[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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