Date: Mon, 19 Dec 2016 15:54:34 +0000 (UTC) From: Sunpoet Po-Chuan Hsieh <sunpoet@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r428941 - in head/biology/p5-BioPerl-Run: . files Message-ID: <201612191554.uBJFsYLx041573@repo.freebsd.org>
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Author: sunpoet Date: Mon Dec 19 15:54:34 2016 New Revision: 428941 URL: https://svnweb.freebsd.org/changeset/ports/428941 Log: - 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 Modified: head/biology/p5-BioPerl-Run/Makefile head/biology/p5-BioPerl-Run/distinfo head/biology/p5-BioPerl-Run/files/patch-Build.PL head/biology/p5-BioPerl-Run/pkg-plist Modified: head/biology/p5-BioPerl-Run/Makefile ============================================================================== --- head/biology/p5-BioPerl-Run/Makefile Mon Dec 19 15:54:29 2016 (r428940) +++ head/biology/p5-BioPerl-Run/Makefile Mon Dec 19 15:54:34 2016 (r428941) @@ -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 Modified: head/biology/p5-BioPerl-Run/distinfo ============================================================================== --- head/biology/p5-BioPerl-Run/distinfo Mon Dec 19 15:54:29 2016 (r428940) +++ head/biology/p5-BioPerl-Run/distinfo Mon Dec 19 15:54:34 2016 (r428941) @@ -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 Modified: head/biology/p5-BioPerl-Run/files/patch-Build.PL ============================================================================== --- head/biology/p5-BioPerl-Run/files/patch-Build.PL Mon Dec 19 15:54:29 2016 (r428940) +++ head/biology/p5-BioPerl-Run/files/patch-Build.PL Mon Dec 19 15:54:34 2016 (r428941) @@ -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' ); Modified: head/biology/p5-BioPerl-Run/pkg-plist ============================================================================== --- head/biology/p5-BioPerl-Run/pkg-plist Mon Dec 19 15:54:29 2016 (r428940) +++ head/biology/p5-BioPerl-Run/pkg-plist Mon Dec 19 15:54:34 2016 (r428941) @@ -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
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