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Use miniforge to update mamba #11

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Use miniforge to update mamba #11

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32 changes: 23 additions & 9 deletions learners/files/macos_setup.Rmd
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Expand Up @@ -16,7 +16,7 @@ Download and install [VSCode][vs_code]

**Install Benten Extension**

[Open Benten in the marketplace](https://marketplace.visualstudio.com/items?itemName=sbg-rabix.benten-cwl) and click the `Install` button or follow the directions.
[Open Benten in the marketplace][benten_vs_code_marketplace] and click the `Install` button or follow the directions.

**Install Redhat Yaml VSCode Extension**

Expand All @@ -38,13 +38,21 @@ Add the following chunk to the VSCode [user settings json][user_settings_json] t

### Docker Installation

[Install docker](https://docs.docker.com/desktop/mac/install)
[Install docker][docker_install]

<br>

### Install MiniConda
### Install Mamba

[Install miniconda](https://docs.conda.io/projects/conda/en/latest/user-guide/install/macos.html)
Mamba is a faster version of conda.

First install miniforge (this will also install conda)

[Install Miniforge][miniforge_install]

Then install mamba.

[Install Mamba][mamba_install]

<br>

Expand Down Expand Up @@ -72,22 +80,24 @@ conda install -y -n base -c conda-forge \
libarchive
```

If you continue to have issues, please re-install conda via miniforge (shown above), or just replace the `mamba` commands below with `conda`.

::::::::::::::::::

#### Create a conda virtual environment
#### Create a virtual environment

Create a virtual environment using conda

```bash
conda create --name cwltutorial python==3.11 mamba
mamba create --name cwltutorial python==3.11 mamba
```

<br>

#### Activate the virtual environment

```bash
conda activate cwltutorial
mamba activate cwltutorial
```

<br>
Expand All @@ -108,12 +118,16 @@ mamba install --yes \
Reactivating the conda virtual environment

The virtual environment needs to be activated every time you start a terminal using
`conda activate cwltutorial`.
`mamba activate cwltutorial`.

::::::::::::::::

[^1]: https://github.com/mamba-org/mamba/issues/1826#issuecomment-1196636463
[^1]: [Mamba libarchive Issue][mamba_libarchive_issue]

[mamba_libarchive_issue]: https://github.com/mamba-org/mamba/issues/1826#issuecomment-1196636463
[docker_install]: https://docs.docker.com/desktop/mac/install
[miniforge]: https://github.com/conda-forge/miniforge
[mamba_install]: https://mamba.readthedocs.io/en/latest/installation/mamba-installation.html
[vs_code]: https://code.visualstudio.com/
[benten_vs_code_marketplace]: https://marketplace.visualstudio.com/items?itemName=sbg-rabix.benten-cwl
[redhat_yaml_vs_code_marketplace]: https://marketplace.visualstudio.com/items?itemName=redhat.vscode-yaml
Expand Down
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