[med-svn] r4949 - in trunk/packages: . qiime qiime/trunk qiime/trunk/debian qiime/trunk/debian/source

Sat Jun 26 23:29:28 UTC 2010

Author: moeller
Date: 2010-06-26 23:29:28 +0000 (Sat, 26 Jun 2010)
New Revision: 4949

Added:
   trunk/packages/qiime/
   trunk/packages/qiime/trunk/
   trunk/packages/qiime/trunk/debian/
   trunk/packages/qiime/trunk/debian/README.Debian
   trunk/packages/qiime/trunk/debian/changelog
   trunk/packages/qiime/trunk/debian/control
   trunk/packages/qiime/trunk/debian/copyright
   trunk/packages/qiime/trunk/debian/docs
   trunk/packages/qiime/trunk/debian/pyversions
   trunk/packages/qiime/trunk/debian/rules
   trunk/packages/qiime/trunk/debian/source/
   trunk/packages/qiime/trunk/debian/source/format
   trunk/packages/qiime/trunk/debian/watch
Log:
Rudimentary packaging attempt



Property changes on: trunk/packages/qiime/trunk/debian
___________________________________________________________________
Added: mergeWithUpstream
   + 1

Added: trunk/packages/qiime/trunk/debian/README.Debian
===================================================================

--- trunk/packages/qiime/trunk/debian/README.Debian	                        (rev 0)
+++ trunk/packages/qiime/trunk/debian/README.Debian	2010-06-26 23:29:28 UTC (rev 4949)
@@ -0,0 +1,8 @@
+QIIME for Debian
+================
+
+QIIME is a very powerful environment, but the core of its power 
+stems from the tools underneath.
+
+Not all those tools that QIIME can work with are yet available 
+with Debian. If you find resources to help - please do.

Added: trunk/packages/qiime/trunk/debian/changelog
===================================================================
--- trunk/packages/qiime/trunk/debian/changelog	                        (rev 0)
+++ trunk/packages/qiime/trunk/debian/changelog	2010-06-26 23:29:28 UTC (rev 4949)
@@ -0,0 +1,6 @@
+qiime (1.1.0-1) unstable; urgency=low
+
+  * Initial release (Closes: #587275)
+
+ -- Sri Girish Srinivasa Murthy <srigirish at evolbio.mpg.de>  Sun, 27 Jun 2010 01:00:47 +0200
+

Added: trunk/packages/qiime/trunk/debian/control
===================================================================
--- trunk/packages/qiime/trunk/debian/control	                        (rev 0)
+++ trunk/packages/qiime/trunk/debian/control	2010-06-26 23:29:28 UTC (rev 4949)
@@ -0,0 +1,42 @@
+Source: qiime
+Section: python
+Priority: extra
+Maintainer: Sri Girish Srinivasa Murthy <srigirish at evolbio.mpg.de>
+Uploaders: Steffen Moeller <moeller at debian.org>
+Build-Depends: debhelper (>= 7), cdbs, python, python-central, python-cogent, python-numpy, python-matplotlib
+Standards-Version: 3.8.4
+Homepage: http://pynast.sourceforge.net/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/qiime/trunk/?rev=0&sc=0
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/qiime/trunk/
+
+Package: qiime
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}, ${misc:Depends}, ${python:Depends}
+Recommends: blast2
+Suggests: muscle, infernal, t-coffee
+Description: Quantitative Insights Into Microbial Ecology
+ QIIME (canonically pronounced ‘Chime’) is a pipeline for performing
+ microbial community analysis that integrates many third party tools which
+ have become standard in the field. A standard QIIME analysis begins with
+ sequence data from one or more sequencing platforms, including Sanger,
+ Roche/454, and Illumina GAIIx. With all the underlying tools installed,
+ of which not all are yet available in Debian (or any other Linux
+ distribution), QIIME can perform library de-multiplexing and quality
+ filtering; denoising with PyroNoise; OTU and representative set picking
+ with uclust, cdhit, mothur, BLAST, or other tools; taxonomy assignment
+ with BLAST or the RDP classifier; sequence alignment with PyNAST, muscle,
+ infernal, or other tools; phylogeny reconstruction with FastTree, raxml,
+ clearcut, or other tools; alpha diversity and rarefaction, including
+ visualization of results, using over 20 metrics including Phylogenetic
+ Diversity, chao1, and observed species; beta diversity and rarefaction,
+ including visualization of results, using over 25 metrics including
+ weighted and unweighted UniFrac, Euclidean distance, and Bray-Curtis;
+ summarization and visualization of taxonomic composition of samples
+ using pie charts and histograms; and many other features.
+ .
+ QIIME includes parallelization capabilities for many of the
+ computationally intensive steps. By default, these are configured to
+ utilize a mutli-core environment, and are easily configured to run in
+ a cluster environment. QIIME is built in Python using the open-source
+ PyCogent toolkit. It makes extensive use of unit tests, and is highly
+ modular to facilitate custom analyses.

Added: trunk/packages/qiime/trunk/debian/copyright
===================================================================
--- trunk/packages/qiime/trunk/debian/copyright	                        (rev 0)
+++ trunk/packages/qiime/trunk/debian/copyright	2010-06-26 23:29:28 UTC (rev 4949)
@@ -0,0 +1,28 @@
+This work was packaged for Debian by:
+
+    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://pynast.sorceforge.net>
+
+Upstream Author:
+
+    Greg Caporaso <gregcaporaso at gmail.com>
+    Kyle Bittinger
+
+Copyright:
+
+    Copyright 2010, The QIIME Project
+
+License:
+
+    GPL-2
+
+The Debian packaging is:
+
+    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'.

Added: trunk/packages/qiime/trunk/debian/docs
===================================================================
--- trunk/packages/qiime/trunk/debian/docs	                        (rev 0)
+++ trunk/packages/qiime/trunk/debian/docs	2010-06-26 23:29:28 UTC (rev 4949)
@@ -0,0 +1,5 @@
+README
+ChangeLog
+qiime_parameters.txt
+qiime_tutorial/
+doc/*

Added: trunk/packages/qiime/trunk/debian/pyversions
===================================================================
--- trunk/packages/qiime/trunk/debian/pyversions	                        (rev 0)
+++ trunk/packages/qiime/trunk/debian/pyversions	2010-06-26 23:29:28 UTC (rev 4949)
@@ -0,0 +1 @@
+2.6

Added: trunk/packages/qiime/trunk/debian/rules
===================================================================
--- trunk/packages/qiime/trunk/debian/rules	                        (rev 0)
+++ trunk/packages/qiime/trunk/debian/rules	2010-06-26 23:29:28 UTC (rev 4949)
@@ -0,0 +1,13 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+export DEB_PYTHON_SYSTEM=pycentral
+
+include /usr/share/cdbs/1/rules/debhelper.mk
+include /usr/share/cdbs/1/class/python-distutils.mk
+
+clean::
+	rm -rf build build-stamp


Property changes on: trunk/packages/qiime/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
   + *

Added: trunk/packages/qiime/trunk/debian/source/format
===================================================================
--- trunk/packages/qiime/trunk/debian/source/format	                        (rev 0)
+++ trunk/packages/qiime/trunk/debian/source/format	2010-06-26 23:29:28 UTC (rev 4949)
@@ -0,0 +1 @@
+3.0 (quilt)

Added: trunk/packages/qiime/trunk/debian/watch
===================================================================
--- trunk/packages/qiime/trunk/debian/watch	                        (rev 0)
+++ trunk/packages/qiime/trunk/debian/watch	2010-06-26 23:29:28 UTC (rev 4949)
@@ -0,0 +1,2 @@
+version=3
+http://sf.net/pynast/PyNAST-([.0-9]+)\.tgz


