[Blends-commit] r2237 - projects/med/trunk/debian-med/tasks

[Debian Pure Blends Subversion Commit]

Author: tille
Date: Mon Jun 28 06:58:53 2010
New Revision: 2237
URL: http://svn.debian.org/viewsvn/blends?rev=2237&view=rev

Log:
Added qiime as propective package


Modified:
   projects/med/trunk/debian-med/tasks/bio

Modified: projects/med/trunk/debian-med/tasks/bio
URL: http://svn.debian.org/viewsvn/blends/projects/med/trunk/debian-med/tasks/bio?rev=2237&view=diff&r1=2237&r2=2236&p1=projects/med/trunk/debian-med/tasks/bio&p2=projects/med/trunk/debian-med/tasks/bio
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio	(original)
+++ projects/med/trunk/debian-med/tasks/bio	Mon Jun 28 06:58:53 2010
@@ -3213,6 +3213,40 @@
  SAM (Sequence Alignment/Map) format is a generic format for storing
  large nucleotide sequence alignments.
 
+Depends: qiime
+WNPP: 587275
+Homepage: http://qiime.sf.net
+License: GPL
+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/
+Responsible: Steffen Moeller <steffen_moeller at gmx.de>
+Pkg-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.
+
 
 Comment: Several related R packages are listed at CRAN:
          http://cran.r-project.org/web/views/Genetics.html