CWL: build docker image with DockerRequirements: dockerFile?
1
0
Entering edit mode
4.4 years ago
ninsch3000 ▴ 10

Hello,

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 http://www.commonwl.org/v1.0/CommandLineTool.html#DockerRequirement 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

cwl docker • 2.2k views
ADD COMMENT
0
Entering edit mode
4.2 years ago
sshinya ▴ 10

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.

hints:
    DockerRequirement:
        dockerImageId: CONTAINER_NAME
        dockerFile:
            $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 COMMENT

Login before adding your answer.

Traffic: 868 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6