[med-svn] r1945 - trunk/packages/t-coffee/trunk/debian/patches

[hanska-guest at alioth.debian.org]

Author: hanska-guest
Date: 2008-05-31 17:27:29 +0000 (Sat, 31 May 2008)
New Revision: 1945

Modified:
   trunk/packages/t-coffee/trunk/debian/patches/Makefiles.patch
   trunk/packages/t-coffee/trunk/debian/patches/dmcoffee.patch
   trunk/packages/t-coffee/trunk/debian/patches/unicode.diff
Log:
Patches updated:
- some stylistic changes to reduce number of difflines
- fixing some fprintf()s


Modified: trunk/packages/t-coffee/trunk/debian/patches/Makefiles.patch
===================================================================
--- trunk/packages/t-coffee/trunk/debian/patches/Makefiles.patch	2008-05-31 17:20:16 UTC (rev 1944)
+++ trunk/packages/t-coffee/trunk/debian/patches/Makefiles.patch	2008-05-31 17:27:29 UTC (rev 1945)
@@ -1,7 +1,5 @@
-Index: t-coffee-5.05/t_coffee_source/makefile
-===================================================================
---- t-coffee-5.05.orig/t_coffee_source/makefile	2007-09-24 15:26:47.028236512 +0200
-+++ t-coffee-5.05/t_coffee_source/makefile	2007-09-24 15:27:26.136696266 +0200
+--- t-coffee-5.68.orig/t_coffee_source/makefile
++++ t-coffee-5.68/t_coffee_source/makefile
 @@ -6,4 +6,4 @@
  all:  t_coffee
  

Modified: trunk/packages/t-coffee/trunk/debian/patches/dmcoffee.patch
===================================================================
--- trunk/packages/t-coffee/trunk/debian/patches/dmcoffee.patch	2008-05-31 17:20:16 UTC (rev 1944)
+++ trunk/packages/t-coffee/trunk/debian/patches/dmcoffee.patch	2008-05-31 17:27:29 UTC (rev 1945)
@@ -1,6 +1,6 @@
 If we do not hardcode these paths, dmcoffee will not work out of the box.
---- a/t_coffee_source/util_constraints_list.c
-+++ b/t_coffee_source/util_constraints_list.c
+--- t-coffee-5.68.orig/t_coffee_source/util_constraints_list.c
++++ t-coffee-5.68/t_coffee_source/util_constraints_list.c
 @@ -1368,13 +1368,13 @@
       else if ( lstrstr ( method, "dialignt_pair"))
          {
@@ -13,7 +13,7 @@
  	  fprintf ( fp, "ALN_MODE   pairwise\n");
  	  fprintf ( fp, "OUT_MODE   aln\n");
 -	  fprintf ( fp, "PARAM1 %s \n", get_mcoffee_4_tcoffee());
-+	  fprintf ( fp, "PARAM1 /usr/share/dialign-tx \n", get_mcoffee_4_tcoffee());
++	  fprintf ( fp, "PARAM1 /usr/share/dialign-tx \n");
  	  fprintf ( fp, "IN_FLAG    &bnsp\n");
  	  fprintf ( fp, "OUT_FLAG   &bnsp\n");
  	  fprintf ( fp, "PARAM      >/dev/null&bnsp2>/dev/null\n"); 
@@ -28,7 +28,7 @@
  	  fprintf ( fp, "ALN_MODE   multiple\n");
  	  fprintf ( fp, "OUT_MODE   aln\n");
 -	  fprintf ( fp, "PARAM1 %s \n", get_mcoffee_4_tcoffee());
-+	  fprintf ( fp, "PARAM1 /usr/share/dialign-tx \n", get_mcoffee_4_tcoffee());
++	  fprintf ( fp, "PARAM1 /usr/share/dialign-tx \n");
  	  fprintf ( fp, "IN_FLAG    &bnsp\n");
  	  fprintf ( fp, "OUT_FLAG   &bnsp\n");
  	  fprintf ( fp, "PARAM      >/dev/null&bnsp2>/dev/null\n"); 
@@ -37,7 +37,7 @@
  	  fprintf ( fp, "IN_FLAG    -read_fasta&bnsp\n");
  	  fprintf ( fp, "OUT_FLAG   -clustal&bnsp\n");
 -	  fprintf ( fp, "PARAM      %s/blosum80.mat&bnsp2>/dev/null\n", get_mcoffee_4_tcoffee()); 
-+	  fprintf ( fp, "PARAM      /usr/share/blosum80.mat&bnsp2>/dev/null\n", get_mcoffee_4_tcoffee()); 
++	  fprintf ( fp, "PARAM      /usr/share/blosum80.mat&bnsp2>/dev/null\n");
  	  fprintf ( fp, "SEQ_TYPE   S\n");
  	  
  	  vfclose (fp); 	   
@@ -46,7 +46,7 @@
  	  fprintf ( fp, "IN_FLAG    -read_fasta&bnsp\n");
  	  fprintf ( fp, "OUT_FLAG   -clustal&bnsp\n");
 -	  fprintf ( fp, "PARAM      %s/blosum80.mat&bnsp2>/dev/null\n", get_mcoffee_4_tcoffee()); 
-+	  fprintf ( fp, "PARAM      /usr/share/poa/blosum80.mat&bnsp2>/dev/null\n", get_mcoffee_4_tcoffee()); 
++	  fprintf ( fp, "PARAM      /usr/share/poa/blosum80.mat&bnsp2>/dev/null\n");
  	  fprintf ( fp, "SEQ_TYPE   S\n");
  	  
  	  vfclose (fp); 	   

Modified: trunk/packages/t-coffee/trunk/debian/patches/unicode.diff
===================================================================
--- trunk/packages/t-coffee/trunk/debian/patches/unicode.diff	2008-05-31 17:20:16 UTC (rev 1944)
+++ trunk/packages/t-coffee/trunk/debian/patches/unicode.diff	2008-05-31 17:27:29 UTC (rev 1945)
@@ -1,5 +1,5 @@
---- a/doc/t_coffee_technical.txt
-+++ b/doc/t_coffee_technical.txt
+--- t-coffee-5.68.orig/doc/t_coffee_technical.txt
++++ t-coffee-5.68/doc/t_coffee_technical.txt
 @@ -4,7 +4,7 @@
  Centre National De LA Recherche scientifique (France)
  
@@ -36,8 +36,8 @@
         Default: -type=<automatically set>
  
         This flag sets the type of the sequences. If  omitted,  the  type  is
---- a/doc/t_coffee_tutorial.txt
-+++ b/doc/t_coffee_tutorial.txt
+--- t-coffee-5.68.orig/doc/t_coffee_tutorial.txt
++++ t-coffee-5.68/doc/t_coffee_tutorial.txt
 @@ -2,7 +2,7 @@
  T-coffee Tutorial