Added an interface in Meadow to deregister agents, i.e. beekeepers, so that...

Added an interface in Meadow to deregister agents, i.e. beekeepers, so that they can run local workers

This allows to "submit" beekeeper to a compute node

modules/Bio/EnsEMBL/Hive/Beekeeper.pm

@@ -56,12 +56,14 @@ sub new_from_Valley {
     my ($class, $valley, @args) = @_;
 
     my ($meadow, $pid, $meadow_host, $meadow_user) = $valley->whereami;
-    unless($meadow->type eq 'LOCAL') {
+    unless($meadow->can('deregister_local_process')) {
         die "beekeeper.pl detected it has been itself submitted to '".$meadow->type."/".$meadow->cached_name."', but this mode of operation is not supported.\n"
            ."Please just run beekeeper.pl on a farm head node, preferably from under a 'screen' session.\n";
     }
+    $meadow->deregister_local_process();
 
     return $class->SUPER::new(
+        'meadow'        => $meadow_host,
         'meadow_host'   => $meadow_host,
         'meadow_user'   => $meadow_user,
         'process_id'    => $pid,
@@ -141,6 +143,13 @@ sub meadow_signatures {
 
 # --------------------------------- Convenient methods ---------------------------------------
 
+sub meadow {
+    my $self = shift;
+    $self->{'_meadow'} = shift if(@_);
+    return $self->{'_meadow'};
+}
+
+
 =head2 set_cause_of_death
 
   Example     : $beekeeper->set_cause_of_death('LOOP_LIMIT');

modules/Bio/EnsEMBL/Hive/Meadow/LOCAL.pm

@@ -50,6 +50,7 @@ sub get_current_worker_process_id {
     return $$;
 }
 
+sub deregister_local_process {}   # Nothing to do
 
 sub _command_line_to_extract_all_running_workers {
     my ($self) = @_;

modules/Bio/EnsEMBL/Hive/Meadow/LSF.pm

@@ -72,6 +72,14 @@ sub get_current_worker_process_id {
 }
 
 
+sub deregister_local_process {
+    my ($self) = @_;
+
+    delete $ENV{'LSB_JOBID'};
+    delete $ENV{'LSB_JOBINDEX'};
+}
+
+
 sub status_of_all_our_workers { # returns an arrayref
     my $self                        = shift @_;
     my $meadow_users_of_interest    = shift @_;