[med-svn] r7538 - in trunk/packages/qiime/1.3.0_ubuntu_lucid/debian: . patches scripts/shell

Timothy Booth tbooth-guest at alioth.debian.org
Wed Aug 24 16:47:14 UTC 2011 

Author: tbooth-guest
Date: 2011-08-24 16:47:14 +0000 (Wed, 24 Aug 2011)
New Revision: 7538

Added:
   trunk/packages/qiime/1.3.0_ubuntu_lucid/debian/patches/fix_shebang_lines.patch
Modified:
   trunk/packages/qiime/1.3.0_ubuntu_lucid/debian/README.source
   trunk/packages/qiime/1.3.0_ubuntu_lucid/debian/changelog
   trunk/packages/qiime/1.3.0_ubuntu_lucid/debian/control
   trunk/packages/qiime/1.3.0_ubuntu_lucid/debian/rules
   trunk/packages/qiime/1.3.0_ubuntu_lucid/debian/scripts/shell/qiime_environment
Log:
Updates and added commentary to README.source


Modified: trunk/packages/qiime/1.3.0_ubuntu_lucid/debian/README.source
===================================================================
--- trunk/packages/qiime/1.3.0_ubuntu_lucid/debian/README.source	2011-08-24 15:46:33 UTC (rev 7537)
+++ trunk/packages/qiime/1.3.0_ubuntu_lucid/debian/README.source	2011-08-24 16:47:14 UTC (rev 7538)
@@ -1,9 +1,42 @@
 QIIME for Debian - source
 =========================
 
+Previous comment by Steffen:
+
 Lintian complains a lot about script-with-language-extension,
 i.e. the .py endings for files ending up in /usr/bin.
 What to do about this is not clear for the moment. For the
 time speaking it seems like lintian is wrong here, too deeply
 embedded is python in the project and Debian does not
 want to become incompatible.
+
+New comments by Tim:
+
+I borrowed the Bio-Linux approach for Qiime which may or may not be the best idea.
+Essentially, the Python scripts are not in the path and instead of running:
+
+% my_qiime_app.py
+
+You run:
+
+% qiime my_qiime_app.py
+
+or equivalently just:
+
+% qiime my_qiime_app
+
+The 'qiime' wrapper script adds the extension if needed and sets the path.  If run with
+no arguments it sets the path and drops to an interactive shell.
+
+The dependencies of Qiime essentially make it non-free despite the DFSG licence on the Qiime
+code itself.  Chief among these is UClust.  This package is supposed to handle the lack of UClust
+gracefully but it is still up to the user to fetch and insatll it.
+
+Other dependencies/TODO:
+
+Everything else needed should be packaged, if not in Debian proper than in the SVN.
+
+denoiser - no longer a dependency as it has been folded into Qiime itself.
+several recommended deps should probably be hard depends, as long as they are available in the archive
+
+

Modified: trunk/packages/qiime/1.3.0_ubuntu_lucid/debian/changelog
===================================================================
--- trunk/packages/qiime/1.3.0_ubuntu_lucid/debian/changelog	2011-08-24 15:46:33 UTC (rev 7537)
+++ trunk/packages/qiime/1.3.0_ubuntu_lucid/debian/changelog	2011-08-24 16:47:14 UTC (rev 7538)
@@ -1,3 +1,9 @@
+qiime (1.3.0-0ubuntu5) lucid; urgency=low
+
+  * Very minor fix to scripts/shell/qiime_environment
+
+ -- Tim Booth <tbooth at ceh.ac.uk>  Tue, 16 Aug 2011 12:35:06 +0100
+
 qiime (1.3.0-0ubuntu4) lucid; urgency=low
 
   * New upstream release.  Needs newer Python-Cogent

Modified: trunk/packages/qiime/1.3.0_ubuntu_lucid/debian/control
===================================================================
--- trunk/packages/qiime/1.3.0_ubuntu_lucid/debian/control	2011-08-24 15:46:33 UTC (rev 7537)
+++ trunk/packages/qiime/1.3.0_ubuntu_lucid/debian/control	2011-08-24 16:47:14 UTC (rev 7538)
@@ -13,7 +13,7 @@
 Package: qiime
 Architecture: any
 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, ampliconnoise
+Recommends: blast2 | blast+-legacy, cd-hit, rdp-classifier, chimeraslayer, muscle, infernal, fasttree, ampliconnoise, python-matplotlib, python-numpy
 Conflicts: denoiser
 Replaces: denoiser
 Suggests: t-coffee, cytoscape

Added: trunk/packages/qiime/1.3.0_ubuntu_lucid/debian/patches/fix_shebang_lines.patch
===================================================================
--- trunk/packages/qiime/1.3.0_ubuntu_lucid/debian/patches/fix_shebang_lines.patch	                        (rev 0)
+++ trunk/packages/qiime/1.3.0_ubuntu_lucid/debian/patches/fix_shebang_lines.patch	2011-08-24 16:47:14 UTC (rev 7538)
@@ -0,0 +1,8 @@
+--- a/scripts/denoiser_postprocess.py
++++ b/scripts/denoiser_postprocess.py
+@@ -1,4 +1,4 @@
+- #!/usr/bin/env python 
++#!/usr/bin/python
+ 
+ __author__ = "Jens Reeder"
+ __copyright__ = "Copyright 2011, The QIIME Project" 

Modified: trunk/packages/qiime/1.3.0_ubuntu_lucid/debian/rules
===================================================================
--- trunk/packages/qiime/1.3.0_ubuntu_lucid/debian/rules	2011-08-24 15:46:33 UTC (rev 7537)
+++ trunk/packages/qiime/1.3.0_ubuntu_lucid/debian/rules	2011-08-24 16:47:14 UTC (rev 7538)
@@ -40,7 +40,8 @@
 	cp -R --no-preserve=all debian/scripts/shell $(ROOTDIR)/usr/lib/qiime
 	rm -rf $(ROOTDIR)/usr/lib/qiime/shell/.svn
 	chmod -R a+rX $(ROOTDIR)/usr/lib/qiime/shell
-	install -m 644 debian/scripts/qiime_config $(ROOTDIR)/etc/qiime/qiime_config	
+	rm -rf $(ROOTDIR)/etc/qiime/qiime_config
+	install -m 644 debian/scripts/qiime_config $(ROOTDIR)/etc/qiime/qiime_config
 	# Lintian complains about case of ChangeLog.gz
 	( cd $(ROOTDIR)/usr/share/doc/`dh_listpackages` ; mv ChangeLog.gz changelog.gz || true )
 	# And about the existence of /usr/qiime

Modified: trunk/packages/qiime/1.3.0_ubuntu_lucid/debian/scripts/shell/qiime_environment
===================================================================
--- trunk/packages/qiime/1.3.0_ubuntu_lucid/debian/scripts/shell/qiime_environment	2011-08-24 15:46:33 UTC (rev 7537)
+++ trunk/packages/qiime/1.3.0_ubuntu_lucid/debian/scripts/shell/qiime_environment	2011-08-24 16:47:14 UTC (rev 7538)
@@ -3,9 +3,9 @@
 
 # Qiime basic environment.  Note that sourcing this file multiple times is not idempotent 
 # and should be avoided!
-# This file needt to be readable by /bin/sh so no bash-isms allowed.
+# This file needs to be readable by /bin/sh and zsh so no bash-isms allowed.
 
-export PYTHONPATH=$PYTHONPATH/:/usr/share/pyshared/qiime:/usr/local/bioinf/denoiser/denoiser
+export PYTHONPATH=$PYTHONPATH/:/usr/share/pyshared/qiime
 export PATH=$PATH:/usr/lib/qiime/bin
 export QIIME_CONFIG_FP=/etc/qiime/qiime_config
 export BLASTMAT=/usr/share/ncbi/data

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