[med-svn] r10023 - in trunk/packages/gmod/chado/trunk/debian: . patches

[Olivier Sallou]

Author: osallou
Date: 2012-03-19 08:54:49 +0000 (Mon, 19 Mar 2012)
New Revision: 10023

Added:
   trunk/packages/gmod/chado/trunk/debian/patches/remove_pl_extension.patch
Modified:
   trunk/packages/gmod/chado/trunk/debian/changelog
   trunk/packages/gmod/chado/trunk/debian/control
   trunk/packages/gmod/chado/trunk/debian/patches/series
Log:
add patch to call binary deps without perl extension

Modified: trunk/packages/gmod/chado/trunk/debian/changelog
===================================================================
--- trunk/packages/gmod/chado/trunk/debian/changelog	2012-03-19 08:53:48 UTC (rev 10022)
+++ trunk/packages/gmod/chado/trunk/debian/changelog	2012-03-19 08:54:49 UTC (rev 10023)
@@ -1,3 +1,10 @@
+libchado-perl (1.22-3) unstable; urgency=low
+
+  * debian/patches/remove_pl_extension.patch:
+    - add patch to use libdbix-dbstag-perl binary without extension 
+
+ -- Olivier Sallou <osallou at debian.org>  Mon, 19 Mar 2012 09:26:00 +0100
+
 libchado-perl (1.22-2) unstable; urgency=low
 
   [Olivier Sallou]

Modified: trunk/packages/gmod/chado/trunk/debian/control
===================================================================
--- trunk/packages/gmod/chado/trunk/debian/control	2012-03-19 08:53:48 UTC (rev 10022)
+++ trunk/packages/gmod/chado/trunk/debian/control	2012-03-19 08:54:49 UTC (rev 10023)
@@ -2,7 +2,7 @@
 Section: perl
 Priority: optional
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Scott Cain <scain at cpan.org>, Steffen Moeller <moeller at debian.org>, Olivier Sallou <olivier.sallou at irisa.fr>
+Uploaders: Scott Cain <scain at cpan.org>, Steffen Moeller <moeller at debian.org>, Olivier Sallou <osallou at debian.org>
 DM-Upload-Allowed: yes
 Build-Depends: debhelper (>= 8)
 Build-Depends-Indep: perl, libclass-dbi-pg-perl, libxml-libxslt-perl, liblog-log4perl-perl,

Added: trunk/packages/gmod/chado/trunk/debian/patches/remove_pl_extension.patch
===================================================================
--- trunk/packages/gmod/chado/trunk/debian/patches/remove_pl_extension.patch	                        (rev 0)
+++ trunk/packages/gmod/chado/trunk/debian/patches/remove_pl_extension.patch	2012-03-19 08:54:49 UTC (rev 10023)
@@ -0,0 +1,48 @@
+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 at 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')
+         );
+ 

Modified: trunk/packages/gmod/chado/trunk/debian/patches/series
===================================================================
--- trunk/packages/gmod/chado/trunk/debian/patches/series	2012-03-19 08:53:48 UTC (rev 10022)
+++ trunk/packages/gmod/chado/trunk/debian/patches/series	2012-03-19 08:54:49 UTC (rev 10023)
@@ -3,3 +3,4 @@
 fix_spelling_manpage
 fix_manpages
 setBinPathForBuilder
+remove_pl_extension.patch