database.ini

[DATABASE]

Sets up four users:

• DB_USER has only select permissions, using a password for this user is untested
• DB_SESSION_USER has read/write access to the DB_SESSION_NAME database, this is the only
  database that must be hosted locally for the site to work
• DB_IMPORT_USER is not required for a simple mirror site but it is convenient to set up this user now
• DB_ROOT_USER must match the password set in the mySQL Docker container

DB_HOST must match the name you give the mySQL Docker container

[DATABASE]
  DB_USER = anonymous
  DB_PASS =

  DB_SESSION_USER = ensrw
  DB_SESSION_PASS = sessionuserpassword
  DB_SESSION_NAME = ensembl_accounts

  DB_IMPORT_USER = importuser
  DB_IMPORT_PASS = importuserpassword

  DB_ROOT_USER = root
  DB_ROOT_PASSWORD = rootuserpassword
  DB_PORT = 3306
  DB_HOST = example-mysql

[WEBSITE]

Set ENSEMBL_WEBSITE_HOST to allow access to the database from any container on a standard Docker network

[WEBSITE]
  ENSEMBL_WEBSITE_HOST = 172.17.0.0/255.255.0.0

[DATA_SOURCE]

At least one core database needs to be hosted locally if you want to import new data as it is used as a
source for analysis names, etc when creating a new core database. The link between the key names in this
section and the urls they are associated with is relatively arbitrary.

• *_DB_URL must be an ftp url under which directories containing database dumps can be found
• *_DB_REPLACE is a flag controlling behaviour if databases with the same name already exist, set to 1 to overwrite
• *_DBs should be a space-separated list of databases to download from this source
• SPECIES_DB_AUTO_EXPAND is a space separated list of other database types to attempt to fetch for each core
  database listed in SPECIES_DBS, e.g. [ variation funcgen ]
• Due to a bug yet to be followes up, the site works with older versions of the ensembl_accounts database
  but not the corresponding release-85 version

[DATA_SOURCE]
  ENSEMBL_DB_URL = ftp://ftp.ensembl.org/pub/release-85/mysql/
  ENSEMBL_DB_REPLACE =
  ENSEMBL_DBS =

  EG_DB_URL = ftp://ftp.ensemblgenomes.org/pub/release-32/pan_ensembl/mysql/
  EG_DB_REPLACE =
  EG_DBS = [ ncbi_taxonomy ]

  SPECIES_DB_URL = ftp://ftp.ensemblgenomes.org/pub/release-32/metazoa/mysql/
  SPECIES_DB_REPLACE =
  SPECIES_DB_AUTO_EXPAND =
  SPECIES_DBS = [ melitaea_cinxia_core_32_85_1 ]

  MISC_DB_URL = ftp://ftp.ensembl.org/pub/release-79/mysql/
  MISC_DB_REPLACE =
  MISC_DBS = [ ensembl_accounts ]