9. 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:

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

e93
e89
e85
$ 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