Hi all, Stupidly enough, I installed a tool shed repo under 'root' of the toolbox. Yes, it was EMBOSS5.0 (btw, installation went flawless!). 1. From the admin menu, I choose to unactivate the repo (manage tool shed repo's) 2. From the admin menu, I reinstalled the tool shed from Main Tool Shed, and chose to put it under a section 'EMBOSS'. This to no avail: all tools still under root. 3. I manually edited the shed_tool_conf.xml and added the section tags 4. The section is now displayed, containing the EMBOSS tools. BUT the tools under the root of the toolbox are still there. Any assistance here? Cheers, Joachim -- Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib