Re: [galaxy-dev] galaxy-dev Digest, Vol 33, Issue 21
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)
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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)"