CROSSMATCH:
1)Need old and new database on the same machine, so if not present copy current database tables dna,contig,clone. Use mysqldump -q -C -T .

2)Get all clones that have changed version between releases: select c1.id from ensembl080.clone c1, ensembl100.clone c2 where c1.embl_version != c2.version and c1.id = c2.id into outfile '/work2/elia/changed.clones';

3)Create crossmatch database:
mysqladmin -u root create cross100
mysql -u root cross100 < src/ensembl/sql/crossmatch.sql

4)Populate clonelist table:
load data infile '/work2/elia/changed.clones' into table clonelist

5)Fill dblocation table:
insert into dblocation values('Bio::EnsEMBL::DBOLD::Obj/host=ecs1c;port=410000;dbname=olddbname;user=ensro;pass=','Bio::EnsEMBL::DBSQL::Adaptor/host=ecs1c;port=410000;dbname=newdbname;user=ensro;pass=');

6)Update the DBOLD directory with the previous branch (using misc-scripts/utilities/dbsql_dbold.pl)

7)Run crossclonemap.pl! (change crossdb name)

8)When all jobs are finished, check for failed jobs, rerun if necessary

9)Run map_genes.pl
