{"_id":"58c10f5a2c3c720f00768ba7","githubsync":"","user":"573592b84b0ab120000b7d44","__v":0,"parentDoc":null,"project":"5735936aafab441700723a50","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"},"category":{"_id":"58c10f5a2c3c720f00768b8a","version":"58c10f5a2c3c720f00768b87","__v":0,"project":"5735936aafab441700723a50","sync":{"url":"","isSync":false},"reference":false,"createdAt":"2016-05-13T09:49:29.176Z","from_sync":false,"order":4,"slug":"quick-start","title":"Importing data"},"updates":[],"next":{"pages":[],"description":""},"createdAt":"2016-05-13T11:15:06.329Z","link_external":false,"link_url":"","sync_unique":"","hidden":false,"api":{"results":{"codes":[]},"settings":"","auth":"required","params":[],"url":""},"isReference":false,"order":8,"body":"[block:callout]\n{\n  \"type\": \"warning\",\n  \"title\": \"Search index\",\n  \"body\": \"Ensembl supports a very basic (direct ``MySQL``) search out of the box, this is best replaced with a search plugin so we have made ``index_database.pl`` available to generate an autocomplete/search index compatible with the GenomeHubs [gh-ensembl-plugin](https://github.com/genomehubs/gh-ensembl-plugin) plugin.\"\n}\n[/block]\n\n[block:code]\n{\n  \"codes\": [\n    {\n      \"code\": \"docker run --rm \\\\\\n           --name easy-import-operophtera_brumata_v1_core_32_85_1 \\\\\\n           --link genomehubs-mysql \\\\\\n           -v ~/demo/genomehubs-import/import/conf:/import/conf \\\\\\n           -v ~/demo/genomehubs-import/import/data:/import/data \\\\\\n           -e DATABASE=operophtera_brumata_v1_core_32_85_1 \\\\\\n           -e FLAGS=\\\"-i\\\" \\\\\\n           genomehubs/easy-import:latest\",\n      \"language\": \"text\",\n      \"name\": \"run index_database.pl\"\n    }\n  ]\n}\n[/block]\n\n[block:api-header]\n{\n  \"type\": \"basic\",\n  \"title\": \"Configuration options\"\n}\n[/block]\n- [[META]](doc:meta-core) \n```\n[META]\n    SPECIES.PRODUCTION_NAME = Operophtera_brumata_v1\n```\n  ``SPECIES.PRODUCTION_NAME`` must match the value used during import to the core database.\n\n- [DATABASE_SEARCH](doc:database_search-core)\n```\n[DATABASE_SEARCH]\n\tNAME = lepbase_search_31_84_1\n\tHOST = localhost\n\tPORT = 3306\n\tRW_USER = importer\n\tRW_PASS = importpassword\n\tRO_USER = anonymous\n\tRO_PASS =\n```\n  Connection details for a search database.  Existing entries for the same ``SPECIES.PRODUCTION_NAME`` will be overwritten each time this script is run.","excerpt":"(optional)","slug":"step-28-generate-search-index","type":"basic","title":"`-i` Generate search index"}

`-i` Generate search index

(optional)

[block:callout] { "type": "warning", "title": "Search index", "body": "Ensembl supports a very basic (direct ``MySQL``) search out of the box, this is best replaced with a search plugin so we have made ``index_database.pl`` available to generate an autocomplete/search index compatible with the GenomeHubs [gh-ensembl-plugin](https://github.com/genomehubs/gh-ensembl-plugin) plugin." } [/block] [block:code] { "codes": [ { "code": "docker run --rm \\\n --name easy-import-operophtera_brumata_v1_core_32_85_1 \\\n --link genomehubs-mysql \\\n -v ~/demo/genomehubs-import/import/conf:/import/conf \\\n -v ~/demo/genomehubs-import/import/data:/import/data \\\n -e DATABASE=operophtera_brumata_v1_core_32_85_1 \\\n -e FLAGS=\"-i\" \\\n genomehubs/easy-import:latest", "language": "text", "name": "run index_database.pl" } ] } [/block] [block:api-header] { "type": "basic", "title": "Configuration options" } [/block] - [[META]](doc:meta-core) ``` [META] SPECIES.PRODUCTION_NAME = Operophtera_brumata_v1 ``` ``SPECIES.PRODUCTION_NAME`` must match the value used during import to the core database. - [DATABASE_SEARCH](doc:database_search-core) ``` [DATABASE_SEARCH] NAME = lepbase_search_31_84_1 HOST = localhost PORT = 3306 RW_USER = importer RW_PASS = importpassword RO_USER = anonymous RO_PASS = ``` Connection details for a search database. Existing entries for the same ``SPECIES.PRODUCTION_NAME`` will be overwritten each time this script is run.