rnakato/rumball repository overview

⁠RumBall: RNA-seq analysis platform with Docker

⁠0. Changelog

See Changelog⁠

⁠1. Installation

⁠1.1 Docker

To use the docker command, type:

# Pull docker image
docker pull rnakato/rumball

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

• user:password
  • ubuntu:ubuntu

⁠1.2 Singularity

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

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

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

Then you can run RumBall with the command:

singularity exec rumball.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 rumball.sif <command>

This command mounts the /work directory.

⁠2. Usage

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

⁠3. Build Docker image from Dockerfile

First clone and move to the repository

git clone https://github.com/rnakato/RumBall.git
cd RumBall/Dockerfiles

Then type:

docker build -f Dockerfile.<version> -t <account>/rumball

⁠4. Reference

• Nagai LAE, Lee S, Nakato R. Protocol for identifying differentially expressed genes using the RumBall RNA-seq analysis platform, STAR Protocols, 2024. doi: 10.1016/j.xpro.2024.102926⁠