In AntonelliLab/outsider: Install and Run Programs, Outside of R, Inside of R

knitr::opts_chunk$set(echo = TRUE, comment = '')

outsider allows users to launch commands on a remote machine. This can be handy if the user wishes to run their external programs on more powerful machines. All that is required is that the remote server has Docker and can be connected to via ssh. To then run outsider module programs on the remote machine, an ssh connection must be set up using the ssh_setup function and the ssh package. Once set-up, all external programs will be run on the external machine, not the local, with all input and output files being automatically sent and retrieved by outsider.

# Libs
library(ssh)
library(outsider)

# SSH
session <- ssh_connect(host = "username@ip.address:port")
ssh_setup(session)

# Run
repo <- 'dombennett/om.hello.world'
if (!is_module_installed(repo = repo)) {
  module_install(repo = repo)
}
module_import(repo = repo, fname = 'hello_world')
# hello world will be run on the remote machine
hello_world()

# Clean up
ssh_teardown()