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12. Start Ensembl browser
Ensembl genome browser.

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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Add details of your Ensembl plugin:
  • update YOUR_PLUGIN_URL to point to the git repository you created in the previous step
  • these details should be added above the GENOMEHUBS_PLUGIN_URL so files in this plugin will overwrite those in the GenomeHubs plugin
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$ nano ~/genomehubs/v1/ensembl/conf/setup.ini
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[REPOSITORIES]
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ENSEMBL_URL = https://github.com/Ensembl
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ENSEMBL_BRANCH = release/93
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BIOPERL_URL = https://github.com/bioperl
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BIOPERL_BRANCH = master
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API_PLUGIN_URL = https://github.com/EnsemblGenomes/ensemblgenomes-api
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API_PLUGIN_BRANCH = release/eg/93
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API_PLUGIN_PACKAGE = EG::API
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YOUR_PLUGIN_URL = https://github.com/YOURACCOUNT/YOUR-PLUGIN-NAME
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YOUR_PLUGIN_BRANCH = master
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YOUR_PLUGIN_PACKAGE = EG::YourPlugin
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GENOMEHUBS_PLUGIN_URL = https://github.com/genomehubs/gh-ensembl-plugin
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GENOMEHUBS_PLUGIN_BRANCH = 18.10
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GENOMEHUBS_PLUGIN_PACKAGE = EG::GenomeHubs
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EG_COMMON_PLUGIN_URL = https://github.com/EnsemblGenomes/eg-web-common
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EG_COMMON_PLUGIN_BRANCH = release/eg/40
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EG_COMMON_PLUGIN_PACKAGE = EG::Common
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PUBLIC_PLUGINS = [ ]
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$ nano ~/genomehubs/v1/ensembl/conf/setup.ini
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[REPOSITORIES]
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ENSEMBL_URL = https://github.com/Ensembl
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ENSEMBL_BRANCH = release/89
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BIOPERL_URL = https://github.com/bioperl
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BIOPERL_BRANCH = master
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API_PLUGIN_URL = https://github.com/EnsemblGenomes/ensemblgenomes-api
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API_PLUGIN_BRANCH = release/eg/36
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API_PLUGIN_PACKAGE = EG::API
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YOUR_PLUGIN_URL = https://github.com/YOURACCOUNT/YOUR-PLUGIN-NAME
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YOUR_PLUGIN_BRANCH = master
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YOUR_PLUGIN_PACKAGE = EG::YourPlugin
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GENOMEHUBS_PLUGIN_URL = https://github.com/genomehubs/gh-ensembl-plugin
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GENOMEHUBS_PLUGIN_BRANCH = 17.06
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GENOMEHUBS_PLUGIN_PACKAGE = EG::GenomeHubs
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EG_COMMON_PLUGIN_URL = https://github.com/EnsemblGenomes/eg-web-common
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EG_COMMON_PLUGIN_BRANCH = release/eg/36
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EG_COMMON_PLUGIN_PACKAGE = EG::Common
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PUBLIC_PLUGINS = [ ]
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$ nano ~/genomehubs/v1/ensembl/conf/setup.ini
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[REPOSITORIES]
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ENSEMBL_URL = https://github.com/Ensembl
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ENSEMBL_BRANCH = release/85
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BIOPERL_URL = https://github.com/bioperl
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BIOPERL_BRANCH = master
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API_PLUGIN_URL = https://github.com/EnsemblGenomes/ensemblgenomes-api
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API_PLUGIN_BRANCH = release/eg/32
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API_PLUGIN_PACKAGE = EG::API
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YOUR_PLUGIN_URL = https://github.com/YOURACCOUNT/YOUR-PLUGIN-NAME
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YOUR_PLUGIN_BRANCH = master
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YOUR_PLUGIN_PACKAGE = EG::YourPlugin
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GENOMEHUBS_PLUGIN_URL = https://github.com/genomehubs/gh-ensembl-plugin
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GENOMEHUBS_PLUGIN_BRANCH = 17.03
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GENOMEHUBS_PLUGIN_PACKAGE = EG::GenomeHubs
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EG_COMMON_PLUGIN_URL = https://github.com/EnsemblGenomes/eg-web-common
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EG_COMMON_PLUGIN_BRANCH = release/eg/32
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EG_COMMON_PLUGIN_PACKAGE = EG::Common
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PUBLIC_PLUGINS = [ ]
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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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mellitaea_cinxia_core_40_93_1
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operophtera_brumata_obru1_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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mellitaea_cinxia_core_36_89_1
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operophtera_brumata_obru1_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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mellitaea_cinxia_core_32_85_1
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operophtera_brumata_obru1_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