singularity_autohic.md

AutoHiC singularity version

Considering that many users run AutoHiC on large clusters, the build dependency environment may not be very free, and Docker has root restrictions, we provide a singularity version. However, the process is currently under active development and there may be some issues during use. We hope to get your feedback to update the process.

• AutoHiC singularity version
  • Usage
    • get image
    • bulid environment
  • run

Usage

First you need to download the AutoHiC singularity environment.

get image

You can also retrieve AutoHiC.sif files directly from the other_tools folder in Google Drive.

bulid environment

# built container
singularity build your_container.sif AutoHiC.sif

# run container
singularity exec your_container.sif bash

# init conda 
/home/autohic/miniconda3/bin/conda init bash
source ~/.bashrc

# activate AutoHiC
conda activate autohic

# clone AutoHiC
git clone https://github.com/Jwindler/AutoHiC.git

# configuration environment
# install dependencies
cd ~/AutoHiC/src/models/swin
pip install -e . -i https://pypi.tuna.tsinghua.edu.cn/simple/

# return to AutoHiC word folder
cd ~/AutoHiC

# This directory(/home/autohic) contains juicer and 3d-dna.

run

Now you can follow this part of the document to prepare data and configuration files to run AutoHiC: Usages