Add p5-Bio-Das 1.02, client-side library for Distributed Genome

Annotation System.

PR:		ports/76379
Submitted by:	Razi Khaja <razi@genet.sickkids.on.ca>

5 files changed, 158 insertions, 0 deletions

diff --git a/biology/Makefile b/biology/Makefile
index 9e958371bc9f..9488229aa980 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -43,6 +43,7 @@
     SUBDIR += nclever
     SUBDIR += ortep3
     SUBDIR += p5-AcePerl
+    SUBDIR += p5-Bio-Das
     SUBDIR += p5-bioperl
     SUBDIR += paml
     SUBDIR += phylip
diff --git a/biology/p5-Bio-Das/Makefile b/biology/p5-Bio-Das/Makefile
new file mode 100644
index 000000000000..e48c99ed2d2c
--- /dev/null
+++ b/biology/p5-Bio-Das/Makefile
@@ -0,0 +1,80 @@
+# New ports collection makefile for:	p5-Bio-Das
+# Date created:				17 January 2005
+# Whom:					Razi Khaja <razi@genet.sickkids.on.ca>
+#
+# $FreeBSD$
+#
+
+PORTNAME=	Bio-Das
+PORTVERSION=	1.02
+CATEGORIES=	biology
+MASTER_SITES=	http://www.biodas.org/download/Bio::Das/ \
+		${MASTER_SITE_PERL_CPAN}
+PKGNAMEPREFIX=	p5-
+
+MAINTAINER=	razi@genet.sickkids.on.ca
+COMMENT=	Client-side library for Distributed Genome Annotation System
+
+BUILD_DEPENDS=	${SITE_PERL}/${PERL_ARCH}/Compress/Zlib.pm:${PORTSDIR}/archivers/p5-Compress-Zlib \
+		${SITE_PERL}/${PERL_ARCH}/HTML/Parser.pm:${PORTSDIR}/www/p5-HTML-Parser \
+		${SITE_PERL}/LWP/UserAgent.pm:${PORTSDIR}/www/p5-libwww \
+		${SITE_PERL}/${PERL_ARCH}/MIME/Base64.pm:${PORTSDIR}/converters/p5-MIME-Base64 \
+		${SITE_PERL}/Bio/Root/Root.pm:${PORTSDIR}/biology/p5-bioperl
+RUN_DEPENDS=	${BUILD_DEPENDS}
+
+PERL_CONFIGURE=	YES
+
+MAN3=	Bio::Das.3 \
+	Bio::Das::AGPServer::Config.3 \
+	Bio::Das::AGPServer::Daemon.3 \
+	Bio::Das::AGPServer::Parser.3 \
+	Bio::Das::AGPServer::SQLStorage.3 \
+	Bio::Das::AGPServer::SQLStorage::CSV::DB.3 \
+	Bio::Das::AGPServer::SQLStorage::MySQL::DB.3 \
+	Bio::Das::DSN.3 \
+	Bio::Das::Feature.3 \
+	Bio::Das::FeatureIterator.3 \
+	Bio::Das::HTTP::Fetch.3 \
+	Bio::Das::Map.3 \
+	Bio::Das::ProServer::Config.3 \
+	Bio::Das::ProServer::Daemon.3 \
+	Bio::Das::ProServer::Loader::agp.3 \
+	Bio::Das::ProServer::SourceAdaptor.3 \
+	Bio::Das::ProServer::SourceAdaptor::Transport::dbi.3 \
+	Bio::Das::ProServer::SourceAdaptor::Transport::file.3 \
+	Bio::Das::ProServer::SourceAdaptor::Transport::generic.3 \
+	Bio::Das::ProServer::SourceAdaptor::Transport::getz.3 \
+	Bio::Das::ProServer::SourceAdaptor::Transport::getzc.3 \
+	Bio::Das::ProServer::SourceAdaptor::Transport::oracle.3 \
+	Bio::Das::ProServer::SourceAdaptor::agp.3 \
+	Bio::Das::ProServer::SourceAdaptor::cosmic.3 \
+	Bio::Das::ProServer::SourceAdaptor::gensat.3 \
+	Bio::Das::ProServer::SourceAdaptor::haplotype.3 \
+	Bio::Das::ProServer::SourceAdaptor::image.3 \
+	Bio::Das::ProServer::SourceAdaptor::interpro.3 \
+	Bio::Das::ProServer::SourceAdaptor::simple.3 \
+	Bio::Das::ProServer::SourceAdaptor::snp.3 \
+	Bio::Das::ProServer::SourceAdaptor::sts.3 \
+	Bio::Das::ProServer::SourceAdaptor::swissprot.3 \
+	Bio::Das::ProServer::SourceAdaptor::trace.3 \
+	Bio::Das::Request.3 \
+	Bio::Das::Request::Dnas.3 \
+	Bio::Das::Request::Dsn.3 \
+	Bio::Das::Request::Entry_points.3 \
+	Bio::Das::Request::Feature2Segments.3 \
+	Bio::Das::Request::Sequences.3 \
+	Bio::Das::Request::Stylesheet.3 \
+	Bio::Das::Request::Types.3 \
+	Bio::Das::Segment.3 \
+	Bio::Das::Stylesheet.3 \
+	Bio::Das::Type.3 \
+	Bio::Das::TypeHandler.3 \
+	Bio::Das::Util.3
+
+.include <bsd.port.pre.mk>
+
+.if (${PERL_LEVEL} < 500601)
+BROKEN=	"Some dependencies doesn't work with Perl < 5.6.1"
+.endif
+
+.include <bsd.port.post.mk>
diff --git a/biology/p5-Bio-Das/distinfo b/biology/p5-Bio-Das/distinfo
new file mode 100644
index 000000000000..09b1eba08788
--- /dev/null
+++ b/biology/p5-Bio-Das/distinfo
@@ -0,0 +1,2 @@
+MD5 (Bio-Das-1.02.tar.gz) = 6b3706f1ca52da18bd7c6376cf89b244
+SIZE (Bio-Das-1.02.tar.gz) = 127150
diff --git a/biology/p5-Bio-Das/pkg-descr b/biology/p5-Bio-Das/pkg-descr
new file mode 100644
index 000000000000..c6e4f07b288b
--- /dev/null
+++ b/biology/p5-Bio-Das/pkg-descr
@@ -0,0 +1,10 @@
+Bio::Das provides access to genome sequencing and annotation databases
+that export their data in Distributed Annotation System (DAS) format
+version 1.5.  This system is described at http://biodas.org.  Both
+unencrypted (http:) and SSL-encrypted (https:) DAS servers are sup-
+ported.  (To run SSL, you will need IO::Socket::SSL and Net::SSLeay
+installed).
+
+WWW: http://www.biodas.org
+
+-- Razi Khaja <razi@genet.sickkids.on.ca>
diff --git a/biology/p5-Bio-Das/pkg-plist b/biology/p5-Bio-Das/pkg-plist
new file mode 100644
index 000000000000..9378ff7eb5ac
--- /dev/null
+++ b/biology/p5-Bio-Das/pkg-plist
@@ -0,0 +1,65 @@
+%%SITE_PERL%%/Bio/Das.pm
+%%SITE_PERL%%/Bio/Das/AGPServer/Config.pm
+%%SITE_PERL%%/Bio/Das/AGPServer/Daemon.pm
+%%SITE_PERL%%/Bio/Das/AGPServer/Parser.pm
+%%SITE_PERL%%/Bio/Das/AGPServer/Proxy.pm
+%%SITE_PERL%%/Bio/Das/AGPServer/SQLStorage.pm
+%%SITE_PERL%%/Bio/Das/AGPServer/SQLStorage/CSV/DB.pm
+%%SITE_PERL%%/Bio/Das/AGPServer/SQLStorage/MySQL/DB.pm
+%%SITE_PERL%%/Bio/Das/DSN.pm
+%%SITE_PERL%%/Bio/Das/Feature.pm
+%%SITE_PERL%%/Bio/Das/FeatureIterator.pm
+%%SITE_PERL%%/Bio/Das/HTTP/Fetch.pm
+%%SITE_PERL%%/Bio/Das/Map.pm
+%%SITE_PERL%%/Bio/Das/ProServer/Config.pm
+%%SITE_PERL%%/Bio/Das/ProServer/Daemon.pm
+%%SITE_PERL%%/Bio/Das/ProServer/Loader/agp.pm
+%%SITE_PERL%%/Bio/Das/ProServer/SourceAdaptor.pm
+%%SITE_PERL%%/Bio/Das/ProServer/SourceAdaptor/Transport/bioseqio.pm
+%%SITE_PERL%%/Bio/Das/ProServer/SourceAdaptor/Transport/dbi.pm
+%%SITE_PERL%%/Bio/Das/ProServer/SourceAdaptor/Transport/file.pm
+%%SITE_PERL%%/Bio/Das/ProServer/SourceAdaptor/Transport/generic.pm
+%%SITE_PERL%%/Bio/Das/ProServer/SourceAdaptor/Transport/getz.pm
+%%SITE_PERL%%/Bio/Das/ProServer/SourceAdaptor/Transport/getzc.pm
+%%SITE_PERL%%/Bio/Das/ProServer/SourceAdaptor/Transport/oracle.pm
+%%SITE_PERL%%/Bio/Das/ProServer/SourceAdaptor/Transport/wgetz.pm
+%%SITE_PERL%%/Bio/Das/ProServer/SourceAdaptor/agp.pm
+%%SITE_PERL%%/Bio/Das/ProServer/SourceAdaptor/bioseq.pm
+%%SITE_PERL%%/Bio/Das/ProServer/SourceAdaptor/cosmic.pm
+%%SITE_PERL%%/Bio/Das/ProServer/SourceAdaptor/gensat.pm
+%%SITE_PERL%%/Bio/Das/ProServer/SourceAdaptor/haplotype.pm
+%%SITE_PERL%%/Bio/Das/ProServer/SourceAdaptor/image.pm
+%%SITE_PERL%%/Bio/Das/ProServer/SourceAdaptor/interpro.pm
+%%SITE_PERL%%/Bio/Das/ProServer/SourceAdaptor/simple.pm
+%%SITE_PERL%%/Bio/Das/ProServer/SourceAdaptor/snp.pm
+%%SITE_PERL%%/Bio/Das/ProServer/SourceAdaptor/sts.pm
+%%SITE_PERL%%/Bio/Das/ProServer/SourceAdaptor/swissprot.pm
+%%SITE_PERL%%/Bio/Das/ProServer/SourceAdaptor/trace.pm
+%%SITE_PERL%%/Bio/Das/Request.pm
+%%SITE_PERL%%/Bio/Das/Request/Dnas.pm
+%%SITE_PERL%%/Bio/Das/Request/Dsn.pm
+%%SITE_PERL%%/Bio/Das/Request/Entry_points.pm
+%%SITE_PERL%%/Bio/Das/Request/Feature2Segments.pm
+%%SITE_PERL%%/Bio/Das/Request/Features.pm
+%%SITE_PERL%%/Bio/Das/Request/Sequences.pm
+%%SITE_PERL%%/Bio/Das/Request/Stylesheet.pm
+%%SITE_PERL%%/Bio/Das/Request/Types.pm
+%%SITE_PERL%%/Bio/Das/Segment.pm
+%%SITE_PERL%%/Bio/Das/Stylesheet.pm
+%%SITE_PERL%%/Bio/Das/Type.pm
+%%SITE_PERL%%/Bio/Das/TypeHandler.pm
+%%SITE_PERL%%/Bio/Das/Util.pm
+%%SITE_PERL%%/mach/auto/Bio/Das/.packlist
+share/nls/POSIX
+share/nls/en_US.US-ASCII
+@dirrm %%SITE_PERL%%/mach/auto/Bio/Das
+@dirrm %%SITE_PERL%%/Bio/Das/Request
+@dirrm %%SITE_PERL%%/Bio/Das/ProServer/SourceAdaptor/Transport
+@dirrm %%SITE_PERL%%/Bio/Das/ProServer/SourceAdaptor
+@dirrm %%SITE_PERL%%/Bio/Das/ProServer/Loader
+@dirrm %%SITE_PERL%%/Bio/Das/ProServer
+@dirrm %%SITE_PERL%%/Bio/Das/HTTP
+@dirrm %%SITE_PERL%%/Bio/Das/AGPServer/SQLStorage/MySQL
+@dirrm %%SITE_PERL%%/Bio/Das/AGPServer/SQLStorage/CSV
+@dirrm %%SITE_PERL%%/Bio/Das/AGPServer/SQLStorage
+@dirrm %%SITE_PERL%%/Bio/Das/AGPServer