Attachment #90932 for bug #128193

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# Date created:		21 November 2005
# Whom:	      		Mauricio Herrera Cuadra <mauricio@arareko.net>
#
# $FreeBSD: ports/biology/p5-bioperl-devel/Makefile,v 1.11 2007/09/08 00:53:11 linimon Exp $
#

PORTNAME=	bioperl

		${SITE_PERL}/Spreadsheet/ParseExcel.pm:${PORTSDIR}/textproc/p5-Spreadsheet-ParseExcel \
		${SITE_PERL}/SVG.pm:${PORTSDIR}/textproc/p5-SVG \
		${SITE_PERL}/SVG/Graph.pm:${PORTSDIR}/graphics/p5-SVG-Graph \
		${SITE_PERL}/Test/Harness.pm:${PORTSDIR}/devel/p5-Test-Harness \
		${SITE_PERL}/Text/Shellwords.pm:${PORTSDIR}/textproc/p5-Text-Shellwords \
		${SITE_PERL}/XML/DOM.pm:${PORTSDIR}/textproc/p5-XML-DOM \
		${SITE_PERL}/XML/DOM/XPath.pm:${PORTSDIR}/textproc/p5-XML-DOM-XPath \

		${SITE_PERL}/${PERL_ARCH}/XML/Parser.pm:${PORTSDIR}/textproc/p5-XML-Parser
RUN_DEPENDS=	${BUILD_DEPENDS}

BROKEN=		missing dependencies

CONFLICTS=	p5-bioperl-1.[02468]*

LATEST_LINK=	p5-bioperl-devel

PERL_MODBUILD=	YES

NOPORTDOCS=	yes
NOPORTEXAMPLES=	yes
NOPORTDATA=	yes

MAN1=		bp_aacomp.pl.1 \
		bp_biblio.pl.1 \
		bp_biofetch_genbank_proxy.pl.1 \

post-install:
	${MKDIR} ${DATADIR}
	${CP} -R ${WRKSRC}/scripts ${WRKSRC}/models ${DATADIR}
.if !defined(NOPORTEXAMPLES)
	${MKDIR} ${EXAMPLESDIR}
	${CP} -R ${WRKSRC}/examples/* ${EXAMPLESDIR}
.endif
.if !defined(NOPORTDOCS)
	${MKDIR} ${DOCSDIR}
.for doc in AUTHORS BUGS Changes DEPENDENCIES DEPRECATED INSTALL LICENSE PLATFORMS README

.endif

.include <bsd.port.post.mk>





--- Build.PL.orig	Wed Feb 14 05:37:47 2007
+++ Build.PL	Sun Jun 15 02:24:07 2008
@@ -32,7 +32,6 @@
                             'Test::More'                => 0,
                             'Module::Build'             => 0.2805,
                             'Test::Harness'             => 2.62,
-                            'CPAN'                      => 1.81
                            },
     recommends          => { # does what you would expect of recommends, except more informative output and generates optional_features in META.yml
                             'Ace'                       => '0/access of ACeDB database/Bio::DB::Ace,Bio::DB::GFF::Adaptor::ace',
@@ -174,7 +173,7 @@
 }
 
 sub prompt_for_biodbgff {
-    my $proceed = $build->y_n("Do you want to run the BioDBGFF live database tests? y/n", 'n');
+    my $proceed = undef; # $build->y_n("Do you want to run the BioDBGFF live database tests? y/n", 'n');
     
     if ($proceed) {
         my @driver_choices;




--- ModuleBuildBioperl.pm.orig	2007-02-14 05:37:47.000000000 -0600
+++ ModuleBuildBioperl.pm	2008-10-17 23:16:52.000000000 -0500
@@ -93,7 +93,7 @@
     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 = $self->prompt($question, 'a');
+    my $prompt = 'a'; # $self->prompt($question, 'a');
     
     if ($prompt =~ /^[aA]/) {
         $self->log_info("  - will install all scripts\n");
@@ -328,7 +328,7 @@
                     
                     $status->{message} .= "\n   (wanted for $why, used by $by_what)";
                     
-                    my $installed = $self->install_optional($modname, $preferred_version, $status->{message});
+                    my $installed = 'skip'; # $self->install_optional($modname, $preferred_version, $status->{message});
                     next if $installed eq 'ok';
                     $status->{message} = $installed unless $installed eq 'skip';
                 }




%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/MANIFEST
%%PORTDOCS%%%%DOCSDIR%%/doc/README
%%PORTDOCS%%%%DOCSDIR%%/doc/makedoc.PL
%%EXAMPLESDIR%%/root/lib/Bio/PrimarySeq.pm
%%EXAMPLESDIR%%/root/lib/Bio/SeqI.pm
%%EXAMPLESDIR%%/root/lib/Bio/Seq.pm
%%EXAMPLESDIR%%/root/lib/Bio/PrimarySeqI.pm
%%EXAMPLESDIR%%/root/lib/TestObject.pm
%%EXAMPLESDIR%%/root/lib/TestInterface.pm
%%EXAMPLESDIR%%/root/exceptions2.pl
%%EXAMPLESDIR%%/root/exceptions4.pl
%%EXAMPLESDIR%%/root/README
%%EXAMPLESDIR%%/root/exceptions1.pl
%%EXAMPLESDIR%%/root/exceptions3.pl
%%EXAMPLESDIR%%/tools/run_genscan.pl
%%EXAMPLESDIR%%/tools/gff2ps.pl
%%EXAMPLESDIR%%/tools/extract_genes.pl
%%EXAMPLESDIR%%/tools/seq_pattern.pl
%%EXAMPLESDIR%%/tools/gb_to_gff.pl
%%EXAMPLESDIR%%/tools/psw.pl
%%EXAMPLESDIR%%/tools/standaloneblast.pl
%%EXAMPLESDIR%%/tools/run_primer3.pl
%%EXAMPLESDIR%%/tools/parse_codeml.pl
%%EXAMPLESDIR%%/tk/gsequence.pl
%%EXAMPLESDIR%%/tk/hitdisplay.pl
%%EXAMPLESDIR%%/tree/paup2phylip.pl
%%EXAMPLESDIR%%/structure/structure-io.pl
%%EXAMPLESDIR%%/sirna/rnai_finder.cgi
%%EXAMPLESDIR%%/sirna/TAG
%%EXAMPLESDIR%%/searchio/custom_writer.pl
%%EXAMPLESDIR%%/searchio/resultwriter.pl
%%EXAMPLESDIR%%/searchio/blast_example.pl
%%EXAMPLESDIR%%/searchio/waba2gff3.pl
%%EXAMPLESDIR%%/searchio/hspwriter.pl
%%EXAMPLESDIR%%/searchio/psiblast_iterations.pl
%%EXAMPLESDIR%%/searchio/waba2gff.pl
%%EXAMPLESDIR%%/searchio/psiblast_features.pl
%%EXAMPLESDIR%%/searchio/htmlwriter.pl
%%EXAMPLESDIR%%/searchio/hitwriter.pl
%%EXAMPLESDIR%%/searchio/rawwriter.pl
%%EXAMPLESDIR%%/db/gb2features.pl
%%EXAMPLESDIR%%/db/dbfetch
%%EXAMPLESDIR%%/db/use_registry.pl
%%EXAMPLESDIR%%/db/est_tissue_query.pl
%%EXAMPLESDIR%%/db/rfetch.pl
%%EXAMPLESDIR%%/db/getGenBank.pl
%%EXAMPLESDIR%%/db/get_seqs.pl
%%EXAMPLESDIR%%/align/clustalw.pl
%%EXAMPLESDIR%%/align/aligntutorial.pl
%%EXAMPLESDIR%%/align/simplealign.pl
%%EXAMPLESDIR%%/align/align_on_codons.pl
%%EXAMPLESDIR%%/biblio/biblio-eutils-example.pl
%%EXAMPLESDIR%%/biblio/biblio_soap.pl
%%EXAMPLESDIR%%/biblio/biblio-soap-example.pl
%%EXAMPLESDIR%%/popgen/parse_calc_stats.pl
%%EXAMPLESDIR%%/biographics/feature_data.gff
%%EXAMPLESDIR%%/biographics/feature_data.txt
%%EXAMPLESDIR%%/biographics/render_sequence.pl
%%EXAMPLESDIR%%/biographics/dynamic_glyphs.pl
%%EXAMPLESDIR%%/biographics/all_glyphs.pl
%%EXAMPLESDIR%%/biographics/lots_of_glyphs.pl
%%EXAMPLESDIR%%/cluster/dbsnp.pl
%%EXAMPLESDIR%%/liveseq/change_gene.pl
%%EXAMPLESDIR%%/contributed/prosite2perl.pl
%%EXAMPLESDIR%%/contributed/nmrpdb_parse.pl
%%EXAMPLESDIR%%/contributed/rebase2list.pl
%%EXAMPLESDIR%%/Bio-DB-GFF/load_ucsc.pl
%%EXAMPLESDIR%%/make_primers.pl
%%EXAMPLESDIR%%/longorf.pl
%%EXAMPLESDIR%%/bioperl.pl
%%EXAMPLESDIR%%/generate_random_seq.pl
%%EXAMPLESDIR%%/rev_and_trans.pl
%%EXAMPLESDIR%%/revcom_dir.pl
%%EXAMPLESDIR%%/subsequence.cgi
%%DATADIR%%/models/map_proposal.txt
%%DATADIR%%/models/bio_liveseq_variation.dia
%%DATADIR%%/models/maps_and_markers.dia

%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/Deobfuscator
%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc
%%PORTDOCS%%@dirrm %%DOCSDIR%%
@dirrm %%EXAMPLESDIR%%/root/lib/Bio
@dirrm %%EXAMPLESDIR%%/root/lib
@dirrm %%EXAMPLESDIR%%/root
@dirrm %%EXAMPLESDIR%%/tools
@dirrm %%EXAMPLESDIR%%/tk
@dirrm %%EXAMPLESDIR%%/tree
@dirrm %%EXAMPLESDIR%%/structure
@dirrm %%EXAMPLESDIR%%/sirna
@dirrm %%EXAMPLESDIR%%/searchio
@dirrm %%EXAMPLESDIR%%/db
@dirrm %%EXAMPLESDIR%%/align
@dirrm %%EXAMPLESDIR%%/biblio
@dirrm %%EXAMPLESDIR%%/popgen
@dirrm %%EXAMPLESDIR%%/biographics
@dirrm %%EXAMPLESDIR%%/cluster
@dirrm %%EXAMPLESDIR%%/liveseq
@dirrm %%EXAMPLESDIR%%/contributed
@dirrm %%EXAMPLESDIR%%/Bio-DB-GFF
@dirrm %%EXAMPLESDIR%%
@dirrm %%DATADIR%%/models
@dirrm %%DATADIR%%/scripts/taxa
@dirrm %%DATADIR%%/scripts/seq

Return to bug 128193

Lines 2-8 Link Here

(-)p5-bioperl-devel/Makefile (-10 / +2 lines)
2	# Date created: 21 November 2005	2	# Date created: 21 November 2005
3	# Whom: Mauricio Herrera Cuadra <mauricio@arareko.net>	3	# Whom: Mauricio Herrera Cuadra <mauricio@arareko.net>
4	#	4	#
5	# $FreeBSD: ports/biology/p5-bioperl-devel/Makefile,v 1.13 2008/07/07 22:57:49 pav Exp $	5	# $FreeBSD: ports/biology/p5-bioperl-devel/Makefile,v 1.11 2007/09/08 00:53:11 linimon Exp $
6	#	6	#
7		7
8	PORTNAME= bioperl	8	PORTNAME= bioperl
Lines 33-38 Link Here
33	${SITE_PERL}/Spreadsheet/ParseExcel.pm:${PORTSDIR}/textproc/p5-Spreadsheet-ParseExcel \	33	${SITE_PERL}/Spreadsheet/ParseExcel.pm:${PORTSDIR}/textproc/p5-Spreadsheet-ParseExcel \
34	${SITE_PERL}/SVG.pm:${PORTSDIR}/textproc/p5-SVG \	34	${SITE_PERL}/SVG.pm:${PORTSDIR}/textproc/p5-SVG \
35	${SITE_PERL}/SVG/Graph.pm:${PORTSDIR}/graphics/p5-SVG-Graph \	35	${SITE_PERL}/SVG/Graph.pm:${PORTSDIR}/graphics/p5-SVG-Graph \
		36	${SITE_PERL}/Test/Harness.pm:${PORTSDIR}/devel/p5-Test-Harness \
36	${SITE_PERL}/Text/Shellwords.pm:${PORTSDIR}/textproc/p5-Text-Shellwords \	37	${SITE_PERL}/Text/Shellwords.pm:${PORTSDIR}/textproc/p5-Text-Shellwords \
37	${SITE_PERL}/XML/DOM.pm:${PORTSDIR}/textproc/p5-XML-DOM \	38	${SITE_PERL}/XML/DOM.pm:${PORTSDIR}/textproc/p5-XML-DOM \
38	${SITE_PERL}/XML/DOM/XPath.pm:${PORTSDIR}/textproc/p5-XML-DOM-XPath \	39	${SITE_PERL}/XML/DOM/XPath.pm:${PORTSDIR}/textproc/p5-XML-DOM-XPath \
Lines 53-70 Link Here
53	${SITE_PERL}/${PERL_ARCH}/XML/Parser.pm:${PORTSDIR}/textproc/p5-XML-Parser	54	${SITE_PERL}/${PERL_ARCH}/XML/Parser.pm:${PORTSDIR}/textproc/p5-XML-Parser
54	RUN_DEPENDS= ${BUILD_DEPENDS}	55	RUN_DEPENDS= ${BUILD_DEPENDS}
55		56
56	BROKEN= missing dependencies
57
58	CONFLICTS= p5-bioperl-1.[02468]*	57	CONFLICTS= p5-bioperl-1.[02468]*
59		58
60	LATEST_LINK= p5-bioperl-devel	59	LATEST_LINK= p5-bioperl-devel
61		60
62	PERL_MODBUILD= YES	61	PERL_MODBUILD= YES
63		62
64	NOPORTDOCS= yes
65	NOPORTEXAMPLES= yes
66	NOPORTDATA= yes
67
68	MAN1= bp_aacomp.pl.1 \	63	MAN1= bp_aacomp.pl.1 \
69	bp_biblio.pl.1 \	64	bp_biblio.pl.1 \
70	bp_biofetch_genbank_proxy.pl.1 \	65	bp_biofetch_genbank_proxy.pl.1 \
Lines 993-1002 Link Here
993	post-install:	988	post-install:
994	${MKDIR} ${DATADIR}	989	${MKDIR} ${DATADIR}
995	${CP} -R ${WRKSRC}/scripts ${WRKSRC}/models ${DATADIR}	990	${CP} -R ${WRKSRC}/scripts ${WRKSRC}/models ${DATADIR}
996	.if !defined(NOPORTEXAMPLES)
997	${MKDIR} ${EXAMPLESDIR}	991	${MKDIR} ${EXAMPLESDIR}
998	${CP} -R ${WRKSRC}/examples/* ${EXAMPLESDIR}	992	${CP} -R ${WRKSRC}/examples/* ${EXAMPLESDIR}
999	.endif
1000	.if !defined(NOPORTDOCS)	993	.if !defined(NOPORTDOCS)
1001	${MKDIR} ${DOCSDIR}	994	${MKDIR} ${DOCSDIR}
1002	.for doc in AUTHORS BUGS Changes DEPENDENCIES DEPRECATED INSTALL LICENSE PLATFORMS README	995	.for doc in AUTHORS BUGS Changes DEPENDENCIES DEPRECATED INSTALL LICENSE PLATFORMS README
Lines 1006-1009 Link Here
1006	.endif	999	.endif
1007		1000
1008	.include <bsd.port.post.mk>	1001	.include <bsd.port.post.mk>
1009

Line 0 Link Here

(-)p5-bioperl-devel/files/patch-Build.PL (+19 lines)
	1	--- Build.PL.orig Wed Feb 14 05:37:47 2007
	2	+++ Build.PL Sun Jun 15 02:24:07 2008
	3	@@ -32,7 +32,6 @@
	4	'Test::More' => 0,
	5	'Module::Build' => 0.2805,
	6	'Test::Harness' => 2.62,
	7	- 'CPAN' => 1.81
	8	},
	9	recommends => { # does what you would expect of recommends, except more informative output and generates optional_features in META.yml
	10	'Ace' => '0/access of ACeDB database/Bio::DB::Ace,Bio::DB::GFF::Adaptor::ace',
	11	@@ -174,7 +173,7 @@
	12	}
	13
	14	sub prompt_for_biodbgff {
	15	- my $proceed = $build->y_n("Do you want to run the BioDBGFF live database tests? y/n", 'n');
	16	+ my $proceed = undef; # $build->y_n("Do you want to run the BioDBGFF live database tests? y/n", 'n');
	17
	18	if ($proceed) {
	19	my @driver_choices;

Line 0 Link Here

(-)p5-bioperl-devel/files/patch-ModuleBuildBioperl.pm (+20 lines)
	1	--- ModuleBuildBioperl.pm.orig 2007-02-14 05:37:47.000000000 -0600
	2	+++ ModuleBuildBioperl.pm 2008-10-17 23:16:52.000000000 -0500
	3	@@ -93,7 +93,7 @@
	4	closedir($scripts_dir);
	5	my $question = $int_ok ? "Install [a]ll Bioperl scripts, [n]one, or choose groups [i]nteractively?" : "Install [a]ll Bioperl scripts or [n]one?";
	6
	7	- my $prompt = $self->prompt($question, 'a');
	8	+ my $prompt = 'a'; # $self->prompt($question, 'a');
	9
	10	if ($prompt =~ /^[aA]/) {
	11	$self->log_info(" - will install all scripts\n");
	12	@@ -328,7 +328,7 @@
	13
	14	$status->{message} .= "\n (wanted for $why, used by $by_what)";
	15
	16	- my $installed = $self->install_optional($modname, $preferred_version, $status->{message});
	17	+ my $installed = 'skip'; # $self->install_optional($modname, $preferred_version, $status->{message});
	18	next if $installed eq 'ok';
	19	$status->{message} = $installed unless $installed eq 'skip';
	20	}

Lines 941-1017 Link Here

(-)p5-bioperl-devel/pkg-plist (-90 / +90 lines)
941	%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/MANIFEST	941	%%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/MANIFEST
942	%%PORTDOCS%%%%DOCSDIR%%/doc/README	942	%%PORTDOCS%%%%DOCSDIR%%/doc/README
943	%%PORTDOCS%%%%DOCSDIR%%/doc/makedoc.PL	943	%%PORTDOCS%%%%DOCSDIR%%/doc/makedoc.PL
944	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/root/lib/Bio/PrimarySeq.pm	944	%%EXAMPLESDIR%%/root/lib/Bio/PrimarySeq.pm
945	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/root/lib/Bio/SeqI.pm	945	%%EXAMPLESDIR%%/root/lib/Bio/SeqI.pm
946	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/root/lib/Bio/Seq.pm	946	%%EXAMPLESDIR%%/root/lib/Bio/Seq.pm
947	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/root/lib/Bio/PrimarySeqI.pm	947	%%EXAMPLESDIR%%/root/lib/Bio/PrimarySeqI.pm
948	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/root/lib/TestObject.pm	948	%%EXAMPLESDIR%%/root/lib/TestObject.pm
949	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/root/lib/TestInterface.pm	949	%%EXAMPLESDIR%%/root/lib/TestInterface.pm
950	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/root/exceptions2.pl	950	%%EXAMPLESDIR%%/root/exceptions2.pl
951	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/root/exceptions4.pl	951	%%EXAMPLESDIR%%/root/exceptions4.pl
952	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/root/README	952	%%EXAMPLESDIR%%/root/README
953	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/root/exceptions1.pl	953	%%EXAMPLESDIR%%/root/exceptions1.pl
954	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/root/exceptions3.pl	954	%%EXAMPLESDIR%%/root/exceptions3.pl
955	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tools/run_genscan.pl	955	%%EXAMPLESDIR%%/tools/run_genscan.pl
956	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tools/gff2ps.pl	956	%%EXAMPLESDIR%%/tools/gff2ps.pl
957	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tools/extract_genes.pl	957	%%EXAMPLESDIR%%/tools/extract_genes.pl
958	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tools/seq_pattern.pl	958	%%EXAMPLESDIR%%/tools/seq_pattern.pl
959	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tools/gb_to_gff.pl	959	%%EXAMPLESDIR%%/tools/gb_to_gff.pl
960	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tools/psw.pl	960	%%EXAMPLESDIR%%/tools/psw.pl
961	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tools/standaloneblast.pl	961	%%EXAMPLESDIR%%/tools/standaloneblast.pl
962	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tools/run_primer3.pl	962	%%EXAMPLESDIR%%/tools/run_primer3.pl
963	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tools/parse_codeml.pl	963	%%EXAMPLESDIR%%/tools/parse_codeml.pl
964	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tk/gsequence.pl	964	%%EXAMPLESDIR%%/tk/gsequence.pl
965	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tk/hitdisplay.pl	965	%%EXAMPLESDIR%%/tk/hitdisplay.pl
966	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tree/paup2phylip.pl	966	%%EXAMPLESDIR%%/tree/paup2phylip.pl
967	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/structure/structure-io.pl	967	%%EXAMPLESDIR%%/structure/structure-io.pl
968	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sirna/rnai_finder.cgi	968	%%EXAMPLESDIR%%/sirna/rnai_finder.cgi
969	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sirna/TAG	969	%%EXAMPLESDIR%%/sirna/TAG
970	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/custom_writer.pl	970	%%EXAMPLESDIR%%/searchio/custom_writer.pl
971	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/resultwriter.pl	971	%%EXAMPLESDIR%%/searchio/resultwriter.pl
972	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/blast_example.pl	972	%%EXAMPLESDIR%%/searchio/blast_example.pl
973	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/waba2gff3.pl	973	%%EXAMPLESDIR%%/searchio/waba2gff3.pl
974	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/hspwriter.pl	974	%%EXAMPLESDIR%%/searchio/hspwriter.pl
975	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/psiblast_iterations.pl	975	%%EXAMPLESDIR%%/searchio/psiblast_iterations.pl
976	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/waba2gff.pl	976	%%EXAMPLESDIR%%/searchio/waba2gff.pl
977	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/psiblast_features.pl	977	%%EXAMPLESDIR%%/searchio/psiblast_features.pl
978	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/htmlwriter.pl	978	%%EXAMPLESDIR%%/searchio/htmlwriter.pl
979	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/hitwriter.pl	979	%%EXAMPLESDIR%%/searchio/hitwriter.pl
980	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/rawwriter.pl	980	%%EXAMPLESDIR%%/searchio/rawwriter.pl
981	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/db/gb2features.pl	981	%%EXAMPLESDIR%%/db/gb2features.pl
982	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/db/dbfetch	982	%%EXAMPLESDIR%%/db/dbfetch
983	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/db/use_registry.pl	983	%%EXAMPLESDIR%%/db/use_registry.pl
984	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/db/est_tissue_query.pl	984	%%EXAMPLESDIR%%/db/est_tissue_query.pl
985	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/db/rfetch.pl	985	%%EXAMPLESDIR%%/db/rfetch.pl
986	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/db/getGenBank.pl	986	%%EXAMPLESDIR%%/db/getGenBank.pl
987	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/db/get_seqs.pl	987	%%EXAMPLESDIR%%/db/get_seqs.pl
988	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/align/clustalw.pl	988	%%EXAMPLESDIR%%/align/clustalw.pl
989	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/align/aligntutorial.pl	989	%%EXAMPLESDIR%%/align/aligntutorial.pl
990	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/align/simplealign.pl	990	%%EXAMPLESDIR%%/align/simplealign.pl
991	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/align/align_on_codons.pl	991	%%EXAMPLESDIR%%/align/align_on_codons.pl
992	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/biblio/biblio-eutils-example.pl	992	%%EXAMPLESDIR%%/biblio/biblio-eutils-example.pl
993	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/biblio/biblio_soap.pl	993	%%EXAMPLESDIR%%/biblio/biblio_soap.pl
994	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/biblio/biblio-soap-example.pl	994	%%EXAMPLESDIR%%/biblio/biblio-soap-example.pl
995	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/popgen/parse_calc_stats.pl	995	%%EXAMPLESDIR%%/popgen/parse_calc_stats.pl
996	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/biographics/feature_data.gff	996	%%EXAMPLESDIR%%/biographics/feature_data.gff
997	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/biographics/feature_data.txt	997	%%EXAMPLESDIR%%/biographics/feature_data.txt
998	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/biographics/render_sequence.pl	998	%%EXAMPLESDIR%%/biographics/render_sequence.pl
999	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/biographics/dynamic_glyphs.pl	999	%%EXAMPLESDIR%%/biographics/dynamic_glyphs.pl
1000	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/biographics/all_glyphs.pl	1000	%%EXAMPLESDIR%%/biographics/all_glyphs.pl
1001	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/biographics/lots_of_glyphs.pl	1001	%%EXAMPLESDIR%%/biographics/lots_of_glyphs.pl
1002	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cluster/dbsnp.pl	1002	%%EXAMPLESDIR%%/cluster/dbsnp.pl
1003	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/liveseq/change_gene.pl	1003	%%EXAMPLESDIR%%/liveseq/change_gene.pl
1004	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/contributed/prosite2perl.pl	1004	%%EXAMPLESDIR%%/contributed/prosite2perl.pl
1005	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/contributed/nmrpdb_parse.pl	1005	%%EXAMPLESDIR%%/contributed/nmrpdb_parse.pl
1006	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/contributed/rebase2list.pl	1006	%%EXAMPLESDIR%%/contributed/rebase2list.pl
1007	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Bio-DB-GFF/load_ucsc.pl	1007	%%EXAMPLESDIR%%/Bio-DB-GFF/load_ucsc.pl
1008	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/make_primers.pl	1008	%%EXAMPLESDIR%%/make_primers.pl
1009	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/longorf.pl	1009	%%EXAMPLESDIR%%/longorf.pl
1010	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bioperl.pl	1010	%%EXAMPLESDIR%%/bioperl.pl
1011	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/generate_random_seq.pl	1011	%%EXAMPLESDIR%%/generate_random_seq.pl
1012	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/rev_and_trans.pl	1012	%%EXAMPLESDIR%%/rev_and_trans.pl
1013	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/revcom_dir.pl	1013	%%EXAMPLESDIR%%/revcom_dir.pl
1014	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/subsequence.cgi	1014	%%EXAMPLESDIR%%/subsequence.cgi
1015	%%DATADIR%%/models/map_proposal.txt	1015	%%DATADIR%%/models/map_proposal.txt
1016	%%DATADIR%%/models/bio_liveseq_variation.dia	1016	%%DATADIR%%/models/bio_liveseq_variation.dia
1017	%%DATADIR%%/models/maps_and_markers.dia	1017	%%DATADIR%%/models/maps_and_markers.dia
Lines 1233-1257 Link Here
1233	%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/Deobfuscator	1233	%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/Deobfuscator
1234	%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc	1234	%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc
1235	%%PORTDOCS%%@dirrm %%DOCSDIR%%	1235	%%PORTDOCS%%@dirrm %%DOCSDIR%%
1236	%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/root/lib/Bio	1236	@dirrm %%EXAMPLESDIR%%/root/lib/Bio
1237	%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/root/lib	1237	@dirrm %%EXAMPLESDIR%%/root/lib
1238	%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/root	1238	@dirrm %%EXAMPLESDIR%%/root
1239	%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/tools	1239	@dirrm %%EXAMPLESDIR%%/tools
1240	%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/tk	1240	@dirrm %%EXAMPLESDIR%%/tk
1241	%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/tree	1241	@dirrm %%EXAMPLESDIR%%/tree
1242	%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/structure	1242	@dirrm %%EXAMPLESDIR%%/structure
1243	%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/sirna	1243	@dirrm %%EXAMPLESDIR%%/sirna
1244	%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/searchio	1244	@dirrm %%EXAMPLESDIR%%/searchio
1245	%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/db	1245	@dirrm %%EXAMPLESDIR%%/db
1246	%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/align	1246	@dirrm %%EXAMPLESDIR%%/align
1247	%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/biblio	1247	@dirrm %%EXAMPLESDIR%%/biblio
1248	%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/popgen	1248	@dirrm %%EXAMPLESDIR%%/popgen
1249	%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/biographics	1249	@dirrm %%EXAMPLESDIR%%/biographics
1250	%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/cluster	1250	@dirrm %%EXAMPLESDIR%%/cluster
1251	%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/liveseq	1251	@dirrm %%EXAMPLESDIR%%/liveseq
1252	%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/contributed	1252	@dirrm %%EXAMPLESDIR%%/contributed
1253	%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/Bio-DB-GFF	1253	@dirrm %%EXAMPLESDIR%%/Bio-DB-GFF
1254	%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%	1254	@dirrm %%EXAMPLESDIR%%
1255	@dirrm %%DATADIR%%/models	1255	@dirrm %%DATADIR%%/models
1256	@dirrm %%DATADIR%%/scripts/taxa	1256	@dirrm %%DATADIR%%/scripts/taxa
1257	@dirrm %%DATADIR%%/scripts/seq	1257	@dirrm %%DATADIR%%/scripts/seq