diff options
| author | Felippe de Meirelles Motta <lippe@FreeBSD.org> | 2008-07-06 23:27:12 +0000 |
|---|---|---|
| committer | Felippe de Meirelles Motta <lippe@FreeBSD.org> | 2008-07-06 23:27:12 +0000 |
| commit | 53ee7131296e8b02193668cc5434737d3ce3ae54 (patch) | |
| tree | acefe79dc88c3c524e00a6c3b2ee29db5f2c37e7 | |
| parent | 1693e5d0702f489aded1f44cada6fe10c7a08f31 (diff) | |
| download | ports-53ee7131296e8b02193668cc5434737d3ce3ae54.tar.gz ports-53ee7131296e8b02193668cc5434737d3ce3ae54.zip | |
Notes
| -rw-r--r-- | biology/p5-bioperl-devel/Makefile | 113 | ||||
| -rw-r--r-- | biology/p5-bioperl-devel/distinfo | 6 | ||||
| -rw-r--r-- | biology/p5-bioperl-devel/files/patch-Makefile.PL | 56 | ||||
| -rw-r--r-- | biology/p5-bioperl-devel/pkg-plist | 2243 |
4 files changed, 1063 insertions, 1355 deletions
diff --git a/biology/p5-bioperl-devel/Makefile b/biology/p5-bioperl-devel/Makefile index c1f007f04d86..4f70181e723f 100644 --- a/biology/p5-bioperl-devel/Makefile +++ b/biology/p5-bioperl-devel/Makefile @@ -6,11 +6,11 @@ # PORTNAME= bioperl -PORTVERSION= 1.5.1 -PORTREVISION= 1 +PORTVERSION= 1.5.2 CATEGORIES= biology perl5 MASTER_SITES= http://bioperl.org/DIST/ PKGNAMEPREFIX= p5- +DISTNAME= ${PORTNAME}-${PORTVERSION}_102 MAINTAINER= mauricio@arareko.net COMMENT= A collection of Perl modules for bioinformatics (developer release) @@ -28,7 +28,9 @@ BUILD_DEPENDS= ${LOCALBASE}/lib/perl5/${PERL_VER}/Text/Wrap.pm:${PORTSDIR}/lang/ ${SITE_PERL}/IO/Scalar.pm:${PORTSDIR}/devel/p5-IO-stringy \ ${SITE_PERL}/IO/String.pm:${PORTSDIR}/devel/p5-IO-String \ ${SITE_PERL}/LWP/UserAgent.pm:${PORTSDIR}/www/p5-libwww \ + ${SITE_PERL}/Set/Scalar.pm:${PORTSDIR}/devel/p5-Set-Scalar \ ${SITE_PERL}/SOAP/Lite.pm:${PORTSDIR}/net/p5-SOAP-Lite \ + ${SITE_PERL}/Spreadsheet/ParseExcel.pm:${PORTSDIR}/textproc/p5-Spreadsheet-ParseExcel \ ${SITE_PERL}/SVG.pm:${PORTSDIR}/textproc/p5-SVG \ ${SITE_PERL}/SVG/Graph.pm:${PORTSDIR}/graphics/p5-SVG-Graph \ ${SITE_PERL}/Text/Shellwords.pm:${PORTSDIR}/textproc/p5-Text-Shellwords \ @@ -42,6 +44,7 @@ BUILD_DEPENDS= ${LOCALBASE}/lib/perl5/${PERL_VER}/Text/Wrap.pm:${PORTSDIR}/lang/ ${SITE_PERL}/XML/Writer.pm:${PORTSDIR}/textproc/p5-XML-Writer \ ${SITE_PERL}/${PERL_ARCH}/Ace.pm:${PORTSDIR}/biology/p5-AcePerl \ ${SITE_PERL}/${PERL_ARCH}/Clone.pm:${PORTSDIR}/devel/p5-Clone \ + ${SITE_PERL}/${PERL_ARCH}/Convert/Binary/C.pm:${PORTSDIR}/converters/p5-Convert-Binary-C \ ${SITE_PERL}/${PERL_ARCH}/DBD/mysql.pm:${PORTSDIR}/databases/p5-DBD-mysql \ ${SITE_PERL}/${PERL_ARCH}/GD.pm:${PORTSDIR}/graphics/p5-GD \ ${SITE_PERL}/${PERL_ARCH}/HTML/Entities.pm:${PORTSDIR}/www/p5-HTML-Parser \ @@ -54,7 +57,11 @@ CONFLICTS= p5-bioperl-1.[02468]* LATEST_LINK= p5-bioperl-devel -PERL_CONFIGURE= YES +PERL_MODBUILD= YES + +NOPORTDOCS= yes +NOPORTEXAMPLES= yes +NOPORTDATA= yes MAN1= bp_aacomp.pl.1 \ bp_biblio.pl.1 \ @@ -209,6 +216,7 @@ MAN3= Bio::Align::AlignI.3 \ Bio::ClusterIO::unigene.3 \ Bio::CodonUsage::IO.3 \ Bio::CodonUsage::Table.3 \ + Bio::ConfigData.3 \ Bio::Coordinate::Chain.3 \ Bio::Coordinate::Collection.3 \ Bio::Coordinate::ExtrapolatingPair.3 \ @@ -231,6 +239,19 @@ MAN3= Bio::Align::AlignI.3 \ Bio::DB::CUTG.3 \ Bio::DB::DBFetch.3 \ Bio::DB::EMBL.3 \ + Bio::DB::EUtilities.3 \ + Bio::DB::EUtilities::Cookie.3 \ + Bio::DB::EUtilities::ElinkData.3 \ + Bio::DB::EUtilities::efetch.3 \ + Bio::DB::EUtilities::egquery.3 \ + Bio::DB::EUtilities::einfo.3 \ + Bio::DB::EUtilities::elink.3 \ + Bio::DB::EUtilities::epost.3 \ + Bio::DB::EUtilities::esearch.3 \ + Bio::DB::EUtilities::esummary.3 \ + Bio::DB::EntrezGene.3 \ + Bio::DB::Expression.3 \ + Bio::DB::Expression::geo.3 \ Bio::DB::Failover.3 \ Bio::DB::Fasta.3 \ Bio::DB::FileCache.3 \ @@ -243,6 +264,7 @@ MAN3= Bio::Align::AlignI.3 \ Bio::DB::Flat::BDB::swissprot.3 \ Bio::DB::Flat::BinarySearch.3 \ Bio::DB::GDB.3 \ + Bio::DB::GenericWebDBI.3 \ Bio::DB::GFF.3 \ Bio::DB::GFF::Adaptor::ace.3 \ Bio::DB::GFF::Adaptor::berkeleydb.3 \ @@ -259,7 +281,9 @@ MAN3= Bio::Align::AlignI.3 \ Bio::DB::GFF::Adaptor::dbi::oracle.3 \ Bio::DB::GFF::Adaptor::dbi::oracleace.3 \ Bio::DB::GFF::Adaptor::dbi::pg.3 \ + Bio::DB::GFF::Adaptor::dbi::pg_fts.3 \ Bio::DB::GFF::Adaptor::memory.3 \ + Bio::DB::GFF::Adaptor::memory::feature_serializer.3 \ Bio::DB::GFF::Adaptor::memory::iterator.3 \ Bio::DB::GFF::Aggregator.3 \ Bio::DB::GFF::Aggregator::alignment.3 \ @@ -290,20 +314,37 @@ MAN3= Bio::Align::AlignI.3 \ Bio::DB::GenBank.3 \ Bio::DB::GenPept.3 \ Bio::DB::InMemoryCache.3 \ + Bio::DB::LocationI.3 \ Bio::DB::MeSH.3 \ Bio::DB::NCBIHelper.3 \ Bio::DB::Query::GenBank.3 \ Bio::DB::Query::WebQuery.3 \ Bio::DB::QueryI.3 \ Bio::DB::RandomAccessI.3 \ + Bio::DB::ReferenceI.3 \ Bio::DB::RefSeq.3 \ Bio::DB::Registry.3 \ + Bio::DB::SeqFeature.3 \ + Bio::DB::SeqFeature::NormalizedFeature.3 \ + Bio::DB::SeqFeature::NormalizedFeatureI.3 \ + Bio::DB::SeqFeature::NormalizedTableFeatureI.3 \ + Bio::DB::SeqFeature::Segment.3 \ + Bio::DB::SeqFeature::Store.3 \ + Bio::DB::SeqFeature::Store::DBI::Iterator.3 \ + Bio::DB::SeqFeature::Store::DBI::mysql.3 \ + Bio::DB::SeqFeature::Store::GFF3Loader.3 \ + Bio::DB::SeqFeature::Store::bdb.3 \ + Bio::DB::SeqFeature::Store::berkeleydb.3 \ + Bio::DB::SeqFeature::Store::memory.3 \ Bio::DB::SeqHound.3 \ Bio::DB::SeqI.3 \ + Bio::DB::SeqVersion.3 \ + Bio::DB::SeqVersion::gi.3 \ Bio::DB::SwissProt.3 \ Bio::DB::Taxonomy.3 \ Bio::DB::Taxonomy::entrez.3 \ Bio::DB::Taxonomy::flatfile.3 \ + Bio::DB::Taxonomy::list.3 \ Bio::DB::Universal.3 \ Bio::DB::UpdateableSeqI.3 \ Bio::DB::WebDBSeqI.3 \ @@ -316,9 +357,15 @@ MAN3= Bio::Align::AlignI.3 \ Bio::DescribableI.3 \ Bio::Event::EventGeneratorI.3 \ Bio::Event::EventHandlerI.3 \ + Bio::Expression::Contact.3 \ + Bio::Expression::DataSet.3 \ Bio::Expression::FeatureGroup.3 \ + Bio::Expression::FeatureGroup::FeatureGroupMas50.3 \ Bio::Expression::FeatureI.3 \ + Bio::Expression::FeatureSet::FeatureSetMas50.3 \ + Bio::Expression::Platform.3 \ Bio::Expression::ProbeI.3 \ + Bio::Expression::Sample.3 \ Bio::Factory::AnalysisI.3 \ Bio::Factory::ApplicationFactoryI.3 \ Bio::Factory::DriverFactory.3 \ @@ -342,6 +389,7 @@ MAN3= Bio::Align::AlignI.3 \ Bio::FeatureIO::gff.3 \ Bio::FeatureIO::gtf.3 \ Bio::FeatureIO::interpro.3 \ + Bio::FeatureIO::ptt.3 \ Bio::Graph::Edge.3 \ Bio::Graph::IO.3 \ Bio::Graph::IO::dip.3 \ @@ -352,6 +400,7 @@ MAN3= Bio::Align::AlignI.3 \ Bio::Graphics.3 \ Bio::Graphics::ConfiguratorI.3 \ Bio::Graphics::Feature.3 \ + Bio::Graphics::FeatureBase.3 \ Bio::Graphics::FeatureFile.3 \ Bio::Graphics::FeatureFile::Iterator.3 \ Bio::Graphics::Glyph.3 \ @@ -373,10 +422,12 @@ MAN3= Bio::Align::AlignI.3 \ Bio::Graphics::Glyph::ex.3 \ Bio::Graphics::Glyph::extending_arrow.3 \ Bio::Graphics::Glyph::flag.3 \ + Bio::Graphics::Glyph::gene.3 \ Bio::Graphics::Glyph::generic.3 \ Bio::Graphics::Glyph::graded_segments.3 \ Bio::Graphics::Glyph::group.3 \ Bio::Graphics::Glyph::heterogeneous_segments.3 \ + Bio::Graphics::Glyph::image.3 \ Bio::Graphics::Glyph::lightning.3 \ Bio::Graphics::Glyph::line.3 \ Bio::Graphics::Glyph::merge_parts.3 \ @@ -387,6 +438,7 @@ MAN3= Bio::Align::AlignI.3 \ Bio::Graphics::Glyph::pinsertion.3 \ Bio::Graphics::Glyph::primers.3 \ Bio::Graphics::Glyph::processed_transcript.3 \ + Bio::Graphics::Glyph::protein.3 \ Bio::Graphics::Glyph::ragged_ends.3 \ Bio::Graphics::Glyph::redgreen_box.3 \ Bio::Graphics::Glyph::redgreen_segment.3 \ @@ -416,6 +468,7 @@ MAN3= Bio::Align::AlignI.3 \ Bio::Graphics::Panel.3 \ Bio::Graphics::Pictogram.3 \ Bio::Graphics::RendererI.3 \ + Bio::Graphics::Util.3 \ Bio::IdCollectionI.3 \ Bio::IdentifiableI.3 \ Bio::Index::Abstract.3 \ @@ -437,7 +490,6 @@ MAN3= Bio::Align::AlignI.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 \ @@ -465,19 +517,25 @@ MAN3= Bio::Align::AlignI.3 \ Bio::Map::CytoMap.3 \ Bio::Map::CytoMarker.3 \ Bio::Map::CytoPosition.3 \ + Bio::Map::EntityI.3 \ Bio::Map::FPCMarker.3 \ Bio::Map::LinkageMap.3 \ Bio::Map::LinkagePosition.3 \ Bio::Map::MapI.3 \ + Bio::Map::Mappable.3 \ Bio::Map::MappableI.3 \ Bio::Map::Marker.3 \ Bio::Map::MarkerI.3 \ Bio::Map::Microsatellite.3 \ Bio::Map::OrderedPosition.3 \ Bio::Map::OrderedPositionWithDistance.3 \ + Bio::Map::PositionHandler.3 \ + Bio::Map::PositionHandlerI.3 \ Bio::Map::Physical.3 \ Bio::Map::Position.3 \ Bio::Map::PositionI.3 \ + Bio::Map::Relative.3 \ + Bio::Map::RelativeI.3 \ Bio::Map::SimpleMap.3 \ Bio::MapIO.3 \ Bio::MapIO::fpc.3 \ @@ -508,9 +566,12 @@ MAN3= Bio::Align::AlignI.3 \ Bio::Ontology::DocumentRegistry.3 \ Bio::Ontology::GOterm.3 \ Bio::Ontology::InterProTerm.3 \ + Bio::Ontology::OBOEngine.3 \ + Bio::Ontology::OBOterm.3 \ Bio::Ontology::Ontology.3 \ Bio::Ontology::OntologyEngineI.3 \ Bio::Ontology::OntologyI.3 \ + Bio::OntologyIO::obo.3 \ Bio::Ontology::OntologyStore.3 \ Bio::Ontology::Path.3 \ Bio::Ontology::PathI.3 \ @@ -567,6 +628,7 @@ MAN3= Bio::Align::AlignI.3 \ Bio::PopGen::Utilities.3 \ Bio::PrimarySeq.3 \ Bio::PrimarySeqI.3 \ + Bio::PullParserI.3 \ Bio::Range.3 \ Bio::RangeI.3 \ Bio::Restriction::Analysis.3 \ @@ -580,20 +642,13 @@ MAN3= Bio::Align::AlignI.3 \ Bio::Restriction::IO::base.3 \ Bio::Restriction::IO::itype2.3 \ Bio::Restriction::IO::withrefm.3 \ - Bio::Root::Err.3 \ Bio::Root::Exception.3 \ - Bio::Root::Global.3 \ Bio::Root::HTTPget.3 \ Bio::Root::IO.3 \ - Bio::Root::IOManager.3 \ - Bio::Root::Object.3 \ Bio::Root::Root.3 \ Bio::Root::RootI.3 \ Bio::Root::Storable.3 \ - Bio::Root::Utilities.3 \ - Bio::Root::Vector.3 \ Bio::Root::Version.3 \ - Bio::Root::Xref.3 \ Bio::Search::BlastStatistics.3 \ Bio::Search::BlastUtils.3 \ Bio::Search::DatabaseI.3 \ @@ -603,24 +658,30 @@ MAN3= Bio::Align::AlignI.3 \ Bio::Search::HSP::FastaHSP.3 \ Bio::Search::HSP::GenericHSP.3 \ Bio::Search::HSP::HMMERHSP.3 \ + Bio::Search::HSP::HmmpfamHSP.3 \ Bio::Search::HSP::HSPFactory.3 \ Bio::Search::HSP::HSPI.3 \ Bio::Search::HSP::PSLHSP.3 \ Bio::Search::HSP::PsiBlastHSP.3 \ + Bio::Search::HSP::PullHSPI.3 \ Bio::Search::HSP::WABAHSP.3 \ Bio::Search::Hit::BlastHit.3 \ Bio::Search::Hit::Fasta.3 \ Bio::Search::Hit::GenericHit.3 \ + Bio::Search::Hit::HmmpfamHit.3 \ Bio::Search::Hit::HMMERHit.3 \ Bio::Search::Hit::HitFactory.3 \ Bio::Search::Hit::HitI.3 \ Bio::Search::Hit::PsiBlastHit.3 \ + Bio::Search::Hit::PullHitI.3 \ Bio::Search::Iteration::GenericIteration.3 \ Bio::Search::Iteration::IterationI.3 \ Bio::Search::Processor.3 \ Bio::Search::Result::BlastResult.3 \ Bio::Search::Result::GenericResult.3 \ + Bio::Search::Result::HmmpfamResult.3 \ Bio::Search::Result::HMMERResult.3 \ + Bio::Search::Result::PullResultI.3 \ Bio::Search::Result::ResultFactory.3 \ Bio::Search::Result::ResultI.3 \ Bio::Search::Result::WABAResult.3 \ @@ -647,6 +708,7 @@ MAN3= Bio::Align::AlignI.3 \ Bio::SearchIO::exonerate.3 \ Bio::SearchIO::fasta.3 \ Bio::SearchIO::hmmer.3 \ + Bio::SearchIO::hmmer_pull.3 \ Bio::SearchIO::megablast.3 \ Bio::SearchIO::psl.3 \ Bio::SearchIO::sim4.3 \ @@ -722,6 +784,7 @@ MAN3= Bio::Align::AlignI.3 \ Bio::SeqIO::ctf.3 \ Bio::SeqIO::embl.3 \ Bio::SeqIO::entrezgene.3 \ + Bio::SeqIO::excel.3 \ Bio::SeqIO::exp.3 \ Bio::SeqIO::fasta.3 \ Bio::SeqIO::fastq.3 \ @@ -736,6 +799,7 @@ MAN3= Bio::Align::AlignI.3 \ Bio::SeqIO::interpro.3 \ Bio::SeqIO::kegg.3 \ Bio::SeqIO::largefasta.3 \ + Bio::SeqIO::lasergene.3 \ Bio::SeqIO::locuslink.3 \ Bio::SeqIO::metafasta.3 \ Bio::SeqIO::phd.3 \ @@ -744,8 +808,10 @@ MAN3= Bio::Align::AlignI.3 \ Bio::SeqIO::qual.3 \ Bio::SeqIO::raw.3 \ Bio::SeqIO::scf.3 \ + Bio::SeqIO::strider.3 \ Bio::SeqIO::swiss.3 \ Bio::SeqIO::tab.3 \ + Bio::SeqIO::table.3 \ Bio::SeqIO::tigr.3 \ Bio::SeqIO::tigrxml.3 \ Bio::SeqIO::tinyseq.3 \ @@ -771,6 +837,7 @@ MAN3= Bio::Align::AlignI.3 \ Bio::Symbol::ProteinAlphabet.3 \ Bio::Symbol::Symbol.3 \ Bio::Symbol::SymbolI.3 \ + Bio::Taxon.3 \ Bio::Taxonomy.3 \ Bio::Taxonomy::FactoryI.3 \ Bio::Taxonomy::Node.3 \ @@ -796,10 +863,6 @@ MAN3= Bio::Align::AlignI.3 \ Bio::Tools::BPlite::Iteration.3 \ Bio::Tools::BPlite::Sbjct.3 \ Bio::Tools::BPpsilite.3 \ - Bio::Tools::Blast.3 \ - Bio::Tools::Blast::HSP.3 \ - Bio::Tools::Blast::HTML.3 \ - Bio::Tools::Blast::Sbjct.3 \ Bio::Tools::Blat.3 \ Bio::Tools::CodonTable.3 \ Bio::Tools::Coil.3 \ @@ -809,6 +872,7 @@ MAN3= Bio::Align::AlignI.3 \ Bio::Tools::ESTScan.3 \ Bio::Tools::Eponine.3 \ Bio::Tools::Est2Genome.3 \ + Bio::Tools::ERPIN.3 \ Bio::Tools::Fgenesh.3 \ Bio::Tools::FootPrinter.3 \ Bio::Tools::GFF.3 \ @@ -852,13 +916,13 @@ MAN3= Bio::Align::AlignI.3 \ Bio::Tools::RandomDistFunctions.3 \ Bio::Tools::RepeatMasker.3 \ Bio::Tools::RestrictionEnzyme.3 \ + Bio::Tools::RNAMotif.3 \ Bio::Tools::Run::GenericParameters.3 \ Bio::Tools::Run::ParametersI.3 \ Bio::Tools::Run::RemoteBlast.3 \ Bio::Tools::Run::StandAloneBlast.3 \ Bio::Tools::Run::WrapperBase.3 \ Bio::Tools::Seg.3 \ - Bio::Tools::SeqAnal.3 \ Bio::Tools::SeqPattern.3 \ Bio::Tools::SeqStats.3 \ Bio::Tools::SeqWords.3 \ @@ -872,8 +936,6 @@ MAN3= Bio::Align::AlignI.3 \ Bio::Tools::Spidey::Exon.3 \ Bio::Tools::Spidey::Results.3 \ Bio::Tools::Tmhmm.3 \ - Bio::Tools::WWW.3 \ - Bio::Tools::WebBlat.3 \ Bio::Tools::dpAlign.3 \ Bio::Tools::ipcress.3 \ Bio::Tools::isPcr.3 \ @@ -914,31 +976,32 @@ MAN3= Bio::Align::AlignI.3 \ Bio::Variation::SNP.3 \ Bio::Variation::SeqDiff.3 \ Bio::Variation::VariantI.3 \ - Bio::WebAgent.3 \ - biodatabases.3 \ - biodesign.3 \ - bioperl.3 \ - bioscripts.3 \ - bptutorial.3 + Bio::WebAgent.3 .include <bsd.port.pre.mk> .if ${PERL_LEVEL} < 500800 BUILD_DEPENDS+= ${SITE_PERL}/File/Temp.pm:${PORTSDIR}/devel/p5-File-Temp +.if ${PERL_LEVEL} < 500600 +IGNORE= requires Perl 5.6 or better +.endif .endif # now install all extra stuff (docs, examples, scripts, models) post-install: ${MKDIR} ${DATADIR} ${CP} -R ${WRKSRC}/scripts ${WRKSRC}/models ${DATADIR} +.if !defined(NOPORTEXAMPLES) ${MKDIR} ${EXAMPLESDIR} ${CP} -R ${WRKSRC}/examples/* ${EXAMPLESDIR} +.endif .if !defined(NOPORTDOCS) ${MKDIR} ${DOCSDIR} -.for doc in AUTHORS BUGS Changes DEPRECATED FAQ INSTALL LICENSE PLATFORMS README +.for doc in AUTHORS BUGS Changes DEPENDENCIES DEPRECATED INSTALL LICENSE PLATFORMS README ${INSTALL_MAN} ${WRKSRC}/${doc} ${DOCSDIR} .endfor ${CP} -R ${WRKSRC}/doc ${DOCSDIR} .endif .include <bsd.port.post.mk> + diff --git a/biology/p5-bioperl-devel/distinfo b/biology/p5-bioperl-devel/distinfo index 670a4e402603..05e52069e19b 100644 --- a/biology/p5-bioperl-devel/distinfo +++ b/biology/p5-bioperl-devel/distinfo @@ -1,3 +1,3 @@ -MD5 (bioperl-1.5.1.tar.gz) = f510c871a1d17ac4ccc8ad3e6c9bad17 -SHA256 (bioperl-1.5.1.tar.gz) = 128ecbdbb22a75e165f844e38795915a909f3134c6558cd3a4d83e5ab597ea1a -SIZE (bioperl-1.5.1.tar.gz) = 6810301 +MD5 (bioperl-1.5.2_102.tar.gz) = 4890481c5beb33e129b65b922fb0c126 +SHA256 (bioperl-1.5.2_102.tar.gz) = 277c74c785afc05ad1d9dbe938677639c33130487d15bdc4a7a10e033137bada +SIZE (bioperl-1.5.2_102.tar.gz) = 5919092 diff --git a/biology/p5-bioperl-devel/files/patch-Makefile.PL b/biology/p5-bioperl-devel/files/patch-Makefile.PL deleted file mode 100644 index 7790c998f8c2..000000000000 --- a/biology/p5-bioperl-devel/files/patch-Makefile.PL +++ /dev/null @@ -1,56 +0,0 @@ ---- Makefile.PL.orig Sun Oct 9 17:16:18 2005 -+++ Makefile.PL Wed Nov 30 13:58:20 2005 -@@ -41,7 +41,7 @@ - 'XML::SAX' => '0.0/New style SAX parser/Parsers/Bio::SeqIO::tigrxml,Bio::SeqIO::bsml_sax', - 'XML::SAX::Base' => '0.0/New style SAX parser/Parsers/Bio::SeqIO::tigrxml,Bio::SeqIO::bsml_sax', - 'XML::SAX::Writer' => '0.0/New style SAX parser/Writers/Bio::SeqIO::tigrxml,Bio::SeqIO::bsml_sax', -- 'Bio::ANS1::EntrezGene' => '0.0/Enztrez Gene Bioperl Parser/Parsers/Bio::SeqIO::entrezgene' -+ 'Bio::ASN1::EntrezGene' => '0.0/Enztrez Gene Bioperl Parser/Parsers/Bio::SeqIO::entrezgene' - # Bio::Microarray is not in core bioperl yet - # 'enum' => '0.0/C style enumerated types and bitmask flags - # in Perl/Bio::Microarray::Affymetrix::*', -@@ -95,7 +95,7 @@ - sub prompt_for_biodbgff { - if( eval { require DBI } && grep {/mysql/} DBI->available_drivers) { - print "\n** Bio::DB::GFF Tests section** \n"; -- my $proceed = prompt("Do you want to run the BioDBGFF tests (requires a mysql, postgres or oracle database) y/n",'n'); -+ my $proceed = 'n'; # prompt("Do you want to run the BioDBGFF tests (requires a mysql, postgres or oracle database) y/n",'n'); - if( $proceed =~ /^[yY]/) { - my $cfg = {dbd_driver => 'mysql'}; - GFFQueryDb($cfg,{'prompt'=>1,'verbose'=>1}); -@@ -129,7 +129,7 @@ - sub get_scripts_to_install { - print "\n*** Script Install Section ****\n"; - print "\nBioperl comes with a number of useful scripts which you may wish to install.\n"; -- my $prompt_mode = prompt("Install [a]ll Bioperl scripts, [n]one, or choose groups [i]nteractively?",'a'); -+ my $prompt_mode = 'a'; # prompt("Install [a]ll Bioperl scripts, [n]one, or choose groups [i]nteractively?",'a'); - return if $prompt_mode =~ /^[nN]/; - my @scripts; - my $script_dir = './scripts'; -@@ -378,16 +378,16 @@ - ); - - --sub MY::manifypods { -- my $self = shift; -- #print STDERR "In manifypods moment\n"; -- if( 1 ) { -- return "\nmanifypods : pure_all\n\t$self->{NOECHO}\$(NOOP)\n" -- } -- else { -- return $self->SUPER::manifypods(@_); -- } --} -+#sub MY::manifypods { -+# my $self = shift; -+# #print STDERR "In manifypods moment\n"; -+# if( 1 ) { -+# return "\nmanifypods : pure_all\n\t$self->{NOECHO}\$(NOOP)\n" -+# } -+# else { -+# return $self->SUPER::manifypods(@_); -+# } -+#} - - sub MY::clean { - package MY; diff --git a/biology/p5-bioperl-devel/pkg-plist b/biology/p5-bioperl-devel/pkg-plist index 7079b9e6f069..ef4214006d49 100644 --- a/biology/p5-bioperl-devel/pkg-plist +++ b/biology/p5-bioperl-devel/pkg-plist @@ -1,1571 +1,1272 @@ -bin/bp_aacomp.pl -bin/bp_biblio.pl -bin/bp_biofetch_genbank_proxy.pl -bin/bp_bioflat_index.pl -bin/bp_biogetseq.pl -bin/bp_blast2tree.pl -bin/bp_bulk_load_gff.pl -bin/bp_chaos_plot.pl -bin/bp_classify_hits_kingdom.pl -bin/bp_composite_LD.pl +bin/bp_sreformat.pl bin/bp_contig_draw.pl -bin/bp_dbsplit.pl -bin/bp_embl2picture.pl -bin/bp_extract_feature_seq.pl -bin/bp_fast_load_gff.pl -bin/bp_fastam9_to_table.pl -bin/bp_feature_draw.pl -bin/bp_fetch.pl -bin/bp_filter_search.pl +bin/bp_tree2pag.pl +bin/bp_meta_gff.pl bin/bp_flanks.pl -bin/bp_frend.pl -bin/bp_gccalc.pl +bin/bp_heterogeneity_test.pl +bin/bp_feature_draw.pl +bin/bp_biogetseq.pl bin/bp_genbank2gff.pl -bin/bp_genbank2gff3.pl -bin/bp_generate_histogram.pl +bin/bp_seqfeature_load.pl +bin/bp_seq_length.pl +bin/bp_frend.pl +bin/bp_fastam9_to_table.pl +bin/bp_taxid4species.pl bin/bp_glyphs1-demo.pl +bin/bp_blast2tree.pl +bin/bp_gccalc.pl +bin/bp_seqret.pl +bin/bp_query_entrez_taxa.pl bin/bp_glyphs2-demo.pl -bin/bp_heterogeneity_test.pl -bin/bp_hmmer_to_table.pl -bin/bp_index.pl -bin/bp_load_gff.pl -bin/bp_local_taxonomydb_query.pl -bin/bp_make_mrna_protein.pl +bin/bp_search2alnblocks.pl +bin/bp_taxonomy2tree.pl bin/bp_mask_by_search.pl -bin/bp_meta_gff.pl -bin/bp_mrtrans.pl -bin/bp_mutate.pl +bin/bp_aacomp.pl +bin/bp_composite_LD.pl +bin/bp_biblio.pl +bin/bp_process_wormbase.pl +bin/bp_embl2picture.pl +bin/bp_local_taxonomydb_query.pl +bin/bp_genbank2gff3.pl +bin/bp_search2BSML.pl +bin/bp_seqconvert.pl +bin/bp_parse_hmmsearch.pl bin/bp_nexus2nh.pl bin/bp_nrdb.pl +bin/bp_split_seq.pl +bin/bp_filter_search.pl +bin/bp_generate_histogram.pl +bin/bp_load_gff.pl +bin/bp_fetch.pl +bin/bp_mutate.pl +bin/bp_process_sgd.pl +bin/bp_index.pl +bin/bp_dbsplit.pl bin/bp_oligo_count.pl -bin/bp_pairwise_kaks.pl -bin/bp_pg_bulk_load_gff.pl bin/bp_process_gadfly.pl -bin/bp_process_sgd.pl -bin/bp_process_wormbase.pl -bin/bp_query_entrez_taxa.pl -bin/bp_remote_blast.pl -bin/bp_search2BSML.pl 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