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common-workflow-library / legacy

Deprecated
https://github.com/common-workflow-library/bio-cwl-tools
Apache License 2.0
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lobSTR example fails: node-engine.cwl is a link to nothing #62

Closed prismofeverything closed 8 years ago

prismofeverything commented 8 years ago

Hi,

Trying to run the lobSTR example, I discover that node-engine.cwl is a link to a file /engines/node-engine.cwl. However, this file does not exist in the repository, and causes the example to blow up.

Is this a directory someone has locally they have not checked in to the repository?

mr-c commented 8 years ago

Thank you Ryan for reporting this issue. The lobSTR example needs updating to the Draft 3 version of CWL as the way JavaScript works changed. Pe 16 mar. 2016 18:25, "Ryan Spangler" notifications@github.com a scris:

Hi,

Trying to run the lobSTR example, I discover that node-engine.cwl is a link to a file /engines/node-engine.cwl. However, this file does not exist in the repository, and causes the example to blow up.

Is this a directory someone has locally they have not checked in to the repository?

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tdanford commented 8 years ago

@mr-c any pointers or high level descriptions, as to what would need to be changed to fix this? I ran into it today too, would be happy to help if there's something I can do.

(I'm assuming that it's related to changes here: http://www.commonwl.org/draft-3/Workflow.html#Expressions is that right?)

mr-c commented 8 years ago

@tdanford Pardon my lack of response. I have this almost finished in https://github.com/common-workflow-language/workflows/pull/70

However the docker load command is failing:

Error response from daemon: invalid argument
Workflow error:
  Docker load returned non-zero exit status 1

I'm running Docker version 1.10.3, build 20f81dd Perhaps @tetron or @portah know what's going on here.

mr-c commented 8 years ago

@tdanford Okay, I just learned that the docker issue I had is because Docker changed the on-disk format in 1.10. I'll update the Readme to reflect that. Otherwise this appears to be working now.