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. Introduction

Demo

PreviousFiles and containersNext1. Prepare

Last updated 4 years ago

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If you already have a server running Docker, the quickest way to try out GenomeHubs is to run our demo import script in the GitHub repository:

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

This sets up a GenomeHub with an Ensembl browser, SequenceServer BLAST server and h5ai downloads server hosting data from one species mirrored from EnsemblGenomes and another imported from FASTA and GFF files in around an hour.

Once loaded the Ensembl site will be available at 127.0.0.1:8881. If are running this demo on another server via ssh you can add an entry to your .ssh/config file so you can ssh dockerserver to forward ports for the Ensembl, BLAST and downloads sites:

  • replace the HostName and User with values relevant to you

$ nano ~/.ssh/config
Host dockerserver
 HostName example.com
 LocalForward 8881 127.0.0.1:8881
 LocalForward 8882 127.0.0.1:8882
 LocalForward 8883 127.0.0.1:8883
 User username
genomehubs/demo