How to install qiime2 on deepthought

Why would I want to do this?

I am not really sure, but if you want to use Qiime2 you should install it on deepthought using conda.

The sysadmins (may they be praised) do provide some qiime installations, but as of this writing they have qiime-1.9.1 and qiime2-2019.4. However, the current version of Qiime2 is qiime2-2021.4` so they are about 2 years out of date. This is why you should use conda, and not rely on the sysadmins to install software for you. (As an aside, if you’ve been using the old version of qiime2 and the sysadmins update it, your results might change now!).

Step 1. Download and install Miniconda3

For the same reason as above, I like to install Miniconda3 manually. Its very easy to do.

Before you begin, do you need to do this? Look at the bottom left of your ssh window to deepthought. Does it say (base) before your username? If so, you don’t need to install conda. You can also make sure by giving the conda command and seeing what happens!

First, get the latest version of miniconda:


and install it


You will need to press space a few times, and it is perfectly fine to accept the default answers!

Once the install is complete, you can remove the installer script:


Step 2. Download and install Qiime2

Start at the Qiime2 website and click on the link Natively installing QIIME 2 (the documents are updated each new version, and I want to make sure you get the latest version!).

Now scroll down to the section Install QIIME 2 within a conda environment and click on the Linux (64 bit) tab.

Copy the text from that window, and paste it into your terminal.

There are two main lines that you need, the line starting wget .... and the line starting conda env create -n ....

If you run those two commands, Qiime2 will install.

Step 3. Activate Qiime2

You will need to do this each time you log in!

We use conda activate to activate an environment and conda deactivate to stop it (or you can just log out!).

When the install has successfully completed, you will see something like:

# To activate this environment, use
#     $ conda activate qiime2-2021.4
# To deactivate an active environment, use
#     $ conda deactivate

So to activate this environment, you should use

conda activate qiime2-2021.4

You can find out your environments with

conda info --envs

Step 4. What next?

Now I suggest you start with one of the tutorials at the Qiime2 website!