make Valley into Configurable and move SubmitWorkersMax into Valley's context,...

make Valley into Configurable and move SubmitWorkersMax into Valley's context, because it is more "global" than a Meadow

hive_config.json

 {
+    "Valley" : {
+        "SubmitWorkersMax"  : 50,       # if set, provides a cut-off on the total number of workers (across all Meadows) submitted each iteration
+    },
     "Meadow" : {    # configure Meadow-specific options here:
         "LSF" : {
             "SubmissionOptions"         : "",   # general options that different Meadows can plug into the submission command
             "TotalRunningWorkersMax"    : 1000, # how many workers can be run on this Meadow in total
             "farm2" : {
-                "SubmitWorkersMax"  : 50,       # if set, provides a cut-off on the number of workers being submitted each iteration
+                "SubmissionOptions"  : "",      # submission options specific for LSF/farm2
             },
             "pcs4" : {
-                "SubmitWorkersMax"  : 30,
+                "SubmissionOptions"  : "",      # submission options specific for LSF/pcs4
             },
             "EBI" : {
-                "SubmitWorkersMax"  : 60,
+                "SubmissionOptions"  : "",      # submission options specific for LSF/EBI
             },
         },
         "LOCAL" : {

modules/Bio/EnsEMBL/Hive/Queen.pm

@@ -814,10 +814,10 @@ sub schedule_workers {
 sub schedule_workers_resync_if_necessary {
     my ($self, $valley, $analysis) = @_;
 
+    my $submit_limit        = $valley->config_get('SubmitWorkersMax');
     my $meadow              = $valley->get_current_meadow();
 
     my $pending_by_rc_name  = $meadow->can('count_pending_workers_by_rc_name') ? $meadow->count_pending_workers_by_rc_name() : {};
-    my $submit_limit        = $meadow->config_get('SubmitWorkersMax');
     my $meadow_limit        = ($meadow->can('count_running_workers') and defined($meadow->config_get('TotalRunningWorkersMax'))) ? $meadow->config_get('TotalRunningWorkersMax') - $meadow->count_running_workers : undef;
 
     my $available_submit_limit = ($submit_limit and $meadow_limit)

modules/Bio/EnsEMBL/Hive/Valley.pm

@@ -26,6 +26,8 @@ use warnings;
 use Sys::Hostname;
 use Bio::EnsEMBL::Hive::Utils ('find_submodules');
 
+use base ('Bio::EnsEMBL::Hive::Configurable');
+
 
 sub meadow_class_path {
 
@@ -38,6 +40,9 @@ sub new {
 
     my $self = bless {}, $class;
 
+    $self->config( $config );
+    $self->context( [ 'Valley' ] );
+
     my $amch = $self->available_meadow_hash( {} );
 
         # make sure modules are loaded and available ones are checked prior to setting the current one

scripts/beekeeper.pl

@@ -156,12 +156,12 @@ sub main {
 
     $meadow_type = 'LOCAL' if($local);
     my $valley = Bio::EnsEMBL::Hive::Valley->new( $config, $meadow_type, $pipeline_name );
+    $valley->config_set('SubmitWorkersMax', $submit_workers_max) if(defined $submit_workers_max);
 
     my $current_meadow = $valley->get_current_meadow();
     warn "Current meadow: ".$current_meadow->signature."\n\n";
 
     $current_meadow->config_set('TotalRunningWorkersMax', $total_running_workers_max) if(defined $total_running_workers_max);
-    $current_meadow->config_set('SubmitWorkersMax', $submit_workers_max) if(defined $submit_workers_max);
     $current_meadow->config_set('SubmissionOptions', $submission_options) if(defined $submission_options);
 
     if($reset_job_id) { $queen->reset_job_by_dbID_and_sync($reset_job_id); }