Example configurations to set up custom Ensembl sites using GenomeHubs
- Basic mirror setup - the simplest Ensembl mirror site setup
- GenomeHubs mirror setup - an Ensembl mirror site using the GenomeHubs plugin, including separate BLAST and download containers
- GenomeHubs import - a full GenomeHubs site hosting the an assembly and gene models imported from FASTA + GFF
Either follow the full tutorials at genomehubs.org or try out the example scripts to get a GenomeHubs Ensembl site up and running as quickly as possible.
demo.sh- set up a GenomeHubs site hosting a mirror of the core database for the Glanville fritillary, Melitaea cinxiaimport.sh- import the genome of the winter moth, Operophtera brumata, into a GenomeHubs site from FASTA and GFF
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If the easy-mirror container is unable to connect to the mysql-server container this is usually because the mysql-server cintainer configuration did not finish before the easy-mirror container started. This will usually be resolved by rerunning the script.
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If the containers already exist when either demo script is run, they will be removed. Rerun the the script to continue.
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If any of the containers fail to run correctly with a permissions error this is likely to be due to running the scripts as a user with a UID other than 1000. There are work arounds for this but we are unable to support problems caused by incompatible users/permissions. Try again on a server/vm wher you are able to run Docker as UID 1000.
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If you are not running Docker on a local machine and are unable to access the site on 127.0.0.1:8081, try following these suggestions to access the site.