[med-svn] r8707 - trunk/packages/qiime/trunk/debian

[Andreas Tille]

Author: tille
Date: 2011-11-29 14:18:21 +0000 (Tue, 29 Nov 2011)
New Revision: 8707

Added:
   trunk/packages/qiime/trunk/debian/qiime-doc.doc-base
   trunk/packages/qiime/trunk/debian/qiime-doc.install
   trunk/packages/qiime/trunk/debian/qiime-doc.links
   trunk/packages/qiime/trunk/debian/upstream-metadata.yaml
Modified:
   trunk/packages/qiime/trunk/debian/changelog
Log:
Created qiime-doc package, incl. doc-base; upstream-metadata.yaml with citation information


Modified: trunk/packages/qiime/trunk/debian/changelog
===================================================================
--- trunk/packages/qiime/trunk/debian/changelog	2011-11-29 13:37:54 UTC (rev 8706)
+++ trunk/packages/qiime/trunk/debian/changelog	2011-11-29 14:18:21 UTC (rev 8707)
@@ -17,6 +17,8 @@
   * debian/{rules,qiime.install}: Adapted to new binary package layout
   * debian/qiime.{doc,links}: Move documentation into place and use
     packaged JavaScript libraries
+  * debian/qiime-doc.doc-base
+  * debian/upstream-metadata.yaml
 
  -- Andreas Tille <tille at debian.org>  Tue, 29 Nov 2011 09:23:18 +0100
 

Added: trunk/packages/qiime/trunk/debian/qiime-doc.doc-base
===================================================================
--- trunk/packages/qiime/trunk/debian/qiime-doc.doc-base	                        (rev 0)
+++ trunk/packages/qiime/trunk/debian/qiime-doc.doc-base	2011-11-29 14:18:21 UTC (rev 8707)
@@ -0,0 +1,38 @@
+Document: qiime
+Title: QIIME: Quantitative Insights Into Microbial Ecology
+Author: Greg Caporaso <gregcaporaso at gmail.com>
+Abstract: 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. 
+ .
+ Rather than reimplementing commonly used algorithms, QIIME wraps popular
+ implementations of those algorithms. This allows us to make use of the
+ many excellent tools available in this area, and allows faster
+ integration of new tools. If you use tools that you think would be
+ useful additions to QIIME, consider submitting a feature request.
+ .
+ A standard QIIME analysis begins with sequence data from one or more
+ sequencing platforms, including Sanger, Roche/454, and Illumina GAIIx.
+ QIIME can perform library de-multiplexing and quality filtering;
+ denoising with AmpliconNoise or the QIIME Denoiser; 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 area, bar and
+ pie charts along with distance histograms; and many other features.
+ While QIIME is primarily used for analysis of amplicon data, many of the
+ downstream analysis pipeline (such as alpha rarefaction and jackknifed
+ beta diversity) can be performed on any type of sample x observation
+ tables if they are formatted correctly.
+Section: Science/Biology
+
+Format: html
+Files: /usr/share/doc/qiime/html/*
+Index: /usr/share/doc/qiime/html/index.html

Added: trunk/packages/qiime/trunk/debian/qiime-doc.install
===================================================================
--- trunk/packages/qiime/trunk/debian/qiime-doc.install	                        (rev 0)
+++ trunk/packages/qiime/trunk/debian/qiime-doc.install	2011-11-29 14:18:21 UTC (rev 8707)
@@ -0,0 +1,3 @@
+qiime_tutorial/	usr/share/doc/qiime
+doc/_build/*	usr/share/doc/qiime
+doc/vb_files	usr/share/doc/qiime

Added: trunk/packages/qiime/trunk/debian/qiime-doc.links
===================================================================
--- trunk/packages/qiime/trunk/debian/qiime-doc.links	                        (rev 0)
+++ trunk/packages/qiime/trunk/debian/qiime-doc.links	2011-11-29 14:18:21 UTC (rev 8707)
@@ -0,0 +1,2 @@
+usr/share/javascript/jquery/jquery.js		usr/share/doc/qiime/html/_static/jquery.js
+usr/share/javascript/underscore/underscore.js	usr/share/doc/qiime/html/_static/underscore.js

Added: trunk/packages/qiime/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/qiime/trunk/debian/upstream-metadata.yaml	                        (rev 0)
+++ trunk/packages/qiime/trunk/debian/upstream-metadata.yaml	2011-11-29 14:18:21 UTC (rev 8707)
@@ -0,0 +1,12 @@
+Name: QIIME
+Homepage: http://www.qiime.org/
+DOI: 10.1038/nmeth.f.303
+PMID: 20383131
+Reference:
+  Author: Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R.
+  Title: QIIME allows analysis of high-throughput community sequencing data
+  Journal: Nature Methods
+  Volume: 7
+  Pages: 335 - 336
+  Year: 2010
+  URL: http://www.nature.com/nmeth/journal/v7/n5/full/nmeth.f.303.html