[Blends-commit] r2793 - in /projects/med/trunk/debian-med/tasks: bio bio-ngs

[tille at users.alioth.debian.org]

Author: tille
Date: Fri Apr 29 06:43:46 2011
New Revision: 2793

URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=2793
Log:
qiime now official package

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

Modified: projects/med/trunk/debian-med/tasks/bio
URL: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/tasks/bio?rev=2793&op=diff
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio (original)
+++ projects/med/trunk/debian-med/tasks/bio Fri Apr 29 06:43:46 2011
@@ -185,8 +185,13 @@
 
 X-End-Category: Sequence alignments and related programs.
 
-Depends:     last-align, maq, ssake, velvet
-Why:         Tools related to high-throughput sequencing.
+X-Begin-Category: high-throughput sequencing
+
+Depends: last-align, maq, ssake, velvet
+
+Depends: qiime
+
+X-End-Category: high-throughput sequencing
 
 X-Begin-Category: Analysis of RNA sequences.
 
@@ -3082,39 +3087,6 @@
  bayesian sampling of phylogenetic trees from these data.
 
 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.
-Remark: Highly important for NGS
 
 Depends: denoiser
 WNPP: 587274

Modified: projects/med/trunk/debian-med/tasks/bio-ngs
URL: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/tasks/bio-ngs?rev=2793&op=diff
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio-ngs (original)
+++ projects/med/trunk/debian-med/tasks/bio-ngs Fri Apr 29 06:43:46 2011
@@ -18,6 +18,8 @@
 	ssake,
 	tabix,
 	velvet
+
+Depends: qiime
 
 Depends: cufflinks
 Homepage: http://cufflinks.cbcb.umd.edu/