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GenomeHubs example configuration and demo script

Example configuration to set up custom Ensembl site using GenomeHubs

  • GenomeHubs import - a full GenomeHubs site hosting the an assembly and gene models imported from FASTA + GFF

Either follow the full tutorial at genomehubs.gitbooks.io or try out the example script to get a GenomeHubs Ensembl site up and running as quickly as possible.

cd
git clone https://github.com/genomehubs/demo
cd demo
./demo.sh

Sets up a GenomeHubs site hosting a mirror of the core database for the Glanville fritillary, Melitaea cinxia and imports the genome of the winter moth, Operophtera brumata, into a GenomeHubs site from FASTA and GFF

Troubleshooting

  • 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.

  • If the containers already exist when either demo script is run, they will be removed. Rerun the the script to continue.

  • 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.

  • If you are not running Docker on a local machine and are unable to access the site on 127.0.0.1:8881, try following these suggestions to access the site.