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

Hi Ross, Hi Greg, Thanks for the elaborate answers. Certainly, having programs installed locally gives lot more control over their execution. In my case I am going to have tools which would be running across Indian "grid" and then the scientist would have the freedom to use the workflow capability to join those tools. I couldn't understand "we can let web service interaction live out in tool space where it already works". Please elaborate.

Thanks, Praveen > 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&gt; 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&gt; >> Subject: Re: [galaxy-dev] Galaxy with web services >> To: Praveen Agrawal <praveen(a)scfbio-iitd.res.in&gt; >> Cc: galaxy-dev(a)bx.psu.edu >> Message-ID: <48E0DDA7.1090200(a)psu.edu&gt; >> 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,&#39;moc.liamg(a)surazal.ssor&#39;); foo.reverse(); > print ''.join(foo)" > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ http://www.scfbio-iitd.res.in ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~