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Summary

Bio::EnsEMBL::Pipeline::BatchSubmission::GridEngine

Package variables

Included modules

Inherit

Bio::EnsEMBL::Pipeline::BatchSubmission

Synopsis

my $batchjob = Bio::EnsEMBL::Pipeline::BatchSubmission::LSF->new(
-STDOUT => $stdout_file,
-STDERR => $stderr_file,
-PARAMETERS => @args,
-PRE_EXEC => $pre_exec,
-QUEUE => $queue,
-JOBNAME => $jobname,
-NODES => $nodes,
-RESOURCE => $resource
);
$batch_job->construct_command_line('test.pl');
$batch_job->open_command_line();

Description

This module provides an interface to the Sun Grid Engine load sharing softwa
re and its commands. It implements the method construct_command_line which is
not defined in the base class and which enables the pipeline to submit jobs
in a distributed environment using Sun Grid Engine.
See base class Bio::EnsEMBL::Pipeline::BatchSubmission for more info

Methods

Methods description

None available.

Methods code

sub construct_command_line {

  my($self, $command, $stdout, $stderr) = @_; 
  #print STDERR "creating the command line\n";
#command must be the first argument then if stdout or stderr aren't definhed the objects own can be used
  if(!$command){
    $self->throw("cannot create qsub if nothing to submit to it : $!\n");
  }
  my $qsub_line;
  $self->command($command);
  if($stdout){
    $qsub_line = "qsub -V -cwd -v FINAL_STDOUT=".$stdout;
  }else{
    $qsub_line = "qsub -V -cwd -v FINAL_STDOUT=".$self->stdout_file;
  }
  if($stderr){
    $qsub_line .= " -v FINAL_STDERR=".$stderr;
  }else{
    $qsub_line .= " -v FINAL_STDERR=".$self->stderr_file;
  }
  $qsub_line .= " -o /tmp -e /tmp";

# Depends on queues being made for each node with name node.q
  if($self->nodes){
    my $nodes = $self->nodes;
    # $nodes needs to be a space-delimited list
    $nodes =~ s/,/.q,/;
    $qsub_line .= " -q ".$nodes." ";
  }

  if (defined($self->queue) && $self->queue ne "") {$qsub_line .= " -l ".$self->queue;}

  $qsub_line .= " -N ".$self->jobname  if defined $self->jobname;

  $qsub_line .= " ".$self->parameters." "  if defined $self->parameters;

  $qsub_line .= " -v PREEXEC=\"".$self->pre_exec."\"" if defined $self->pre_exec; 

  ## must ensure the prexec is in quotes ##
  my $ge_wrapper = "ge_wrapper.pl";
  unless (-x $ge_wrapper) {
    $ge_wrapper = __FILE__;
    $ge_wrapper =~ s:GridEngine.pm:../../../../../scripts/ge_wrapper.pl:;
    print $ge_wrapper . "\n";
    my $caller = caller(0);
    $self->throw("ge_wrapper not found - needs to be set in $caller\n") unless -x $ge_wrapper;
  }

  $qsub_line .= " $ge_wrapper\" ".$command . "\"";
  $self->qsub($qsub_line);
  #print "have command line\n";

}

sub new {

  my ($class, @args) = @_;
  my $self = $class->SUPER::new(@args);

  return $self;
 
}


##################
#accessor methods#
##################

}

sub open_command_line {

  my ($self)= @_;

  print STDERR $self->qsub."\n";
  print STDERR "opening command line\n";
  open(SUB, $self->qsub." 2>&1 |");
  my $geid;
  while(<SUB>){
    if (/your job (\d+)/) {
      $geid = $1;
    }
  }
  print STDERR "have opened ".$self->qsub."\n";
  print STDERR "geid ".$geid."\n";
  $self->id($geid);
  close(SUB);

}

sub qsub {

  my ($self,$qsub_line) = @_;

  if (defined($qsub_line)) {
    $self->{_qsub} = $qsub_line;
  }
  return $self->{_qsub};
}

##other accessor are in base class##

######################
#command line methods#
######################

}

General documentation

Post general queries to ensembl-dev@ebi.ac.uk

The rest of the documentation details each of the object methods. Interna
l
methods are usually preceded with a _