biology/p5-BioPerl-Run/pkg-plist
new file mode 100644
index 000000000000..51b2742be490
--- /dev/null
+++ b/biology/p5-BioPerl-Run/pkg-plist
@@ -0,0 +1,263 @@
+bin/bp_bioperl_application_installer
+bin/bp_multi_hmmsearch
+bin/bp_panalysis
+bin/bp_papplmaker
+bin/bp_run_neighbor
+bin/bp_run_protdist
+%%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/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/Clustalw.pm
+%%SITE_PERL%%/Bio/Tools/Run/Alignment/DBA.pm
+%%SITE_PERL%%/Bio/Tools/Run/Alignment/Exonerate.pm
+%%SITE_PERL%%/Bio/Tools/Run/Alignment/Gmap.pm
+%%SITE_PERL%%/Bio/Tools/Run/Alignment/Kalign.pm
+%%SITE_PERL%%/Bio/Tools/Run/Alignment/Lagan.pm
+%%SITE_PERL%%/Bio/Tools/Run/Alignment/MAFFT.pm
+%%SITE_PERL%%/Bio/Tools/Run/Alignment/MSAProbs.pm
+%%SITE_PERL%%/Bio/Tools/Run/Alignment/Muscle.pm
+%%SITE_PERL%%/Bio/Tools/Run/Alignment/Pal2Nal.pm
+%%SITE_PERL%%/Bio/Tools/Run/Alignment/Probalign.pm
+%%SITE_PERL%%/Bio/Tools/Run/Alignment/Probcons.pm
+%%SITE_PERL%%/Bio/Tools/Run/Alignment/Proda.pm
+%%SITE_PERL%%/Bio/Tools/Run/Alignment/Sim4.pm
+%%SITE_PERL%%/Bio/Tools/Run/Alignment/StandAloneFasta.pm
+%%SITE_PERL%%/Bio/Tools/Run/Alignment/TCoffee.pm
+%%SITE_PERL%%/Bio/Tools/Run/Analysis.pm
+%%SITE_PERL%%/Bio/Tools/Run/Analysis/soap.pm
+%%SITE_PERL%%/Bio/Tools/Run/AnalysisFactory.pm
+%%SITE_PERL%%/Bio/Tools/Run/AnalysisFactory/soap.pm
+%%SITE_PERL%%/Bio/Tools/Run/AssemblerBase.pm
+%%SITE_PERL%%/Bio/Tools/Run/BEDTools.pm
+%%SITE_PERL%%/Bio/Tools/Run/BEDTools/Config.pm
+%%SITE_PERL%%/Bio/Tools/Run/BWA.pm
+%%SITE_PERL%%/Bio/Tools/Run/BWA/Config.pm
+%%SITE_PERL%%/Bio/Tools/Run/BlastPlus.pm
+%%SITE_PERL%%/Bio/Tools/Run/BlastPlus/Config.pm
+%%SITE_PERL%%/Bio/Tools/Run/Bowtie.pm
+%%SITE_PERL%%/Bio/Tools/Run/Bowtie/Config.pm
+%%SITE_PERL%%/Bio/Tools/Run/Cap3.pm
+%%SITE_PERL%%/Bio/Tools/Run/Coil.pm
+%%SITE_PERL%%/Bio/Tools/Run/EMBOSSApplication.pm
+%%SITE_PERL%%/Bio/Tools/Run/EMBOSSacd.pm
+%%SITE_PERL%%/Bio/Tools/Run/ERPIN.pm
+%%SITE_PERL%%/Bio/Tools/Run/Ensembl.pm
+%%SITE_PERL%%/Bio/Tools/Run/Eponine.pm
+%%SITE_PERL%%/Bio/Tools/Run/FootPrinter.pm
+%%SITE_PERL%%/Bio/Tools/Run/Genemark.pm
+%%SITE_PERL%%/Bio/Tools/Run/Genewise.pm
+%%SITE_PERL%%/Bio/Tools/Run/Genscan.pm
+%%SITE_PERL%%/Bio/Tools/Run/Glimmer.pm
+%%SITE_PERL%%/Bio/Tools/Run/Hmmer.pm
+%%SITE_PERL%%/Bio/Tools/Run/Infernal.pm
+%%SITE_PERL%%/Bio/Tools/Run/MCS.pm
+%%SITE_PERL%%/Bio/Tools/Run/Maq.pm
+%%SITE_PERL%%/Bio/Tools/Run/Maq/Config.pm
+%%SITE_PERL%%/Bio/Tools/Run/Match.pm
+%%SITE_PERL%%/Bio/Tools/Run/Mdust.pm
+%%SITE_PERL%%/Bio/Tools/Run/Meme.pm
+%%SITE_PERL%%/Bio/Tools/Run/Minimo.pm
+%%SITE_PERL%%/Bio/Tools/Run/Newbler.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phrap.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/FastTree.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/Gerp.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/Gumby.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/Hyphy/Base.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/Hyphy/BatchFile.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/Hyphy/FEL.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/Hyphy/Modeltest.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/Hyphy/REL.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/Hyphy/SLAC.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/LVB.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/Molphy/ProtML.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/Njtree/Best.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/PAML/Baseml.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/PAML/Codeml.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/PAML/Evolver.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/PAML/Yn00.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/Phast/PhastCons.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/Phast/PhyloFit.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/Base.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/Consense.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/DrawGram.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/DrawTree.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/Neighbor.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/PhylipConf.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/ProtDist.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/ProtPars.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/SeqBoot.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/PhyloBase.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/Phyml.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/QuickTree.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/Raxml.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/SLR.pm
+%%SITE_PERL%%/Bio/Tools/Run/Phylo/Semphy.pm
+%%SITE_PERL%%/Bio/Tools/Run/Primate.pm
+%%SITE_PERL%%/Bio/Tools/Run/Primer3.pm
+%%SITE_PERL%%/Bio/Tools/Run/Prints.pm
+%%SITE_PERL%%/Bio/Tools/Run/Profile.pm
+%%SITE_PERL%%/Bio/Tools/Run/Promoterwise.pm
+%%SITE_PERL%%/Bio/Tools/Run/Pseudowise.pm
+%%SITE_PERL%%/Bio/Tools/Run/RNAMotif.pm
+%%SITE_PERL%%/Bio/Tools/Run/RepeatMasker.pm
+%%SITE_PERL%%/Bio/Tools/Run/Samtools.pm
+%%SITE_PERL%%/Bio/Tools/Run/Samtools/Config.pm
+%%SITE_PERL%%/Bio/Tools/Run/Seg.pm
+%%SITE_PERL%%/Bio/Tools/Run/Signalp.pm
+%%SITE_PERL%%/Bio/Tools/Run/Simprot.pm
+%%SITE_PERL%%/Bio/Tools/Run/StandAloneBlastPlus.pm
+%%SITE_PERL%%/Bio/Tools/Run/StandAloneBlastPlus/BlastMethods.pm
+%%SITE_PERL%%/Bio/Tools/Run/TigrAssembler.pm
+%%SITE_PERL%%/Bio/Tools/Run/Tmhmm.pm
+%%SITE_PERL%%/Bio/Tools/Run/TribeMCL.pm
+%%SITE_PERL%%/Bio/Tools/Run/Vista.pm
+%%SITE_PERL%%/Bio/Tools/Run/tRNAscanSE.pm
+%%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
+%%PORTDOCS%%%%DOCSDIR%%/AUTHORS
+%%PORTDOCS%%%%DOCSDIR%%/Changes
+%%PORTDOCS%%%%DOCSDIR%%/INSTALL.PROGRAMS
+%%PORTDOCS%%%%DOCSDIR%%/README