maker_wq_worker

#!/usr/bin/env perl
use strict "vars";
use strict "refs";
use warnings;

use FindBin;
use vars qw($RANK $LOG $CMD_ARGS);

BEGIN{
   if (not ($ENV{CGL_SO_SOURCE})) {
      $ENV{CGL_SO_SOURCE} = "$FindBin::Bin/../lib/CGL/so.obo";
   }
   if (not ($ENV{CGL_GO_SOURCE})) {
      $ENV{CGL_GO_SOURCE} = "$FindBin::Bin/../lib/CGL/gene_ontology.obo"
   }
   
   $CMD_ARGS = join(' ', @ARGV);
   
   #what to do on ^C
   $SIG{'INT'} = sub {
      print STDERR "\n\nMaker aborted by user!!\n\n" unless($main::qq);
      exit (1);
   };    
   
   #supress warnings from storable module
   $SIG{'__WARN__'} = sub {
      warn $_[0] if ( $_[0] !~ /Not a CODE reference/ &&
		      $_[0] !~ /Can\'t store item / &&
		      $_[0] !~ /Find\:\:skip_pattern|File\/Find\.pm/
		    );
   };

   #output to log file of seq that caused rank to die
   $SIG{'__DIE__'} =
   sub {
      if (defined ($LOG) && defined $_[0]) {
	 my $die_count = $LOG->get_die_count();
	 $die_count++;
	 
	 $LOG->add_entry("DIED","RANK",$RANK);
	 $LOG->add_entry("DIED","COUNT",$die_count);
      }

      die $_[0]."\n".
	  "FATAL ERROR\n";
   };
}

my $link_output = `find -name "*" -exec ln -s {} . \\\;`;

my $numArgs = $#ARGV + 1;
if ($numArgs < 1) {
        print "Usage: maker_wq_worker counter\n";
        exit;
}

my $counter = $ARGV[0];
my $tier;

use lib "./lib"; 
use Storable qw(retrieve);
use ds_utility;
use runlog;
use Error qw(:try);
use Error::Simple;
use Process::MpiTiers;
use Proc::Signal;
#use Fasta;
#use maker::auto_annotator;
#use FastaChunker;
#use cluster;
#use repeat_mask_seq;
#use GFFDB;
#use Process::MpiChunk;
#use GI;
#use Cwd;
#use FileHandle;
#use File::Path;
#use Getopt::Long qw(:config no_ignore_case);
#use Dumper::GFF::GFFV3;
#use Iterator::Any;
#use Iterator::Fasta;
#use Iterator::GFF3;

my @ts = @ARGV; 
foreach my $c (@ts) {
	my $inFile = $c."_todo.tier";
	my $total = scalar(@ts); 
	print "On component $c of $#ts, $total, $counter\n"; 

	#tier files were generated with the nstore command from the Storable Perl module
	#This simply stores a hash to disk in a convenient format. 
	$tier = ${retrieve($inFile)};
	$tier->CTL_OPT->{out_name} = "."; 
	$tier->CTL_OPT->{out_base} = "."; 
	$tier->CTL_OPT->{the_void} = ".";
	$tier->{the_void} = ".";  

	#use Process::MpiTiers;
	print time." :: Worker $counter :: starting \n";
	$tier->run_all;
	print time." :: Worker $counter :: finished \n";

	if($tier->failed) { print "EXIT:-1 \n"; last; }
	elsif($tier->terminated) { print "EXIT:1 \n"; next; }
}