Starting and customizing Galaxy on Terra

Allie Cliffe
  • Updated

Interactive applications such as Galaxy run on virtual machines in your workspace Cloud Environment. This article describes how to start your Galaxy analysis and adjust the configuration of your Galaxy Cloud Environment to fit your computational needs.

Galaxy Cloud Components Overview

The Galaxy Cloud Environment is the virtual machine that runs your Galaxy app. It includes:

  • A virtual machine (VM) engine (compute profile)
  • Software (the current version of Galaxy in the application configuration)
  • A boot boot disk
  • VM storage (persistent disk).

Galaxy-Cloud-Environment-components_diagram.png

You can adjust the compute profile and persistent disk size of your Galaxy instance VM (white boxes in the diagram above) to meet your analysis needs. Note that all Galaxy Cloud Environments come pre-installed with the latest version of Galaxy and a standard boot disk (gray boxes).

How to start a Galaxy instance (default settings)

To start your Galaxy instance (using the default or a customized compute profile and storage size) follow the directions below. Note that the steps are slightly different depending on your display (Notebooks tab or Analyses tab).

  • 1. Start in the Notebooks tab of a workspace where you have permission to launch a VM (at least writer, "can-compute").

    2. Click the Create a Cloud Environment for Galaxy button on the left.
    2021-06-09_12-45-14.png

    3. This will call up the Cloud Environment pane on the right of your screen, where you can customize the compute power of your virtual machine and size of the associated persistent disk. Note that the cost of running this environment is higher than for the default notebook configuration, so make sure you use your time wisely!

    The default Galaxy environment includes up-to-date version of Galaxy, 1 node with 8 CPUs, 52 GB of RAM, and 500 GB of persistent disk storage.
    galaxy-default-Cloud-Environment_Screen_shot.png

    4. Click Next and then Create on the screen that follows.
    image__1_.png

    You'll see at the top of your screen a notification that your Galaxy environment is being precreeating and then provisioned (this can take about 10 minutes).

    5. When this process is complete, you'll see the following pop-up. Clicking Launch Galaxy will take you directly to your very own Galaxy instance (in a new browser tab).
    Screen_Shot_2020-10-21_at_4.05.05_PM.png

  • 1. Go to the Analyses tab in your workspace.

    2. Click the + Start button next to Your Analyses.
    Analyses-tab_plus-Create-button_Screen_shot.png

    3. Select the Galaxy application.

    4. In the Galaxy Cloud Environment pane, choose your Cloud compute profile (number of nodes, CPUs and memory) and Persistent disk size. Note that the cost of running the default Galaxy environment is higher than for the default notebook configuration. Make sure you use your resources wisely!

    The default Galaxy environment includes up-to-date version of Galaxy, 1 node with 8 CPUs, 52 GB of RAM, and 500 GB of persistent disk storage.
    galaxy-default-Cloud-Environment_Screen_shot.png

    5. Click Next to finalize your configuration.

    6. On the screen that follows, click Create to spin up your Galaxy instance. 
    image__1_.png

    You'll see a new Galaxy icon with a blue dot in the right sidebar. The dot will change to green when the VM is done creating (this can take 10 minutes).
    Galaxy-Cloud-Environment-provisioning_Galaxy-logo-Screen_shot.png

    7. When provisioning is complete, a pop-up lets you know your Galaxy Cloud Environment is ready. Clicking Launch Galaxy will take you directly to your very own Galaxy instance (in a new browser tab).
    .Screen_Shot_2020-10-21_at_4.05.05_PM.png

About the Galaxy Cloud Environment paneNote that you'll see the Galaxy Cloud Environment pane both when you first create your Galaxy app instance, then again after the Galaxy app has been created in case you'd like to view what configs you chose.

The Galaxy Cloud Environment pane displays the current configuration and a cost estimate for either that configuration or another hypothetical configuration you're thinking of using instead.

How to customize Galaxy 

You can customize the compute profile and storage size of your Galaxy instance from the Galaxy Cloud Environment pane. Follow the steps below to access the Galaxy Cloud Environment pane while Galaxy is running. Note that the steps are different depending on whether you are using the Notebooks tab or Analyses tab display.

You must recreate (i.e. delete) your Galaxy VM to change any customizations Terra does not currently support the ability to update the compute configuration of a Galaxy application that is already running. If you decide you want to change an existing configuration, you'll need to delete that instance and recreate it with a different configuration.

  • 1. Click the Galaxy widget at the top of any workspace page.
    Galaxy-widget_Screen_shot.png

    2. In the Galaxy Cloud Environment pane, click the Delete Environment button at the bottom.

    3. In the next screen, leave the persistent disk intact and click Delete.

    4. After deleting the Galaxy Cloud Environment, click the Create a Cloud Environment for Galaxy button to expose the configuration pane and customize (follow step-by-step directions above).

     Galaxy cloud environment configuration pane.png

  • 1. Go to the Analyses tab in your workspace.

    2. Click the Galaxy icon with the green dot in the sidebar.

    3. In the Galaxy Environment Details pane, click the gear icon (environment settings). 

    4. In the Galaxy Cloud Environment pane, click Delete Environment.

    5. Leave the radio button to keep the persistent disk but delete application configuration and compute profile.

    6. Click Delete (bottom right).

    Once the old instance is deleted, you can click the cloud icon in the sidebar and follow directions above to customize and start a new Galaxy instance. You'll be able to adjust your Cloud compute profile (number of nodes, CPUs and memory) and Persistent disk size. 
    image.png

Cost-saving recommendations

Size your compute power appropriately

You pay a fixed amount while Galaxy is running, whether or not you are doing active calculations. The cost is based on the compute power of your virtual machine or cluster, not how much computation is being done. So you want to have enough power to do your computations in a reasonable amount of time, but not a lot of extra that you will be paying for and not using. Note that Terra automatically pauses a notebook after twenty minutes of inactivity.

Avoid runaway costs

Don't forget to shut off your Galaxy instance when you're done! You will continue to pay the cost displayed in blue on your Galaxy Cloud Configuration pane as long as your instance is running. To avoid runaway costs, don't forget to delete your Galaxy VM when you are done working! 

You will find a list of all Cloud Environment VMs and all persistent disks and their status at https://app.terra.bio/#clusters (go to Main Menu > Your name > Cloud Environments). You can delete directly from this page. 

In the Notebooks or Analyses tab
Return to the Terra workspace and click the Cloud Environment widget (Notebooks tab) or the Galaxy logo (Analyses tab) to expose the Galaxy Cloud Environment configuration pane. 

Click the Delete button at the bottom.

To learn more about controlling cloud costs, see Controlling cloud costs - sample use cases.

How to save Galaxy outputs to the Workspace bucket

To share outputs with collaborators, use generated data as input for a workflow, or copy to external or local long-term storage, make sure to explicitly save your outputs in the workspace bucket. Galaxy has a built-in upload/download system where you can pull data to and from the bucket to the PD.

Copy-data-in-Galaxy-instance_Screen-shot.png

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