Index: head/biology/p5-BioPerl-Run/Makefile =================================================================== --- head/biology/p5-BioPerl-Run/Makefile (revision 493447) +++ head/biology/p5-BioPerl-Run/Makefile (revision 493448) @@ -1,53 +1,49 @@ # Created by: Mauricio Herrera Cuadra # $FreeBSD$ 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+ LICENSE_COMB= dual 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 \ 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 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 Index: head/biology/p5-BioPerl-Run/distinfo =================================================================== --- head/biology/p5-BioPerl-Run/distinfo (revision 493447) +++ head/biology/p5-BioPerl-Run/distinfo (revision 493448) @@ -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 Index: head/biology/p5-BioPerl-Run/files/patch-Build.PL =================================================================== --- head/biology/p5-BioPerl-Run/files/patch-Build.PL (revision 493447) +++ head/biology/p5-BioPerl-Run/files/patch-Build.PL (revision 493448) @@ -1,12 +1,12 @@ ---- 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' ); -my $accept = $build->args->{accept}; +# my $accept = $build->args->{accept}; +my $accept = 1; # Optionally have script files installed. if ($build->args('install_scripts') or $accept ? 0 : $build->y_n("Install scripts? y/n", 'n')) { Index: head/biology/p5-BioPerl-Run/pkg-plist =================================================================== --- head/biology/p5-BioPerl-Run/pkg-plist (revision 493447) +++ head/biology/p5-BioPerl-Run/pkg-plist (revision 493448) @@ -1,251 +1,204 @@ -bin/bp_bioperl_application_installer bin/bp_multi_hmmsearch bin/bp_panalysis bin/bp_papplmaker bin/bp_run_neighbor bin/bp_run_protdist %%SITE_PERL%%/Bio/DB/ESoap.pm %%SITE_PERL%%/Bio/DB/ESoap/WSDL.pm %%SITE_PERL%%/Bio/DB/SoapEUtilities.pm %%SITE_PERL%%/Bio/DB/SoapEUtilities/DocSumAdaptor.pm %%SITE_PERL%%/Bio/DB/SoapEUtilities/FetchAdaptor.pm %%SITE_PERL%%/Bio/DB/SoapEUtilities/FetchAdaptor/seq.pm %%SITE_PERL%%/Bio/DB/SoapEUtilities/FetchAdaptor/species.pm 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