Installation

DecoDen is available as a python package on PyPi and Bioconda (SOON). To ensure the dependencies are satisfied with the correct package version, we recommend the use of Anaconda to create suitable environment. Alternative solutions like https://virtualenv.pypa.io/en/latest/ and Poetry work as well, however you will need to ensure the installation of the external dependencies BEDOPS and bedtools.

Temporary development instructions

Section to remove once the package is published. Clone the github repository and run the following commands

# Create and activate the environment
conda create -n dden python=3.9
conda activate dden

# Install the external dependencies and DecoDen
conda install -c bioconda bedops bedtools

# From the cloned folder
poetry install

Setup with Conda

To setup a suitable environment with Conda, use the following commands:

# Create and activate the environment
conda create -n dden python=3.9
conda activate dden

# Install the external dependencies and DecoDen
conda install -c bioconda bedops bedtools decoden

# Verify the correct installation of DecoDen
decoden --version
decoden --help