Creating a Workflow Using an iPlant Analytic Tool

What are workflows? The BioExtract Server workflow system allows users the ability to save a series of BioExtract Server tasks (e.g. querying a data source, saving a data extract and executing analytic tools) as a workflow. Any series of tasks performed on data is a possible candidate for workflow automation.

BioExtract Server's most unique feature may be its ability to record your tasks as you perform them and then turn those tasks into a workflow. This means that you create a workflow by simply performing the tasks in your analysis job. It's that easy!

How it works: As you perform the tasks in your job, BioExtract Server records each task as a step. Once you've finished all of your tasks, simply click Save, and the BioExtract Server connects the steps together to form a complete workflow.

When you execute the workflow, you can execute it as one unit or each step in the workflow can be run individually. Execution can also be paused to allow you to check progress or adjust input into a step.

Steps in the workflow can be modified. This allows you to repeat the workflow on different data or with modified parameters. A detailed report can also be generated for personal review, publishing or for sharing with colleagues.

As a registered user, you are able to create, modify and share workflows with colleagues.

Example: Creating a workflow using an iPlant tool

  1. In the Workflow tab, click on the 'Create and Import Workflow' node in the Workflow list on the left. Click the 'Record Workflow' button in the panel on the right. This will clear out any previously executed tasks during the current session.

    iPlant Query
  2. In the Query tab, search NCBI for all Arabidopsis 'Argonaute' proteins.

    iPlant Query
  3. Optionally, click the "Extracts" tab to view the results of the query.

    iPlant tool selection
  4. In the Tools tab, select the 'xmknr' tool under the 'Edit Tools' node. Specify that the tool should 'Use records on the Extracts page' as input and the 'Sequence type' is set to 'protein'. Click the 'Execute' button. This tool is being executed to remove possible duplicates. This tool also is able to modify the list of records in the current extract.

    iPlant tool selection
  5. Click on the Extracts Tab to observe the change is the list of records. iPlant tool execution
  6. In the Tools tab, select the 'clustalo-lonestar' (Clustal Omega running on Lonestar) tool under the 'iPlant' node. Specify 'User records on Extracts page ' as input and verify that the 'Force sequence input file format' is 'fasta'. Click the 'Execute' button.

    iPlant tool selection
  7. After the Clustal Omega tool execution has completed, on the Workflow tab, click on the 'Create and Import Workflow' node in the Workflow list on the left. Enter a name and a description for the executed steps and click the 'Save' button.

    iPlant tool execution
  8. Click on the name of the new workflow in the list of Workflows on the left. The workflow will appear in the panel on the right. Click the 'Start' button at the top of the panel to execute the workflow. iPlant tool execution
  9. To view the results of the workflow execution:
    1. Right click on the final node
    2. Select 'More information'
    3. Click on the 'View File' button below the Output File heading
    iPlant tool execution