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Manage groups & tools

The menu bar's Manage menu allows you to manage either Groups or Private Tools. This includes creating, editing and deleting groups and private tools.

Groups are GenomeSpace user lists much like a group email list that become available from drop-down menus when sharing files, folders, and private tools. You have the option of viewing my groups and all groups. My groups are groups in which you are a member and all groups are groups defined by other GenomeSpace users of which you are not a member. When you create a group, you automatically become a member and the administrator of the group.

Private tools are your own private instances of GenomeSpace-enabled tools that are sharable with groups. This may be a local instance of GenePattern, Galaxy, or any other GenomeSpace-enabled tool. Private tools show up in the tool catalog and from there you can add them to a toolbar for one-click launches. To GenomeSpace-enable your tool, developers see Adding a Tool to GenomeSpace in the Developer's guide.

 

Manage Groups

Click on the Manage menu and select Groups. The Manage User Groups dialog displays (Screenshot 2015.1.30). For a given group, all members can view members but only those with administrative privileges can edit or delete the group. When viewing a group for which you are not an admin, disabled button options turn gray.

  1. Groups in which you are a member display under Group Names. Click on a group to select.
    • Click Delete Selected Group button to delete the group (admins only).
  2. The selected group's description and members display.
    • Members with administrative priviledges have red icons next to their name while those that do not are labeled with a blue icon.
    • Remove a member by clicking on the red x next to their name (admins only).
  3. Add a member to the selected group by entering the username in the text field and clicking Add user to [group name] button (admins only).
    • If a member has a searchable name, as described in Share Data, then you can search for them with a partial username or an email address by clicking on the magnifying glass icon .  Otherwise, you must know the exact username.
    • Make a user a group administrator by checking User can administer group.
  4. Create a new group by inputing a Group name and group Description in the text fields. Click the Add New Group button.
    • To allow non-member GenomeSpace users to view members of a group, check the box. This is a future feature.

 

Manage Private Tools

You can add any GenomeSpace-enabled tool to your GenomeSpace toolbar as a private instance. For example, you can add your private GenePattern or Galaxy server as a private tool.

  • You and groups you share it with can see and use this instance.
  • Private tools show up in the tool catalog for addition to a toolbar. From the tool catalog, add the tool to your toolbar as outlined in Customizing the interface.

To manage private tools, select Manage>Private Tools. The Manage My Tools dialog box displays and lists private tools you administer. Only tools you have added can be edited or deleted by you.

  • To delete a listed tool, click the red x next to the tool name.
  • To modify a listed tool, click the Modify link in line with the tool name. An Edit dialog appears.
  • To add a new private tool, click the Add new button. An Add a new private tool dialog appears.

The Edit and Add a new private tool dialog boxes have the same input fields. Edit or fill out the parameters summarized in the table below and press Save. To display instructions within the dialog box, click the blue quesiton mark ? button.

Field

(* required)

 Description
Name*
  • Tool name
Description
  • Optional description
Tool Provider*
  • Institution, group, or user providing the tool
Base URL*
  • The page in the web-based application that will be launched or the URL of a JNLP launch file for desktop applications. For example, a GenePattern server might have the base URL <http://gpdev.broadinstitute.org/gp/pages/genomespace/receiveFile.jsf>.
Help URL
  • Optional tool documentation web address
File Parameter
  • Optional parameter to pass GenomeSpace file URLs to the tool when launched. Without this GenomeSpace cannot pass a file to your tool.
  • We recommend as a minimum that you add the ability to transfer data between your tool and GenomeSpace.
  • The File Parameter name is added to the Base URL for the call. File parameters are defined by the application you are adding. If you do not know the file parameter, contact the help desk for the tool you are adding.
  • Check the Allow multiple files box to allow multiple files to be passed to the tool at once. Specify a Multiple file Delimiter to separate the multiple file URLs. 
  • Select as many as apply from the list file formats your tool natively accepts. Files in these selected formats are sent directly to the tool and GenomeSpace will not ask to convert them.
  • If another compatible format is selected, meaning the conversion between formats is supported, GenomeSpace will automatically convert when a file is sent to the tool. See Help menu>Format Converters for supported conversions.
  • If your tool's accepted format is not listed, contact gs-help@broadinstitute.org to request the addition.
Icon
  • Optional custom icon to display in the tool catalog and toolbar for the tool. By default, a GenomeSpace icon is provided.
  • Use GIF, JPG, or PNG files.
  • Icon is scaled to 44x44 or less pixels within GenomeSpace. 
  • Sharing the tool adds people icons to the tool icon.
Share with groups
  • Optionally share your private tool with your groups. Your groups are groups in which you are a member.
  • Shared group users will be able to see and launch the tool, but cannot edit or delete it.
  • Click the wrench icon  to create or edit user groups as described in the preceding section.

 

Additional considerations

  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. If GenomeSpace-enabled, the tool should point to the GenomeSpace production environment as detailed in the technical documentation.
  3. Some GenomeSpace tools have instructions in their help for managing private instances in GenomeSpace. For example, Galaxy on their Customizing Galaxy's GenomeSpace Integration help page.
  4. You may not share tools with the gs-public group via this mechanism. If you'd like to make your tool available to all members of the GS community, contact the development team at gs-help@broadinstitute.org.
  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.

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