[med-svn] r7556 - trunk/packages/qiime/trunk/debian

[Steffen Möller]

Author: moeller
Date: 2011-08-26 13:24:12 +0000 (Fri, 26 Aug 2011)
New Revision: 7556

Modified:
   trunk/packages/qiime/trunk/debian/README.Debian
   trunk/packages/qiime/trunk/debian/changelog
   trunk/packages/qiime/trunk/debian/control
Log:
Some updates parallel to the ubuntu branch.


Modified: trunk/packages/qiime/trunk/debian/README.Debian
===================================================================
--- trunk/packages/qiime/trunk/debian/README.Debian	2011-08-26 13:19:44 UTC (rev 7555)
+++ trunk/packages/qiime/trunk/debian/README.Debian	2011-08-26 13:24:12 UTC (rev 7556)
@@ -18,17 +18,10 @@
 first to profit from now joint forces on getting the packages to a
 best-possible shape for everyone.
 
-The package is in experimental since:
- * it depends on python-pynast that is in experimental - and since like
-   pynast it uses the sphinx documentation system that it not yet uses
-   to streamline the orig.tar.gz and recreate the documentation from
-   its sources.  When adding python-sphinx the build fails because of
-   a conflict to orig.tar.gz that could not yet be resolved.
- * qiime still lacks a man page
-
 The distribution is set to contrib because of
  * the strong recommends to use uclust that is not shipped with
    Debian as a binary only package.
+ * python-cogent is a dependency that is non-free
 
 
 Disambiguation of versions in bio-linux, Debian and Ubuntu

Modified: trunk/packages/qiime/trunk/debian/changelog
===================================================================
--- trunk/packages/qiime/trunk/debian/changelog	2011-08-26 13:19:44 UTC (rev 7555)
+++ trunk/packages/qiime/trunk/debian/changelog	2011-08-26 13:24:12 UTC (rev 7556)
@@ -1,11 +1,11 @@
 qiime (1.3.0-1) UNRELEASED; urgency=low
 
-Why should this be kept in experimental???
-
   * New upstream version
   * debian/control:
     - Added myself to uploaders
     - needs higher version of python-cogent
+  [Steffen, Tim]
+  * Escaping from experimental since pynast has escaped it.
 
  -- Andreas Tille <tille at debian.org>  Wed, 03 Aug 2011 10:59:42 +0200
 

Modified: trunk/packages/qiime/trunk/debian/control
===================================================================
--- trunk/packages/qiime/trunk/debian/control	2011-08-26 13:19:44 UTC (rev 7555)
+++ trunk/packages/qiime/trunk/debian/control	2011-08-26 13:24:12 UTC (rev 7556)
@@ -23,21 +23,28 @@
  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