still working on docs

scripts/beekeeper.pl

 #!/usr/bin/env perl
 
-use warnings;
 use strict;
+use warnings;
 use DBI;
 use Getopt::Long;
 
@@ -61,8 +61,7 @@ sub main {
     $self->{'reg_name'}             = 'hive';
     $self->{'maximise_concurrency'} = 0;
 
-    GetOptions('help'              => \$help,
-
+    GetOptions(
                     # connection parameters
                'conf=s'            => \$conf_file,
                'regfile=s'         => \$self->{'reg_file'},
@@ -96,6 +95,7 @@ sub main {
                'maximise_concurrency' => \$self->{'maximise_concurrency'},
 
                     # other commands/options
+               'h|help'            => \$help,
                'sync'              => \$sync,
                'dead'              => \$check_for_dead,
                'killworker=i'      => \$kill_worker_id,
@@ -549,5 +549,9 @@ beekeeper.pl -url mysql://username:secret@hostname:port/long_mult_test -dead
   -reset_all_jobs_for_analysis <logic_name>
                          : reset jobs back to READY so it can be rerun
 
+=head1 CONTACT
+
+  Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
+
 =cut
 

scripts/cmd_hive.pl

-#!/usr/local/bin/perl -w
+#!/usr/bin/env perl
 
 # cmd_hive.pl
 #
 # Cared for by Albert Vilella <>
-#
 # Copyright Albert Vilella
 #
 # You may distribute this module under the same terms as perl itself
 
 use strict;
+use warnings;
 use DBI;
 use Getopt::Long;
 use Bio::EnsEMBL::Hive::DBSQL::DBAdaptor;
@@ -57,7 +57,7 @@ GetOptions(
            'hashed_b=s'        => \$self->{'hashed_b'},
 
 # other options:
-           'help'              => \$help,
+           'h|help'            => \$help,
            'debug=s'           => \$self->{'debug'},
 );
 
@@ -345,10 +345,9 @@ Always use single quotes to protect the values of -input_id and -parameters.
 
   -help                          : print this help
 
-=head1 AUTHORS
+=head1 CONTACT
 
- Albert Vilella
- Leo Gordon
+  Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
 
 =cut
 

scripts/runWorker.pl

 #!/usr/bin/env perl
 
-use warnings;
 use strict;
+use warnings;
 use DBI;
 use Getopt::Long;
 use Bio::EnsEMBL::Hive::DBSQL::DBAdaptor;
@@ -68,7 +68,7 @@ GetOptions(
            'maximise_concurrency' => \$self->{'maximise_concurrency'},
 
 # Other commands
-           'help'           => \$help,
+           'h|help'         => \$help,
            'debug=i'        => \$self->{'debug'},
           );
 
@@ -270,12 +270,25 @@ runWorker.pl
 
 =head1 DESCRIPTION
 
- runWorker.pl is an eHive script that does the work of a single Worker -
+ runWorker.pl is an eHive component script that does the work of a single Worker -
  specializes in one of the analyses and starts executing jobs of that analysis one-by-one or batch-by-batch.
 
-=head1 USAGE
+ Most of the functionality of the eHive is accessible via beekeeper.pl script,
+ but feel free to run the runWorker.pl if you think you know what you are doing :)
+
+=head1 USAGE EXAMPLES
+
+    # Run one local worker process in ehive_dbname and let the system pick up the analysis
+runWorker.pl --host=hostname --port=3306 --user=username --password=secret --database=ehive_dbname
 
-runWorker.pl [options]
+    # Run one local worker process in ehive_dbname and let the system pick up the analysis (another connection syntax)
+runWorker.pl -url mysql://username:secret@hostname:port/ehive_dbname
+
+    # Run one local worker process in ehive_dbname and specify the logic_name
+runWorker.pl -url mysql://username:secret@hostname:port/ehive_dbname -logic_name fast_blast
+
+    # Create a job outside the eHive to test the specified input_id
+runWorker.pl -url mysql://username:secret@hostname:port/ehive_dbname -logic_name fast_blast -input_id '{ "foo" => 1500 }'
 
 =head1 OPTIONS
 
@@ -312,5 +325,9 @@ runWorker.pl [options]
   -help                  : print this help
   -debug <level>         : turn on debug messages at <level>
 
+=head1 CONTACT
+
+  Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
+
 =cut