Difference between revisions of "Setting up a Genome Explorer repository"

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== Repository file format ==
 
== Repository file format ==
−
The repository file is a tab-delimited file where each column has a special meaning.
+
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
 
# repository identifier
−
# display name for repository, should be reasonably short and informative people
+
# display name for session, should be reasonably short and informative people
−
# display image for repository, this should be a URL
+
# display image for session, this should be a URL
−
# description text, this can be html code.
+
# description text for individual session, this can be html code.
 
# url to the session file.
 
# url to the session file.
  
−
For example  
+
An example row could be:
−
{-
+
{|
 
|fusobac
 
|fusobac
−
|Fusobacterium nucleatum animalis ATCC51191
+
|Fusobacterium nucleatum animalis
−
|http://www.broadinstitute.org/software/genomeview/supplemental/fusobacterium/broadlogo.png
+
|http://genomeview.org/manual/images/6/69/Gv_logo-96px.png
−
|Fusobacterium nucleatum animalis ATCC51191 is from a colon sample.  This strain was sequenced at Baylor College of Medicine.
+
|Fusobacterium nucleatum animalis is from a colon sample.  This strain was sequenced at Baylor College of Medicine.
−
|http://www.broadinstitute.org/software/genomeview/supplemental/fusobacterium/Fuso_animalis_ATCC51191.session
+
|<nowiki>http://myuniversity.org/fusobacterium/Fuso_animalis.session</nowiki>
 
|}
 
|}
 +
 +
 +
== 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>
 +
 +
For example:
 +
<nowiki>external:repository=http://myuniversity.org/my/repository/file.txt</nowiki>
 +
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 <nowiki>http://myuniversity.org/my/repository/config.txt</nowiki>, then the launch URL would be:
 +
<nowiki>http://genomeview.org/start/launch.jnlp?--config http://myuniversity.org/my/repository/config.txt</nowiki>

Latest revision as of 00:09, 16 November 2013

GenomeView allows you to set up a custom repository of genomes that will be loaded as primary view in the Genome Explorer

Recipe

  1. Set up a repository file
  2. Set up configuration file
  3. 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.

  1. repository identifier
  2. display name for session, should be reasonably short and informative people
  3. display image for session, this should be a URL
  4. description text for individual session, this can be html code.
  5. 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>

For example: 

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: 

http://genomeview.org/start/launch.jnlp?--config http://myuniversity.org/my/repository/config.txt
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