p5-Bio-MAGETAB contains the core MAGE-TAB Utilities Perl modules. This

is a beta release. All functions have now been implemented and most
have test suites; the exceptions include the modules involved in
export of MAGE-TAB documents, which are still a little experimental in
nature. The API is mostly finalised (and fully documented), but some
details may yet change where necessary to improve usability.

WWW: http://search.cpan.org/dist/Bio-MAGETAB/

PR:		ports/136021
Submitted by:	Wen Heping <wenheping at gmail.com>

4 files changed, 176 insertions, 0 deletions

diff --git a/biology/p5-Bio-MAGETAB/Makefile b/biology/p5-Bio-MAGETAB/Makefile
new file mode 100644
index 000000000000..e6ece989286a
--- /dev/null
+++ b/biology/p5-Bio-MAGETAB/Makefile
@@ -0,0 +1,96 @@
+# New ports collection makefile for:	p5-Bio-MAGETAB
+# Date created:				23 June, 2009
+# Whom:					Wen Heping <wenheping@gmail.com>
+#
+# $FreeBSD$
+#
+
+PORTNAME=	Bio-MAGETAB
+PORTVERSION=	0.98
+CATEGORIES=	biology perl5
+MASTER_SITES=	CPAN
+PKGNAMEPREFIX=	p5-
+
+MAINTAINER=	wenheping@gmail.com
+COMMENT=	A data model and utility API for the MAGE-TAB format
+
+BUILD_DEPENDS=	p5-Test-Exception>=0.26:${PORTSDIR}/devel/p5-Test-Exception \
+		p5-DateTime-Format-DateManip>=0.04:${PORTSDIR}/devel/p5-DateTime-Format-DateManip \
+		p5-Moose-Policy>=0.03:${PORTSDIR}/devel/p5-Moose-Policy \
+		p5-MooseX-Types>=0.10:${PORTSDIR}/devel/p5-MooseX-Types \
+		p5-Parse-RecDescent>=1.96:${PORTSDIR}/devel/p5-Parse-RecDescent \
+		p5-Params-Coerce>=0.14:${PORTSDIR}/devel/p5-Params-Coerce \
+		p5-URI>=1.35:${PORTSDIR}/net/p5-URI \
+		p5-Test-Exception>=0.26:${PORTSDIR}/devel/p5-Test-Exception \
+		p5-Date-Manip>=5.44:${PORTSDIR}/devel/p5-Date-Manip \
+		p5-DateTime>=0.43:${PORTSDIR}/devel/p5-DateTime \
+		p5-Text-CSV_XS>=0.32:${PORTSDIR}/textproc/p5-Text-CSV_XS \
+		p5-Email-Valid>=0.179:${PORTSDIR}/mail/p5-Email-Valid \
+		p5-Moose>=0.43:${PORTSDIR}/devel/p5-Moose
+RUN_DEPENDS=	${BUILD_DEPENDS}
+
+PERL_CONFIGURE=	YES
+
+MAN3=	Bio::MAGETAB::Material.3 \
+	Bio::MAGETAB::Types.3 \
+	Bio::MAGETAB::ControlledTerm.3 \
+	Bio::MAGETAB::Util::Reader::DataMatrix.3 \
+	Bio::MAGETAB::DesignElement.3 \
+	Bio::MAGETAB::Contact.3 \
+	Bio::MAGETAB::Investigation.3 \
+	Bio::MAGETAB::Comment.3 \
+	Bio::MAGETAB::Sample.3 \
+	Bio::MAGETAB::Publication.3 \
+	Bio::MAGETAB::DataFile.3 \
+	Bio::MAGETAB::Event.3 \
+	Bio::MAGETAB::Edge.3 \
+	Bio::MAGETAB::ArrayDesign.3 \
+	Bio::MAGETAB.3 \
+	Bio::MAGETAB::Util::Writer::ADF.3 \
+	Bio::MAGETAB::MatrixColumn.3 \
+	Bio::MAGETAB::Normalization.3 \
+	Bio::MAGETAB::Util::Reader::TagValueFile.3 \
+	Bio::MAGETAB::ParameterValue.3 \
+	Bio::MAGETAB::Util::Reader::Tabfile.3 \
+	Bio::MAGETAB::Util::Writer.3 \
+	Bio::MAGETAB::Util::Writer::Tabfile.3 \
+	Bio::MAGETAB::DataAcquisition.3 \
+	Bio::MAGETAB::Util::Reader::SDRF.3 \
+	Bio::MAGETAB::Assay.3 \
+	Bio::MAGETAB::SDRFRow.3 \
+	Bio::MAGETAB::Util::Writer::IDF.3 \
+	Bio::MAGETAB::SDRF.3 \
+	Bio::MAGETAB::MatrixRow.3 \
+	Bio::MAGETAB::Data.3 \
+	Bio::MAGETAB::Util::Reader.3 \
+	Bio::MAGETAB::Extract.3 \
+	Bio::MAGETAB::Util::Reader::IDF.3 \
+	Bio::MAGETAB::TermSource.3 \
+	Bio::MAGETAB::Measurement.3 \
+	Bio::MAGETAB::Util::Builder.3 \
+	Bio::MAGETAB::CompositeElement.3 \
+	Bio::MAGETAB::Node.3 \
+	Bio::MAGETAB::Util::DBLoader.3 \
+	Bio::MAGETAB::BaseClass.3 \
+	Bio::MAGETAB::Util::Writer::SDRF.3 \
+	Bio::MAGETAB::Protocol.3 \
+	Bio::MAGETAB::Reporter.3 \
+	Bio::MAGETAB::Util::Reader::ADF.3 \
+	Bio::MAGETAB::Factor.3 \
+	Bio::MAGETAB::DatabaseEntry.3 \
+	Bio::MAGETAB::Feature.3 \
+	Bio::MAGETAB::LabeledExtract.3 \
+	Bio::MAGETAB::ProtocolApplication.3 \
+	Bio::MAGETAB::Util::RewriteAE.3 \
+	Bio::MAGETAB::Source.3 \
+	Bio::MAGETAB::Util::Persistence.3 \
+	Bio::MAGETAB::Util::Writer::GraphViz.3 \
+	Bio::MAGETAB::DataMatrix.3 \
+	Bio::MAGETAB::FactorValue.3 \
+	Bio::MAGETAB::ProtocolParameter.3
+
+post-extract:
+	@${REINPLACE_CMD} -e 's?auto_install?#auto_install?g' \
+		${WRKSRC}/Makefile.PL
+
+.include <bsd.port.mk>
diff --git a/biology/p5-Bio-MAGETAB/distinfo b/biology/p5-Bio-MAGETAB/distinfo
new file mode 100644
index 000000000000..b5519c68ec6f
--- /dev/null
+++ b/biology/p5-Bio-MAGETAB/distinfo
@@ -0,0 +1,3 @@
+MD5 (Bio-MAGETAB-0.98.tar.gz) = 91ddd45bdbe836a9be1f09a7049bb98a
+SHA256 (Bio-MAGETAB-0.98.tar.gz) = 2a8bf1eb1883f9b9afa9c9caf2ebae74345fb3e0e1a1faf891f3790ebb223151
+SIZE (Bio-MAGETAB-0.98.tar.gz) = 240502
diff --git a/biology/p5-Bio-MAGETAB/pkg-descr b/biology/p5-Bio-MAGETAB/pkg-descr
new file mode 100644
index 000000000000..c847b27165b5
--- /dev/null
+++ b/biology/p5-Bio-MAGETAB/pkg-descr
@@ -0,0 +1,8 @@
+p5-Bio-MAGETAB contains the core MAGE-TAB Utilities Perl modules. This
+is a beta release. All functions have now been implemented and most
+have test suites; the exceptions include the modules involved in
+export of MAGE-TAB documents, which are still a little experimental in
+nature. The API is mostly finalised (and fully documented), but some
+details may yet change where necessary to improve usability.
+
+WWW: http://search.cpan.org/dist/Bio-MAGETAB/
diff --git a/biology/p5-Bio-MAGETAB/pkg-plist b/biology/p5-Bio-MAGETAB/pkg-plist
new file mode 100644
index 000000000000..02398f400a64
--- /dev/null
+++ b/biology/p5-Bio-MAGETAB/pkg-plist
@@ -0,0 +1,69 @@
+bin/deploy_magetab_db.pl
+bin/fix_ae_magetab.pl
+bin/read_magetab.pl
+bin/unload_magetab_namespace.pl
+%%SITE_PERL%%/mach/auto/Bio/MAGETAB/.packlist
+%%SITE_PERL%%/Bio/MAGETAB/Util/Reader/DataMatrix.pm
+%%SITE_PERL%%/Bio/MAGETAB/Util/Reader/TagValueFile.pm
+%%SITE_PERL%%/Bio/MAGETAB/Util/Reader/Tabfile.pm
+%%SITE_PERL%%/Bio/MAGETAB/Util/Reader/SDRF.pm
+%%SITE_PERL%%/Bio/MAGETAB/Util/Reader/IDF.pm
+%%SITE_PERL%%/Bio/MAGETAB/Util/Reader/ADF.pm
+%%SITE_PERL%%/Bio/MAGETAB/Util/Writer/ADF.pm
+%%SITE_PERL%%/Bio/MAGETAB/Util/Writer/Tabfile.pm
+%%SITE_PERL%%/Bio/MAGETAB/Util/Writer/IDF.pm
+%%SITE_PERL%%/Bio/MAGETAB/Util/Writer/SDRF.pm
+%%SITE_PERL%%/Bio/MAGETAB/Util/Writer/GraphViz.pm
+%%SITE_PERL%%/Bio/MAGETAB/Util/Writer.pm
+%%SITE_PERL%%/Bio/MAGETAB/Util/Reader.pm
+%%SITE_PERL%%/Bio/MAGETAB/Util/Builder.pm
+%%SITE_PERL%%/Bio/MAGETAB/Util/DBLoader.pm
+%%SITE_PERL%%/Bio/MAGETAB/Util/RewriteAE.pm
+%%SITE_PERL%%/Bio/MAGETAB/Util/Persistence.pm
+%%SITE_PERL%%/Bio/MAGETAB/Material.pm
+%%SITE_PERL%%/Bio/MAGETAB/Types.pm
+%%SITE_PERL%%/Bio/MAGETAB/ControlledTerm.pm
+%%SITE_PERL%%/Bio/MAGETAB/Contact.pm
+%%SITE_PERL%%/Bio/MAGETAB/DesignElement.pm
+%%SITE_PERL%%/Bio/MAGETAB/Investigation.pm
+%%SITE_PERL%%/Bio/MAGETAB/Comment.pm
+%%SITE_PERL%%/Bio/MAGETAB/Publication.pm
+%%SITE_PERL%%/Bio/MAGETAB/Sample.pm
+%%SITE_PERL%%/Bio/MAGETAB/DataFile.pm
+%%SITE_PERL%%/Bio/MAGETAB/ArrayDesign.pm
+%%SITE_PERL%%/Bio/MAGETAB/Event.pm
+%%SITE_PERL%%/Bio/MAGETAB/Edge.pm
+%%SITE_PERL%%/Bio/MAGETAB/MatrixColumn.pm
+%%SITE_PERL%%/Bio/MAGETAB/Normalization.pm
+%%SITE_PERL%%/Bio/MAGETAB/ParameterValue.pm
+%%SITE_PERL%%/Bio/MAGETAB/DataAcquisition.pm
+%%SITE_PERL%%/Bio/MAGETAB/Assay.pm
+%%SITE_PERL%%/Bio/MAGETAB/SDRFRow.pm
+%%SITE_PERL%%/Bio/MAGETAB/SDRF.pm
+%%SITE_PERL%%/Bio/MAGETAB/Data.pm
+%%SITE_PERL%%/Bio/MAGETAB/MatrixRow.pm
+%%SITE_PERL%%/Bio/MAGETAB/Extract.pm
+%%SITE_PERL%%/Bio/MAGETAB/Measurement.pm
+%%SITE_PERL%%/Bio/MAGETAB/TermSource.pm
+%%SITE_PERL%%/Bio/MAGETAB/CompositeElement.pm
+%%SITE_PERL%%/Bio/MAGETAB/BaseClass.pm
+%%SITE_PERL%%/Bio/MAGETAB/Node.pm
+%%SITE_PERL%%/Bio/MAGETAB/Protocol.pm
+%%SITE_PERL%%/Bio/MAGETAB/Reporter.pm
+%%SITE_PERL%%/Bio/MAGETAB/Factor.pm
+%%SITE_PERL%%/Bio/MAGETAB/ProtocolApplication.pm
+%%SITE_PERL%%/Bio/MAGETAB/LabeledExtract.pm
+%%SITE_PERL%%/Bio/MAGETAB/Feature.pm
+%%SITE_PERL%%/Bio/MAGETAB/DatabaseEntry.pm
+%%SITE_PERL%%/Bio/MAGETAB/Source.pm
+%%SITE_PERL%%/Bio/MAGETAB/ProtocolParameter.pm
+%%SITE_PERL%%/Bio/MAGETAB/FactorValue.pm
+%%SITE_PERL%%/Bio/MAGETAB/DataMatrix.pm
+%%SITE_PERL%%/Bio/MAGETAB.pm
+@dirrm %%SITE_PERL%%/mach/auto/Bio/MAGETAB
+@dirrmtry %%SITE_PERL%%/mach/auto/Bio
+@dirrm %%SITE_PERL%%/Bio/MAGETAB/Util/Reader
+@dirrm %%SITE_PERL%%/Bio/MAGETAB/Util/Writer
+@dirrm %%SITE_PERL%%/Bio/MAGETAB/Util
+@dirrm %%SITE_PERL%%/Bio/MAGETAB
+@dirrmtry %%SITE_PERL%%/Bio