Date: Sun, 8 Dec 2019 16:49:25 +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: r519319 - in head/biology: . p5-Bio-DB-NCBIHelper Message-ID: <201912081649.xB8GnP7O054282@repo.freebsd.org>
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Author: sunpoet Date: Sun Dec 8 16:49:25 2019 New Revision: 519319 URL: https://svnweb.freebsd.org/changeset/ports/519319 Log: Add p5-Bio-DB-NCBIHelper 1.7.6 Bio::DB::NCBIHelper provides a single place to setup some common methods for querying NCBI web databases. This module just centralizes the methods for constructing a URL for querying NCBI GenBank and NCBI GenPept and the common HTML stripping done in postprocess_data(). WWW: https://metacpan.org/release/Bio-DB-NCBIHelper Added: head/biology/p5-Bio-DB-NCBIHelper/ head/biology/p5-Bio-DB-NCBIHelper/Makefile (contents, props changed) head/biology/p5-Bio-DB-NCBIHelper/distinfo (contents, props changed) head/biology/p5-Bio-DB-NCBIHelper/pkg-descr (contents, props changed) head/biology/p5-Bio-DB-NCBIHelper/pkg-plist (contents, props changed) Modified: head/biology/Makefile Modified: head/biology/Makefile ============================================================================== --- head/biology/Makefile Sun Dec 8 16:49:19 2019 (r519318) +++ head/biology/Makefile Sun Dec 8 16:49:25 2019 (r519319) @@ -87,6 +87,7 @@ SUBDIR += p5-Bio-Cluster SUBDIR += p5-Bio-Coordinate SUBDIR += p5-Bio-DB-EMBL + SUBDIR += p5-Bio-DB-NCBIHelper SUBDIR += p5-Bio-Das SUBDIR += p5-Bio-Das-Lite SUBDIR += p5-Bio-FeatureIO Added: head/biology/p5-Bio-DB-NCBIHelper/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/p5-Bio-DB-NCBIHelper/Makefile Sun Dec 8 16:49:25 2019 (r519319) @@ -0,0 +1,36 @@ +# Created by: Po-Chuan Hsieh <sunpoet@FreeBSD.org> +# $FreeBSD$ + +PORTNAME= Bio-DB-NCBIHelper +PORTVERSION= 1.7.6 +CATEGORIES= biology perl5 +MASTER_SITES= CPAN +PKGNAMEPREFIX= p5- + +MAINTAINER= sunpoet@FreeBSD.org +COMMENT= Collection of routines useful for queries to NCBI databases + +LICENSE= ART10 GPLv1+ +LICENSE_COMB= dual +LICENSE_FILE= ${WRKSRC}/LICENSE + +BUILD_DEPENDS= ${RUN_DEPENDS} +RUN_DEPENDS= p5-Bio-ASN1-EntrezGene>=0:biology/p5-Bio-ASN1-EntrezGene \ + p5-BioPerl>=1.007007:biology/p5-BioPerl \ + p5-CGI>=0:www/p5-CGI \ + p5-Cache-Cache>=0:devel/p5-Cache-Cache \ + p5-HTTP-Message>=0:www/p5-HTTP-Message \ + p5-LWP-Protocol-https>=0:www/p5-LWP-Protocol-https \ + p5-URI>=0:net/p5-URI \ + p5-XML-Twig>=0:textproc/p5-XML-Twig \ + p5-libwww>=0:www/p5-libwww +TEST_DEPENDS= p5-Test-Exception>=0:devel/p5-Test-Exception \ + p5-Test-Most>=0:devel/p5-Test-Most \ + p5-Test-RequiresInternet>=0:devel/p5-Test-RequiresInternet + +USES= perl5 +USE_PERL5= configure + +NO_ARCH= yes + +.include <bsd.port.mk> Added: head/biology/p5-Bio-DB-NCBIHelper/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/p5-Bio-DB-NCBIHelper/distinfo Sun Dec 8 16:49:25 2019 (r519319) @@ -0,0 +1,3 @@ +TIMESTAMP = 1575793785 +SHA256 (Bio-DB-NCBIHelper-1.7.6.tar.gz) = 6475fef8475e9491fec352b4fe3a6249be7b0bee92e7bad62c3f81ca31e3bcc7 +SIZE (Bio-DB-NCBIHelper-1.7.6.tar.gz) = 45150 Added: head/biology/p5-Bio-DB-NCBIHelper/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/p5-Bio-DB-NCBIHelper/pkg-descr Sun Dec 8 16:49:25 2019 (r519319) @@ -0,0 +1,6 @@ +Bio::DB::NCBIHelper provides a single place to setup some common methods for +querying NCBI web databases. This module just centralizes the methods for +constructing a URL for querying NCBI GenBank and NCBI GenPept and the common +HTML stripping done in postprocess_data(). + +WWW: https://metacpan.org/release/Bio-DB-NCBIHelper Added: head/biology/p5-Bio-DB-NCBIHelper/pkg-plist ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/p5-Bio-DB-NCBIHelper/pkg-plist Sun Dec 8 16:49:25 2019 (r519319) @@ -0,0 +1,18 @@ +bin/bp_biofetch_genbank_proxy +bin/bp_download_query_genbank +bin/bp_query_entrez_taxa +%%SITE_PERL%%/Bio/DB/EntrezGene.pm +%%SITE_PERL%%/Bio/DB/GenBank.pm +%%SITE_PERL%%/Bio/DB/GenPept.pm +%%SITE_PERL%%/Bio/DB/NCBIHelper.pm +%%SITE_PERL%%/Bio/DB/Query/GenBank.pm +%%SITE_PERL%%/Bio/DB/Taxonomy/entrez.pm +%%PERL5_MAN1%%/bp_biofetch_genbank_proxy.1.gz +%%PERL5_MAN1%%/bp_download_query_genbank.1.gz +%%PERL5_MAN1%%/bp_query_entrez_taxa.1.gz +%%PERL5_MAN3%%/Bio::DB::EntrezGene.3.gz +%%PERL5_MAN3%%/Bio::DB::GenBank.3.gz +%%PERL5_MAN3%%/Bio::DB::GenPept.3.gz +%%PERL5_MAN3%%/Bio::DB::NCBIHelper.3.gz +%%PERL5_MAN3%%/Bio::DB::Query::GenBank.3.gz +%%PERL5_MAN3%%/Bio::DB::Taxonomy::entrez.3.gz
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