added environment variables episode

Author: Toby Hodges

_episodes/12-env.md

@@ -0,0 +1,42 @@
+---
+title: "Environment Variables"
+teaching: 10
+exercises: 0
+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."
+keypoints:
+- "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."
+---
+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*
+
+```
+{% include cwl/env.cwl %}
+```
+
+*echo-job.yml*
+
+```
+{% include cwl/echo-job.yml %}
+```
+
+Now invoke `cwl-runner` with the tool wrapper and the input object on the
+command line:
+
+```
+$ cwl-runner env.cwl echo-job.yml
+[job 140710387785808] /home/example$ env
+PATH=/bin:/usr/bin:/usr/local/bin
+HELLO=Hello world!
+TMPDIR=/tmp/tmp63Obpk
+Final process status is success
+{}
+```