Hi-C analysis tools by Python3
Project description
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
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