Hi-C analysis tools by Python3
Project description
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
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 .
6. Reference
- 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
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