Install

Get the Chr3D pipeline running locally.

Prerequisites

• Conda (Miniconda or Anaconda)
• Git

1. Clone the repository

git clone https://github.com/rudrajoshi2481/Chr3D.git
cd Chr3D

2. Run the install script

The repository includes an automated install script that sets up everything.

chmod +x install.sh
./install.sh

What the script does:

1. Configures conda channels (defaults, bioconda, conda-forge)
2. Creates a conda environment named chr3d with Python 3.12
3. Installs bioinformatics tools:
   • BWA (alignment)
   • SAMtools (BAM processing)
   • MACS3 (peak calling)
   • pairtools (Hi-C pairs processing)
   • cooler (Hi-C matrix generation)
   • cooltools (Hi-C analysis)
4. Installs Python dependencies (numpy, pandas, scipy, biopython, pysam, etc.)
5. Installs the Chr3D package in editable mode

Customize the environment name

To use a different environment name, edit the install.sh file:

ENV_NAME="your_env_name"  # Change this line

3. Activate and use

conda activate chr3d
chr3d --help

Or use the Python API:

import chr3d as c3d
print(c3d.__version__)

Installed Tools

Troubleshooting

• Conda not found: Make sure conda is installed and initialized in your shell
• Permission denied: Run chmod +x install.sh before executing
• Environment conflicts: Remove existing environment with conda env remove -n chr3d before reinstalling