1. Getting Started¶
1.1. 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.
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.
- (Optional) Create and activate python virtualenv
virtualenv ~/venv/clubcpg -p python3
source activate ~/venv/clubcpg/bin/activate
- Install CluBCpG with the following command
pip install clubcpg
1.2.2. conda¶
Coming soon
1.3. 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