Quick Start
Prerequisites
The quick start requires having a registered user account in a tenant with access to the platform. The user should be added to a workgroup with permission to use the application.
Procedure
The quick start will begin by creating a project in the web application GUI. With a project created, a basic analysis pipeline will be constructed. Finally, we'll launch the pipeline and examine the results.
Create a Project
In order to get started on the platform, first we'll create a project. Navigate to your domain login URL and click into the ICA application to be directed to the web application GUI.
When the platform GUI loads, you'll be presented with the projects dashboard. Click the new project button to create a project.
Enter a project name and set the project entitlement (entitlement will vary based on the subscription purchased). Then click save.
Add Workgroup to a Project
From the Project Dashboard, select the newly created project to enter into the Project Details page. Navigate to the Team tab and click Add workgroup and set role button to add workgroups and associate roles to project.
Create a Tool
To build an analysis pipeline in the GUI, we'll first need to construct a Tool - a containerized application step within a pipeline. Tools are a core component in the Common Workflow Language (CWL) specification for describing the resources and environment for executing an application. In this quick start, we'll be creating a Tool that executes an echo command.
Add a docker image
In order to create a Tool, a docker image is required to run the application in a containerized environment. Before creating a Tool, we'll add a docker image to the Docker Repository in the platform GUI. To run the echo command, we'll use an external docker image reference to the alpine:latest docker image publicly available on docker hub. Navigate to the Docker Repository and click to add a new external image. In the Url add the URL to the alpine image on docker hub:
The Docker Name and Version properties are auto-populated based on the URL. Then click Save.
Add a Tool
The Tool we'll create for this quick start provides a simple example as an introduction to the pieces that construct a Tool. Navigate to the Tool Repository in the GUI and click the button to add a new tool.
In the new tool menu, select the Information tab and fill in the mandatory fields:
Add a name for the Tool (ie, "echo")
Select the Docker Image from the Docker Repository
alpine:latestAdd a Tool Version (ie, 1.0.0)
Navigate to the General Tool tab and make the following changes:
Add an entry to the Base command field with value "echo"
Navigate to the Tool Settings tab and make the following changes:
Add a row to create a Tool Setting entry
Add an ID for the setting (ie, "message")
Set a default value (ie, "testMessage")
Set the Binding Position to 1
Navigate to the Tool Outputs tab and make the following changes:
Add a row to create a Tool Output entry
Add an ID for the output (ie, "echoOutput")
Change the Type to Stdout
Click save. The Tool will be saved to the Tool Repository and is now accessible when creating pipelines.
Create a Pipeline
Now that you have a Tool created, you can create a simple single-step pipeline. Pipelines are created and launched from within a project where the output data will be stored. Navigate to the projects dashboard and enter the project created in previous steps. In the project, navigate to the Pipelines section under the Flow expandable region in the left pane. Click Create Pipeline in the buttons at the top of the Pipelines screen.
In the Information tab of the pipeline creation view, fill in the mandatory fields:
Enter a Code (name) for the pipeline (ie, "echo-pipeline")
Enter a Description (ie, "Quick Start echo pipeline")
Navigate to the Definition tab. You'll be presented with a drag-and-drop Graphical User Interface (GUI) for creating a pipeline. The pipeline will execute our simple echo tool and the output of the tool will be captured as the final pipeline output and saved to the Data section in the project.
Expand the Tool Repository menu on the right pane adjacent to the editor. Click and drag the echo tool onto the pipeline editor screen. The echo tool created has a single output file from the standard output of the echo command. To create a pipeline output mapped to the tool's output, drag the output file icon into the pipeline editor. Connect the tool output to the pipeline output file by dragging the output node from the echo tool to the output file icon in the editor. With the output file selected, set the Format property to "TXT".
Click to save the pipeline. In the Pipelines view, you'll see the new pipeline created.
Launch a Pipeline
Select the newly created pipeline in the Pipelines view. Click the button to Start New Run at the top of the screen.
In the launch pipeline view, fill in the mandatory information:
Enter a "User Reference" to name the pipeline run (ie, "echo-pipeline-run1")
Choose an Entitlement Bundle
(Optional) Change the input string in the Settings to a custom input
Click Start Run to launch the pipeline.
Navigate to the Runs tab in the project to view the progress of the pipeline run.
The run shows as "In Progress", indicating the run has been launched and is currently running. The run will take 5-10 minutes depending on compute resource availability. Click the run to navigate the Run view. The Run view contains information about the run in progress, including the run ID, the status, a visual status of the progress of each step, output logs from each step, and resource utilization.
When the pipeline run completes, the output files will be displayed in the Run details view. To verify the output file contains the expected content, the output file can be previewed in the GUI. Click the "task-stdouterr-0.log" file to view the file details. Navigate to the View tab to see a preview of the contents.
The file content will show the standard output of the echo command based on the input string provided in to the pipeline at launch.
That concludes the quick start. This introduction only scrapes the surface of the platform capabilities. Explore the user documentation to find more in depth information about specific aspects.
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