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
