Environment Variables

Overview

Teaching: 10 min
Exercises: 0 min

Questions

• How do I set the value of environment variables for a tool’s execution?

Objectives

• Learn how to pass environment variables to a tool’s runtime.

Tools run in a restricted environment and do not inherit most environment variables from the parent process. You can set environment variables for the tool using EnvVarRequirement.

env.cwl

#!/usr/bin/env cwl-runner

cwlVersion: v1.0
class: CommandLineTool
baseCommand: env
requirements:
  EnvVarRequirement:
    envDef:
      HELLO: $(inputs.message)
inputs:
  message: string
outputs:
  example_out:
    type: stdout
stdout: output.txt

echo-job.yml

message: Hello world!

Now invoke cwl-runner with the tool wrapper and the input object on the command line:

$ cwl-runner env.cwl echo-job.yml
[job env.cwl] /home/example$ env > /home/example/output.txt
[job env.cwl] completed success
{
    "example_out": {
        "location": "file:///home/example/output.txt",
        "basename": "output.txt",
        "class": "File",
        "checksum": "sha1$1ca16a840b14807b2fd3323022c476b06a150e2f",
        "size": 94,
        "path": "/home/example/output.txt"
    }
}
Final process status is success
$ cat output.txt
HELLO=Hello world!
PATH=/bin:/usr/bin:/usr/local/bin
HOME=/home/example
TMPDIR=/tmp/tmp63Obpk

Key Points

• Tools run in a restricted environment with a minimal set of environment variables.

• Use the EnvVarRequirement field to set environment variables inside a tool’s environment.