Restarting Galaxy after adding a new tool

Whenever we add a tool to the tool_conf.xml file in galaxy-dist, there is a second xml file (integrated_tool_panel.xml) that changes as well. This second xml should mirror tool_conf.xml, and it is the xml that determines the workflow tool menu.

The integrated_tool_panel.xml gets re-written every time galaxy restarts. So, if you add a new tool, delete the integrated_tool_panel.xml file in galaxy-dist. When you restart galaxy, the file will be re-written and will mirror the tool_conf.xml file.

This probably sounds a bit confusing and convoluted, but I hope it makes some sense! Here is a link with more detail from the galaxy wiki:

http://wiki.g2.bx.psu.edu/Tool%20Shed#Managing_the_layout_of_your_Galaxy_tool_panel