Commit b891ee83 authored by Leo Gordon's avatar Leo Gordon
Browse files

more doc

parent e0e4e7b6
......@@ -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
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