Index: head/biology/p5-bioperl/pkg-descr
===================================================================
--- head/biology/p5-bioperl/pkg-descr	(revision 428867)
+++ head/biology/p5-bioperl/pkg-descr	(nonexistent)
@@ -1,11 +0,0 @@
-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
-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/

Property changes on: head/biology/p5-bioperl/pkg-descr
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Deleted: fbsd:nokeywords
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-yes
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-native
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Index: head/biology/p5-bioperl/distinfo
===================================================================
--- head/biology/p5-bioperl/distinfo	(revision 428867)
+++ head/biology/p5-bioperl/distinfo	(nonexistent)
@@ -1,2 +0,0 @@
-SHA256 (BioPerl-1.6.924.tar.gz) = 616a7546bb3c58504de27304a0f6cb904e18b6bbcdb6a4ec8454f2bd37bb76d0
-SIZE (BioPerl-1.6.924.tar.gz) = 12623118

Property changes on: head/biology/p5-bioperl/distinfo
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Deleted: fbsd:nokeywords
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-yes
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Index: head/biology/p5-bioperl/pkg-plist
===================================================================
--- head/biology/p5-bioperl/pkg-plist	(revision 428867)
+++ head/biology/p5-bioperl/pkg-plist	(nonexistent)
@@ -1,1939 +0,0 @@
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-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_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
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-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
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-bin/bp_search2alnblocks.pl
-bin/bp_search2gff.pl
-bin/bp_search2table.pl
-bin/bp_search2tribe.pl
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-bin/bp_sreformat.pl
-bin/bp_taxid4species.pl
-bin/bp_taxonomy2tree.pl
-bin/bp_translate_seq.pl
-bin/bp_tree2pag.pl
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-%%DATADIR%%/scripts/searchio/README
-%%DATADIR%%/scripts/searchio/TAG
-%%DATADIR%%/scripts/searchio/bp_fastam9_to_table.pl
-%%DATADIR%%/scripts/searchio/bp_filter_search.pl
-%%DATADIR%%/scripts/searchio/bp_hmmer_to_table.pl
-%%DATADIR%%/scripts/searchio/bp_parse_hmmsearch.pl
-%%DATADIR%%/scripts/searchio/bp_search2table.pl
-%%DATADIR%%/scripts/seq/TAG
-%%DATADIR%%/scripts/seq/bp_extract_feature_seq.pl
-%%DATADIR%%/scripts/seq/bp_make_mrna_protein.pl
-%%DATADIR%%/scripts/seq/bp_seqconvert.pl
-%%DATADIR%%/scripts/seq/bp_seqcut.pl
-%%DATADIR%%/scripts/seq/bp_seqpart.pl
-%%DATADIR%%/scripts/seq/bp_seqretsplit.pl
-%%DATADIR%%/scripts/seq/bp_split_seq.pl
-%%DATADIR%%/scripts/seq/bp_translate_seq.pl
-%%DATADIR%%/scripts/seq/bp_unflatten_seq.pl
-%%DATADIR%%/scripts/seqstats/TAG
-%%DATADIR%%/scripts/seqstats/bp_aacomp.pl
-%%DATADIR%%/scripts/seqstats/bp_chaos_plot.pl
-%%DATADIR%%/scripts/seqstats/bp_gccalc.pl
-%%DATADIR%%/scripts/seqstats/bp_oligo_count.pl
-%%DATADIR%%/scripts/taxa/TAG
-%%DATADIR%%/scripts/taxa/bp_classify_hits_kingdom.pl
-%%DATADIR%%/scripts/taxa/bp_local_taxonomydb_query.pl
-%%DATADIR%%/scripts/taxa/bp_query_entrez_taxa.pl
-%%DATADIR%%/scripts/taxa/bp_taxid4species.pl
-%%DATADIR%%/scripts/taxa/bp_taxonomy2tree.pl
-%%DATADIR%%/scripts/tree/TAG
-%%DATADIR%%/scripts/tree/bp_blast2tree.pl
-%%DATADIR%%/scripts/tree/bp_nexus2nh.pl
-%%DATADIR%%/scripts/tree/bp_tree2pag.pl
-%%DATADIR%%/scripts/utilities/README
-%%DATADIR%%/scripts/utilities/TAG
-%%DATADIR%%/scripts/utilities/bp_dbsplit.pl
-%%DATADIR%%/scripts/utilities/bp_download_query_genbank.pl
-%%DATADIR%%/scripts/utilities/bp_mask_by_search.pl
-%%DATADIR%%/scripts/utilities/bp_mrtrans.pl
-%%DATADIR%%/scripts/utilities/bp_mutate.pl
-%%DATADIR%%/scripts/utilities/bp_netinstall.pl
-%%DATADIR%%/scripts/utilities/bp_nrdb.pl
-%%DATADIR%%/scripts/utilities/bp_pairwise_kaks.pl
-%%DATADIR%%/scripts/utilities/bp_remote_blast.pl
-%%DATADIR%%/scripts/utilities/bp_revtrans-motif.pl
-%%DATADIR%%/scripts/utilities/bp_search2BSML.pl
-%%DATADIR%%/scripts/utilities/bp_search2alnblocks.pl
-%%DATADIR%%/scripts/utilities/bp_search2gff.pl
-%%DATADIR%%/scripts/utilities/bp_search2tribe.pl
-%%DATADIR%%/scripts/utilities/bp_seq_length.pl
-%%DATADIR%%/scripts/utilities/bp_sreformat.pl
-%%PORTDOCS%%%%DOCSDIR%%/AUTHORS
-%%PORTDOCS%%%%DOCSDIR%%/BUGS
-%%PORTDOCS%%%%DOCSDIR%%/Changes
-%%PORTDOCS%%%%DOCSDIR%%/DEPENDENCIES
-%%PORTDOCS%%%%DOCSDIR%%/DEPRECATED
-%%PORTDOCS%%%%DOCSDIR%%/INSTALL
-%%PORTDOCS%%%%DOCSDIR%%/LICENSE
-%%PORTDOCS%%%%DOCSDIR%%/MANIFEST
-%%PORTDOCS%%%%DOCSDIR%%/README
-%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/Build.PL
-%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/Changes
-%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/LICENSE
-%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/MANIFEST
-%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/META.yml
-%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/Makefile.PL
-%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/README
-%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/bin/deob_index.pl
-%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/bin/run-deobfuscator-update.pl
-%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/cgi-bin/deob_detail.cgi
-%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/cgi-bin/deob_flowchart.png
-%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/cgi-bin/deob_help.html
-%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/cgi-bin/deob_interface.cgi
-%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/excluded_modules.txt
-%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/lib/Deobfuscator.pm
-%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/t/00.load.t
-%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/t/pod.t
-%%PORTDOCS%%%%DOCSDIR%%/doc/README
-%%PORTDOCS%%%%DOCSDIR%%/doc/makedoc.PL
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Bio-DB-GFF/load_ucsc.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/align/FastAlign.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/align/align_on_codons.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/align/aligntutorial.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/align/clustalw.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/align/simplealign.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bioperl.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cluster/dbsnp.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/contributed/nmrpdb_parse.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/contributed/prosite2perl.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/contributed/rebase2list.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/db/dbfetch
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/db/est_tissue_query.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/db/gb2features.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/db/getGenBank.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/db/get_seqs.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/db/rfetch.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/db/use_registry.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/generate_random_seq.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/liveseq/change_gene.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/longorf.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/make_primers.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/popgen/parse_calc_stats.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/quality/svgtrace.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/rev_and_trans.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/revcom_dir.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/root/README
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/root/exceptions1.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/root/exceptions2.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/root/exceptions3.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/root/exceptions4.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/root/lib/TestInterface.pm
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/root/lib/TestObject.pm
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/blast_example.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/custom_writer.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/hitwriter.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/hspwriter.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/htmlwriter.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/psiblast_features.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/psiblast_iterations.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/rawwriter.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/resultwriter.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/waba2gff.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/waba2gff3.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sirna/TAG
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sirna/rnai_finder.cgi
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/structure/structure-io.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/subsequence.cgi
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tk/gsequence.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tk/hitdisplay.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tools/extract_genes.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tools/gb_to_gff.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tools/gff2ps.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tools/parse_codeml.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tools/psw.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tools/reverse-translate.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tools/run_genscan.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tools/run_primer3.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tools/seq_pattern.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tools/standaloneblast.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tree/paup2phylip.pl

Property changes on: head/biology/p5-bioperl/pkg-plist
___________________________________________________________________
Deleted: fbsd:nokeywords
## -1 +0,0 ##
-yes
\ No newline at end of property
Deleted: svn:eol-style
## -1 +0,0 ##
-native
\ No newline at end of property
Deleted: svn:mime-type
## -1 +0,0 ##
-text/plain
\ No newline at end of property
Index: head/biology/p5-bioperl/Makefile
===================================================================
--- head/biology/p5-bioperl/Makefile	(revision 428867)
+++ head/biology/p5-bioperl/Makefile	(nonexistent)
@@ -1,94 +0,0 @@
-# Created by: Johann Visagie <johann@egenetics.com>
-# $FreeBSD$
-
-PORTNAME=	bioperl
-PORTVERSION=	1.6.924
-PORTREVISION=	4
-CATEGORIES=	biology perl5
-MASTER_SITES=	CPAN
-MASTER_SITE_SUBDIR=	CPAN:CJFIELDS
-PKGNAMEPREFIX=	p5-
-DISTNAME=	BioPerl-${PORTVERSION}
-
-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-Data-Stag>=0:devel/p5-Data-Stag \
-		p5-DBD-mysql>=0:databases/p5-DBD-mysql \
-		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-GraphViz>=0:graphics/p5-GraphViz \
-		p5-HTML-Parser>=0:www/p5-HTML-Parser \
-		p5-HTML-TableExtract>=2:www/p5-HTML-TableExtract \
-		p5-IO-stringy>=0:devel/p5-IO-stringy \
-		p5-IO-String>=0:devel/p5-IO-String \
-		p5-Math-Random>=0:math/p5-Math-Random \
-		p5-PostScript>=0:print/p5-PostScript \
-		p5-SOAP-Lite>=0:net/p5-SOAP-Lite \
-		p5-Set-Scalar>=0:devel/p5-Set-Scalar \
-		p5-Sort-Naturally>=1:textproc/p5-Sort-Naturally \
-		p5-Spreadsheet-ParseExcel>=0:textproc/p5-Spreadsheet-ParseExcel \
-		p5-SVG>=0:textproc/p5-SVG \
-		p5-SVG-Graph>=0:graphics/p5-SVG-Graph \
-		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-Writer>=0:textproc/p5-XML-SAX-Writer \
-		p5-XML-Simple>=2:textproc/p5-XML-Simple \
-		p5-XML-Twig>=0:textproc/p5-XML-Twig \
-		p5-XML-Writer>=0:textproc/p5-XML-Writer \
-		p5-YAML>=0:textproc/p5-YAML \
-		p5-libwww>=0:www/p5-libwww \
-		p5-libxml>=0:textproc/p5-libxml
-
-RUN_DEPENDS:=	${BUILD_DEPENDS}
-
-USES=		perl5
-USE_PERL5=	modbuild
-NO_ARCH=	yes
-
-OPTIONS_DEFINE=	DOCS EXAMPLES PGTEST SQLITETEST
-PGTEST_DESC=	Test PostGreSQL
-SQLITETEST_DESC=	Test SQLite
-PGTEST_RUN_DEPENDS=	p5-DBD-Pg>=3:databases/p5-DBD-Pg
-PGTEST_BUILD_DEPENDS=	p5-DBD-Pg>=3:databases/p5-DBD-Pg
-SQLITETEST_RUN_DEPENDS=	p5-DBD-SQLite>=1:databases/p5-DBD-SQLite
-SQLITETEST_BUILD_DEPENDS=	p5-DBD-SQLite>=1:databases/p5-DBD-SQLite
-
-post-patch:
-	@${FIND} ${WRKSRC}/examples ${WRKSRC}/doc -name "*.pl" -o -name "*.cgi" \
-		-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}
-.endfor
-	${CP} -R ${WRKSRC}/doc ${STAGEDIR}${DOCSDIR}
-
-post-install-EXAMPLES-on:
-	@${MKDIR} ${STAGEDIR}${EXAMPLESDIR}
-	${CP} -R ${WRKSRC}/examples/* ${STAGEDIR}${EXAMPLESDIR}
-
-.include <bsd.port.mk>

Property changes on: head/biology/p5-bioperl/Makefile
___________________________________________________________________
Deleted: svn:eol-style
## -1 +0,0 ##
-native
\ No newline at end of property
Deleted: svn:keywords
## -1 +0,0 ##
-FreeBSD=%H
\ No newline at end of property
Deleted: svn:mime-type
## -1 +0,0 ##
-text/plain
\ No newline at end of property
Index: head/biology/p5-bioperl/files/patch-Bio-Root-Build.pm
===================================================================
--- head/biology/p5-bioperl/files/patch-Bio-Root-Build.pm	(revision 428867)
+++ head/biology/p5-bioperl/files/patch-Bio-Root-Build.pm	(nonexistent)
@@ -1,80 +0,0 @@
---- 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
-@@ -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

Property changes on: head/biology/p5-bioperl/files/patch-Bio-Root-Build.pm
___________________________________________________________________
Deleted: fbsd:nokeywords
## -1 +0,0 ##
-yes
\ No newline at end of property
Deleted: svn:eol-style
## -1 +0,0 ##
-native
\ No newline at end of property
Deleted: svn:mime-type
## -1 +0,0 ##
-text/plain
\ No newline at end of property
Index: head/biology/p5-bioperl/files/patch-Build.PL
===================================================================
--- head/biology/p5-bioperl/files/patch-Build.PL	(revision 428867)
+++ head/biology/p5-bioperl/files/patch-Build.PL	(nonexistent)
@@ -1,99 +0,0 @@
---- 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_requires      => {
--                            'CPAN'                      => 1.81,
-                             'Module::Build'             => 0.2805,
-                             'Test::Harness'             => 2.62,
-                             'Test::Most'                => 0,
-@@ -376,86 +375,8 @@
- 
- sub prompt_for_biodb {
-     my $accept = shift;
--    my $proceed = $accept ? 0 : $build->y_n("Do you want to run the Bio::DB::GFF or ".
--                              "Bio::DB::SeqFeature::Store live database tests? ".
--                              "y/n", 'n');
--
--    if ($proceed) {
--        my @driver_choices;
--        foreach my $poss ('SQLite', 'mysql', 'Pg', 'Oracle') {
--            if (grep {/$poss/i} @drivers) {
--                my $choice = $poss;
--                $choice =~ s/^(.)/[$1]/;
--                push(@driver_choices, $choice);
--            }
--        }
--
--        my $driver;
--        if (@driver_choices > 1) {
--            my ($default) = $driver_choices[0] =~ /\[(.)/;
--            $driver = $build->prompt("Which database driver should be used? ".join(" ", @driver_choices), $default);
--        }
--        else {
--            ($driver) = $driver_choices[0] =~ /\[(.)/;
--        }
--        if ($driver =~ /^[mM]/) {
--            $driver = 'mysql';
--        }
--        elsif ($driver =~ /^[pP]/) {
--            $driver = 'Pg';
--        }
--        elsif ($driver =~ /^[oO]/) {
--            $driver = 'Oracle';
--        }
--        elsif ($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 $use_host = 1;
--        if ($test_host eq 'undef' || $test_host eq 'localhost') {
--            $use_host = 0;
--        }
--
--        my $test_dsn;
--        if ($driver eq 'Pg' || $driver eq 'SQLite') {
--            $test_dsn = "dbi:$driver:dbname=$test_db";
--            $mysql_ok = 0;
--        }
--        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);
--
--        $build->log_info("  - will run tests with database driver '$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;
- }

Property changes on: head/biology/p5-bioperl/files/patch-Build.PL
___________________________________________________________________
Deleted: fbsd:nokeywords
## -1 +0,0 ##
-yes
\ No newline at end of property
Deleted: svn:eol-style
## -1 +0,0 ##
-native
\ No newline at end of property
Deleted: svn:mime-type
## -1 +0,0 ##
-text/plain
\ No newline at end of property
Index: head/biology/Makefile
===================================================================
--- head/biology/Makefile	(revision 428867)
+++ head/biology/Makefile	(revision 428868)
@@ -1,112 +1,112 @@
 # $FreeBSD$
 #
 
     COMMENT = Biology
 
     SUBDIR += ariadne
     SUBDIR += artemis
     SUBDIR += avida
     SUBDIR += babel
     SUBDIR += bcftools
     SUBDIR += bedtools
     SUBDIR += biococoa
     SUBDIR += biojava
     SUBDIR += blat
     SUBDIR += bowtie
     SUBDIR += bowtie2
     SUBDIR += bwa
     SUBDIR += cd-hit
     SUBDIR += cdbfasta
     SUBDIR += chemeq
     SUBDIR += clustalw
     SUBDIR += consed
     SUBDIR += crux
     SUBDIR += diamond
     SUBDIR += emboss
     SUBDIR += fasta
     SUBDIR += fasta3
     SUBDIR += fastdnaml
     SUBDIR += fastool
     SUBDIR += fasttree
     SUBDIR += fastx-toolkit
     SUBDIR += fluctuate
     SUBDIR += garlic
     SUBDIR += gff2ps
     SUBDIR += gmap
     SUBDIR += gperiodic
     SUBDIR += grappa
     SUBDIR += hmmer
     SUBDIR += htslib
     SUBDIR += iolib
     SUBDIR += jalview
     SUBDIR += jellyfish
     SUBDIR += lagan
     SUBDIR += lamarc
     SUBDIR += libgtextutils
     SUBDIR += libsbml
     SUBDIR += linux-foldingathome
     SUBDIR += mafft
     SUBDIR += mapm3
     SUBDIR += migrate
     SUBDIR += molden
     SUBDIR += mopac
     SUBDIR += mrbayes
     SUBDIR += mummer
     SUBDIR += muscle
     SUBDIR += ncbi-blast+
     SUBDIR += ncbi-toolkit
     SUBDIR += njplot
     SUBDIR += p5-AcePerl
     SUBDIR += p5-Bio-ASN1-EntrezGene
     SUBDIR += p5-Bio-Das
     SUBDIR += p5-Bio-Das-Lite
     SUBDIR += p5-Bio-GFF3
     SUBDIR += p5-Bio-Glite
     SUBDIR += p5-Bio-Graphics
     SUBDIR += p5-Bio-MAGETAB
     SUBDIR += p5-Bio-NEXUS
     SUBDIR += p5-Bio-Phylo
     SUBDIR += p5-Bio-SCF
-    SUBDIR += p5-bioperl
+    SUBDIR += p5-BioPerl
     SUBDIR += p5-bioperl-run
     SUBDIR += p5-transdecoder
     SUBDIR += paml
     SUBDIR += phrap
     SUBDIR += phred
     SUBDIR += phylip
     SUBDIR += phyml
     SUBDIR += plink
     SUBDIR += plinkseq
     SUBDIR += primer3
     SUBDIR += protomol
     SUBDIR += psi88
     SUBDIR += py-biom-format
     SUBDIR += py-biopython
     SUBDIR += pycogent
     SUBDIR += pyfasta
     SUBDIR += python-nexus
     SUBDIR += recombine
     SUBDIR += ruby-bio
     SUBDIR += samtools
     SUBDIR += seaview
     SUBDIR += seqan
     SUBDIR += seqan-apps
     SUBDIR += seqan1
     SUBDIR += seqio
     SUBDIR += seqtools
     SUBDIR += sim4
     SUBDIR += slclust
     SUBDIR += ssaha
     SUBDIR += tRNAscan-SE
     SUBDIR += t_coffee
     SUBDIR += tinker
     SUBDIR += treepuzzle
     SUBDIR += treeviewx
     SUBDIR += trimmomatic
     SUBDIR += ugene
     SUBDIR += vcftools
     SUBDIR += velvet
     SUBDIR += wise
     SUBDIR += xmolwt
 
 .include <bsd.port.subdir.mk>
Index: head/biology/p5-BioPerl/Makefile
===================================================================
--- head/biology/p5-BioPerl/Makefile	(nonexistent)
+++ head/biology/p5-BioPerl/Makefile	(revision 428868)
@@ -0,0 +1,92 @@
+# Created by: Johann Visagie <johann@egenetics.com>
+# $FreeBSD$
+
+PORTNAME=	BioPerl
+PORTVERSION=	1.6.924
+PORTREVISION=	5
+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-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-GraphViz>=0:graphics/p5-GraphViz \
+		p5-HTML-Parser>=0:www/p5-HTML-Parser \
+		p5-HTML-TableExtract>=2:www/p5-HTML-TableExtract \
+		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-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-Set-Scalar>=0:devel/p5-Set-Scalar \
+		p5-Sort-Naturally>=1: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-Writer>=0:textproc/p5-XML-SAX-Writer \
+		p5-XML-Simple>=2:textproc/p5-XML-Simple \
+		p5-XML-Twig>=0:textproc/p5-XML-Twig \
+		p5-XML-Writer>=0:textproc/p5-XML-Writer \
+		p5-YAML>=0:textproc/p5-YAML \
+		p5-libwww>=0:www/p5-libwww \
+		p5-libxml>=0:textproc/p5-libxml
+RUN_DEPENDS:=	${BUILD_DEPENDS}
+
+USES=		perl5
+USE_PERL5=	modbuild
+NO_ARCH=	yes
+
+OPTIONS_DEFINE=	DOCS EXAMPLES PGTEST SQLITETEST
+PGTEST_DESC=	Test PostGreSQL
+SQLITETEST_DESC=	Test SQLite
+PGTEST_RUN_DEPENDS=	p5-DBD-Pg>=3:databases/p5-DBD-Pg
+PGTEST_BUILD_DEPENDS=	p5-DBD-Pg>=3:databases/p5-DBD-Pg
+SQLITETEST_RUN_DEPENDS=	p5-DBD-SQLite>=1:databases/p5-DBD-SQLite
+SQLITETEST_BUILD_DEPENDS=	p5-DBD-SQLite>=1:databases/p5-DBD-SQLite
+
+post-patch:
+	@${FIND} ${WRKSRC}/examples ${WRKSRC}/doc -name "*.pl" -o -name "*.cgi" \
+		-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}
+.endfor
+	${CP} -R ${WRKSRC}/doc ${STAGEDIR}${DOCSDIR}
+
+post-install-EXAMPLES-on:
+	@${MKDIR} ${STAGEDIR}${EXAMPLESDIR}
+	${CP} -R ${WRKSRC}/examples/* ${STAGEDIR}${EXAMPLESDIR}
+
+.include <bsd.port.mk>

Property changes on: head/biology/p5-BioPerl/Makefile
___________________________________________________________________
Added: svn:eol-style
## -0,0 +1 ##
+native
\ No newline at end of property
Added: svn:keywords
## -0,0 +1 ##
+FreeBSD=%H
\ No newline at end of property
Added: svn:mime-type
## -0,0 +1 ##
+text/plain
\ No newline at end of property
Index: head/biology/p5-BioPerl/pkg-descr
===================================================================
--- head/biology/p5-BioPerl/pkg-descr	(nonexistent)
+++ head/biology/p5-BioPerl/pkg-descr	(revision 428868)
@@ -0,0 +1,11 @@
+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
+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/

Property changes on: head/biology/p5-BioPerl/pkg-descr
___________________________________________________________________
Added: fbsd:nokeywords
## -0,0 +1 ##
+yes
\ No newline at end of property
Added: svn:eol-style
## -0,0 +1 ##
+native
\ No newline at end of property
Added: svn:mime-type
## -0,0 +1 ##
+text/plain
\ No newline at end of property
Index: head/biology/p5-BioPerl/pkg-plist
===================================================================
--- head/biology/p5-BioPerl/pkg-plist	(nonexistent)
+++ head/biology/p5-BioPerl/pkg-plist	(revision 428868)
@@ -0,0 +1,1939 @@
+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_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
+%%SITE_PERL%%/Bio/Assembly/ContigAnalysis.pm
+%%SITE_PERL%%/Bio/Assembly/IO.pm
+%%SITE_PERL%%/Bio/Assembly/IO/ace.pm
+%%SITE_PERL%%/Bio/Assembly/IO/bowtie.pm
+%%SITE_PERL%%/Bio/Assembly/IO/maq.pm
+%%SITE_PERL%%/Bio/Assembly/IO/phrap.pm
+%%SITE_PERL%%/Bio/Assembly/IO/sam.pm
+%%SITE_PERL%%/Bio/Assembly/IO/tigr.pm
+%%SITE_PERL%%/Bio/Assembly/Scaffold.pm
+%%SITE_PERL%%/Bio/Assembly/ScaffoldI.pm
+%%SITE_PERL%%/Bio/Assembly/Singlet.pm
+%%SITE_PERL%%/Bio/Assembly/Tools/ContigSpectrum.pm
+%%SITE_PERL%%/Bio/Cluster/ClusterFactory.pm
+%%SITE_PERL%%/Bio/Cluster/FamilyI.pm
+%%SITE_PERL%%/Bio/Cluster/SequenceFamily.pm
+%%SITE_PERL%%/Bio/Cluster/UniGene.pm
+%%SITE_PERL%%/Bio/Cluster/UniGeneI.pm
+%%SITE_PERL%%/Bio/ClusterI.pm
+%%SITE_PERL%%/Bio/ClusterIO.pm
+%%SITE_PERL%%/Bio/ClusterIO/dbsnp.pm
+%%SITE_PERL%%/Bio/ClusterIO/unigene.pm
+%%SITE_PERL%%/Bio/CodonUsage/IO.pm
+%%SITE_PERL%%/Bio/CodonUsage/Table.pm
+%%SITE_PERL%%/Bio/Coordinate/Chain.pm
+%%SITE_PERL%%/Bio/Coordinate/Collection.pm
+%%SITE_PERL%%/Bio/Coordinate/ExtrapolatingPair.pm
+%%SITE_PERL%%/Bio/Coordinate/GeneMapper.pm
+%%SITE_PERL%%/Bio/Coordinate/Graph.pm
+%%SITE_PERL%%/Bio/Coordinate/MapperI.pm
+%%SITE_PERL%%/Bio/Coordinate/Pair.pm
+%%SITE_PERL%%/Bio/Coordinate/Result.pm
+%%SITE_PERL%%/Bio/Coordinate/Result/Gap.pm
+%%SITE_PERL%%/Bio/Coordinate/Result/Match.pm
+%%SITE_PERL%%/Bio/Coordinate/ResultI.pm
+%%SITE_PERL%%/Bio/Coordinate/Utils.pm
+%%SITE_PERL%%/Bio/DB/Ace.pm
+%%SITE_PERL%%/Bio/DB/BioFetch.pm
+%%SITE_PERL%%/Bio/DB/CUTG.pm
+%%SITE_PERL%%/Bio/DB/DBFetch.pm
+%%SITE_PERL%%/Bio/DB/EMBL.pm
+%%SITE_PERL%%/Bio/DB/EntrezGene.pm
+%%SITE_PERL%%/Bio/DB/Expression.pm
+%%SITE_PERL%%/Bio/DB/Expression/geo.pm
+%%SITE_PERL%%/Bio/DB/Failover.pm
+%%SITE_PERL%%/Bio/DB/Fasta.pm
+%%SITE_PERL%%/Bio/DB/FileCache.pm
+%%SITE_PERL%%/Bio/DB/Flat.pm
+%%SITE_PERL%%/Bio/DB/Flat/BDB.pm
+%%SITE_PERL%%/Bio/DB/Flat/BDB/embl.pm
+%%SITE_PERL%%/Bio/DB/Flat/BDB/fasta.pm
+%%SITE_PERL%%/Bio/DB/Flat/BDB/genbank.pm
+%%SITE_PERL%%/Bio/DB/Flat/BDB/swiss.pm
+%%SITE_PERL%%/Bio/DB/Flat/BinarySearch.pm
+%%SITE_PERL%%/Bio/DB/GFF.pm
+%%SITE_PERL%%/Bio/DB/GFF/Adaptor/ace.pm
+%%SITE_PERL%%/Bio/DB/GFF/Adaptor/berkeleydb.pm
+%%SITE_PERL%%/Bio/DB/GFF/Adaptor/berkeleydb/iterator.pm
+%%SITE_PERL%%/Bio/DB/GFF/Adaptor/biofetch.pm
+%%SITE_PERL%%/Bio/DB/GFF/Adaptor/biofetch_oracle.pm
+%%SITE_PERL%%/Bio/DB/GFF/Adaptor/dbi.pm
+%%SITE_PERL%%/Bio/DB/GFF/Adaptor/dbi/caching_handle.pm
+%%SITE_PERL%%/Bio/DB/GFF/Adaptor/dbi/iterator.pm
+%%SITE_PERL%%/Bio/DB/GFF/Adaptor/dbi/mysql.pm
+%%SITE_PERL%%/Bio/DB/GFF/Adaptor/dbi/mysqlace.pm
+%%SITE_PERL%%/Bio/DB/GFF/Adaptor/dbi/mysqlcmap.pm
+%%SITE_PERL%%/Bio/DB/GFF/Adaptor/dbi/mysqlopt.pm
+%%SITE_PERL%%/Bio/DB/GFF/Adaptor/dbi/oracle.pm
+%%SITE_PERL%%/Bio/DB/GFF/Adaptor/dbi/oracleace.pm
+%%SITE_PERL%%/Bio/DB/GFF/Adaptor/dbi/pg.pm
+%%SITE_PERL%%/Bio/DB/GFF/Adaptor/dbi/pg_fts.pm
+%%SITE_PERL%%/Bio/DB/GFF/Adaptor/memory.pm
+%%SITE_PERL%%/Bio/DB/GFF/Adaptor/memory/feature_serializer.pm
+%%SITE_PERL%%/Bio/DB/GFF/Adaptor/memory/iterator.pm
+%%SITE_PERL%%/Bio/DB/GFF/Aggregator.pm
+%%SITE_PERL%%/Bio/DB/GFF/Aggregator/alignment.pm
+%%SITE_PERL%%/Bio/DB/GFF/Aggregator/clone.pm
+%%SITE_PERL%%/Bio/DB/GFF/Aggregator/coding.pm
+%%SITE_PERL%%/Bio/DB/GFF/Aggregator/gene.pm
+%%SITE_PERL%%/Bio/DB/GFF/Aggregator/match.pm
+%%SITE_PERL%%/Bio/DB/GFF/Aggregator/none.pm
+%%SITE_PERL%%/Bio/DB/GFF/Aggregator/orf.pm
+%%SITE_PERL%%/Bio/DB/GFF/Aggregator/processed_transcript.pm
+%%SITE_PERL%%/Bio/DB/GFF/Aggregator/so_transcript.pm
+%%SITE_PERL%%/Bio/DB/GFF/Aggregator/transcript.pm
+%%SITE_PERL%%/Bio/DB/GFF/Aggregator/ucsc_acembly.pm
+%%SITE_PERL%%/Bio/DB/GFF/Aggregator/ucsc_ensgene.pm
+%%SITE_PERL%%/Bio/DB/GFF/Aggregator/ucsc_genscan.pm
+%%SITE_PERL%%/Bio/DB/GFF/Aggregator/ucsc_refgene.pm
+%%SITE_PERL%%/Bio/DB/GFF/Aggregator/ucsc_sanger22.pm
+%%SITE_PERL%%/Bio/DB/GFF/Aggregator/ucsc_sanger22pseudo.pm
+%%SITE_PERL%%/Bio/DB/GFF/Aggregator/ucsc_softberry.pm
+%%SITE_PERL%%/Bio/DB/GFF/Aggregator/ucsc_twinscan.pm
+%%SITE_PERL%%/Bio/DB/GFF/Aggregator/ucsc_unigene.pm
+%%SITE_PERL%%/Bio/DB/GFF/Featname.pm
+%%SITE_PERL%%/Bio/DB/GFF/Feature.pm
+%%SITE_PERL%%/Bio/DB/GFF/Homol.pm
+%%SITE_PERL%%/Bio/DB/GFF/RelSegment.pm
+%%SITE_PERL%%/Bio/DB/GFF/Segment.pm
+%%SITE_PERL%%/Bio/DB/GFF/Typename.pm
+%%SITE_PERL%%/Bio/DB/GFF/Util/Binning.pm
+%%SITE_PERL%%/Bio/DB/GFF/Util/Rearrange.pm
+%%SITE_PERL%%/Bio/DB/GenBank.pm
+%%SITE_PERL%%/Bio/DB/GenPept.pm
+%%SITE_PERL%%/Bio/DB/GenericWebAgent.pm
+%%SITE_PERL%%/Bio/DB/HIV.pm
+%%SITE_PERL%%/Bio/DB/HIV/HIVAnnotProcessor.pm
+%%SITE_PERL%%/Bio/DB/HIV/HIVQueryHelper.pm
+%%SITE_PERL%%/Bio/DB/HIV/lanl-schema.xml
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+%%PERL5_MAN3%%/Bio::Tree::Tree.3.gz
+%%PERL5_MAN3%%/Bio::Tree::TreeFunctionsI.3.gz
+%%PERL5_MAN3%%/Bio::Tree::TreeI.3.gz
+%%PERL5_MAN3%%/Bio::TreeIO.3.gz
+%%PERL5_MAN3%%/Bio::TreeIO::NewickParser.3.gz
+%%PERL5_MAN3%%/Bio::TreeIO::TreeEventBuilder.3.gz
+%%PERL5_MAN3%%/Bio::TreeIO::cluster.3.gz
+%%PERL5_MAN3%%/Bio::TreeIO::lintree.3.gz
+%%PERL5_MAN3%%/Bio::TreeIO::newick.3.gz
+%%PERL5_MAN3%%/Bio::TreeIO::nexml.3.gz
+%%PERL5_MAN3%%/Bio::TreeIO::nexus.3.gz
+%%PERL5_MAN3%%/Bio::TreeIO::nhx.3.gz
+%%PERL5_MAN3%%/Bio::TreeIO::pag.3.gz
+%%PERL5_MAN3%%/Bio::TreeIO::phyloxml.3.gz
+%%PERL5_MAN3%%/Bio::TreeIO::svggraph.3.gz
+%%PERL5_MAN3%%/Bio::TreeIO::tabtree.3.gz
+%%PERL5_MAN3%%/Bio::UpdateableSeqI.3.gz
+%%PERL5_MAN3%%/Bio::Variation::AAChange.3.gz
+%%PERL5_MAN3%%/Bio::Variation::AAReverseMutate.3.gz
+%%PERL5_MAN3%%/Bio::Variation::Allele.3.gz
+%%PERL5_MAN3%%/Bio::Variation::DNAMutation.3.gz
+%%PERL5_MAN3%%/Bio::Variation::IO.3.gz
+%%PERL5_MAN3%%/Bio::Variation::IO::flat.3.gz
+%%PERL5_MAN3%%/Bio::Variation::IO::xml.3.gz
+%%PERL5_MAN3%%/Bio::Variation::RNAChange.3.gz
+%%PERL5_MAN3%%/Bio::Variation::SNP.3.gz
+%%PERL5_MAN3%%/Bio::Variation::SeqDiff.3.gz
+%%PERL5_MAN3%%/Bio::Variation::VariantI.3.gz
+%%PERL5_MAN3%%/Bio::WebAgent.3.gz
+%%PERL5_MAN1%%/bp_aacomp.pl.1.gz
+%%PERL5_MAN1%%/bp_biofetch_genbank_proxy.pl.1.gz
+%%PERL5_MAN1%%/bp_bioflat_index.pl.1.gz
+%%PERL5_MAN1%%/bp_biogetseq.pl.1.gz
+%%PERL5_MAN1%%/bp_blast2tree.pl.1.gz
+%%PERL5_MAN1%%/bp_bulk_load_gff.pl.1.gz
+%%PERL5_MAN1%%/bp_chaos_plot.pl.1.gz
+%%PERL5_MAN1%%/bp_classify_hits_kingdom.pl.1.gz
+%%PERL5_MAN1%%/bp_composite_LD.pl.1.gz
+%%PERL5_MAN1%%/bp_dbsplit.pl.1.gz
+%%PERL5_MAN1%%/bp_download_query_genbank.pl.1.gz
+%%PERL5_MAN1%%/bp_extract_feature_seq.pl.1.gz
+%%PERL5_MAN1%%/bp_fast_load_gff.pl.1.gz
+%%PERL5_MAN1%%/bp_fastam9_to_table.pl.1.gz
+%%PERL5_MAN1%%/bp_fetch.pl.1.gz
+%%PERL5_MAN1%%/bp_filter_search.pl.1.gz
+%%PERL5_MAN1%%/bp_flanks.pl.1.gz
+%%PERL5_MAN1%%/bp_gccalc.pl.1.gz
+%%PERL5_MAN1%%/bp_genbank2gff.pl.1.gz
+%%PERL5_MAN1%%/bp_genbank2gff3.pl.1.gz
+%%PERL5_MAN1%%/bp_generate_histogram.pl.1.gz
+%%PERL5_MAN1%%/bp_heterogeneity_test.pl.1.gz
+%%PERL5_MAN1%%/bp_hivq.pl.1.gz
+%%PERL5_MAN1%%/bp_hmmer_to_table.pl.1.gz
+%%PERL5_MAN1%%/bp_index.pl.1.gz
+%%PERL5_MAN1%%/bp_load_gff.pl.1.gz
+%%PERL5_MAN1%%/bp_local_taxonomydb_query.pl.1.gz
+%%PERL5_MAN1%%/bp_make_mrna_protein.pl.1.gz
+%%PERL5_MAN1%%/bp_mask_by_search.pl.1.gz
+%%PERL5_MAN1%%/bp_meta_gff.pl.1.gz
+%%PERL5_MAN1%%/bp_mrtrans.pl.1.gz
+%%PERL5_MAN1%%/bp_mutate.pl.1.gz
+%%PERL5_MAN1%%/bp_netinstall.pl.1.gz
+%%PERL5_MAN1%%/bp_nexus2nh.pl.1.gz
+%%PERL5_MAN1%%/bp_nrdb.pl.1.gz
+%%PERL5_MAN1%%/bp_oligo_count.pl.1.gz
+%%PERL5_MAN1%%/bp_pairwise_kaks.pl.1.gz
+%%PERL5_MAN1%%/bp_parse_hmmsearch.pl.1.gz
+%%PERL5_MAN1%%/bp_process_gadfly.pl.1.gz
+%%PERL5_MAN1%%/bp_process_sgd.pl.1.gz
+%%PERL5_MAN1%%/bp_process_wormbase.pl.1.gz
+%%PERL5_MAN1%%/bp_query_entrez_taxa.pl.1.gz
+%%PERL5_MAN1%%/bp_remote_blast.pl.1.gz
+%%PERL5_MAN1%%/bp_revtrans-motif.pl.1.gz
+%%PERL5_MAN1%%/bp_search2BSML.pl.1.gz
+%%PERL5_MAN1%%/bp_search2alnblocks.pl.1.gz
+%%PERL5_MAN1%%/bp_search2gff.pl.1.gz
+%%PERL5_MAN1%%/bp_search2table.pl.1.gz
+%%PERL5_MAN1%%/bp_search2tribe.pl.1.gz
+%%PERL5_MAN1%%/bp_seq_length.pl.1.gz
+%%PERL5_MAN1%%/bp_seqconvert.pl.1.gz
+%%PERL5_MAN1%%/bp_seqcut.pl.1.gz
+%%PERL5_MAN1%%/bp_seqfeature_load.pl.1.gz
+%%PERL5_MAN1%%/bp_seqpart.pl.1.gz
+%%PERL5_MAN1%%/bp_seqret.pl.1.gz
+%%PERL5_MAN1%%/bp_seqretsplit.pl.1.gz
+%%PERL5_MAN1%%/bp_split_seq.pl.1.gz
+%%PERL5_MAN1%%/bp_sreformat.pl.1.gz
+%%PERL5_MAN1%%/bp_taxid4species.pl.1.gz
+%%PERL5_MAN1%%/bp_taxonomy2tree.pl.1.gz
+%%PERL5_MAN1%%/bp_translate_seq.pl.1.gz
+%%PERL5_MAN1%%/bp_tree2pag.pl.1.gz
+%%PERL5_MAN1%%/bp_unflatten_seq.pl.1.gz
+%%DATADIR%%/models/README
+%%DATADIR%%/models/biblio.dia
+%%DATADIR%%/models/bio_liveseq_variation.dia
+%%DATADIR%%/models/bio_map.dia
+%%DATADIR%%/models/bio_restriction.dia
+%%DATADIR%%/models/bioperl.dia
+%%DATADIR%%/models/coordinatemapper.dia
+%%DATADIR%%/models/map_proposal.txt
+%%DATADIR%%/models/maps_and_markers.dia
+%%DATADIR%%/models/popgen.dia
+%%DATADIR%%/models/population_proposal.txt
+%%DATADIR%%/scripts/Bio-DB-GFF/README
+%%DATADIR%%/scripts/Bio-DB-GFF/bp_bulk_load_gff.pl
+%%DATADIR%%/scripts/Bio-DB-GFF/bp_fast_load_gff.pl
+%%DATADIR%%/scripts/Bio-DB-GFF/bp_genbank2gff.pl
+%%DATADIR%%/scripts/Bio-DB-GFF/bp_genbank2gff3.pl
+%%DATADIR%%/scripts/Bio-DB-GFF/bp_generate_histogram.pl
+%%DATADIR%%/scripts/Bio-DB-GFF/bp_load_gff.pl
+%%DATADIR%%/scripts/Bio-DB-GFF/bp_meta_gff.pl
+%%DATADIR%%/scripts/Bio-DB-GFF/bp_process_gadfly.pl
+%%DATADIR%%/scripts/Bio-DB-GFF/bp_process_sgd.pl
+%%DATADIR%%/scripts/Bio-DB-GFF/bp_process_wormbase.pl
+%%DATADIR%%/scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_delete.pl
+%%DATADIR%%/scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_gff3.pl
+%%DATADIR%%/scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_load.pl
+%%DATADIR%%/scripts/DB-HIV/bp_hivq.pl
+%%DATADIR%%/scripts/DB/TAG
+%%DATADIR%%/scripts/DB/bp_biofetch_genbank_proxy.pl
+%%DATADIR%%/scripts/DB/bp_bioflat_index.pl
+%%DATADIR%%/scripts/DB/bp_biogetseq.pl
+%%DATADIR%%/scripts/DB/bp_flanks.pl
+%%DATADIR%%/scripts/README
+%%DATADIR%%/scripts/das/README
+%%DATADIR%%/scripts/das/TAG
+%%DATADIR%%/scripts/das/bp_das_server.pl
+%%DATADIR%%/scripts/index/TAG
+%%DATADIR%%/scripts/index/bp_fetch.pl
+%%DATADIR%%/scripts/index/bp_index.pl
+%%DATADIR%%/scripts/index/bp_seqret.pl
+%%DATADIR%%/scripts/popgen/bp_composite_LD.pl
+%%DATADIR%%/scripts/popgen/bp_heterogeneity_test.pl
+%%DATADIR%%/scripts/searchio/README
+%%DATADIR%%/scripts/searchio/TAG
+%%DATADIR%%/scripts/searchio/bp_fastam9_to_table.pl
+%%DATADIR%%/scripts/searchio/bp_filter_search.pl
+%%DATADIR%%/scripts/searchio/bp_hmmer_to_table.pl
+%%DATADIR%%/scripts/searchio/bp_parse_hmmsearch.pl
+%%DATADIR%%/scripts/searchio/bp_search2table.pl
+%%DATADIR%%/scripts/seq/TAG
+%%DATADIR%%/scripts/seq/bp_extract_feature_seq.pl
+%%DATADIR%%/scripts/seq/bp_make_mrna_protein.pl
+%%DATADIR%%/scripts/seq/bp_seqconvert.pl
+%%DATADIR%%/scripts/seq/bp_seqcut.pl
+%%DATADIR%%/scripts/seq/bp_seqpart.pl
+%%DATADIR%%/scripts/seq/bp_seqretsplit.pl
+%%DATADIR%%/scripts/seq/bp_split_seq.pl
+%%DATADIR%%/scripts/seq/bp_translate_seq.pl
+%%DATADIR%%/scripts/seq/bp_unflatten_seq.pl
+%%DATADIR%%/scripts/seqstats/TAG
+%%DATADIR%%/scripts/seqstats/bp_aacomp.pl
+%%DATADIR%%/scripts/seqstats/bp_chaos_plot.pl
+%%DATADIR%%/scripts/seqstats/bp_gccalc.pl
+%%DATADIR%%/scripts/seqstats/bp_oligo_count.pl
+%%DATADIR%%/scripts/taxa/TAG
+%%DATADIR%%/scripts/taxa/bp_classify_hits_kingdom.pl
+%%DATADIR%%/scripts/taxa/bp_local_taxonomydb_query.pl
+%%DATADIR%%/scripts/taxa/bp_query_entrez_taxa.pl
+%%DATADIR%%/scripts/taxa/bp_taxid4species.pl
+%%DATADIR%%/scripts/taxa/bp_taxonomy2tree.pl
+%%DATADIR%%/scripts/tree/TAG
+%%DATADIR%%/scripts/tree/bp_blast2tree.pl
+%%DATADIR%%/scripts/tree/bp_nexus2nh.pl
+%%DATADIR%%/scripts/tree/bp_tree2pag.pl
+%%DATADIR%%/scripts/utilities/README
+%%DATADIR%%/scripts/utilities/TAG
+%%DATADIR%%/scripts/utilities/bp_dbsplit.pl
+%%DATADIR%%/scripts/utilities/bp_download_query_genbank.pl
+%%DATADIR%%/scripts/utilities/bp_mask_by_search.pl
+%%DATADIR%%/scripts/utilities/bp_mrtrans.pl
+%%DATADIR%%/scripts/utilities/bp_mutate.pl
+%%DATADIR%%/scripts/utilities/bp_netinstall.pl
+%%DATADIR%%/scripts/utilities/bp_nrdb.pl
+%%DATADIR%%/scripts/utilities/bp_pairwise_kaks.pl
+%%DATADIR%%/scripts/utilities/bp_remote_blast.pl
+%%DATADIR%%/scripts/utilities/bp_revtrans-motif.pl
+%%DATADIR%%/scripts/utilities/bp_search2BSML.pl
+%%DATADIR%%/scripts/utilities/bp_search2alnblocks.pl
+%%DATADIR%%/scripts/utilities/bp_search2gff.pl
+%%DATADIR%%/scripts/utilities/bp_search2tribe.pl
+%%DATADIR%%/scripts/utilities/bp_seq_length.pl
+%%DATADIR%%/scripts/utilities/bp_sreformat.pl
+%%PORTDOCS%%%%DOCSDIR%%/AUTHORS
+%%PORTDOCS%%%%DOCSDIR%%/BUGS
+%%PORTDOCS%%%%DOCSDIR%%/Changes
+%%PORTDOCS%%%%DOCSDIR%%/DEPENDENCIES
+%%PORTDOCS%%%%DOCSDIR%%/DEPRECATED
+%%PORTDOCS%%%%DOCSDIR%%/INSTALL
+%%PORTDOCS%%%%DOCSDIR%%/LICENSE
+%%PORTDOCS%%%%DOCSDIR%%/MANIFEST
+%%PORTDOCS%%%%DOCSDIR%%/README
+%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/Build.PL
+%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/Changes
+%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/LICENSE
+%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/MANIFEST
+%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/META.yml
+%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/Makefile.PL
+%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/README
+%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/bin/deob_index.pl
+%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/bin/run-deobfuscator-update.pl
+%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/cgi-bin/deob_detail.cgi
+%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/cgi-bin/deob_flowchart.png
+%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/cgi-bin/deob_help.html
+%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/cgi-bin/deob_interface.cgi
+%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/excluded_modules.txt
+%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/lib/Deobfuscator.pm
+%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/t/00.load.t
+%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/t/pod.t
+%%PORTDOCS%%%%DOCSDIR%%/doc/README
+%%PORTDOCS%%%%DOCSDIR%%/doc/makedoc.PL
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Bio-DB-GFF/load_ucsc.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/align/FastAlign.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/align/align_on_codons.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/align/aligntutorial.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/align/clustalw.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/align/simplealign.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bioperl.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cluster/dbsnp.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/contributed/nmrpdb_parse.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/contributed/prosite2perl.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/contributed/rebase2list.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/db/dbfetch
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/db/est_tissue_query.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/db/gb2features.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/db/getGenBank.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/db/get_seqs.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/db/rfetch.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/db/use_registry.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/generate_random_seq.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/liveseq/change_gene.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/longorf.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/make_primers.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/popgen/parse_calc_stats.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/quality/svgtrace.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/rev_and_trans.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/revcom_dir.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/root/README
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/root/exceptions1.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/root/exceptions2.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/root/exceptions3.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/root/exceptions4.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/root/lib/TestInterface.pm
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/root/lib/TestObject.pm
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/blast_example.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/custom_writer.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/hitwriter.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/hspwriter.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/htmlwriter.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/psiblast_features.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/psiblast_iterations.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/rawwriter.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/resultwriter.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/waba2gff.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/waba2gff3.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sirna/TAG
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sirna/rnai_finder.cgi
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/structure/structure-io.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/subsequence.cgi
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tk/gsequence.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tk/hitdisplay.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tools/extract_genes.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tools/gb_to_gff.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tools/gff2ps.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tools/parse_codeml.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tools/psw.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tools/reverse-translate.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tools/run_genscan.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tools/run_primer3.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tools/seq_pattern.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tools/standaloneblast.pl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tree/paup2phylip.pl

Property changes on: head/biology/p5-BioPerl/pkg-plist
___________________________________________________________________
Added: fbsd:nokeywords
## -0,0 +1 ##
+yes
\ No newline at end of property
Added: svn:eol-style
## -0,0 +1 ##
+native
\ No newline at end of property
Added: svn:mime-type
## -0,0 +1 ##
+text/plain
\ No newline at end of property
Index: head/biology/p5-BioPerl/distinfo
===================================================================
--- head/biology/p5-BioPerl/distinfo	(nonexistent)
+++ head/biology/p5-BioPerl/distinfo	(revision 428868)
@@ -0,0 +1,2 @@
+SHA256 (BioPerl-1.6.924.tar.gz) = 616a7546bb3c58504de27304a0f6cb904e18b6bbcdb6a4ec8454f2bd37bb76d0
+SIZE (BioPerl-1.6.924.tar.gz) = 12623118

Property changes on: head/biology/p5-BioPerl/distinfo
___________________________________________________________________
Added: fbsd:nokeywords
## -0,0 +1 ##
+yes
\ No newline at end of property
Added: svn:eol-style
## -0,0 +1 ##
+native
\ No newline at end of property
Added: svn:mime-type
## -0,0 +1 ##
+text/plain
\ No newline at end of property
Index: head/biology/p5-BioPerl/files/patch-Bio-Root-Build.pm
===================================================================
--- head/biology/p5-BioPerl/files/patch-Bio-Root-Build.pm	(nonexistent)
+++ head/biology/p5-BioPerl/files/patch-Bio-Root-Build.pm	(revision 428868)
@@ -0,0 +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
+@@ -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

Property changes on: head/biology/p5-BioPerl/files/patch-Bio-Root-Build.pm
___________________________________________________________________
Added: fbsd:nokeywords
## -0,0 +1 ##
+yes
\ No newline at end of property
Added: svn:eol-style
## -0,0 +1 ##
+native
\ No newline at end of property
Added: svn:mime-type
## -0,0 +1 ##
+text/plain
\ No newline at end of property
Index: head/biology/p5-BioPerl/files/patch-Build.PL
===================================================================
--- head/biology/p5-BioPerl/files/patch-Build.PL	(nonexistent)
+++ head/biology/p5-BioPerl/files/patch-Build.PL	(revision 428868)
@@ -0,0 +1,99 @@
+--- 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_requires      => {
+-                            'CPAN'                      => 1.81,
+                             'Module::Build'             => 0.2805,
+                             'Test::Harness'             => 2.62,
+                             'Test::Most'                => 0,
+@@ -376,86 +375,8 @@
+ 
+ sub prompt_for_biodb {
+     my $accept = shift;
+-    my $proceed = $accept ? 0 : $build->y_n("Do you want to run the Bio::DB::GFF or ".
+-                              "Bio::DB::SeqFeature::Store live database tests? ".
+-                              "y/n", 'n');
+-
+-    if ($proceed) {
+-        my @driver_choices;
+-        foreach my $poss ('SQLite', 'mysql', 'Pg', 'Oracle') {
+-            if (grep {/$poss/i} @drivers) {
+-                my $choice = $poss;
+-                $choice =~ s/^(.)/[$1]/;
+-                push(@driver_choices, $choice);
+-            }
+-        }
+-
+-        my $driver;
+-        if (@driver_choices > 1) {
+-            my ($default) = $driver_choices[0] =~ /\[(.)/;
+-            $driver = $build->prompt("Which database driver should be used? ".join(" ", @driver_choices), $default);
+-        }
+-        else {
+-            ($driver) = $driver_choices[0] =~ /\[(.)/;
+-        }
+-        if ($driver =~ /^[mM]/) {
+-            $driver = 'mysql';
+-        }
+-        elsif ($driver =~ /^[pP]/) {
+-            $driver = 'Pg';
+-        }
+-        elsif ($driver =~ /^[oO]/) {
+-            $driver = 'Oracle';
+-        }
+-        elsif ($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 $use_host = 1;
+-        if ($test_host eq 'undef' || $test_host eq 'localhost') {
+-            $use_host = 0;
+-        }
+-
+-        my $test_dsn;
+-        if ($driver eq 'Pg' || $driver eq 'SQLite') {
+-            $test_dsn = "dbi:$driver:dbname=$test_db";
+-            $mysql_ok = 0;
+-        }
+-        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);
+-
+-        $build->log_info("  - will run tests with database driver '$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;
+ }

Property changes on: head/biology/p5-BioPerl/files/patch-Build.PL
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+yes
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+native
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