[med-svn] r8695 - trunk/packages/qiime/trunk/debian
Andreas Tille
tille at alioth.debian.org
Tue Nov 29 10:15:16 UTC 2011
Author: tille
Date: 2011-11-29 10:15:16 +0000 (Tue, 29 Nov 2011)
New Revision: 8695
Removed:
trunk/packages/qiime/trunk/debian/qiime-denoiser.README.Debian
trunk/packages/qiime/trunk/debian/qiime-denoiser.install
Modified:
trunk/packages/qiime/trunk/debian/changelog
trunk/packages/qiime/trunk/debian/control
trunk/packages/qiime/trunk/debian/qiime.docs
trunk/packages/qiime/trunk/debian/qiime.install
Log:
Drop qiime-denoiser extra packaging but rather move documentation to qiime-doc package; TODO: doc-base + manpages
Modified: trunk/packages/qiime/trunk/debian/changelog
===================================================================
--- trunk/packages/qiime/trunk/debian/changelog 2011-11-29 09:27:09 UTC (rev 8694)
+++ trunk/packages/qiime/trunk/debian/changelog 2011-11-29 10:15:16 UTC (rev 8695)
@@ -5,10 +5,8 @@
- moved from contrib/science to science because there are
no non-free components used any more
- Removed duplicated entry ${misc:Depends}
- - Additional binary package qiime-denoiser arch any to avoid
- having large arch all content in arch any package
- - Removed denoiser from Recommends because it is included
- in the package itself
+ - Extra package qiime-doc arch all to avoid
+ - Provides/Replaces/Conflicts denoiser
- Fix Vcs fields
- DM-Upload-Allowed: yes
- Build-Depends:
@@ -17,10 +15,8 @@
* debian/rules: short dh notation instead of cdbs
Closes: #639389
* debian/{rules,qiime.install}: Adapted to new binary package layout
- * debian/qiime-denoiser.install: Move denoiser into place
- * debian/{qiime,qiime-denoiser}.README.Debian: Provide a different
- README.Debian for qiime-denoiser explaining the purpose of the
- separate packaging and asking for enhancement if needed
+ * debian/qiime.{doc,links}: Move documentation into place and use
+ packaged JavaScript libraries
-- Andreas Tille <tille at debian.org> Tue, 29 Nov 2011 09:23:18 +0100
Modified: trunk/packages/qiime/trunk/debian/control
===================================================================
--- trunk/packages/qiime/trunk/debian/control 2011-11-29 09:27:09 UTC (rev 8694)
+++ trunk/packages/qiime/trunk/debian/control 2011-11-29 10:15:16 UTC (rev 8695)
@@ -14,13 +14,15 @@
XS-Python-Version: >= 2.6
Package: qiime
-Architecture: all
+Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends}, ${python:Depends},
- python-pynast (>= 1.1)|pynast (>= 1.1), python-cogent ( >= 1.5.1 ),
- qiime-denoiser
+ 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
Suggests: t-coffee, cytoscape
+Replaces: denoiser
+Conflicts: denoiser
+Provides: denoiser
XB-Python-Version: ${python:Versions}
Description: Quantitative Insights Into Microbial Ecology
QIIME (canonically pronounced ‘Chime’) is a pipeline for performing
@@ -57,19 +59,43 @@
PyCogent toolkit. It makes extensive use of unit tests, and is highly
modular to facilitate custom analyses.
-Package: qiime-denoiser
-Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}, python-cogent, python
-Replaces: denoiser
-Conflicts: denoiser
-Provides: denoiser
-Description: Rapid denoising of pyrosequencing amplicon data
- To denoise pyrosequencing amplicon data, the package exploits the
- rank-abundance distribution. PyroNoise uses an expectation maximization
- (EM) algorithm to figure out the most likely sequence for every read. We,
- instead, use a greedy scheme that can be seen as an approximation to
- PyroNoise. According to several test data sets, the approximation gives
- very similar results in a fraction of the time.
+Package: qiime-doc
+Section: doc
+Architecture: all
+Depends: ${misc:Depends}, libjs-jquery, libjs-underscore
+Description: Quantitative Insights Into Microbial Ecology (tutorial)
+ 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.
.
- This package is split from the Qiime binary package because it has
- architecture dependent code.
+ 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.
+ .
+ This package contains the documentation and a tutorial.
\ No newline at end of file
Deleted: trunk/packages/qiime/trunk/debian/qiime-denoiser.README.Debian
===================================================================
--- trunk/packages/qiime/trunk/debian/qiime-denoiser.README.Debian 2011-11-29 09:27:09 UTC (rev 8694)
+++ trunk/packages/qiime/trunk/debian/qiime-denoiser.README.Debian 2011-11-29 10:15:16 UTC (rev 8695)
@@ -1,8 +0,0 @@
-Denoiser used to be a separate program but is now bundled together with
-qiime. Currently the packaging does not allow a separate use of
-denoiser - it is just bundled separately to enable qiime beeing arch=all
-while denoiser contains the architecture dependent code. If there is
-any interest in having a separate denoiser package simple file a bug
-report and let us (= Debian Med team) know.
-
- -- Andreas Tille <tille at debian.org> Tue, 29 Nov 2011 09:23:18 +0100
Deleted: trunk/packages/qiime/trunk/debian/qiime-denoiser.install
===================================================================
--- trunk/packages/qiime/trunk/debian/qiime-denoiser.install 2011-11-29 09:27:09 UTC (rev 8694)
+++ trunk/packages/qiime/trunk/debian/qiime-denoiser.install 2011-11-29 10:15:16 UTC (rev 8695)
@@ -1 +0,0 @@
-qiime/support_files/denoiser/FlowgramAlignment/FlowgramAli_4frame usr/lib/qiime/support_files/denoiser/bin
Modified: trunk/packages/qiime/trunk/debian/qiime.docs
===================================================================
--- trunk/packages/qiime/trunk/debian/qiime.docs 2011-11-29 09:27:09 UTC (rev 8694)
+++ trunk/packages/qiime/trunk/debian/qiime.docs 2011-11-29 10:15:16 UTC (rev 8695)
@@ -1,5 +1,2 @@
README
qiime_parameters.txt
-qiime_tutorial/
-doc/_build/*
-doc/vb_files
Modified: trunk/packages/qiime/trunk/debian/qiime.install
===================================================================
--- trunk/packages/qiime/trunk/debian/qiime.install 2011-11-29 09:27:09 UTC (rev 8694)
+++ trunk/packages/qiime/trunk/debian/qiime.install 2011-11-29 10:15:16 UTC (rev 8695)
@@ -4,3 +4,4 @@
debian/scripts/qiime_config etc/qiime
debian/scripts/uclust usr/lib/qiime/bin
debian/tmp/usr/bin/*.py usr/lib/qiime/bin
+qiime/support_files/denoiser/FlowgramAlignment/FlowgramAli_4frame usr/lib/qiime/support_files/denoiser/bin
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