[med-svn] r5823 - trunk/packages/tm-align/trunk/debian

[Timothy Booth]

Author: tbooth-guest
Date: 2011-01-30 14:02:47 +0000 (Sun, 30 Jan 2011)
New Revision: 5823

Modified:
   trunk/packages/tm-align/trunk/debian/changelog
   trunk/packages/tm-align/trunk/debian/control
   trunk/packages/tm-align/trunk/debian/copyright
   trunk/packages/tm-align/trunk/debian/rules
Log:
Updated and some fixes at sprint


Modified: trunk/packages/tm-align/trunk/debian/changelog
===================================================================
--- trunk/packages/tm-align/trunk/debian/changelog	2011-01-30 13:59:12 UTC (rev 5822)
+++ trunk/packages/tm-align/trunk/debian/changelog	2011-01-30 14:02:47 UTC (rev 5823)
@@ -1,3 +1,34 @@
+tm-align (20110124-1) unstable; urgency=low
+
+  * New upstream version
+    - 2005/06/01: A small bug of two-point superposition was fixed.
+    - 2005/10/19: the program was reformed so that the alignment results
+                  are not dependent on the specific compilers.
+    - 2006/06/20: select 'A' if there is altLoc when reading PDB file.
+    - 2007/02/27: rotation matrix from Chain-1 to Chain-2 was added.
+    - 2007/04/18: added options with TM-score normalized by average
+                  length, shorter length, or longer length of two
+                  structures.
+    - 2007/05/23: added additional output file 'TM.sup_all' for showing
+                  all atoms while 'TM.sup' is only for aligned atoms
+    - 2007/09/19: added a new feature alignment to deal with the problem
+                  of aligning fractional structures (e.g. protein
+                  interfaces).
+    - 2007/10/16: A bug for irregular bond-length models was fixed.
+    - 2009/03/14: A new initial alignment was added and previous initial
+                  alignments are further enhanced. This change increased
+                  accuracy by 4% but increases CPU cost by 40%.
+    - 2009/08/20: A bug for asymmetry alignment result was fixed.
+    - 2010/08/02: A new RMSD matrix was used to remove obsolete
+                  statements. Staled subroutines were deleted.
+    - 2011/01/03: The length of pdb file names were extended to 500
+    - 2011/01/24: Fixed a bug on output file name created on 2011/01/03 
+  * Tweaked get-orig-source in rules to spot version in upstream file
+
+  * New standards version 3.9.4
+
+ -- Tim Booth <tbooth at ceh.ac.uk>  Sun, 30 Jan 2011 13:34:53 +0000
+
 tm-align (20050601-2) UNRELEASED; urgency=low
 
   * Updated to Standards-Version 3.7.3 (no changes needed)

Modified: trunk/packages/tm-align/trunk/debian/control
===================================================================
--- trunk/packages/tm-align/trunk/debian/control	2011-01-30 13:59:12 UTC (rev 5822)
+++ trunk/packages/tm-align/trunk/debian/control	2011-01-30 14:02:47 UTC (rev 5823)
@@ -3,9 +3,9 @@
 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>
+Uploaders: Steffen Moeller <moeller at debian.org>, Tim Booth <tbooth at ceh.ac.uk>
 Build-Depends: debhelper (>= 5), gfortran
-Standards-Version: 3.7.3
+Standards-Version: 3.9.4
 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/tm-align/trunk/?rev=0&sc=0
 Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/tm-align/trunk/
 Homepage: http://zhang.bioinformatics.ku.edu/TM-align/

Modified: trunk/packages/tm-align/trunk/debian/copyright
===================================================================
--- trunk/packages/tm-align/trunk/debian/copyright	2011-01-30 13:59:12 UTC (rev 5822)
+++ trunk/packages/tm-align/trunk/debian/copyright	2011-01-30 14:02:47 UTC (rev 5823)
@@ -9,9 +9,9 @@
     Jeffrey Skolnick
 
 
-right: 
+Copyright: 
 
-    Yang Zhang <yzhang at ku.edu>
+    2005-2011 Yang Zhang <yzhang at ku.edu>
     Jeffrey Skolnick
 
     The copyrights of the employing universities is still unclear,
@@ -21,6 +21,6 @@
 
     The program can be freely copied or modified or redistributed.
 
-The Debian packaging is (C) 2007, Steffen Moeller <moeller at debian.org> and
+The Debian packaging is (C) 2011, Steffen Moeller <moeller at debian.org> and
 is licensed under the GPL, see `/usr/share/common-licenses/GPL'.
 

Modified: trunk/packages/tm-align/trunk/debian/rules
===================================================================
--- trunk/packages/tm-align/trunk/debian/rules	2011-01-30 13:59:12 UTC (rev 5822)
+++ trunk/packages/tm-align/trunk/debian/rules	2011-01-30 14:02:47 UTC (rev 5823)
@@ -65,8 +65,8 @@
 
 get-orig-source:
 	mkdir tm-align-tmp
-	( cd tm-align-tmp && wget http://zhang.bioinformatics.ku.edu/TM-align/TMalign.f ) ; \
-	version=`grep -A1 history tm-align-tmp/TMalign.f | tail -1 | cut -f1 -d: | tr -d ' */'` ; \
+	( cd tm-align-tmp && wget http://zhanglab.ccmb.med.umich.edu/TM-align/TMalign.f ) ; \
+	version=`egrep '\*     [0-9]{4}/[0-9]{2}/[0-9]{2}: ' tm-align-20050601/TMalign.f | tail -n 1 | cut -f 1 -d : | sed 's/[* /]//g'` ; \
 	newname="tm-align-$$version" ;\
 	[ -d "$$newname" ] && rm -rf $$newname  ; \
 	mv tm-align-tmp $$newname ; \