Adding Private Tools

Introduction

The GenomeSpace team is working on a new feature to allow you to add your own private tools to the GenomeSpace toolbar.  This will allow you to add your own versions of existing tools (e.g., your lab's GenePattern or Galaxy instance) or other tools that are not part of the public GenomeSpace installation into your toolbar.

For the first version of this feature, the GenomeSpace team must add the tools for you.  However, this will be followed shortly with an update to GenomeSpace that will let you add and remove tools yourself.

Image 1: Notice the 'Teds GenePattern' tool at the left edge of the toolbar

Getting Started

While it's no problem to add a tool as-is with no GenomeSpace features added, we recommend as a minimum that you add the ability to transfer data between your tool and GenomeSpace. You can find instructions on how to do this on our technical documentation page. That page also shows you how to implement login and authentication, launch a tool on a file, and add other GenomeSpace functionality.

To have a tool added send an email to gs-help(at)broadinstitute.org with a subject line  "Add a private tool to GenomeSpace".  The body of the message should include the following information:

  • Tool name, e.g., "GenePattern"
  • Author/organization - who provided the tool, e.g., "GenePattern team from the Broad Instittute"
  • Short description - what the tool can do, e.g., "Performs a variety of genomic analyses"
  • Base URL - The URL to launch the tool, meaning either its web address or the address of a JNLP launcher for desktop applications, e.g., http://tedsserver.broadinstitute.org:8080/gp/receiveFile.jsf
  • (optional) Input file parameter - if the tool can be launched on a file, this is the parameter that should precede input file URLs
    • (optional) Allowable file formats for the input files
      • include extension, name, and a brief description
  • (optional) JRAC launch port - the port that desktop applications implementing the Java Relaunch Avoidance Code (JRAC) specification listens to
  • (optional) Tool icon (~128x128 pixels).
  • (optional) The name of the GenomeSpace user groups with whom you want to share the tool.  Members of these groups will also see the tool in their toolbar.

Shortly after your email is received, the GenomeSpace administrators will enter these details into the GenomeSpace database and the tool will become available for testing on your toolbar.

Limitations

  1. All tools need to be web-launchable.  Desktop applications like Excel cannot be handled at this time. If your tool is a Java-based application, it must be implemented as a Java Web start jnlp file.
  2. Tool icons may take a while to show up.  In the meantime, they will use the default GenomeSpace icon in the toolbar.
  3. You may not share tools with the gs-public group via this mechanism.
  4. You may only share tools to groups of which you are yourself a member.
  5. If you are using a private tool and would like to see it use more GenomeSpace features, please let us know and we will try to work with the developers to have it added.
  6. If GenomeSpace-enabled, the tool should point to the GenomeSpace production environment as detailed in the technical documentation.

Conclusion

That's it!  Once your tool has been added, you should be able to launch it from GenomeSpace.  In the months to come, we will be adding functionality to GenomeSpace so that you will be able to add tools easily yourself.