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1 =pod
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2
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3 =head1 NAME
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4
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5 Bio::EnsEMBL::Hive::RunnableDB::Funcgen::SetupAnnotationPipeline
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6
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7 =head1 DESCRIPTION
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8
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9 'SetupAnnotationPipeline' Checks cell types and creates annotation processes for each
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10 This Runnable CANNOT be run multiple times in parallell!
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11
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12 =cut
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13
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14 package Bio::EnsEMBL::Funcgen::RunnableDB::SetupAnnotationPipeline;
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15
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16 use warnings;
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17 use strict;
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18 use Bio::EnsEMBL::DBSQL::DBAdaptor;
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19 use Bio::EnsEMBL::Funcgen::DBSQL::DBAdaptor;
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20 use Bio::EnsEMBL::Utils::Exception qw(throw warning stack_trace_dump);
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21
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22 use base ('Bio::EnsEMBL::Funcgen::RunnableDB::Annotation');
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23
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24 sub fetch_input { # fetch parameters...
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25 my $self = shift @_;
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26
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27 $self->SUPER::fetch_input();
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28
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29 #Sets up the output dir
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30 my $output_dir = $self->_output_dir();
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31 if(! -d $output_dir){
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32 system("mkdir -p $output_dir") && throw("Couldn't create output directory $output_dir");
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33 }
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34
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35 return 1;
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36 }
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37
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38 sub run { # Check parameters and do appropriate database/file operations...
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39 my $self = shift @_;
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40
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41 my $efgdba = $self->_efgdba();
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42 #Check how many different cell types exist with regulatory features for current species
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43 #Creates the appropriate jobs
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44 my @reg_sets = @{$efgdba->get_FeatureSetAdaptor->fetch_all_by_type('regulatory')};
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45 my @cell_types;
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46 foreach my $set (@reg_sets){
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47 if($set->cell_type->name ne 'MultiCell'){
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48 push @cell_types, $set->cell_type->name;
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49 }
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50 }
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51 $self->_cell_types_to_run(\@cell_types);
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52
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53 return 1;
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54 }
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55
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56
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57 sub write_output { # Create the relevant job
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58 my $self = shift @_;
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59
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60 foreach my $cell_type (@{$self->_cell_types_to_run()}){
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61 my $new_input_id = eval($self->input_id);
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62 $new_input_id->{"cell_type"} = $cell_type;
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63 $self->dataflow_output_id($new_input_id, 2, { } );
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64 }
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65
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66 return 1;
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67
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68 }
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69
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70 #Private getter / setter to the cell_types_to_run list
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71 sub _cell_types_to_run {
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72 return $_[0]->_getter_setter('cell_types_to_run',$_[1]);
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73 }
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74
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75 1;
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