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From Gale Naylor <Ga...@noventussolutions.com>
Subject Re: Common workflow language
Date Mon, 14 Dec 2015 18:12:09 GMT
Creating JIRA issues makes sense to me. Unless we have another way to keep
track of proposed or potential actions.

Gale

On Fri, Dec 11, 2015 at 6:02 AM Ian Dunlop <ian.dunlop@manchester.ac.uk>
wrote:

> Hello,
>
> I know this is a crazy suggestion, but......are there some issues that
> we can add to JIRA around CWL or jbatch. Otherwise it will be lost in
> the email thread.
>
> eg
> * CWL reader for SCUFL2
> * Docker image for taverna activities (docker compose based?)
> * Integrate with CWL tool registries (which I guess means getting the
> workbench working!)
>
> Cheers,
>
> Ian
>
> On 10/12/2015 09:35, Stian Soiland-Reyes wrote:
> >  I've signed up for the CWL hackathon, but I hope others would join!
> >
> >
> > I find CWL interesting as it has focused on the tool descriptions, and
> > packaging them using Docker. This is a pragmatic approach that means
> > lots of issues on reproducibility, installation and repurposability is
> > pretty much solved.
> >
> > It does however means it is hard to use non-local tools like REST
> > services, as you would need an equivalent command line tool.  Message
> > parsing and shims are trickier, but on the plus side you could use
> > your favourite scripting language (as long as it works on Linux :)).
> >
> >
> > Docker is also an important part of http://bioboxes.org/
> >
> >
> > CWL Tool descriptions are annotated with the EDAM ontology, which
> > includes many ELIXIR folks. ELIXIR is building a tool registry.
> >
> > Now I think it would be nice if we could also use such a tool registry
> > and descriptions from Taverna.
> >
> >
> > CWL focuses on data as files, in a way that is very similar to the
> > current Tool service.
> >
> > I think we could update the Tool Service to handle "CWL tools" or at
> > least handle docker images.  Of course you could do this today with
> > just having a command line tool that is "docker run blablabla".
> >
> >
> > I would like to start work on a CWL reader for SCUFL2, which would
> > create such Tool instances in the first place.
> >
> >
> > Representing any SCUFL2/Taverna workflow in CWL can be tricky, as you
> > would need to extend the tool type to have REST, WSDL, etc/. This is
> > an extension point in CWL though - and so it would perhaps raise the
> > question of why use CWL with custom extensions if nobody else can run
> > such the Taverna services. Still, the workflow structure can be
> > repurposed, with a different activity inserted in other CWL engines.
> > There's a danger here of "standards mutation" - like we saw a decade
> > ago with WSDL being modified beyond recognition in Globus web services
> > and WSRF.
> >
> >
> > Another approach could be to create Docker images that can execute
> > Taverna activities (e.g. using the wsdl-generic command line). This
> > would be more of an interesting research angle, perhaps, as it means
> > we would be more freely able to try to run a Taverna workflow with an
> > alternate CWL workflow engine.
> >
> >
> > Taverna workflows allow various control mechanisms like Retry,
> > Failover, Parallelism, inplicit iterations, dot/cross product - which
> > could be tricky to represent in CWL. I think only a subset of Taverna
> > workflows could be run as CWL - without again adding customizations -
> > kind of like a CWL profile.
> >
> >
> > I think one aspect is that CWL is also a focus opportunity for Taverna
> > - coordinating command line tools is simpler than trying to integrate
> > "everything". I think also this is more of the growing space we find
> > Taverna in now, rather than 8 years ago when Taverna aimed to be
> > bioinformatician's best friend and we added lots of GUI and activity
> > plugins for various bioinformatics-centric services. (however
> > AstroTaverna is one landscape which is still open to be claimed in
> > such a way.).  CWL is a bit more on a "hacker level" - which I think
> > we can be more comfortable with catering for.
> >
> >
> > For CWL, Taverna is a valuable proposition as we know how to handle
> > workflow provenance, we can easily add preservation aspects (e.g.
> > packaging all the docker images used in a run).  The Taverna Workbench
> > has a pluggable way to add service descriptions, so we could connect
> > to CWL tool registries and turn Taverna into a "CWL editor".
> >
> >
> > On 4 December 2015 at 17:05, Alan Williams <alaninmcr@googlemail.com>
> wrote:
> >> On 04-Dec-15 15:28, Ian Dunlop wrote:
> >>>
> >>> -----BEGIN PGP SIGNED MESSAGE-----
> >>> Hash: SHA256
> >>>
> >>> Hello,
> >>>
> >>> Does anyone have views on how Apache Taverna fits into the goals of
> >>> the Common Workflow Language project
> >>> https://github.com/common-workflow-language/common-workflow-language ?
> >>> Should taverna adopt CWL instead of SCUFL2. Are there things that
> >>> SCUFL2 or the current taverna engine offers that CWL does not?
> >>
> >>
> >> Stian is probably the best person to answer this as he has been quite
> >> involved with CWL. To the best of my knowledge, CWL started off very
> similar
> >> to SCUFL2 but diverged.
> >>
> >> There is a CWL/Taverna/Galaxy hackathon planned for May 2016 in Paris. I
> >> think (hope) I sent around the Doodle poll for it.
> >>
> >>> Cheers,
> >>>
> >>> Ian
> >>
> >>
> >> Alan
> >>
> >
> >
> >
>
> --
> Ian Dunlop, eScience Lab
> School of Computer Science
> The University of Manchester
> http://orcid.org/0000-0001-7066-3350
>

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