GenomeHubs
Search…
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.
1
$ docker run -d \
2
--name genomehubs-search \
3
--network genomehubs-network \
4
-p 8884:8080 \
5
genomehubs/search:19.05
Copied!
Optionally add a custom apache configuration file to override defaults
1
mkdir -p ~/genomehubs/v1/search/conf
2
nano ~/genomehubs/v1/search/conf/search.genomehubs.org.conf
Copied!
~/genomehubs/v1/search/conf/search.genomehubs.org.conf:
1
Listen 8080
2
3
<VirtualHost *:8080>
4
5
RewriteEngine on
6
RewriteRule "^/lbsearchquot; "/cgi-bin/lbsearch" [PT]
7
RewriteRule "^/autocompletequot; "/cgi-bin/autocomplete" [PT]
8
9
ServerAdmin [email protected]
10
ServerName search.genomehubs.org
11
ServerAlias search.genomehubs.org
12
DocumentRoot /var/www/search.genomehubs.org/httpdocs
13
ErrorLog /var/www/search.genomehubs.org/logs/error.log
14
CustomLog /var/www/search.genomehubs.org/logs/access.log combined
15
ScriptAlias "/cgi-bin/" "/var/www/search.genomehubs.org/cgi-bin/"
16
<Directory "/var/www/search.genomehubs.org/cgi-bin/">
17
Options +ExecCGI
18
SetHandler cgi-script
19
</Directory>
20
</VirtualHost>
Copied!
1
$ docker run -d \
2
--name genomehubs-search \
3
-v ~/genomehubs/v1/search/conf:/conf:ro \
4
--network genomehubs-network \
5
-p 8884:8080 \
6
genomehubs/search:19.05
Copied!

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.
Last modified 1yr ago
Copy link