Installation

Cloning the Repository

First, clone the ArtiCull repository from GitHub to your local machine:

git clone https://github.com/shahcompbio/ArtiCull.git
cd ArtiCull

Setting up the Conda Environment

The recommended way to set up ArtiCull is using conda. Alternatively, you can ensure all packages listed in requirements.yml are available.

First, ensure you have conda installed on your machine. Then run:

conda env create -f requirements.yml -n articull-env
conda activate articull-env

Downloading Reference Data Tracks

Use the provided script to download and process the reference genome mappability track. Note that the download requires ~1GB of space and expands to ~5GB when uncompressed. By default, files are saved to the resources directory unless an alternative output directory is specified.

bash scripts/setup_mappability_track.bash [optional: output_directory]

Currently only hg19/GRCh37 is supported. Support for additional reference genomes coming soon. For other genome versions, please open an issue on the ArtiCull GitHub repo.