Updating a previously installed repository to a revision that includes tool dependency installation information

Let's assume that you installed the Emboss 5.0.0 tools using the migration process, specifically revision 1:7334f6d0ac17 of the emboss_5 repository from the main Galaxy Tool Shed. If you look at the emboss_5 repository, you notices that it has been updated to revision 2:a52e6cbbb469. This revision added the following tool_dependencies.xml file to the repository.

<?xml version="1.0"?>
<tool_dependency>
    <package name="emboss" version="5.0.0">
        <install version="1.0">
            <actions>
                <action type="download_by_url">ftp://emboss.open-bio.org/pub/EMBOSS/old/5.0.0/EMBOSS-5.0.0.tar.gz</action>
                <action type="shell_command">./configure --without-x --prefix=$INSTALL_DIR</action>
                <action type="shell_command">make</action>
                <action type="shell_command">make install</action>
            </actions>
            <actions>
                <action type="download_by_url">ftp://emboss.open-bio.org/pub/EMBOSS/old/5.0.0/PHYLIP-3.6b.tar.gz</action>
                <action type="shell_command">./configure --without-x --prefix=$INSTALL_DIR</action>
                <action type="shell_command">make</action>
                <action type="shell_command">make install</action>
            </actions>
        </install>
        <readme>
            These links provide information for building the Emboss package in most environments.
            System requirementshttp://emboss.sourceforge.net/download/#RequirementsPlatform-dependent noteshttp://emboss.sourceforge.net/download/#Platforms
        </readme>
    </package>
</tool_dependency>

If you have the enable_tool_shed_check = True setting defined in your universe_wsgi.ini file and the defined time interval passes or you stop and start your Galaxy server, then clicking the Manage installed Tool Shed repositories link on the Admin menu will display a page like the following (ignore the change set revision hash tags - I'm using a test environment here). Notice that the installed emboss_5 repository is highlighted in yellow since there are updates available from the Tool Shed. We can use the pop-up menu to retrieve the updates from the Tool Shed.

Updating the installed emboss_5 repository to the revision that includes the tool_dependencies.xml file will result in the following message being displayed.

Clicking the Repository actions popup menu will display the following options. Notice that you now have the option to Manage tool dependencies.

Clicking the Manage tool dependencies option displays the following page where you can install the dependency now defined in the repository.