[med-svn] r7555 - trunk/packages/qiime/1.3.0_ubuntu_lucid/debian

[Steffen Möller]

Author: moeller
Date: 2011-08-26 13:19:44 +0000 (Fri, 26 Aug 2011)
New Revision: 7555

Modified:
   trunk/packages/qiime/1.3.0_ubuntu_lucid/debian/control
Log:
Some formatting on the control file.


Modified: trunk/packages/qiime/1.3.0_ubuntu_lucid/debian/control
===================================================================
--- trunk/packages/qiime/1.3.0_ubuntu_lucid/debian/control	2011-08-26 13:01:08 UTC (rev 7554)
+++ trunk/packages/qiime/1.3.0_ubuntu_lucid/debian/control	2011-08-26 13:19:44 UTC (rev 7555)
@@ -4,7 +4,7 @@
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 Uploaders: Sri Girish Srinivasa Murthy <srigirish at evolbio.mpg.de>, Steffen Moeller <moeller at debian.org>, Tim Booth <tbooth at ceh.ac.uk>
 Build-Depends: debhelper (>= 8), cdbs, python, python-central, python-cogent ( >= 1.5.1 ), python-numpy, python-matplotlib, ghc6
-Standards-Version: 3.9.1
+Standards-Version: 3.9.2
 Homepage: http://qiime.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/
@@ -12,31 +12,39 @@
 
 Package: qiime
 Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}, ${misc:Depends}, ${python:Depends}, python-pynast, python-cogent ( >= 1.5.1 )
+Depends: ${shlibs:Depends}, ${misc:Depends}, ${misc:Depends}, ${python:Depends}, python-pynast (>= 1.1)|pynast (>= 1.1), python-cogent ( >= 1.5.1 )
 Recommends: blast2 | blast+-legacy, cd-hit, rdp-classifier, chimeraslayer, muscle, infernal, fasttree, ampliconnoise, python-matplotlib, python-numpy
 Conflicts: denoiser
 Replaces: denoiser
+#Provides: denoiser # matter of discussion
 Suggests: t-coffee, cytoscape
 XB-Python-Version:  ${python:Versions}
 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,
+ 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.
+ 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