(optional) Test Ensembl browser

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

    $ nano ~/genomehubs/v1/ensembl/conf/setup.ini
    [DATA_SOURCE]
    SPECIES_DBS = [
    melitaea_cinxia_core_40_93_1
    ]
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$ 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 container

Start the EasyMirror Docker container:

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$ 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