Install runHiC

Requirements

runHiC is developed and tested on UNIX-like operating systems, and following packages or softwares are required:

Python requirements:

• Python 3.7+

• matplotlib 2.0+

• biopython 1.78+

• pairtools 0.3.0+

• cooler 0.8.6+

Other requirements:

• sra-tools 2.10.8+

• bwa 0.7.17+

• minimap2 2.17+

• chromap 0.1+

• samtools 1.10+

• pigz 2.3.4+

Install Requirements through Mamba

To satisfy the requirements above, just install mamba on your machine, and execute the commands below:

$ conda config --add channels defaults
$ conda config --add channels bioconda
$ conda config --add channels conda-forge
$ mamba create -n runHiC matplotlib biopython cooler sra-tools bwa minimap2 samtools pigz chromap "pairtools==0.3" "numpy<=1.23"
$ mamba activate runHiC

Install runHiC

Then runHiC can be installed from PyPI using pip:

$ pip install runHiC

You should have runHiC installed successfully if no exception occurs in the above processes.