Date: Wed, 20 Feb 2019 20:46:59 +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: r493448 - in head/biology/p5-BioPerl-Run: . files Message-ID: <201902202046.x1KKkxxi082535@repo.freebsd.org>
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Author: sunpoet Date: Wed Feb 20 20:46:58 2019 New Revision: 493448 URL: https://svnweb.freebsd.org/changeset/ports/493448 Log: Update to 1.007003 - Take maintainership Changes: https://metacpan.org/changes/distribution/BioPerl-Run 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 Wed Feb 20 20:46:53 2019 (r493447) +++ head/biology/p5-BioPerl-Run/Makefile Wed Feb 20 20:46:58 2019 (r493448) @@ -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> Modified: head/biology/p5-BioPerl-Run/distinfo ============================================================================== --- head/biology/p5-BioPerl-Run/distinfo Wed Feb 20 20:46:53 2019 (r493447) +++ head/biology/p5-BioPerl-Run/distinfo Wed Feb 20 20:46:58 2019 (r493448) @@ -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 Modified: head/biology/p5-BioPerl-Run/files/patch-Build.PL ============================================================================== --- head/biology/p5-BioPerl-Run/files/patch-Build.PL Wed Feb 20 20:46:53 2019 (r493447) +++ head/biology/p5-BioPerl-Run/files/patch-Build.PL Wed Feb 20 20:46:58 2019 (r493448) @@ -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' ); Modified: head/biology/p5-BioPerl-Run/pkg-plist ============================================================================== --- head/biology/p5-BioPerl-Run/pkg-plist Wed Feb 20 20:46:53 2019 (r493447) +++ head/biology/p5-BioPerl-Run/pkg-plist Wed Feb 20 20:46:58 2019 (r493448) @@ -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
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