Hey Greg & Galaxy Team, Galaxy doesn't load tool sections from multiple files in a consistent manner. This is a minimal example that demonstrates the problem: https://bitbucket.org/jmchilton/galaxy-central-tool-load-example https://bitbucket.org/jmchilton/galaxy-central-tool-load-example/compare This example specifies two sections, Section 1 and Section 2. The first time you load up Galaxy, Section 1 appears first followed by Section 2. On every subsequent time Galaxy is loaded, Section 2 appears first followed by Section 1. I have attached the smallest patch I could come up with to fix this problem. While I was in that file, I noticed that a standing request I had the defunct bug tracker to allow directories to appear in the tool_config_file option is easy to implement, so I have attached a patch for that as well if you are so inclined. Thanks for your time, -John ------------------------------------------------ John Chilton Senior Software Developer University of Minnesota Supercomputing Institute Office: 612-625-0917 Cell: 612-226-9223 Bitbucket: https://bitbucket.org/jmchilton Github: https://github.com/jmchilton Web: http://jmchilton.net