Bio::NEXUS package provides an object-oriented, Perl-based

applications programming interface (API) to the NEXUS file
format of Maddison, et al., 1997 (Syst. Biol. 46:590-621).
NEXUS is a powerful and extensible format designed for use
in evolutionary analysis, including the analysis of molecular
sequence data as well as classical morphological and life-history
data. NEXUS is the input or output format for software such as
PAUP*, MacClade, Mesquite, SIMMAP, MrBayes, Nexplorer, and
so on.  This package also contains the demonstration applications
nexplot.pl (plot character data with a tree) and nextool.pl
(allowing programmatic editing, e.g., selecting particular
clades or subsets of data).

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

PR:		ports/137983
Submitted by:	Wen Heping <wenheping at gmail.com>

4 files changed, 90 insertions, 0 deletions

diff --git a/biology/p5-Bio-NEXUS/Makefile b/biology/p5-Bio-NEXUS/Makefile
new file mode 100644
index 000000000000..c76c1038d592
--- /dev/null
+++ b/biology/p5-Bio-NEXUS/Makefile
@@ -0,0 +1,38 @@
+# New ports collection makefile for:	Bio-NEXUS
+# Date created:				20 Sug, 2009
+# Whom:					Wen Heping <wenheping@gmail.com>
+#
+# $FreeBSD$
+#
+
+PORTNAME=	Bio-NEXUS
+PORTVERSION=	0.72
+CATEGORIES=	biology perl5
+MASTER_SITES=	CPAN
+PKGNAMEPREFIX=	p5-
+
+MAINTAINER=	wenheping@gmail.com
+COMMENT=	An object-oriented Perl API for the NEXUS file format
+
+BUILD_DEPENDS=	p5-Clone-PP>=1.02:${PORTSDIR}/devel/p5-Clone-PP \
+		p5-Test-Deep>=0.106:${PORTSDIR}/devel/p5-Test-Deep
+RUN_DEPENDS=	${BUILD_DEPENDS}
+
+PERL_CONFIGURE=	yes
+
+MAN1=		nextool.pl.1 nex2text_tree.pl.1 nexplot.pl.1
+MAN3=		Bio::NEXUS::DataBlock.3 Bio::NEXUS::CodonsBlock.3 \
+		Bio::NEXUS::NotesBlock.3 Bio::NEXUS::NHXCmd.3 \
+		Bio::NEXUS::HistoryBlock.3 Bio::NEXUS::TaxUnit.3 \
+		Bio::NEXUS::CharactersBlock.3 Bio::NEXUS::SpanBlock.3 \
+		Bio::NEXUS::UnalignedBlock.3 Bio::NEXUS::TaxUnitSet.3 \
+		Bio::NEXUS::DistancesBlock.3 Bio::NEXUS::UnknownBlock.3 \
+		Bio::NEXUS::Node.3 Bio::NEXUS::Matrix.3 \
+		Bio::NEXUS::Tree.3 Bio::NEXUS::WeightSet.3 \
+		Bio::NEXUS::TreesBlock.3 Bio::NEXUS::Util::Exceptions.3 \
+		Bio::NEXUS::SetsBlock.3 Bio::NEXUS::TaxaBlock.3 \
+		Bio::NEXUS::Util::Logger.3 Bio::NEXUS::AssumptionsBlock.3 \
+		Bio::NEXUS::Block.3 Bio::NEXUS::Functions.3 \
+		Bio::NEXUS.3
+
+.include <bsd.port.mk>
diff --git a/biology/p5-Bio-NEXUS/distinfo b/biology/p5-Bio-NEXUS/distinfo
new file mode 100644
index 000000000000..b84ab8be2d08
--- /dev/null
+++ b/biology/p5-Bio-NEXUS/distinfo
@@ -0,0 +1,3 @@
+MD5 (Bio-NEXUS-0.72.tar.gz) = 2dc7506f6d9fa9bea615f0855b8ff2dd
+SHA256 (Bio-NEXUS-0.72.tar.gz) = 645203f64b61df3d403108dd4b9057c492e67dfa46ecd1c280980b3e58a1fb40
+SIZE (Bio-NEXUS-0.72.tar.gz) = 946520
diff --git a/biology/p5-Bio-NEXUS/pkg-descr b/biology/p5-Bio-NEXUS/pkg-descr
new file mode 100644
index 000000000000..a267b121c6e8
--- /dev/null
+++ b/biology/p5-Bio-NEXUS/pkg-descr
@@ -0,0 +1,14 @@
+Bio::NEXUS package provides an object-oriented, Perl-based
+applications programming interface (API) to the NEXUS file
+format of Maddison, et al., 1997 (Syst. Biol. 46:590-621).
+NEXUS is a powerful and extensible format designed for use
+in evolutionary analysis, including the analysis of molecular
+sequence data as well as classical morphological and life-history
+data. NEXUS is the input or output format for software such as
+PAUP*, MacClade, Mesquite, SIMMAP, MrBayes, Nexplorer, and
+so on.  This package also contains the demonstration applications
+nexplot.pl (plot character data with a tree) and nextool.pl
+(allowing programmatic editing, e.g., selecting particular
+clades or subsets of data). 
+
+WWW: http://search.cpan.org/dist/Bio-NEXUS/
diff --git a/biology/p5-Bio-NEXUS/pkg-plist b/biology/p5-Bio-NEXUS/pkg-plist
new file mode 100644
index 000000000000..38c1170da430
--- /dev/null
+++ b/biology/p5-Bio-NEXUS/pkg-plist
@@ -0,0 +1,35 @@
+bin/nex2text_tree.pl
+bin/nexplot.pl
+bin/nextool.pl
+%%SITE_PERL%%/Bio/NEXUS.pm
+%%SITE_PERL%%/Bio/NEXUS/DataBlock.pm
+%%SITE_PERL%%/Bio/NEXUS/._Functions.pm
+%%SITE_PERL%%/Bio/NEXUS/CodonsBlock.pm
+%%SITE_PERL%%/Bio/NEXUS/NotesBlock.pm
+%%SITE_PERL%%/Bio/NEXUS/NHXCmd.pm
+%%SITE_PERL%%/Bio/NEXUS/HistoryBlock.pm
+%%SITE_PERL%%/Bio/NEXUS/TaxUnit.pm
+%%SITE_PERL%%/Bio/NEXUS/CharactersBlock.pm
+%%SITE_PERL%%/Bio/NEXUS/SpanBlock.pm
+%%SITE_PERL%%/Bio/NEXUS/UnalignedBlock.pm
+%%SITE_PERL%%/Bio/NEXUS/TaxUnitSet.pm
+%%SITE_PERL%%/Bio/NEXUS/DistancesBlock.pm
+%%SITE_PERL%%/Bio/NEXUS/UnknownBlock.pm
+%%SITE_PERL%%/Bio/NEXUS/Node.pm
+%%SITE_PERL%%/Bio/NEXUS/Matrix.pm
+%%SITE_PERL%%/Bio/NEXUS/Tree.pm
+%%SITE_PERL%%/Bio/NEXUS/WeightSet.pm
+%%SITE_PERL%%/Bio/NEXUS/SetsBlock.pm
+%%SITE_PERL%%/Bio/NEXUS/TaxaBlock.pm
+%%SITE_PERL%%/Bio/NEXUS/TreesBlock.pm
+%%SITE_PERL%%/Bio/NEXUS/AssumptionsBlock.pm
+%%SITE_PERL%%/Bio/NEXUS/Block.pm
+%%SITE_PERL%%/Bio/NEXUS/Functions.pm
+%%SITE_PERL%%/Bio/NEXUS/Util/Exceptions.pm
+%%SITE_PERL%%/Bio/NEXUS/Util/Logger.pm
+%%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio/NEXUS/.packlist
+@dirrmtry %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio/NEXUS
+@dirrmtry %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio
+@dirrmtry %%SITE_PERL%%/Bio/NEXUS/Util
+@dirrmtry %%SITE_PERL%%/Bio/NEXUS
+@dirrmtry %%SITE_PERL%%/Bio