Update: July 26, 2019
This section of the forum is now closed; we are working on a new support model for WDL that we will share here shortly. For Cromwell-specific issues, see the Cromwell docs and post questions on Github.

(Internal Broad only) How to create docker images using Broad filesystems?

I'm trying to create my first docker, but I'm stymied by the first step "Get and install Docker on your local machine". My local machine is a Windows laptop, but I never use this for any programming -- instead I just use the Windows laptop to get a terminal with which to access Broad linux filesystems. All my computer programs are within the Broad's linux system (where I install software using dotkits, and then run them using the linux operating system).

It does not make sense to me to install Docker on my local PC, since I never use or install needed software (Java, R, Python) or run programs on the PC.

But I can't find any instructions on how to create a docker from the Broad unix filesystems (eg when I'm logged in to a linux login server).

Thanks for any help,
Sarah Calvo



  • RuchiRuchi Member, Broadie, Moderator, Dev admin

    Hey Sarah,

    I'm not 100% on this, but I believe one isn't allowed to install Docker on the Broad's linux system.

    If you are hoping to run Cromwell jobs locally on the Broad's linux system, then your tasks can't use docker and rely on software installed by dotkits.

    Else, if you are hopping to run Cromwell jobs in the cloud, then its worthwhile to:

    • install docker on your local PC
    • copy some of your files from the Broad FS to the cloud

    Because this way you can orchestrate jobs from your local laptop that actually compute on cloud infrastructure using data that lives in cloud buckets. When you install Docker locally, you're not required to install all the tools locally as well -- you just need to write a Dockerfile that contains instructions on how to download the required tools. Here's a nice example of a Dockerfile that is used to build a Docker image that contains bwa https://hub.docker.com/r/biocontainers/bwa/~/dockerfile/

    Hope this helps

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