Question: CWL: build docker image with DockerRequirements: dockerFile?
gravatar for ninsch3000
3.1 years ago by
ninsch300010 wrote:


I'd like to run CWL with docker, but don't entirely understand DockerRequirements.

My question: Do I always have to provide a pre-built docker image (works for me with dockerPull and/or dockerImageId), or can cwltool call docker build if the Dockerfile is specified (with dockerFile). The latter option sounds tempting on but doesn't work for me ('Docker is not available for this tool'). Am I just misunderstanding the specifications, or is my system not set up correctly?

Thanks in advance for any comments!

cwltool 1.0.20171017195544

Docker version 17.12.0-ce

docker cwl • 1.7k views
ADD COMMENTlink modified 2.9 years ago by sshinya10 • written 3.1 years ago by ninsch300010
gravatar for sshinya
2.9 years ago by
sshinya10 wrote:

Hi ninsche3000

I'm not sure how did you wrote your CWL scripts, but DockerRequirement part may be incorrect. If you have Dockerfile in foo/bar/Dockerfile as a relative path, you have to write following format. This issue will help you.

        dockerImageId: CONTAINER_NAME
            $include: foo/bar/Dockerfile

It should be noted that you have to give dockerImageId additionally in current cwltool implementation(See this issue).

(Edited on 2018-04-17): Removed triangle

ADD COMMENTlink modified 2.9 years ago • written 2.9 years ago by sshinya10
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