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Update the Getting Started instructions
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alancleary authored Jan 8, 2025
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## **Getting Started**

To begin, we must understand how this repository is organized.
After following the [Before Starting](#before-starting) instructions, the JupyterLab launcher (File -> New Launcher) will contain a "Submodule Notebooks" section.
This section contains an ordered list of the notebooks in this module, one for each submodule.
Clicking on a submodule in this section will open the corresponding notebook.
To begin, click on the "Environment Setup."

Alternatively, you can use the JupyterLab file browser.
Here is the location and file structure of the module notebooks:
```
NIGMIS-Sandbox-Pangenomics-Module/
└── module_notebooks/
   ├── 00-environment-setup.ipynb
   ├── 01-intro-to-pangenomics.ipynb
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   ├── 06-searching-graphs-with-blast.ipynb
   └── 07-visualization.ipynb
```

`module_notebooks/` contains Jupyter notebooks - one for each submodule.
To open a notebook, simply double-click on it in your Workbench instance.
To open a notebook, simply double-click on it it.
To begin this module, open the `00-environment-setup.ipynb` notebook.
This notebook will introduce you to Jupyter notebooks and instruct you on how to install the software for this module.


## **Software Requirements**
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