Churros: Docker image for ChIP-seq/ATAC-seq analysis

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/churros

# Container login
docker run --rm -it rnakato/churros /bin/bash
# Execute a command
docker run -it --rm rnakato/churros <command>

1.2 Singularity

Singularity is the alternative way to use the docker image. With this command you can build the singularity file (.sif) of Churros:

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

Instead, you can download the Churros singularity image from our Dropbox (We use singularity version 3.8.5).

Then you can run Churros with the command:

singularity exec churros.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 churros.sif <command>

This command mounts the /work directory.

2. Quickstart

churros command executes all steps from mapping to visualization.

# download Churros/tutorial directory
git clone https://github.com/rnakato/Churros.git
cd Churros/tutorial/

# download fastq and genome data and make index
bash 00_getdata.sh

# Execute Churros pipeline
bash Quickstart.sh

Then the results are output in Churros_result directory.

3. Usage

See https://churros.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/Churros.git
cd Churros/Dockerfiles/

Then type:

docker build -f Dokerfile.<version> -t <account>/churros

5. Reference

• Wang J, Nakato R, Churros: a Docker-based pipeline for large-scale epigenomic analysis, DNA Research, 2023. doi: 10.1093/dnares/dsad026