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`-i` Generate search index

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Search index

Ensembl supports a very basic (direct MySQL) search out of the box, this is best replaced with a search plugin so we have made index_database.pl available to generate an autocomplete/search index compatible with the GenomeHubs gh-ensembl-plugin plugin.

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="-i" \
           genomehubs/easy-import:latest

Configuration options

[META]
    SPECIES.PRODUCTION_NAME = Operophtera_brumata_v1

SPECIES.PRODUCTION_NAME must match the value used during import to the core database.

[DATABASE_SEARCH]
    NAME = lepbase_search_31_84_1
    HOST = localhost
    PORT = 3306
    RW_USER = importer
    RW_PASS = importpassword
    RO_USER = anonymous
    RO_PASS =

Connection details for a search database. Existing entries for the same SPECIES.PRODUCTION_NAME will be overwritten each time this script is run.

Updated less than a minute ago