Getting Started

Install PrimerLab and run your first primer design

Installation Options

PrimerLab offers multiple installation methods. Choose the one that best fits your needs:

Method	Best For	Includes External Tools
Docker	Zero-setup, cross-platform	✅ ViennaRNA, BLAST
Conda	Bioinformatics users	✅ ViennaRNA, BLAST
Pip	Python developers	❌ Manual install

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Option 1: Docker (Recommended for beginners)

# Pull the image
docker pull ghcr.io/engkinandatama/primerlab-genomic:latest

# Run with your config file
docker run -v $(pwd):/data primerlab-genomic run pcr --config /data/config.yaml

No installation needed - everything is included!

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Option 2: Conda/Mamba

# Clone repository
git clone https://github.com/engkinandatama/primerlab-genomic.git
cd primerlab-genomic

# Create environment (includes ViennaRNA, BLAST)
conda env create -f environment.yml
conda activate primerlab

# Install PrimerLab
pip install -e .

For faster install, use Mamba:

mamba env create -f environment.yml

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Option 3: Pip (Advanced)

Requires manual installation of system tools.

Linux (Ubuntu/Debian):

# Install system dependencies
sudo apt-get update
sudo apt-get install -y vienna-rna ncbi-blast+ build-essential

# Install PrimerLab
pip install git+https://github.com/engkinandatama/primerlab-genomic.git@v0.9.0

macOS:

brew install viennarna blast
pip install git+https://github.com/engkinandatama/primerlab-genomic.git@v0.9.0

Windows:

Use WSL (Windows Subsystem for Linux) and follow Linux instructions.

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Option 4: From Source (Development)

git clone https://github.com/engkinandatama/primerlab-genomic.git
cd primerlab-genomic
pip install -e ".[dev]"

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Verify Installation

primerlab --version
# Output: PrimerLab v0.9.0

primerlab health
# Shows dependency status (ViennaRNA, BLAST, Primer3)

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Quick Start

1. Check Your Sequence

primerlab stats input.fasta

2. Create Config File

primerlab init --workflow pcr --output my_config.yaml

3. Run Primer Design

primerlab run pcr --config my_config.yaml

4. View Results

Results are saved in the output directory:

• result.json - Machine-readable results
• report.md - Human-readable report
• audit.json - Reproducibility log

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Troubleshooting

primer3-py fails to install

# Install build tools first
sudo apt-get install -y build-essential python3-dev

ViennaRNA not found

# Check if installed
RNAfold --version

# If not, install via apt or conda
sudo apt-get install vienna-rna
# or
conda install -c bioconda viennarna

BLAST not found

# Check if installed
blastn -version

# If not, install
sudo apt-get install ncbi-blast+

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Next Steps

• CLI Reference - All available commands
• Configuration - Config file options
• Examples - Example configurations