1. Installation

Docker image of RumBall (based on Ubuntu 22.04) is available at DockerHub. This image contains various tools for RNA-seq analysis as below:

• Mapping tools

  • BWA v0.7.17

  • Bowtie v1.3.1

  • Bowtie2 v2.5.3

  • chromap v0.2.5

• Mapping tools for RNA-seq

  • STAR 2.7.11b

  • salmon v1.10.0

  • HISAT2 v2.2.1

  • kallisto v0.46.1

• Gene expression estimation

  • RSEM v1.3.3

  • StringTie v2.2.1

• Differential expression analysis

  • edgeR v3.38.1

  • DESeq2 v1.36.0

  • ballgown v2.18.0

  • sleuth v0.30.0

• Gene onthology (GO) analysis

  • ClusterProfiler v4.4.4

  • gprofiler2 v0.2.1

• Quality assessment

  • FastQC v0.11.9

• Utility tools

  • SRAtoolkit v3.0.10

  • SAMtools v1.19.2

  • BEDtools v2.31.0

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.