[med-svn] r7573 - in trunk/packages/qiime: . trunk/debian

Andreas Tille tille at alioth.debian.org
Mon Aug 29 06:54:01 UTC 2011


Author: tille
Date: 2011-08-29 06:54:01 +0000 (Mon, 29 Aug 2011)
New Revision: 7573

Added:
   trunk/packages/qiime/trunk/
   trunk/packages/qiime/trunk/debian/changelog
   trunk/packages/qiime/trunk/debian/control
Removed:
   trunk/packages/qiime/trunk/debian/changelog
   trunk/packages/qiime/trunk/debian/conffiles
   trunk/packages/qiime/trunk/debian/control
Modified:
   trunk/packages/qiime/trunk/debian/README.Debian
Log:
Move from contrib to main; hopefully better up to date and better understandable README.Debian


Modified: trunk/packages/qiime/trunk/debian/README.Debian
===================================================================
--- trunk/packages/qiime/trunk_debhelper/debian/README.Debian	2011-08-28 22:45:23 UTC (rev 7570)
+++ trunk/packages/qiime/trunk/debian/README.Debian	2011-08-29 06:54:01 UTC (rev 7573)
@@ -18,28 +18,9 @@
 first to profit from now joint forces on getting the packages to a
 best-possible shape for everyone.
 
-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
-----------------------------------------------------------
-
-The conflict reports in the control file is originally indiciated against
-bio-linux-qiime (<= bl1.1.x). The prefix "bl" is unfortunate since the
-Debian packaging tools demand (and the Debian policy) demand the version
-to start with a number, not a character. The version is now removed from
-that indicated conflict.
-
-Depending on who was performing the last editing of the package, versions
-are either specified with a suffix "-N", N numeric, for uploads to Debian,
-or with the suffix "-ubuntuN". The changelog shall show the Ns to increase
-and be reset for new upstream versions. This is yet slightly different
-from the common practice to have the Ubuntu vesion keep the last Debian
-version (or start a new one as 0) and have the version extended to
-"NubuntuM" with M reset to 1 with every new Debian version. Either way
-makes sense. The current approach indiciates better that some upload
-to Debian may not yet have happened.
-
+Qiime wants very much to use the UClust binary, but this is not free software.
+However, it is available right now free-of-charge if:
+  a) You are an academic user and only want the 32-bit version.
+  b) You promise to use the UClust application only as part of Qiime.
+You can download uclust from
+  http://www.drive5.com/uclust/downloads1_2_21q.html

Deleted: trunk/packages/qiime/trunk/debian/changelog
===================================================================
--- trunk/packages/qiime/trunk_debhelper/debian/changelog	2011-08-28 22:45:23 UTC (rev 7570)
+++ trunk/packages/qiime/trunk/debian/changelog	2011-08-29 06:54:01 UTC (rev 7573)
@@ -1,78 +0,0 @@
-qiime (1.3.0-1) UNRELEASED; urgency=low
-
-  * 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
-
-qiime (1.2.1-6) experimental; urgency=low
-
-  [Andreas Tille]
-  * Dropped cdbs in favour of dh
-  * Debhelper 8 (compat+control)
-  * Use debian/{install,dirs) to enable better readable debian/rules
-  * debian/rules:
-    - override_dh_compress
-    - override_dh_installchangelogs
-
-  [Steffen Moeller]
-  * Updates to debian/README.Debian
-  * Policy updated to 3.9.2
-
- -- Steffen Moeller <moeller at debian.org>  Fri, 29 Apr 2011 22:56:37 +0200
-
-qiime (1.2.1-ubuntu5) lucid; urgency=low
-
-  * Fixed silly error in qiime wrapper script
-  * Added uclust wrapper to deal with uclust being expected but missing
-
- -- Tim Booth <tbooth at ceh.ac.uk>  Thu, 24 Mar 2011 16:52:43 +0000
-
-qiime (1.2.1-ubuntu4) lucid; urgency=low
-
-  * Fixed dependency - needs python-cogent >= 1.5
-
- -- Tim Booth <tbooth at ceh.ac.uk>  Thu, 24 Mar 2011 15:33:03 +0000
-
-qiime (1.2.1-ubuntu3) lucid; urgency=low
-
-  * Moved .py scripts out of /usr/bin
-  * Added /usr/bin/qiime wrapper script as per Bio-Linux
-  * Added default configuration file
-  * Cleaned up documentation
-  * Added many dependencies (some of which are still not packaged) 
-
- -- Tim Booth <tbooth at ceh.ac.uk>  Thu, 24 Mar 2011 11:35:58 +0000
-
-qiime (1.2.1-ubuntu2) lucid; urgency=low
-
-  * Pulled 1.2.1 source and tried a rebuild.
-  * Fixed Lintian changelog warning.
-
- -- Tim Booth <tbooth at ceh.ac.uk>  Tue, 22 Mar 2011 13:55:49 +0000
-
-qiime (1.2.1-2) experimental; urgency=low
-
-  * Initial release (Closes: #587275)
-  * Fixed Python 2.6 incompatibility.
-
- -- Steffen Moeller <moeller at debian.org>  Wed, 02 Mar 2011 22:33:45 +0100
-
-qiime (1.2.1-1) experimental; urgency=low
-
-  * Corrected home page
-  * Updated policy to 3.9.1
-  * Updated debian/README.Debian
-
- -- Steffen Moeller <moeller at debian.org>  Wed, 02 Mar 2011 18:19:39 +0100
-
-qiime (1.1.0-1) experimental; urgency=low
-
-  * Initial release.
-
- -- Sri Girish Srinivasa Murthy <srigirish at evolbio.mpg.de>  Tue, 20 Jul 2010 00:03:02 +0200
-

Copied: trunk/packages/qiime/trunk/debian/changelog (from rev 7571, trunk/packages/qiime/trunk_debhelper/debian/changelog)
===================================================================
--- trunk/packages/qiime/trunk/debian/changelog	                        (rev 0)
+++ trunk/packages/qiime/trunk/debian/changelog	2011-08-29 06:54:01 UTC (rev 7573)
@@ -0,0 +1,92 @@
+qiime (1.3.0-1) UNRELEASED; urgency=low
+
+  [Andreas Tille]
+  * New upstream version
+  * debian/control:
+    - Added myself to uploaders
+    - needs higher version of python-cogent
+    - moved from contrib/science to science because there are
+      no non-free components used any more
+  * Removed denoiser from Recommends because it is included
+    in the package itself
+  * Removed empty file debian/conffiles
+  * debian/README.Debian:
+    - Removed non-free remark about cogent
+    - Added remark about uclust
+    - Removed explanation of version numbers refering to BioLinux.
+      The remark was hard to understand either for Debian or Ubuntu
+      users because they do not see in their packages what is
+      described inside README.Debian.
+
+  [Steffen Möller, Tim Booth]
+  * Escaping from experimental since pynast has escaped it.
+
+ -- Andreas Tille <tille at debian.org>  Wed, 03 Aug 2011 10:59:42 +0200
+
+qiime (1.2.1-6) experimental; urgency=low
+
+  [Andreas Tille]
+  * Dropped cdbs in favour of dh
+  * Debhelper 8 (compat+control)
+  * Use debian/{install,dirs) to enable better readable debian/rules
+  * debian/rules:
+    - override_dh_compress
+    - override_dh_installchangelogs
+
+  [Steffen Moeller]
+  * Updates to debian/README.Debian
+  * Policy updated to 3.9.2
+
+ -- Steffen Moeller <moeller at debian.org>  Fri, 29 Apr 2011 22:56:37 +0200
+
+qiime (1.2.1-ubuntu5) lucid; urgency=low
+
+  * Fixed silly error in qiime wrapper script
+  * Added uclust wrapper to deal with uclust being expected but missing
+
+ -- Tim Booth <tbooth at ceh.ac.uk>  Thu, 24 Mar 2011 16:52:43 +0000
+
+qiime (1.2.1-ubuntu4) lucid; urgency=low
+
+  * Fixed dependency - needs python-cogent >= 1.5
+
+ -- Tim Booth <tbooth at ceh.ac.uk>  Thu, 24 Mar 2011 15:33:03 +0000
+
+qiime (1.2.1-ubuntu3) lucid; urgency=low
+
+  * Moved .py scripts out of /usr/bin
+  * Added /usr/bin/qiime wrapper script as per Bio-Linux
+  * Added default configuration file
+  * Cleaned up documentation
+  * Added many dependencies (some of which are still not packaged) 
+
+ -- Tim Booth <tbooth at ceh.ac.uk>  Thu, 24 Mar 2011 11:35:58 +0000
+
+qiime (1.2.1-ubuntu2) lucid; urgency=low
+
+  * Pulled 1.2.1 source and tried a rebuild.
+  * Fixed Lintian changelog warning.
+
+ -- Tim Booth <tbooth at ceh.ac.uk>  Tue, 22 Mar 2011 13:55:49 +0000
+
+qiime (1.2.1-2) experimental; urgency=low
+
+  * Initial release (Closes: #587275)
+  * Fixed Python 2.6 incompatibility.
+
+ -- Steffen Moeller <moeller at debian.org>  Wed, 02 Mar 2011 22:33:45 +0100
+
+qiime (1.2.1-1) experimental; urgency=low
+
+  * Corrected home page
+  * Updated policy to 3.9.1
+  * Updated debian/README.Debian
+
+ -- Steffen Moeller <moeller at debian.org>  Wed, 02 Mar 2011 18:19:39 +0100
+
+qiime (1.1.0-1) experimental; urgency=low
+
+  * Initial release.
+
+ -- Sri Girish Srinivasa Murthy <srigirish at evolbio.mpg.de>  Tue, 20 Jul 2010 00:03:02 +0200
+

Deleted: trunk/packages/qiime/trunk/debian/conffiles
===================================================================
Deleted: trunk/packages/qiime/trunk/debian/control
===================================================================
--- trunk/packages/qiime/trunk_debhelper/debian/control	2011-08-28 22:45:23 UTC (rev 7570)
+++ trunk/packages/qiime/trunk/debian/control	2011-08-29 06:54:01 UTC (rev 7573)
@@ -1,54 +0,0 @@
-Source: qiime
-Section: contrib/science
-Priority: extra
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Steffen Moeller <moeller at debian.org>,
- Tim Booth <tbooth at ceh.ac.uk>,
- Andreas Tille <tille at debian.org>
-Build-Depends: debhelper (>= 8), python, python-central, python-cogent, python-numpy, python-matplotlib
-Standards-Version: 3.9.2
-Homepage: http://qiime.sourceforge.net/
-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/
-XS-Python-Version: >= 2.5
-
-Package: qiime
-Architecture: all
-Depends: ${shlibs:Depends}, ${misc:Depends}, ${misc:Depends}, ${python:Depends}, python-pynast, python-cogent ( >= 1.5.1 )
-Recommends: blast2, cd-hit, denoiser, rdp-classifier, chimeraslayer, muscle, infernal, fasttree
-Suggests: t-coffee, cytoscape
-Conflicts: bio-linux-qiime
-XB-Python-Version:  ${python:Versions}
-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.

Copied: trunk/packages/qiime/trunk/debian/control (from rev 7571, trunk/packages/qiime/trunk_debhelper/debian/control)
===================================================================
--- trunk/packages/qiime/trunk/debian/control	                        (rev 0)
+++ trunk/packages/qiime/trunk/debian/control	2011-08-29 06:54:01 UTC (rev 7573)
@@ -0,0 +1,54 @@
+Source: qiime
+Section: science
+Priority: extra
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Steffen Moeller <moeller at debian.org>,
+ Tim Booth <tbooth at ceh.ac.uk>,
+ Andreas Tille <tille at debian.org>
+Build-Depends: debhelper (>= 8), python, python-central, python-cogent, python-numpy, python-matplotlib
+Standards-Version: 3.9.2
+Homepage: http://qiime.sourceforge.net/
+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/
+XS-Python-Version: >= 2.5
+
+Package: qiime
+Architecture: all
+Depends: ${shlibs:Depends}, ${misc:Depends}, ${misc:Depends}, ${python:Depends}, python-pynast, python-cogent ( >= 1.5.1 )
+Recommends: blast2, cd-hit, rdp-classifier, chimeraslayer, muscle, infernal, fasttree
+Suggests: t-coffee, cytoscape
+Conflicts: bio-linux-qiime
+XB-Python-Version:  ${python:Versions}
+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.




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