[med-svn] r4208 - in trunk/packages/clustalx/trunk/debian: . patches

Charles Plessy plessy at alioth.debian.org
Wed Oct 14 10:25:32 UTC 2009 

Author: plessy
Date: 2009-10-14 10:25:32 +0000 (Wed, 14 Oct 2009)
New Revision: 4208

Added:
   trunk/packages/clustalx/trunk/debian/patches/hardcode-accessory-file-locations.patch
   trunk/packages/clustalx/trunk/debian/patches/series
   trunk/packages/clustalx/trunk/debian/upstream-metadata.yaml
Removed:
   trunk/packages/clustalx/trunk/debian/clustalx.dirs
Modified:
   trunk/packages/clustalx/trunk/debian/changelog
   trunk/packages/clustalx/trunk/debian/clustalx.install
   trunk/packages/clustalx/trunk/debian/compat
   trunk/packages/clustalx/trunk/debian/control
   trunk/packages/clustalx/trunk/debian/copyright
   trunk/packages/clustalx/trunk/debian/rules
   trunk/packages/clustalx/trunk/debian/watch
Log:
Preparation of 2.0.x package, not that the license of Qt allows linking to non-free.


Modified: trunk/packages/clustalx/trunk/debian/changelog
===================================================================
--- trunk/packages/clustalx/trunk/debian/changelog	2009-10-14 09:54:04 UTC (rev 4207)
+++ trunk/packages/clustalx/trunk/debian/changelog	2009-10-14 10:25:32 UTC (rev 4208)
@@ -1,8 +1,18 @@
-clustalx (2.0.1-1) unstable; urgency=low
+clustalx (2.0.12-1) UNRELEASED; urgency=low
 
+  TODO: update manpage, check copyright file and Policy.
+        Access the xml and help files from /usr/share/clustalx (the patch does not work).
+        Annotate and forward patch
+        Misc stuff found by Lintian
+
+  * New upstream release (LP: #423648, #393769):
+    - Uses Qt instead of lesstif.
+    - Includes new code for UPGMA guide trees.
+    - Includes iterative alignment facility.
+
   [ Steffen Moeller ]
   * New upstream release.
-  * Updated watch file.
+  * Updated watch file (Closes: #550893).
   * Removed LICENSE from debian/clustalx.docs
   * rename to clustalx seems no longer required in debian/rules
   * moved clustalx.1 into debian folder (eases working with svn-buildpackage)
@@ -10,18 +20,16 @@
 
   [ Charles Plessy ]
   * Updated my email address.
-  * New upstream release:
-    - Uses Qt instead of lesstif.
-    - Includes new code for UPGMA guide trees.
-    - Includes iterative alignment facility.
   * debian/copyright made machine-readable.
-  * Association between Clustal X and .aln files:
-    - text/x-clustalw-alignment associated to clustalx in clustalx.desktop.
-    - .aln declared as text/x-clustalw-alignment in clustalx.sharedmimeinfo.
-    - text/x-clustalw-alignment associated to clustalx in clustalx.mime.
-    - debian/rules calls dh_installmime.
+  * Added various informations in debian/upstream-metadata.yaml.
+  * Switched to Debhelper 7.
+    (debian/rules, debian/control, debian/patches, debian/compat)
+  * Removed useless Debhelper file debian/clustalx.dirs.
+  * Updated package description.
+  * Hardcoded the localisation of accessory files in /usr/share/clustalx.
+    (debian/patches/hardcode-accessory-file-locations.patch)
 
- -- Charles Plessy <charles-debian-nospam at plessy.org>  Thu, 17 Jan 2008 22:55:41 +0900
+ -- Charles Plessy <plessy at debian.org>  Wed, 14 Oct 2009 18:49:45 +0900
 
 clustalx (1.83-4) unstable; urgency=low
 

Deleted: trunk/packages/clustalx/trunk/debian/clustalx.dirs
===================================================================
--- trunk/packages/clustalx/trunk/debian/clustalx.dirs	2009-10-14 09:54:04 UTC (rev 4207)
+++ trunk/packages/clustalx/trunk/debian/clustalx.dirs	2009-10-14 10:25:32 UTC (rev 4208)
@@ -1 +0,0 @@
-usr/share/applications

Modified: trunk/packages/clustalx/trunk/debian/clustalx.install
===================================================================
--- trunk/packages/clustalx/trunk/debian/clustalx.install	2009-10-14 09:54:04 UTC (rev 4207)
+++ trunk/packages/clustalx/trunk/debian/clustalx.install	2009-10-14 10:25:32 UTC (rev 4208)
@@ -1,3 +1,4 @@
 clustalx usr/bin
-clustalx.hlp usr/share/clustalw
+clustalx.hlp	usr/share/clustalx
+*xml		usr/share/clustalx
 debian/clustalx.desktop usr/share/applications

Modified: trunk/packages/clustalx/trunk/debian/compat
===================================================================
--- trunk/packages/clustalx/trunk/debian/compat	2009-10-14 09:54:04 UTC (rev 4207)
+++ trunk/packages/clustalx/trunk/debian/compat	2009-10-14 10:25:32 UTC (rev 4208)
@@ -1 +1 @@
-5
+7

Modified: trunk/packages/clustalx/trunk/debian/control
===================================================================
--- trunk/packages/clustalx/trunk/debian/control	2009-10-14 09:54:04 UTC (rev 4207)
+++ trunk/packages/clustalx/trunk/debian/control	2009-10-14 10:25:32 UTC (rev 4208)
@@ -3,20 +3,20 @@
 Priority: optional
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 DM-Upload-Allowed: yes
-Uploaders: Steffen Moeller <moeller at debian.org>, Charles Plessy <charles-debian-nospam at plessy.org>
-Build-Depends: debhelper (>= 5), libqt4-dev, quilt
+Uploaders: Steffen Moeller <moeller at debian.org>, Charles Plessy <plessy at debian.org>
+Build-Depends: debhelper (>= 7), libqt4-dev, quilt
 Standards-Version: 3.7.3
 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/clustalx/trunk/?rev=0&sc=0
 Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/clustalx/trunk/
 XS-Autobuild: yes
-Homepage: http://www.ebi.ac.uk/Tools/clustalw2/
+Homepage: http://www.clustal.org/
 
 Package: clustalx
 Architecture: any
-Depends: ${shlibs:Depends}
+Depends: ${shlibs:Depends}, ${misc:Depends}
 Suggests: clustalw, texshade|texlive-latex-extra, boxshade
-Description: GUI for clustalw
- This package offers a GUI interface for the Clustal W multiple sequence
+Description: Multiple alignment of nucleic acid and protein sequences (graphical interface)
+ This package offers a GUI interface for the Clustal multiple sequence
  alignment program. It provides an integrated environment for performing
  multiple sequence- and profile-alignments to analyse the results.
  The sequence alignment is displayed in a window on the screen.
@@ -32,6 +32,3 @@
  .
  An alignment quality analysis can be performed and low-scoring segments or
  exceptional residues can be highlighted.
- .
- For details and citation purposes see paper "Clustal W and Clustal X version 
- 2.0", Larkin M., et al. Bioinformatics 2007 23(21):2947-2948

Modified: trunk/packages/clustalx/trunk/debian/copyright
===================================================================
--- trunk/packages/clustalx/trunk/debian/copyright	2009-10-14 09:54:04 UTC (rev 4207)
+++ trunk/packages/clustalx/trunk/debian/copyright	2009-10-14 10:25:32 UTC (rev 4208)
@@ -1,7 +1,7 @@
 X-Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat
 X-Debianized-By: Stephane Bortzmeyer <bortzmeyer at debian.org>
 X-Debianized-Date: Fri, 28 Aug 1998 16:09:48 +0200
-X-Source-Downloaded-From: ftp://ftp.ebi.ac.uk/pub/software/clustalw2
+X-Source-Downloaded-From: http://www.clustal.org/download/current/clustalx-2.0.12.tar.gz
 X-Upstream-Author: Des Higgins, Julie Thompson and Toby Gibson
 
 Files: debian/*

Added: trunk/packages/clustalx/trunk/debian/patches/hardcode-accessory-file-locations.patch
===================================================================
--- trunk/packages/clustalx/trunk/debian/patches/hardcode-accessory-file-locations.patch	                        (rev 0)
+++ trunk/packages/clustalx/trunk/debian/patches/hardcode-accessory-file-locations.patch	2009-10-14 10:25:32 UTC (rev 4208)
@@ -0,0 +1,26 @@
+--- clustalx-2.0.12.orig/ClustalQtParams.h
++++ clustalx-2.0.12/ClustalQtParams.h
+@@ -13,9 +13,9 @@
+ #include "clustalW/alignment/Alignment.h"
+ #include <vector>
+ 
+-static QString psColorFile = "colprot.xml";
+-static QString psDNAFile = "coldna.xml";
+-static QString psPrintFile = "colprint.xml";
++static QString psColorFile = "/usr/share/clustalx/colprot.xml";
++static QString psDNAFile = "/usr/share/clustalx/coldna.xml";
++static QString psPrintFile = "/usr/share/clustalx/colprint.xml";
+ 
+ static const int BlackAndWhite = 1;
+ static const int ColorsBackGround = 2;
+--- clustalx-2.0.12.orig/HelpDisplayWidget.cpp
++++ clustalx-2.0.12/HelpDisplayWidget.cpp
+@@ -19,7 +19,7 @@
+ #include <QtGui>
+ #include "Resources.h"
+ 
+-const string HelpDisplayWidget::helpFileName = "clustalx.hlp";
++const string HelpDisplayWidget::helpFileName = "/usr/share/clustalx/clustalx.hlp";
+ 
+ HelpDisplayWidget::HelpDisplayWidget(char helpPointer)
+ {

Added: trunk/packages/clustalx/trunk/debian/patches/series
===================================================================
--- trunk/packages/clustalx/trunk/debian/patches/series	                        (rev 0)
+++ trunk/packages/clustalx/trunk/debian/patches/series	2009-10-14 10:25:32 UTC (rev 4208)
@@ -0,0 +1 @@
+hardcode-accessory-file-locations.patch

Modified: trunk/packages/clustalx/trunk/debian/rules
===================================================================
--- trunk/packages/clustalx/trunk/debian/rules	2009-10-14 09:54:04 UTC (rev 4207)
+++ trunk/packages/clustalx/trunk/debian/rules	2009-10-14 10:25:32 UTC (rev 4208)
@@ -3,48 +3,21 @@
 include /usr/share/quilt/quilt.make
 
 build: build-stamp
-build-stamp:
+build-stamp: patch
 	dh_testdir
 	qmake-qt4
-	$(MAKE)
-	# no longer required?
-	#mv clustalQtcurrent clustalx
-	touch build-stamp
+	dh build
 
-clean:
-	dh_testdir
-	dh_testroot
-	[ ! -f Makefile ] || $(MAKE) distclean
-	dh_clean build-stamp
+clean: unpatch
+	dh clean
 
 install:
 install: build
-	dh_testdir
-	dh_testroot
-	dh_clean -k
-	dh_installdirs
-	dh_install
+	dh install
 
 # Build architecture-dependent files here.
 binary-arch: build install
-	dh_testdir
-	dh_testroot
-	dh_installdocs
-	dh_installexamples
-	dh_installmenu
-	dh_desktop
-	dh_installmime
-	dh_installman
-	dh_installchangelogs
-	dh_strip
-	dh_link
-	dh_compress
-	dh_fixperms
-	dh_installdeb
-	dh_shlibdeps
-	dh_gencontrol
-	dh_md5sums
-	dh_builddeb
+	dh binary-arch
 
 binary: binary-arch
 binary-indep: # does nothing

Added: trunk/packages/clustalx/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/clustalx/trunk/debian/upstream-metadata.yaml	                        (rev 0)
+++ trunk/packages/clustalx/trunk/debian/upstream-metadata.yaml	2009-10-14 10:25:32 UTC (rev 4208)
@@ -0,0 +1,20 @@
+Bugs: http://bioinf.ucd.ie/bugzilla/buglist.cgi?quicksearch=clustal
+Commercial: http://www.clustal.org/download/LICENSE
+Contact: clustalw at ucd.ie
+DOI: 10.1093/bioinformatics/btm404
+Homepage: http://www.clustal.org/
+PubMed: 17846036
+Reference: |
+ @article{M.A.Larkin11012007,
+ author = {Larkin, M.A. and Blackshields, G. and Brown, N.P. and Chenna, R. and McGettigan, P.A. and McWilliam, H. and Valentin, F. and Wallace, I.M. and Wilm, A. and Lopez, R. and Thompson, J.D. and Gibson, T.J. and Higgins, D.G.},
+ title = {{Clustal W and Clustal X version 2.0}},
+ journal = {Bioinformatics},
+ volume = {23},
+ number = {21},
+ pages = {2947-2948},
+ doi = {10.1093/bioinformatics/btm404},
+ year = {2007},
+ },
+ URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/21/2947},
+ eprint = {http://bioinformatics.oxfordjournals.org/cgi/reprint/23/21/2947.pdf}
+ }

Modified: trunk/packages/clustalx/trunk/debian/watch
===================================================================
--- trunk/packages/clustalx/trunk/debian/watch	2009-10-14 09:54:04 UTC (rev 4207)
+++ trunk/packages/clustalx/trunk/debian/watch	2009-10-14 10:25:32 UTC (rev 4208)
@@ -1,2 +1,2 @@
 version=3
-ftp://ftp.ebi.ac.uk/pub/software/clustalw2/clustalx-(.*)-src\.tar\.gz
+http://www.clustal.org/download/current/clustalx-([\.\d]*).tar.gz

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