Ensembl minimum install

You need the fasta and AGP files for an assembly. Ensembl supports multiple coordinate systems: Any piece of DNA can be referenced by it's chromosomal location (1:1000), its super_contig location (NT_039500:1-1000) or other coordinates

• Create an empty database named mouse37_mini_ref and populate it with the CORE schema:

 mysql -uens-training -pworkshop -h127.0.0.1 -P3306 -D mouse37_mini_ref < $HOME/cvs_checkout/ensembl/sql/table.sql

• Load sequences into the empty core database:

 perl $PS/load_seq_region.pl -dbhost 127.0.0.1 -dbuser ens-training -dbport 3306 -dbname mouse37_mini_ref -dbpass workshop -coord_system_name chromosome -coord_system_version NCBIM37 -rank 1 -default_version -agp_file $HOME/workshop/genebuild/assembly/mini_chr_contig.agp