Subject: remove extension to call libdbix-dbstag-perl binaries
Description: libdbix-dbstag-perl binaries have perl extension removed,
 current scripts must call those binaries without extension too
Author: Olivier Sallou <osallou@debian.org>
Last-Updated: 19/03/2012
--- a/INSTALL.Chado
+++ b/INSTALL.Chado
@@ -360,17 +360,17 @@
 the Sequence Ontology (SO) is absolutely required for proper
 functioning of the database.  The commands to load an ontology are:
 
-      $  go2fmt.pl -p obo_text -w xml /path/to/obofile | \
+      $  go2fmt -p obo_text -w xml /path/to/obofile | \
             go-apply-xslt oboxml_to_chadoxml - > obo_text.xml
 
 This creates a chadoxml file of the obo file - then execute:
 
-     $ stag-storenode.pl \
+     $ stag-storenode \
      -d 'dbi:Pg:dbname=$CHADO_DB_NAME;host=$CHADO_DB_HOST;port=$CHADO_DB_PORT' \
      --user $CHADO_DB_USERNAME --password $CHADO_DB_PASSWORD obo_text.xml
 
 If you have other ontology format files, the commands are similar;
-consult the documentation for go2fmt.pl and go-apply-xslt for your
+consult the documentation for go2fmt and go-apply-xslt for your
 file format.
 
 It is a good idea at this point to make a back up of the database,
--- a/lib/Bio/Chado/Builder.pm
+++ b/lib/Bio/Chado/Builder.pm
@@ -350,7 +350,7 @@
       }
 
       # loading chadoxml
-      my $stag_string = "stag-storenode.pl -d 'dbi:Pg:dbname=$db_name;host=$db_host;port=$db_port'";
+      my $stag_string = "stag-storenode -d 'dbi:Pg:dbname=$db_name;host=$db_host;port=$db_port'";
       $stag_string .= " --user $db_user " if $db_user;
       $stag_string .= " --password $db_pass " if $db_pass;
       $sys_call = join( ' ',
@@ -387,7 +387,7 @@
 
 
         $sys_call = join( ' ',
-          "stag-storenode.pl -d 'dbi:Pg:dbname=$db_name;host=$db_host;port=$db_port'",
+          "stag-storenode -d 'dbi:Pg:dbname=$db_name;host=$db_host;port=$db_port'",
           catfile( $conf->{'path'}{'data'}, $deffile->{'local'}.'xml')
         );