Metadata-Version: 2.1
Name: custardpy
Version: 0.4.2
Summary: Hi-C analysis tools by Python3
Home-page: https://github.com/rnakato/custardpy
Author: Ryuichiro Nakato
Author-email: rnakato@iqb.u-tokyo.ac.jp
License: GPL3.0
Keywords: Hi-C analysis,3D genome,NGS
Classifier: Programming Language :: Python :: 3
Classifier: Operating System :: OS Independent
Requires-Python: >=3.7
Description-Content-Type: text/markdown
Requires-Dist: numpy (>=1.18)
Requires-Dist: pandas (>=1.3.0)
Requires-Dist: scipy (>=1.3)
Requires-Dist: scikit-learn (>=1.0.0)
Requires-Dist: matplotlib (>=3.2.2)
Requires-Dist: seaborn (>=0.11.1)
Requires-Dist: h1d (>=0.2.0)
Requires-Dist: hic-straw (>=1.3.0)

# 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](https://custardpy.readthedocs.io), and
- Tutorial data of Hi-C and Micro-C analysis using demo data.

## 0. Changelog

See [Changelog](https://github.com/rnakato/CustardPy/blob/master/ChangeLog.md)

## 1. Installation

Docker image is available at [DockerHub](https://hub.docker.com/r/rnakato/custardpy).

### 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](https://www.biorxiv.org/content/10.1101/2022.05.24.493188v1)

## 7. Contact

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