Running Tools Inside Docker


Teaching: 10 min
Exercises: 0 min
  • How do I run tools inside a Docker container?

  • Learn how to invoke tools inside a complete controlled runtime.

Docker containers simplify software installation by providing a complete known-good runtime for software and its dependencies. However, containers are also purposefully isolated from the host system, so in order to run a tool inside a Docker container there is additional work to ensure that input files are available inside the container and output files can be recovered from the container. A CWL runner can perform this work automatically, allowing you to use Docker to simplify your software management while avoiding the complexity of invoking and managing Docker containers.

One of the responsibilities of the CWL runner is to adjust the paths of input files to reflect the location where they appear inside the container.

This example runs a simple Node.js script inside a Docker container.


#!/usr/bin/env cwl-runner

cwlVersion: v1.0
class: CommandLineTool
baseCommand: node
    dockerPull: node:slim
    type: File
      position: 1
    type: stdout
stdout: output.txt


  class: File
  path: hello.js

Provide a “hello.js” and invoke cwl-runner providing the tool wrapper and the input object on the command line:

$ echo "console.log(\"Hello World\");" > hello.js
$ cwl-runner docker.cwl docker-job.yml
[job docker.cwl] /tmp/tmpgugLND$ docker \
    run \
    -i \
    --volume=/tmp/tmpgugLND:/var/spool/cwl:rw \
    --volume=/tmp/tmpSs5JoN:/tmp:rw \
    --volume=/home/me/cwl/user_guide/hello.js:/var/lib/cwl/job369354770_examples/hello.js:ro \
    --workdir=/var/spool/cwl \
    --read-only=true \
    --user=1000 \
    --rm \
    --env=TMPDIR=/tmp \
    --env=HOME=/var/spool/cwl \
    node:slim \
    node \
    /var/lib/cwl/job369354770_examples/hello.js > /tmp/tmpgugLND/output.txt
[job docker.cwl] completed success
    "example_out": {
        "location": "file:///home/me/cwl/user_guide/output.txt",
        "basename": "output.txt",
        "class": "File",
        "checksum": "sha1$648a6a6ffffdaa0badb23b8baf90b6168dd16b3a",
        "size": 12,
        "path": "/home/me/cwl/user_guide/output.txt"
Final process status is success
$ cat output.txt
Hello World

Notice the CWL runner has constructed a Docker command line to run the script.

In this example, the path to the script hello.js is /home/me/cwl/user_guide/hello.js outside the container but /var/lib/cwl/job369354770_examples/hello.js inside the container, as reflected in the invocation of the node command.

Key Points

  • Containers can help to simplify management of the software requirements of a tool.

  • Specify a Docker image for a tool with DockerRequirement in the hints section.