- Update to 1.007000

- Change MASTER_SITES back to CPAN
- Update LICENSE
- Add LICENSE_FILE
- Use PORTDOCS
- Convert to options target helper
- Use INSTALL_SCRIPT
- Pet portlint: fix diff header of patch file

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

4 files changed, 29 insertions, 20 deletions

diff --git a/biology/p5-BioPerl-Run/Makefile b/biology/p5-BioPerl-Run/Makefile
index 881c35fd26d5..d0e60ede9355 100644
--- a/biology/p5-BioPerl-Run/Makefile
+++ b/biology/p5-BioPerl-Run/Makefile
@@ -2,48 +2,50 @@
 # $FreeBSD$
 
 PORTNAME=	BioPerl-Run
-PORTVERSION=	1.6.901
-PORTREVISION=	2
+PORTVERSION=	1.007000
 CATEGORIES=	biology perl5
+MASTER_SITES=	CPAN
+MASTER_SITE_SUBDIR=	CPAN:CJFIELDS
 PKGNAMEPREFIX=	p5-
 
 MAINTAINER=	perl@FreeBSD.org
 COMMENT=	Wrapper modules for common bioinformatics tools
 
-LICENSE=	ART10 GPLv3
+LICENSE=	ART10 GPLv1
 LICENSE_COMB=	dual
+LICENSE_FILE_ART10=	${WRKSRC}/LICENSE
 
 BUILD_DEPENDS=	p5-Algorithm-Diff>=0:devel/p5-Algorithm-Diff \
-		p5-BioPerl>=1.6.0:biology/p5-BioPerl \
+		p5-BioPerl>=1.007000:biology/p5-BioPerl \
 		p5-Config-Any>=0:devel/p5-Config-Any \
 		p5-File-Sort>=0:misc/p5-File-Sort \
+		p5-IO-String>=0:devel/p5-IO-String \
 		p5-IPC-Run>=0:devel/p5-IPC-Run \
 		p5-XML-Twig>=0:textproc/p5-XML-Twig
 RUN_DEPENDS:=	${BUILD_DEPENDS}
 
 CONFLICTS=	p5-bioperl-run-1.[13579]*
 
-USE_GITHUB=	yes
-GH_ACCOUNT=	bioperl
-GH_PROJECT=	bioperl-run
-GH_TAGNAME=	96ccd93
+OPTIONS_DEFINE=	DOCS
 
 NO_ARCH=	yes
 USES=		perl5 shebangfix
 USE_PERL5=	modbuild
 SHEBANG_FILES=	scripts/*
 
-OPTIONS_DEFINE=	DOCS
+PORTDOCS=	*
 
 post-build:
 	(cd ${WRKSRC} && ${PERL} ./Build manifest)
 
 post-install:
 .for i in bioperl_application_installer multi_hmmsearch panalysis papplmaker run_neighbor run_protdist
-	${CP} ${WRKSRC}/scripts/${i}.PLS ${STAGEDIR}${PREFIX}/bin/bp_${i}
+	${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
+.for doc in AUTHORS Changes INSTALL.PROGRAMS README.md
 	${INSTALL_DATA} ${WRKSRC}/${doc} ${STAGEDIR}${DOCSDIR}
 .endfor
 
diff --git a/biology/p5-BioPerl-Run/distinfo b/biology/p5-BioPerl-Run/distinfo
index 1005fa30a806..59b23c36b2b6 100644
--- a/biology/p5-BioPerl-Run/distinfo
+++ b/biology/p5-BioPerl-Run/distinfo
@@ -1,2 +1,3 @@
-SHA256 (bioperl-bioperl-run-1.6.901-96ccd93_GH0.tar.gz) = 13f6c0b47b70a2bc5e9f633bc011378a85f78a7f0c0d334246acbc1a8f3b343c
-SIZE (bioperl-bioperl-run-1.6.901-96ccd93_GH0.tar.gz) = 13941085
+TIMESTAMP = 1482075945
+SHA256 (BioPerl-Run-1.007000.tar.gz) = 7345ad504301bc156c8bb153be157a5626612fd7af7a3abae0f5be9c6fa635c0
+SIZE (BioPerl-Run-1.007000.tar.gz) = 14548111
diff --git a/biology/p5-BioPerl-Run/files/patch-Build.PL b/biology/p5-BioPerl-Run/files/patch-Build.PL
index 8af6e19b1a04..dab7bca6f278 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 04:49:03.000000000 +0200
-+++ ./Build.PL	2014-08-04 09:33:15.000000000 +0200
-@@ -42,7 +42,8 @@
+--- Build.PL.orig	2014-07-26 02:49:03 UTC
++++ Build.PL
+@@ -50,7 +50,8 @@ my $build = Module::Build->new(
      #create_makefile_pl  => 'passthrough'
  );
  
diff --git a/biology/p5-BioPerl-Run/pkg-plist b/biology/p5-BioPerl-Run/pkg-plist
index 51b2742be490..483cfc7a23ae 100644
--- a/biology/p5-BioPerl-Run/pkg-plist
+++ b/biology/p5-BioPerl-Run/pkg-plist
@@ -124,12 +124,17 @@ bin/bp_run_protdist
 %%SITE_PERL%%/Bio/Tools/Run/Seg.pm
 %%SITE_PERL%%/Bio/Tools/Run/Signalp.pm
 %%SITE_PERL%%/Bio/Tools/Run/Simprot.pm
+%%SITE_PERL%%/Bio/Tools/Run/StandAloneBlast.pm
 %%SITE_PERL%%/Bio/Tools/Run/StandAloneBlastPlus.pm
 %%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
@@ -250,14 +255,15 @@ bin/bp_run_protdist
 %%PERL5_MAN3%%/Bio::Tools::Run::Seg.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::Signalp.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::Simprot.3.gz
+%%PERL5_MAN3%%/Bio::Tools::Run::StandAloneBlast.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::StandAloneBlastPlus.3.gz
 %%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