rev-docker

For using RevBayes with Docker

The RevBayes Docker image currently has the following applications and libraries installed:

• RevBayes
• TensorPhylo
• R
• Python
• Julia
• Java
• Beast/Beagle

The RevBayes Docker image can be found at hub.docker.com/r/sswiston/rb_tp, alongside a README containing information about different tag options and program versions.

For a full tutorial about using RevBayes with Docker: revbayes.github.io/tutorials/docker/

Prerequisites

• Download and install Docker Desktop
• Create DockerHub account and login
• Download the RevBayes Docker image by with this shell command: docker pull sswiston/rb_tp:latest

Command-line job

• Open Docker Desktop to launch the Docker daemon
• Use helper script to launch a RevBayes container and execute a job script
  • Usage: ./run_revbayes_docker.sh test.Rev my_job_name
• Use docker run command to launch a RevBayes container and execute a job script
  • Usage: `docker run --name my_job_name --volume /Users/Sarah/projects/rev-docker:/mnt/project sswiston/rb_tp:latest rb /mnt/project/test.Rev"

Interactive job (through GUI)

• Open Docker Desktop
• Go to Images tab
• Click Run on image you want to run (e.g. sswiston/rb_tp:latest)
• Optional settings:
  • Set container name (optional)
  • Set Volume -> Host Path: the location of the RevBayes project and scripts for the analysis (e.g. /Users/Sarah/projects/rev-docker)
  • Set Volume -> Container Path: the volume mount location within the container (e.g. /mnt/project)
• Click Run to boot container
• Go to Containers tab
• Click CLI for Command Line Interface
• Enter the container and run commands as needed, for example:

  •    cd /mnt/project
       rb test.Rev