diff --git a/notebooks/scRNA-seq/03_vertex_workbench.md b/notebooks/scRNA-seq/03_vertex_workbench.md index b73a291..878c3f4 100644 --- a/notebooks/scRNA-seq/03_vertex_workbench.md +++ b/notebooks/scRNA-seq/03_vertex_workbench.md @@ -41,7 +41,7 @@ scrna_notebook ``` ### Region / Zone -- Region: `us-central1` +- Region: `us-central1` (or your preferred region) - Zone: `us-central1-a` (or your preferred zone) ### Machine Type @@ -88,23 +88,51 @@ You are now inside your notebook VM. # Part 3 – Install Required Python Packages +In this section, you will open a terminal inside your JupyterLab environment, clone the course repository, and install the required Python packages. + +--- + ## 1. Open a Terminal in JupyterLab -1. Click the **"+"** button (Launcher) -2. Scroll to **Other** -3. Click **Terminal** +1. Click the **"+"** button (Launcher). +2. Scroll down to the **Other** section. +3. Click **Terminal**. -You should see a prompt like: +A new terminal window will open. + +You should see a prompt similar to: ``` jupyter@instance:~$ ``` -⚠️ This terminal is running inside your notebook VM (NOT Cloud Shell). +⚠️ Make sure this terminal is running inside your **notebook VM**. +Do **not** use Cloud Shell for these steps. --- -## 2. Install Required Libraries +## 2. Clone the Course Repository + +In the JupyterLab terminal, run: + +```bash +git clone https://github.com/STRIDES/NIHCloudLabGCP.git +``` + +This will create a directory called: + +``` +NIHCloudLabGCP/ +``` + +Navigate into the notebooks directory: + +```bash +cd NIHCloudLabGCP/notebooks/scRNAseq +``` + + +## 3. Install Required Libraries Run: