[med-svn] r7574 - trunk/packages/qiime/trunk/debian

Andreas Tille tille at alioth.debian.org
Mon Aug 29 08:12:57 UTC 2011 

Author: tille
Date: 2011-08-29 08:12:57 +0000 (Mon, 29 Aug 2011)
New Revision: 7574

Added:
   trunk/packages/qiime/trunk/debian/qiime-denoiser.install
   trunk/packages/qiime/trunk/debian/qiime.dirs
   trunk/packages/qiime/trunk/debian/qiime.docs
   trunk/packages/qiime/trunk/debian/qiime.install
Removed:
   trunk/packages/qiime/trunk/debian/dirs
   trunk/packages/qiime/trunk/debian/docs
   trunk/packages/qiime/trunk/debian/install
Modified:
   trunk/packages/qiime/trunk/debian/changelog
   trunk/packages/qiime/trunk/debian/control
   trunk/packages/qiime/trunk/debian/rules
Log:
New binary package qiime-denoiser which makes sure that the large amount of payload does not need to be arch any;  There is another way to go: strip out qiime-tutorial as arch all.


Modified: trunk/packages/qiime/trunk/debian/changelog
===================================================================
--- trunk/packages/qiime/trunk/debian/changelog	2011-08-29 06:54:01 UTC (rev 7573)
+++ trunk/packages/qiime/trunk/debian/changelog	2011-08-29 08:12:57 UTC (rev 7574)
@@ -7,6 +7,10 @@
     - needs higher version of python-cogent
     - 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
+    - Reformated long description to have all lines < 80 characters
   * Removed denoiser from Recommends because it is included
     in the package itself
   * Removed empty file debian/conffiles
@@ -17,6 +21,8 @@
       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.
+  * debian/{rules,qiime.install}: Adapted to new binary package layout
+  * debian/qiime-denoiser.install: Move denoiser into place
 
   [Steffen Möller, Tim Booth]
   * Escaping from experimental since pynast has escaped it.

Modified: trunk/packages/qiime/trunk/debian/control
===================================================================
--- trunk/packages/qiime/trunk/debian/control	2011-08-29 06:54:01 UTC (rev 7573)
+++ trunk/packages/qiime/trunk/debian/control	2011-08-29 08:12:57 UTC (rev 7574)
@@ -5,7 +5,8 @@
 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
+Build-Depends: debhelper (>= 8), python, python-central, python-cogent, python-numpy,
+ python-matplotlib, ghc6
 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
@@ -14,7 +15,8 @@
 
 Package: qiime
 Architecture: all
-Depends: ${shlibs:Depends}, ${misc:Depends}, ${misc:Depends}, ${python:Depends}, python-pynast, python-cogent ( >= 1.5.1 )
+Depends: ${shlibs:Depends}, ${misc:Depends}, ${python:Depends}, python-pynast,
+ python-cogent (>= 1.5.1), qiime-denoiser
 Recommends: blast2, cd-hit, rdp-classifier, chimeraslayer, muscle, infernal, fasttree
 Suggests: t-coffee, cytoscape
 Conflicts: bio-linux-qiime
@@ -32,7 +34,8 @@
  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;
+  * 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;
@@ -52,3 +55,20 @@
  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.
+
+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.
+ .
+ This package is split from the Qiime binary package because it has
+ architecture dependent code.

Deleted: trunk/packages/qiime/trunk/debian/dirs
===================================================================
--- trunk/packages/qiime/trunk/debian/dirs	2011-08-29 06:54:01 UTC (rev 7573)
+++ trunk/packages/qiime/trunk/debian/dirs	2011-08-29 08:12:57 UTC (rev 7574)
@@ -1,2 +0,0 @@
-usr/lib/qiime/bin
-etc/qiime

Deleted: trunk/packages/qiime/trunk/debian/docs
===================================================================
--- trunk/packages/qiime/trunk/debian/docs	2011-08-29 06:54:01 UTC (rev 7573)
+++ trunk/packages/qiime/trunk/debian/docs	2011-08-29 08:12:57 UTC (rev 7574)
@@ -1,5 +0,0 @@
-README
-qiime_parameters.txt
-qiime_tutorial/
-doc/_build/*
-doc/vb_files

Deleted: trunk/packages/qiime/trunk/debian/install
===================================================================
--- trunk/packages/qiime/trunk/debian/install	2011-08-29 06:54:01 UTC (rev 7573)
+++ trunk/packages/qiime/trunk/debian/install	2011-08-29 08:12:57 UTC (rev 7574)
@@ -1,3 +0,0 @@
-debian/scripts/qiime		usr/bin
-debian/scripts/shell		usr/lib/qiime
-debian/scripts/qiime_config	etc/qiime/qiime_config

Added: trunk/packages/qiime/trunk/debian/qiime-denoiser.install
===================================================================
--- trunk/packages/qiime/trunk/debian/qiime-denoiser.install	                        (rev 0)
+++ trunk/packages/qiime/trunk/debian/qiime-denoiser.install	2011-08-29 08:12:57 UTC (rev 7574)
@@ -0,0 +1 @@
+qiime/support_files/denoiser/FlowgramAlignment/FlowgramAli_4frame    usr/lib/qiime/bin

Added: trunk/packages/qiime/trunk/debian/qiime.dirs
===================================================================
--- trunk/packages/qiime/trunk/debian/qiime.dirs	                        (rev 0)
+++ trunk/packages/qiime/trunk/debian/qiime.dirs	2011-08-29 08:12:57 UTC (rev 7574)
@@ -0,0 +1 @@
+usr/lib/qiime/bin

Added: trunk/packages/qiime/trunk/debian/qiime.docs
===================================================================
--- trunk/packages/qiime/trunk/debian/qiime.docs	                        (rev 0)
+++ trunk/packages/qiime/trunk/debian/qiime.docs	2011-08-29 08:12:57 UTC (rev 7574)
@@ -0,0 +1,5 @@
+README
+qiime_parameters.txt
+qiime_tutorial/
+doc/_build/*
+doc/vb_files

Added: trunk/packages/qiime/trunk/debian/qiime.install
===================================================================
--- trunk/packages/qiime/trunk/debian/qiime.install	                        (rev 0)
+++ trunk/packages/qiime/trunk/debian/qiime.install	2011-08-29 08:12:57 UTC (rev 7574)
@@ -0,0 +1,6 @@
+debian/scripts/qiime		usr/bin
+debian/scripts/shell/*		usr/lib/qiime/shell
+debian/scripts/shell/.[bz]*	usr/lib/qiime/shell
+debian/scripts/qiime_config	etc/qiime/qiime_config
+debian/scripts/uclust           usr/lib/qiime/bin
+usr/bin/*.py                    usr/lib/qiime/bin

Modified: trunk/packages/qiime/trunk/debian/rules
===================================================================
--- trunk/packages/qiime/trunk/debian/rules	2011-08-29 06:54:01 UTC (rev 7573)
+++ trunk/packages/qiime/trunk/debian/rules	2011-08-29 08:12:57 UTC (rev 7574)
@@ -21,8 +21,10 @@
 override_dh_clean:
 	dh_clean
 	rm -rf doc/_build
+	( cd qiime/support_files/denoiser/FlowgramAlignment && make clean ) || true
+	rm -f qiime/support_files/denoiser/bin/*
 
-export ROOTDIR=debian/`dh_listpackages`
+export ROOTDIR=debian/qiime
 
 #Lots of shuffling to be done...
 # Python scripts go into /usr/lib/qiime/bin (not /usr/bin)
@@ -32,9 +34,7 @@
 # ...or maybe it should be copied to $HOME/.qiime_config on 1st run?
 override_dh_install:
 	dh_install
-	mv $(ROOTDIR)/usr/bin/*.py  $(ROOTDIR)/usr/lib/qiime/bin
-	install -m 755 debian/scripts/uclust $(ROOTDIR)/usr/lib/qiime/bin
-	rm -rf $(ROOTDIR)/usr/lib/qiime/shell/.svn
+	chmod a+x $(ROOTDIR)/usr/lib/qiime/bin/uclust
 	chmod -R a+rX $(ROOTDIR)/usr/lib/qiime/shell
 
 override_dh_installchangelogs:

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