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Diffstat (limited to 'biology/p5-bioperl-devel/Makefile')
| -rw-r--r-- | biology/p5-bioperl-devel/Makefile | 230 |
1 files changed, 230 insertions, 0 deletions
diff --git a/biology/p5-bioperl-devel/Makefile b/biology/p5-bioperl-devel/Makefile new file mode 100644 index 000000000000..2a1fd99762de --- /dev/null +++ b/biology/p5-bioperl-devel/Makefile @@ -0,0 +1,230 @@ +# New ports collection makefile for: p5-bioperl-devel +# Date created: 13 August 2001 +# Whom: Johann Visagie <wjv@FreeBSD.org> +# +# $FreeBSD$ +# + +PORTNAME= bioperl +PORTVERSION= 0.9.0 +CATEGORIES= biology perl5 +MASTER_SITES= ftp://bioperl.org/pub/DIST/ \ + http://bioperl.org/Core/Latest/ +PKGNAMEPREFIX= p5- +PKGNAMESUFFIX= -devel +DISTFILES= ${DISTNAME}${EXTRACT_SUFX} + +MAINTAINER= wjv@FreeBSD.org + +# These are all run-time dependencies, but listing them in ${BUILD_DEPENDS} +# prevents a flood of build-time warnings. +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}/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/Twig.pm:${PORTSDIR}/textproc/p5-XML-Twig \ + ${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/XML/Writer.pm:${PORTSDIR}/textproc/p5-XML-Writer +RUN_DEPENDS= ${BUILD_DEPENDS} + +PERL_CONFIGURE= YES + +.if defined(WITH_CORBA) +WITH_CORBA_CLIENT= YES +WITH_CORBA_SERVER= YES +.endif + +EXT_VERSION= 0.6 +CORBA_CLIENT_VERSION= 0.2 +CORBA_SERVER_VERSION= 0.2 +GUI_VERSION= 0.7 +DISTFILES+= bioperl-ext-${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 +RUN_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 +RUN_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::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 +MANPREFIX= ${PREFIX}/lib/perl5/${PERL_VERSION} + +pre-fetch: +.if !defined(BATCH) && (!defined(WITH_CORBA_CLIENT) || \ + !defined(WITH_CORBA_SERVER) || !defined(WITH_GUI)) + @ ${CAT} ${FILESDIR}/ext.msg +.endif + +post-configure: + @ cd ${EXT_WRKSRC} && \ + ${SETENV} ${CONFIGURE_ENV} \ + ${PERL5} ./${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} +.for ext in ${EXTLIST} + @ cd ${${ext}_WRKSRC} && ${SETENV} ${MAKE_ENV} \ + ${MAKE} ${MAKE_FLAGS} ${MAKEFILE} ${MAKE_ARGS} ${ALL_TARGET} +.endfor + +post-install: + @ 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} +.endfor + +.include <bsd.port.mk> |