Start BLAST server

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:

  • keys in taxa should match your database name(s), values should match the corresponding SPECIES.URL
  • modify the url = "http://ensembl.genomehubs.org/#{assembly}" to match your domain name
$ 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}"
...
$ 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}"
...

Start SequenceServer BLAST container

Start the SequenceServer Docker container:

$ docker run -d \
             --name genomehubs-sequenceserver \
             -v ~/genomehubs/v1/blast/conf:/conf:ro \
             -v ~/genomehubs/v1/blast/data:/dbs:ro \
             -p 8083:4567 \
             genomehubs/sequenceserver:latest

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