dnanexus / dxCompiler

WDL and CWL compiler for the DNAnexus platform
Apache License 2.0
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difficulty setting a default docker image #392

Closed 23andme-jaredo closed 2 years ago

23andme-jaredo commented 2 years ago

Hi there,

I am having trouble getting a global docker image working via my extras.json:

{
    "defaultRuntimeAttributes" : {
                "docker" : "dx://ukbb_wgs_test1:/docker_images/wgs_phaser.tar.gz"
      }
}

I then compile with:

java -jar ~/software/dxCompiler-2.10.4.jar compile phase_wgs_noruntime.wdl  -project ukbb_wgs_test1 -folder /workflows/test/ -f -extras extras.json

but get various runtime errors since it is not using the docker image.

If I add:

    runtime {
        docker: "dx://ukbb_wgs_test1:/docker_images/wgs_phaser.tar.gz"
    }

to each task then it works fine so the docker path is correct etc.

23andme-jaredo commented 2 years ago

looks like:

{
      "default_runtime_attributes": {
        "docker" : "dx://ukbb_wgs_test1:/docker_images/wgs_phaser.tar.gz"
    }
}

works. I think the documentation here might need to be updated.