JBrowse

InterMine 1.3.1 supports the JBrowse REST web-service specification (see configuring JBrowse) which means that you can run a JBrowse installation directly off the InterMine web-services.

This documentation has been tested with JBrowse-1.11.5.

NOTE: If you already have a JBrowse installation working and just want to embed it in your report pages then see: Embedding JBrowse.

Build Your InterMine Database

Add this to the <post-processing> section of your project XML file and then build your database:

<post-process name="populate-child-features"/>

See Post processing for details.

Install JBrowse

You will need an installation of JBrowse for this task. Instructions on doing this can be found at installing JBrowse.

Add JBrowse to InterMine

Add JBrowse to your report pages by adding this entry to your webconfig-model.xml file:

<reportdisplayer javaClass="org.intermine.bio.web.displayer.JBrowseDisplayer"
                 jspName="model/jbrowseDisplayer.jsp"
                 replacesFields=""
                 placement="Genomics"
                 types="SequenceFeature"/>

See Report Displayers Examples for more information.

Add the location of your JBrowse installation to your web.properties or mine properties file, for example:

jbrowse.install.url = http://jbrowse.intermine.org

Point JBrowse at your InterMine

Add your new mine-based dataset to your configuration file. For example to add D. melanogaster data from FlyMine as a JBrowse dataset, the following configuration in jbrowse_conf.json would suffice:

{
  "datasets": {
     "FlyMine-7227": {
      "url": "?data=http://www.flymine.org/query/service/jbrowse/config/7227",
      "name": "FlyMine"
    },
    ...
  }
}

Once in place, you can visit your JBrowse index.html and see the data from FlyMine.

Configuring InterMine’s JBrowse integration

By default, all InterMine classes that inherit from the SequenceFeature model class will have tracks.

However, this can be inappropriate since some of those classes may not have data.

You can make entries in web.properties to configure which tracks appear. For instance, if you just want Gene, CDS, UTR and Promoter tracks then in <mine>/webapp/resources/web.properties configure

org.intermine.webservice.server.jbrowse.genomic.track.Gene.class=Gene
org.intermine.webservice.server.jbrowse.genomic.track.CDS.class=CDS
org.intermine.webservice.server.jbrowse.genomic.track.UTR.class=UTR
org.intermine.webservice.server.jbrowse.genomic.track.Promoter.class=Promoter

Here, track names are the first component of the key after org.intermine.webservice.server.jbrowse.genomic.track (e.g. Gene on the first line). These track names are used to group related properties and are not used in JBrowse display. The rest of the key name (here always class) specifies the InterMine class to be used for this track.

JBrowse parameters can also be set for individual tracks within InterMine. For instance, in web.properties, if one wanted to give all 4 of the tracks defined above different colours then one would set

org.intermine.webservice.server.jbrowse.genomic.track.Gene.style.color=red
org.intermine.webservice.server.jbrowse.genomic.track.CDS.style.color=yellow
org.intermine.webservice.server.jbrowse.genomic.track.UTR.style.color=green
org.intermine.webservice.server.jbrowse.genomic.track.Promoter.style.color=blue

For the full list of properties, please see the canvas section of the JBrowse Configuration Guide.