GenomeHubs
  • Introduction
  • Introduction
    • GenomeHubs
    • Files and containers
    • Demo
  • Quick Start
    • 1. Prepare
    • 2. Setup MySQL database server
    • (optional) Test Ensembl browser
    • 3. Import assembly and gene models
    • 4. Export files
    • 5. Run analyses
    • 6. Import analysis results
    • 7. Update meta
    • 8. Start download site
    • 9. Start BLAST server
    • 10. Start search container
    • 11. Edit Ensembl plugin
    • 12. Start Ensembl browser
  • Next Steps
    • Setup with multiple hosts
    • Understand the GFF parser
    • Import additional assemblies
    • Run comparative analyses
    • Import variation data
    • Add track hubs
    • Connect using Perl API
    • Set up REST API
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  1. Quick Start

6. Import analysis results

Previous5. Run analysesNext7. Update meta

Last updated 4 years ago

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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