Setting up a Genome Explorer repository
GenomeView allows you to set up a custom repository of genomes that will be loaded as primary view in the Genome Explorer
- Set up a repository file
- Set up configuration file
- Make launch URL
Repository file format
The repository file is a tab-delimited file where each column has a special meaning. These should be one row per session, i.e. per data set.
- repository identifier
- display name for session, should be reasonably short and informative people
- display image for session, this should be a URL
- description text for individual session, this can be html code.
- url to the session file.
An example row could be:
|fusobac||Fusobacterium nucleatum animalis||http://genomeview.org/manual/images/6/69/Gv_logo-96px.png||Fusobacterium nucleatum animalis is from a colon sample. This strain was sequenced at Baylor College of Medicine.||http://myuniversity.org/fusobacterium/Fuso_animalis.session|
Setting up the configuration file
In order to work with the new repository file, you need to create a config file that specifies where GenomeView has to look for it.
The key options you need to set are:
# Make sure the Genome Explorer is enabled general:enableGenomeExplorer=true # Point GenomeView to your repository external:repository=<URL> # Provide display names for the repository identifier you used in the first column external:repository:labels=<repository identifier>:<repository display name>
For each repository identifier you also need to fill out the description field:
external:repository:description:<repository identifier>=<long HTML formatted description>
external:repository=http://myuniversity.org/my/repository/file.txt external:repository:labels=fusobac:Fusobacterium Repository external:repository:description:fusobac=Welcome to the Fusobacterium GenomeView portal. Blah blah blah...
Setting up launch URL
The final step is to start GenomeView with this configuration file. Suppose you make the config file available at http://myuniversity.org/my/repository/config.txt, then the launch URL would be: