Adding port biology/p5-Bio-Phylo, Phylogenetic analysis using perl.

Approved by:	tobez (implicit)

5 files changed, 110 insertions, 0 deletions

diff --git a/biology/Makefile b/biology/Makefile
index 4e3db30..dff99da 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -48,6 +48,7 @@
     SUBDIR += p5-AcePerl
     SUBDIR += p5-Bio-ASN1-EntrezGene
     SUBDIR += p5-Bio-Das
+    SUBDIR += p5-Bio-Phylo
     SUBDIR += p5-bioperl
     SUBDIR += p5-bioperl-devel
     SUBDIR += p5-bioperl-run
diff --git a/biology/p5-Bio-Phylo/Makefile b/biology/p5-Bio-Phylo/Makefile
new file mode 100644
index 0000000..edd4ea9
--- /dev/null
+++ b/biology/p5-Bio-Phylo/Makefile
@@ -0,0 +1,58 @@
+# New ports collection makefile for:	Bio-Phylo
+# Date created:				12 Mar 2006
+# Whom:					Aaron Dalton <aaron@FreeBSD.org>
+#
+# $FreeBSD$
+#
+
+PORTNAME=	Bio-Phylo
+PORTVERSION=	0.07
+CATEGORIES=	biology perl5
+MASTER_SITES=	${MASTER_SITE_PERL_CPAN}
+MASTER_SITE_SUBDIR=	Bio
+PKGNAMEPREFIX=	p5-
+
+MAINTAINER=	aaron@FreeBSD.org
+COMMENT=	Phylogenetic analysis using perl
+
+BUILD_DEPENDS=	${SITE_PERL}/${PERL_ARCH}/Math/Random.pm:${PORTSDIR}/math/p5-Math-Random \
+		${SITE_PERL}/SVG.pm:${PORTSDIR}/textproc/p5-SVG \
+		${SITE_PERL}/Exception/Class.pm:${PORTSDIR}/devel/p5-Exception-Class \
+		${SITE_PERL}/${PERL_ARCH}/Scalar/Util.pm:${PORTSDIR}/lang/p5-Scalar-List-Utils
+RUN_DEPENDS=	${BUILD_DEPENDS}
+
+MAN3=	Bio::Phylo.3 \
+	Bio::Phylo::CONSTANT.3 \
+	Bio::Phylo::Exceptions.3 \
+	Bio::Phylo::Forest.3 \
+	Bio::Phylo::Forest::Node.3 \
+	Bio::Phylo::Forest::Tree.3 \
+	Bio::Phylo::Generator.3 \
+	Bio::Phylo::IO.3 \
+	Bio::Phylo::Listable.3 \
+	Bio::Phylo::Manual.3 \
+	Bio::Phylo::Matrices.3 \
+	Bio::Phylo::Matrices::Alignment.3 \
+	Bio::Phylo::Matrices::Datum.3 \
+	Bio::Phylo::Matrices::Matrix.3 \
+	Bio::Phylo::Matrices::Sequence.3 \
+	Bio::Phylo::Parsers::Newick.3 \
+	Bio::Phylo::Parsers::Nexus.3 \
+	Bio::Phylo::Parsers::Table.3 \
+	Bio::Phylo::Parsers::Taxlist.3 \
+	Bio::Phylo::Taxa.3 \
+	Bio::Phylo::Taxa::Taxon.3 \
+	Bio::Phylo::Treedrawer.3 \
+	Bio::Phylo::Treedrawer::SVG.3 \
+	Bio::Phylo::Unparsers::Newick.3 \
+	Bio::Phylo::Unparsers::Pagel.3
+
+PERL_CONFIGURE=	yes
+
+.include <bsd.port.pre.mk>
+
+.if ${PERL_LEVEL} < 500800
+IGNORE=	requires at least Perl 5.8 due to dependencies.  Please install lang/perl5.8 and try again
+.endif
+
+.include <bsd.port.post.mk>
diff --git a/biology/p5-Bio-Phylo/distinfo b/biology/p5-Bio-Phylo/distinfo
new file mode 100644
index 0000000..3c4ba97
--- /dev/null
+++ b/biology/p5-Bio-Phylo/distinfo
@@ -0,0 +1,3 @@
+MD5 (Bio-Phylo-0.07.tar.gz) = 12b6ca632bc25e5c3fd647990cb5c959
+SHA256 (Bio-Phylo-0.07.tar.gz) = c98ab09053b9b0e9b30c72f7b09448e908ddde71c5db2489b6924c710f654923
+SIZE (Bio-Phylo-0.07.tar.gz) = 69580
diff --git a/biology/p5-Bio-Phylo/pkg-descr b/biology/p5-Bio-Phylo/pkg-descr
new file mode 100644
index 0000000..dd1319b
--- /dev/null
+++ b/biology/p5-Bio-Phylo/pkg-descr
@@ -0,0 +1,6 @@
+This is the base class for the Bio::Phylo package. All other modules 
+inherit from it, the methods defined here are applicable to all. Consult 
+the manual for usage examples: Bio::Phylo::Manual.
+
+WWW: http://search.cpan.org/dist/Bio-Phylo
+Author: Rutger Vos <rvosa@sfu.ca>
diff --git a/biology/p5-Bio-Phylo/pkg-plist b/biology/p5-Bio-Phylo/pkg-plist
new file mode 100644
index 0000000..19f9db9
--- /dev/null
+++ b/biology/p5-Bio-Phylo/pkg-plist
@@ -0,0 +1,42 @@
+bin/LRmb.pl
+bin/age2bl.pl
+bin/bremer.pl
+bin/dnd2svg.pl
+bin/droptip.pl
+bin/postmb.pl
+%%SITE_PERL%%/Bio/Phylo.pm
+%%SITE_PERL%%/Bio/Phylo/CONSTANT.pm
+%%SITE_PERL%%/Bio/Phylo/Exceptions.pm
+%%SITE_PERL%%/Bio/Phylo/Forest.pm
+%%SITE_PERL%%/Bio/Phylo/Forest/Node.pm
+%%SITE_PERL%%/Bio/Phylo/Forest/Tree.pm
+%%SITE_PERL%%/Bio/Phylo/Generator.pm
+%%SITE_PERL%%/Bio/Phylo/IO.pm
+%%SITE_PERL%%/Bio/Phylo/Listable.pm
+%%SITE_PERL%%/Bio/Phylo/Manual.pod
+%%SITE_PERL%%/Bio/Phylo/Matrices.pm
+%%SITE_PERL%%/Bio/Phylo/Matrices/Alignment.pm
+%%SITE_PERL%%/Bio/Phylo/Matrices/Datum.pm
+%%SITE_PERL%%/Bio/Phylo/Matrices/Matrix.pm
+%%SITE_PERL%%/Bio/Phylo/Matrices/Sequence.pm
+%%SITE_PERL%%/Bio/Phylo/Parsers/Newick.pm
+%%SITE_PERL%%/Bio/Phylo/Parsers/Nexus.pm
+%%SITE_PERL%%/Bio/Phylo/Parsers/Table.pm
+%%SITE_PERL%%/Bio/Phylo/Parsers/Taxlist.pm
+%%SITE_PERL%%/Bio/Phylo/Taxa.pm
+%%SITE_PERL%%/Bio/Phylo/Taxa/Taxon.pm
+%%SITE_PERL%%/Bio/Phylo/Treedrawer.pm
+%%SITE_PERL%%/Bio/Phylo/Treedrawer/SVG.pm
+%%SITE_PERL%%/Bio/Phylo/Unparsers/Newick.pm
+%%SITE_PERL%%/Bio/Phylo/Unparsers/Pagel.pm
+%%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio/Phylo/.packlist
+@dirrm %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio/Phylo
+@dirrmtry %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio
+@dirrm %%SITE_PERL%%/Bio/Phylo/Unparsers
+@dirrm %%SITE_PERL%%/Bio/Phylo/Treedrawer
+@dirrm %%SITE_PERL%%/Bio/Phylo/Taxa
+@dirrm %%SITE_PERL%%/Bio/Phylo/Parsers
+@dirrm %%SITE_PERL%%/Bio/Phylo/Matrices
+@dirrm %%SITE_PERL%%/Bio/Phylo/Forest
+@dirrm %%SITE_PERL%%/Bio/Phylo
+@dirrmtry %%SITE_PERL%%/Bio