GenomeHubs
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Introduction
Quick Start
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/imgdirectory if you wish to include them on your site - further changes to the appearance can be made by editing the styles in
custom.css
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$ cd ~/genomehubs/v1/blast/conf
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# if you have a google analytics code to track usage
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$ sed 's/UA-00000000-0/your analytics code/' Masthead.html
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$ nano Masthead.html
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# replace references to example.com with your domain name
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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
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$ nano links.rb
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...
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def genomehubs
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...
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url = "http://localhost:8881/#{assembly}"
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...
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$ nano links.rb
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...
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def genomehubs
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taxa = {}
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taxa["operophtera_brumata_obru1_core_36_89_1"] = "Operophtera_brumata_Obru1"
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...
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accession = encode accession
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colon = ':'
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url = "http://ensembl.genomehubs.org/#{assembly}"
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...
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$ nano links.rb
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...
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def genomehubs
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taxa = {}
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taxa["operophtera_brumata_obru1_core_32_85_1"] = "Operophtera_brumata_Obru1"
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...
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accession = encode accession
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colon = ':'
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url = "http://ensembl.genomehubs.org/#{assembly}"
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...
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Start SequenceServer BLAST container
Start the SequenceServer Docker container:
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$ docker run -d \
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--name genomehubs-sequenceserver \
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--network genomehubs-network \
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-v ~/genomehubs/v1/blast/conf:/conf:ro \
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-v ~/genomehubs/v1/blast/data:/dbs \
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-p 8883:4567 \
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genomehubs/sequenceserver:19.05
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Last modified 1yr ago
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