Embarrassingly long overdue update to 0.7.0, including optional support for
GUI (Tk) and CORBA extensions.
This commit is contained in:
Johann Visagie
parent
092f55b30a
commit
4ff56da9dd
Notes:
svn2git
2021-03-31 03:12:20 +00:00
svn path=/head/; revision=44463
@ -6,78 +6,166 @@
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#
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PORTNAME= bioperl
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PORTVERSION= 0.6.2
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PORTVERSION= 0.7.0
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CATEGORIES= biology perl5
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MASTER_SITES= ftp://bio.perl.org/pub/DIST/ \
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http://bio.perl.org/Core/Latest/ \
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MASTER_SITES= ftp://bioperl.org/pub/DIST/ \
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http://bioperl.org/Core/Latest/ \
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${MASTER_SITE_PERL_CPAN}
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MASTER_SITE_SUBDIR=Bio
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MASTER_SITE_SUBDIR= Bio
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PKGNAMEPREFIX= p5-
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DISTFILES= ${DISTNAME}${EXTRACT_SUFX} bioperl-ext-0.6.tar.gz
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DISTFILES= ${DISTNAME}${EXTRACT_SUFX}
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MAINTAINER= johann@egenetics.com
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MAINTAINER= wjv@FreeBSD.org
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BUILD_DEPENDS= ${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/HTTP/Request/Common.pm:${PORTSDIR}/www/p5-libwww \
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BUILD_DEPENDS= ${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/${PERL_ARCH}/Ace.pm:${PORTSDIR}/biology/p5-AcePerl \
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${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/${PERL_ARCH}/XML/Parser.pm:${PORTSDIR}/textproc/p5-XML-Parser \
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${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/File/Temp.pm:${PORTSDIR}/devel/p5-File-Temp \
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${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/HTTP/Request/Common.pm:${PORTSDIR}/www/p5-libwww \
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${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/IO/Scalar.pm:${PORTSDIR}/devel/p5-IO-stringy \
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${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/IO/String.pm:${PORTSDIR}/devel/p5-IO-String \
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${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/LWP/UserAgent.pm:${PORTSDIR}/www/p5-libwww \
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${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/${PERL_ARCH}/Ace.pm:${PORTSDIR}/biology/p5-AcePerl \
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${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/IO/Scalar.pm:${PORTSDIR}/devel/p5-IO-stringy
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${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/XML/Node.pm:${PORTSDIR}/textproc/p5-XML-Node \
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${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/XML/Parser/PerlSAX.pm:${PORTSDIR}/textproc/p5-libxml \
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${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/XML/Writer.pm:${PORTSDIR}/textproc/p5-XML-Writer
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PERL_CONFIGURE= YES
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MAN3= Bio::Annotation.3 Bio::Annotation::Comment.3 \
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Bio::Annotation::DBLink.3 Bio::Annotation::Reference.3 \
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Bio::DB::Ace.3 Bio::DB::GenBank.3 Bio::DB::GenPept.3 \
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Bio::DB::RandomAccessI.3 Bio::DB::SeqI.3 \
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Bio::Index::Abstract.3 Bio::Index::AbstractSeq.3 \
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Bio::Index::EMBL.3 Bio::Index::Fasta.3 \
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Bio::Index::SwissPfam.3 Bio::LocatableSeq.3 \
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Bio::PrimarySeq.3 Bio::PrimarySeqI.3 Bio::Range.3 \
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Bio::RangeI.3 Bio::Root::Err.3 Bio::Root::Global.3 \
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Bio::Root::IOManager.3 Bio::Root::Object.3 \
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Bio::Root::RootI.3 Bio::Root::Utilities.3 \
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Bio::Root::Vector.3 Bio::Root::Xref.3 \
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Bio::Search::Hit::Fasta.3 Bio::Search::Hit::HitI.3 \
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Bio::Search::Processor.3 Bio::Search::Processor::Fasta.3 \
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Bio::Search::Processor::ProcessorI.3 \
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Bio::Search::Result::Fasta.3 \
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Bio::Search::Result::ResultI.3 Bio::SearchDist.3 \
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Bio::Seq.3 Bio::SeqFeature::FeaturePair.3 \
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Bio::SeqFeature::Generic.3 Bio::SeqFeatureI.3 Bio::SeqI.3 \
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Bio::SeqIO.3 Bio::SeqIO::FTHelper.3 \
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Bio::SeqIO::MultiFile.3 Bio::SeqIO::embl.3 \
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Bio::SeqIO::fasta.3 Bio::SeqIO::gcg.3 \
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Bio::SeqIO::genbank.3 Bio::SeqIO::pir.3 Bio::SeqIO::raw.3 \
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Bio::SeqIO::scf.3 Bio::SeqIO::swiss.3 Bio::SimpleAlign.3 \
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Bio::Species.3 Bio::Tools::AlignFactory.3 \
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Bio::Tools::Blast.3 Bio::Tools::Blast::HSP.3 \
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Bio::Tools::Blast::HTML.3 \
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Bio::Tools::Blast::Run::LocalBlast.3 \
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Bio::Tools::Blast::Run::Webblast.3 \
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Bio::Tools::Blast::Sbjct.3 Bio::Tools::CodonTable.3 \
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Bio::Tools::Fasta.3 Bio::Tools::HMMER::Domain.3 \
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Bio::Tools::HMMER::Results.3 Bio::Tools::HMMER::Set.3 \
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Bio::Tools::IUPAC.3 Bio::Tools::RestrictionEnzyme.3 \
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Bio::Tools::SeqAnal.3 Bio::Tools::SeqPattern.3 \
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Bio::Tools::SeqStats.3 Bio::Tools::SeqWords.3 \
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Bio::Tools::Sigcleave.3 Bio::Tools::WWW.3 \
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Bio::Tools::pSW.3 Bio::UnivAln.3 \
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bioback.3 biodesign.3 bioperl.3 biostart.3
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MANPREFIX= ${PREFIX}/lib/perl5/${PERL_VERSION}
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.if defined(WITH_CORBA)
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WITH_CORBA_CLIENT= YES
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WITH_CORBA_SERVER= YES
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.endif
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EXT_VERSION= 0.6
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CORBA_CLIENT_VERSION= 0.2
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CORBA_SERVER_VERSION= 0.2
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GUI_VERSION= 0.7
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DISTFILES+= bioperl-ext-${EXT_VERSION}${EXTRACT_SUFX}
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EXT_WRKSRC= ${WRKDIR}/bioperl-ext-06/Bio/Ext/Align
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.if defined(WITH_CORBA_CLIENT)
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BUILD_DEPENDS+= ${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/${PERL_ARCH}/CORBA/ORBit.pm:${PORTSDIR}/devel/p5-ORBit
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.endif
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.if defined(WITH_CORBA_SERVER)
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BUILD_DEPENDS+= ${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/${PERL_ARCH}/CORBA/ORBit.pm:${PORTSDIR}/devel/p5-ORBit
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.endif
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.if defined(WITH_GUI)
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RUN_DEPENDS+= ptksh:${PORTSDIR}/x11-toolkits/p5-Tk
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.endif
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.for ext in CORBA_CLIENT CORBA_SERVER GUI
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.if defined(WITH_${ext})
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EXTLIST+= ${ext}
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DISTFILES+= bioperl-${ext:L:S/_/-/}-${${ext}_VERSION}${EXTRACT_SUFX}
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${ext}_WRKSRC= ${WRKDIR}/bioperl-${ext:L:S/_/-/}
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PLIST_${ext}= ""
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.else
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PLIST_${ext}= "@comment "
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.endif
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PLIST_SUB+= PLIST_${ext}=${PLIST_${ext}}
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.endfor
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MAN3= Bio::AlignIO.3 Bio::AlignIO::bl2seq.3 \
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Bio::AlignIO::clustalw.3 Bio::AlignIO::fasta.3 \
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Bio::AlignIO::mase.3 Bio::AlignIO::msf.3 Bio::AlignIO::pfam.3 \
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Bio::AlignIO::prodom.3 Bio::AlignIO::selex.3 \
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Bio::AlignIO::stockholm.3 Bio::DB::GDB.3 \
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Bio::DB::NCBIHelper.3 Bio::DB::SwissProt.3 \
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Bio::DB::UpdateableSeqI.3 Bio::DB::WebDBSeqI.3 \
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Bio::DBLinkContainerI.3 Bio::Factory::DriverFactory.3 \
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Bio::Factory::SeqAnalysisParserFactory.3 \
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Bio::Factory::SeqAnalysisParserFactoryI.3 \
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Bio::Index::GenBank.3 Bio::Index::Swissprot.3 \
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Bio::LiveSeq::AARange.3 Bio::LiveSeq::Chain.3 \
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Bio::LiveSeq::ChainI.3 Bio::LiveSeq::DNA.3 \
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Bio::LiveSeq::Exon.3 Bio::LiveSeq::Gene.3 \
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Bio::LiveSeq::IO::BioPerl.3 Bio::LiveSeq::IO::Loader.3 \
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Bio::LiveSeq::IO::SRS.3 Bio::LiveSeq::Intron.3 \
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Bio::LiveSeq::Mutation.3 Bio::LiveSeq::Mutator.3 \
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Bio::LiveSeq::Prim_Transcript.3 Bio::LiveSeq::Range.3 \
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Bio::LiveSeq::Repeat_Region.3 Bio::LiveSeq::Repeat_Unit.3 \
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Bio::LiveSeq::SeqI.3 Bio::LiveSeq::Transcript.3 \
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Bio::LiveSeq::Translation.3 \
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Bio::Location::AvWithinCoordPolicy.3 \
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Bio::Location::CoordinatePolicyI.3 Bio::Location::Fuzzy.3 \
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Bio::Location::FuzzyLocationI.3 \
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Bio::Location::NarrowestCoordPolicy.3 Bio::Location::Simple.3 \
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Bio::Location::Split.3 Bio::Location::SplitLocationI.3 \
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Bio::Location::WidestCoordPolicy.3 Bio::LocationI.3 \
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Bio::Root::IO.3 Bio::Seq::LargePrimarySeq.3 \
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Bio::Seq::LargeSeq.3 Bio::Seq::RichSeq.3 Bio::Seq::RichSeqI.3 \
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Bio::SeqAnalysisParserI.3 Bio::SeqFeature::Gene::Exon.3 \
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Bio::SeqFeature::Gene::ExonI.3 \
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Bio::SeqFeature::Gene::GeneStructure.3 \
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Bio::SeqFeature::Gene::GeneStructureI.3 \
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Bio::SeqFeature::Gene::Transcript.3 \
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Bio::SeqFeature::Gene::TranscriptI.3 \
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Bio::SeqFeature::Similarity.3 \
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Bio::SeqFeature::SimilarityPair.3 Bio::SeqIO::ace.3 \
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Bio::SeqIO::game.3 Bio::SeqIO::largefasta.3 Bio::SeqUtils.3 \
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Bio::Tools::AnalysisResult.3 Bio::Tools::BPbl2seq.3 \
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Bio::Tools::BPlite.3 Bio::Tools::BPlite::Iteration.3 \
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Bio::Tools::BPpsilite.3 Bio::Tools::ESTScan.3 \
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Bio::Tools::GFF.3 Bio::Tools::Genscan.3 Bio::Tools::MZEF.3 \
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Bio::Tools::OddCodes.3 Bio::Tools::Prediction::Exon.3 \
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Bio::Tools::Prediction::Gene.3 \
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Bio::Tools::Run::Alignment::Clustalw.3 \
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Bio::Tools::Run::Alignment::TCoffee.3 \
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Bio::Tools::Run::StandAloneBlast.3 Bio::Tools::Sim4::Exon.3 \
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Bio::Tools::Sim4::Results.3 Bio::Variation::AAChange.3 \
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Bio::Variation::AAReverseMutate.3 Bio::Variation::Allele.3 \
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Bio::Variation::DNAMutation.3 Bio::Variation::IO.3 \
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Bio::Variation::IO::flat.3 Bio::Variation::IO::xml.3 \
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Bio::Variation::RNAChange.3 Bio::Variation::SeqDiff.3 \
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Bio::Variation::VariantI.3 bptutorial.3
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.if defined(WITH_CORBA_CLIENT)
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MAN3+= Bio::CorbaClient::PrimarySeq.3 Bio::CorbaClient::Seq.3 \
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Bio::CorbaClient::SeqFeature.3 Bio::CorbaClient::Base.3 \
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Bio::SeqIO::biocorba.3 Bio::DB::Biocorba.3 \
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Bio::CorbaClient::Client.3 Bio::CorbaClient::ORB.3
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.endif
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.if defined(WITH_CORBA_SERVER)
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MAN3+= Bio::CorbaServer::BioEnv.3 Bio::CorbaServer::AnonymousSeq.3 \
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Bio::CorbaServer::PrimarySeq.3 Bio::CorbaServer::SeqFeature.3 \
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Bio::CorbaServer::PrimarySeqDB.3 \
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Bio::CorbaServer::PrimarySeqIterator.3 \
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Bio::CorbaServer::PrimarySeqVector.3 \
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Bio::CorbaServer::Seq.3 \
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Bio::CorbaServer::SeqDB.3 Bio::CorbaServer::Base.3 \
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Bio::CorbaServer::SeqFeatureIterator.3 \
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Bio::CorbaServer::SeqFeatureVector.3 \
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Bio::CorbaServer::Server.3
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.endif
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.if defined(WITH_GUI)
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MAN3+= Bio::Tk::HitDisplay.3 Bio::Tk::SeqCanvas.3
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.endif
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MANPREFIX= ${PREFIX}/lib/perl5/${PERL_VERSION}
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post-configure:
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@ (cd ${EXT_WRKSRC} && \
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@ cd ${EXT_WRKSRC} && \
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${SETENV} ${CONFIGURE_ENV} \
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${PERL5} ${CONFIGURE_SCRIPT} ${CONFIGURE_ARGS})
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${PERL5} ./${CONFIGURE_SCRIPT} ${CONFIGURE_ARGS}
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.for ext in ${EXTLIST}
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@ cd ${${ext}_WRKSRC} && \
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${PERL5} ./${CONFIGURE_SCRIPT} ${CONFIGURE_ARGS}
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.endfor
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post-build:
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@ (cd ${EXT_WRKSRC} && \
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${MAKE} ${MAKE_FLAGS} ${MAKEFILE} ${MAKE_ARGS} ${ALL_TARGET})
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@ cd ${EXT_WRKSRC} && \
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${MAKE} ${MAKE_FLAGS} ${MAKEFILE} ${MAKE_ARGS} ${ALL_TARGET}
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.for ext in ${EXTLIST}
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@ cd ${${ext}_WRKSRC} && ${SETENV} ${MAKE_ENV} \
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${MAKE} ${MAKE_FLAGS} ${MAKEFILE} ${MAKE_ARGS} ${ALL_TARGET}
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.endfor
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post-install:
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@ (cd ${EXT_WRKSRC} && \
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@ cd ${EXT_WRKSRC} && \
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${SETENV} ${MAKE_ENV} ${MAKE} ${MAKE_FLAGS} \
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${MAKEFILE} ${MAKE_ARGS} ${INSTALL_TARGET})
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${MAKEFILE} ${MAKE_ARGS} ${INSTALL_TARGET}
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.for ext in ${EXTLIST}
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@ cd ${${ext}_WRKSRC} && \
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${SETENV} ${MAKE_ENV} ${MAKE} ${MAKE_FLAGS} \
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${MAKEFILE} ${MAKE_ARGS} ${INSTALL_TARGET}
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.endfor
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.include <bsd.port.mk>
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@ -1,2 +1,5 @@
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MD5 (bioperl-0.6.2.tar.gz) = 26330f4f0c1e08a4f5cbcbe8b05b72f1
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MD5 (bioperl-0.7.0.tar.gz) = 10b4d196346495fdd6f4337bac115776
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MD5 (bioperl-ext-0.6.tar.gz) = 5bf87e0cf94d3d41fabbfd209971d240
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MD5 (bioperl-corba-client-0.2.tar.gz) = 9635488e779d771bc5f976bf56826590
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MD5 (bioperl-corba-server-0.2.tar.gz) = d5e3353ed6c8717de06e0db8f5bbc0f5
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MD5 (bioperl-gui-0.7.tar.gz) = 07b50934c5dc8fcbbb89d2d35c758dea
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@ -1,62 +1,166 @@
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%%PLIST_CORBA_CLIENT%%lib/perl5/site_perl/5.6.0/Bio/CorbaClient/Base.pm
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%%PLIST_CORBA_CLIENT%%lib/perl5/site_perl/5.6.0/Bio/CorbaClient/Client.pm
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%%PLIST_CORBA_CLIENT%%lib/perl5/site_perl/5.6.0/Bio/CorbaClient/ORB.pm
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%%PLIST_CORBA_CLIENT%%lib/perl5/site_perl/5.6.0/Bio/CorbaClient/PrimarySeq.pm
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%%PLIST_CORBA_CLIENT%%lib/perl5/site_perl/5.6.0/Bio/CorbaClient/Seq.pm
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%%PLIST_CORBA_CLIENT%%lib/perl5/site_perl/5.6.0/Bio/CorbaClient/SeqFeature.pm
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%%PLIST_CORBA_CLIENT%%lib/perl5/site_perl/5.6.0/Bio/DB/Biocorba.pm
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%%PLIST_CORBA_CLIENT%%lib/perl5/site_perl/5.6.0/Bio/SeqIO/biocorba.pm
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%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/5.6.0/Bio/CorbaServer/AnonymousSeq.pm
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%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/5.6.0/Bio/CorbaServer/Base.pm
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%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/5.6.0/Bio/CorbaServer/BioEnv.pm
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%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/5.6.0/Bio/CorbaServer/PrimarySeq.pm
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%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/5.6.0/Bio/CorbaServer/PrimarySeqDB.pm
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%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/5.6.0/Bio/CorbaServer/PrimarySeqIterator.pm
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%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/5.6.0/Bio/CorbaServer/PrimarySeqVector.pm
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%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/5.6.0/Bio/CorbaServer/Seq.pm
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%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/5.6.0/Bio/CorbaServer/SeqDB.pm
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%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/5.6.0/Bio/CorbaServer/SeqFeature.pm
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%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/5.6.0/Bio/CorbaServer/SeqFeatureIterator.pm
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%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/5.6.0/Bio/CorbaServer/SeqFeatureVector.pm
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||||
%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/5.6.0/Bio/CorbaServer/Server.pm
|
||||
%%PLIST_GUI%%lib/perl5/site_perl/5.6.0/Bio/Tk/AnnotMap.pm
|
||||
%%PLIST_GUI%%lib/perl5/site_perl/5.6.0/Bio/Tk/BioTkPerl8_1.pm
|
||||
%%PLIST_GUI%%lib/perl5/site_perl/5.6.0/Bio/Tk/GO_Browser.pm
|
||||
%%PLIST_GUI%%lib/perl5/site_perl/5.6.0/Bio/Tk/HitDisplay.pm
|
||||
%%PLIST_GUI%%lib/perl5/site_perl/5.6.0/Bio/Tk/README
|
||||
%%PLIST_GUI%%lib/perl5/site_perl/5.6.0/Bio/Tk/SeqCanvas.pm
|
||||
%%PLIST_GUI%%lib/perl5/site_perl/5.6.0/Bio/Tk/Tkpsh.pl
|
||||
%%PLIST_GUI%%lib/perl5/site_perl/5.6.0/Bio/Tk/bioTk_Map.pm
|
||||
%%PLIST_GUI%%lib/perl5/site_perl/5.6.0/Bio/Tk/bioTk_SeqSubs.pm
|
||||
%%PLIST_GUI%%lib/perl5/site_perl/5.6.0/Bio/Tk/bioTk_Sequence.pm
|
||||
%%PLIST_GUI%%lib/perl5/site_perl/5.6.0/Bio/Tk/bioTk_Utilities.pm
|
||||
%%PLIST_GUI%%lib/perl5/site_perl/5.6.0/mach/auto/Bio/Tk/.packlist
|
||||
lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Bio/Ext/Align.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio/.packlist
|
||||
lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio/Ext/Align/.packlist
|
||||
lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio/Ext/Align/Align.bs
|
||||
lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio/Ext/Align/Align.so
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/AlignIO.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/AlignIO/bl2seq.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/AlignIO/clustalw.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/AlignIO/fasta.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/AlignIO/mase.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/AlignIO/msf.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/AlignIO/pfam.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/AlignIO/prodom.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/AlignIO/selex.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/AlignIO/stockholm.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Annotation.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Annotation/Comment.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Annotation/DBLink.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Annotation/Reference.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/DB/Ace.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/DB/GDB.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/DB/GenBank.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/DB/GenPept.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/DB/NCBIHelper.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/DB/RandomAccessI.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/DB/SeqI.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/DB/SwissProt.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/DB/UpdateableSeqI.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/DB/WebDBSeqI.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/DBLinkContainerI.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Factory/DriverFactory.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Factory/SeqAnalysisParserFactory.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Factory/SeqAnalysisParserFactoryI.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Index/Abstract.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Index/AbstractSeq.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Index/EMBL.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Index/Fasta.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Index/GenBank.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Index/SwissPfam.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Index/Swissprot.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/AARange.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/Chain.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/ChainI.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/DNA.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/Exon.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/Gene.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/IO/BioPerl.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/IO/Loader.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/IO/SRS.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/Intron.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/Mutation.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/Mutator.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/Prim_Transcript.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/Range.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/Repeat_Region.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/Repeat_Unit.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/SeqI.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/Transcript.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/Translation.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/LocatableSeq.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Location/AvWithinCoordPolicy.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Location/CoordinatePolicyI.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Location/Fuzzy.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Location/FuzzyLocationI.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Location/NarrowestCoordPolicy.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Location/Simple.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Location/Split.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Location/SplitLocationI.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Location/WidestCoordPolicy.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/LocationI.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/PrimarySeq.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/PrimarySeqI.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Range.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/RangeI.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Root/Err.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Root/Global.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Root/IO.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Root/IOManager.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Root/Object.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Root/RootI.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Root/Utilities.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Root/Vector.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Root/Xref.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Hit/Fasta.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Hit/HitI.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Processor.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Processor/Fasta.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Processor/ProcessorI.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Result/Fasta.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Result/ResultI.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/SearchDist.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Seq.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Seq/LargePrimarySeq.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Seq/LargeSeq.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Seq/RichSeq.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Seq/RichSeqI.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqAnalysisParserI.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeature/FeaturePair.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeature/Gene/Exon.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeature/Gene/ExonI.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeature/Gene/GeneStructure.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeature/Gene/GeneStructureI.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeature/Gene/Transcript.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeature/Gene/TranscriptI.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeature/Generic.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeature/Similarity.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeature/SimilarityPair.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeatureI.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqI.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/FTHelper.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/MultiFile.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/ace.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/embl.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/fasta.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/game.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/game/featureHandler.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/game/idHandler.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/game/seqHandler.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/gcg.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/genbank.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/largefasta.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/pir.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/raw.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/scf.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/swiss.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqUtils.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/SimpleAlign.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Species.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/AlignFactory.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/AnalysisResult.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/BPbl2seq.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/BPlite.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/BPlite/HSP.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/BPlite/Iteration.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/BPlite/Sbjct.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/BPpsilite.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/CHANGES
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/HSP.pm
|
||||
@ -68,38 +172,77 @@ lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/Run/Webblast.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/Run/postclient.pl
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/Sbjct.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/CodonTable.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/ESTScan.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Fasta.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/GFF.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Genscan.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/HMMER/Domain.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/HMMER/Results.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/HMMER/Set.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/IUPAC.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/MZEF.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/OddCodes.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Prediction/Exon.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Prediction/Gene.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/RestrictionEnzyme.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Run/Alignment/Clustalw.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Run/Alignment/TCoffee.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Run/StandAloneBlast.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/SeqAnal.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/SeqPattern.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/SeqStats.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/SeqWords.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Sigcleave.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Sim4/Exon.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Sim4/Results.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/WWW.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/pSW.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/UnivAln.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Variation/AAChange.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Variation/AAReverseMutate.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Variation/Allele.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Variation/DNAMutation.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Variation/IO.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Variation/IO/flat.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Variation/IO/xml.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Variation/README
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Variation/RNAChange.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Variation/SeqDiff.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/Bio/Variation/VariantI.pm
|
||||
lib/perl5/site_perl/%%PERL_VER%%/bioback.pod
|
||||
lib/perl5/site_perl/%%PERL_VER%%/biodesign.pod
|
||||
lib/perl5/site_perl/%%PERL_VER%%/bioperl.pod
|
||||
lib/perl5/site_perl/%%PERL_VER%%/biostart.pod
|
||||
lib/perl5/site_perl/%%PERL_VER%%/bptutorial.pl
|
||||
%%PLIST_GUI%%@dirrm lib/perl5/site_perl/5.6.0/mach/auto/Bio/Tk
|
||||
%%PLIST_GUI%%@dirrm lib/perl5/site_perl/5.6.0/Bio/Tk
|
||||
%%PLIST_CORBA_SERVER%%@dirrm lib/perl5/site_perl/5.6.0/Bio/CorbaServer
|
||||
%%PLIST_CORBA_CLIENT%%@dirrm lib/perl5/site_perl/5.6.0/Bio/CorbaClient
|
||||
@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Variation/IO
|
||||
@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Variation
|
||||
@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Sim4
|
||||
@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Run/Alignment
|
||||
@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Run
|
||||
@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Prediction
|
||||
@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/HMMER
|
||||
@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/Run
|
||||
@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast
|
||||
@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/BPlite
|
||||
@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools
|
||||
@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/game
|
||||
@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO
|
||||
@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeature/Gene
|
||||
@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeature
|
||||
@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Result
|
||||
@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Processor
|
||||
@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Hit
|
||||
@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Search
|
||||
@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Seq
|
||||
@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Root
|
||||
@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Location
|
||||
@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/IO
|
||||
@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq
|
||||
@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Index
|
||||
@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Factory
|
||||
@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/DB
|
||||
@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Annotation
|
||||
@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/AlignIO
|
||||
@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio
|
||||
@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio/Ext/Align
|
||||
@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio/Ext
|
||||
|
||||
Loading…
Reference in New Issue
Block a user