simple_example_hello.rst

hello

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

see Before_using_Tibanna

3. Install Tibanna on your local machine

see Installation

4. Deploy Tibanna (link it to the AWS account)

see Installation

5. Run workflow as below.

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

6. Check status

   tibanna stat

7. 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!