Using Galaxy with Terra
Galaxy is an open web-based platform for highly accessible bioinformatic research, similar to Terra. You can learn. more about how to use Galaxy in the platform's documentation or by visiting the Galaxy community hub. To use Galaxy through Terra, you need to be logged into the AnVIL-linked Terra (https://anvil.terra.bio):
For step-by-step instructions on how to link Gen3 and AnVIL to Terra, see this article. Once you're logged into your AnVIL-linked Terra account, you can launch your own instance of Galaxy through one of your workspaces.
Launching a Galaxy instance
- Start by entering a workspace for which you have the permission necessary to launch a notebook VM, and navigate to the Notebooks tab of that workspace. There, you'll click a button labeled "Create a Cloud Environment for Galaxy"
- This will call up the following panel on the right of your screen. This is where you can customize the compute power of your virtual machine and size of the associated 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!
- Click "Next" and confirm on the screen that follows. Once you've done that, you'll see at the top of your screen a notification that says your Galaxy environment is being provisioned (this can take about 10 minutes):
- 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
Navigating Galaxy's Interface
After clicking "Launch Galaxy" you'll be taken to the main screen of your new Galaxy instance. The Galaxy interface has three panels:
- The left panel is the Tool panel, where you can see a list of all of the tools that have been pre-installed on this Galaxy instance.
- The middle panel is for running tools and examining data.
- The right panel is the History panel, which serves as a convenient place to track your analysis and perform certain actions.
How to import data to your Galaxy instance through the Tool panel
- To add data to your Galaxy instance, you'll want to click the upload icon at the top of the Tool panel.
- This will call a pop up that allows you to either upload files from a local machine or to link to other data. Clicking "Choose remote files" will allow you to select the files from your Terra workspace.
- Once you've selected your desired files, the "Start" button, and the files you've selected will appear in the History panel. Once an upload is complete, the item in the History panel turns green.
- You'll be able to manipulate the files in your history to use them as workflow inputs or data visualization outputs. Once the files are uploaded, you can use, copy, share, or extract them:
Note that when selecting files, Galaxy will need to be told what format to expect for each of those files. Galaxy does have auto-detecting capabilities, but sometimes it's better to select the filetype yourself:
How to install additional tools in the Galaxy Tool panel
- To add a tool to your Tool panel, start by clicking "Admin" in the masthead at the top of your screen:
- Now, 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:
- This will allow you to search thousands of repositories for the tools that best suit your workflow. The search results give 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)
- Click "Ok" to install and choose the section in your Tool panel where you'd like the new tool to appear:
How to create a new history in Galaxy
- Select the “multiple histories” button at the top right of the Galaxy history panel.
- On the new page, choose “Create new”.
- Click the words “Untitled history” on the new pane, and rename the new history.
- Add datasets by clicking and dragging them over from previous History panes.
- Click “Switch to” on the old history to return.