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-rw-r--r--biology/p5-bioperl-devel/Makefile128
-rw-r--r--biology/p5-bioperl-devel/files/Makefile.man235
2 files changed, 240 insertions, 123 deletions
diff --git a/biology/p5-bioperl-devel/Makefile b/biology/p5-bioperl-devel/Makefile
index 2a1fd99762de..555482386ca9 100644
--- a/biology/p5-bioperl-devel/Makefile
+++ b/biology/p5-bioperl-devel/Makefile
@@ -69,128 +69,10 @@ PLIST_${ext}= "@comment "
PLIST_SUB+= PLIST_${ext}=${PLIST_${ext}}
.endfor
-MAN3= Bio::AlignIO.3 Bio::AlignIO::bl2seq.3 \
- Bio::AlignIO::clustalw.3 Bio::AlignIO::fasta.3 \
- Bio::AlignIO::mase.3 Bio::AlignIO::meme.3 Bio::AlignIO::msf.3 \
- Bio::AlignIO::nexus.3 Bio::AlignIO::pfam.3 \
- Bio::AlignIO::phylip.3 Bio::AlignIO::prodom.3 \
- Bio::AlignIO::selex.3 Bio::AlignIO::stockholm.3 \
- Bio::Annotation.3 Bio::Annotation::Comment.3 \
- Bio::Annotation::DBLink.3 Bio::Annotation::Reference.3 \
- Bio::DB::Ace.3 Bio::DB::EMBL.3 Bio::DB::Fasta.3 \
- Bio::DB::GDB.3 Bio::DB::GFF.3 Bio::DB::GFF::Adaptor::dbi.3 \
- Bio::DB::GFF::Aggregator.3 \
- Bio::DB::GFF::Aggregator::alignment.3 \
- Bio::DB::GFF::Aggregator::clone.3 \
- Bio::DB::GFF::Aggregator::none.3 \
- Bio::DB::GFF::Aggregator::transcript.3 \
- Bio::DB::GFF::Featname.3 Bio::DB::GFF::Feature.3 \
- Bio::DB::GFF::Homol.3 Bio::DB::GFF::RelSegment.3 \
- Bio::DB::GFF::Segment.3 Bio::DB::GFF::Typename.3 \
- Bio::DB::GenBank.3 Bio::DB::GenPept.3 Bio::DB::NCBIHelper.3 \
- Bio::DB::RandomAccessI.3 Bio::DB::SeqI.3 Bio::DB::SwissProt.3 \
- Bio::DB::Universal.3 Bio::DB::UpdateableSeqI.3 \
- Bio::DB::WebDBSeqI.3 Bio::DBLinkContainerI.3 \
- Bio::Factory::ApplicationFactoryI.3 \
- Bio::Factory::DriverFactory.3 Bio::Factory::EMBOSS.3 \
- Bio::Factory::SeqAnalysisParserFactory.3 \
- Bio::Factory::SeqAnalysisParserFactoryI.3 \
- Bio::Index::Abstract.3 Bio::Index::AbstractSeq.3 \
- Bio::Index::EMBL.3 Bio::Index::Fasta.3 Bio::Index::GenBank.3 \
- Bio::Index::SwissPfam.3 Bio::Index::Swissprot.3 \
- Bio::LiveSeq::AARange.3 Bio::LiveSeq::Chain.3 \
- Bio::LiveSeq::ChainI.3 Bio::LiveSeq::DNA.3 \
- Bio::LiveSeq::Exon.3 Bio::LiveSeq::Gene.3 \
- Bio::LiveSeq::IO::BioPerl.3 Bio::LiveSeq::IO::Loader.3 \
- Bio::LiveSeq::IO::SRS.3 Bio::LiveSeq::Intron.3 \
- Bio::LiveSeq::Mutation.3 Bio::LiveSeq::Mutator.3 \
- Bio::LiveSeq::Prim_Transcript.3 Bio::LiveSeq::Range.3 \
- Bio::LiveSeq::Repeat_Region.3 Bio::LiveSeq::Repeat_Unit.3 \
- Bio::LiveSeq::SeqI.3 Bio::LiveSeq::Transcript.3 \
- Bio::LiveSeq::Translation.3 Bio::LocatableSeq.3 \
- Bio::Location::AvWithinCoordPolicy.3 \
- Bio::Location::CoordinatePolicyI.3 Bio::Location::Fuzzy.3 \
- Bio::Location::FuzzyLocationI.3 \
- Bio::Location::NarrowestCoordPolicy.3 Bio::Location::Simple.3 \
- Bio::Location::Split.3 Bio::Location::SplitLocationI.3 \
- Bio::Location::WidestCoordPolicy.3 Bio::LocationI.3 \
- Bio::PrimarySeq.3 Bio::PrimarySeqI.3 Bio::Range.3 \
- Bio::RangeI.3 Bio::Root::Err.3 Bio::Root::Global.3 \
- Bio::Root::IO.3 Bio::Root::IOManager.3 Bio::Root::Object.3 \
- Bio::Root::RootI.3 Bio::Root::Utilities.3 Bio::Root::Vector.3 \
- Bio::Root::Xref.3 Bio::SearchDist.3 Bio::Seq.3 \
- Bio::Seq::LargePrimarySeq.3 Bio::Seq::LargeSeq.3 \
- Bio::Seq::RichSeq.3 Bio::Seq::RichSeqI.3 \
- Bio::SeqAnalysisParserI.3 Bio::SeqFeature::Computation.3 \
- Bio::SeqFeature::Exon.3 Bio::SeqFeature::FeaturePair.3 \
- Bio::SeqFeature::Gene::Exon.3 Bio::SeqFeature::Gene::ExonI.3 \
- Bio::SeqFeature::Gene::GeneStructure.3 \
- Bio::SeqFeature::Gene::GeneStructureI.3 \
- Bio::SeqFeature::Gene::Transcript.3 \
- Bio::SeqFeature::Gene::TranscriptI.3 \
- Bio::SeqFeature::Generic.3 Bio::SeqFeature::Intron.3 \
- Bio::SeqFeature::PolyA.3 Bio::SeqFeature::Promoter.3 \
- Bio::SeqFeature::Similarity.3 \
- Bio::SeqFeature::SimilarityPair.3 Bio::SeqFeature::UTR3.3 \
- Bio::SeqFeature::UTR5.3 Bio::SeqFeatureI.3 Bio::SeqI.3 \
- Bio::SeqIO.3 Bio::SeqIO::FTHelper.3 Bio::SeqIO::MultiFile.3 \
- Bio::SeqIO::ace.3 Bio::SeqIO::embl.3 Bio::SeqIO::fasta.3 \
- Bio::SeqIO::game.3 Bio::SeqIO::game::featureHandler.3 \
- Bio::SeqIO::game::idHandler.3 Bio::SeqIO::game::seqHandler.3 \
- Bio::SeqIO::gcg.3 Bio::SeqIO::genbank.3 \
- Bio::SeqIO::largefasta.3 Bio::SeqIO::pir.3 Bio::SeqIO::raw.3 \
- Bio::SeqIO::scf.3 Bio::SeqIO::swiss.3 Bio::SeqUtils.3 \
- Bio::SimpleAlign.3 Bio::Species.3 Bio::Tools::AlignFactory.3 \
- Bio::Tools::AnalysisResult.3 Bio::Tools::BPbl2seq.3 \
- Bio::Tools::BPlite.3 Bio::Tools::BPlite::Iteration.3 \
- Bio::Tools::BPpsilite.3 Bio::Tools::Blast.3 \
- Bio::Tools::Blast::HSP.3 Bio::Tools::Blast::HTML.3 \
- Bio::Tools::Blast::Run::LocalBlast.3 \
- Bio::Tools::Blast::Run::Webblast.3 Bio::Tools::Blast::Sbjct.3 \
- Bio::Tools::CodonTable.3 Bio::Tools::EPCR.3 \
- Bio::Tools::ESTScan.3 Bio::Tools::Fasta.3 Bio::Tools::GFF.3 \
- Bio::Tools::Genemark.3 Bio::Tools::Genscan.3 \
- Bio::Tools::Grail.3 Bio::Tools::HMMER::Domain.3 \
- Bio::Tools::HMMER::Results.3 Bio::Tools::HMMER::Set.3 \
- Bio::Tools::IUPAC.3 Bio::Tools::MZEF.3 Bio::Tools::OddCodes.3 \
- Bio::Tools::Prediction::Exon.3 Bio::Tools::Prediction::Gene.3 \
- Bio::Tools::RestrictionEnzyme.3 \
- Bio::Tools::Run::Alignment::Clustalw.3 \
- Bio::Tools::Run::Alignment::TCoffee.3 \
- Bio::Tools::Run::EMBOSSApplication.3 \
- Bio::Tools::Run::RemoteBlast.3 \
- Bio::Tools::Run::StandAloneBlast.3 Bio::Tools::SeqAnal.3 \
- Bio::Tools::SeqPattern.3 Bio::Tools::SeqStats.3 \
- Bio::Tools::SeqWords.3 Bio::Tools::Sigcleave.3 \
- Bio::Tools::Sim4::Exon.3 Bio::Tools::Sim4::Results.3 \
- Bio::Tools::WWW.3 Bio::Tools::pSW.3 Bio::UnivAln.3 \
- Bio::Variation::AAChange.3 Bio::Variation::AAReverseMutate.3 \
- Bio::Variation::Allele.3 Bio::Variation::DNAMutation.3 \
- Bio::Variation::IO.3 Bio::Variation::IO::flat.3 \
- Bio::Variation::IO::xml.3 Bio::Variation::RNAChange.3 \
- Bio::Variation::SeqDiff.3 Bio::Variation::VariantI.3 \
- bioback.3 biodesign.3 bioperl.3 biostart.3 bptutorial.3
-.if defined(WITH_CORBA_CLIENT)
-MAN3+= Bio::CorbaClient::PrimarySeq.3 Bio::CorbaClient::Seq.3 \
- Bio::CorbaClient::SeqFeature.3 Bio::CorbaClient::Base.3 \
- Bio::SeqIO::biocorba.3 Bio::DB::Biocorba.3 \
- Bio::CorbaClient::Client.3 Bio::CorbaClient::ORB.3
-.endif
-.if defined(WITH_CORBA_SERVER)
-MAN3+= Bio::CorbaServer::BioEnv.3 Bio::CorbaServer::AnonymousSeq.3 \
- Bio::CorbaServer::PrimarySeq.3 Bio::CorbaServer::SeqFeature.3 \
- Bio::CorbaServer::PrimarySeqDB.3 \
- Bio::CorbaServer::PrimarySeqIterator.3 \
- Bio::CorbaServer::PrimarySeqVector.3 \
- Bio::CorbaServer::Seq.3 \
- Bio::CorbaServer::SeqDB.3 Bio::CorbaServer::Base.3 \
- Bio::CorbaServer::SeqFeatureIterator.3 \
- Bio::CorbaServer::SeqFeatureVector.3 \
- Bio::CorbaServer::Server.3
-.endif
-.if defined(WITH_GUI)
-MAN3+= Bio::Tk::HitDisplay.3 Bio::Tk::SeqCanvas.3
-.endif
+.include <bsd.port.pre.mk>
+
+# Include the (extremely) long list of manpages from a separate file:
+.include "${FILESDIR}/Makefile.man"
MANPREFIX= ${PREFIX}/lib/perl5/${PERL_VERSION}
pre-fetch:
@@ -227,4 +109,4 @@ post-install:
${MAKEFILE} ${MAKE_ARGS} ${INSTALL_TARGET}
.endfor
-.include <bsd.port.mk>
+.include <bsd.port.post.mk>
diff --git a/biology/p5-bioperl-devel/files/Makefile.man b/biology/p5-bioperl-devel/files/Makefile.man
new file mode 100644
index 000000000000..4d3b300f0cb9
--- /dev/null
+++ b/biology/p5-bioperl-devel/files/Makefile.man
@@ -0,0 +1,235 @@
+# $FreeBSD$
+
+MAN3= Bio::AlignIO.3 \
+ Bio::AlignIO::bl2seq.3 \
+ Bio::AlignIO::clustalw.3 \
+ Bio::AlignIO::fasta.3 \
+ Bio::AlignIO::mase.3 \
+ Bio::AlignIO::meme.3 \
+ Bio::AlignIO::msf.3 \
+ Bio::AlignIO::nexus.3 \
+ Bio::AlignIO::pfam.3 \
+ Bio::AlignIO::phylip.3 \
+ Bio::AlignIO::prodom.3 \
+ Bio::AlignIO::selex.3 \
+ Bio::AlignIO::stockholm.3 \
+ Bio::Annotation.3 \
+ Bio::Annotation::Comment.3 \
+ Bio::Annotation::DBLink.3 \
+ Bio::Annotation::Reference.3 \
+ Bio::DB::Ace.3 \
+ Bio::DB::EMBL.3 \
+ Bio::DB::Fasta.3 \
+ Bio::DB::GDB.3 \
+ Bio::DB::GFF.3 \
+ Bio::DB::GFF::Adaptor::dbi.3 \
+ Bio::DB::GFF::Aggregator.3 \
+ Bio::DB::GFF::Aggregator::alignment.3 \
+ Bio::DB::GFF::Aggregator::clone.3 \
+ Bio::DB::GFF::Aggregator::none.3 \
+ Bio::DB::GFF::Aggregator::transcript.3 \
+ Bio::DB::GFF::Featname.3 \
+ Bio::DB::GFF::Feature.3 \
+ Bio::DB::GFF::Homol.3 \
+ Bio::DB::GFF::RelSegment.3 \
+ Bio::DB::GFF::Segment.3 \
+ Bio::DB::GFF::Typename.3 \
+ Bio::DB::GenBank.3 \
+ Bio::DB::GenPept.3 \
+ Bio::DB::NCBIHelper.3 \
+ Bio::DB::RandomAccessI.3 \
+ Bio::DB::SeqI.3 \
+ Bio::DB::SwissProt.3 \
+ Bio::DB::Universal.3 \
+ Bio::DB::UpdateableSeqI.3 \
+ Bio::DB::WebDBSeqI.3 \
+ Bio::DBLinkContainerI.3 \
+ Bio::Factory::ApplicationFactoryI.3 \
+ Bio::Factory::DriverFactory.3 \
+ Bio::Factory::EMBOSS.3 \
+ Bio::Factory::SeqAnalysisParserFactory.3 \
+ Bio::Factory::SeqAnalysisParserFactoryI.3 \
+ Bio::Index::Abstract.3 \
+ Bio::Index::AbstractSeq.3 \
+ Bio::Index::EMBL.3 \
+ Bio::Index::Fasta.3 \
+ Bio::Index::GenBank.3 \
+ Bio::Index::SwissPfam.3 \
+ Bio::Index::Swissprot.3 \
+ Bio::LiveSeq::AARange.3 \
+ Bio::LiveSeq::Chain.3 \
+ Bio::LiveSeq::ChainI.3 \
+ Bio::LiveSeq::DNA.3 \
+ Bio::LiveSeq::Exon.3 \
+ Bio::LiveSeq::Gene.3 \
+ Bio::LiveSeq::IO::BioPerl.3 \
+ Bio::LiveSeq::IO::Loader.3 \
+ Bio::LiveSeq::IO::SRS.3 \
+ Bio::LiveSeq::Intron.3 \
+ Bio::LiveSeq::Mutation.3 \
+ Bio::LiveSeq::Mutator.3 \
+ Bio::LiveSeq::Prim_Transcript.3 \
+ Bio::LiveSeq::Range.3 \
+ Bio::LiveSeq::Repeat_Region.3 \
+ Bio::LiveSeq::Repeat_Unit.3 \
+ Bio::LiveSeq::SeqI.3 \
+ Bio::LiveSeq::Transcript.3 \
+ Bio::LiveSeq::Translation.3 \
+ Bio::LocatableSeq.3 \
+ Bio::Location::AvWithinCoordPolicy.3 \
+ Bio::Location::CoordinatePolicyI.3 \
+ Bio::Location::Fuzzy.3 \
+ Bio::Location::FuzzyLocationI.3 \
+ Bio::Location::NarrowestCoordPolicy.3 \
+ Bio::Location::Simple.3 \
+ Bio::Location::Split.3 \
+ Bio::Location::SplitLocationI.3 \
+ Bio::Location::WidestCoordPolicy.3 \
+ Bio::LocationI.3 \
+ Bio::PrimarySeq.3 \
+ Bio::PrimarySeqI.3 \
+ Bio::Range.3 \
+ Bio::RangeI.3 \
+ Bio::Root::Err.3 \
+ Bio::Root::Global.3 \
+ Bio::Root::IO.3 \
+ Bio::Root::IOManager.3 \
+ Bio::Root::Object.3 \
+ Bio::Root::RootI.3 \
+ Bio::Root::Utilities.3 \
+ Bio::Root::Vector.3 \
+ Bio::Root::Xref.3 \
+ Bio::SearchDist.3 \
+ Bio::Seq.3 \
+ Bio::Seq::LargePrimarySeq.3 \
+ Bio::Seq::LargeSeq.3 \
+ Bio::Seq::RichSeq.3 \
+ Bio::Seq::RichSeqI.3 \
+ Bio::SeqAnalysisParserI.3 \
+ Bio::SeqFeature::Computation.3 \
+ Bio::SeqFeature::Exon.3 \
+ Bio::SeqFeature::FeaturePair.3 \
+ Bio::SeqFeature::Gene::Exon.3 \
+ Bio::SeqFeature::Gene::ExonI.3 \
+ Bio::SeqFeature::Gene::GeneStructure.3 \
+ Bio::SeqFeature::Gene::GeneStructureI.3 \
+ Bio::SeqFeature::Gene::Transcript.3 \
+ Bio::SeqFeature::Gene::TranscriptI.3 \
+ Bio::SeqFeature::Generic.3 \
+ Bio::SeqFeature::Intron.3 \
+ Bio::SeqFeature::PolyA.3 \
+ Bio::SeqFeature::Promoter.3 \
+ Bio::SeqFeature::Similarity.3 \
+ Bio::SeqFeature::SimilarityPair.3 \
+ Bio::SeqFeature::UTR3.3 \
+ Bio::SeqFeature::UTR5.3 \
+ Bio::SeqFeatureI.3 \
+ Bio::SeqI.3 \
+ Bio::SeqIO.3 \
+ Bio::SeqIO::FTHelper.3 \
+ Bio::SeqIO::MultiFile.3 \
+ Bio::SeqIO::ace.3 \
+ Bio::SeqIO::embl.3 \
+ Bio::SeqIO::fasta.3 \
+ Bio::SeqIO::game.3 \
+ Bio::SeqIO::game::featureHandler.3 \
+ Bio::SeqIO::game::idHandler.3 \
+ Bio::SeqIO::game::seqHandler.3 \
+ Bio::SeqIO::gcg.3 \
+ Bio::SeqIO::genbank.3 \
+ Bio::SeqIO::largefasta.3 \
+ Bio::SeqIO::pir.3 \
+ Bio::SeqIO::raw.3 \
+ Bio::SeqIO::scf.3 \
+ Bio::SeqIO::swiss.3 \
+ Bio::SeqUtils.3 \
+ Bio::SimpleAlign.3 \
+ Bio::Species.3 \
+ Bio::Tools::AlignFactory.3 \
+ Bio::Tools::AnalysisResult.3 \
+ Bio::Tools::BPbl2seq.3 \
+ Bio::Tools::BPlite.3 \
+ Bio::Tools::BPlite::Iteration.3 \
+ Bio::Tools::BPpsilite.3 \
+ Bio::Tools::Blast.3 \
+ Bio::Tools::Blast::HSP.3 \
+ Bio::Tools::Blast::HTML.3 \
+ Bio::Tools::Blast::Run::LocalBlast.3 \
+ Bio::Tools::Blast::Run::Webblast.3 \
+ Bio::Tools::Blast::Sbjct.3 \
+ Bio::Tools::CodonTable.3 \
+ Bio::Tools::EPCR.3 \
+ Bio::Tools::ESTScan.3 \
+ Bio::Tools::Fasta.3 \
+ Bio::Tools::GFF.3 \
+ Bio::Tools::Genemark.3 \
+ Bio::Tools::Genscan.3 \
+ Bio::Tools::Grail.3 \
+ Bio::Tools::HMMER::Domain.3 \
+ Bio::Tools::HMMER::Results.3 \
+ Bio::Tools::HMMER::Set.3 \
+ Bio::Tools::IUPAC.3 \
+ Bio::Tools::MZEF.3 \
+ Bio::Tools::OddCodes.3 \
+ Bio::Tools::Prediction::Exon.3 \
+ Bio::Tools::Prediction::Gene.3 \
+ Bio::Tools::RestrictionEnzyme.3 \
+ Bio::Tools::Run::Alignment::Clustalw.3 \
+ Bio::Tools::Run::Alignment::TCoffee.3 \
+ Bio::Tools::Run::EMBOSSApplication.3 \
+ Bio::Tools::Run::RemoteBlast.3 \
+ Bio::Tools::Run::StandAloneBlast.3 \
+ Bio::Tools::SeqAnal.3 \
+ Bio::Tools::SeqPattern.3 \
+ Bio::Tools::SeqStats.3 \
+ Bio::Tools::SeqWords.3 \
+ Bio::Tools::Sigcleave.3 \
+ Bio::Tools::Sim4::Exon.3 \
+ Bio::Tools::Sim4::Results.3 \
+ Bio::Tools::WWW.3 \
+ Bio::Tools::pSW.3 \
+ Bio::UnivAln.3 \
+ Bio::Variation::AAChange.3 \
+ Bio::Variation::AAReverseMutate.3 \
+ Bio::Variation::Allele.3 \
+ Bio::Variation::DNAMutation.3 \
+ Bio::Variation::IO.3 \
+ Bio::Variation::IO::flat.3 \
+ Bio::Variation::IO::xml.3 \
+ Bio::Variation::RNAChange.3 \
+ Bio::Variation::SeqDiff.3 \
+ Bio::Variation::VariantI.3 \
+ bioback.3 \
+ biodesign.3 \
+ bioperl.3 \
+ biostart.3 \
+ bptutorial.3
+.if defined(WITH_CORBA_CLIENT)
+MAN3+= Bio::CorbaClient::PrimarySeq.3 \
+ Bio::CorbaClient::Seq.3 \
+ Bio::CorbaClient::SeqFeature.3 \
+ Bio::CorbaClient::Base.3 \
+ Bio::SeqIO::biocorba.3 \
+ Bio::DB::Biocorba.3 \
+ Bio::CorbaClient::Client.3 \
+ Bio::CorbaClient::ORB.3
+.endif
+.if defined(WITH_CORBA_SERVER)
+MAN3+= Bio::CorbaServer::BioEnv.3 \
+ Bio::CorbaServer::AnonymousSeq.3 \
+ Bio::CorbaServer::PrimarySeq.3 \
+ Bio::CorbaServer::SeqFeature.3 \
+ Bio::CorbaServer::PrimarySeqDB.3 \
+ Bio::CorbaServer::PrimarySeqIterator.3 \
+ Bio::CorbaServer::PrimarySeqVector.3 \
+ Bio::CorbaServer::Seq.3 \
+ Bio::CorbaServer::SeqDB.3 \
+ Bio::CorbaServer::Base.3 \
+ Bio::CorbaServer::SeqFeatureIterator.3 \
+ Bio::CorbaServer::SeqFeatureVector.3 \
+ Bio::CorbaServer::Server.3
+.endif
+.if defined(WITH_GUI)
+MAN3+= Bio::Tk::HitDisplay.3 \
+ Bio::Tk::SeqCanvas.3
+.endif
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-08 19:05:27 +0000