GenomeHubs
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(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
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$ nano ~/genomehubs/v1/ensembl/conf/setup.ini
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[DATABASE]
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DB_HOST = genomehubs-mysql
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DB_PORT = 3306
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DB_USER = anonymous
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DB_PASS =
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DB_FALLBACK_HOST = mysql-eg-publicsql.ebi.ac.uk
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DB_FALLBACK_PORT = 4157
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DB_FALLBACK_USER = anonymous
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DB_FALLBACK_PASS =
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DB_SESSION_HOST = genomehubs-mysql
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DB_SESSION_PORT = 3306
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DB_SESSION_USER = ensrw
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DB_SESSION_PASS = CHANGEME
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Set database names to load:
  • Assemblies will be listed on your Ensembl site homepage in the order they are added to SPECIES_DBS
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$ nano ~/genomehubs/v1/ensembl/conf/setup.ini
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[DATA_SOURCE]
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SPECIES_DBS = [
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melitaea_cinxia_core_40_93_1
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]
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$ nano ~/genomehubs/v1/ensembl/conf/setup.ini
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[DATA_SOURCE]
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SPECIES_DBS = [
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melitaea_cinxia_core_36_89_1
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]
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$ nano ~/genomehubs/v1/ensembl/conf/setup.ini
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[DATA_SOURCE]
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SPECIES_DBS = [
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melitaea_cinxia_core_32_85_1
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]
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Start the EasyMirror container

Start the EasyMirror Docker container:
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$ docker run -d \
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--name genomehubs-ensembl \
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-v ~/genomehubs/v1/ensembl/conf:/conf:ro \
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--network genomehubs-network \
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-p 8881:8080 \
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genomehubs/easy-mirror:19.05
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$ docker run -d \
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--name genomehubs-ensembl \
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-v ~/genomehubs/v1/ensembl/conf:/conf:ro \
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--link genomehubs-mysql \
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-p 8081:8080 \
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genomehubs/easy-mirror:17.06
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$ docker run -d \
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--name genomehubs-ensembl \
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-v ~/genomehubs/v1/ensembl/conf:/ensembl/conf:ro \
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--link genomehubs-mysql \
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-p 8081:8080 \
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genomehubs/easy-mirror:17.03
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Last modified 1yr ago