Date: Mon, 17 Jan 2005 22:33:41 GMT From: Razi Khaja <razi@genet.sickkids.on.ca> To: freebsd-gnats-submit@FreeBSD.org Subject: ports/76379: New port:biology/p5-Bio-Das Message-ID: <200501172233.j0HMXfLK042219@www.freebsd.org> Resent-Message-ID: <200501172240.j0HMeK3X064290@freefall.freebsd.org>
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>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 <razi@genet.sickkids.on.ca>
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 <bsd.port.mk>
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 <razi@genet.sickkids.on.ca>
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:
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