[med-svn] r5484 - trunk/packages/clustalx/trunk/debian

[Andreas Tille]

Author: tille
Date: 2010-11-24 13:34:23 +0000 (Wed, 24 Nov 2010)
New Revision: 5484

Modified:
   trunk/packages/clustalx/trunk/debian/CHANGELOG.upstream
   trunk/packages/clustalx/trunk/debian/changelog
   trunk/packages/clustalx/trunk/debian/rules
Log:
New upstream version


Modified: trunk/packages/clustalx/trunk/debian/CHANGELOG.upstream
===================================================================
--- trunk/packages/clustalx/trunk/debian/CHANGELOG.upstream	2010-11-24 13:21:50 UTC (rev 5483)
+++ trunk/packages/clustalx/trunk/debian/CHANGELOG.upstream	2010-11-24 13:34:23 UTC (rev 5484)
@@ -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/clustalx/trunk/debian/changelog
===================================================================
--- trunk/packages/clustalx/trunk/debian/changelog	2010-11-24 13:21:50 UTC (rev 5483)
+++ trunk/packages/clustalx/trunk/debian/changelog	2010-11-24 13:34:23 UTC (rev 5484)
@@ -1,3 +1,11 @@
+clustalx (2.1-1) unstable; urgency=low
+
+  * New upstream version
+  * debian/rules: added get-upstream-changelog target and used
+    it to obtain upstream changelog in debian/CHANGELOG.upstream
+
+ -- Andreas Tille <tille at debian.org>  Wed, 24 Nov 2010 14:24:10 +0100
+
 clustalx (2.0.12-3) unstable; urgency=low
 
   * debian/clustalx.desktop: Fixed typo

Modified: trunk/packages/clustalx/trunk/debian/rules
===================================================================
--- trunk/packages/clustalx/trunk/debian/rules	2010-11-24 13:21:50 UTC (rev 5483)
+++ trunk/packages/clustalx/trunk/debian/rules	2010-11-24 13:34:23 UTC (rev 5484)
@@ -26,4 +26,8 @@
 override_dh_installchangelogs:
 	dh_installchangelogs debian/CHANGELOG.upstream
 
+get-upstream-changelog:
+	# Get upstream changelog
+	cd debian; wget -N --output-document=CHANGELOG.upstream http://www.clustal.org/download/current/CHANGELOG
+
 .PHONY: build clean binary-arch binary install