[med-svn] r6728 - trunk/packages/qiime/trunk/debian

Fri Apr 29 21:03:18 UTC 2011

Author: moeller
Date: 2011-04-29 21:03:16 +0000 (Fri, 29 Apr 2011)
New Revision: 6728

Modified:
   trunk/packages/qiime/trunk/debian/README.Debian
   trunk/packages/qiime/trunk/debian/changelog
   trunk/packages/qiime/trunk/debian/control
Log:
Uploaded all those nice improvements to Qiime by Tim and Andreas.


Modified: trunk/packages/qiime/trunk/debian/README.Debian
===================================================================

--- trunk/packages/qiime/trunk/debian/README.Debian	2011-04-29 18:23:44 UTC (rev 6727)
+++ trunk/packages/qiime/trunk/debian/README.Debian	2011-04-29 21:03:16 UTC (rev 6728)
@@ -1,32 +1,52 @@
 Quick Start
 ===========
 
-Type 'qiime' at the shell prompt before running any of the standard qiime
-commands.
+Type 'qiime' at the shell prompt before running any of the standard
+qiime commands.
 
-QIIME for Debian
-================
+QIIME for Debian and Ubuntu
+===========================
 
-QIIME is a very powerful environment, but the core of its power 
-stems from the tools underneath.
+QIIME is a very powerful environment, but the core of its power stems
+from the tools underneath.
 
-Not all those tools that QIIME can work with are yet available 
-with Debian. If you find resources to help - please do.
+Not all those tools that QIIME can work with are yet available with
+Debian. If you find resources to help - please do.
 
-Most of the needed tools are available via the Bio-Linux
-project: http://nebc.nerc.ac.uk/tools/bio-linux - efforts
-are underway by the Bio-Linux devlopers to port this work into Debian.
+Most of the needed tools are available via the Bio-Linux project:
+http://nebc.nerc.ac.uk/tools/bio-linux . This package was one of the
+first to profit from now joint forces on getting the packages to a
+best-possible shape for everyone.
 
 The package is in experimental since:
- * it depends on python-pynast that is in experimental - and
-   since like pynast it uses the sphinx documentation system
-   that it not yet uses to streamline the orig.tar.gz and
-   recreate the documentation from its sources.
-   When adding python-sphinx the build fails because of a conflict
-   to orig.tar.gz that could not yet be resolved.
+ * it depends on python-pynast that is in experimental - and since like
+   pynast it uses the sphinx documentation system that it not yet uses
+   to streamline the orig.tar.gz and recreate the documentation from
+   its sources.  When adding python-sphinx the build fails because of
+   a conflict to orig.tar.gz that could not yet be resolved.
+ * qiime still lacks a man page
 
-The distribution set to contrib because of
- * a build dependency to pynast from the cogent library that
-   incorporates some "free for academia only" code fragment.
- * the strong suggest to use uclust that is not shipped with
+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.
+
+
+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.
+

Modified: trunk/packages/qiime/trunk/debian/changelog
===================================================================
--- trunk/packages/qiime/trunk/debian/changelog	2011-04-29 18:23:44 UTC (rev 6727)
+++ trunk/packages/qiime/trunk/debian/changelog	2011-04-29 21:03:16 UTC (rev 6728)
@@ -1,5 +1,6 @@
-qiime (1.2.1-1) UNRELEASED; urgency=low
+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
@@ -7,8 +8,12 @@
     - override_dh_compress
     - override_dh_installchangelogs
 
- -- Andreas Tille <tille at debian.org>  Thu, 24 Mar 2011 22:39:55 +0100
+  [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

Modified: trunk/packages/qiime/trunk/debian/control
===================================================================
--- trunk/packages/qiime/trunk/debian/control	2011-04-29 18:23:44 UTC (rev 6727)
+++ trunk/packages/qiime/trunk/debian/control	2011-04-29 21:03:16 UTC (rev 6728)
@@ -2,9 +2,9 @@
 Section: contrib/science
 Priority: extra
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Sri Girish Srinivasa Murthy <srigirish at evolbio.mpg.de>, Steffen Moeller <moeller at debian.org>, Tim Booth <tbooth at ceh.ac.uk>
+Uploaders: Steffen Moeller <moeller at debian.org>, Tim Booth <tbooth at ceh.ac.uk>
 Build-Depends: debhelper (>= 8), python, python-central, python-cogent, python-numpy, python-matplotlib
-Standards-Version: 3.9.1
+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/
@@ -15,7 +15,7 @@
 Depends: ${shlibs:Depends}, ${misc:Depends}, ${misc:Depends}, ${python:Depends}, python-pynast, python-cogent ( >= 1.5 )
 Recommends: blast2, cd-hit, denoiser, rdp-classifier, chimeraslayer, muscle, infernal, fasttree
 Suggests: t-coffee, cytoscape
-Conflicts: bio-linux-qiime (<= bl1.1.x)
+Conflicts: bio-linux-qiime
 XB-Python-Version:  ${python:Versions}
 Description: Quantitative Insights Into Microbial Ecology
  QIIME (canonically pronounced ‘Chime’) is a pipeline for performing


