Index: head/biology/p5-bioperl-run/Makefile =================================================================== --- head/biology/p5-bioperl-run/Makefile (revision 377368) +++ head/biology/p5-bioperl-run/Makefile (revision 377369) @@ -1,60 +1,55 @@ # Created by: Mauricio Herrera Cuadra # $FreeBSD$ PORTNAME= bioperl-run PORTVERSION= 1.6.901 PORTREVISION= 1 CATEGORIES= biology perl5 PKGNAMEPREFIX= p5- -MAINTAINER= ports@FreeBSD.org +MAINTAINER= perl@FreeBSD.org COMMENT= Wrapper modules for common bioinformatics tools 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:${PORTSDIR}/devel/p5-Algorithm-Diff \ p5-XML-Twig>=0:${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_GITHUB= yes -GH_ACCOUNT= bioperl +USE_GITHUB= yes +GH_ACCOUNT= bioperl GH_COMMIT= 96ccd93 -GH_TAGNAME= ${GH_COMMIT} +GH_TAGNAME= ${GH_COMMIT} 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 - 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 -.if ${PORT_OPTIONS:MDOCS} ${MKDIR} ${STAGEDIR}${DOCSDIR} .for doc in AUTHORS Changes INSTALL.PROGRAMS README ${INSTALL_DATA} ${WRKSRC}/${doc} ${STAGEDIR}${DOCSDIR} .endfor -.endif .include Index: head/biology/p5-bioperl-run/pkg-plist =================================================================== --- head/biology/p5-bioperl-run/pkg-plist (revision 377368) +++ head/biology/p5-bioperl-run/pkg-plist (revision 377369) @@ -1,263 +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 -%%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/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