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

$ 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

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
[REPOSITORIES]
ENSEMBL_URL = https://github.com/Ensembl
ENSEMBL_BRANCH = release/93
BIOPERL_URL = https://github.com/bioperl
BIOPERL_BRANCH = master
API_PLUGIN_URL = https://github.com/EnsemblGenomes/ensemblgenomes-api
API_PLUGIN_BRANCH = release/eg/93
API_PLUGIN_PACKAGE = EG::API
YOUR_PLUGIN_URL = https://github.com/YOURACCOUNT/YOUR-PLUGIN-NAME
YOUR_PLUGIN_BRANCH = master
YOUR_PLUGIN_PACKAGE = EG::YourPlugin
GENOMEHUBS_PLUGIN_URL = https://github.com/genomehubs/gh-ensembl-plugin
GENOMEHUBS_PLUGIN_BRANCH = 18.10
GENOMEHUBS_PLUGIN_PACKAGE = EG::GenomeHubs
EG_COMMON_PLUGIN_URL = https://github.com/EnsemblGenomes/eg-web-common
EG_COMMON_PLUGIN_BRANCH = release/eg/40
EG_COMMON_PLUGIN_PACKAGE = EG::Common
PUBLIC_PLUGINS = [ ]
$ nano ~/genomehubs/v1/ensembl/conf/setup.ini
[REPOSITORIES]
ENSEMBL_URL = https://github.com/Ensembl
ENSEMBL_BRANCH = release/89
BIOPERL_URL = https://github.com/bioperl
BIOPERL_BRANCH = master
API_PLUGIN_URL = https://github.com/EnsemblGenomes/ensemblgenomes-api
API_PLUGIN_BRANCH = release/eg/36
API_PLUGIN_PACKAGE = EG::API
YOUR_PLUGIN_URL = https://github.com/YOURACCOUNT/YOUR-PLUGIN-NAME
YOUR_PLUGIN_BRANCH = master
YOUR_PLUGIN_PACKAGE = EG::YourPlugin
GENOMEHUBS_PLUGIN_URL = https://github.com/genomehubs/gh-ensembl-plugin
GENOMEHUBS_PLUGIN_BRANCH = 17.06
GENOMEHUBS_PLUGIN_PACKAGE = EG::GenomeHubs
EG_COMMON_PLUGIN_URL = https://github.com/EnsemblGenomes/eg-web-common
EG_COMMON_PLUGIN_BRANCH = release/eg/36
EG_COMMON_PLUGIN_PACKAGE = EG::Common
PUBLIC_PLUGINS = [ ]
$ nano ~/genomehubs/v1/ensembl/conf/setup.ini
[REPOSITORIES]
ENSEMBL_URL = https://github.com/Ensembl
ENSEMBL_BRANCH = release/85
BIOPERL_URL = https://github.com/bioperl
BIOPERL_BRANCH = master
API_PLUGIN_URL = https://github.com/EnsemblGenomes/ensemblgenomes-api
API_PLUGIN_BRANCH = release/eg/32
API_PLUGIN_PACKAGE = EG::API
YOUR_PLUGIN_URL = https://github.com/YOURACCOUNT/YOUR-PLUGIN-NAME
YOUR_PLUGIN_BRANCH = master
YOUR_PLUGIN_PACKAGE = EG::YourPlugin
GENOMEHUBS_PLUGIN_URL = https://github.com/genomehubs/gh-ensembl-plugin
GENOMEHUBS_PLUGIN_BRANCH = 17.03
GENOMEHUBS_PLUGIN_PACKAGE = EG::GenomeHubs
EG_COMMON_PLUGIN_URL = https://github.com/EnsemblGenomes/eg-web-common
EG_COMMON_PLUGIN_BRANCH = release/eg/32
EG_COMMON_PLUGIN_PACKAGE = EG::Common
PUBLIC_PLUGINS = [ ]

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
[DATA_SOURCE]
SPECIES_DBS = [
mellitaea_cinxia_core_40_93_1
operophtera_brumata_obru1_core_40_93_1
]
$ nano ~/genomehubs/v1/ensembl/conf/setup.ini
[DATA_SOURCE]
SPECIES_DBS = [
mellitaea_cinxia_core_36_89_1
operophtera_brumata_obru1_core_36_89_1
]
$ nano ~/genomehubs/v1/ensembl/conf/setup.ini
[DATA_SOURCE]
SPECIES_DBS = [
mellitaea_cinxia_core_32_85_1
operophtera_brumata_obru1_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