TL;DR I have a tool that generates other tools. Where should those tools go, and how should I add them (without modifying Galaxy code)?
I apologize, in advance, for the wall of text. I would like some advice on what the best way to go about setting up a tool that generates other tools... As some of you (especially those who saw my boss's talk at GCC) already know, I'm working on a tool that lets galaxy users add web service operations as tools to Galaxy. We have a general purpose client for invoking web services, and we have a tool that let's a user enter a WSDL/WADL URL, select the operations they want to add, and generates tool config XML files for Galaxy. Right now, I'm in the process of making our tool "tool shed" compatible, and that's going along great (I especially like the tool dependency installation stuff), but I'm trying to determine the best course of action on the following: 1. Where is the best place to put the tool config (XML) files that are generated by my tool? My predecessors just placed them in a subdirectory under our tool's directory. I'm ok with this, but does that mean that all the generated files will get removed if they upgrade our tool via the tool shed (haven't taken the time to see if Galaxy just does an "hg pull" or if it's more complicated than that)? Would it be better to have my tool create a local tool shed repository (just for these generated tools), and if so, can the tool shed API let my tool install this repository? Having not looked at install_tool_shed_repositories.py yet, it's unclear from the wiki documentation whether or not POST /api/tool_shed_repositories/install_repository_revision requires that the tool shed already registered in tool_sheds_conf.xml)? 2. What's the best way to add the generated tools to Galaxy? My predecessors modified the tool_config.xml directly and required users to restart Galaxy. Now, If these tools are in a tool shed repo, I know that I can use the add_to_tool_panel() method in lib/tool_shed/util/tool_util.py if these tools are in a tool shed repo, however, if that's not the recommended course of action, then I'd like some advice on what to do? Thanks! Sincerely, Michael E. Cotterell Ph.D. Student in Computer Science, University of Georgia Instructor of Record, Graduate RA & TA, University of Georgia Faculty Liaison, CS Graduate Student Association, University of Georgia mepcotter...@gmail.com (mailto:mepcotter...@gmail.com) mepc...@uga.edu (mailto:mepc...@uga.edu) m...@cs.uga.edu (mailto:m...@cs.uga.edu) http://michaelcotterell.com/ ___________________________________________________________ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
