3 files changed, 42 insertions, 7 deletions

diff --git a/biology/p5-bioperl-devel/Makefile b/biology/p5-bioperl-devel/Makefile
index bee2b490e0eb..8a7685235279 100644
--- a/biology/p5-bioperl-devel/Makefile
+++ b/biology/p5-bioperl-devel/Makefile
@@ -33,6 +33,7 @@ BUILD_DEPENDS=	${LOCALBASE}/lib/perl5/${PERL_VER}/Text/Wrap.pm:${PORTSDIR}/lang/
 		${SITE_PERL}/Spreadsheet/ParseExcel.pm:${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 \
@@ -53,18 +54,12 @@ BUILD_DEPENDS=	${LOCALBASE}/lib/perl5/${PERL_VER}/Text/Wrap.pm:${PORTSDIR}/lang/
 		${SITE_PERL}/${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 \
@@ -106,6 +101,7 @@ MAN1=		bp_aacomp.pl.1 \
 		bp_nrdb.pl.1 \
 		bp_oligo_count.pl.1 \
 		bp_pairwise_kaks.pl.1 \
+		bp_parse_hmmsearch.pl.1 \
 		bp_process_gadfly.pl.1 \
 		bp_process_sgd.pl.1 \
 		bp_process_wormbase.pl.1 \
@@ -123,6 +119,7 @@ MAN1=		bp_aacomp.pl.1 \
 		bp_split_seq.pl.1 \
 		bp_sreformat.pl.1 \
 		bp_taxid4species.pl.1 \
+		bp_taxonomy2tree.pl.1 \
 		bp_translate_seq.pl.1 \
 		bp_tree2pag.pl.1 \
 		bp_unflatten_seq.pl.1
@@ -1006,4 +1003,3 @@ post-install:
 .endif
 
 .include <bsd.port.post.mk>
-
diff --git a/biology/p5-bioperl-devel/files/patch-Build.PL b/biology/p5-bioperl-devel/files/patch-Build.PL
new file mode 100644
index 000000000000..58442ee46006
--- /dev/null
+++ b/biology/p5-bioperl-devel/files/patch-Build.PL
@@ -0,0 +1,19 @@
+--- 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;
diff --git a/biology/p5-bioperl-devel/files/patch-ModuleBuildBioperl.pm b/biology/p5-bioperl-devel/files/patch-ModuleBuildBioperl.pm
new file mode 100644
index 000000000000..5f627035c3f3
--- /dev/null
+++ b/biology/p5-bioperl-devel/files/patch-ModuleBuildBioperl.pm
@@ -0,0 +1,20 @@
+--- 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';
+                 }