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?
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...