How to execute workflow locally without docker
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!
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.
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