Content developed by Jared Johnson

Module Objectives

• Install Nextstrain
• Install all other tools used in later modules into a single Micromamba environment

Nextstrain

Install Nextstrain following the Conda runtime instructions on the docs page.

Other Software

Install

Use the command below to create a new environment with micromamba and install the other software that will be used in future lessions.

micromamba create -n flu_env \
  -c bioconda \
  -c conda-forge \
  -c defaults \
  "sra-tools=3.4.1" \
  "samtools=1.1" \
  "nextflow=26.04.1" \
  --yes

Verify

# activate the environment
micromamba activate flu_env

# check for installed tools
fasterq-dump -v
samtools
nextflow version -v

# deactivate the environment
micromamba deactivate