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 <[email protected]> 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 @@ _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
