Installation

Download the CPhasing and activate environments by the activate_cphasing 

LATEST_URL=$(curl -s https://api.github.com/repos/wangyibin/CPhasing/releases/latest | grep "browser_download_url.*linux-x86.tar.gz" | cut -d '"' -f 4)
wget $LATEST_URL

tar xzvf CPhasing*.tar.gz

source ./CPhasing*/bin/activate_cphasing

### activate environment
source ./CPhasing*/bin/activate_cphasing

### deactivate
source deactivate

Note

For the first configuration, run it when the network is accessible.

Note

If you can not download the pixi, you can download it from the github release page: 

mkdir -p ~/.pixi/bin
cd ~/.pixi/bin
wget https://github.com/prefix-dev/pixi/releases/download/v0.60.0/pixi-x86_64-unknown-linux-musl.tar.gz
tar xzvf pixi-x86_64-unknown-linux-musl.tar.gz

And rerun the activate_cphasing to install the dependencies of CPhasing

Note

If you do not have direct access to the anaconda repository, you can set the mirror for pixi.

Note

For the platform of linux-aarch64, please download from github release.

Download the CPhasing and install environment by conda 

git clone https://github.com/wangyibin/CPhasing.git

cd CPhasing
conda env create -f environment.yml
conda activate cphasing
Add the following to the ~/.bash_profile
~/.bash_profile
export PATH=/path/to/CPhasing/bin:$PATH
export PYTHONPATH=/path/to/CPhasing:$PYTHONPATH

Note

The hic pipeline require GLIBCXX_3.4.29, or you can add the following to the start of cphasing execute script, e.g.: run.sh

run.sh
export LD_LIBRARY_PATH=/path/to/anaconda3/envs/cphasing/lib:$LD_LIBRARY_PATH

Install C-Phasing

## Download C-Phasing and install python dependencies
git clone https://github.com/wangyibin/CPhasing.git
cd CPhasing
pip install .
Add following to the ~/.bash_profile or ~/.bashrc
~/.bash_profile
export PATH=/path/to/CPhasing/bin:$PATH

Dependencies

  1. For core function
    - bedtools
    - seqkit
    - pigz
  2. For Pore-C pipeline
    - minimap2(>= v2.24)