activate environment

Hi, I was able to install qiime2 within a new conda environment in windows10 with miniconda using linux. However, I get error massege trying to reopen the environment.

(base) [email protected]:/mnt/c/Users/USER/Desktop/qiime2$ conda info --envs

conda environments:


base * /mnt/c/Users/USER/Desktop/qiime2/[miniconda]

(base) [email protected]:/mnt/c/Users/USER/Desktop/qiime2$ conda activate qiime2-2021.11
Could not find conda environment: qiime2-2021.11
You can list all discoverable environments with conda info --envs.

(base) [email protected]:/mnt/c/Users/USER/Desktop/qiime2$

I dont know what is the meaning of /home/omerkamer/miniconda3/envs/ since I dont have a folder named miniconda3

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Hi @Omer,

Happy New Year :fireworks: and welcome to the :qiime2: forum!

From the looks of it, your conda environments weren't created with name-based references (which is why conda activate qiime2-2021.11 was unsuccessful). There are a couple of options to address this:

  1. You can activate this environment using the path (vs. the name), like so:

conda activate /home/omerkamer/miniconda3/envs/qiime2-2021.11

  1. You can delete this environment and re-create it with a name-based reference (which is what I'd recommend doing, so that you don't have to type in the full path each time you want to activate this environment). Here's how you'll do this:
  • Delete this environment by typing in the following command:
    conda remove /home/omerkamer/miniconda3/envs/qiime2-2021.11

  • Re-create the environment by following the QIIME 2 installation instructions here. Note that since you're on a Windows machine, we do recommend performing a native conda installation in the Windows Subsystem for Linux (WSL). If you don't have WSL set up, you can do so by following these instructions.

Once you've created a new conda environment and installed QIIME 2 on it, you should be able to deactivate and activate your conda env without any issues - but please let us know if you're still having difficulties!

Cheers :lizard:

The first option worked, thanks!

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