Adding Private Tools: Part 2

Posted by Ted Liefeld on Wednesday, October 03, 2012 at 10:53AM

About a month ago, we posted that GenomeSpace had added the ability to let you put your own tools into the tool bar so that you could use your local instance of GenePattern, Galaxy, or any other GenomeSpace enabled tool.  It has now gotten easier to add your tools into GenomeSpace with the release of the Manage Private Tools dialog.

To add a tool to your toolbar, first, make sure it is GenomeSpace enabled.

Once the tool is ready, start at the System menu and select Manage Private Tools.

This will open up the list of private tools that you have available.  Most people will start with an empty list like this (below).  Click Add new to start the process of adding a new tool.

This will present you with the dialog for adding your tool to the tool bar.

As we discussed in the earlier post, you now need to enter the information about the tool that you are adding.  Here you will need to enter:

  • Name
  • (optional) Description
  • Tool Provider, that is, the group or institution that developed the tool
  • URL for launching the tool (Base URL)
  • (optional) Help URL
  • The parameter used to send files from GenomeSpace to the tool
    • (optional) The file formats that the tool natively accepts.  Files in these formats will be sent directly to the tool and GenomeSpace will not try to convert them.  If another format is selected and there is a conversion to one of the formats selected here, GenomeSpace will try to automatically convert it when a file is sent to your tool.
  • (optional)The tool icon
    • A default icon (as shown above) will be used if not icon is uploaded.
  • (optional) Sharing
    • Sharing of tools uses the same user groups as the sharing of files with one exception: you may not share to public.  If you have a tool you would like to make available to all members of the GenomeSpace community, please contact the development team at gs-help@broadinstitute.org.

Help about what to use in each of the fields is available if you click the help icons (blue question marks) at the right side of the dialog.  A completed tool information dialog (with the help showing) will look something like this:

That's it!  Once your tool has been added, you should be able to launch it from GenomeSpace.