let jobs decide whether it makes any sense to restart them or not

modules/Bio/EnsEMBL/Hive/AnalysisJob.pm

@@ -139,6 +139,8 @@ sub stderr_file {
   return $self->{'_stderr_file'};
 }
 
+##-----------------[indicators to the Worker]--------------------------------
+
 sub lethal_for_worker {     # Job should set this to 1 prior to dying (or before running code that might cause death - such as RunnableDB's compilation)
                             # if it believes that the state of things will not allow the Worker to continue normally.
                             # The Worker will check the flag and commit suicide if it is set to true.
@@ -147,6 +149,18 @@ sub lethal_for_worker {     # Job should set this to 1 prior to dying (or before
   return $self->{'_lethal_for_worker'};
 }
 
+sub transient_error {       # Job should set this to 1 prior to dying (or before running code that might cause death)
+                            # if it believes that it makes sense to retry the same job without any changes.
+                            # It may also set it to 0 prior to dying (or before running code that might cause death)
+                            # if it believes that there is no point in re-trying (say, if the parameters are wrong).
+                            # The Worker will check the flag and make necessary adjustments to the database state.
+  my $self = shift;
+  $self->{'_transient_error'} = shift if(@_);
+  return $self->{'_transient_error'};
+}
+
+##-----------------[/indicators to the Worker]-------------------------------
+
 sub print_job {
   my $self = shift;
   my $logic_name = $self->adaptor()

modules/Bio/EnsEMBL/Hive/Worker.pm

@@ -515,7 +515,11 @@ sub run
             my $job_status_when_died = $job->status();
             warn "Job with id=$job_id died in status '$job_status_when_died' for the following reason: $error_msg\n";
             $self->db()->get_JobErrorAdaptor()->register_error($job_id, $error_msg);
-            $job->update_status('FAILED');
+            if($job->transient_error) {
+                $job->adaptor->reset_dead_job_by_dbID($job_id);
+            } else {
+                $job->update_status('FAILED');
+            }
 
             if($job->lethal_for_worker) {    # either a compilation error or other job-sanctioned contamination
                 warn "Job's error has contaminated the Worker, so the Worker will now die\n";