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-1.16.4.
If you want to be able to have a hierarchical view of your features on JBrowse, add this to the
<post-processing> section of your project XML file and then build your database:
See Post processing for details.
You will need an installation of JBrowse for this task. Instructions on doing this can be found at installing JBrowse.
Note: you need to set
in the index.html file of your JBrowse installation.
Add JBrowse to your report pages by adding this entry to the
webconfig-model.xml file of your mine (see FlyMine example):
See Report Displayers Examples for more information.
Add the location of your JBrowse installation to your
web.properties or mine properties file, for example:
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:
Once in place, you can visit your JBrowse
index.html and see the data from FlyMine.
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
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. <div class="jbrowse" id="GenomeBrowser" data-config="allowCrossOriginDataroot":true> 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:
For the full list of properties, please see the canvas section of the JBrowse Configuration Guide.