With the exception of the session/ensembl_accounts database, EasyMirror will attempt to find
each database listed in
DB_HOST, if it cannot connect it will try
DB_FALLBACK2_HOST so databases used in the final site can be hosted
in multiple locations.
DB_SESSION_HOST should match the mySQL Docker container name, other hosts can be set to any
accessible mysql hostname.
[DATABASE] DB_HOST = example-mysql DB_PORT = 3306 DB_USER = anonymous DB_PASS = DB_SESSION_HOST = example-mysql DB_SESSION_PORT = 3306 DB_SESSION_USER = ensrw DB_SESSION_PASS = sessionuserpassword DB_FALLBACK_HOST = mysql-eg-publicsql.ebi.ac.uk DB_FALLBACK_PORT = 4157 DB_FALLBACK_USER = anonymous DB_FALLBACK_PASS = DB_FALLBACK2_HOST = ensembldb.ensembl.org DB_FALLBACK2_PORT = 3306 DB_FALLBACK2_USER = anonymous DB_FALLBACK2_PASS =
A list of plugins to use,
ENSEMBL_* (which fetches a number of repositories) and
are essential, the others are optional. Branches should match the release versions of the
databases (currently 85/32 for Ensembl/EnsemblGenomes).
To customise the site, create and add your own plugin repository, after
BIOPERL, repositories higher
up the list will be loaded after those below so can overwrite specific settings.
[REPOSITORIES] ENSEMBL_URL = https://github.com/Ensembl ENSEMBL_BRANCH = release/85 BIOPERL_URL = https://github.com/bioperl BIOPERL_BRANCH = master EG_METAZOA_PLUGIN_URL = https://github.com/EnsemblGenomes/eg-web-metazoa EG_METAZOA_PLUGIN_BRANCH = release/eg/32 EG_METAZOA_PLUGIN_PACKAGE = EG::Metazoa API_PLUGIN_URL = https://github.com/EnsemblGenomes/ensemblgenomes-api API_PLUGIN_BRANCH = release/eg/32 API_PLUGIN_PACKAGE = EG::API 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 = [ ]
There should be no need to change these values
[WEBSITE] HTTP_PORT = 8080 SERVER_ROOT = /ensembl
All databases listed here should be available on at least one of the database hosts listed under
SPECIES_DBSa space separated list of core databases to include in the site. After importing
new assemblies, add the database name to this list before reloading
SPECIES_DB_AUTO_EXPANDto also include variation, etc. databases for one or more core databases,
list the types to attempt to load here
MULTI_DBSdatabases that are needed for an EnsemblGenomes site
COMPARA_DBScompara databases should be listed separately
[DATA_SOURCE] SPECIES_DBS = [ melitaea_cinxia_core_32_85_1 ] SPECIES_DB_AUTO_EXPAND [ ] MULTI_DBS = [ ensemblgenomes_ontology_32_85 ensemblgenomes_info_32 ensembl_archive_85 ensembl_website_85 ] COMPARA_DBS = [ ensembl_compara_metazoa_32_85 ensembl_compara_pan_homology_32_85 ]
Updated less than a minute ago