1. Getting Started

1.1. Requirements

  • Python 3.9

  • Installation of samtools on your PATH

  • Any *nix operating system

    • (tested on Ubuntu, CentOS, RHEL)

Note

CluBCpG utilized Pysam, which is a wrapper around the htslib and samtools C-APIs, to read from BAM files. These tools do not support Windows, therefore, CluBCpG cannot be run on Windows.

1.2. Installation

1.2.1. pip install

These steps will install CluBCpG.

Note

While optional, it is highly recommended to install CluBCpG in a virtual environment.

  1. (Optional) Create and activate python virtualenv

virtualenv ~/venv/clubcpg -p python3
source ~/venv/clubcpg/bin/activate

  1. Install CluBCpG with the following command

pip install clubcpg

1.3. Running Tests

Included tests can be run to verify CluBCpG is correctly interacting with samtools to read form BAM files. The source code can be downloaded from GitHub and the following can be run:

python -m unittest -v clubcpg/tests/test_Module.py

Running this will download a small amount of test data in BAM format and will verify all dependencies are met to correctly run CluBCpG