Heads up:
We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
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.

How to develop WDL workflows using Docker images locally which can be used seamlessly in the cloud

dannykwellsdannykwells San FranciscoMember ✭✭

Hi Broad/WDL folks,

I love WDL and we're really excited it's potential (good work!)
One question that I have about it is about what the workflow looks like for developing WDL programs locally (on a Mac) and then deploying those on the cloud (Google). How do you do this at Broad?

From here (https://docs.google.com/document/d/1jv4FFWC0RJUWoQagh7wA7L7K6lHNz72zGttwEfVKgnA/edit?ts=5601ad23#heading=h.16u3o9piptvm) it seems that you work within a VM when making Docker images on a Mac (although this is no longer required in the latest Docker release - https://docs.docker.com/engine/installation/mac/ - is this required if I want to call containers inside a WDL program? Said another way, is it possible to use containers made on a Mac within a WDL program from the standard Mac terminal? In turn, are there substantial changes to these programs needs before they can be deployed on a cluster?

In general, any help using WDL to write pipelines using Docker containers holding needed functions (bwa, picard, GATK) that can be developed and executed locally on a mac and ported easily to a cluster computing environment would be really helpful!

Thank you!

Best Answer

Answers

  • dannykwellsdannykwells San FranciscoMember ✭✭

    Hi @KateN, thank you! This helped and I have WDL et al running both on my laptop and GCP!

Sign In or Register to comment.