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> 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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