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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