svn commit: r428941 - in head/biology/p5-BioPerl-Run: . files
Sunpoet Po-Chuan Hsieh
sunpoet at FreeBSD.org
Mon Dec 19 15:54:35 UTC 2016
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 at 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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