Date: Mon, 4 Aug 2014 08:54:10 +0000 (UTC) From: Kurt Jaeger <pi@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r363975 - in head/biology/p5-bioperl-run: . files Message-ID: <53df4a32.5c2b.60176c28@svn.freebsd.org>
next in thread | raw e-mail | index | archive | help
Author: pi Date: Mon Aug 4 08:54:10 2014 New Revision: 363975 URL: http://svnweb.freebsd.org/changeset/ports/363975 QAT: https://qat.redports.org/buildarchive/r363975/ Log: biology/p5-bioperl-run: 1.6.1 -> 1.6.901, unbreak, stagify Added: head/biology/p5-bioperl-run/files/ head/biology/p5-bioperl-run/files/patch-Build.PL (contents, props changed) Modified: head/biology/p5-bioperl-run/Makefile head/biology/p5-bioperl-run/distinfo head/biology/p5-bioperl-run/pkg-descr head/biology/p5-bioperl-run/pkg-plist Modified: head/biology/p5-bioperl-run/Makefile ============================================================================== --- head/biology/p5-bioperl-run/Makefile Mon Aug 4 08:29:06 2014 (r363974) +++ head/biology/p5-bioperl-run/Makefile Mon Aug 4 08:54:10 2014 (r363975) @@ -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 Modified: head/biology/p5-bioperl-run/distinfo ============================================================================== --- head/biology/p5-bioperl-run/distinfo Mon Aug 4 08:29:06 2014 (r363974) +++ head/biology/p5-bioperl-run/distinfo Mon Aug 4 08:54:10 2014 (r363975) @@ -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 Added: head/biology/p5-bioperl-run/files/patch-Build.PL ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/p5-bioperl-run/files/patch-Build.PL Mon Aug 4 08:54:10 2014 (r363975) @@ -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')) { Modified: head/biology/p5-bioperl-run/pkg-descr ============================================================================== --- head/biology/p5-bioperl-run/pkg-descr Mon Aug 4 08:29:06 2014 (r363974) +++ head/biology/p5-bioperl-run/pkg-descr Mon Aug 4 08:54:10 2014 (r363975) @@ -2,4 +2,4 @@ Bioperl-run contain modules that provide bioinformatics applications. This allows various applications to be used with common Bioperl objects. -WWW: http://bioperl.org/ +WWW: https://github.com/bioperl/bioperl-run Modified: head/biology/p5-bioperl-run/pkg-plist ============================================================================== --- head/biology/p5-bioperl-run/pkg-plist Mon Aug 4 08:29:06 2014 (r363974) +++ head/biology/p5-bioperl-run/pkg-plist Mon Aug 4 08:54:10 2014 (r363975) @@ -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 -%%SITE_PERL%%/Bio/Tools/Run/Alignment/Pal2Nal.pm -%%SITE_PERL%%/Bio/Tools/Run/Alignment/Probcons.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/MAFFT.pm -%%SITE_PERL%%/Bio/Tools/Run/Alignment/TCoffee.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/Exonerate.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/Phylo/Hyphy/REL.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/Modeltest.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/Codeml.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/SeqBoot.pm -%%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/PhylipConf.pm -%%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/ProtPars.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/Consense.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/DrawGram.pm -%%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/Base.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/LVB.pm %%SITE_PERL%%/Bio/Tools/Run/Phylo/Semphy.pm -%%SITE_PERL%%/Bio/Tools/Run/Phylo/Gerp.pm -%%SITE_PERL%%/Bio/Tools/Run/Phylo/Gumby.pm -%%SITE_PERL%%/Bio/Tools/Run/Phylo/QuickTree.pm -%%SITE_PERL%%/Bio/Tools/Run/EMBOSSacd.pm -%%SITE_PERL%%/Bio/Tools/Run/ERPIN.pm -%%SITE_PERL%%/Bio/Tools/Run/Phrap.pm -%%SITE_PERL%%/Bio/Tools/Run/FootPrinter.pm -%%SITE_PERL%%/Bio/Tools/Run/Match.pm %%SITE_PERL%%/Bio/Tools/Run/Primate.pm -%%SITE_PERL%%/Bio/Tools/Run/Pseudowise.pm -%%SITE_PERL%%/Bio/Tools/Run/AnalysisFactory.pm -%%SITE_PERL%%/Bio/Tools/Run/Genscan.pm -%%SITE_PERL%%/Bio/Tools/Run/Infernal.pm -%%SITE_PERL%%/Bio/Tools/Run/Simprot.pm -%%SITE_PERL%%/Bio/Tools/Run/MCS.pm -%%SITE_PERL%%/Bio/Tools/Run/Coil.pm -%%SITE_PERL%%/Bio/Tools/Run/Analysis.pm +%%SITE_PERL%%/Bio/Tools/Run/Primer3.pm %%SITE_PERL%%/Bio/Tools/Run/Prints.pm -%%SITE_PERL%%/Bio/Tools/Run/Hmmer.pm -%%SITE_PERL%%/Bio/Tools/Run/Vista.pm -%%SITE_PERL%%/Bio/Tools/Run/TigrAssembler.pm -%%SITE_PERL%%/Bio/Tools/Run/Eponine.pm -%%SITE_PERL%%/Bio/Tools/Run/TribeMCL.pm +%%SITE_PERL%%/Bio/Tools/Run/Profile.pm %%SITE_PERL%%/Bio/Tools/Run/Promoterwise.pm -%%SITE_PERL%%/Bio/Tools/Run/tRNAscanSE.pm -%%SITE_PERL%%/Bio/Tools/Run/Cap3.pm -%%SITE_PERL%%/Bio/Tools/Run/Glimmer.pm -%%SITE_PERL%%/Bio/Tools/Run/EMBOSSApplication.pm -%%SITE_PERL%%/Bio/Tools/Run/Signalp.pm -%%SITE_PERL%%/Bio/Tools/Run/Meme.pm +%%SITE_PERL%%/Bio/Tools/Run/Pseudowise.pm %%SITE_PERL%%/Bio/Tools/Run/RNAMotif.pm -%%SITE_PERL%%/Bio/Tools/Run/Seg.pm -%%SITE_PERL%%/Bio/Tools/Run/Genemark.pm -%%SITE_PERL%%/Bio/Tools/Run/Mdust.pm %%SITE_PERL%%/Bio/Tools/Run/RepeatMasker.pm -%%SITE_PERL%%/Bio/Tools/Run/Genewise.pm -%%SITE_PERL%%/Bio/Tools/Run/Profile.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/Ensembl.pm -%%SITE_PERL%%/Bio/Tools/Run/Primer3.pm -%%SITE_PERL%%/Bio/Installer/EMBOSS.pm -%%SITE_PERL%%/Bio/Installer/Muscle.pm -%%SITE_PERL%%/Bio/Installer/Clustalw.pm -%%SITE_PERL%%/Bio/Installer/SLR.pm -%%SITE_PERL%%/Bio/Installer/Probcons.pm -%%SITE_PERL%%/Bio/Installer/TCoffee.pm -%%SITE_PERL%%/Bio/Installer/Hyphy.pm -%%SITE_PERL%%/Bio/Installer/Generic.pm -%%SITE_PERL%%/Bio/Installer/PAML.pm -@dirrm %%SITE_PERL%%/Bio/Installer -@dirrm %%SITE_PERL%%/Bio/Tools/Run/Analysis -@dirrm %%SITE_PERL%%/Bio/Tools/Run/Alignment -@dirrm %%SITE_PERL%%/Bio/Tools/Run/AnalysisFactory -@dirrm %%SITE_PERL%%/Bio/Tools/Run/Phylo/Hyphy -@dirrm %%SITE_PERL%%/Bio/Tools/Run/Phylo/Molphy -@dirrm %%SITE_PERL%%/Bio/Tools/Run/Phylo/Njtree -@dirrm %%SITE_PERL%%/Bio/Tools/Run/Phylo/PAML -@dirrm %%SITE_PERL%%/Bio/Tools/Run/Phylo/Phast -@dirrm %%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip -@dirrm %%SITE_PERL%%/Bio/Tools/Run/Phylo -@dirrmtry %%SITE_PERL%%/Bio/Tools/Run -@dirrmtry %%SITE_PERL%%/Bio/Tools -@dirrmtry %%SITE_PERL%%/Bio +%%SITE_PERL%%/Bio/Tools/Run/TribeMCL.pm +%%SITE_PERL%%/Bio/Tools/Run/Vista.pm +%%SITE_PERL%%/Bio/Tools/Run/tRNAscanSE.pm +%%PORTDOCS%%%%DOCSDIR%%/AUTHORS +%%PORTDOCS%%%%DOCSDIR%%/Changes +%%PORTDOCS%%%%DOCSDIR%%/INSTALL.PROGRAMS +%%PORTDOCS%%%%DOCSDIR%%/README +@dirrmtry %%SITE_PERL%%/Bio/DB/ESoap +@dirrmtry %%SITE_PERL%%/Bio/DB/SoapEUtilities/FetchAdaptor +@dirrmtry %%SITE_PERL%%/Bio/DB/SoapEUtilities +@dirrmtry %%SITE_PERL%%/Bio/Installer +@dirrmtry %%SITE_PERL%%/Bio/Tools/Run/Alignment +@dirrmtry %%SITE_PERL%%/Bio/Tools/Run/Analysis +@dirrmtry %%SITE_PERL%%/Bio/Tools/Run/AnalysisFactory +@dirrmtry %%SITE_PERL%%/Bio/Tools/Run/BEDTools +@dirrmtry %%SITE_PERL%%/Bio/Tools/Run/BWA +@dirrmtry %%SITE_PERL%%/Bio/Tools/Run/BlastPlus +@dirrmtry %%SITE_PERL%%/Bio/Tools/Run/Bowtie +@dirrmtry %%SITE_PERL%%/Bio/Tools/Run/Maq +@dirrmtry %%SITE_PERL%%/Bio/Tools/Run/Phylo/Hyphy +@dirrmtry %%SITE_PERL%%/Bio/Tools/Run/Phylo/Molphy +@dirrmtry %%SITE_PERL%%/Bio/Tools/Run/Phylo/Njtree +@dirrmtry %%SITE_PERL%%/Bio/Tools/Run/Phylo/PAML +@dirrmtry %%SITE_PERL%%/Bio/Tools/Run/Phylo/Phast +@dirrmtry %%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip +@dirrmtry %%SITE_PERL%%/Bio/Tools/Run/Phylo +@dirrmtry %%SITE_PERL%%/Bio/Tools/Run/Samtools +@dirrmtry %%SITE_PERL%%/Bio/Tools/Run/StandAloneBlastPlus +%%PORTDOCS%%@dirrmtry %%DOCSDIR%%
Want to link to this message? Use this URL: <https://mail-archive.FreeBSD.org/cgi/mid.cgi?53df4a32.5c2b.60176c28>