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readme clear mandatory instructions
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adamovanja committed Nov 27, 2023
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Expand Up @@ -18,7 +18,6 @@ For both options 1 and 2 make sure to start by installing [mamba](https://mamba.
```shell
conda install mamba -n base -c conda-forge
```
Also, don't forget to run the mandatory configuration step [at the end]((#mandatory-configuration-for-both-options-1-and-2))!

### Option 1: Minimal fondue environment:
* Create and activate a conda environment with the required dependencies:
Expand All @@ -30,6 +29,7 @@ mamba create -y -n fondue \

conda activate fondue
```
Now, don't forget to run [the mandatory configuration step](#mandatory-configuration-for-both-options-1-and-2)!

### Option 2: Install fondue within existing QIIME 2 environment
* Install QIIME 2 within a conda environment as described in [the official user documentation](https://docs.qiime2.org/).
Expand All @@ -41,6 +41,7 @@ mamba install -y \
-c conda-forge -c bioconda -c defaults \
q2-fondue
```
Now, don't forget to run [the mandatory configuration step](#mandatory-configuration-for-both-options-1-and-2)!

### Mandatory configuration for both options 1 and 2
* Refresh the QIIME 2 CLI cache and see that everything worked:
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