Found the link to the externalTools / UseCases definitions - http://usecase.taverna.org.uk/sharedRepository/index.php
Jits Jiten Bhagat wrote: > Hi Alan, > > Alan R Williams wrote: > >> Hello Jits, >> >> I have two immediate questions: >> >> (1) How does your definition of a workflow component as including "Anything >> that does >> some processing" relate to the idea of data sources as first-class objects >> in the >> next gen workbench? >> >> > > At the moment, we're not quite sure and don't have a concrete proposal > for handling data sources and data items. Though we definitely want to > make them first class objects that can be easily added to workflows. > > In earlier work, we thought that data could be "wrapped" using the same > components mechanism, but this quickly conflated the design discussions > and led to some analysis paralysis. So in the interest of moving forward > we focused on the process side of things first. > > There are a few considerations: > - Based on discussions, users tend to want a clear separation between > the "things that do some processing" and data sources. Hence the > workbench has a "Components Palette" and a "Data" view (maybe we should > call it "Data Palette"?) > - There are very likely to be cases where components can be > pre-packaged with data. For simple cases, like example data and default > values, this is handled directly in the component definition. Or string > constants within nested workflows can be used. But for more elaborate > data packaging we need to think about this some more. > > Any thoughts / ideas on how we might do this? > > Internally, we will possibly use the Eclipse Resources framework [1] as > there is a whole load of support for that in Eclipse RCP. We're also > looking at VBrowser. > > >> (2) How does the workbench component definition relate to, say, Galaxy tool >> descriptions >> Network Workbench algorithms or externalTool (was UseCase) definitions? >> >> > > I've had a close look at Galaxy tool descriptions [2] and UseCase > definitions (please could you remind me of the URL), but don't think > I've come across NWB algorithms. Could you point me to the > spec/template/examples please? > > In terms of Galaxy and externalTool, they cater for a bit simpler > situation - wrapping command line tools only (I believe) so they have > simple mappings to the underlying tech. There is still significant > overlap with our components work, especially things like the UI > configuration/fields in Galaxy tool configs. > > I can imagine we would be able to easily write a script to generate > component definitions from externalTool definitions, or even just build > a lightweight facade API over them. > > One thing, they don't seem to focus as much on metadata. I think things > like help docs, tags, annotations, linking to related resources and > helpers will (hopefully) add value once these workflow components live > in repositories like a components library (building on our experiences > with myExperiment and BioCatalogue). > > Cheers, > Jits > > [1] > http://help.eclipse.org/helios/index.jsp?topic=/org.eclipse.platform.doc.isv/guide/resInt.htm > [2] http://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax > >> Alan >> >> >> ------------------------------------------------------------------------------ >> Increase Visibility of Your 3D Game App & Earn a Chance To Win $500! >> Tap into the largest installed PC base & get more eyes on your game by >> optimizing for Intel(R) Graphics Technology. Get started today with the >> Intel(R) Software Partner Program. Five $500 cash prizes are up for grabs. >> http://p.sf.net/sfu/intelisp-dev2dev >> _______________________________________________ >> taverna-hackers mailing list >> [email protected] >> Web site: http://www.taverna.org.uk >> Mailing lists: http://www.taverna.org.uk/about/contact-us/ >> Developers Guide: http://www.taverna.org.uk/developers/ >> >> > > > > ------------------------------------------------------------------------------ > Increase Visibility of Your 3D Game App & Earn a Chance To Win $500! > Tap into the largest installed PC base & get more eyes on your game by > optimizing for Intel(R) Graphics Technology. Get started today with the > Intel(R) Software Partner Program. Five $500 cash prizes are up for grabs. > http://p.sf.net/sfu/intelisp-dev2dev > _______________________________________________ > taverna-hackers mailing list > [email protected] > Web site: http://www.taverna.org.uk > Mailing lists: http://www.taverna.org.uk/about/contact-us/ > Developers Guide: http://www.taverna.org.uk/developers/ > ------------------------------------------------------------------------------ Increase Visibility of Your 3D Game App & Earn a Chance To Win $500! Tap into the largest installed PC base & get more eyes on your game by optimizing for Intel(R) Graphics Technology. Get started today with the Intel(R) Software Partner Program. Five $500 cash prizes are up for grabs. http://p.sf.net/sfu/intelisp-dev2dev _______________________________________________ taverna-hackers mailing list [email protected] Web site: http://www.taverna.org.uk Mailing lists: http://www.taverna.org.uk/about/contact-us/ Developers Guide: http://www.taverna.org.uk/developers/
