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revision 1.1, Thu Aug 27 19:54:22 2009 UTC revision 1.2, Wed May 4 21:06:07 2011 UTC
# Line 81  Line 81 
81  C<out>I<User>C<.log>, respectively, where I<User> is the value of the  C<out>I<User>C<.log>, respectively, where I<User> is the value of the
82  B<user> option above.  B<user> option above.
83    
84    =item dbName
85    
86    SQL name of the target database. If not specified, the default name is used.
87    This option allows you to specify a backup or alternate database that can
88    be updated without compromising the main database.
89    
90    =item dbhost
91    
92    Name of the MySQL database host. If not specified, the default host is used.
93    This option is required when the default host is restricted to read-only
94    database access.
95    
96  =item help  =item help
97    
98  Display this command's parameters and options.  Display this command's parameters and options.
# Line 100  Line 112 
112  # Get the command-line options and parameters.  # Get the command-line options and parameters.
113  my ($options, @parameters) = StandardSetup([qw(FC Sapling) ],  my ($options, @parameters) = StandardSetup([qw(FC Sapling) ],
114                                             {                                             {
115                                                  dbName => ["", "if specified, the SQL name of the target database"],
116                                                  dbhost => ["", "if specified, the name of the target database"],
117                                                incomplete => ["", "if specified, incomplete genomes will be processed"],                                                incomplete => ["", "if specified, incomplete genomes will be processed"],
118                                                trace => ["2", "tracing level"],                                                trace => ["2", "tracing level"],
119                                                genomes => ["", "specific genomes to process"],                                                genomes => ["", "specific genomes to process"],
# Line 116  Line 130 
130  # Insure we catch errors.  # Insure we catch errors.
131  eval {  eval {
132      # Create the SAPLING object.      # Create the SAPLING object.
133      my $sap = ERDB::GetDatabase('Sapling');      my $sap = ERDB::GetDatabase('Sapling', undef, %$options);
134      # We'll put our list of genomes to process in here.      # We'll put our list of genomes to process in here.
135      my @genomes;      my @genomes;
136      # Check for genomes specified on the command line.      # Check for genomes specified on the command line.

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