Installation¶

HOMERun can be installed three ways. Conda is recommended, because it also installs the external bioinformatics tools HOMERun depends on (HOMER, STAR, HISAT2, samtools, and skewer).

If you do not already have Conda installed, see the Conda installation guide.

The other two installation methods install only the Python package, so you will need to install the required bioinformatics tools separately.

Recommended: Conda (Bioconda)¶

conda install -c bioconda homerun

This pulls in every required tool automatically. Verify the install:

homerun --help

PyPI (pip)¶

pip install homerun

pip installs the Python package only. The external tools must already be on your PATH. The easiest way is a dedicated conda environment:

conda create -n homerun-tools -c bioconda homer star hisat2 samtools skewer

From source (git clone)¶

git clone https://github.com/NguyenThomas986/homerun.git
cd homerun
pip install -e .

Requirements¶

Python >= 3.9
A SLURM-based HPC cluster
External tools: HOMER, STAR, HISAT2, samtools, skewer