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  
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