Contributor

Khaoula Ferchichi, Bioinformatician

• Scientist, HPC@HRZ University of Bonn.
• Postdoctoral researcher, University hospital Bonn, Section Psychiatric Genomics and Epigenomics.

🧰 Installing Git, Anaconda, and Python on Windows via Git Bash

📦 Install Git on Windows

1. Download Git

• Visit the Git for Windows website.
• Click Download to get the latest version.

2. Run the Installer

• Locate the downloaded .exe file.
• Double-click to launch the installer.

3. Follow Installation Steps

• Click Next in the setup wizard.
• Accept the License Agreement.
• Choose the installation directory (default is fine).
• Select components – default is fine.
• Choose Nano as the default editor (recommended).
• Set “Let Git decide” for naming the initial branch after git init.
• For PATH environment:
  • Choose: Git from the command line and also from 3rd-party software.
• Use bundled OpenSSH.
• Select native Windows Secure Channel library for HTTPS.
• Configure line endings: choose the first option.
• Terminal emulator: Windows default console window.
• git pull behavior: Fast-forward or merge.
• Enable:
  • Git Credential Manager.
  • File system caching.
• Click Install.
• Click Finish after installation.

🐍 Install Anaconda Using Git Bash

Step 1: Download the Installer

curl -O https://repo.anaconda.com/archive/Anaconda3-2024.10-1-Windows-x86_64.exe

Step 2: Run the Installer

./Anaconda3-2024.10-1-Windows-x86_64.exe

• Follow the graphical installer prompts.

Step 3: Configure Environment Variables

• Add to PATH during installation or set it manually:

  C:\Users\<YourUsername>\anaconda3
  

Note: Replace <YourUsername> with your Windows username.

✅ Verify Anaconda Installation

Step 4: Confirm conda Exists

1. Open Git Bash.
2. Navigate:

   cd /c/Users/<YourUsername>/anaconda3
   cd Scripts
   ls -all
   

3. Confirm that conda.exe exists.

⚙️ Add Anaconda to Git Bash PATH

Step 5: Modify .bashrc or .bash_profile

nano ~/.bashrc

Add the following:

export PATH="/c/Users/<YourUsername>/Anaconda3:/c/Users/<YourUsername>/Anaconda3/Scripts:$PATH"

Replace <YourUsername> with your actual Windows username.
To save in nano: CTRL + X, then Y, then Enter.

Step 6: Apply the Changes

source ~/.bashrc

Step 7: Restart Git Bash

🔍 Check Conda Functionality

Step 8: Check Version

conda --version

If the above doesn’t work:

/c/Users/<YourUsername>/anaconda3/Scripts/conda --version

If it shows the version, Conda is working correctly.

Step 9: Update Conda

conda update conda

🐍 Install Python via Conda Environment

Step 1: Create a New Conda Environment

conda create --name myenv

Step 2: Initialize Conda for Bash

conda init bash

Step 3: Restart Git Bash

Step 4: Activate the Environment

conda activate myenv

Step 5: Install Specific Python Version (e.g., Python 3.8)

conda install python=3.8

Step 6: Verify Python

python --version

💡 Note: Ensure you have at least 6 GB of free disk space for successful installation.