my $self = shift;

  if($self->input_job->retry_count >= 5) {
    $self->input_job->update_status('FAILED');

    throw("HclusterRun job failed >=5 times: try something else and FAIL it");
  }
}

1;

  my $self = shift;

  my $treeDBA = $self->{'comparaDBA'}->get_ProteinTreeAdaptor;
  my $starttime = time();

  my $clusterset;
  $clusterset = $treeDBA->fetch_node_by_node_id($self->{'clusterset_id'});
  if (!defined($clusterset)) {
    $clusterset = $self->{'ccEngine'}->clusterset;
  }
  my $clusters = $clusterset->children;
  foreach my $cluster (@{$clusters}) {
    my $output_id = sprintf("{'protein_tree_id'=>%d, 'clusterset_id'=>%d}", 
                            $cluster->node_id, $clusterset->node_id);
    if (defined($self->{retry})) {
      my $readded_cluster_tag = $cluster->get_tagvalue("readded_cluster");
      next unless (1 == $readded_cluster_tag); # Will skip flow unless is one of the readded
    }
    $self->dataflow_output_id($output_id, 2);
  }

  my( $self) = @_;

  $self->{'species_set'} = undef;
  $self->{'clusterset_id'} = 1;
  $self->throw("No input_id") unless defined($self->input_id);

  #create a Compara::DBAdaptor which shares the same DBI handle
  #with the Pipeline::DBAdaptor that is based into this runnable
  $self->{'comparaDBA'} = Bio::EnsEMBL::Compara::DBSQL::DBAdaptor->new(-DBCONN=>$self->db->dbc);

  $self->get_params($self->parameters);

  my @species_set = @{$self->{'species_set'}};
  $self->{'cluster_mlss'} = new Bio::EnsEMBL::Compara::MethodLinkSpeciesSet;
  $self->{'cluster_mlss'}->method_link_type('PROTEIN_TREES');
  my @genomeDB_set;
  foreach my $gdb_id (@species_set) {
    my $gdb = $self->{'comparaDBA'}->get_GenomeDBAdaptor->fetch_by_dbID($gdb_id);
    throw("print gdb not defined for gdb_id = $gdb_id\n") unless (defined $gdb);
    push @genomeDB_set, $gdb;
  }
  $self->{'cluster_mlss'}->species_set(\@genomeDB_set);

  #  $self->{gdba} = $self->{'comparaDBA'}->get_GenomeDBAdaptor;
  #   my $input_gdb_id = $self->input_id;
  #   my $gdb = $self->{gdba}->fetch_by_dbID($input_gdb_id);
  #   throw("no genome_db for $input_gdb_id") unless(defined($gdb));
  #   $self->{gdb} = $gdb;

  return 1;

  my $self = shift;

  my $starttime = time();
  return undef if ($self->input_job->retry_count > 10);

  my $fasta_dir = $self->{fasta_dir};
  my $output_dir = $self->worker_temp_directory;
  my $cmd;
  print "gathering input in $output_dir\n" if ($self->debug);

  $cmd ="cat $fasta_dir/*.hcluster.cat > $output_dir/hcluster.cat";
  unless(system($cmd) == 0) {
    $self->check_job_fail_options;
    throw("error gathering category files for Hcluster, $!\n");
  }
  printf("%1.3f secs to gather category entries\n", (time()-$starttime));
  $cmd ="cat $fasta_dir/*.hcluster.txt > $output_dir/hcluster.txt";
  unless(system($cmd) == 0) {
    $self->check_job_fail_options;
    throw("error gathering distance files for Hcluster, $!\n");
  }
  printf("%1.3f secs to gather distance entries\n", (time()-$starttime));

  my $self         = shift;
  my $param_string = shift;

  return if ($param_string eq "1");

  return unless($param_string);
  print("parsing parameter string : ",$param_string,"\n");

  my $params = eval($param_string);
  return unless($params);

  foreach my $key (keys %$params) {
    print("  $key : ", $params->{$key}, "\n");
  }

  if (defined $params->{'species_set'}) {
    $self->{'species_set'} = $params->{'species_set'};
  }
  if (defined $params->{'fasta_dir'}) {
    $self->{'fasta_dir'} = $params->{'fasta_dir'};
  }
  if (defined $params->{'outgroups'}) {
    foreach my $outgroup (@{$params->{'outgroups'}}) {
      $self->{outgroups}{$outgroup} = 1;
    }
  }
  if (defined $params->{'max_gene_count'}) {
    $self->{'max_gene_count'} = $params->{'max_gene_count'};
  }

  print("parameters...\n");
  printf("  fasta_dir      : %d\n", $self->{'fasta_dir'});
  printf("  species_set    : (%s)\n", join(',', @{$self->{'species_set'}}));
  printf("  outgroups      : (%s)\n", join(',', keys %{$self->{'outgroups'}}));
  printf("  max_gene_count : %d\n", $self->{'max_gene_count'});

  return;

  my $self = shift;

  $self->gather_input();
  $self->run_hcluster();
  return 1;

  my $self = shift;

  my $starttime = time();
  return undef if ($self->input_job->retry_count > 10);

  my $hcluster_executable = $self->analysis->program_file;
  unless (-e $hcluster_executable) {
    if (`uname -m` =~ /ia64/) {
      $hcluster_executable
        = "/nfs/acari/avilella/src/treesoft/trunk/ia64/hcluster/hcluster_sg";
    } else {
      $hcluster_executable
        = "/nfs/acari/avilella/src/treesoft/trunk/hcluster/hcluster_sg";
    }
  }

  $self->{'comparaDBA'}->dbc->disconnect_when_inactive(1);

  my $cmd = $hcluster_executable;
  my $max_count = int($self->{'max_gene_count'}/2); # hcluster can joint up to (max_count+(max_count-1))
  $cmd .= " ". "-m $max_count -w 0 -s 0.34 -O ";
  $cmd .= "-C " . $self->worker_temp_directory . "hcluster.cat ";
  $cmd .= "-o " . $self->worker_temp_directory . "hcluster.out ";
  $cmd .= " " . $self->worker_temp_directory . "hcluster.txt";
  print("Ready to execute:\n") if($self->debug);
  print("$cmd\n") if($self->debug);
  unless(system($cmd) == 0) {
    $self->check_job_fail_options;
    throw("error running hcluster, $!\n");
  }
  $self->{'comparaDBA'}->dbc->disconnect_when_inactive(0);
  printf("%1.3f secs to execute\n", (time()-$starttime));

  return 1;

  my $self = shift;

  $self->{retry} = $self->input_job->retry_count if ($self->input_job->retry_count > 10);

  my $mlssDBA = $self->{'comparaDBA'}->get_MethodLinkSpeciesSetAdaptor;
  my $pafDBA = $self->{'comparaDBA'}->get_PeptideAlignFeatureAdaptor;
  my $treeDBA = $self->{'comparaDBA'}->get_ProteinTreeAdaptor;
  my $starttime = time();

  my $clusterset;
  $clusterset = $treeDBA->fetch_node_by_node_id($self->{'clusterset_id'});
  if (!defined($clusterset)) {
    $self->{'ccEngine'} = new Bio::EnsEMBL::Compara::Graph::ConnectedComponents;
    $clusterset = $self->{'ccEngine'}->clusterset;
    throw("no clusters generated") unless($clusterset);

    $clusterset->name("PROTEIN_TREES");
    $treeDBA->store_node($clusterset);
    printf("root_id %d\n", $clusterset->node_id);
    $self->{'clusterset_id'} = $clusterset->node_id;
    $mlssDBA->store($self->{'cluster_mlss'});
    printf("MLSS %d\n", $self->{'cluster_mlss'}->dbID);
  }

  my $mlss_id = $self->{'cluster_mlss'}->dbID;
  $mlss_id = $self->{comparaDBA}->get_MethodLinkSpeciesSetAdaptor->fetch_by_method_link_type_GenomeDBs($self->{cluster_mlss}->method_link_type,$self->{cluster_mlss}->species_set)->dbID unless (defined($mlss_id));

  my $filename;
  if (defined($self->{retry})) {
    my $fasta_dir = $self->{fasta_dir};
    $filename = $fasta_dir . "/" . "hcluster.out";
  } else {
    $filename = $self->worker_temp_directory . "/" . "hcluster.out";
  }
  $self->{memberDBA} = $self->{'comparaDBA'}->get_MemberAdaptor;
  $self->{treeDBA} = $self->{'comparaDBA'}->get_ProteinTreeAdaptor;

  open FILE, "$filename" or die $!;
  my $counter=1;
  while (<FILE>) {
    # 0       0       0       1.000   2       1       697136_68,
    # 1       0       39      1.000   3       5       1213317_31,1135561_22,288182_42,426893_62,941130_38,
    chomp $_;

    my ($cluster_id, $dummy1, $dummy2, $dummy3, $dummy4, $dummy5, $cluster_list) = split("\t",$_);

    next if ($dummy5 < 2);
    $cluster_list =~ s/\,^//;
    my @cluster_list = split(",",$cluster_list);

    # If it's a singleton, we don't store it as a protein tree
    next if (2 > scalar(@cluster_list));

    if($counter % 20 == 0) { printf("%10d clusters\n", $counter); }
    $counter++;

    my $cluster = new Bio::EnsEMBL::Compara::NestedSet;
    $clusterset->add_child($cluster);

    my $already_present;
    my $number_raw_cluster = scalar(@cluster_list);
    my $number_filtered_cluster = 0;
    if (defined($self->{retry}) && $self->{retry} >= 20) {
      foreach my $member_hcluster_id (@cluster_list) {
        my ($pmember_id,$genome_db_id) = split("_",$member_hcluster_id);
        my $aligned_member = $self->{treeDBA}->fetch_AlignedMember_by_member_id_root_id($pmember_id, 1);
        if (defined($aligned_member)) {
          $already_present->{$aligned_member->member_id} = 1;
        }
      }
      next if ($number_raw_cluster == (scalar keys %$already_present));
    }

    $DB::single=1;1;
    foreach my $member_hcluster_id (@cluster_list) {
      my ($pmember_id,$genome_db_id) = split("_",$member_hcluster_id);
      if (defined($self->{retry}) && $self->{retry} >= 20) {
        my $member = $self->{memberDBA}->fetch_by_dbID($pmember_id);
        my $longest_member = $member->gene_member->get_longest_peptide_Member;
        next unless ($longest_member->member_id eq $member->member_id);
        next if (defined($already_present->{$member->member_id}));
      }
      my $node = new Bio::EnsEMBL::Compara::NestedSet;
      $node->node_id($pmember_id);
      $cluster->add_child($node);
      #leaves are NestedSet objects, bless to make into AlignedMember objects
      bless $node, "Bio::EnsEMBL::Compara::AlignedMember";

      #the building method uses member_id's to reference unique nodes
      #which are stored in the node_id value, copy to member_id
      $node->member_id($node->node_id);
      $node->method_link_species_set_id($mlss_id);
    }

    # Store the cluster
    $treeDBA->store($cluster);
    #calc residue count total
    my $leafcount = scalar(@{$cluster->get_all_leaves});
    $cluster->store_tag('gene_count', $leafcount);
    if (defined($self->{retry}) && $self->{retry} >= 20) {
      $cluster->store_tag('readded_cluster', 1);
      print STDERR "Re-adding cluster ", $cluster->node_id, "with $leafcount members\n";
    }
    # $cluster->store_tag('include_brh', $self->{'include_brh'});
    # $cluster->store_tag('bsr_threshold', $self->{'bsr_threshold'});
  }

  return 1;
}

##########################################
#
# internal methods
#
##########################################

  my $self = shift;

  $self->store_clusters();
  $self->dataflow_clusters;

  # modify input_job so that it now contains the clusterset_id
  my $outputHash = {};
  $outputHash = eval($self->input_id) if(defined($self->input_id) && $self->input_id =~ /^\s*\{.*\}\s*$/);
  $outputHash->{'clusterset_id'} = $self->{'clusterset_id'};
  my $output_id = $self->encode_hash($outputHash);

  return 1;

  Contact Albert Vilella on module implemetation/design detail: avilella@ebi.ac.uk
  Contact Abel Ureta-Vidal on EnsEMBL/Compara: abel@ebi.ac.uk
  Contact Ewan Birney on EnsEMBL in general: birney@sanger.ac.uk