I may be missing something, but right now, and without any changes to
Galaxy, there's no reason why a new tool should not wrap an existing
(or new) command line executable program that uses web services to do
something interesting!
I have an rgenetics tool that uses the Haploview java executable in
command line mode to prepare image files of LD patterns in the Hapmap
populations with an inhouse sample over a region, and then stitches
them together into a single image so they can be visually compared -
Galaxy doesn't know or care if the tool executable uses web services -
the job runner sets up the call and then deals with the resulting tool
outputs correctly - as long as the cluster node executing the tool has
internet access, it can interact with the web services transparently -
as Greg says, the tool will be fragile to changes in the web service
call syntax but that's always a problem in the long term.
I agree with Greg that bringing web services interfaces *directly*
into the existing Galaxy framework does not appear to have a high
priority at this time and I'm not even sure that it makes an awful lot
of sense in the long term - especially since we can let web service
interaction live out in tool space where it already works? Is there a
specific use-case anyone has in mind where the web services interface
really needs to be brought inside the framework itself?
On Tue, Sep 30, 2008 at 2:00 AM, <galaxy-dev-request(a)bx.psu.edu> wrote:
>
> Today's Topics:
>
> 1. Re: Galaxy with web services (Greg Von Kuster)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 29 Sep 2008 09:52:39 -0400
> From: Greg Von Kuster <ghv2(a)psu.edu>
> Subject: Re: [galaxy-dev] Galaxy with web services
> To: Praveen Agrawal <praveen(a)scfbio-iitd.res.in>
> Cc: galaxy-dev(a)bx.psu.edu
> Message-ID: <48E0DDA7.1090200(a)psu.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hello Praveen,
>
> Currently web-based interaction is only used for external data sources
> (biomart, UCSC table browser, most other things under "Get Data"). For
> the other tools, we generate a command line based on the user input,
> which Galaxy then runs. The motivation for this is control and trust.
> One of our major goals with Galaxy is to ensure reproducibility, and
> relying on web services which can change their interfaces or behavior
> makes this very challenging. We are certainly interested in supporting
> web services in the Galaxy framework, but implementation is not yet
> under way. Several of the methods currently in ~/tools/__init__.py (
> among others ) will need to evolve and grow in order to support a web
> services interface for remote tools. We'll certainly keep you informed
> as we begin to support this, but it may be a while...
>
> Greg Von Kuster
> Galaxy Development Team
>
>
> Praveen Agrawal wrote:
>> Hi,
>> I am trying to use Galaxy at my site and cann't figure out Galaxy with web
>> services. I understand that it's possible to integrate a data source using
>> WSDL/SOAP. Is the same possible for a remote tool as well?
--
python -c "foo = map(None,'moc.liamg(a)surazal.ssor'); foo.reverse();
print ''.join(foo)"