giulianonetto/run-job

R pkg and infrastructure for simulation using sockeye

Run job

Standard script for running jobs using instructions from an yaml file. Depends on packages:

• docopt (v. 0.7.1)
• yaml (v. 2.2.1)
• logger (v. 0.2.2)

Usage:

Assuming you are in the same directory as the run_job.R script:

./run_job.R --instructions example-instructions.yaml

In the instructions file, you should include at least a call key with the exact executable call you would run if using bash. Optionally, you can add a log key with the file path where logging should be stored.

Not necessary, but I use this docker image (source files stored here).