6. Import analysis results

The results of common analyses can be imported into an Ensembl database to provide functional annotations.

Running the file export after this stage will add additional information to the exported FASTA headers and json files. Updating the index (with the -i flag) will index the descriptions imported from blastp and interproscan results.

Run the import script:

-b will import blastp and InterProScan results
-r will import RepeatMasker results (omit this flag if you have used RepeatDetector in place of RepeatMasker as the results cannot be imported)
-c will import CEGMA and BUSCO results

$ docker run --rm \
             -u $UID:$GROUPS \
             --name easy-import-operophtera_brumata_v1_core_40_93_1 \
             --network genomehubs-network \
             -v ~/genomehubs/v1/import/conf:/import/conf \
             -v ~/genomehubs/v1/import/data:/import/data \
             -v ~/genomehubs/v1/download/data:/import/download \
             -e DATABASE=operophtera_brumata_obru1_core_40_93_1 \
             -e FLAGS="-b -r -c" \
             genomehubs/easy-import:19.05

$ docker run --rm \
             -u $UID:$GROUPS \
             --name easy-import-operophtera_brumata_v1_core_36_89_1 \
             --link genomehubs-mysql \
             -v ~/genomehubs/v1/import/conf:/import/conf \
             -v ~/genomehubs/v1/import/data:/import/data \
             -v ~/genomehubs/v1/download/data:/download/data \
             -e DATABASE=operophtera_brumata_obru1_core_36_89_1 \
             -e FLAGS="-b -r -c" \
             genomehubs/easy-import:17.06

$ docker run --rm \
             -u $UID:$GROUPS \
             --name easy-import-operophtera_brumata_v1_core_32_85_1 \
             --link genomehubs-mysql \
             -v ~/genomehubs/v1/import/conf:/import/conf \
             -v ~/genomehubs/v1/import/data:/import/data \
             -v ~/genomehubs/v1/download/data:/download/data \
             -e DATABASE=operophtera_brumata_obru1_core_32_85_1 \
             -e FLAGS="-b -r -c" \
             genomehubs/easy-import:17.06

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$ docker run --rm \ -u $UID:$GROUPS \ --name easy-import-operophtera_brumata_v1_core_40_93_1 \ --network genomehubs-network \ -v ~/genomehubs/v1/import/conf:/import/conf \ -v ~/genomehubs/v1/import/data:/import/data \ -v ~/genomehubs/v1/download/data:/import/download \ -e DATABASE=operophtera_brumata_obru1_core_40_93_1 \ -e FLAGS="-b -r -c" \ genomehubs/easy-import:19.05

$ docker run --rm \ -u $UID:$GROUPS \ --name easy-import-operophtera_brumata_v1_core_36_89_1 \ --link genomehubs-mysql \ -v ~/genomehubs/v1/import/conf:/import/conf \ -v ~/genomehubs/v1/import/data:/import/data \ -v ~/genomehubs/v1/download/data:/download/data \ -e DATABASE=operophtera_brumata_obru1_core_36_89_1 \ -e FLAGS="-b -r -c" \ genomehubs/easy-import:17.06

$ docker run --rm \ -u $UID:$GROUPS \ --name easy-import-operophtera_brumata_v1_core_32_85_1 \ --link genomehubs-mysql \ -v ~/genomehubs/v1/import/conf:/import/conf \ -v ~/genomehubs/v1/import/data:/import/data \ -v ~/genomehubs/v1/download/data:/download/data \ -e DATABASE=operophtera_brumata_obru1_core_32_85_1 \ -e FLAGS="-b -r -c" \ genomehubs/easy-import:17.06