The 'conda' command is not available in the shell /bin/bash that will be used by Snakemake

Hi, there:

please see the screenshot below. I am keeping getting an error.

Is this because that “Setting default environment to docker” instead of “native”? If so, how to change the default environment to native?

Thank you & Best regards,

Hi @jiehuang001 - you can run each individual nextstrain command in a native (non-docker) environment by adding --native, e.g. nextstrain build --native ....

Changing the defaults is a work in progress!