Running Galaxy in Terra

Anton Kovalsky
  • Updated

Galaxy is an open, web-based platform for highly accessible bioinformatic research, similar to Terra. You can set up and run a Galaxy instance from within your Terra workspace.  To learn more about using Galaxy, see the platform's documentation or visit the Galaxy Community Hub

Launch a Galaxy instance

When you launch a Galaxy instance in Terra, you can use the tools on the Galaxy platform to analyze and visualize data from your Terra workspace. For step-by-step instructions for creating, customizing, and launching a Galaxy instance in Terra, see Starting and customizing your Galaxy VM.

You'll see the Galaxy Cloud Environment dialog box when you first create your Galaxy app instance and then again after the Galaxy app has been created. 

  • After the app is created, the dialog box displays the current configuration and a cost estimate for either the current configuration or any other configuration you might use.
  • Currently, Terra does not support updating the configuration of a Galaxy application that is already running. To change an existing configuration, you'll need to delete that instance and re-create it with a different configuration.

Galaxy Cloud Environment persistence

The Galaxy app runs in a virtual Cloud Environment that includes a virtual machine (VM) or cluster, preinstalled Galaxy software, and persistent disk storage.  The persistent disk storage retains package configurations and generated outputs, so you don't lose configurations or data if you have to delete and re-create your Galaxy instance.

When you delete a Galaxy instance, you have the option to either keep or delete the associated persistent disk. If you choose to keep the disk, the next time you create a Galaxy instance, the old disk is automatically attached to the new Galaxy instance.

To learn more about how persistent disks function in all of our cloud environments, see our article on detachable persistent disks. There are two notable differences between Galaxy Persistent Disks and those for other cloud environments:

  • You can't access a terminal view through our Galaxy instance, so the mounted directory is not visible to you through command-line tools.
  • The option to change the disk size upon Galaxy creation will be disabled if you already have a persistent disk (because currently, Terra doesn’t support updating a Galaxy Persistent Disk once created).

Working in Galaxy on Terra

After clicking Launch Galaxy, you'll be taken to the main screen of your new Galaxy instance. The Galaxy interface has three panels.

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  • The Tools panel (left) lists all the tools preinstalled on your Galaxy instance.
  • The middle panel is for running tools and examining data.
  • The History panel (right) is a place to track your analysis and perform certain actions.

Import data to your Galaxy instance through the Tool panel

1. To add data to your Galaxy instance, first click Upload Data at the top of the Tool panel.

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2. This will create a popup that lets you upload files from a local machine or link to other data. To select files from your Terra workspace storage or data table, click Choose remote files.

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3. After you select your files, click the Start button. The files you've chosen will appear in the History panel. Once an upload is complete, the item in the History panel turns green.

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4. You can manipulate the files in the history panel to use as workflow inputs or data visualization outputs. Once the files are uploaded, you can use, copy, share, or extract them.

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When selecting files, you'll need to specify the format of each file. Galaxy does have auto-detecting capabilities, but sometimes it's better to select the filetype yourself.

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Install additional tools in the Galaxy Tool panel

If your Tool panel is missing something you need for your analysis, you can add tools from a variety of repositories.

1. To add a tool to your Tool panel, start by clicking Admin in the masthead at the top of your screen.

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2. You'll see a menu on the left side of your screen that includes a Tool Management section near the bottom. Click the Install and Uninstall option in that section.

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3. Now you can search various repositories for the tools that best suit your workflow. The search results provide some useful information to help you make the best selection.

  • How up-to-date is this tool? (Updated date)
  • How popular is this tool? (Number of downloads)
  • Who published this tool? (Please note: "IUC" stands for Intergalactic Utilities Commission - a Galaxy community effort to publish best practices)

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4. Click OK to install and choose the section in your Tool panel where you'd like the new tool to appear.

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Create a new history in Galaxy

1. Select the View all histories button at the top right of the Galaxy History panel.

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>2. On the new page, choose Create new.
3. Click Unnamed history on the new pane, and rename the new history.
4. Add datasets by clicking and dragging them over from previous History panes.
5. Click Switch to on the old history to return.

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