{"_id":"58c10f5a2c3c720f00768b9c","category":{"_id":"58c10f5a2c3c720f00768b90","project":"5735936aafab441700723a50","__v":0,"version":"58c10f5a2c3c720f00768b87","sync":{"url":"","isSync":false},"reference":false,"createdAt":"2016-05-13T14:33:40.982Z","from_sync":false,"order":11,"slug":"configuration-options-database","title":"Configuration Options (Database)"},"version":{"_id":"58c10f5a2c3c720f00768b87","project":"5735936aafab441700723a50","__v":4,"createdAt":"2017-03-09T08:16:26.385Z","releaseDate":"2017-03-09T08:16:26.385Z","categories":["58c10f5a2c3c720f00768b88","58c10f5a2c3c720f00768b89","58c10f5a2c3c720f00768b8a","58c10f5a2c3c720f00768b8b","58c10f5a2c3c720f00768b8c","58c10f5a2c3c720f00768b8d","58c10f5a2c3c720f00768b8e","58c10f5a2c3c720f00768b8f","58c10f5a2c3c720f00768b90","58c10f5a2c3c720f00768b91","58c10f5a2c3c720f00768b92","58c10f5a2c3c720f00768b93","58c11574b36d8c0f006fda47","58c2cdcafc6eed3900e97640","58c2ce8afc6eed3900e97663"],"is_deprecated":false,"is_hidden":false,"is_beta":false,"is_stable":true,"codename":"","version_clean":"2.0.0","version":"2.0"},"parentDoc":null,"user":"573592b84b0ab120000b7d44","githubsync":"","project":"5735936aafab441700723a50","__v":0,"updates":[],"next":{"pages":[],"description":""},"createdAt":"2016-05-13T15:08:27.168Z","link_external":false,"link_url":"","sync_unique":"","hidden":false,"api":{"settings":"","results":{"codes":[]},"auth":"required","params":[],"url":""},"isReference":false,"order":0,"body":"```\nDATA_SOURCE]\n  ENSEMBL_DB_URL = ftp://ftp.ensembl.org/pub/current_mysql/\n  ENSEMBL_DB_REPLACE =\n  ENSEMBL_DBS = [ ensembl_accounts ]\n\n  EG_DB_URL = ftp://ftp.ensemblgenomes.org/pub/current/pan_ensembl/mysql/\n  EG_DB_REPLACE = 1\n  EG_DBS = [ ncbi_taxonomy ensembl_website_84 ]\n\n  SPECIES_DB_URL = ftp://ftp.ensemblgenomes.org/pub/current/metazoa/mysql/\n  SPECIES_DB_REPLACE =\n  SPECIES_DB_AUTO_EXPAND =\n  SPECIES_DBS = [ bombyx_mori_core_31_84_1 ]\n\n  MISC_DB_URL =\n  MISC_DB_REPLACE =\n  MISC_DBS =\n```\n\n- ``ENSEMBL_DB_URL`` - the URL containing the Ensembl database dumps\n- ``ENSEMBL_DB_REPLACE`` - a flag to specify whether to overwrite databases that already exist on the ``DB_HOST``\n- ``ENSEMBL_DBS`` - a space separated list of database dump names in square braces. ``ensembl_accounts`` is required, all others are optional\n- The equivalent variables may be set for ``EG_DB_URL`` to fetch and download EnsemblGenomes database dumps and for ``MISC_DB_URL`` to support situations where the required databases are spread across multiple hosts.\n- An additional variable may be set for species databases, ``SPECIES_DB_AUTO_EXPAND`` - a space separated list of database types to use as replacement strings for ``core`` to facilitate downloading multiple database types for each species in ``SPECIES_DBS``","excerpt":"Locations and names of database dumps to fetch and load locally","slug":"data_source-db","type":"basic","title":"[DATA_SOURCE]"}

[DATA_SOURCE]

Locations and names of database dumps to fetch and load locally

``` DATA_SOURCE] ENSEMBL_DB_URL = ftp://ftp.ensembl.org/pub/current_mysql/ ENSEMBL_DB_REPLACE = ENSEMBL_DBS = [ ensembl_accounts ] EG_DB_URL = ftp://ftp.ensemblgenomes.org/pub/current/pan_ensembl/mysql/ EG_DB_REPLACE = 1 EG_DBS = [ ncbi_taxonomy ensembl_website_84 ] SPECIES_DB_URL = ftp://ftp.ensemblgenomes.org/pub/current/metazoa/mysql/ SPECIES_DB_REPLACE = SPECIES_DB_AUTO_EXPAND = SPECIES_DBS = [ bombyx_mori_core_31_84_1 ] MISC_DB_URL = MISC_DB_REPLACE = MISC_DBS = ``` - ``ENSEMBL_DB_URL`` - the URL containing the Ensembl database dumps - ``ENSEMBL_DB_REPLACE`` - a flag to specify whether to overwrite databases that already exist on the ``DB_HOST`` - ``ENSEMBL_DBS`` - a space separated list of database dump names in square braces. ``ensembl_accounts`` is required, all others are optional - The equivalent variables may be set for ``EG_DB_URL`` to fetch and download EnsemblGenomes database dumps and for ``MISC_DB_URL`` to support situations where the required databases are spread across multiple hosts. - An additional variable may be set for species databases, ``SPECIES_DB_AUTO_EXPAND`` - a space separated list of database types to use as replacement strings for ``core`` to facilitate downloading multiple database types for each species in ``SPECIES_DBS``