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