[med-svn] r12734 - in trunk/packages/gmod/chado/trunk/debian: . patches

[Olivier Sallou]

Author: osallou
Date: 2013-01-03 10:36:04 +0000 (Thu, 03 Jan 2013)
New Revision: 12734

Modified:
   trunk/packages/gmod/chado/trunk/debian/changelog
   trunk/packages/gmod/chado/trunk/debian/patches/fix_perl_headers
   trunk/packages/gmod/chado/trunk/debian/patches/fix_spelling_manpage
   trunk/packages/gmod/chado/trunk/debian/patches/remove_pl_extension.patch
Log:
new upstream release, update patches

Modified: trunk/packages/gmod/chado/trunk/debian/changelog
===================================================================
--- trunk/packages/gmod/chado/trunk/debian/changelog	2013-01-03 10:24:39 UTC (rev 12733)
+++ trunk/packages/gmod/chado/trunk/debian/changelog	2013-01-03 10:36:04 UTC (rev 12734)
@@ -1,3 +1,9 @@
+libchado-perl (1.23-1) UNRELEASED; urgency=low
+
+  * New upstream release 
+
+ -- Olivier Sallou <osallou at debian.org>  Thu, 03 Jan 2013 11:24:54 +0100
+
 libchado-perl (1.22-4) unstable; urgency=low
 
   * debian/rules: fix permissions on gmod-chado file

Modified: trunk/packages/gmod/chado/trunk/debian/patches/fix_perl_headers
===================================================================
--- trunk/packages/gmod/chado/trunk/debian/patches/fix_perl_headers	2013-01-03 10:24:39 UTC (rev 12733)
+++ trunk/packages/gmod/chado/trunk/debian/patches/fix_perl_headers	2013-01-03 10:36:04 UTC (rev 12734)
@@ -26,38 +26,6 @@
  =head1 NAME
  
   load_taxonomy_cvterms.pl
---- a/modules/bin/makedep.pl
-+++ b/modules/bin/makedep.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/perl -w
-+#!/usr/bin/perl -w
- #
- # (c) Hilmar Lapp, hlapp at gmx.net, 2007.
- #
---- a/modules/bin/mk.pl
-+++ b/modules/bin/mk.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/perl
-+#!/usr/bin/perl
- 
- foreach $f (@ARGV) {
-     open(F,$f) || die("no $f");
---- a/modules/cv/bridges/bin/create-bridge-sql.pl
-+++ b/modules/cv/bridges/bin/create-bridge-sql.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/perl -w
-+#!/usr/bin/perl -w
- 
- use strict;
- use Data::Stag;
---- a/modules/sequence/bridges/bin/create-sofa-bridge.pl
-+++ b/modules/sequence/bridges/bin/create-sofa-bridge.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/perl -w
-+#!/usr/bin/perl -w
- 
- use strict;
- 
 --- a/load/bin/bulk_load_gff3.PLS
 +++ b/load/bin/bulk_load_gff3.PLS
 @@ -1,4 +1,4 @@
@@ -74,43 +42,3 @@
  
  use Config;
  use File::Basename qw(&basename &dirname);
---- a/soi/cgi/get_xml.pl
-+++ b/soi/cgi/get_xml.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/perl
-+#!/usr/bin/perl
- 
- BEGIN{
-     eval{do "config.pl"};
---- a/soi/scripts/dump_fasta.pl
-+++ b/soi/scripts/dump_fasta.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/perl 
-+#!/usr/bin/perl 
- 
- # generegion_soi.pl
- 
---- a/soi/scripts/dump_segment.pl
-+++ b/soi/scripts/dump_segment.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/perl
-+#!/usr/bin/perl
- 
- use FindBin qw($RealBin);
- use lib (($ENV{SOI_ROOT}) ||
---- a/soi/scripts/generegion.pl
-+++ b/soi/scripts/generegion.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/perl 
-+#!/usr/bin/perl 
- 
- # generegion_soi.pl
- 
---- a/soi/t/t_soi_parse_intersect
-+++ b/soi/t/t_soi_parse_intersect
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/perl -w
-+#!/usr/bin/perl -w
- 
- use lib "../";
- BEGIN {

Modified: trunk/packages/gmod/chado/trunk/debian/patches/fix_spelling_manpage
===================================================================
--- trunk/packages/gmod/chado/trunk/debian/patches/fix_spelling_manpage	2013-01-03 10:24:39 UTC (rev 12733)
+++ trunk/packages/gmod/chado/trunk/debian/patches/fix_spelling_manpage	2013-01-03 10:36:04 UTC (rev 12734)
@@ -151,7 +151,7 @@
     
 --- a/bin/gmod_gff3_preprocessor.pl
 +++ b/bin/gmod_gff3_preprocessor.pl
-@@ -23,7 +23,7 @@
+@@ -24,7 +24,7 @@
   --gfffile        The file containing GFF3 (optional, can read
                       from stdin)
   --outfile        The name kernel that will be used for naming result files
@@ -160,7 +160,7 @@
                       an argument to control splitting
   --onlysplit      Split the files and then quit (ie, don't sort)
   --nosplit        Don't split the files (ie, only sort)
-@@ -60,7 +60,7 @@
+@@ -61,7 +61,7 @@
  =head2 FASTA sequence
  
  If the GFF3 file contains FASTA sequence at the end, the sequence
@@ -182,7 +182,7 @@
  The script tries several options for identifying the accession in the
 --- a/bin/gmod_materialized_view_tool.pl
 +++ b/bin/gmod_materialized_view_tool.pl
-@@ -58,7 +58,7 @@
+@@ -59,7 +59,7 @@
  =item 1 Data syncronisity
  
  When normal tables are updated with values that are reflected in a MV,

Modified: trunk/packages/gmod/chado/trunk/debian/patches/remove_pl_extension.patch
===================================================================
--- trunk/packages/gmod/chado/trunk/debian/patches/remove_pl_extension.patch	2013-01-03 10:24:39 UTC (rev 12733)
+++ trunk/packages/gmod/chado/trunk/debian/patches/remove_pl_extension.patch	2013-01-03 10:36:04 UTC (rev 12734)
@@ -35,7 +35,7 @@
 -      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;
+       $stag_string .= " --password '$db_pass' " if $db_pass;
        $sys_call = join( ' ',
 @@ -387,7 +387,7 @@