AnVIL: Galaxy on Terra FAQ

Anton Kovalsky
  • Updated

This article provides supplementary information about using Galaxy on Terra. For detailed instruction on running Galaxy through Terra, check out our main article on Galaxy interactive environments.

Please note that while these FAQs are based on information about Galaxy-on-AnVIL, the implementations of Galaxy on Terra's non-AnVIL versions use the same code on the backend, so most of the information is universal to Galaxy on Terra.

1. Where can I find tutorials on using Galaxy?

You can find a variety of tutorials on the Galaxy training page here.

2. Can I use an FTP client to transfer files to my Galaxy virtual machine?

Yes, although this requires administrative configuration of the server. For instructions on uploading files to Galaxy via FTP, check out the Galaxy documentation here.

3. Can I set up a backend job without using the Galaxy GUI?

Yes, there is an API and a Python library called Bioblend that allows you to interact with almost all of Galaxy’s features (the exception being the interactive visualization features, which are part of the GUI). You can find more information in the developer-focused Galaxy training materials here.

4. Why am I charged when Galaxy is paused if there is no job running?

If you pause (rather than delete) a Galaxy instance, you’re still paying for the storage required for your data and storage for the instance itself even if you haven’t stored or generated any data.

5. Is Galaxy FISMA certified (what is FISMA)?

The Federal Information Security Modernization Act (FISMA) is a law that establishes levels of accreditation for certifying a platform as being secure enough to host various types of protected data. Galaxy-on-AnVIL has been certified “FISMA moderate.” In short, this means that the assets associated with Galaxy-on-AnVIL are considered "moderate impact" - meaning that a failure of security can have serious adverse effects on mission capability and cause significant harm to assets, but not serious injury or loss of life - and that the NIST 800-53 security framework has been implemented to protect the system.

6. Is Galaxy-on-AnVIL CLIA certified?

Galaxy-on-AnVIL is not CLIA certified.  

7. Is Galaxy-on-AnVIL HIPAA compliant?

Galaxy-on-AnVIL is not HIPAA compliant.

8. Is it possible to export workflows from Galaxy?

Yes, to export a workflow, go to the workflows tab in Galaxy, click on the workflow of interest to see the dropdown menu, and then click “Download”. For more detailed instructions, check out the Galaxy documentation on extracting workflows.

9. Is it possible to export a “History” from Galaxy?

While this is possible with Galaxy in general, this feature has not yet been implemented for Galaxy-on-AnVIL as of June 2021.

10. Can I access Galaxy from outside the country/region for that particular UseGalaxy url 

e.g. can I use UseGalaxy.au if I am in the United States?
Yes, in most cases. For a few infrastructures, you have to be in the right country (e.g. UseGalaxy.no must be used in Norway). But you can use any listed in the "Use Galaxy" tab from any place in the world.

11. Is there terminal access through Galaxy?

Terminal access to your Galaxy virtual machine is not through the Galaxy GUI, to use the command line terminal, you should go back to the Terra workspace. If you click on the terminal icon (as described here) in the workspace from which you’ve launched your Galaxy instance, this will be a terminal for that Galaxy instance.

12. What if a tool I need isn't in the preinstalled tools available when I create my Galaxy instance?

The Galaxy ToolShed includes thousands of bioinformatics tools that have been wrapped for use in Galaxy.  When AnVIL creates a Galaxy instance, it automatically logs you in as the server admin, which enables you to install tools from the ToolShed on to your instance. This means that you can add it yourself via the Galaxy Admin interface and the Galaxy ToolShed. If you are an experienced Galaxy administrator you can also add it yourself, behind the scenes, via the AnVIL shell. If the tool you’re interested in isn’t available in the ToolShed, you can find support on the Galaxy Project page to see how it can be added. You can also contact the Intergalactic Utilities Commission.

13. Where can I send tools that I've wrapped for Galaxy to be reviewed?

Absolutely! The Intergalactic Utilities Commission maintains best practices for tools, and also accepts pull requests for tools.

14. Is there any advantage between Docker and Conda with respect to wrapping tools for Galaxy?

The performance tends to be pretty similar from the perspective of Galaxy.

15. If my tool is already in IUC, what is the next step to get it onto a public server like UseGalaxy?

You should post in the help forum so that your tool can be upvoted, or you can make a pull request against a publicly available repository. The main requirement is that it be a tool with wide applicability. 

16. How difficult is it publish in the ToolShed and/or make dependencies available if they are not already available in Conda?

We recommend adding your tool first to something like BioConda, as this will create a Docker container for that tool, this way your tool is available in Conda. If that's not an option you prefer, you can create your own Docker image and specify your namespace.

17. Can interactive environments be integrated in my personal Galaxy instance?

You can write a Galaxy tool that references a Docker container where you've wrapped an application for Galaxy.

18. Can I have separate accounts on multiple servers and move data between those accounts?

Yes, you can have accounts on multiple servers (you can have separate accounts on all 134 public Galaxy servers, and this would not be considered abusive in anyway). These accounts will be completely independent of one another. You can export and import things like workflows and history between different Galaxy servers (although importing history has not yet been implemented for Galaxy-on-AnVIL as of June 2021).

 

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