- Update to 1.5.3

- Trim Makefile headers

3 files changed, 37 insertions, 11 deletions

diff --git a/biology/pycogent/Makefile b/biology/pycogent/Makefile
index 91e85b355e42..0f620c546a9b 100644
--- a/biology/pycogent/Makefile
+++ b/biology/pycogent/Makefile
@@ -1,12 +1,8 @@
-# New ports collection makefile for:	pycogent
-# Date created:		20 June, 2009
-# Whom:			Wen Heping <wenheping@gmail.com>
-#
+# Created by: Wen Heping <wenheping@gmail.com>
 # $FreeBSD$
-#
 
 PORTNAME=	pycogent
-PORTVERSION=	1.5.1
+PORTVERSION=	1.5.3
 CATEGORIES=	biology python
 MASTER_SITES=	SF/${PORTNAME}/PyCogent/${PORTVERSION}
 DISTNAME=	PyCogent-${PORTVERSION}
diff --git a/biology/pycogent/distinfo b/biology/pycogent/distinfo
index ba89cd329511..a8fa5014327f 100644
--- a/biology/pycogent/distinfo
+++ b/biology/pycogent/distinfo
@@ -1,2 +1,2 @@
-SHA256 (PyCogent-1.5.1.tgz) = 572345eb5f9ef0c4c5307145d27c2c69277dc7dffdbb772219532dce749513d7
-SIZE (PyCogent-1.5.1.tgz) = 3057837
+SHA256 (PyCogent-1.5.3.tgz) = ad883cf4f8bbedd797b934a6ba75a20df2313736e84bff3d5a0e54ac41ea425c
+SIZE (PyCogent-1.5.3.tgz) = 3360039
diff --git a/biology/pycogent/pkg-plist b/biology/pycogent/pkg-plist
index addc2b2622df..085ee15f5ef0 100644
--- a/biology/pycogent/pkg-plist
+++ b/biology/pycogent/pkg-plist
@@ -25,9 +25,6 @@
 %%PYTHON_SITELIBDIR%%/cogent/align/pairwise.py
 %%PYTHON_SITELIBDIR%%/cogent/align/pairwise.pyc
 %%PYTHON_SITELIBDIR%%/cogent/align/pairwise.pyo
-%%PYTHON_SITELIBDIR%%/cogent/align/partial_order_graph.py
-%%PYTHON_SITELIBDIR%%/cogent/align/partial_order_graph.pyc
-%%PYTHON_SITELIBDIR%%/cogent/align/partial_order_graph.pyo
 %%PYTHON_SITELIBDIR%%/cogent/align/progressive.py
 %%PYTHON_SITELIBDIR%%/cogent/align/progressive.pyc
 %%PYTHON_SITELIBDIR%%/cogent/align/progressive.pyo
@@ -52,6 +49,12 @@
 %%PYTHON_SITELIBDIR%%/cogent/app/blast.py
 %%PYTHON_SITELIBDIR%%/cogent/app/blast.pyc
 %%PYTHON_SITELIBDIR%%/cogent/app/blast.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/blat.py
+%%PYTHON_SITELIBDIR%%/cogent/app/blat.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/blat.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/bwa.py
+%%PYTHON_SITELIBDIR%%/cogent/app/bwa.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/bwa.pyo
 %%PYTHON_SITELIBDIR%%/cogent/app/carnac.py
 %%PYTHON_SITELIBDIR%%/cogent/app/carnac.pyc
 %%PYTHON_SITELIBDIR%%/cogent/app/carnac.pyo
@@ -103,6 +106,9 @@
 %%PYTHON_SITELIBDIR%%/cogent/app/gctmpca.py
 %%PYTHON_SITELIBDIR%%/cogent/app/gctmpca.pyc
 %%PYTHON_SITELIBDIR%%/cogent/app/gctmpca.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/guppy.py
+%%PYTHON_SITELIBDIR%%/cogent/app/guppy.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/guppy.pyo
 %%PYTHON_SITELIBDIR%%/cogent/app/ilm.py
 %%PYTHON_SITELIBDIR%%/cogent/app/ilm.pyc
 %%PYTHON_SITELIBDIR%%/cogent/app/ilm.pyo
@@ -127,21 +133,33 @@
 %%PYTHON_SITELIBDIR%%/cogent/app/muscle.py
 %%PYTHON_SITELIBDIR%%/cogent/app/muscle.pyc
 %%PYTHON_SITELIBDIR%%/cogent/app/muscle.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/muscle_v38.py
+%%PYTHON_SITELIBDIR%%/cogent/app/muscle_v38.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/muscle_v38.pyo
 %%PYTHON_SITELIBDIR%%/cogent/app/nupack.py
 %%PYTHON_SITELIBDIR%%/cogent/app/nupack.pyc
 %%PYTHON_SITELIBDIR%%/cogent/app/nupack.pyo
 %%PYTHON_SITELIBDIR%%/cogent/app/parameters.py
 %%PYTHON_SITELIBDIR%%/cogent/app/parameters.pyc
 %%PYTHON_SITELIBDIR%%/cogent/app/parameters.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/parsinsert.py
+%%PYTHON_SITELIBDIR%%/cogent/app/parsinsert.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/parsinsert.pyo
 %%PYTHON_SITELIBDIR%%/cogent/app/pfold.py
 %%PYTHON_SITELIBDIR%%/cogent/app/pfold.pyc
 %%PYTHON_SITELIBDIR%%/cogent/app/pfold.pyo
 %%PYTHON_SITELIBDIR%%/cogent/app/pknotsrg.py
 %%PYTHON_SITELIBDIR%%/cogent/app/pknotsrg.pyc
 %%PYTHON_SITELIBDIR%%/cogent/app/pknotsrg.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/pplacer.py
+%%PYTHON_SITELIBDIR%%/cogent/app/pplacer.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/pplacer.pyo
 %%PYTHON_SITELIBDIR%%/cogent/app/raxml.py
 %%PYTHON_SITELIBDIR%%/cogent/app/raxml.pyc
 %%PYTHON_SITELIBDIR%%/cogent/app/raxml.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/raxml_v730.py
+%%PYTHON_SITELIBDIR%%/cogent/app/raxml_v730.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/raxml_v730.pyo
 %%PYTHON_SITELIBDIR%%/cogent/app/rdp_classifier.py
 %%PYTHON_SITELIBDIR%%/cogent/app/rdp_classifier.pyc
 %%PYTHON_SITELIBDIR%%/cogent/app/rdp_classifier.pyo
@@ -160,6 +178,9 @@
 %%PYTHON_SITELIBDIR%%/cogent/app/rnaview.py
 %%PYTHON_SITELIBDIR%%/cogent/app/rnaview.pyc
 %%PYTHON_SITELIBDIR%%/cogent/app/rnaview.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/rtax.py
+%%PYTHON_SITELIBDIR%%/cogent/app/rtax.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/rtax.pyo
 %%PYTHON_SITELIBDIR%%/cogent/app/sfffile.py
 %%PYTHON_SITELIBDIR%%/cogent/app/sfffile.pyc
 %%PYTHON_SITELIBDIR%%/cogent/app/sfffile.pyo
@@ -178,6 +199,9 @@
 %%PYTHON_SITELIBDIR%%/cogent/app/unafold.py
 %%PYTHON_SITELIBDIR%%/cogent/app/unafold.pyc
 %%PYTHON_SITELIBDIR%%/cogent/app/unafold.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/usearch.py
+%%PYTHON_SITELIBDIR%%/cogent/app/usearch.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/usearch.pyo
 %%PYTHON_SITELIBDIR%%/cogent/app/util.py
 %%PYTHON_SITELIBDIR%%/cogent/app/util.pyc
 %%PYTHON_SITELIBDIR%%/cogent/app/util.pyo
@@ -337,6 +361,9 @@
 %%PYTHON_SITELIBDIR%%/cogent/draw/dinuc.py
 %%PYTHON_SITELIBDIR%%/cogent/draw/dinuc.pyc
 %%PYTHON_SITELIBDIR%%/cogent/draw/dinuc.pyo
+%%PYTHON_SITELIBDIR%%/cogent/draw/distribution_plots.py
+%%PYTHON_SITELIBDIR%%/cogent/draw/distribution_plots.pyc
+%%PYTHON_SITELIBDIR%%/cogent/draw/distribution_plots.pyo
 %%PYTHON_SITELIBDIR%%/cogent/draw/dotplot.py
 %%PYTHON_SITELIBDIR%%/cogent/draw/dotplot.pyc
 %%PYTHON_SITELIBDIR%%/cogent/draw/dotplot.pyo
@@ -418,6 +445,9 @@
 %%PYTHON_SITELIBDIR%%/cogent/format/alignment.py
 %%PYTHON_SITELIBDIR%%/cogent/format/alignment.pyc
 %%PYTHON_SITELIBDIR%%/cogent/format/alignment.pyo
+%%PYTHON_SITELIBDIR%%/cogent/format/bedgraph.py
+%%PYTHON_SITELIBDIR%%/cogent/format/bedgraph.pyc
+%%PYTHON_SITELIBDIR%%/cogent/format/bedgraph.pyo
 %%PYTHON_SITELIBDIR%%/cogent/format/clustal.py
 %%PYTHON_SITELIBDIR%%/cogent/format/clustal.pyc
 %%PYTHON_SITELIBDIR%%/cogent/format/clustal.pyo