Installation¶

Prerequisites¶

• Python >= 3.6
• Bowtie2 (bowtie2 and bowtie2-build) for genome masking and index building

If you plan to use genome masking (enabled by default), register a reference species with fetchMouseIndex or buildGenomeIndex after installing.

Install from PyPI¶

pip install hcrprobedesign

Install from source¶

git clone https://github.com/gofflab/HCRProbeDesign.git
cd HCRProbeDesign

# Optional: use the provided conda environment
conda env create -f environment.yaml
conda activate HCRProbeDesign

# Install the package
pip install -e .

Documentation build dependencies¶

If you want to build the documentation locally:

pip install -r docs/requirements.txt
mkdocs serve