This step imports the data from the prepared
.gff file (Step 2.3) into the specified core database.
docker run --rm \ --name easy-import-operophtera_brumata_v1_core_32_85_1 \ --link genomehubs-mysql \ -v ~/demo/genomehubs-import/import/conf:/import/conf \ -v ~/demo/genomehubs-import/import/data:/import/data \ -e DATABASE=operophtera_brumata_v1_core_32_85_1 \ -e FLAGS="-g" \ genomehubs/easy-import:latest
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 (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.
[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.
[MODIFY] TRUNCATE_GENE_TABLES = 1
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.
Updated less than a minute ago