[med-svn] r12035 - in trunk/packages/qiime/trunk/debian: . patches
Timothy Booth
tbooth-guest at alioth.debian.org
Fri Aug 10 17:27:51 UTC 2012
Author: tbooth-guest
Date: 2012-08-10 17:27:51 +0000 (Fri, 10 Aug 2012)
New Revision: 12035
Removed:
trunk/packages/qiime/trunk/debian/patches/python26_trim_sff_primers.patch
Modified:
trunk/packages/qiime/trunk/debian/changelog
trunk/packages/qiime/trunk/debian/control
trunk/packages/qiime/trunk/debian/qiime-doc.install
trunk/packages/qiime/trunk/debian/qiime.install
trunk/packages/qiime/trunk/debian/rules
Log:
See changelog
Still need to test this properly
Older packages had the various data files in place but they seem to
have vanished in the later version so I added them back
Modified: trunk/packages/qiime/trunk/debian/changelog
===================================================================
--- trunk/packages/qiime/trunk/debian/changelog 2012-08-10 17:22:42 UTC (rev 12034)
+++ trunk/packages/qiime/trunk/debian/changelog 2012-08-10 17:27:51 UTC (rev 12035)
@@ -1,11 +1,15 @@
-qiime (1.5.0-2ubuntu1) precise; urgency=low
+qiime (1.5.0-2ubuntu2) precise; urgency=low
* Remove python26_trim_sff_primers.patch as Qiime now requires
2.7 anyway
* Avoid calling dh_auto_clean at all as it triggers a partial
rebuild
+ * Added various support files in /usr/share/qiime/support_files
+ * Added various symlinks as Qiime wants everything in one place
+ * Set python-biom-format as a hard dependency because even built-in
+ self-test won't start without it
- -- Tim Booth <tbooth at ceh.ac.uk> Fri, 10 Aug 2012 14:42:10 +0100
+ -- Tim Booth <tbooth at ceh.ac.uk> Fri, 10 Aug 2012 17:52:06 +0100
qiime (1.5.0-2) unstable; urgency=low
Modified: trunk/packages/qiime/trunk/debian/control
===================================================================
--- trunk/packages/qiime/trunk/debian/control 2012-08-10 17:22:42 UTC (rev 12034)
+++ trunk/packages/qiime/trunk/debian/control 2012-08-10 17:27:51 UTC (rev 12035)
@@ -17,9 +17,9 @@
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends}, ${python:Depends},
python-pynast (>= 1.1)|pynast (>= 1.1), python-cogent ( >= 1.5.1 ),
- king
+ king, python-biom-format
Recommends: blast2 | blast+-legacy, cd-hit, rdp-classifier, chimeraslayer, muscle, infernal,
- fasttree, ampliconnoise, python-matplotlib, python-numpy, python-biom-format
+ fasttree, ampliconnoise, python-matplotlib, python-numpy, libjs-jquery
Suggests: t-coffee, cytoscape
Replaces: denoiser
Conflicts: denoiser
Deleted: trunk/packages/qiime/trunk/debian/patches/python26_trim_sff_primers.patch
===================================================================
--- trunk/packages/qiime/trunk/debian/patches/python26_trim_sff_primers.patch 2012-08-10 17:22:42 UTC (rev 12034)
+++ trunk/packages/qiime/trunk/debian/patches/python26_trim_sff_primers.patch 2012-08-10 17:27:51 UTC (rev 12035)
@@ -1,13 +0,0 @@
---- Qiime-1.5.0.orig/qiime/trim_sff_primers.py
-+++ Qiime-1.5.0/qiime/trim_sff_primers.py
-@@ -101,8 +101,8 @@
- clipped_header, clipped_reads = set_clip_qual_left(sff_data, readlength)
-
- _, temp_fp = tempfile.mkstemp(dir=sff_dir)
-- with open(temp_fp, 'w') as f:
-- write_binary_sff(f, clipped_header, clipped_reads)
-+ f = open(temp_fp, 'w')
-+ write_binary_sff(f, clipped_header, clipped_reads)
-
- shutil.move(temp_fp, sff_fp)
-
Modified: trunk/packages/qiime/trunk/debian/qiime-doc.install
===================================================================
--- trunk/packages/qiime/trunk/debian/qiime-doc.install 2012-08-10 17:22:42 UTC (rev 12034)
+++ trunk/packages/qiime/trunk/debian/qiime-doc.install 2012-08-10 17:27:51 UTC (rev 12035)
@@ -1,3 +1,4 @@
qiime_tutorial/ usr/share/doc/qiime
doc/_build/* usr/share/doc/qiime
doc/vb_files usr/share/doc/qiime
+qiime/support_files/denoiser/TestData usr/lib/qiime/support_files/denoiser
Modified: trunk/packages/qiime/trunk/debian/qiime.install
===================================================================
--- trunk/packages/qiime/trunk/debian/qiime.install 2012-08-10 17:22:42 UTC (rev 12034)
+++ trunk/packages/qiime/trunk/debian/qiime.install 2012-08-10 17:27:51 UTC (rev 12035)
@@ -9,3 +9,8 @@
qiime/denoiser usr/share/pyshared/qiime
qiime/parallel usr/share/pyshared/qiime
qiime/pycogent_backports usr/share/pyshared/qiime
+qiime/support_files/denoiser/Data usr/share/qiime/support_files/denoiser
+qiime/support_files/css/* usr/share/qiime/support_files/css
+qiime/support_files/images/* usr/share/qiime/support_files/images
+qiime/support_files/R/* usr/share/qiime/support_files/R
+qiime/support_files/js/* usr/share/qiime/support_files/js
Modified: trunk/packages/qiime/trunk/debian/rules
===================================================================
--- trunk/packages/qiime/trunk/debian/rules 2012-08-10 17:22:42 UTC (rev 12034)
+++ trunk/packages/qiime/trunk/debian/rules 2012-08-10 17:27:51 UTC (rev 12035)
@@ -23,9 +23,6 @@
--exclude=.fna \
--exclude=.fna.txt
-override_dh_builddeb:
- dh_builddeb -- -Z xz
-
override_dh_auto_clean:
#Calling "python setup.py clean -a" actually triggers a
#rebuild, so don't do it.
@@ -41,11 +38,20 @@
# Helper script goes into /usr/bin
# 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?
+# ...see debian/*.install files
override_dh_install:
dh_install
- chmod a+x $(ROOTDIR)/usr/lib/$(pkg)/bin/uclust
- chmod -R a+rX $(ROOTDIR)/usr/lib/$(pkg)/shell
+ chmod a+x $(ROOTDIR)/usr/lib/qiime/bin/uclust || true
+ chmod -R a+rX $(ROOTDIR)/usr/lib/qiime/shell || true
+ chmod a-x $(ROOTDIR)/usr/share/qiime/support_files/R/* || true
+ chmod a-x $(ROOTDIR)/usr/share/qiime/support_files/js/* || true
+ #Fix lintian warning for jquery
+ rm $(ROOTDIR)/usr/share/qiime/support_files/js/jquery.js && \
+ ln -s /usr/share/javascript/jquery/jquery.js $(ROOTDIR)/usr/share/qiime/support_files/js
+ #Make some symlinks as Qiime assumes a single dir structure
+ for path in denoiser/Data css images R js ; do \
+ dh_link -pqiime /usr/share/qiime/support_files/"$$path" /usr/lib/qiime/support_files/"$$path" ;\
+ done
override_dh_installchangelogs:
dh_installchangelogs ChangeLog
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