[med-svn] r8781 - trunk/packages/gmod/chado/trunk/debian/patches

[olivier sallou]

Author: osallou-guest
Date: 2011-12-06 09:59:18 +0000 (Tue, 06 Dec 2011)
New Revision: 8781

Added:
   trunk/packages/gmod/chado/trunk/debian/patches/setBinPathForBuilder
Modified:
   trunk/packages/gmod/chado/trunk/debian/patches/series
Log:
fix binary path in builder

Modified: trunk/packages/gmod/chado/trunk/debian/patches/series
===================================================================
--- trunk/packages/gmod/chado/trunk/debian/patches/series	2011-12-06 09:04:22 UTC (rev 8780)
+++ trunk/packages/gmod/chado/trunk/debian/patches/series	2011-12-06 09:59:18 UTC (rev 8781)
@@ -2,3 +2,4 @@
 force_SIMPLE
 fix_spelling_manpage
 fix_manpages
+setBinPathForBuilder

Added: trunk/packages/gmod/chado/trunk/debian/patches/setBinPathForBuilder
===================================================================
--- trunk/packages/gmod/chado/trunk/debian/patches/setBinPathForBuilder	                        (rev 0)
+++ trunk/packages/gmod/chado/trunk/debian/patches/setBinPathForBuilder	2011-12-06 09:59:18 UTC (rev 8781)
@@ -0,0 +1,31 @@
+Author: Olivier Sallou <olivier.sallou at irisa.fr>
+Subject: set binary path
+Last-Updated: 06/12/11
+Description:
+update path for binaries to match gmod chado installation
+--- a/lib/Bio/Chado/Builder.pm
++++ b/lib/Bio/Chado/Builder.pm
+@@ -96,12 +96,12 @@
+       my $result = `bin/gmod_add_organism.pl --name_only --common_name $db_org`;
+       unless ($result) {
+           print "Adding $db_org to the database...\n";
+-          system('bin/gmod_add_organism.pl','--common_name',$db_org);
++          system('/usr/share/gmod/chado/bin/gmod_add_organism.pl','--common_name',$db_org);
+       }  
+   } 
+ 
+   #set the chado schema version in the database
+-  system("gmod_chado_properties.pl --dbprofile $db_name --force --version $schema_version"); 
++  system("/usr/share/gmod/chado/bin/gmod_chado_properties.pl --dbprofile $db_name --force --version $schema_version"); 
+ 
+ }
+ 
+@@ -133,7 +133,7 @@
+ 
+   if (looks_like_number($version) and $version < $schema_version) {
+     print "Attempting schema update.\n";
+-    system("gmod_update_chado.pl --dbprofile $db_name");
++    system("/usr/share/gmod/chado/bin/gmod_update_chado.pl --dbprofile $db_name");
+   } 
+   elsif (looks_like_number($version) and $version >= $schema_version) {
+     print "No update necessary.\n";