At this stage you may wish to start up a basic Ensembl mirror site using the local copy of the Ensembl core database(s) from the previous step. This will lack many of the additional features of a complete GenomeHubs site but provides a useful opportunity to check that the basic components are working before continuing with the instructions to import your own data.
Edit setup.ini
Edit database settings:
for the default setup, only DB_SESSION_PASS should need changing
database hosts should match the name of your mysql container
DB_FALLBACK_HOST is used to allow additional databases to be loaded from a remote host (in this case EnsemblGenomes) so not all databases need to be hosted locally
$ nano ~/genomehubs/v1/ensembl/conf/setup.ini
[DATABASE]
DB_HOST = genomehubs-mysql
DB_PORT = 3306
DB_USER = anonymous
DB_PASS =
​
DB_FALLBACK_HOST = mysql-eg-publicsql.ebi.ac.uk
DB_FALLBACK_PORT = 4157
DB_FALLBACK_USER = anonymous
DB_FALLBACK_PASS =
​
DB_SESSION_HOST = genomehubs-mysql
DB_SESSION_PORT = 3306
DB_SESSION_USER = ensrw
DB_SESSION_PASS = CHANGEME
Set database names to load:
Assemblies will be listed on your Ensembl site homepage in the order they are added to SPECIES_DBS