custardpy 0.0.10

Hi-C analysis tools by Python3

CustardPy

Hi-C analysis tools by Python3 and Docker

Requirements

The following are required before installing CustardPy:

• Python 3.7+

Installation

From PyPI

Core components of CustardPy can by installed using pip:

pip3 install custardpy

Docker image

We recommend to use the CustardPy Docker image that contains additional scripts for Hi-C/Micro-C analysis.

Docker

To use docker command, type:

docker pull rnakato/custardpy
docker run -it --rm rnakato/custardpy <command>

Singularity

Singularity can also be used to execute the docker image:

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

Usage

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

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