From owner-svn-ports-all@freebsd.org Sun Dec 8 16:49:26 2019 Return-Path: Delivered-To: svn-ports-all@mailman.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.nyi.freebsd.org (Postfix) with ESMTP id EF8A51E7ABE; Sun, 8 Dec 2019 16:49:26 +0000 (UTC) (envelope-from sunpoet@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) server-signature RSA-PSS (4096 bits) client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "Let's Encrypt Authority X3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 47WC3B68h3z4CwH; Sun, 8 Dec 2019 16:49:26 +0000 (UTC) (envelope-from sunpoet@FreeBSD.org) Received: from repo.freebsd.org (repo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:0]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id CE9145208; Sun, 8 Dec 2019 16:49:26 +0000 (UTC) (envelope-from sunpoet@FreeBSD.org) Received: from repo.freebsd.org ([127.0.1.37]) by repo.freebsd.org (8.15.2/8.15.2) with ESMTP id xB8GnQqE054287; Sun, 8 Dec 2019 16:49:26 GMT (envelope-from sunpoet@FreeBSD.org) Received: (from sunpoet@localhost) by repo.freebsd.org (8.15.2/8.15.2/Submit) id xB8GnP7O054282; Sun, 8 Dec 2019 16:49:25 GMT (envelope-from sunpoet@FreeBSD.org) Message-Id: <201912081649.xB8GnP7O054282@repo.freebsd.org> X-Authentication-Warning: repo.freebsd.org: sunpoet set sender to sunpoet@FreeBSD.org using -f From: Sunpoet Po-Chuan Hsieh Date: Sun, 8 Dec 2019 16:49:25 +0000 (UTC) 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 X-SVN-Group: ports-head X-SVN-Commit-Author: sunpoet X-SVN-Commit-Paths: in head/biology: . p5-Bio-DB-NCBIHelper X-SVN-Commit-Revision: 519319 X-SVN-Commit-Repository: ports MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-BeenThere: svn-ports-all@freebsd.org X-Mailman-Version: 2.1.29 Precedence: list List-Id: SVN commit messages for the ports tree List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sun, 08 Dec 2019 16:49:27 -0000 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 +# $FreeBSD$ + +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 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