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Description:
clubcpg 0.3.0
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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License
For personal and professional use. You cannot resell or redistribute these repositories in their original state.
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