We will run a command that prints hello world through Tibanna. To do this, we just need to prepare for a job description json and run tibanna.

Job description

To run the pipeline on a specific input file using Tibanna, we need to create an job description file for each execution (or a dictionary object if you’re using Tibanna as a python module).

The job description for running shell commands requires command and container_image fields. The former is a list of commands and the latter is the Docker image name. Here, we use ubuntu:16.04 image and use an echo command. Notice that double-quotes are escaped inside the command string. We’re passing an environment variable $NAME through the field input_env. Also notice that the environment variable’s $ sign is prefixed with an escaped backslash in the command string.

In the following example, the output file hello.txt in the same directory is copied to the output bucket my-tibanna-test-bucket as some_sub_dirname/my_first_hello.txt.

This json can be found at https://github.com/4dn-dcic/tibanna/blob/master/examples/hello/hello_shell_input.json

  "args": {
    "container_image": "ubuntu:16.04",
    "command": ["echo \"Hello world, \\$NAME!\" > hello.txt"],
    "language": "shell",
    "input_files": {},
    "secondary_files": {},
    "input_parameters": {},
    "input_env": {"NAME": "Soo"},
    "output_S3_bucket": "my-tibanna-test-bucket",
    "output_target": {
      "file:///data1/shell/hello.txt": "some_sub_dirname/my_first_hello.txt"
    "secondary_output_target": {}
  "config": {
    "ebs_size": 10,
    "instance_type": "t3.micro",
    "EBS_optimized": true,
    "password": "whateverpasswordworks",
    "log_bucket": "my-tibanna-test-bucket"

Tibanna run

To run Tibanna,

  1. Sign up for AWS
  2. Install and configure awscli
  1. Install Tibanna on your local machine
  1. Deploy Tibanna (link it to the AWS account)
  1. Run workflow as below.

    cd tibanna
    tibanna run_workflow --input-json=examples/hello/hello_shell_input.json
  2. Check status

    tibanna stat
  3. Check output file

    Let’s try downloading the output file to check the content.

    aws s3 cp s3://my-tibanna-test-bucket/some_sub_dirname/my_first_hello.txt .

    The output file my_first_hello.txt would look as below.

    Hello world, Soo!