diff --git a/learners/files/macos_setup.Rmd b/learners/files/macos_setup.Rmd index d1404829..733acaf9 100644 --- a/learners/files/macos_setup.Rmd +++ b/learners/files/macos_setup.Rmd @@ -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** @@ -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]
-### 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]
@@ -72,14 +80,16 @@ 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 ```
@@ -87,7 +97,7 @@ conda create --name cwltutorial python==3.11 mamba #### Activate the virtual environment ```bash -conda activate cwltutorial +mamba activate cwltutorial ```
@@ -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