From owner-svn-ports-head@freebsd.org Sun Dec 8 16:49:20 2019 Return-Path: Delivered-To: svn-ports-head@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 DCFD21E7A90; Sun, 8 Dec 2019 16:49:20 +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 47WC345bGFz4Cr1; Sun, 8 Dec 2019 16:49:20 +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 BB2E75207; Sun, 8 Dec 2019 16:49:20 +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 xB8GnKoE054101; Sun, 8 Dec 2019 16:49:20 GMT (envelope-from sunpoet@FreeBSD.org) Received: (from sunpoet@localhost) by repo.freebsd.org (8.15.2/8.15.2/Submit) id xB8GnJP0054096; Sun, 8 Dec 2019 16:49:19 GMT (envelope-from sunpoet@FreeBSD.org) Message-Id: <201912081649.xB8GnJP0054096@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 16:49:19 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r519318 - in head/biology: . p5-Bio-DB-EMBL X-SVN-Group: ports-head X-SVN-Commit-Author: sunpoet X-SVN-Commit-Paths: in head/biology: . p5-Bio-DB-EMBL X-SVN-Commit-Revision: 519318 X-SVN-Commit-Repository: ports MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-BeenThere: svn-ports-head@freebsd.org X-Mailman-Version: 2.1.29 Precedence: list List-Id: SVN commit messages for the ports tree for head List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sun, 08 Dec 2019 16:49:20 -0000 Author: sunpoet Date: Sun Dec 8 16:49:19 2019 New Revision: 519318 URL: https://svnweb.freebsd.org/changeset/ports/519318 Log: Add p5-Bio-DB-EMBL 1.7.4 Bio::DB::EMBL allows the dynamic retrieval of sequence objects Bio::Seq from the EMBL database using the dbfetch script at EBI. In order to make changes transparent we have host type (currently only ebi) and location (defaults to ebi) separated out. This allows later additions of more servers in different geographical locations. The functionality of this module is inherited from Bio::DB::DBFetch which implements Bio::DB::WebDBSeqI. WWW: https://metacpan.org/release/Bio-DB-EMBL Added: head/biology/p5-Bio-DB-EMBL/ head/biology/p5-Bio-DB-EMBL/Makefile (contents, props changed) head/biology/p5-Bio-DB-EMBL/distinfo (contents, props changed) head/biology/p5-Bio-DB-EMBL/pkg-descr (contents, props changed) head/biology/p5-Bio-DB-EMBL/pkg-plist (contents, props changed) Modified: head/biology/Makefile Modified: head/biology/Makefile ============================================================================== --- head/biology/Makefile Sun Dec 8 16:49:13 2019 (r519317) +++ head/biology/Makefile Sun Dec 8 16:49:19 2019 (r519318) @@ -86,6 +86,7 @@ SUBDIR += p5-Bio-ASN1-EntrezGene SUBDIR += p5-Bio-Cluster SUBDIR += p5-Bio-Coordinate + SUBDIR += p5-Bio-DB-EMBL SUBDIR += p5-Bio-Das SUBDIR += p5-Bio-Das-Lite SUBDIR += p5-Bio-FeatureIO Added: head/biology/p5-Bio-DB-EMBL/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/p5-Bio-DB-EMBL/Makefile Sun Dec 8 16:49:19 2019 (r519318) @@ -0,0 +1,27 @@ +# Created by: Po-Chuan Hsieh +# $FreeBSD$ + +PORTNAME= Bio-DB-EMBL +PORTVERSION= 1.7.4 +CATEGORIES= biology perl5 +MASTER_SITES= CPAN +PKGNAMEPREFIX= p5- + +MAINTAINER= sunpoet@FreeBSD.org +COMMENT= Database object interface for EMBL entry retrieval + +LICENSE= ART10 GPLv1+ +LICENSE_COMB= dual +LICENSE_FILE= ${WRKSRC}/LICENSE + +BUILD_DEPENDS= ${RUN_DEPENDS} +RUN_DEPENDS= p5-BioPerl>=0:biology/p5-BioPerl +TEST_DEPENDS= 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-EMBL/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/p5-Bio-DB-EMBL/distinfo Sun Dec 8 16:49:19 2019 (r519318) @@ -0,0 +1,3 @@ +TIMESTAMP = 1575793783 +SHA256 (Bio-DB-EMBL-1.7.4.tar.gz) = fce080c4b3db7bcc529fd0cf0d29700d0b86ef8bbe7f77ad87f429a3ae7e1a27 +SIZE (Bio-DB-EMBL-1.7.4.tar.gz) = 13927 Added: head/biology/p5-Bio-DB-EMBL/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/p5-Bio-DB-EMBL/pkg-descr Sun Dec 8 16:49:19 2019 (r519318) @@ -0,0 +1,11 @@ +Bio::DB::EMBL allows the dynamic retrieval of sequence objects Bio::Seq from the +EMBL database using the dbfetch script at EBI. + +In order to make changes transparent we have host type (currently only ebi) and +location (defaults to ebi) separated out. This allows later additions of more +servers in different geographical locations. + +The functionality of this module is inherited from Bio::DB::DBFetch which +implements Bio::DB::WebDBSeqI. + +WWW: https://metacpan.org/release/Bio-DB-EMBL Added: head/biology/p5-Bio-DB-EMBL/pkg-plist ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/p5-Bio-DB-EMBL/pkg-plist Sun Dec 8 16:49:19 2019 (r519318) @@ -0,0 +1,2 @@ +%%SITE_PERL%%/Bio/DB/EMBL.pm +%%PERL5_MAN3%%/Bio::DB::EMBL.3.gz