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Getting Started

Requirements

  • Python 3.5+ (Fully tested on Python 3.5, 3.6, and 3.7)

  • 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.

Installation

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 activate ~/venv/clubcpg/bin/activate
  1. Install CluBCpG with the following command
pip install clubcpg

conda

Coming soon

Running Tests

Included tests can be run to verify CluBCpG is correctly interacting with samtools to read form BAM files.

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