{"__v":7,"_id":"5735afb9afab441700723ab3","category":{"__v":0,"_id":"5735a32931a73b1700887c94","project":"5735936aafab441700723a50","version":"5735936aafab441700723a53","sync":{"url":"","isSync":false},"reference":false,"createdAt":"2016-05-13T09:49:29.176Z","from_sync":false,"order":2,"slug":"quick-start","title":"Stage 2 - Core Import"},"parentDoc":null,"project":"5735936aafab441700723a50","user":"573592b84b0ab120000b7d44","version":{"__v":12,"_id":"5735936aafab441700723a53","project":"5735936aafab441700723a50","createdAt":"2016-05-13T08:42:18.615Z","releaseDate":"2016-05-13T08:42:18.615Z","categories":["5735936aafab441700723a54","5735a32931a73b1700887c94","5735b55beceb872200abbc6c","5735b56eb667601700d3bd6f","5735b9ba4b0ab120000b7dd4","5735b9c94b0ab120000b7dd5","5735cb131f16241700c8a0f7","5735e5c4e4824c3400aa1f21","5735e5d9e4824c3400aa1f23","5735e5f2ec67f6290013ac72","573ecfe0804f901700a9dfc7","573f276c7eeb8b190094ca7d"],"is_deprecated":false,"is_hidden":false,"is_beta":false,"is_stable":false,"codename":"","version_clean":"1.0.0","version":"1.0"},"updates":[],"next":{"pages":[],"description":""},"createdAt":"2016-05-13T10:43:05.481Z","link_external":false,"link_url":"","githubsync":"","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\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 [Step 2.3](doc:step-23-prepare-the-gff-file-for-import) (due to exceptions that required different pattern matching), each of the ``.ini`` files can be passed to this step in a single command to load all gene models at once.\n\n```\nperl ../ei/core/import_gene_models.pl ../ei/conf/core-import.ini /path/to/exception.ini\n```\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":"Step 2.4: Import gff from prepared file"}

Step 2.4: 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. ``` cd ~/import perl ../ei/core/import_gene_models.pl ../ei/conf/core-import.ini ``` If more than one ``.gff`` was prepared during [Step 2.3](doc:step-23-prepare-the-gff-file-for-import) (due to exceptions that required different pattern matching), each of the ``.ini`` files can be passed to this step in a single command to load all gene models at once. ``` perl ../ei/core/import_gene_models.pl ../ei/conf/core-import.ini /path/to/exception.ini ``` [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.