On Apr 30, 2018, at 10:01 AM, Martin Čech <marten(a)bx.psu.edu&gt; wrote: Hi Nancy, for the list of tools on Main that were installed from Tool Shed please look at https://github.com/galaxyproject/usegalaxy-playbook/blob/master/env/main/... <https://github.com/galaxyproject/usegalaxy-playbook/blob/master/env/main/... The tool_conf.xml.main file only consists of tools that are not from the Tool Shed, which is a minority nowadays. Martin On Mon, Apr 30, 2018 at 9:57 AM Nancy Ide <ide(a)vassar.edu <mailto:ide@vassar.edu>> wrote: Hello I’m trying to include some of the tools available from usegalaxy.org <http://usegalaxy.org/> in the tool menu of our instance of Galaxy. When I look at the list of tools in the Galaxy tool_conf.xml.main file, it does not seem to line up with what you see in the menu at usegalaxy.org <http://usegalaxy.org/>;. I’ve searched through various versions etc. on GitHub, but no luck—they all seem to be identical and do not seem to correspond with the menu at usegalaxy.org <http://usegalaxy.org/> (I am looking specifically at the Text Manipulation part of the menu). Any clues on where I should look? Thanks, Nancy Ide ----------------------------------------------------- Nancy Ide Professor of Computer Science Department of Computer Science Vassar College Poughkeepsie, New York 12604-0520 USA tel: (+1 845) 437 5988 <tel:(845)%20437-5988> fax: (+1 845) 437 7498 <tel:(845)%20437-7498> email: ide(a)cs.vassar.edu <mailto:ide@cs.vassar.edu> http://www.cs.vassar.edu/~ide <http://www.cs.vassar.edu/~ide> ----------------------------------------------------- ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ <https://lists.galaxyproject.org/> To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/ <http://galaxyproject.org/search/>