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 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-mysqlDB_PORT = 3306DB_USER = anonymousDB_PASS =​DB_FALLBACK_HOST = mysql-eg-publicsql.ebi.ac.ukDB_FALLBACK_PORT = 4157DB_FALLBACK_USER = anonymousDB_FALLBACK_PASS =​DB_SESSION_HOST = genomehubs-mysqlDB_SESSION_PORT = 3306DB_SESSION_USER = ensrwDB_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
$ nano ~/genomehubs/v1/ensembl/conf/setup.ini[DATA_SOURCE]SPECIES_DBS = [melitaea_cinxia_core_40_93_1]
$ nano ~/genomehubs/v1/ensembl/conf/setup.ini[DATA_SOURCE]SPECIES_DBS = [melitaea_cinxia_core_36_89_1]
$ nano ~/genomehubs/v1/ensembl/conf/setup.ini[DATA_SOURCE]SPECIES_DBS = [melitaea_cinxia_core_32_85_1]
Start the EasyMirror Docker container:
$ docker run -d \--name genomehubs-ensembl \-v ~/genomehubs/v1/ensembl/conf:/conf:ro \--network genomehubs-network \-p 8881:8080 \genomehubs/easy-mirror:19.05
$ docker run -d \--name genomehubs-ensembl \-v ~/genomehubs/v1/ensembl/conf:/conf:ro \--link genomehubs-mysql \-p 8081:8080 \genomehubs/easy-mirror:17.06
$ docker run -d \--name genomehubs-ensembl \-v ~/genomehubs/v1/ensembl/conf:/ensembl/conf:ro \--link genomehubs-mysql \-p 8081:8080 \genomehubs/easy-mirror:17.03