[med-svn] r4935 - in trunk/packages: . python-nast python-nast/trunk python-nast/trunk/debian
Steffen Möller
moeller at alioth.debian.org
Fri Jun 25 23:01:38 UTC 2010
Author: moeller
Date: 2010-06-25 23:01:25 +0000 (Fri, 25 Jun 2010)
New Revision: 4935
Added:
trunk/packages/python-nast/
trunk/packages/python-nast/trunk/
trunk/packages/python-nast/trunk/debian/
trunk/packages/python-nast/trunk/debian/source/
trunk/packages/python-nast/trunk/debian/watch
Removed:
trunk/packages/python-nast/trunk/debian/compat
trunk/packages/python-nast/trunk/debian/patches/
trunk/packages/python-nast/trunk/debian/python-cogent.doc-base.EX
trunk/packages/python-nast/trunk/debian/python-cogent.prerm.debhelper
trunk/packages/python-nast/trunk/debian/python-cogent.substvars
trunk/packages/python-nast/trunk/debian/watch
Modified:
trunk/packages/python-nast/trunk/debian/README.source
trunk/packages/python-nast/trunk/debian/changelog
trunk/packages/python-nast/trunk/debian/control
trunk/packages/python-nast/trunk/debian/copyright
trunk/packages/python-nast/trunk/debian/docs
trunk/packages/python-nast/trunk/debian/pyversions
Log:
Iinital attempt to package python-nast
Modified: trunk/packages/python-nast/trunk/debian/README.source
===================================================================
--- trunk/packages/python-cogent/trunk/debian/README.source 2010-06-25 16:33:10 UTC (rev 4931)
+++ trunk/packages/python-nast/trunk/debian/README.source 2010-06-25 23:01:25 UTC (rev 4935)
@@ -1,8 +1,2 @@
-python-cogent for Debian
---------------------------
-
-All source is left intact, except for obvious adjustments to the shebang
-line to have it point to /usr/bin/python.
-
-
-
+python-nast for Debian
+----------------------
Modified: trunk/packages/python-nast/trunk/debian/changelog
===================================================================
--- trunk/packages/python-cogent/trunk/debian/changelog 2010-06-25 16:33:10 UTC (rev 4931)
+++ trunk/packages/python-nast/trunk/debian/changelog 2010-06-25 23:01:25 UTC (rev 4935)
@@ -1,6 +1,6 @@
-python-cogent (1.4.1-1) unstable; urgency=low
+python-nast (1.1-1) unstable; urgency=low
- * Initial release (Closes: #587161)
+ * Initial release (Closes: #587189)
-- Sri Girish Srinivasa Murthy <srigirish at evolbio.mpg.de> Fri, 25 Jun 2010 17:23:58 +0200
Deleted: trunk/packages/python-nast/trunk/debian/compat
===================================================================
--- trunk/packages/python-cogent/trunk/debian/compat 2010-06-25 16:33:10 UTC (rev 4931)
+++ trunk/packages/python-nast/trunk/debian/compat 2010-06-25 23:01:25 UTC (rev 4935)
@@ -1 +0,0 @@
-7
Modified: trunk/packages/python-nast/trunk/debian/control
===================================================================
--- trunk/packages/python-cogent/trunk/debian/control 2010-06-25 16:33:10 UTC (rev 4931)
+++ trunk/packages/python-nast/trunk/debian/control 2010-06-25 23:01:25 UTC (rev 4935)
@@ -1,19 +1,38 @@
-Source: python-cogent
+Source: python-nast
Section: python
Priority: extra
Maintainer: Sri Girish Srinivasa Murthy <srigirish at evolbio.mpg.de>
-Build-Depends: debhelper (>= 7), cdbs, python, python-central, python-numpy (>= 1.3.0)
+Uploaders: Steffen Moeller <moeller at debian.org>
+Build-Depends: debhelper (>= 7), cdbs, python, python-central, python-cogent
Standards-Version: 3.8.4
-Homepage: http://pycogent.sourceforge.net/
+Homepage: http://pynast.sourceforge.net/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/python-nast/trunk/?rev=0&sc=0
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/python-nast/trunk/
-Package: python-cogent
+Package: python-nast
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends}, ${misc:Depends}, ${python:Depends}
-Description: framework for genomic biology
- PyCogent is a software library for genomic biology. It is a fully
- integrated and thoroughly tested framework for: controlling third-party
- applications; devising workflows; querying databases; conducting novel
- probabilistic analyses of biological sequence evolution; and generating
- publication quality graphics. It is distinguished by many unique built-in
- capabilities (such as true codon alignment) and the frequent addition
- of entirely new methods for the analysis of genomic data.
+Description: alignment of short DNA sequences
+ The package provices a reimplementation of the Nearest Alignment
+ Space Termination tool in python. It was prepared for next generation
+ sequencers.
+ .
+ Given a set of sequences and a template alignment, PyNAST will align the
+ input sequences against the template alignment, and return a multiple
+ sequence alignment which contains the same number of positions (or
+ columns) as the template alignment. This facilitates the analysis of new
+ sequences in the context of existing alignments, and additional data
+ derived from existing alignments such as phylogenetic trees. Because
+ any protein or nucleic acid sequences and template alignments can be
+ provided, PyNAST is not limited to the analysis of 16s rDNA sequences.
+ .
+ Since version 1.1, PyNAST no longer exactly matches the output
+ of the origianl NAST program. Instead it focuses on getting better
+ alignments. Users who wish to exactly match the results of NAST should
+ download PyNAST 1.0.
+ .
+ PyNAST: a flexible tool for aligning sequences to a template
+ alignment. J. Gregory Caporaso, Kyle Bittinger, Frederic D. Bushman,
+ Todd Z. DeSantis, Gary L. Andersen, and Rob Knight. January 15, 2010,
+ DOI 10.1093/bioinformatics/btp636. Bioinformatics 26: 266-267.
+
Modified: trunk/packages/python-nast/trunk/debian/copyright
===================================================================
--- trunk/packages/python-cogent/trunk/debian/copyright 2010-06-25 16:33:10 UTC (rev 4931)
+++ trunk/packages/python-nast/trunk/debian/copyright 2010-06-25 23:01:25 UTC (rev 4935)
@@ -1,27 +1,27 @@
This work was packaged for Debian by:
- root <root at unknown> on Fri, 25 Jun 2010 17:23:58 +0200
+ Sri Girish Srinivasa Murthy <srigirish at evolbio.mpg.de>
+ and Steffen Moeller <moeller at debian.org>
+ on Fri, 25 Jun 2010 17:23:58 +0200
-It was downloaded from <http://pycogent.sorceforge.net>
+It was downloaded from <http://pynast.sorceforge.net>
-Upstream Authors:
+Upstream Author:
- Gavin Huttley <gavin.huttley at anu.edu.au>
- Andrew Butterfield
- Peter Maxwell
- Rob Knight
+ Greg Caporaso
Copyright:
- Copyright 2007-2009, The Cogent Project"
+ Copyright 2010, The PyNAST Project
License:
- GPL-2+
+ GPL-2
The Debian packaging is:
- Copyright (C) 2010 root <root at unknown>
+ Copyright (C) 2010 Sri Girish Srinivasa Murthy <srigirish at evolbio.mpg.de>
+ and Steffen Moeller <moeller at debian.org>
and is licensed under the same copyright,
see `/usr/share/common-licenses/GPL-2'.
Modified: trunk/packages/python-nast/trunk/debian/docs
===================================================================
--- trunk/packages/python-cogent/trunk/debian/docs 2010-06-25 16:33:10 UTC (rev 4931)
+++ trunk/packages/python-nast/trunk/debian/docs 2010-06-25 23:01:25 UTC (rev 4935)
@@ -1,3 +1,2 @@
-cogent-requirements.txt
-NumpyPortingNotes.txt
README
+doc/*
Deleted: trunk/packages/python-nast/trunk/debian/python-cogent.doc-base.EX
===================================================================
--- trunk/packages/python-cogent/trunk/debian/python-cogent.doc-base.EX 2010-06-25 16:33:10 UTC (rev 4931)
+++ trunk/packages/python-nast/trunk/debian/python-cogent.doc-base.EX 2010-06-25 23:01:25 UTC (rev 4935)
@@ -1,20 +0,0 @@
-Document: python-pycogent
-Title: Debian python-pycogent Manual
-Author: <insert document author here>
-Abstract: This manual describes what python-pycogent is
- and how it can be used to
- manage online manuals on Debian systems.
-Section: unknown
-
-Format: debiandoc-sgml
-Files: /usr/share/doc/python-pycogent/python-pycogent.sgml.gz
-
-Format: postscript
-Files: /usr/share/doc/python-pycogent/python-pycogent.ps.gz
-
-Format: text
-Files: /usr/share/doc/python-pycogent/python-pycogent.text.gz
-
-Format: HTML
-Index: /usr/share/doc/python-pycogent/html/index.html
-Files: /usr/share/doc/python-pycogent/html/*.html
Deleted: trunk/packages/python-nast/trunk/debian/python-cogent.prerm.debhelper
===================================================================
--- trunk/packages/python-cogent/trunk/debian/python-cogent.prerm.debhelper 2010-06-25 16:33:10 UTC (rev 4931)
+++ trunk/packages/python-nast/trunk/debian/python-cogent.prerm.debhelper 2010-06-25 23:01:25 UTC (rev 4935)
@@ -1,45 +0,0 @@
-# Automatically added by dh_pycentral
-case "$1" in remove|upgrade)
- pkgremove=y
-esac
-if [ -f /var/lib/pycentral/python-cogent.pkgremove ] || [ -f /var/lib/pycentral/pkgremove ]; then
- pkgremove=y
-fi
-if [ "$pkgremove" = y ]; then
-if which python >/dev/null 2>&1 && which pycentral >/dev/null 2>&1; then
- pycentral pkgremove python-cogent
-else
- flist=$(tempfile)
- slist=$(tempfile)
- dpkg -L python-cogent | tee $flist | \
- while read n; do
- case "$n" in
- /usr/share/pyshared/*)
- n2=${n#/usr/share/pyshared/*}
- case "$n" in
- *.py) echo "p $n";;
- *) [ -d "$n" ] && echo "d $n2" || echo "f $n2"
- esac
- ;;
- *) continue
- esac
- done > $slist
- if [ -s $slist ]; then
- for d in /usr/lib/python[0-9].[0-9]/????-packages; do
- case "$d" in */python2.1/*|*/python2.2/*) continue; esac
- while read t n; do
- case "$t" in
- p) rm -f $d/$n $d/${n}[co];;
- d) rmdir $d/$n 2>/dev/null || true;;
- *) rm -f $d/$n
- esac
- done < $slist
- done
- fi
- awk '/\/usr\/share\/pyshared/ {next} /\.py$/ {print $0"c\n" $0"o"}' $flist \
- | xargs -r rm -f >&2
- rm -f $flist $slist
-fi
-rm -f /var/lib/pycentral/python-cogent.pkgremove
-fi
-# End automatically added section
Deleted: trunk/packages/python-nast/trunk/debian/python-cogent.substvars
===================================================================
--- trunk/packages/python-cogent/trunk/debian/python-cogent.substvars 2010-06-25 16:33:10 UTC (rev 4931)
+++ trunk/packages/python-nast/trunk/debian/python-cogent.substvars 2010-06-25 23:01:25 UTC (rev 4935)
@@ -1,5 +0,0 @@
-python:Versions=2.6
-python:Provides=python2.6-cogent
-python:Depends=python (<< 2.7), python (>= 2.6), python-central (>= 0.6.11)
-shlibs:Depends=libc6 (>= 2.3.4)
-misc:Depends=
Modified: trunk/packages/python-nast/trunk/debian/pyversions
===================================================================
--- trunk/packages/python-cogent/trunk/debian/pyversions 2010-06-25 16:33:10 UTC (rev 4931)
+++ trunk/packages/python-nast/trunk/debian/pyversions 2010-06-25 23:01:25 UTC (rev 4935)
@@ -1 +1 @@
-2.6
+all
Deleted: trunk/packages/python-nast/trunk/debian/watch
===================================================================
--- trunk/packages/python-cogent/trunk/debian/watch 2010-06-25 16:33:10 UTC (rev 4931)
+++ trunk/packages/python-nast/trunk/debian/watch 2010-06-25 23:01:25 UTC (rev 4935)
@@ -1,2 +0,0 @@
-version=3
-http://sf.net/pycogent/PyCogent-(.*)\.tar\.gz
Copied: trunk/packages/python-nast/trunk/debian/watch (from rev 4932, trunk/packages/python-cogent/trunk/debian/watch)
===================================================================
--- trunk/packages/python-nast/trunk/debian/watch (rev 0)
+++ trunk/packages/python-nast/trunk/debian/watch 2010-06-25 23:01:25 UTC (rev 4935)
@@ -0,0 +1,2 @@
+version=3
+http://sf.net/pynast/PyNAST-([.0-9]+)\.tgz
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