Add Git and RStudio setup documentation for Windows

docs/Computing-Hardware.md

@@ -14,6 +14,12 @@ You will need accounts with the following services in order to minimally functio
 
 - [Slack](https://slack.com): Needed for participation in the [Roberts Lab Slack channels](https://genefish.slack.com)
 
+## Software Setup
+
+If you're using a Windows computer and need to set up Git and RStudio, see our comprehensive guide:
+
+- [Git and RStudio Setup for Windows](Git-RStudio-Setup-Windows.md)
+
 ## Computers
 You're free to use your own computer for any computing task that you wish. However, some of the computing work that you will perform will require lengthy run times. As such, we have computers available for you to use. Plus, Roberts Lab computers have better processors and much more RAM, which will allow you to keep your computer free for doing fun stuff, like reading Facebook (or scientific papers).
 

docs/Git-RStudio-Setup-Windows.md

@@ -0,0 +1,241 @@
+# Installing Git and Connecting to RStudio on Windows
+
+This guide will walk you through installing Git on a Windows machine and connecting it to RStudio, which is essential for version control and collaboration in the Roberts Lab.
+
+## Prerequisites
+
+- A Windows computer with administrator access
+- An internet connection
+- A [GitHub account](https://github.com) (see [Computing Hardware](Computing-Hardware.md#accounts) for more info)
+
+---
+
+## Step 1: Install Git for Windows
+
+1. **Download Git for Windows**
+   - Visit the official Git website: [https://git-scm.com/download/win](https://git-scm.com/download/win)
+   - The download should start automatically. If not, click the appropriate link for your system (typically 64-bit)
+
+2. **Run the Installer**
+   - Locate the downloaded file (typically in your Downloads folder) and double-click to run it
+   - Click "Yes" if prompted by User Account Control
+
+3. **Installation Options**
+
+   During installation, you'll be presented with several configuration screens. Here are the recommended settings:
+
+   - **Select Components**: Keep the default selections
+     - Windows Explorer integration
+     - Git Bash Here
+     - Git GUI Here
+     - Associate .git* configuration files with the default text editor
+     - Associate .sh files to be run with Bash
+
+   - **Choosing the default editor**: Select your preferred text editor (Notepad++ or Visual Studio Code are good options if installed, otherwise the default is fine)
+
+   - **Adjusting your PATH environment**: Select **"Git from the command line and also from 3rd-party software"** (recommended)
+
+   - **Choosing HTTPS transport backend**: Select **"Use the OpenSSL library"** (default)
+
+   - **Configuring line ending conversions**: Select **"Checkout Windows-style, commit Unix-style line endings"** (default)
+
+   - **Configuring the terminal emulator**: Select **"Use MinTTY"** (default)
+
+   - **Choose the default behavior of `git pull`**: Select **"Default (fast-forward or merge)"**
+
+   - **Choose a credential helper**: Select **"Git Credential Manager"** (default)
+
+   - **Configuring extra options**: Keep the defaults
+     - Enable file system caching
+     - Enable symbolic links
+
+   - Click **"Install"** to complete the installation
+
+4. **Verify Git Installation**
+   - Open Command Prompt (press `Windows Key + R`, type `cmd`, press Enter)
+   - Type `git --version` and press Enter
+   - You should see output like: `git version 2.x.x.windows.x`
+
+---
+
+## Step 2: Configure Git
+
+Before using Git, you need to set up your identity. This information will be attached to your commits.
+
+1. **Open Git Bash**
+   - Right-click on your desktop or in any folder
+   - Select "Git Bash Here" from the context menu
+
+2. **Set Your Name**
+   ```bash
+   git config --global user.name "Your Name"
+   ```
+   Replace "Your Name" with your actual name (use the same name as your GitHub account)
+
+3. **Set Your Email**
+   ```bash
+   git config --global user.email "your.email@example.com"
+   ```
+   Replace with the email address associated with your GitHub account
+
+4. **Verify Your Configuration**
+   ```bash
+   git config --global --list
+   ```
+   You should see your name and email listed
+
+---
+
+## Step 3: Install RStudio (if not already installed)
+
+1. **Download RStudio Desktop**
+   - Visit: [https://posit.co/download/rstudio-desktop/](https://posit.co/download/rstudio-desktop/)
+   - First, ensure R is installed (install from [https://cran.r-project.org/](https://cran.r-project.org/) if needed)
+   - Download the RStudio installer for Windows
+   - Run the installer and follow the prompts
+
+---
+
+## Step 4: Connect Git to RStudio
+
+1. **Open RStudio**
+
+2. **Configure Git in RStudio**
+   - Go to **Tools** → **Global Options**
+   - Select **Git/SVN** from the left sidebar
+
+3. **Verify Git Path**
+   - RStudio should automatically detect Git
+   - The "Git executable" field should show the path to git.exe (typically `C:/Program Files/Git/bin/git.exe`)
+   - If it's blank or incorrect:
+     - Click **Browse**
+     - Navigate to `C:\Program Files\Git\bin\`
+     - Select `git.exe`
+     - Click **Open**
+
+4. **Enable Version Control**
+   - Check the box for **"Enable version control interface for RStudio projects"**
+
+5. **Set Up SSH Key (Recommended for GitHub)**
+
+   SSH keys allow you to connect to GitHub without entering your password each time.
+
+   - In the Git/SVN options window, click **"Create RSA Key..."**
+   - Click **"Create"** in the dialog box (you can optionally add a passphrase for extra security)
+   - Click **"Close"** when the key generation is complete
+   - Click **"View public key"**
+   - Copy the entire key (it starts with `ssh-rsa`)
+
+6. **Add SSH Key to GitHub**
+   - Go to [GitHub.com](https://github.com) and log in
+   - Click your profile picture (top right) → **Settings**
+   - Click **SSH and GPG keys** in the left sidebar
+   - Click **"New SSH key"** or **"Add SSH key"**
+   - Give it a title (e.g., "Lab Windows PC")
+   - Paste your public key into the "Key" field
+   - Click **"Add SSH key"**
+
+7. **Click OK** to close the RStudio options window
+
+---
+
+## Step 5: Test Git Integration in RStudio
+
+### Option A: Clone an Existing Repository
+
+1. In RStudio, go to **File** → **New Project**
+2. Select **Version Control**
+3. Select **Git**
+4. Enter the repository URL (e.g., `https://github.com/RobertsLab/resources.git`)
+5. Choose where to save the project on your computer
+6. Click **Create Project**
+
+If successful, RStudio will download the repository and you'll see a "Git" tab in the upper-right pane.
+
+### Option B: Create a New Git Repository
+
+1. In RStudio, go to **File** → **New Project**
+2. Select **New Directory**
+3. Select **New Project**
+4. Enter a directory name
+5. Check **"Create a git repository"**
+6. Click **Create Project**
+
+You should now see a "Git" tab in the upper-right pane.
+
+---
+
+## Step 6: Using Git in RStudio
+
+Once Git is connected to RStudio, you can use version control for your projects:
+
+1. **View Changes**: The Git tab shows all modified files
+2. **Stage Files**: Check the boxes next to files you want to commit
+3. **Commit**: Click the "Commit" button, write a commit message, and click "Commit"
+4. **Push**: Click the green "Push" arrow to send your changes to GitHub
+5. **Pull**: Click the blue "Pull" arrow to get updates from GitHub
+
+---
+
+## Troubleshooting
+
+### Git Not Found by RStudio
+
+**Problem**: RStudio can't find Git, or the Git executable field is empty.
+
+**Solution**:
+1. Verify Git is installed by opening Command Prompt and typing `git --version`
+2. If Git is installed, manually set the path in RStudio:
+   - Tools → Global Options → Git/SVN
+   - Browse to `C:\Program Files\Git\bin\git.exe`
+
+### Authentication Issues with GitHub
+
+**Problem**: Getting errors when trying to push/pull from GitHub.
+
+**Solution 1 - Use Personal Access Token**:
+1. Go to GitHub → Settings → Developer settings → Personal access tokens → Tokens (classic)
+2. Click "Generate new token (classic)"
+3. Give it a name and select scopes (at minimum: `repo`)
+4. Click "Generate token" and copy the token
+5. When RStudio prompts for a password, paste the token instead
+
+**Solution 2 - Use SSH** (if you completed Step 4.5):
+1. When cloning or setting up a repository, use the SSH URL instead of HTTPS
+   - SSH URL format: `git@github.com:username/repository.git`
+   - HTTPS URL format: `https://github.com/username/repository.git`
+
+### Path Issues
+
+**Problem**: Git works in Git Bash but not in RStudio or Command Prompt.
+
+**Solution**: Git might not be in your system PATH.
+1. Right-click "This PC" or "My Computer" → Properties
+2. Click "Advanced system settings"
+3. Click "Environment Variables"
+4. Under "System variables", find and select "Path"
+5. Click "Edit"
+6. Add `C:\Program Files\Git\bin` if it's not already there
+7. Click OK on all windows
+8. Restart RStudio
+
+---
+
+## Additional Resources
+
+- **Git Documentation**: [https://git-scm.com/doc](https://git-scm.com/doc)
+- **RStudio Git Integration**: [https://support.posit.co/hc/en-us/articles/200532077-Version-Control-with-Git-and-SVN](https://support.posit.co/hc/en-us/articles/200532077-Version-Control-with-Git-and-SVN)
+- **Happy Git with R**: [https://happygitwithr.com/](https://happygitwithr.com/) - Comprehensive guide for using Git with R and RStudio
+- **Software Carpentry Git Lesson**: [https://swcarpentry.github.io/git-novice/](https://swcarpentry.github.io/git-novice/)
+- **Roberts Lab Computing Best Practices**: [Computing-Best-Practices.md](Computing-Best-Practices.md) - includes video tutorial on working with Git and RStudio on Raven
+
+---
+
+## Getting Help
+
+If you encounter issues not covered in this guide:
+
+1. Check the [Troubleshooting](#troubleshooting) section above
+2. Search for your error message on [Stack Overflow](https://stackoverflow.com/)
+3. Post a question in the [Roberts Lab Slack](https://genefish.slack.com)
+4. [Submit a GitHub Issue](https://github.com/RobertsLab/resources/issues) with details about your problem

docs/Onboarding.md

@@ -28,9 +28,11 @@ Get on [lab Slack](https://genefish.slack.com/), added to [the lab GitHub Organi
 - shell
 - git    
 - GitHub Desktop   
-- RStudio   
+- RStudio
 
-#### What do you recommend for learning more about the process and output of the labs's scientific endevours?
+**Windows users**: See our [Git and RStudio Setup guide for Windows](Git-RStudio-Setup-Windows.md) for detailed installation instructions.
+
+#### What do you recommend for learning more about the process and output of the labs's scientific endeavours?
 
 - [tusk](https://robertslab.github.io/tusk/)
 - [FISH546](https://sr320.github.io/course-fish546-2023/schedule.html)

mkdocs.yml

@@ -54,6 +54,7 @@ nav:
      - Code Snippets: 'code_Snippets.md'
      - Computing Hardware: 'Computing-Hardware.md'
      - Lab Software: 'Lab-Software.md'
+     - Git and RStudio Setup (Windows): 'Git-RStudio-Setup-Windows.md'
 
      - 'Klone Guides':
        - Quick Start: 'klone_quick-start.md'