Date: Thu, 24 Nov 2005 16:22:10 GMT From: Mauricio Herrera Cuadra <mauricio@arareko.net> To: freebsd-gnats-submit@FreeBSD.org Subject: ports/89497: New port: biology/p5-bioperl-devel A collection of Perl modules for bioinformatics (developer release) Message-ID: <200511241622.jAOGMA7r055863@www.freebsd.org> Resent-Message-ID: <200511241630.jAOGU3I9087639@freefall.freebsd.org>
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>Number: 89497
>Category: ports
>Synopsis: New port: biology/p5-bioperl-devel A collection of Perl modules for bioinformatics (developer release)
>Confidential: no
>Severity: non-critical
>Priority: low
>Responsible: freebsd-ports-bugs
>State: open
>Quarter:
>Keywords:
>Date-Required:
>Class: change-request
>Submitter-Id: current-users
>Arrival-Date: Thu Nov 24 16:30:02 GMT 2005
>Closed-Date:
>Last-Modified:
>Originator: Mauricio Herrera Cuadra
>Release: FreeBSD 5.4-STABLE i386
>Organization:
>Environment:
FreeBSD nordwand.arareko.net 5.4-STABLE FreeBSD 5.4-STABLE #0: Wed Oct 12 03:34:59 CDT 2005 root@nordwand.arareko.net:/usr/obj/usr/src/sys/nordwand i386
>Description:
This port installs the developer release (1.5.1) of the BioPerl software.
The MAN3 pages were not listed in the Makefile because of the large amount of new modules incorporated into the suite. Listing them in the Makefile produced an install error due to shell limitations (e.g. /bin/sh:Argument list too long), so putting them into pkg-plist was a necessary workaround. I've tested the port thoroughly and it works fine (install, deinstall, pkg_create, reinstall, etc.).
>How-To-Repeat:
>Fix:
# This is a shell archive. Save it in a file, remove anything before
# this line, and then unpack it by entering "sh file". Note, it may
# create directories; files and directories will be owned by you and
# have default permissions.
#
# This archive contains:
#
# biology/p5-bioperl-devel
# biology/p5-bioperl-devel/pkg-descr
# biology/p5-bioperl-devel/Makefile
# biology/p5-bioperl-devel/pkg-plist
# biology/p5-bioperl-devel/files
# biology/p5-bioperl-devel/files/patch-Makefile.PL
# biology/p5-bioperl-devel/distinfo
#
echo c - biology/p5-bioperl-devel
mkdir -p biology/p5-bioperl-devel > /dev/null 2>&1
echo x - biology/p5-bioperl-devel/pkg-descr
sed 's/^X//' >biology/p5-bioperl-devel/pkg-descr << 'END-of-biology/p5-bioperl-devel/pkg-descr'
XThe Bioperl Project is an international association of developers of open
Xsource Perl tools for bioinformatics, genomics and life science research.
X
XBioperl is a collection of object-oriented Perl modules created by the
XBioperl Project. It forms the basis of a large number of bioinformatics and
Xgenomics applications.
X
X(For an interesting aside on "How Perl saved the Human Genome Project", see
Xhttp://bioperl.org/GetStarted/tpj_ls_bio.html)
X
XWWW: http://bioperl.org/
X
X-- Johann Visagie <wjv@FreeBSD.org>
END-of-biology/p5-bioperl-devel/pkg-descr
echo x - biology/p5-bioperl-devel/Makefile
sed 's/^X//' >biology/p5-bioperl-devel/Makefile << 'END-of-biology/p5-bioperl-devel/Makefile'
X# New ports collection makefile for: biology/p5-bioperl-devel
X# Date created: 21 November 2005
X# Whom: Mauricio Herrera Cuadra <mauricio@arareko.net>
X#
X# $FreeBSD$
X#
X
XPORTNAME= bioperl
XPORTVERSION= 1.5.1
XCATEGORIES= biology perl5
XMASTER_SITES= http://bioperl.org/DIST/
XPKGNAMEPREFIX= p5-
X
XMAINTAINER= mauricio@arareko.net
XCOMMENT= A collection of Perl modules for bioinformatics (developer release)
X
X# These are all run-time dependencies, but listing them in ${BUILD_DEPENDS}
X# prevents a flood of build-time warnings.
XBUILD_DEPENDS= ${LOCALBASE}/lib/perl5/${PERL_VER}/Text/Wrap.pm:${PORTSDIR}/lang/perl5.8 \
X ${LOCALBASE}/lib/perl5/${PERL_VER}/${PERL_ARCH}/DB_File.pm:${PORTSDIR}/lang/perl5.8 \
X ${SITE_PERL}/Bio/ASN1/EntrezGene.pm:${PORTSDIR}/biology/p5-Bio-ASN1-EntrezGene \
X ${SITE_PERL}/Class/AutoClass.pm:${PORTSDIR}/devel/p5-Class-AutoClass \
X ${SITE_PERL}/Data/Stag/ITextWriter.pm:${PORTSDIR}/devel/p5-Data-Stag \
X ${SITE_PERL}/Data/Stag/SxprWriter.pm:${PORTSDIR}/devel/p5-Data-Stag \
X ${SITE_PERL}/Data/Stag/XMLWriter.pm:${PORTSDIR}/devel/p5-Data-Stag \
X ${SITE_PERL}/GD/SVG.pm:${PORTSDIR}/graphics/p5-GD-SVG \
X ${SITE_PERL}/Graph/Directed.pm:${PORTSDIR}/math/p5-Graph \
X ${SITE_PERL}/HTTP/Request/Common.pm:${PORTSDIR}/www/p5-libwww \
X ${SITE_PERL}/IO/Scalar.pm:${PORTSDIR}/devel/p5-IO-stringy \
X ${SITE_PERL}/IO/String.pm:${PORTSDIR}/devel/p5-IO-String \
X ${SITE_PERL}/LWP/UserAgent.pm:${PORTSDIR}/www/p5-libwww \
X ${SITE_PERL}/SOAP/Lite.pm:${PORTSDIR}/net/p5-SOAP-Lite \
X ${SITE_PERL}/SVG.pm:${PORTSDIR}/textproc/p5-SVG \
X ${SITE_PERL}/SVG/Graph.pm:${PORTSDIR}/graphics/p5-SVG-Graph \
X ${SITE_PERL}/Text/Shellwords.pm:${PORTSDIR}/textproc/p5-Text-Shellwords \
X ${SITE_PERL}/XML/DOM.pm:${PORTSDIR}/textproc/p5-XML-DOM \
X ${SITE_PERL}/XML/DOM/XPath.pm:${PORTSDIR}/textproc/p5-XML-DOM-XPath \
X ${SITE_PERL}/XML/Parser/PerlSAX.pm:${PORTSDIR}/textproc/p5-libxml \
X ${SITE_PERL}/XML/SAX.pm:${PORTSDIR}/textproc/p5-XML-SAX \
X ${SITE_PERL}/XML/SAX/Base.pm:${PORTSDIR}/textproc/p5-XML-SAX \
X ${SITE_PERL}/XML/SAX/Writer.pm:${PORTSDIR}/textproc/p5-XML-SAX-Writer \
X ${SITE_PERL}/XML/Twig.pm:${PORTSDIR}/textproc/p5-XML-Twig \
X ${SITE_PERL}/XML/Writer.pm:${PORTSDIR}/textproc/p5-XML-Writer \
X ${SITE_PERL}/${PERL_ARCH}/Ace.pm:${PORTSDIR}/biology/p5-AcePerl \
X ${SITE_PERL}/${PERL_ARCH}/Clone.pm:${PORTSDIR}/devel/p5-Clone \
X ${SITE_PERL}/${PERL_ARCH}/DBD/mysql.pm:${PORTSDIR}/databases/p5-DBD-mysql \
X ${SITE_PERL}/${PERL_ARCH}/GD.pm:${PORTSDIR}/graphics/p5-GD \
X ${SITE_PERL}/${PERL_ARCH}/HTML/Entities.pm:${PORTSDIR}/www/p5-HTML-Parser \
X ${SITE_PERL}/${PERL_ARCH}/HTML/Parser.pm:${PORTSDIR}/www/p5-HTML-Parser \
X ${SITE_PERL}/${PERL_ARCH}/Storable.pm:${PORTSDIR}/devel/p5-Storable \
X ${SITE_PERL}/${PERL_ARCH}/XML/Parser.pm:${PORTSDIR}/textproc/p5-XML-Parser
XRUN_DEPENDS= ${BUILD_DEPENDS}
X
XCONFLICTS= p5-bioperl-1.[0-46-9]*
X
XPERL_CONFIGURE= YES
X
XMAN1= bp_aacomp.pl.1 \
X bp_biblio.pl.1 \
X bp_biofetch_genbank_proxy.pl.1 \
X bp_bioflat_index.pl.1 \
X bp_biogetseq.pl.1 \
X bp_blast2tree.pl.1 \
X bp_bulk_load_gff.pl.1 \
X bp_chaos_plot.pl.1 \
X bp_classify_hits_kingdom.pl.1 \
X bp_composite_LD.pl.1 \
X bp_contig_draw.pl.1 \
X bp_dbsplit.pl.1 \
X bp_embl2picture.pl.1 \
X bp_extract_feature_seq.pl.1 \
X bp_fast_load_gff.pl.1 \
X bp_fastam9_to_table.pl.1 \
X bp_feature_draw.pl.1 \
X bp_fetch.pl.1 \
X bp_filter_search.pl.1 \
X bp_flanks.pl.1 \
X bp_frend.pl.1 \
X bp_gccalc.pl.1 \
X bp_genbank2gff.pl.1 \
X bp_genbank2gff3.pl.1 \
X bp_generate_histogram.pl.1 \
X bp_glyphs1-demo.pl.1 \
X bp_glyphs2-demo.pl.1 \
X bp_heterogeneity_test.pl.1 \
X bp_hmmer_to_table.pl.1 \
X bp_index.pl.1 \
X bp_load_gff.pl.1 \
X bp_local_taxonomydb_query.pl.1 \
X bp_make_mrna_protein.pl.1 \
X bp_mask_by_search.pl.1 \
X bp_meta_gff.pl.1 \
X bp_mrtrans.pl.1 \
X bp_mutate.pl.1 \
X bp_nexus2nh.pl.1 \
X bp_nrdb.pl.1 \
X bp_oligo_count.pl.1 \
X bp_pairwise_kaks.pl.1 \
X bp_process_gadfly.pl.1 \
X bp_process_sgd.pl.1 \
X bp_process_wormbase.pl.1 \
X bp_query_entrez_taxa.pl.1 \
X bp_remote_blast.pl.1 \
X bp_search_overview.pl.1 \
X bp_search2alnblocks.pl.1 \
X bp_search2BSML.pl.1 \
X bp_search2gff.pl.1 \
X bp_search2table.pl.1 \
X bp_search2tribe.pl.1 \
X bp_seq_length.pl.1 \
X bp_seqconvert.pl.1 \
X bp_seqret.pl.1 \
X bp_split_seq.pl.1 \
X bp_sreformat.pl.1 \
X bp_taxid4species.pl.1 \
X bp_translate_seq.pl.1 \
X bp_tree2pag.pl.1 \
X bp_unflatten_seq.pl.1
X
X.include <bsd.port.pre.mk>
X
X.if ${PERL_LEVEL} < 500800
XBUILD_DEPENDS+= ${SITE_PERL}/File/Temp.pm:${PORTSDIR}/devel/p5-File-Temp
X.if ${PERL_LEVEL} < 500600
XIGNORE= This port requires Perl 5.6 or better
X.endif
X.endif
X
X# now install all extra stuff (docs, examples, scripts, models)
Xpost-install:
X ${MKDIR} ${DATADIR}
X ${CP} -R ${WRKSRC}/scripts ${WRKSRC}/models ${DATADIR}
X ${MKDIR} ${EXAMPLESDIR}
X ${CP} -R ${WRKSRC}/examples/* ${EXAMPLESDIR}
X.if !defined(NOPORTDOCS)
X ${MKDIR} ${DOCSDIR}
X.for doc in AUTHORS BUGS Changes DEPRECATED FAQ INSTALL LICENSE PLATFORMS README
X ${INSTALL_MAN} ${WRKSRC}/${doc} ${DOCSDIR}
X.endfor
X ${CP} -R ${WRKSRC}/doc ${DOCSDIR}
X.endif
X
X.include <bsd.port.post.mk>
END-of-biology/p5-bioperl-devel/Makefile
echo x - biology/p5-bioperl-devel/pkg-plist
sed 's/^X//' >biology/p5-bioperl-devel/pkg-plist << 'END-of-biology/p5-bioperl-devel/pkg-plist'
Xbin/bp_aacomp.pl
Xbin/bp_biblio.pl
Xbin/bp_biofetch_genbank_proxy.pl
Xbin/bp_bioflat_index.pl
Xbin/bp_biogetseq.pl
Xbin/bp_blast2tree.pl
Xbin/bp_bulk_load_gff.pl
Xbin/bp_chaos_plot.pl
Xbin/bp_classify_hits_kingdom.pl
Xbin/bp_composite_LD.pl
Xbin/bp_contig_draw.pl
Xbin/bp_dbsplit.pl
Xbin/bp_embl2picture.pl
Xbin/bp_extract_feature_seq.pl
Xbin/bp_fast_load_gff.pl
Xbin/bp_fastam9_to_table.pl
Xbin/bp_feature_draw.pl
Xbin/bp_fetch.pl
Xbin/bp_filter_search.pl
Xbin/bp_flanks.pl
Xbin/bp_frend.pl
Xbin/bp_gccalc.pl
Xbin/bp_genbank2gff.pl
Xbin/bp_genbank2gff3.pl
Xbin/bp_generate_histogram.pl
Xbin/bp_glyphs1-demo.pl
Xbin/bp_glyphs2-demo.pl
Xbin/bp_heterogeneity_test.pl
Xbin/bp_hmmer_to_table.pl
Xbin/bp_index.pl
Xbin/bp_load_gff.pl
Xbin/bp_local_taxonomydb_query.pl
Xbin/bp_make_mrna_protein.pl
Xbin/bp_mask_by_search.pl
Xbin/bp_meta_gff.pl
Xbin/bp_mrtrans.pl
Xbin/bp_mutate.pl
Xbin/bp_nexus2nh.pl
Xbin/bp_nrdb.pl
Xbin/bp_oligo_count.pl
Xbin/bp_pairwise_kaks.pl
Xbin/bp_pg_bulk_load_gff.pl
Xbin/bp_process_gadfly.pl
Xbin/bp_process_sgd.pl
Xbin/bp_process_wormbase.pl
Xbin/bp_query_entrez_taxa.pl
Xbin/bp_remote_blast.pl
Xbin/bp_search2BSML.pl
Xbin/bp_search2alnblocks.pl
Xbin/bp_search2gff.pl
Xbin/bp_search2table.pl
Xbin/bp_search2tribe.pl
Xbin/bp_search_overview.pl
Xbin/bp_seq_length.pl
Xbin/bp_seqconvert.pl
Xbin/bp_seqret.pl
Xbin/bp_split_seq.pl
Xbin/bp_sreformat.pl
Xbin/bp_taxid4species.pl
Xbin/bp_translate_seq.pl
Xbin/bp_tree2pag.pl
Xbin/bp_unflatten_seq.pl
Xlib/perl5/5.8.7/man/man3/Bio::Align::AlignI.3
Xlib/perl5/5.8.7/man/man3/Bio::Align::DNAStatistics.3
Xlib/perl5/5.8.7/man/man3/Bio::Align::PairwiseStatistics.3
Xlib/perl5/5.8.7/man/man3/Bio::Align::ProteinStatistics.3
Xlib/perl5/5.8.7/man/man3/Bio::Align::StatisticsI.3
Xlib/perl5/5.8.7/man/man3/Bio::Align::Utilities.3
Xlib/perl5/5.8.7/man/man3/Bio::AlignIO.3
Xlib/perl5/5.8.7/man/man3/Bio::AlignIO::bl2seq.3
Xlib/perl5/5.8.7/man/man3/Bio::AlignIO::clustalw.3
Xlib/perl5/5.8.7/man/man3/Bio::AlignIO::emboss.3
Xlib/perl5/5.8.7/man/man3/Bio::AlignIO::fasta.3
Xlib/perl5/5.8.7/man/man3/Bio::AlignIO::largemultifasta.3
Xlib/perl5/5.8.7/man/man3/Bio::AlignIO::maf.3
Xlib/perl5/5.8.7/man/man3/Bio::AlignIO::mase.3
Xlib/perl5/5.8.7/man/man3/Bio::AlignIO::mega.3
Xlib/perl5/5.8.7/man/man3/Bio::AlignIO::meme.3
Xlib/perl5/5.8.7/man/man3/Bio::AlignIO::metafasta.3
Xlib/perl5/5.8.7/man/man3/Bio::AlignIO::msf.3
Xlib/perl5/5.8.7/man/man3/Bio::AlignIO::nexus.3
Xlib/perl5/5.8.7/man/man3/Bio::AlignIO::pfam.3
Xlib/perl5/5.8.7/man/man3/Bio::AlignIO::phylip.3
Xlib/perl5/5.8.7/man/man3/Bio::AlignIO::po.3
Xlib/perl5/5.8.7/man/man3/Bio::AlignIO::prodom.3
Xlib/perl5/5.8.7/man/man3/Bio::AlignIO::psi.3
Xlib/perl5/5.8.7/man/man3/Bio::AlignIO::selex.3
Xlib/perl5/5.8.7/man/man3/Bio::AlignIO::stockholm.3
Xlib/perl5/5.8.7/man/man3/Bio::AnalysisI.3
Xlib/perl5/5.8.7/man/man3/Bio::AnalysisParserI.3
Xlib/perl5/5.8.7/man/man3/Bio::AnalysisResultI.3
Xlib/perl5/5.8.7/man/man3/Bio::AnnotatableI.3
Xlib/perl5/5.8.7/man/man3/Bio::Annotation::AnnotationFactory.3
Xlib/perl5/5.8.7/man/man3/Bio::Annotation::Collection.3
Xlib/perl5/5.8.7/man/man3/Bio::Annotation::Comment.3
Xlib/perl5/5.8.7/man/man3/Bio::Annotation::DBLink.3
Xlib/perl5/5.8.7/man/man3/Bio::Annotation::OntologyTerm.3
Xlib/perl5/5.8.7/man/man3/Bio::Annotation::Reference.3
Xlib/perl5/5.8.7/man/man3/Bio::Annotation::SimpleValue.3
Xlib/perl5/5.8.7/man/man3/Bio::Annotation::StructuredValue.3
Xlib/perl5/5.8.7/man/man3/Bio::Annotation::Target.3
Xlib/perl5/5.8.7/man/man3/Bio::Annotation::TypeManager.3
Xlib/perl5/5.8.7/man/man3/Bio::AnnotationCollectionI.3
Xlib/perl5/5.8.7/man/man3/Bio::AnnotationI.3
Xlib/perl5/5.8.7/man/man3/Bio::Assembly::Contig.3
Xlib/perl5/5.8.7/man/man3/Bio::Assembly::ContigAnalysis.3
Xlib/perl5/5.8.7/man/man3/Bio::Assembly::IO.3
Xlib/perl5/5.8.7/man/man3/Bio::Assembly::IO::ace.3
Xlib/perl5/5.8.7/man/man3/Bio::Assembly::IO::phrap.3
Xlib/perl5/5.8.7/man/man3/Bio::Assembly::Scaffold.3
Xlib/perl5/5.8.7/man/man3/Bio::Assembly::ScaffoldI.3
Xlib/perl5/5.8.7/man/man3/Bio::Assembly::Singlet.3
Xlib/perl5/5.8.7/man/man3/Bio::Biblio.3
Xlib/perl5/5.8.7/man/man3/Bio::Biblio::Article.3
Xlib/perl5/5.8.7/man/man3/Bio::Biblio::BiblioBase.3
Xlib/perl5/5.8.7/man/man3/Bio::Biblio::Book.3
Xlib/perl5/5.8.7/man/man3/Bio::Biblio::BookArticle.3
Xlib/perl5/5.8.7/man/man3/Bio::Biblio::IO.3
Xlib/perl5/5.8.7/man/man3/Bio::Biblio::IO::medline2ref.3
Xlib/perl5/5.8.7/man/man3/Bio::Biblio::IO::medlinexml.3
Xlib/perl5/5.8.7/man/man3/Bio::Biblio::IO::pubmed2ref.3
Xlib/perl5/5.8.7/man/man3/Bio::Biblio::IO::pubmedxml.3
Xlib/perl5/5.8.7/man/man3/Bio::Biblio::Journal.3
Xlib/perl5/5.8.7/man/man3/Bio::Biblio::JournalArticle.3
Xlib/perl5/5.8.7/man/man3/Bio::Biblio::MedlineArticle.3
Xlib/perl5/5.8.7/man/man3/Bio::Biblio::MedlineBook.3
Xlib/perl5/5.8.7/man/man3/Bio::Biblio::MedlineBookArticle.3
Xlib/perl5/5.8.7/man/man3/Bio::Biblio::MedlineJournal.3
Xlib/perl5/5.8.7/man/man3/Bio::Biblio::MedlineJournalArticle.3
Xlib/perl5/5.8.7/man/man3/Bio::Biblio::Organisation.3
Xlib/perl5/5.8.7/man/man3/Bio::Biblio::Patent.3
Xlib/perl5/5.8.7/man/man3/Bio::Biblio::Person.3
Xlib/perl5/5.8.7/man/man3/Bio::Biblio::Proceeding.3
Xlib/perl5/5.8.7/man/man3/Bio::Biblio::Provider.3
Xlib/perl5/5.8.7/man/man3/Bio::Biblio::PubmedArticle.3
Xlib/perl5/5.8.7/man/man3/Bio::Biblio::PubmedBookArticle.3
Xlib/perl5/5.8.7/man/man3/Bio::Biblio::PubmedJournalArticle.3
Xlib/perl5/5.8.7/man/man3/Bio::Biblio::Ref.3
Xlib/perl5/5.8.7/man/man3/Bio::Biblio::Service.3
Xlib/perl5/5.8.7/man/man3/Bio::Biblio::TechReport.3
Xlib/perl5/5.8.7/man/man3/Bio::Biblio::Thesis.3
Xlib/perl5/5.8.7/man/man3/Bio::Biblio::WebResource.3
Xlib/perl5/5.8.7/man/man3/Bio::Cluster::ClusterFactory.3
Xlib/perl5/5.8.7/man/man3/Bio::Cluster::FamilyI.3
Xlib/perl5/5.8.7/man/man3/Bio::Cluster::SequenceFamily.3
Xlib/perl5/5.8.7/man/man3/Bio::Cluster::UniGene.3
Xlib/perl5/5.8.7/man/man3/Bio::Cluster::UniGeneI.3
Xlib/perl5/5.8.7/man/man3/Bio::ClusterI.3
Xlib/perl5/5.8.7/man/man3/Bio::ClusterIO.3
Xlib/perl5/5.8.7/man/man3/Bio::ClusterIO::dbsnp.3
Xlib/perl5/5.8.7/man/man3/Bio::ClusterIO::unigene.3
Xlib/perl5/5.8.7/man/man3/Bio::CodonUsage::IO.3
Xlib/perl5/5.8.7/man/man3/Bio::CodonUsage::Table.3
Xlib/perl5/5.8.7/man/man3/Bio::Coordinate::Chain.3
Xlib/perl5/5.8.7/man/man3/Bio::Coordinate::Collection.3
Xlib/perl5/5.8.7/man/man3/Bio::Coordinate::ExtrapolatingPair.3
Xlib/perl5/5.8.7/man/man3/Bio::Coordinate::GeneMapper.3
Xlib/perl5/5.8.7/man/man3/Bio::Coordinate::Graph.3
Xlib/perl5/5.8.7/man/man3/Bio::Coordinate::MapperI.3
Xlib/perl5/5.8.7/man/man3/Bio::Coordinate::Pair.3
Xlib/perl5/5.8.7/man/man3/Bio::Coordinate::Result.3
Xlib/perl5/5.8.7/man/man3/Bio::Coordinate::Result::Gap.3
Xlib/perl5/5.8.7/man/man3/Bio::Coordinate::Result::Match.3
Xlib/perl5/5.8.7/man/man3/Bio::Coordinate::ResultI.3
Xlib/perl5/5.8.7/man/man3/Bio::Coordinate::Utils.3
Xlib/perl5/5.8.7/man/man3/Bio::DB::Ace.3
Xlib/perl5/5.8.7/man/man3/Bio::DB::Biblio::biofetch.3
Xlib/perl5/5.8.7/man/man3/Bio::DB::Biblio::eutils.3
Xlib/perl5/5.8.7/man/man3/Bio::DB::Biblio::pdf.3
Xlib/perl5/5.8.7/man/man3/Bio::DB::Biblio::soap.3
Xlib/perl5/5.8.7/man/man3/Bio::DB::BiblioI.3
Xlib/perl5/5.8.7/man/man3/Bio::DB::BioFetch.3
Xlib/perl5/5.8.7/man/man3/Bio::DB::CUTG.3
Xlib/perl5/5.8.7/man/man3/Bio::DB::DBFetch.3
Xlib/perl5/5.8.7/man/man3/Bio::DB::EMBL.3
Xlib/perl5/5.8.7/man/man3/Bio::DB::Failover.3
Xlib/perl5/5.8.7/man/man3/Bio::DB::Fasta.3
Xlib/perl5/5.8.7/man/man3/Bio::DB::FileCache.3
Xlib/perl5/5.8.7/man/man3/Bio::DB::Flat.3
Xlib/perl5/5.8.7/man/man3/Bio::DB::Flat::BDB.3
Xlib/perl5/5.8.7/man/man3/Bio::DB::Flat::BDB::embl.3
Xlib/perl5/5.8.7/man/man3/Bio::DB::Flat::BDB::fasta.3
Xlib/perl5/5.8.7/man/man3/Bio::DB::Flat::BDB::genbank.3
Xlib/perl5/5.8.7/man/man3/Bio::DB::Flat::BDB::swiss.3
Xlib/perl5/5.8.7/man/man3/Bio::DB::Flat::BDB::swissprot.3
Xlib/perl5/5.8.7/man/man3/Bio::DB::Flat::BinarySearch.3
Xlib/perl5/5.8.7/man/man3/Bio::DB::GDB.3
Xlib/perl5/5.8.7/man/man3/Bio::DB::GFF.3
Xlib/perl5/5.8.7/man/man3/Bio::DB::GFF::Adaptor::ace.3
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X%%EXAMPLESDIR%%/db/use_registry.pl
X%%EXAMPLESDIR%%/generate_random_seq.pl
X%%EXAMPLESDIR%%/liveseq/change_gene.pl
X%%EXAMPLESDIR%%/longorf.pl
X%%EXAMPLESDIR%%/make_primers.pl
X%%EXAMPLESDIR%%/popgen/parse_calc_stats.pl
X%%EXAMPLESDIR%%/rev_and_trans.pl
X%%EXAMPLESDIR%%/revcom_dir.pl
X%%EXAMPLESDIR%%/root/README
X%%EXAMPLESDIR%%/root/exceptions1.pl
X%%EXAMPLESDIR%%/root/exceptions2.pl
X%%EXAMPLESDIR%%/root/exceptions3.pl
X%%EXAMPLESDIR%%/root/exceptions4.pl
X%%EXAMPLESDIR%%/root/lib/Bio/PrimarySeq.pm
X%%EXAMPLESDIR%%/root/lib/Bio/PrimarySeqI.pm
X%%EXAMPLESDIR%%/root/lib/Bio/Seq.pm
X%%EXAMPLESDIR%%/root/lib/Bio/SeqI.pm
X%%EXAMPLESDIR%%/root/lib/Error.pm
X%%EXAMPLESDIR%%/root/lib/TestInterface.pm
X%%EXAMPLESDIR%%/root/lib/TestObject.pm
X%%EXAMPLESDIR%%/searchio/blast_example.pl
X%%EXAMPLESDIR%%/searchio/custom_writer.pl
X%%EXAMPLESDIR%%/searchio/hitwriter.pl
X%%EXAMPLESDIR%%/searchio/hspwriter.pl
X%%EXAMPLESDIR%%/searchio/htmlwriter.pl
X%%EXAMPLESDIR%%/searchio/psiblast_features.pl
X%%EXAMPLESDIR%%/searchio/psiblast_iterations.pl
X%%EXAMPLESDIR%%/searchio/rawwriter.pl
X%%EXAMPLESDIR%%/searchio/resultwriter.pl
X%%EXAMPLESDIR%%/searchio/waba2gff.pl
X%%EXAMPLESDIR%%/searchio/waba2gff3.pl
X%%EXAMPLESDIR%%/sirna/TAG
X%%EXAMPLESDIR%%/sirna/rnai_finder.cgi
X%%EXAMPLESDIR%%/structure/structure-io.pl
X%%EXAMPLESDIR%%/subsequence.cgi
X%%EXAMPLESDIR%%/tk/gsequence.pl
X%%EXAMPLESDIR%%/tk/hitdisplay.pl
X%%EXAMPLESDIR%%/tools/gb_to_gff.pl
X%%EXAMPLESDIR%%/tools/gff2ps.pl
X%%EXAMPLESDIR%%/tools/parse_codeml.pl
X%%EXAMPLESDIR%%/tools/psw.pl
X%%EXAMPLESDIR%%/tools/run_genscan.pl
X%%EXAMPLESDIR%%/tools/seq_pattern.pl
X%%EXAMPLESDIR%%/tools/standaloneblast.pl
X%%EXAMPLESDIR%%/tree/paup2phylip.pl
X@dirrm %%EXAMPLESDIR%%/tree
X@dirrm %%EXAMPLESDIR%%/tools
X@dirrm %%EXAMPLESDIR%%/tk
X@dirrm %%EXAMPLESDIR%%/structure
X@dirrm %%EXAMPLESDIR%%/sirna
X@dirrm %%EXAMPLESDIR%%/searchio
X@dirrm %%EXAMPLESDIR%%/root/lib/Bio
X@dirrm %%EXAMPLESDIR%%/root/lib
X@dirrm %%EXAMPLESDIR%%/root
X@dirrm %%EXAMPLESDIR%%/popgen
X@dirrm %%EXAMPLESDIR%%/liveseq
X@dirrm %%EXAMPLESDIR%%/db
X@dirrm %%EXAMPLESDIR%%/contributed
X@dirrm %%EXAMPLESDIR%%/cluster
X@dirrm %%EXAMPLESDIR%%/biographics
X@dirrm %%EXAMPLESDIR%%/biblio
X@dirrm %%EXAMPLESDIR%%/align
X@dirrm %%EXAMPLESDIR%%/Bio-DB-GFF
X@dirrm %%EXAMPLESDIR%%
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/howto/xml/xsl/xhtml
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/howto/xml/xsl/profiling
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/howto/xml/xsl/lib
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/howto/xml/xsl/html
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/howto/xml/xsl/fo
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/howto/xml/xsl/common
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/howto/xml/xsl
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/howto/xml/stylesheet
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/howto/xml/ent
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/howto/xml
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/howto/txt
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/howto/pdf
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/howto/html/images
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/howto/html
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/howto/figs/graphics
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/howto/figs
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/howto/examples/graphics
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/howto/examples
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/howto
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/faq
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc
X%%PORTDOCS%%@dirrm %%DOCSDIR%%
X@dirrm %%DATADIR%%/scripts/utilities
X@dirrm %%DATADIR%%/scripts/tree
X@dirrm %%DATADIR%%/scripts/taxa
X@dirrm %%DATADIR%%/scripts/seqstats
X@dirrm %%DATADIR%%/scripts/seq
X@dirrm %%DATADIR%%/scripts/searchio
X@dirrm %%DATADIR%%/scripts/popgen
X@dirrm %%DATADIR%%/scripts/index
X@dirrm %%DATADIR%%/scripts/graphics
X@dirrm %%DATADIR%%/scripts/das
X@dirrm %%DATADIR%%/scripts/biographics
X@dirrm %%DATADIR%%/scripts/biblio
X@dirrm %%DATADIR%%/scripts/DB
X@dirrm %%DATADIR%%/scripts/Bio-DB-GFF
X@dirrm %%DATADIR%%/scripts
X@dirrm %%DATADIR%%/models
X@dirrm %%DATADIR%%
X@unexec rmdir %D/%%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Variation/IO 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Variation 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/TreeIO 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Tree/Draw 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Tree 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Tools/Spidey 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Tools/Sim4 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Tools/SiRNA/Ruleset 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Tools/SiRNA 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Tools/Run 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Tools/Primer/Assessor 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Tools/Primer 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Tools/Prediction 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Tools/Phylo/Phylip 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Tools/Phylo/PAML 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Tools/Phylo/Molphy 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Tools/Phylo 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Tools/HMMER 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Tools/EMBOSS 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Tools/Blast 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Tools/BPlite 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Tools/Analysis/Protein 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Tools/Analysis/DNA 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Tools/Analysis 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Tools/Alignment 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Tools 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Taxonomy 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Symbol 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Structure/SecStr/STRIDE 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Structure/SecStr/DSSP 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Structure/SecStr 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Structure/IO 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Structure 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/SeqIO/tinyseq 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/SeqIO/game 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/SeqIO 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/SeqFeature/Tools 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/SeqFeature/SiRNA 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/SeqFeature/Gene 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/SeqFeature 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Seq/Meta 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Seq 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/SearchIO/Writer 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/SearchIO 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Search/Result 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Search/Iteration 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Search/Hit 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Search/HSP 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Search 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Root 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Restriction/IO 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Restriction/Enzyme 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Restriction 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/PopGen/Simulation 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/PopGen/IO 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/PopGen 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Phenotype/OMIM 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Phenotype/MeSH 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Phenotype 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/OntologyIO/Handlers 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/OntologyIO 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Ontology/SimpleGOEngine 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Ontology 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Matrix/PSM/IO 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Matrix/PSM 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Matrix/IO 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Matrix 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/MapIO 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Map 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Location 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/LiveSeq/IO 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/LiveSeq 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Index 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Graphics/Glyph 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Graphics/FeatureFile 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Graphics 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Graph/SimpleGraph 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Graph/IO 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Graph 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/FeatureIO 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Factory 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Expression/FeatureSet 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Expression/FeatureGroup 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Expression 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Event 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Das 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/DB/Taxonomy 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/DB/Query 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/DB/GFF/Util 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/DB/GFF/Aggregator 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/DB/GFF/Adaptor/memory 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/DB/GFF/Adaptor/dbi 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/DB/GFF/Adaptor/berkeleydb 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/DB/GFF/Adaptor 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/DB/GFF 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/DB/Flat/BDB 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/DB/Flat 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/DB/Biblio 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/DB 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Coordinate/Result 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Coordinate 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/CodonUsage 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/ClusterIO 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Cluster 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Biblio/IO 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Biblio 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Assembly/IO 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Assembly 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Annotation 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/AlignIO 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio/Align 2>/dev/null || true
X@unexec rmdir %D/%%SITE_PERL%%/Bio 2>/dev/null || true
END-of-biology/p5-bioperl-devel/pkg-plist
echo c - biology/p5-bioperl-devel/files
mkdir -p biology/p5-bioperl-devel/files > /dev/null 2>&1
echo x - biology/p5-bioperl-devel/files/patch-Makefile.PL
sed 's/^X//' >biology/p5-bioperl-devel/files/patch-Makefile.PL << 'END-of-biology/p5-bioperl-devel/files/patch-Makefile.PL'
X--- Makefile.PL.orig Sun Oct 9 10:16:18 2005
X+++ Makefile.PL Tue Nov 22 17:38:36 2005
X@@ -41,7 +41,7 @@
X 'XML::SAX' => '0.0/New style SAX parser/Parsers/Bio::SeqIO::tigrxml,Bio::SeqIO::bsml_sax',
X 'XML::SAX::Base' => '0.0/New style SAX parser/Parsers/Bio::SeqIO::tigrxml,Bio::SeqIO::bsml_sax',
X 'XML::SAX::Writer' => '0.0/New style SAX parser/Writers/Bio::SeqIO::tigrxml,Bio::SeqIO::bsml_sax',
X- 'Bio::ANS1::EntrezGene' => '0.0/Enztrez Gene Bioperl Parser/Parsers/Bio::SeqIO::entrezgene'
X+ 'Bio::ASN1::EntrezGene' => '0.0/Enztrez Gene Bioperl Parser/Parsers/Bio::SeqIO::entrezgene'
X # Bio::Microarray is not in core bioperl yet
X # 'enum' => '0.0/C style enumerated types and bitmask flags
X # in Perl/Bio::Microarray::Affymetrix::*',
X@@ -378,16 +378,16 @@
X );
X
X
X-sub MY::manifypods {
X- my $self = shift;
X- #print STDERR "In manifypods moment\n";
X- if( 1 ) {
X- return "\nmanifypods : pure_all\n\t$self->{NOECHO}\$(NOOP)\n"
X- }
X- else {
X- return $self->SUPER::manifypods(@_);
X- }
X-}
X+#sub MY::manifypods {
X+# my $self = shift;
X+# #print STDERR "In manifypods moment\n";
X+# if( 1 ) {
X+# return "\nmanifypods : pure_all\n\t$self->{NOECHO}\$(NOOP)\n"
X+# }
X+# else {
X+# return $self->SUPER::manifypods(@_);
X+# }
X+#}
X
X sub MY::clean {
X package MY;
END-of-biology/p5-bioperl-devel/files/patch-Makefile.PL
echo x - biology/p5-bioperl-devel/distinfo
sed 's/^X//' >biology/p5-bioperl-devel/distinfo << 'END-of-biology/p5-bioperl-devel/distinfo'
XMD5 (bioperl-1.5.1.tar.gz) = f510c871a1d17ac4ccc8ad3e6c9bad17
XSHA256 (bioperl-1.5.1.tar.gz) = 128ecbdbb22a75e165f844e38795915a909f3134c6558cd3a4d83e5ab597ea1a
XSIZE (bioperl-1.5.1.tar.gz) = 6810301
END-of-biology/p5-bioperl-devel/distinfo
exit
>Release-Note:
>Audit-Trail:
>Unformatted:
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