Configuration 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 configurations
connections.js	choice of database - local, mongo, mysql, … (we use local by default.) The DB file is in the `./data/localDiskDb.db`.

globals.js¶

To view aggregate configuration: ./jbutil --config

The aggregate config is the merged globals.js combined with the globals.js of server hook modules.

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

Edit config file: nano config/globals.js

jbrowse: {
    jbrowseRest: "http://localhost:1337",
    jbrowsePath: jbPath,                        // or "/var/www/jbrowse/"
    routePrefix: "jbrowse",                     // jbrowse is accessed with http://<addr>/jbrowse

    dataSet: {
         Volvox: {path: "sample_data/json/volvox"}
    },

    // search service settings
    serverSearch: {
        resultPath: "ServerSearch",
        resultCategory: "Search Results",
        trackTemplate: "ServerSearchTrackTemplate.json",
        workflowScript: "ServerSearch.workflow.js",
        processScript:   'ServerSearchProcess.html'
    },
    // search job service registration
    services: {
        'serverSearchService': {name: 'serverSearchService',  type: 'service'}
    },

    /*
     * Virtual Routes
     * These routes reference node_modules that are used by the client and
     * accessed by virtual route.
     */
    libRoutes: {
        // name         node_modules dir            virtual route
        'jquery':       {module: 'jquery',          vroute:'/jblib/jquery'},
        'bootstrap':    {module: 'bootstrap',       vroute:'/jblib/bootstrap'},
        'jqueryui':     {module: 'jquery-ui-dist',  vroute:'/jblib/jquery-ui'},
        'mbextruder':   {module: 'jquery.mb.extruder', vroute:'/jblib/mb.extruder'}
    },
    /*
     * Web Includes
     * These includes are injected into JBrowse ``index.html`` upon ``sails lift``.
     */
    webIncludes: {
        // key                    virtual route
        "css-bootstrap":         {lib: "/jblib/bootstrap/dist/css/bootstrap.min.css"},
        "css-mbextruder":        {lib: "/jblib/mb.extruder/css/mbExtruder.css"},
        "css-jqueryui":          {lib: "/jblib/jquery-ui/jquery-ui.min.css"},
        "css-jqueryuistructure": {lib: "/jblib/jquery-ui/jquery-ui.structure.min.css"},
        "css-jqueryuitheme":     {lib: "/jblib/jquery-ui/jquery-ui.theme.min.css"},
        "js-sailsio":            {lib: "/js/dependencies/sails.io.js"},
        "js-jquery":             {lib: "/jblib/jquery/dist/jquery.min.js" },
        "js-jqueryui":           {lib: "/jblib/jquery-ui/jquery-ui.min.js" },
        "js-bootstrap":          {lib: "/jblib/bootstrap/dist/js/bootstrap.min.js"},
        "js-mbextruderHover":    {lib: "/jblib/mb.extruder/inc/jquery.hoverIntent.min.js"},
        "js-mbextruderFlip":     {lib: "/jblib/mb.extruder/inc/jquery.mb.flipText.js"},
        "js-mbextruder":         {lib: "/jblib/mb.extruder/inc/mbExtruder.js"}
    }
}

Limiting Query Size¶

The query size (# of base pairs) can be limited. This might be necessary to contain the processing or contain memory consumption of client and server., particularly with operations like BLAST where the BLAST database may be very large.

Add the following option to the trackList.json of the dataset configuration:

{
    ...
    "bpSizeLimit": 25000,
    ...
},

This will cause an alert message when the selected query size exceeds 25000 bp.

If omitted, the allowed size will be unlimited.

We definitely recommend using this setting for larger assemblies.

Installing JBConnect jbh-hooks¶

A ‘JBConnect Hook’ is basically an installable sails hook with specific methods for extending JBConnect. JBConnect 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). JBConnect will automatically integrate a number of features of the hook directly into JBConnect upon sails lift.

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

Extend models, controllers, policies and services
Integrated client-side JBrowse plugins injection
Integrated client-side npm module injection
Integrated job services (see: jbs-jobservice_)
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: JBConnect 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"
],

Job Service Configuration¶

Job services (jservice) 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.js 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 and RESTful interfaces
service - service only serves RESTful interfaces

Job service config in config/globals.js:

// 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'}
},

Extending jbutil¶

jbutil is a command line utility that is used to configure JBConnect in various ways. jbutil can be extended by a installable hook through bin/jbutil-ext.js.

jbutil-ext.js must imeplement these function:

module.exports = {
    // this return the options that the module support.  In this example,
    // we add -t or --test and --thing options to jbutil.

    getOptions: function() {
        return [
            ['t' , 'test=ARG', '(jbh-myhook) this is a test option'],
            ['' , 'thing',   , '(jbh-myhook) this is another test option']
        ];
    },

    // Extends the help display
    // In this example, we describe how to use --test with a parameter value "abc"

    getHelpText: function() {
        return "\nExample: ./jbutil --test abc\n";
    },

    // process options
    // where opt - the option list.
    //       path - path of the module that will process the option (i.e. "./node_modules/jbh-jblast"
    //       config - the aggregate globals.js config.

    process: function(opt,path,config) {
        var tool = opt.options['setupindex'];
        if (typeof tool !== 'undefined') {
            jblib.exec_setupindex(this.config);
            jblib.exec_setupPlugins(this.config);
        }

        var tool = opt.options['dbreset'];
        if (typeof tool !== 'undefined') {
    }

See npm module node-getopt for more info.