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lib/Bio/InterProScanWrapper/External/LSFInterProScan.pm  view on Meta::CPAN

package Bio::InterProScanWrapper::External::LSFInterProScan;

# ABSTRACT: Run interproscan via LSF jobs


use Moose;
use LSF;
use LSF::JobManager;
use File::Basename;
use Bio::InterProScanWrapper::Exceptions;

has 'input_file'          => ( is => 'ro', isa => 'Str',        required => 1);
has 'output_file'         => ( is => 'ro', isa => 'Str',        required => 1);
has 'temp_directory_name' => ( is => 'ro', isa => 'Str',        required => 1);
has 'input_files'         => ( is => 'ro', isa => 'ArrayRef',        required => 1 );
has 'memory_in_mb'        => ( is => 'ro', isa => 'Int',             default  => 5000 );
has 'queue'               => ( is => 'ro', isa => 'Str',             default  => 'normal' );
has '_job_manager'        => ( is => 'ro', isa => 'LSF::JobManager', lazy     => 1, builder => '_build__job_manager' );
has 'exec'                => ( is => 'ro', isa => 'Str', default  => '/software/pathogen/external/apps/usr/local/iprscan-5.0.7/interproscan.sh' );
has 'output_type'         => ( is => 'ro', isa => 'Str', default => 'gff3' );
has '_output_suffix'      => ( is => 'ro', isa => 'Str', default  => '.out' );
has 'tokens_per_job'      => ( is => 'ro', isa => 'Int', default  => 25 );

                          
# A single instance uses more than 1 cpu so you need to reserve more slots
has '_cpus_per_command'  => ( is => 'ro', isa => 'Int',  default  => 4 );

sub _build__job_manager {
    my ($self) = @_;
    return LSF::JobManager->new( -q => $self->queue );
}

sub _generate_memory_parameter {
    my ($self) = @_;
    return "select[mem > ".$self->memory_in_mb."] rusage[mem=".$self->memory_in_mb.", iprscantok=".$self->tokens_per_job."] span[hosts=1]";
}

sub _submit_job {
    my ( $self, $sequence_temp_files_directory, $number_of_files ) = @_;

    my($filename, $directories, $suffix) = fileparse($self->input_file);
    $filename =~ s!\W!_!gi;
    my $job_array_name = "iprscan_".$filename."_".int(rand(100))."[1-$number_of_files]";
    
    $self->_job_manager->submit(
        -o => ".iprscan.o",
        -e => ".iprscan.e",
        -M => $self->memory_in_mb,
        -R => $self->_generate_memory_parameter,
        -n => $self->_cpus_per_command,
        -J => $job_array_name,
        $self->_construct_cmd($sequence_temp_files_directory)
    );
}

sub _construct_cmd
{ 
  my ($self, $sequence_temp_files_directory) = @_;
  my $cmd = join(
      ' ',
      (
          $self->exec, '-f', $self->output_type, '--goterms', '--iprlookup',
          '--pathways', '-i', $sequence_temp_files_directory.'/'.'$LSB_JOBINDEX'.'.seq', '--outfile', $sequence_temp_files_directory.'/'.'$LSB_JOBINDEX'.'.seq'. $self->_output_suffix
      )
  );
}

sub _construct_dependancy_params
{
   my ($self, $ids) = @_;
   return '' if((! defined($ids)) || @{$ids} == 0);
   
   my @done_ids;
   for my $id ( @{$ids})
   {