Index: head/biology/p5-BioPerl/Makefile =================================================================== --- head/biology/p5-BioPerl/Makefile (revision 428939) +++ head/biology/p5-BioPerl/Makefile (revision 428940) @@ -1,92 +1,100 @@ # Created by: Johann Visagie # $FreeBSD$ PORTNAME= BioPerl -PORTVERSION= 1.6.924 -PORTREVISION= 5 +PORTVERSION= 1.007001 CATEGORIES= biology perl5 MASTER_SITES= CPAN MASTER_SITE_SUBDIR= CPAN:CJFIELDS PKGNAMEPREFIX= p5- MAINTAINER= perl@FreeBSD.org COMMENT= Collection of Perl modules for bioinformatics LICENSE= ART10 GPLv1 LICENSE_COMB= dual BUILD_DEPENDS= p5-Algorithm-Munkres>=0:math/p5-Algorithm-Munkres \ p5-Array-Compare>=0:misc/p5-Array-Compare \ - p5-Class-AutoClass>=0:devel/p5-Class-AutoClass \ p5-Clone>=0:devel/p5-Clone \ p5-Convert-Binary-C>=0:converters/p5-Convert-Binary-C \ p5-DBD-mysql>=0:databases/p5-DBD-mysql \ - p5-Data-Stag>=0:devel/p5-Data-Stag \ + p5-DBI>=0:databases/p5-DBI \ + p5-Data-Stag>=0.11:devel/p5-Data-Stag \ p5-Error>=0:lang/p5-Error \ p5-GD>=0:graphics/p5-GD \ - p5-GD-SVG>=0:graphics/p5-GD-SVG \ - p5-Graph>=0:math/p5-Graph \ + p5-Graph>=0.50:math/p5-Graph \ p5-GraphViz>=0:graphics/p5-GraphViz \ - p5-HTML-Parser>=0:www/p5-HTML-Parser \ - p5-HTML-TableExtract>=2:www/p5-HTML-TableExtract \ + p5-HTML-Parser>=3:www/p5-HTML-Parser \ + p5-HTML-TableExtract>=0:www/p5-HTML-TableExtract \ + p5-HTTP-Message>=0:www/p5-HTTP-Message \ p5-IO-String>=0:devel/p5-IO-String \ p5-IO-stringy>=0:devel/p5-IO-stringy \ - p5-Math-Random>=0:math/p5-Math-Random \ + p5-Inline-C>=0.67:devel/p5-Inline-C \ + p5-List-MoreUtils>=0:lang/p5-List-MoreUtils \ p5-PostScript>=0:print/p5-PostScript \ - p5-SOAP-Lite>=0:net/p5-SOAP-Lite \ - p5-SVG>=0:textproc/p5-SVG \ - p5-SVG-Graph>=0:graphics/p5-SVG-Graph \ + p5-SVG>=2.26:textproc/p5-SVG \ + p5-SVG-Graph>=0.01:graphics/p5-SVG-Graph \ p5-Set-Scalar>=0:devel/p5-Set-Scalar \ - p5-Sort-Naturally>=1:textproc/p5-Sort-Naturally \ + p5-Sort-Naturally>=0:textproc/p5-Sort-Naturally \ p5-Spreadsheet-ParseExcel>=0:textproc/p5-Spreadsheet-ParseExcel \ - p5-Test-Most>=0:devel/p5-Test-Most \ - p5-Text-Shellwords>=0:textproc/p5-Text-Shellwords \ - p5-Text-Tabs+Wrap>=0:textproc/p5-Text-Tabs+Wrap \ - p5-URI>=0:net/p5-URI \ p5-XML-DOM>=0:textproc/p5-XML-DOM \ p5-XML-DOM-XPath>=0:textproc/p5-XML-DOM-XPath \ p5-XML-LibXML>=0:textproc/p5-XML-LibXML \ p5-XML-Parser>=0:textproc/p5-XML-Parser \ - p5-XML-SAX>=0:textproc/p5-XML-SAX \ + p5-XML-SAX>=0.15:textproc/p5-XML-SAX \ p5-XML-SAX-Writer>=0:textproc/p5-XML-SAX-Writer \ - p5-XML-Simple>=2:textproc/p5-XML-Simple \ + p5-XML-Simple>=0:textproc/p5-XML-Simple \ p5-XML-Twig>=0:textproc/p5-XML-Twig \ - p5-XML-Writer>=0:textproc/p5-XML-Writer \ + p5-XML-Writer>=0.400:textproc/p5-XML-Writer \ p5-YAML>=0:textproc/p5-YAML \ p5-libwww>=0:www/p5-libwww \ p5-libxml>=0:textproc/p5-libxml RUN_DEPENDS:= ${BUILD_DEPENDS} +TEST_DEPENDS= p5-Test-Most>=0:devel/p5-Test-Most \ + p5-URI>=0:net/p5-URI USES= perl5 USE_PERL5= modbuild NO_ARCH= yes +PORTDATA= * +PORTDOCS= * +PORTEXAMPLES= * + OPTIONS_DEFINE= DOCS EXAMPLES PGTEST SQLITETEST PGTEST_DESC= Test PostGreSQL SQLITETEST_DESC= Test SQLite PGTEST_RUN_DEPENDS= p5-DBD-Pg>=3:databases/p5-DBD-Pg PGTEST_BUILD_DEPENDS= p5-DBD-Pg>=3:databases/p5-DBD-Pg SQLITETEST_RUN_DEPENDS= p5-DBD-SQLite>=1:databases/p5-DBD-SQLite SQLITETEST_BUILD_DEPENDS= p5-DBD-SQLite>=1:databases/p5-DBD-SQLite post-patch: - @${FIND} ${WRKSRC}/examples ${WRKSRC}/doc -name "*.pl" -o -name "*.cgi" \ + @${FIND} ${WRKSRC}/examples ${WRKSRC}/deobfuscator -name "*.pl" -o -name "*.cgi" \ -o -name "*.PL" | ${XARGS} ${REINPLACE_CMD} -i '' -Ee \ '1s|(/usr)?/bin/perl|${PERL}|' post-install: @${MKDIR} ${STAGEDIR}${DATADIR} ${CP} -R ${WRKSRC}/scripts ${WRKSRC}/models ${STAGEDIR}${DATADIR} post-install-DOCS-on: @${MKDIR} ${STAGEDIR}${DOCSDIR} -.for doc in AUTHORS BUGS Changes DEPENDENCIES DEPRECATED INSTALL LICENSE MANIFEST README - ${INSTALL_MAN} ${WRKSRC}/${doc} ${STAGEDIR}${DOCSDIR} +.for doc in AUTHORS BUGS Changes DEPENDENCIES DEPRECATED INSTALL.md MANIFEST README.md + ${INSTALL_DATA} ${WRKSRC}/${doc} ${STAGEDIR}${DOCSDIR} .endfor - ${CP} -R ${WRKSRC}/doc ${STAGEDIR}${DOCSDIR} + ${CP} -R ${WRKSRC}/deobfuscator ${STAGEDIR}${DOCSDIR} post-install-EXAMPLES-on: @${MKDIR} ${STAGEDIR}${EXAMPLESDIR} ${CP} -R ${WRKSRC}/examples/* ${STAGEDIR}${EXAMPLESDIR} -.include +.include + +.if ${PERL_LEVEL} >= 502200 +BUILD_DEPENDS+= p5-CGI>=0:www/p5-CGI +RUN_DEPENDS+= p5-CGI>=0:www/p5-CGI +.endif + +.include Index: head/biology/p5-BioPerl/distinfo =================================================================== --- head/biology/p5-BioPerl/distinfo (revision 428939) +++ head/biology/p5-BioPerl/distinfo (revision 428940) @@ -1,2 +1,3 @@ -SHA256 (BioPerl-1.6.924.tar.gz) = 616a7546bb3c58504de27304a0f6cb904e18b6bbcdb6a4ec8454f2bd37bb76d0 -SIZE (BioPerl-1.6.924.tar.gz) = 12623118 +TIMESTAMP = 1479828383 +SHA256 (BioPerl-1.007001.tar.gz) = 9da1dbcd10452f53194c98c6cc2f604a59124507dcc1e6a8440565f44dd07b40 +SIZE (BioPerl-1.007001.tar.gz) = 12486953 Index: head/biology/p5-BioPerl/files/patch-Bio-Root-Build.pm =================================================================== --- head/biology/p5-BioPerl/files/patch-Bio-Root-Build.pm (revision 428939) +++ head/biology/p5-BioPerl/files/patch-Bio-Root-Build.pm (revision 428940) @@ -1,80 +1,80 @@ ---- Bio/Root/Build.pm.orig 2014-07-10 22:13:23.000000000 +0200 -+++ Bio/Root/Build.pm 2014-07-24 11:55:59.000000000 +0200 +--- Bio/Root/Build.pm.orig 2014-07-10 20:13:23 UTC ++++ Bio/Root/Build.pm @@ -83,49 +83,9 @@ } } closedir($scripts_dir); - my $question = $int_ok ? "Install [a]ll BioPerl scripts, [n]one, ". - "or choose groups [i]nteractively?" : "Install [a]ll BioPerl scripts ". - "or [n]one?"; - - my $prompt = $accept ? 'a' : $self->prompt($question, 'a'); - - if ($prompt =~ /^[aA]/) { - $self->log_info(" - will install all scripts\n"); - $self->notes(chosen_scripts => 'all'); - } - elsif ($prompt =~ /^[iI]/) { - $self->log_info(" - will install interactively:\n"); - - my @chosen_scripts; - foreach my $group_dir (@group_dirs) { - my $group = File::Basename::basename($group_dir); - print " * group '$group' has:\n"; - - my @script_files = @{$self->rscan_dir($group_dir, qr/\.PLS$|\.pl$/)}; - foreach my $script_file (@script_files) { - my $script = File::Basename::basename($script_file); - print " $script\n"; - } - - my $result = $self->prompt(" Install scripts for group '$group'? [y]es [n]o [q]uit", 'n'); - die if $result =~ /^[qQ]/; - if ($result =~ /^[yY]/) { - $self->log_info(" + will install group '$group'\n"); - push(@chosen_scripts, @script_files); - } - else { - $self->log_info(" - will not install group '$group'\n"); - } - } - my $chosen_scripts = @chosen_scripts ? join("|", @chosen_scripts) : 'none'; - - $self->notes(chosen_scripts => $chosen_scripts); - } - else { - $self->log_info(" - won't install any scripts\n"); - $self->notes(chosen_scripts => 'none'); - } + $self->log_info(" - willt install all scripts\n"); + $self->notes(chosen_scripts => 'all'); print "\n"; } @@ -1153,22 +1113,9 @@ sub prompt_for_network { my ($self, $accept) = @_; - my $proceed = $accept ? 0 : $self->y_n( "Do you want to run tests that require connection to servers across the internet\n" - . "(likely to cause some failures)? y/n", 'n'); - - if ($proceed) { - $self->notes('network' => 1); - $self->log_info(" - will run internet-requiring tests\n"); - my $use_email = $self->y_n("Do you want to run tests requiring a valid email address? y/n",'n'); - if ($use_email) { - my $address = $self->prompt("Enter email address:"); - $self->notes(email => $address); - } - } - else { - $self->notes(network => 0); - $self->log_info(" - will not run internet-requiring tests\n"); - } + my $proceed = 0; + $self->notes(network => 0); + $self->log_info(" - will not run internet-requiring tests\n"); } =head2 print_build_script Index: head/biology/p5-BioPerl/files/patch-Build.PL =================================================================== --- head/biology/p5-BioPerl/files/patch-Build.PL (revision 428939) +++ head/biology/p5-BioPerl/files/patch-Build.PL (revision 428940) @@ -1,99 +1,114 @@ ---- Build.PL.orig 2009-09-30 00:33:45.000000000 +0800 -+++ Build.PL 2009-12-01 10:25:51.000000000 +0800 -@@ -187,7 +187,6 @@ - }, +--- Build.PL.orig 2016-11-06 03:59:41 UTC ++++ Build.PL +@@ -226,7 +226,6 @@ my $build = Bio::Root::Build->new( - build_requires => { -- 'CPAN' => 1.81, - 'Module::Build' => 0.2805, - 'Test::Harness' => 2.62, - 'Test::Most' => 0, -@@ -376,86 +375,8 @@ + build_requires => { + 'Module::Build' => 0.42, +- 'CPAN' => 1.81, + 'Test::Harness' => 2.62, + 'Test::Most' => 0, + 'URI::Escape' => 0 +@@ -413,101 +412,8 @@ sub test_biodbgff { sub prompt_for_biodb { my $accept = shift; -- my $proceed = $accept ? 0 : $build->y_n("Do you want to run the Bio::DB::GFF or ". -- "Bio::DB::SeqFeature::Store live database tests? ". -- "y/n", 'n'); +- my $proceed = $accept ? 0 : $build->y_n( +- "Do you want to run the Bio::DB::GFF or " +- . "Bio::DB::SeqFeature::Store live database tests? " . "y/n", +- 'n' +- ); - - if ($proceed) { - my @driver_choices; -- foreach my $poss ('SQLite', 'mysql', 'Pg', 'Oracle') { -- if (grep {/$poss/i} @drivers) { +- foreach my $poss ( 'SQLite', 'mysql', 'Pg', 'Oracle' ) { +- if ( grep {/$poss/i} @drivers ) { - my $choice = $poss; - $choice =~ s/^(.)/[$1]/; -- push(@driver_choices, $choice); +- push( @driver_choices, $choice ); - } - } - - my $driver; -- if (@driver_choices > 1) { +- if ( @driver_choices > 1 ) { - my ($default) = $driver_choices[0] =~ /\[(.)/; -- $driver = $build->prompt("Which database driver should be used? ".join(" ", @driver_choices), $default); -- } -- else { +- $driver = $build->prompt( +- "Which database driver should be used? " +- . join( " ", @driver_choices ), +- $default +- ); +- } else { - ($driver) = $driver_choices[0] =~ /\[(.)/; - } -- if ($driver =~ /^[mM]/) { +- if ( $driver =~ /^[mM]/ ) { - $driver = 'mysql'; -- } -- elsif ($driver =~ /^[pP]/) { +- } elsif ( $driver =~ /^[pP]/ ) { - $driver = 'Pg'; -- } -- elsif ($driver =~ /^[oO]/) { +- } elsif ( $driver =~ /^[oO]/ ) { - $driver = 'Oracle'; -- } -- elsif ($driver =~ /^[sS]/) { +- } elsif ( $driver =~ /^[sS]/ ) { - $driver = 'SQLite'; - } - -- my $test_db = $build->prompt("Which database should I use for testing the $driver driver?\n". -- "This database should already be present but doesn't have to ". -- "be preloaded for any schema", 'test'); -- my $test_host = $build->prompt("On which host is database '$test_db' running (hostname, ip address or host:port)", 'localhost'); -- my $test_user = $build->prompt("User name for connecting to database '$test_db'?", 'undef'); -- my $test_pass = $build->prompt("Password for connecting to database '$test_db'?", 'undef'); +- my $test_db = $build->prompt( +- "Which database should I use for testing the $driver driver?\n" +- . "This database should already be present but doesn't have to " +- . "be preloaded for any schema", +- 'test' +- ); +- my $test_host = $build->prompt( +- "On which host is database '$test_db' running (hostname, ip address or host:port)", +- 'localhost' +- ); +- my $test_user = $build->prompt( +- "User name for connecting to database '$test_db'?", 'undef' ); +- my $test_pass = $build->prompt( +- "Password for connecting to database '$test_db'?", 'undef' ); - - my $use_host = 1; -- if ($test_host eq 'undef' || $test_host eq 'localhost') { +- if ( $test_host eq 'undef' || $test_host eq 'localhost' ) { - $use_host = 0; - } - - my $test_dsn; -- if ($driver eq 'Pg' || $driver eq 'SQLite') { +- if ( $driver eq 'Pg' || $driver eq 'SQLite' ) { - $test_dsn = "dbi:$driver:dbname=$test_db"; - $mysql_ok = 0; -- } -- else { +- } else { - $test_dsn = "dbi:$driver:database=$test_db"; - $mysql_ok = 0; - } - if ($use_host) { - $test_dsn .= ";host=$test_host"; - } - -- $build->notes(dbd_driver => $driver); -- $build->notes(test_db => $test_db); -- $build->notes(test_host => $test_host); -- $build->notes(test_user => $test_user eq 'undef' ? undef : $test_user); -- $build->notes(test_pass => $test_pass eq 'undef' ? undef : $test_pass); -- $build->notes(test_dsn => $test_dsn); +- $build->notes( dbd_driver => $driver ); +- $build->notes( test_db => $test_db ); +- $build->notes( test_host => $test_host ); +- $build->notes( +- test_user => $test_user eq 'undef' ? undef : $test_user ); +- $build->notes( +- test_pass => $test_pass eq 'undef' ? undef : $test_pass ); +- $build->notes( test_dsn => $test_dsn ); - -- $build->log_info(" - will run tests with database driver '$driver' and these settings:\n", -- " Database $test_db\n", -- " Host $test_host\n", -- " DSN $test_dsn\n", -- " User $test_user\n", -- " Password $test_pass\n"); -- $build->log_info(" - will not run the BioDBSeqFeature live ". -- "database tests (requires MySQL or Pg driver)\n") unless ($driver eq 'mysql' or $driver eq 'Pg'); -- } -- else { -- $build->log_info(" - will not run the BioDBGFF or BioDBSeqFeature live database tests\n"); +- $build->log_info( +- " - will run tests with database driver '$driver' and these settings:\n", +- " Database $test_db\n", +- " Host $test_host\n", +- " DSN $test_dsn\n", +- " User $test_user\n", +- " Password $test_pass\n" +- ); +- $build->log_info( " - will not run the BioDBSeqFeature live " +- . "database tests (requires MySQL or Pg driver)\n" ) +- unless ( $driver eq 'mysql' or $driver eq 'Pg' ); +- } else { +- $build->log_info( +- " - will not run the BioDBGFF or BioDBSeqFeature live database tests\n" +- ); - } - + my $proceed = 0; + $build->log_info(" - will not run the BioDBGFF or BioDBSeqFeature live database tests\n"); $build->log_info("\n"); return $proceed; } Index: head/biology/p5-BioPerl/pkg-descr =================================================================== --- head/biology/p5-BioPerl/pkg-descr (revision 428939) +++ head/biology/p5-BioPerl/pkg-descr (revision 428940) @@ -1,11 +1,11 @@ -The Bioperl Project is an international association of developers of open +The BioPerl Project is an international association of developers of open source Perl tools for bioinformatics, genomics and life science research. -Bioperl is a collection of object-oriented Perl modules created by the -Bioperl Project. It forms the basis of a large number of bioinformatics and +BioPerl is a collection of object-oriented Perl modules created by the +BioPerl Project. It forms the basis of a large number of bioinformatics and genomics applications. (For an interesting aside on "How Perl saved the Human Genome Project", see http://www.bioperl.org/wiki/How_Perl_saved_human_genome) WWW: http://bioperl.org/ Index: head/biology/p5-BioPerl/pkg-plist =================================================================== --- head/biology/p5-BioPerl/pkg-plist (revision 428939) +++ head/biology/p5-BioPerl/pkg-plist (revision 428940) @@ -1,1939 +1,1712 @@ bin/bp_aacomp.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_das_server.pl bin/bp_dbsplit.pl bin/bp_download_query_genbank.pl bin/bp_extract_feature_seq.pl bin/bp_fast_load_gff.pl bin/bp_fastam9_to_table.pl bin/bp_fetch.pl bin/bp_filter_search.pl +bin/bp_find-blast-matches.pl bin/bp_flanks.pl bin/bp_gccalc.pl bin/bp_genbank2gff.pl bin/bp_genbank2gff3.pl bin/bp_generate_histogram.pl bin/bp_heterogeneity_test.pl bin/bp_hivq.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_mask_by_search.pl bin/bp_meta_gff.pl bin/bp_mrtrans.pl bin/bp_mutate.pl bin/bp_netinstall.pl bin/bp_nexus2nh.pl bin/bp_nrdb.pl bin/bp_oligo_count.pl bin/bp_pairwise_kaks.pl bin/bp_parse_hmmsearch.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_revtrans-motif.pl -bin/bp_search2BSML.pl bin/bp_search2alnblocks.pl bin/bp_search2gff.pl bin/bp_search2table.pl bin/bp_search2tribe.pl bin/bp_seq_length.pl bin/bp_seqconvert.pl bin/bp_seqcut.pl bin/bp_seqfeature_delete.pl bin/bp_seqfeature_gff3.pl bin/bp_seqfeature_load.pl bin/bp_seqpart.pl bin/bp_seqret.pl bin/bp_seqretsplit.pl bin/bp_split_seq.pl bin/bp_sreformat.pl bin/bp_taxid4species.pl bin/bp_taxonomy2tree.pl bin/bp_translate_seq.pl bin/bp_tree2pag.pl bin/bp_unflatten_seq.pl %%SITE_PERL%%/Bio/Align/AlignI.pm %%SITE_PERL%%/Bio/Align/DNAStatistics.pm %%SITE_PERL%%/Bio/Align/Graphics.pm %%SITE_PERL%%/Bio/Align/PairwiseStatistics.pm %%SITE_PERL%%/Bio/Align/ProteinStatistics.pm %%SITE_PERL%%/Bio/Align/StatisticsI.pm %%SITE_PERL%%/Bio/Align/Utilities.pm %%SITE_PERL%%/Bio/AlignIO.pm %%SITE_PERL%%/Bio/AlignIO/Handler/GenericAlignHandler.pm %%SITE_PERL%%/Bio/AlignIO/arp.pm %%SITE_PERL%%/Bio/AlignIO/bl2seq.pm %%SITE_PERL%%/Bio/AlignIO/clustalw.pm %%SITE_PERL%%/Bio/AlignIO/emboss.pm %%SITE_PERL%%/Bio/AlignIO/fasta.pm %%SITE_PERL%%/Bio/AlignIO/largemultifasta.pm %%SITE_PERL%%/Bio/AlignIO/maf.pm %%SITE_PERL%%/Bio/AlignIO/mase.pm %%SITE_PERL%%/Bio/AlignIO/mega.pm %%SITE_PERL%%/Bio/AlignIO/meme.pm %%SITE_PERL%%/Bio/AlignIO/metafasta.pm %%SITE_PERL%%/Bio/AlignIO/msf.pm %%SITE_PERL%%/Bio/AlignIO/nexml.pm %%SITE_PERL%%/Bio/AlignIO/nexus.pm %%SITE_PERL%%/Bio/AlignIO/pfam.pm %%SITE_PERL%%/Bio/AlignIO/phylip.pm %%SITE_PERL%%/Bio/AlignIO/po.pm %%SITE_PERL%%/Bio/AlignIO/proda.pm %%SITE_PERL%%/Bio/AlignIO/prodom.pm %%SITE_PERL%%/Bio/AlignIO/psi.pm %%SITE_PERL%%/Bio/AlignIO/selex.pm %%SITE_PERL%%/Bio/AlignIO/stockholm.pm %%SITE_PERL%%/Bio/AlignIO/xmfa.pm %%SITE_PERL%%/Bio/AnalysisI.pm %%SITE_PERL%%/Bio/AnalysisParserI.pm %%SITE_PERL%%/Bio/AnalysisResultI.pm %%SITE_PERL%%/Bio/AnnotatableI.pm %%SITE_PERL%%/Bio/Annotation/AnnotationFactory.pm %%SITE_PERL%%/Bio/Annotation/Collection.pm %%SITE_PERL%%/Bio/Annotation/Comment.pm %%SITE_PERL%%/Bio/Annotation/DBLink.pm %%SITE_PERL%%/Bio/Annotation/OntologyTerm.pm %%SITE_PERL%%/Bio/Annotation/Reference.pm %%SITE_PERL%%/Bio/Annotation/Relation.pm %%SITE_PERL%%/Bio/Annotation/SimpleValue.pm %%SITE_PERL%%/Bio/Annotation/StructuredValue.pm %%SITE_PERL%%/Bio/Annotation/TagTree.pm %%SITE_PERL%%/Bio/Annotation/Target.pm %%SITE_PERL%%/Bio/Annotation/Tree.pm %%SITE_PERL%%/Bio/Annotation/TypeManager.pm %%SITE_PERL%%/Bio/AnnotationCollectionI.pm %%SITE_PERL%%/Bio/AnnotationI.pm %%SITE_PERL%%/Bio/Assembly/Contig.pm 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