{"metadata":{"image":[],"title":"","description":""},"api":{"url":"","auth":"required","params":[],"results":{"codes":[]},"settings":""},"next":{"description":"","pages":[]},"title":"`-g` Import gff from prepared file","type":"basic","slug":"step-24-import-gff-from-prepared-file","excerpt":"","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.","updates":[],"order":4,"isReference":false,"hidden":false,"sync_unique":"","link_url":"","link_external":false,"_id":"58c10f5a2c3c720f00768ba3","__v":0,"category":{"sync":{"isSync":false,"url":""},"pages":[],"title":"Importing data","slug":"quick-start","order":4,"from_sync":false,"reference":false,"_id":"58c10f5a2c3c720f00768b8a","version":"58c10f5a2c3c720f00768b87","createdAt":"2016-05-13T09:49:29.176Z","__v":0,"project":"5735936aafab441700723a50"},"parentDoc":null,"user":"573592b84b0ab120000b7d44","githubsync":"","project":"5735936aafab441700723a50","createdAt":"2016-05-13T10:43:05.481Z","version":{"version":"2.0","version_clean":"2.0.0","codename":"","is_stable":true,"is_beta":false,"is_hidden":false,"is_deprecated":false,"categories":["58c10f5a2c3c720f00768b88","58c10f5a2c3c720f00768b89","58c10f5a2c3c720f00768b8a","58c10f5a2c3c720f00768b8b","58c10f5a2c3c720f00768b8c","58c10f5a2c3c720f00768b8d","58c10f5a2c3c720f00768b8e","58c10f5a2c3c720f00768b8f","58c10f5a2c3c720f00768b90","58c10f5a2c3c720f00768b91","58c10f5a2c3c720f00768b92","58c10f5a2c3c720f00768b93","58c11574b36d8c0f006fda47","58c2cdcafc6eed3900e97640","58c2ce8afc6eed3900e97663"],"_id":"58c10f5a2c3c720f00768b87","project":"5735936aafab441700723a50","releaseDate":"2017-03-09T08:16:26.385Z","createdAt":"2017-03-09T08:16:26.385Z","__v":4}}

`-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.