Local installation of Augur and Auspice with conda

1

I was trying to install Augur and Auspice using coda following this link: Installing Nextstrain — Nextstrain documentation. While when I was checking the status, I got some un-expected responses from the terminal as the following.

(nextstrain) Amandas-MacBook-Pro:~ amanda$ auspice -h
-bash: auspice: command not found
Moreover,

(nextstrain) Amandas-MacBook-Pro:~ amanda$ nextstrain check-setup --set-default

nextstrain-cli is up to date!

Testing your setup…

# docker is not supported

✘ no: docker is installed

✘ no: docker run works

? unknown: containers have access to >2 GiB of memory

:heavy_check_mark: yes: image is new enough for this CLI version

# native is not supported

:heavy_check_mark: yes: snakemake is installed

:heavy_check_mark: yes: augur is installed

✘ no: auspice is installed

# aws-batch is not supported

✘ no: job description “nextstrain-job” exists

✘ no: job queue “nextstrain-job-queue” exists

✘ no: S3 bucket “nextstrain-jobs” exists

No good. No support for any Nextstrain environment.

Could anyone please clarify a bit? Any comments are greatly appreciated.

2

Hi @emtf! Apologies that your post fell through the cracks; hopefully you’ve long-since solved the problem. In case not, and for anyone finding this post in the future, this looks like the install step for Auspice (npm install --global auspice) wasn’t run after activating the Conda env with conda activate nextstrain.