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adamovanja committed Jul 8, 2024
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Expand Up @@ -20,11 +20,11 @@ There are multiple options to install q2-fondue - each targeted towards differen
To install q2-fondue with a version <= 2023.7 see [this](#installing-q2-fondue-with-older-versions) section.

### Option 1: Install q2-fondue with QIIME 2 metagenome distribution
* Install q2-fondue together with the QIIME 2 metagenome distribution as outlined [here](https://docs.qiime2.org/2024.5/install/native/#qiime-2-metagenome-distribution).
* Now, don't forget to run **[the mandatory configuration step](#mandatory-configuration-for-all-three-options)**!
q2-fondue is a part of the QIIME 2 metagenome distribution and you can install it as outlined in the [QIIME 2 installation instructions](https://docs.qiime2.org/).
After that, don't forget to run **[the mandatory configuration step](#mandatory-configuration-for-all-three-options)**!

### Option 2: Install q2-fondue within a QIIME 2 amplicon conda environment
* Install the QIIME 2 amplicon distribution within a conda environment as described in [the official user documentation](https://docs.qiime2.org/2024.5/install/native/#qiime-2-amplicon-distribution).
* Install the QIIME 2 amplicon distribution within a conda environment as described in [the official QIIME 2 documentation](https://docs.qiime2.org/).
* Activate the QIIME 2 environment (v2024.5 or higher) and install q2-fondue within while making sure that the used conda channel matches the version of the QIIME 2 environment (replace below `{ENV_VERSION}` with the version number of your QIIME 2 environment):
```
conda activate qiime2-amplicon-{ENV_VERSION}
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