clubcpg 0.3.0

CluBCpG is a software package built to analyze whole genome bisulfite sequencing (WGBS) data.

CluBCpG: Cluster-Based analysis of CpG methylation

Whats new?

v0.3.0

• A major overhaul and modernization of the ClubCpG dependencies.
• setup.py removed in favor of a pyproject.toml
• All project dependencies updated to modern versions
• Support of python 3.5, 3.6, 3.7, and 3.8 dropped
• Minimum version of python is now 3.9
• Added GitHub Actions workflows to automate testing of python 3.9 and 3.10
• Updated readthedocs build configuration ahead of deprecation of old method

What is CluBCpG?

CluBCpG is a software package built to analyze whole genome bisulfite sequencing (WGBS) data. This toolkit will divide each chromosome into small user-defined intervals, extract all WGBS reads within those intervals, cluster them based on identity, and write a final report to the use containing all identified CpG methylation patterns.

How do I use this?

Full documentation is available on ReadTheDocs

Requirements

• Python >= 3.9, <3.11
• Installation of Samtools on your PATH

Install

• (Optional, but HIGHLY recommended) Create a new python virtual environment and activate that virualenv
• Execute pip install clubcpg to install the package. Requirements will automatically be installed if not already present.

Developer Install

• Ensure all dependencies in ubuntu-preinsatll.sh are installed on the system. (Or equivilant packages if using fedora based system)
• Install samtools, use install-samtools.sh
• Make sure you have a compatible version of python installed
• Install Poetry pip3 install poetry
• Run poetry install to install required packages and clubcpg
• To install optional packages for docs building. Run poetry install --with docs

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