Configuring a Data Server

By default, the File>Load from Server option in IGV provides access to public datasets stored on the IGV data server. You can host your own web accessible datasets by creating server registry and configuration files.

 To create a custom load from server menu

1. For each top level node in the hierarchy, create an XML file that describes the datafiles accessible under that node.  Each datafile is specified by a Resource element which has 2 attributes: a name to be displayed to the user and a URL to the file.   The resources can be organized into categories, which in turn can be nested to form a tree structure.  An example follows.
   
   <?xml version="1.0" encoding="UTF-8"?>
   <Global name="Example Project"  infolink="http://www.broadinstitute.org/igv/" version="1">
       <Category name="Category">
           <Category name="Subcategory One">
           <Resource name="pi.12mer.tdf"
                     path="http://www.broadinstitute.org/igvdata/annotations/hg18/conservation/pi.12mer.wig.tdf" />
           </Category>
           <Category name="Subcategory One">
           <Resource name="omega.12mer.tdf"
                     path="http://www.broadinstitute.org/igvdata/annotations/hg18/conservation/omega.12mer.tdf" />
           </Category>
       </Category>
   </Global>
   
   The infolink attribute, which displays an information link for the resource, may be included in any <Global> or <Category> element.
    
2. Create a registry (text) file that lists the XML files. For example:
   

   http://www.broadinstitute.org/igvdata/annotations/hg18/hg18_annotations.xml
   http://www.broadinstitute.org/igvdata/tcga_external.xml
   http://www.broadinstitute.org/igvdata/mmgp.xml
   http://www.broadinstitute.org/igvdata/epigenetics_public.xml
   http://www.broadinstitute.org/igvdata/1KG/1KG.xml
   http://www.mycompany.org/igvdata/example_project.xml

3. In IGV, on the Advanced tab of the Preferences window, update the Data Registry URL to point to your registry file.

IGV points to exactly one data registry file. If you'd like your data server to provide access to the public datasets on the IGV data server, include them in your registry file, as shown above.