[
  { TYPE => SPECIES,
    'abrev'          => 'Mm37',
    'genome_db_id'   => 134,
    'taxon_id'       => 10090,
    'phylum'         => 'Vertebrata',
    'module'         => 'Bio::EnsEMBL::DBSQL::DBAdaptor',
    'host'           => "ens-livemirror",
    'port'           => 3306,
    'user'           => "ensro",
    'dbname'         => "mus_musculus_core_73_38",
    'species'        => "mus_musculus"
  },

  { TYPE => SPECIES,
    'abrev'          => 'Hs37',
    'genome_db_id'   => 90,
    'taxon_id'       => 9606,
    'phylum'         => 'Vertebrata',
    'module'         => 'Bio::EnsEMBL::DBSQL::DBAdaptor',
    'host'           => "ens-livemirror",
    'port'           => 3306,
    'user'           => "ensro",
    'dbname'         => "homo_sapiens_core_73_37",
    'species'        => "homo_sapiens"
  },

  { TYPE => SPECIES,
    'abrev'          => 'Rn',
    'genome_db_id'   => 140,
    'taxon_id'       => 10116,
    'phylum'         => 'Vertebrata',
    'module'         => 'Bio::EnsEMBL::DBSQL::DBAdaptor',
    'host'           => "ens-livemirror",
    'port'           => 3306,
    'user'           => "ensro",
    'dbname'         => "rattus_norvegicus_core_73_5",
    'species'        => "rattus_norvegicus"
  },

  { TYPE => DNA_COLLECTION,
    'collection_name'       => 'human all',
    'genome_db_id'          => 90,
    'genome_name_assembly'  => 'homo_sapiens:NCBI37',
    'chunk_size'            => 30000000,
    'overlap'               => 0,
    'region'                => "chromosome:22",
    'masking_options_file' => '/nfs/users/nfs_k/kb3/src/ensembl_main/ensembl-compara/scripts/pipeline/human36.spec'
  },

  { TYPE => DNA_COLLECTION,
    'collection_name'       => 'mouse all',
    'genome_db_id'          => 134,
    'genome_name_assembly'  => 'mus_musculus:GRCm38',
    'chunk_size'            => 10100000,
    'group_set_size'        => 10100000,
    'overlap'               => 100000,
    'region'                => "chromosome:16",
    'masking_options'       => '{default_soft_masking => 1}'
  },

  { TYPE => DNA_COLLECTION,
    'collection_name'       => 'rat all',
    'genome_db_id'          => 3,
    'genome_name_assembly'  => 'rattus_norvegicus:RGSC3.4',
    'chunk_size'            => 10100000,
    'group_set_size'        => 10100000,
    'overlap'               => 100000,
    'region'                => "chromosome:11",
    'masking_options'       => '{default_soft_masking => 1}'
  },


  { TYPE => PAIR_ALIGNER,
    'method_link' => [1001, 'LASTZ_RAW'],
    'analysis_template' => {
        '-program'       => 'lastz',
        '-parameters'    => "{method_link=>'LASTZ_RAW',options=>'T=1 L=3000 H=2200 O=400 E=30'}",
        '-module'        => 'Bio::EnsEMBL::Compara::RunnableDB::PairAligner::LastZ',
    },
    'non_reference_collection_name'   => 'mouse all',
    'reference_collection_name'  => 'human all',
  },

  { TYPE => PAIR_ALIGNER,
    'method_link' => [1001, 'LASTZ_RAW'],
    'analysis_template' => {
        '-program'       => 'lastz',
        '-parameters'    => "{method_link=>'LASTZ_RAW',options=>'T=1 L=3000 H=2200 O=400 E=30'}",
        '-module'        => 'Bio::EnsEMBL::Compara::RunnableDB::PairAligner::LastZ',
    },
    'non_reference_collection_name'   => 'rat all',
    'reference_collection_name'  => 'human all',
  },

   #########second half of the pipeline ###########
  { TYPE => DNA_COLLECTION,
    'collection_name'       => 'mouse for chain',        # The collection_name needs to be unique to avoid confusion
    'genome_db_id'          => 134, 
    'genome_name_assembly'  => 'mus_musculus:GRCm38',
    'region'                => "chromosome:16",
    'dump_loc'              => '/lustre/scratch109/ensembl/kb3/scratch/hive/tests/test_pairaligner_conf/nib_files/mus_musculus_nib_for_chain'
  },

  { TYPE => DNA_COLLECTION,
    'collection_name'       => 'rat for chain', # The collection_name needs to be unique to avoid confusion
    'genome_db_id'          => 3, 
    'genome_name_assembly'  => 'rattus_norvegicus:RGSC3.4',
       'region'                => "chromosome:11",
    'dump_loc'              => '/lustre/scratch109/ensembl/kb3/scratch/hive/tests/test_pairaligner_conf/nib_files/rattus_norvegicus_nib_for_chain'
  },

  { TYPE => DNA_COLLECTION,
    'collection_name'       => 'human for chain', # The collection_name needs to be unique to avoid confusion
    'genome_db_id'          => 90,
    'genome_name_assembly'  => 'Homo sapiens:NCBI37',
    'include_non_reference' => 1, #include haplotypes   
    'dump_loc'              => '/lustre/scratch109/ensembl/kb3/scratch/hive/tests/test_pairaligner_conf/nib_files/homo_sapiens_nib_for_chain',
    'region'                => "chromosome:22",
  },


  { TYPE => CHAIN_CONFIG,
    'input_method_link' => [1001, 'LASTZ_RAW'],
    'output_method_link' => [1002, 'LASTZ_CHAIN'],

    'reference_collection_name' => 'human for chain',
    'non_reference_collection_name' => 'mouse for chain',
              
    'max_gap' => 50,
    'output_group_type' => 'chain',
    'linear_gap' => 'medium'
  },

  { TYPE => CHAIN_CONFIG,
    'input_method_link' => [1001, 'LASTZ_RAW'],
    'output_method_link' => [1002, 'LASTZ_CHAIN'],

    'reference_collection_name' => 'human for chain',
    'non_reference_collection_name' => 'rat for chain',
              
    'max_gap' => 50,
    'output_group_type' => 'chain',
    'linear_gap' => 'medium'
  },

  { TYPE => NET_CONFIG,
    'input_method_link' => [1002, 'LASTZ_CHAIN'],
   'output_method_link' => [16, 'LASTZ_NET'],

    'reference_collection_name' => 'human for chain',
    'non_reference_collection_name' => 'mouse for chain',
              
    'max_gap' => 50,
    'input_group_type' => 'chain',
    'output_group_type' => 'default'
  },

  { TYPE => NET_CONFIG,
    'input_method_link' => [1002, 'LASTZ_CHAIN'],
   'output_method_link' => [16, 'LASTZ_NET'],

    'reference_collection_name' => 'human for chain',
    'non_reference_collection_name' => 'rat for chain',
              
    'max_gap' => 50,
    'input_group_type' => 'chain',
    'output_group_type' => 'default'
  },

  { TYPE => END }
]
