Skip to content

Installing QIIME2

Sometimes you will need to install a different version of QIIME 2. For example, you may be continuing an analysis that was started in an older version, or you may need to reproduce results from a previous project. Below is a guide for installing QIIME 2 on Alpine.

Installing QIIME2 on Alpine

Log into Alpine using OnDemand

Use ls -la to list all files in your HOME directory. See if you have a .condarc file. If you do not, use nano .condarc to make one.

Using nano, add the following to your .condarc file which is found in your HOME directory.

pkgs_dirs:
  - /projects/.colostate.edu/$USER/.conda_pkgs
envs_dirs:
  - /projects/.colostate.edu/$USER/software/anaconda/envs

NOTE: replace $USER with your NetID for example: /projects/.colostate.edu/vfn/.conda_pkgs)

The HOME directory does not have enough storage to save all your conda packages so we will tell conda to store those in our PROJECTS directory.

Navigate to the COMPILE node using:

acompile --ntasks=4 --time=04:00:00

Purge modules using: 

module purge

Load Anaconda by using:

module load anaconda

Navigate to https://library.qiime2.org/quickstart/qiime2 to find the latest Qiime2 install directions.

Note: If you are pulling the information from the website yourself, make sure to use the Linux instructions. If you are installing on your own computer, make sure to use the proper instructions for your computer.

  • For installing on QIIME2 on alpine you do not need to do steps 1 and 2 on the qiime2docs website.

Create a new conda environment using the .yml file

conda env create \
  --name qiime2-amplicon-2026.4 \
  --file https://raw.githubusercontent.com/qiime2/distributions/refs/heads/dev/2026.4/qiime2/released/rachis-qiime2-linux-64-conda.yml
  • Note that qiime2-amplicon-2026.4 is just the name of the conda environment. You can choose a different name if you prefer, but you will need to use that same name whenever you activate the environment.

Activate the environment using:

conda activate qiime2-amplicon-2026.4

Test the install using:

qiime --help

Remove the .yml file using (optional):

rm rachis-qiime2-linux-64-conda.yml

Type exit to leave the COMPILE node. This will bring you back to the LOGIN node.

Congratulations! You are now well equipped to begin learning about and doing microbiome analyses.

Intalling QIIME2 on your computer

To install QIIME2 on your own computer you can follow the same steps from https://library.qiime2.org/quickstart/qiime2 . Make sure to select the base distribution’s conda environment that matches your computer.

Windows Users

If you have a windows computer and would like to install qiime2 on your computer you will have to install Windows Subsystem for Linux(WSL) first. Then you will follow the linux instruction on the qiime2 website. Info for WSL can be found here: https://learn.microsoft.com/en-us/windows/wsl/install