{"_id":"58c10f5a2c3c720f00768ba3","__v":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"},"parentDoc":null,"user":"573592b84b0ab120000b7d44","githubsync":"","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"},"updates":[],"next":{"pages":[],"description":""},"createdAt":"2016-05-13T10:43:05.481Z","link_external":false,"link_url":"","sync_unique":"","hidden":false,"api":{"results":{"codes":[]},"settings":"","auth":"required","params":[],"url":""},"isReference":false,"order":4,"body":"This step imports the data from the prepared ``.gff`` file ([Step 2.3](doc:step-23-prepare-the-gff-file-for-import)) into the specified core database.  \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=\\\"-g\\\" \\\\\\n           genomehubs/easy-import:latest\",\n      \"language\": \"text\",\n      \"name\": \"run import_gene_models.pl\"\n    }\n  ]\n}\n[/block]\n```\ncd ~/import\nperl ../ei/core/import_gene_models.pl ../ei/conf/core-import.ini\n```\n\nIf more than one ``.gff`` was prepared during [`-p` Prepare the gff file for import](doc:step-23-prepare-the-gff-file-for-import) (due to exceptions that required different pattern matching), each of the ``.ini`` files will be passed to this step in a single command to load all gene models at once.\n[block:api-header]\n{\n  \"type\": \"basic\",\n  \"title\": \"Configuration options\"\n}\n[/block]\n- [[DATABASE_CORE]](doc:database_core-core)\n```\n[DATABASE_CORE]\n\tNAME = operophtera_brumata_v1_core_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  This must refer to the same database as used in [Step 2.2: Create database and load sequence data](doc:step-22-create-database-and-load-sequence-data).\n\n- [[MODIFY]](doc:modify-core)\n```\n[MODIFY]\n\tTRUNCATE_GENE_TABLES = 1\n```\n  If ``TRUNCATE_GENE_TABLES`` is set, all tables that are associated with specific gene models will be truncated allowing for a fresh import of the data.  Otherwise, only additional data will be imported.","excerpt":"","slug":"step-24-import-gff-from-prepared-file","type":"basic","title":"`-g` Import gff from prepared file"}

`-g` Import gff from prepared file


This step imports the data from the prepared ``.gff`` file ([Step 2.3](doc:step-23-prepare-the-gff-file-for-import)) into the specified core database. [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=\"-g\" \\\n genomehubs/easy-import:latest", "language": "text", "name": "run import_gene_models.pl" } ] } [/block] ``` cd ~/import perl ../ei/core/import_gene_models.pl ../ei/conf/core-import.ini ``` If more than one ``.gff`` was prepared during [`-p` Prepare the gff file for import](doc:step-23-prepare-the-gff-file-for-import) (due to exceptions that required different pattern matching), each of the ``.ini`` files will be passed to this step in a single command to load all gene models at once. [block:api-header] { "type": "basic", "title": "Configuration options" } [/block] - [[DATABASE_CORE]](doc:database_core-core) ``` [DATABASE_CORE] NAME = operophtera_brumata_v1_core_31_84_1 HOST = localhost PORT = 3306 RW_USER = importer RW_PASS = importpassword RO_USER = anonymous RO_PASS = ``` This must refer to the same database as used in [Step 2.2: Create database and load sequence data](doc:step-22-create-database-and-load-sequence-data). - [[MODIFY]](doc:modify-core) ``` [MODIFY] TRUNCATE_GENE_TABLES = 1 ``` If ``TRUNCATE_GENE_TABLES`` is set, all tables that are associated with specific gene models will be truncated allowing for a fresh import of the data. Otherwise, only additional data will be imported.