HiC-rs

This part is the python-rust interface for the iterative matrix correction

Install

First: Make sure you have Python and Conda installed properly.

To install smb (short for stochastic matrix balancing) on a Ubuntu 18.04, simply execute conda install -c kargf smb.

For using, not building, installation of Rust is not needed.

Build

To build it, execute the commands applicable to you:

# first, install rust:
curl https://sh.rustup.rs -sSf | sh -s -- -y

# alternatively install rust with conda:
conda install -c conda-forge rust

# confirm install:
cargo --version
rustc --version

# download repository and navigate in it
git clone https://github.com/fkarg/HiC-rs
cd HiC-rs

# navigate to the rust code and compile (optional)
cd smb
cargo build
cd ..

# install missing python dependencies
pip install -r requirements.txt

# execute the setup.py (will also compile rust if not done yet)
python setup.py build
pip install .