[arvados] running cwl workflow on arvados

[Sehrish Kanwal]

Thanks for getting back Peter.
I was later able to solve the issue and successfully run the pipeline.



Kind Regards,
Sehrish Kanwal
PhD Research Scholar
Computing and Information Systems, Melbourne School of Engineering
The University of Melbourne


On Mon, Jun 26, 2017 at 9:45 AM, Peter Amstutz <peter.amstutz at curoverse.com>
wrote:

> Hi Sehrish,
>
> Can you provide the whole output, and the command line you used?
>
> Thanks,
> Peter
>
>
> On Jun 25, 2017 11:15, "Sehrish Kanwal" <skanwal at student.unimelb.edu.au>
> wrote:
>
>> Hi,
>>
>> I am new to arvados and trying to run my cwl workflow using it. I have
>> setup my VM and have the directory structure setup like the one I had at my
>> local machine.
>> I am getting an error: Field `run` contains undefined reference to
>> `file:///data-sdc/home/skanw al/keep2/home/New%20collection/BWA-mem.cwl`
>> I think that is something to do with referencing files using/in keep. Can
>> someone help me with that? More specifically how can I run my cwl workflow
>> on arvados? What requirements do I need to fulfil before trying that?
>> Thanks.
>>
>>
>> Kind Regards,
>> Sehrish Kanwal
>> PhD Research Scholar
>> Computing and Information Systems, Melbourne School of Engineering
>> The University of Melbourne
>>
>>
>> _______________________________________________
>> arvados mailing list
>> arvados at arvados.org
>> http://lists.arvados.org/mailman/listinfo/arvados
>>
>>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.arvados.org/pipermail/arvados/attachments/20170627/a1496c8d/attachment.html>