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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