10. Start search container

Starting with version 19.05 which runs Ensembl release 93, it is necessary to start an additional container to run searches against the Ensembl database.

We anticipate adding functionality to search across additional GenomeHubs resources in future releases.

$ docker run -d \
             --name genomehubs-search \
             --network genomehubs-network \
             -p 8884:8080 \
             genomehubs/search:19.05

Optionally add a custom apache configuration file to override defaults

mkdir -p ~/genomehubs/v1/search/conf
nano ~/genomehubs/v1/search/conf/search.genomehubs.org.conf

~/genomehubs/v1/search/conf/search.genomehubs.org.conf:

Listen 8080

<VirtualHost *:8080>

    RewriteEngine  on
    RewriteRule    "^/lbsearch$"  "/cgi-bin/lbsearch" [PT]
    RewriteRule    "^/autocomplete$"  "/cgi-bin/autocomplete" [PT]

    ServerAdmin [e-mail]
    ServerName search.genomehubs.org
    ServerAlias search.genomehubs.org
    DocumentRoot /var/www/search.genomehubs.org/httpdocs
    ErrorLog /var/www/search.genomehubs.org/logs/error.log 
    CustomLog /var/www/search.genomehubs.org/logs/access.log combined
    ScriptAlias "/cgi-bin/" "/var/www/search.genomehubs.org/cgi-bin/"
    <Directory "/var/www/search.genomehubs.org/cgi-bin/">
        Options +ExecCGI
        SetHandler cgi-script
    </Directory>    
</VirtualHost>

$ docker run -d \
             --name genomehubs-search \
             -v ~/genomehubs/v1/search/conf:/conf:ro \
             --network genomehubs-network \
             -p 8884:8080 \
             genomehubs/search:19.05

Troubleshooting

• Earlier 19.05 container versions contained a search bug, if you are having trouble with search please pull the updated easy-mirror and search container images:

  • docker pull genomehubs/easy-mirror:19.05

  • docker pull genomehubs/search:19.05

• This container must be named genomehubs-search and be made available on the same docker network as the genomehubs-ensembl container for the search configuration to work.