diff options
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/p5-bioperl-run/Makefile | 445 | ||||
| -rw-r--r-- | biology/p5-bioperl-run/distinfo | 6 | ||||
| -rw-r--r-- | biology/p5-bioperl-run/pkg-plist | 448 |
3 files changed, 216 insertions, 683 deletions
diff --git a/biology/p5-bioperl-run/Makefile b/biology/p5-bioperl-run/Makefile index 3d733736464a..679c9ca1af79 100644 --- a/biology/p5-bioperl-run/Makefile +++ b/biology/p5-bioperl-run/Makefile @@ -6,362 +6,133 @@ # PORTNAME= bioperl-run -PORTVERSION= 1.4 -PORTREVISION= 1 +PORTVERSION= 1.6.1 CATEGORIES= biology perl5 MASTER_SITES= http://bioperl.org/DIST/ \ CPAN PKGNAMEPREFIX= p5- +DISTNAME= BioPerl-run-${PORTVERSION} MAINTAINER= mauricio@arareko.net COMMENT= Wrapper modules for common bioinformatics tools -BUILD_DEPENDS= p5-bioperl=1.4_2:${PORTSDIR}/biology/p5-bioperl \ +BUILD_DEPENDS= p5-bioperl=1.6.0:${PORTSDIR}/biology/p5-bioperl \ + ${SITE_PERL}/IPC/Run.pm:${PORTSDIR}/devel/p5-IPC-Run \ ${SITE_PERL}/Algorithm/Diff.pm:${PORTSDIR}/devel/p5-Algorithm-Diff RUN_DEPENDS= ${BUILD_DEPENDS} CONFLICTS= p5-bioperl-run-1.[13579]* -PERL_CONFIGURE= YES +PERL_MODBUILD= YES +WRKSRC= ${WRKDIR}/BioPerl-run-1.6.0 -MAN3= Bio::Factory::EMBOSS.3 \ - Bio::Tools::Run::Alignment::Blat.3 \ - Bio::Tools::Run::Alignment::Clustalw.3 \ - Bio::Tools::Run::Alignment::DBA.3 \ - Bio::Tools::Run::Alignment::Lagan.3 \ - Bio::Tools::Run::Alignment::Sim4.3 \ - Bio::Tools::Run::Alignment::StandAloneFasta.3 \ - Bio::Tools::Run::Alignment::TCoffee.3 \ - Bio::Tools::Run::Analysis.3 \ - Bio::Tools::Run::Analysis::soap.3 \ - Bio::Tools::Run::AnalysisFactory.3 \ - Bio::Tools::Run::AnalysisFactory::Pise.3 \ - Bio::Tools::Run::AnalysisFactory::soap.3 \ - Bio::Tools::Run::Coil.3 \ - Bio::Tools::Run::EMBOSSApplication.3 \ - Bio::Tools::Run::EMBOSSacd.3 \ - Bio::Tools::Run::Eponine.3 \ - Bio::Tools::Run::FootPrinter.3 \ - Bio::Tools::Run::Genewise.3 \ - Bio::Tools::Run::Genscan.3 \ - Bio::Tools::Run::Hmmer.3 \ - Bio::Tools::Run::Hmmpfam.3 \ - Bio::Tools::Run::Mdust.3 \ - Bio::Tools::Run::Phylo::Molphy::ProtML.3 \ - Bio::Tools::Run::Phylo::PAML::Codeml.3 \ - Bio::Tools::Run::Phylo::PAML::Yn00.3 \ - Bio::Tools::Run::Phylo::Phylip::Base.3 \ - Bio::Tools::Run::Phylo::Phylip::Consense.3 \ - Bio::Tools::Run::Phylo::Phylip::DrawGram.3 \ - Bio::Tools::Run::Phylo::Phylip::DrawTree.3 \ - Bio::Tools::Run::Phylo::Phylip::Neighbor.3 \ - Bio::Tools::Run::Phylo::Phylip::PhylipConf.3 \ - Bio::Tools::Run::Phylo::Phylip::ProtDist.3 \ - Bio::Tools::Run::Phylo::Phylip::ProtPars.3 \ - Bio::Tools::Run::Phylo::Phylip::SeqBoot.3 \ - Bio::Tools::Run::PiseApplication.3 \ - Bio::Tools::Run::PiseApplication::CSR.3 \ - Bio::Tools::Run::PiseApplication::Puzzle.3 \ - Bio::Tools::Run::PiseApplication::abiview.3 \ - Bio::Tools::Run::PiseApplication::addquart.3 \ - Bio::Tools::Run::PiseApplication::align2model.3 \ - Bio::Tools::Run::PiseApplication::alistat.3 \ - Bio::Tools::Run::PiseApplication::antigenic.3 \ - Bio::Tools::Run::PiseApplication::assp.3 \ - Bio::Tools::Run::PiseApplication::backtranseq.3 \ - Bio::Tools::Run::PiseApplication::bambe.3 \ - Bio::Tools::Run::PiseApplication::banana.3 \ - Bio::Tools::Run::PiseApplication::bionj.3 \ - Bio::Tools::Run::PiseApplication::biosed.3 \ - Bio::Tools::Run::PiseApplication::bl2seq.3 \ - Bio::Tools::Run::PiseApplication::blast2.3 \ - Bio::Tools::Run::PiseApplication::blimps.3 \ - Bio::Tools::Run::PiseApplication::blimps_block.3 \ - Bio::Tools::Run::PiseApplication::blimps_matrix.3 \ - Bio::Tools::Run::PiseApplication::boxshade.3 \ - Bio::Tools::Run::PiseApplication::btwisted.3 \ - Bio::Tools::Run::PiseApplication::cai.3 \ - Bio::Tools::Run::PiseApplication::cap.3 \ - Bio::Tools::Run::PiseApplication::cds.3 \ - Bio::Tools::Run::PiseApplication::chaos.3 \ - Bio::Tools::Run::PiseApplication::charge.3 \ - Bio::Tools::Run::PiseApplication::checktrans.3 \ - Bio::Tools::Run::PiseApplication::chips.3 \ - Bio::Tools::Run::PiseApplication::cirdna.3 \ - Bio::Tools::Run::PiseApplication::clique.3 \ - Bio::Tools::Run::PiseApplication::clustalw.3 \ - Bio::Tools::Run::PiseApplication::clustalw_convert.3 \ - Bio::Tools::Run::PiseApplication::codcmp.3 \ - Bio::Tools::Run::PiseApplication::coderet.3 \ - Bio::Tools::Run::PiseApplication::codnocod.3 \ - Bio::Tools::Run::PiseApplication::codontree.3 \ - Bio::Tools::Run::PiseApplication::codonw.3 \ - Bio::Tools::Run::PiseApplication::comalign.3 \ - Bio::Tools::Run::PiseApplication::combat.3 \ - Bio::Tools::Run::PiseApplication::compseq.3 \ - Bio::Tools::Run::PiseApplication::con_filter.3 \ - Bio::Tools::Run::PiseApplication::confmat.3 \ - Bio::Tools::Run::PiseApplication::cons.3 \ - Bio::Tools::Run::PiseApplication::consense.3 \ - Bio::Tools::Run::PiseApplication::consensus.3 \ - Bio::Tools::Run::PiseApplication::cpgplot.3 \ - Bio::Tools::Run::PiseApplication::cpgreport.3 \ - Bio::Tools::Run::PiseApplication::cusp.3 \ - Bio::Tools::Run::PiseApplication::cutseq.3 \ - Bio::Tools::Run::PiseApplication::dan.3 \ - Bio::Tools::Run::PiseApplication::dca.3 \ - Bio::Tools::Run::PiseApplication::decorate.3 \ - Bio::Tools::Run::PiseApplication::degapseq.3 \ - Bio::Tools::Run::PiseApplication::descseq.3 \ - Bio::Tools::Run::PiseApplication::dialign2.3 \ - Bio::Tools::Run::PiseApplication::diffseq.3 \ - Bio::Tools::Run::PiseApplication::digest.3 \ - Bio::Tools::Run::PiseApplication::distmat.3 \ - Bio::Tools::Run::PiseApplication::distquart.3 \ - Bio::Tools::Run::PiseApplication::dnadist.3 \ - Bio::Tools::Run::PiseApplication::dnapars.3 \ - Bio::Tools::Run::PiseApplication::dollop.3 \ - Bio::Tools::Run::PiseApplication::domainer.3 \ - Bio::Tools::Run::PiseApplication::dotmatcher.3 \ - Bio::Tools::Run::PiseApplication::dotpath.3 \ - Bio::Tools::Run::PiseApplication::dottup.3 \ - Bio::Tools::Run::PiseApplication::drawgram.3 \ - Bio::Tools::Run::PiseApplication::drawpyr.3 \ - Bio::Tools::Run::PiseApplication::drawtree.3 \ - Bio::Tools::Run::PiseApplication::dreg.3 \ - Bio::Tools::Run::PiseApplication::druid.3 \ - Bio::Tools::Run::PiseApplication::dsc.3 \ - Bio::Tools::Run::PiseApplication::dssp.3 \ - Bio::Tools::Run::PiseApplication::einverted.3 \ - Bio::Tools::Run::PiseApplication::emma.3 \ - Bio::Tools::Run::PiseApplication::emowse.3 \ - Bio::Tools::Run::PiseApplication::environ.3 \ - Bio::Tools::Run::PiseApplication::eprimer3.3 \ - Bio::Tools::Run::PiseApplication::equicktandem.3 \ - Bio::Tools::Run::PiseApplication::est2genome.3 \ - Bio::Tools::Run::PiseApplication::etandem.3 \ - Bio::Tools::Run::PiseApplication::extractfeat.3 \ - Bio::Tools::Run::PiseApplication::extractseq.3 \ - Bio::Tools::Run::PiseApplication::fasta.3 \ - Bio::Tools::Run::PiseApplication::fastdnaml.3 \ - Bio::Tools::Run::PiseApplication::fastrna.3 \ - Bio::Tools::Run::PiseApplication::filtersites.3 \ - Bio::Tools::Run::PiseApplication::findkm.3 \ - Bio::Tools::Run::PiseApplication::fitch.3 \ - Bio::Tools::Run::PiseApplication::fmtseq.3 \ - Bio::Tools::Run::PiseApplication::freak.3 \ - Bio::Tools::Run::PiseApplication::fuzznuc.3 \ - Bio::Tools::Run::PiseApplication::fuzzpro.3 \ - Bio::Tools::Run::PiseApplication::fuzztran.3 \ - Bio::Tools::Run::PiseApplication::gb2xml.3 \ - Bio::Tools::Run::PiseApplication::geecee.3 \ - Bio::Tools::Run::PiseApplication::genscan.3 \ - Bio::Tools::Run::PiseApplication::getblock.3 \ - Bio::Tools::Run::PiseApplication::getorf.3 \ - Bio::Tools::Run::PiseApplication::gff2ps.3 \ - Bio::Tools::Run::PiseApplication::gibbs.3 \ - Bio::Tools::Run::PiseApplication::gibbs_scan.3 \ - Bio::Tools::Run::PiseApplication::golden.3 \ - Bio::Tools::Run::PiseApplication::grailclnt.3 \ - Bio::Tools::Run::PiseApplication::gruppi.3 \ - Bio::Tools::Run::PiseApplication::helixturnhelix.3 \ - Bio::Tools::Run::PiseApplication::hmmalign.3 \ - Bio::Tools::Run::PiseApplication::hmmbuild.3 \ - Bio::Tools::Run::PiseApplication::hmmcalibrate.3 \ - Bio::Tools::Run::PiseApplication::hmmconvert.3 \ - Bio::Tools::Run::PiseApplication::hmmemit.3 \ - Bio::Tools::Run::PiseApplication::hmmer2sam.3 \ - Bio::Tools::Run::PiseApplication::hmmfetch.3 \ - Bio::Tools::Run::PiseApplication::hmmpfam.3 \ - Bio::Tools::Run::PiseApplication::hmmscore.3 \ - Bio::Tools::Run::PiseApplication::hmmsearch.3 \ - Bio::Tools::Run::PiseApplication::hmoment.3 \ - Bio::Tools::Run::PiseApplication::homology.3 \ - Bio::Tools::Run::PiseApplication::html4blast.3 \ - Bio::Tools::Run::PiseApplication::iep.3 \ - Bio::Tools::Run::PiseApplication::infoalign.3 \ - Bio::Tools::Run::PiseApplication::infoseq.3 \ - Bio::Tools::Run::PiseApplication::interface.3 \ - Bio::Tools::Run::PiseApplication::isochore.3 \ - Bio::Tools::Run::PiseApplication::kitsch.3 \ - Bio::Tools::Run::PiseApplication::lassap.3 \ - Bio::Tools::Run::PiseApplication::lgicsearch.3 \ - Bio::Tools::Run::PiseApplication::lindna.3 \ - Bio::Tools::Run::PiseApplication::listor.3 \ - Bio::Tools::Run::PiseApplication::loadseq.3 \ - Bio::Tools::Run::PiseApplication::lvb.3 \ - Bio::Tools::Run::PiseApplication::makehist.3 \ - Bio::Tools::Run::PiseApplication::map.3 \ - Bio::Tools::Run::PiseApplication::marscan.3 \ - Bio::Tools::Run::PiseApplication::maskfeat.3 \ - Bio::Tools::Run::PiseApplication::maskseq.3 \ - Bio::Tools::Run::PiseApplication::matcher.3 \ - Bio::Tools::Run::PiseApplication::megamerger.3 \ - Bio::Tools::Run::PiseApplication::melting.3 \ - Bio::Tools::Run::PiseApplication::merger.3 \ - Bio::Tools::Run::PiseApplication::mfold.3 \ - Bio::Tools::Run::PiseApplication::mix.3 \ - Bio::Tools::Run::PiseApplication::modelfromalign.3 \ - Bio::Tools::Run::PiseApplication::most.3 \ - Bio::Tools::Run::PiseApplication::mreps.3 \ - Bio::Tools::Run::PiseApplication::msa.3 \ - Bio::Tools::Run::PiseApplication::msbar.3 \ - Bio::Tools::Run::PiseApplication::mspcrunch.3 \ - Bio::Tools::Run::PiseApplication::mview_alig.3 \ - Bio::Tools::Run::PiseApplication::mview_blast.3 \ - Bio::Tools::Run::PiseApplication::mwfilter.3 \ - Bio::Tools::Run::PiseApplication::needle.3 \ - Bio::Tools::Run::PiseApplication::neighbor.3 \ - Bio::Tools::Run::PiseApplication::newcpgreport.3 \ - Bio::Tools::Run::PiseApplication::newcpgseek.3 \ - Bio::Tools::Run::PiseApplication::newseq.3 \ - Bio::Tools::Run::PiseApplication::njdist.3 \ - Bio::Tools::Run::PiseApplication::nnssp.3 \ - Bio::Tools::Run::PiseApplication::notseq.3 \ - Bio::Tools::Run::PiseApplication::nrscope.3 \ - Bio::Tools::Run::PiseApplication::nthseq.3 \ - Bio::Tools::Run::PiseApplication::octanol.3 \ - Bio::Tools::Run::PiseApplication::oddcomp.3 \ - Bio::Tools::Run::PiseApplication::palindrome.3 \ - Bio::Tools::Run::PiseApplication::pam.3 \ - Bio::Tools::Run::PiseApplication::parciquart.3 \ - Bio::Tools::Run::PiseApplication::pars.3 \ - Bio::Tools::Run::PiseApplication::pasteseq.3 \ - Bio::Tools::Run::PiseApplication::patmatdb.3 \ - Bio::Tools::Run::PiseApplication::patmatmotifs.3 \ - Bio::Tools::Run::PiseApplication::patser.3 \ - Bio::Tools::Run::PiseApplication::pdbsearch.3 \ - Bio::Tools::Run::PiseApplication::pepcoil.3 \ - Bio::Tools::Run::PiseApplication::pepinfo.3 \ - Bio::Tools::Run::PiseApplication::pepnet.3 \ - Bio::Tools::Run::PiseApplication::pepstats.3 \ - Bio::Tools::Run::PiseApplication::pepwheel.3 \ - Bio::Tools::Run::PiseApplication::pepwindow.3 \ - Bio::Tools::Run::PiseApplication::pepwindowall.3 \ - Bio::Tools::Run::PiseApplication::pestfind.3 \ - Bio::Tools::Run::PiseApplication::pftools.3 \ - Bio::Tools::Run::PiseApplication::phiblast.3 \ - Bio::Tools::Run::PiseApplication::pima.3 \ - Bio::Tools::Run::PiseApplication::plotcon.3 \ - Bio::Tools::Run::PiseApplication::plotorf.3 \ - Bio::Tools::Run::PiseApplication::plsearch.3 \ - Bio::Tools::Run::PiseApplication::polydot.3 \ - Bio::Tools::Run::PiseApplication::pratt.3 \ - Bio::Tools::Run::PiseApplication::predator.3 \ - Bio::Tools::Run::PiseApplication::preg.3 \ - Bio::Tools::Run::PiseApplication::prettyalign.3 \ - Bio::Tools::Run::PiseApplication::prettyplot.3 \ - Bio::Tools::Run::PiseApplication::prettyseq.3 \ - Bio::Tools::Run::PiseApplication::primersearch.3 \ - Bio::Tools::Run::PiseApplication::primo.3 \ - Bio::Tools::Run::PiseApplication::prodom.3 \ - Bio::Tools::Run::PiseApplication::profit.3 \ - Bio::Tools::Run::PiseApplication::prophecy.3 \ - Bio::Tools::Run::PiseApplication::prophet.3 \ - Bio::Tools::Run::PiseApplication::prose.3 \ - Bio::Tools::Run::PiseApplication::prot_nucml.3 \ - Bio::Tools::Run::PiseApplication::protal2dna.3 \ - Bio::Tools::Run::PiseApplication::protdist.3 \ - Bio::Tools::Run::PiseApplication::protpars.3 \ - Bio::Tools::Run::PiseApplication::pscan.3 \ - Bio::Tools::Run::PiseApplication::psiblast.3 \ - Bio::Tools::Run::PiseApplication::psort2.3 \ - Bio::Tools::Run::PiseApplication::pyramids.3 \ - Bio::Tools::Run::PiseApplication::pyreval.3 \ - Bio::Tools::Run::PiseApplication::qstar.3 \ - Bio::Tools::Run::PiseApplication::quicktree.3 \ - Bio::Tools::Run::PiseApplication::readnexus.3 \ - Bio::Tools::Run::PiseApplication::readseq.3 \ - Bio::Tools::Run::PiseApplication::recoder.3 \ - Bio::Tools::Run::PiseApplication::redata.3 \ - Bio::Tools::Run::PiseApplication::remap.3 \ - Bio::Tools::Run::PiseApplication::repeats.3 \ - Bio::Tools::Run::PiseApplication::restover.3 \ - Bio::Tools::Run::PiseApplication::restrict.3 \ - Bio::Tools::Run::PiseApplication::revseq.3 \ - Bio::Tools::Run::PiseApplication::rnadistance.3 \ - Bio::Tools::Run::PiseApplication::rnaeval.3 \ - Bio::Tools::Run::PiseApplication::rnafold.3 \ - Bio::Tools::Run::PiseApplication::rnaga.3 \ - Bio::Tools::Run::PiseApplication::rnaheat.3 \ - Bio::Tools::Run::PiseApplication::rnainverse.3 \ - Bio::Tools::Run::PiseApplication::rnapdist.3 \ - Bio::Tools::Run::PiseApplication::rnasubopt.3 \ - Bio::Tools::Run::PiseApplication::sam2hmmer.3 \ - Bio::Tools::Run::PiseApplication::sampleseqs.3 \ - Bio::Tools::Run::PiseApplication::saps.3 \ - Bio::Tools::Run::PiseApplication::satellites.3 \ - Bio::Tools::Run::PiseApplication::scan_for_matches.3 \ - Bio::Tools::Run::PiseApplication::scope.3 \ - Bio::Tools::Run::PiseApplication::scopparse.3 \ - Bio::Tools::Run::PiseApplication::seqboot.3 \ - Bio::Tools::Run::PiseApplication::seqgen.3 \ - Bio::Tools::Run::PiseApplication::seqmatchall.3 \ - Bio::Tools::Run::PiseApplication::seqsblast.3 \ - Bio::Tools::Run::PiseApplication::seqstat.3 \ - Bio::Tools::Run::PiseApplication::showalign.3 \ - Bio::Tools::Run::PiseApplication::showfeat.3 \ - Bio::Tools::Run::PiseApplication::showorf.3 \ - Bio::Tools::Run::PiseApplication::showseq.3 \ - Bio::Tools::Run::PiseApplication::shuffleseq.3 \ - Bio::Tools::Run::PiseApplication::sigcleave.3 \ - Bio::Tools::Run::PiseApplication::siggen.3 \ - Bio::Tools::Run::PiseApplication::sigscan.3 \ - Bio::Tools::Run::PiseApplication::silent.3 \ - Bio::Tools::Run::PiseApplication::sirna.3 \ - Bio::Tools::Run::PiseApplication::splitter.3 \ - Bio::Tools::Run::PiseApplication::sreformat.3 \ - Bio::Tools::Run::PiseApplication::stretcher.3 \ - Bio::Tools::Run::PiseApplication::stride.3 \ - Bio::Tools::Run::PiseApplication::stssearch.3 \ - Bio::Tools::Run::PiseApplication::supermatcher.3 \ - Bio::Tools::Run::PiseApplication::syco.3 \ - Bio::Tools::Run::PiseApplication::tacg.3 \ - Bio::Tools::Run::PiseApplication::tfscan.3 \ - Bio::Tools::Run::PiseApplication::tipdate.3 \ - Bio::Tools::Run::PiseApplication::tmap.3 \ - Bio::Tools::Run::PiseApplication::toppred.3 \ - Bio::Tools::Run::PiseApplication::tranalign.3 \ - Bio::Tools::Run::PiseApplication::transeq.3 \ - Bio::Tools::Run::PiseApplication::treealign.3 \ - Bio::Tools::Run::PiseApplication::trimest.3 \ - Bio::Tools::Run::PiseApplication::trimseq.3 \ - Bio::Tools::Run::PiseApplication::trnascan.3 \ - Bio::Tools::Run::PiseApplication::twofeat.3 \ - Bio::Tools::Run::PiseApplication::unroot.3 \ - Bio::Tools::Run::PiseApplication::vectorstrip.3 \ - Bio::Tools::Run::PiseApplication::water.3 \ - Bio::Tools::Run::PiseApplication::weighbor.3 \ - Bio::Tools::Run::PiseApplication::whichdb.3 \ - Bio::Tools::Run::PiseApplication::wise2.3 \ - Bio::Tools::Run::PiseApplication::wobble.3 \ - Bio::Tools::Run::PiseApplication::wordcount.3 \ - Bio::Tools::Run::PiseApplication::wordmatch.3 \ - Bio::Tools::Run::PiseApplication::wublast2.3 \ - Bio::Tools::Run::PiseApplication::xblast.3 \ - Bio::Tools::Run::PiseApplication::xpound.3 \ - Bio::Tools::Run::PiseJob.3 \ - Bio::Tools::Run::PiseJobParser.3 \ - Bio::Tools::Run::PiseWorkflow.3 \ - Bio::Tools::Run::Primate.3 \ - Bio::Tools::Run::Primer3.3 \ - Bio::Tools::Run::Prints.3 \ - Bio::Tools::Run::Profile.3 \ - Bio::Tools::Run::Promoterwise.3 \ - Bio::Tools::Run::Pseudowise.3 \ - Bio::Tools::Run::RepeatMasker.3 \ - Bio::Tools::Run::Seg.3 \ - Bio::Tools::Run::Signalp.3 \ - Bio::Tools::Run::Tmhmm.3 \ - Bio::Tools::Run::TribeMCL.3 \ - Bio::Tools::Run::Vista.3 +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 # now install all extra stuff (docs, examples, scripts) post-install: ${MKDIR} ${DATADIR} @${CP} -Rv ${WRKSRC}/scripts ${DATADIR} - ${MKDIR} ${EXAMPLESDIR} - @${CP} -Rv ${WRKSRC}/examples/* ${EXAMPLESDIR} .if !defined(NOPORTDOCS) ${MKDIR} ${DOCSDIR} .for doc in AUTHORS Changes INSTALL.PROGRAMS README diff --git a/biology/p5-bioperl-run/distinfo b/biology/p5-bioperl-run/distinfo index 889ee4b564d2..b6ef133afd6e 100644 --- a/biology/p5-bioperl-run/distinfo +++ b/biology/p5-bioperl-run/distinfo @@ -1,3 +1,3 @@ -MD5 (bioperl-run-1.4.tar.gz) = 25914ab48d1ab0393ebb067a8f68a821 -SHA256 (bioperl-run-1.4.tar.gz) = 54eea327c8f80061d6c45e56b64d5c51daa20b723390eed1a3377f3a61645d86 -SIZE (bioperl-run-1.4.tar.gz) = 830774 +MD5 (BioPerl-run-1.6.1.tar.gz) = 15f53f5232b9ed58fa27662431935da8 +SHA256 (BioPerl-run-1.6.1.tar.gz) = 1ecf2f3a0dd606a1522642d6dd05f8641cd5c8788f3b53e19243f4121c4d4b80 +SIZE (BioPerl-run-1.6.1.tar.gz) = 4082463 diff --git a/biology/p5-bioperl-run/pkg-plist b/biology/p5-bioperl-run/pkg-plist index ddc2754cc27a..eb1451a811cd 100644 --- a/biology/p5-bioperl-run/pkg-plist +++ b/biology/p5-bioperl-run/pkg-plist @@ -1,366 +1,128 @@ +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%%/ %%SITE_PERL%%/Bio/Factory/EMBOSS.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/Lagan.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/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/Kalign.pm +%%SITE_PERL%%/Bio/Tools/Run/Alignment/MAFFT.pm %%SITE_PERL%%/Bio/Tools/Run/Alignment/TCoffee.pm -%%SITE_PERL%%/Bio/Tools/Run/Analysis.pm +%%SITE_PERL%%/Bio/Tools/Run/Alignment/Lagan.pm +%%SITE_PERL%%/Bio/Tools/Run/Alignment/Proda.pm +%%SITE_PERL%%/Bio/Tools/Run/Alignment/Exonerate.pm %%SITE_PERL%%/Bio/Tools/Run/Analysis/soap.pm -%%SITE_PERL%%/Bio/Tools/Run/AnalysisFactory.pm -%%SITE_PERL%%/Bio/Tools/Run/AnalysisFactory/Pise.pm %%SITE_PERL%%/Bio/Tools/Run/AnalysisFactory/soap.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/Eponine.pm -%%SITE_PERL%%/Bio/Tools/Run/FootPrinter.pm -%%SITE_PERL%%/Bio/Tools/Run/Genewise.pm -%%SITE_PERL%%/Bio/Tools/Run/Genscan.pm -%%SITE_PERL%%/Bio/Tools/Run/Hmmer.pm -%%SITE_PERL%%/Bio/Tools/Run/Hmmpfam.pm -%%SITE_PERL%%/Bio/Tools/Run/Mdust.pm +%%SITE_PERL%%/Bio/Tools/Run/Phylo/Hyphy/REL.pm +%%SITE_PERL%%/Bio/Tools/Run/Phylo/Hyphy/Base.pm 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