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lib/AlignAid.pm  view on Meta::CPAN

    if ( !$PP_loaded && ($arg{queue} eq 'LSF' || $arg{queue} eq 'PBS') ) {
        croak "The PP module is required for submitting jobs to LSF or PBS queues.";
    }
    
    if ( $arg{queue} ne 'single' && $arg{queue} ne 'LSF' && $arg{queue} ne 'PBS') {
	    croak "$arg{queue} is not a supported queue type";
    }
    $arg{program} = defined( $arg{program} ) ? $arg{program} : 'blastn';
    $arg{chunk}   = defined( $arg{chunk} )   ? $arg{chunk}   : 1;

    # verify all paths are absolute paths
    $arg{db}        = File::Spec->rel2abs( $arg{db} );
    $arg{dir}       = File::Spec->rel2abs( $arg{dir} );
    $arg{fasta}     = File::Spec->rel2abs( $arg{fasta} );
    $arg{prog_name} = $arg{program};
    $arg{program}   = `which $arg{program}`;
    chomp $arg{program};

    # setup the object
    my $self = {
        _queue     => $arg{queue},

lib/AlignAid.pm  view on Meta::CPAN

                        pp_type => 'lsf',
                        command => $command,
                        q       => 'long',
                        eo      => $error_file,
                        output  => $out_file,
                    );

		    # actually start job (it's been holding up til now)
                    $pp->start();

                    # verify job made it onto the queue
                    if ( $pp->is_in_queue(1) ) {
                        push @jobs, $pp;
                    }
                    else {
                        $ret_val = 0;
                        warn "job didn't get submitted!";
                    }

                }
                elsif ( $class->{_queue} eq 'PBS' ) {

lib/AlignAid.pm  view on Meta::CPAN

                my $pp = PP->run(
                    pp_type => 'lsf',
                    command =>
"$class->{_program} $class->{_database} $fa_file $class->{_prog_args}",
                    q => 'long',
                    e => $error_file,
                    o => $out_file,
                );

                # verify job made it onto the queue
                if ( $pp->is_in_queue(1) ) {
                    push @jobs, $pp;
                }
                else {
                    warn "job didn't get submitted!";
                    $ret_val = 0;
                }
            }
            elsif ( $class->{_queue} eq 'PBS' ) {
                croak "Sorry! PBS queueing not implemented yet!\n";