I have a partial *solution, *when I have already enabled Global Properties:

<https://lh4.googleusercontent.com/-EJJeUHpiDSs/VO4yDdXk2vI/AAAAAAAAACY/UDR7x-oUvJo/s1600/Configure%2BSystem%2B[Jenkins]%2B2015-02-25%2B21-35-00.png>


the following script works for me:


import jenkins.*

import jenkins.model.*

import hudson.*

import hudson.model.*


nodes = Jenkins.getInstance().getGlobalNodeProperties()

nodes.getAll(hudson.slaves.EnvironmentVariablesNodeProperty.class)

if ( nodes.size() != 1 ) {

  println("error: unexpected number of environment variable containers: "

          + nodes.size()

          + " expected: 1")

} else {

  envVars= nodes.get(0).getEnvVars()

  envVars.put("FOO", "foo")

  ...

  Jenkins.getInstance().save()

  println("okay")

}

I send this script to Jenkins with:

java -jar /tmp/jenkins-cli.jar -s http://localhost:8080/jenkins/ groovy 
/tmp/jenkins_global_vars.groovy

and the variables are set and persisted. What I haven't yet figured out, is 
how to enable the Global Properties in the first place

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