[med-svn] r8692 - in trunk/packages/qiime/trunk/debian: . patches

Andreas Tille tille at alioth.debian.org
Tue Nov 29 09:04:14 UTC 2011 

Author: tille
Date: 2011-11-29 09:04:14 +0000 (Tue, 29 Nov 2011)
New Revision: 8692

Added:
   trunk/packages/qiime/trunk/debian/patches/fix_binary_helper_location.patch
   trunk/packages/qiime/trunk/debian/patches/fix_shebang_lines.patch
   trunk/packages/qiime/trunk/debian/qiime-denoiser.README.Debian
   trunk/packages/qiime/trunk/debian/qiime.README.Debian
   trunk/packages/qiime/trunk/debian/qiime.links
Removed:
   trunk/packages/qiime/trunk/debian/README.Debian
Modified:
   trunk/packages/qiime/trunk/debian/README.source
   trunk/packages/qiime/trunk/debian/changelog
   trunk/packages/qiime/trunk/debian/control
   trunk/packages/qiime/trunk/debian/patches/series
   trunk/packages/qiime/trunk/debian/qiime-denoiser.install
   trunk/packages/qiime/trunk/debian/qiime.install
   trunk/packages/qiime/trunk/debian/rules
Log:
Several changes merging BioLinux (lucid) branch with current Debian packaging; not finished yet


Deleted: trunk/packages/qiime/trunk/debian/README.Debian
===================================================================
--- trunk/packages/qiime/trunk/debian/README.Debian	2011-11-29 08:13:31 UTC (rev 8691)
+++ trunk/packages/qiime/trunk/debian/README.Debian	2011-11-29 09:04:14 UTC (rev 8692)
@@ -1,26 +0,0 @@
-Quick Start
-===========
-
-Type 'qiime' at the shell prompt before running any of the standard
-qiime commands.
-
-QIIME for Debian and Ubuntu
-===========================
-
-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.
-
-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.
-
-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

Modified: trunk/packages/qiime/trunk/debian/README.source
===================================================================
--- trunk/packages/qiime/trunk/debian/README.source	2011-11-29 08:13:31 UTC (rev 8691)
+++ trunk/packages/qiime/trunk/debian/README.source	2011-11-29 09:04:14 UTC (rev 8692)
@@ -1,9 +1,46 @@
 QIIME for Debian - source
 =========================
 
+.py endings and the qiime wrapper of Bio-Linux
+----------------------------------------------
+
+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 install it.
+
+Other dependencies/TODO:
+------------------------
+
+Everything else needed should be packaged, if not in Debian proper then 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/trunk/debian/changelog
===================================================================
--- trunk/packages/qiime/trunk/debian/changelog	2011-11-29 08:13:31 UTC (rev 8691)
+++ trunk/packages/qiime/trunk/debian/changelog	2011-11-29 09:04:14 UTC (rev 8692)
@@ -1,52 +1,62 @@
-qiime (1.3.0-1) UNRELEASED; urgency=low
+qiime (1.3.0-2) 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 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
     - Fix Vcs fields
     - DM-Upload-Allowed: yes
-  * 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.
+    - Build-Depends:
+       + python-all-dev (>= 2.6) (instead of python-central)
+       + python-sphinx to create python documentation
+  * debian/rules: short dh notation instead of cdbs
+    Closes: #639389
   * debian/{rules,qiime.install}: Adapted to new binary package layout
   * debian/qiime-denoiser.install: Move denoiser into place
+  * debian/{qiime,qiime-denoiser}.README.Debian: Provide a different
+    README.Debian for qiime-denoiser explaining the purpose of the
+    separate packaging and asking for enhancement if needed
 
-  [Steffen Möller, Tim Booth]
-  * Escaping from experimental since pynast has escaped it.
+ -- Andreas Tille <tille at debian.org>  Tue, 29 Nov 2011 09:23:18 +0100
 
- -- Andreas Tille <tille at debian.org>  Wed, 03 Aug 2011 10:59:42 +0200
+qiime (1.3.0-0ubuntu6) lucid; urgency=low
 
-qiime (1.2.1-6) experimental; urgency=low
+  * Attempt to fix some errors reported by print_qiime_config -t
+    Fixes to environment, configuration and small patches 
 
-  [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
+ -- Tim Booth <tbooth at ceh.ac.uk>  Wed, 02 Nov 2011 18:06:37 +0000
 
-  [Steffen Moeller]
-  * Updates to debian/README.Debian
-  * Policy updated to 3.9.2
+qiime (1.3.0-1) unstable; urgency=low
 
- -- Steffen Moeller <moeller at debian.org>  Fri, 29 Apr 2011 22:56:37 +0200
+  * Bringing qiime to Debian
+  [Steffen]
+  * Some reformatting of debian/control
 
+ -- Tim Booth <tbooth at ceh.ac.uk>  Fri, 26 Aug 2011 17:48:30 +0200
+
+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
+    and includes built-in denoiser, so I have now aliased
+    denoiser to run the qiime wrapper.
+  * As the upstream now contains a tiny compiled package I've had
+    to make it arch dependent (support_files/denoiser/FlowgramAlignment
+    code written in Haskell).
+  * Added build dep on ghc6 for the same reson
+
+ -- Tim Booth <tbooth at ceh.ac.uk>  Tue, 19 Jul 2011 17:38:28 +0100
+
 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	2011-11-29 08:13:31 UTC (rev 8691)
+++ trunk/packages/qiime/trunk/debian/control	2011-11-29 09:04:14 UTC (rev 8692)
@@ -2,25 +2,25 @@
 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>,
+Uploaders: Steffen Moeller <moeller at debian.org>, Tim Booth <tbooth at ceh.ac.uk>,
  Andreas Tille <tille at debian.org>
 DM-Upload-Allowed: yes
-Build-Depends: debhelper (>= 8), python, python-central, python-cogent, python-numpy,
- python-matplotlib, ghc6
+Build-Depends: debhelper (>= 8), python-all-dev (>= 2.6), python-cogent ( >= 1.5.1 ),
+ python-numpy, python-matplotlib, ghc6, python-sphinx
 Standards-Version: 3.9.2
-Homepage: http://qiime.sourceforge.net/
+Homepage: http://www.qiime.org/
 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/qiime/trunk/
 Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/qiime/trunk/
-XS-Python-Version: >= 2.5
+XS-Python-Version: >= 2.6
 
 Package: qiime
 Architecture: all
-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
+Depends: ${shlibs:Depends}, ${misc:Depends}, ${python:Depends},
+ python-pynast (>= 1.1)|pynast (>= 1.1), python-cogent ( >= 1.5.1 ),
+ qiime-denoiser
+Recommends: blast2 | blast+-legacy, cd-hit, rdp-classifier, chimeraslayer, muscle, infernal,
+ fasttree, ampliconnoise, python-matplotlib, python-numpy
 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
@@ -28,7 +28,7 @@
  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
+  * Roche/454, and 
   * Illumina GAIIx.
  With all the underlying tools installed,
  of which not all are yet available in Debian (or any other Linux

Added: trunk/packages/qiime/trunk/debian/patches/fix_binary_helper_location.patch
===================================================================
--- trunk/packages/qiime/trunk/debian/patches/fix_binary_helper_location.patch	                        (rev 0)
+++ trunk/packages/qiime/trunk/debian/patches/fix_binary_helper_location.patch	2011-11-29 09:04:14 UTC (rev 8692)
@@ -0,0 +1,18 @@
+--- a/qiime/denoiser/utils.py
++++ b/qiime/denoiser/utils.py
+@@ -41,9 +41,12 @@
+ def get_flowgram_ali_exe():
+     """Return the path to the flowgram alignment prog
+     """
+-    fp = get_qiime_project_dir() +\
+-        "/qiime/support_files/denoiser/bin/FlowgramAli_4frame"
+-    return fp
++    """fp = get_qiime_project_dir() +\
++    """    "/qiime/support_files/denoiser/bin/FlowgramAli_4frame"
++
++    """ Modified for Debian to allow this file to live somewhere more sensible:
++    """
++    return "/usr/lib/qiime/support_files/denoiser/bin/FlowgramAli_4frame"
+ 
+ def check_flowgram_ali_exe():
+    """Check if we have a working FlowgramAligner"""

Added: trunk/packages/qiime/trunk/debian/patches/fix_shebang_lines.patch
===================================================================
--- trunk/packages/qiime/trunk/debian/patches/fix_shebang_lines.patch	                        (rev 0)
+++ trunk/packages/qiime/trunk/debian/patches/fix_shebang_lines.patch	2011-11-29 09:04:14 UTC (rev 8692)
@@ -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/trunk/debian/patches/series
===================================================================
--- trunk/packages/qiime/trunk/debian/patches/series	2011-11-29 08:13:31 UTC (rev 8691)
+++ trunk/packages/qiime/trunk/debian/patches/series	2011-11-29 09:04:14 UTC (rev 8692)
@@ -1 +1,3 @@
 python26_trim_sff_primers.patch
+fix_shebang_lines.patch
+fix_binary_helper_location.patch

Added: trunk/packages/qiime/trunk/debian/qiime-denoiser.README.Debian
===================================================================
--- trunk/packages/qiime/trunk/debian/qiime-denoiser.README.Debian	                        (rev 0)
+++ trunk/packages/qiime/trunk/debian/qiime-denoiser.README.Debian	2011-11-29 09:04:14 UTC (rev 8692)
@@ -0,0 +1,8 @@
+Denoiser used to be a separate program but is now bundled together with
+qiime.  Currently the packaging does not allow a separate use of
+denoiser - it is just bundled separately to enable qiime beeing arch=all
+while denoiser contains the architecture dependent code.  If there is
+any interest in having a separate denoiser package simple file a bug
+report and let us (= Debian Med team) know.
+
+ -- Andreas Tille <tille at debian.org>  Tue, 29 Nov 2011 09:23:18 +0100

Modified: trunk/packages/qiime/trunk/debian/qiime-denoiser.install
===================================================================
--- trunk/packages/qiime/trunk/debian/qiime-denoiser.install	2011-11-29 08:13:31 UTC (rev 8691)
+++ trunk/packages/qiime/trunk/debian/qiime-denoiser.install	2011-11-29 09:04:14 UTC (rev 8692)
@@ -1 +1 @@
-qiime/support_files/denoiser/FlowgramAlignment/FlowgramAli_4frame    usr/lib/qiime/bin
+qiime/support_files/denoiser/FlowgramAlignment/FlowgramAli_4frame	usr/lib/qiime/support_files/denoiser/bin

Added: trunk/packages/qiime/trunk/debian/qiime.README.Debian
===================================================================
--- trunk/packages/qiime/trunk/debian/qiime.README.Debian	                        (rev 0)
+++ trunk/packages/qiime/trunk/debian/qiime.README.Debian	2011-11-29 09:04:14 UTC (rev 8692)
@@ -0,0 +1,52 @@
+Quick Start
+===========
+
+Type 'qiime' at the shell prompt before running any of the standard
+qiime commands.
+
+QIIME for Debian and Ubuntu
+===========================
+
+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.
+
+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.
+ * qiime still lacks a man page
+
+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/qiime.install
===================================================================
--- trunk/packages/qiime/trunk/debian/qiime.install	2011-11-29 08:13:31 UTC (rev 8691)
+++ trunk/packages/qiime/trunk/debian/qiime.install	2011-11-29 09:04:14 UTC (rev 8692)
@@ -1,6 +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/qiime_config	etc/qiime
 debian/scripts/uclust           usr/lib/qiime/bin
-usr/bin/*.py                    usr/lib/qiime/bin
+qiime/*.py			usr/lib/qiime/bin

Added: trunk/packages/qiime/trunk/debian/qiime.links
===================================================================
--- trunk/packages/qiime/trunk/debian/qiime.links	                        (rev 0)
+++ trunk/packages/qiime/trunk/debian/qiime.links	2011-11-29 09:04:14 UTC (rev 8692)
@@ -0,0 +1 @@
+usr/bin/qiime	usr/bin/denoiser

Modified: trunk/packages/qiime/trunk/debian/rules
===================================================================
--- trunk/packages/qiime/trunk/debian/rules	2011-11-29 08:13:31 UTC (rev 8691)
+++ trunk/packages/qiime/trunk/debian/rules	2011-11-29 09:04:14 UTC (rev 8692)
@@ -7,6 +7,8 @@
 # Uncomment this to turn on verbose mode.
 #export DH_VERBOSE=1
 
+pkg := $(shell dpkg-parsechangelog | sed -n 's/^Source: //p')
+
 %:
 	dh $@ --with python2
 
@@ -21,21 +23,21 @@
 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/*
+	( cd $(pkg)/support_files/denoiser/FlowgramAlignment && make clean ) || true
+	rm -f $(pkg)/support_files/denoiser/bin/*
 
-export ROOTDIR=debian/qiime
+export ROOTDIR=debian/$(pkg)
 
 #Lots of shuffling to be done...
-# Python scripts go into /usr/lib/qiime/bin (not /usr/bin)
+# Python scripts go into /usr/lib/$(pkg)/bin (not /usr/bin)
 # Helper script goes into /usr/bin
-# Setup scripts go into /usr/lib/qiime/shell
-# Default configuration goes into /etc/qiime/default_qiime_config
+# Setup scripts go into /usr/lib/$(pkg)/shell
+# Default configuration goes into /etc/$(pkg)/default_qiime_config
 # ...or maybe it should be copied to $HOME/.qiime_config on 1st run?
 override_dh_install:
 	dh_install
-	chmod a+x $(ROOTDIR)/usr/lib/qiime/bin/uclust
-	chmod -R a+rX $(ROOTDIR)/usr/lib/qiime/shell
+	chmod a+x $(ROOTDIR)/usr/lib/$(pkg)/bin/uclust
+	chmod -R a+rX $(ROOTDIR)/usr/lib/$(pkg)/shell
 
 override_dh_installchangelogs:
 	dh_installchangelogs ChangeLog

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