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76 changes: 76 additions & 0 deletions docs/setup/package-managers/micromamba.md
Original file line number Diff line number Diff line change
Expand Up @@ -59,6 +59,82 @@ Strict channel priority helps keep dependency resolution more predictable.
:::


## Computational Workstations & Shared Environments

On shared computational workstations (e.g. `kmer`), micromamba is often pre-installed with a shared conda root.

### Verify installation

```sh
micromamba --version
micromamba info
```

Make sure the root prefix is set correctly (example):

```text
/home/ndemo/.conda
```

### Create a personal environment

```sh
micromamba create -n test python=3.12 numpy scipy -y
```

Activate and verify it:

```sh
micromamba activate test
which python
python --version
```

The expected path should look like:

```text
/home/ndemo/.conda/envs/test/bin/python
```

Deactivate when done:

```sh
micromamba deactivate
```

### Create and use shared environments (managed by root)

On shared servers, system administrators can create environments in a shared location (e.g. `/data/conda/shared_envs/`) that all users can activate.

::: warning
Only root/administrators can create or update shared environments.
:::

As root:

```sh
micromamba create \
-p /data/conda/shared_envs/scientific \
-c conda-forge \
python=3.12 numpy scipy pandas matplotlib \
-y
```

As any user, you can activate it directly by path:

```sh
micromamba activate /data/conda/shared_envs/scientific
```

To add packages to a shared environment, only the administrator can do so:

```sh
micromamba install \
-p /data/conda/shared_envs/scientific \
scikit-learn -y
```


## Core Workflow

::: warning
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