dnanexus/dxCompiler

difficulty setting a default docker image

Closed this issue · 1 comments

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.

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.