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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  • Mirror additional species from Ensembl/EnsemblGenomes
  • Import additional assemblies from FASTA+GFF

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  1. Next Steps

Import additional assemblies

The Quick Start guide shows an example set up with one species mirrored from an existing Ensembl database and a second species imported directly from FASTA and GFF files. Further assemblies (for the same or different species) can be added from either of these sources to provide a consistent interface to multiple assemblies and to support comparative analyses across a suite of related taxa.

Mirror additional species from Ensembl/EnsemblGenomes

To mirror additional assemblies from Ensembl/EnsemblGenomes, add then to the database.ini file and re-run the database import. Existing databases will not be re-imported unless you set the corresponding _DB_REPLACE value to 1.

To import additional database types (e.g. variation, funcgen, etc) in addition to the core database add a list of database types to download to SPECIES_DB_AUTO_EXPAND:

$ nano ~/genomehubs/v1/ensembl/conf/database.ini
SPECIES_DB_AUTO_EXPAND = [ variation funcgen ]

Import additional assemblies from FASTA+GFF

To import additional assemblies, repeat steps 3 to 7 (substituting the new assembly name and details) then remove the SequenceServer and EasyMirror containers:

$ docker rm -f genomehubs-sequenceserver
$ docker rm -f genomehubs-ensembl

Then follow steps 9 to 11, adding the new assembly database name to setup.ini before restarting the EasyMirror container.

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Last updated 4 years ago

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