Installation¶

This guide covers different methods to install circDNA Detection on your system.

Requirements¶

System Requirements¶

• Operating System: Linux, macOS, or Windows (with WSL)
• Python: Python 3.7 or higher
• Memory: At least 4GB RAM (8GB+ recommended for large datasets)
• Storage: Sufficient space for BAM files and output

Python Dependencies¶

The following Python packages are required:

• pysam >= 0.19.0 - For BAM file handling
• numpy >= 1.19.0 - For numerical computations
• scipy >= 1.6.0 - For statistical analysis

Installation Methods¶

Method 1: Install from GitHub (Recommended)¶

Install directly from the GitHub repository:

pip install git+https://github.com/samarth8392/circDNA_detection.git

This method automatically installs all dependencies and provides the latest stable version.

Method 2: Development Installation¶

For development or to contribute to the project:

# Clone the repository
git clone https://github.com/samarth8392/circDNA_detection.git
cd circDNA_detection

# Install in development mode
pip install -e .

This method allows you to modify the code and have changes reflected immediately.

Method 3: Virtual Environment Installation¶

It's recommended to install in a virtual environment to avoid dependency conflicts:

# Create a virtual environment
python -m venv circDNA_env

# Activate the virtual environment
# On Linux/macOS:
source circDNA_env/bin/activate
# On Windows:
circDNA_env\Scripts\activate

# Install circDNA Detection
pip install git+https://github.com/samarth8392/circDNA_detection.git

Method 4: Conda Environment¶

If you use Conda, you can create a dedicated environment:

# Create a new conda environment
conda create -n circDNA python=3.8

# Activate the environment
conda activate circDNA

# Install dependencies
conda install -c bioconda pysam numpy scipy

# Install circDNA Detection
pip install git+https://github.com/samarth8392/circDNA_detection.git

Verification¶

After installation, verify that circDNA Detection is correctly installed:

Command Line Tool¶

circDNA-detect --help

You should see the help message with available options.

Python Import¶

import circDNA_detection
print(circDNA_detection.__version__)

Quick Test¶

Create a simple test to ensure everything works:

from circDNA_detection import CircularDNADetector

# Create detector instance
detector = CircularDNADetector()
print("Installation successful!")

Troubleshooting¶

Common Issues¶

Issue: ModuleNotFoundError: No module named 'pysam'¶

Solution: Install pysam manually:

pip install pysam

Issue: ImportError: libhts.so.3: cannot open shared object file¶

Solution: Install system dependencies:

# On Ubuntu/Debian:
sudo apt-get install libhts-dev

# On CentOS/RHEL:
sudo yum install htslib-devel

# On macOS:
brew install htslib

Issue: Permission denied during installation¶

Solution: Use --user flag:

pip install --user git+https://github.com/samarth8392/circDNA_detection.git

Issue: Version conflicts¶

Solution: Use a fresh virtual environment:

python -m venv fresh_env
source fresh_env/bin/activate  # On Linux/macOS
pip install git+https://github.com/samarth8392/circDNA_detection.git

Getting Help¶

If you encounter issues not covered here:

1. Check the GitHub Issues page
2. Create a new issue with:
3. Your operating system
4. Python version (python --version)
5. Complete error message
6. Installation method used

Updating¶

To update to the latest version:

pip install --upgrade git+https://github.com/samarth8392/circDNA_detection.git

For development installations:

cd circDNA_detection
git pull origin main
pip install -e .

Uninstalling¶

To remove circDNA Detection:

pip uninstall circDNA-detection