`-g` Import gff from prepared file

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" \
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.

Configuration options

    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.


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.