svn commit: r449922 - in head/biology: . p5-Bio-FeatureIO

Fri Sep 15 19:17:19 UTC 2017

Author: sunpoet
Date: Fri Sep 15 19:17:17 2017
New Revision: 449922
URL: https://svnweb.freebsd.org/changeset/ports/449922

Log:
  Add p5-Bio-FeatureIO 1.6.905
  
  Bio::FeatureIO is an iterator subsystem for genomic sequence features.
  
  Bio::FeatureIO is a handler module for the formats in the FeatureIO set (eg,
  Bio::FeatureIO::GFF). It is the officially sanctioned way of getting at the
  format objects, which most people should use.
  
  The Bio::FeatureIO system can be thought of like biological file handles. They
  are attached to filehandles with smart formatting rules (eg, GFF format, or BED
  format) and can either read or write feature objects (Bio::SeqFeature objects,
  or more correctly, Bio::FeatureHolderI implementing objects, of which
  Bio::SeqFeature is one such object). If you want to know what to do with a
  Bio::SeqFeatureI object, read Bio::SeqFeatureI.
  
  The idea is that you request a stream object for a particular format. All the
  stream objects have a notion of an internal file that is read from or written
  to. A particular FeatureIO object instance is configured for either input or
  output. A specific example of a stream object is the Bio::FeatureIO::gff object.
  
  WWW: http://search.cpan.org/dist/Bio-FeatureIO/

Added:
  head/biology/p5-Bio-FeatureIO/
  head/biology/p5-Bio-FeatureIO/Makefile   (contents, props changed)
  head/biology/p5-Bio-FeatureIO/distinfo   (contents, props changed)
  head/biology/p5-Bio-FeatureIO/pkg-descr   (contents, props changed)
  head/biology/p5-Bio-FeatureIO/pkg-plist   (contents, props changed)
Modified:
  head/biology/Makefile

Modified: head/biology/Makefile
==============================================================================

--- head/biology/Makefile	Fri Sep 15 18:48:38 2017	(r449921)
+++ head/biology/Makefile	Fri Sep 15 19:17:17 2017	(r449922)
@@ -60,6 +60,7 @@
     SUBDIR += p5-Bio-Coordinate
     SUBDIR += p5-Bio-Das
     SUBDIR += p5-Bio-Das-Lite
+    SUBDIR += p5-Bio-FeatureIO
     SUBDIR += p5-Bio-GFF3
     SUBDIR += p5-Bio-Glite
     SUBDIR += p5-Bio-Graphics

Added: head/biology/p5-Bio-FeatureIO/Makefile
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/p5-Bio-FeatureIO/Makefile	Fri Sep 15 19:17:17 2017	(r449922)
@@ -0,0 +1,28 @@
+# Created by: Po-Chuan Hsieh <sunpoet at FreeBSD.org>
+# $FreeBSD$
+
+PORTNAME=	Bio-FeatureIO
+PORTVERSION=	1.6.905
+CATEGORIES=	biology perl5
+MASTER_SITES=	CPAN
+PKGNAMEPREFIX=	p5-
+
+MAINTAINER=	sunpoet at FreeBSD.org
+COMMENT=	Handler for FeatureIO
+
+LICENSE=	ART10 GPLv1+
+LICENSE_COMB=	dual
+LICENSE_FILE=	${WRKSRC}/LICENSE
+
+BUILD_DEPENDS=	p5-BioPerl>=0:biology/p5-BioPerl \
+		p5-Tree-DAG_Node>=0:devel/p5-Tree-DAG_Node \
+		p5-URI>=0:net/p5-URI \
+		p5-XML-DOM>=0:textproc/p5-XML-DOM \
+		p5-XML-DOM-XPath>=0:textproc/p5-XML-DOM-XPath
+RUN_DEPENDS:=	${BUILD_DEPENDS}
+
+NO_ARCH=	yes
+USE_PERL5=	configure
+USES=		perl5
+
+.include <bsd.port.mk>

Added: head/biology/p5-Bio-FeatureIO/distinfo
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/p5-Bio-FeatureIO/distinfo	Fri Sep 15 19:17:17 2017	(r449922)
@@ -0,0 +1,3 @@
+TIMESTAMP = 1505488503
+SHA256 (Bio-FeatureIO-1.6.905.tar.gz) = 322e5757b374f2fb90b8f20bdbdc75631f5cb4d122f81a4d35c3a177cf950c7a
+SIZE (Bio-FeatureIO-1.6.905.tar.gz) = 54906

Added: head/biology/p5-Bio-FeatureIO/pkg-descr
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/p5-Bio-FeatureIO/pkg-descr	Fri Sep 15 19:17:17 2017	(r449922)
@@ -0,0 +1,19 @@
+Bio::FeatureIO is an iterator subsystem for genomic sequence features.
+
+Bio::FeatureIO is a handler module for the formats in the FeatureIO set (eg,
+Bio::FeatureIO::GFF). It is the officially sanctioned way of getting at the
+format objects, which most people should use.
+
+The Bio::FeatureIO system can be thought of like biological file handles. They
+are attached to filehandles with smart formatting rules (eg, GFF format, or BED
+format) and can either read or write feature objects (Bio::SeqFeature objects,
+or more correctly, Bio::FeatureHolderI implementing objects, of which
+Bio::SeqFeature is one such object). If you want to know what to do with a
+Bio::SeqFeatureI object, read Bio::SeqFeatureI.
+
+The idea is that you request a stream object for a particular format. All the
+stream objects have a notion of an internal file that is read from or written
+to. A particular FeatureIO object instance is configured for either input or
+output. A specific example of a stream object is the Bio::FeatureIO::gff object.
+
+WWW: http://search.cpan.org/dist/Bio-FeatureIO/

Added: head/biology/p5-Bio-FeatureIO/pkg-plist
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/p5-Bio-FeatureIO/pkg-plist	Fri Sep 15 19:17:17 2017	(r449922)
@@ -0,0 +1,16 @@
+%%SITE_PERL%%/Bio/FeatureIO.pm
+%%SITE_PERL%%/Bio/FeatureIO/bed.pm
+%%SITE_PERL%%/Bio/FeatureIO/gff.pm
+%%SITE_PERL%%/Bio/FeatureIO/gtf.pm
+%%SITE_PERL%%/Bio/FeatureIO/interpro.pm
+%%SITE_PERL%%/Bio/FeatureIO/ptt.pm
+%%SITE_PERL%%/Bio/FeatureIO/vecscreen_simple.pm
+%%SITE_PERL%%/Bio/SeqFeature/Annotated.pm
+%%PERL5_MAN3%%/Bio::FeatureIO.3.gz
+%%PERL5_MAN3%%/Bio::FeatureIO::bed.3.gz
+%%PERL5_MAN3%%/Bio::FeatureIO::gff.3.gz
+%%PERL5_MAN3%%/Bio::FeatureIO::gtf.3.gz
+%%PERL5_MAN3%%/Bio::FeatureIO::interpro.3.gz
+%%PERL5_MAN3%%/Bio::FeatureIO::ptt.3.gz
+%%PERL5_MAN3%%/Bio::FeatureIO::vecscreen_simple.3.gz
+%%PERL5_MAN3%%/Bio::SeqFeature::Annotated.3.gz
