Raw content of Bio::EnsEMBL::Analysis::RunnableDB::Funcgen::Chipotle # Ensembl module for Bio::EnsEMBL::Analysis::RunnableDB::Funcgen::Chipotle # # Copyright (c) 2007 Ensembl # =head1 NAME Bio::EnsEMBL::Analysis::RunnableDB::Funcgen::Chipotle =head1 SYNOPSIS my $runnable = Bio::EnsEMBL::Analysis::RunnableDB::Funcgen::Chipotle->new ( -db => $db, -input_id => 'chromosome::20:1:100000:1', -analysis => $analysis, ); $runnable->fetch_input; $runnable->run; $runnable->write_output; =head1 DESCRIPTION This module provides an interface between the ensembl database and the Runnable Chipotle which wraps the program ChIPoTle =head1 AUTHOR Stefan Graf, Ensembl Functional Genomics - / =head1 CONTACT Post questions to the Ensembl development list: ensembl-dev@ebi.ac.uk =cut package Bio::EnsEMBL::Analysis::RunnableDB::Funcgen::Chipotle; use strict; use warnings; use Data::Dumper; use Bio::EnsEMBL::Analysis::Config::General; use Bio::EnsEMBL::Analysis::Config::Funcgen::Chipotle; use Bio::EnsEMBL::Analysis::RunnableDB; use Bio::EnsEMBL::Analysis::RunnableDB::Funcgen; use Bio::EnsEMBL::Analysis::Runnable::Funcgen::Chipotle; use Bio::EnsEMBL::Utils::Exception qw(throw warning stack_trace_dump); use vars qw(@ISA); @ISA = qw(Bio::EnsEMBL::Analysis::RunnableDB::Funcgen); =head2 new Arg [1] : Arg [2] : Description : Instantiates new Chipotle runnabledb Returntype : Bio::EnsEMBL::Analysis::RunnableDB::Funcgen::Chipotle object Exceptions : Example : =cut sub new { print "Analysis::RunnableDB::Funcgen::Chipotle::new\n"; my ($class,@args) = @_; my $self = $class->SUPER::new(@args); $self->read_and_check_config($CONFIG); # add some runnable/program special params to analysis here # make sure we have the correct analysis object $self->check_Analysis(); # make sure we can store the correct feature_set, data_sets, and result_sets $self->check_Sets(); return $self; } 1;