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Author: Olivier Sallou <olivier.sallou@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
@@ -97,12 +97,12 @@
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 $schema_version");
}
@@ -134,7 +134,7 @@
if (looks_like_number($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";
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