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
mepcotterell(a)gmail.com (mailto:mepcotterell@gmail.com)
mepcott(a)uga.edu (mailto:mepcott@uga.edu)
mec(a)cs.uga.edu (mailto:mec@cs.uga.edu)
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 <mepcotterell(a)gmail.com
(mailto:mepcotterell@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
> mepcotterell(a)gmail.com (mailto:mepcotterell@gmail.com)
(mailto:mepcotterell@gmail.com)
> mepcott(a)uga.edu (mailto:mepcott@uga.edu) (mailto:mepcott@uga.edu)
> mec(a)cs.uga.edu (mailto:mec@cs.uga.edu) (mailto:mec@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.gruening(a)pharmazie.uni-freiburg.de
(mailto:bjoern.gruening@pharmazie.uni-freiburg.de)
(mailto:bjoern.gruening@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
> >
>