Raw content of Bio::EnsEMBL::Pipeline::BatchSubmission
<![CDATA[# Base Class for handling job submission via Load Sharing software
#
# Cared for by Laura Clarke
#
# Copyright Laura Clarke
#
# You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code
=pod
=head1 NAME
Bio::EnsEMBL::Pipeline::BatchSubmission
=head1 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');
$batch_job->open_command_line();
=head1 DESCRIPTION
Generic base class for specific BatchSubmission modules found in
BatchSubmission directory for handling pipeline jobs in a distributed
environment with load sharing software such as LSF, PBS,etc.
All get/sets and generic methods found here, while specific methods such as
construct_command_line have to be implemented in the specific child
classes Bio::EnsEMBL::Pipeline::BatchSubmission::*
the specific methods which must be implemented are
construct_command_line, a method to build the submission statement
open_command_line, a method to open the submission statement
copy_output ,a method copy the output of a job at to the defined
destination if desired
delete_output, a method to delete the output from the temporary location
that held it
=head1 CONTACT
Post general queries to B<ensembl-dev@ebi.ac.uk>
=head1 APPENDIX
The rest of the documentation details each of the object methods. Internal
methods are usually preceded with a _
=cut
package Bio::EnsEMBL::Pipeline::BatchSubmission;
use vars qw(@ISA);
use strict;
use Bio::EnsEMBL::Root;
use Bio::EnsEMBL::Utils::Exception qw(verbose throw warning info);
use Bio::EnsEMBL::Utils::Argument qw( rearrange );
@ISA = qw();
sub new{
my ($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 $self;
}
##################
#accessor methods#
##################
sub stdout_file{
my ($self, $arg) = @_;
if($arg){
$self->{'stdout'} = $arg;
}
return $self->{'stdout'};
}
sub stderr_file{
my ($self, $arg) = @_;
if($arg){
$self->{'stderr'} = $arg;
}
return $self->{'stderr'};
}
sub id{
my ($self, $arg) = @_;
if($arg){
$self->{'id'} = $arg;
}
return $self->{'id'};
}
sub parameters{
my ($self, $arg) = @_;
if($arg){
$self->{'parameters'} = $arg;
}
return $self->{'parameters'};
}
sub pre_exec{
my ($self, $arg) = @_;
if($arg){
$self->{'pre_exec'} = $arg;
}
return $self->{'pre_exec'};
}
sub command{
my ($self, $arg) = @_;
if($arg){
$self->{'command'} = $arg;
}
return $self->{'command'};
}
sub queue{
my ($self, $arg) = @_;
if($arg){
$self->{'queue'} = $arg;
}
return $self->{'queue'};
}
sub jobname{
my ($self, $arg) = @_;
if($arg){
$self->{'jobname'} = $arg;
}
return $self->{'jobname'};
}
sub nodes{
my ($self, $arg) = @_;
if($arg){
$self->{'nodes'} = $arg;
}
return $self->{'nodes'};
}
sub resource{
my ($self, $arg) = @_;
if($arg){
$self->{'resource'} = $arg;
}
return $self->{'resource'};
}
#############
#run methods#
#############
sub construct_command_line{
my ($self) = @_;
throw("this method construct command line must be implemented");
}
sub open_command_line{
my ($self)= @_;
throw("open_command_line isn't implemented yet");
}
sub copy_output{
my ($self) = @_;
throw("this method copy_output must be implemented");
}
sub delete_output{
my ($self) = @_;
throw("this method delete_output must be implemented");
}
1;
]]>