[med-svn] r7374 - in trunk/packages/qiime: . 1.3.0_ubuntu_lucid/debian 1.3.0_ubuntu_lucid/debian/patches
Timothy Booth
tbooth-guest at alioth.debian.org
Tue Aug 2 17:10:08 UTC 2011
Author: tbooth-guest
Date: 2011-08-02 17:10:08 +0000 (Tue, 02 Aug 2011)
New Revision: 7374
Added:
trunk/packages/qiime/1.3.0_ubuntu_lucid/
Modified:
trunk/packages/qiime/1.3.0_ubuntu_lucid/debian/changelog
trunk/packages/qiime/1.3.0_ubuntu_lucid/debian/compat
trunk/packages/qiime/1.3.0_ubuntu_lucid/debian/control
trunk/packages/qiime/1.3.0_ubuntu_lucid/debian/patches/series
trunk/packages/qiime/1.3.0_ubuntu_lucid/debian/rules
Log:
This is a update of the Qiime 1.2.1 package to build Qiime 1.3.
Unfortunately, this is now a fork from the Debian trunk because current versions
of Debian/Ubuntu now build Python with "dh --with python2" but I can't use this for
backports to Lucid Lynx.
Anyone wanting to package Qiime 1.3 or above for Deb Med should ignore this fork, and
work from the much neater trunk. However, you should take a look at my last changelog
entry as there are some important changes from the packaging point of view - primarily
the inclusion of a small piece of compiled code and the incorporation of Denoiser within
the core Qiime codebase.
Modified: trunk/packages/qiime/1.3.0_ubuntu_lucid/debian/changelog
===================================================================
--- trunk/packages/qiime/trunk/debian/changelog 2011-08-02 13:08:20 UTC (rev 7373)
+++ trunk/packages/qiime/1.3.0_ubuntu_lucid/debian/changelog 2011-08-02 17:10:08 UTC (rev 7374)
@@ -1,19 +1,14 @@
-qiime (1.2.1-6) experimental; urgency=low
+qiime (1.3.0-0ubuntu4) lucid; 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
+ * 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.
+ * Added build dep on ghc6 for the same reson
- [Steffen Moeller]
- * Updates to debian/README.Debian
- * Policy updated to 3.9.2
+ -- Tim Booth <tbooth at ceh.ac.uk> Tue, 19 Jul 2011 17:38:28 +0100
- -- 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/1.3.0_ubuntu_lucid/debian/compat
===================================================================
--- trunk/packages/qiime/trunk/debian/compat 2011-08-02 13:08:20 UTC (rev 7373)
+++ trunk/packages/qiime/1.3.0_ubuntu_lucid/debian/compat 2011-08-02 17:10:08 UTC (rev 7374)
@@ -1 +1 @@
-8
+5
Modified: trunk/packages/qiime/1.3.0_ubuntu_lucid/debian/control
===================================================================
--- trunk/packages/qiime/trunk/debian/control 2011-08-02 13:08:20 UTC (rev 7373)
+++ trunk/packages/qiime/1.3.0_ubuntu_lucid/debian/control 2011-08-02 17:10:08 UTC (rev 7374)
@@ -2,20 +2,21 @@
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>
-Build-Depends: debhelper (>= 8), python, python-central, python-cogent, python-numpy, python-matplotlib
-Standards-Version: 3.9.2
+Uploaders: Sri Girish Srinivasa Murthy <srigirish at evolbio.mpg.de>, Steffen Moeller <moeller at debian.org>, Tim Booth <tbooth at ceh.ac.uk>
+Build-Depends: debhelper (>= 8), cdbs, python, python-central, python-cogent ( >= 1.5.1 ), python-numpy, python-matplotlib, ghc6
+Standards-Version: 3.9.1
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
+XS-Python-Version: >= 2.6
Package: qiime
-Architecture: all
-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
+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
+Conflicts: denoiser
+Replaces: denoiser
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
Modified: trunk/packages/qiime/1.3.0_ubuntu_lucid/debian/patches/series
===================================================================
--- trunk/packages/qiime/trunk/debian/patches/series 2011-08-02 13:08:20 UTC (rev 7373)
+++ trunk/packages/qiime/1.3.0_ubuntu_lucid/debian/patches/series 2011-08-02 17:10:08 UTC (rev 7374)
@@ -1 +1,2 @@
python26_trim_sff_primers.patch
+fix_shebang_lines.patch
Modified: trunk/packages/qiime/1.3.0_ubuntu_lucid/debian/rules
===================================================================
--- trunk/packages/qiime/trunk/debian/rules 2011-08-02 13:08:20 UTC (rev 7373)
+++ trunk/packages/qiime/1.3.0_ubuntu_lucid/debian/rules 2011-08-02 17:10:08 UTC (rev 7374)
@@ -1,41 +1,47 @@
#!/usr/bin/make -f
# -*- makefile -*-
-# debian/rules for Qiime
-# Tim Booth <tbooth at ceh.ac.uk>, Andreas Tille <tille at debian.org>
-# GPL
+#
+# FIXME - don't edit this file any more. Pull Steffen's version and work from there.
+# Except that won't work with Ubuntu 10.04 so we're stuffed.
# Uncomment this to turn on verbose mode.
#export DH_VERBOSE=1
-%:
- dh $@ --with python2
+export DEB_PYTHON_SYSTEM=pycentral
+export DEB_COMPRESS_EXCLUDE=.js .sff .qual .fna .fna.txt
-override_dh_compress:
- dh_compress \
- --exclude=.js \
- --exclude=.sff \
- --exclude=.qual \
- --exclude=.fna \
- --exclude=.fna.txt
+include /usr/share/cdbs/1/rules/debhelper.mk
+include /usr/share/cdbs/1/class/python-distutils.mk
-override_dh_clean:
- dh_clean
- rm -rf doc/_build
-
export ROOTDIR=debian/`dh_listpackages`
+# Apparently the override_dh_* mechanism doesn't work with the above includes??
+# Yes, see http://lists.debian.org/debian-med/2011/03/msg00211.html
+# TODO - redo this file as Andreas suggested.
+clean::
+ rm -rf doc/_build/*
+ ( cd qiime/support_files/denoiser/FlowgramAlignment && make clean ) || true
+ rm -f qiime/support_files/denoiser/bin/*
+
#Lots of shuffling to be done...
# Python scripts go into /usr/lib/qiime/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
# ...or maybe it should be copied to $HOME/.qiime_config on 1st run?
-override_dh_install:
- dh_install
+# Since 3.0, denoiser is aliased to Qiime
+common-binary-fixup-arch::
+ install -m 755 -d $(ROOTDIR)/usr/lib/qiime/bin
+ install -m 755 -d $(ROOTDIR)/etc/qiime
mv $(ROOTDIR)/usr/bin/*.py $(ROOTDIR)/usr/lib/qiime/bin
+ install -m 755 debian/scripts/qiime $(ROOTDIR)/usr/bin
+ ln -sf qiime $(ROOTDIR)/usr/bin/denoiser
install -m 755 debian/scripts/uclust $(ROOTDIR)/usr/lib/qiime/bin
+ 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
-
-override_dh_installchangelogs:
- dh_installchangelogs ChangeLog
+ 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
+ mv $(ROOTDIR)/usr/qiime/support_files $(ROOTDIR)/usr/lib/qiime && rmdir $(ROOTDIR)/usr/qiime
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