custardpy 0.3.0

Hi-C analysis tools by Python3

CustardPy: Docker image for 3D genome analysis

Major Release! (v1.0.0)

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 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, suppy --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

1.2 Singularity

Singularity can also be used to execute the docker image:

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

# execute a command
singularity exec custardpy.sif <command>

Singularity mounts the current directory automatically. If you access the files in the other directory, please mount by --bind option, for instance:

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

This command mounts /work directory.

When calling loops using Juicer HICCUPS, suppy --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 .

6. Reference

• Nakato R, Sakata T, Wang J, Nagai LAE, Oba GM, Bando M, Shirahige K, Context-dependent 3D genome regulation by cohesin and related factors, bioRxiv, 2022. doi: 10.1101/2022.05.24.493188

7. Contact

Ryuichiro Nakato: rnakato AT iqb.u-tokyo.ac.jp