Installation#

Required Package#

BandHiC can be installed on Linux-like systems and requires the following dependencies:

  1. python >= 3.11

  2. numpy >= 2.3

  3. pandas >= 2.3

  4. scipy >= 1.16

  5. cooler >= 0.10

  6. hic_straw >= 1.3

There are two recommended ways to install BandHiC:

Option 1: Install via pip#

If you already have Python >= 3.11 installed:

pip install bandhic

Option 2: Install from source with conda#

# 1. Clone the repository
git clone https://github.com/xdwwb/BandHiC-Master.git
cd BandHiC-Master

# 2. Create the environment and activate it
conda env create -f environment.yml
conda activate bandhic

# 3. Install BandHiC
pip install .

Build Troubleshooting for hic-straw#

If you encounter an error like the following while installing or building hic-straw:

fatal error: curl/curl.h: No such file or directory

This means the C++ extension in hic-straw requires the libcurl development headers, which are not installed by default on many systems.

Solution 1: Install system dependencies (for pip installation)

You need to install the libcurl development package before building:

  • On Ubuntu/Debian:

    sudo apt-get update
sudo apt-get install libcurl4-openssl-dev

  • On Fedora/CentOS/RHEL:

    sudo dnf install libcurl-devel

  • On macOS (with Homebrew):

    brew install curl

    If Homebrew’s curl is not found automatically, you may need to set environment variables:

    export CPATH="$(brew --prefix curl)/include"
export LIBRARY_PATH="$(brew --prefix curl)/lib"

Solution 2: Use Conda (recommended for convenience)

Instead of building hic-straw from source, you can install a prebuilt binary via Bioconda:

conda install -c bioconda hic-straw

To avoid conflicts and ensure reproducibility, we recommend installing it in a fresh Conda environment:

conda create -n bandhic-env python=3.11
conda activate bandhic-env
conda install -c bioconda hic-straw

# Install BandHiC
pip install bandhic