Hi , Now i am familiar with working apache taverna.But what modules do i need to study in the git modules to understand how it is implemented.From what i understand currently Taverna workflows are implemented using Scufl2 Taverna Language.So CWL is used to bring different work flow implementation into one platform .Am i correct ?.So what part do i need to study in order to get better idea about project "Browse and use CWL tool descriptions from the workbench " ?.
regards Thilina. On Mon, Feb 29, 2016 at 5:51 PM, Stian Soiland-Reyes <[email protected]> wrote: > Here's a getting started guide for Taverna > > http://taverna.incubator.apache.org/documentation/quick-start-guide/ > > Also a video: > > https://www.youtube.com/watch?v=Zh0tn8amjAY > > And more tutorials for 2.5: > > http://dev.mygrid.org.uk/wiki/display/tav250/Tutorials > > (You don't need to go through all of those, just like the first one) > > On 28 February 2016 at 02:00, Stian Soiland-Reyes <[email protected]> > wrote: > > Hi, thanks for showing early interest! > > > > Perhaps you would like to tell us a bit about yourself and your > background? > > Are you studying Computer Science? > > > > First of all you probably want to have a quick look at the Getting > Started > > documentation for Taverna, and try the Taverna Workbench Core 2.5 > download. > > There should be a tutorial for building a hello world workflow somewhere, > > I'll see if I can find it. > > > > Basically what this task you mention is about is to add support for > finding > > CWL tools under the top-left Available Services panel, so they can be > > dragged into the workflow. > > > > The remaining tasks deal with how to execute such CWL tools, and how to > > represent a Taverna workflow in CWL (or vice versa) > > > > The Jira issue gives an introduction and various links to related > material. > > > > As for the Workbench integration we have already this plugin developer > > tutorial: > > > > > http://dev.mygrid.org.uk/wiki/display/developer/Tutorial+-+Service+discovery+plugin > > > > Unfortunately this tutorial relates to Taverna 2, while now we develop > > Taverna 3. Naturally we would hope for your potential contribution to > apply > > to Taverna 3, which has a slightly different mechanism for Taverna > Activity > > configuration (JSON object instead of a Java Bean). > > > > We have not yet released the Taverna 3 Workbench, so testing your work > might > > require other modifications to the T3 Workbench code to get it running. > We > > would appreciate any general fixes there (e.g. if we have the wrong > import > > statements after moving to org apache.taverna) - but it could be > sufficient > > for you to track such issues and discuss them on our mailing list > > > > However for your discovery side I think it should be fine for you to > start > > work in Taverna 2 and with a dummy Activity that just keeps a Jackson > JSON > > object, and then adapting your code to Taverna 3 would be a nice second > > phase. > > > > As for discovery side this is still early days in the CWL community, so > you > > want to engage them to ask what are the plans for a tool registry. I know > > they are working with the http://bio.tools/ guys, but I am not sure how > easy > > it is to add CWL Tool YAML/JSON directly there (or by reference). > > > > As far as I've seen CWL used, each tool is typically stored in a separate > > YAML file. Perhaps a good start is to just "discover" within a fixed or > > configured directory which we can populate manually with from CWLs Github > > examples. > > > > The Service Discovery mechanism in Taverna can do searches over fields, > so > > an add-on task could be to expose some of the metadata that could be in > the > > tool description, e.g. function:sequencing. However I think again > metadata > > work in CWL is early days and you might need to work with the CWL > community > > to get good examples. > > > > On 27 Feb 2016 12:23, "Thilina Manamgoda" <[email protected]> wrote: > >> > >> Hi, > >> > >> I am interested in "Browse and use CWL tool descriptions from the > >> workbench" task and to get better idea about this project can you > provide > >> me a guide line please. > >> > >> Regards > >> ,Thilina > >> > >> On Sat, Feb 27, 2016 at 4:40 PM, Alan Williams < > [email protected]> > >> wrote: > >> > >> > On 27-Feb-16 09:05, Thilina Manamgoda wrote: > >> > > >> >> HI, > >> >> > >> > > >> > Hello > >> > > >> > Source: https://issues.apache.org/jira/browse/TAVERNA-900 > >> >> > >> >> I am Thilina Manamgoda undergraduate from University of Perandeniya. > I > >> >> would like to contribute this project for GSOC 2016. > >> >> > >> > > >> > That is great. > >> > > >> > In order to add CWL support to Taverna following steps should be > taken. > >> >> > >> >> 1.Save Taverna workflows as CWL > >> >> 2.Read CWL workflows > >> >> 3.Execute CWL tool descriptions > >> >> 4.Browse and use CWL tool descriptions from the workbench > >> >> 5.Create a Docker tool for executing Taverna activities > >> >> > >> >> So for Gsoc 2016 i need to get better idea about the project ,am i > >> >> supposed > >> >> to do one of above task or all of them ?. > >> >> > >> > > >> > As the issue says, "the GSOC student can ... choose to pursue one or > two > >> > of these tasks in detail" > >> > > >> > So, if you are interested in (for example) Docker, you might want to > >> > concentrate on #5. > >> > > >> > As part of a submission to become a GSOC student, you do a proposal of > >> > what you plan to do. That proposal will depend on which task(s) you > are > >> > interested in working on. The content of a proposal from someone > >> > interested > >> > in #1 would be very different to that for someone working on #4. > >> > > >> > Which task(s) are you interested in? > >> > > >> > Feel free to ask as many questions as you want. > >> > > >> > Regards, > >> >> Thilina. > >> >> > >> > > >> > Alan > >> > > >> > > > > > -- > Stian Soiland-Reyes > Apache Taverna (incubating), Apache Commons RDF (incubating) > http://orcid.org/0000-0001-9842-9718 >
