Setup Options

JBrowse Installed In Separate Directory

The JBrowse directory can also be configured manually. (See jbs-globals-js)

Configuration Files

A number of configuration files are in the ./config directory. A few of the more important ones (ones that JBSserver touches) are described mentioned in the table below. See Sails Configuration for a better description of the configuration framework.

jbs-globals-js	global configuration file
http.js	custom middleware and /jbrowse route is setup here.
passport.js, policies.js	passport framework and auth policies config
routes.js	various route config
connections.js	choice of database - local, mongo, mysql, … (we use local by default.) The DB file is in the ./data/localDiskDb.db.

globals.js

Modify the configuration file as necessary.

To view aggregate configuration: ./jbutil --config

The aggregate config file is the merged config of JBServer and its installed jbh- (hook) modules.

Edit config file: nano config/globals.js

jbrowse: {
    jbrowseRest: "http://localhost:1337",       // path accessible by web browser
    jbrowsePath: jbPath,                        // or point to jbrowse directory (ie. "/var/www/jbrowse/")
    routePrefix: "jbrowse",                     // jbrowse is accessed with http://<addr>/jbrowse
    dataSet: [
        {
            dataPath: "sample_data/json/volvox" // datasets.
        }
    ]
}

Installing JBServer jbh-hooks

A ‘JBServer Hook’ is basically an installable sails hook with specific methods for extending JBServer. JBServer hooks must have the prefix jbh- prepended to the name. For example: jbh-jblast. When the hook is installed (i.e. npm install jbh-jblast). JBServer will automatically integrate a number of features of the hook directly into JBServer upon sails lift.

The jbh- hook can extend JBServer in the following ways:

• Extend models, controllers, policies and services
• Integrated client-side JBrowse plugins injection
• Integrated client-side npm module injection
• Integrated configuration tool (jbutil)
• Aggregated configurations

Installing a hook:

npm install jbh-<hook name> (i.e. jbh-jblast)

For detailed info on jbh-hooks, see: JBServer jbh-hooks

JBClient Plugin

JBrowse GUI intetrated interfaces are available when the JBClient plugin is configured on in the JBrowse client.

To enable integrated features within the JBrowse app, modify the dataset’s trackList.json, adding JBClient plugin to the configuration.

Note: the JBClient plugin is not physically in the JBrowse plugin directory. It is available as a route.

"plugins": [
  "JBClient",                    <-----
  "NeatHTMLFeatures",
  "NeatCanvasFeatures",
  "HideTrackLabels"
],

Jservice Configuration

Jservices are a special type of service that are used to extend RESTful api service and serve processing for job operations.

Configuration is defined in config/globals under the jbrowse section under service.

A definition: <indexname>: {name: <servicename>, type:<type>, alias:<alias> }

where:

• indexname - is the reference name service (generally the same as servicename)
• servicename - is the name of the service reference the service code in api/services.
• type - is the type of service. either “workflow” or “service”
• alias - (optional) if specified, the service can also be referenced by the alias name.

jservice type:

• workflow - service can serve job execution
• service - service only serves RESTful interfaces

// list of services that will get registered.
services: {
    'basicWorkflowService':     {name: 'basicWorkflowService',  type: 'workflow', alias: "jblast"},
    'filterService':            {name: 'filterService',         type: 'service'},
    'entrezService':            {name: 'entrezService',         type: 'service'}
},