Sorry if my post was rambling and unclear. Here's the executive summary for what it's worth: IMHO, a Galaxy tool that generates tools should emit them as tool shed compatible artefacts, ready for uploading to a TS repository for automated installation to any target instance.
On Thu, Jul 18, 2013 at 11:25 AM, Michael E. Cotterell < mepcotter...@gmail.com> wrote: > Ross, > > Thanks for the comments. > > I've already made my main tool "tool_shed" compatible. What I'm wondering > about is what do I do with the tools that my tool creates? > > 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/ > > > On Wednesday, July 17, 2013 at 7:44 PM, Ross wrote: > > > Hi, Michael, > > > > As others have said, in the long term, tool wrappers and their > dependencies will be distributed and installed through tool sheds rather > than being distributed with Galaxy source, so you might want to plan to > generate and upload tool shed compatible archives from the get-go. The test > and main tool sheds contain plenty of examples and Björn's tools exercise > pretty much all of the functionality - you can browse the repo structure > which is identical to the gz archive structure you need to upload to a new > repo, or download the repo as a gz, unpack it and get exactly the kind of > directory structure and contents you need to emulate for your tools. Once > you have a working tool packaging the archive up is straightforward. > > > > The format for tool shed repo uploads and syntax for the tags used to > define dependencies is very well documented in the tool shed section of the > wiki. As Björn points out, the tool factory python wrapper might be a > useful source of ideas and perhaps code. Your tool generator will need to > do something similar to write the content and generate complete tool shed > archives. When generating a new tool, the TF uses an ugly XML wrapper > generator (contributed improvements would be very welcome!) and (probably > more usefully) the few lines of code you need to package up the functional > test data and the XML and wrapper if you need one in toolshed archive > format. > > > > > > On Thu, Jul 18, 2013 at 5:30 AM, Björn Grüning < > bjoern.gruen...@pharmazie.uni-freiburg.de (mailto: > bjoern.gruen...@pharmazie.uni-freiburg.de)> wrote: > > > Hi Michael, > > > > > > I think you will enter new ground with your tool. The closest tool that > > > will do something similar is Ross toolfactory, I think: > > > > > > http://toolshed.g2.bx.psu.edu/view/fubar/toolfactory > > > > > > For me one question is, do you really want to offer that service to > > > every user and is it save? > > > > > > > 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)? > > > > > > > > > It is mainly a hg pull. But if you deinstall that repository and > > > reinstall it, all your files are lost. > > > > > > > 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)? > > > > > > > > > I think that is a better way to do it. The API can be used to install > > > your tools. But it need to be configured beforehand from the user, > > > administrator. > > > > > > > 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? > > > > > > > > > There is a feature request, that you can specify in your > > > toolshed-repository the preferred location in the tool panel. For now I > > > would ignore it and just install the tools somewhere and hope that > > > feature request is quiet high in Gregs ToDo list :) > > > > > > Cheers, > > > Bjoern > > >
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