Dear all,<div><br></div><div>I installed and uninstalled some shed tools for my Galaxy instance. And I have found some weird things which I don&#39;t think they are as expected.</div><div><br></div><div>1.  After I installed a shed tool using the Galaxy web UI and the tool can run successfully, I didn&#39;t find any change of the &quot;shed_tool_conf.xml&quot; file.  According to the instructions under the link <a href="http://wiki.g2.bx.psu.edu/Tool%20Shed#Automatic_installation_of_Galaxy_tool_shed_repository_tools_into_a_local_Galaxy_instance">http://wiki.g2.bx.psu.edu/Tool%20Shed#Automatic_installation_of_Galaxy_tool_shed_repository_tools_into_a_local_Galaxy_instance</a>,  a entry of the newly added tool should be added.  Thus I don&#39;t know where I go to modify the tools information(such as the section name..) like I did in the &quot;tool_conf.xml&quot; file.</div>
<div><br></div><div>2. When I go to &quot;Admin |<a href="http://localhost/admin_toolshed/browse_repositories" target="galaxy_main" style="color:rgb(48,48,48);font-family:&#39;Lucida Grande&#39;,verdana,arial,helvetica,sans-serif;font-size:12px;background-color:rgb(193,201,229)">Manage installed tool shed repositories</a> &quot;, I can&#39;t find all the installed tools. Only some of them are displayed there. </div>
<div><br></div><div>3. After I uninstalled a shed tool, all the related files are deleted, which is good. But the empty directories(under the Shed_tools) are left. </div><div><br></div><div>4. Last, I have one question: if I install a shed tool into a new section(which means it doesn&#39;t exist before) , how could we modify the section&#39;s name?</div>
<div><br></div><div><br></div><div>Anyone have encounter the same problems? Hope someone can explain to me. Thanks in advance!!!</div><div><br></div><div>Cheers,</div><div>Tyler</div><div><br></div>