custardpy 0.7.7

Hi-C analysis tools by Python3

CustardPy: Docker image for 3D genome analysis

This repository contains

• Source code of CustardPy (PyPI),
• Dockerfile of CustardPy Docker image,
• Full Manual, and
• Tutorial data of Hi-C and Micro-C analysis using demo data.

0. Changelog

See Changelog

1. Installation

Docker image is available at DockerHub.

1.1 Docker

To use the docker command, type:

# Pull docker image
docker pull rnakato/custardpy

# Container login
docker run --rm -it rnakato/custardpy /bin/bash
# Execute a command
docker run --rm -it -v (your directory):/opt/work rnakato/custardpy <command>

When calling loops using Juicer HICCUPS, supply the --gpus all option to allow GPU computation (GPU card needed):

docker run --gpus all -it --rm -it -v (your directory):/opt/work rnakato/custardpy call_HiCCUPS.sh

• user:password
  • ubuntu:ubuntu

1.2 Singularity/Apptainer

Singularity is the alternative way to use CustardPy. With this command, you can build the singularity file (.sif) of CustardPy:

singularity build custardpy.sif docker://rnakato/custardpy

Instead, you can download the CustardPy singularity image from our Dropbox (We use singularity version 3.8.5).

Then you can run CustardPy with the command:

singularity exec custardpy.sif <command>

Singularity will automatically mount the current directory. If you want to access the files in the other directory, use the --bind option, for instance:

singularity exec --bind /work custardpy.sif <command>

This command mounts the /work directory.

When calling loops using Juicer HICCUPS, supply --nv option to allow GPU computation (GPU card needed):

singularity exec --bind /work custardpy.sif call_HiCCUPS.sh

2. Quickstart

# download Churros/tutorial directory
git clone https://github.com/rnakato/CustardPy.git
cd CustardPy/tutorial/Hi-C/

# download fastq and genome data and make index
bash 00_getdata.sh

# Execute Juicer pipeline
bash QuickStart_juicer.sh

3. Usage

See https://custardpy.readthedocs.io for the detailed Manual.

4. Build Docker image from Dockerfile

First clone and move to the repository

git clone https://github.com/rnakato/CustardPy.git
cd CustardPy/Docker

Then type:

docker build -f Dokerfile.<version> -t <account>/custardpy_juicer .

5. Citation

Please cite this reference when using CustardPy in your study.

• Nakato R, Sakata T, Wang J, Nagai LAE, Nagaoka Y, Oba GM, Bando M, Shirahige K, Context-dependent perturbations in chromatin folding and the transcriptome by cohesin and related factors, Nature Communications, 2023. doi: 10.1038/s41467-023-41316-4