Embarrassingly long overdue update to 0.7.0, including optional support for

GUI (Tk) and CORBA extensions.

1 files changed, 142 insertions, 54 deletions

diff --git a/biology/p5-bioperl/Makefile b/biology/p5-bioperl/Makefile
index 302592a9a251..59fb85f02cfb 100644
--- a/biology/p5-bioperl/Makefile
+++ b/biology/p5-bioperl/Makefile
@@ -6,78 +6,166 @@
 #
 
 PORTNAME=	bioperl
-PORTVERSION=	0.6.2
+PORTVERSION=	0.7.0
 CATEGORIES=	biology perl5
-MASTER_SITES=	ftp://bio.perl.org/pub/DIST/ \
-		http://bio.perl.org/Core/Latest/ \
+MASTER_SITES=	ftp://bioperl.org/pub/DIST/ \
+		http://bioperl.org/Core/Latest/ \
 		${MASTER_SITE_PERL_CPAN}
-MASTER_SITE_SUBDIR=Bio
+MASTER_SITE_SUBDIR=	Bio
 PKGNAMEPREFIX=	p5-
-DISTFILES=	${DISTNAME}${EXTRACT_SUFX} bioperl-ext-0.6.tar.gz
+DISTFILES=	${DISTNAME}${EXTRACT_SUFX}
 
-MAINTAINER=	johann@egenetics.com
+MAINTAINER=	wjv@FreeBSD.org
 
-BUILD_DEPENDS=	${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/HTTP/Request/Common.pm:${PORTSDIR}/www/p5-libwww \
+BUILD_DEPENDS=	${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/${PERL_ARCH}/Ace.pm:${PORTSDIR}/biology/p5-AcePerl \
+		${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/${PERL_ARCH}/XML/Parser.pm:${PORTSDIR}/textproc/p5-XML-Parser \
+		${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/File/Temp.pm:${PORTSDIR}/devel/p5-File-Temp \
+		${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/HTTP/Request/Common.pm:${PORTSDIR}/www/p5-libwww \
+		${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/IO/Scalar.pm:${PORTSDIR}/devel/p5-IO-stringy \
+		${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/IO/String.pm:${PORTSDIR}/devel/p5-IO-String \
 		${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/LWP/UserAgent.pm:${PORTSDIR}/www/p5-libwww \
-		${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/${PERL_ARCH}/Ace.pm:${PORTSDIR}/biology/p5-AcePerl \
-		${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/IO/Scalar.pm:${PORTSDIR}/devel/p5-IO-stringy
+		${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/XML/Node.pm:${PORTSDIR}/textproc/p5-XML-Node \
+		${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/XML/Parser/PerlSAX.pm:${PORTSDIR}/textproc/p5-libxml \
+		${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/XML/Writer.pm:${PORTSDIR}/textproc/p5-XML-Writer
 
 PERL_CONFIGURE=	YES
 
-MAN3=		Bio::Annotation.3 Bio::Annotation::Comment.3 \
-		Bio::Annotation::DBLink.3 Bio::Annotation::Reference.3 \
-		Bio::DB::Ace.3 Bio::DB::GenBank.3 Bio::DB::GenPept.3 \
-		Bio::DB::RandomAccessI.3 Bio::DB::SeqI.3 \
-		Bio::Index::Abstract.3 Bio::Index::AbstractSeq.3 \
-		Bio::Index::EMBL.3 Bio::Index::Fasta.3 \
-		Bio::Index::SwissPfam.3 Bio::LocatableSeq.3 \
-		Bio::PrimarySeq.3 Bio::PrimarySeqI.3 Bio::Range.3 \
-		Bio::RangeI.3 Bio::Root::Err.3 Bio::Root::Global.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::Search::Hit::Fasta.3 Bio::Search::Hit::HitI.3 \
-		Bio::Search::Processor.3 Bio::Search::Processor::Fasta.3 \
-		Bio::Search::Processor::ProcessorI.3 \
-		Bio::Search::Result::Fasta.3 \
-		Bio::Search::Result::ResultI.3 Bio::SearchDist.3 \
-		Bio::Seq.3 Bio::SeqFeature::FeaturePair.3 \
-		Bio::SeqFeature::Generic.3 Bio::SeqFeatureI.3 Bio::SeqI.3 \
-		Bio::SeqIO.3 Bio::SeqIO::FTHelper.3 \
-		Bio::SeqIO::MultiFile.3 Bio::SeqIO::embl.3 \
-		Bio::SeqIO::fasta.3 Bio::SeqIO::gcg.3 \
-		Bio::SeqIO::genbank.3 Bio::SeqIO::pir.3 Bio::SeqIO::raw.3 \
-		Bio::SeqIO::scf.3 Bio::SeqIO::swiss.3 Bio::SimpleAlign.3 \
-		Bio::Species.3 Bio::Tools::AlignFactory.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::Fasta.3 Bio::Tools::HMMER::Domain.3 \
-		Bio::Tools::HMMER::Results.3 Bio::Tools::HMMER::Set.3 \
-		Bio::Tools::IUPAC.3 Bio::Tools::RestrictionEnzyme.3 \
-		Bio::Tools::SeqAnal.3 Bio::Tools::SeqPattern.3 \
-		Bio::Tools::SeqStats.3 Bio::Tools::SeqWords.3 \
-		Bio::Tools::Sigcleave.3 Bio::Tools::WWW.3 \
-		Bio::Tools::pSW.3 Bio::UnivAln.3 \
-		bioback.3 biodesign.3 bioperl.3 biostart.3
-MANPREFIX=	${PREFIX}/lib/perl5/${PERL_VERSION}
+.if defined(WITH_CORBA)
+WITH_CORBA_CLIENT=	YES
+WITH_CORBA_SERVER=	YES
+.endif
 
+EXT_VERSION=	0.6
+CORBA_CLIENT_VERSION=	0.2
+CORBA_SERVER_VERSION=	0.2
+GUI_VERSION=	0.7
+DISTFILES+=	bioperl-ext-${EXT_VERSION}${EXTRACT_SUFX}
 EXT_WRKSRC=	${WRKDIR}/bioperl-ext-06/Bio/Ext/Align
 
+.if defined(WITH_CORBA_CLIENT)
+BUILD_DEPENDS+=	${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/${PERL_ARCH}/CORBA/ORBit.pm:${PORTSDIR}/devel/p5-ORBit
+.endif
+.if defined(WITH_CORBA_SERVER)
+BUILD_DEPENDS+=	${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/${PERL_ARCH}/CORBA/ORBit.pm:${PORTSDIR}/devel/p5-ORBit
+.endif
+.if defined(WITH_GUI)
+RUN_DEPENDS+=	ptksh:${PORTSDIR}/x11-toolkits/p5-Tk
+.endif
+
+.for ext in CORBA_CLIENT CORBA_SERVER GUI
+.if defined(WITH_${ext})
+EXTLIST+=	${ext}
+DISTFILES+=	bioperl-${ext:L:S/_/-/}-${${ext}_VERSION}${EXTRACT_SUFX}
+${ext}_WRKSRC=	${WRKDIR}/bioperl-${ext:L:S/_/-/}
+PLIST_${ext}=	""
+.else
+PLIST_${ext}=	"@comment "
+.endif
+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::msf.3 Bio::AlignIO::pfam.3 \
+		Bio::AlignIO::prodom.3 Bio::AlignIO::selex.3 \
+		Bio::AlignIO::stockholm.3 Bio::DB::GDB.3 \
+		Bio::DB::NCBIHelper.3 Bio::DB::SwissProt.3 \
+		Bio::DB::UpdateableSeqI.3 Bio::DB::WebDBSeqI.3 \
+		Bio::DBLinkContainerI.3 Bio::Factory::DriverFactory.3 \
+		Bio::Factory::SeqAnalysisParserFactory.3 \
+		Bio::Factory::SeqAnalysisParserFactoryI.3 \
+		Bio::Index::GenBank.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::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::Root::IO.3 Bio::Seq::LargePrimarySeq.3 \
+		Bio::Seq::LargeSeq.3 Bio::Seq::RichSeq.3 Bio::Seq::RichSeqI.3 \
+		Bio::SeqAnalysisParserI.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::Similarity.3 \
+		Bio::SeqFeature::SimilarityPair.3 Bio::SeqIO::ace.3 \
+		Bio::SeqIO::game.3 Bio::SeqIO::largefasta.3 Bio::SeqUtils.3 \
+		Bio::Tools::AnalysisResult.3 Bio::Tools::BPbl2seq.3 \
+		Bio::Tools::BPlite.3 Bio::Tools::BPlite::Iteration.3 \
+		Bio::Tools::BPpsilite.3 Bio::Tools::ESTScan.3 \
+		Bio::Tools::GFF.3 Bio::Tools::Genscan.3 Bio::Tools::MZEF.3 \
+		Bio::Tools::OddCodes.3 Bio::Tools::Prediction::Exon.3 \
+		Bio::Tools::Prediction::Gene.3 \
+		Bio::Tools::Run::Alignment::Clustalw.3 \
+		Bio::Tools::Run::Alignment::TCoffee.3 \
+		Bio::Tools::Run::StandAloneBlast.3 Bio::Tools::Sim4::Exon.3 \
+		Bio::Tools::Sim4::Results.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 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
+MANPREFIX=	${PREFIX}/lib/perl5/${PERL_VERSION}
+
 post-configure:
-	@ (cd ${EXT_WRKSRC} && \
+	@ cd ${EXT_WRKSRC} && \
 	  ${SETENV} ${CONFIGURE_ENV} \
-	  ${PERL5} ${CONFIGURE_SCRIPT} ${CONFIGURE_ARGS})
+	  ${PERL5} ./${CONFIGURE_SCRIPT} ${CONFIGURE_ARGS}
+
+.for ext in ${EXTLIST}
+	@ cd ${${ext}_WRKSRC} && \
+	  ${PERL5} ./${CONFIGURE_SCRIPT} ${CONFIGURE_ARGS}
+.endfor
 
 post-build:
-	@ (cd ${EXT_WRKSRC} && \
-	  ${MAKE} ${MAKE_FLAGS} ${MAKEFILE} ${MAKE_ARGS} ${ALL_TARGET})
+	@ cd ${EXT_WRKSRC} && \
+	  ${MAKE} ${MAKE_FLAGS} ${MAKEFILE} ${MAKE_ARGS} ${ALL_TARGET}
+.for ext in ${EXTLIST}
+	@ cd ${${ext}_WRKSRC} && ${SETENV} ${MAKE_ENV} \
+	  ${MAKE} ${MAKE_FLAGS} ${MAKEFILE} ${MAKE_ARGS} ${ALL_TARGET}
+.endfor
 
 post-install:
-	@ (cd ${EXT_WRKSRC} && \
+	@ cd ${EXT_WRKSRC} && \
+	  ${SETENV} ${MAKE_ENV} ${MAKE} ${MAKE_FLAGS} \
+	  ${MAKEFILE} ${MAKE_ARGS} ${INSTALL_TARGET}
+.for ext in ${EXTLIST}
+	@ cd ${${ext}_WRKSRC} && \
 	  ${SETENV} ${MAKE_ENV} ${MAKE} ${MAKE_FLAGS} \
-	  ${MAKEFILE} ${MAKE_ARGS} ${INSTALL_TARGET})
+	  ${MAKEFILE} ${MAKE_ARGS} ${INSTALL_TARGET}
+.endfor
 
 .include <bsd.port.mk>