Help Me!

So you’re new to Galaxy (welcome!), or you’re an old hand with an esoteric Galaxy problem (good for you!), this is the page that collates help resources to get you an answer to your question. There are many Galaxy help resources, aimed at many different users and navigating them can be a bit overwhelming. Hopefully the lists below will give you a good place to start digging.

I have a question about:

The right tool or visualisation to use

The method or best practice of using a tool in a science experiment

I’m getting a weird error from my tool

The Galaxy interface

I need a new tool

Adding my own data

Administering my specific Galaxy installation

Finding training to go on

Developing new software for galaxy

Sharing workflows, histories and data

Citing Galaxy or individual tools

Which tool or visualisation should I use?

This is a thorny topic indeed many issues can confound an easy decision and the final answer is totally dependent on the scientific question you have. Of course, Galaxy’s main tool headings give a high-level categorisation. The scientific literature is the best place to answer this in depth but here are some links that will help clarify classes of tools and what they do.

Wikipedia Open Source Bioinformatics Tools

Galaxy Tools and Visualisation

What is the best practice for the tool I am using? How do I know it is working for me?

All the Galaxy tools have help sections at the bottom of the page providing information and help on how to use the tools. As many of Galaxy tools are available as command line tools, they often have online documentation, which is usually linked-to in the Help section

What does this error message mean?

When you run a tool in Galaxy, if all goes well your history item will turn green once it has finished. If an error occurs, your history item will turn red. You can find out more about the error by clicking on the green ‘bug’ icon in the history item and you can then report this error to your Galaxy administrator. Before you do that though, have a read of the error. Maybe it’s telling you something about a problem with your data or something that you can fix yourself.

How do I work with the interface?

The Galaxy interface is designed so you don’t have to learn how to run tools from the command line. The interface generally consists of drop-down lists and text boxes. The drop-down lists usually consist of either data from the history that the tool can accept or a restricted set of parameters that you must choose from before running the tool (e.g. when selecting a reference sequence you might have to chose ‘Use a built-in index’ or ‘Use one from the history’). Often, selecting a certain option in a drop-down list will result in extra drop-down lists and boxes for additional parameters being displayed to you. The text boxes are areas where you write parameters that have large ranges, e.g. a tool might need to know what cut-off to use between 1-100.

There are lots of help videos on the Galaxy Vimeo site to assist you

How do I get a new tool added to my / a public Galaxy

If you know of a new tool that you think could be of help to you, contact the Galaxy administrator. It might be the case that there is already a Galaxy implementation of the tool and you could be using it in next to no time. Otherwise, the administrator might be kind enough to implement the tool for you.

How do I add my own big data set to Galaxy?

There are three commonly used ways of adding data to Galaxy. For small datasets there is an upload tool that uploads files from your local machine into either your Galaxy history or your data library (a place for data that you might want to use more than once). For bigger datasets, some instances (e.g. Galaxy Main) have the facility to upload data by FTP. See the Galaxy Wiki for more information. The final option, for those who have a local Galaxy instance, is to merely create symbolic links to big data in a directory on a mass-storage device that Galaxy can read and then use the data library ‘Add datasets’ to import those links. This way the original data is never moved or replicated, just read by Galaxy. Thereafter, any datasets created by tools in Galaxy will be stored in the Galaxy database.

How can I troubleshoot my own Galaxy installation

There are a number of places you can seek assistance from for troubleshooting your own Galaxy instance. Your first port-of-call should be the Galaxy Wiki Admin page, which provides help and advice for a whole range of administration subjects. If that doesn’t help, then you can ask the Galaxy-development email group, which has a large list of active members (including of course all the Galaxy Development Team) and questions are generally answered quite quickly.

Where is the best training near me?

Training courses and other Galaxy-related events can be found on this site! Check out the Training and Tools page for further information.

How can I add my great new tool into Galaxy?

You’ve written a new tool and you know think that it would be useful for other people to use in Galaxy – great! Most tools that do not rely on any third-party dependencies just need a simple ‘wrapper script’ creating and can then be loaded into Galaxy. There’s plenty of help for creating wrapper scripts on the The Galaxy Wiki Tool page.

How can I publish/share my workflow, histories and/or data?

If you have a Galaxy workflow or some data that you want to share with others on the same Galaxy instance, it’s just a few simple clicks to share your data. In most instances, it’s just a matter of going to what you want to share, clicking on it and either sharing it with a particular user or making it public (viewable by everyone). Workflows can also be downloaded as files and upload by users of other Galaxy instances. They can also be shared on the Toolshed and become available to anyone. Here’s how. Finally, if you have a Galaxy Workflow that you’re particularly proud of and would like to get it published, see our Workflow publishing page.

How do I cite Galaxy?

There are a number of ways to cite Galaxy. It normally involves citing the three major Galaxy papers. Follow the instructions on the Galaxy ‘Cite’ page for more information.