BashCommand step

Cloudgene supports the execution of executable binaries.

Tip

All HDFS inputs are automatically exported to the local filesystem and can be used without manual exportation in any executable binary.

Parameters

Parameter Required Description
cmd yes The command that should be executed
bash no Enables or disable Bash specific features like pipes and loops (default: false)
stdout no Use stdout as step's output (default: false)

Examples

This example shows how to forward stdout directly to the output of a step in order to display it the web-application.

name: cmd example
version: 1.0
workflow:
  steps:
    - name: Print text to terminal
      cmd: /bin/echo $message
      stdout: true
  inputs:
    - id: message
      description: Message
      type: text

Write message to a file using stdout streaming

This example shows how to use Bash specific features by setting the bash property to true:

name: bash example
version: 1.0
workflow:
  steps:
    - name: Write text to file using pipes
      cmd: /bin/echo $message > $output
      bash: true
  inputs:
    - id: message
      description: Message
      type: text
  outputs:
    - id: output
      description: Output File
      type: local_file

Working with HDFS files

All HDFS inputs are automatically exported to the local filesystem and can be used without manual exportation. In this example we use the cat command to show the content of an hdfs-file input parameter:

name: hdfs example
version: 1.0
workflow:
  steps:
    - name: Print text to file using pipes
      cmd: /bin/cat $input
      stdout: true
  inputs:
    - id: input
      description: Output File
      type: hdfs_file