[med-svn] r5482 - in trunk/packages/clustalw/trunk/debian: . source

[Andreas Tille]

Author: tille
Date: 2010-11-24 13:20:17 +0000 (Wed, 24 Nov 2010)
New Revision: 5482

Added:
   trunk/packages/clustalw/trunk/debian/source/
   trunk/packages/clustalw/trunk/debian/source/format
Removed:
   trunk/packages/clustalw/trunk/debian/patches/
Modified:
   trunk/packages/clustalw/trunk/debian/CHANGELOG.upstream
   trunk/packages/clustalw/trunk/debian/changelog
   trunk/packages/clustalw/trunk/debian/control
   trunk/packages/clustalw/trunk/debian/rules
Log:
New upstream version; adapted packaging to current standards in Debian Med


Modified: trunk/packages/clustalw/trunk/debian/CHANGELOG.upstream
===================================================================
--- trunk/packages/clustalw/trunk/debian/CHANGELOG.upstream	2010-11-24 12:52:08 UTC (rev 5481)
+++ trunk/packages/clustalw/trunk/debian/CHANGELOG.upstream	2010-11-24 13:20:17 UTC (rev 5482)
@@ -1,4 +1,32 @@
 ----------------------------------------------------------------------
+Version 2.1
+----------------------------------------------------------------------
+* Fixed bug 196 "clustalx: user feedback about use of secondary structure 
+  printed to console" - secondary structure is now used if specified
+  in Alignment -> Alignment Parameters -> Secondary Structure Parameters
+  UserParameters->getGui() should be used when ClustalW code needs to 
+  know if a function has been called from ClustalX
+  
+* Fixed bug 204 "Nexus alignment format contain invalid line" - the amino
+  acid alphabet line has been removed
+
+* Missing/corrupted file names in ClustalX status messages have been
+  fixed
+  
+* Fixed bug 175 "msf/pileup files cannot be read if sequences names are 
+  all numbers" - this happened if a line such as
+528244          .......... .......... .......... .......... .......... 
+  was present in the first block of the file  
+  
+* Fixed bug 192 "Alignment in Phylip Format broken for big Alignments"
+
+* Fixed bug 198 "Warning about divergent sequences gets printed to 
+  console in ClustalX"
+  
+* Fixed bug 151 "clustalx doesn't switch to profile alignment mode when 
+  profile12 is given on cmdline"
+
+----------------------------------------------------------------------
 Version 2.0.12
 ----------------------------------------------------------------------
 
@@ -247,3 +275,4 @@
 * Fixed bug 91
 Clustalw2.0 now handles pseudo-FASTA/MoST format files. Strips out
 numbers and spaces.
+

Modified: trunk/packages/clustalw/trunk/debian/changelog
===================================================================
--- trunk/packages/clustalw/trunk/debian/changelog	2010-11-24 12:52:08 UTC (rev 5481)
+++ trunk/packages/clustalw/trunk/debian/changelog	2010-11-24 13:20:17 UTC (rev 5482)
@@ -1,3 +1,14 @@
+clustalw (2.1-1) unstable; urgency=low
+
+  * New upstream version
+  * Added myself to uploaders
+  * Standards-Version: 3.9.1 (no changes needed)
+  * debian/rules: added get-upstream-changelog target and used
+    it to obtain upstream changelog in debian/CHANGELOG.upstream
+  * debian/source/format: 3.0 (quilt)
+
+ -- Andreas Tille <tille at debian.org>  Wed, 24 Nov 2010 14:07:24 +0100
+
 clustalw (2.0.12-1) unstable; urgency=low
 
   * New upstream release fixing many bugs

Modified: trunk/packages/clustalw/trunk/debian/control
===================================================================
--- trunk/packages/clustalw/trunk/debian/control	2010-11-24 12:52:08 UTC (rev 5481)
+++ trunk/packages/clustalw/trunk/debian/control	2010-11-24 13:20:17 UTC (rev 5482)
@@ -3,9 +3,10 @@
 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 <plessy at debian.org>
+Uploaders: Steffen Moeller <moeller at debian.org>, Charles Plessy <plessy at debian.org>,
+ Andreas Tille <tille at debian.org>
 Build-Depends: debhelper (>= 7), cdbs, autotools-dev
-Standards-Version: 3.8.3
+Standards-Version: 3.9.1
 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/clustalw/trunk/?rev=0&sc=0
 Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/clustalw/trunk/
 XS-Autobuild: yes

Modified: trunk/packages/clustalw/trunk/debian/rules
===================================================================
--- trunk/packages/clustalw/trunk/debian/rules	2010-11-24 12:52:08 UTC (rev 5481)
+++ trunk/packages/clustalw/trunk/debian/rules	2010-11-24 13:20:17 UTC (rev 5482)
@@ -12,3 +12,8 @@
 
 	# That is a bit ugly and should be better investigated.
 	rmdir $(CURDIR)/debian/clustalw/usr/share/aclocal/
+
+get-upstream-changelog:
+	# Get upstream changelog
+	cd debian; wget -N --output-document=CHANGELOG.upstream http://www.clustal.org/download/current/CHANGELOG
+

Added: trunk/packages/clustalw/trunk/debian/source/format
===================================================================
--- trunk/packages/clustalw/trunk/debian/source/format	                        (rev 0)
+++ trunk/packages/clustalw/trunk/debian/source/format	2010-11-24 13:20:17 UTC (rev 5482)
@@ -0,0 +1 @@
+3.0 (quilt)