3. Installation

cobind is written in Python. Python3 (v3.5.x) is required to run all programs in cobind.

3.1. Dependencies

• pandas

• numpy

• scipy

• bx-python

• pyBigWig

Note

These packages will be automatically installed when you use pip3 to install cobind.

3.2. Install pip

Please install pip (Package Installer for Python) first if you do not have it.

#check if pip is available.
$ pip --version
pip 23.0.1 from /Users/m102324/miniconda3/lib/python3.10/site-packages/pip (python 3.10)

3.3. Install to virtual environment

Python’s Virtual Environments allow Python packages to be installed in an isolated location rather than being installed globally. If you would like to install cobind into a virtual environment, please follow these instructions. Specifically, follow these steps:

$python3 -m venv cobind
$source cobind/bin/activate
$pip install cobind

3.4. Install globally

Install cobind using pip from PyPI or GitHub

$ pip install cobind
#or
$ pip install git+https://github.com/liguowang/cobind.git

3.5. Upgrade

$ pip install cobind --upgrade

3.6. Uninstall

$ pip uninstall cobind