Update to 1.007002

Changes:	http://search.cpan.org/dist/BioPerl-Run/Changes

3 files changed, 5 insertions, 23 deletions

diff --git a/biology/p5-BioPerl-Run/Makefile b/biology/p5-BioPerl-Run/Makefile
index 090f5923d5af..27a06f98bcb8 100644
--- a/biology/p5-BioPerl-Run/Makefile
+++ b/biology/p5-BioPerl-Run/Makefile
@@ -2,8 +2,7 @@
 # $FreeBSD$
 
 PORTNAME=	BioPerl-Run
-PORTVERSION=	1.007001
-PORTREVISION=	1
+PORTVERSION=	1.007002
 CATEGORIES=	biology perl5
 MASTER_SITES=	CPAN
 MASTER_SITE_SUBDIR=	CPAN:CJFIELDS
@@ -17,6 +16,7 @@ LICENSE_COMB=	dual
 LICENSE_FILE_ART10=	${WRKSRC}/LICENSE
 
 BUILD_DEPENDS=	p5-Algorithm-Diff>=0:devel/p5-Algorithm-Diff \
+		p5-Bio-FeatureIO>=0:biology/p5-Bio-FeatureIO \
 		p5-BioPerl>=1.007000:biology/p5-BioPerl \
 		p5-Config-Any>=0:devel/p5-Config-Any \
 		p5-File-Sort>=0:misc/p5-File-Sort \
diff --git a/biology/p5-BioPerl-Run/distinfo b/biology/p5-BioPerl-Run/distinfo
index 2cc94d39027f..60e04988a375 100644
--- a/biology/p5-BioPerl-Run/distinfo
+++ b/biology/p5-BioPerl-Run/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1482241323
-SHA256 (BioPerl-Run-1.007001.tar.gz) = 55fd632ff24af9b3b1ecf655906cd34c0460a48cb45faabc72dd327ee5e1b0cc
-SIZE (BioPerl-Run-1.007001.tar.gz) = 14548613
+TIMESTAMP = 1505487295
+SHA256 (BioPerl-Run-1.007002.tar.gz) = 29806fc407183a936897d49d01d227877f52c946e3ed96c0675ed1ed14e1ce07
+SIZE (BioPerl-Run-1.007002.tar.gz) = 14493777
diff --git a/biology/p5-BioPerl-Run/pkg-plist b/biology/p5-BioPerl-Run/pkg-plist
index 483cfc7a23ae..cb33191c5e2d 100644
--- a/biology/p5-BioPerl-Run/pkg-plist
+++ b/biology/p5-BioPerl-Run/pkg-plist
@@ -15,18 +15,14 @@ bin/bp_run_protdist
 %%SITE_PERL%%/Bio/DB/SoapEUtilities/LinkAdaptor.pm
 %%SITE_PERL%%/Bio/DB/SoapEUtilities/Result.pm
 %%SITE_PERL%%/Bio/Factory/EMBOSS.pm
-%%SITE_PERL%%/Bio/Installer/Clustalw.pm
 %%SITE_PERL%%/Bio/Installer/EMBOSS.pm
 %%SITE_PERL%%/Bio/Installer/Generic.pm
 %%SITE_PERL%%/Bio/Installer/Hyphy.pm
 %%SITE_PERL%%/Bio/Installer/Muscle.pm
-%%SITE_PERL%%/Bio/Installer/PAML.pm
 %%SITE_PERL%%/Bio/Installer/Probcons.pm
 %%SITE_PERL%%/Bio/Installer/SLR.pm
-%%SITE_PERL%%/Bio/Installer/TCoffee.pm
 %%SITE_PERL%%/Bio/Tools/Run/Alignment/Amap.pm
 %%SITE_PERL%%/Bio/Tools/Run/Alignment/Blat.pm
-%%SITE_PERL%%/Bio/Tools/Run/Alignment/Clustalw.pm
 %%SITE_PERL%%/Bio/Tools/Run/Alignment/DBA.pm
 %%SITE_PERL%%/Bio/Tools/Run/Alignment/Exonerate.pm
 %%SITE_PERL%%/Bio/Tools/Run/Alignment/Gmap.pm
@@ -41,7 +37,6 @@ bin/bp_run_protdist
 %%SITE_PERL%%/Bio/Tools/Run/Alignment/Proda.pm
 %%SITE_PERL%%/Bio/Tools/Run/Alignment/Sim4.pm
 %%SITE_PERL%%/Bio/Tools/Run/Alignment/StandAloneFasta.pm
-%%SITE_PERL%%/Bio/Tools/Run/Alignment/TCoffee.pm
 %%SITE_PERL%%/Bio/Tools/Run/Analysis.pm
 %%SITE_PERL%%/Bio/Tools/Run/Analysis/soap.pm
 %%SITE_PERL%%/Bio/Tools/Run/AnalysisFactory.pm
@@ -90,10 +85,6 @@ bin/bp_run_protdist
 %%SITE_PERL%%/Bio/Tools/Run/Phylo/LVB.pm
 %%SITE_PERL%%/Bio/Tools/Run/Phylo/Molphy/ProtML.pm
 %%SITE_PERL%%/Bio/Tools/Run/Phylo/Njtree/Best.pm
-%%SITE_PERL%%/Bio/Tools/Run/Phylo/PAML/Baseml.pm
-%%SITE_PERL%%/Bio/Tools/Run/Phylo/PAML/Codeml.pm
-%%SITE_PERL%%/Bio/Tools/Run/Phylo/PAML/Evolver.pm
-%%SITE_PERL%%/Bio/Tools/Run/Phylo/PAML/Yn00.pm
 %%SITE_PERL%%/Bio/Tools/Run/Phylo/Phast/PhastCons.pm
 %%SITE_PERL%%/Bio/Tools/Run/Phylo/Phast/PhyloFit.pm
 %%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/Base.pm
@@ -147,18 +138,14 @@ bin/bp_run_protdist
 %%PERL5_MAN3%%/Bio::DB::SoapEUtilities::LinkAdaptor.3.gz
 %%PERL5_MAN3%%/Bio::DB::SoapEUtilities::Result.3.gz
 %%PERL5_MAN3%%/Bio::Factory::EMBOSS.3.gz
-%%PERL5_MAN3%%/Bio::Installer::Clustalw.3.gz
 %%PERL5_MAN3%%/Bio::Installer::EMBOSS.3.gz
 %%PERL5_MAN3%%/Bio::Installer::Generic.3.gz
 %%PERL5_MAN3%%/Bio::Installer::Hyphy.3.gz
 %%PERL5_MAN3%%/Bio::Installer::Muscle.3.gz
-%%PERL5_MAN3%%/Bio::Installer::PAML.3.gz
 %%PERL5_MAN3%%/Bio::Installer::Probcons.3.gz
 %%PERL5_MAN3%%/Bio::Installer::SLR.3.gz
-%%PERL5_MAN3%%/Bio::Installer::TCoffee.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::Alignment::Amap.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::Alignment::Blat.3.gz
-%%PERL5_MAN3%%/Bio::Tools::Run::Alignment::Clustalw.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::Alignment::DBA.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::Alignment::Exonerate.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::Alignment::Gmap.3.gz
@@ -173,7 +160,6 @@ bin/bp_run_protdist
 %%PERL5_MAN3%%/Bio::Tools::Run::Alignment::Proda.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::Alignment::Sim4.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::Alignment::StandAloneFasta.3.gz
-%%PERL5_MAN3%%/Bio::Tools::Run::Alignment::TCoffee.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::Analysis.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::Analysis::soap.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::AnalysisFactory.3.gz
@@ -221,10 +207,6 @@ bin/bp_run_protdist
 %%PERL5_MAN3%%/Bio::Tools::Run::Phylo::LVB.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::Phylo::Molphy::ProtML.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::Phylo::Njtree::Best.3.gz
-%%PERL5_MAN3%%/Bio::Tools::Run::Phylo::PAML::Baseml.3.gz
-%%PERL5_MAN3%%/Bio::Tools::Run::Phylo::PAML::Codeml.3.gz
-%%PERL5_MAN3%%/Bio::Tools::Run::Phylo::PAML::Evolver.3.gz
-%%PERL5_MAN3%%/Bio::Tools::Run::Phylo::PAML::Yn00.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::Phylo::Phast::PhastCons.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::Phylo::Phast::PhyloFit.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::Phylo::Phylip::Base.3.gz