Applied wait constraints to all three calls. Could have refactored, but the...

Applied wait constraints to all three calls. Could have refactored, but the system calls are fiddly and I'll probably make more mistakes that way.

misc-scripts/xref_projection/submit_projections.pl

@@ -258,22 +258,26 @@ foreach my $species (keys %names_1_1) {
 }
 
 # 1:1
+
+my $last_name; # for waiting in queue
+
 foreach my $from (@execution_order) {
-    if (not exists($names_1_1{$from})) {next;}
     my $last_name; # for waiting in queue
+    if (not exists($names_1_1{$from})) {next;}
     foreach my $to (@{$names_1_1{$from}}) {
         my $o = "$dir/names_${from}_$to.out";
         my $e = "$dir/names_${from}_$to.err";
         my $n = substr("n_${from}_$to", 0, 10); # job name display limited to 10 chars
         my $all = ($from eq "human") ? "" : "--all_sources"; # non-human from species -> use all sources
         my $wait;
-        if ($last_name) { $wait = "-w 'done($last_name)'";}
+        if ($last_name) { $wait = "-w 'ended(${last_name}*)'";}
         
         print "Submitting name projection from $from to $to\n";
         system "bsub $bsub_opts -o $o -e $e -J $n $wait perl project_display_xrefs.pl $script_opts -from $from -to $to -names -no_database $all\n";
-        $last_name = $n;
     }
+    $last_name = "n_".$from;
 }
+$last_name = "";
 
 print "Deleting projected names (one to many)\n";
 foreach my $from (keys %names_1_many) {
@@ -289,11 +293,18 @@ foreach my $from (@execution_order) {
         my $o = "$dir/names_${from}_$to.out";        
         my $e = "$dir/names_${from}_$to.err";
         my $n = substr("n_${from}_$to", 0, 10);
+        
+        my $wait;
+        if ($last_name) { $wait = "-w 'ended(${last_name}*)'";}
+        
         print "Submitting name projection from $from to $to (1:many)\n";
-        system "bsub $bsub_opts -o $o -e $e -J $n perl project_display_xrefs.pl $script_opts -from $from -to $to -names -no_database -one_to_many\n";
+        system "bsub $bsub_opts -o $o -e $e -J $n $wait perl project_display_xrefs.pl $script_opts -from $from -to $to -names -no_database -one_to_many\n";
     }
+    $last_name = "n_".$from;    
 }
 
+$last_name = "";
+
 # ----------------------------------------
 # GO terms
 
@@ -314,9 +325,14 @@ foreach my $from (@execution_order) {
         my $o = "$dir/go_${from}_$to.out";
         my $e = "$dir/go_${from}_$to.err";
         my $n = substr("g_${from}_$to", 0, 10);
+        
+        my $wait;
+        if ($last_name) { $wait = "-w 'ended(${last_name}*)'";}
+        
         print "Submitting GO term projection from $from to $to\n";
-        system "bsub $bsub_opts -q long -o $o -e $e -J $n perl project_display_xrefs.pl $script_opts -from $from -to $to -go_terms\n";
+        system "bsub $bsub_opts -q long -o $o -e $e -J $n $wait perl project_display_xrefs.pl $script_opts -from $from -to $to -go_terms\n";
     }
+    $last_name = "n_".$from;   
 }