created by jneff
on 2016-02-18
If you are building a pipeline or tools to run on FireCloud, you may benefit from existing Docker images. For example, when you write the WDL for your tool, it could be easier to reference a Docker image that already contains Matlab or other dependencies.
You may have found the Broad Institute’s public Docker Hub repository: (https://hub.docker.com/r/broadinstitute/). This repository includes a Docker image for the (https://hub.docker.com/r/broadinstitute/firecloud-cli/) that enables you to upload tools to FireCloud. However, this repo is not particularly helpful if you are building tools.
Eventually, FireCloud may support a Docker Hub repository with best practice images for tool developers. In the meantime, you can check out the Broad GDAC repository: (https://hub.docker.com/r/broadgdac/). Here you can find Docker images for R, Matlab, Nozzle, and other GDAC tools (e.g., GISTIC2.0) that could integrate with your pipeline.
For more information on Docker, refer to (https://docs.google.com/document/d/1SExJeNoxKGBClPYKtGFfQ0K0bGN2nQeuh_iIkxEt3TY/) and (http://gatkforums.broadinstitute.org/gatk/discussion/6886/best-practices-for-docker-images-and-dockerfiles#latest).