From owner-freebsd-ports-bugs@FreeBSD.ORG Mon Jan 17 22:40:21 2005 Return-Path: Delivered-To: freebsd-ports-bugs@hub.freebsd.org Received: from mx1.FreeBSD.org (mx1.freebsd.org [216.136.204.125]) by hub.freebsd.org (Postfix) with ESMTP id 7B9EB16A4CF for ; Mon, 17 Jan 2005 22:40:21 +0000 (GMT) Received: from freefall.freebsd.org (freefall.freebsd.org [216.136.204.21]) by mx1.FreeBSD.org (Postfix) with ESMTP id C673043D39 for ; Mon, 17 Jan 2005 22:40:20 +0000 (GMT) (envelope-from gnats@FreeBSD.org) Received: from freefall.freebsd.org (gnats@localhost [127.0.0.1]) by freefall.freebsd.org (8.13.1/8.13.1) with ESMTP id j0HMeKiK064291 for ; Mon, 17 Jan 2005 22:40:20 GMT (envelope-from gnats@freefall.freebsd.org) Received: (from gnats@localhost) by freefall.freebsd.org (8.13.1/8.13.1/Submit) id j0HMeK3X064290; Mon, 17 Jan 2005 22:40:20 GMT (envelope-from gnats) Resent-Date: Mon, 17 Jan 2005 22:40:20 GMT Resent-Message-Id: <200501172240.j0HMeK3X064290@freefall.freebsd.org> Resent-From: FreeBSD-gnats-submit@FreeBSD.org (GNATS Filer) Resent-To: freebsd-ports-bugs@FreeBSD.org Resent-Reply-To: FreeBSD-gnats-submit@FreeBSD.org, Razi Khaja Received: from mx1.FreeBSD.org (mx1.freebsd.org [216.136.204.125]) by hub.freebsd.org (Postfix) with ESMTP id DD33D16A4CE for ; Mon, 17 Jan 2005 22:33:41 +0000 (GMT) Received: from www.freebsd.org (www.freebsd.org [216.136.204.117]) by mx1.FreeBSD.org (Postfix) with ESMTP id 7177143D2F for ; Mon, 17 Jan 2005 22:33:41 +0000 (GMT) (envelope-from nobody@FreeBSD.org) Received: from www.freebsd.org (localhost [127.0.0.1]) by www.freebsd.org (8.13.1/8.13.1) with ESMTP id j0HMXfsg042223 for ; Mon, 17 Jan 2005 22:33:41 GMT (envelope-from nobody@www.freebsd.org) Received: (from nobody@localhost) by www.freebsd.org (8.13.1/8.13.1/Submit) id j0HMXfLK042219; Mon, 17 Jan 2005 22:33:41 GMT (envelope-from nobody) Message-Id: <200501172233.j0HMXfLK042219@www.freebsd.org> Date: Mon, 17 Jan 2005 22:33:41 GMT From: Razi Khaja To: freebsd-gnats-submit@FreeBSD.org X-Send-Pr-Version: www-2.3 Subject: ports/76379: New port:biology/p5-Bio-Das X-BeenThere: freebsd-ports-bugs@freebsd.org X-Mailman-Version: 2.1.1 Precedence: list List-Id: Ports bug reports List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 17 Jan 2005 22:40:21 -0000 >Number: 76379 >Category: ports >Synopsis: New port:biology/p5-Bio-Das >Confidential: no >Severity: non-critical >Priority: high >Responsible: freebsd-ports-bugs >State: open >Quarter: >Keywords: >Date-Required: >Class: update >Submitter-Id: current-users >Arrival-Date: Mon Jan 17 22:40:20 GMT 2005 >Closed-Date: >Last-Modified: >Originator: Razi Khaja >Release: FreeBSD 5.3 >Organization: The Hospital for Sick Children >Environment: >Description: >How-To-Repeat: >Fix: # This is a shell archive. Save it in a file, remove anything before # this line, and then unpack it by entering "sh file". Note, it may # create directories; files and directories will be owned by you and # have default permissions. # # This archive contains: # # p5-Bio-Das # p5-Bio-Das/Makefile # p5-Bio-Das/pkg-descr # p5-Bio-Das/distinfo # p5-Bio-Das/pkg-plist # echo c - p5-Bio-Das mkdir -p p5-Bio-Das > /dev/null 2>&1 echo x - p5-Bio-Das/Makefile sed 's/^X//' >p5-Bio-Das/Makefile << 'END-of-p5-Bio-Das/Makefile' X# New ports collection makefile for: p5-Bio-Das X# Date created: 17 January 2005 X# Whom: Razi Khaja X# X# $FreeBSD$ X# X XPORTNAME= Bio-Das XPORTVERSION= 0.99 XCATEGORIES= biology XMASTER_SITES= http://www.biodas.org/download/Bio::Das/ \ X ${MASTER_SITE_PERL_CPAN} XPKGNAMEPREFIX= p5- X XMAINTAINER= razi@genet.sickkids.on.ca XCOMMENT= Client-side library for Distributed Genome Annotation System X XBUILD_DEPENDS= ${SITE_PERL}/${PERL_ARCH}/Compress/Zlib.pm:${PORTSDIR}/archivers/p5-Compress-Zlib \ X ${SITE_PERL}/${PERL_ARCH}/HTML/Parser.pm:${PORTSDIR}/www/p5-HTML-Parser \ X ${SITE_PERL}/LWP/UserAgent.pm:${PORTSDIR}/www/p5-libwww \ X ${SITE_PERL}/${PERL_ARCH}/MIME/Base64.pm:${PORTSDIR}/converters/p5-MIME-Base64 \ X ${SITE_PERL}/Bio/Root/Root.pm:${PORTSDIR}/biology/p5-bioperl X XRUN_DEPENDS= ${BUILD_DEPENDS} X XPERL_CONFIGURE= YES X XMAN3= Bio::Das.3 \ X Bio::Das::AGPServer::Config.3 \ X Bio::Das::AGPServer::Daemon.3 \ X Bio::Das::AGPServer::Parser.3 \ X Bio::Das::AGPServer::SQLStorage.3 \ X Bio::Das::AGPServer::SQLStorage::CSV::DB.3 \ X Bio::Das::AGPServer::SQLStorage::MySQL::DB.3 \ X Bio::Das::DSN.3 \ X Bio::Das::Feature.3 \ X Bio::Das::FeatureIterator.3 \ X Bio::Das::HTTP::Fetch.3 \ X Bio::Das::Map.3 \ X Bio::Das::ProServer::Config.3 \ X Bio::Das::ProServer::Daemon.3 \ X Bio::Das::ProServer::Loader::agp.3 \ X Bio::Das::ProServer::SourceAdaptor.3 \ X Bio::Das::ProServer::SourceAdaptor::Transport::dbi.3 \ X Bio::Das::ProServer::SourceAdaptor::Transport::file.3 \ X Bio::Das::ProServer::SourceAdaptor::Transport::generic.3 \ X Bio::Das::ProServer::SourceAdaptor::Transport::getz.3 \ X Bio::Das::ProServer::SourceAdaptor::Transport::getzc.3 \ X Bio::Das::ProServer::SourceAdaptor::Transport::oracle.3 \ X Bio::Das::ProServer::SourceAdaptor::agp.3 \ X Bio::Das::ProServer::SourceAdaptor::cosmic.3 \ X Bio::Das::ProServer::SourceAdaptor::gensat.3 \ X Bio::Das::ProServer::SourceAdaptor::haplotype.3 \ X Bio::Das::ProServer::SourceAdaptor::image.3 \ X Bio::Das::ProServer::SourceAdaptor::interpro.3 \ X Bio::Das::ProServer::SourceAdaptor::simple.3 \ X Bio::Das::ProServer::SourceAdaptor::snp.3 \ X Bio::Das::ProServer::SourceAdaptor::sts.3 \ X Bio::Das::ProServer::SourceAdaptor::swissprot.3 \ X Bio::Das::ProServer::SourceAdaptor::trace.3 \ X Bio::Das::Request.3 \ X Bio::Das::Request::Dnas.3 \ X Bio::Das::Request::Dsn.3 \ X Bio::Das::Request::Entry_points.3 \ X Bio::Das::Request::Feature2Segments.3 \ X Bio::Das::Request::Stylesheet.3 \ X Bio::Das::Request::Types.3 \ X Bio::Das::Segment.3 \ X Bio::Das::Stylesheet.3 \ X Bio::Das::Type.3 \ X Bio::Das::TypeHandler.3 \ X Bio::Das::Util.3 X X.include END-of-p5-Bio-Das/Makefile echo x - p5-Bio-Das/pkg-descr sed 's/^X//' >p5-Bio-Das/pkg-descr << 'END-of-p5-Bio-Das/pkg-descr' XBio::Das provides access to genome sequencing and annotation databases Xthat export their data in Distributed Annotation System (DAS) format Xversion 1.5. This system is described at http://biodas.org. Both Xunencrypted (http:) and SSL-encrypted (https:) DAS servers are sup- Xported. (To run SSL, you will need IO::Socket::SSL and Net::SSLeay Xinstalled). X XWWW: http://www.biodas.org X X-- Razi Khaja END-of-p5-Bio-Das/pkg-descr echo x - p5-Bio-Das/distinfo sed 's/^X//' >p5-Bio-Das/distinfo << 'END-of-p5-Bio-Das/distinfo' XMD5 (Bio-Das-0.99.tar.gz) = fc9f965815603b4de148a7f46e3bce4e XSIZE (Bio-Das-0.99.tar.gz) = 124838 END-of-p5-Bio-Das/distinfo echo x - p5-Bio-Das/pkg-plist sed 's/^X//' >p5-Bio-Das/pkg-plist << 'END-of-p5-Bio-Das/pkg-plist' Xlib/perl5/site_perl/5.8.5/Bio/Das.pm Xlib/perl5/site_perl/5.8.5/Bio/Das/AGPServer/Config.pm Xlib/perl5/site_perl/5.8.5/Bio/Das/AGPServer/Daemon.pm Xlib/perl5/site_perl/5.8.5/Bio/Das/AGPServer/Parser.pm Xlib/perl5/site_perl/5.8.5/Bio/Das/AGPServer/Proxy.pm Xlib/perl5/site_perl/5.8.5/Bio/Das/AGPServer/SQLStorage.pm Xlib/perl5/site_perl/5.8.5/Bio/Das/AGPServer/SQLStorage/CSV/DB.pm Xlib/perl5/site_perl/5.8.5/Bio/Das/AGPServer/SQLStorage/MySQL/DB.pm Xlib/perl5/site_perl/5.8.5/Bio/Das/DSN.pm Xlib/perl5/site_perl/5.8.5/Bio/Das/Feature.pm Xlib/perl5/site_perl/5.8.5/Bio/Das/FeatureIterator.pm Xlib/perl5/site_perl/5.8.5/Bio/Das/HTTP/Fetch.pm Xlib/perl5/site_perl/5.8.5/Bio/Das/Map.pm Xlib/perl5/site_perl/5.8.5/Bio/Das/ProServer/Config.pm Xlib/perl5/site_perl/5.8.5/Bio/Das/ProServer/Daemon.pm Xlib/perl5/site_perl/5.8.5/Bio/Das/ProServer/Loader/agp.pm Xlib/perl5/site_perl/5.8.5/Bio/Das/ProServer/SourceAdaptor.pm Xlib/perl5/site_perl/5.8.5/Bio/Das/ProServer/SourceAdaptor/Transport/bioseqio.pm Xlib/perl5/site_perl/5.8.5/Bio/Das/ProServer/SourceAdaptor/Transport/dbi.pm Xlib/perl5/site_perl/5.8.5/Bio/Das/ProServer/SourceAdaptor/Transport/file.pm Xlib/perl5/site_perl/5.8.5/Bio/Das/ProServer/SourceAdaptor/Transport/generic.pm Xlib/perl5/site_perl/5.8.5/Bio/Das/ProServer/SourceAdaptor/Transport/getz.pm Xlib/perl5/site_perl/5.8.5/Bio/Das/ProServer/SourceAdaptor/Transport/getzc.pm Xlib/perl5/site_perl/5.8.5/Bio/Das/ProServer/SourceAdaptor/Transport/oracle.pm Xlib/perl5/site_perl/5.8.5/Bio/Das/ProServer/SourceAdaptor/Transport/wgetz.pm Xlib/perl5/site_perl/5.8.5/Bio/Das/ProServer/SourceAdaptor/agp.pm Xlib/perl5/site_perl/5.8.5/Bio/Das/ProServer/SourceAdaptor/bioseq.pm Xlib/perl5/site_perl/5.8.5/Bio/Das/ProServer/SourceAdaptor/cosmic.pm Xlib/perl5/site_perl/5.8.5/Bio/Das/ProServer/SourceAdaptor/gensat.pm Xlib/perl5/site_perl/5.8.5/Bio/Das/ProServer/SourceAdaptor/haplotype.pm Xlib/perl5/site_perl/5.8.5/Bio/Das/ProServer/SourceAdaptor/image.pm Xlib/perl5/site_perl/5.8.5/Bio/Das/ProServer/SourceAdaptor/interpro.pm Xlib/perl5/site_perl/5.8.5/Bio/Das/ProServer/SourceAdaptor/simple.pm Xlib/perl5/site_perl/5.8.5/Bio/Das/ProServer/SourceAdaptor/snp.pm Xlib/perl5/site_perl/5.8.5/Bio/Das/ProServer/SourceAdaptor/sts.pm Xlib/perl5/site_perl/5.8.5/Bio/Das/ProServer/SourceAdaptor/swissprot.pm Xlib/perl5/site_perl/5.8.5/Bio/Das/ProServer/SourceAdaptor/trace.pm Xlib/perl5/site_perl/5.8.5/Bio/Das/Request.pm Xlib/perl5/site_perl/5.8.5/Bio/Das/Request/Dnas.pm Xlib/perl5/site_perl/5.8.5/Bio/Das/Request/Dsn.pm Xlib/perl5/site_perl/5.8.5/Bio/Das/Request/Entry_points.pm Xlib/perl5/site_perl/5.8.5/Bio/Das/Request/Feature2Segments.pm Xlib/perl5/site_perl/5.8.5/Bio/Das/Request/Features.pm Xlib/perl5/site_perl/5.8.5/Bio/Das/Request/Stylesheet.pm Xlib/perl5/site_perl/5.8.5/Bio/Das/Request/Types.pm Xlib/perl5/site_perl/5.8.5/Bio/Das/Segment.pm Xlib/perl5/site_perl/5.8.5/Bio/Das/Stylesheet.pm Xlib/perl5/site_perl/5.8.5/Bio/Das/Type.pm Xlib/perl5/site_perl/5.8.5/Bio/Das/TypeHandler.pm Xlib/perl5/site_perl/5.8.5/Bio/Das/Util.pm Xlib/perl5/site_perl/5.8.5/mach/auto/Bio/Das/.packlist Xshare/nls/POSIX Xshare/nls/en_US.US-ASCII X@dirrm lib/perl5/site_perl/5.8.5/mach/auto/Bio/Das X@dirrm lib/perl5/site_perl/5.8.5/Bio/Das/Request X@dirrm lib/perl5/site_perl/5.8.5/Bio/Das/ProServer/SourceAdaptor/Transport X@dirrm lib/perl5/site_perl/5.8.5/Bio/Das/ProServer/SourceAdaptor X@dirrm lib/perl5/site_perl/5.8.5/Bio/Das/ProServer/Loader X@dirrm lib/perl5/site_perl/5.8.5/Bio/Das/ProServer X@dirrm lib/perl5/site_perl/5.8.5/Bio/Das/HTTP X@dirrm lib/perl5/site_perl/5.8.5/Bio/Das/AGPServer/SQLStorage/MySQL X@dirrm lib/perl5/site_perl/5.8.5/Bio/Das/AGPServer/SQLStorage/CSV X@dirrm lib/perl5/site_perl/5.8.5/Bio/Das/AGPServer/SQLStorage X@dirrm lib/perl5/site_perl/5.8.5/Bio/Das/AGPServer X END-of-p5-Bio-Das/pkg-plist exit >Release-Note: >Audit-Trail: >Unformatted: