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From Stian Soiland-Reyes <st...@apache.org>
Subject Re: GSOC: Add CWL support to Taverna
Date Sun, 28 Feb 2016 02:00:26 GMT
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


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

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

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

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" <maanafunedu@gmail.com> 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 <alaninmcr@googlemail.com>
> 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
> >
> >

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