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Summary

Bio::EnsEMBL::Pipeline::BatchSubmission

Package variables

Included modules

Inherit

Synopsis

This is just a base class: objects should be created via child classes
Bio::EnsEMBL::Pipeline::BatchSubmission::*
my $batchjob = Bio::EnsEMBL::Pipeline::BatchSubmission::XXX->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

Generic base class for specific BatchSubmission modules found in
BatchSubmission directory for handling pipeline jobs in a distributed
environment with load sharing software such as LSF, PBS,etc.
All get/sets and generic methods found here, while specific methods such as
construct_command_line have to be implemented in the specific child
classes Bio::EnsEMBL::Pipeline::BatchSubmission::*
the specific methods which must be implemented are
construct_command_line, a method to build the submission statement
open_command_line, a method to open the submission statement
copy_output ,a method copy the output of a job at to the defined
destination if desired
delete_output, a method to delete the output from the temporary location
that held it

Methods

Methods description

None available.

Methods code

sub command {

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

   if($arg){
     $self->{'command'} = $arg;
   }

   return $self->{'command'};

}

sub construct_command_line {

  my ($self) = @_;

  throw("this method construct command line must be implemented");

}

sub copy_output {

  my ($self) = @_;

  throw("this method copy_output must be implemented");

}

sub delete_output {

  my ($self) = @_;

  throw("this method delete_output must be implemented");
}

1;

}

sub id {

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

   if($arg){
     $self->{'id'} = $arg;
   }

   return $self->{'id'};

}

sub jobname {

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

   if($arg){
     $self->{'jobname'} = $arg;
   }

   return $self->{'jobname'};

}

sub new {

  my ($class, @args) = @_;
  my $self = bless {},$class;   
  $self->{'stdout'} = undef;
  $self->{'stderr'} = undef;
  $self->{'id'} = undef;
  $self->{'parameters'} = undef;
  $self->{'pre_exec'} = undef;
  $self->{'command'} = undef;
  $self->{'queue'} = undef;
  $self->{'jobname'} = undef;
  $self->{'nodes'} = undef; #must by a space delimited line of nodes
  $self->{'resource'} = undef;

  my($stdout, $stderr, $parameters, $pre_exec, $command,$queue, $jobname,
     $resource, $nodes) = rearrange([qw(STDOUT
                                        STDERR
                                        PARAMETERS
                                        PRE_EXEC 
                                        COMMAND 
                                        QUEUE 
                                        JOBNAME
                                        RESOURCE
                                        NODES)],@args);
  
  if($stdout){
    $self->stdout_file($stdout);
  }
  if($stderr){
    $self->stderr_file($stderr);
  }
  if($parameters){
    $self->parameters($parameters);
  }
  if($pre_exec){
    $self->pre_exec($pre_exec);
  }
  if($command){
    $self->command($command);
  }
  if($queue){
    $self->queue($queue);
  }
  if($jobname){
    $self->jobname($jobname);
  }
  if($resource){
    $self->resource($resource);
  }
  if($nodes){
    $self->nodes($nodes);
  }

  return $self;
}

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

}

sub nodes {

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

   if($arg){
     $self->{'nodes'} = $arg;
   }

   return $self->{'nodes'};

}

sub open_command_line {

  my ($self)= @_;
  
  throw("open_command_line isn't implemented yet");

}

sub parameters {

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

   if($arg){
     $self->{'parameters'} = $arg;
   }

   return $self->{'parameters'};

}

sub pre_exec {

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

   if($arg){
     $self->{'pre_exec'} = $arg;
   }

   return $self->{'pre_exec'};

}

sub queue {

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

   if($arg){
     $self->{'queue'} = $arg;
   }

   return $self->{'queue'};

}

sub resource {

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

   if($arg){
     $self->{'resource'} = $arg;
   }

   return $self->{'resource'};
}


#############
#run methods#
#############

}

sub stderr_file {

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

   if($arg){
     $self->{'stderr'} = $arg;
   }

   return $self->{'stderr'};

}

sub stdout_file {

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

   if($arg){
     $self->{'stdout'} = $arg;
   }

   return $self->{'stdout'};

}

General documentation

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

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