{"_id":"58c116463384df0f0000eaaa","user":"573592b84b0ab120000b7d44","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"},"__v":0,"category":{"_id":"58c11574b36d8c0f006fda47","project":"5735936aafab441700723a50","version":"58c10f5a2c3c720f00768b87","__v":0,"sync":{"url":"","isSync":false},"reference":false,"createdAt":"2017-03-09T08:42:28.884Z","from_sync":false,"order":1,"slug":"files","title":"Files"},"parentDoc":null,"project":"5735936aafab441700723a50","githubsync":"","updates":[],"next":{"pages":[],"description":""},"createdAt":"2017-03-09T08:45:58.882Z","link_external":false,"link_url":"","sync_unique":"","hidden":false,"api":{"results":{"codes":[]},"settings":"","auth":"required","params":[],"url":""},"isReference":false,"order":1,"body":"## `[DATABASE]`\n\nWith the exception of the session/ensembl_accounts database, EasyMirror will attempt to find\neach database listed in `[DATA_SOURCE]` at `DB_HOST`, if it cannot connect it will try\n`DB_FALLBACK_HOST`, then `DB_FALLBACK2_HOST` so databases used in the final site can be hosted\nin multiple locations.\n\n`DB_SESSION_HOST` should match the mySQL Docker container name, other hosts can be set to any\naccessible mysql hostname.\n\n```\n[DATABASE]\n  DB_HOST = example-mysql\n  DB_PORT = 3306\n  DB_USER = anonymous\n  DB_PASS =\n\n  DB_SESSION_HOST = example-mysql\n  DB_SESSION_PORT = 3306\n  DB_SESSION_USER = ensrw\n  DB_SESSION_PASS = sessionuserpassword\n\n  DB_FALLBACK_HOST = mysql-eg-publicsql.ebi.ac.uk\n  DB_FALLBACK_PORT = 4157\n  DB_FALLBACK_USER = anonymous\n  DB_FALLBACK_PASS =\n\n  DB_FALLBACK2_HOST = ensembldb.ensembl.org\n  DB_FALLBACK2_PORT = 3306\n  DB_FALLBACK2_USER = anonymous\n  DB_FALLBACK2_PASS =\n```\n\n## `[REPOSITORIES]`\n\nA list of plugins to use, `ENSEMBL_*` (which fetches a number of repositories) and `BIOPERL_*`\nare essential, the others are optional. Branches should match the release versions of the\ndatabases (currently 85/32 for Ensembl/EnsemblGenomes).\n\nTo customise the site, create and add your own plugin repository, after `BIOPERL`, repositories higher\nup the list will be loaded after those below so can overwrite specific settings.\n\n```\n[REPOSITORIES]\n  ENSEMBL_URL = https://github.com/Ensembl\n  ENSEMBL_BRANCH = release/85\n\n  BIOPERL_URL = https://github.com/bioperl\n  BIOPERL_BRANCH = master\n\n  EG_METAZOA_PLUGIN_URL = https://github.com/EnsemblGenomes/eg-web-metazoa\n  EG_METAZOA_PLUGIN_BRANCH = release/eg/32\n  EG_METAZOA_PLUGIN_PACKAGE = EG::Metazoa\n\n  API_PLUGIN_URL = https://github.com/EnsemblGenomes/ensemblgenomes-api\n  API_PLUGIN_BRANCH = release/eg/32\n  API_PLUGIN_PACKAGE = EG::API\n\n  EG_COMMON_PLUGIN_URL = https://github.com/EnsemblGenomes/eg-web-common\n  EG_COMMON_PLUGIN_BRANCH = release/eg/32\n  EG_COMMON_PLUGIN_PACKAGE = EG::Common\n\n  PUBLIC_PLUGINS = [ ]\n```\n\n## `[WEBSITE]`\n\nThere should be no need to change these values\n\n```\n[WEBSITE]\n  HTTP_PORT = 8080\n  SERVER_ROOT = /ensembl\n```\n\n## `[DATA_SOURCE]`\n\nAll databases listed here should be available on at least one of the database hosts listed under `[DATABASE]`.\n\n- `SPECIES_DBS` a space separated list of core databases to include in the site. After importing\n  new assemblies, add the database name to this list before reloading\n- `SPECIES_DB_AUTO_EXPAND` to also include variation, etc. databases for one or more core databases,\n  list the types to attempt to load here\n- `MULTI_DBS` databases that are needed for an EnsemblGenomes site\n- `COMPARA_DBS` compara databases should be listed separately\n\n```\n[DATA_SOURCE]\n  SPECIES_DBS = [\n\tmelitaea_cinxia_core_32_85_1\n\t]\n  SPECIES_DB_AUTO_EXPAND [ ]\n  MULTI_DBS = [ ensemblgenomes_ontology_32_85 ensemblgenomes_info_32 ensembl_archive_85 ensembl_website_85 ]\n  COMPARA_DBS = [ ensembl_compara_metazoa_32_85 ensembl_compara_pan_homology_32_85 ]\n```","excerpt":"","slug":"setupini","type":"basic","title":"setup.ini"}
## `[DATABASE]` With the exception of the session/ensembl_accounts database, EasyMirror will attempt to find each database listed in `[DATA_SOURCE]` at `DB_HOST`, if it cannot connect it will try `DB_FALLBACK_HOST`, then `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 = ``` ## `[REPOSITORIES]` A list of plugins to use, `ENSEMBL_*` (which fetches a number of repositories) and `BIOPERL_*` 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 = [ ] ``` ## `[WEBSITE]` There should be no need to change these values ``` [WEBSITE] HTTP_PORT = 8080 SERVER_ROOT = /ensembl ``` ## `[DATA_SOURCE]` All databases listed here should be available on at least one of the database hosts listed under `[DATABASE]`. - `SPECIES_DBS` a 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_EXPAND` to also include variation, etc. databases for one or more core databases, list the types to attempt to load here - `MULTI_DBS` databases that are needed for an EnsemblGenomes site - `COMPARA_DBS` compara 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 ] ```