Installation

From PyPI

Multiple binaries are distributed via PyPI to accommodate different operating systems, Python versions (3.11 - 3.14), and architectures.

To install the latest version, run:

% python -m pip install consenrich --upgrade

If a binary is not available for your platform or you wish to optimize compiler flags for your hardware, consider building from source.

Conda

You can easily create a conda, mamba virtual environment and ensure all dependencies are met.

For instance, save the following contents to a file named environment.yaml:

name: consenrichEnv
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - c-compiler
  - python
  - pip
  - setuptools
  - wheel
  - cython>=3.0
  - numpy>=2.3.0
  - scipy>=1.16.0
  - pandas>=2.3.0
  - samtools>=1.20
  - bedtools>=2.30.0
  - pybedtools>=0.11.2
  - ucsc-bedgraphtobigwig
  - PyYAML>=6.0.2
  - PyWavelets>=1.9.0

  - pip:
      - consenrich

Then, run the following to create and activate the environment, named consenrichEnv:

% conda config --set channel_priority strict
% conda create -n consenrichEnv -f environment.yaml
% conda activate consenrichEnv

If using mamba, or micromamba, replace conda with mamba or micromamba.

From Source

Some features require samtools and bedtools in your $PATH.

Guidance: C Compiler

To build from source, you will need a C compiler such as gcc or clang.

A compiler is often already present. Check with gcc --version or clang --version.

If not, try one of the following:

  • macOS: xcode-select --install

  • Ubuntu/Debian Linux: sudo apt install build-essential

  • For Fedora Linux: sudo dnf groupinstall "Development Tools"

First, clone the repository:

% git clone https://github.com/nolan-h-hamilton/Consenrich.git

Set the working directory and install:

% cd Consenrich
% python -m pip install .