1. Installation

bhive is written in Python. Python3 is required to run all programs. Some programs also need R and R libraries to generate graphs.

1.1. Prerequisites

You need to install these tools if they are not available from your computer.

• Python3
• pip3
• R

1.2. R libraries required

• R library ggplot2
• R library cowplot
• R library pheatmap

Note

These R libraries will be automatically installed the first time they are used. Please manually install them if you encounter error like: Error in library(XYZ) : there is no package called ‘XYZ’

1.3. Python packages required

• pandas
• numpy
• sklearn
• logomaker
• pysam

Note

Note: These Python packages will be automatically installed if you use pip3 to install bhive.

1.4. Install bhive

$ pip3 install bhive
or
$ pip3 install git+https://github.com/liguowang/bhive.git

1.5. Upgrade bhive

$ pip3 install bhive --upgrade