more doc

scripts/runWorker.pl

@@ -37,14 +37,20 @@ my ($help, $host, $user, $pass, $dbname, $port, $adaptor, $url);
 my $reg_conf  = undef;
 my $reg_alias = 'hive';
 
-GetOptions('help'           => \$help,
-           'url=s'          => \$url,
+GetOptions(
+
+# Connection parameters:
            'conf=s'         => \$conf_file,
+           'regfile=s'      => \$reg_conf,
+           'regname=s'      => \$reg_alias,
+           'url=s'          => \$url,
            'host|dbhost=s'  => \$host,
            'port|dbport=i'  => \$port,
            'user|dbuser=s'  => \$user,
            'password|dbpass=s'  => \$pass,
            'database|dbname=s'  => \$dbname,
+
+# Job/Analysis control parameters:
            'job_id=i'       => \$self->{'job_id'},
            'analysis_id=i'  => \$self->{'analysis_id'},
            'logic_name=s'   => \$self->{'logic_name'},
@@ -57,12 +63,13 @@ GetOptions('help'           => \$help,
            'input_id=s'     => \$self->{'input_id'},
            'no_cleanup'     => \$self->{'no_global_cleanup'},
            'analysis_stats' => \$self->{'show_analysis_stats'},
-           'debug=i'        => \$self->{'debug'},
            'no_write'       => \$self->{'no_write'},
            'nowrite'        => \$self->{'no_write'},
-           'regfile=s'      => \$reg_conf,
-           'regname=s'      => \$reg_alias,
            'maximise_concurrency' => \$self->{'maximise_concurrency'},
+
+# Other commands
+           'help'           => \$help,
+           'debug=i'        => \$self->{'debug'},
           );
 
 $self->{'analysis_id'} = shift if(@_);
@@ -272,16 +279,20 @@ runWorker.pl [options]
 
 =head1 OPTIONS
 
-  -help                  : print this help\n";
+=head2 Connection parameters
+
+  -conf <path>           : config file describing db connection\n";
   -regfile <path>        : path to a Registry configuration file\n";
   -regname <string>      : species/alias name for the Hive DBAdaptor\n";
   -url <url string>      : url defining where database is located\n";
-  -conf <path>           : config file describing db connection\n";
-  -dbhost <machine>      : mysql database host <machine>\n";
-  -dbport <port#>        : mysql port number\n";
-  -dbname <name>         : mysql database <name>\n";
-  -dbuser <name>         : mysql connection user <name>\n";
-  -dbpass <pass>         : mysql connection password\n";
+  -host <machine>        : mysql database host <machine>\n";
+  -port <port#>          : mysql port number\n";
+  -user <name>           : mysql connection user <name>\n";
+  -password <pass>       : mysql connection password\n";
+  -database <name>       : mysql database <name>\n";
+
+=head2 Job/Analysis control parameters:
+
   -analysis_id <id>      : analysis_id in db\n";
   -logic_name <string>   : logic_name of analysis to make this worker\n";
   -batch_size <num>      : #jobs to claim at a time\n";
@@ -292,10 +303,14 @@ runWorker.pl [options]
   -pid <string>          : externally set process_id descriptor (e.g. lsf job_id, array_id)\n";
   -input_id <string>     : test input_id on specified analysis (analysis_id or logic_name)\n";
   -job_id <id>           : run specific job defined by analysis_job_id\n";
-  -debug <level>         : turn on debug messages at <level> \n";
   -analysis_stats        : show status of each analysis in hive\n";
   -no_cleanup            : don't perform global_cleanup when worker exits\n";
   -no_write              : don't write_output or auto_dataflow input_job\n";
 
+=head2 Other options:
+
+  -help                  : print this help\n";
+  -debug <level>         : turn on debug messages at <level> \n";
+
 =cut