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Summary

Bio::EnsEMBL::Hive::RunnableDB::SystemCmd

Package variables

Included modules

Inherit

Bio::EnsEMBL::Hive::Process

Synopsis

my $db = Bio::EnsEMBL::DBAdaptor->new($locator);
my $runDB = Bio::EnsEMBL::Hive::RunnableDB::SystemCmd->new (
-db => $db,
-input_id => $input_id
-analysis => $analysis );
$runDB->fetch_input(); #reads from DB
$runDB->run();
$runDB->output();
$runDB->write_output(); #writes to DB

Description

This object is a very simple module. It takes the input_id
and runs it as a system command.

Methods

Methods description

None available.

Methods code

sub fetch_input {

  my $self = shift;

  print("input_id\n  ", $self->input_id,"\n");
  $self->{'cmd'} = $self->input_id;

  if($self->input_id =~ /^{/) {
    my $input_hash = eval($self->input_id);
    if($input_hash) {
      $self->{'cmd'} = $input_hash->{'cmd'} if($input_hash->{'cmd'});
      if($input_hash->{'did'}) {
        $self->{'cmd'} = $self->db->get_AnalysisDataAdaptor->fetch_by_dbID($input_hash->{'did'});
      }
    }
  }
  print("cmd\n  ", $self->{'cmd'},"\n");
  return 1;

}

sub run {

  my $self = shift;
  system($self->{'cmd'}) == 0 or die "system ".$self->{'cmd'}." failed: $?";
  return 1;

}

sub write_output {

  my $self = shift;
  return 1;
}

1;

}

General documentation

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