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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  • Edit files in conf directory
  • Start SequenceServer BLAST container

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  1. Quick Start

9. Start BLAST server

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Last updated 4 years ago

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A SequenceServer BLAST server container provides a user friendly BLAST interface to genomes hosted in a GenomeHub.

Edit files in conf directory

Edit Masthead.html to change the site name, logos and link urls:

  • add images to the ~/genomehubs/v1/blast/conf/img directory if you wish to include them on your site

  • further changes to the appearance can be made by editing the styles in custom.css

$ cd ~/genomehubs/v1/blast/conf
# if you have a google analytics code to track usage
$ sed 's/UA-00000000-0/your analytics code/' Masthead.html
$ nano Masthead.html
# replace references to example.com with your domain name

Edit links.rb to ensure that links from BLAST results are directed to your Ensembl site:

  • modify the url = "http://localhost:8881/#{assembly}" to match your domain name

$ nano links.rb
...
    def genomehubs
...
      url = "http://localhost:8881/#{assembly}"
...
$ nano links.rb
...
    def genomehubs
      taxa = {}
      taxa["operophtera_brumata_obru1_core_36_89_1"] = "Operophtera_brumata_Obru1"
...
      accession = encode accession
      colon = ':'
      url = "http://ensembl.genomehubs.org/#{assembly}"
...
$ nano links.rb
...
    def genomehubs
      taxa = {}
      taxa["operophtera_brumata_obru1_core_32_85_1"] = "Operophtera_brumata_Obru1"
...
      accession = encode accession
      colon = ':'
      url = "http://ensembl.genomehubs.org/#{assembly}"
...

Start SequenceServer BLAST container

Start the SequenceServer Docker container:

$ docker run -d \
             --name genomehubs-sequenceserver \
             --network genomehubs-network \
             -v ~/genomehubs/v1/blast/conf:/conf:ro \
             -v ~/genomehubs/v1/blast/data:/dbs \
             -p 8883:4567 \
             genomehubs/sequenceserver:19.05