Update to 1.007003

- Take maintainership

Changes:	https://metacpan.org/changes/distribution/BioPerl-Run

4 files changed, 16 insertions, 67 deletions

diff --git a/biology/p5-BioPerl-Run/Makefile b/biology/p5-BioPerl-Run/Makefile
index 7c344b617cf9..e3206f3d3945 100644
--- a/biology/p5-BioPerl-Run/Makefile
+++ b/biology/p5-BioPerl-Run/Makefile
@@ -2,13 +2,13 @@
 # $FreeBSD$
 
 PORTNAME=	BioPerl-Run
-PORTVERSION=	1.007002
+PORTVERSION=	1.007003
 CATEGORIES=	biology perl5
 MASTER_SITES=	CPAN
 MASTER_SITE_SUBDIR=	CPAN:CJFIELDS
 PKGNAMEPREFIX=	p5-
 
-MAINTAINER=	perl@FreeBSD.org
+MAINTAINER=	sunpoet@FreeBSD.org
 COMMENT=	Wrapper modules for common bioinformatics tools
 
 LICENSE=	ART10 GPLv1+
@@ -17,6 +17,7 @@ LICENSE_FILE_ART10=	${WRKSRC}/LICENSE
 
 BUILD_DEPENDS=	${RUN_DEPENDS}
 RUN_DEPENDS=	p5-Algorithm-Diff>=0:devel/p5-Algorithm-Diff \
+		p5-Bio-Cluster>=0:biology/p5-Bio-Cluster \
 		p5-Bio-FeatureIO>=0:biology/p5-Bio-FeatureIO \
 		p5-BioPerl>=1.007000:biology/p5-BioPerl \
 		p5-Config-Any>=0:devel/p5-Config-Any \
@@ -29,25 +30,20 @@ CONFLICTS=	p5-bioperl-run-1.[13579]*
 
 OPTIONS_DEFINE=	DOCS
 
-NO_ARCH=	yes
 USES=		perl5 shebangfix
 USE_PERL5=	modbuild
-SHEBANG_FILES=	scripts/*
 
-PORTDOCS=	*
+NO_ARCH=	yes
 
-post-build:
-	(cd ${WRKSRC} && ${PERL} ./Build manifest)
+SHEBANG_FILES=	scripts/*
 
 post-install:
-.for i in bioperl_application_installer multi_hmmsearch panalysis papplmaker run_neighbor run_protdist
+.for i in multi_hmmsearch panalysis papplmaker run_neighbor run_protdist
 	${INSTALL_SCRIPT} ${WRKSRC}/scripts/${i}.PLS ${STAGEDIR}${PREFIX}/bin/bp_${i}
 .endfor
 
 post-install-DOCS-on:
 	@${MKDIR} ${STAGEDIR}${DOCSDIR}
-.for doc in AUTHORS Changes INSTALL.PROGRAMS README.md
-	${INSTALL_DATA} ${WRKSRC}/${doc} ${STAGEDIR}${DOCSDIR}
-.endfor
+	cd ${WRKSRC} && ${INSTALL_DATA} AUTHORS Changes INSTALL.PROGRAMS README.md ${STAGEDIR}${DOCSDIR}
 
 .include <bsd.port.mk>
diff --git a/biology/p5-BioPerl-Run/distinfo b/biology/p5-BioPerl-Run/distinfo
index 60e04988a375..31d105061f30 100644
--- a/biology/p5-BioPerl-Run/distinfo
+++ b/biology/p5-BioPerl-Run/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1505487295
-SHA256 (BioPerl-Run-1.007002.tar.gz) = 29806fc407183a936897d49d01d227877f52c946e3ed96c0675ed1ed14e1ce07
-SIZE (BioPerl-Run-1.007002.tar.gz) = 14493777
+TIMESTAMP = 1549711722
+SHA256 (BioPerl-Run-1.007003.tar.gz) = e62e529352f0644bc26509065595d0a47fb6217e5f1301acad76182c2f062071
+SIZE (BioPerl-Run-1.007003.tar.gz) = 5138162
diff --git a/biology/p5-BioPerl-Run/files/patch-Build.PL b/biology/p5-BioPerl-Run/files/patch-Build.PL
index dab7bca6f278..26146d6a87a0 100644
--- a/biology/p5-BioPerl-Run/files/patch-Build.PL
+++ b/biology/p5-BioPerl-Run/files/patch-Build.PL
@@ -1,6 +1,6 @@
---- Build.PL.orig	2014-07-26 02:49:03 UTC
+--- Build.PL.orig	2019-02-08 19:53:38 UTC
 +++ Build.PL
-@@ -50,7 +50,8 @@ my $build = Module::Build->new(
+@@ -75,7 +75,8 @@ my $build = Module::Build->subclass(
      #create_makefile_pl  => 'passthrough'
  );
  
diff --git a/biology/p5-BioPerl-Run/pkg-plist b/biology/p5-BioPerl-Run/pkg-plist
index cb33191c5e2d..b726134761b0 100644
--- a/biology/p5-BioPerl-Run/pkg-plist
+++ b/biology/p5-BioPerl-Run/pkg-plist
@@ -1,4 +1,3 @@
-bin/bp_bioperl_application_installer
 bin/bp_multi_hmmsearch
 bin/bp_panalysis
 bin/bp_papplmaker
@@ -15,12 +14,6 @@ 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/EMBOSS.pm
-%%SITE_PERL%%/Bio/Installer/Generic.pm
-%%SITE_PERL%%/Bio/Installer/Hyphy.pm
-%%SITE_PERL%%/Bio/Installer/Muscle.pm
-%%SITE_PERL%%/Bio/Installer/Probcons.pm
-%%SITE_PERL%%/Bio/Installer/SLR.pm
 %%SITE_PERL%%/Bio/Tools/Run/Alignment/Amap.pm
 %%SITE_PERL%%/Bio/Tools/Run/Alignment/Blat.pm
 %%SITE_PERL%%/Bio/Tools/Run/Alignment/DBA.pm
@@ -37,20 +30,12 @@ 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/Analysis.pm
 %%SITE_PERL%%/Bio/Tools/Run/Analysis/soap.pm
-%%SITE_PERL%%/Bio/Tools/Run/AnalysisFactory.pm
 %%SITE_PERL%%/Bio/Tools/Run/AnalysisFactory/soap.pm
-%%SITE_PERL%%/Bio/Tools/Run/AssemblerBase.pm
 %%SITE_PERL%%/Bio/Tools/Run/BEDTools.pm
 %%SITE_PERL%%/Bio/Tools/Run/BEDTools/Config.pm
-%%SITE_PERL%%/Bio/Tools/Run/BWA.pm
-%%SITE_PERL%%/Bio/Tools/Run/BWA/Config.pm
 %%SITE_PERL%%/Bio/Tools/Run/BlastPlus.pm
 %%SITE_PERL%%/Bio/Tools/Run/BlastPlus/Config.pm
-%%SITE_PERL%%/Bio/Tools/Run/Bowtie.pm
-%%SITE_PERL%%/Bio/Tools/Run/Bowtie/Config.pm
-%%SITE_PERL%%/Bio/Tools/Run/Cap3.pm
 %%SITE_PERL%%/Bio/Tools/Run/Coil.pm
 %%SITE_PERL%%/Bio/Tools/Run/EMBOSSApplication.pm
 %%SITE_PERL%%/Bio/Tools/Run/EMBOSSacd.pm
@@ -65,17 +50,10 @@ bin/bp_run_protdist
 %%SITE_PERL%%/Bio/Tools/Run/Hmmer.pm
 %%SITE_PERL%%/Bio/Tools/Run/Infernal.pm
 %%SITE_PERL%%/Bio/Tools/Run/MCS.pm
-%%SITE_PERL%%/Bio/Tools/Run/Maq.pm
-%%SITE_PERL%%/Bio/Tools/Run/Maq/Config.pm
 %%SITE_PERL%%/Bio/Tools/Run/Match.pm
 %%SITE_PERL%%/Bio/Tools/Run/Mdust.pm
-%%SITE_PERL%%/Bio/Tools/Run/Meme.pm
-%%SITE_PERL%%/Bio/Tools/Run/Minimo.pm
-%%SITE_PERL%%/Bio/Tools/Run/Newbler.pm
-%%SITE_PERL%%/Bio/Tools/Run/Phrap.pm
 %%SITE_PERL%%/Bio/Tools/Run/Phylo/FastTree.pm
 %%SITE_PERL%%/Bio/Tools/Run/Phylo/Gerp.pm
-%%SITE_PERL%%/Bio/Tools/Run/Phylo/Gumby.pm
 %%SITE_PERL%%/Bio/Tools/Run/Phylo/Hyphy/Base.pm
 %%SITE_PERL%%/Bio/Tools/Run/Phylo/Hyphy/BatchFile.pm
 %%SITE_PERL%%/Bio/Tools/Run/Phylo/Hyphy/FEL.pm
@@ -96,7 +74,6 @@ bin/bp_run_protdist
 %%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/ProtDist.pm
 %%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/ProtPars.pm
 %%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/SeqBoot.pm
-%%SITE_PERL%%/Bio/Tools/Run/Phylo/PhyloBase.pm
 %%SITE_PERL%%/Bio/Tools/Run/Phylo/Phyml.pm
 %%SITE_PERL%%/Bio/Tools/Run/Phylo/QuickTree.pm
 %%SITE_PERL%%/Bio/Tools/Run/Phylo/Raxml.pm
@@ -120,12 +97,9 @@ bin/bp_run_protdist
 %%SITE_PERL%%/Bio/Tools/Run/StandAloneBlastPlus/BlastMethods.pm
 %%SITE_PERL%%/Bio/Tools/Run/StandAloneNCBIBlast.pm
 %%SITE_PERL%%/Bio/Tools/Run/StandAloneWUBlast.pm
-%%SITE_PERL%%/Bio/Tools/Run/TigrAssembler.pm
 %%SITE_PERL%%/Bio/Tools/Run/Tmhmm.pm
 %%SITE_PERL%%/Bio/Tools/Run/TribeMCL.pm
 %%SITE_PERL%%/Bio/Tools/Run/Vista.pm
-%%SITE_PERL%%/Bio/Tools/Run/WrapperBase.pm
-%%SITE_PERL%%/Bio/Tools/Run/WrapperBase/CommandExts.pm
 %%SITE_PERL%%/Bio/Tools/Run/tRNAscanSE.pm
 %%PERL5_MAN3%%/Bio::DB::ESoap.3.gz
 %%PERL5_MAN3%%/Bio::DB::ESoap::WSDL.3.gz
@@ -138,12 +112,6 @@ 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::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::Probcons.3.gz
-%%PERL5_MAN3%%/Bio::Installer::SLR.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::DBA.3.gz
@@ -160,19 +128,11 @@ 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::Analysis.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::Analysis::soap.3.gz
-%%PERL5_MAN3%%/Bio::Tools::Run::AnalysisFactory.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::AnalysisFactory::soap.3.gz
-%%PERL5_MAN3%%/Bio::Tools::Run::AssemblerBase.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::BEDTools.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::BEDTools::Config.3.gz
-%%PERL5_MAN3%%/Bio::Tools::Run::BWA.3.gz
-%%PERL5_MAN3%%/Bio::Tools::Run::BWA::Config.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::BlastPlus.3.gz
-%%PERL5_MAN3%%/Bio::Tools::Run::Bowtie.3.gz
-%%PERL5_MAN3%%/Bio::Tools::Run::Bowtie::Config.3.gz
-%%PERL5_MAN3%%/Bio::Tools::Run::Cap3.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::Coil.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::EMBOSSApplication.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::EMBOSSacd.3.gz
@@ -187,17 +147,10 @@ bin/bp_run_protdist
 %%PERL5_MAN3%%/Bio::Tools::Run::Hmmer.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::Infernal.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::MCS.3.gz
-%%PERL5_MAN3%%/Bio::Tools::Run::Maq.3.gz
-%%PERL5_MAN3%%/Bio::Tools::Run::Maq::Config.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::Match.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::Mdust.3.gz
-%%PERL5_MAN3%%/Bio::Tools::Run::Meme.3.gz
-%%PERL5_MAN3%%/Bio::Tools::Run::Minimo.3.gz
-%%PERL5_MAN3%%/Bio::Tools::Run::Newbler.3.gz
-%%PERL5_MAN3%%/Bio::Tools::Run::Phrap.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::Phylo::FastTree.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::Phylo::Gerp.3.gz
-%%PERL5_MAN3%%/Bio::Tools::Run::Phylo::Gumby.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::Phylo::Hyphy::Base.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::Phylo::Hyphy::BatchFile.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::Phylo::Hyphy::FEL.3.gz
@@ -218,7 +171,6 @@ bin/bp_run_protdist
 %%PERL5_MAN3%%/Bio::Tools::Run::Phylo::Phylip::ProtDist.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::Phylo::Phylip::ProtPars.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::Phylo::Phylip::SeqBoot.3.gz
-%%PERL5_MAN3%%/Bio::Tools::Run::Phylo::PhyloBase.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::Phylo::Phyml.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::Phylo::QuickTree.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::Phylo::Raxml.3.gz
@@ -242,10 +194,11 @@ bin/bp_run_protdist
 %%PERL5_MAN3%%/Bio::Tools::Run::StandAloneBlastPlus::BlastMethods.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::StandAloneNCBIBlast.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::StandAloneWUBlast.3.gz
-%%PERL5_MAN3%%/Bio::Tools::Run::TigrAssembler.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::Tmhmm.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::TribeMCL.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::Vista.3.gz
-%%PERL5_MAN3%%/Bio::Tools::Run::WrapperBase.3.gz
-%%PERL5_MAN3%%/Bio::Tools::Run::WrapperBase::CommandExts.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::tRNAscanSE.3.gz
+%%PORTDOCS%%%%DOCSDIR%%/AUTHORS
+%%PORTDOCS%%%%DOCSDIR%%/Changes
+%%PORTDOCS%%%%DOCSDIR%%/INSTALL.PROGRAMS
+%%PORTDOCS%%%%DOCSDIR%%/README.md