From peter.amstutz at curoverse.com Mon May 1 10:15:22 2017 From: peter.amstutz at curoverse.com (Peter Amstutz) Date: Mon, 1 May 2017 10:15:22 -0400 Subject: [arvados] Fwd: help with errors arvados-cwl In-Reply-To: References: <67e578ca58ad4a98bb0fc99e6f897eb7@cchmc.org> Message-ID: Hi Roberto, This means that the API server's internal clone of the "arvados" git repository is out of date. It needs to contain this commit: https://dev.arvados.org/projects/arvados/repository?utf8=%E2%9C%93&rev=570509ab4d2ef93d870fd2b1f2eab1 Thanks, Peter On Fri, Mar 24, 2017 at 12:20 PM, Perea, Roberto wrote: > Hi, > > > > Could you explain about the following error that I get when running > ?arvados-cwl-runner bwa-mem.cwl bwa-mem-input.yml? > > > > "error searching arvados from '570509ab4d2ef93d870fd2b1f2eab178afb1bad9' to > 'master', excluding []"> > > > > Thanks, > > > > > > Roberto Perea, PhD > > Sr. Analyst-Linux Systems > > Biomedical Informatics > > CCHMC > > Ext. 61005 > > > > > _______________________________________________ > arvados mailing list > arvados at arvados.org > http://lists.arvados.org/mailman/listinfo/arvados > From skanwal at student.unimelb.edu.au Fri May 12 01:58:28 2017 From: skanwal at student.unimelb.edu.au (Sehrish Kanwal) Date: Fri, 12 May 2017 05:58:28 -0000 Subject: [arvados] running cwl workflow on arvados Message-ID: 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: