How to execute workflow locally without docker

Follow

jiawei

• July 11, 2020 15:28

Hello! I want to use the workflow locally. But I cannot use docker because  I don't have root access. 

I do find the tutorial "(How to) Install and use Conda for GATK4". But I am confused if it can be used instead of  docker to execute workflow. If yes, what's the specific steps?

Thank you so much!

0

• 

  Genevieve Brandt (she/her)

  • July 15, 2020 16:50

  Hi jiawei, a conda environment can be used to run the tools individually (https://github.com/broadinstitute/gatk/#quickstart). If you want to run the pipelines, please see the getting started blog post (https://gatk.broadinstitute.org/hc/en-us/articles/360036194592-Getting-started-with-GATK4) under #9 Run Pipelines. You can use cromwell locally on your computer.

  1

  Comment actions Permalink

Please sign in to leave a comment.