Install Nextstrain by Conda

This is a note of install Nextstrain-cli by conda.

1. Prerequisites

Latest Conda (Minoconda or Anaconda) is installed.

Update conda if necessary.

$ conda update conda --all

2. Installation

1. Create a nextstrain environment:

$ conda create -n nextstrain

# Then activate this environment
$ conda activate nextstrain

2. Install nextstrain-cli

(nextstrain) $ conda install nextstrain-cli \
  -c conda-forge -c bioconda \
  --strict-channel-priority \
  --override-channels

3. Install nextstrain runtime

(nextstrain) $ nextstrain setup --set-default conda

4. (Optional) Try running Augur and Auspice

(1) Enter an interactive Nextstrain shell in the current directory (.).

(nextstrain) $ nextstrain shell .

(2) Run Augur.

(nextstrain) $ augur --help

(3) Run Auspice.

(nextstrain) $ auspice --help

(4) Exit the Nextstrain shell.

(nextstrain) $ exit

Reference

1. Nextstain cli documentation
2. Installing Nextstrain