[med-svn] r850 - in trunk/packages/t-coffee/trunk/debian: . patches

[charles-guest at alioth.debian.org]

Author: charles-guest
Date: 2007-11-23 02:41:08 +0000 (Fri, 23 Nov 2007)
New Revision: 850

Added:
   trunk/packages/t-coffee/trunk/debian/patches/dmcoffee.patch
Modified:
   trunk/packages/t-coffee/trunk/debian/changelog
   trunk/packages/t-coffee/trunk/debian/patches/series
Log:
dmcoffee works out of the box now

Modified: trunk/packages/t-coffee/trunk/debian/changelog
===================================================================
--- trunk/packages/t-coffee/trunk/debian/changelog	2007-11-23 02:11:29 UTC (rev 849)
+++ trunk/packages/t-coffee/trunk/debian/changelog	2007-11-23 02:41:08 UTC (rev 850)
@@ -1,8 +1,11 @@
-t-coffee (5.05-2) UNRELEASED; urgency=low
+t-coffee (5.31-1) UNRELEASED; urgency=low
 
+  * New upstream version.
   * Debian menu transition: updated debian/t-coffee-doc.doc-base.
+  * debian/patches/dmcoffee.patch: to make dmcoffee work
+    out of the box.
 
- -- Charles Plessy <charles-debian-nospam at plessy.org>  Mon, 08 Oct 2007 16:22:43 +0900
+ -- Charles Plessy <charles-debian-nospam at plessy.org>  Fri, 23 Nov 2007 11:38:49 +0900
 
 t-coffee (5.05-1) unstable; urgency=low
 

Added: trunk/packages/t-coffee/trunk/debian/patches/dmcoffee.patch
===================================================================
--- trunk/packages/t-coffee/trunk/debian/patches/dmcoffee.patch	                        (rev 0)
+++ trunk/packages/t-coffee/trunk/debian/patches/dmcoffee.patch	2007-11-23 02:41:08 UTC (rev 850)
@@ -0,0 +1,41 @@
+If we do not hardcode these paths, dmcoffee will not work out of the box.
+Index: T-COFFEE_distribution_Version_5.31/t_coffee_source/util_constraints_list.c
+===================================================================
+--- T-COFFEE_distribution_Version_5.31.orig/t_coffee_source/util_constraints_list.c
++++ T-COFFEE_distribution_Version_5.31/t_coffee_source/util_constraints_list.c
+@@ -1306,7 +1306,7 @@
+ 	  fprintf ( fp, "EXECUTABLE %s\n",(getenv("DIALIGNT_4_TCOFFEE"))?getenv("DIALIGNT_4_TCOFFEE"):DIALIGNT_4_TCOFFEE );
+ 	  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-t \n", get_mcoffee_4_tcoffee());
+ 	  fprintf ( fp, "IN_FLAG    &bnsp\n");
+ 	  fprintf ( fp, "OUT_FLAG   &bnsp\n");
+ 	  fprintf ( fp, "PARAM      >/dev/null&bnsp2>/dev/null\n"); 
+@@ -1324,7 +1324,7 @@
+ 	  fprintf ( fp, "EXECUTABLE %s\n",(getenv("DIALIGNT_4_TCOFFEE"))?getenv("DIALIGNT_4_TCOFFEE"):DIALIGNT_4_TCOFFEE );
+ 	  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-t \n", get_mcoffee_4_tcoffee());
+ 	  fprintf ( fp, "IN_FLAG    &bnsp\n");
+ 	  fprintf ( fp, "OUT_FLAG   &bnsp\n");
+ 	  fprintf ( fp, "PARAM      >/dev/null&bnsp2>/dev/null\n"); 
+@@ -1346,7 +1346,7 @@
+ 	  fprintf ( fp, "PARAM1 -toupper \n");
+ 	  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, "SEQ_TYPE   S\n");
+ 	  
+ 	  vfclose (fp); 	   
+@@ -1364,7 +1364,7 @@
+ 	  fprintf ( fp, "PARAM1 -toupper \n");
+ 	  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, "SEQ_TYPE   S\n");
+ 	  
+ 	  vfclose (fp); 	   

Modified: trunk/packages/t-coffee/trunk/debian/patches/series
===================================================================
--- trunk/packages/t-coffee/trunk/debian/patches/series	2007-11-23 02:11:29 UTC (rev 849)
+++ trunk/packages/t-coffee/trunk/debian/patches/series	2007-11-23 02:41:08 UTC (rev 850)
@@ -1,2 +1,3 @@
+dmcoffee.patch
 manpage.patch
 Makefiles.patch