Dear all, I installed and uninstalled some shed tools for my Galaxy instance. And I have found some weird things which I don't think they are as expected. 1. After I installed a shed tool using the Galaxy web UI and the tool can run successfully, I didn't find any change of the "shed_tool_conf.xml" file. According to the instructions under the link http://wiki.g2.bx.psu.edu/Tool%20Shed#Automatic_installation_of_Galaxy_tool_..., a entry of the newly added tool should be added. Thus I don't know where I go to modify the tools information(such as the section name..) like I did in the "tool_conf.xml" file. 2. When I go to "Admin |Manage installed tool shed repositories<http://localhost/admin_toolshed/browse_repositories> ", I can't find all the installed tools. Only some of them are displayed there. 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. 4. Last, I have one question: if I install a shed tool into a new section(which means it doesn't exist before) , how could we modify the section's name? Anyone have encounter the same problems? Hope someone can explain to me. Thanks in advance!!! Cheers, Tyler