Bio-Grid-Run-SGE

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lib/Bio/Grid/Run/SGE/Log/Notify/Jabber.pm  view on Meta::CPAN

    },
    error => sub {
      my ( $con, $error ) = @_;
      warn "Error: " . $error->string . "\n";
      $msg_send_failed = 1;
      $j->broadcast;
    },
  );

  $con->connect;
  my $timer
    = AnyEvent->timer( after => $self->wait_time, cb => sub { $self->log->info("close"); $j->broadcast; } );

  $j->wait;
  $con->disconnect;
  return $msg_send_failed;
}

__PACKAGE__->meta->make_immutable();

lib/Bio/Grid/Run/SGE/Util.pm  view on Meta::CPAN

@EXPORT      = qw();
%EXPORT_TAGS = ();
@EXPORT_OK   = qw(
  my_glob
  glob_list
  delete_by_regex
  expand_path
  my_mkdir
  concat_files
  my_glob_non_fatal
  timer
  expand_path_rel
  poll_interval
);

our $LOG =  Bio::Gonzales::Util::Log->new();

sub my_glob_non_fatal {
  my (@dirs) = @_;

  return unless defined wantarray;    # don't bother doing more

lib/Bio/Grid/Run/SGE/Util.pm  view on Meta::CPAN

  $concat_fh->close;

  for my $f (@to_be_unlinked) {
    $LOG->info("Deleting $f");
    unlink $f;
  }

  return;
}

sub timer {

  my ( $time_start, $time_end );

  return sub {
    unless ( defined $time_start ) {
      $time_start = time;
      return ( localtime($time_start) );
    } else {
      $time_end = time;

lib/Bio/Grid/Run/SGE/Util.pm  view on Meta::CPAN

=head1 SYNOPSIS

    use Bio::Grid::Run::SGE::Util qw(
      my_glob
      delete_by_regex
      expand_path
      my_mkdir
      concat_files
      my_glob_non_fatal
      timer
      expand_path_rel
    );

=head1 DESCRIPTION

Provides utility functions for the Bio::Grid::Run::SGE module.

=head1 SUBROUTINES

=over 4

lib/Bio/Grid/Run/SGE/Util.pm  view on Meta::CPAN

    (?:\..*)? #suffix
    $/x;

If your toolwrapper makes use of it, you can also invoke it by hand. In the
working dir of your job run:

    ~/script/<toolwrapper>.pl -p <job_id> <tmp>/<job_name>.config

B<TAKE CARE, IT DELETES THE RESULT FILES AND OVERWRITES THE LAST RESULT.CONCAT FILE>

=item B<< $timer = timer() >>

Time something. Usage:

  # get a timer
  my $timer = timer();

  # start
  my $start_time = $timer->();

  # stop
  my $stop_time = $timer->();
  my ($stop_time, $elapsed_time_as_string) = $timer->();

=back

=head1 SEE ALSO

L<Bio::Grid::Run::SGE>

=head1 AUTHOR

jw bargsten, C<< <joachim.bargsten at wur.nl> >>