Ah. Forgive me for not paying attention to that requirement. Tools usually
run as the Galaxy user so only local admins can do that at present because
allowing a non-admin user to install a newly generated tool, especially on
a public site opens up some interesting security challenges. I think it
would be hard to sell as a new feature unless you've figured out how to
prevent potential mischief from miscreant users?


On Thu, Jul 18, 2013 at 11:33 PM, Michael E. Cotterell <
mepcotter...@gmail.com> wrote:

> This doesn't seem to fit into the use case that my colleagues have
> described to me. Our tool, used within Galaxy, creates/builds/generates new
> tools for Web service operations. Once a user uses our tool to generate a
> Web service tool, it should be visible and usable to them.
>
> Currently, in order to accomplish this, we have to manually modify the
> tool_config.xml file, however, I don't think we should release a tool that
> does that.
>
> 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 10:26 PM, Ross wrote:
>
> > AFAIK it's not yet possible, but a tool shed API to expose subversion
> hooks for repository creation and update is a logical development which is
> already on the radar AFAIK.
> >
> > For the bigger picture of complexity for the user, I think some key
> clarifications required include:
> > which 'user' is experiencing complexity;
> > how big a barrier it is to generating tools;
> > how readily can we make it go away;
> > how much will it help?
> >
> > Tool builders (even 'users' of the TF) might reasonably be expected to
> have a capacity for substantial complexity that the end user of the
> generated tools should not need to possess - after all, once a generated
> tool is installed in Galaxy, the Galaxy user can't tell the difference and
> sees no more complexity from the generated tool than a hand written one.
> >
> > On absent local tool sheds: it's trivial to run a toolshed on a dev
> laptop and not hard to run in production - but tool makers can always use
> the public test and main TS if they want to distribute new tools so I'm not
> sure how big a barrier a missing local toolshed really is.
> >
> >
> > On Thu, Jul 18, 2013 at 12:08 PM, Michael E. Cotterell <
> mepcotter...@gmail.com (mailto:mepcotter...@gmail.com)> wrote:
> > > I didn't mean to imply it was unclear. It definitely made sense.
> > >
> > > I completely agree with you. However, is there for a way (maybe via
> the toolshed api) for my tool to push these tools to a TS repo? Also,
> doesn't that add some more complexity for the user? Not everyone runs a
> local tool shed.
> > >
> > > 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) (mailto:
> mepcotter...@gmail.com)
> > > mepc...@uga.edu (mailto:mepc...@uga.edu) (mailto:mepc...@uga.edu)
> > > m...@cs.uga.edu (mailto:m...@cs.uga.edu) (mailto:m...@cs.uga.edu)
> > > http://michaelcotterell.com/
> > >
> > >
> > > On Wednesday, July 17, 2013 at 10:05 PM, Ross wrote:
> > >
> > > > 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 (mailto:mepcotter...@gmail.com) (mailto:
> 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) (mailto:
> mepcotter...@gmail.com) (mailto:mepcotter...@gmail.com)
> > > > > mepc...@uga.edu (mailto:mepc...@uga.edu) (mailto:mepc...@uga.edu)
> (mailto:mepc...@uga.edu)
> > > > > m...@cs.uga.edu (mailto:m...@cs.uga.edu) (mailto: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) (mailto:
> 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
> > > > > >
> > > > >
> > > >
> > >
> >
> >
> >
> > --
> > Ross Lazarus MBBS MPH;
> > Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444
> > http://scholar.google.com/citations?hl=en&user=UCUuEM4AAAAJ
> > ___________________________________________________________
> > Please keep all replies on the list by using "reply all"
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> >
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>
>
>
>


-- 
Ross Lazarus MBBS MPH;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444
http://scholar.google.com/citations?hl=en&user=UCUuEM4AAAAJ
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