text: -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
  -- Copyright [2016-2020] EMBL-European Bioinformatics Institute
  -- 
  -- Licensed under the Apache License, Version 2.0 (the "License");
  -- you may not use this file except in compliance with the License.
  -- You may obtain a copy of the License at
  -- 
  --      http://www.apache.org/licenses/LICENSE-2.0
  -- 
  -- Unless required by applicable law or agreed to in writing, software
  -- distributed under the License is distributed on an "AS IS" BASIS,
  -- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
  -- See the License for the specific language governing permissions and
  -- limitations under the License.
  
  -- Updating the schema version
  UPDATE meta SET meta_value = 56 where meta_key = "schema_version";
  
  
  -- Add strand info to constrained_element for EPO anchor generation
  alter table constrained_element add column dnafrag_strand int(2);
  
  
  -- Adding lr_index_offset if not already there (introduced into 55 post release).
  CREATE TABLE IF NOT EXISTS lr_index_offset (
  	table_name  varchar(64) NOT NULL,
  	lr_index    int(10) unsigned NOT NULL,
  	PRIMARY KEY (table_name)
  ) COLLATE=latin1_swedish_ci;
  
  
  -- Increasing the size of 3 columns in analysis
  ALTER TABLE analysis MODIFY COLUMN db_file varchar(255);
  ALTER TABLE analysis MODIFY COLUMN program varchar(255);
  ALTER TABLE analysis MODIFY COLUMN program_file varchar(255);
  
  
  -- extra values for the enum type:
  ALTER TABLE homology MODIFY COLUMN description enum('ortholog_one2one','apparent_ortholog_one2one','ortholog_one2many','ortholog_many2many','within_species_paralog','other_paralog','putative_gene_split','contiguous_gene_split','between_species_paralog ','UBRH','BRH','MBRH','RHS') DEFAULT NULL;
  
  
  -- extra table for protein pipeline:
  CREATE TABLE `protein_tree_hmmprofile` (
      `node_id` int(10) unsigned NOT NULL,
      `type` varchar(40) NOT NULL DEFAULT '',
      `hmmprofile` mediumtext,
      UNIQUE KEY `type_node_id` (`type`,`node_id`),
      KEY `node_id` (`node_id`)
  ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
  
  
  -- 3 more extra tables for protein pipeline:
  CREATE TABLE super_protein_tree_node LIKE protein_tree_node;
  CREATE TABLE super_protein_tree_member LIKE protein_tree_member;
  CREATE TABLE super_protein_tree_tag LIKE protein_tree_tag;
  
  