howto.qmd

# How to run the notebooks

## Option 1. Using BiocWorkshop (Preferred)

If you are attending the workshop at Bioconductor:

1. Open [BiocWorkshops](https://workshop.bioconductor.org/) in a new tab.
2. Select "R/Bioconductor Jupyter Workshop" as shown in the screenshot.

![](./assets/biocworkshop_select_rjupyter.png)

3. Click the "Run the tool".

![](./assets/biocworkshop_run_tool.png)

4. Click on "Interactive Tools" in the left sidebar to check on the status of the session. Once the session is ready, click on the "BiocPy" to open the Jupyter notebook.

![](./assets/biocworkshop_open_session.png)

5. You should be able to see the BiocWorkshop repository cloned into the session.

![](./assets/biocworkshop_jupyter.png)

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## Option 2: Using Google Colab

To open the session in Google Colab:

1. Open [Google colab](https://colab.research.google.com/) in a new tab.
2. On the page, it should open up a dialog to "Open notebook" as shown in the screenshot below. 
   * If no dialog appears, go to File -> Open Notebook from the menu (in the top left).
3. Choose Github and enter the repository url for the workshop: `https://github.com/BiocPy/BiocWorkshop2024`. This will automatically find the python notebooks available in the repository.

![](./assets/colab_session.png)

4. Choose the open icon to explore this notebook

![](./assets/colab_open_notebook.png)

:::{.callout-important}
This process does not download the [RDS file](https://github.com/BiocPy/BiocWorkshop2024/tree/master/notebook) available in the repository. Folks might have to manually download this to their Google Colab sessions.
:::

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## Option 3: Run notebooks locally

If you want to run locally, please clone the repository and install the python packages used for the workshop.

```sh
git clone https://github.com/BiocPy/BiocWorkshop2024
cd BiocWorkshop2024

# Assuming python is available
# You are free to use mamba, conda or virtualenv's
pip install -r requirements.txt

# Start the jupyter server
jupyter lab
```

Then checkout the [notebook](https://github.com/BiocPy/BiocWorkshop2024/tree/master/notebook) directory that contain Jupyter notebooks.